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IPKM:master IPKM:306-sigmoid IPKM:dev IPKM:pyside IPKM:gga_relaxation IPKM:packaging IPKM:csv_broken IPKM:drawing IPKM:bootstrap dominik:master dominik:dev dominik:pyside dominik:gga_relaxation dominik:packaging dominik:csv_broken dominik:drawing dominik:bootstrap
IPKM:v1.0.0 dominik:v1.0.0

1 Commits
packaging ... csv_broken

Author SHA1 Message Date
Dominik Demuth
35e89176be datawidget.py: raise AttributeError manually if item is graph, was not always raised; maybe problem of #52 2023-04-27 12:13:20 +02:00
140 changed files with 21726 additions and 7776 deletions
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1
.gitignore vendored
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@ -5,4 +5,3 @@ AppDir
NMReval*.zsync
.idea
*.zs-old
docs

47
AppImageBuilder.yml
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@ -12,9 +12,7 @@ script:
# Copy the python application code into the AppDir
- cp bin/evaluate.py $TARGET_APPDIR/usr/bin/
- cp -r src/* $TARGET_APPDIR/usr/src/
- cp src/resources/pkm.vogel.nmreval.desktop $TARGET_APPDIR/usr/share/applications
# set current date as version info
- sed -i "s/CURRENT_DATE/$(date +'%Y-%m-%d')/" $TARGET_APPDIR/usr/src/nmreval/version.py
- cp src/pkm.vogel.nmreval.desktop $TARGET_APPDIR/usr/share/applications
AppDir:
@ -32,50 +30,35 @@ AppDir:
arch: amd64
allow_unauthenticated: true
sources:
- sourceline: 'deb [arch=amd64] http://ftp.uni-mainz.de/debian bullseye main contrib non-free'
- sourceline: 'deb [arch=amd64] http://mirror.infra.pkm/ bullseye main contrib non-free'
include:
# for /usr/bin/env
# - coreutils
# - dash
# - zsync
# - hicolor-icon-theme
- coreutils
- dash
- zsync
- hicolor-icon-theme
- libatlas3-base
- gnuplot-nox
- python3-minimal
- python3.9-minimal
- python3-numpy
- python3-scipy
# - python3-matplotlib
# - python-matplotlib-data
- python3-bsddb3
- python3-h5py
- python3-pyqt5
- python3-pyqtgraph
- python3-requests
- python3-urllib3
# - python3-tk
exclude:
# lots of qt stuff we do not use
- libqt5designer5
- libqt5help5
- libqt5network5
- libqt5sql5
- libqt5test5
- libqt5xml5
- qtbase5-dev-tools
- pyqt5-dev-tools
- libavahi-client3
- libavahi-common-data
- libavahi-common3
- libwacom2
- libwacom-common
files:
exclude:
- usr/share/man
- usr/share/doc/*/README.*
- usr/share/doc/*/changelog.*
- usr/share/doc/*/NEWS.*
- usr/share/doc/*/TODO.*
after_bundle: |
echo "MONSTER SED FOLLOWING...(uncomment if needed for mpl-data)"
#sed -i s,\'/usr/share/matplotlib/mpl-data\',"f\"\{os.environ.get\('APPDIR'\,'/'\)\}/usr/share/matplotlib/mpl-data\"", ${TARGET_APPDIR}/usr/lib/python3/dist-packages/matplotlib/__init__.py
runtime:
# if needed, apparently replaces hardcoded location with APPDIR location
# path_mappings:
# - /usr/share/matplotlib/mpl-data:$APPDIR/usr/share/matplotlib/mpl-data
version: "continuous"
env:
PATH: '${APPDIR}/usr/bin:${PATH}'

30
Makefile
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@ -5,37 +5,31 @@ PYUIC = pyuic5
PYRCC = pyrcc5
#Directory with ui files
RESOURCE_DIR = src/resources/_ui
RESOURCE_DIR = resources/_ui
#Directory for compiled resources
PYQT_DIR = src/gui_qt/_py
COMPILED_DIR = nmreval/gui_qt/_py
#UI files to compile, uses every *.ui found in RESOURCE_DIR
UI_FILES = $(foreach dir, $(RESOURCE_DIR), $(notdir $(wildcard $(dir)/*.ui)))
PYQT_UI = $(UI_FILES:%.ui=$(PYQT_DIR)/%.py)
COMPILED_UI = $(UI_FILES:%.ui=$(COMPILED_DIR)/%.py)
SVG_FILES = $(foreach dir, $(RCC_DIR), $(notdir $(wildcard $(dir)/*.svg)))
PNG_FILES = $(SVG_FILES:%.svg=$(RCC_DIR)/%.png)
CC = gcc
CFLAGS = -O2 -fPIC
LDFLAGS = -shared
all : ui
ui : $(COMPILED_UI)
C_DIR = src/nmreval/clib
all : ui compile
ui : $(PYQT_UI)
rcc : $(PNG_FILES)
# only one C file at the moment
compile : $(C_DIR)/integrate.c
$(CC) $(LDFLAGS) $(CFLAGS) -o $(C_DIR)/integrate.so $<
rcc: $(PNG_FILES)
$(COMPILED_DIR)/%.py : $(RESOURCE_DIR)/%.ui
$(PYUIC) $< -o $@
# replace import of ressource to correct path
# @sed -i s/images_rc/nmrevalqt.$(COMPILED_DIR).images_rc/g $@
# @sed -i /images_rc/d $@
$(RCC_DIR)/%.png : $(RCC_DIR)/%.svg
convert -background none $< $@
$(PYRCC) $(RCC_DIR)/images.qrc -o $(COMPILED_DIR)/images_rc.py

27
bin/evaluate.py Executable file
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@ -0,0 +1,27 @@
#!/usr/bin/env python3
import sys
import pathlib
sys.path.append(str(pathlib.Path(__file__).absolute().parent.parent / 'src'))
from nmreval.configs import check_for_config
# does a directory for config stuff exist? create it if not
check_for_config()
# pyqtgraph warns on Mac if QApplication is created when it is imported
# import pyqtgraph
from nmreval.lib.logger import handle_exception
sys.excepthook = handle_exception
from gui_qt import App
app = App(['Team Rocket FTW!'])
from gui_qt.main.mainwindow import NMRMainWindow
mplQt = NMRMainWindow()
mplQt.show()
sys.exit(app.exec())

91
pyproject.toml
View File

@ -1,53 +1,54 @@
[build-system]
requires = ["setuptools", "wheel", "setuptools-scm"]
build-backend = "setuptools.build_meta"
[project]
name = "nmreval"
version = "0.1"
description = "Evaluation of NMR and orther data"
authors = [
{ name = "Dominik Demuth", email = "dominik.demuth@pkm.tu-darmstadt.de" },
[metadata]
name = nmreval
version = 0.1
description = Evaluation of data
long_description = file: README.md
author = Dominik Demuth
author_email = dominik.demuth@physik.tu-darmstadt.de
install_requires = [
'numpy',
'scipy',
'matplotlib',
'bsddb3',
'pyqtgraph',
'pyqt',
'h5py',
]
maintainers = [
{ name = "Dominik Demuth", email = "dominik.demuth@pkm.tu-darmstadt.de" },
]
requires-python = ">=3.7"
keywords = ['nmr', 'physics', 'science']
classifiers = [
"Development Status :: 3 - Alpha",
"Intended Audience :: Science/Research",
"Topic :: Scientific/Engineering :: Physics",
"License :: OSI Approved :: BSD License",
"Programming Language :: Python :: 3",
"Programming Language :: Python :: 3.7",
"Programming Language :: Python :: 3.8",
"Programming Language :: Python :: 3.9",
"Programming Language :: Python :: 3.10",
"Programming Language :: Python :: 3.10",
"Programming Language :: Python :: 3.11",
"Programming Language :: Python :: 3.12",
"Programming Language :: Python :: 3 :: only",
"Operating System :: POSIX :: Linux"
]
keywords = ["nmr", "physics", "science"]
license = { text = "BSD 3-Clause License" }
dependencies = [
"numpy",
"scipy",
"h5py",
"PyQt5",
"pyqtgraph",
'Development Status :: 3 - Alpha',
'Intended Audience :: End Users/Desktop',
'Intended Audience :: Science/Research',
'Topic :: Scientific/Engineering :: Physics',
'Topic :: Scientific/Engineering :: Visualization',
'Programming Language :: Python :: 3',
'Programming Language :: Python :: 3.7',
'Programming Language :: Python :: 3.8',
'Programming Language :: Python :: 3.9',
'Programming Language :: Python :: 3.10',
'Programming Language :: Python :: 3 :: only',
]
license = {text = "BSD 3-Clause License"}
[project.optional-dependencies]
legacy = ["bsddb3"]
[tool.setuptools]
include_package_data = true
[project.urls]
Repository = "https://gitea.pkm.physik.tu-darmstadt.de/IPKM/nmreval"
Issues = "https://gitea.pkm.physik.tu-darmstadt.de/IPKM/nmreval/issues"
[project.gui-scripts]
nmreval = "gui_qt.cli:main"
[tool.setuptools.packages]
find = {}
scripts = bin/evaluate.py
[tool.setuptools.packages.find]
where = ["src"]
include =[
'nmreval*',
'gui_qt*',
'resources*',
]
[tool.setuptools.package_data]
* = *.txt, *.npz, *.png, *.json

8
requirements.txt Normal file
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@ -0,0 +1,8 @@
matplotlib
numpy
scipy
PyQt5
h5py
pyqtgraph
bsddb3
requests

4
setup.py Executable file
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@ -0,0 +1,4 @@
# Always prefer setuptools over distutils
from setuptools import setup
setup()

226
src/gui_qt/_py/apod_dialog.py
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@ -1,11 +1,10 @@
# -*- coding: utf-8 -*-
# Form implementation generated from reading ui file 'src/resources/_ui/apod_dialog.ui'
# Form implementation generated from reading ui file '_ui/apod_dialog.ui'
#
# Created by: PyQt5 UI code generator 5.15.9
# Created by: PyQt5 UI code generator 5.12.3
#
# WARNING: Any manual changes made to this file will be lost when pyuic5 is
# run again. Do not edit this file unless you know what you are doing.
# WARNING! All changes made in this file will be lost!
from PyQt5 import QtCore, QtGui, QtWidgets
@ -14,223 +13,62 @@ from PyQt5 import QtCore, QtGui, QtWidgets
class Ui_ApodEdit(object):
def setupUi(self, ApodEdit):
ApodEdit.setObjectName("ApodEdit")
ApodEdit.resize(1144, 655)
ApodEdit.resize(784, 484)
sizePolicy = QtWidgets.QSizePolicy(QtWidgets.QSizePolicy.Preferred, QtWidgets.QSizePolicy.Preferred)
sizePolicy.setHorizontalStretch(0)
sizePolicy.setVerticalStretch(0)
sizePolicy.setHeightForWidth(ApodEdit.sizePolicy().hasHeightForWidth())
ApodEdit.setSizePolicy(sizePolicy)
self.gridLayout = QtWidgets.QGridLayout(ApodEdit)
self.gridLayout.setContentsMargins(9, 9, 9, 9)
self.gridLayout.setContentsMargins(3, 3, 3, 3)
self.gridLayout.setSpacing(3)
self.gridLayout.setObjectName("gridLayout")
self.freq_graph = NMRPlotWidget(ApodEdit)
self.freq_graph.setObjectName("freq_graph")
self.gridLayout.addWidget(self.freq_graph, 2, 2, 1, 1)
self.time_graph = NMRPlotWidget(ApodEdit)
self.graphicsView = PlotWidget(ApodEdit)
sizePolicy = QtWidgets.QSizePolicy(QtWidgets.QSizePolicy.MinimumExpanding, QtWidgets.QSizePolicy.Expanding)
sizePolicy.setHorizontalStretch(0)
sizePolicy.setVerticalStretch(0)
sizePolicy.setHeightForWidth(self.time_graph.sizePolicy().hasHeightForWidth())
self.time_graph.setSizePolicy(sizePolicy)
self.time_graph.setObjectName("time_graph")
self.gridLayout.addWidget(self.time_graph, 2, 1, 1, 1)
self.widget = QtWidgets.QWidget(ApodEdit)
sizePolicy = QtWidgets.QSizePolicy(QtWidgets.QSizePolicy.Maximum, QtWidgets.QSizePolicy.Preferred)
sizePolicy.setHeightForWidth(self.graphicsView.sizePolicy().hasHeightForWidth())
self.graphicsView.setSizePolicy(sizePolicy)
self.graphicsView.setObjectName("graphicsView")
self.gridLayout.addWidget(self.graphicsView, 2, 0, 1, 1)
self.graphicsView_2 = PlotWidget(ApodEdit)
self.graphicsView_2.setObjectName("graphicsView_2")
self.gridLayout.addWidget(self.graphicsView_2, 2, 1, 1, 1)
self.apodcombobox = QtWidgets.QComboBox(ApodEdit)
sizePolicy = QtWidgets.QSizePolicy(QtWidgets.QSizePolicy.MinimumExpanding, QtWidgets.QSizePolicy.Fixed)
sizePolicy.setHorizontalStretch(0)
sizePolicy.setVerticalStretch(0)
sizePolicy.setHeightForWidth(self.widget.sizePolicy().hasHeightForWidth())
self.widget.setSizePolicy(sizePolicy)
self.widget.setObjectName("widget")
self.verticalLayout = QtWidgets.QVBoxLayout(self.widget)
self.verticalLayout.setObjectName("verticalLayout")
self.baseline_box = QtWidgets.QCheckBox(self.widget)
self.baseline_box.setObjectName("baseline_box")
self.verticalLayout.addWidget(self.baseline_box)
self.shift_box = QtWidgets.QGroupBox(self.widget)
self.shift_box.setFlat(True)
self.shift_box.setCheckable(True)
self.shift_box.setChecked(False)
self.shift_box.setObjectName("shift_box")
self.gridLayout_4 = QtWidgets.QGridLayout(self.shift_box)
self.gridLayout_4.setContentsMargins(3, 3, 3, 3)
self.gridLayout_4.setSpacing(3)
self.gridLayout_4.setObjectName("gridLayout_4")
self.ls_lineedit = QtWidgets.QLineEdit(self.shift_box)
self.ls_lineedit.setObjectName("ls_lineedit")
self.gridLayout_4.addWidget(self.ls_lineedit, 1, 1, 1, 1)
self.ls_spinbox = QtWidgets.QSpinBox(self.shift_box)
self.ls_spinbox.setMaximum(999999)
self.ls_spinbox.setObjectName("ls_spinbox")
self.gridLayout_4.addWidget(self.ls_spinbox, 0, 1, 1, 1)
self.ls_combobox = QtWidgets.QComboBox(self.shift_box)
self.ls_combobox.setObjectName("ls_combobox")
self.ls_combobox.addItem("")
self.ls_combobox.addItem("")
self.gridLayout_4.addWidget(self.ls_combobox, 0, 0, 2, 1)
self.verticalLayout.addWidget(self.shift_box)
self.apod_box = QtWidgets.QGroupBox(self.widget)
self.apod_box.setFlat(True)
self.apod_box.setCheckable(True)
self.apod_box.setChecked(False)
self.apod_box.setObjectName("apod_box")
self.verticalLayout_2 = QtWidgets.QVBoxLayout(self.apod_box)
self.verticalLayout_2.setContentsMargins(3, 3, 3, 3)
self.verticalLayout_2.setSpacing(3)
self.verticalLayout_2.setObjectName("verticalLayout_2")
self.apodcombobox = QtWidgets.QComboBox(self.apod_box)
sizePolicy.setHeightForWidth(self.apodcombobox.sizePolicy().hasHeightForWidth())
self.apodcombobox.setSizePolicy(sizePolicy)
self.apodcombobox.setObjectName("apodcombobox")
self.verticalLayout_2.addWidget(self.apodcombobox)
self.eqn_label = QtWidgets.QLabel(self.apod_box)
self.eqn_label.setIndent(3)
self.eqn_label.setObjectName("eqn_label")
self.verticalLayout_2.addWidget(self.eqn_label)
self.gridLayout.addWidget(self.apodcombobox, 0, 0, 1, 1)
self.widget_layout = QtWidgets.QHBoxLayout()
self.widget_layout.setContentsMargins(-1, 6, -1, -1)
self.widget_layout.setSpacing(20)
self.widget_layout.setObjectName("widget_layout")
self.verticalLayout_2.addLayout(self.widget_layout)
self.verticalLayout.addWidget(self.apod_box)
self.zerofill_box = QtWidgets.QGroupBox(self.widget)
self.zerofill_box.setFlat(True)
self.zerofill_box.setCheckable(True)
self.zerofill_box.setChecked(False)
self.zerofill_box.setObjectName("zerofill_box")
self.horizontalLayout = QtWidgets.QHBoxLayout(self.zerofill_box)
self.horizontalLayout.setContentsMargins(3, 3, 3, 3)
self.horizontalLayout.setSpacing(3)
self.horizontalLayout.setObjectName("horizontalLayout")
self.label = QtWidgets.QLabel(self.zerofill_box)
self.label.setObjectName("label")
self.horizontalLayout.addWidget(self.label)
self.zf_spinbox = QtWidgets.QSpinBox(self.zerofill_box)
self.zf_spinbox.setMinimum(1)
self.zf_spinbox.setMaximum(3)
self.zf_spinbox.setObjectName("zf_spinbox")
self.horizontalLayout.addWidget(self.zf_spinbox)
self.verticalLayout.addWidget(self.zerofill_box)
self.phase_box = QtWidgets.QGroupBox(self.widget)
self.phase_box.setFlat(True)
self.phase_box.setCheckable(True)
self.phase_box.setChecked(False)
self.phase_box.setObjectName("phase_box")
self.gridLayout_2 = QtWidgets.QGridLayout(self.phase_box)
self.gridLayout_2.setContentsMargins(3, 3, 3, 3)
self.gridLayout_2.setSpacing(3)
self.gridLayout_2.setObjectName("gridLayout_2")
self.label_3 = QtWidgets.QLabel(self.phase_box)
self.label_3.setObjectName("label_3")
self.gridLayout_2.addWidget(self.label_3, 1, 0, 1, 1)
self.label_4 = QtWidgets.QLabel(self.phase_box)
self.label_4.setObjectName("label_4")
self.gridLayout_2.addWidget(self.label_4, 2, 0, 1, 1)
self.ph0_spinbox = QtWidgets.QDoubleSpinBox(self.phase_box)
self.ph0_spinbox.setWrapping(True)
self.ph0_spinbox.setDecimals(1)
self.ph0_spinbox.setMinimum(-180.0)
self.ph0_spinbox.setMaximum(180.0)
self.ph0_spinbox.setSingleStep(0.5)
self.ph0_spinbox.setObjectName("ph0_spinbox")
self.gridLayout_2.addWidget(self.ph0_spinbox, 0, 1, 1, 1)
self.pivot_lineedit = QtWidgets.QLineEdit(self.phase_box)
self.pivot_lineedit.setObjectName("pivot_lineedit")
self.gridLayout_2.addWidget(self.pivot_lineedit, 2, 1, 1, 1)
self.label_2 = QtWidgets.QLabel(self.phase_box)
self.label_2.setObjectName("label_2")
self.gridLayout_2.addWidget(self.label_2, 0, 0, 1, 1)
self.ph1_spinbox = QtWidgets.QDoubleSpinBox(self.phase_box)
self.ph1_spinbox.setWrapping(True)
self.ph1_spinbox.setDecimals(2)
self.ph1_spinbox.setMinimum(-720.0)
self.ph1_spinbox.setMaximum(720.0)
self.ph1_spinbox.setSingleStep(0.05)
self.ph1_spinbox.setObjectName("ph1_spinbox")
self.gridLayout_2.addWidget(self.ph1_spinbox, 1, 1, 1, 1)
self.verticalLayout.addWidget(self.phase_box)
self.ft_box = QtWidgets.QGroupBox(self.widget)
self.ft_box.setCheckable(True)
self.ft_box.setChecked(False)
self.ft_box.setObjectName("ft_box")
self.verticalLayout_3 = QtWidgets.QVBoxLayout(self.ft_box)
self.verticalLayout_3.setContentsMargins(3, 3, 3, 3)
self.verticalLayout_3.setSpacing(3)
self.verticalLayout_3.setObjectName("verticalLayout_3")
self.phase_before_button = QtWidgets.QRadioButton(self.ft_box)
self.phase_before_button.setChecked(True)
self.phase_before_button.setObjectName("phase_before_button")
self.buttonGroup = QtWidgets.QButtonGroup(ApodEdit)
self.buttonGroup.setObjectName("buttonGroup")
self.buttonGroup.addButton(self.phase_before_button)
self.verticalLayout_3.addWidget(self.phase_before_button)
self.phase_after_button = QtWidgets.QRadioButton(self.ft_box)
self.phase_after_button.setObjectName("phase_after_button")
self.buttonGroup.addButton(self.phase_after_button)
self.verticalLayout_3.addWidget(self.phase_after_button)
self.verticalLayout.addWidget(self.ft_box)
spacerItem = QtWidgets.QSpacerItem(20, 40, QtWidgets.QSizePolicy.Minimum, QtWidgets.QSizePolicy.Expanding)
self.verticalLayout.addItem(spacerItem)
self.gridLayout.addWidget(self.widget, 2, 0, 1, 1)
self.gridLayout.addLayout(self.widget_layout, 1, 0, 1, 2)
self.buttonBox = QtWidgets.QDialogButtonBox(ApodEdit)
self.buttonBox.setOrientation(QtCore.Qt.Horizontal)
self.buttonBox.setStandardButtons(QtWidgets.QDialogButtonBox.Cancel|QtWidgets.QDialogButtonBox.Ok)
self.buttonBox.setObjectName("buttonBox")
self.gridLayout.addWidget(self.buttonBox, 4, 1, 1, 2)
self.log_freq_widget = QtWidgets.QWidget(ApodEdit)
self.log_freq_widget.setObjectName("log_freq_widget")
self.horizontalLayout_3 = QtWidgets.QHBoxLayout(self.log_freq_widget)
self.horizontalLayout_3.setObjectName("horizontalLayout_3")
spacerItem1 = QtWidgets.QSpacerItem(40, 20, QtWidgets.QSizePolicy.Expanding, QtWidgets.QSizePolicy.Minimum)
self.horizontalLayout_3.addItem(spacerItem1)
self.logx_freq = QtWidgets.QCheckBox(self.log_freq_widget)
self.logx_freq.setObjectName("logx_freq")
self.horizontalLayout_3.addWidget(self.logx_freq)
self.logy_freq = QtWidgets.QCheckBox(self.log_freq_widget)
self.logy_freq.setObjectName("logy_freq")
self.horizontalLayout_3.addWidget(self.logy_freq)
self.gridLayout.addWidget(self.log_freq_widget, 3, 2, 1, 1)
self.logtime_widget = QtWidgets.QWidget(ApodEdit)
self.logtime_widget.setObjectName("logtime_widget")
self.horizontalLayout_2 = QtWidgets.QHBoxLayout(self.logtime_widget)
self.horizontalLayout_2.setContentsMargins(-1, 1, -1, -1)
self.horizontalLayout_2.setObjectName("horizontalLayout_2")
spacerItem2 = QtWidgets.QSpacerItem(40, 20, QtWidgets.QSizePolicy.Expanding, QtWidgets.QSizePolicy.Minimum)
self.horizontalLayout_2.addItem(spacerItem2)
self.logx_time = QtWidgets.QCheckBox(self.logtime_widget)
self.logx_time.setObjectName("logx_time")
self.horizontalLayout_2.addWidget(self.logx_time)
self.logy_time = QtWidgets.QCheckBox(self.logtime_widget)
self.logy_time.setObjectName("logy_time")
self.horizontalLayout_2.addWidget(self.logy_time)
self.gridLayout.addWidget(self.logtime_widget, 3, 1, 1, 1)
self.gridLayout.addWidget(self.buttonBox, 4, 0, 1, 2)
self.eqn_label = QtWidgets.QLabel(ApodEdit)
sizePolicy = QtWidgets.QSizePolicy(QtWidgets.QSizePolicy.MinimumExpanding, QtWidgets.QSizePolicy.Preferred)
sizePolicy.setHorizontalStretch(0)
sizePolicy.setVerticalStretch(0)
sizePolicy.setHeightForWidth(self.eqn_label.sizePolicy().hasHeightForWidth())
self.eqn_label.setSizePolicy(sizePolicy)
self.eqn_label.setIndent(3)
self.eqn_label.setObjectName("eqn_label")
self.gridLayout.addWidget(self.eqn_label, 0, 1, 1, 1)
self.retranslateUi(ApodEdit)
self.buttonBox.accepted.connect(ApodEdit.accept) # type: ignore
self.buttonBox.rejected.connect(ApodEdit.close) # type: ignore
self.buttonBox.accepted.connect(ApodEdit.accept)
self.buttonBox.rejected.connect(ApodEdit.close)
QtCore.QMetaObject.connectSlotsByName(ApodEdit)
def retranslateUi(self, ApodEdit):
_translate = QtCore.QCoreApplication.translate
ApodEdit.setWindowTitle(_translate("ApodEdit", "Apodization"))
self.baseline_box.setText(_translate("ApodEdit", "Baseline"))
self.shift_box.setTitle(_translate("ApodEdit", "Shift"))
self.ls_lineedit.setText(_translate("ApodEdit", "0"))
self.ls_combobox.setItemText(0, _translate("ApodEdit", "Points"))
self.ls_combobox.setItemText(1, _translate("ApodEdit", "Seconds"))
self.apod_box.setTitle(_translate("ApodEdit", "Apodization"))
self.eqn_label.setText(_translate("ApodEdit", "TextLabel"))
self.zerofill_box.setTitle(_translate("ApodEdit", "Zero fill"))
self.label.setText(_translate("ApodEdit", "Double length"))
self.zf_spinbox.setSuffix(_translate("ApodEdit", "x"))
self.phase_box.setTitle(_translate("ApodEdit", "Phase correction"))
self.label_3.setText(_translate("ApodEdit", "Phase 1"))
self.label_4.setText(_translate("ApodEdit", "Pivot"))
self.pivot_lineedit.setText(_translate("ApodEdit", "0"))
self.label_2.setText(_translate("ApodEdit", "Phase 0"))
self.ft_box.setTitle(_translate("ApodEdit", "Fourier transform"))
self.phase_before_button.setText(_translate("ApodEdit", "before phase correction"))
self.phase_after_button.setText(_translate("ApodEdit", "after phase correction"))
self.logx_freq.setText(_translate("ApodEdit", "Log X"))
self.logy_freq.setText(_translate("ApodEdit", "Log Y"))
self.logx_time.setText(_translate("ApodEdit", "Log X"))
self.logy_time.setText(_translate("ApodEdit", "Log Y"))
from ..lib.graph_items import NMRPlotWidget
from pyqtgraph import PlotWidget

298
src/gui_qt/_py/asciidialog.py
View File

@ -2,7 +2,7 @@
# Form implementation generated from reading ui file 'src/resources/_ui/asciidialog.ui'
#
# Created by: PyQt5 UI code generator 5.15.9
# Created by: PyQt5 UI code generator 5.15.7
#
# WARNING: Any manual changes made to this file will be lost when pyuic5 is
# run again. Do not edit this file unless you know what you are doing.
@ -14,7 +14,7 @@ from PyQt5 import QtCore, QtGui, QtWidgets
class Ui_ascii_reader(object):
def setupUi(self, ascii_reader):
ascii_reader.setObjectName("ascii_reader")
ascii_reader.resize(665, 904)
ascii_reader.resize(627, 703)
self.verticalLayout = QtWidgets.QVBoxLayout(ascii_reader)
self.verticalLayout.setObjectName("verticalLayout")
self.tabWidget = QtWidgets.QTabWidget(ascii_reader)
@ -28,111 +28,18 @@ class Ui_ascii_reader(object):
self.header_widget.setObjectName("header_widget")
self.verticalLayout_3.addWidget(self.header_widget)
self.groupBox = QtWidgets.QGroupBox(self.tabWidgetPage1)
sizePolicy = QtWidgets.QSizePolicy(QtWidgets.QSizePolicy.Preferred, QtWidgets.QSizePolicy.Maximum)
sizePolicy.setHorizontalStretch(0)
sizePolicy.setVerticalStretch(0)
sizePolicy.setHeightForWidth(self.groupBox.sizePolicy().hasHeightForWidth())
self.groupBox.setSizePolicy(sizePolicy)
self.groupBox.setObjectName("groupBox")
self.horizontalLayout_4 = QtWidgets.QHBoxLayout(self.groupBox)
self.horizontalLayout_4.setContentsMargins(3, 3, 3, 3)
self.horizontalLayout_4.setObjectName("horizontalLayout_4")
self.verticalLayout_6 = QtWidgets.QVBoxLayout()
self.verticalLayout_6.setObjectName("verticalLayout_6")
self.column_checkBox = QtWidgets.QCheckBox(self.groupBox)
sizePolicy = QtWidgets.QSizePolicy(QtWidgets.QSizePolicy.MinimumExpanding, QtWidgets.QSizePolicy.Preferred)
sizePolicy.setHorizontalStretch(0)
sizePolicy.setVerticalStretch(0)
sizePolicy.setHeightForWidth(self.column_checkBox.sizePolicy().hasHeightForWidth())
self.column_checkBox.setSizePolicy(sizePolicy)
self.column_checkBox.setObjectName("column_checkBox")
self.verticalLayout_6.addWidget(self.column_checkBox)
self.line_spinBox = QtWidgets.QSpinBox(self.groupBox)
sizePolicy = QtWidgets.QSizePolicy(QtWidgets.QSizePolicy.Preferred, QtWidgets.QSizePolicy.Fixed)
sizePolicy.setHorizontalStretch(0)
sizePolicy.setVerticalStretch(0)
sizePolicy.setHeightForWidth(self.line_spinBox.sizePolicy().hasHeightForWidth())
self.line_spinBox.setSizePolicy(sizePolicy)
self.line_spinBox.setMinimum(1)
self.line_spinBox.setObjectName("line_spinBox")
self.verticalLayout_6.addWidget(self.line_spinBox)
self.label_6 = QtWidgets.QLabel(self.groupBox)
self.label_6.setObjectName("label_6")
self.verticalLayout_6.addWidget(self.label_6)
self.preview_spinBox = QtWidgets.QSpinBox(self.groupBox)
self.preview_spinBox.setMinimum(1)
self.preview_spinBox.setProperty("value", 10)
self.preview_spinBox.setObjectName("preview_spinBox")
self.verticalLayout_6.addWidget(self.preview_spinBox)
spacerItem = QtWidgets.QSpacerItem(20, 40, QtWidgets.QSizePolicy.Minimum, QtWidgets.QSizePolicy.Expanding)
self.verticalLayout_6.addItem(spacerItem)
self.horizontalLayout_4.addLayout(self.verticalLayout_6)
self.verticalLayout_5 = QtWidgets.QVBoxLayout()
self.verticalLayout_5.setObjectName("verticalLayout_5")
self.label = QtWidgets.QLabel(self.groupBox)
sizePolicy = QtWidgets.QSizePolicy(QtWidgets.QSizePolicy.MinimumExpanding, QtWidgets.QSizePolicy.Preferred)
sizePolicy.setHorizontalStretch(0)
sizePolicy.setVerticalStretch(0)
sizePolicy.setHeightForWidth(self.label.sizePolicy().hasHeightForWidth())
self.label.setSizePolicy(sizePolicy)
self.label.setObjectName("label")
self.verticalLayout_5.addWidget(self.label)
self.pts_radioButton = QtWidgets.QRadioButton(self.groupBox)
self.pts_radioButton.setChecked(True)
self.pts_radioButton.setAutoExclusive(True)
self.pts_radioButton.setObjectName("pts_radioButton")
self.buttonGroup = QtWidgets.QButtonGroup(ascii_reader)
self.buttonGroup.setObjectName("buttonGroup")
self.buttonGroup.addButton(self.pts_radioButton)
self.verticalLayout_5.addWidget(self.pts_radioButton)
self.dsc_radioButton = QtWidgets.QRadioButton(self.groupBox)
self.dsc_radioButton.setObjectName("dsc_radioButton")
self.buttonGroup.addButton(self.dsc_radioButton)
self.verticalLayout_5.addWidget(self.dsc_radioButton)
self.gridLayout = QtWidgets.QGridLayout(self.groupBox)
self.gridLayout.setContentsMargins(3, 3, 3, 3)
self.gridLayout.setHorizontalSpacing(9)
self.gridLayout.setObjectName("gridLayout")
self.FID_radioButton = QtWidgets.QRadioButton(self.groupBox)
self.FID_radioButton.setAutoExclusive(True)
self.FID_radioButton.setObjectName("FID_radioButton")
self.buttonGroup = QtWidgets.QButtonGroup(ascii_reader)
self.buttonGroup.setObjectName("buttonGroup")
self.buttonGroup.addButton(self.FID_radioButton)
self.verticalLayout_5.addWidget(self.FID_radioButton)
self.spectrum_radioButton = QtWidgets.QRadioButton(self.groupBox)
self.spectrum_radioButton.setObjectName("spectrum_radioButton")
self.buttonGroup.addButton(self.spectrum_radioButton)
self.verticalLayout_5.addWidget(self.spectrum_radioButton)
self.bds_radioButton = QtWidgets.QRadioButton(self.groupBox)
self.bds_radioButton.setObjectName("bds_radioButton")
self.buttonGroup.addButton(self.bds_radioButton)
self.verticalLayout_5.addWidget(self.bds_radioButton)
self.horizontalLayout_4.addLayout(self.verticalLayout_5)
self.gridLayout_2 = QtWidgets.QGridLayout()
self.gridLayout_2.setObjectName("gridLayout_2")
self.deltay_lineEdit = QtWidgets.QLineEdit(self.groupBox)
sizePolicy = QtWidgets.QSizePolicy(QtWidgets.QSizePolicy.Maximum, QtWidgets.QSizePolicy.Fixed)
sizePolicy.setHorizontalStretch(0)
sizePolicy.setVerticalStretch(0)
sizePolicy.setHeightForWidth(self.deltay_lineEdit.sizePolicy().hasHeightForWidth())
self.deltay_lineEdit.setSizePolicy(sizePolicy)
self.deltay_lineEdit.setObjectName("deltay_lineEdit")
self.gridLayout_2.addWidget(self.deltay_lineEdit, 3, 1, 1, 1)
self.label_7 = QtWidgets.QLabel(self.groupBox)
sizePolicy = QtWidgets.QSizePolicy(QtWidgets.QSizePolicy.MinimumExpanding, QtWidgets.QSizePolicy.Preferred)
sizePolicy.setHorizontalStretch(0)
sizePolicy.setVerticalStretch(0)
sizePolicy.setHeightForWidth(self.label_7.sizePolicy().hasHeightForWidth())
self.label_7.setSizePolicy(sizePolicy)
self.label_7.setObjectName("label_7")
self.gridLayout_2.addWidget(self.label_7, 0, 0, 1, 2)
self.y_lineedit = QtWidgets.QLineEdit(self.groupBox)
sizePolicy = QtWidgets.QSizePolicy(QtWidgets.QSizePolicy.Maximum, QtWidgets.QSizePolicy.Fixed)
sizePolicy.setHorizontalStretch(0)
sizePolicy.setVerticalStretch(0)
sizePolicy.setHeightForWidth(self.y_lineedit.sizePolicy().hasHeightForWidth())
self.y_lineedit.setSizePolicy(sizePolicy)
self.y_lineedit.setInputMethodHints(QtCore.Qt.ImhFormattedNumbersOnly|QtCore.Qt.ImhPreferNumbers)
self.y_lineedit.setObjectName("y_lineedit")
self.gridLayout_2.addWidget(self.y_lineedit, 2, 1, 1, 1)
self.y_label = QtWidgets.QLabel(self.groupBox)
self.y_label.setObjectName("y_label")
self.gridLayout_2.addWidget(self.y_label, 2, 0, 1, 1)
self.gridLayout.addWidget(self.FID_radioButton, 2, 1, 1, 1)
self.x_lineedit = QtWidgets.QLineEdit(self.groupBox)
sizePolicy = QtWidgets.QSizePolicy(QtWidgets.QSizePolicy.Maximum, QtWidgets.QSizePolicy.Fixed)
sizePolicy.setHorizontalStretch(0)
@ -141,10 +48,64 @@ class Ui_ascii_reader(object):
self.x_lineedit.setSizePolicy(sizePolicy)
self.x_lineedit.setInputMethodHints(QtCore.Qt.ImhFormattedNumbersOnly|QtCore.Qt.ImhPreferNumbers)
self.x_lineedit.setObjectName("x_lineedit")
self.gridLayout_2.addWidget(self.x_lineedit, 1, 1, 1, 1)
self.gridLayout.addWidget(self.x_lineedit, 1, 3, 1, 1)
self.y_label = QtWidgets.QLabel(self.groupBox)
self.y_label.setObjectName("y_label")
self.gridLayout.addWidget(self.y_label, 2, 2, 1, 1)
self.pts_radioButton = QtWidgets.QRadioButton(self.groupBox)
self.pts_radioButton.setChecked(True)
self.pts_radioButton.setAutoExclusive(True)
self.pts_radioButton.setObjectName("pts_radioButton")
self.buttonGroup.addButton(self.pts_radioButton)
self.gridLayout.addWidget(self.pts_radioButton, 1, 1, 1, 1)
self.deltay_lineEdit = QtWidgets.QLineEdit(self.groupBox)
sizePolicy = QtWidgets.QSizePolicy(QtWidgets.QSizePolicy.Maximum, QtWidgets.QSizePolicy.Fixed)
sizePolicy.setHorizontalStretch(0)
sizePolicy.setVerticalStretch(0)
sizePolicy.setHeightForWidth(self.deltay_lineEdit.sizePolicy().hasHeightForWidth())
self.deltay_lineEdit.setSizePolicy(sizePolicy)
self.deltay_lineEdit.setObjectName("deltay_lineEdit")
self.gridLayout.addWidget(self.deltay_lineEdit, 3, 3, 1, 1)
self.label_5 = QtWidgets.QLabel(self.groupBox)
self.label_5.setObjectName("label_5")
self.gridLayout_2.addWidget(self.label_5, 3, 0, 1, 1)
self.gridLayout.addWidget(self.label_5, 3, 2, 1, 1)
self.column_checkBox = QtWidgets.QCheckBox(self.groupBox)
sizePolicy = QtWidgets.QSizePolicy(QtWidgets.QSizePolicy.MinimumExpanding, QtWidgets.QSizePolicy.Fixed)
sizePolicy.setHorizontalStretch(0)
sizePolicy.setVerticalStretch(0)
sizePolicy.setHeightForWidth(self.column_checkBox.sizePolicy().hasHeightForWidth())
self.column_checkBox.setSizePolicy(sizePolicy)
self.column_checkBox.setObjectName("column_checkBox")
self.gridLayout.addWidget(self.column_checkBox, 0, 0, 1, 1)
self.label = QtWidgets.QLabel(self.groupBox)
sizePolicy = QtWidgets.QSizePolicy(QtWidgets.QSizePolicy.MinimumExpanding, QtWidgets.QSizePolicy.Preferred)
sizePolicy.setHorizontalStretch(0)
sizePolicy.setVerticalStretch(0)
sizePolicy.setHeightForWidth(self.label.sizePolicy().hasHeightForWidth())
self.label.setSizePolicy(sizePolicy)
self.label.setObjectName("label")
self.gridLayout.addWidget(self.label, 0, 1, 1, 1)
self.label_7 = QtWidgets.QLabel(self.groupBox)
sizePolicy = QtWidgets.QSizePolicy(QtWidgets.QSizePolicy.MinimumExpanding, QtWidgets.QSizePolicy.Preferred)
sizePolicy.setHorizontalStretch(0)
sizePolicy.setVerticalStretch(0)
sizePolicy.setHeightForWidth(self.label_7.sizePolicy().hasHeightForWidth())
self.label_7.setSizePolicy(sizePolicy)
self.label_7.setObjectName("label_7")
self.gridLayout.addWidget(self.label_7, 0, 2, 1, 2)
self.y_lineedit = QtWidgets.QLineEdit(self.groupBox)
sizePolicy = QtWidgets.QSizePolicy(QtWidgets.QSizePolicy.Maximum, QtWidgets.QSizePolicy.Fixed)
sizePolicy.setHorizontalStretch(0)
sizePolicy.setVerticalStretch(0)
sizePolicy.setHeightForWidth(self.y_lineedit.sizePolicy().hasHeightForWidth())
self.y_lineedit.setSizePolicy(sizePolicy)
self.y_lineedit.setInputMethodHints(QtCore.Qt.ImhFormattedNumbersOnly|QtCore.Qt.ImhPreferNumbers)
self.y_lineedit.setObjectName("y_lineedit")
self.gridLayout.addWidget(self.y_lineedit, 2, 3, 1, 1)
self.spectrum_radioButton = QtWidgets.QRadioButton(self.groupBox)
self.spectrum_radioButton.setObjectName("spectrum_radioButton")
self.buttonGroup.addButton(self.spectrum_radioButton)
self.gridLayout.addWidget(self.spectrum_radioButton, 3, 1, 1, 1)
self.x_label = QtWidgets.QLabel(self.groupBox)
sizePolicy = QtWidgets.QSizePolicy(QtWidgets.QSizePolicy.Maximum, QtWidgets.QSizePolicy.Preferred)
sizePolicy.setHorizontalStretch(0)
@ -152,61 +113,26 @@ class Ui_ascii_reader(object):
sizePolicy.setHeightForWidth(self.x_label.sizePolicy().hasHeightForWidth())
self.x_label.setSizePolicy(sizePolicy)
self.x_label.setObjectName("x_label")
self.gridLayout_2.addWidget(self.x_label, 1, 0, 1, 1)
spacerItem1 = QtWidgets.QSpacerItem(20, 40, QtWidgets.QSizePolicy.Minimum, QtWidgets.QSizePolicy.Expanding)
self.gridLayout_2.addItem(spacerItem1, 4, 1, 1, 1)
self.horizontalLayout_4.addLayout(self.gridLayout_2)
self.gridLayout.addWidget(self.x_label, 1, 2, 1, 1)
self.line_spinBox = QtWidgets.QSpinBox(self.groupBox)
sizePolicy = QtWidgets.QSizePolicy(QtWidgets.QSizePolicy.Preferred, QtWidgets.QSizePolicy.Fixed)
sizePolicy.setHorizontalStretch(0)
sizePolicy.setVerticalStretch(0)
sizePolicy.setHeightForWidth(self.line_spinBox.sizePolicy().hasHeightForWidth())
self.line_spinBox.setSizePolicy(sizePolicy)
self.line_spinBox.setMinimum(1)
self.line_spinBox.setObjectName("line_spinBox")
self.gridLayout.addWidget(self.line_spinBox, 1, 0, 1, 1)
self.preview_spinBox = QtWidgets.QSpinBox(self.groupBox)
self.preview_spinBox.setMinimum(1)
self.preview_spinBox.setProperty("value", 10)
self.preview_spinBox.setObjectName("preview_spinBox")
self.gridLayout.addWidget(self.preview_spinBox, 3, 0, 1, 1)
self.label_6 = QtWidgets.QLabel(self.groupBox)
self.label_6.setObjectName("label_6")
self.gridLayout.addWidget(self.label_6, 2, 0, 1, 1)
self.verticalLayout_3.addWidget(self.groupBox)
self.dsdfsf = QtWidgets.QLabel(self.tabWidgetPage1)
self.dsdfsf.setObjectName("dsdfsf")
self.verticalLayout_3.addWidget(self.dsdfsf)
self.gridLayout = QtWidgets.QGridLayout()
self.gridLayout.setObjectName("gridLayout")
self.re_match_index = QtWidgets.QSpinBox(self.tabWidgetPage1)
self.re_match_index.setMinimum(1)
self.re_match_index.setObjectName("re_match_index")
self.gridLayout.addWidget(self.re_match_index, 1, 3, 1, 1)
self.label_9 = QtWidgets.QLabel(self.tabWidgetPage1)
self.label_9.setObjectName("label_9")
self.gridLayout.addWidget(self.label_9, 1, 2, 1, 1)
self.regex_input = QtWidgets.QLineEdit(self.tabWidgetPage1)
sizePolicy = QtWidgets.QSizePolicy(QtWidgets.QSizePolicy.Preferred, QtWidgets.QSizePolicy.Fixed)
sizePolicy.setHorizontalStretch(0)
sizePolicy.setVerticalStretch(0)
sizePolicy.setHeightForWidth(self.regex_input.sizePolicy().hasHeightForWidth())
self.regex_input.setSizePolicy(sizePolicy)
self.regex_input.setObjectName("regex_input")
self.gridLayout.addWidget(self.regex_input, 1, 1, 1, 1)
self.re_button = QtWidgets.QRadioButton(self.tabWidgetPage1)
self.re_button.setChecked(True)
self.re_button.setObjectName("re_button")
self.buttonGroup_2 = QtWidgets.QButtonGroup(ascii_reader)
self.buttonGroup_2.setObjectName("buttonGroup_2")
self.buttonGroup_2.addButton(self.re_button)
self.gridLayout.addWidget(self.re_button, 1, 0, 1, 1)
self.custom_input = QtWidgets.QLineEdit(self.tabWidgetPage1)
sizePolicy = QtWidgets.QSizePolicy(QtWidgets.QSizePolicy.Preferred, QtWidgets.QSizePolicy.Fixed)
sizePolicy.setHorizontalStretch(0)
sizePolicy.setVerticalStretch(0)
sizePolicy.setHeightForWidth(self.custom_input.sizePolicy().hasHeightForWidth())
self.custom_input.setSizePolicy(sizePolicy)
self.custom_input.setObjectName("custom_input")
self.gridLayout.addWidget(self.custom_input, 2, 1, 1, 1)
self.custom_button = QtWidgets.QRadioButton(self.tabWidgetPage1)
self.custom_button.setObjectName("custom_button")
self.buttonGroup_2.addButton(self.custom_button)
self.gridLayout.addWidget(self.custom_button, 2, 0, 1, 1)
self.label_8 = QtWidgets.QLabel(self.tabWidgetPage1)
self.label_8.setWordWrap(True)
self.label_8.setObjectName("label_8")
self.gridLayout.addWidget(self.label_8, 0, 0, 1, 4)
self.verticalLayout_3.addLayout(self.gridLayout)
self.groupBox_2 = QtWidgets.QGroupBox(self.tabWidgetPage1)
sizePolicy = QtWidgets.QSizePolicy(QtWidgets.QSizePolicy.Preferred, QtWidgets.QSizePolicy.MinimumExpanding)
sizePolicy.setHorizontalStretch(0)
sizePolicy.setVerticalStretch(0)
sizePolicy.setHeightForWidth(self.groupBox_2.sizePolicy().hasHeightForWidth())
self.groupBox_2.setSizePolicy(sizePolicy)
self.groupBox_2.setObjectName("groupBox_2")
self.verticalLayout_2 = QtWidgets.QVBoxLayout(self.groupBox_2)
self.verticalLayout_2.setContentsMargins(3, 3, 3, 3)
@ -289,19 +215,24 @@ class Ui_ascii_reader(object):
self.pushButton.setSizePolicy(sizePolicy)
self.pushButton.setObjectName("pushButton")
self.formLayout.setWidget(5, QtWidgets.QFormLayout.FieldRole, self.pushButton)
spacerItem2 = QtWidgets.QSpacerItem(20, 40, QtWidgets.QSizePolicy.Minimum, QtWidgets.QSizePolicy.Expanding)
self.formLayout.setItem(6, QtWidgets.QFormLayout.FieldRole, spacerItem2)
spacerItem = QtWidgets.QSpacerItem(20, 40, QtWidgets.QSizePolicy.Minimum, QtWidgets.QSizePolicy.Expanding)
self.formLayout.setItem(6, QtWidgets.QFormLayout.FieldRole, spacerItem)
self.horizontalLayout_3.addLayout(self.formLayout)
self.tabWidget.addTab(self.tabWidgetPage2, "")
self.verticalLayout.addWidget(self.tabWidget)
self.horizontalLayout = QtWidgets.QHBoxLayout()
self.horizontalLayout.setObjectName("horizontalLayout")
spacerItem1 = QtWidgets.QSpacerItem(40, 20, QtWidgets.QSizePolicy.Expanding, QtWidgets.QSizePolicy.Minimum)
self.horizontalLayout.addItem(spacerItem1)
self.verticalLayout.addLayout(self.horizontalLayout)
self.horizontalLayout_2 = QtWidgets.QHBoxLayout()
self.horizontalLayout_2.setContentsMargins(-1, 0, -1, -1)
self.horizontalLayout_2.setObjectName("horizontalLayout_2")
spacerItem3 = QtWidgets.QSpacerItem(40, 20, QtWidgets.QSizePolicy.Expanding, QtWidgets.QSizePolicy.Minimum)
self.horizontalLayout_2.addItem(spacerItem3)
self.skippy_checkbox = QtWidgets.QCheckBox(ascii_reader)
self.skippy_checkbox.setObjectName("skippy_checkbox")
self.horizontalLayout_2.addWidget(self.skippy_checkbox)
spacerItem2 = QtWidgets.QSpacerItem(40, 20, QtWidgets.QSizePolicy.Expanding, QtWidgets.QSizePolicy.Minimum)
self.horizontalLayout_2.addItem(spacerItem2)
self.verticalLayout.addLayout(self.horizontalLayout_2)
self.buttonbox = QtWidgets.QDialogButtonBox(ascii_reader)
self.buttonbox.setStandardButtons(QtWidgets.QDialogButtonBox.Apply|QtWidgets.QDialogButtonBox.Cancel|QtWidgets.QDialogButtonBox.Ok)
@ -316,20 +247,14 @@ class Ui_ascii_reader(object):
ascii_reader.setTabOrder(self.column_checkBox, self.line_spinBox)
ascii_reader.setTabOrder(self.line_spinBox, self.preview_spinBox)
ascii_reader.setTabOrder(self.preview_spinBox, self.pts_radioButton)
ascii_reader.setTabOrder(self.pts_radioButton, self.dsc_radioButton)
ascii_reader.setTabOrder(self.dsc_radioButton, self.FID_radioButton)
ascii_reader.setTabOrder(self.pts_radioButton, self.FID_radioButton)
ascii_reader.setTabOrder(self.FID_radioButton, self.spectrum_radioButton)
ascii_reader.setTabOrder(self.spectrum_radioButton, self.bds_radioButton)
ascii_reader.setTabOrder(self.bds_radioButton, self.x_lineedit)
ascii_reader.setTabOrder(self.spectrum_radioButton, self.x_lineedit)
ascii_reader.setTabOrder(self.x_lineedit, self.y_lineedit)
ascii_reader.setTabOrder(self.y_lineedit, self.deltay_lineEdit)
ascii_reader.setTabOrder(self.deltay_lineEdit, self.re_button)
ascii_reader.setTabOrder(self.re_button, self.regex_input)
ascii_reader.setTabOrder(self.regex_input, self.re_match_index)
ascii_reader.setTabOrder(self.re_match_index, self.custom_button)
ascii_reader.setTabOrder(self.custom_button, self.custom_input)
ascii_reader.setTabOrder(self.custom_input, self.ascii_table)
ascii_reader.setTabOrder(self.ascii_table, self.delay_textfield)
ascii_reader.setTabOrder(self.deltay_lineEdit, self.ascii_table)
ascii_reader.setTabOrder(self.ascii_table, self.skippy_checkbox)
ascii_reader.setTabOrder(self.skippy_checkbox, self.delay_textfield)
ascii_reader.setTabOrder(self.delay_textfield, self.delay_lineedit)
ascii_reader.setTabOrder(self.delay_lineedit, self.start_lineedit)
ascii_reader.setTabOrder(self.start_lineedit, self.end_lineedit)
@ -337,33 +262,24 @@ class Ui_ascii_reader(object):
ascii_reader.setTabOrder(self.log_checkBox, self.staggered_checkBox)
ascii_reader.setTabOrder(self.staggered_checkBox, self.stag_lineEdit)
ascii_reader.setTabOrder(self.stag_lineEdit, self.pushButton)
ascii_reader.setTabOrder(self.pushButton, self.skippy_checkbox)
def retranslateUi(self, ascii_reader):
_translate = QtCore.QCoreApplication.translate
ascii_reader.setWindowTitle(_translate("ascii_reader", "Read text file"))
self.groupBox.setTitle(_translate("ascii_reader", "Options"))
self.FID_radioButton.setText(_translate("ascii_reader", "FID"))
self.x_lineedit.setToolTip(_translate("ascii_reader", "<html><head/><body><p>Specify which column is used as x-value.</p></body></html>"))
self.y_label.setText(_translate("ascii_reader", "y"))
self.pts_radioButton.setText(_translate("ascii_reader", "Points"))
self.label_5.setText(_translate("ascii_reader", "<html><head/><body><p>Δy</p></body></html>"))
self.column_checkBox.setText(_translate("ascii_reader", "Column name"))
self.label.setText(_translate("ascii_reader", "Import as"))
self.label_7.setText(_translate("ascii_reader", "Use columns as"))
self.y_lineedit.setToolTip(_translate("ascii_reader", "<html><head/><body><p>Specify which columns are read for y-values. (\'Points\': Every number creates a new data set;\'FID\'/\'Spectrum\': Numbers at even positions are used for real parts, at odd positions for imaginary parts.)</p></body></html>"))
self.spectrum_radioButton.setText(_translate("ascii_reader", "Spectrum"))
self.x_label.setText(_translate("ascii_reader", "x"))
self.line_spinBox.setPrefix(_translate("ascii_reader", "header line "))
self.label_6.setText(_translate("ascii_reader", "Preview length"))
self.label.setText(_translate("ascii_reader", "Import as"))
self.pts_radioButton.setText(_translate("ascii_reader", "Points"))
self.dsc_radioButton.setText(_translate("ascii_reader", "DSC"))
self.FID_radioButton.setText(_translate("ascii_reader", "FID"))
self.spectrum_radioButton.setText(_translate("ascii_reader", "Spectrum"))
self.bds_radioButton.setText(_translate("ascii_reader", "BDS"))
self.label_7.setText(_translate("ascii_reader", "Use columns as"))
self.y_lineedit.setToolTip(_translate("ascii_reader", "<html><head/><body><p>Specify which columns are used for y values.</p><p>- \'Points\': Every number creates a new data set;<br/>- \'FID\'/\'Spectrum\': Numbers at even positions are used for real parts, at odd positions for imaginary parts.</p></body></html>"))
self.y_label.setText(_translate("ascii_reader", "y"))
self.x_lineedit.setToolTip(_translate("ascii_reader", "<html><head/><body><p>Specify which column is used for x values, write <span style=\" font-style:italic;\">index</span> to use row numbers (starting with 0). </p></body></html>"))
self.label_5.setText(_translate("ascii_reader", "<html><head/><body><p>Δy</p></body></html>"))
self.x_label.setText(_translate("ascii_reader", "x"))
self.dsdfsf.setText(_translate("ascii_reader", "Numerical value"))
self.label_9.setText(_translate("ascii_reader", "Match index"))
self.regex_input.setToolTip(_translate("ascii_reader", "<html><head/><body><p>Token:<br/>[abc]: Matches any of a, b, or c<br/>[a-z]: Matches any digit in the range a-z<br/>\\d: Matches any digit in the range 0-9 (equal to [0-9}</p><p>Quantifiers:<br/>a*: 0 or more of a<br/>a*: 1 or more of a<br/>a?: 0 or 1 of a</p></body></html>"))
self.re_button.setText(_translate("ascii_reader", "Regex"))
self.custom_button.setText(_translate("ascii_reader", "Custom value"))
self.label_8.setText(_translate("ascii_reader", "Filename"))
self.groupBox_2.setTitle(_translate("ascii_reader", "Preview"))
self.tabWidget.setTabText(self.tabWidget.indexOf(self.tabWidgetPage1), _translate("ascii_reader", "Data"))
self.label_2.setText(_translate("ascii_reader", "Number of delays"))

15
src/gui_qt/_py/baseline_dialog.py
View File

@ -1,11 +1,10 @@
# -*- coding: utf-8 -*-
# Form implementation generated from reading ui file 'src/resources/_ui/baseline_dialog.ui'
# Form implementation generated from reading ui file '_ui/baseline_dialog.ui'
#
# Created by: PyQt5 UI code generator 5.15.9
# Created by: PyQt5 UI code generator 5.12.3
#
# WARNING: Any manual changes made to this file will be lost when pyuic5 is
# run again. Do not edit this file unless you know what you are doing.
# WARNING! All changes made in this file will be lost!
from PyQt5 import QtCore, QtGui, QtWidgets
@ -45,7 +44,7 @@ class Ui_SignalEdit(object):
self.buttonBox.setStandardButtons(QtWidgets.QDialogButtonBox.Cancel|QtWidgets.QDialogButtonBox.Ok)
self.buttonBox.setObjectName("buttonBox")
self.gridLayout.addWidget(self.buttonBox, 1, 0, 1, 3)
self.graphicsView = NMRPlotWidget(SignalEdit)
self.graphicsView = PlotWidget(SignalEdit)
sizePolicy = QtWidgets.QSizePolicy(QtWidgets.QSizePolicy.MinimumExpanding, QtWidgets.QSizePolicy.Expanding)
sizePolicy.setHorizontalStretch(0)
sizePolicy.setVerticalStretch(0)
@ -55,11 +54,11 @@ class Ui_SignalEdit(object):
self.gridLayout.addWidget(self.graphicsView, 0, 2, 1, 1)
self.retranslateUi(SignalEdit)
self.buttonBox.accepted.connect(SignalEdit.accept) # type: ignore
self.buttonBox.rejected.connect(SignalEdit.close) # type: ignore
self.buttonBox.accepted.connect(SignalEdit.accept)
self.buttonBox.rejected.connect(SignalEdit.close)
QtCore.QMetaObject.connectSlotsByName(SignalEdit)
def retranslateUi(self, SignalEdit):
_translate = QtCore.QCoreApplication.translate
SignalEdit.setWindowTitle(_translate("SignalEdit", "Dialog"))
from ..lib.graph_items import NMRPlotWidget
from pyqtgraph import PlotWidget

37
src/gui_qt/_py/basewindow.py
View File

@ -2,7 +2,7 @@
# Form implementation generated from reading ui file 'src/resources/_ui/basewindow.ui'
#
# Created by: PyQt5 UI code generator 5.15.9
# Created by: PyQt5 UI code generator 5.15.7
#
# WARNING: Any manual changes made to this file will be lost when pyuic5 is
# run again. Do not edit this file unless you know what you are doing.
@ -70,7 +70,7 @@ class Ui_BaseWindow(object):
self.integralwidget = IntegralWidget()
self.integralwidget.setObjectName("integralwidget")
self.tabWidget.addTab(self.integralwidget, "")
self.area = MdiAreaTile(self.splitter)
self.area = QtWidgets.QMdiArea(self.splitter)
self.area.setObjectName("area")
self.horizontalLayout.addWidget(self.splitter)
BaseWindow.setCentralWidget(self.centralwidget)
@ -117,8 +117,6 @@ class Ui_BaseWindow(object):
self.menuStuff = QtWidgets.QMenu(self.menubar)
self.menuStuff.setTitle("")
self.menuStuff.setObjectName("menuStuff")
self.menuDSC = QtWidgets.QMenu(self.menubar)
self.menuDSC.setObjectName("menuDSC")
BaseWindow.setMenuBar(self.menubar)
self.toolBar = QtWidgets.QToolBar(BaseWindow)
sizePolicy = QtWidgets.QSizePolicy(QtWidgets.QSizePolicy.Preferred, QtWidgets.QSizePolicy.Fixed)
@ -263,10 +261,6 @@ class Ui_BaseWindow(object):
self.actionMaximize.setObjectName("actionMaximize")
self.actionTile = QtWidgets.QAction(BaseWindow)
self.actionTile.setObjectName("actionTile")
self.actionTileVertical = QtWidgets.QAction(BaseWindow)
self.actionTileVertical.setObjectName("actionTileVertical")
self.actionTileHorizontal = QtWidgets.QAction(BaseWindow)
self.actionTileHorizontal.setObjectName("actionTileHorizontal")
self.actionMinimize = QtWidgets.QAction(BaseWindow)
self.actionMinimize.setCheckable(True)
self.actionMinimize.setVisible(False)
@ -364,16 +358,6 @@ class Ui_BaseWindow(object):
self.actionBugs.setObjectName("actionBugs")
self.actionShow_error_log = QtWidgets.QAction(BaseWindow)
self.actionShow_error_log.setObjectName("actionShow_error_log")
self.actionCreate_starter = QtWidgets.QAction(BaseWindow)
self.actionCreate_starter.setObjectName("actionCreate_starter")
self.actionAbout = QtWidgets.QAction(BaseWindow)
self.actionAbout.setObjectName("actionAbout")
self.actionTNMH_model = QtWidgets.QAction(BaseWindow)
self.actionTNMH_model.setObjectName("actionTNMH_model")
self.actionBinning = QtWidgets.QAction(BaseWindow)
self.actionBinning.setObjectName("actionBinning")
self.actionTNMH = QtWidgets.QAction(BaseWindow)
self.actionTNMH.setObjectName("actionTNMH")
self.menuSave.addAction(self.actionSave)
self.menuSave.addAction(self.actionExportGraphic)
self.menuSave.addAction(self.action_save_fit_parameter)
@ -399,9 +383,9 @@ class Ui_BaseWindow(object):
self.menuData.addSeparator()
self.menuData.addAction(self.actionChange_datatypes)
self.menuHelp.addAction(self.actionShow_error_log)
self.menuHelp.addAction(self.actionDocumentation)
self.menuHelp.addAction(self.actionUpdate)
self.menuHelp.addAction(self.actionBugs)
self.menuHelp.addAction(self.actionAbout)
self.menuNormalize.addAction(self.action_norm_max)
self.menuNormalize.addAction(self.action_norm_max_abs)
self.menuNormalize.addSeparator()
@ -417,7 +401,6 @@ class Ui_BaseWindow(object):
self.menuExtra.addSeparator()
self.menuExtra.addAction(self.menuNormalize.menuAction())
self.menuExtra.addAction(self.actionInterpolation)
self.menuExtra.addAction(self.actionBinning)
self.menuExtra.addAction(self.actionRunning_values)
self.menuExtra.addAction(self.actionShift)
self.menuExtra.addSeparator()
@ -439,10 +422,7 @@ class Ui_BaseWindow(object):
self.menuOptions.addSeparator()
self.menuOptions.addAction(self.action_colorcycle)
self.menuOptions.addAction(self.actionConfiguration)
self.menuOptions.addAction(self.actionCreate_starter)
self.menuView.addAction(self.actionTile)
self.menuView.addAction(self.actionTileVertical)
self.menuView.addAction(self.actionTileHorizontal)
self.menuView.addAction(self.actionCascade_windows)
self.menuWindow.addAction(self.actionNew_window)
self.menuWindow.addAction(self.actionDelete_window)
@ -471,7 +451,6 @@ class Ui_BaseWindow(object):
self.menuStuff.addAction(self.actionLife)
self.menuStuff.addAction(self.actionTetris)
self.menuStuff.addAction(self.actionMine)
self.menuDSC.addAction(self.actionTNMH_model)
self.menubar.addAction(self.menuFile.menuAction())
self.menubar.addAction(self.menuWindow.menuAction())
self.menubar.addAction(self.menuData.menuAction())
@ -480,7 +459,6 @@ class Ui_BaseWindow(object):
self.menubar.addAction(self.menuFit.menuAction())
self.menubar.addAction(self.menuNMR.menuAction())
self.menubar.addAction(self.menuBDS.menuAction())
self.menubar.addAction(self.menuDSC.menuAction())
self.menubar.addAction(self.menuOptions.menuAction())
self.menubar.addAction(self.menuHelp.menuAction())
self.menubar.addAction(self.menuStuff.menuAction())
@ -533,7 +511,6 @@ class Ui_BaseWindow(object):
self.menuNMR.setTitle(_translate("BaseWindow", "NMR"))
self.menuBDS.setTitle(_translate("BaseWindow", "BDS"))
self.menuSpectrum.setTitle(_translate("BaseWindow", "Spectrum"))
self.menuDSC.setTitle(_translate("BaseWindow", "DSC"))
self.toolBar.setWindowTitle(_translate("BaseWindow", "Main"))
self.toolbar_edit.setWindowTitle(_translate("BaseWindow", "Math"))
self.toolBar_nmr.setWindowTitle(_translate("BaseWindow", "NMR"))
@ -589,8 +566,6 @@ class Ui_BaseWindow(object):
self.actionGuide_lines.setText(_translate("BaseWindow", "Draw lines..."))
self.actionMaximize.setText(_translate("BaseWindow", "Maximize"))
self.actionTile.setText(_translate("BaseWindow", "Tile windows"))
self.actionTileVertical.setText(_translate("BaseWindow", "Tile windows vertically"))
self.actionTileHorizontal.setText(_translate("BaseWindow", "Tile windows horizontally"))
self.actionMinimize.setText(_translate("BaseWindow", "Minimize"))
self.actionNew_window.setText(_translate("BaseWindow", "New graph"))
self.actionDelete_window.setText(_translate("BaseWindow", "Delete graph"))
@ -637,11 +612,6 @@ class Ui_BaseWindow(object):
self.action_draw_object.setText(_translate("BaseWindow", "Draw objects..."))
self.actionBugs.setText(_translate("BaseWindow", "Bugs! Problems! Wishes!"))
self.actionShow_error_log.setText(_translate("BaseWindow", "Show error log"))
self.actionCreate_starter.setText(_translate("BaseWindow", "Create starter.."))
self.actionAbout.setText(_translate("BaseWindow", "About..."))
self.actionTNMH_model.setText(_translate("BaseWindow", "Tg , Hodge, TNMH,,,"))
self.actionBinning.setText(_translate("BaseWindow", "Binning..."))
self.actionTNMH.setText(_translate("BaseWindow", "TNMH..."))
from ..data.datawidget.datawidget import DataWidget
from ..data.integral_widget import IntegralWidget
from ..data.point_select import PointSelectWidget
@ -649,5 +619,4 @@ from ..data.signaledit.editsignalwidget import EditSignalWidget
from ..data.valueeditwidget import ValueEditWidget
from ..fit.fitwindow import QFitDialog
from ..graphs.drawings import DrawingsWidget
from ..lib.mdiarea import MdiAreaTile
from ..nmr.t1widget import QT1Widget

18
src/gui_qt/_py/bdsdialog.py
View File

@ -1,16 +1,13 @@
# -*- coding: utf-8 -*-
# Form implementation generated from reading ui file 'src/resources/_ui/bdsdialog.ui'
# Form implementation generated from reading ui file 'resources/_ui/bdsdialog.ui'
#
# Created by: PyQt5 UI code generator 5.15.9
# Created by: PyQt5 UI code generator 5.9.2
#
# WARNING: Any manual changes made to this file will be lost when pyuic5 is
# run again. Do not edit this file unless you know what you are doing.
# WARNING! All changes made in this file will be lost!
from PyQt5 import QtCore, QtGui, QtWidgets
class Ui_Dialog(object):
def setupUi(self, Dialog):
Dialog.setObjectName("Dialog")
@ -19,13 +16,12 @@ class Ui_Dialog(object):
self.gridLayout.setContentsMargins(3, 3, 3, 3)
self.gridLayout.setSpacing(3)
self.gridLayout.setObjectName("gridLayout")
self.listWidget = QListWidgetSelect(Dialog)
self.listWidget = QtWidgets.QListWidget(Dialog)
sizePolicy = QtWidgets.QSizePolicy(QtWidgets.QSizePolicy.Expanding, QtWidgets.QSizePolicy.MinimumExpanding)
sizePolicy.setHorizontalStretch(0)
sizePolicy.setVerticalStretch(0)
sizePolicy.setHeightForWidth(self.listWidget.sizePolicy().hasHeightForWidth())
self.listWidget.setSizePolicy(sizePolicy)
self.listWidget.setSelectionMode(QtWidgets.QAbstractItemView.ExtendedSelection)
self.listWidget.setObjectName("listWidget")
self.gridLayout.addWidget(self.listWidget, 1, 0, 2, 1)
self.groupBox_2 = QtWidgets.QGroupBox(Dialog)
@ -97,8 +93,8 @@ class Ui_Dialog(object):
self.gridLayout.addWidget(self.label, 0, 0, 1, 2)
self.retranslateUi(Dialog)
self.buttonBox.accepted.connect(Dialog.accept) # type: ignore
self.buttonBox.rejected.connect(Dialog.reject) # type: ignore
self.buttonBox.accepted.connect(Dialog.accept)
self.buttonBox.rejected.connect(Dialog.reject)
QtCore.QMetaObject.connectSlotsByName(Dialog)
Dialog.setTabOrder(self.freq_button, self.temp_button)
Dialog.setTabOrder(self.temp_button, self.eps_checkBox)
@ -121,4 +117,4 @@ class Ui_Dialog(object):
self.temp_checkBox.setText(_translate("Dialog", "Meas. temperature"))
self.time_checkBox.setText(_translate("Dialog", "Meas. time"))
self.label.setText(_translate("Dialog", "Found entries"))
from ..lib.listwidget import QListWidgetSelect

258
src/gui_qt/_py/dscfile_dialog.py
View File

@ -1,113 +1,29 @@
# -*- coding: utf-8 -*-
# Form implementation generated from reading ui file 'src/resources/_ui/dscfile_dialog.ui'
# Form implementation generated from reading ui file 'resources/_ui/dscfile_dialog.ui'
#
# Created by: PyQt5 UI code generator 5.15.9
# Created by: PyQt5 UI code generator 5.9.2
#
# WARNING: Any manual changes made to this file will be lost when pyuic5 is
# run again. Do not edit this file unless you know what you are doing.
# WARNING! All changes made in this file will be lost!
from PyQt5 import QtCore, QtGui, QtWidgets
class Ui_Dialog(object):
def setupUi(self, Dialog):
Dialog.setObjectName("Dialog")
Dialog.resize(1341, 799)
self.verticalLayout_5 = QtWidgets.QVBoxLayout(Dialog)
self.verticalLayout_5.setObjectName("verticalLayout_5")
self.splitter = QtWidgets.QSplitter(Dialog)
self.splitter.setOrientation(QtCore.Qt.Horizontal)
self.splitter.setObjectName("splitter")
self.verticalLayoutWidget = QtWidgets.QWidget(self.splitter)
self.verticalLayoutWidget.setObjectName("verticalLayoutWidget")
self.verticalLayout_4 = QtWidgets.QVBoxLayout(self.verticalLayoutWidget)
self.verticalLayout_4.setContentsMargins(6, 6, 6, 6)
self.verticalLayout_4.setObjectName("verticalLayout_4")
self.groupBox = QtWidgets.QGroupBox(self.verticalLayoutWidget)
self.groupBox.setFlat(False)
self.groupBox.setObjectName("groupBox")
self.verticalLayout = QtWidgets.QVBoxLayout(self.groupBox)
self.verticalLayout.setContentsMargins(6, 6, 6, 6)
self.verticalLayout.setObjectName("verticalLayout")
self.step_listWidget = QtWidgets.QListWidget(self.groupBox)
sizePolicy = QtWidgets.QSizePolicy(QtWidgets.QSizePolicy.MinimumExpanding, QtWidgets.QSizePolicy.Minimum)
sizePolicy.setHorizontalStretch(0)
sizePolicy.setVerticalStretch(0)
sizePolicy.setHeightForWidth(self.step_listWidget.sizePolicy().hasHeightForWidth())
self.step_listWidget.setSizePolicy(sizePolicy)
self.step_listWidget.setMinimumSize(QtCore.QSize(0, 0))
self.step_listWidget.setObjectName("step_listWidget")
self.verticalLayout.addWidget(self.step_listWidget)
self.verticalLayout_4.addWidget(self.groupBox)
self.groupBox_2 = QtWidgets.QGroupBox(self.verticalLayoutWidget)
self.groupBox_2.setObjectName("groupBox_2")
self.verticalLayout_2 = QtWidgets.QVBoxLayout(self.groupBox_2)
self.verticalLayout_2.setContentsMargins(6, 6, 6, 6)
self.verticalLayout_2.setObjectName("verticalLayout_2")
self.groupBox_4 = QtWidgets.QGroupBox(self.groupBox_2)
self.groupBox_4.setObjectName("groupBox_4")
self.verticalLayout_6 = QtWidgets.QVBoxLayout(self.groupBox_4)
self.verticalLayout_6.setContentsMargins(6, 6, 6, 6)
self.verticalLayout_6.setObjectName("verticalLayout_6")
self.empty_label = QtWidgets.QLabel(self.groupBox_4)
self.empty_label.setObjectName("empty_label")
self.verticalLayout_6.addWidget(self.empty_label)
self.horizontalLayout_2 = QtWidgets.QHBoxLayout()
self.horizontalLayout_2.setSpacing(3)
self.horizontalLayout_2.setObjectName("horizontalLayout_2")
self.loadempty_button = QtWidgets.QPushButton(self.groupBox_4)
self.loadempty_button.setObjectName("loadempty_button")
self.horizontalLayout_2.addWidget(self.loadempty_button)
self.delempty_button = QtWidgets.QPushButton(self.groupBox_4)
self.delempty_button.setObjectName("delempty_button")
self.horizontalLayout_2.addWidget(self.delempty_button)
self.verticalLayout_6.addLayout(self.horizontalLayout_2)
self.verticalLayout_2.addWidget(self.groupBox_4)
self.groupBox_5 = QtWidgets.QGroupBox(self.groupBox_2)
self.groupBox_5.setObjectName("groupBox_5")
self.verticalLayout_7 = QtWidgets.QVBoxLayout(self.groupBox_5)
self.verticalLayout_7.setContentsMargins(6, 6, 6, 6)
self.verticalLayout_7.setSpacing(3)
self.verticalLayout_7.setObjectName("verticalLayout_7")
self.none_radioButton = QtWidgets.QRadioButton(self.groupBox_5)
self.none_radioButton.setObjectName("none_radioButton")
self.buttonGroup = QtWidgets.QButtonGroup(Dialog)
self.buttonGroup.setObjectName("buttonGroup")
self.buttonGroup.addButton(self.none_radioButton)
self.verticalLayout_7.addWidget(self.none_radioButton)
self.isotherm_radioButton = QtWidgets.QRadioButton(self.groupBox_5)
self.isotherm_radioButton.setChecked(True)
self.isotherm_radioButton.setObjectName("isotherm_radioButton")
self.buttonGroup.addButton(self.isotherm_radioButton)
self.verticalLayout_7.addWidget(self.isotherm_radioButton)
self.slope_radioButton = QtWidgets.QRadioButton(self.groupBox_5)
self.slope_radioButton.setObjectName("slope_radioButton")
self.buttonGroup.addButton(self.slope_radioButton)
self.verticalLayout_7.addWidget(self.slope_radioButton)
self.widget = QtWidgets.QWidget(self.groupBox_5)
self.widget.setMinimumSize(QtCore.QSize(0, 33))
self.widget.setObjectName("widget")
self.horizontalLayout_3 = QtWidgets.QHBoxLayout(self.widget)
self.horizontalLayout_3.setContentsMargins(3, 3, 3, 3)
self.horizontalLayout_3.setObjectName("horizontalLayout_3")
self.limit1_lineedit = QtWidgets.QLineEdit(self.widget)
self.limit1_lineedit.setObjectName("limit1_lineedit")
self.horizontalLayout_3.addWidget(self.limit1_lineedit)
self.limit2_lineedit = QtWidgets.QLineEdit(self.widget)
self.limit2_lineedit.setText("")
self.limit2_lineedit.setObjectName("limit2_lineedit")
self.horizontalLayout_3.addWidget(self.limit2_lineedit)
self.verticalLayout_7.addWidget(self.widget)
self.verticalLayout_2.addWidget(self.groupBox_5)
self.verticalLayout_4.addWidget(self.groupBox_2)
self.groupBox_3 = QtWidgets.QGroupBox(self.verticalLayoutWidget)
self.groupBox_3.setObjectName("groupBox_3")
self.verticalLayout_3 = QtWidgets.QVBoxLayout(self.groupBox_3)
self.verticalLayout_3.setContentsMargins(6, 6, 6, 6)
self.verticalLayout_3.setObjectName("verticalLayout_3")
self.cp_checkBox = QtWidgets.QCheckBox(self.groupBox_3)
Dialog.resize(962, 662)
self.gridLayout_2 = QtWidgets.QGridLayout(Dialog)
self.gridLayout_2.setObjectName("gridLayout_2")
self.buttonBox = QtWidgets.QDialogButtonBox(Dialog)
self.buttonBox.setOrientation(QtCore.Qt.Horizontal)
self.buttonBox.setStandardButtons(QtWidgets.QDialogButtonBox.Apply|QtWidgets.QDialogButtonBox.Cancel|QtWidgets.QDialogButtonBox.Ok|QtWidgets.QDialogButtonBox.Save)
self.buttonBox.setObjectName("buttonBox")
self.gridLayout_2.addWidget(self.buttonBox, 1, 1, 1, 1)
self.gridLayout_4 = QtWidgets.QGridLayout()
self.gridLayout_4.setContentsMargins(-1, 0, 0, -1)
self.gridLayout_4.setSpacing(3)
self.gridLayout_4.setObjectName("gridLayout_4")
self.cp_checkBox = QtWidgets.QCheckBox(Dialog)
sizePolicy = QtWidgets.QSizePolicy(QtWidgets.QSizePolicy.Minimum, QtWidgets.QSizePolicy.MinimumExpanding)
sizePolicy.setHorizontalStretch(0)
sizePolicy.setVerticalStretch(0)
@ -115,8 +31,36 @@ class Ui_Dialog(object):
self.cp_checkBox.setSizePolicy(sizePolicy)
self.cp_checkBox.setChecked(True)
self.cp_checkBox.setObjectName("cp_checkBox")
self.verticalLayout_3.addWidget(self.cp_checkBox)
self.reference_tableWidget = QtWidgets.QTableWidget(self.groupBox_3)
self.gridLayout_4.addWidget(self.cp_checkBox, 11, 0, 1, 4)
self.horizontalLayout_2 = QtWidgets.QHBoxLayout()
self.horizontalLayout_2.setSpacing(3)
self.horizontalLayout_2.setObjectName("horizontalLayout_2")
self.loadempty_button = QtWidgets.QPushButton(Dialog)
self.loadempty_button.setObjectName("loadempty_button")
self.horizontalLayout_2.addWidget(self.loadempty_button)
self.delempty_button = QtWidgets.QPushButton(Dialog)
self.delempty_button.setObjectName("delempty_button")
self.horizontalLayout_2.addWidget(self.delempty_button)
self.gridLayout_4.addLayout(self.horizontalLayout_2, 5, 0, 1, 4)
spacerItem = QtWidgets.QSpacerItem(20, 40, QtWidgets.QSizePolicy.Minimum, QtWidgets.QSizePolicy.Expanding)
self.gridLayout_4.addItem(spacerItem, 12, 0, 1, 1)
self.isotherm_radioButton = QtWidgets.QRadioButton(Dialog)
self.isotherm_radioButton.setChecked(True)
self.isotherm_radioButton.setObjectName("isotherm_radioButton")
self.buttonGroup = QtWidgets.QButtonGroup(Dialog)
self.buttonGroup.setObjectName("buttonGroup")
self.buttonGroup.addButton(self.isotherm_radioButton)
self.gridLayout_4.addWidget(self.isotherm_radioButton, 6, 1, 1, 1)
self.label_4 = QtWidgets.QLabel(Dialog)
sizePolicy = QtWidgets.QSizePolicy(QtWidgets.QSizePolicy.Preferred, QtWidgets.QSizePolicy.Maximum)
sizePolicy.setHorizontalStretch(0)
sizePolicy.setVerticalStretch(0)
sizePolicy.setHeightForWidth(self.label_4.sizePolicy().hasHeightForWidth())
self.label_4.setSizePolicy(sizePolicy)
self.label_4.setStyleSheet("font-weight: bold")
self.label_4.setObjectName("label_4")
self.gridLayout_4.addWidget(self.label_4, 0, 0, 1, 4)
self.reference_tableWidget = QtWidgets.QTableWidget(Dialog)
sizePolicy = QtWidgets.QSizePolicy(QtWidgets.QSizePolicy.MinimumExpanding, QtWidgets.QSizePolicy.Maximum)
sizePolicy.setHorizontalStretch(0)
sizePolicy.setVerticalStretch(0)
@ -131,11 +75,57 @@ class Ui_Dialog(object):
self.reference_tableWidget.horizontalHeader().setVisible(False)
self.reference_tableWidget.horizontalHeader().setStretchLastSection(True)
self.reference_tableWidget.verticalHeader().setVisible(False)
self.verticalLayout_3.addWidget(self.reference_tableWidget)
self.gridLayout_4.addWidget(self.reference_tableWidget, 9, 0, 1, 4)
self.step_listWidget = QtWidgets.QListWidget(Dialog)
sizePolicy = QtWidgets.QSizePolicy(QtWidgets.QSizePolicy.MinimumExpanding, QtWidgets.QSizePolicy.Minimum)
sizePolicy.setHorizontalStretch(0)
sizePolicy.setVerticalStretch(0)
sizePolicy.setHeightForWidth(self.step_listWidget.sizePolicy().hasHeightForWidth())
self.step_listWidget.setSizePolicy(sizePolicy)
self.step_listWidget.setMinimumSize(QtCore.QSize(0, 0))
self.step_listWidget.setObjectName("step_listWidget")
self.gridLayout_4.addWidget(self.step_listWidget, 1, 0, 1, 4)
self.label = QtWidgets.QLabel(Dialog)
self.label.setObjectName("label")
self.gridLayout_4.addWidget(self.label, 6, 0, 1, 1)
self.slope_radioButton = QtWidgets.QRadioButton(Dialog)
self.slope_radioButton.setObjectName("slope_radioButton")
self.buttonGroup.addButton(self.slope_radioButton)
self.gridLayout_4.addWidget(self.slope_radioButton, 6, 2, 1, 1)
self.empty_label = QtWidgets.QLabel(Dialog)
self.empty_label.setObjectName("empty_label")
self.gridLayout_4.addWidget(self.empty_label, 4, 0, 1, 4)
self.label_3 = QtWidgets.QLabel(Dialog)
sizePolicy = QtWidgets.QSizePolicy(QtWidgets.QSizePolicy.Preferred, QtWidgets.QSizePolicy.Maximum)
sizePolicy.setHorizontalStretch(0)
sizePolicy.setVerticalStretch(0)
sizePolicy.setHeightForWidth(self.label_3.sizePolicy().hasHeightForWidth())
self.label_3.setSizePolicy(sizePolicy)
self.label_3.setStyleSheet("font-weight: bold")
self.label_3.setObjectName("label_3")
self.gridLayout_4.addWidget(self.label_3, 8, 0, 1, 4)
self.label_2 = QtWidgets.QLabel(Dialog)
sizePolicy = QtWidgets.QSizePolicy(QtWidgets.QSizePolicy.Preferred, QtWidgets.QSizePolicy.Maximum)
sizePolicy.setHorizontalStretch(0)
sizePolicy.setVerticalStretch(0)
sizePolicy.setHeightForWidth(self.label_2.sizePolicy().hasHeightForWidth())
self.label_2.setSizePolicy(sizePolicy)
self.label_2.setStyleSheet("font-weight: bold")
self.label_2.setObjectName("label_2")
self.gridLayout_4.addWidget(self.label_2, 3, 0, 1, 4)
self.line = QtWidgets.QFrame(Dialog)
self.line.setFrameShape(QtWidgets.QFrame.HLine)
self.line.setFrameShadow(QtWidgets.QFrame.Sunken)
self.line.setObjectName("line")
self.gridLayout_4.addWidget(self.line, 7, 0, 1, 4)
self.none_radioButton = QtWidgets.QRadioButton(Dialog)
self.none_radioButton.setObjectName("none_radioButton")
self.buttonGroup.addButton(self.none_radioButton)
self.gridLayout_4.addWidget(self.none_radioButton, 6, 3, 1, 1)
self.horizontalLayout = QtWidgets.QHBoxLayout()
self.horizontalLayout.setSpacing(3)
self.horizontalLayout.setObjectName("horizontalLayout")
self.ref_add_pushButton = QtWidgets.QPushButton(self.groupBox_3)
self.ref_add_pushButton = QtWidgets.QPushButton(Dialog)
sizePolicy = QtWidgets.QSizePolicy(QtWidgets.QSizePolicy.MinimumExpanding, QtWidgets.QSizePolicy.Maximum)
sizePolicy.setHorizontalStretch(0)
sizePolicy.setVerticalStretch(0)
@ -143,7 +133,7 @@ class Ui_Dialog(object):
self.ref_add_pushButton.setSizePolicy(sizePolicy)
self.ref_add_pushButton.setObjectName("ref_add_pushButton")
self.horizontalLayout.addWidget(self.ref_add_pushButton)
self.ref_remove_pushButton = QtWidgets.QPushButton(self.groupBox_3)
self.ref_remove_pushButton = QtWidgets.QPushButton(Dialog)
sizePolicy = QtWidgets.QSizePolicy(QtWidgets.QSizePolicy.MinimumExpanding, QtWidgets.QSizePolicy.Maximum)
sizePolicy.setHorizontalStretch(0)
sizePolicy.setVerticalStretch(0)
@ -151,22 +141,16 @@ class Ui_Dialog(object):
self.ref_remove_pushButton.setSizePolicy(sizePolicy)
self.ref_remove_pushButton.setObjectName("ref_remove_pushButton")
self.horizontalLayout.addWidget(self.ref_remove_pushButton)
self.verticalLayout_3.addLayout(self.horizontalLayout)
self.verticalLayout_4.addWidget(self.groupBox_3)
spacerItem = QtWidgets.QSpacerItem(20, 40, QtWidgets.QSizePolicy.Minimum, QtWidgets.QSizePolicy.Expanding)
self.verticalLayout_4.addItem(spacerItem)
self.buttonBox = QtWidgets.QDialogButtonBox(self.verticalLayoutWidget)
self.buttonBox.setOrientation(QtCore.Qt.Horizontal)
self.buttonBox.setStandardButtons(QtWidgets.QDialogButtonBox.Apply|QtWidgets.QDialogButtonBox.Cancel|QtWidgets.QDialogButtonBox.Ok|QtWidgets.QDialogButtonBox.Save)
self.buttonBox.setCenterButtons(True)
self.buttonBox.setObjectName("buttonBox")
self.verticalLayout_4.addWidget(self.buttonBox)
self.layoutWidget = QtWidgets.QWidget(self.splitter)
self.layoutWidget.setObjectName("layoutWidget")
self.gridLayout = QtWidgets.QGridLayout(self.layoutWidget)
self.gridLayout.setContentsMargins(0, 0, 0, 0)
self.gridLayout_4.addLayout(self.horizontalLayout, 10, 0, 1, 4)
self.line_2 = QtWidgets.QFrame(Dialog)
self.line_2.setFrameShape(QtWidgets.QFrame.HLine)
self.line_2.setFrameShadow(QtWidgets.QFrame.Sunken)
self.line_2.setObjectName("line_2")
self.gridLayout_4.addWidget(self.line_2, 2, 0, 1, 4)
self.gridLayout_2.addLayout(self.gridLayout_4, 0, 0, 1, 1)
self.gridLayout = QtWidgets.QGridLayout()
self.gridLayout.setObjectName("gridLayout")
self.raw_graph = NMRPlotWidget(self.layoutWidget)
self.raw_graph = PlotWidget(Dialog)
sizePolicy = QtWidgets.QSizePolicy(QtWidgets.QSizePolicy.MinimumExpanding, QtWidgets.QSizePolicy.MinimumExpanding)
sizePolicy.setHorizontalStretch(0)
sizePolicy.setVerticalStretch(0)
@ -175,7 +159,7 @@ class Ui_Dialog(object):
self.raw_graph.setMinimumSize(QtCore.QSize(300, 200))
self.raw_graph.setObjectName("raw_graph")
self.gridLayout.addWidget(self.raw_graph, 0, 0, 1, 1)
self.calib_graph = NMRPlotWidget(self.layoutWidget)
self.calib_graph = PlotWidget(Dialog)
sizePolicy = QtWidgets.QSizePolicy(QtWidgets.QSizePolicy.MinimumExpanding, QtWidgets.QSizePolicy.MinimumExpanding)
sizePolicy.setHorizontalStretch(0)
sizePolicy.setVerticalStretch(0)
@ -184,7 +168,7 @@ class Ui_Dialog(object):
self.calib_graph.setMinimumSize(QtCore.QSize(300, 200))
self.calib_graph.setObjectName("calib_graph")
self.gridLayout.addWidget(self.calib_graph, 1, 0, 1, 1)
self.baseline_graph = NMRPlotWidget(self.layoutWidget)
self.baseline_graph = PlotWidget(Dialog)
sizePolicy = QtWidgets.QSizePolicy(QtWidgets.QSizePolicy.MinimumExpanding, QtWidgets.QSizePolicy.MinimumExpanding)
sizePolicy.setHorizontalStretch(0)
sizePolicy.setVerticalStretch(0)
@ -193,7 +177,7 @@ class Ui_Dialog(object):
self.baseline_graph.setMinimumSize(QtCore.QSize(300, 200))
self.baseline_graph.setObjectName("baseline_graph")
self.gridLayout.addWidget(self.baseline_graph, 0, 1, 1, 1)
self.end_graph = NMRPlotWidget(self.layoutWidget)
self.end_graph = PlotWidget(Dialog)
sizePolicy = QtWidgets.QSizePolicy(QtWidgets.QSizePolicy.MinimumExpanding, QtWidgets.QSizePolicy.MinimumExpanding)
sizePolicy.setHorizontalStretch(0)
sizePolicy.setVerticalStretch(0)
@ -202,30 +186,28 @@ class Ui_Dialog(object):
self.end_graph.setMinimumSize(QtCore.QSize(0, 0))
self.end_graph.setObjectName("end_graph")
self.gridLayout.addWidget(self.end_graph, 1, 1, 1, 1)
self.verticalLayout_5.addWidget(self.splitter)
self.gridLayout_2.addLayout(self.gridLayout, 0, 1, 1, 1)
self.retranslateUi(Dialog)
self.buttonBox.accepted.connect(Dialog.accept) # type: ignore
self.buttonBox.rejected.connect(Dialog.reject) # type: ignore
self.buttonBox.accepted.connect(Dialog.accept)
self.buttonBox.rejected.connect(Dialog.reject)
QtCore.QMetaObject.connectSlotsByName(Dialog)
def retranslateUi(self, Dialog):
_translate = QtCore.QCoreApplication.translate
Dialog.setWindowTitle(_translate("Dialog", "Read DSC file"))
self.groupBox.setTitle(_translate("Dialog", "Detected steps"))
self.groupBox_2.setTitle(_translate("Dialog", "Baseline corrections"))
self.groupBox_4.setTitle(_translate("Dialog", "Empty measurement"))
self.empty_label.setText(_translate("Dialog", "No emtpy measurement"))
self.cp_checkBox.setText(_translate("Dialog", "Convert to heat capacity"))
self.loadempty_button.setText(_translate("Dialog", "Load empty"))
self.delempty_button.setText(_translate("Dialog", "Remove empty"))
self.groupBox_5.setTitle(_translate("Dialog", "Slope correction"))
self.none_radioButton.setText(_translate("Dialog", "None"))
self.isotherm_radioButton.setText(_translate("Dialog", "Isotherms"))
self.slope_radioButton.setText(_translate("Dialog", "Curve slope"))
self.limit1_lineedit.setPlaceholderText(_translate("Dialog", "start (in min)"))
self.limit2_lineedit.setPlaceholderText(_translate("Dialog", "stop (in min)"))
self.groupBox_3.setTitle(_translate("Dialog", "References"))
self.cp_checkBox.setText(_translate("Dialog", "Use reference to convert to heat capacity"))
self.label_4.setText(_translate("Dialog", "Detected steps"))
self.label.setText(_translate("Dialog", "Slope"))
self.slope_radioButton.setText(_translate("Dialog", "Initial slope"))
self.empty_label.setText(_translate("Dialog", "Empty measurement"))
self.label_3.setText(_translate("Dialog", "Calibration"))
self.label_2.setText(_translate("Dialog", "Baseline"))
self.none_radioButton.setText(_translate("Dialog", "None"))
self.ref_add_pushButton.setText(_translate("Dialog", "Add reference"))
self.ref_remove_pushButton.setText(_translate("Dialog", "Remove reference"))
from ..lib.graph_items import NMRPlotWidget
from pyqtgraph import PlotWidget

14
src/gui_qt/_py/eval_expr_dialog.py
View File

@ -1,11 +1,10 @@
# -*- coding: utf-8 -*-
# Form implementation generated from reading ui file 'src/resources/_ui/eval_expr_dialog.ui'
# Form implementation generated from reading ui file 'resources/_ui/eval_expr_dialog.ui'
#
# Created by: PyQt5 UI code generator 5.15.2
# Created by: PyQt5 UI code generator 5.12.3
#
# WARNING: Any manual changes made to this file will be lost when pyuic5 is
# run again. Do not edit this file unless you know what you are doing.
# WARNING! All changes made in this file will be lost!
from PyQt5 import QtCore, QtGui, QtWidgets
@ -37,14 +36,14 @@ class Ui_CalcDialog(object):
self.label_2 = QtWidgets.QLabel(self.page)
self.label_2.setObjectName("label_2")
self.verticalLayout_2.addWidget(self.label_2)
self.listWidget = QListWidgetSelect(self.page)
self.listWidget = QtWidgets.QListWidget(self.page)
sizePolicy = QtWidgets.QSizePolicy(QtWidgets.QSizePolicy.Preferred, QtWidgets.QSizePolicy.MinimumExpanding)
sizePolicy.setHorizontalStretch(0)
sizePolicy.setVerticalStretch(0)
sizePolicy.setHeightForWidth(self.listWidget.sizePolicy().hasHeightForWidth())
self.listWidget.setSizePolicy(sizePolicy)
self.listWidget.setEditTriggers(QtWidgets.QAbstractItemView.NoEditTriggers)
self.listWidget.setSelectionMode(QtWidgets.QAbstractItemView.ExtendedSelection)
self.listWidget.setSelectionMode(QtWidgets.QAbstractItemView.SingleSelection)
self.listWidget.setObjectName("listWidget")
self.verticalLayout_2.addWidget(self.listWidget)
self.overwrite_checkbox = QtWidgets.QCheckBox(self.page)
@ -203,7 +202,7 @@ class Ui_CalcDialog(object):
self.label_8.setBuddy(self.line_doubleSpinBox)
self.retranslateUi(CalcDialog)
self.stackedWidget.setCurrentIndex(0)
self.stackedWidget.setCurrentIndex(2)
QtCore.QMetaObject.connectSlotsByName(CalcDialog)
CalcDialog.setTabOrder(self.calc_edit, self.listWidget)
CalcDialog.setTabOrder(self.listWidget, self.overwrite_checkbox)
@ -238,5 +237,4 @@ class Ui_CalcDialog(object):
self.label_11.setText(_translate("CalcDialog", "Style"))
self.label.setText(_translate("CalcDialog", "Expressions are evaluated line by line and change previous values"))
from ..lib.delegates import ColorListEditor, LineStyleEditor, SymbolStyleEditor
from ..lib.listwidget import QListWidgetSelect
from ..lib.namespace import QNamespaceWidget

9
src/gui_qt/_py/fitdialog.py
View File

@ -1,11 +1,10 @@
# -*- coding: utf-8 -*-
# Form implementation generated from reading ui file 'src/resources/_ui/fitdialog.ui'
# Form implementation generated from reading ui file 'resources/_ui/fitdialog.ui'
#
# Created by: PyQt5 UI code generator 5.15.2
# Created by: PyQt5 UI code generator 5.12.3
#
# WARNING: Any manual changes made to this file will be lost when pyuic5 is
# run again. Do not edit this file unless you know what you are doing.
# WARNING! All changes made in this file will be lost!
from PyQt5 import QtCore, QtGui, QtWidgets
@ -38,6 +37,7 @@ class Ui_FitDialog(object):
self.weight_combobox.addItem("")
self.weight_combobox.addItem("")
self.weight_combobox.addItem("")
self.weight_combobox.addItem("")
self.gridLayout_2.addWidget(self.weight_combobox, 6, 1, 1, 1)
self.newmodel_button = QtWidgets.QPushButton(self.scrollAreaWidgetContents_2)
self.newmodel_button.setEnabled(False)
@ -143,6 +143,7 @@ class Ui_FitDialog(object):
self.weight_combobox.setItemText(1, _translate("FitDialog", "y"))
self.weight_combobox.setItemText(2, _translate("FitDialog", "y²"))
self.weight_combobox.setItemText(3, _translate("FitDialog", "Δy"))
self.weight_combobox.setItemText(4, _translate("FitDialog", "log(y)"))
self.newmodel_button.setText(_translate("FitDialog", "New model"))
self.deletemodel_button.setText(_translate("FitDialog", "Delete model"))
self.label_3.setText(_translate("FitDialog", "Weight"))

19
src/gui_qt/_py/fitmodelwidget.py
View File

@ -1,11 +1,10 @@
# -*- coding: utf-8 -*-
# Form implementation generated from reading ui file 'src/resources/_ui/fitmodelwidget.ui'
# Form implementation generated from reading ui file 'resources/_ui/fitmodelwidget.ui'
#
# Created by: PyQt5 UI code generator 5.15.9
# Created by: PyQt5 UI code generator 5.12.3
#
# WARNING: Any manual changes made to this file will be lost when pyuic5 is
# run again. Do not edit this file unless you know what you are doing.
# WARNING! All changes made in this file will be lost!
from PyQt5 import QtCore, QtGui, QtWidgets
@ -14,7 +13,7 @@ from PyQt5 import QtCore, QtGui, QtWidgets
class Ui_FitParameter(object):
def setupUi(self, FitParameter):
FitParameter.setObjectName("FitParameter")
FitParameter.resize(365, 66)
FitParameter.resize(365, 78)
sizePolicy = QtWidgets.QSizePolicy(QtWidgets.QSizePolicy.Preferred, QtWidgets.QSizePolicy.MinimumExpanding)
sizePolicy.setHorizontalStretch(0)
sizePolicy.setVerticalStretch(0)
@ -37,7 +36,7 @@ class Ui_FitParameter(object):
self.parametername.setObjectName("parametername")
self.horizontalLayout_2.addWidget(self.parametername)
self.parameter_line = LineEdit(FitParameter)
sizePolicy = QtWidgets.QSizePolicy(QtWidgets.QSizePolicy.MinimumExpanding, QtWidgets.QSizePolicy.Fixed)
sizePolicy = QtWidgets.QSizePolicy(QtWidgets.QSizePolicy.Fixed, QtWidgets.QSizePolicy.Fixed)
sizePolicy.setHorizontalStretch(0)
sizePolicy.setVerticalStretch(0)
sizePolicy.setHeightForWidth(self.parameter_line.sizePolicy().hasHeightForWidth())
@ -45,12 +44,20 @@ class Ui_FitParameter(object):
self.parameter_line.setText("")
self.parameter_line.setObjectName("parameter_line")
self.horizontalLayout_2.addWidget(self.parameter_line)
spacerItem = QtWidgets.QSpacerItem(40, 20, QtWidgets.QSizePolicy.Expanding, QtWidgets.QSizePolicy.Minimum)
self.horizontalLayout_2.addItem(spacerItem)
self.fixed_check = QtWidgets.QCheckBox(FitParameter)
self.fixed_check.setObjectName("fixed_check")
self.horizontalLayout_2.addWidget(self.fixed_check)
self.global_checkbox = QtWidgets.QCheckBox(FitParameter)
self.global_checkbox.setObjectName("global_checkbox")
self.horizontalLayout_2.addWidget(self.global_checkbox)
self.toolButton = QtWidgets.QToolButton(FitParameter)
self.toolButton.setText("")
self.toolButton.setPopupMode(QtWidgets.QToolButton.InstantPopup)
self.toolButton.setArrowType(QtCore.Qt.RightArrow)
self.toolButton.setObjectName("toolButton")
self.horizontalLayout_2.addWidget(self.toolButton)
self.verticalLayout.addLayout(self.horizontalLayout_2)
self.frame = QtWidgets.QFrame(FitParameter)
sizePolicy = QtWidgets.QSizePolicy(QtWidgets.QSizePolicy.Maximum, QtWidgets.QSizePolicy.Maximum)

226
src/gui_qt/_py/fitresult.py
View File

@ -1,8 +1,8 @@
# -*- coding: utf-8 -*-
# Form implementation generated from reading ui file 'src/resources/_ui/fitresult.ui'
# Form implementation generated from reading ui file '/autohome/dominik/nmreval-gitea/src/resources/_ui/fitresult.ui'
#
# Created by: PyQt5 UI code generator 5.15.9
# Created by: PyQt5 UI code generator 5.15.7
#
# WARNING: Any manual changes made to this file will be lost when pyuic5 is
# run again. Do not edit this file unless you know what you are doing.
@ -14,105 +14,37 @@ from PyQt5 import QtCore, QtGui, QtWidgets
class Ui_Dialog(object):
def setupUi(self, Dialog):
Dialog.setObjectName("Dialog")
Dialog.resize(969, 974)
Dialog.resize(864, 649)
self.gridLayout = QtWidgets.QGridLayout(Dialog)
self.gridLayout.setObjectName("gridLayout")
self.stack = QtWidgets.QTabWidget(Dialog)
sizePolicy = QtWidgets.QSizePolicy(QtWidgets.QSizePolicy.MinimumExpanding, QtWidgets.QSizePolicy.Preferred)
self.sets_comboBox = ElideComboBox(Dialog)
sizePolicy = QtWidgets.QSizePolicy(QtWidgets.QSizePolicy.Maximum, QtWidgets.QSizePolicy.Fixed)
sizePolicy.setHorizontalStretch(0)
sizePolicy.setVerticalStretch(0)
sizePolicy.setHeightForWidth(self.stack.sizePolicy().hasHeightForWidth())
self.stack.setSizePolicy(sizePolicy)
self.stack.setObjectName("stack")
self.stackPage1 = QtWidgets.QWidget()
self.stackPage1.setObjectName("stackPage1")
self.gridLayout_3 = QtWidgets.QGridLayout(self.stackPage1)
self.gridLayout_3.setContentsMargins(3, 3, 3, 3)
self.gridLayout_3.setSpacing(3)
self.gridLayout_3.setObjectName("gridLayout_3")
self.logy_box = QtWidgets.QCheckBox(self.stackPage1)
self.logy_box.setLayoutDirection(QtCore.Qt.RightToLeft)
self.logy_box.setObjectName("logy_box")
self.gridLayout_3.addWidget(self.logy_box, 2, 1, 1, 1)
self.logx_box = QtWidgets.QCheckBox(self.stackPage1)
self.logx_box.setLayoutDirection(QtCore.Qt.RightToLeft)
self.logx_box.setObjectName("logx_box")
self.gridLayout_3.addWidget(self.logx_box, 2, 0, 1, 1)
self.graphicsView = GraphicsLayoutWidget(self.stackPage1)
self.graphicsView.setObjectName("graphicsView")
self.gridLayout_3.addWidget(self.graphicsView, 0, 0, 1, 2)
self.stack.addTab(self.stackPage1, "")
self.stackPage2 = QtWidgets.QWidget()
self.stackPage2.setObjectName("stackPage2")
self.verticalLayout_2 = QtWidgets.QVBoxLayout(self.stackPage2)
self.verticalLayout_2.setContentsMargins(3, 3, 3, 3)
self.verticalLayout_2.setSpacing(3)
self.verticalLayout_2.setObjectName("verticalLayout_2")
self.stats_tableWidget = QtWidgets.QTableWidget(self.stackPage2)
self.stats_tableWidget.setFrameShape(QtWidgets.QFrame.Box)
self.stats_tableWidget.setGridStyle(QtCore.Qt.NoPen)
self.stats_tableWidget.setColumnCount(1)
self.stats_tableWidget.setObjectName("stats_tableWidget")
self.stats_tableWidget.setRowCount(0)
self.stats_tableWidget.horizontalHeader().setVisible(False)
self.stats_tableWidget.horizontalHeader().setSortIndicatorShown(True)
self.verticalLayout_2.addWidget(self.stats_tableWidget)
self.stack.addTab(self.stackPage2, "")
self.stackPage3 = QtWidgets.QWidget()
self.stackPage3.setObjectName("stackPage3")
self.verticalLayout_3 = QtWidgets.QVBoxLayout(self.stackPage3)
self.verticalLayout_3.setContentsMargins(3, 3, 3, 3)
self.verticalLayout_3.setSpacing(3)
self.verticalLayout_3.setObjectName("verticalLayout_3")
self.corr_tableWidget = QtWidgets.QTableWidget(self.stackPage3)
self.corr_tableWidget.setFrameShape(QtWidgets.QFrame.Box)
self.corr_tableWidget.setEditTriggers(QtWidgets.QAbstractItemView.NoEditTriggers)
self.corr_tableWidget.setGridStyle(QtCore.Qt.NoPen)
self.corr_tableWidget.setObjectName("corr_tableWidget")
self.corr_tableWidget.setColumnCount(4)
self.corr_tableWidget.setRowCount(0)
item = QtWidgets.QTableWidgetItem()
self.corr_tableWidget.setHorizontalHeaderItem(0, item)
item = QtWidgets.QTableWidgetItem()
self.corr_tableWidget.setHorizontalHeaderItem(1, item)
item = QtWidgets.QTableWidgetItem()
self.corr_tableWidget.setHorizontalHeaderItem(2, item)
item = QtWidgets.QTableWidgetItem()
self.corr_tableWidget.setHorizontalHeaderItem(3, item)
self.corr_tableWidget.horizontalHeader().setStretchLastSection(True)
self.corr_tableWidget.verticalHeader().setVisible(False)
self.verticalLayout_3.addWidget(self.corr_tableWidget)
self.stack.addTab(self.stackPage3, "")
self.gridLayout.addWidget(self.stack, 0, 1, 5, 1)
sizePolicy.setHeightForWidth(self.sets_comboBox.sizePolicy().hasHeightForWidth())
self.sets_comboBox.setSizePolicy(sizePolicy)
self.sets_comboBox.setMaximumSize(QtCore.QSize(400, 16777215))
self.sets_comboBox.setBaseSize(QtCore.QSize(200, 0))
self.sets_comboBox.setSizeAdjustPolicy(QtWidgets.QComboBox.AdjustToMinimumContentsLength)
self.sets_comboBox.setObjectName("sets_comboBox")
self.gridLayout.addWidget(self.sets_comboBox, 0, 0, 1, 1)
self.buttonBox = QtWidgets.QDialogButtonBox(Dialog)
self.buttonBox.setStandardButtons(QtWidgets.QDialogButtonBox.Cancel|QtWidgets.QDialogButtonBox.Ok|QtWidgets.QDialogButtonBox.Retry)
self.buttonBox.setObjectName("buttonBox")
self.gridLayout.addWidget(self.buttonBox, 8, 0, 1, 2)
self.gridLayout.addWidget(self.buttonBox, 6, 0, 1, 2)
self.param_tableWidget = QtWidgets.QTableWidget(Dialog)
sizePolicy = QtWidgets.QSizePolicy(QtWidgets.QSizePolicy.Preferred, QtWidgets.QSizePolicy.Expanding)
sizePolicy.setHorizontalStretch(0)
sizePolicy.setVerticalStretch(0)
sizePolicy.setHeightForWidth(self.param_tableWidget.sizePolicy().hasHeightForWidth())
self.param_tableWidget.setSizePolicy(sizePolicy)
self.param_tableWidget.setHorizontalScrollBarPolicy(QtCore.Qt.ScrollBarAsNeeded)
self.param_tableWidget.setSizeAdjustPolicy(QtWidgets.QAbstractScrollArea.AdjustIgnored)
self.param_tableWidget.setEditTriggers(QtWidgets.QAbstractItemView.NoEditTriggers)
self.param_tableWidget.setAlternatingRowColors(True)
self.param_tableWidget.setSelectionMode(QtWidgets.QAbstractItemView.NoSelection)
self.param_tableWidget.setColumnCount(1)
self.param_tableWidget.setSelectionMode(QtWidgets.QAbstractItemView.SingleSelection)
self.param_tableWidget.setSelectionBehavior(QtWidgets.QAbstractItemView.SelectColumns)
self.param_tableWidget.setShowGrid(False)
self.param_tableWidget.setColumnCount(0)
self.param_tableWidget.setObjectName("param_tableWidget")
self.param_tableWidget.setRowCount(0)
self.param_tableWidget.horizontalHeader().setVisible(False)
self.param_tableWidget.horizontalHeader().setStretchLastSection(True)
self.param_tableWidget.horizontalHeader().setStretchLastSection(False)
self.gridLayout.addWidget(self.param_tableWidget, 1, 0, 1, 1)
self.del_prev_checkBox = QtWidgets.QCheckBox(Dialog)
self.del_prev_checkBox.setObjectName("del_prev_checkBox")
self.gridLayout.addWidget(self.del_prev_checkBox, 3, 0, 1, 1)
self.line = QtWidgets.QFrame(Dialog)
self.line.setFrameShape(QtWidgets.QFrame.HLine)
self.line.setFrameShadow(QtWidgets.QFrame.Sunken)
self.line.setObjectName("line")
self.gridLayout.addWidget(self.line, 5, 0, 1, 2)
self.groupBox = QtWidgets.QGroupBox(Dialog)
self.groupBox.setObjectName("groupBox")
self.gridLayout_2 = QtWidgets.QGridLayout(self.groupBox)
@ -180,21 +112,89 @@ class Ui_Dialog(object):
self.partial_checkBox.setObjectName("partial_checkBox")
self.horizontalLayout.addWidget(self.partial_checkBox)
self.gridLayout_2.addLayout(self.horizontalLayout, 0, 0, 1, 4)
self.gridLayout.addWidget(self.groupBox, 7, 0, 1, 2)
self.sets_comboBox = ElideComboBox(Dialog)
sizePolicy = QtWidgets.QSizePolicy(QtWidgets.QSizePolicy.Maximum, QtWidgets.QSizePolicy.Fixed)
sizePolicy.setHorizontalStretch(0)
sizePolicy.setVerticalStretch(0)
sizePolicy.setHeightForWidth(self.sets_comboBox.sizePolicy().hasHeightForWidth())
self.sets_comboBox.setSizePolicy(sizePolicy)
self.sets_comboBox.setMaximumSize(QtCore.QSize(400, 16777215))
self.sets_comboBox.setBaseSize(QtCore.QSize(200, 0))
self.sets_comboBox.setSizeAdjustPolicy(QtWidgets.QComboBox.AdjustToMinimumContentsLength)
self.sets_comboBox.setObjectName("sets_comboBox")
self.gridLayout.addWidget(self.sets_comboBox, 0, 0, 1, 1)
self.gridLayout.addWidget(self.groupBox, 5, 0, 1, 2)
self.horizontalLayout_2 = QtWidgets.QHBoxLayout()
self.horizontalLayout_2.setSpacing(3)
self.horizontalLayout_2.setObjectName("horizontalLayout_2")
self.reject_fit_checkBox = QtWidgets.QCheckBox(Dialog)
self.reject_fit_checkBox.setObjectName("reject_fit_checkBox")
self.gridLayout.addWidget(self.reject_fit_checkBox, 2, 0, 1, 1)
self.horizontalLayout_2.addWidget(self.reject_fit_checkBox)
self.del_prev_checkBox = QtWidgets.QCheckBox(Dialog)
self.del_prev_checkBox.setObjectName("del_prev_checkBox")
self.horizontalLayout_2.addWidget(self.del_prev_checkBox)
self.gridLayout.addLayout(self.horizontalLayout_2, 2, 0, 1, 1)
self.line = QtWidgets.QFrame(Dialog)
self.line.setFrameShape(QtWidgets.QFrame.HLine)
self.line.setFrameShadow(QtWidgets.QFrame.Sunken)
self.line.setObjectName("line")
self.gridLayout.addWidget(self.line, 3, 0, 1, 2)
self.stack = QtWidgets.QTabWidget(Dialog)
sizePolicy = QtWidgets.QSizePolicy(QtWidgets.QSizePolicy.MinimumExpanding, QtWidgets.QSizePolicy.Preferred)
sizePolicy.setHorizontalStretch(0)
sizePolicy.setVerticalStretch(0)
sizePolicy.setHeightForWidth(self.stack.sizePolicy().hasHeightForWidth())
self.stack.setSizePolicy(sizePolicy)
self.stack.setObjectName("stack")
self.stackPage1 = QtWidgets.QWidget()
self.stackPage1.setObjectName("stackPage1")
self.gridLayout_3 = QtWidgets.QGridLayout(self.stackPage1)
self.gridLayout_3.setContentsMargins(3, 3, 3, 3)
self.gridLayout_3.setSpacing(3)
self.gridLayout_3.setObjectName("gridLayout_3")
self.logy_box = QtWidgets.QCheckBox(self.stackPage1)
self.logy_box.setLayoutDirection(QtCore.Qt.RightToLeft)
self.logy_box.setObjectName("logy_box")
self.gridLayout_3.addWidget(self.logy_box, 2, 1, 1, 1)
self.logx_box = QtWidgets.QCheckBox(self.stackPage1)
self.logx_box.setLayoutDirection(QtCore.Qt.RightToLeft)
self.logx_box.setObjectName("logx_box")
self.gridLayout_3.addWidget(self.logx_box, 2, 0, 1, 1)
self.graphicsView = GraphicsLayoutWidget(self.stackPage1)
self.graphicsView.setObjectName("graphicsView")
self.gridLayout_3.addWidget(self.graphicsView, 0, 0, 1, 2)
self.stack.addTab(self.stackPage1, "")
self.stackPage2 = QtWidgets.QWidget()
self.stackPage2.setObjectName("stackPage2")
self.verticalLayout_2 = QtWidgets.QVBoxLayout(self.stackPage2)
self.verticalLayout_2.setContentsMargins(3, 3, 3, 3)
self.verticalLayout_2.setSpacing(3)
self.verticalLayout_2.setObjectName("verticalLayout_2")
self.stats_tableWidget = QtWidgets.QTableWidget(self.stackPage2)
self.stats_tableWidget.setFrameShape(QtWidgets.QFrame.Box)
self.stats_tableWidget.setGridStyle(QtCore.Qt.NoPen)
self.stats_tableWidget.setColumnCount(1)
self.stats_tableWidget.setObjectName("stats_tableWidget")
self.stats_tableWidget.setRowCount(0)
self.stats_tableWidget.horizontalHeader().setVisible(False)
self.stats_tableWidget.horizontalHeader().setSortIndicatorShown(True)
self.verticalLayout_2.addWidget(self.stats_tableWidget)
self.stack.addTab(self.stackPage2, "")
self.stackPage3 = QtWidgets.QWidget()
self.stackPage3.setObjectName("stackPage3")
self.verticalLayout_3 = QtWidgets.QVBoxLayout(self.stackPage3)
self.verticalLayout_3.setContentsMargins(3, 3, 3, 3)
self.verticalLayout_3.setSpacing(3)
self.verticalLayout_3.setObjectName("verticalLayout_3")
self.corr_tableWidget = QtWidgets.QTableWidget(self.stackPage3)
self.corr_tableWidget.setFrameShape(QtWidgets.QFrame.Box)
self.corr_tableWidget.setEditTriggers(QtWidgets.QAbstractItemView.NoEditTriggers)
self.corr_tableWidget.setGridStyle(QtCore.Qt.NoPen)
self.corr_tableWidget.setObjectName("corr_tableWidget")
self.corr_tableWidget.setColumnCount(4)
self.corr_tableWidget.setRowCount(0)
item = QtWidgets.QTableWidgetItem()
self.corr_tableWidget.setHorizontalHeaderItem(0, item)
item = QtWidgets.QTableWidgetItem()
self.corr_tableWidget.setHorizontalHeaderItem(1, item)
item = QtWidgets.QTableWidgetItem()
self.corr_tableWidget.setHorizontalHeaderItem(2, item)
item = QtWidgets.QTableWidgetItem()
self.corr_tableWidget.setHorizontalHeaderItem(3, item)
self.corr_tableWidget.horizontalHeader().setStretchLastSection(True)
self.corr_tableWidget.verticalHeader().setVisible(False)
self.verticalLayout_3.addWidget(self.corr_tableWidget)
self.stack.addTab(self.stackPage3, "")
self.gridLayout.addWidget(self.stack, 0, 1, 3, 1)
self.retranslateUi(Dialog)
self.stack.setCurrentIndex(0)
@ -203,20 +203,6 @@ class Ui_Dialog(object):
def retranslateUi(self, Dialog):
_translate = QtCore.QCoreApplication.translate
Dialog.setWindowTitle(_translate("Dialog", "Fit results"))
self.logy_box.setText(_translate("Dialog", "logarithmic y axis"))
self.logx_box.setText(_translate("Dialog", "logarithmic x axis"))
self.stack.setTabText(self.stack.indexOf(self.stackPage1), _translate("Dialog", "Plot"))
self.stack.setTabText(self.stack.indexOf(self.stackPage2), _translate("Dialog", "Statistics"))
item = self.corr_tableWidget.horizontalHeaderItem(0)
item.setText(_translate("Dialog", "Parameter 1"))
item = self.corr_tableWidget.horizontalHeaderItem(1)
item.setText(_translate("Dialog", "Parameter 2"))
item = self.corr_tableWidget.horizontalHeaderItem(2)
item.setText(_translate("Dialog", "Corr."))
item = self.corr_tableWidget.horizontalHeaderItem(3)
item.setText(_translate("Dialog", "Partial Corr."))
self.stack.setTabText(self.stack.indexOf(self.stackPage3), _translate("Dialog", "Correlations"))
self.del_prev_checkBox.setText(_translate("Dialog", "Delete previous fits of this set"))
self.groupBox.setTitle(_translate("Dialog", "Output"))
self.extrapolate_box.setToolTip(_translate("Dialog", "Extrapolates only main function"))
self.extrapolate_box.setText(_translate("Dialog", "Extrapolate curves"))
@ -230,5 +216,19 @@ class Ui_Dialog(object):
self.curve_checkbox.setText(_translate("Dialog", "Plot fit curve"))
self.partial_checkBox.setText(_translate("Dialog", "Plot partial functions"))
self.reject_fit_checkBox.setText(_translate("Dialog", "Reject this fit"))
self.del_prev_checkBox.setText(_translate("Dialog", "Delete previous fits"))
self.logy_box.setText(_translate("Dialog", "logarithmic y axis"))
self.logx_box.setText(_translate("Dialog", "logarithmic x axis"))
self.stack.setTabText(self.stack.indexOf(self.stackPage1), _translate("Dialog", "Plot"))
self.stack.setTabText(self.stack.indexOf(self.stackPage2), _translate("Dialog", "Statistics"))
item = self.corr_tableWidget.horizontalHeaderItem(0)
item.setText(_translate("Dialog", "Parameter 1"))
item = self.corr_tableWidget.horizontalHeaderItem(1)
item.setText(_translate("Dialog", "Parameter 2"))
item = self.corr_tableWidget.horizontalHeaderItem(2)
item.setText(_translate("Dialog", "Corr."))
item = self.corr_tableWidget.horizontalHeaderItem(3)
item.setText(_translate("Dialog", "Partial Corr."))
self.stack.setTabText(self.stack.indexOf(self.stackPage3), _translate("Dialog", "Correlations"))
from ..lib.forms import ElideComboBox
from pyqtgraph import GraphicsLayoutWidget

15
src/gui_qt/_py/graph.py
View File

@ -1,11 +1,10 @@
# -*- coding: utf-8 -*-
# Form implementation generated from reading ui file 'src/resources/_ui/graph.ui'
# Form implementation generated from reading ui file 'resources/_ui/graph.ui'
#
# Created by: PyQt5 UI code generator 5.15.9
# Created by: PyQt5 UI code generator 5.12.3
#
# WARNING: Any manual changes made to this file will be lost when pyuic5 is
# run again. Do not edit this file unless you know what you are doing.
# WARNING! All changes made in this file will be lost!
from PyQt5 import QtCore, QtGui, QtWidgets
@ -197,20 +196,19 @@ class Ui_GraphWindow(object):
self.gridLayout.setHorizontalSpacing(3)
self.gridLayout.setVerticalSpacing(0)
self.gridLayout.setObjectName("gridLayout")
self.listWidget = QListWidgetSelect(GraphWindow)
self.listWidget = QtWidgets.QListWidget(GraphWindow)
sizePolicy = QtWidgets.QSizePolicy(QtWidgets.QSizePolicy.Maximum, QtWidgets.QSizePolicy.MinimumExpanding)
sizePolicy.setHorizontalStretch(0)
sizePolicy.setVerticalStretch(0)
sizePolicy.setHeightForWidth(self.listWidget.sizePolicy().hasHeightForWidth())
self.listWidget.setSizePolicy(sizePolicy)
self.listWidget.setSelectionMode(QtWidgets.QAbstractItemView.ExtendedSelection)
self.listWidget.setObjectName("listWidget")
self.gridLayout.addWidget(self.listWidget, 1, 1, 1, 1)
self.checkBox = QtWidgets.QCheckBox(GraphWindow)
self.checkBox.setChecked(True)
self.checkBox.setObjectName("checkBox")
self.gridLayout.addWidget(self.checkBox, 0, 1, 1, 1)
self.graphic = NMRPlotWidget(GraphWindow)
self.graphic = PlotWidget(GraphWindow)
sizePolicy = QtWidgets.QSizePolicy(QtWidgets.QSizePolicy.MinimumExpanding, QtWidgets.QSizePolicy.MinimumExpanding)
sizePolicy.setHorizontalStretch(0)
sizePolicy.setVerticalStretch(0)
@ -274,5 +272,4 @@ class Ui_GraphWindow(object):
self.label_6.setText(_translate("GraphWindow", "X Axis"))
self.label_7.setText(_translate("GraphWindow", "Y Axis"))
self.checkBox.setText(_translate("GraphWindow", "Show legend"))
from ..lib.graph_items import NMRPlotWidget
from ..lib.listwidget import QListWidgetSelect
from pyqtgraph import PlotWidget

5
src/gui_qt/_py/integral_widget.py
View File

@ -1,8 +1,8 @@
# -*- coding: utf-8 -*-
# Form implementation generated from reading ui file 'src/resources/_ui/integral_widget.ui'
# Form implementation generated from reading ui file '/autohome/dominik/nmreval/src/resources/_ui/integral_widget.ui'
#
# Created by: PyQt5 UI code generator 5.15.9
# Created by: PyQt5 UI code generator 5.15.4
#
# WARNING: Any manual changes made to this file will be lost when pyuic5 is
# run again. Do not edit this file unless you know what you are doing.
@ -26,6 +26,7 @@ class Ui_Form(object):
self.set_combobox.setObjectName("set_combobox")
self.verticalLayout.addWidget(self.set_combobox)
self.treeWidget = QtWidgets.QTreeWidget(Form)
self.treeWidget.setEditTriggers(QtWidgets.QAbstractItemView.NoEditTriggers)
self.treeWidget.setSelectionBehavior(QtWidgets.QAbstractItemView.SelectRows)
self.treeWidget.setHeaderHidden(True)
self.treeWidget.setObjectName("treeWidget")

17
src/gui_qt/_py/integratederive_dialog.py
View File

@ -1,11 +1,10 @@
# -*- coding: utf-8 -*-
# Form implementation generated from reading ui file 'src/resources/_ui/integratederive_dialog.ui'
# Form implementation generated from reading ui file 'resources/_ui/integratederive_dialog.ui'
#
# Created by: PyQt5 UI code generator 5.15.9
# Created by: PyQt5 UI code generator 5.12.3
#
# WARNING: Any manual changes made to this file will be lost when pyuic5 is
# run again. Do not edit this file unless you know what you are doing.
# WARNING! All changes made in this file will be lost!
from PyQt5 import QtCore, QtGui, QtWidgets
@ -14,7 +13,7 @@ from PyQt5 import QtCore, QtGui, QtWidgets
class Ui_Dialog(object):
def setupUi(self, Dialog):
Dialog.setObjectName("Dialog")
Dialog.resize(400, 375)
Dialog.resize(400, 308)
self.verticalLayout = QtWidgets.QVBoxLayout(Dialog)
self.verticalLayout.setObjectName("verticalLayout")
self.listWidget = QtWidgets.QListWidget(Dialog)
@ -50,9 +49,6 @@ class Ui_Dialog(object):
self.log_checkbox = QtWidgets.QCheckBox(Dialog)
self.log_checkbox.setObjectName("log_checkbox")
self.verticalLayout.addWidget(self.log_checkbox)
self.freq_box = QtWidgets.QCheckBox(Dialog)
self.freq_box.setObjectName("freq_box")
self.verticalLayout.addWidget(self.freq_box)
self.horizontalLayout_2 = QtWidgets.QHBoxLayout()
self.horizontalLayout_2.setContentsMargins(-1, 0, -1, -1)
self.horizontalLayout_2.setSpacing(3)
@ -71,8 +67,8 @@ class Ui_Dialog(object):
self.verticalLayout.addWidget(self.buttonBox)
self.retranslateUi(Dialog)
self.buttonBox.accepted.connect(Dialog.accept) # type: ignore
self.buttonBox.rejected.connect(Dialog.reject) # type: ignore
self.buttonBox.accepted.connect(Dialog.accept)
self.buttonBox.rejected.connect(Dialog.reject)
QtCore.QMetaObject.connectSlotsByName(Dialog)
def retranslateUi(self, Dialog):
@ -84,5 +80,4 @@ class Ui_Dialog(object):
self.ft_comboBox.setItemText(1, _translate("Dialog", "Imag"))
self.ft_comboBox.setItemText(2, _translate("Dialog", "Complex"))
self.log_checkbox.setText(_translate("Dialog", "use logarithmic x axis"))
self.freq_box.setText(_translate("Dialog", "return x axis as f, not omega"))
self.newgraph_checkbox.setText(_translate("Dialog", "New graph"))

15
src/gui_qt/_py/interpol_dialog.py
View File

@ -1,11 +1,10 @@
# -*- coding: utf-8 -*-
# Form implementation generated from reading ui file 'src/resources/_ui/interpol_dialog.ui'
# Form implementation generated from reading ui file 'resources/_ui/interpol_dialog.ui'
#
# Created by: PyQt5 UI code generator 5.15.9
# Created by: PyQt5 UI code generator 5.12.3
#
# WARNING: Any manual changes made to this file will be lost when pyuic5 is
# run again. Do not edit this file unless you know what you are doing.
# WARNING! All changes made in this file will be lost!
from PyQt5 import QtCore, QtGui, QtWidgets
@ -66,13 +65,12 @@ class Ui_Dialog(object):
self.label_2 = QtWidgets.QLabel(Dialog)
self.label_2.setObjectName("label_2")
self.gridLayout.addWidget(self.label_2, 6, 0, 1, 1)
self.listWidget = QListWidgetSelect(Dialog)
self.listWidget = QtWidgets.QListWidget(Dialog)
sizePolicy = QtWidgets.QSizePolicy(QtWidgets.QSizePolicy.MinimumExpanding, QtWidgets.QSizePolicy.Expanding)
sizePolicy.setHorizontalStretch(0)
sizePolicy.setVerticalStretch(0)
sizePolicy.setHeightForWidth(self.listWidget.sizePolicy().hasHeightForWidth())
self.listWidget.setSizePolicy(sizePolicy)
self.listWidget.setSelectionMode(QtWidgets.QAbstractItemView.MultiSelection)
self.listWidget.setObjectName("listWidget")
self.gridLayout.addWidget(self.listWidget, 1, 0, 1, 2)
self.sampling_widget = QtWidgets.QWidget(Dialog)
@ -132,8 +130,8 @@ class Ui_Dialog(object):
self.label_8.setBuddy(self.dest_combobox)
self.retranslateUi(Dialog)
self.buttonBox.accepted.connect(Dialog.accept) # type: ignore
self.buttonBox.rejected.connect(Dialog.reject) # type: ignore
self.buttonBox.accepted.connect(Dialog.accept)
self.buttonBox.rejected.connect(Dialog.reject)
QtCore.QMetaObject.connectSlotsByName(Dialog)
Dialog.setTabOrder(self.listWidget, self.ylog_checkBox)
Dialog.setTabOrder(self.ylog_checkBox, self.interp_comboBox)
@ -166,4 +164,3 @@ class Ui_Dialog(object):
self.xaxis_comboBox.setItemText(1, _translate("Dialog", "from data"))
self.label_8.setText(_translate("Dialog", "Add interpolated data to"))
self.xlog_checkBox.setText(_translate("Dialog", "use log(x)"))
from ..lib.listwidget import QListWidgetSelect

12
src/gui_qt/_py/phase_corr_dialog.py
View File

@ -1,8 +1,8 @@
# -*- coding: utf-8 -*-
# Form implementation generated from reading ui file 'src/resources/_ui/phase_corr_dialog.ui'
# Form implementation generated from reading ui file 'resources/_ui/phase_corr_dialog.ui'
#
# Created by: PyQt5 UI code generator 5.15.9
# Created by: PyQt5 UI code generator 5.15.4
#
# WARNING: Any manual changes made to this file will be lost when pyuic5 is
# run again. Do not edit this file unless you know what you are doing.
@ -24,7 +24,7 @@ class Ui_SignalEdit(object):
self.gridLayout.setContentsMargins(6, 6, 6, 6)
self.gridLayout.setSpacing(3)
self.gridLayout.setObjectName("gridLayout")
self.graphicsView = NMRPlotWidget(SignalEdit)
self.graphicsView = PlotWidget(SignalEdit)
sizePolicy = QtWidgets.QSizePolicy(QtWidgets.QSizePolicy.MinimumExpanding, QtWidgets.QSizePolicy.Expanding)
sizePolicy.setHorizontalStretch(0)
sizePolicy.setVerticalStretch(0)
@ -83,8 +83,8 @@ class Ui_SignalEdit(object):
self.gridLayout.addItem(spacerItem1, 1, 5, 1, 1)
self.retranslateUi(SignalEdit)
self.buttonBox.accepted.connect(SignalEdit.accept) # type: ignore
self.buttonBox.rejected.connect(SignalEdit.close) # type: ignore
self.buttonBox.accepted.connect(SignalEdit.accept)
self.buttonBox.rejected.connect(SignalEdit.close)
QtCore.QMetaObject.connectSlotsByName(SignalEdit)
def retranslateUi(self, SignalEdit):
@ -94,4 +94,4 @@ class Ui_SignalEdit(object):
self.label_8.setText(_translate("SignalEdit", "Pivot"))
self.label_6.setText(_translate("SignalEdit", "Phase 1"))
self.label.setText(_translate("SignalEdit", "Phase 0"))
from ..lib.graph_items import NMRPlotWidget
from pyqtgraph import PlotWidget

15
src/gui_qt/_py/shift_scale_dialog.py
View File

@ -1,11 +1,10 @@
# -*- coding: utf-8 -*-
# Form implementation generated from reading ui file 'src/resources/_ui/shift_scale_dialog.ui'
# Form implementation generated from reading ui file 'resources/_ui/shift_scale_dialog.ui'
#
# Created by: PyQt5 UI code generator 5.15.9
# Created by: PyQt5 UI code generator 5.12.3
#
# WARNING: Any manual changes made to this file will be lost when pyuic5 is
# run again. Do not edit this file unless you know what you are doing.
# WARNING! All changes made in this file will be lost!
from PyQt5 import QtCore, QtGui, QtWidgets
@ -163,7 +162,7 @@ class Ui_shift_dialog(object):
self.verticalLayout_2 = QtWidgets.QVBoxLayout(self.verticalFrame_2)
self.verticalLayout_2.setSpacing(3)
self.verticalLayout_2.setObjectName("verticalLayout_2")
self.graphicsView = NMRPlotWidget(self.verticalFrame_2)
self.graphicsView = PlotWidget(self.verticalFrame_2)
sizePolicy = QtWidgets.QSizePolicy(QtWidgets.QSizePolicy.Expanding, QtWidgets.QSizePolicy.MinimumExpanding)
sizePolicy.setHorizontalStretch(0)
sizePolicy.setVerticalStretch(0)
@ -268,8 +267,8 @@ class Ui_shift_dialog(object):
self.retranslateUi(shift_dialog)
self.tabWidget.setCurrentIndex(0)
self.buttonBox.accepted.connect(shift_dialog.accept) # type: ignore
self.buttonBox.rejected.connect(shift_dialog.reject) # type: ignore
self.buttonBox.accepted.connect(shift_dialog.accept)
self.buttonBox.rejected.connect(shift_dialog.reject)
QtCore.QMetaObject.connectSlotsByName(shift_dialog)
shift_dialog.setTabOrder(self.tabWidget, self.shift_table)
shift_dialog.setTabOrder(self.shift_table, self.x_shift_spinbox)
@ -311,5 +310,5 @@ class Ui_shift_dialog(object):
self.overwrite_checkbox.setText(_translate("shift_dialog", "Overwrite data"))
self.data_newgraph.setText(_translate("shift_dialog", "New graph"))
self.values_newgraph.setText(_translate("shift_dialog", "New graph"))
from ..lib.graph_items import NMRPlotWidget
from ..lib.spinboxes import SciSpinBox
from pyqtgraph import PlotWidget

8
src/gui_qt/_py/t1dialog.py
View File

@ -1,11 +1,10 @@
# -*- coding: utf-8 -*-
# Form implementation generated from reading ui file 'src/resources/_ui/t1dialog.ui'
# Form implementation generated from reading ui file 'resources/_ui/t1dialog.ui'
#
# Created by: PyQt5 UI code generator 5.15.9
# Created by: PyQt5 UI code generator 5.12.3
#
# WARNING: Any manual changes made to this file will be lost when pyuic5 is
# run again. Do not edit this file unless you know what you are doing.
# WARNING! All changes made in this file will be lost!
from PyQt5 import QtCore, QtGui, QtWidgets
@ -161,7 +160,6 @@ class Ui_t1dialog(object):
self.tau_combox.addItem("")
self.gridLayout_4.addWidget(self.tau_combox, 1, 0, 1, 2)
self.checkBox_interpol = QtWidgets.QCheckBox(self.groupBox_3)
self.checkBox_interpol.setEnabled(False)
self.checkBox_interpol.setObjectName("checkBox_interpol")
self.gridLayout_4.addWidget(self.checkBox_interpol, 2, 0, 1, 2)
self.graph_checkbox = QtWidgets.QCheckBox(self.groupBox_3)

253
src/gui_qt/_py/tnmh_dialog.py
View File

@ -1,253 +0,0 @@
# -*- coding: utf-8 -*-
# Form implementation generated from reading ui file 'src/resources/_ui/tnmh_dialog.ui'
#
# Created by: PyQt5 UI code generator 5.15.9
#
# WARNING: Any manual changes made to this file will be lost when pyuic5 is
# run again. Do not edit this file unless you know what you are doing.
from PyQt5 import QtCore, QtGui, QtWidgets
class Ui_DSCEvalDialog(object):
def setupUi(self, DSCEvalDialog):
DSCEvalDialog.setObjectName("DSCEvalDialog")
DSCEvalDialog.resize(996, 712)
self.gridLayout = QtWidgets.QGridLayout(DSCEvalDialog)
self.gridLayout.setObjectName("gridLayout")
self.listWidget = QListWidgetSelect(DSCEvalDialog)
sizePolicy = QtWidgets.QSizePolicy(QtWidgets.QSizePolicy.Maximum, QtWidgets.QSizePolicy.Expanding)
sizePolicy.setHorizontalStretch(0)
sizePolicy.setVerticalStretch(0)
sizePolicy.setHeightForWidth(self.listWidget.sizePolicy().hasHeightForWidth())
self.listWidget.setSizePolicy(sizePolicy)
self.listWidget.setSelectionMode(QtWidgets.QAbstractItemView.ExtendedSelection)
self.listWidget.setObjectName("listWidget")
self.gridLayout.addWidget(self.listWidget, 0, 0, 1, 1)
self.stackedWidget = QtWidgets.QStackedWidget(DSCEvalDialog)
sizePolicy = QtWidgets.QSizePolicy(QtWidgets.QSizePolicy.MinimumExpanding, QtWidgets.QSizePolicy.Preferred)
sizePolicy.setHorizontalStretch(0)
sizePolicy.setVerticalStretch(0)
sizePolicy.setHeightForWidth(self.stackedWidget.sizePolicy().hasHeightForWidth())
self.stackedWidget.setSizePolicy(sizePolicy)
self.stackedWidget.setFrameShape(QtWidgets.QFrame.Box)
self.stackedWidget.setObjectName("stackedWidget")
self.page = QtWidgets.QWidget()
self.page.setObjectName("page")
self.gridLayout_2 = QtWidgets.QGridLayout(self.page)
self.gridLayout_2.setObjectName("gridLayout_2")
self.gridLayout_9 = QtWidgets.QGridLayout()
self.gridLayout_9.setObjectName("gridLayout_9")
self.tg_export_check = QtWidgets.QCheckBox(self.page)
self.tg_export_check.setChecked(True)
self.tg_export_check.setObjectName("tg_export_check")
self.gridLayout_9.addWidget(self.tg_export_check, 0, 0, 1, 1)
spacerItem = QtWidgets.QSpacerItem(20, 40, QtWidgets.QSizePolicy.Minimum, QtWidgets.QSizePolicy.Expanding)
self.gridLayout_9.addItem(spacerItem, 3, 0, 1, 1)
self.tglines_export_check = QtWidgets.QCheckBox(self.page)
self.tglines_export_check.setChecked(True)
self.tglines_export_check.setObjectName("tglines_export_check")
self.gridLayout_9.addWidget(self.tglines_export_check, 0, 1, 1, 1)
self.tg_export_button = QtWidgets.QPushButton(self.page)
self.tg_export_button.setObjectName("tg_export_button")
self.gridLayout_9.addWidget(self.tg_export_button, 2, 0, 1, 2)
self.gridLayout_2.addLayout(self.gridLayout_9, 2, 1, 1, 1)
self.tg_tree = QtWidgets.QTreeWidget(self.page)
self.tg_tree.setObjectName("tg_tree")
self.tg_tree.headerItem().setText(0, "1")
self.tg_tree.header().setVisible(False)
self.gridLayout_2.addWidget(self.tg_tree, 2, 0, 1, 1)
self.dsc_plot = NMRPlotWidget(self.page)
sizePolicy = QtWidgets.QSizePolicy(QtWidgets.QSizePolicy.MinimumExpanding, QtWidgets.QSizePolicy.MinimumExpanding)
sizePolicy.setHorizontalStretch(0)
sizePolicy.setVerticalStretch(0)
sizePolicy.setHeightForWidth(self.dsc_plot.sizePolicy().hasHeightForWidth())
self.dsc_plot.setSizePolicy(sizePolicy)
self.dsc_plot.setObjectName("dsc_plot")
self.gridLayout_2.addWidget(self.dsc_plot, 1, 0, 1, 2)
self.horizontalLayout_4 = QtWidgets.QHBoxLayout()
self.horizontalLayout_4.setObjectName("horizontalLayout_4")
self.label = QtWidgets.QLabel(self.page)
self.label.setObjectName("label")
self.horizontalLayout_4.addWidget(self.label)
self.calctg_button = QtWidgets.QPushButton(self.page)
sizePolicy = QtWidgets.QSizePolicy(QtWidgets.QSizePolicy.Preferred, QtWidgets.QSizePolicy.Preferred)
sizePolicy.setHorizontalStretch(0)
sizePolicy.setVerticalStretch(0)
sizePolicy.setHeightForWidth(self.calctg_button.sizePolicy().hasHeightForWidth())
self.calctg_button.setSizePolicy(sizePolicy)
self.calctg_button.setObjectName("calctg_button")
self.horizontalLayout_4.addWidget(self.calctg_button)
self.gridLayout_2.addLayout(self.horizontalLayout_4, 0, 0, 1, 2)
self.stackedWidget.addWidget(self.page)
self.page_2 = QtWidgets.QWidget()
self.page_2.setObjectName("page_2")
self.gridLayout_3 = QtWidgets.QGridLayout(self.page_2)
self.gridLayout_3.setObjectName("gridLayout_3")
self.label_4 = QtWidgets.QLabel(self.page_2)
self.label_4.setObjectName("label_4")
self.gridLayout_3.addWidget(self.label_4, 2, 0, 1, 1)
self.tghodge_graph = NMRPlotWidget(self.page_2)
self.tghodge_graph.setObjectName("tghodge_graph")
self.gridLayout_3.addWidget(self.tghodge_graph, 1, 0, 1, 1)
self.tau_plot = NMRPlotWidget(self.page_2)
sizePolicy = QtWidgets.QSizePolicy(QtWidgets.QSizePolicy.Expanding, QtWidgets.QSizePolicy.MinimumExpanding)
sizePolicy.setHorizontalStretch(0)
sizePolicy.setVerticalStretch(0)
sizePolicy.setHeightForWidth(self.tau_plot.sizePolicy().hasHeightForWidth())
self.tau_plot.setSizePolicy(sizePolicy)
self.tau_plot.setObjectName("tau_plot")
self.gridLayout_3.addWidget(self.tau_plot, 1, 1, 1, 1)
self.horizontalLayout_3 = QtWidgets.QHBoxLayout()
self.horizontalLayout_3.setObjectName("horizontalLayout_3")
self.label_2 = QtWidgets.QLabel(self.page_2)
self.label_2.setObjectName("label_2")
self.horizontalLayout_3.addWidget(self.label_2)
self.hodge_button = QtWidgets.QPushButton(self.page_2)
sizePolicy = QtWidgets.QSizePolicy(QtWidgets.QSizePolicy.Preferred, QtWidgets.QSizePolicy.Preferred)
sizePolicy.setHorizontalStretch(0)
sizePolicy.setVerticalStretch(0)
sizePolicy.setHeightForWidth(self.hodge_button.sizePolicy().hasHeightForWidth())
self.hodge_button.setSizePolicy(sizePolicy)
self.hodge_button.setObjectName("hodge_button")
self.horizontalLayout_3.addWidget(self.hodge_button)
self.gridLayout_3.addLayout(self.horizontalLayout_3, 0, 0, 1, 2)
self.export_hodge_button = QtWidgets.QPushButton(self.page_2)
self.export_hodge_button.setObjectName("export_hodge_button")
self.gridLayout_3.addWidget(self.export_hodge_button, 5, 1, 1, 1)
self.hodge_graph_combo = QtWidgets.QComboBox(self.page_2)
self.hodge_graph_combo.setEnabled(False)
self.hodge_graph_combo.setObjectName("hodge_graph_combo")
self.gridLayout_3.addWidget(self.hodge_graph_combo, 4, 1, 1, 1)
self.hodge_graph_check = QtWidgets.QCheckBox(self.page_2)
self.hodge_graph_check.setChecked(True)
self.hodge_graph_check.setObjectName("hodge_graph_check")
self.gridLayout_3.addWidget(self.hodge_graph_check, 4, 0, 1, 1)
self.horizontalLayout_5 = QtWidgets.QHBoxLayout()
self.horizontalLayout_5.setObjectName("horizontalLayout_5")
self.onset_check = QtWidgets.QCheckBox(self.page_2)
self.onset_check.setChecked(True)
self.onset_check.setObjectName("onset_check")
self.horizontalLayout_5.addWidget(self.onset_check)
self.mid_check = QtWidgets.QCheckBox(self.page_2)
self.mid_check.setChecked(True)
self.mid_check.setObjectName("mid_check")
self.horizontalLayout_5.addWidget(self.mid_check)
self.end_check = QtWidgets.QCheckBox(self.page_2)
self.end_check.setChecked(True)
self.end_check.setObjectName("end_check")
self.horizontalLayout_5.addWidget(self.end_check)
self.inflection_check = QtWidgets.QCheckBox(self.page_2)
self.inflection_check.setChecked(True)
self.inflection_check.setObjectName("inflection_check")
self.horizontalLayout_5.addWidget(self.inflection_check)
self.fictive_check = QtWidgets.QCheckBox(self.page_2)
self.fictive_check.setChecked(True)
self.fictive_check.setObjectName("fictive_check")
self.horizontalLayout_5.addWidget(self.fictive_check)
spacerItem1 = QtWidgets.QSpacerItem(40, 20, QtWidgets.QSizePolicy.Expanding, QtWidgets.QSizePolicy.Minimum)
self.horizontalLayout_5.addItem(spacerItem1)
self.gridLayout_3.addLayout(self.horizontalLayout_5, 3, 0, 1, 2)
self.stackedWidget.addWidget(self.page_2)
self.page_3 = QtWidgets.QWidget()
self.page_3.setObjectName("page_3")
self.gridLayout_6 = QtWidgets.QGridLayout(self.page_3)
self.gridLayout_6.setObjectName("gridLayout_6")
self.tnmh_graphics = NMRPlotWidget(self.page_3)
self.tnmh_graphics.setObjectName("tnmh_graphics")
self.gridLayout_6.addWidget(self.tnmh_graphics, 1, 0, 1, 2)
self.tnmh_tree = QtWidgets.QTreeWidget(self.page_3)
self.tnmh_tree.setObjectName("tnmh_tree")
self.tnmh_tree.headerItem().setText(0, "1")
self.tnmh_tree.header().setVisible(False)
self.gridLayout_6.addWidget(self.tnmh_tree, 2, 0, 1, 1)
self.gridLayout_5 = QtWidgets.QGridLayout()
self.gridLayout_5.setObjectName("gridLayout_5")
self.tnmh_graph_check = QtWidgets.QCheckBox(self.page_3)
self.tnmh_graph_check.setChecked(True)
self.tnmh_graph_check.setObjectName("tnmh_graph_check")
self.gridLayout_5.addWidget(self.tnmh_graph_check, 1, 0, 1, 1)
self.tnmhfit_export_check = QtWidgets.QCheckBox(self.page_3)
self.tnmhfit_export_check.setChecked(True)
self.tnmhfit_export_check.setObjectName("tnmhfit_export_check")
self.gridLayout_5.addWidget(self.tnmhfit_export_check, 0, 0, 1, 1)
self.tnmh_export_button = QtWidgets.QPushButton(self.page_3)
self.tnmh_export_button.setObjectName("tnmh_export_button")
self.gridLayout_5.addWidget(self.tnmh_export_button, 2, 0, 1, 2)
self.fictive_export_check = QtWidgets.QCheckBox(self.page_3)
self.fictive_export_check.setChecked(True)
self.fictive_export_check.setObjectName("fictive_export_check")
self.gridLayout_5.addWidget(self.fictive_export_check, 0, 1, 1, 1)
self.tnmh_graph_combo = QtWidgets.QComboBox(self.page_3)
self.tnmh_graph_combo.setEnabled(False)
self.tnmh_graph_combo.setObjectName("tnmh_graph_combo")
self.gridLayout_5.addWidget(self.tnmh_graph_combo, 1, 1, 1, 1)
spacerItem2 = QtWidgets.QSpacerItem(20, 40, QtWidgets.QSizePolicy.Minimum, QtWidgets.QSizePolicy.Expanding)
self.gridLayout_5.addItem(spacerItem2, 3, 0, 1, 1)
self.gridLayout_6.addLayout(self.gridLayout_5, 2, 1, 1, 1)
self.horizontalLayout_2 = QtWidgets.QHBoxLayout()
self.horizontalLayout_2.setObjectName("horizontalLayout_2")
self.label_3 = QtWidgets.QLabel(self.page_3)
self.label_3.setObjectName("label_3")
self.horizontalLayout_2.addWidget(self.label_3)
self.tnhm_fitbutton = QtWidgets.QPushButton(self.page_3)
self.tnhm_fitbutton.setObjectName("tnhm_fitbutton")
self.horizontalLayout_2.addWidget(self.tnhm_fitbutton)
self.gridLayout_6.addLayout(self.horizontalLayout_2, 0, 0, 1, 2)
self.stackedWidget.addWidget(self.page_3)
self.gridLayout.addWidget(self.stackedWidget, 0, 1, 1, 1)
self.horizontalLayout = QtWidgets.QHBoxLayout()
self.horizontalLayout.setObjectName("horizontalLayout")
spacerItem3 = QtWidgets.QSpacerItem(40, 20, QtWidgets.QSizePolicy.Expanding, QtWidgets.QSizePolicy.Minimum)
self.horizontalLayout.addItem(spacerItem3)
self.back_button = QtWidgets.QToolButton(DSCEvalDialog)
self.back_button.setToolButtonStyle(QtCore.Qt.ToolButtonTextBesideIcon)
self.back_button.setArrowType(QtCore.Qt.LeftArrow)
self.back_button.setObjectName("back_button")
self.horizontalLayout.addWidget(self.back_button)
self.next_button = QtWidgets.QToolButton(DSCEvalDialog)
self.next_button.setToolButtonStyle(QtCore.Qt.ToolButtonTextBesideIcon)
self.next_button.setArrowType(QtCore.Qt.RightArrow)
self.next_button.setObjectName("next_button")
self.horizontalLayout.addWidget(self.next_button)
self.close_button = QtWidgets.QPushButton(DSCEvalDialog)
self.close_button.setObjectName("close_button")
self.horizontalLayout.addWidget(self.close_button)
self.gridLayout.addLayout(self.horizontalLayout, 1, 0, 1, 2)
self.retranslateUi(DSCEvalDialog)
self.stackedWidget.setCurrentIndex(0)
self.close_button.clicked.connect(DSCEvalDialog.close) # type: ignore
QtCore.QMetaObject.connectSlotsByName(DSCEvalDialog)
def retranslateUi(self, DSCEvalDialog):
_translate = QtCore.QCoreApplication.translate
DSCEvalDialog.setWindowTitle(_translate("DSCEvalDialog", "To boldly go where no man has gone before"))
self.tg_export_check.setText(_translate("DSCEvalDialog", "Export Tg"))
self.tglines_export_check.setText(_translate("DSCEvalDialog", "Export lines"))
self.tg_export_button.setText(_translate("DSCEvalDialog", "Export"))
self.label.setText(_translate("DSCEvalDialog", "<html><head/><body><p><span style=\" font-weight:600;\">Glass transition</span></p></body></html>"))
self.calctg_button.setText(_translate("DSCEvalDialog", "Calculate Tg"))
self.label_4.setText(_translate("DSCEvalDialog", "Export tau:"))
self.label_2.setText(_translate("DSCEvalDialog", "<html><head/><body><p><span style=\" font-weight:600;\">Hodge tau</span></p></body></html>"))
self.hodge_button.setText(_translate("DSCEvalDialog", "Make it so."))
self.export_hodge_button.setText(_translate("DSCEvalDialog", "Export"))
self.hodge_graph_check.setText(_translate("DSCEvalDialog", "New graph"))
self.onset_check.setText(_translate("DSCEvalDialog", "Onset"))
self.mid_check.setText(_translate("DSCEvalDialog", "Midpoint"))
self.end_check.setText(_translate("DSCEvalDialog", "End"))
self.inflection_check.setText(_translate("DSCEvalDialog", "Inflection"))
self.fictive_check.setText(_translate("DSCEvalDialog", "Fictive"))
self.tnmh_graph_check.setText(_translate("DSCEvalDialog", "New graph"))
self.tnmhfit_export_check.setText(_translate("DSCEvalDialog", "Export fit"))
self.tnmh_export_button.setText(_translate("DSCEvalDialog", "Export"))
self.fictive_export_check.setText(_translate("DSCEvalDialog", "Export dTf / dT"))
self.label_3.setText(_translate("DSCEvalDialog", "<html><head/><body><p><span style=\" font-weight:600;\">dTf/dT and TNMH </span></p></body></html>"))
self.tnhm_fitbutton.setText(_translate("DSCEvalDialog", "Engage!"))
self.back_button.setText(_translate("DSCEvalDialog", "Back"))
self.next_button.setText(_translate("DSCEvalDialog", "Next"))
self.close_button.setText(_translate("DSCEvalDialog", "Close"))
from ..lib.graph_items import NMRPlotWidget
from ..lib.listwidget import QListWidgetSelect

4
src/gui_qt/_py/valueeditor.py
View File

@ -1,8 +1,8 @@
# -*- coding: utf-8 -*-
# Form implementation generated from reading ui file 'src/resources/_ui/valueeditor.ui'
# Form implementation generated from reading ui file 'resources/_ui/valueeditor.ui'
#
# Created by: PyQt5 UI code generator 5.15.9
# Created by: PyQt5 UI code generator 5.15.4
#
# WARNING: Any manual changes made to this file will be lost when pyuic5 is
# run again. Do not edit this file unless you know what you are doing.

28
src/gui_qt/cli.py
View File

@ -1,28 +0,0 @@
def main():
import sys
from nmreval.configs import check_for_config
# does a directory for config stuff exist? create it if not
check_for_config()
# pyqtgraph warns on Mac if QApplication is created when it is imported
# import pyqtgraph
from nmreval.lib.logger import handle_exception
sys.excepthook = handle_exception
from gui_qt import App
app = App(['Team Rocket FTW!'])
from gui_qt.main.mainwindow import NMRMainWindow
mplQt = NMRMainWindow()
mplQt.show()
sys.exit(app.exec())
if __name__ == '__main__':
main()

155
src/gui_qt/data/container.py
View File

@ -8,10 +8,8 @@ from pyqtgraph import mkPen
from nmreval.data.points import Points
from nmreval.data.signals import Signal
from nmreval.lib.logger import logger
from nmreval.utils.text import convert
from nmreval.data.bds import BDS
from nmreval.data.dsc import DSC
from nmreval.lib.colors import BaseColor, TUColors
from nmreval.lib.lines import LineStyle
from nmreval.lib.symbols import SymbolStyle, symbolcycle
@ -34,7 +32,6 @@ class ExperimentContainer(QtCore.QObject):
self.id = str(identifier)
self._fits = []
self._relations = kwargs.get('relations', {})
self._data = data
self._manager = kwargs.get('manager')
self.graph = ''
@ -47,7 +44,6 @@ class ExperimentContainer(QtCore.QObject):
self.actions = {}
self._update_actions()
@plot_update
def _init_plot(self):
raise NotImplementedError
@ -230,8 +226,6 @@ class ExperimentContainer(QtCore.QObject):
return self.plot_real, self.plot_imag, self.plot_error
def get_state(self):
# TODO preserve relationships
ret_dic = {
'id': self.id,
'data': self._data.get_state(),
@ -273,32 +267,6 @@ class ExperimentContainer(QtCore.QObject):
else:
self._fits.extend(value)
def has_relation(self, relation_type):
return relation_type in self._relations
def get_relation(self, relation_type: int):
return self._relations.get(relation_type, [])
def add_relation(self, relation_type: int, value: str):
if relation_type not in self._relations:
self._relations[relation_type] = []
self._relations[relation_type].append(value)
def remove_relation(self, relation_type: int, value: str):
if relation_type not in self._relations:
raise ValueError(f'Relationship {relation_type!r} with id {value!r} doe not exist for {self.name}')
related_id_value = self._relations[relation_type]
idx = related_id_value.index(value)
if idx == -1:
raise ValueError(f'Relationship {relation_type!r} with id {value!r} doe not exist for {self.name}')
related_id_value.pop(idx)
if len(related_id_value) == 0:
self._relations.pop(relation_type)
def _update_actions(self):
self.actions.update({'sort': self._data.sort,
'cut': self._data.cut,
@ -344,10 +312,12 @@ class ExperimentContainer(QtCore.QObject):
err_pen.setColor(QtGui.QColor(*self.plot_real.symbolcolor.rgb()))
self.plot_error.setData(pen=err_pen)
if mode in ['imag', 'all'] and self.plot_imag is not None:
elif mode == 'imag' and self.plot_imag is not None:
self.plot_imag.set_color(color, symbol=symbol, line=line)
else:
print('Updating color failed for ' + str(self.id))
def setSymbol(self, *, symbol=None, color=None, size=None, mode='real'):
def setSymbol(self, symbol=None, color=None, size=None, mode='real'):
if mode in ['real', 'all']:
self.plot_real.set_symbol(symbol=symbol, size=size, color=color)
if color is not None and self.plot_error is not None and self.plot_real.symbol != SymbolStyle.No:
@ -357,9 +327,9 @@ class ExperimentContainer(QtCore.QObject):
elif mode in ['imag', 'all'] and self.plot_imag is not None:
self.plot_imag.set_symbol(symbol=symbol, size=size, color=color)
else:
logger.warning(f'Updating symbol failed for {self.id}')
print('Updating symbol failed for ' + str(self.id))
def setLine(self, *, width=None, style=None, color=None, mode='real'):
def setLine(self, width=None, style=None, color=None, mode='real'):
if mode in ['real', 'all']:
self.plot_real.set_line(width=width, style=style, color=color)
if color is not None and self.plot_error is not None and self.plot_real.symbol == SymbolStyle.No:
@ -369,7 +339,7 @@ class ExperimentContainer(QtCore.QObject):
elif mode in ['imag', 'all'] and self.plot_imag is not None:
self.plot_imag.set_line(width=width, style=style, color=color)
else:
logger.warning(f'Updating line failed for {self.id}')
print('Updating line failed for ' + str(self.id))
def update_property(self, key1: str, key2: str, value: Any):
keykey = key2.split()
@ -464,21 +434,11 @@ class ExperimentContainer(QtCore.QObject):
return offset
@plot_update
def shift_scale(self, shift_factor: tuple[float, float], scaling_factor: tuple[float, float]):
scale_x, scale_y = scaling_factor
shift_x, shift_y = shift_factor
self.data.x = self.data.x * scale_x + shift_x
self.data.y = self.data.y * scale_y + shift_y
self.data.y_err = self.data.y_err * scale_y
self.update({'shift': scaling_factor, 'scale': shift_factor})
def get_namespace(self, i: int = None, j: int = None) -> dict:
if (i is None) and (j is None):
prefix = ''
else:
prefix = f'g[{i}].s[{j}].'
prefix = 'g[%i].s[%i].' % (i, j)
namespace = {prefix + 'x': (self.x, 'x values'),
prefix + 'y': [self.y, 'y values'],
@ -499,50 +459,27 @@ class ExperimentContainer(QtCore.QObject):
return namespace
def eval_expression(self, cmds, namespace, i=None, j=None):
if i is not None:
namespace['i'] = i
def eval_expression(self, cmds, namespace):
namespace.update({'x': self.x, 'y': self.y, 'y_err': self.y_err, 'value': self.value})
if j is not None:
namespace['j'] = j
namespace.update({'x': self._data.x, 'y': self._data.y, 'y_err': self._data.y_err, 'value': self.value})
namespace['fit'] = {}
if isinstance(self, FitContainer):
namespace['fit'].update({
'%s' % convert(pname, old='latex', new='plain'): pvalue.value
for (pname, pvalue) in self._data.parameter.items()
})
elif len(self._fits) == 1:
namespace['fit'].update({
'%s' % convert(pname, old='tex', new='str'): pvalue.value
for (pname, pvalue) in self._manager[self._fits[0]].parameter.items()
})
if len(self._fits) == 1:
namespace.update({"fit['%s']" % (convert(pname, old='tex', new='str')): pvalue.value
for (pname, pvalue) in self._manager[self._fits[0]].parameter.items()})
else:
for k, f in enumerate(self._fits):
namespace['fit'].update({
"%s_%i" % (convert(pname, old='tex', new='str'), k): pvalue.value
for (pname, pvalue) in self._manager[f].parameter.items()
})
namespace.update({"fit['%s_%i']" % (convert(pname, old='tex', new='str'), k): pvalue.value
for (pname, pvalue) in self._manager[f].parameter.items()})
new_data = self.copy()
for c in cmds:
if c:
exec(c, globals(), namespace)
new_data.set_data(x=namespace['x'], y=namespace['y'], y_err=namespace['y_err'], replace_mask=False)
new_data.set_data(x=namespace['x'], y=namespace['y'], y_err=namespace['y_err'])
new_data.value = namespace['value']
return new_data
def binning(self, digits: float):
new_data = self.copy(full=True)
new_data.data = self._data.binning(value=digits)
return new_data
class PointContainer(ExperimentContainer):
symbols = symbolcycle()
@ -553,9 +490,6 @@ class PointContainer(ExperimentContainer):
self.mode = 'pts'
self._init_plot(**kwargs)
if isinstance(self._data, DSC):
self.mode = 'dsc'
def _init_plot(self, **kwargs):
self.plot_imag = None
@ -592,17 +526,17 @@ class PointContainer(ExperimentContainer):
line_kwargs['style'] = LineStyle.No
sym_kwargs['symbol'] = next(PointContainer.symbols)
self.plot_real = PlotItem(x=self.x, y=self.y, name=self.name,
self.plot_real = PlotItem(x=self._data.x, y=self._data.y, name=self.name,
symbol=None, pen=None, connect='finite')
self.setSymbol(mode='real', **sym_kwargs)
self.setLine(mode='real', **line_kwargs)
if sym_kwargs['symbol'] != SymbolStyle.No:
self.plot_error = ErrorBars(x=self.x, y=self.y, top=self.y_err, bottom=self.y_err,
self.plot_error = ErrorBars(x=self._data.x, y=self._data.y, top=self._data.y_err, bottom=self._data.y_err,
pen=mkPen({'color': self.plot_real.symbolcolor.rgb()}))
else:
self.plot_error = ErrorBars(x=self.x, y=self.y, top=self.y_err, bottom=self.y_err,
self.plot_error = ErrorBars(x=self._data.x, y=self._data.y, top=self._data.y_err, bottom=self._data.y_err,
pen=mkPen({'color': self.plot_real.linecolor.rgb()}))
@ -625,12 +559,12 @@ class FitContainer(ExperimentContainer):
if isinstance(color, BaseColor):
color = color.rgb()
self.plot_real = PlotItem(x=self.x, y=self.y.real, name=self.name,
self.plot_real = PlotItem(x=self._data.x, y=self._data.y.real, name=self.name,
pen=mkPen({'color': color}),
connect='finite', symbol=None)
if np.iscomplexobj(self._data.y):
self.plot_imag = PlotItem(x=self.x, y=self.y.imag, name=self.name,
self.plot_imag = PlotItem(x=self._data.x, y=self._data.y.imag, name=self.name,
pen=mkPen({'color': color}),
connect='finite', symbol=None)
@ -663,9 +597,9 @@ class SignalContainer(ExperimentContainer):
self._init_plot(symbol=symbol, **kwargs)
def _init_plot(self, **kwargs):
self.plot_real = PlotItem(x=self.x, y=self.y.real, name=self.name,
self.plot_real = PlotItem(x=self._data.x, y=self._data.y.real, name=self.name,
symbol=None, pen=None, connect='finite')
self.plot_imag = PlotItem(x=self.x, y=self.y.imag, name=self.name,
self.plot_imag = PlotItem(x=self._data.x, y=self._data.y.imag, name=self.name,
symbol=None, pen=None, connect='finite')
color = kwargs.get('color', None)
@ -749,46 +683,3 @@ class SignalContainer(ExperimentContainer):
self._update_actions()
return self
@plot_update
def edit_signal(
self: SignalContainer,
baseline: tuple[None | bool],
leftshift: tuple[None | float, str],
zerofill: tuple[None, int],
apod: tuple[None, list[float], type[object]],
phase: tuple[None | float, float, float],
fourier: tuple[None | bool]
):
"""
Function for EditUndoCommand to call if a timesignal or spectra must be worked on.
This avoids to update the plot for every action we do and makes it slightly faster.
"""
if baseline[0] is not None:
self._data.baseline()
if leftshift[0] is not None:
self._data.shift(*leftshift)
if zerofill[0] is not None:
self._data.zerofill(*zerofill)
if apod[0] is not None:
self._data.apod(*apod)
# ft with three options: None, True, False
if fourier[0] is None:
# ft None -> only phase correct
if phase[0] is not None:
self._data.manual_phase(*phase)
elif fourier[0] == True:
# ft True -> first phase correct then fft
if phase[0] is not None:
self._data.manual_phase(*phase)
self.fourier()
else:
# ft False -> first fft then phase correct
self.fourier()
if phase[0] is not None:
self._data.manual_phase(*phase)

94
src/gui_qt/data/datawidget/datawidget.py
View File

@ -5,7 +5,7 @@ from nmreval.lib.colors import available_cycles
from .properties import PropWidget
from ...Qt import QtWidgets, QtGui, QtCore
from ..._py.datawidget import Ui_DataWidget
from ...lib.iconloading import make_action_icons
from ...lib import make_action_icons
from ...lib.delegates import HeaderDelegate
@ -19,7 +19,6 @@ class DataTree(QtWidgets.QTreeWidget):
saveFits = QtCore.pyqtSignal(list)
extendFits = QtCore.pyqtSignal(list)
# noinspection PyUnresolvedReferences
def __init__(self, parent=None):
super().__init__(parent=parent)
@ -61,16 +60,15 @@ class DataTree(QtWidgets.QTreeWidget):
self.update_indexes()
def add_item(self, items: (tuple | list[tuple]), gid: str, update: bool = True):
def add_item(self, items: (tuple | list[tuple]), gid: str):
if isinstance(items, tuple):
items = [items]
for row in range(self.invisibleRootItem().childCount()):
graph = self.invisibleRootItem().child(row)
if graph.data(0, QtCore.Qt.UserRole) == gid:
for (idd, name, value) in items:
for (idd, name) in items:
item = QtWidgets.QTreeWidgetItem([name])
item.setToolTip(0, f'Value: {value}')
item.setData(0, QtCore.Qt.UserRole, idd)
item.setCheckState(0, QtCore.Qt.Checked)
item.setFlags(QtCore.Qt.ItemIsSelectable | QtCore.Qt.ItemIsDragEnabled | QtCore.Qt.ItemIsEditable |
@ -80,11 +78,11 @@ class DataTree(QtWidgets.QTreeWidget):
self.resizeColumnToContents(0)
break
if update:
self.update_indexes()
self.update_indexes()
@QtCore.pyqtSlot(QtWidgets.QTreeWidgetItem)
def data_change(self, item: QtWidgets.QTreeWidgetItem, emit: bool = True) -> tuple[set, set]:
def data_change(self, item: QtWidgets.QTreeWidgetItem) -> tuple[set, set]:
idd = item.data(0, QtCore.Qt.UserRole)
is_selected = item.checkState(0) == QtCore.Qt.Checked
to_be_hidden = set()
@ -142,10 +140,9 @@ class DataTree(QtWidgets.QTreeWidget):
pass
else:
if emit:
self.keyChanged.emit(idd, item.text(0))
self.keyChanged.emit(idd, item.text(0))
if (to_be_shown or to_be_hidden) and emit:
if to_be_shown or to_be_hidden:
self.stateChanged.emit(list(to_be_shown), list(to_be_hidden))
return to_be_shown, to_be_hidden
@ -232,7 +229,7 @@ class DataTree(QtWidgets.QTreeWidget):
def sort(self, graph_item: QtWidgets.QTreeWidgetItem, mode: str = 'value'):
graph_id = graph_item.data(0, QtCore.Qt.UserRole)
sets = self.management.get_attributes(graph_id, mode)
sets = self.management.get_attributes(graph_id, mode)
sets = [el[0] for el in sorted(sets.items(), key=lambda x: x[1])]
self.management.move_sets(sets, graph_id, graph_id, pos=-1)
@ -250,11 +247,11 @@ class DataTree(QtWidgets.QTreeWidget):
self.blockSignals(False)
def update_indexes(self):
graph_cnt = -1
set_cnt = 0
iterator = QtWidgets.QTreeWidgetItemIterator(self)
self.blockSignals(True)
while iterator.value():
item = iterator.value()
if item is not None:
@ -269,7 +266,6 @@ class DataTree(QtWidgets.QTreeWidget):
iterator += 1
self.resizeColumnToContents(1)
self.blockSignals(False)
def set_name(self, sid, name):
iterator = QtWidgets.QTreeWidgetItemIterator(self)
@ -291,20 +287,13 @@ class DataTree(QtWidgets.QTreeWidget):
for idx in self.selectedIndexes():
if idx.column() == 1:
continue
item = self.itemFromIndex(idx)
if item.parent() is None:
for c_i in range(item.childCount()):
# add sets inside graph to removal
child_data = item.child(c_i).data(0, QtCore.Qt.UserRole)
if child_data not in rm_sets:
rm_sets.append(child_data)
rm_sets.append(item.child(c_i).data(0, QtCore.Qt.UserRole))
rm_graphs.append(item.data(0, QtCore.Qt.UserRole))
else:
item_data = item.data(0, QtCore.Qt.UserRole)
if item_data not in rm_sets:
rm_sets.append(item_data)
rm_sets.append(item.data(0, QtCore.Qt.UserRole))
# self.deleteItem.emit(rm_sets+rm_graphs)
self.management.delete_sets(rm_sets+rm_graphs)
@ -317,24 +306,26 @@ class DataTree(QtWidgets.QTreeWidget):
if idx.column() != 0:
continue
item = self.itemFromIndex(idx)
if item.parent() is None:
is_selected = item.checkState(0)
self.blockSignals(True)
for i in range(item.childCount()):
child = item.child(i)
from_parent.append(child)
sets.append(item)
self.blockSignals(False)
if is_selected == QtCore.Qt.Checked:
item.setCheckState(0, QtCore.Qt.Unchecked)
else:
item.setCheckState(0, QtCore.Qt.Checked)
else:
sets.append(item)
to_be_hidden = set()
to_be_shown = set()
self.blockSignals(True)
for it in sets:
if it in from_parent:
continue
it.setCheckState(0, QtCore.Qt.Unchecked if it.checkState(0) == QtCore.Qt.Checked else QtCore.Qt.Checked)
s1, s2 = self.data_change(it, emit=False)
to_be_hidden |= s2
to_be_shown |= s1
self.blockSignals(False)
self.stateChanged.emit(list(to_be_shown), list(to_be_hidden))
else:
super().keyPressEvent(evt)
@ -344,47 +335,27 @@ class DataTree(QtWidgets.QTreeWidget):
self.setDragEnabled(idx.column() == 0)
super().mousePressEvent(evt)
def remove_item(self, ids: list[str]):
def remove_item(self, ids: list):
iterator = QtWidgets.QTreeWidgetItemIterator(self)
toberemoved = []
graph_removal = []
# find all items that have to be removed
while iterator.value():
item = iterator.value()
_id = item.data(0, QtCore.Qt.UserRole)
if _id in ids:
try:
item_parent = item.parent()
if item_parent is None:
if item.parent() is None:
raise AttributeError
idx = item_parent.indexOfChild(item)
# item.parent().takeChild(idx)
toberemoved.append((item_parent, idx))
idx = item.parent().indexOfChild(item)
item.parent().takeChild(idx)
if _id in self._checked_sets:
self._checked_sets.remove(_id)
except AttributeError:
idx = self.invisibleRootItem().indexOfChild(item)
# self.invisibleRootItem().takeChild(idx)
graph_removal.append(idx)
if _id in self._checked_graphs:
self._checked_graphs.remove(_id)
self.invisibleRootItem().takeChild(idx)
self._checked_graphs.remove(_id)
iterator += 1
for (item, set_idx) in sorted(toberemoved, key=lambda x: x[1], reverse=True):
item.takeChild(set_idx)
for graph_idx in sorted(graph_removal, reverse=True):
self.invisibleRootItem().takeChild(graph_idx)
self.update_indexes()
def contextMenuEvent(self, evt):
@ -548,7 +519,6 @@ class DataWidget(QtWidgets.QWidget, Ui_DataWidget):
self.setupUi(self)
self.tree = DataTree(self)
self.verticalLayout.addWidget(self.tree)
# noinspection PyUnresolvedReferences
self.tree.selectionModel().selectionChanged.connect(lambda x, y: self.show_property(x))
self.tree.keyChanged.connect(lambda x, y: self.keyChanged.emit(x, y))
@ -566,9 +536,9 @@ class DataWidget(QtWidgets.QWidget, Ui_DataWidget):
self.tree.add_graph(idd, name)
self.tree.blockSignals(False)
def add_item(self, idd: str, name: str, value: str, gid: str, update: bool= True):
def add_item(self, idd: str, name: str, gid: str):
self.tree.blockSignals(True)
self.tree.add_item((idd, name, value), gid, update=update)
self.tree.add_item((idd, name), gid)
self.tree.blockSignals(False)
def add_item_list(self, loi: list, gid: str):
@ -576,7 +546,7 @@ class DataWidget(QtWidgets.QWidget, Ui_DataWidget):
self.tree.add_item(loi, gid)
self.tree.blockSignals(False)
def remove_item(self, key: list[str]):
def remove_item(self, key):
self.tree.remove_item(key)
def show_property(self, _: QtCore.QModelIndex = None):

39
src/gui_qt/data/integral_widget.py
View File

@ -42,8 +42,6 @@ class IntegralWidget(QtWidgets.QWidget, Ui_Form):
self.max_y = inf
self.min_y = -inf
self.treeWidget.itemChanged.connect(self._update_by_tree)
def __call__(self, graph_name, items):
self.label_2.setText(f'Connected to {graph_name}\nChanging tab will remove all integration limits.')
@ -79,6 +77,7 @@ class IntegralWidget(QtWidgets.QWidget, Ui_Form):
for idx, rnge in enumerate(self.ranges):
self._update_values(idx, rnge)
def add(self, pos):
x = pos[0]
self.ranges.append((x, x*1.1))
@ -109,10 +108,7 @@ class IntegralWidget(QtWidgets.QWidget, Ui_Form):
item_list = []
for text, val in [('Start', pts_i[0]), ('Stop', pts_i[1]), ('Areas', 0), ('Ratio', 1.)]:
child = QtWidgets.QTreeWidgetItem()
if text.startswith('S'):
child.setFlags(child.flags() | QtCore.Qt.ItemIsEditable)
else:
child.setFlags(QtCore.Qt.NoItemFlags)
child.setFlags(QtCore.Qt.NoItemFlags)
child.setText(0, f'{text}: {val:.5g}')
child.setForeground(0, QtGui.QBrush(QtGui.QColor('black')))
@ -125,27 +121,8 @@ class IntegralWidget(QtWidgets.QWidget, Ui_Form):
self._update_values(len(self.ranges) - 1, pts_i)
def _update_by_tree(self, item: QtWidgets.QTreeWidgetItem) -> None:
parent_item = item.parent()
idx = self.treeWidget.invisibleRootItem().indexOfChild(parent_item)
is_left_border = parent_item.indexOfChild(item) == 0
current_region = self.lines[idx][0]
current_limits = current_region.getRegion()
new_value = item.text(0)
try:
new_value = float(new_value)
if is_left_border:
current_region.setRegion((new_value, current_limits[1]))
else:
current_region.setRegion((current_limits[0], new_value))
except ValueError:
self._update_values(idx, current_limits)
def _update_integral(self):
idx = None
reg = None
sender = self.sender()
for i, (reg, _) in enumerate(self.lines):
if sender == reg:
@ -155,20 +132,19 @@ class IntegralWidget(QtWidgets.QWidget, Ui_Form):
if idx is None:
return
self._update_values(idx, reg.getRegion())
self._update_values(idx, sender.getRegion())
def _update_values(self, idx, new_range):
self.ranges[idx] = new_range
area = self.make_integral(idx, *new_range)
self.treeWidget.blockSignals(True)
item = self.treeWidget.topLevelItem(idx)
item.child(0).setText(0, f'Start: {new_range[0]:.5g}')
item.child(1).setText(0, f'Stop: {new_range[1]:.5g}')
if area is not None:
self.areas[idx] = area
item.child(2).setText(0, f'Area: {area:.5g}')
if self.max_area > 0:
self._set_ratios(idx, self.max_area)
@ -181,12 +157,9 @@ class IntegralWidget(QtWidgets.QWidget, Ui_Form):
self._set_ratios(i, curr_max)
self.max_area = curr_max
self.treeWidget.blockSignals(False)
def _set_ratios(self, idx, max_value):
item = self.treeWidget.invisibleRootItem().child(idx)
area_i = self.areas[idx]
item.child(3).setText(0, f'Ratio: {area_i / max_value:.3g}')
integral_line = self.lines[idx][1]
@ -203,9 +176,7 @@ class IntegralWidget(QtWidgets.QWidget, Ui_Form):
if integral.size != 0:
area = integral[-1, 1]
scale = (self.max_y-self.min_y) / area
self.lines[idx][1].setData(x=integral[:, 0], y=integral[:, 1]*scale + self.min_y)
self.areas[idx] = area
self.lines[idx][1].setData(x=integral[:, 0], y=integral[:, 1]*scale + self.min_y)
return area

10
src/gui_qt/data/point_select.py
View File

@ -177,7 +177,7 @@ class PointSelectWidget(QtWidgets.QWidget, Ui_Form):
it.setText(f'{pos[0]:.5g} - {pos[1]:.5g}')
self.peaktable.blockSignals(False)
it_pts.blockSignals(True)
it_pts.setRegion(pos, use_log=True)
it_pts.setRegion(pos)
it_pts.blockSignals(False)
undo = False
@ -187,15 +187,9 @@ class PointSelectWidget(QtWidgets.QWidget, Ui_Form):
self.peaktable.blockSignals(False)
def set_graphs(self, graphs: list):
last_graph = self.graph_combobox.currentData()
self.graph_combobox.clear()
idx = 0
for i, g in enumerate(graphs):
for g in graphs:
self.graph_combobox.addItem(g[1], userData=g[0])
if g[0] == last_graph:
idx = i
self.graph_combobox.setCurrentIndex(idx)
@QtCore.pyqtSlot(int, name='on_graph_checkbox_stateChanged')
def changed_state(self, checked):

14
src/gui_qt/data/shift_graphs.py
View File

@ -1,7 +1,7 @@
import numpy as np
from itertools import cycle
from pyqtgraph import mkColor, mkPen, mkBrush
from pyqtgraph import mkColor, mkPen
from nmreval.lib.colors import Tab10
@ -42,17 +42,11 @@ class QShift(QtWidgets.QDialog, Ui_shift_dialog):
def add_item(self, idx, name, x, y):
color = mkColor(next(self._colors).rgb())
if len(y) == 1:
sym_kwds = {'symbol': 'o', 'symbolBrush': mkBrush(color=color), 'symbolPen': mkPen(color=color)}
else:
sym_kwds = {'symbol': None, 'symbolBrush': mkBrush(color=color), 'symbolPen': mkPen(color=color)}
if np.iscomplexobj(y):
pl = [PlotItem(x=x, y=y.real, name=name, pen=mkPen(color=color), **sym_kwds),
PlotItem(x=x, y=y.imag, name=name, pen=mkPen(color=color), **sym_kwds)]
pl = [PlotItem(x=x, y=y.real, name=name, pen=mkPen(color=color)),
PlotItem(x=x, y=y.imag, name=name, pen=mkPen(color=color))]
else:
pl = [PlotItem(x=x, y=y, name=name, pen=mkPen(color=color), **sym_kwds)]
pl = [PlotItem(x=x, y=y, name=name, pen=mkPen(color=color))]
self.data[idx] = (pl, x, y)

2
src/gui_qt/data/signaledit/__init__.py
View File

@ -1,2 +1,2 @@
from .phase_dialog import QPreviewDialog
from .phase_dialog import QApodDialog, QPhasedialog
from .baseline_dialog import QBaselineDialog

5
src/gui_qt/data/signaledit/editsignalwidget.py
View File

@ -1,4 +1,3 @@
from nmreval.lib.logger import logger
from nmreval.math import apodization
from nmreval.lib.importer import find_models
from nmreval.utils.text import convert
@ -47,7 +46,7 @@ class EditSignalWidget(QtWidgets.QWidget, Ui_Form):
stype = 'pts'
else:
try:
_nop = float(self.ls_lineEdit.text())
_nop = float(self.lineEdit.text())
except ValueError:
_nop = 0.0
stype = 'time'
@ -68,7 +67,7 @@ class EditSignalWidget(QtWidgets.QWidget, Ui_Form):
self.do_something.emit(sender, (ph0, ph1, pvt))
else:
logger.warning(f'You should never reach this by accident, invalid sender {sender!r}')
print('You should never reach this by accident.')
@QtCore.pyqtSlot(int, name='on_apodcombobox_currentIndexChanged')
def change_apodization(self, index):

491
src/gui_qt/data/signaledit/phase_dialog.py
View File

@ -1,43 +1,119 @@
from __future__ import annotations
from pyqtgraph import mkPen
import numpy as np
from numpy import pi
from numpy.fft import fft, fftshift, fftfreq
from pyqtgraph import mkPen
from numpy import inf, linspace
from numpy.fft import fft, fftfreq, fftshift
from nmreval.data import FID, Spectrum
from ...lib.pg_objects import PlotItem, LogInfiniteLine
from nmreval.lib.importer import find_models
from nmreval.math import apodization as apodization
from nmreval.utils.text import convert
from ...Qt import QtCore, QtWidgets, QtGui
from ...Qt import QtCore, QtWidgets
from ..._py.apod_dialog import Ui_ApodEdit
from ..._py.phase_corr_dialog import Ui_SignalEdit
from ...lib.forms import FormWidget
class QPreviewDialog(QtWidgets.QDialog, Ui_ApodEdit):
class QPreviewDialogs(QtWidgets.QDialog):
finished = QtCore.pyqtSignal(str, tuple)
def __init__(self, parent=None):
super().__init__(parent=parent)
self.setupUi(self)
self.data = []
self.graphs = []
self.mode = ''
def setRange(self, xlim: list, ylim: list, logmode: list[bool]):
self.graphicsView.getPlotItem().setLogMode(x=logmode[0], y=logmode[1])
if logmode[0]:
xlim = [np.log10(x) for x in xlim]
if logmode[1]:
ylim = [np.log10(y) for y in ylim]
self.graphicsView.setRange(xRange=xlim, yRange=ylim, padding=0, disableAutoRange=True)
def add_data(self, x, y):
self.data.append((x, y))
real_plt = PlotItem(x=x, y=y.real, pen=mkPen('b'), )
imag_plt = PlotItem(x=x, y=y.imag, pen=mkPen('r'))
self.graphs.append((real_plt, imag_plt))
self.graphicsView.addItem(real_plt)
self.graphicsView.addItem(imag_plt)
def done(self, val):
self.cleanup()
super().done(val)
def close(self):
self.cleanup()
super().close()
def accept(self):
self.finished.emit(self.mode, self.get_value())
super().accept()
def get_value(self):
raise NotImplementedError
def cleanup(self):
self.blockSignals(True)
for line in self.graphs:
for g in line:
self.graphicsView.removeItem(g)
del g
self.graphicsView.clear()
self.data = []
self.graphs = []
self._tmp_data_bl = []
self._tmp_data_zf = []
self._tmp_data_ls = []
self._tmp_data_ap = []
self._tmp_data_ph = []
self.blockSignals(False)
class QPhasedialog(QPreviewDialogs, Ui_SignalEdit):
def __init__(self, parent=None):
super().__init__(parent=parent)
self.setupUi(self)
self.mode = 'ph'
self.pvt_line = LogInfiniteLine(pos=0, movable=True)
self.freq_graph.addItem(self.pvt_line)
self.graphicsView.addItem(self.pvt_line)
self.pvt_line.sigPositionChanged.connect(self.move_line)
self.ls_lineedit.hide()
@QtCore.pyqtSlot(float, name='on_ph1slider_valueChanged')
@QtCore.pyqtSlot(float, name='on_ph0slider_valueChanged')
def _temp_phase(self, *args):
ph0, ph1, pvt = self.get_value()
self.pvt_line.setValue(pvt)
for i, (x, y) in enumerate(self.data):
phasecorr = np.exp(-1j * (ph0 + ph1*(x-pvt)/np.max(x))*np.pi/180.)
_y = y * phasecorr
self.graphs[i][0].setData(x=x, y=_y.real)
self.graphs[i][1].setData(x=x, y=_y.imag)
def get_value(self):
return float(self.ph0slider.text()), float(self.ph1slider.text()), float(self.pivot_lineedit.text())
def move_line(self, evt):
self.pivot_lineedit.setText(f'{evt.value():.5g}')
class QApodDialog(QPreviewDialogs, Ui_ApodEdit):
def __init__(self, parent=None):
super().__init__(parent=parent)
self.setupUi(self)
self._limits = (-inf, inf), -inf
self.apods = []
self.apods = find_models(apodization)
self.apodcombobox.blockSignals(True)
@ -46,262 +122,72 @@ class QPreviewDialog(QtWidgets.QDialog, Ui_ApodEdit):
self.apodcombobox.blockSignals(False)
self.apod_graph = PlotItem(x=[], y=[])
self.time_graph.addItem(self.apod_graph)
self.graphicsView.addItem(self.apod_graph)
for g in [self.freq_graph, self.time_graph]:
pl = g.getPlotItem()
pl.hideButtons()
pl.setMenuEnabled(False)
self._all_time = None
self._all_freq = None
self.mode = 'ap'
self.change_apodization(0)
self.shift_box.clicked.connect(self._update_shift)
self.ls_spinbox.valueChanged.connect(self._update_shift)
self.ls_lineedit.setValidator(QtGui.QDoubleValidator())
self.ls_lineedit.textChanged.connect(self._update_shift)
def add_data(self, x, y):
real_plt = PlotItem(x=x, y=y.real, pen=mkPen('b'))
# imag_plt = (x=x, y=y.imag, pen=pg.mkPen('r'))
self.graphicsView.addItem(real_plt)
# self.graphicsView.addItem(imag_plt)
self.zerofill_box.clicked.connect(self._update_zf)
self.zf_spinbox.valueChanged.connect(self._update_zf)
self.apod_box.clicked.connect(self._update_apod)
self.phase_box.clicked.connect(self._update_phase)
self.ph0_spinbox.valueChanged.connect(self._update_phase)
self.ph1_spinbox.valueChanged.connect(self._update_phase)
self.pivot_lineedit.setValidator(QtGui.QDoubleValidator())
self.pivot_lineedit.textChanged.connect(self._update_phase)
self.pivot_lineedit.textEdited.connect(lambda x: self.pvt_line.setValue(float(x)))
def add_data(self: QPreviewDialog, data: FID | Spectrum) -> bool:
if isinstance(data, FID):
if self._all_freq:
msg = QtWidgets.QMessageBox.warning(self, 'Mixed types',
'Timesignals and spectra cannot be edited at the same time.')
return False
else:
self._all_time = True
self._all_freq = False
elif isinstance(data, Spectrum):
if self._all_time:
msg = QtWidgets.QMessageBox.warning(self, 'Mixed types',
'Timesignals and spectra cannot be edited at the same time.')
return False
else:
self._all_time = False
self._all_freq = True
fid = data.copy()
spec = self._temp_fft_time(fid.x, fid.y, self.baseline_box.isChecked())
x_len = data.x.size
self.zf_spinbox.setMaximum(min(2**17//x_len, 3))
real_plt = PlotItem(x=fid.x, y=fid.y.real, pen=mkPen('b'))
imag_plt = PlotItem(x=fid.x, y=fid.y.imag, pen=mkPen('r'))
self.time_graph.addItem(imag_plt)
self.time_graph.addItem(real_plt)
real_plt_fft = PlotItem(x=spec[0], y=spec[1].real, pen=mkPen('b'))
imag_plt_fft = PlotItem(x=spec[0], y=spec[1].imag, pen=mkPen('r'))
self.freq_graph.addItem(imag_plt_fft)
self.freq_graph.addItem(real_plt_fft)
self.data.append(data)
for p in [self._tmp_data_bl, self._tmp_data_ls]:
p.append(data.y.copy())
for p in [self._tmp_data_zf, self._tmp_data_ap]:
p.append((data.x, data.y.copy()))
self._tmp_data_ph.append((data.x, data.y, spec[0], spec[1]))
self.graphs.append((real_plt, imag_plt, real_plt_fft, imag_plt_fft))
return True
@QtCore.pyqtSlot(name='on_baseline_box_clicked')
def _update_bl(self):
if self.baseline_box.isChecked():
for y in self._tmp_data_bl:
self._temp_baseline(y)
else:
for i, d in enumerate(self.data):
self._tmp_data_bl[i] = d.y.copy()
self._update_shift()
def _update_shift(self):
if self.shift_box.isChecked():
if self.ls_combobox.currentIndex() == 0:
num_points = self.ls_spinbox.value()
is_time = False
else:
num_points = float(self.ls_lineedit.text())
is_time = True
for i, y in enumerate(self._tmp_data_bl):
self._tmp_data_ls[i] = self._temp_leftshift(self.data[i].dx, y, num_points, is_time)
else:
for i, y in enumerate(self._tmp_data_bl):
self._tmp_data_ls[i] = y
self._update_zf()
def _update_zf(self):
zf_padding = self.zf_spinbox.value()
if self.zerofill_box.isChecked():
for i, y in enumerate(self._tmp_data_ls):
self._tmp_data_zf[i] = self._temp_zerofill(self.data[i].x, y, zf_padding)
else:
for i, y in enumerate(self._tmp_data_ls):
self._tmp_data_zf[i] = self.data[i].x, y
self._update_apod()
def _update_apod(self):
if self.apod_box.isChecked():
model = self.apods[self.apodcombobox.currentIndex()]
p = self._get_parameter()
x_limit = np.inf, -np.inf
y_limit = -np.inf
for i, (x, y) in enumerate(self._tmp_data_zf):
self._tmp_data_ap[i] = x, y * model.apod(x, *p)
y_limit = max(y.real.max(), y_limit)
x_limit = min(x_limit[0], x.min()), max(x_limit[1], x.max())
_x_apod = np.linspace(*x_limit, num=150)
_y_apod = model.apod(_x_apod, *p)
self.apod_graph.setData(x=_x_apod, y=y_limit * _y_apod)
self.apod_graph.show()
else:
for i, (x, y) in enumerate(self._tmp_data_zf):
self._tmp_data_ap[i] = x, y
self.apod_graph.hide()
self._update_phase()
def _update_phase(self):
if self.phase_box.isChecked():
pvt = float(self.pivot_lineedit.text())
self.pvt_line.show()
ph0 = self.ph0_spinbox.value()
ph1 = self.ph1_spinbox.value()
for i, (x, y) in enumerate(self._tmp_data_ap):
x_fft, y_fft = self._temp_fft_time(x, y, self.baseline_box.isChecked())
if ph0 != 0:
y = self._temp_phase(x, y, ph0, 0, 0)
y_fft = self._temp_phase(x, y_fft, ph0, ph1, pvt)
elif ph1 != 0:
y_fft = self._temp_phase(x, y_fft, ph0, ph1, pvt)
self._tmp_data_ph[i] = x, y, x_fft, y_fft
else:
self.pvt_line.hide()
for i, (x, y) in enumerate(self._tmp_data_ap):
self._tmp_data_ph[i] = x, y, *self._temp_fft_time(x, y, self.baseline_box.isChecked())
self._update_plots()
def _update_plots(self):
for i, (x, y, xf, yf) in enumerate(self._tmp_data_ph):
self.graphs[i][0].setData(x=x, y=y.real)
self.graphs[i][1].setData(x=x, y=y.imag)
self.graphs[i][2].setData(x=xf, y=yf.real)
self.graphs[i][3].setData(x=xf, y=yf.imag)
@staticmethod
def _temp_baseline_time(y):
y -= y[int(-0.12 * y.size):].mean()
@staticmethod
def _temp_baseline_freq(y):
region = int(0.12 * y.size)
y -= np.mean([y[-region:], y[:region]])
@staticmethod
def _temp_phase(x: np.ndarray, y: np.ndarray, ph0: float, ph1: float, pvt: float) -> np.ndarray:
phase_correction = np.exp(-1j * (ph0 + ph1 * (x - pvt) / x.max()) * pi / 180.)
_y = y * phase_correction
return _y
@staticmethod
def _temp_zerofill(x: np.ndarray, y: np.ndarray, num_padding: int) -> tuple[np.ndarray, np.ndarray]:
length = x.size
factor = 2**num_padding
_y = np.r_[y, np.zeros((factor-1) * length)]
_temp_x = np.arange(1, (factor-1) * length+1) * (x[1]-x[0]) + np.max(x)
_x = np.r_[x, _temp_x]
return _x, _y
@staticmethod
def _temp_leftshift(dx: np.ndarray, y: np.ndarray, points: float | int, is_time: bool) -> np.ndarray:
if is_time:
points = int(points//dx)
_y = np.roll(y, -points)
_y[-points-1:] = 0
return _y
@staticmethod
def _temp_fft_time(x: np.ndarray, y: np.ndarray, baseline: bool = False) -> tuple[np.ndarray, np.ndarray]:
y_fft = fftshift(fft(y))
x_fft = fftshift(fftfreq(len(x), d=x[1]-x[0]))
real_plt_fft = PlotItem(x=x_fft, y=y_fft.real, pen=mkPen('b'))
# imag_plt_fft = pg.PlotDataItem(x=x_fft, y=y_fft.imag, pen=pg.mkPen('b'))
self.graphicsView_2.addItem(real_plt_fft)
# self.graphicsView_2.addItem(imag_plt_fft)
if baseline:
QPreviewDialog._temp_baseline_freq(y_fft)
self.graphs.append((real_plt, real_plt_fft))
self.data.append((x, y, x_fft))
return x_fft, y_fft
@staticmethod
def _temp_fft_freq(x: np.ndarray, y: np.ndarray, _=None):
return x, y
def move_line(self, evt):
self.pivot_lineedit.setText(f'{evt.value():.5g}')
xlimits = (max(x.min(), self._limits[0][0]), min(x.max(), self._limits[0][1]))
ylimit = max(self._limits[1], y.real.max())
self._limits = xlimits, ylimit
@QtCore.pyqtSlot(int, name='on_apodcombobox_currentIndexChanged')
def change_apodization(self, index: int) -> None:
def change_apodization(self, index):
# delete old widgets
self.eqn_label.setText(convert(self.apods[index].equation))
while self.widget_layout.count():
item = self.widget_layout.takeAt(0)
if isinstance(item, FormWidget):
item.disconnect()
try:
item.widget().deleteLater()
except AttributeError:
pass
# set up parameter widgets for new model
for k, v in enumerate(self.apods[index].params):
widget = FormWidget(name=v)
widget.value = 1
widget.valueChanged.connect(self._update_apod)
self.widget_layout.addWidget(widget)
for k, v in enumerate(self.apods[index]().params):
widgt = FormWidget(name=v)
widgt.valueChanged.connect(self._temp_apod)
self.widget_layout.addWidget(widgt)
self.widget_layout.addStretch()
self._update_apod()
self._temp_apod()
def _temp_apod(self):
apodmodel = self.apods[self.apodcombobox.currentIndex()]
p = self._get_parameter()
if self.data:
for i, (x, y, x_fft) in enumerate(self.data):
y2 = apodmodel.apod(x, *p)
_y = y2 * y
self.graphs[i][0].setData(x=x, y=_y.real)
# self.graphs[i][1].setData(y=_y.imag)
y_fft = fftshift(fft(_y))
self.graphs[i][1].setData(x=x_fft, y=y_fft.real)
# self.graphs[i][3].setData(y=y_fft.imag)
_x_apod = linspace(self._limits[0][0], self._limits[0][1])
try:
_y_apod = apodmodel.apod(_x_apod, *p)
self.apod_graph.setData(x=_x_apod, y=self._limits[1]*_y_apod)
except IndexError:
pass
def _get_parameter(self):
p = []
@ -315,113 +201,8 @@ class QPreviewDialog(QtWidgets.QDialog, Ui_ApodEdit):
return p
@QtCore.pyqtSlot(int, name='on_ls_combobox_currentIndexChanged')
def change_ls(self, idx: int) -> None:
self.ls_lineedit.setVisible(bool(idx))
self.ls_spinbox.setVisible(not bool(idx))
@QtCore.pyqtSlot(bool, name='on_ft_checkbox_stateChanged')
def change_ft(self, state: bool):
self.ph1_spinbox.setEnabled(state)
self.pivot_lineedit.setEnabled(state)
def cleanup(self):
self.blockSignals(True)
for line in self.graphs:
for g in line:
self.time_graph.removeItem(g)
self.freq_graph.removeItem(g)
del g
self.time_graph.clear()
self.freq_graph.clear()
self._tmp_data_ap = []
self._tmp_data_bl = []
self._tmp_data_ls = []
self._tmp_data_ph = []
self._tmp_data_zf = []
self.data = []
self.graphs = []
self.freq_graph.removeItem(self.pvt_line)
self.time_graph.removeItem(self.pvt_line)
self.blockSignals(False)
def get_value(self):
edits = [(None,), (None,), (None,), (None,), (None,), (None,)]
if self.baseline_box.isChecked():
edits[0] = (True,)
if self.zerofill_box.isChecked():
edits[2] = (self.zf_spinbox.value(),)
if self.shift_box.isChecked():
if self.ls_combobox.currentIndex() == 0:
edits[1] = (self.ls_spinbox.value(), 'pts')
else:
edits[1] = (float(self.ls_lineedit.text()), 'time')
if self.apod_box.isChecked():
edits[3] = (self._get_parameter(), self.apods[self.apodcombobox.currentIndex()])
if self.phase_box.isChecked():
edits[4] = (self.ph0_spinbox.value(), self.ph1_spinbox.value(), float(self.pivot_lineedit.text()))
if self.ft_box.isChecked():
edits[5] = (self.phase_before_button.isChecked(),)
return edits
def exec(self):
self._prepare_ui()
return super().exec()
def _prepare_ui(self):
"""Stuff we have to do before showing the window but after all the data was added"""
vb = self.freq_graph.getPlotItem().getViewBox()
vb.disableAutoRange(axis=vb.YAxis)
vb = self.time_graph.getPlotItem().getViewBox()
vb.disableAutoRange(axis=vb.YAxis)
self.zerofill_box.setVisible(self._all_time)
self.apod_box.setVisible(self._all_time)
self.shift_box.setVisible(self._all_time)
self.time_graph.setVisible(self._all_time)
self.logtime_widget.setVisible(self._all_time)
@QtCore.pyqtSlot(int, name='on_logx_time_stateChanged')
@QtCore.pyqtSlot(int, name='on_logy_time_stateChanged')
@QtCore.pyqtSlot(int, name='on_logx_freq_stateChanged')
@QtCore.pyqtSlot(int, name='on_logy_freq_stateChanged')
def set_log(self, state: int):
switch = {
self.logx_time: lambda _x: self.time_graph.setLogMode(x=_x),
self.logy_time: lambda _x: self.time_graph.setLogMode(y=_x),
self.logx_freq: lambda _x: self.freq_graph.setLogMode(x=_x),
self.logy_freq: lambda _x: self.freq_graph.setLogMode(y=_x),
}[self.sender()]
switch(state == QtCore.Qt.Checked)
vb = self.freq_graph.getPlotItem().getViewBox()
vb.disableAutoRange(axis=vb.YAxis)
vb = self.time_graph.getPlotItem().getViewBox()
vb.disableAutoRange(axis=vb.YAxis)
self._temp_baseline = self._temp_baseline_time if self._all_time else self._temp_baseline_freq
self._temp_fft = self._temp_fft_time if self._all_time else self._temp_fft_freq
self.freq_graph.setVisible(self._all_time)
if self._all_freq:
self.time_graph.addItem(self.pvt_line)
else:
self.freq_graph.addItem(self.pvt_line)
apodmodel = self.apods[self.apodcombobox.currentIndex()]
p = self._get_parameter()
return p, apodmodel

25
src/gui_qt/data/valueeditwidget.py
View File

@ -188,15 +188,7 @@ class ValueEditWidget(QtWidgets.QWidget, Ui_MaskDialog):
new_value = complex(val)
new_value = new_value.real if new_value.imag == 0 else new_value
# table view loses focus when itemChanged is emitted
# if edit of item is cause of change resume editing at next item
prev_state = self.tableView.state()
idx = self.tableView.currentIndex()
idx = idx.sibling((col+1)//3+row, (col+1) % 3)
self.itemChanged.emit(sid, (col, row), new_value)
if prev_state == self.tableView.State.EditingState:
self.tableView.setCurrentIndex(idx)
self.tableView.edit(idx)
@QtCore.pyqtSlot(QtCore.QItemSelection, QtCore.QItemSelection)
def show_position(self, *_):
@ -267,7 +259,10 @@ class ValueModel(QtCore.QAbstractTableModel):
row = idx.row()
if role in [QtCore.Qt.DisplayRole, QtCore.Qt.EditRole]:
val = self._data[row][idx.column()]
return self.as_string(val)
if isinstance(val, complex):
return f'{val.real:.8g}{val.imag:+.8g}j'
else:
return f'{val:.8g}'
elif role == QtCore.Qt.BackgroundRole:
pal = QtGui.QGuiApplication.palette()
@ -300,16 +295,11 @@ class ValueModel(QtCore.QAbstractTableModel):
if value:
if role == QtCore.Qt.EditRole:
if value == self.as_string(self._data[row][col]):
return True
try:
value = complex(value)
except ValueError:
# not a number
return False
value = value.real if value.imag == 0 else value
self._data[row][col] = value.real if value.imag == 0 else value
self.itemChanged.emit(col, row, str(value))
self.dataChanged.emit(self.index(0, 0), self.index(0, 1), [role])
@ -378,10 +368,3 @@ class ValueModel(QtCore.QAbstractTableModel):
def unmask(self):
self.mask = [True] * self.total_rows
self.dataChanged.emit(self.index(0, 0), self.index(0, 1), [ValueModel.maskRole])
@staticmethod
def as_string(value) -> str:
if isinstance(value, complex):
return f'{value.real:.8g}{value.imag:+.8g}j'
else:
return f'{value:.8g}'

0
src/gui_qt/dsc/__init__.py
View File

375
src/gui_qt/dsc/glass_dialog.py
View File

@ -1,375 +0,0 @@
from itertools import cycle
from numpy import array, nan, isnan
from pyqtgraph import mkPen, mkBrush
from nmreval.dsc.hodge import tau_hodge
from nmreval.lib.colors import Tab10
from ..Qt import QtWidgets, QtCore
from .._py.tnmh_dialog import Ui_DSCEvalDialog
from ..lib.pg_objects import PlotItem, RegionItem
from nmreval.data import DSC, Points
class TgCalculator(QtWidgets.QWizard, Ui_DSCEvalDialog):
newData = QtCore.pyqtSignal(dict, str)
def __init__(self, management, parent=None):
super().__init__(parent=parent)
self.setupUi(self)
self._management = management
self._colors = cycle(Tab10)
self._dsc = {}
self._plots = {}
self._tg_value = {}
self._fit = {}
self._hodge = {
'onset': (
PlotItem(x=[], y=[], pen=None, symbol='o', symbolBrush=Tab10.TabBlue.rgb(), name='Onset'),
None,
(PlotItem(x=[], y=[], pen=mkPen({'color': Tab10.TabBlue.rgb()})),
PlotItem(x=[], y=[], pen=None, symbol='o', symbolBrush=Tab10.TabBlue.rgb())),
None,
),
'midpoint': (
PlotItem(x=[], y=[], pen=None, symbol='s', symbolBrush=Tab10.TabOrange.rgb(), name='Midpoint'),
None,
(PlotItem(x=[], y=[], pen=mkPen({'color': Tab10.TabOrange.rgb()})),
PlotItem(x=[], y=[], pen=None, symbol='s', symbolBrush=Tab10.TabOrange.rgb())),
None,
),
'end': (
PlotItem(x=[], y=[], pen=None, symbol='t', symbolBrush=Tab10.TabGreen.rgb(), name='End'),
None,
(PlotItem(x=[], y=[], pen=mkPen({'color': Tab10.TabGreen.rgb()})),
PlotItem(x=[], y=[], pen=None, symbol='t', symbolBrush=Tab10.TabGreen.rgb())),
None,
),
'inflection': (
PlotItem(x=[], y=[], pen=None, symbol='d', symbolBrush=Tab10.TabRed.rgb(), name='Inflection'),
None,
(PlotItem(x=[], y=[], pen=mkPen({'color': Tab10.TabRed.rgb()})),
PlotItem(x=[], y=[], pen=None, symbol='d', symbolBrush=Tab10.TabRed.rgb())),
None,
),
'fictive': (
PlotItem(x=[], y=[], pen=None, symbol='t1', symbolBrush=Tab10.TabPurple.rgb(), name='Fictive'),
None,
(PlotItem(x=[], y=[], pen=mkPen({'color': Tab10.TabPurple.rgb()})),
PlotItem(x=[], y=[], pen=None, symbol='t1', symbolBrush=Tab10.TabPurple.rgb())),
None,
),
}
self._lines = {}
self.tau_plot.getPlotItem().addLegend()
for plt, _, fitplt, _ in self._hodge.values():
self.tau_plot.addItem(plt)
self.tghodge_graph.addItem(fitplt[0])
self.tghodge_graph.addItem(fitplt[1])
self.tau_plot.setLogMode(y=True)
self.tghodge_graph.setLogMode(y=True)
self.limits = RegionItem(), RegionItem()
for lim in self.limits:
self.dsc_plot.addItem(lim)
self._limitless = True
self.add_sets()
self.tnmh_graph_check.stateChanged.connect(lambda state: self.tnmh_graph_combo.setEnabled(not bool(state)))
self.hodge_graph_check.stateChanged.connect(lambda state: self.hodge_graph_combo.setEnabled(not bool(state)))
self.next_button.clicked.connect(lambda: self.stackedWidget.setCurrentIndex((self.stackedWidget.currentIndex() + 1) % 3))
self.back_button.clicked.connect(lambda: self.stackedWidget.setCurrentIndex((self.stackedWidget.currentIndex() + 2) % 3))
self.listWidget.itemChanged.connect(self.change_visibility)
def __call__(self):
self.clear()
self._colors = cycle(Tab10)
self.add_sets()
return self
def clear(self):
self.listWidget.clear()
self.tg_tree.clear()
self.tnmh_tree.clear()
for plots in self._plots.values():
for val in plots:
self.dsc_plot.removeItem(val)
self.tnmh_graphics.removeItem(val)
for key, plt in self._hodge.items():
plt[0].setData(x=[], y=[])
plt[2][0].setData(x=[], y=[])
plt[2][1].setData(x=[], y=[])
self._hodge[key] = (plt[0], None, plt[2], None)
self._dsc = {}
self._plots = {}
self._tg_value = {}
self._lines = {}
self._fit = {}
self.stackedWidget.setCurrentIndex(0)
def add_sets(self):
for w in (self.tnmh_graph_combo, self.hodge_graph_combo):
w.clear()
for graphs in self._management.graphs.list():
w.addItem(graphs[1], userData=graphs[0])
min_x = 10_000_000
max_x = -10_000_000
for (key, name), c in zip(self._management.active_sets, self._colors):
data = self._management[key].data
if not isinstance(data, DSC):
continue
min_x = min(min_x, data.x.min())
max_x = max(max_x, data.x.max())
item = QtWidgets.QListWidgetItem(name)
item.setCheckState(QtCore.Qt.Checked)
item.setData(QtCore.Qt.UserRole, key)
item.setForeground(mkBrush(c.rgb()))
self.listWidget.addItem(item)
self._dsc[key] = (data, None)
data_plot = PlotItem(x=data.x, y=data.y, pen=mkPen(c.rgb()))
self.dsc_plot.addItem(data_plot)
glass = PlotItem()
glass.set_line(style=2, color=c)
self.dsc_plot.addItem(glass)
liquid = PlotItem()
liquid.set_line(style=2, color=c)
self.dsc_plot.addItem(liquid)
tangent = PlotItem()
tangent.set_line(style=2, color=c)
self.dsc_plot.addItem(tangent)
tg_plot = PlotItem(pen=None, symbolBrush=c.rgb(), symbol='o')
self.dsc_plot.addItem(tg_plot)
fictive_cp = PlotItem(pen=mkPen(c.rgb()))
self.tnmh_graphics.addItem(fictive_cp)
tnmh_fit = PlotItem()
tnmh_fit.set_line(style=2, color=c)
self.tnmh_graphics.addItem(tnmh_fit)
self._plots[key] = (data_plot, tg_plot, glass, liquid, tangent, fictive_cp, tnmh_fit)
self._tg_value[key] = {
'onset': (nan, nan),
'midpoint': (nan, nan),
'end': (nan, nan),
'inflection': (nan, nan),
# 'fictive': (nan, nan),
}
if self._limitless and max_x != -10000000 and min_x != 10000000 :
dist = max_x - min_x
self.limits[0].setRegion((min_x, min_x+min(0.1*dist, 5)))
self.limits[1].setRegion((max_x-min(5, 0.1*dist), max_x))
self._limitless = False
@QtCore.pyqtSlot(name='on_calctg_button_clicked')
def calc_tg(self):
baselines = tuple(lim.getRegion() for lim in self.limits)
if baselines[0][0] > baselines[1][0]:
baselines = baselines[1], baselines[0]
for idx in range(self.listWidget.count()):
item = self.listWidget.item(idx)
if item.checkState() == QtCore.Qt.Unchecked:
continue
key = item.data(QtCore.Qt.UserRole)
plot = self._plots[key]
data, _ = self._dsc[key]
tg_results, glass, liquid, tangent = data.glass_transition(*baselines)
self._lines[key] = (glass, liquid, tangent)
for i, line in enumerate((glass, liquid, tangent)):
plot[i+2].setData(x=line.x, y=line.y)
self._tg_value[key].update(tg_results)
self._update_tg_plots()
def _update_tg_plots(self):
self.tg_tree.clear()
for idx in range(self.listWidget.count()):
item = self.listWidget.item(idx)
tree_item = QtWidgets.QTreeWidgetItem([item.text()])
values = self._tg_value.get(item.data(QtCore.Qt.UserRole))
if values is not None:
for name, pos in values.items():
child_item = QtWidgets.QTreeWidgetItem([f'{name.capitalize()}: {pos[0]:.2f} K'])
tree_item.addChild(child_item)
self.tg_tree.addTopLevelItem(tree_item)
key = item.data(QtCore.Qt.UserRole)
plot = self._plots[key]
data, _ = self._dsc[key]
plot[1].setData(array(list(self._tg_value[key].values())))
@QtCore.pyqtSlot(name='on_tg_export_button_clicked')
def export_tg(self):
ret_dic = {}
for key, tg in self._tg_value.items():
tgx = [x for x, y in tg.values()]
tgy = [y for x, y in tg.values()]
if self.tg_export_check.isChecked():
tg_pts = Points(x=tgx, y=tgy, name=self._management[key].name + ' (Tg)', value=self._management[key].value)
else:
tg_pts = None
line = []
if self.tglines_export_check.isChecked():
line = self._lines.get(key, [])
ret_dic[key] = (tg_pts, line)
self.newData.emit(ret_dic, 'tg')
@QtCore.pyqtSlot(QtWidgets.QListWidgetItem)
def change_visibility(self, item: QtWidgets.QListWidgetItem):
is_checked = bool(item.checkState())
plot = self._plots[item.data(QtCore.Qt.UserRole)]
for val in plot:
val.setVisible(is_checked)
def get_fictive(self, key, baselines):
plot = self._plots[key]
data, _ = self._dsc[key]
cp, tg = data.get_fictive_cp(*baselines)
plot[5].setData(cp.x, cp.y)
self._dsc[key] = (data, cp)
return cp
@QtCore.pyqtSlot(name='on_tnhm_fitbutton_clicked')
def make_tnmh(self):
baselines = tuple(lim.getRegion() for lim in self.limits)
if baselines[0][0] > baselines[1][0]:
baselines = baselines[1], baselines[0]
self.tnmh_tree.clear()
for idx in range(self.listWidget.count()):
item = self.listWidget.item(idx)
if item.checkState() == QtCore.Qt.Unchecked:
continue
key = item.data(QtCore.Qt.UserRole)
data = self.get_fictive(key, baselines)
res = data.calculate_tnmh([60, 0.5, 1, 2e5], *baselines, return_fictive=False)
self._fit[key] = res
plot = self._plots[key]
plot[-1].setData(res.x, res.y)
for idx in range(self.listWidget.count()):
item = self.listWidget.item(idx)
tree_item = QtWidgets.QTreeWidgetItem([item.text()])
values = self._fit.get(item.data(QtCore.Qt.UserRole))
if values is not None:
child_item = QtWidgets.QTreeWidgetItem([values.parameter_string()])
tree_item.addChild(child_item)
self.tnmh_tree.addTopLevelItem(tree_item)
@QtCore.pyqtSlot(name='on_tnmh_export_button_clicked')
def export_tnmh(self):
ret_dic = {}
for idx in range(self.listWidget.count()):
item = self.listWidget.item(idx)
if item.checkState() == QtCore.Qt.Unchecked:
continue
key = item.data(QtCore.Qt.UserRole)
cp = None
if self.fictive_export_check.isChecked():
_, cp = self._dsc[key]
line = None
if self.tnmhfit_export_check.isChecked():
line = self._fit.get(key)
ret_dic[key] = (cp, line)
ret_dic['graph'] = '' if self.tnmh_graph_check.isChecked() else self.tnmh_graph_combo.currentData()
self.newData.emit(ret_dic, 'tnmh')
@QtCore.pyqtSlot(name='on_hodge_button_clicked')
def hodge(self):
for tg_type, (plot, data, fitplots, fit) in self._hodge.items():
m = []
for idx in range(self.listWidget.count()):
item = self.listWidget.item(idx)
if item.checkState() == QtCore.Qt.Unchecked:
continue
key = item.data(QtCore.Qt.UserRole)
data, _ = self._dsc[key]
try:
tg_value = self._tg_value[key][tg_type][0]
if isnan(tg_value):
continue
except KeyError:
continue
m.append([tg_value, data.value])
if len(m) > 1:
data, fit = tau_hodge(*array(m).T)
data.name = f'{data.name} ({tg_type.capitalize()})'
plot.setData(data.x, data.y)
fitplots[0].setData(fit.x, fit.y)
fitplots[1].setData(fit.x_data, fit.y_data)
self._hodge[tg_type] = (plot, data, fitplots, fit)
@QtCore.pyqtSlot(name='on_export_hodge_button_clicked')
def export_hodge(self):
ret_dic = {}
for cb in (self.onset_check, self.mid_check, self.end_check, self.inflection_check, self.fictive_check):
if cb.isChecked():
item = cb.text().lower()
data = self._hodge.get(item)
if data[1] is not None:
ret_dic[item] = data[1]
ret_dic['graph'] = '' if self.hodge_graph_check.isChecked() else self.hodge_graph_combo.currentData()
self.newData.emit(ret_dic, 'hodge')
def close(self) -> bool:
self.clear()
return super().close()

178
src/gui_qt/fit/fit_forms.py
View File

@ -5,48 +5,51 @@ from nmreval.utils.text import convert
from ..Qt import QtCore, QtWidgets, QtGui
from .._py.fitmodelwidget import Ui_FitParameter
from .._py.save_fitmodel_dialog import Ui_SaveDialog
from ..lib.iconloading import get_icon
from ..lib.tables import TableWidget
from ..lib import get_icon
class FitModelWidget(QtWidgets.QWidget, Ui_FitParameter):
value_requested = QtCore.pyqtSignal(object)
value_changed = QtCore.pyqtSignal(str)
state_changed = QtCore.pyqtSignal()
replace_single_value = QtCore.pyqtSignal(object)
def __init__(self, label: str = 'Fitparameter', parent=None, fixed: bool = False):
super().__init__(parent)
self.setupUi(self)
self.name = label
self.parametername.setText(convert(label) + ' ')
self.parametername.setText(label + ' ')
validator = QtGui.QDoubleValidator()
validator.setDecimals(9)
self.parameter_line.setValidator(validator)
self.parameter_line.setText('1')
self.parameter_line.setMaximumWidth(160)
self.lineEdit.setMaximumWidth(100)
self.lineEdit_2.setMaximumWidth(100)
self.parameter_line.setMaximumWidth(60)
self.lineEdit.setMaximumWidth(60)
self.lineEdit_2.setMaximumWidth(60)
self.label_3.setText(f'&lt; {convert(label)} &lt;')
self.label_3.setText(f'&lt; {label} &lt;')
self.checkBox.stateChanged.connect(self.enableBounds)
self.global_checkbox.stateChanged.connect(lambda: self.state_changed.emit())
self.parameter_line.editingFinished.connect(self.update_parameter)
self.parameter_line.values_requested.connect(lambda: self.value_requested.emit(self))
self.parameter_line.replace_single_values.connect(lambda: self.replace_single_value.emit(None))
self.parameter_line.editingFinished.connect(lambda: self.value_changed.emit(self.parameter_line.text()))
self.fixed_check.toggled.connect(self.set_fixed)
if fixed:
self.fixed_check.hide()
self.menu = QtWidgets.QMenu(self)
self.add_links()
self.is_linked = None
self.parameter_pos = None
self.func_idx = None
self._linetext = '1'
self.menu = QtWidgets.QMenu(self)
@property
def name(self):
return convert(self.parametername.text().strip(), old='html', new='str')
def set_parameter_string(self, p: str):
self.parameter_line.setText(p)
@ -66,67 +69,123 @@ class FitModelWidget(QtWidgets.QWidget, Ui_FitParameter):
def set_parameter(self, p: float | None, bds: tuple[float, float, bool] = None,
fixed: bool = None, glob: bool = None):
ptext = f'{p:.4g}'
if p is None:
# bad hack: linked parameter return (None, linked parameter)
# if p is None -> parameter is linked to argument given by bds
self.link_parameter(linkto=bds)
else:
ptext = f'{p:.4g}'
self.set_parameter_string(ptext)
self.set_parameter_string(ptext)
if bds is not None:
self.set_bounds(*bds)
if bds is not None:
self.set_bounds(*bds)
if fixed is not None:
self.fixed_check.setCheckState(QtCore.Qt.Unchecked if fixed else QtCore.Qt.Checked)
if fixed is not None:
self.fixed_check.setCheckState(QtCore.Qt.Unchecked if fixed else QtCore.Qt.Checked)
if glob is not None:
self.global_checkbox.setCheckState(QtCore.Qt.Checked if glob else QtCore.Qt.Unchecked)
if glob is not None:
self.global_checkbox.setCheckState(QtCore.Qt.Checked if glob else QtCore.Qt.Unchecked)
def get_parameter(self):
try:
p = float(self.parameter_line.text().replace(',', '.'))
except ValueError:
p = self.parameter_line.text().replace(',', '.')
if self.is_linked:
try:
p = float(self._linetext)
except ValueError:
p = 1.0
else:
try:
p = float(self.parameter_line.text().replace(',', '.'))
except ValueError:
_ = QtWidgets.QMessageBox().warning(self, 'Invalid value',
f'{self.parametername.text()} contains invalid values',
QtWidgets.QMessageBox.Cancel)
return None
if self.checkBox.isChecked():
lb_text = self.lineEdit.text()
lb = None
if lb_text:
try:
lb = float(lb_text.replace(',', '.'))
except ValueError:
lb = lb_text
try:
lb = float(self.lineEdit.text().replace(',', '.'))
except ValueError:
lb = None
ub_text = self.lineEdit_2.text()
rb = None
if ub_text:
try:
rb = float(ub_text.replace(',', '.'))
except ValueError:
rb = ub_text
try:
rb = float(self.lineEdit_2.text().replace(',', '.'))
except ValueError:
rb = None
else:
lb = rb = None
bounds = (lb, rb)
return p, bounds, not self.fixed_check.isChecked(), self.global_checkbox.isChecked()
return p, bounds, not self.fixed_check.isChecked(), self.global_checkbox.isChecked(), self.is_linked
@QtCore.pyqtSlot(bool)
def set_fixed(self, state: bool):
# self.global_checkbox.setVisible(not state)
self.frame.setVisible(not state)
def add_links(self, parameter: dict = None):
if parameter is None:
parameter = {}
self.menu.clear()
ac = QtWidgets.QAction('Link to...', self)
ac.triggered.connect(self.link_parameter)
self.menu.addAction(ac)
for model_key, model_funcs in parameter.items():
m = QtWidgets.QMenu('Model ' + model_key, self)
for func_name, func_params in model_funcs.items():
m2 = QtWidgets.QMenu(func_name, m)
for p_name, idx in func_params:
ac = QtWidgets.QAction(p_name, m2)
ac.setData((model_key, *idx))
ac.triggered.connect(self.link_parameter)
m2.addAction(ac)
m.addMenu(m2)
self.menu.addMenu(m)
self.toolButton.setMenu(self.menu)
@QtCore.pyqtSlot()
def update_parameter(self):
new_value = self.parameter_line.text()
if not new_value:
self.parameter_line.setText('1')
def link_parameter(self, linkto=None):
if linkto is None:
action = self.sender()
else:
action = False
for m in self.menu.actions():
if m.menu():
for a in m.menu().actions():
if a.data() == linkto:
action = a
break
if action:
break
if (self.func_idx, self.parameter_pos) == action.data():
return
try:
float(new_value)
is_text = False
except ValueError:
is_text = True
self.global_checkbox.setCheckState(False)
new_text = f'Linked to {action.parentWidget().title()}.{action.text()}'
self._linetext = self.parameter_line.text()
self.parameter_line.setText(new_text)
self.parameter_line.setEnabled(False)
self.global_checkbox.hide()
self.global_checkbox.blockSignals(True)
self.global_checkbox.setCheckState(QtCore.Qt.Checked)
self.global_checkbox.blockSignals(False)
self.frame.hide()
self.is_linked = action.data()
self.set_fixed(is_text)
except AttributeError:
self.parameter_line.setText(self._linetext)
self.parameter_line.setEnabled(True)
if self.fixed_check.isEnabled():
self.global_checkbox.show()
self.frame.show()
self.is_linked = None
self.state_changed.emit()
class QSaveModelDialog(QtWidgets.QDialog, Ui_SaveDialog):
@ -221,17 +280,8 @@ class FitModelTree(QtWidgets.QTreeWidget):
idx = item.data(0, self.counterRole)
self.itemRemoved.emit(idx)
def add_function(self,
idx: int,
cnt: int,
op: int,
name: str,
color: QtGui.QColor | str | tuple,
parent: QtWidgets.QTreeWidgetItem = None,
children: list = None,
active: bool = True,
param_names: list[str] = None,
**kwargs):
def add_function(self, idx: int, cnt: int, op: int, name: str, color: QtGui.QColor | str | tuple,
parent: QtWidgets.QTreeWidgetItem = None, children: list = None, active: bool = True, **kwargs):
"""
Add function to tree and dictionary of functions.
"""
@ -246,10 +296,6 @@ class FitModelTree(QtWidgets.QTreeWidget):
it.setData(0, self.counterRole, cnt)
it.setData(0, self.operatorRole, op)
it.setText(0, name)
if param_names is not None:
it.setToolTip(0,
'Parameter names:\n' +
'\n'.join(f'{pn}({cnt})' for pn in param_names))
it.setForeground(0, QtGui.QBrush(color))
it.setIcon(0, get_icon(self.icons[op]))
@ -319,7 +365,7 @@ class FitModelTree(QtWidgets.QTreeWidget):
return funcs
class FitTableWidget(TableWidget):
class FitTableWidget(QtWidgets.QTableWidget):
def __init__(self, parent=None):
super().__init__(parent=parent)

124
src/gui_qt/fit/fit_parameter.py
View File

@ -1,8 +1,5 @@
from __future__ import annotations
from typing import Optional
from nmreval.fit.parameter import Parameter
from nmreval.utils.text import convert
from ..Qt import QtWidgets, QtCore, QtGui
@ -65,7 +62,8 @@ class QFitParameterWidget(QtWidgets.QWidget, Ui_FormFit):
self.glob_values = [1] * len(func.params)
for k, v in enumerate(func.params):
widgt = FitModelWidget(label=v, parent=self.scrollwidget)
name = convert(v)
widgt = FitModelWidget(label=name, parent=self.scrollwidget)
widgt.parameter_pos = k
widgt.func_idx = idx
try:
@ -80,12 +78,11 @@ class QFitParameterWidget(QtWidgets.QWidget, Ui_FormFit):
widgt.state_changed.connect(self.make_global)
widgt.value_requested.connect(self.look_for_value)
widgt.value_changed.connect(self.change_global_parameter)
widgt.replace_single_value.connect(self.delete_single_parameter)
self.global_parameter.append(widgt)
self.scrollwidget.layout().addWidget(widgt)
widgt2 = ParameterSingleWidget(name=v, parent=self.scrollwidget2)
widgt2 = ParameterSingleWidget(name=name, parent=self.scrollwidget2)
widgt2.valueChanged.connect(self.change_single_parameter)
widgt2.removeSingleValue.connect(self.change_single_parameter)
widgt2.installEventFilter(self)
@ -117,22 +114,20 @@ class QFitParameterWidget(QtWidgets.QWidget, Ui_FormFit):
self.scrollwidget.layout().addStretch(1)
self.scrollwidget2.layout().addStretch(1)
# def set_links(self, parameter):
# for w in self.global_parameter:
# if isinstance(w, FitModelWidget):
# w.add_links(parameter)
def set_links(self, parameter):
for w in self.global_parameter:
if isinstance(w, FitModelWidget):
w.add_links(parameter)
@QtCore.pyqtSlot(str)
def change_global_parameter(self, value: str, idx: int = None):
if idx is None:
idx = self.global_parameter.index(self.sender())
# self.glob_values[idx] = float(value)
self.glob_values[idx] = value
self.glob_values[idx] = float(value)
if self.data_values[self.comboBox.currentData()][idx] is None:
self.data_parameter[idx].blockSignals(True)
# self.data_parameter[idx].value = float(value)
self.data_parameter[idx].value = value
self.data_parameter[idx].value = float(value)
self.data_parameter[idx].blockSignals(False)
@QtCore.pyqtSlot(str, object)
@ -153,13 +148,6 @@ class QFitParameterWidget(QtWidgets.QWidget, Ui_FormFit):
if value is None:
self.change_data(self.comboBox.currentIndex())
def delete_single_parameter(self):
idx = self.global_parameter.index(self.sender())
for i in range(self.comboBox.count()):
set_id = self.comboBox.itemData(i)
self.data_values[set_id][idx] = None
self.change_data(self.comboBox.currentIndex())
def change_single_choice(self, _, value, sender=None):
if sender is None:
sender = self.sender()
@ -175,7 +163,7 @@ class QFitParameterWidget(QtWidgets.QWidget, Ui_FormFit):
# disable single parameter if it is set global, enable if global is unset
widget = self.sender()
idx = self.global_parameter.index(widget)
enable = (widget.global_checkbox.checkState() == QtCore.Qt.Unchecked)
enable = (widget.global_checkbox.checkState() == QtCore.Qt.Unchecked) and (widget.is_linked is None)
self.data_parameter[idx].setEnabled(enable)
def select_next_preview(self, direction):
@ -193,11 +181,6 @@ class QFitParameterWidget(QtWidgets.QWidget, Ui_FormFit):
for i, value in enumerate(self.data_values[sid]):
w = self.data_parameter[i]
w.blockSignals(True)
try:
w.show_as_local_parameter(value is not None)
except AttributeError:
pass
if value is None:
w.value = self.glob_values[i]
else:
@ -208,50 +191,64 @@ class QFitParameterWidget(QtWidgets.QWidget, Ui_FormFit):
if sid not in self.data_values:
self.data_values[sid] = [None] * len(self.data_parameter)
def get_parameter(self, use_func=None) -> tuple[dict, list]:
def get_parameter(self, use_func=None):
bds = []
is_global = []
is_fixed = []
param_general = []
globs = []
is_linked = []
for g in self.global_parameter:
if isinstance(g, FitModelWidget):
p_i, bds_i, fixed_i, global_i = g.get_parameter()
parameter_i = Parameter(name=g.name, value=p_i, lb=bds_i[0], ub=bds_i[1], var=fixed_i)
param_general.append(parameter_i)
p_i, bds_i, fixed_i, global_i, link_i = g.get_parameter()
globs.append(p_i)
bds.append(bds_i)
is_fixed.append(fixed_i)
is_global.append(global_i)
is_linked.append(link_i)
lb, ub = list(zip(*bds))
data_parameter = {}
if use_func is None:
use_func = list(self.data_values.keys())
global_p = None
for sid, parameter in self.data_values.items():
if sid not in use_func:
continue
kw_p = {}
p = []
if global_p is None:
global_p = {'p': [], 'idx': [], 'var': [], 'ub': [], 'lb': []}
for i, (p_i, g) in enumerate(zip(parameter, self.global_parameter)):
if isinstance(g, FitModelWidget):
if (p_i is None) or is_global[i]:
# set has no oen value
p.append(param_general[i].copy())
p.append(globs[i])
if is_global[i]:
if i not in global_p['idx']:
global_p['p'].append(globs[i])
global_p['idx'].append(i)
global_p['var'].append(is_fixed[i])
global_p['ub'].append(ub[i])
global_p['lb'].append(lb[i])
else:
lb, ub = bds[i]
try:
if not ((lb < p_i < ub) or (not is_fixed[i])):
raise ValueError(f'Parameter {g.name} is outside bounds ({lb}, {ub})')
except TypeError:
pass
p.append(p_i)
# create Parameter
p.append(
Parameter(name=g.name, value=p_i, lb=lb, ub=ub, var=is_fixed[i])
)
try:
if p[i] > ub[i]:
raise ValueError(f'Parameter {g.name} is outside bounds ({lb[i]}, {ub[i]})')
except TypeError:
pass
try:
if p[i] < lb[i]:
raise ValueError(f'Parameter {g.name} is outside bounds ({lb[i]}, {ub[i]})')
except TypeError:
pass
else:
if p_i is None:
@ -263,28 +260,20 @@ class QFitParameterWidget(QtWidgets.QWidget, Ui_FormFit):
data_parameter[sid] = (p, kw_p)
global_parameter = []
for param, global_flag in zip(param_general, is_global):
if global_flag:
param.is_global = True
global_parameter.append(param)
else:
global_parameter.append(None)
return data_parameter, global_parameter
return data_parameter, lb, ub, is_fixed, global_p, is_linked
def set_parameter(self, set_id: str | None, parameter: list[float]) -> int:
num_parameter = list(filter(lambda g: not isinstance(g, SelectionWidget), self.global_parameter))
param_len = len(num_parameter)
param_len = len(list(filter(lambda g: not isinstance(g, SelectionWidget), self.global_parameter)))
if set_id is None:
for i, g in enumerate(num_parameter):
val = parameter[i]
for val, g in zip(parameter, self.global_parameter):
if isinstance(g, SelectionWidget):
continue
g.set_parameter(val)
self.glob_values[i] = val
else:
new_param = self.data_values[set_id]
min_len = min(param_len, len(new_param))
min_len = min(param_len, len(new_param), len(new_param))
for i in range(min_len):
new_param[i] = parameter[i]
@ -302,12 +291,10 @@ class ParameterSingleWidget(QtWidgets.QWidget):
self._init_ui()
self.name = name
self._name = name
self.label.setText(convert(name))
self.label.setToolTip('If this is bold then this parameter is only for this data. '
'Otherwise, the general parameter is used and displayed')
# self.value_line.setValidator(QtGui.QDoubleValidator())
self.value_line.setValidator(QtGui.QDoubleValidator())
self.value_line.textChanged.connect(lambda: self.valueChanged.emit(self.value) if self.value is not None else 0)
self.reset_button.clicked.connect(lambda x: self.removeSingleValue.emit())
@ -322,12 +309,10 @@ class ParameterSingleWidget(QtWidgets.QWidget):
layout.addSpacerItem(QtWidgets.QSpacerItem(0, 0, QtWidgets.QSizePolicy.Expanding, QtWidgets.QSizePolicy.Minimum))
self.value_line = QtWidgets.QLineEdit(self)
self.value_line.textEdited.connect(lambda x: self.show_as_local_parameter(True))
layout.addWidget(self.value_line)
self.reset_button = QtWidgets.QToolButton(self)
self.reset_button.setText('Use global')
self.reset_button.clicked.connect(lambda: self.show_as_local_parameter(False))
layout.addWidget(self.reset_button)
self.setLayout(layout)
@ -341,11 +326,4 @@ class ParameterSingleWidget(QtWidgets.QWidget):
@value.setter
def value(self, val):
# self.value_line.setText(f'{float(val):.5g}')
self.value_line.setText(f'{val}')
def show_as_local_parameter(self, is_local: bool):
if is_local:
self.label.setStyleSheet('font-weight: bold;')
else:
self.label.setStyleSheet('')
self.value_line.setText(f'{float(val):.5g}')

6
src/gui_qt/fit/fitfunction.py
View File

@ -8,11 +8,10 @@ from nmreval.lib.importer import find_models
from nmreval.lib.colors import BaseColor, Tab10
from nmreval.utils.text import convert
from ..lib.iconloading import get_icon
from ..lib import get_icon
from .._py.fitfunctionwidget import Ui_Form
from ..Qt import QtWidgets, QtCore, QtGui
class QFunctionWidget(QtWidgets.QWidget, Ui_Form):
func_cnt = count()
func_colors = cycle(Tab10)
@ -128,7 +127,7 @@ class QFunctionWidget(QtWidgets.QWidget, Ui_Form):
self.newFunction.emit(idx, cnt)
self.add_function(idx, cnt, op, name, col, param_names=self.functions[idx].params)
self.add_function(idx, cnt, op, name, col)
def add_function(self, idx: int, cnt: int, op: int,
name: str, color: str | tuple[float, float, float] | BaseColor, **kwargs):
@ -141,7 +140,6 @@ class QFunctionWidget(QtWidgets.QWidget, Ui_Form):
qcolor = QtGui.QColor.fromRgbF(*color)
else:
qcolor = QtGui.QColor(color)
self.functree.add_function(idx, cnt, op, name, qcolor, **kwargs)
f = self.functions[idx]

131
src/gui_qt/fit/fitwindow.py
View File

@ -9,14 +9,10 @@ import numpy as np
from pyqtgraph import mkPen
from nmreval.fit._meta import MultiModel, ModelFactory
from nmreval.fit.data import Data
from nmreval.fit.model import Model
from nmreval.fit.parameter import Parameters
from nmreval.fit.result import FitResult
from .fit_forms import FitTableWidget
from .fit_parameter import QFitParameterWidget
from ..lib import Relations
from ..lib.pg_objects import PlotItem
from ..Qt import QtGui, QtCore, QtWidgets
from .._py.fitdialog import Ui_FitDialog
@ -53,7 +49,7 @@ class QFitDialog(QtWidgets.QWidget, Ui_FitDialog):
self._func_list = {}
self._complex = {}
self.connected_figure = None
self.connected_figure = ''
self.model_frame.hide()
self.preview_button.hide()
@ -81,11 +77,16 @@ class QFitDialog(QtWidgets.QWidget, Ui_FitDialog):
w.deleteLater()
del self.param_widgets[idx]
self._current_function = None
if len(self.param_widgets) == 0:
if len(self.functionwidget) == 0:
# empty model
self.newmodel_button.setEnabled(False)
self.deletemodel_button.setEnabled(False)
self._current_function = None
else:
f_tree = self.functionwidget.functree
func_idx = f_tree.currentItem().data(0, f_tree.counterRole)
self._current_function = self.functionwidget.functions[func_idx]
@QtCore.pyqtSlot(int)
def show_function_parameter(self, function_id: int, function_idx: int = None):
@ -119,7 +120,7 @@ class QFitDialog(QtWidgets.QWidget, Ui_FitDialog):
# collect parameter names etc. to allow linkage
self._func_list[self._current_model] = self.functionwidget.get_parameter_list()
# dialog.set_links(self._func_list)
dialog.set_links(self._func_list)
# show same tab (general parameter/Data parameter)
tab_idx = 0
@ -147,13 +148,6 @@ class QFitDialog(QtWidgets.QWidget, Ui_FitDialog):
Add name and id of dataset to list.
"""
self.data_table.load(ids)
# deselect all fit sets
for i in range(self.data_table.rowCount()):
data_id = self.data_table.item(i, 0).data(QtCore.Qt.UserRole+1)
if self._management[data_id].mode == 'fit' or self._management[data_id].has_relation(Relations.isFitPartOf):
self.data_table.item(i, 0).setCheckState(QtCore.Qt.Unchecked)
if self.models:
for m in self.models.keys():
self.data_table.add_model(m)
@ -222,49 +216,57 @@ class QFitDialog(QtWidgets.QWidget, Ui_FitDialog):
def _prepare(self, model: list, function_use: list = None,
parameter: dict = None, add_idx: bool = False, cnt: int = 0) -> tuple[dict, int]:
if parameter is None:
parameter = {
'data_parameter': {},
'global_parameter': [],
'links': [],
'color': [],
}
parameter = {'parameter': {}, 'lb': (), 'ub': (), 'var': [],
'glob': {'idx': [], 'p': [], 'var': [], 'lb': [], 'ub': []},
'links': [], 'color': []}
for i, f in enumerate(model):
if not f['active']:
continue
try:
p, glob = self.param_widgets[f['cnt']].get_parameter(function_use)
p, lb, ub, var, glob, links = self.param_widgets[f['cnt']].get_parameter(function_use)
except ValueError as e:
_ = QtWidgets.QMessageBox().warning(self, 'Invalid value', str(e),
QtWidgets.QMessageBox.Ok)
return {}, -1
parameter['color'].append(f['color'])
parameter['global_parameter'].extend(glob)
p_len = len(parameter['lb'])
parameter['lb'] += lb
parameter['ub'] += ub
parameter['var'] += var
parameter['links'] += links
parameter['color'] += [f['color']]
cnt = f['cnt']
for p_k, v_k in p.items():
if add_idx:
kw_k = {f'{k}_{cnt}': v for k, v in v_k[1].items()}
else:
kw_k = v_k[1]
if p_k in parameter['data_parameter']:
params, kw = parameter['data_parameter'][p_k]
if p_k in parameter['parameter']:
params, kw = parameter['parameter'][p_k]
params += v_k[0]
kw.update(kw_k)
else:
parameter['data_parameter'][p_k] = (v_k[0], kw_k)
parameter['parameter'][p_k] = (v_k[0], kw_k)
for g_k, g_v in glob.items():
if g_k != 'idx':
parameter['glob'][g_k] += g_v
else:
parameter['glob']['idx'] += [idx_i + p_len for idx_i in g_v]
if add_idx:
cnt += 1
if f['children']:
# recurse for children
_, cnt = self._prepare(f['children'], parameter=parameter, add_idx=add_idx, cnt=cnt)
child_parameter, cnt = self._prepare(f['children'], parameter=parameter, add_idx=add_idx, cnt=cnt)
return parameter, cnt
@ -275,43 +277,30 @@ class QFitDialog(QtWidgets.QWidget, Ui_FitDialog):
data = self.data_table.collect_data(default=self.default_combobox.currentData())
func_dict = {}
for model_name, model_parameter in self.models.items():
func, order, param_len = ModelFactory.create_from_list(model_parameter)
for k, mod in self.models.items():
func, order, param_len = ModelFactory.create_from_list(mod)
if func is None:
continue
func = Model(func)
if model_name in data:
parameter, _ = self._prepare(model_parameter, function_use=data[model_name], add_idx=isinstance(func, MultiModel))
if k in data:
parameter, _ = self._prepare(mod, function_use=data[k], add_idx=isinstance(func, MultiModel))
if parameter is None:
return
for (data_parameter, _) in parameter['data_parameter'].values():
for pname, param in zip(func.params, data_parameter):
param.name = pname
if self._complex[model_name] is not None:
for p_k, p_v in parameter['data_parameter'].items():
p_v[1].update({'complex_mode': self._complex[model_name]})
parameter['data_parameter'][p_k] = p_v[0], p_v[1]
for pname, param_value in zip(func.params, parameter['global_parameter']):
if param_value is not None:
param_value.name = pname
func.set_global_parameter(param_value)
parameter['func'] = func
parameter['order'] = order
parameter['len'] = param_len
parameter['complex'] = self._complex[model_name]
parameter['complex'] = self._complex[k]
if self._complex[k] is not None:
for p_k, p_v in parameter['parameter'].items():
p_v[1].update({'complex_mode': self._complex[k]})
parameter['parameter'][p_k] = p_v[0], p_v[1]
func_dict[model_name] = parameter
func_dict[k] = parameter
replaceable = []
for model_name, v in func_dict.items():
for k, v in func_dict.items():
for i, link_i in enumerate(v['links']):
if link_i is None:
continue
@ -342,7 +331,7 @@ class QFitDialog(QtWidgets.QWidget, Ui_FitDialog):
QtWidgets.QMessageBox.Ok)
return
replaceable.append((model_name, i, rep_model, repl_idx))
replaceable.append((k, i, rep_model, repl_idx))
replace_value = None
for p_k in f['parameter'].values():
@ -420,37 +409,31 @@ class QFitDialog(QtWidgets.QWidget, Ui_FitDialog):
def make_previews(self, x, models_parameters: dict):
self.preview_lines = []
# needed to create namespace
param_dict = Parameters()
cnt = 0
for model in models_parameters.values():
f = model['func']
for parameter_list in model['data_parameter'].values():
for i, p_value in enumerate(parameter_list[0]):
p_value.name = f.params[i]
param_dict.add_parameter(f'a{cnt}', p_value)
cnt += 1
for k, model in models_parameters.items():
f = model['func']
is_complex = self._complex[k]
parameters = model['data_parameter']
parameters = model['parameter']
color = model['color']
seen_parameter = []
for p, kwargs in parameters.values():
p_value = [pp.value for pp in p]
if (p, kwargs) in seen_parameter:
# plot only previews with different parameter
continue
seen_parameter.append((p, kwargs))
if is_complex is not None:
y = f.func(x, *p_value, complex_mode=is_complex, **kwargs)
y = f.func(x, *p, complex_mode=is_complex, **kwargs)
if np.iscomplexobj(y):
self.preview_lines.append(PlotItem(x=x, y=y.real, pen=mkPen(width=3)))
self.preview_lines.append(PlotItem(x=x, y=y.imag, pen=mkPen(width=3)))
else:
self.preview_lines.append(PlotItem(x=x, y=y, pen=mkPen(width=3)))
else:
y = f.func(x, *p_value, **kwargs)
y = f.func(x, *p, **kwargs)
self.preview_lines.append(PlotItem(x=x, y=y, pen=mkPen(width=3)))
if isinstance(f, MultiModel):
@ -458,7 +441,7 @@ class QFitDialog(QtWidgets.QWidget, Ui_FitDialog):
if is_complex is not None:
sub_kwargs.update({'complex_mode': is_complex})
for i, s in enumerate(f.subs(x, *p_value, **sub_kwargs)):
for i, s in enumerate(f.subs(x, *p, **sub_kwargs)):
pen_i = mkPen(QtGui.QColor.fromRgbF(*color[i]))
if np.iscomplexobj(s):
self.preview_lines.append(PlotItem(x=x, y=s.real, pen=pen_i))
@ -466,17 +449,15 @@ class QFitDialog(QtWidgets.QWidget, Ui_FitDialog):
else:
self.preview_lines.append(PlotItem(x=x, y=s, pen=pen_i))
param_dict.clear()
return self.preview_lines
def set_parameter(self, parameter: dict[str, FitResult]):
# which data uses which model
data = self.data_table.collect_data(default=self.default_combobox.currentData())
for fitted_model, fitted_data in data.items():
glob_fit_parameter = []
glob_fit_parameter = []
for fitted_model, fitted_data in data.items():
for fit_id, fit_curve in parameter.items():
if fit_id in fitted_data:
fit_parameter = list(fit_curve.parameter.values())

9
src/gui_qt/fit/function_creation_dialog.py
View File

@ -14,7 +14,7 @@ from gui_qt.lib.namespace import QNamespaceWidget
__all__ = ['QUserFitCreator']
validator = QtGui.QRegExpValidator(QtCore.QRegExp('[_A-Za-z][_A-Za-z0-9]*'))
validator = QtGui.QRegExpValidator(QtCore.QRegExp('[A-Za-z]\S*'))
pattern = re.compile(r'def func\(.*\):', flags=re.MULTILINE)
@ -145,7 +145,6 @@ class QUserFitCreator(QtWidgets.QDialog, Ui_Dialog):
self.classCreated.emit()
super().accept()
class KwargsWidget(QtWidgets.QWidget):
Changed = QtCore.pyqtSignal()
@ -210,7 +209,7 @@ class KwargsWidget(QtWidgets.QWidget):
def get_strings(self) -> str:
kwargs = []
if self.use_nuclei.isChecked():
kwargs.append(r"(r'\gamma', 'nucleus', gamma)")
kwargs.append("(r'\gamma', 'nucleus', gamma)")
for i in range(self.choices.count()):
kwargs.append(self.choices.widget(i).get_strings())
@ -301,7 +300,7 @@ class ChoiceWidget(QtWidgets.QWidget):
def get_strings(self) -> str:
opts = []
for i in range(self.table.rowCount()):
name = self.table.cellWidget(i, 0).text()
name = self.table.item(i, 0).text()
val = self._make_value(i)
opts.append(f'{name!r}: {val!r}')
@ -472,7 +471,7 @@ class DescWidget(QtWidgets.QWidget):
stringi = f'class {self.klass_lineedit.text()}:\n' \
f' name = {self.name_lineedit.text()!r}\n' \
f' type = {self.group_lineedit.text()!r}\n' \
f" equation = r'{self.eq_lineedit.text()}'\n"
f' equation = {self.eq_lineedit.text()!r}\n'
return stringi

223
src/gui_qt/fit/result.py
View File

@ -1,9 +1,8 @@
from math import isnan
from pyqtgraph import mkBrush, mkPen
from pyqtgraph import mkBrush
from nmreval.utils.text import convert
from ..lib.graph_items import logTickValues
from ..lib.utils import RdBuCMap
from ..Qt import QtWidgets, QtGui, QtCore
@ -28,82 +27,70 @@ class QFitResult(QtWidgets.QDialog, Ui_Dialog):
self.extrapolate_box.stateChanged.connect(lambda x: self.minx_line.setEnabled(x))
self.extrapolate_box.stateChanged.connect(lambda x: self.numx_line.setEnabled(x))
self._previous_fits = {}
self._opts = []
self._results = {}
self.graph_opts = {}
self.last_idx = None
self._prevs = {}
self._models = {}
self.fit_plot = self.graphicsView.addPlot(row=1, col=0, title='Fit')
self.resid_plot = self.graphicsView.addPlot(row=0, col=0, title='Residual')
for res in results:
idx = res.idx
data_k = management.data[idx]
for orient in ['top', 'bottom', 'left', 'right']:
self.fit_plot.getAxis(orient).logTickValues = logTickValues
self.resid_plot.getAxis(orient).logTickValues = logTickValues
if res.name not in self._models:
self._models[res.name] = []
self.graphicsView.ci.layout.setRowStretchFactor(0, 1)
self.graphicsView.ci.layout.setRowStretchFactor(1, 2)
self._models[res.name].append(idx)
self._prevs[idx] = []
for fit in data_k.get_fits():
self._prevs[idx].append((fit.name, fit.statistics, fit.nobs-fit.nvar))
self._results = {res.idx: res for res in results}
self._opts = [(False, False) for _ in range(len(self._results))]
self.residplot = self.graphicsView.addPlot(row=0, col=0)
self.resid_graph = PlotItem(x=[], y=[],
symbol='o', symbolPen=None, symbolBrush=mkBrush(color=(31, 119, 180)),
pen=None)
self.resid_graph_imag = PlotItem(x=[], y=[],
symbol='s', symbolPen=None, symbolBrush=mkBrush(color=(255, 127, 14)),
pen=None)
self.resid_plot.addItem(self.resid_graph)
self.resid_plot.addItem(self.resid_graph_imag)
self.residplot.addItem(self.resid_graph)
self.residplot.addItem(self.resid_graph_imag)
self.residplot.setLabel('left', 'Residual')
self.fitplot = self.graphicsView.addPlot(row=1, col=0)
self.data_graph = PlotItem(x=[], y=[],
symbol='o', symbolPen=None, symbolBrush=mkBrush(color=(31, 119, 180)),
pen=None)
self.data_graph_imag = PlotItem(x=[], y=[],
symbol='s', symbolPen=None, symbolBrush=mkBrush(color=(255, 127, 14)),
pen=None)
self.fit_plot.addItem(self.data_graph)
self.fit_plot.addItem(self.data_graph_imag)
self.fitplot.addItem(self.data_graph)
self.fitplot.addItem(self.data_graph_imag)
self.fitplot.setLabel('left', 'Function')
self.fit_graph = PlotItem(x=[], y=[])
self.fit_graph_imag = PlotItem(x=[], y=[])
self.fit_plot.addItem(self.fit_graph)
self.fit_plot.addItem(self.fit_graph_imag)
self.fitplot.addItem(self.fit_graph)
self.fitplot.addItem(self.fit_graph_imag)
self.cmap = RdBuCMap(vmin=-1, vmax=1)
self.graph_checkBox.stateChanged.connect(lambda x: self.graph_comboBox.setEnabled(x == QtCore.Qt.Unchecked))
self.logy_box.stateChanged.connect(lambda x: self.fit_plot.setLogMode(y=bool(x)))
self.logx_box.stateChanged.connect(lambda x: self.fit_plot.setLogMode(x=bool(x)))
self.resid_plot.setXLink(self.fit_plot)
self.set_results(results)
def __call__(self, results: list):
self._previous_fits = {}
self.sets_comboBox.blockSignals(True)
self.sets_comboBox.clear()
for n in self._models.keys():
self.sets_comboBox.addItem(n)
self.sets_comboBox.blockSignals(False)
self._results = {}
self._opts = {}
self.set_results(results)
def set_results(self, results: list):
self.sets_comboBox.blockSignals(True)
for res in results:
idx = res.idx
data_k = self._management.data[idx]
self._previous_fits[idx] = []
for fit in data_k.get_fits():
self._previous_fits[idx].append((fit.name, fit.statistics, fit.nobs - fit.nvar))
self.sets_comboBox.addItem(data_k.name, userData=idx)
self.sets_comboBox.blockSignals(False)
self._results = {res.idx: res for res in results}
self._opts = [(False, False) for _ in range(len(self._results))]
self.set_parameter(0)
self.buttonBox.accepted.connect(self.accept)
self.param_tableWidget.itemClicked.connect(self.show_results)
self.param_tableWidget.horizontalHeader().sectionClicked.connect(lambda i: self.show_results(None, idx=i))
self.graph_checkBox.stateChanged.connect(lambda x: self.graph_comboBox.setEnabled(x == QtCore.Qt.Unchecked))
self.logy_box.stateChanged.connect(lambda x: self.fitplot.setLogMode(y=bool(x)))
self.logx_box.stateChanged.connect(lambda x: self.fitplot.setLogMode(x=bool(x)))
self.residplot.setXLink(self.fitplot)
def add_graphs(self, graphs: list):
self.graph_comboBox.clear()
@ -112,40 +99,56 @@ class QFitResult(QtWidgets.QDialog, Ui_Dialog):
@QtCore.pyqtSlot(int, name='on_sets_comboBox_currentIndexChanged')
def set_parameter(self, idx: int):
set_id = self.sets_comboBox.itemData(idx, QtCore.Qt.UserRole)
model_name = self.sets_comboBox.itemText(idx)
sets = self._models[model_name]
self.param_tableWidget.setColumnCount(len(sets))
res = self._results[set_id]
self.param_tableWidget.setRowCount(len(res.parameter))
for j, (pkey, pvalue) in enumerate(res.parameter.items()):
name = pkey
p_header = QtWidgets.QTableWidgetItem(convert(name, 'tex', 'str', brackets=True))
self.param_tableWidget.setVerticalHeaderItem(j, p_header)
r = self._results[sets[0]]
self.param_tableWidget.setRowCount(len(r.parameter))
item_text = f'{pvalue.value:.4g}'
if pvalue.error is not None:
item_text += f' \u00b1 {pvalue.error:.4g}'
self.param_tableWidget.setItem(2*j+1, 0, QtWidgets.QTableWidgetItem('-'))
else:
self.param_tableWidget.setItem(2*j+1, 0, QtWidgets.QTableWidgetItem())
item = QtWidgets.QTableWidgetItem(item_text)
self.param_tableWidget.setItem(j, 0, item)
for i, pval in enumerate(r.parameter.values()):
name = pval.full_name
p_header = QtWidgets.QTableWidgetItem(convert(name, 'tex', 'html', brackets=False))
self.param_tableWidget.setVerticalHeaderItem(i, p_header)
self.param_tableWidget.resizeColumnToContents(0)
self.show_results(idx)
for i, set_id in enumerate(sets):
data_i = self._management[set_id]
header_item = QtWidgets.QTableWidgetItem(data_i.name)
header_item.setData(QtCore.Qt.UserRole, set_id)
self.param_tableWidget.setHorizontalHeaderItem(i, header_item)
res = self._results[set_id]
for j, pvalue in enumerate(res.parameter.values()):
item_text = f'{pvalue.value:.4g}'
if pvalue.error is not None:
item_text += f' \u00b1 {pvalue.error:.4g}'
self.param_tableWidget.setItem(2*j+1, i, QtWidgets.QTableWidgetItem('-'))
else:
self.param_tableWidget.setItem(2*j+1, i, QtWidgets.QTableWidgetItem())
item = QtWidgets.QTableWidgetItem(item_text)
self.param_tableWidget.setItem(j, i, item)
self.param_tableWidget.resizeColumnsToContents()
self.param_tableWidget.selectColumn(0)
self.show_results(None, idx=0)
@QtCore.pyqtSlot(int, name='on_reject_fit_checkBox_stateChanged')
@QtCore.pyqtSlot(int, name='on_del_prev_checkBox_stateChanged')
def change_opts(self, _):
idx = self.sets_comboBox.currentIndex()
idx = self.param_tableWidget.currentIndex().column()
self._opts[idx] = (self.reject_fit_checkBox.checkState() == QtCore.Qt.Checked,
self.del_prev_checkBox.checkState() == QtCore.Qt.Checked)
def show_results(self, idx):
set_id = self.sets_comboBox.itemData(idx, QtCore.Qt.UserRole)
def show_results(self, item, idx=None):
if item is not None:
idx = self.param_tableWidget.indexFromItem(item).column()
set_id = self.param_tableWidget.horizontalHeaderItem(idx).data(QtCore.Qt.UserRole)
self.set_plot(set_id)
self.set_correlation(set_id)
self.set_statistics(set_id)
self.reject_fit_checkBox.blockSignals(True)
self.reject_fit_checkBox.setChecked(self._opts[idx][0])
self.reject_fit_checkBox.blockSignals(False)
@ -154,22 +157,9 @@ class QFitResult(QtWidgets.QDialog, Ui_Dialog):
self.del_prev_checkBox.blockSignals(False)
def set_plot(self, idx: str):
if self.last_idx is not None:
self.graph_opts[self.last_idx] = (
self.fit_plot.viewRange(),
self.logx_box.isChecked(),
self.logy_box.isChecked(),
)
self.last_idx = idx
res = self._results[idx]
iscomplex = res.iscomplex
sub_funcs = res.sub(res.x)
for item in self.fit_plot.items[::-1]:
if item not in [self.data_graph, self.data_graph_imag, self.fit_graph, self.fit_graph_imag]:
self.fit_plot.removeItem(item)
if iscomplex:
self.data_graph.setData(x=res.x_data, y=res.y_data.real)
self.data_graph_imag.setData(x=res.x_data, y=res.y_data.imag)
@ -177,13 +167,6 @@ class QFitResult(QtWidgets.QDialog, Ui_Dialog):
self.fit_graph_imag.setData(x=res.x, y=res.y.imag)
self.resid_graph.setData(x=res.x_data, y=res.residual.real)
self.resid_graph_imag.setData(x=res.x_data, y=res.residual.imag)
for i, f in enumerate(sub_funcs):
item = PlotItem(x=f.x, y=f.y.real, pen=mkPen({'color': i, 'style': 2}))
self.fit_plot.addItem(item)
item = PlotItem(x=f.x, y=f.y.imag, pen=mkPen({'color': i, 'style': 2}))
self.fit_plot.addItem(item)
else:
self.resid_graph.setData(x=res.x_data, y=res.residual)
self.resid_graph_imag.setData(x=[], y=[])
@ -192,27 +175,8 @@ class QFitResult(QtWidgets.QDialog, Ui_Dialog):
self.fit_graph.setData(x=res.x, y=res.y)
self.fit_graph_imag.setData(x=[], y=[])
for i, f in enumerate(sub_funcs):
item = PlotItem(x=f.x, y=f.y, pen=mkPen({'color': i, 'style': 2}))
self.fit_plot.addItem(item)
self.logx_box.blockSignals(True)
self.logx_box.setChecked(res.islog)
self.logx_box.blockSignals(False)
self.fit_plot.setLogMode(x=res.islog)
self.resid_plot.setLogMode(x=res.islog)
if idx in self.graph_opts:
view_range, logx, logy = self.graph_opts[idx]
self.fit_plot.setRange(xRange=view_range[0], yRange=view_range[1], padding=0)
self.fit_plot.setLogMode(x=logx, y=logy)
self.logx_box.blockSignals(True)
self.logx_box.setChecked(logx)
self.logx_box.blockSignals(False)
self.logy_box.blockSignals(True)
self.logy_box.setChecked(logy)
self.logy_box.blockSignals(False)
self.fitplot.setLogMode(x=res.islog)
self.residplot.setLogMode(x=res.islog)
def set_correlation(self, idx: str):
while self.corr_tableWidget.rowCount():
@ -243,7 +207,7 @@ class QFitResult(QtWidgets.QDialog, Ui_Dialog):
res = self._results[idx]
self.stats_tableWidget.setColumnCount(1 + len(self._previous_fits[idx]))
self.stats_tableWidget.setColumnCount(1 + len(self._prevs[idx]))
self.stats_tableWidget.setRowCount(len(res.statistics)+3)
it = QtWidgets.QTableWidgetItem(f'{res.dof}')
@ -251,7 +215,7 @@ class QFitResult(QtWidgets.QDialog, Ui_Dialog):
self.stats_tableWidget.setVerticalHeaderItem(0, QtWidgets.QTableWidgetItem('DoF'))
self.stats_tableWidget.setItem(0, 0, it)
for col, (name, _, dof) in enumerate(self._previous_fits[idx], start=1):
for col, (name, _, dof) in enumerate(self._prevs[idx], start=1):
self.stats_tableWidget.setHorizontalHeaderItem(0, QtWidgets.QTableWidgetItem(name))
it = QtWidgets.QTableWidgetItem(f'{dof}')
it.setFlags(it.flags() ^ QtCore.Qt.ItemIsEditable)
@ -265,7 +229,7 @@ class QFitResult(QtWidgets.QDialog, Ui_Dialog):
best_idx = -1
best_val = v
for col, (_, stats, _) in enumerate(self._previous_fits[idx], start=1):
for col, (_, stats, _) in enumerate(self._prevs[idx], start=1):
if k in ['adj. R^2', 'R^2']:
best_idx = col if best_val < stats[k] else max(0, best_idx)
else:
@ -285,7 +249,7 @@ class QFitResult(QtWidgets.QDialog, Ui_Dialog):
self.stats_tableWidget.setVerticalHeaderItem(row+1, QtWidgets.QTableWidgetItem('Pr(>F)'))
self.stats_tableWidget.setItem(row+1, 0, QtWidgets.QTableWidgetItem('-'))
for col, (_, stats, dof) in enumerate(self._previous_fits[idx], start=1):
for col, (_, stats, dof) in enumerate(self._prevs[idx], start=1):
f_value, prob_f = res.f_test(stats['chi^2'], dof)
it = QtWidgets.QTableWidgetItem(f'{f_value:.4g}')
it.setFlags(it.flags() ^ QtCore.Qt.ItemIsEditable)
@ -315,30 +279,27 @@ class QFitResult(QtWidgets.QDialog, Ui_Dialog):
plot_fits = self.curve_checkbox.isChecked()
parts = self.partial_checkBox.checkState() == QtCore.Qt.Checked
extrapolate = [None, None, None]
error = []
if self.extrapolate_box.isChecked():
try:
extrapolate[0] = float(self.minx_line.text())
except (TypeError, ValueError):
error.append('Start value is missing')
except TypeError:
pass
try:
extrapolate[1] = float(self.maxx_line.text())
except (TypeError, ValueError):
error.append('End value is missing')
except TypeError:
pass
try:
extrapolate[2] = int(self.numx_line.text())
except (TypeError, ValueError):
error.append('Number of points is missing')
except TypeError:
pass
if error:
msg = QtWidgets.QMessageBox.warning(self, 'Error', 'Extrapolation failed because:\n' + '\n'.join(error))
return
else:
self.closed.emit(self._results, self._opts, graph, plot_fits, parts, extrapolate)
self.accept()
self.closed.emit(self._results, self._opts, graph, plot_fits, parts, extrapolate)
self.accept()
else:
self.reject()
@ -372,7 +333,7 @@ class FitExtension(QtWidgets.QDialog):
self.buttonBox = QtWidgets.QDialogButtonBox()
self.buttonBox.setOrientation(QtCore.Qt.Horizontal)
self.buttonBox.setStandardButtons(QtWidgets.QDialogButtonBox.Cancel | QtWidgets.QDialogButtonBox.Ok)
self.buttonBox.setStandardButtons(QtWidgets.QDialogButtonBox.Cancel|QtWidgets.QDialogButtonBox.Ok)
gridLayout.addWidget(self.buttonBox, 3, 0, 1, 2)
self.setLayout(gridLayout)
@ -389,4 +350,4 @@ class FitExtension(QtWidgets.QDialog):
except TypeError:
return None
return xmin, xmax, nums
return xmin, xmax, nums

2
src/gui_qt/graphs/drawings.py
View File

@ -138,7 +138,9 @@ class DrawingsWidget(QtWidgets.QWidget, Ui_Form):
graph_id = self.graph_comboBox.currentData()
current_lines = self.lines[graph_id]
print(remove_rows)
for i in reversed(remove_rows):
print(i)
self.tableWidget.removeRow(i)
self.line_deleted.emit(current_lines[i], graph_id)

113
src/gui_qt/graphs/graphwindow.py
View File

@ -4,21 +4,19 @@ import itertools
import os
import uuid
from math import isfinite
from math import isnan
from pathlib import Path
import numpy as np
from numpy import errstate, floor, log10
from pyqtgraph import GraphicsObject, getConfigOption, mkColor
from nmreval.lib.logger import logger
from nmreval.utils.text import convert
from ..io.filedialog import FileDialog
from ..lib.pg_objects import LegendItemBlock, RegionItem
from ..Qt import QtCore, QtWidgets, QtGui
from .._py.graph import Ui_GraphWindow
from ..lib.iconloading import make_action_icons
from ..lib import make_action_icons
from ..lib.configurations import GraceMsgBox
@ -26,7 +24,7 @@ class QGraphWindow(QtWidgets.QGraphicsView, Ui_GraphWindow):
mousePositionChanged = QtCore.pyqtSignal(float, float)
mouseDoubleClicked = QtCore.pyqtSignal()
positionClicked = QtCore.pyqtSignal(tuple, bool)
aboutToClose = QtCore.pyqtSignal(list)
aboutToClose = QtCore.pyqtSignal(str)
counter = itertools.count()
@ -45,7 +43,7 @@ class QGraphWindow(QtWidgets.QGraphicsView, Ui_GraphWindow):
self.id = str(uuid.uuid4())
self.sets = []
self._active = []
self.active = []
self.real_plots = {}
self.imag_plots = {}
@ -55,8 +53,6 @@ class QGraphWindow(QtWidgets.QGraphicsView, Ui_GraphWindow):
self._external_items = []
self.closable = True
self._block = False
self.log = [False, False]
self.scene = self.plotItem.scene()
@ -75,8 +71,6 @@ class QGraphWindow(QtWidgets.QGraphicsView, Ui_GraphWindow):
self.scene.contextMenu[0].disconnect()
self.scene.contextMenu[0].triggered.connect(self.export_dialog)
self.bwbutton.toggled.connect(self.change_background)
def _init_gui(self):
self.setWindowTitle('Graph ' + str(next(QGraphWindow.counter)))
@ -116,11 +110,11 @@ class QGraphWindow(QtWidgets.QGraphicsView, Ui_GraphWindow):
return iter(self.active)
def __len__(self):
return len(self._active)
return len(self.active)
def curves(self) -> tuple:
for set_id in self.sets:
if set_id in self._active:
if set_id in self.active:
if self.real_button.isChecked():
if self.error_plots[set_id] is not None:
yield self.real_plots[set_id], self.error_plots[set_id]
@ -143,43 +137,19 @@ class QGraphWindow(QtWidgets.QGraphicsView, Ui_GraphWindow):
r = self.plotItem.getViewBox().viewRange()
for i in [0, 1]:
if self.log[i]:
tmp = [np.nan, np.nan]
for j, x in enumerate(r[i]):
try:
tmp[j] = 10**min(x, 199)
except OverflowError:
pass
r[i] = tuple(tmp)
r[i] = tuple([10**x for x in r[i]])
else:
r[i] = tuple(r[i])
return tuple(r)
@property
def active(self) -> list:
return [set_id for set_id in self.sets if set_id in self._active]
@active.setter
def active(self, value: list):
self._active = value
def block(self, state: bool):
self._block = state
if not self._block:
self.graphic.enableAutoRange()
self._update_zorder()
self.show_legend()
else:
self.graphic.disableAutoRange()
def add(self, name: str | list, plots: list):
if isinstance(name, str):
name = [name]
plots = [plots]
toplevel = len(self.sets)
self.listWidget.blockSignals(True)
for (real_plot, imag_plot, err_plot), n in zip(plots, name):
toplevel = len(self.sets)
self.sets.append(n)
if real_plot:
@ -199,16 +169,7 @@ class QGraphWindow(QtWidgets.QGraphicsView, Ui_GraphWindow):
list_item.setCheckState(QtCore.Qt.Checked)
self.listWidget.addItem(list_item)
toplevel += 1
self.listWidget.blockSignals(False)
if len(name) < 200:
self.show_item(name)
else:
QtWidgets.QMessageBox.warning(self, 'Display disabled',
'If more than 200 sets are added at once, they are not displayed to avoid major performance issues.\n'
'The checkmark in the data tree is invalid.\n'
'Please display them manually in smaller batches, thank you!')
self.show_item(name)
def remove(self, name: str | list):
if isinstance(name, str):
@ -220,8 +181,8 @@ class QGraphWindow(QtWidgets.QGraphicsView, Ui_GraphWindow):
for plot in [self.real_plots, self.imag_plots, self.error_plots]:
self.graphic.removeItem(plot[n])
if n in self._active:
self._active.remove(n)
if n in self.active:
self.active.remove(n)
# remove from label list
self.listWidget.blockSignals(True)
@ -233,9 +194,8 @@ class QGraphWindow(QtWidgets.QGraphicsView, Ui_GraphWindow):
self.listWidget.blockSignals(False)
if not self._block:
self._update_zorder()
self.show_legend()
self._update_zorder()
self.show_legend()
def move_sets(self, sets: list, position: int):
move_plots = []
@ -265,8 +225,8 @@ class QGraphWindow(QtWidgets.QGraphicsView, Ui_GraphWindow):
return
for a in idlist:
if a not in self._active:
self._active.append(a)
if a not in self.active:
self.active.append(a)
for (bttn, plot_dic) in [
(self.real_button, self.real_plots),
@ -285,8 +245,8 @@ class QGraphWindow(QtWidgets.QGraphicsView, Ui_GraphWindow):
return
for r in idlist:
if r in self._active:
self._active.remove(r)
if r in self.active:
self.active.remove(r)
for plt in [self.real_plots, self.imag_plots, self.error_plots]:
item = plt[r]
@ -308,7 +268,7 @@ class QGraphWindow(QtWidgets.QGraphicsView, Ui_GraphWindow):
else:
func = self.graphic.removeItem
for a in self._active:
for a in self.active:
item = plots[a]
if item is not None:
func(item)
@ -325,12 +285,12 @@ class QGraphWindow(QtWidgets.QGraphicsView, Ui_GraphWindow):
return
if visible:
for a in self._active:
for a in self.active:
item = self.error_plots[a]
if (item is not None) and (item not in self.graphic.items()):
self.graphic.addItem(item)
else:
for a in self._active:
for a in self.active:
item = self.error_plots[a]
if (item is not None) and (item in self.graphic.items()):
self.graphic.removeItem(item)
@ -394,7 +354,7 @@ class QGraphWindow(QtWidgets.QGraphicsView, Ui_GraphWindow):
QtWidgets.QMessageBox.Yes, QtWidgets.QMessageBox.No)
if res == QtWidgets.QMessageBox.Yes:
self.aboutToClose.emit([self.id])
self.aboutToClose.emit(self.id)
evt.accept()
else:
evt.ignore()
@ -442,9 +402,6 @@ class QGraphWindow(QtWidgets.QGraphicsView, Ui_GraphWindow):
def set_logmode(self, xmode: bool = None, ymode: bool = None):
r = self.ranges
self.plotItem.setXRange(*r[0])
self.plotItem.setYRange(*r[1])
if xmode is None:
xmode = self.plotItem.ctrl.logXCheck.isChecked()
else:
@ -461,7 +418,6 @@ class QGraphWindow(QtWidgets.QGraphicsView, Ui_GraphWindow):
item.logmode[0] = self.log[:]
self.plotItem.updateLogMode()
self.set_range(x=r[0], y=r[1])
self.plotItem.enableAutoRange()
@ -504,9 +460,9 @@ class QGraphWindow(QtWidgets.QGraphicsView, Ui_GraphWindow):
with errstate(all='ignore'):
xy = [log10(val) for val in xy]
if not isfinite(xy[1]):
if isnan(xy[1]):
xy = [-1, 1]
elif not isfinite(xy[0]):
elif isnan(xy[0]):
xy[0] = xy[1]-4
func(xy[0], xy[1], padding=0)
@ -538,9 +494,6 @@ class QGraphWindow(QtWidgets.QGraphicsView, Ui_GraphWindow):
self.checkBox.setVisible(visible)
def update_legend(self, sid, name):
if self._block:
return
self.listWidget.blockSignals(True)
for i in range(self.listWidget.count()):
@ -567,14 +520,16 @@ class QGraphWindow(QtWidgets.QGraphicsView, Ui_GraphWindow):
elif other_item in self.graphic.items():
self.legend.addItem(other_item, convert(other_item.opts.get('name', ''), old='tex', new='html'))
def export_dialog(self, _=None):
def export_dialog(self, path=None):
filters = 'All files (*.*);;AGR (*.agr);;SVG (*.svg);;PDF (*.pdf)'
for imgformat in QtGui.QImageWriter.supportedImageFormats():
str_format = imgformat.data().decode('utf-8')
filters += ';;' + str_format.upper() + ' (*.' + str_format + ')'
if path is None:
path = ''
outfile = None
f = FileDialog(caption='Export graphic', filter=filters, mode='save')
f = FileDialog(caption='Export graphic', directory=str(path), filter=filters, mode='save')
f.setOption(FileDialog.DontConfirmOverwrite)
mode = f.exec()
if mode == QtWidgets.QDialog.Accepted:
@ -653,7 +608,7 @@ class QGraphWindow(QtWidgets.QGraphicsView, Ui_GraphWindow):
try:
item_dic = plot_item.get_data_opts()
except Exception as e:
logger.exception(f'{item} could not exported because {e.args}')
print(f'{item} could not exported because {e.args}')
continue
if len(item) == 2:
@ -667,7 +622,7 @@ class QGraphWindow(QtWidgets.QGraphicsView, Ui_GraphWindow):
try:
dic['items'].append(item.get_data_opts())
except Exception as e:
logger.exception(f'{item} could not be exported because {e.args}')
print(f'{item} could not be exported because {e.args}')
continue
in_legend.append(False)
@ -690,7 +645,7 @@ class QGraphWindow(QtWidgets.QGraphicsView, Ui_GraphWindow):
'legend': self.legend.isVisible(),
'plots': (self.real_button.isChecked(), self.imag_button.isChecked(), self.error_button.isChecked()),
'children': self.sets,
'active': self._active,
'active': self.active,
}
in_legend = []
@ -753,7 +708,7 @@ class QGraphWindow(QtWidgets.QGraphicsView, Ui_GraphWindow):
if background is not None:
self._bgcolor = mkColor(background)
self.graphic.setBackground(self._bgcolor)
# self.legend.setBrush(self._bgcolor)
self.legend.setBrush(self._bgcolor)
if foreground is not None:
self._fgcolor = mkColor(foreground)
@ -770,7 +725,7 @@ class QGraphWindow(QtWidgets.QGraphicsView, Ui_GraphWindow):
self.show_legend()
title = self.plotItem.titleLabel.text
if title is not None and title != '':
if title is not None:
self.plotItem.setTitle(title, **{'size': '10pt', 'color': self._fgcolor})
x = self.plotItem.getAxis('bottom').labelText
@ -781,8 +736,8 @@ class QGraphWindow(QtWidgets.QGraphicsView, Ui_GraphWindow):
if y is not None:
self.plotItem.setLabel('left', y, **{'font-size': '10pt', 'color': self._fgcolor.name()})
@QtCore.pyqtSlot(bool, name='on_bwbutton_toggled')
def change_background(self, _):
temp = self._fgcolor, self._bgcolor
self.set_color(foreground=self._prev_colors[0], background=self._prev_colors[1])
self._prev_colors = temp

89
src/gui_qt/io/asciireader.py
View File

@ -1,9 +1,4 @@
from __future__ import annotations
import re
from nmreval.io.asciireader import AsciiReader
from nmreval.utils import NUMBER_RE
from ..Qt import QtGui, QtCore, QtWidgets
from .._py.asciidialog import Ui_ascii_reader
@ -18,9 +13,6 @@ class QAsciiReader(QtWidgets.QDialog, Ui_ascii_reader):
self.setupUi(self)
self.reader = None
self._matches = []
self.regex_input.setText(NUMBER_RE.pattern)
self.custom_input.setValidator(QtGui.QDoubleValidator())
self.comment_textfield = QtWidgets.QPlainTextEdit(self.header_widget)
self.comment_textfield.setReadOnly(True)
@ -49,8 +41,6 @@ class QAsciiReader(QtWidgets.QDialog, Ui_ascii_reader):
def __call__(self, fname, *args, **kwargs):
self.reader = AsciiReader(fname)
self.check_filename(self.regex_input.text())
if self.skip:
self.accept()
return
@ -62,7 +52,6 @@ class QAsciiReader(QtWidgets.QDialog, Ui_ascii_reader):
self.log_checkBox.setChecked(False)
self.set_gui()
self.set_column_names(1)
self.skippy_checkbox.blockSignals(True)
self.skippy_checkbox.setCheckState(QtCore.Qt.Unchecked)
@ -74,14 +63,12 @@ class QAsciiReader(QtWidgets.QDialog, Ui_ascii_reader):
for text in self.reader.header:
self.comment_textfield.appendPlainText(text)
tmp = self.line_spinBox.value()
if self.reader.header:
self.line_spinBox.setMaximum(len(self.reader.header))
else:
self.line_spinBox.setValue(0)
self.line_spinBox.setEnabled(False)
self.show_preview(10)
self.line_spinBox.setValue(tmp)
if self.reader.delays is not None:
set_string = ''.join(str(d) + '\n' for d in self.reader.delays)
@ -111,19 +98,15 @@ class QAsciiReader(QtWidgets.QDialog, Ui_ascii_reader):
@QtCore.pyqtSlot(int, name='on_preview_spinBox_valueChanged')
def show_preview(self, line_no: int):
preview, width, comments = self.reader.make_preview(line_no)
preview, width = self.reader.make_preview(line_no)
self.ascii_table.setRowCount(min(line_no, len(preview)))
self.ascii_table.setColumnCount(width + 1)
self.ascii_table.setColumnCount(width)
for i, line in enumerate(preview):
comment_line = comments[i]
for j, field in enumerate(line):
it = QtWidgets.QTableWidgetItem(field)
self.ascii_table.setItem(i, j, it)
it = QtWidgets.QTableWidgetItem(comment_line)
self.ascii_table.setItem(i, len(line), it)
self.ascii_table.resizeColumnsToContents()
@QtCore.pyqtSlot(int, name='on_column_checkBox_stateChanged')
@ -151,7 +134,7 @@ class QAsciiReader(QtWidgets.QDialog, Ui_ascii_reader):
staggered_range = 0
except ValueError:
_ = QtWidgets.QMessageBox.information(self, 'No delays',
'Delays cannot be calculated: Not enough or wrong arguments.')
'Delays cannot be calculated: Not enough or wrong arguments.')
return
self.reader.calc_delays(start, stop, num_delays, log=self.log_checkBox.isChecked(),
@ -182,13 +165,10 @@ class QAsciiReader(QtWidgets.QDialog, Ui_ascii_reader):
def apply(self):
# default row for x is the first row, it will be superseded if an integer number is given.
x = self.x_lineedit.text()
if x:
try:
x = int(x)-1
except ValueError:
pass
else:
try:
x = int(self.x_lineedit.text())-1
print(x)
except ValueError:
x = None
try:
@ -214,17 +194,12 @@ class QAsciiReader(QtWidgets.QDialog, Ui_ascii_reader):
col_header = [col_header[i] for i in range(len(col_header)) if i in y]
try:
ret_dic = self.reader.export(
x=x,
y=y,
yerr=y_err,
mode=self.buttonGroup.checkedButton().text(),
col_names=col_header,
num_value=self.get_numerical_value(),
)
ret_dic = self.reader.export(x=x, y=y, yerr=y_err,
mode=self.buttonGroup.checkedButton().text(),
col_names=col_header)
self.data_read.emit(ret_dic)
except ImportError as e:
except Exception as e:
_ = QtWidgets.QMessageBox.information(self, 'Reading failed',
f'Import data failed with {e.args}')
@ -236,45 +211,5 @@ class QAsciiReader(QtWidgets.QDialog, Ui_ascii_reader):
@QtCore.pyqtSlot(int, name='on_skippy_checkbox_stateChanged')
def skip_next_dial(self, _: int):
print('skippy das buschkänguru', _)
self.skip = self.skippy_checkbox.isChecked()
@QtCore.pyqtSlot(str, name='on_regex_input_textChanged')
def check_filename(self, pattern: str = NUMBER_RE.pattern):
if self.reader is None:
return
try:
pattern = re.compile(pattern)
self.regex_input.setStyleSheet('color: rgb(0, 0, 0)')
self._matches = [m for m in pattern.finditer(str(self.reader.fname.stem))]
except re.error:
self._matches = []
if self._matches:
self.re_match_index.blockSignals(True)
self.re_match_index.setMaximum(len(self._matches))
self.re_match_index.blockSignals(False)
else:
self.regex_input.setStyleSheet('color: rgb(255, 0, 0)')
self.show_match(self.re_match_index.value())
@QtCore.pyqtSlot(int, name='on_re_match_index_valueChanged')
def show_match(self, idx: int = 0):
fname = str(self.reader.fname.stem)
if self._matches:
m = self._matches[idx-1]
self.label_8.setText(f'{fname[:m.start()]}<b>{fname[m.start():m.end()]}</b>{fname[m.end():]}')
else:
self.label_8.setText(fname)
def get_numerical_value(self):
val = 0
if self.re_button.isChecked() and self._matches:
m = self._matches[self.re_match_index.value()-1]
val = float(NUMBER_RE.search(m.group()).group().replace('p', '.'))
elif self.custom_button.isChecked():
val = float(self.custom_input.text())
return val

41
src/gui_qt/io/dscreader.py
View File

@ -5,7 +5,7 @@ from pathlib import Path
import numpy as np
from pyqtgraph import PlotDataItem
from nmreval.data import DSC
from nmreval.data.points import Points
from nmreval.io.dsc import Cyclohexane, DSCCalibrator, DSCSample
from ..Qt import QtWidgets, QtCore
@ -83,7 +83,7 @@ class QDSCReader(QtWidgets.QDialog, Ui_Dialog):
if opts[0] == 'i':
item.setFlags(QtCore.Qt.NoItemFlags)
item.setText(f'{opts[1]:.2f} K for {opts[2] / 60:.0f} min')
item.setText(f'{opts[1]:.2f} K for {opts[1] / 60:.0f} min')
else:
item.setFlags(QtCore.Qt.ItemIsEnabled | QtCore.Qt.ItemIsSelectable | QtCore.Qt.ItemIsUserCheckable)
item.setText(f'{opts[2]:.2f} K to {opts[3]:.2f} K with {opts[1]} K/min')
@ -97,7 +97,7 @@ class QDSCReader(QtWidgets.QDialog, Ui_Dialog):
if empty:
self.empty = self.calibrator.set_measurement(empty, mode='empty')
self.empty_label.setText('~/' + str(self.empty.fname.relative_to(Path.home())))
self.empty_label.setText(str(self.empty.fname.name))
self.update_plots()
@ -158,28 +158,20 @@ class QDSCReader(QtWidgets.QDialog, Ui_Dialog):
self.sample_idx = None
self.clear_plots()
def get_data(self):
def get_data(self, ):
if self.sample_idx is None:
return
rate = self.current_run[0]
slope_type = {
self.none_radioButton: None,
self.isotherm_radioButton: 'iso',
self.slope_radioButton: 'curve',
}[self.buttonGroup.checkedButton()]
limit = None
if slope_type == 'curve':
try:
limit = float(self.limit1_lineedit.text())*60, float(self.limit2_lineedit.text())*60
except ValueError:
limit = None
slope_type = {self.none_radioButton: None,
self.isotherm_radioButton: 'iso',
self.slope_radioButton: 'curve'}[self.buttonGroup.checkedButton()]
try:
raw_sample, drift_value, sample_data, empty_data, slope = self.calibrator.get_data(self.sample_idx, slope=slope_type, limits=limit)
raw_sample, drift_value, sample_data, empty_data, slope = self.calibrator.get_data(self.sample_idx,
slope=slope_type)
except ValueError as e:
_msg = QtWidgets.QMessageBox.warning(self, f'Data collection with error', e.args[0])
_msg = QtWidgets.QMessageBox.warning(self, 'No rate found', e.args[0])
return
self.calibrator.ref_list = []
@ -202,14 +194,8 @@ class QDSCReader(QtWidgets.QDialog, Ui_Dialog):
@QtCore.pyqtSlot(QtWidgets.QAbstractButton, name='on_buttonGroup_buttonClicked')
@QtCore.pyqtSlot(int, name='on_cp_checkBox_stateChanged')
@QtCore.pyqtSlot(str, name='on_limit1_lineedit_textChanged')
@QtCore.pyqtSlot(str, name='on_limit2_lineedit_textChanged')
def update_plots(self, _=None):
res = self.get_data()
if res is None:
return
sample_data, raw_sample, empty_data, drift_value, slope, calib_x, calib_y, regions = res
sample_data, raw_sample, empty_data, drift_value, slope, calib_x, calib_y, regions = self.get_data()
self.raw_sample.setData(x=raw_sample[0], y=raw_sample[1])
self.drift_sample.setData(x=drift_value[0], y=drift_value[1])
@ -250,11 +236,10 @@ class QDSCReader(QtWidgets.QDialog, Ui_Dialog):
return
rate, mode = self.current_run
new_val = DSC(sample_data[0], sample_data[1], value=rate, name=f'{self.fname.stem} {rate} ({mode})')
new_val = Points(sample_data[0], sample_data[1], value=rate, name=f'{self.fname.stem} {rate} ({mode})')
if filesave:
new_val.savetxt(self.fname.with_name(f'{self.fname.stem} {rate}K-min {mode}.dat'.replace(' ', '_')))
close_after = False
else:
self.data_read.emit([new_val])
@ -265,7 +250,7 @@ class QDSCReader(QtWidgets.QDialog, Ui_Dialog):
def button_clicked(self, bttn: QtWidgets.QAbstractButton):
bttn_value = self.buttonBox.standardButton(bttn)
if bttn_value in (self.buttonBox.Ok, self.buttonBox.Apply, self.buttonBox.Save):
self.export_data(filesave=bttn_value == self.buttonBox.Save, close_after=bttn_value == self.buttonBox.Ok)
self.export_data(filesave=bttn_value==self.buttonBox.Save, close_after=bttn_value==self.buttonBox.Ok)
else:
super().close()

6
src/gui_qt/io/exporters.py
View File

@ -55,9 +55,9 @@ class GraceExporter:
break
if c_num == -1:
c_num = max(colors.keys())+1
colors[c_num] = (f'color{c_num}', sc)
new_colors.append((c_num, f'color{c_num}', sc))
c_num = max(colors.keys())
colors[c_num + 1] = (f'color{c_num + 1}', sc)
new_colors.append((c_num + 1, f'color{c_num + 1}', sc))
new_s.set_symbol(**{'symbol': item['symbol'].value, 'size': item['symbolsize'] / 10., 'color': c_num,
'fill color': c_num, 'fill pattern': 1})

20
src/gui_qt/io/fcbatchreader.py
View File

@ -1,5 +1,3 @@
from __future__ import annotations
import pathlib
from nmreval.io.fcbatchreader import FCReader
@ -33,10 +31,6 @@ class QFCReader(QtWidgets.QDialog, Ui_FCEval_dialog):
return super().eventFilter(src, evt)
def add_graphs(self, graphs: list[tuple[str, str]]):
for gid, graph_name in graphs:
self.graph_comboBox.addItem(graph_name, gid)
@QtCore.pyqtSlot(int, name='on_region_checkBox_stateChanged')
def use_region(self, state: int):
self.start_lineedit.setEnabled(state == QtCore.Qt.Checked)
@ -49,17 +43,17 @@ class QFCReader(QtWidgets.QDialog, Ui_FCEval_dialog):
infiles, _ = QtWidgets.QFileDialog.getOpenFileNames(caption='Select HDF files',
directory=str(self.path),
filter='HDF files (*.h5)')
if infiles:
self.listWidget.addItems(infiles)
self.label.setText(str(pathlib.Path(infiles[-1]).parent))
else:
infiles = QtWidgets.QFileDialog.getExistingDirectory(caption='Select input directory',
directory=str(self.path),
options=QtWidgets.QFileDialog.ShowDirsOnly)
infiles = [infiles] if infiles else infiles
if infiles:
self.listWidget.addItems(infiles)
self.path = pathlib.Path(infiles[-1]).parent
self.label.setText(str(self.path))
if infiles:
self.listWidget.addItem(infiles)
self.label.setText(str(pathlib.Path(infiles).parent))
@QtCore.pyqtSlot(name='on_savebutton_clicked')
def save_path(self):
@ -78,7 +72,7 @@ class QFCReader(QtWidgets.QDialog, Ui_FCEval_dialog):
self.close()
def read(self, items):
region = None
region = (None, None)
if self.region_box.isChecked():
start = None
if self.start_lineedit.text():

15
src/gui_qt/io/gracereader.py
View File

@ -4,7 +4,6 @@ from nmreval.lib.lines import LineStyle
from nmreval.lib.symbols import SymbolStyle
from nmreval.data.points import Points
from nmreval.io.graceeditor import GraceEditor
from nmreval.utils.text import convert
from ..Qt import QtCore, QtWidgets, QtGui
from .._py.gracereader import Ui_Dialog
@ -56,12 +55,8 @@ class QGraceReader(QtWidgets.QDialog, Ui_Dialog):
if ds is None:
continue
legend = gset.get_property('legend')
legend_str = convert(legend, old='agr', new='str') if legend is not None else ''
item_2 = QtWidgets.QTreeWidgetItem([f'Set {gset.idx} (Label: {legend_str}, '
item_2 = QtWidgets.QTreeWidgetItem([f'Set {gset.idx} (Label: {gset.get_property("legend")}, '
f'shape: {ds.shape})'])
item_2.setCheckState(0, QtCore.Qt.Checked)
item_2.setData(0, QtCore.Qt.UserRole, (graphs.idx, gset.idx))
item.addChild(item_2)
@ -94,12 +89,8 @@ class QGraceReader(QtWidgets.QDialog, Ui_Dialog):
item = iterator.value()
key = (item.data(0, QtCore.Qt.UserRole))
s = self._reader.dataset(*key)
label = self._reader.get_property(*key, 'legend')
if label is None:
label = ''
else:
label = label.replace('"', '')
label = convert(label, old='agr', new='str')
label = self._reader.get_property(*key, 'legend').replace('"', '')
# label = self._reader.graphs[key[0]].sets[key[1]]['legend'].replace('"', '')
sd = s.data
sd = np.atleast_2d(sd)
if s.type == 'xydy':

81
src/gui_qt/lib/__init__.py
View File

@ -1 +1,80 @@
from .enums import Relations
import sys
if sys.version_info < (3, 7):
HAS_IMPORTLIB_RESOURCE = False
from pkg_resources import resource_filename
else:
HAS_IMPORTLIB_RESOURCE = True
from importlib.resources import path
from ..Qt import QtGui, QtWidgets
# def get_path_importlib(package, resource):
# return path(package, resource)
#
#
# def _get_path_pkg(package, resource):
# return resource_filename(package, resource)
#
#
# if HAS_IMPORTLIB_RESOURCE:
# get_path = get_path_importlib
# else:
# get_path = _get_path_pkg
def make_action_icons(widget):
global HAS_IMPORTLIB_RESOURCE
icon_type = QtWidgets.QApplication.instance().theme
from json import loads
if HAS_IMPORTLIB_RESOURCE:
with path('resources.icons', 'icons.json') as fp:
with fp.open('r') as f:
icon_list = loads(f.read())
for ac, img in icon_list[widget.objectName()].items():
dirname = 'resources.icons.%s_light' % icon_type
with path(dirname, img+'.png') as imgpath:
icon = QtGui.QIcon()
icon.addPixmap(QtGui.QPixmap(str(imgpath)), QtGui.QIcon.Normal, QtGui.QIcon.Off)
getattr(widget, ac).setIcon(icon)
else:
with open(resource_filename('resources.icons', 'icons.json'), 'r') as f:
icon_list = loads(f.read())
for ac, img in icon_list[widget.objectName()].items():
dirname = 'resources.icons.%s_light' % icon_type
imgpath = resource_filename(dirname, img+'.png')
icon = QtGui.QIcon()
icon.addPixmap(QtGui.QPixmap(str(imgpath)), QtGui.QIcon.Normal, QtGui.QIcon.Off)
getattr(widget, ac).setIcon(icon)
def get_icon(icon_name):
try:
icon_type = QtWidgets.QApplication.instance().theme
except AttributeError:
icon_type = 'normal'
global HAS_IMPORTLIB_RESOURCE
if icon_name != 'logo':
dirname = f'resources.icons.{icon_type}_light'
else:
dirname = 'resources.icons'
if HAS_IMPORTLIB_RESOURCE:
with path(dirname, icon_name+'.png') as imgpath:
icon = QtGui.QIcon()
icon.addPixmap(QtGui.QPixmap(str(imgpath)), QtGui.QIcon.Normal, QtGui.QIcon.Off)
return icon
else:
imgpath = resource_filename(dirname, icon_name+'.png')
icon = QtGui.QIcon()
icon.addPixmap(QtGui.QPixmap(imgpath), QtGui.QIcon.Normal, QtGui.QIcon.Off)
return icon

2
src/gui_qt/lib/codeeditor.py
View File

@ -237,7 +237,7 @@ class CodeEditor(QtWidgets.QPlainTextEdit):
if block.isVisible() and (bottom >= evt.rect().top()):
number = str(block_number + 1)
painter.setPen(QtCore.Qt.black)
painter.drawText(0, int(top), self.current_linenumber.width() - 3, height,
painter.drawText(0, top, self.current_linenumber.width() - 3, height,
QtCore.Qt.AlignRight, number)
block = block.next()

8
src/gui_qt/lib/delegates.py
View File

@ -30,7 +30,7 @@ class PropertyDelegate(QtWidgets.QStyledItemDelegate):
rect = options.rect
rect.adjust(5, 0, -5, 0)
mid = int((rect.bottom()+rect.top()) / 2)
mid = (rect.bottom()+rect.top()) / 2
painter.drawLine(rect.left(), mid, rect.right(), mid)
painter.restore()
@ -42,7 +42,7 @@ class PropertyDelegate(QtWidgets.QStyledItemDelegate):
painter.setPen(pen)
pm = make_symbol_pixmap(r)
painter.drawPixmap(options.rect.topLeft()+QtCore.QPoint(3, int((options.rect.height()-pm.height())/2)), pm)
painter.drawPixmap(options.rect.topLeft()+QtCore.QPoint(3, (options.rect.height()-pm.height())/2), pm)
style = QtWidgets.QApplication.style()
text_rect = style.subElementRect(QtWidgets.QStyle.SE_ItemViewItemText, options, None)
@ -171,7 +171,7 @@ class LineStyleEditor(QtWidgets.QComboBox):
rect = painter.style().subControlRect(QtWidgets.QStyle.CC_ComboBox,
opt, QtWidgets.QStyle.SC_ComboBoxEditField, None)
rect.adjust(+10, 0, -10, 0)
mid = int((rect.bottom() + rect.top()) / 2)
mid = (rect.bottom() + rect.top()) / 2
painter.drawLine(rect.left(), mid, rect.right(), mid)
painter.end()
else:
@ -193,7 +193,7 @@ class LineStyleDelegate(QtWidgets.QStyledItemDelegate):
rect = option.rect
rect.adjust(+10, 0, -10, 0)
mid = int((rect.bottom()+rect.top()) / 2)
mid = (rect.bottom()+rect.top()) / 2
painter.drawLine(rect.left(), mid, rect.right(), mid)
else:
QtWidgets.QStyledItemDelegate.paint(self, painter, option, index)

8
src/gui_qt/lib/enums.py
View File

@ -1,8 +0,0 @@
from enum import IntEnum, auto
class Relations(IntEnum):
isFitOf = auto()
hasFit = auto()
isFitPartOf = auto()
hasFitPart = auto()

27
src/gui_qt/lib/forms.py
View File

@ -1,5 +1,3 @@
from typing import Any
from numpy import inf
from nmreval.utils.text import convert
@ -52,24 +50,19 @@ class QDelayWidget(QtWidgets.QWidget):
class LineEdit(QtWidgets.QLineEdit):
values_requested = QtCore.pyqtSignal()
replace_single_values = QtCore.pyqtSignal()
def __init__(self, parent=None):
super().__init__(parent=parent)
def contextMenuEvent(self, evt):
menu = self.createStandardContextMenu()
request_action = menu.addAction('Use numeric value of sets')
set_value_action = menu.addAction('Replace single set values')
request_action = menu.addAction('Use value of sets')
action = menu.exec(evt.globalPos())
if action == request_action:
self.values_requested.emit()
elif action == set_value_action:
self.replace_single_values.emit()
class LineEditPost(QtWidgets.QLineEdit):
values_requested = QtCore.pyqtSignal()
@ -411,21 +404,3 @@ class ElideComboBox(QtWidgets.QComboBox):
opt.currentText = painter.fontMetrics().elidedText(opt.currentText, QtCore.Qt.ElideRight, rect.width())
painter.drawControl(QtWidgets.QStyle.CE_ComboBoxLabel, opt)
class CheckCombobox(QtWidgets.QComboBox):
def addItem(self, text: str, userData: Any=None) -> None:
super().addItem(text, userData=userData)
item = self.model().item(self.count()-1)
item.setFlags(QtCore.Qt.ItemIsEnabled | QtCore.Qt.ItemIsUserCheckable)
item.setCheckState(QtCore.Qt.Checked)
def addItems(self, text):
for text_i in text:
self.addItem(text_i)
def isChecked(self, idx: int) -> bool:
return bool(self.model().item(idx).checkState())

53
src/gui_qt/lib/graph_items.py
View File

@ -1,53 +0,0 @@
from numpy import log10, arange, floor, ceil
from pyqtgraph import PlotWidget, PlotItem
__all__ = ['NMRPlotWidget', 'logTickValues']
class NMRPlotWidget(PlotWidget):
def __init__(self, *args, **kwargs):
super().__init__(*args, **kwargs)
for orient in ['top', 'bottom', 'left', 'right']:
# BAD HACK!!! but seems to work, see function for explanation
self.plotItem.getAxis(orient).logTickValues = logTickValues
class NMRPlotItem(PlotItem):
def __init__(self, *args, **kwargs):
super().__init__(*args, **kwargs)
for orient in ['top', 'bottom', 'left', 'right']:
self.plotItem.getAxis(orient).logTickValues = logTickValues
def logTickValues(minVal, maxVal, size, stdTicks):
# TODO FIND A BETTER SOLUTION!!!
# Sometimes minVal and maxVal are not log-scaled values and the loop from v1 to v2 is humongous,
# The minor list then fills the RAM completely and freezes everything
# Until there is a better solution, we overwrite this function for every AxesItem
# and do not draw minor ticks at all if there are too many
# start with the tick spacing given by tickValues().
# Any level whose spacing is < 1 needs to be converted to log scale
ticks = []
for (spacing, t) in stdTicks:
if spacing >= 1.0:
ticks.append((spacing, t))
if len(ticks) < 3:
v1 = int(floor(minVal))
v2 = int(ceil(maxVal))
# major = list(range(v1+1, v2))
minor = []
if v2 - v1 < 400:
for v in range(v1, v2):
minor.extend(v + log10(arange(1, 10)))
minor = [x for x in minor if minVal < x < maxVal]
ticks.append((None, minor))
return ticks

66
src/gui_qt/lib/iconloading.py
View File

@ -1,66 +0,0 @@
import sys
if sys.version_info < (3, 7):
HAS_IMPORTLIB_RESOURCE = False
from pkg_resources import resource_filename
else:
HAS_IMPORTLIB_RESOURCE = True
from importlib.resources import path
from ..Qt import QtGui, QtWidgets
def make_action_icons(widget):
global HAS_IMPORTLIB_RESOURCE
icon_type = QtWidgets.QApplication.instance().theme
from json import loads
if HAS_IMPORTLIB_RESOURCE:
with path('resources.icons', 'icons.json') as fp:
with fp.open('r') as f:
icon_list = loads(f.read())
for ac, img in icon_list[widget.objectName()].items():
dirname = 'resources.icons.%s_light' % icon_type
with path(dirname, img+'.png') as imgpath:
icon = QtGui.QIcon()
icon.addPixmap(QtGui.QPixmap(str(imgpath)), QtGui.QIcon.Normal, QtGui.QIcon.Off)
getattr(widget, ac).setIcon(icon)
else:
with open(resource_filename('resources.icons', 'icons.json'), 'r') as f:
icon_list = loads(f.read())
for ac, img in icon_list[widget.objectName()].items():
dirname = 'resources.icons.%s_light' % icon_type
imgpath = resource_filename(dirname, img+'.png')
icon = QtGui.QIcon()
icon.addPixmap(QtGui.QPixmap(str(imgpath)), QtGui.QIcon.Normal, QtGui.QIcon.Off)
getattr(widget, ac).setIcon(icon)
def get_icon(icon_name):
try:
icon_type = QtWidgets.QApplication.instance().theme
except AttributeError:
icon_type = 'normal'
global HAS_IMPORTLIB_RESOURCE
if icon_name != 'logo':
dirname = f'resources.icons.{icon_type}_light'
else:
dirname = 'resources.icons'
if HAS_IMPORTLIB_RESOURCE:
with path(dirname, icon_name+'.png') as imgpath:
icon = QtGui.QIcon()
icon.addPixmap(QtGui.QPixmap(str(imgpath)), QtGui.QIcon.Normal, QtGui.QIcon.Off)
return icon
else:
imgpath = resource_filename(dirname, icon_name+'.png')
icon = QtGui.QIcon()
icon.addPixmap(QtGui.QPixmap(imgpath), QtGui.QIcon.Normal, QtGui.QIcon.Off)
return icon

20
src/gui_qt/lib/listwidget.py
View File

@ -1,20 +0,0 @@
from ..Qt import QtWidgets, QtGui, QtCore
class QListWidgetSelect(QtWidgets.QListWidget):
"""
Extension of QListWidget to change the check state of all selected QListWidgetItems with space key
"""
def __init__(self, parent=None):
super().__init__(parent=parent)
def keyPressEvent(self, evt: QtGui.QKeyEvent):
if evt.key() == QtCore.Qt.Key.Key_Space:
for idx in self.selectedIndexes():
item = self.itemFromIndex(idx)
cs = item.checkState()
item.setCheckState(QtCore.Qt.CheckState.Unchecked if cs == QtCore.Qt.CheckState.Checked
else QtCore.Qt.CheckState.Checked)
else:
super().keyPressEvent(evt)

49
src/gui_qt/lib/mdiarea.py
View File

@ -1,49 +0,0 @@
from __future__ import annotations
from ..Qt import QtWidgets, QtCore
from nmreval.lib.logger import logger
from ..graphs.graphwindow import QGraphWindow
class MdiAreaTile(QtWidgets.QMdiArea):
def __init__(self, parent=None):
super().__init__(parent=parent)
def tileSubWindowsVertically(self):
window_list = self.subWindowList()
rect = QtCore.QRect(0, 0, self.width(), int(self.height() / len(window_list)))
pos = QtCore.QPoint(0, 0)
for win in window_list:
win.setGeometry(rect)
win.move(pos)
pos.setY(pos.y() + win.height())
def tileSubWindowsHorizontally(self):
window_list = self.subWindowList()
rect = QtCore.QRect(0, 0, int(self.width() / len(window_list)), self.height())
pos = QtCore.QPoint(0, 0)
for win in window_list:
win.setGeometry(rect)
win.move(pos)
pos.setX(pos.x() + win.width())
def addSubWindow(self, widget: QtWidgets.QWidget, flags: QtCore.Qt.WindowFlags = QtCore.Qt.WindowFlags()) -> QtWidgets.QMdiSubWindow | None:
subwindow = super().addSubWindow(widget)
subwindow.setOption(QtWidgets.QMdiSubWindow.RubberBandMove, True)
subwindow.setOption(QtWidgets.QMdiSubWindow.RubberBandResize, True)
subwindow.setMinimumHeight(240)
subwindow.setMinimumWidth(360)
return subwindow
def setActiveSubWidget(self, key: str):
for win in self.subWindowList():
wdgt = win.widget()
if isinstance(wdgt, QGraphWindow) and wdgt.id == key:
self.setActiveSubWindow(win)
break

87
src/gui_qt/lib/namespace.py
View File

@ -21,53 +21,36 @@ class Namespace:
self.top_levels = {}
if basic:
self.add_namespace(
{'x': (None, 'x values'),
'y': (None, 'x values'),
'y_err': (None, 'y error values'),
'fit': (None, 'dictionary of fit parameter', 'fit["PIKA"]'),
'np': (np, 'numpy module'),
},
parents=('Basic', 'General'),
)
self.add_namespace({'x': (None, 'x values'), 'y': (None, 'x values'), 'y_err': (None, 'y error values'),
'fit': (None, 'dictionary of fit parameter', 'fit["PIKA"]'), 'np': (np, 'numpy module')},
parents=('Basic', 'General'))
self.add_namespace(
{'sin': (np.sin, 'Sine', 'sin(PIKA)'),
'cos': (np.cos, 'Cosine', 'cos(PIKA)'),
'tan': (np.tan, 'Tangens', 'tan(PIKA)'),
'ln': (np.log, 'Natural Logarithm', 'ln(PIKA)'),
'log': (np.log10, 'Logarithm (base 10)', 'log(PIKA)'),
'exp': (np.exp, 'Exponential', 'exp(PIKA)'),
'sqrt': (np.sqrt, 'Root', 'sqrt(PIKA)'),
'lin_range': (np.linspace, 'N evenly spaced over interval [start, stop]', 'lin_range(start, stop, N)'),
'log_range': (np.geomspace, 'N evenly spaced (log-scale) over interval [start, stop]', 'lin_range(start, stop, N)'),
},
parents=('Basic', 'Functions'))
self.add_namespace(
{'max': (np.max, 'Maximum value', 'max(PIKA)'),
'min': (np.min, 'Minimum value', 'min(PIKA)'),
'argmax': (np.argmax, 'Index of maximum value', 'argmax(PIKA)'),
'argmin': (np.argmax, 'Index of minimum value', 'argmin(PIKA)'),
},
parents=('Basic', 'Values')),
self.add_namespace({'sin': (np.sin, 'Sine', 'sin(PIKA)'), 'cos': (np.cos, 'Cosine', 'cos(PIKA)'),
'tan': (np.tan, 'Tangens', 'tan(PIKA)'), 'ln': (np.log, 'Natural Logarithm', 'ln(PIKA)'),
'log': (np.log10, 'Logarithm (base 10)', 'log(PIKA)'),
'exp': (np.exp, 'Exponential', 'exp(PIKA)'), 'sqrt': (np.sqrt, 'Root', 'sqrt(PIKA)'),
'lin_range': (np.linspace, 'N evenly spaced over interval [start, stop]',
'lin_range(start, stop, N)'),
'log_range': (np.geomspace, 'N evenly spaced (log-scale) over interval [start, stop]',
'lin_range(start, stop, N)')},
parents=('Basic', 'Functions'))
self.add_namespace({'max': (np.max, 'Maximum value', 'max(PIKA)'),
'min': (np.min, 'Minimum value', 'min(PIKA)'),
'argmax': (np.argmax, 'Index of maximum value', 'argmax(PIKA)'),
'argmin': (np.argmax, 'Index of minimum value', 'argmin(PIKA)')},
parents=('Basic', 'Values'))
if const:
self.add_namespace(
{'e': (constants.e, 'e / As'),
'eps0': (constants.epsilon0, 'epsilon0 / As/Vm'),
'Eu': (constants.Eu,), 'h': (constants.h, 'h / eVs'),
'hbar': (constants.hbar, 'hbar / eVs'), 'kB': (constants.kB, 'kB / eV/K'),
'mu0': (constants.mu0, 'mu0 / Vs/Am'), 'NA': (constants.NA, 'NA / 1/mol'),
'pi': (constants.pi,), 'R': (constants.R, 'R / eV'),
},
parents=('Constants', 'Maybe useful'),
)
self.add_namespace({'e': (constants.e, 'e / As'), 'eps0': (constants.epsilon0, 'epsilon0 / As/Vm'),
'Eu': (constants.Eu,), 'h': (constants.h, 'h / eVs'),
'hbar': (constants.hbar, 'hbar / eVs'), 'kB': (constants.kB, 'kB / eV/K'),
'mu0': (constants.mu0, 'mu0 / Vs/Am'), 'NA': (constants.NA, 'NA / 1/mol'),
'pi': (constants.pi,), 'R': (constants.R, 'R / eV')},
parents=('Constants', 'Maybe useful'))
self.add_namespace(
{f'gamma["{k}"]': (v, k, f'gamma["{k}"]') for k, v in constants.gamma.items()},
parents=('Constants', 'Magnetogyric ratios (in 1/(sT))')
)
self.add_namespace({f'gamma["{k}"]': (v, k, f'gamma["{k}"]') for k, v in constants.gamma.items()},
parents=('Constants', 'Magnetogyric ratios (in 1/(sT))'))
if fitfuncs:
self.make_dict_from_fitmodule(models)
@ -121,18 +104,9 @@ class Namespace:
graph = namedtuple('graphs', ['s'])
sets = namedtuple('sets', ['x', 'y', 'y_err', 'value', 'fit'], defaults=(None,))
gamma = {}
gs = re.compile(r'g\[(\d+)].s\[(\d+)].(x|y(?:_err)*|value|fit)')
gamma_re = re.compile(r'gamma\["(\w+)"\]')
for k, v in self.namespace.items():
m = gamma_re.match(k)
if m:
gamma[m.group(1)] = v[0]
continue
m = gs.match(k)
if m:
if 'g' not in ret_dic:
@ -144,7 +118,7 @@ class Namespace:
gg = ret_dic['g'][int(g_num)]
if int(s_num) not in gg.s:
gg.s[int(s_num)] = sets('', '', '', '', {})
gg.s[int(s_num)] = sets('', '', '', '')
ss = gg.s[int(s_num)]
if pos == 'fit':
@ -156,11 +130,8 @@ class Namespace:
else:
ret_dic['g'][int(g_num)].s[int(s_num)] = ss._replace(**{pos: v[0]})
continue
ret_dic[k] = v[0]
ret_dic['gamma'] = gamma
else:
ret_dic[k] = v[0]
return ret_dic

37
src/gui_qt/lib/pg_objects.py
View File

@ -174,7 +174,6 @@ class PlotItem(PlotDataItem):
pen = self.opts['pen']
if isinstance(pen, tuple):
self.opts['linecolor'] = pen
self.opts['pen'] = mkPen(color=pen)
else:
c = pen.color()
self.opts['linecolor'] = c.red(), c.green(), c.blue()
@ -280,7 +279,7 @@ class PlotItem(PlotDataItem):
else:
self.scatter.hide()
def set_symbol(self, *, symbol=None, size=None, color=None):
def set_symbol(self, symbol=None, size=None, color=None):
if symbol is not None:
if isinstance(symbol, int):
self.setSymbol(SymbolStyle(symbol).to_str())
@ -314,13 +313,14 @@ class PlotItem(PlotDataItem):
self.opts['pen'] = pen
self.updateItems()
def set_line(self, *, style=None, width=None, color=None):
def set_line(self, style=None, width=None, color=None):
pen = self.opts['pen']
if pen is None:
pen = mkPen(style=QtCore.Qt.NoPen)
if width is not None:
pen.setWidthF(width)
if style is not None:
if isinstance(style, LineStyle):
style = style.value
@ -375,6 +375,7 @@ class PlotItem(PlotDataItem):
class RegionItem(LinearRegionItem):
def __init__(self, *args, **kwargs):
self.mode = kwargs.pop('mode', 'half')
super().__init__(*args, **kwargs)
self.logmode = False
@ -382,10 +383,6 @@ class RegionItem(LinearRegionItem):
if not hasattr(self, '_bounds') and hasattr(self, '_boundingRectCache'):
self._bounds = self._boundingRectCache
for l in self.lines:
# higher z for borderlines improves chances that you can move it when multiple regions overlap
l.setZValue(self.zValue() + 1)
def setLogMode(self, xmode, _):
if self.logmode == xmode:
return
@ -421,15 +418,6 @@ class RegionItem(LinearRegionItem):
else:
return region
def setRegion(self, region, use_log=False):
if self.logmode and use_log:
region = np.log10(region[0]), np.log10(region[1])
if not np.all(np.isfinite(region)):
raise ValueError(f'Invalid region limits ({region[0]}, {region[1]})')
else:
super().setRegion(region)
def boundingRect(self):
# overwrite to draw correct rect in logmode
@ -472,18 +460,11 @@ class LegendItemBlock(LegendItem):
def mouseDragEvent(self, ev):
if ev.button() == QtCore.Qt.LeftButton:
ev.accept()
dpos = ev.pos() - ev.lastPos()
upper_left = self.pos()
lower_right = self.pos()
lower_right.setX(lower_right.x() + self.width())
lower_right.setY(lower_right.y() + self.height())
vb_rect = self.parentItem().rect()
# upper left and lower right corner must be inside viewbox
if vb_rect.contains(upper_left + dpos) and vb_rect.contains(lower_right + dpos):
self.autoAnchor(upper_left + dpos)
pos = self.pos()
# upper left corner and a point a little more to the bottom right must be inside
if vb_rect.contains(pos+dpos) and vb_rect.contains(pos+dpos+QtCore.QPointF(20., 20.)):
self.autoAnchor(pos + dpos)
else:
self.autoAnchor(upper_left)
self.autoAnchor(pos)

110
src/gui_qt/lib/randpok.py Normal file
View File

@ -0,0 +1,110 @@
import os.path
import json
import urllib.request
import webbrowser
import random
from ..Qt import QtGui, QtCore, QtWidgets
from .._py.pokemon import Ui_Dialog
random.seed()
class QPokemon(QtWidgets.QDialog, Ui_Dialog):
def __init__(self, number=None, parent=None):
super().__init__(parent=parent)
self.setupUi(self)
self._js = json.load(open(os.path.join(path_to_module, 'utils', 'pokemon.json'), 'r'), encoding='UTF-8')
self._id = 0
if number is not None and number in range(1, len(self._js)+1):
poke_nr = f'{number:03d}'
self._id = number
else:
poke_nr = f'{random.randint(1, len(self._js)):03d}'
self._id = int(poke_nr)
self._pokemon = None
self.show_pokemon(poke_nr)
self.label_15.linkActivated.connect(lambda x: webbrowser.open(x))
self.buttonBox.clicked.connect(self.randomize)
self.next_button.clicked.connect(self.show_next)
self.prev_button.clicked.connect(self.show_prev)
def show_pokemon(self, nr):
self._pokemon = self._js[nr]
self.setWindowTitle('Pokémon: ' + self._pokemon['Deutsch'])
for i in range(self.tabWidget.count(), -1, -1):
print('i', self.tabWidget.count(), i)
try:
self.tabWidget.widget(i).deleteLater()
except AttributeError:
pass
for n, img in self._pokemon['Bilder']:
w = QtWidgets.QWidget()
vl = QtWidgets.QVBoxLayout()
l = QtWidgets.QLabel(self)
l.setAlignment(QtCore.Qt.AlignHCenter)
pixmap = QtGui.QPixmap()
try:
pixmap.loadFromData(urllib.request.urlopen(img, timeout=0.5).read())
except IOError:
l.setText(n)
else:
sc_pixmap = pixmap.scaled(256, 256, QtCore.Qt.KeepAspectRatio)
l.setPixmap(sc_pixmap)
vl.addWidget(l)
w.setLayout(vl)
self.tabWidget.addTab(w, n)
if len(self._pokemon['Bilder']) <= 1:
self.tabWidget.tabBar().setVisible(False)
else:
self.tabWidget.tabBar().setVisible(True)
self.tabWidget.adjustSize()
self.name.clear()
keys = ['National-Dex', 'Kategorie', 'Typ', 'Größe', 'Gewicht', 'Farbe', 'Link']
label_list = [self.pokedex_nr, self.category, self.poketype, self.weight, self.height, self.color, self.info]
for (k, label) in zip(keys, label_list):
v = self._pokemon[k]
if isinstance(v, list):
v = os.path.join('', *v)
if k == 'Link':
v = '<a href={}>{}</a>'.format(v, v)
label.setText(v)
for k in ['Deutsch', 'Japanisch', 'Englisch', 'Französisch']:
v = self._pokemon[k]
self.name.addItem(k + ': ' + v)
self.adjustSize()
def randomize(self, idd):
if idd.text() == 'Retry':
new_number = f'{random.randint(1, len(self._js)):03d}'
self._id = int(new_number)
self.show_pokemon(new_number)
else:
self.close()
def show_next(self):
new_number = self._id + 1
if new_number > len(self._js):
new_number = 1
self._id = new_number
self.show_pokemon(f'{new_number:03d}')
def show_prev(self):
new_number = self._id - 1
if new_number == 0:
new_number = len(self._js)
self._id = new_number
self.show_pokemon(f'{new_number:03d}')

100
src/gui_qt/lib/starter.py
View File

@ -1,100 +0,0 @@
from __future__ import annotations
import re
from shutil import copyfile
from pathlib import Path
import os
from configparser import ConfigParser
from importlib.resources import path as resource_path
from nmreval.configs import config_paths
from nmreval.lib.logger import logger
def make_starter(app_file: str | None):
if app_file is not None:
make_starter_appimage(Path(app_file))
else:
make_starter_src()
def make_starter_appimage(app_file: Path):
new_path = Path.home() / '.local' / 'bin'
if not new_path.exists():
new_path.mkdir(parents=True)
new_path /= app_file.name
if app_file != new_path:
app_file.rename(new_path)
create_desktop_file(new_path)
def make_starter_src():
home = Path.home()
p = Path.home()
for p in Path(__file__).parents:
if p.stem == 'src':
break
elif p == home:
break
success = p != Path.home()
if success:
bin_path = p.with_name('bin') / 'evaluate.py'
success = bin_path.exists()
if not success:
logger.warning('Location of evaluate.py could not be determined')
return False
create_desktop_file(bin_path)
def create_desktop_file(new_path: Path):
logo_path = config_paths() / 'logo.png'
if not logo_path.exists():
with resource_path('resources', 'logo.png') as fp:
copyfile(fp, logo_path)
desktop_entry = f"""\
[Desktop Entry]
Name=NMReval
Comment=Best program ever (maybe)
Exec={new_path}
Icon={logo_path}
Type=Application
Terminal=false
Categories=Science;NumericalAnalysis;Physics;DataVisualization;Other;
NoDisplay=false
"""
file_name = 'pkm.vogel.nmreval.desktop'
with Path('~/.local/share/applications/', file_name).expanduser().open('w') as f:
f.write(desktop_entry)
desktop_dir = get_xkg_user_dirs('desktop')
if desktop_dir is not None:
desk_file = Path(desktop_dir, file_name)
with desk_file.open('w') as f:
f.write(desktop_entry)
desk_file.chmod(0o755)
def get_xkg_user_dirs(dir_type: str) -> str | None:
xdg_conf_home = os.getenv('XDG_CONFIG_HOME') or str(Path.home() / '.config')
with Path(xdg_conf_home, 'user-dirs.dirs').open('r') as f:
conf_string = '[XDG_USER_DIRS]\n' + f.read()
conf_string = re.sub(r'\$HOME', str(Path.home()), conf_string)
conf_string = re.sub('"', '', conf_string)
config = ConfigParser()
config.read_string(conf_string)
return config['XDG_USER_DIRS'].get(f'xdg_{dir_type}_dir')
if __name__ == '__main__':
make_starter()

2
src/gui_qt/lib/stuff.py
View File

@ -6,7 +6,7 @@ import numpy as np
from ..Qt import QtWidgets, QtCore, QtGui
__all__ = ['Game', 'QMines']
__all__ = ['Game']
class Game(QtWidgets.QDialog):

2
src/gui_qt/lib/styles.py
View File

@ -1,4 +1,4 @@
from .iconloading import HAS_IMPORTLIB_RESOURCE
from . import HAS_IMPORTLIB_RESOURCE
from ..Qt import QtGui, QtWidgets, QtCore

15
src/gui_qt/lib/tables.py
View File

@ -28,17 +28,4 @@ class TreeWidget(QtWidgets.QTreeWidget):
continue
it.setCheckState(0, QtCore.Qt.Unchecked if it.checkState(0) == QtCore.Qt.Checked else QtCore.Qt.Checked)
else:
super().keyPressEvent(evt)
class TableWidget(QtWidgets.QTableWidget):
def keyPressEvent(self, evt: QtGui.QKeyEvent):
if evt.key() == QtCore.Qt.Key.Key_Space:
for idx in self.selectedIndexes():
item = self.itemFromIndex(idx)
cs = item.checkState()
item.setCheckState(QtCore.Qt.CheckState.Unchecked if cs == QtCore.Qt.CheckState.Checked
else QtCore.Qt.CheckState.Checked)
else:
super().keyPressEvent(evt)
super().keyPressEvent(evt)

88
src/gui_qt/lib/undos.py
View File

@ -1,10 +1,7 @@
from __future__ import annotations
import copy
from numpy import argsort
from . import Relations
from ..Qt import QtWidgets, QtCore
from ..data.container import FitContainer
from ..graphs.graphwindow import QGraphWindow
@ -87,21 +84,6 @@ class ShiftCommand(QtWidgets.QUndoCommand):
self.__data.apply('ls', self.__args)
class EditCommand(QtWidgets.QUndoCommand):
def __init__(self, data, *args):
super().__init__('Edit signal')
self.__data = data
self.__arguments = args
self.__original = copy.deepcopy(self.__data.data)
def undo(self):
self.__data.data = copy.deepcopy(self.__original)
def redo(self):
self.__data.edit_signal(*self.__arguments)
class NormCommand(QtWidgets.QUndoCommand):
def __init__(self, data, mode):
super().__init__('Normalize')
@ -234,69 +216,33 @@ class DeleteGraphCommand(QtWidgets.QUndoCommand):
class DeleteCommand(QtWidgets.QUndoCommand):
def __init__(self, container: dict, keys: list[str], graphs: dict, graphid: str,
signal1: QtCore.pyqtSignal, signal2: QtCore.pyqtSignal):
def __init__(self, container, key, signal1, signal2):
super().__init__('Delete data')
self.__container = container
self.__graph_container = graphs
self.__graph_key = graphid
self.__value = {}
for k in keys:
self.__value[k] = self.__container[k]
self.__keys = tuple(keys)
self.__value = self.__container[key]
self.__key = key
self.__signal_add = signal1
self.__signal_remove = signal2
def redo(self):
# stop graph from rescaling and updating legend
self.__graph_container[self.__graph_key].block(True)
self.__signal_remove.emit(list(self.__keys[::-1]))
for sid in self.__keys[::-1]:
val = self.__value[sid]
if isinstance(val, FitContainer):
try:
self.__container[val.fitted_key]._fits.remove(sid)
except KeyError:
pass
for (flag1, flag2) in ((Relations.isFitPartOf, Relations.hasFitPart), (Relations.hasFitPart, Relations.isFitPartOf)):
for related_item in val.get_relation(flag1):
try:
self.__container[related_item].remove_relation(flag2, sid)
except KeyError:
pass
del self.__container[sid]
self.__graph_container[self.__graph_key].block(False)
self.__signal_remove.emit(self.__key)
if isinstance(self.__value, FitContainer):
try:
self.__container[self.__value.fitted_key]._fits.remove(self.__key)
except KeyError:
pass
del self.__container[self.__key]
def undo(self):
# stop graph from rescaling and updating legend
self.__graph_container[self.__graph_key].block(True)
self.__container[self.__key] = self.__value
if isinstance(self.__value, FitContainer):
try:
self.__container[self.__value.fitted_key]._fits.append(self.__key)
except KeyError:
pass
for sid in self.__keys:
val = self.__value[sid]
self.__container[sid] = val
if isinstance(val, FitContainer):
try:
self.__container[val.fitted_key]._fits.append(sid)
except KeyError:
pass
for (flag1, flag2) in (('isFitPartOf', 'hasFitPartOf'), ('hasFitPartOf', 'isFitPartOf')):
for related_item in val.get_relation(flag1):
try:
self.__container[related_item].add_relation(flag2, sid)
except KeyError:
pass
self.__signal_add.emit(list(self.__keys), self.__graph_key)
self.__graph_container[self.__graph_key].block(False)
self.__signal_add.emit([self.__key], self.__value.graph)
class EvalCommand(QtWidgets.QUndoCommand):

179
src/gui_qt/lib/utils.py
View File

@ -1,7 +1,7 @@
from __future__ import annotations
import os
import urllib.request
import sys
from functools import lru_cache
from os import getenv, stat
from os.path import exists
import hashlib
@ -9,7 +9,8 @@ import subprocess
from datetime import datetime
from contextlib import contextmanager
from pathlib import Path
from urllib.error import HTTPError
import requests
from numpy import linspace
from scipy.interpolate import interp1d
@ -58,13 +59,13 @@ class RdBuCMap:
elif val < self.min:
col = QtGui.QColor.fromRgb(*RdBuCMap._rdbu[-1])
else:
col = QtGui.QColor.fromRgb(*(int(self.spline[i](val)) for i in range(3)))
col = QtGui.QColor.fromRgb(*(float(self.spline[i](val)) for i in range(3)))
return col
class UpdateDialog(QtWidgets.QDialog):
startDownload = QtCore.pyqtSignal(tuple)
startDownload = QtCore.pyqtSignal(list)
def __init__(self, filename: str = None, parent=None):
super().__init__(parent=parent)
@ -74,6 +75,7 @@ class UpdateDialog(QtWidgets.QDialog):
filename = getenv('APPIMAGE')
self._appfile = filename
self.success = False
self.updater = Updater()
self.thread = QtCore.QThread(self)
@ -114,28 +116,28 @@ class UpdateDialog(QtWidgets.QDialog):
# Download zsync file of latest Appimage, look for SHA-1 hash and compare with hash of AppImage
is_updateble, m_time_file, m_time_zsync = self.updater.get_update_information(filename)
label_text = ''
if is_updateble is None:
label_text += '<p>Could not determine if this version is newer, please update manually (if necessary).</p>'
dialog_bttns = QtWidgets.QDialogButtonBox.Close
elif is_updateble:
label_text += '<p>Newer version available. Press Ok to download new version, Cancel to ignore.</p>'
dialog_bttns = QtWidgets.QDialogButtonBox.Ok | QtWidgets.QDialogButtonBox.Cancel
else:
label_text += '<p>Version may be already up-to-date.</p>'
dialog_bttns = QtWidgets.QDialogButtonBox.Close
if m_time_zsync is None:
label_text += '<p>Creation date of remote version is unknown.</p>'
label_text = '<p>Retrieval of version information failed.</p>' \
'<p>Please try later (or complain to people that it does not work).</p>'
dialog_bttns = QtWidgets.QDialogButtonBox.Close
else:
label_text += f'<p>Date of most recent AppImage: {m_time_zsync.strftime("%d %B %Y %H:%M")}</p>'
label_text = f'<p>Date of most recent AppImage: {m_time_zsync.strftime("%d %B %Y %H:%M")}</p>'
if m_time_file is None:
label_text += 'No AppImage file found, press Ok to download latest version.'
dialog_bttns = QtWidgets.QDialogButtonBox.Ok | QtWidgets.QDialogButtonBox.Close
else:
label_text += f'<p>Date of used AppImage: {m_time_file.strftime("%d %B %Y %H:%M")}</p>'
if m_time_file is None:
label_text += 'No AppImage file found, press Ok to download latest version.'
dialog_bttns = QtWidgets.QDialogButtonBox.Ok|QtWidgets.QDialogButtonBox.Close
else:
label_text += f'<p>Date of used AppImage: {m_time_file.strftime("%d %B %Y %H:%M")}</p>'
if is_updateble is None:
self.status.setText('Could not determine if this version is newer, please update manually (if necessary).')
dialog_bttns = QtWidgets.QDialogButtonBox.Close
elif is_updateble:
self.status.setText(f'<p>Newer version available. Press Ok to download new version, Cancel to ignore.')
dialog_bttns = QtWidgets.QDialogButtonBox.Ok|QtWidgets.QDialogButtonBox.Cancel
else:
self.status.setText(f'Version may be already up-to-date.')
dialog_bttns = QtWidgets.QDialogButtonBox.Close
self.label.setText(label_text)
self.dialog_button.setStandardButtons(dialog_bttns)
@ -143,20 +145,24 @@ class UpdateDialog(QtWidgets.QDialog):
@QtCore.pyqtSlot()
def update_appimage(self):
if self._appfile is None:
args = (self.updater.zsync_url,)
args = [self.updater.zsync_url]
else:
# this breaks the download for some reason
args = (self.updater.zsync_url, self._appfile)
args = ['-i', self._appfile, self.updater.zsync_url]
args = [self.updater.zsync_url]
self.dialog_button.setEnabled(False)
self.startDownload.emit(args)
self.status.show()
@QtCore.pyqtSlot(int, str)
def finish_update(self, retcode: int, file_loc: str):
@QtCore.pyqtSlot(int)
def finish_update(self, retcode: int):
# print('finished with', retcode)
self.success = retcode == 0
if retcode == 0:
self.status.setText(f'Download complete.New AppImage lies in <p><em>{file_loc}</em>.</p>')
self.status.setText('Download complete.')
else:
self.status.setText(f'Download failed :( with return code {retcode}.')
self.dialog_button.setStandardButtons(QtWidgets.QDialogButtonBox.Close)
@ -166,85 +172,78 @@ class UpdateDialog(QtWidgets.QDialog):
self.thread.quit()
self.thread.wait()
if self.success:
appname = self.updater.get_zsync()[2]
if self._appfile is not None:
appimage_path = appname
old_version = Path(self._appfile).rename(self._appfile+'.old')
appimage_path = Path(appimage_path).replace(self._appfile)
else:
appimage_path = Path().cwd() / appname
# rename to version-agnostic name
appimage_path = appimage_path.rename('NMReval.AppImage')
appimage_path.chmod(appimage_path.stat().st_mode | 73) # 73 = 0o111 = a+x
_ = QtWidgets.QMessageBox.information(self, 'Complete',
f'New AppImage available at<br>{appimage_path}')
super().closeEvent(evt)
class Downloader(QtCore.QObject):
started = QtCore.pyqtSignal()
finished = QtCore.pyqtSignal(int, str)
finished = QtCore.pyqtSignal(int)
progressChanged = QtCore.pyqtSignal(str)
@QtCore.pyqtSlot(tuple)
def run_download(self, args: tuple[str]):
status = 0
appimage_location = args[0][:-6]
logger.info(f'Download {appimage_location}')
if len(args) == 2:
new_file = Path(args[1])
else:
new_file = Path.home() / 'Downloads' / 'NMReval-latest-x86_64.AppImage'
@QtCore.pyqtSlot(list)
def run_download(self, args: list[str]):
logger.info(f'Download with args {args}')
process = subprocess.Popen(['zsync'] + args, stdout=subprocess.PIPE, stderr=subprocess.PIPE, bufsize=1, universal_newlines=True)
while True:
nextline = process.stdout.readline().strip()
if nextline:
self.progressChanged.emit(nextline)
if new_file.exists():
os.rename(new_file, new_file.with_suffix('.AppImage.old'))
# line = process.stderr.readline().strip()
try:
with urllib.request.urlopen(appimage_location) as response:
with new_file.open('wb') as f:
f.write(response.read())
if process.poll() is not None:
break
new_file.chmod(0o755)
except HTTPError as e:
logger.exception(f'Download failed with {e}')
status = 3
except Exception as e:
logger.exception(f'Download failed with {e.args}')
status = 1
if status != 0:
logger.warning('Download failed, restore previous AppImage')
try:
os.rename(new_file.with_suffix('.AppImage.old'), new_file)
except FileNotFoundError:
pass
# zsync does not support https
self.finished.emit(status, str(new_file))
self.finished.emit(process.returncode)
class Updater:
host = 'gitea.pkm.physik.tu-darmstadt.de/api/packages/IPKM/generic/NMReval/latest/'
host = 'mirror.infra.pkm'
bucket = 'nmreval'
version = 'NMReval-latest-x86_64'
@property
def zsync_url(self):
return f'https://{Updater.host}/{Updater.version}.AppImage.zsync'
return f'http://{Updater.host}/{Updater.bucket}/{Updater.version}.AppImage.zsync'
@staticmethod
@lru_cache(3)
def get_zsync():
url_zsync = f'https://{Updater.host}/{Updater.version}.AppImage.zsync'
url_zsync = f'http://{Updater.host}/{Updater.bucket}/{Updater.version}.AppImage.zsync'
m_time_zsync = None
checksum_zsync = None
zsync_file = None
filename = None
try:
with urllib.request.urlopen(url_zsync) as response:
zsync_file = response.read()
except HTTPError as e:
logger.error(f'Request for zsync returned code {e}')
except Exception as e:
logger.exception(f'Download of zsync failed with exception {e.args}')
response = requests.get(url_zsync)
if response.status_code == requests.codes['\o/']:
zsync_file = response.content
else:
logger.error(f'Request for zsync returned code {response.statuse_code}')
except Exception:
logger.exception('Download of zsync failed')
if zsync_file is not None:
for line in zsync_file.split(b'\n'):
try:
kw, val = line.split(b': ')
time_string = str(val, encoding='utf-8')
time_format = '%a, %d %b %Y %H:%M:%S %z'
if kw == b'MTime':
try:
m_time_zsync = datetime.strptime(time_string, time_format).astimezone(None)
except ValueError:
logger.warning(f'zsync time "{time_string}" does not match "{time_format}"')
m_time_zsync = datetime.strptime(str(val, encoding='utf-8'), '%a, %d %b %Y %H:%M:%S %z').astimezone(None)
elif kw == b'SHA-1':
checksum_zsync = str(val, encoding='utf-8')
elif kw == b'Filename':
@ -268,8 +267,6 @@ class Updater:
m_time_file = datetime.fromtimestamp(stat_mtime).replace(microsecond=0)
with open(filename, 'rb') as f:
checksum_file = hashlib.sha1(f.read()).hexdigest()
if checksum_file is None:
logger.warning('No checksum for AppImage calculated')
return m_time_file, checksum_file
@ -278,10 +275,30 @@ class Updater:
m_time_zsync, checksum_zsync, appname = Updater.get_zsync()
m_time_file, checksum_file = Updater.get_appimage_info(filename)
logger.debug(f'zsync information {m_time_zsync}, {checksum_zsync}, {appname}')
logger.debug(f'file information {m_time_file}, {checksum_file}')
logger.info(f'zsync information {m_time_zsync}, {checksum_zsync}, {appname}')
logger.info(f'file information {m_time_file}, {checksum_zsync}')
if not ((checksum_file is not None) and (checksum_zsync is not None)):
return None, m_time_file, m_time_zsync
else:
return checksum_file != checksum_zsync, m_time_file, m_time_zsync
def open_bug_report():
form_entries = {
'description': 'Please state the nature of the medical emergency.',
'title': 'Everything is awesome?',
'assign[0]': 'dominik',
'subscribers[0]': 'dominik',
'tag': 'nmreval',
'priority': 'normal',
'status': 'open',
}
full_url = 'https://chaos3.fkp.physik.tu-darmstadt.de/maniphest/task/edit/?'
for k, v in form_entries.items():
full_url += f'{k}={v}&'
full_url.replace(' ', '+')
import webbrowser
webbrowser.open(full_url)

304
src/gui_qt/main/mainwindow.py
View File

@ -1,7 +1,7 @@
from __future__ import annotations
import datetime
import os
import pathlib
import re
from pathlib import Path
@ -9,23 +9,18 @@ from numpy import geomspace, linspace
from pyqtgraph import ViewBox
from nmreval.configs import *
from nmreval.lib.logger import logger
from nmreval.io.sessionwriter import NMRWriter
from .management import UpperManagement
from ..Qt import QtGui, QtPrintSupport
from ..data.shift_graphs import QShift
from ..data.signaledit import QPreviewDialog, QBaselineDialog
from ..dsc.glass_dialog import TgCalculator
from ..data.signaledit import QApodDialog, QBaselineDialog, QPhasedialog
from ..fit.result import FitExtension, QFitResult
from ..graphs.graphwindow import QGraphWindow
from ..graphs.movedialog import QMover
from ..io.fcbatchreader import QFCReader
from ..io.filedialog import *
from ..lib.iconloading import make_action_icons, get_icon
from ..lib import get_icon, make_action_icons
from ..lib.pg_objects import RegionItem
from ..lib.starter import make_starter
from ..math.binning import BinningWindow
from ..math.evaluation import QEvalDialog
from ..math.interpol import InterpolDialog
from ..math.mean_dialog import QMeanTimes
@ -33,7 +28,7 @@ from ..math.smooth import QSmooth
from ..nmr.coupling_calc import QCoupCalcDialog
from ..nmr.t1_from_tau import QRelaxCalc
from .._py.basewindow import Ui_BaseWindow
from ..lib.utils import UpdateDialog, Updater
from ..lib.utils import UpdateDialog, open_bug_report, Updater
class NMRMainWindow(QtWidgets.QMainWindow, Ui_BaseWindow):
@ -58,8 +53,6 @@ class NMRMainWindow(QtWidgets.QMainWindow, Ui_BaseWindow):
self.fitpreview = []
self._fit_plot_id = None
self.savefitdialog = None
self._tg_dialog = None
self.fitresult_dialog = None
self.eval = None
self.editor = None
@ -70,6 +63,7 @@ class NMRMainWindow(QtWidgets.QMainWindow, Ui_BaseWindow):
self._block_window_change = False
self.fname = None
self.tim = QtCore.QTimer()
self.settings = QtCore.QSettings('NMREVal', 'settings')
self._init_gui()
@ -79,18 +73,6 @@ class NMRMainWindow(QtWidgets.QMainWindow, Ui_BaseWindow):
if Updater.get_update_information(os.getenv('APPIMAGE'))[0]:
self.look_for_update()
self.check_for_backup()
self.__timer = QtCore.QTimer()
self.__backup_path = config_paths() / f'{datetime.datetime.now().strftime("%Y-%m-%d_%H%M%S")}.nmr'
self.__timer.start(3*60*1000) # every three minutes
self.__timer.timeout.connect(self._autosave)
self.fit_timer = QtCore.QTimer()
self.fit_timer.setInterval(500)
self.fit_timer.timeout.connect(
lambda: self.status.setText(f'Fit running... ({self.management.fitter.step} evaluations)'))
def _init_gui(self):
self.setupUi(self)
make_action_icons(self)
@ -121,10 +103,7 @@ class NMRMainWindow(QtWidgets.QMainWindow, Ui_BaseWindow):
self.mousepos = QtWidgets.QLabel('')
self.status = QtWidgets.QLabel('')
# noinspection PyUnresolvedReferences
self.statusBar.addWidget(self.status)
# noinspection PyUnresolvedReferences
self.statusBar.addWidget(self.mousepos)
self.fitregion = RegionItem()
@ -135,7 +114,7 @@ class NMRMainWindow(QtWidgets.QMainWindow, Ui_BaseWindow):
self.datawidget.management = self.management
self.integralwidget.management = self.management
# self.drawingswidget.graphs = self.management.graphs
self.drawingswidget.graphs = self.management.graphs
self.ac_group = QtWidgets.QActionGroup(self)
self.ac_group.addAction(self.action_lm_fit)
@ -160,23 +139,20 @@ class NMRMainWindow(QtWidgets.QMainWindow, Ui_BaseWindow):
self.actionUndo.setIcon(icon)
self.menuData.insertAction(self.actionRedo, self.actionUndo)
# # self.actionSave.triggered.connect(lambda: self.management.save('/autohome/dominik/nmreval/testdata/test.nmr', ''))
# self.actionSave.triggered.connect(self.save)
self.action_save_fit_parameter.triggered.connect(self.save_fit_parameter)
self.ac_group2.triggered.connect(self.change_fit_limits)
self.t1action.triggered.connect(lambda: self._show_tab('t1_temp'))
self.action_edit.triggered.connect(self.do_preview)
self.action_edit.triggered.connect(lambda: self._show_tab('signal'))
self.actionPick_position.triggered.connect(lambda: self._show_tab('pick'))
self.actionIntegration.triggered.connect(lambda: self._show_tab('integrate'))
self.action_FitWidget.triggered.connect(lambda: self._show_tab('fit'))
self.action_draw_object.triggered.connect(lambda: self._show_tab('drawing'))
self.action_new_set.triggered.connect(self.management.create_empty)
self.actionDelete_window.triggered.connect(self.management.delete_sets)
self.actionCascade_windows.triggered.connect(self.area.cascadeSubWindows)
self.actionTile.triggered.connect(self.area.tileSubWindows)
self.actionTileHorizontal.triggered.connect(self.area.tileSubWindowsHorizontally)
self.actionTileVertical.triggered.connect(self.area.tileSubWindowsVertically)
self.datawidget.keyChanged.connect(self.management.change_keys)
self.datawidget.tree.deleteItem.connect(self.management.delete_sets)
self.datawidget.tree.moveItem.connect(self.management.move_sets)
@ -190,8 +166,7 @@ class NMRMainWindow(QtWidgets.QMainWindow, Ui_BaseWindow):
self.datawidget.tree.saveFits.connect(self.save_fit_parameter)
self.datawidget.tree.extendFits.connect(self.extend_fit)
self.management.newData[list, str].connect(self.show_new_data)
self.management.newData[list, str, bool].connect(self.show_new_data)
self.management.newData.connect(self.show_new_data)
self.management.newGraph.connect(self.new_graph)
self.management.dataChanged.connect(self.update_data)
self.management.deleteData.connect(self.delete_data)
@ -204,7 +179,7 @@ class NMRMainWindow(QtWidgets.QMainWindow, Ui_BaseWindow):
self.fit_dialog._management = self.management
self.fit_dialog.preview_emit.connect(self.show_fit_preview)
self.fit_dialog.fitStartSig.connect(self.start_fit)
self.fit_dialog.abortFit.connect(lambda: self.management.stopFit.emit())
self.fit_dialog.abortFit.connect(lambda : self.management.stopFit.emit())
self.movedialog.moveData.connect(self.move_sets)
self.movedialog.copyData.connect(self.management.copy_sets)
@ -214,7 +189,7 @@ class NMRMainWindow(QtWidgets.QMainWindow, Ui_BaseWindow):
self.t1tauwidget.newData.connect(self.management.add_new_data)
self.editsignalwidget.do_something.connect(self.management.apply)
# self.editsignalwidget.preview_triggered.connect(self.do_preview)
self.editsignalwidget.preview_triggered.connect(self.do_preview)
self.action_sort_pts.triggered.connect(lambda: self.management.apply('sort', ()))
self.action_calc_eps_derivative.triggered.connect(self.management.bds_deriv)
@ -242,9 +217,7 @@ class NMRMainWindow(QtWidgets.QMainWindow, Ui_BaseWindow):
self.action_norm_area.triggered.connect(lambda: self.management.apply('norm', ('area',)))
self.action_cut.triggered.connect(lambda: self.management.cut())
self.actionConcatenate_sets.triggered.connect(lambda: self.management.cat())
self.management.graphs.valueChanged.connect(self.update_graph_list)
self.actionConcatenate_sets.triggered.connect(lambda : self.management.cat())
@QtCore.pyqtSlot(name='on_action_open_triggered')
def open(self):
@ -269,7 +242,6 @@ class NMRMainWindow(QtWidgets.QMainWindow, Ui_BaseWindow):
@QtCore.pyqtSlot(name='on_actionOpen_FC_triggered')
def read_fc(self):
reader = QFCReader(path=self.path, parent=self)
reader.add_graphs(self.management.graphs.list())
reader.data_read.connect(self.management.add_new_data)
reader.exec()
@ -290,11 +262,10 @@ class NMRMainWindow(QtWidgets.QMainWindow, Ui_BaseWindow):
selected_filter = save_dialog.selectedNameFilter()
if savefile is not None:
self.path = savefile.parent
use_underscore = save_dialog.checkBox.isChecked()
self.management.save(savefile, selected_filter, strip_spaces=use_underscore)
param_outfile = re.sub(r'[_\s-]?<label>[_\s-]?', '', savefile.stem)
param_outfile = re.sub('[_\s-]?<label>[_\s-]?', '', savefile.stem)
bad_character = r'/*<>\|:"'
for c in bad_character:
@ -336,15 +307,10 @@ class NMRMainWindow(QtWidgets.QMainWindow, Ui_BaseWindow):
return w.id
@QtCore.pyqtSlot(list, str)
@QtCore.pyqtSlot(list, str, bool)
def show_new_data(self, sets: list, graph: str, skip_change: bool = False):
def show_new_data(self, sets: list, graph: str):
if len(sets) == 0:
return
prev_graph = ''
if skip_change:
prev_graph = self.management.current_graph
if graph == '':
graph = self.new_graph()
@ -353,21 +319,22 @@ class NMRMainWindow(QtWidgets.QMainWindow, Ui_BaseWindow):
for idd in sets:
new_item = self.management[idd]
self.datawidget.blockSignals(True)
self.datawidget.add_item(new_item.id, new_item.name, new_item.value, graph, update=False)
self.datawidget.add_item(new_item.id, new_item.name, graph)
self.datawidget.blockSignals(False)
self.datawidget.tree.update_indexes()
# if graph == self.fit_dialog.connected_figure:
# self.fit_dialog.load(self.management.graphs.active(graph))
if skip_change:
self.area.setActiveSubWidget(prev_graph)
if graph == self.fit_dialog.connected_figure:
self.fit_dialog.load(self.management.graphs.active(graph))
if self.valuewidget.isVisible():
self.valuewidget(self.management.graphs.tree())
@QtCore.pyqtSlot(name='on_actionDelete_window_triggered')
def delete_windows(self):
self.management.delete_sets()
@QtCore.pyqtSlot(str)
def remove_graph(self, gid: str):
self.datawidget.remove_item([gid])
self.datawidget.remove_item(gid)
val_figure = self.valuewidget.connected_figure
self.valuewidget.remove_graph()
@ -380,15 +347,10 @@ class NMRMainWindow(QtWidgets.QMainWindow, Ui_BaseWindow):
if wdgt == self.current_graph_widget:
if self.ptsselectwidget.connected_figure == gid:
self.ptsselectwidget.connected_figure = None
for line in self.ptsselectwidget.pts_lines:
self.current_graph_widget.remove_external(line)
self.tabWidget.removeTab(self.tabWidget.indexOf(self.ptsselectwidget))
if self.t1tauwidget.connected_figure == gid:
self.t1tauwidget.connected_figure = None
self.current_graph_widget.add_external(self.t1tauwidget.min_pos)
self.current_graph_widget.add_external(self.t1tauwidget.parabola)
self.tabWidget.removeTab(self.tabWidget.indexOf(self.t1tauwidget))
if self.fit_dialog.connected_figure == gid:
@ -397,14 +359,12 @@ class NMRMainWindow(QtWidgets.QMainWindow, Ui_BaseWindow):
self.current_graph_widget.remove_external(item)
if val_figure == gid:
self.current_graph_widget.remove_external(self.valuewidget.selection_real)
self.current_graph_widget.remove_external(self.valuewidget.selection_imag)
self.tabWidget.setCurrentIndex(0)
self.current_graph_widget.enable_picking(False)
self.current_graph_widget = None
self.management.current_graph = None
self.management.current_graph = ''
self.current_plotitem = None
wdgt.setParent(None)
@ -415,6 +375,7 @@ class NMRMainWindow(QtWidgets.QMainWindow, Ui_BaseWindow):
break
if w is not None:
self.area.removeSubWindow(w)
w.close()
@ -427,12 +388,6 @@ class NMRMainWindow(QtWidgets.QMainWindow, Ui_BaseWindow):
if self.area.subWindowList():
self.area.activateNextSubWindow()
@QtCore.pyqtSlot()
def update_graph_list(self):
graph_list = self.management.graphs.list()
self.t1tauwidget.set_graphs(graph_list)
self.ptsselectwidget.set_graphs(graph_list)
@QtCore.pyqtSlot(str)
def set_graph(self, key: str):
w = self.management.graphs[key]
@ -450,7 +405,7 @@ class NMRMainWindow(QtWidgets.QMainWindow, Ui_BaseWindow):
self.datawidget.blockSignals(False)
w.mousePositionChanged.connect(self.mousemoved)
w.aboutToClose.connect(self.management.delete_sets)
w.aboutToClose.connect(self.delete_windows)
w.positionClicked.connect(self.point_selected)
w.show()
@ -461,36 +416,42 @@ class NMRMainWindow(QtWidgets.QMainWindow, Ui_BaseWindow):
@QtCore.pyqtSlot(QtWidgets.QMdiSubWindow, name='on_area_subWindowActivated')
def change_window(self, wd):
""" Called every time focus moves from or to a subwindow. Returns None if current focus is not on a subwindow"""
if wd is None:
return
if wd is not None:
if self.current_graph_widget is not None:
self.current_graph_widget.closable = True
if self.current_graph_widget is not None:
self.current_graph_widget.closable = True
if self.ptsselectwidget.isVisible():
self._select_ptswidget(False, False, False)
if self.fit_dialog.isVisible():
self._select_fitwidget(False, False)
self.current_graph_widget = wd.widget()
self.management.current_graph = wd.widget().id
self.current_plotitem = self.current_graph_widget.graphic
self.change_mouse_mode(self.actionMouse_behaviour.isChecked())
pick = False
block = False
if self.ptsselectwidget.isVisible():
self._select_ptswidget(False, False, False)
pick, block = self._select_ptswidget(True, pick, block)
if self.fit_dialog.isVisible():
self._select_fitwidget(False, False)
block = self._select_fitwidget(True, block)
self.current_graph_widget = wd.widget()
self.management.current_graph = wd.widget().id
self.current_plotitem = self.current_graph_widget.graphic
self._set_pick_block(pick, block)
self.change_mouse_mode(self.actionMouse_behaviour.isChecked())
self.datawidget.tree.blockSignals(True)
self.datawidget.tree.highlight(self.management.current_graph)
self.datawidget.tree.blockSignals(False)
pick = False
block = False
if self.ptsselectwidget.isVisible():
pick, block = self._select_ptswidget(True, pick, block)
if self.fit_dialog.isVisible():
block = self._select_fitwidget(True, block)
self._set_pick_block(pick, block)
self.datawidget.tree.blockSignals(True)
self.datawidget.tree.highlight(self.management.current_graph)
self.datawidget.tree.blockSignals(False)
@QtCore.pyqtSlot(name='on_actionCascade_windows_triggered')
@QtCore.pyqtSlot(name='on_actionTile_triggered')
def change_window_size(self):
if self.sender() == self.actionCascade_windows:
self.area.cascadeSubWindows()
elif self.sender() == self.actionTile:
self.area.tileSubWindows()
@QtCore.pyqtSlot(name='on_actionChange_datatypes_triggered')
def type_change_dialog(self):
@ -514,6 +475,7 @@ class NMRMainWindow(QtWidgets.QMainWindow, Ui_BaseWindow):
'signal': (self.editsignalwidget, 'Signals'),
'pick': (self.ptsselectwidget, 'Pick points'),
'fit': (self.fit_dialog, 'Fit'),
'drawing': (self.drawingswidget, 'Draw'),
'integrate': (self.integralwidget, 'Integrate'),
}[mode]
@ -549,6 +511,7 @@ class NMRMainWindow(QtWidgets.QMainWindow, Ui_BaseWindow):
self._select_valuewidget(widget == self.valuewidget)
pick_required, block_window = self._select_t1tauwidget(widget == self.t1tauwidget, pick_required, block_window)
block_window = self._select_fitwidget(widget == self.fit_dialog, block_window)
self._select_drawingswidget(widget == self.drawingswidget)
pick_required = self._select_integralwidget(widget == self.integralwidget, pick_required, block_window)
self._set_pick_block(pick_required, block_window)
@ -581,9 +544,8 @@ class NMRMainWindow(QtWidgets.QMainWindow, Ui_BaseWindow):
self.management.graphs[current_graph].add_external(self.valuewidget.selection_imag)
else:
if self.valuewidget.connected_figure is not None:
conn_fig = self.valuewidget.connected_figure
self.management.graphs[conn_fig].remove_external(self.valuewidget.selection_real)
self.management.graphs[conn_fig].remove_external(self.valuewidget.selection_imag)
self.management.graphs[self.valuewidget.connected_figure].remove_external(self.valuewidget.selection_real)
self.management.graphs[self.valuewidget.connected_figure].remove_external(self.valuewidget.selection_imag)
def _select_integralwidget(self, onoff: bool, pick_required: bool, block_window: bool) -> tuple[bool, bool]:
if self.current_graph_widget is None:
@ -637,10 +599,17 @@ class NMRMainWindow(QtWidgets.QMainWindow, Ui_BaseWindow):
return pick_required, block_window
def _select_drawingswidget(self, onoff):
if onoff:
if self.drawingswidget.graphs is None:
self.drawingswidget.graphs = self.management.graphs
self.drawingswidget.update_tree()
else:
self.drawingswidget.clear()
@QtCore.pyqtSlot(str)
def get_data(self, key: str):
if hasattr(self.sender(), 'set_data'):
self.sender().set_data(self.management[key])
self.sender().set_data(self.management[key])
@QtCore.pyqtSlot(name='on_actionCalculateT1_triggered')
def show_t1calc_dialog(self):
@ -714,14 +683,6 @@ class NMRMainWindow(QtWidgets.QMainWindow, Ui_BaseWindow):
self.eval.exec()
@QtCore.pyqtSlot(name='on_actionBinning_triggered')
def open_binning(self):
dialog = BinningWindow(self)
res = dialog.exec()
if res:
digits = float(dialog.spinbox.text())
self.management.binning(digits)
@QtCore.pyqtSlot(name='on_actionDerivation_triggered')
# @QtCore.pyqtSlot(name='on_actionIntegration_triggered')
@QtCore.pyqtSlot(name='on_actionFilon_triggered')
@ -758,11 +719,10 @@ class NMRMainWindow(QtWidgets.QMainWindow, Ui_BaseWindow):
self.datawidget.set_name(sid, self.management[sid].name)
@QtCore.pyqtSlot(list)
def delete_data(self, sid: list[str]):
for key in sid:
if self.valuewidget.shown_set == key:
self.tabWidget.setCurrentIndex(0)
@QtCore.pyqtSlot(str)
def delete_data(self, sid):
if self.valuewidget.shown_set == sid:
self.tabWidget.setCurrentIndex(0)
self.datawidget.remove_item(sid)
@ -784,22 +744,29 @@ class NMRMainWindow(QtWidgets.QMainWindow, Ui_BaseWindow):
editor.finished.connect(self.management.apply)
editor.exec()
@QtCore.pyqtSlot()
def do_preview(self):
dialog = QPreviewDialog(self)
@QtCore.pyqtSlot(str)
def do_preview(self, mode):
success = True
if mode == 'ap':
dialog = QApodDialog(parent=self)
elif mode == 'ph':
dialog = QPhasedialog(parent=self)
else:
raise ValueError('Unknown preview mode %s' % str(mode))
dialog.setRange(*self.current_graph_widget.ranges, self.current_graph_widget.log)
for sid in self.current_graph_widget.active:
data_mode = self.management[sid].mode
if data_mode in ('fid', 'spectrum'):
success = dialog.add_data(self.management[sid].data)
tobeadded = False
if (data_mode == 'fid') or (data_mode == 'spectrum' and mode == 'ph'):
tobeadded = True
if not success:
break
if tobeadded:
dialog.add_data(*self.management.get_data(sid, xy_only=True))
if success and dialog.exec() == QtWidgets.QDialog.Accepted:
self.management.edit_signals(dialog.get_value())
if dialog.exec() == QtWidgets.QDialog.Accepted:
self.management.apply(mode, dialog.get_value())
@QtCore.pyqtSlot(name='on_actionMove_between_plots_triggered')
def move_sets_dialog(self):
@ -850,7 +817,6 @@ class NMRMainWindow(QtWidgets.QMainWindow, Ui_BaseWindow):
except KeyError:
ret_val = None
# noinspection PyUnresolvedReferences
self.sender().receive_data(ret_val)
return ret_val
@ -866,7 +832,7 @@ class NMRMainWindow(QtWidgets.QMainWindow, Ui_BaseWindow):
self.t1tauwidget.t1min_picked(pos)
elif w == self.integralwidget:
region, integral_plot = self.integralwidget.add(pos)
region, integral_plot = self.integralwidget.add(pos)
self.current_graph_widget.add_external(region)
self.current_graph_widget.add_external(integral_plot)
@ -910,18 +876,12 @@ class NMRMainWindow(QtWidgets.QMainWindow, Ui_BaseWindow):
self.action_odr_fit: 'odr'
}[self.ac_group.checkedAction()]
fit_is_ready = self.management.prepare_fit(parameter, links, fit_options)
if fit_is_ready:
self.management.start_fit()
self.fit_dialog.fit_button.setEnabled(False)
self.status.setText('Fit running...'.format(self.management.fitter.step))
self.fit_timer.start(500)
self.fit_dialog.fit_button.setEnabled(False)
self.management.start_fit(parameter, links, fit_options)
@QtCore.pyqtSlot(dict, int, bool)
def show_fit_preview(self, funcs: dict, num: int, show: bool):
if not self.fit_dialog.connected_figure:
logger.warning(f'Fit dialog is not connected graph: Fit {self.fit_dialog.connected_figure}, '
f'current graph: {self.management.current_graph} ({self.management.current_graph in self.management.graphs})')
if self.fit_dialog.connected_figure is None:
return
g = self.management.graphs[self.fit_dialog.connected_figure]
@ -941,22 +901,15 @@ class NMRMainWindow(QtWidgets.QMainWindow, Ui_BaseWindow):
@QtCore.pyqtSlot(list)
def show_fit_results(self, results: list):
self.fit_dialog.fit_button.setEnabled(True)
self.fit_timer.stop()
self.status.setText('')
if results:
if self.fitresult_dialog is None:
self.fitresult_dialog = QFitResult(results, self.management, parent=self)
self.fitresult_dialog.add_graphs(self.management.graphs.list())
self.fitresult_dialog.closed.connect(self.accepts_fit)
self.fitresult_dialog.redoFit.connect(self.management.redo_fits)
else:
self.fitresult_dialog(results)
self.fitresult_dialog.add_graphs(self.management.graphs.list())
self.fitresult_dialog.show()
res_dialog = QFitResult(results, self.management, parent=self)
res_dialog.add_graphs(self.management.graphs.list())
res_dialog.closed.connect(self.accepts_fit)
res_dialog.redoFit.connect(self.management.redo_fits)
res_dialog.show()
@QtCore.pyqtSlot(dict, list, str, bool, bool, list)
def accepts_fit(self, res: dict, opts: list, param_graph: str,
show_fit: bool, parts: bool, extrapolate: list) -> None:
def accepts_fit(self, res: dict, opts: list, param_graph: str, show_fit: bool, parts: bool, extrapolate: list) -> None:
self.fit_dialog.set_parameter(res)
self.management.make_fits(res, opts, param_graph, show_fit, parts, extrapolate)
@ -974,6 +927,7 @@ class NMRMainWindow(QtWidgets.QMainWindow, Ui_BaseWindow):
def extend_fit(self, sets: list):
w = FitExtension(self)
res = w.exec()
print(res)
if res:
p = w.values
x = linspace(p[0], p[1], num=p[2])
@ -1066,9 +1020,6 @@ class NMRMainWindow(QtWidgets.QMainWindow, Ui_BaseWindow):
def close(self):
write_state({'History': {'recent path': str(self.path)}})
# remove backup file when closing
self.__backup_path.unlink(missing_ok=True)
super().close()
def read_state(self):
@ -1092,56 +1043,3 @@ class NMRMainWindow(QtWidgets.QMainWindow, Ui_BaseWindow):
QLog(parent=self).show()
def _autosave(self):
# TODO better separate thread may it takes some time to save
self.status.setText('Autosave...')
success = NMRWriter(self.management.graphs, self.management.data).export(self.__backup_path.with_suffix('.nmr.0'))
if success:
self.__backup_path.with_suffix('.nmr.0').rename(self.__backup_path)
self.status.setText('')
def check_for_backup(self):
backups = []
for filename in config_paths().glob('*.nmr'):
try:
backups.append((filename, datetime.datetime.strptime(filename.stem, "%Y-%m-%d_%H%M%S")))
except ValueError:
continue
if backups:
backup_by_date = sorted(backups, key=lambda x: x[1])
msg = QtWidgets.QMessageBox.information(
self, 'Backup found',
f'{len(backups)} backup files in directory {backup_by_date[-1][0].parent} found.\n\n'
f'Latest backup date: {backup_by_date[-1][1]}\n\n'
f'Press Ok to load, Cancel to delete backup, Close to do nothing.',
QtWidgets.QMessageBox.Ok | QtWidgets.QMessageBox.Cancel | QtWidgets.QMessageBox.Close
)
if msg == QtWidgets.QMessageBox.Ok:
self.management.load_files([str(backup_by_date[-1][0])])
backup_by_date[-1][0].unlink()
elif msg == QtWidgets.QMessageBox.Cancel:
backup_by_date[-1][0].unlink()
else:
pass
@QtCore.pyqtSlot(name='on_actionCreate_starter_triggered')
def create_starter(self):
make_starter(os.getenv('APPIMAGE'))
@QtCore.pyqtSlot(name='on_actionAbout_triggered')
def show_version(self):
from nmreval.version import __version__
QtWidgets.QMessageBox.about(self, 'Version', f'Build date of AppImage: {__version__}')
@QtCore.pyqtSlot(name='on_actionTNMH_model_triggered')
@QtCore.pyqtSlot(name='on_actionTNMH_triggered')
def show_tg_dialog(self):
if self._tg_dialog is None:
self._tg_dialog = TgCalculator(self.management, parent=self)
self._tg_dialog.newData.connect(self.management.addTg)
else:
self._tg_dialog()
self._tg_dialog.show()

370
src/gui_qt/main/management.py
View File

@ -18,7 +18,6 @@ from nmreval.math.smooth import smooth
from nmreval.nmr.relaxation import Relaxation
from ..Qt import QtCore, QtWidgets
from ..lib import Relations
from ..lib.undos import *
from ..data.container import *
from ..io.filereaders import QFileReader
@ -58,18 +57,11 @@ class GraphDict(OrderedDict):
def list(self):
return [(k, v.title) for k, v in self.items()]
def active(self, key: str, return_val: str = 'both'):
if not key:
return []
def active(self, key: str):
if key:
return [(self._data[i].id, self._data[i].name) for i in self[key]]
else:
if return_val == 'both':
return [(self._data[i].id, self._data[i].name) for i in self[key]]
elif return_val == 'id':
return [self._data[i].id for i in self[key]]
elif return_val == 'name':
return [self._data[i].name for i in self[key]]
else:
raise ValueError(f'return_val got wrong value {return_val!r}')
return []
def current_sets(self, key: str):
if key:
@ -82,8 +74,8 @@ class UpperManagement(QtCore.QObject):
newGraph = QtCore.pyqtSignal()
restoreGraph = QtCore.pyqtSignal(str)
deleteGraph = QtCore.pyqtSignal(str)
newData = QtCore.pyqtSignal([list, str], [list, str, bool])
deleteData = QtCore.pyqtSignal(list)
newData = QtCore.pyqtSignal(list, str)
deleteData = QtCore.pyqtSignal(str)
dataChanged = QtCore.pyqtSignal(str)
fitFinished = QtCore.pyqtSignal(list)
stopFit = QtCore.pyqtSignal()
@ -118,7 +110,7 @@ class UpperManagement(QtCore.QObject):
self.counter = 0
self.data = OrderedDict()
self.window = window
self.current_graph = None
self.current_graph = ''
self.graphs = GraphDict(self.data)
self.namespace = None
self.undostack = QtWidgets.QUndoStack()
@ -155,10 +147,6 @@ class UpperManagement(QtCore.QObject):
def active_sets(self):
return self.graphs.active(self.current_graph)
@property
def active_id(self):
return self.graphs.active(self.current_graph, return_val='id')
def get_attributes(self, graph_id: str, attr: str) -> dict[str, Any]:
return {self.data[i].id: getattr(self.data[i], attr) for i in self.graphs[graph_id].sets}
@ -192,10 +180,7 @@ class UpperManagement(QtCore.QObject):
graph.active = active
graph.listWidget.blockSignals(True)
for i, l in enumerate(g['in_legend']):
try:
graph.listWidget.item(i).setCheckState(QtCore.Qt.Checked if l else QtCore.Qt.Unchecked)
except AttributeError:
pass
graph.listWidget.item(i).setCheckState(l)
graph.listWidget.blockSignals(False)
# set unchecked in tree and hide/show in plot
@ -246,17 +231,9 @@ class UpperManagement(QtCore.QObject):
for k in plotkeys:
self.data[k].graph = gid
@QtCore.pyqtSlot(list)
def plot_from_graph(self, key: list[str]):
sort_graph = {}
for sid in key:
v = self.data[sid].graph
if v not in sort_graph:
sort_graph[v] = []
sort_graph[v].append(sid)
for gid, sets in sort_graph.items():
self.graphs[gid].remove(sets)
@QtCore.pyqtSlot(str)
def plot_from_graph(self, key: str):
self.graphs[self.data[key].graph].remove(key)
@QtCore.pyqtSlot(list, str, str)
def move_sets(self, sets: list, dest: str, src: (str|list), pos: int = -1):
@ -299,7 +276,6 @@ class UpperManagement(QtCore.QObject):
@QtCore.pyqtSlot(list)
@QtCore.pyqtSlot(str)
@QtCore.pyqtSlot()
def delete_sets(self, rm_sets: list = None):
rm_graphs = []
@ -308,25 +284,12 @@ class UpperManagement(QtCore.QObject):
self.undostack.beginMacro('Delete')
rm_set_by_graph = {}
for k in rm_sets[::-1]:
if k in self.data:
parent_graph = self.data[k].graph
if parent_graph not in rm_set_by_graph:
rm_set_by_graph[parent_graph] = []
rm_set_by_graph[parent_graph].append(k)
elif k in self.graphs:
rm_graphs.append(k)
cmd = DeleteCommand(self.data, k, self.newData, self.deleteData)
self.undostack.push(cmd)
else:
logger.warning(f'delete_sets: {k} is not in data or graph found')
for gid, sid_list in rm_set_by_graph.items():
cmd = DeleteCommand(self.data, sid_list, self.graphs, gid, self.newData, self.deleteData)
self.undostack.push(cmd)
rm_graphs.append(k)
for k in rm_graphs:
cmd = DeleteGraphCommand(self.graphs, k, self.restoreGraph, self.deleteGraph)
@ -355,7 +318,7 @@ class UpperManagement(QtCore.QObject):
if joined is None:
joined = data_i.copy()
else:
joined.append(data_i.data.x, data_i.data.y, y_err=data_i.data.y_err, mask=data_i.data.mask)
joined.append(data_i.x, data_i.y, data_i.y_err)
name_set.add(data_i.name)
group_set.add(data_i.group)
@ -385,16 +348,12 @@ class UpperManagement(QtCore.QObject):
def change_visibility(self, selected: list, deselected: list):
"""Change status of list of ids after status change in datawidget"""
for item_list, func in [(selected, 'show_item'), (deselected, 'hide_item')]:
grouping = {}
for s in item_list:
g = self.data[s].graph
if g not in grouping:
grouping[g] = []
grouping[g].append(s)
for k, v in grouping.items():
getattr(self.graphs[k], func)(v)
for s in selected:
self.graphs[self.data[s].graph].show_item([s])
for d in deselected:
self.graphs[self.data[d].graph].hide_item([d])
@QtCore.pyqtSlot(str, str)
def change_keys(self, identifier: str, name: str):
@ -418,13 +377,6 @@ class UpperManagement(QtCore.QObject):
self.undostack.push(single_undo)
self.undostack.endMacro()
def edit_signals(self: UpperManagement, args: list[tuple]) -> None:
self.undostack.beginMacro('Edit signals')
for sid in self.graphs[self.current_graph]:
single_undo = EditCommand(self.data[sid], *args)
self.undostack.push(single_undo)
self.undostack.endMacro()
def cut(self):
if self.current_graph:
xlim, _ = self.graphs[self.current_graph].ranges
@ -435,105 +387,68 @@ class UpperManagement(QtCore.QObject):
for d in self.data.values():
d.mask = np.ones_like(d.mask, dtype=bool)
def prepare_fit(self, parameter: dict, links: list, fit_options: dict) -> bool:
def start_fit(self, parameter: dict, links: list, fit_options: dict):
if self._fit_active:
return False
return
self.__fit_options = (parameter, links, fit_options)
self.fitter = FitRoutine()
fitter = FitRoutine()
models = {}
fit_limits = fit_options['limits']
fit_mode = fit_options['fit_mode']
we_option = fit_options['we']
we = fit_options['we']
self.fitter.fitmethod = fit_mode
for model_id, model_p in parameter.items():
m = Model(model_p['func'])
models[model_id] = m
# all-encompassing error catch
try:
for model_id, model_p in parameter.items():
m = model_p['func']
models[model_id] = m
m_complex = model_p['complex']
m_complex = model_p['complex']
for set_id, set_params in model_p['parameter'].items():
data_i = self.data[set_id]
if we.lower() == 'deltay':
we = data_i.y_err**2
# sets are not in active order but in order they first appeared in fit dialog
# iterate over order of set id in active order and access parameter inside loop
# instead of directly looping
try:
list_ids = list(self.active_id)
set_order = [self.active_id.index(i) for i in model_p['data_parameter'].keys()]
except ValueError as e:
raise Exception('Getting order failed') from e
if m_complex is None or m_complex == 1:
_y = data_i.y.real
elif m_complex == 2 and np.iscomplexobj(data_i.y):
_y = data_i.y.imag
else:
_y = data_i.y
for pos in set_order:
set_id = list_ids[pos]
_x = data_i.x
try:
data_i = self.data[set_id]
except KeyError as e:
raise KeyError(f'{set_id} not found') from e
if fit_limits == 'none':
inside = slice(None)
elif fit_limits == 'x':
x_lim, _ = self.graphs[self.current_graph].ranges
inside = np.where((_x >= x_lim[0]) & (_x <= x_lim[1]))
else:
inside = np.where((_x >= fit_limits[0]) & (_x <= fit_limits[1]))
try:
set_params = model_p['data_parameter'][set_id]
except KeyError as e:
raise KeyError(f'No parameter found for {set_id}') from e
if isinstance(we, str):
d = fit_d.Data(_x[inside], _y[inside], we=we, idx=set_id)
else:
d = fit_d.Data(_x[inside], _y[inside], we=we[inside], idx=set_id)
if we_option.lower() == 'deltay':
we = data_i.y_err**2
else:
we = we_option
d.set_model(m)
d.set_parameter(set_params[0], var=model_p['var'],
lb=model_p['lb'], ub=model_p['ub'],
fun_kwargs=set_params[1])
if m_complex is None or m_complex == 1:
_y = data_i.y.real
elif m_complex == 2 and np.iscomplexobj(data_i.y):
_y = data_i.y.imag
else:
_y = data_i.y
fitter.add_data(d)
_x = data_i.x
model_globs = model_p['glob']
if model_globs:
m.set_global_parameter(**model_p['glob'])
if fit_limits == 'none':
inside = slice(None)
elif fit_limits == 'x':
x_lim, _ = self.graphs[self.current_graph].ranges
inside = np.where((_x >= x_lim[0]) & (_x <= x_lim[1]))
else:
inside = np.where((_x >= fit_limits[0]) & (_x <= fit_limits[1]))
for links_i in links:
fitter.set_link_parameter((models[links_i[0]], links_i[1]),
(models[links_i[2]], links_i[3]))
try:
if isinstance(we, str):
d = fit_d.Data(_x[inside], _y[inside], we=we, idx=set_id)
else:
d = fit_d.Data(_x[inside], _y[inside], we=we[inside], idx=set_id)
except Exception as e:
raise Exception(f'Setting data failed for {set_id}')
d.set_model(m)
try:
d.set_parameter(set_params[0], fun_kwargs=set_params[1])
except Exception as e:
raise Exception('Setting parameter failed') from e
self.fitter.add_data(d)
for links_i in links:
self.fitter.set_link_parameter((models[links_i[0]], links_i[1]),
(models[links_i[2]], links_i[3]))
return True
except Exception as e:
logger.error('Fit preparation failed', *e.args)
QtWidgets.QMessageBox.warning(QtWidgets.QWidget(),
'Fit prep failed',
f'Fit preparation failed:\n'
'Message:\n'
f'{e.args}:\n')
return False
def start_fit(self):
with busy_cursor():
self.fit_worker = FitWorker(self.fitter)
self.fit_worker = FitWorker(fitter, fit_mode)
self.fit_thread = QtCore.QThread()
self.fit_worker.moveToThread(self.fit_thread)
@ -549,14 +464,12 @@ class UpperManagement(QtCore.QObject):
@QtCore.pyqtSlot(list, bool)
def end_fit(self, result: list, success: bool):
print('FIT FINISHED')
if success:
logger.info('Successful fit')
self.fitFinished.emit(result)
else:
e = result[0]
logger.exception(e, exc_info=True)
QtWidgets.QMessageBox.warning(QtWidgets.QWidget(), 'Fit failed',
f'Fit kaput with exception: \n\n{e!r}')
'Fit kaput with exception: \n' + "\n".join(result[0]))
self.fitFinished.emit([])
self._fit_active = False
@ -569,8 +482,7 @@ class UpperManagement(QtCore.QObject):
for set_id, set_parameter in parameter.items():
new_values = [v.value for v in res[set_id].parameter.values()]
parameter[set_id] = (new_values, set_parameter[1])
if self.prepare_fit(*self.__fit_options):
self.start_fit()
self.start_fit(*self.__fit_options)
def make_fits(self, res: dict, opts: list, param_graph: str, show_fit: bool, parts: bool, extrapolate: list) -> None:
"""
@ -646,9 +558,6 @@ class UpperManagement(QtCore.QObject):
subfunc.name += data_name
sub_f_id = self.add(subfunc, color=col, linestyle=LineStyle.Dashed, symbol=SymbolStyle.No)
self[sub_f_id].add_relation(Relations.isFitPartOf, f_id)
self[f_id].add_relation(Relations.hasFitPart, sub_f_id)
f_id_list.append(sub_f_id)
gid = data_k.graph
self.delete_sets(tobedeleted)
@ -691,11 +600,11 @@ class UpperManagement(QtCore.QObject):
if not graph_id:
graph_id = ''
self.newData[list, str, bool].emit(p_id_list, graph_id, True)
self.newData.emit(p_id_list, graph_id)
def save_fit_parameter(self, fname: str | pathlib.Path, fit_sets: list[str] = None):
if fit_sets is None:
fit_sets = [s for s in self.active_id]
fit_sets = [s for (s, _) in self.active_sets]
for set_id in fit_sets:
data = self.data[set_id]
@ -717,10 +626,12 @@ class UpperManagement(QtCore.QObject):
else:
continue
for fit_key, pvalue in data.parameter.items():
for key, pvalue in data.parameter.items():
name = pvalue.full_name
fit_key = key + data.model_name
if fit_key not in fit_dict:
fit_dict[fit_key] = [[], fit_key]
fit_dict[fit_key] = [[], name]
err = 0 if pvalue.error is None else pvalue.error
@ -757,7 +668,7 @@ class UpperManagement(QtCore.QObject):
key = self.add(Points(x=new_x_axis, y=_temp[:, i, 1], y_err=_temp[:, i, 2], name=label))
key_list.append(key)
self.newData[list, str, bool].emit(key_list, gid, True)
self.newData.emit(key_list, gid)
@QtCore.pyqtSlot(list)
def get_properties(self, sid: list) -> dict:
@ -828,47 +739,6 @@ class UpperManagement(QtCore.QObject):
self.newData.emit(new_key, dest_graph)
def binning(self, digits: float):
_active = self.graphs[self.current_graph].active
new_data = []
for sid in _active:
key = self.add(self.data[sid].binning(digits=digits))
new_data.append(key)
self.newData.emit(new_data, self.current_graph)
@QtCore.pyqtSlot(dict, str)
def addTg(self, dic: dict, dtype: str):
graph_id = self.current_graph if dtype == 'tg' else dic.pop('graph')
set_id_list = []
if dtype == 'hodge':
for v in dic.values():
set_id_list.append(self.add(v))
else:
for k, (data, lines) in dic.items():
p: ExperimentContainer = self[k]
col = p.plot_real.linecolor
if data is not None:
set_id_list.append(self.add(data, color=col))
if dtype == 'tnmh':
if lines is not None:
lines = [lines]
else:
lines = []
for line in lines:
set_id = self.add(line, color=col)
self[set_id].setLine(style=LineStyle.Dashed)
self[set_id].setSymbol(symbol=SymbolStyle.No)
set_id_list.append(set_id)
self.newData.emit(set_id_list, graph_id)
@QtCore.pyqtSlot(int, dict)
def smooth_data(self, npoints, param_kwargs):
_active = self.graphs[self.current_graph].active
@ -901,10 +771,13 @@ class UpperManagement(QtCore.QObject):
d_k = self.data[k]
if copy_data is None:
d_k.shift_scale(v[0], v[1])
d_k.x = d_k.x*v[1][0] + v[0][0]
d_k.y = d_k.y*v[1][1] + v[0][1]
else:
new_data = d_k.copy(full=True)
new_data.shift_scale(v[0], v[1])
new_data.update({'shift': v[0], 'scale': v[1]})
new_data.data.x = new_data.x*v[1][0] + v[0][0]
new_data.y = new_data.y*v[1][1] + v[0][1]
sid = self.add(new_data)
sid_list.append(sid)
@ -1000,26 +873,21 @@ class UpperManagement(QtCore.QObject):
self.undostack.beginMacro('Evaluate expression')
failures = []
for i, g in enumerate(self.graphs.values()):
for j, sid in enumerate(g.sets):
if sid not in set_ids:
continue
data_i = self.data[sid]
try:
# use a copy of original namespace
new_data = data_i.eval_expression(cmds, dict(ns), i=i, j=j)
if overwrite:
cmd = EvalCommand(self.data, sid, new_data, 'Evaluate expression')
self.undostack.push(cmd)
else:
new_id = self.copy_sets(sets=[sid])
self.data[new_id[0]].data = new_data
except Exception as e:
failures.append((data_i, e))
logger.warning(str(data_i) + ' failed with Exception: ' + ''.join(e.args))
continue
for sid in set_ids:
data_i = self.data[sid]
try:
# use a copy of original namespace
new_data = data_i.eval_expression(cmds, dict(ns))
if overwrite:
cmd = EvalCommand(self.data, sid, new_data, 'Evaluate expression')
self.undostack.push(cmd)
else:
new_id = self.copy_sets(sets=[sid])
self.data[new_id[0]].data = new_data
except Exception as e:
failures.append((data_i, e))
print(str(data_i) + ' failed with Exception: ' + ''.join(e.args))
continue
if overwrite:
self.undostack.endMacro()
@ -1053,9 +921,9 @@ class UpperManagement(QtCore.QObject):
self.newData.emit([s_id], graph)
except Exception as err:
logger.exception('Creation failed with error: ' + ', '.join(err.args))
print('Creation failed with error: ' + ', '.join(err.args))
err_msg = QtWidgets.QMessageBox(parent=self.sender())
err_msg.setText('One or more errors occurred during evaluation.')
err_msg.setText('One or more errors occured during evaluation.')
err_msg.setDetailedText('Creation failed with error: ' + ', '.join(err.args))
err_msg.exec()
@ -1064,7 +932,7 @@ class UpperManagement(QtCore.QObject):
def show_statistics(self, mode):
x, y, = [], []
for i in self.active_id:
for i, _ in self.active_sets:
_temp = self.data[i]
try:
x.append(float(_temp.name))
@ -1075,7 +943,7 @@ class UpperManagement(QtCore.QObject):
@QtCore.pyqtSlot()
def calc_magn(self):
new_id = []
for k in self.active_id:
for k, _ in self.active_sets:
dataset = self.data[k]
if isinstance(dataset, SignalContainer):
new_value = dataset.copy(full=True)
@ -1087,7 +955,7 @@ class UpperManagement(QtCore.QObject):
@QtCore.pyqtSlot()
def center(self):
new_id = []
for k in self.active_id:
for k, _ in self.active_sets:
new_value = self.data[k].copy(full=True)
new_value.x -= new_value.x[np.argmax(new_value.y.real)]
new_id.append(self.add(new_value))
@ -1126,7 +994,7 @@ class UpperManagement(QtCore.QObject):
def bds_deriv(self):
new_sets = []
for set_id in self.active_id:
for (set_id, _) in self.active_sets:
data_i = self.data[set_id]
diff = data_i.data.diff(log=True)
new_data = Points(x=diff.x, y=-np.pi/2*diff.y.real)
@ -1139,14 +1007,13 @@ class UpperManagement(QtCore.QObject):
def logft(self, **kwargs):
new_sets = []
ft_mode = kwargs['ft_mode']
return_f = kwargs['return_f']
for set_id in kwargs['sets']:
data_i = self.data[set_id]
if ft_mode in ['cos', 'sin']:
new_data = Points(*logft(data_i.x, data_i.y, mode=ft_mode, return_f=return_f))
new_data = Points(*logft(data_i.x, data_i.y, mode=ft_mode))
else:
new_data = Signal(*logft(data_i.x, data_i.y, mode=ft_mode, return_f=return_f))
new_data = Signal(*logft(data_i.x, data_i.y, mode=ft_mode))
new_sets.append(self.add(new_data, color=data_i['color'], symbol=data_i['symbol'], line=data_i['line']))
self.data[new_sets[-1]].update(data_i.data.meta)
@ -1154,7 +1021,7 @@ class UpperManagement(QtCore.QObject):
self.newData.emit(new_sets, kwargs['graph'])
def skip_points(self, offset: int, step: int, invert: bool = False, copy: bool = False):
for k in self.active_id:
for k, _ in self.active_sets:
src = self.data[k]
if invert:
mask = np.mod(np.arange(offset, src.x.size+offset), step) != 0
@ -1180,11 +1047,9 @@ class UpperManagement(QtCore.QObject):
params = opts['pts']
if len(params) == 4:
if params[3]:
_x = np.geomspace(params[0], params[1], num=params[2])
x1 = np.geomspace(params[0], params[1], num=params[2])
_x = x1 = np.geomspace(params[0], params[1], num=params[2])
else:
_x = np.linspace(params[0], params[1], num=params[2])
x1 = np.linspace(params[0], params[1], num=params[2])
_x = x1 = np.linspace(params[0], params[1], num=params[2])
if opts['axis1'] in ['t', 'invt1000']:
t_p = opts['t_param']
@ -1203,23 +1068,21 @@ class UpperManagement(QtCore.QObject):
_x = x1 = self.data[params[0]].x
x2 = opts['val2']
sd = opts['spec_dens']
sd_param = list(zip(*[self.data[p].y.real if isinstance(p, str) else [p]*len(_x) for p in opts['sd_param'][0]]))
sd_param = [self.data[p].y.real if isinstance(p, str) else p for p in opts['sd_param'][0]]
sd.convert(_x, *sd_param, from_=opts['tau_type'], to_='raw')
relax = Relaxation()
relax.set_distribution(sd, keywords=opts['sd_param'][1])
relax.set_distribution(sd, parameter=sd_param, keywords=opts['sd_param'][1])
cp_param = list(zip(*[self.data[p].y.real if isinstance(p, str) else [p]*len(_x) for p in opts['cp_param'][0]]))
# relax.set_coupling(opts['coup'], parameter=cp_param, keywords=opts['cp_param'][1])
cp_param = [self.data[p].y.real if isinstance(p, str) else p for p in opts['cp_param'][0]]
relax.set_coupling(opts['coup'], parameter=cp_param, keywords=opts['cp_param'][1])
relax_func = relax.t1 if opts['out'] == 't1' else relax.t2
y = np.zeros(_x.size)
for i in range(_x.size):
_x_i = sd.convert(_x[i], *sd_param[i], from_=opts['tau_type'], to_='raw')
relax.dist_parameter = sd_param[i]
relax.set_coupling(opts['coup'], parameter=cp_param[i], keywords=opts['cp_param'][1])
y[i] = relax_func(x2, _x_i)
if opts['out'] == 't1':
y = relax.t1(x2, _x)
else:
y = relax.t2(x2, _x)
pts = Points(x1, y, name=sd.name)
pts.meta.update(opts)
@ -1313,17 +1176,18 @@ class UpperManagement(QtCore.QObject):
class FitWorker(QtCore.QObject):
finished = QtCore.pyqtSignal(list, bool)
def __init__(self, fitter):
def __init__(self, fitter, mode):
super().__init__()
self.fitter = fitter
self.mode = mode
@QtCore.pyqtSlot()
def run(self):
try:
res = self.fitter.run()
res = self.fitter.run(mode=self.mode)
success = True
except Exception as e:
res = [e]
res = [e.args]
success = False
self.finished.emit(res, success)

21
src/gui_qt/math/binning.py
View File

@ -1,21 +0,0 @@
from ..Qt import QtWidgets, QtGui
class BinningWindow(QtWidgets.QDialog):
def __init__(self, parent=None):
super().__init__(parent=parent)
layout = QtWidgets.QFormLayout()
self.label = QtWidgets.QLabel('Digits (negative values position left of decimal point)')
self.spinbox = QtWidgets.QLineEdit()
self.spinbox.setValidator(QtGui.QDoubleValidator())
self.spinbox.setText('1')
layout.addRow(self.label, self.spinbox)
self.dialogbox = QtWidgets.QDialogButtonBox(QtWidgets.QDialogButtonBox.Ok | QtWidgets.QDialogButtonBox.Cancel)
self.dialogbox.accepted.connect(self.accept)
self.dialogbox.rejected.connect(self.reject)
layout.addWidget(self.dialogbox)
self.setLayout(layout)

34
src/gui_qt/math/evaluation.py
View File

@ -31,35 +31,13 @@ class QEvalDialog(QtWidgets.QDialog, Ui_CalcDialog):
self.namespace_widget.set_namespace(self.namespace)
def add_data(self, data):
# self.listWidget.clear()
tmp = []
while self.listWidget.count():
tmp.append(self.listWidget.takeItem(0))
self.listWidget.clear()
for set_id, name in data:
# search if set was used before
new_one = True
for i in range(len(tmp)):
w = tmp[i]
if w.data(QtCore.Qt.UserRole) == set_id:
w.setText(name)
self.listWidget.addItem(w)
tmp.pop(i)
new_one = False
break
# new set, create item
if new_one:
item = QtWidgets.QListWidgetItem(name)
item.setData(QtCore.Qt.UserRole, set_id)
item.setFlags(item.flags() ^ QtCore.Qt.ItemIsEditable)
item.setCheckState(QtCore.Qt.Checked)
self.listWidget.addItem(item)
while len(tmp):
# delete remaining ListWidgetItems
w = tmp.pop()
del w
item = QtWidgets.QListWidgetItem(name)
item.setData(QtCore.Qt.UserRole, set_id)
item.setFlags(item.flags() ^ QtCore.Qt.ItemIsEditable)
item.setCheckState(QtCore.Qt.Checked)
self.listWidget.addItem(item)
def set_graphs(self, graphs: list):
self.graph_comboBox.clear()

10
src/gui_qt/math/integrate_derive.py
View File

@ -16,19 +16,16 @@ class QDeriveIntegrate(QtWidgets.QDialog, Ui_Dialog):
self.start_lineedit.setValidator(QtGui.QDoubleValidator())
self.stop_lineedit.setValidator(QtGui.QDoubleValidator())
self.ft_comboBox.hide()
self.freq_box.hide()
elif self.mode == 'd':
self.setWindowTitle('Differentiation dialog')
self.widget.hide()
self.ft_comboBox.hide()
self.freq_box.hide()
elif self.mode == 'l':
self.setWindowTitle('Logarithmic FT dialog')
self.log_checkbox.hide()
self.widget.hide()
self.freq_box.show()
else:
raise ValueError(f'Unknown mode {mode}, use "d", "i", or "l".')
@ -57,10 +54,8 @@ class QDeriveIntegrate(QtWidgets.QDialog, Ui_Dialog):
self.stop_lineedit.setEnabled(full_range != QtCore.Qt.Checked)
def get_options(self):
opts = {
'graph': '' if self.newgraph_checkbox.isChecked() else self.graph_combobox.currentData(),
'mode': self.mode, 'sets': []
}
opts = {'graph': '' if self.newgraph_checkbox.isChecked() else self.graph_combobox.currentData(),
'mode': self.mode, 'sets': []}
if self.mode == 'i':
start = None
@ -80,7 +75,6 @@ class QDeriveIntegrate(QtWidgets.QDialog, Ui_Dialog):
if self.mode == 'l':
opts['ft_mode'] = ['cos', 'sin', 'complex'][self.ft_comboBox.currentIndex()]
opts['return_f'] = self.freq_box.isChecked()
else:
opts['log'] = self.log_checkbox.isChecked()

10
src/gui_qt/nmr/t1_from_tau.py
View File

@ -19,7 +19,7 @@ class QRelaxCalc(QtWidgets.QDialog, Ui_Dialog):
self.graphs = {}
self.specdens = [ColeCole, ColeDavidson, HavriliakNegami, KWW, LogGaussian]
self.specdens = [ColeCole, ColeDavidson, HavriliakNegami, KWW]
self.coupling = [Quadrupolar, HomoDipolar, Czjzek]
self.tau_parameter = []
@ -131,7 +131,7 @@ class QRelaxCalc(QtWidgets.QDialog, Ui_Dialog):
self.verticalLayout_3.addWidget(_temp)
def get_taus(self, dic: dict):
dic['tau_type'] = {0: 'raw', 1: 'peak', 2: 'mean', 3: 'logmean'}[self.xtype_combobox.currentIndex()]
dic['tau_type'] = {0: 'raw', 1: 'mean', 2: 'peak', 3: 'logmean'}[self.xtype_combobox.currentIndex()]
dic['axis1'] = {self.radioButton: 'tau', self.radioButton_2: 'omega',
self.radioButton_3: 't', self.radioButton_4: 'invt1000'}[self.buttonGroup.checkedButton()]
@ -199,9 +199,3 @@ class QRelaxCalc(QtWidgets.QDialog, Ui_Dialog):
def accept(self):
self.calc_relaxation()
super().accept()
@QtCore.pyqtSlot(QtWidgets.QAbstractButton)
def on_buttonBox_clicked(self, button: QtWidgets.QAbstractButton):
role = self.buttonBox.buttonRole(button)
if role == self.buttonBox.ApplyRole:
self.calc_relaxation()

2
src/gui_qt/nmr/t1widget.py
View File

@ -61,8 +61,6 @@ class QT1Widget(QtWidgets.QDialog, Ui_t1dialog):
self.freq_combox.currentIndexChanged.connect(lambda x: self.update_model())
self.freq_spinbox.valueChanged.connect(lambda x: self.update_model())
self.checkBox_interpol.setVisible(False)
self.update_specdens(0)
self.update_coupling(0)

158
src/nmreval/clib/integrate.c
View File

@ -1,158 +0,0 @@
/* integrands used in quadrature integration with scipy's LowLevelCallables */
#include <math.h>
const double KB = 8.617333262145179e-05;
/* FFHS functions */
double ffhsSD(double x, void *user_data) {
double *c = (double *)user_data;
double omega = c[0];
double tau = c[1];
double u = x*x;
double res = u*u * tau;
res /= 81. + 9.*u - 2.*u*u + u*u*u;
res /= u*u + omega*omega * tau*tau;
return res;
}
/* log-gaussian functions */
double logNormalDist(double tau, double tau0, double sigma) {
return exp(- pow((log(tau/tau0) / sigma), 2) / 2.) / sqrt(2*M_PI)/sigma;
}
double logGaussian_imag_high(double u, void *user_data) {
double *c = (double *)user_data;
double omega = c[0];
double tau = c[1];
double sigma = c[2];
double uu = exp(-u);
double dist = logNormalDist(1./uu, tau, sigma);
return dist * omega * uu / (pow(uu, 2) + pow(omega, 2));
}
double logGaussian_imag_low(double u, void *user_data) {
double *c = (double *)user_data;
double omega = c[0];
double tau = c[1];
double sigma = c[2];
double uu = exp(u);
double dist = logNormalDist(uu, tau, sigma);
return dist * omega * uu / (1. + pow(omega*uu, 2));
}
double logGaussian_real_high(double u, void *user_data) {
double *c = (double *)user_data;
double omega = c[0];
double tau = c[1];
double sigma = c[2];
double uu = exp(-2.*u);
double dist = logNormalDist(exp(uu), tau, sigma);
return dist * uu / (uu + pow(omega, 2));
}
double logGaussian_real_low(double u, void *user_data) {
double *c = (double *)user_data;
double omega = c[0];
double tau = c[1];
double sigma = c[2];
double uu = exp(u);
double dist = logNormalDist(uu, tau, sigma);
return dist / (1. + pow(omega*uu, 2));
}
double logGaussianCorrelation(double x, void *user_data) {
double *c = (double *)user_data;
double t = c[0];
double tau = c[1];
double sigma = c[2];
double uu = exp(x);
double dist = logNormalDist(uu, tau, sigma);
return dist * exp(-t/uu);
}
// functions for distribution of energy
double normalDist(double x, double x0, double sigma) {
return exp(- pow((x-x0) / sigma, 2) / 2.) / sqrt(2 * M_PI) / sigma;
}
double rate(double tau0, double ea, double t) {
return exp(-ea / t / KB) / tau0;
}
double energyDist_SD(double x, void *user_data) {
double *c = (double *)user_data;
double omega = c[0];
double tau0 = c[1];
double e_m = c[2];
double e_b = c[3];
double temp = c[4];
double r = rate(tau0, x, temp);
return r/(pow(r, 2) + pow(omega, 2)) * normalDist(x, e_m, e_b);
}
double energyDistSuscReal(double x, void *user_data) {
double *c = (double *)user_data;
double omega = c[0];
double tau0 = c[1];
double e_m = c[2];
double e_b = c[3];
double temp = c[4];
double r = rate(tau0, x, temp);
return 1 / (pow(r, 2) + pow(omega, 2)) * normalDist(x, e_m, e_b);
}
double energyDistSuscImag(double x, void *user_data) {
double *c = (double *)user_data;
double omega = c[0];
double tau0 = c[1];
double e_m = c[2];
double e_b = c[3];
double temp = c[4];
double r = rate(tau0, x, temp);
return omega * r / (pow(r, 2) + pow(omega, 2)) * normalDist(x, e_m, e_b);
}
double energyDistCorrelation(double x, void *user_data) {
double *c = (double *)user_data;
double t = c[0];
double tau0 = c[1];
double e_m = c[2];
double e_b = c[3];
double temp = c[4];
double r = rate(tau0, x, temp);
return normalDist(x, e_m, e_b) * exp(-t * r);
}

BIN
src/nmreval/clib/integrate.so
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Binary file not shown.

16
src/nmreval/configs.py
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@ -10,25 +10,19 @@ __all__ = ['config_paths', 'check_for_config', 'read_configuration', 'write_conf
def check_for_config(make=True):
try:
conf_path = config_paths()
config_paths()
except FileNotFoundError as e:
if make:
conf_path = pathlib.Path('~/.auswerten').expanduser()
conf_path.mkdir(parents=True)
cwd = pathlib.Path(__file__).parent
copyfile(cwd / 'models' / 'usermodels.py', conf_path / 'usermodels.py')
with resource_path('resources', 'Default.agr') as fp:
copyfile(fp, conf_path / 'Default.agr')
else:
raise e
for filename in ('Default.agr', 'logo.png'):
_file = conf_path / filename
if not _file.exists():
with resource_path('resources', filename) as fp:
copyfile(fp, _file)
if not (conf_path / 'usermodels.py').exists():
cwd = pathlib.Path(__file__).parent
copyfile(cwd / 'models' / 'usermodels.py', conf_path / 'usermodels.py')
def config_paths() -> pathlib.Path:
searchpaths = ['~/.config/nmreval', '~/.auswerten', '/usr/share/nmreval']

134
src/nmreval/data/dsc.py
View File

@ -1,138 +1,6 @@
from __future__ import annotations
from typing import Optional
import numpy as np
from scipy.optimize import fsolve
from scipy.signal import savgol_filter
try:
from scipy.integrate import cumulative_trapezoid
except ImportError:
from scipy.integrate import cumtrapz as cumulative_trapezoid
from scipy.stats import linregress
from .points import Points
from ..dsc.tnmh_model import TNMH
class DSC(Points):
def __init__(self, x, y, **kwargs):
y = np.asarray(y).reshape(np.asarray(x).shape)
x, unique = np.unique(x, return_index=True)
if kwargs.get('y_err', None) is not None:
_yerr = np.asarray(kwargs['y_err']).reshape(np.asarray(x).shape)
kwargs['y_err'] = _yerr[unique]
self.tg = {'onset': np.nan, 'mid': np.nan, 'end': np.nan, 'inflection': np.nan, 'fictive': np.nan}
super().__init__(x, y[unique], **kwargs)
def get_fictive_cp(self, glass: tuple[float, float], liquid: tuple[float, float]) -> ('DSC', float):
min_glass, max_glass = min(glass), max(glass)
min_liquid, max_liquid = min(liquid), max(liquid)
region = self.copy()
region.cut(min_glass, max_liquid)
glass_regime = (min_glass < region.x) & (region.x < max_glass)
regress = linregress(region.x[glass_regime], region.y[glass_regime])
glass_extrapolation = regress.slope * region.x + regress.intercept
liquid_regime = (min_liquid < region.x) & (region.x < max_liquid)
regress2 = linregress(region.x[liquid_regime], region.y[liquid_regime])
region.y -= glass_extrapolation
real_area = cumulative_trapezoid(region.y, region.x, initial=0)
real_area -= real_area[-1]
t = regress2.intercept - regress.intercept
m = regress2.slope - regress.slope
c0 = 0.5 * m * region.x.max() ** 2 + t * region.x.max()
def equiv(_x, _i):
return (0.5 * m * _x ** 2 + t * _x - c0) - real_area[_i]
def equiv_prime(_x, _i):
return m * _x + t
fictive_temperature = np.array(
[fsolve(equiv, region.x[i], fprime=equiv_prime, args=(i,))[0] for i in range(len(region.x))])
t_g_fictive = fictive_temperature[:20].mean()
region.y = np.gradient(fictive_temperature, region.x)
return region, t_g_fictive
def calculate_tnmh(self, p0: list, glass: tuple[float, float], liquid: tuple[float, float],
tg: float = None, num_points: int = 200, return_fictive: bool = True) \
-> ('FitResult', Optional[float], Optional[DSC]):
dtf_dt, fictive_tg = self.get_fictive_cp(glass, liquid)
if tg is None:
tg = fictive_tg
temp_equidist = np.linspace(dtf_dt.x[0], dtf_dt.x[-1], num_points)
dtf_dt_equidist = np.interp(temp_equidist, dtf_dt.x, dtf_dt.y)
from ..fit.minimizer import FitRoutine
fitter = FitRoutine()
fitter.set_model(TNMH)
data = fitter.add_data(temp_equidist, dtf_dt_equidist)
data.set_parameter(p0 + [tg, self.value], var=[True] * 4 + [False] * 2, default_bounds=True)
res = fitter.run()[0]
if return_fictive:
return res, tg, dtf_dt
else:
return res
def glass_transition(self, glass, liquid):
low_idx = tuple(np.argmin(np.abs(self.x - g)) for g in glass)
high_idx = tuple(np.argmin(np.abs(self.x - l)) for l in liquid)
x = self.x[low_idx[0]:high_idx[1]]
y = self.y[low_idx[0]:high_idx[1]]
win_len = min(len(x) // 20, 51)
if win_len % 2 == 0:
win_len += 1
yy = savgol_filter(y, window_length=win_len, polyorder=1, deriv=1) / np.mean(np.diff(x))
high_idx = (high_idx[0] - low_idx[0], high_idx[1] - low_idx[0])
low_idx = (0, low_idx[1] - low_idx[0])
inflection = np.argmax(yy)
p1 = linregress(x[low_idx[0]:low_idx[1]], y[low_idx[0]:low_idx[1]])
glass_baseline = p1.slope * x + p1.intercept
p2 = linregress(x[high_idx[0]:high_idx[1]], y[high_idx[0]:high_idx[1]])
liquid_baseline = p2.slope * x + p2.intercept
tangent_line = yy[inflection] * (x - x[inflection]) + y[inflection]
onset = np.argmin(np.abs(tangent_line - glass_baseline))
end = np.argmin(np.abs(tangent_line - liquid_baseline))
midpoint = np.argmin(np.abs(y - 0.5 * (liquid_baseline[end] - glass_baseline[onset])))
cut_tangent = np.where((tangent_line > y.min() - 1) & (tangent_line < y.max() + 1))
glass = Points(x, glass_baseline, name=f'Glass baseline ({self.name})', value=self.value)
tangent = Points(x[cut_tangent], tangent_line[cut_tangent], name=f'Tangent ({self.name})', value=self.value)
liquid = Points(x, liquid_baseline, name=f'Liquid baseline ({self.name})', value=self.value)
ret_dic = {
'onset': (x[onset], glass_baseline[onset]),
'midpoint': (x[midpoint], y[midpoint]),
'end': (x[end], liquid_baseline[end]),
'inflection': (x[inflection], y[inflection]),
}
self.tg.update(ret_dic)
return ret_dic, glass, liquid, tangent
super().__init__(x, y, **kwargs)

4
src/nmreval/data/nmr.py
View File

@ -62,10 +62,6 @@ class FID(Signal):
return self
def manual_phase(self, ph0: float = 0., ph1: float = 0., pvt: float = 0):
"""FID knows only how to phase correct in zeroth order"""
super().manual_phase(ph0=ph0)
def fourier(self) -> 'Spectrum':
ft = np.fft.fftshift(np.fft.fft(self._y)) / self.dx
freq = np.fft.fftshift(np.fft.fftfreq(self.length, self.dx))

71
src/nmreval/data/points.py
View File

@ -1,7 +1,6 @@
from __future__ import annotations
import copy
from math import log10
from numbers import Number, Real
from pathlib import Path
from typing import Any, TypeVar
@ -319,21 +318,20 @@ class Points:
if pts is None:
pts = []
if idx is not None:
for x in idx:
if isinstance(x, tuple):
x_idx = np.argmin(np.abs(self._x[self.mask] - (x[0]+x[1])/2))
left_b = np.argmin(np.abs(self._x[self.mask] - x[0]))
right_b = np.argmin(np.abs(self._x[self.mask] - x[1]))
else:
x_idx = np.argmin(np.abs(self._x[self.mask]-x))
left_b = int(max(0, x_idx - avg_range[0]))
right_b = int(min(len(self), x_idx + avg_range[1] + 1))
for x in idx:
if isinstance(x, tuple):
x_idx = np.argmin(np.abs(self._x[self.mask] - (x[0]+x[1])/2))
left_b = np.argmin(np.abs(self._x[self.mask] - x[0]))
right_b = np.argmin(np.abs(self._x[self.mask] - x[1]))
else:
x_idx = np.argmin(np.abs(self._x[self.mask]-x))
left_b = int(max(0, x_idx - avg_range[0]))
right_b = int(min(len(self), x_idx + avg_range[1] + 1))
if left_b < right_b:
pts.append([self._x[x_idx], *self._average(avg_mode, x_idx, left_b, right_b)])
else:
pts.append([self._x[x_idx], self._y[x_idx], self._y_err[x_idx]])
if left_b < right_b:
pts.append([self._x[x_idx], *self._average(avg_mode, x_idx, left_b, right_b)])
else:
pts.append([self._x[x_idx], self._y[x_idx], self._y_err[x_idx]])
if special is not None:
if special not in ['max', 'min', 'absmax', 'absmin']:
@ -485,25 +483,20 @@ class Points:
return self
def set_data(self, x: np.ndarray = None, y: np.ndarray = None, y_err: np.ndarray | float = None, replace_mask: bool = True) -> PointLike:
def set_data(self, x: np.ndarray = None, y: np.ndarray = None, y_err: np.ndarray = None) -> PointLike:
if x is None:
x = self._x
if y is None:
y = self._y
if y_err is None:
if y_err is not None:
y_err = self._y_err
self._x, self._y, self._y_err, mask = self._prepare_xy(x, y, y_err)
if replace_mask:
self.mask = mask
self._x, self._y, self._y_err, self.mask = self._prepare_xy(x, y, y_err)
return self
def append(self, x: ArrayLike, y: ArrayLike, y_err: ArrayLike = None, mask: ArrayLike = None):
if mask is None:
x, y, y_err, mask = self._prepare_xy(x, y, y_err)
else:
x, y, y_err, _ = self._prepare_xy(x, y, y_err)
def append(self, x: ArrayLike, y: ArrayLike, y_err: ArrayLike = None):
x, y, y_err, mask = self._prepare_xy(x, y, y_err)
self._x = np.r_[self._x, x]
self._y = np.r_[self._y, y]
@ -548,34 +541,6 @@ class Points:
return self
def binning(self, value: float):
if value <= 0:
raise ValueError('value must be a positive number')
copy = self.copy()
upper_lim = (self.x[-1]//value + 1) * value
lower_lim = (self.x[0]//value) * value
offset = value / 2
xbins = np.linspace(lower_lim - offset, upper_lim + offset, num=int((upper_lim-lower_lim)/value + 2))
n, _ = np.histogram(copy.x, bins=xbins)
sum_y, _ = np.histogram(copy.x, bins=xbins, weights=copy.y)
sum_yerr_2, _ = np.histogram(copy.x, bins=xbins, weights=copy.y_err**2)
isnan = n != 0
n = n[isnan]
sum_y = sum_y[isnan]
sum_yerr_2 = sum_yerr_2[isnan]
xaxis = (xbins[:-1] + offset)[isnan]
copy.set_data(xaxis, sum_y/n, y_err=np.sqrt(sum_yerr_2/n))
return copy
def shift(self, points: int) -> PointLike:
"""
Shift indexes of y values.

2
src/nmreval/distributions/base.py
View File

@ -29,7 +29,7 @@ class Distribution(abc.ABC):
@staticmethod
@abc.abstractmethod
def susceptibility(omega: ArrayLike, tau: ArrayLike, *args: Any):
def susceptibility(omega, tau, *args):
pass
@classmethod

3
src/nmreval/distributions/colecole.py
View File

@ -54,9 +54,6 @@ class ColeCole(Distribution):
tau (array_like):
alpha (float):
"""
if alpha == 1:
return tau / (1 + omega**2 * tau**2)
omtau = (omega*tau)**alpha
return np.sin(alpha*np.pi/2) * omtau / (1 + omtau**2 + 2*np.cos(alpha*np.pi/2)*omtau) / omega

122
src/nmreval/distributions/energy.py
View File

@ -1,18 +1,13 @@
from itertools import product
from ctypes import c_double, cast, pointer, c_void_p
import numpy as np
from scipy import LowLevelCallable
from scipy.integrate import quad, simps as simpson
from .base import Distribution
from ..lib.utils import ArrayLike
from ..utils.constants import kB
from .helper import HAS_C_FUNCS, lib
# noinspection PyMethodOverriding
class EnergyBarriers(Distribution):
name = 'Energy barriers'
parameter = [r'\tau_{0}', r'E_{m}', r'\Delta E']
@ -28,30 +23,24 @@ class EnergyBarriers(Distribution):
return np.exp(-e_a / (kB * te)) / t0
@staticmethod
def energy_distribution(e_a, mu, sigma):
def energydistribution(e_a, mu, sigma):
return np.exp(-0.5 * ((mu-e_a) / sigma) ** 2) / (np.sqrt(2 * np.pi) * sigma)
@staticmethod
def correlation(t: ArrayLike, temperature: ArrayLike, tau0: float, e_m: float, e_b: float) -> ArrayLike:
def correlation(t, temperature, *args):
tau0, e_m, e_b = args
def integrand(e_a, ti, t0, mu, sigma, te):
# correlation time would go to inf for higher energies, so we use rate
return np.exp(-ti*EnergyBarriers.rate(t0, e_a, te)) * EnergyBarriers.energydistribution(e_a, mu, sigma)
t = np.atleast_1d(t)
temperature = np.atleast_1d(temperature)
if HAS_C_FUNCS:
ret_val = _integrate_c(lib.energyDistCorrelation, t, temperature, tau0, e_m, e_b)
else:
ret_val = _integrate_py(_integrand_time, t, temperature, tau0, e_m, e_b)
e_axis = np.linspace(max(0, e_m-50*e_b), e_m+50*e_b, num=5001)
return ret_val
@staticmethod
def specdens(omega: ArrayLike, temperature: ArrayLike, tau0: float, e_m: float, e_b: float) -> ArrayLike:
omega = np.atleast_1d(omega)
temperature = np.atleast_1d(temperature)
if HAS_C_FUNCS:
ret_val = _integrate_c(lib.energyDist_SD, omega, temperature, tau0, e_m, e_b)
else:
ret_val = _integrate_py(_integrand_sd, omega, temperature, tau0, e_m, e_b)
ret_val = np.array([simpson(integrand(e_axis, o, tau0, e_m, e_b, tt), e_axis)
for o in t for tt in temperature])
return ret_val
@ -62,73 +51,70 @@ class EnergyBarriers(Distribution):
omega = np.atleast_1d(omega)
temperature = np.atleast_1d(temperature)
if HAS_C_FUNCS:
ret_val = _integrate_c(lib.energyDistSuscReal, omega, temperature, tau0, e_m, e_b) + \
1j * _integrate_c(lib.energyDistSuscImag, omega, temperature, tau0, e_m, e_b)
else:
ret_val = _integrate_py(_integrand_susc_real, omega, temperature, tau0, e_m, e_b) + \
1j * _integrate_py(_integrand_susc_imag, omega, temperature, tau0, e_m, e_b)
e_axis = np.linspace(max(0, e_m-50*e_b), e_m+50*e_b, num=5001)
ret_val = []
for o, tt in product(omega, temperature):
ret_val.append(simpson(_integrand_freq_real(e_axis, o, tau0, e_m, e_b, tt), e_axis) -
1j * simpson(_integrand_freq_imag(e_axis, o, tau0, e_m, e_b, tt), e_axis))
return np.array(ret_val)
@staticmethod
def specdens(omega, temperature, *args):
# in contrast to other spectral densities, it's omega and temperature
tau0, e_m, e_b = args
def integrand(e_a, w, t0, mu, sigma, t):
r = EnergyBarriers.rate(t0, e_a, t)
return r/(r**2 + w**2) * EnergyBarriers.energydistribution(e_a, mu, sigma)
omega = np.atleast_1d(omega)
temperature = np.atleast_1d(temperature)
e_axis = np.linspace(max(0, e_m-50*e_b), e_m+50*e_b, num=5001)
ret_val = np.array([simpson(integrand(e_axis, o, tau0, e_m, e_b, tt), e_axis)
for o in omega for tt in temperature])
return ret_val
@staticmethod
def mean(temperature, tau0, ea):
return tau0*np.exp(ea/(kB*temperature))
def mean(*args):
return args[1]*np.exp(args[2]/(kB*args[0]))
@staticmethod
def logmean(temperature, tau0, ea):
return tau0 + ea / (kB * temperature)
def logmean(*args):
return args[1] + args[2] / (kB * args[0])
@staticmethod
def max(*args):
return args[1] * np.exp(args[2] / (kB * args[0]))
# helper functions
def _integrate_c(func, omega: np.ndarray, temperature: np.ndarray, tau0: float, e_m: float, e_b: float) -> np.ndarray:
res = []
for o, t in product(omega, temperature):
c = (c_double * 5)(o, tau0, e_m, e_b, t)
user_data = cast(pointer(c), c_void_p)
area = quad(LowLevelCallable(func, user_data), 0, np.infty, epsabs=1e-13)[0]
res.append(area)
ret_val = np.array(res).reshape(omega.shape[0], temperature.shape[0])
return ret_val.squeeze()
def _integrate_process_imag(args):
pass
def _integrate_py(func, axis, temp, tau0, e_m, e_b):
x = np.atleast_1d(axis)
temperature = np.atleast_1d(temp)
e_axis = np.linspace(max(0., e_m - 50*e_b), e_m + 50*e_b, num=5001)
ret_val = []
for o, tt in product(x, temperature):
ret_val.append(simpson(func(e_axis, o, tau0, e_m, e_b, tt), e_axis))
ret_val = np.array(ret_val).reshape(x.shape[0], temperature.shape[0])
return ret_val.squeeze()
def _integrate_process_real(args):
omega_i, t, tau0, mu, sigma, temp_j = args
return quad(_integrand_freq_real(), 0, 10, args=(omega_i, t, tau0, mu, sigma, temp_j))[0]
# python integrands
def _integrand_sd(u, omega, tau0, mu, sigma, temp):
def _integrate_process_time(args):
omega_i, t, tau0, mu, sigma, temp_j = args
return quad(_integrand_time, 0, 10, args=(omega_i, t, tau0, mu, sigma, temp_j))[0]
def _integrand_freq_real(u, omega, tau0, mu, sigma, temp):
r = EnergyBarriers.rate(tau0, u, temp)
return r / (r**2 + omega**2) * EnergyBarriers.energy_distribution(u, mu, sigma)
return 1 / (r**2 + omega**2) * EnergyBarriers.energydistribution(u, mu, sigma)
def _integrand_susc_real(u, omega, tau0, mu, sigma, temp):
r = EnergyBarriers.rate(tau0, u, temp)
return 1 / (r**2 + omega**2) * EnergyBarriers.energy_distribution(u, mu, sigma)
def _integrand_susc_imag(u, omega, tau0, mu, sigma, temp):
def _integrand_freq_imag(u, omega, tau0, mu, sigma, temp):
rate = EnergyBarriers.rate(tau0, u, temp)
return omega * rate / (rate**2 + omega**2) * EnergyBarriers.energy_distribution(u, mu, sigma)
return omega * rate / (rate**2 + omega**2) * EnergyBarriers.energydistribution(u, mu, sigma)
def _integrand_time(u, t, tau0, mu, sigma, temp):
rate = EnergyBarriers.rate(tau0, u, temp)
return EnergyBarriers.energy_distribution(u, mu, sigma) * np.exp(-t*rate)
return EnergyBarriers.energydistribution(u, mu, sigma) * np.exp(-t*rate)

48
src/nmreval/distributions/helper.py
View File

@ -1,48 +0,0 @@
from pathlib import Path
from ctypes import CDLL, c_double, c_void_p
from ..lib.logger import logger
lib = None
try:
lib = CDLL(str(Path(__file__).parents[1] / 'clib' / 'integrate.so'))
# FFHS integrand
lib.ffhsSD.restype = c_double
lib.ffhsSD.argtypes = (c_double, c_void_p)
# Log-Gaussian integrands
lib.logGaussian_imag_high.restype = c_double
lib.logGaussian_imag_high.argtypes = (c_double, c_void_p)
lib.logGaussian_imag_low.restype = c_double
lib.logGaussian_imag_low.argtypes = (c_double, c_void_p)
lib.logGaussian_real_high.restype = c_double
lib.logGaussian_real_high.argtypes = (c_double, c_void_p)
lib.logGaussian_real_low.restype = c_double
lib.logGaussian_real_low.argtypes = (c_double, c_void_p)
lib.logGaussianCorrelation.restype = c_double
lib.logGaussianCorrelation.argtypes = (c_double, c_void_p)
# integrands for distribution of energies
lib.energyDist_SD.restype = c_double
lib.energyDist_SD.argtypes = (c_double, c_void_p)
lib.energyDistCorrelation.restype = c_double
lib.energyDistCorrelation.argtypes = (c_double, c_void_p)
lib.energyDistSuscReal.restype = c_double
lib.energyDistSuscReal.argtypes = (c_double, c_void_p)
lib.energyDistSuscImag.restype = c_double
lib.energyDistSuscImag.argtypes = (c_double, c_void_p)
HAS_C_FUNCS = True
logger.info('Use C functions')
except OSError:
HAS_C_FUNCS = False
logger.info('Use python functions')

35
src/nmreval/distributions/intermolecular.py
View File

@ -1,16 +1,9 @@
import ctypes
import numpy as np
from scipy import LowLevelCallable
from scipy.integrate import quad
from .helper import HAS_C_FUNCS, lib
from .base import Distribution
# Everything except spectral density is implemented in Python only because the only use case of FFHS is NMR
# field cycling measurements with T1 results
class FFHS(Distribution):
name = 'Intermolecular (FFHS)'
parameter = None
@ -26,30 +19,19 @@ class FFHS(Distribution):
def integrand(u, tt, tau0):
return FFHS.distribution(u, tau0) * np.exp(-tt/u) / u
ret_val = np.array([quad(integrand, 0, np.infty, args=(tt, tau0))[0] for tt in t])
ret_val = np.array([quad(integrand, 0, np.infty, args=(tt, tau0), epsabs=1e-12, epsrel=1e-12)[0] for tt in t])
return ret_val
@staticmethod
def specdens_py(omega, tau0):
def specdens(omega, tau0, *args):
def integrand(u, o, tau0):
return u**4 * tau0 / (81 + 9*u**2 - 2*u**4 + u**6) / (u**4 + (o*tau0)**2)
# return FFHS.distribution(u, tau0) * u / (1+o**2 * u**2)
ret_val = np.array([quad(integrand, 0, np.infty, args=(o, tau0))[0] for o in omega])
ret_val = np.array([quad(integrand, 0, np.infty, args=(o, tau0), epsabs=1e-12, epsrel=1e-12)[0] for o in omega])
return ret_val * 54 / np.pi
@staticmethod
def specdens_c(omega, tau0):
res = []
for o in omega:
c = (ctypes.c_double * 2)(o, tau0)
user_data = ctypes.cast(ctypes.pointer(c), ctypes.c_void_p)
func = LowLevelCallable(lib.ffhsSD, user_data)
res.append(quad(func, 0, np.infty)[0])
return np.array(res) * 54 / np.pi
return ret_val
@staticmethod
def susceptibility(omega, tau0, *args):
@ -59,16 +41,15 @@ class FFHS(Distribution):
def integrand_imag(u, o, tau0):
return FFHS.distribution(u, tau0) * o*u / (1+o**2 * u**2)
ret_val = np.array([quad(integrand_real, 0, np.infty, args=(o, tau0))[0] for o in omega], dtype=complex)
ret_val = np.array([quad(integrand_real, 0, np.infty, args=(o, tau0),
epsabs=1e-12, epsrel=1e-12)[0] for o in omega], dtype=complex)
ret_val.imag += np.array([quad(integrand_imag, 0, np.infty, args=(o, tau0))[0] for o in omega])
ret_val.imag += np.array([quad(integrand_imag, 0, np.infty, args=(o, tau0),
epsabs=1e-12, epsrel=1e-12)[0] for o in omega])
return ret_val
FFHS.specdens = FFHS.specdens_c if HAS_C_FUNCS else FFHS.specdens_py
# class Bessel(Distribution):
# name = 'Intermolecular (Bessel)'
# parameter = None

165
src/nmreval/distributions/loggaussian.py
View File

@ -1,13 +1,7 @@
import ctypes
from multiprocessing import Pool, cpu_count
from itertools import product
from typing import Callable
import numpy as np
from scipy import LowLevelCallable
from scipy.special import erf
from nmreval.lib.utils import ArrayLike
try:
from scipy.integrate import simpson
@ -15,146 +9,89 @@ except ImportError:
from scipy.integrate import simps as simpson
from scipy.integrate import quad
from nmreval.distributions.helper import HAS_C_FUNCS, lib
from nmreval.distributions.base import Distribution
from .base import Distribution
__all__ = ['LogGaussian']
# noinspection PyMethodOverriding
class LogGaussian(Distribution):
name = 'Log-Gaussian'
parameter = [r'\sigma']
bounds = [(0, 10)]
@staticmethod
def distribution(tau: ArrayLike, tau0: ArrayLike, sigma: float) -> ArrayLike:
def distribution(tau, tau0, sigma: float):
return np.exp(-0.5*(np.log(tau/tau0)/sigma)**2)/np.sqrt(2*np.pi)/sigma
@staticmethod
def correlation(t: ArrayLike, tau0: ArrayLike, sigma: float):
def correlation(t, tau0, sigma: float):
_t = np.atleast_1d(t)
_tau = np.atleast_1d(tau0)
if HAS_C_FUNCS:
res = _integrate_correlation_c(_t, _tau, sigma)
else:
res = _integration_parallel(_t, _tau, sigma, _integrate_process_time)
pool = Pool(processes=min(cpu_count(), 4))
integration_ranges = [(omega_i, tau_j, sigma) for (omega_i, tau_j) in product(_t, _tau)]
return res.squeeze()
@staticmethod
def susceptibility(omega: ArrayLike, tau0: ArrayLike, sigma: float):
_omega = np.atleast_1d(omega)
_tau = np.atleast_1d(tau0)
if HAS_C_FUNCS:
res_real = _integrate_susc_real_c(_omega, _tau, sigma)
res_imag = _integrate_susc_imag_c(_omega, _tau, sigma)
else:
res_real = _integration_parallel(_omega, _tau, sigma, _integrate_process_imag)
res_imag = _integration_parallel(_omega, _tau, sigma, _integrate_process_real)
return (res_real + 1j * res_imag).squeeze()
@staticmethod
def specdens(omega: ArrayLike, tau: ArrayLike, sigma: float) -> np.ndarray:
_omega = np.atleast_1d(omega)
_tau = np.atleast_1d(tau)
if HAS_C_FUNCS:
ret_val = _integrate_susc_imag_c(_omega, _tau, sigma)
else:
ret_val = _integration_parallel(_omega, _tau, sigma, _integrate_process_imag)
ret_val /= _omega[:, None]
ret_val[_omega == 0, :] = _tau[None, :] * np.exp(sigma**2 / 2)
with np.errstate(divide='ignore'):
res = np.array(pool.map(_integrate_process_time, integration_ranges))
ret_val = res.reshape((_t.shape[0], _tau.shape[0]))
return ret_val.squeeze()
@staticmethod
def mean(tau, sigma):
return tau*np.exp(sigma**2 / 2)
def susceptibility(omega, tau0, sigma: float):
_omega = np.atleast_1d(omega)
_tau = np.atleast_1d(tau0)
pool = Pool(processes=min(cpu_count(), 4))
integration_ranges = [(omega_i, tau_j, sigma) for (omega_i, tau_j) in product(_omega, _tau)]
with np.errstate(divide='ignore'):
res_real = np.array(pool.map(_integrate_process_imag, integration_ranges))
res_imag = np.array(pool.map(_integrate_process_real, integration_ranges))
ret_val = (res_real+1j*res_imag).reshape((_omega.shape[0], _tau.shape[0]))
return ret_val.squeeze()
@staticmethod
def specdens(omega, tau0, sigma):
_omega = np.atleast_1d(omega)
_tau = np.atleast_1d(tau0)
pool = Pool(processes=min(cpu_count(), 4))
integration_ranges = [(omega_i, tau_j, sigma) for (omega_i, tau_j) in product(_omega, _tau)]
with np.errstate(divide='ignore'):
res = np.array(pool.map(_integrate_process_imag, integration_ranges))
ret_val = res.reshape((_omega.shape[0], _tau.shape[0]))
ret_val /= _omega[:, None]
return ret_val.squeeze()
def mean(*args):
return args[0]*np.exp(args[1]**2 / 2)
def _integration_parallel(x: np.ndarray, tau: np.ndarray, sigma: float, func: Callable) -> np.ndarray:
pool = Pool(processes=min(cpu_count(), 4))
integration_ranges = [(x_i, tau_j, sigma) for (x_i, tau_j) in product(x, tau)]
with np.errstate(divide='ignore'):
res = pool.map(func, integration_ranges)
res = np.array(res).reshape((x.shape[0], tau.shape[0]))
return res
def _integrate_susc_imag_c(omega: np.ndarray, tau: np.ndarray, sigma: float) -> np.ndarray:
return _integrate_susc_c(lib.logGaussian_imag_low, lib.logGaussian_imag_high, omega, tau, sigma)
def _integrate_susc_real_c(omega: np.ndarray, tau: np.ndarray, sigma: float) -> np.ndarray:
return _integrate_susc_c(lib.logGaussian_real_low, lib.logGaussian_real_high, omega, tau, sigma)
def _integrate_susc_c(lowfunc, highfunc, omega, tau, sigma):
res = []
for o, t in product(omega, tau):
c = (ctypes.c_double * 3)(o, t, sigma)
user_data = ctypes.cast(ctypes.pointer(c), ctypes.c_void_p)
area = 0
for (func, limits) in [(highfunc, (0, np.inf)), (lowfunc, (-np.infty, 0))]:
epsabs = 1e-12
while epsabs > 1e-25:
a = quad(LowLevelCallable(func, user_data), *limits, epsabs=epsabs, epsrel=1e-12, full_output=1)
if a[2]['last'] > 2 or a[0] < 1e-48:
break
epsabs /= 10.
area += a[0]
res.append(area)
res = np.asanyarray(res).reshape((omega.shape[0], tau.shape[0]))
return res
def _integrate_process_imag(omega, tau, sigma):
area = quad(_integrand_freq_imag_high, 0, 50, args=(omega, tau, sigma), epsabs=1e-12, epsrel=1e-12)[0]
area += quad(_integrand_freq_imag_low, -50, 0, args=(omega, tau, sigma), epsabs=1e-12, epsrel=1e-12)[0]
def _integrate_process_imag(args):
omega_i, tau_j, sigma = args
area = quad(_integrand_freq_imag_high, 0, 50, args=(omega_i, tau_j, sigma))[0]
area += quad(_integrand_freq_imag_low, -50, 0, args=(omega_i, tau_j, sigma))[0]
return area
def _integrate_process_real(omega: float, tau: float, sigma: float):
area = quad(_integrand_freq_real_high, 0, 50, args=(omega, tau, sigma))[0]
area += quad(_integrand_freq_real_low, -50, 0, args=(omega, tau, sigma))[0]
def _integrate_process_real(args):
omega_i, tau_j, sigma = args
area = quad(_integrand_freq_real_high, 0, 50, args=(omega_i, tau_j, sigma))[0]
area += quad(_integrand_freq_real_low, -50, 0, args=(omega_i, tau_j, sigma))[0]
return area
def _integrate_correlation_c(t, tau, sigma):
res = []
for t_i, tau_i in product(t, tau):
c = (ctypes.c_double * 3)(t_i, tau_i, sigma)
user_data = ctypes.cast(ctypes.pointer(c), ctypes.c_void_p)
area = quad(LowLevelCallable(lib.logGaussianCorrelation, user_data), -np.infty, np.infty)[0]
res.append(area)
res = np.asanyarray(res).reshape((t.shape[0], tau.shape[0]))
return res
def _integrate_process_time(omega, tau, sigma):
return quad(_integrand_time, -50, 50, args=(omega, tau, sigma), epsabs=1e-12, epsrel=1e-12)[0]
def _integrate_process_time(args):
omega_i, tau_j, sigma = args
return quad(_integrand_time, -50, 50, args=(omega_i, tau_j, sigma))[0]
def _integrand_time(u, t, tau, sigma):

289
src/nmreval/dsc/calibration.py Normal file
View File

@ -0,0 +1,289 @@
import os
import argparse
import sys
import numpy as np
import matplotlib.pyplot as plt
import scipy.interpolate
from scipy.integrate import simps
from ..io.dsc import DSCSample, Cyclohexane
parser = argparse.ArgumentParser(description='Calibrate DSC data')
parser.add_argument('sample', type=str, help='filename of DSC sample')
parser.add_argument('empty', type=str, help='filename of empty pan')
parser.add_argument('reference', help='filename of reference', type=str)
parser.add_argument('--cooling', help='Show figure of found cooling rates', action='store_true')
def evaluate(sample, empty, reference, ref_points=Cyclohexane, show_cooling=False):
sample = DSCSample(sample)
empty = DSCSample(empty)
reference = DSCSample(reference)
if show_cooling:
fig, ax = plt.subplots()
print('\n')
for k, v in sample.cooling.items():
print('Plot run {} with cooling rate {} K/min'.format(k, v))
c = sample.flow_data(v, mode='c')
ax.plot(c[0], c[1], label=str(v)+' K/min')
ax.set_xlabel('T / K')
plt.legend()
plt.show()
return
run_list = []
if len(sample.heating) > 1:
run = None
print('\nMultiple heat rates found:')
for k, v in sample.heating.items():
print(' run {}: {} K/min'.format(k, v))
while run not in sample.heating:
# choose your own adventure!!!
value = input('\nPlease select a run (press Enter for all heat rates): ')
if value == '':
run_list = list(sample.heating.keys())
break
else:
run = int(value)
run_list = [run]
else:
run_list = list(sample.heating.keys())
for run in run_list:
rate = sample.heating[run]
print('\nProcessing heat rate {} K/min'.format(rate))
print('Load data of heating data')
len_sample = sample.length(run)
# sanity checks
try:
reference_data = reference.flow_data(rate)
except IndexError:
print('ERROR: Reference measurement has no heat rate {} K/min'.format(rate))
print('Stop evaluation')
sys.exit()
try:
run_baseline = empty.get_run(rate)
except ValueError:
print('ERROR: Empty measurement has no heat rate {} K/min'.format(rate))
print('Stop evaluation')
sys.exit()
len_baseline = empty.length(run_baseline)
if len_baseline != len_sample:
print('WARNING: measurements differ by {} points'.format(abs(len_baseline - len_sample)))
# max_length = min(len_baseline, len_sample)
sample_data = sample.flow_data(rate, length=None)
empty_data = empty.flow_data(rate, length=None)
# plot input data
fig1, ax1 = plt.subplots(2, 3, **{'figsize': (10, 6)})
ax1[0, 0].set_title('raw data')
ax1[0, 0].set_xlabel('T / K')
ax1[0, 0].plot(sample_data[0], sample_data[1], 'k-', label='Sample')
ax1[0, 0].plot(empty_data[0], empty_data[1], 'b-', label='Empty')
ax1[0, 0].plot(reference_data[0], reference_data[1], 'r-', label='Reference')
ax1[0, 0].legend()
print('Substract empty data\n')
sample_baseline = sample_data.copy()
empty_y = empty_data[1]
if len_sample != len_baseline:
with np.errstate(all='ignore'):
empty_y = scipy.interpolate.interp1d(empty_data[0], empty_data[1],
fill_value='extrapolate')(sample_data[0])
sample_baseline[1] = sample_data[1] - empty_y
# plot baseline correction
ax1[0, 1].set_title('baseline correction')
ax1[0, 1].set_xlabel('T / K')
ax1[0, 1].plot(sample_data[0], sample_data[1], 'k--', label='Raw')
ax1[0, 1].plot(sample_baseline[0], sample_baseline[1], 'k-', label='Baseline corrected')
ax1[0, 1].plot(empty_data[0], empty_data[1], 'b-', label='Empty')
ax1[0, 1].legend()
print('Load isothermal data around heat rate')
mean_isotherms = []
for offset, where, ls in [(-1, 'low', '-'), (1, 'high', '--')]:
# read isotherms and baseline correct
len_baseline = empty.length(run_baseline+offset)
len_sample = sample.length(run+offset)
if len_baseline != len_sample:
print('WARNING: {} T isotherms differ by {} points'.format(where, abs(len_baseline-len_sample)))
max_length = min(len_baseline, len_sample)
isotherm_sample = sample.isotherm_data(run_baseline+offset, length=max_length)
isotherm_empty = empty.isotherm_data(run+offset, length=max_length)
isotherm_sample[1] -= isotherm_empty[1]
# get mean isotherm value
m = np.polyfit(isotherm_sample[0, 200:-200], isotherm_sample[1, 200:-200], 0)[0]
mean_isotherms.append(m)
print('Calculated {} heat flow: {:.4} mW'.format(where, m))
ax1[0, 2].plot(isotherm_sample[0], isotherm_sample[1], 'k--')
# calculate slope from difference between isotherms
slope = (mean_isotherms[1]-mean_isotherms[0]) / (sample_data[2, -1] - empty_data[2, 0])
print('Heat flow slope from isotherms: {:.4} per minute'.format(slope*60))
# calculate mean slope of heat flow at points in the beginning
slope_baseline = np.gradient(sample_baseline[1, int(4000/rate):int(9000/rate)],
sample_baseline[2, 300]-sample_baseline[2, 299]).mean()
print('Heat flow slope from initial heating: {:.4f} per minute\n'.format(slope_baseline*60))
drift_corrected = sample_baseline[1] - mean_isotherms[0] - (sample_baseline[2]-empty_data[2, 0])*slope
drift_from_slope = sample_baseline[1] - mean_isotherms[0] - (sample_baseline[2]-empty_data[2, 0])*slope_baseline
# plot
ax1[0, 2].axhline(mean_isotherms[0], linestyle=':')
ax1[0, 2].axhline(mean_isotherms[1], linestyle=':')
ax1[0, 2].plot(sample_baseline[2], sample_baseline[1], 'k-', label='Baseline corrected')
ax1[0, 2].plot(sample_baseline[2], drift_corrected, 'g-', label='Corrected (isotherm)')
ax1[0, 2].plot(sample_baseline[2], drift_from_slope, 'b-', label='Corrected (heating)')
ax1[0, 2].plot(sample_baseline[2], mean_isotherms[0] + (sample_baseline[2]-empty_data[2, 0])*slope, 'g--')
ax1[0, 2].plot(sample_baseline[2], mean_isotherms[0] + slope_baseline*(sample_baseline[2]-empty_data[2, 0]),
'b--')
ax1[0, 2].plot(sample_baseline[2, int(4000/rate):int(9000/rate)],
sample_baseline[1, int(4000/rate):int(9000/rate)], 'r--')
ax1[0, 2].set_title('time dependence')
ax1[0, 2].set_xlabel('t / s')
ax1[0, 2].legend()
melts = []
for i, (ref_temp, enthalpy) in enumerate(ref_points.transitions):
# region around reference peaks
t_low_lim = ref_temp - 15
t_high_lim = ref_temp + 15
low_border = np.argmin(np.abs(reference_data[0]-t_low_lim))
high_border = np.argmin(np.abs(reference_data[0]-t_high_lim))
ref_zoom = reference_data[:, low_border:high_border]
x_val = np.array([[ref_zoom[0, 0], 1],
[ref_zoom[0, -1], 1]])
y_val = np.array([ref_zoom[1, 0],
ref_zoom[1, -1]])
print('Baseline correct reference of %.2f transition' % ref_temp)
sol = np.linalg.solve(x_val, y_val)
ref_zoom[1] -= (ref_zoom[0] * sol[0] + sol[1])
peak_max = ref_zoom[:, np.argmax(ref_zoom[1])]
integration_limit = np.argmin(abs(ref_zoom[0]-peak_max[0]+3)), np.argmin(abs(ref_zoom[0]-peak_max[0]-3))
# substract baseline around reference peaks
x_val = np.array([[ref_zoom[0, integration_limit[0]], 1],
[ref_zoom[0, integration_limit[1]], 1]])
y_val = np.array([ref_zoom[1, integration_limit[0]],
ref_zoom[1, integration_limit[1]]])
print('Baseline correct reference of %.2f transition' % ref_temp)
sol = np.linalg.solve(x_val, y_val)
ref_zoom[1] -= (ref_zoom[0] * sol[0] + sol[1])
# calculate onset slope (use points at position of maximum gradient +/- 100/rate)
ref_grad = np.gradient(ref_zoom[1])
max_grad = np.argmax(ref_grad)
x_val = np.array([[ref_zoom[0, max_grad-int(100/rate)], 1],
[ref_zoom[0, max_grad+int(100/rate)+1], 1]])
y_val = np.array([ref_zoom[1, max_grad-int(100/rate)],
ref_zoom[1, max_grad+int(100/rate)+1]])
sol = np.linalg.solve(x_val, y_val)
onset = sol[0]*ref_zoom[0] + sol[1]
melts.append(-sol[1]/sol[0])
# plot
ax1[1, i].set_title(f'reference: {ref_temp:.2f}')
ax1[1, i].set_xlabel('T / K')
ax1[1, i].plot(reference_data[0], reference_data[1], 'r-')
ax1[1, i].plot(ref_zoom[0, max_grad], ref_zoom[0, max_grad], 'kx')
ax1[1, i].plot(ref_zoom[0], onset, 'k--')
ax1[1, i].axhline(0, color='k', linestyle='--')
ax1[1, i].set_xlim(ref_zoom[0, integration_limit[0]], ref_zoom[0, integration_limit[1]])
ax1[1, i].set_ylim(-max(ref_zoom[1])/10, max(ref_zoom[1])*1.1)
print('Onset of transition: %.2f K found at %.2f' % (ref_temp, melts[-1]))
if enthalpy is not None:
# integrate over low temperature peak to calibrate y axis
# delta H in J/g: Integrate Peak over time and divide by weight
area = 1e-3 * simps(ref_zoom[1, integration_limit[0]:integration_limit[1]],
ref_zoom[2, integration_limit[0]:integration_limit[1]],
even='avg')
calib_y_axis = enthalpy / (area / reference.weight)
print("Calibration factor of peak: %f\n" % calib_y_axis)
sample_baseline[1] *= calib_y_axis
fig1.delaxes(ax1[1, 2])
fig1.tight_layout()
plt.show()
# give a choice how to compensate for long-time drift
mode = None
while mode not in ['i', 'h']:
mode = input('\nUse [i]sotherms or initial [h]eating for long-time correction? (Default: i) ')
if mode == '':
mode = 'i'
if mode == 'h':
print('\nCorrect slope from initial heating')
sample_baseline[1] = drift_from_slope
else:
print('\nCorrect slope from isotherm')
sample_baseline[1] = drift_corrected
# calibrate T axis
print('\nCalibrate temperature')
real_trans = np.array([temp for (temp, _) in ref_points.transitions])
t_vals = np.array([[melts[0], 1],
[melts[1], 1]])
calibration_temp = np.linalg.solve(t_vals, real_trans)
print('T_real = {:.4f} * T_meas {:+.4f}'.format(*calibration_temp))
sample_baseline[0] = calibration_temp[0] * sample_baseline[0] + calibration_temp[1]
print('Convert to capacity')
cp = sample_baseline[1] * 60. / rate / sample.weight / 1000.
if sample.weight is None:
raise ValueError('No sample weight given')
# plot final results in separate figure
fig2, ax2 = plt.subplots()
ax2.set_title('{} K/min: Heat flow vs. heat capacity (close to cont.)'.format(rate))
ax2.set_xlabel('Temperature / K')
ax2.plot(sample_baseline[0], sample_baseline[1], label='heat flow')
ax2.plot(sample_baseline[0], cp, label='heat capacity')
plt.legend()
plt.show()
outname = os.path.splitext(sample.name)[0] + '_' + str(rate) + 'K-min.dat'
header = 'Made with version: {}\n'.format(__version__)
header += 'T/K\tCp/J/(gK)\theat flow/mW'
print()
print('Save to', outname)
np.savetxt(outname, np.c_[sample_baseline[0], cp, sample_baseline[1]], header=header)
if __name__ == '__main__':
args = parser.parse_args()
evaluate(args.sample, args.empty, args.reference, show_cooling=args.cooling)

292
src/nmreval/dsc/dsc_calibration_fast_neu.py Normal file
View File

@ -0,0 +1,292 @@
from __future__ import annotations
__version__ = '0.1.2'
import os
from argparse import ArgumentParser
from pathlib import Path
import sys
import numpy as np
import matplotlib.pyplot as plt
from scipy.integrate import simps
from nmreval.io.dsc import DSCReader, Cyclohexane, ReferenceValue
parser = ArgumentParser(description='Calibrate DSC data')
parser.add_argument('sample', type=str, help='filename of DSC sample')
parser.add_argument('empty', type=str, help='filename of empty pan')
parser.add_argument('reference', help='filename of reference', type=str)
parser.add_argument('--cooling', help='Plot found cooling rates', action='store_true')
def evaluate(sample: str|Path, empty: str|Path, reference: str|Path,
ref_points: ReferenceValue = Cyclohexane, show_cooling: bool = False):
sample = DSCReader(sample)
empty = DSCReader(empty)
reference = DSCReader(reference)
print(sample)
if show_cooling:
fig, ax = plt.subplots()
print('\n')
for k, v in sample.cooling.items():
print('Plot run {} with cooling rate {} K/min'.format(k, v))
c = sample.flow_data(v, mode='c')
ax.plot(c[0], c[1], label=str(v)+' K/min')
ax.set_xlabel('T / K')
plt.legend()
plt.show()
return
run_list = []
if len(sample.heating) > 1:
run = None
print('\nMultiple heat rates found:')
for k, v in sample.heating.items():
print(' run {}: {} K/min'.format(k, v))
while run not in sample.heating:
# choose your own adventure!!!
value = input('\nPlease select a run (press Enter for all heat rates): ')
if value == '':
run_list = list(sample.heating.keys())
break
else:
run = int(value)
run_list = [run]
else:
run_list = list(sample.heating.keys())
for run in run_list:
rate = sample.heating[run]
print('\nProcessing heat rate {} K/min'.format(rate))
print('Load data of heating data')
len_sample = sample.length(run)
# sanity checks
try:
reference_data = reference.flow_data(rate)
except IndexError:
print('ERROR: Reference measurement has no heat rate {} K/min'.format(rate))
print('Stop evaluation')
sys.exit()
try:
run_baseline = empty.get_run(rate)
except ValueError:
print('ERROR: Empty measurement has no heat rate {} K/min'.format(rate))
print('Stop evaluation')
sys.exit()
len_baseline = empty.length(run_baseline)
max_length = None
if len_baseline != len_sample:
print('WARNING: measurements differ by {} points'.format(abs(len_baseline - len_sample)))
max_length = min(len_baseline, len_sample)
sample_data = sample.flow_data(rate, length=max_length)
empty_data = empty.flow_data(rate, length=max_length)
# plot input data
fig1, ax1 = plt.subplots(2, 3, **{'figsize': (10, 6)})
ax1[0, 0].set_title('raw data')
ax1[0, 0].set_xlabel('T / K')
ax1[0, 0].plot(sample_data[0], sample_data[1], 'k-', label='Sample')
ax1[0, 0].plot(empty_data[0], empty_data[1], 'b-', label='Empty')
ax1[0, 0].plot(reference_data[0], reference_data[1], 'r-', label='Reference')
ax1[0, 0].legend()
print('Substract empty data')
sample_baseline = sample_data.copy()
sample_baseline[1] = sample_data[1] - empty_data[1]
# plot baseline correction
ax1[0, 1].set_title('baseline correction')
ax1[0, 1].set_xlabel('T / K')
ax1[0, 1].plot(sample_data[0], sample_data[1], 'k--', label='Raw')
ax1[0, 1].plot(sample_baseline[0], sample_baseline[1], 'k-', label='Baseline corrected')
ax1[0, 1].plot(empty_data[0], empty_data[1], 'b-', label='Empty')
ax1[0, 1].legend()
print('Load isothermal data around heat rate')
mean_isotherms = []
for offset, where, ls in [(-1, 'low', '-'), (1, 'high', '--')]:
# read isotherms and baseline correct
len_baseline = empty.length(run_baseline+offset)
len_sample = sample.length(run+offset)
if len_baseline != len_sample:
print('WARNING: {} T isotherms differ by {} points'.format(where, abs(len_baseline-len_sample)))
max_length = min(len_baseline, len_sample)
isotherm_sample = sample.isotherm_data(run_baseline+offset, length=max_length)
isotherm_empty = empty.isotherm_data(run+offset, length=max_length)
isotherm_sample[1] -= isotherm_empty[1]
# get mean isotherm value
m = np.polyfit(isotherm_sample[0, 200:-200], isotherm_sample[1, 200:-200], 0)[0]
mean_isotherms.append(m)
print('Calculated {} heat flow: {} mW'.format(where, m))
ax1[0, 2].plot(isotherm_sample[0], isotherm_sample[1], 'k--')
# calculate slope from difference between isotherms
slope = (mean_isotherms[1]-mean_isotherms[0]) / (sample_data[2, -1] - empty_data[2, 0])
print('Heat flow slope from isotherms: {} per minute'.format(slope*60))
# calculate mean slope of heat flow at points in the beginning
slope_baseline = np.gradient(sample_baseline[1, int(4000/rate):int(9000/rate)],
sample_baseline[2, 300]-sample_baseline[2, 299]).mean()
print('Heat flow slope from initial heating: {} per minute'.format(slope_baseline*60))
drift_corrected = sample_baseline[1] - mean_isotherms[0] - (sample_baseline[2]-empty_data[2, 0])*slope
drift_from_slope = sample_baseline[1] - mean_isotherms[0] - (sample_baseline[2]-empty_data[2, 0])*slope_baseline
# plot
ax1[0, 2].axhline(mean_isotherms[0], linestyle=':')
ax1[0, 2].axhline(mean_isotherms[1], linestyle=':')
ax1[0, 2].plot(sample_baseline[2], sample_baseline[1], 'k-', label='Baseline corrected')
ax1[0, 2].plot(sample_baseline[2], drift_corrected, 'g-', label='Corrected (isotherm)')
ax1[0, 2].plot(sample_baseline[2], drift_from_slope, 'b-', label='Corrected (heating)')
ax1[0, 2].plot(sample_baseline[2], mean_isotherms[0] + (sample_baseline[2]-empty_data[2, 0])*slope, 'g--')
ax1[0, 2].plot(sample_baseline[2], mean_isotherms[0] + slope_baseline*(sample_baseline[2]-empty_data[2, 0]),
'b--')
ax1[0, 2].plot(sample_baseline[2, int(4000/rate):int(9000/rate)],
sample_baseline[1, int(4000/rate):int(9000/rate)], 'r--')
ax1[0, 2].set_title('time dependence')
ax1[0, 2].set_xlabel('t / s')
ax1[0, 2].legend()
melts = []
for i, (trans_temp, enthalpy) in enumerate(ref_points.transitions):
print(trans_temp, enthalpy)
# region around reference peaks
# NOTE: limits are hard coded for cyclohexane, other references need other limits
low_border = np.argmin(abs(reference_data[0]-(trans_temp-15)))
high_border = np.argmin(abs(reference_data[0]-(trans_temp+15)))
ref_zoom = reference_data[:, low_border:high_border]
x_val = np.array([[ref_zoom[0, 0], 1],
[ref_zoom[0, -1], 1]])
y_val = np.array([ref_zoom[1, 0],
ref_zoom[1, -1]])
print('Baseline correct reference of {} transition'.format(trans_temp))
sol = np.linalg.solve(x_val, y_val)
ref_zoom[1] -= (ref_zoom[0] * sol[0] + sol[1])
peak_max = ref_zoom[:, np.argmax(ref_zoom[1])]
integration_limit = np.argmin(abs(ref_zoom[0]-peak_max[0]+3)), np.argmin(abs(ref_zoom[0]-peak_max[0]-3))
# substract baseline around reference peaks
x_val = np.array([[ref_zoom[0, integration_limit[0]], 1],
[ref_zoom[0, integration_limit[1]], 1]])
y_val = np.array([ref_zoom[1, integration_limit[0]],
ref_zoom[1, integration_limit[1]]])
print('Baseline correct reference of {} transition'.format(trans_temp))
sol = np.linalg.solve(x_val, y_val)
ref_zoom[1] -= (ref_zoom[0] * sol[0] + sol[1])
# calculate onset slope (use points at position of maximum gradient +/- 100/rate)
ref_grad = np.gradient(ref_zoom[1])
max_grad = np.argmax(ref_grad)
x_val = np.array([[ref_zoom[0, max_grad-int(100/rate)], 1],
[ref_zoom[0, max_grad+int(100/rate)+1], 1]])
y_val = np.array([ref_zoom[1, max_grad-int(100/rate)],
ref_zoom[1, max_grad+int(100/rate)+1]])
sol = np.linalg.solve(x_val, y_val)
onset = sol[0]*ref_zoom[0] + sol[1]
melts.append(-sol[1]/sol[0])
# plot
ax1[1, i].set_title('reference: {:.2f} K'.format(trans_temp))
ax1[1, i].set_xlabel('T / K')
ax1[1, i].plot(reference_data[0], reference_data[1], 'r-')
ax1[1, i].plot(ref_zoom[0, max_grad], ref_zoom[0, max_grad], 'kx')
ax1[1, i].plot(ref_zoom[0], onset, 'k--')
ax1[1, i].axhline(0, color='k', linestyle='--')
ax1[1, i].set_xlim(ref_zoom[0, integration_limit[0]], ref_zoom[0, integration_limit[1]])
ax1[1, i].set_ylim(-max(ref_zoom[1])/10, max(ref_zoom[1])*1.1)
print('Onset of transition: {:.2f} K, should be at {:.2f}'.format(melts[-1], trans_temp))
if enthalpy is not None:
# integrate over low temperature peak to calibrate y axis
# NOTE: again, this is only valid for cyclohexane
# delta H in J/g: Integrate Peak over time and divide by weight
area = 1e-3 * simps(ref_zoom[1, integration_limit[0]:integration_limit[1]],
ref_zoom[2, integration_limit[0]:integration_limit[1]],
even='avg')
calib_y_axis = enthalpy / (area / reference.weight)
print("Calibration factor of peak: {}".format(calib_y_axis))
sample_baseline[1] *= calib_y_axis
fig1.delaxes(ax1[1, 2])
fig1.tight_layout()
plt.show()
# give a choice how to compensate for long-time drift
mode = None
while mode not in ['i', 'h']:
mode = input('\nUse [i]sotherms or initial [h]eating for long-time correction? (Default: i) ')
if mode == '':
mode = 'i'
if mode == 'h':
print('\nCorrect slope from initial heating')
sample_baseline[1] = drift_from_slope
else:
print('\nCorrect slope from isotherm')
sample_baseline[1] = drift_corrected
# calibrate T axis
print('\nCalibrate temperature')
real_trans = np.array([ref_points.transition1, ref_points.transition2])
t_vals = np.array([[melts[0], 1],
[melts[1], 1]])
calibration_temp = np.linalg.solve(t_vals, real_trans)
print('T_real = {:.4f} * T_meas {:+.4f}'.format(*calibration_temp))
sample_baseline[0] = calibration_temp[0] * sample_baseline[0] + calibration_temp[1]
print('Convert to capacity')
cp = sample_baseline[1] * 60. / rate / sample.weight / 1000.
if sample.weight is None:
raise ValueError('No sample weight given')
# plot final results in separate figure
fig2, ax2 = plt.subplots()
ax2.set_title('{} K/min: Heat flow vs. heat capacity (close to cont.)'.format(rate))
ax2.set_xlabel('Temperature / K')
ax2.plot(sample_baseline[0], sample_baseline[1], label='heat flow')
ax2.plot(sample_baseline[0], cp, label='heat capacity')
plt.legend()
plt.show()
outname = os.path.splitext(sample.name)[0] + '_' + str(rate) + 'K-min.dat'
header = 'Made with version: {}\n'.format(__version__)
header += 'T/K\tCp/J/(gK)\theat flow/mW'
print()
print('Save to', outname)
np.savetxt(outname, np.c_[sample_baseline[0], cp, sample_baseline[1]], header=header)
if __name__ == '__main__':
args = parser.parse_args()
evaluate(args.sample, args.empty, args.reference, show_cooling=args.cooling)

27
src/nmreval/dsc/hodge.py
View File

@ -1,27 +0,0 @@
import numpy as np
from scipy.stats import linregress
from nmreval.data import Points
from nmreval.fit.minimizer import FitRoutine
from nmreval.fit.result import FitResult
from nmreval.lib.utils import ArrayLike
from nmreval.models import Arrhenius
from nmreval.utils import kB
def tau_hodge(tg: ArrayLike, rate: ArrayLike) -> (Points, FitResult):
rate = np.asanyarray(rate)
tg = np.asanyarray(tg)
fitter = FitRoutine()
fitter.set_model(Arrhenius)
d = fitter.add_data(1000/tg, rate, we='y')
init = linregress(1000/tg, np.log(rate))
d.set_parameter([np.exp(init.intercept), 1000*init.slope*kB], fun_kwargs={'invt': 'invt1000'})
res = fitter.run()[0]
de = res.parameter['E_{A}']
tau = kB*tg**2/np.abs(de.value)/rate*60
return Points(x=1000/tg, y=tau, y_err=tau*de.error/np.abs(de.value), name='Hodge'), res

46
src/nmreval/dsc/tnmh_model.py
View File

@ -1,46 +0,0 @@
import numpy as np
from nmreval.utils.constants import R_joule as R
class TNMH:
type = 'DSC'
name = 'TNMH model'
equation = r''
params = [r'\tau_{g}', 'x', r'\beta', r'\Delta H', 'T_{g}', 'rate']
bounds = [(0, None), (0, 1), (0, 1), (0, None), (0, None), (0, None)]
@staticmethod
def func(x: np.ndarray, tau_g: float, xx: float, beta: float, energy: float, tg: float, rate: float) -> np.ndarray:
model_temp = np.r_[x[::-1], x[1:]]
curve = TNMH.tnm_function(model_temp, tau_g, xx, beta, energy, tg, rate)[x.size - 1:]
res = np.gradient(curve, x)
return res
@staticmethod
def tnm_function(x: np.ndarray, tau_g: float, xx: float, beta: float, energy: float, tg: float, rate: float) -> np.ndarray:
step = x.size
Tf = np.empty(step)
Tf[0] = x[0]
delta_temp = np.diff(x)
delta_time = np.abs(delta_temp) * 60 / rate
tau = np.empty(step)
dt_by_tau = np.zeros(step)
temp_0 = x[0]
for i in range(0, step - 1):
tau[i] = TNMH.relax(x[i+1], Tf[i], tau_g, tg, energy, xx)
dt_by_tau[:i] += delta_time[i] / tau[i]
Tf[i + 1] = np.sum(delta_temp[:i] * (1 - np.exp(-dt_by_tau[:i] ** beta))) + temp_0
return Tf
@staticmethod
def relax(t, tf, tau_g, t_glass, ea, x):
h = ea/R
return tau_g * np.exp((x*h / t) + ((1 - x) * h / tf) - h / t_glass)

16
src/nmreval/fit/_meta.py
View File

@ -24,10 +24,9 @@ class ModelFactory:
param_len.append(len(func['func'].params))
if func['children']:
right, _, _ = ModelFactory.create_from_list(func['children'], left_cnt=func['pos'],
right, _, _ = ModelFactory.create_from_list(func['children'], left=func['func'], left_cnt=func['pos'],
func_order=func_order, param_len=param_len)
right_cnt = None
right = MultiModel(func['func'], right, func['children'][0]['op'], left_idx=func['cnt'], right_idx=None)
else:
right = func['func']
right_cnt = func['cnt']
@ -47,13 +46,7 @@ class MultiModel:
str_op = {'+': operator.add, '*': operator.mul, '-': operator.sub, '/': operator.truediv}
int_op = {0: operator.add, 1: operator.mul, 2: operator.sub, 3: operator.truediv}
def __init__(self,
left: Any,
right: Any,
op: str | Callable | int = '+',
left_idx: int | None = 0,
right_idx: int | None = 1,
):
def __init__(self, left: Any, right: Any, op: str | Callable | int = '+', left_idx=0, right_idx=1):
self._left = left
self._right = right
@ -75,7 +68,6 @@ class MultiModel:
self._kwargs_right = {}
self._kwargs_left = {}
self.fun_kwargs = {}
self.idx = (left_idx, right_idx)
# mapping kwargs to kwargs of underlying functions
self._ext_int_kw = {}
@ -186,13 +178,13 @@ class MultiModel:
if isinstance(self._left, MultiModel):
yield from self._left.sub_name()
elif hasattr(self._left, 'name'):
yield f'{self._left.name}({self.idx[0]})'
yield self._left.name
else:
yield self.name + '(lhs)'
if isinstance(self._right, MultiModel):
yield from self._right.sub_name()
elif hasattr(self._right, 'name'):
yield f'{self._right.name}({self.idx[1]})'
yield self._right.name
else:
yield self.name + '(rhs)'

91
src/nmreval/fit/data.py
View File

@ -1,9 +1,7 @@
from __future__ import annotations
import numpy as np
from .model import Model
from .parameter import Parameters, Parameter
from .parameter import Parameters
class Data(object):
@ -13,27 +11,27 @@ class Data(object):
if self.y.shape[0] != self.x.shape[0]:
raise ValueError(f'x and y have different lengths {self.x.shape[0]} and {self.y.shape[0]}')
self.we, self.we_string = self._calc_weights(we)
self.we = self._calc_weights(we)
self.idx = idx
self.model = None
self.minimizer = None
self.parameter = Parameters()
self.para_keys: list = []
self.para_keys = None
self.fun_kwargs = {}
def __len__(self):
return self.y.shape[0]
def _calc_weights(self, we: str | np.ndarray | None) -> tuple[np.ndarray, str]:
if isinstance(we, str) or we is None:
if we is None or we.lower() == 'none':
we_string = 'None'
we_func = lambda yy: np.ones_like(len(yy))
elif we == 'y2':
we_string = we
def _calc_weights(self, we):
if we is None:
return 1.
if isinstance(we, str):
if we == 'y2':
we_func = lambda yy: 1. / yy**2
elif we.lower() == 'none':
we_func = lambda yy: np.ones_like(len(yy))
else:
we_string = we
we_func = lambda yy: 1. / np.abs(yy)
if np.iscomplexobj(self.y):
@ -42,7 +40,6 @@ class Data(object):
weights = we_func(self.y)
else:
we_string = 'yerr' # This is pure speculation that array equals error
we = 1. / np.asarray(we)
if np.iscomplexobj(self.y):
if np.iscomplexobj(we):
@ -54,7 +51,7 @@ class Data(object):
weights[weights == np.inf] = np.finfo(float).max
return weights, we_string
return weights
def set_model(self, func, *args, **kwargs):
if isinstance(func, Model):
@ -71,19 +68,12 @@ class Data(object):
def get_model(self):
return self.model
def set_parameter(self,
values: list[float | Parameter],
*,
var: list[bool] = None,
ub: list[float] = None,
lb: list[float] = None,
default_bounds: bool = False,
fun_kwargs: dict = None
):
def set_parameter(self, parameter, var=None, ub=None, lb=None,
default_bounds=False, fun_kwargs=None):
"""
Creates parameter for this data.
If no Model is available, it falls back to the model
:param values: list of parameters
:param parameter: list of parameters
:param var: list of boolean or boolean; False fixes parameter at given list index.
Single value is broadcast to all parameter
:param ub: list of upper boundaries or float; Single value is broadcast to all parameter.
@ -97,46 +87,23 @@ class Data(object):
model = self.model
if model is None:
# Data has no unique
if self.minimizer is not None:
if self.minimizer is None:
model = None
else:
model = self.minimizer.fit_model
self.fun_kwargs.update(model.fun_kwargs)
if model is None:
raise ValueError('No model found, please set model before parameters')
if len(values) != len(model.params):
raise ValueError('Number of given parameter does not match number of model parameters')
is_parameter = [isinstance(v, Parameter) for v in values]
if all(is_parameter):
for p_i in values:
key = f"p{next(Parameters.parameter_counter)}"
self.parameter.add_parameter(key, p_i)
elif any(is_parameter):
raise ValueError('list of parameter are not all float of Parameter')
else:
if var is None:
var = [True] * len(values)
if default_bounds:
if lb is None:
if default_bounds:
lb = model.lb
else:
lb = [None] * len(values)
lb = model.lb
if ub is None:
if default_bounds:
ub = model.ub
else:
ub = [None] * len(values)
ub = model.ub
arg_names = ['name', 'value', 'var', 'lb', 'ub']
for parameter_arg in zip(model.params, values, var, lb, ub):
self.parameter.add(**{arg_name: arg_value for arg_name, arg_value in zip(arg_names, parameter_arg)})
self.para_keys = self.parameter.add_parameter(parameter, var=var, lb=lb, ub=ub)
self.para_keys = list(self.parameter.keys())
self.fun_kwargs.update(model.fun_kwargs)
if fun_kwargs is not None:
self.fun_kwargs.update(fun_kwargs)
@ -156,18 +123,6 @@ class Data(object):
else:
return [p.value for p in self.minimizer.parameters[self.parameter]]
def replace_parameter(self, key: str, parameter: Parameter) -> None:
tobereplaced = None
for k, v in self.parameter.items():
if v.name == parameter.name:
tobereplaced = k
break
if tobereplaced is None:
raise KeyError(f'Global parameter {key} not found in list of parameters')
self.para_keys[self.para_keys.index(tobereplaced)] = key
self.parameter.replace_parameter(tobereplaced, key, parameter)
def cost(self, p):
"""
Cost function :math:`y-f(p, x)`

297
src/nmreval/fit/minimizer.py
View File

@ -1,5 +1,3 @@
from __future__ import annotations
import warnings
from itertools import product
@ -16,81 +14,21 @@ from .result import FitResultCreator
__all__ = ['FitRoutine', 'FitAbortException']
from ..lib.logger import logger
class FitAbortException(Exception):
pass
# COST FUNCTIONS: f(x) - y (least_square, minimize), and f(x) (ODR)
def _cost_scipy_glob(p: list[float], data: list[Data], varpars: list[str], used_pars: list[list[str]]):
# replace values
for keys, values in zip(varpars, p):
for data_i in data:
if keys in data_i.parameter.keys():
# TODO move this to scaled_value setter
data_i.parameter[keys].scaled_value = values
data_i.parameter[keys].namespace[keys] = data_i.parameter[keys].value
r = []
# unpack parameter and calculate y values and concatenate all
for values, p_idx in zip(data, used_pars):
actual_parameters = [values.parameter[keys].value for keys in p_idx]
r = np.r_[r, values.cost(actual_parameters)]
return r
def _cost_scipy(p, data, varpars, used_pars):
for keys, values in zip(varpars, p):
data.parameter[keys].scaled_value = values
data.parameter[keys].namespace[keys] = data.parameter[keys].value
actual_parameters = [data.parameter[keys].value for keys in used_pars]
return data.cost(actual_parameters)
def _cost_odr(p: list[float], data: Data, varpars: list[str], used_pars: list[str], fitmode: int=0):
for keys, values in zip(varpars, p):
data.parameter[keys].scaled_value = values
data.parameter[keys].namespace[keys] = data.parameter[keys].value
actual_parameters = [data.parameter[keys].value for keys in used_pars]
return data.func(actual_parameters, data.x)
def _cost_odr_glob(p: list[float], data: list[Data], var_pars: list[str], used_pars: list[str]):
# replace values
for data_i in data:
_update_parameter(data_i, var_pars, p)
r = []
# unpack parameter and calculate y values and concatenate all
for values, p_idx in zip(data, used_pars):
actual_parameters = [values.parameter[keys].value for keys in p_idx]
r = np.r_[r, values.func(actual_parameters, values.x)]
return r
def _update_parameter(data: Data, varied_keys: list[str], parameter: list[float]):
for keys, values in zip(varied_keys, parameter):
if keys in data.parameter.keys():
data.parameter[keys].scaled_value = values
data.parameter[keys].namespace[keys] = data.parameter[keys].value
class FitRoutine(object):
def __init__(self, mode='lsq'):
self.fitmethod = mode
self._fitmethod = mode
self.data = []
self.fit_model = None
self._no_own_model = []
self.parameter = Parameters()
self.result = []
self.linked = []
self._abort = False
self.step = 0
def add_data(self, x, y=None, we=None, idx=None):
if isinstance(x, Data):
@ -140,27 +78,29 @@ class FitRoutine(object):
return self.fit_model
def set_link_parameter(self, dismissed_param: tuple[Model | Data, str], replacement: tuple[Model, str]):
def set_link_parameter(self, parameter: tuple, replacement: tuple):
if isinstance(replacement[0], Model):
if replacement[1] not in replacement[0].parameter:
raise KeyError(f'Parameter {replacement[1]} of '
f'model {replacement[0]} is not global')
if replacement[1] not in replacement[0].global_parameter:
raise KeyError(f'Parameter at pos {replacement[1]} of '
f'model {str(replacement[0])} is not global')
if isinstance(dismissed_param[0], Model):
warnings.warn(f'Replaced parameter {dismissed_param[1]} in {dismissed_param[0]} '
if isinstance(parameter[0], Model):
warnings.warn(f'Replaced parameter at pos {parameter[1]} in {str(parameter[0])} '
f'becomes global with linkage.')
self.linked.append((*dismissed_param, *replacement))
self.linked.append((*parameter, *replacement))
def prepare_links(self):
self._no_own_model = []
self.parameter = Parameters()
_found_models = {}
linked_sender = {}
for v in self.data:
linked_sender[v] = set()
self.parameter.update(v.parameter.copy())
# set temporary model
# set temporaray model
if v.model is None:
v.model = self.fit_model
self._no_own_model.append(v)
@ -168,6 +108,8 @@ class FitRoutine(object):
# register model
if v.model not in _found_models:
_found_models[v.model] = []
m_param = v.model.parameter.copy()
self.parameter.update(m_param)
_found_models[v.model].append(v)
@ -175,21 +117,24 @@ class FitRoutine(object):
linked_sender[v.model] = set()
linked_parameter = {}
for dismiss_model, dismiss_param, replace_model, replace_param in self.linked:
linked_sender[replace_model].add(dismiss_model)
linked_sender[replace_model].add(replace_model)
for par, par_parm, repl, repl_par in self.linked:
if isinstance(par, Data):
if isinstance(repl, Data):
linked_parameter[par.para_keys[par_parm]] = repl.para_keys[repl_par]
else:
linked_parameter[par.para_keys[par_parm]] = repl.global_parameter[repl_par]
replace_key = replace_model.parameter.get_key(replace_param)
dismiss_key = dismiss_model.parameter.get_key(dismiss_param)
if isinstance(replace_model, Data):
linked_parameter[dismiss_key] = replace_key
else:
p = dismiss_model.set_global_parameter(dismiss_param, replace_key)
p._expr_disp = replace_param
if isinstance(repl, Data):
par.global_parameter[par_parm] = repl.para_keys[repl_par]
else:
par.global_parameter[par_parm] = repl.global_parameter[repl_par]
linked_sender[repl].add(par)
linked_sender[par].add(repl)
for mm, m_data in _found_models.items():
if mm.parameter:
if mm.global_parameter:
for dd in m_data:
linked_sender[mm].add(dd)
linked_sender[dd].add(mm)
@ -218,16 +163,15 @@ class FitRoutine(object):
self.find_paths(neighbor, graph, coupled_nodes, visited_nodes)
def abort(self):
logger.info('Fit aborted by user')
print('ABORT ???')
self._abort = True
def run(self, mode: str = None):
def run(self, mode='lsq'):
self._abort = False
if mode is None:
mode = self.fitmethod
self.parameter = Parameters()
fit_groups, linked_parameter = self.prepare_links()
for data_groups in fit_groups:
if len(data_groups) == 1 and not self.linked:
data = data_groups[0]
@ -258,32 +202,17 @@ class FitRoutine(object):
self.unprep_run()
for r in self.result:
r.pprint()
return self.result
def make_preview(self, x: np.ndarray) -> list[np.ndarray]:
y_pred = []
fit_groups, linked_parameter = self.prepare_links()
for data_groups in fit_groups:
data = data_groups[0]
actual_parameters = [p.value for p in data.parameter.values()]
y_pred.append(data.func(actual_parameters, x))
return y_pred
def _prep_data(self, data):
if data.get_model() is None:
data._model = self.fit_model
self._no_own_model.append(data)
# data.parameter.prepare_bounds()
return self._prep_parameter(data.parameter)
@staticmethod
def _prep_parameter(parameter: Parameters):
def _prep_parameter(parameter):
vals = []
var_pars = []
for p_k, v_k in parameter.items():
@ -295,26 +224,29 @@ class FitRoutine(object):
return pp, lb, ub, var_pars
@staticmethod
def _prep_global(data_group: list[Data], linked):
def _prep_global(self, data_group, linked):
p0 = []
lb = []
ub = []
var = []
data_pars = []
# loopy-loop over data that belong to one fit (linked or global)
# loopyloop over data that belong to one fit (linked or global)
for data in data_group:
# is parameter replaced by global parameter?
for k, v in data.model.parameter.items():
data.replace_parameter(k, v)
# data.parameter.prepare_bounds()
actual_pars = []
for i, p_k in enumerate(data.para_keys):
for i, (p_k, v_k) in enumerate(data.parameter.items()):
p_k_used = p_k
v_k_used = data.parameter[p_k]
v_k_used = v_k
# is parameter replaced by global parameter?
if i in data.model.global_parameter:
p_k_used = data.model.global_parameter[i]
v_k_used = self.parameter[p_k_used]
# links trump global parameter
if p_k_used in linked:
p_k_used = linked[p_k_used]
v_k_used = self.parameter[p_k_used]
actual_pars.append(p_k_used)
# parameter is variable and was not found before as shared parameter
@ -333,20 +265,58 @@ class FitRoutine(object):
d._model = None
self._no_own_model = []
Parameters.reset()
# COST FUNCTIONS: f(x) - y (least_square, minimize), and f(x) (ODR)
def __cost_scipy(self, p, data, varpars, used_pars):
for keys, values in zip(varpars, p):
self.parameter[keys].scaled_value = values
actual_parameters = [self.parameter[keys].value for keys in used_pars]
return data.cost(actual_parameters)
def __cost_odr(self, p, data, varpars, used_pars):
for keys, values in zip(varpars, p):
self.parameter[keys].scaled_value = values
actual_parameters = [self.parameter[keys].value for keys in used_pars]
return data.func(actual_parameters, data.x)
def __cost_scipy_glob(self, p, data, varpars, used_pars):
# replace values
for keys, values in zip(varpars, p):
self.parameter[keys].scaled_value = values
r = []
# unpack parameter and calculate y values and concatenate all
for values, p_idx in zip(data, used_pars):
actual_parameters = [self.parameter[keys].value for keys in p_idx]
r = np.r_[r, values.cost(actual_parameters)]
return r
def __cost_odr_glob(self, p, data, varpars, used_pars):
# replace values
for keys, values in zip(varpars, p):
self.parameter[keys].scaled_value = values
r = []
# unpack parameter and calculate y values and concatenate all
for values, p_idx in zip(data, used_pars):
actual_parameters = [self.parameter[keys].value for keys in p_idx]
r = np.r_[r, values.func(actual_parameters, values.x)]
return r
def _least_squares_single(self, data, p0, lb, ub, var):
self.step = 0
def cost(p):
self.step += 1
if self._abort:
raise FitAbortException(f'Fit aborted by user')
return _cost_scipy(p, data, var, data.para_keys)
return self.__cost_scipy(p, data, var, data.para_keys)
with np.errstate(all='ignore'):
res = optimize.least_squares(cost, p0, bounds=(lb, ub), max_nfev=500 * len(p0))
res = optimize.least_squares(cost, p0, bounds=(lb, ub), max_nfev=1000 * len(p0))
err, corr, partial_corr = self._calc_error(res.jac, np.sum(res.fun**2), *res.jac.shape)
self.make_results(data, res.x, var, data.para_keys, res.jac.shape,
@ -354,13 +324,12 @@ class FitRoutine(object):
def _least_squares_global(self, data, p0, lb, ub, var, data_pars):
def cost(p):
self.step += 1
if self._abort:
raise FitAbortException(f'Fit aborted by user')
return _cost_scipy_glob(p, data, var, data_pars)
return self.__cost_scipy_glob(p, data, var, data_pars)
with np.errstate(all='ignore'):
res = optimize.least_squares(cost, p0, bounds=(lb, ub), max_nfev=500 * len(p0))
res = optimize.least_squares(cost, p0, bounds=(lb, ub), max_nfev=1000 * len(p0))
err, corr, partial_corr = self._calc_error(res.jac, np.sum(res.fun**2), *res.jac.shape)
for v, var_pars_k in zip(data, data_pars):
@ -369,27 +338,25 @@ class FitRoutine(object):
def _nm_single(self, data, p0, lb, ub, var):
def cost(p):
self.step += 1
if self._abort:
raise FitAbortException(f'Fit aborted by user')
return (_cost_scipy(p, data, var, data.para_keys) ** 2).sum()
return (self.__cost_scipy(p, data, var, data.para_keys)**2).sum()
with np.errstate(all='ignore'):
res = optimize.minimize(cost, p0, bounds=[(b1, b2) for (b1, b2) in zip(lb, ub)],
method='Nelder-Mead', options={'maxiter': 500 * len(p0)})
method='Nelder-Mead', options={'maxiter': 1000 * len(p0)})
self.make_results(data, res.x, var, data.para_keys, (len(data), len(p0)))
def _nm_global(self, data, p0, lb, ub, var, data_pars):
def cost(p):
self.step += 1
if self._abort:
raise FitAbortException(f'Fit aborted by user')
return (_cost_scipy_glob(p, data, var, data_pars) ** 2).sum()
return (self.__cost_scipy_glob(p, data, var, data_pars)**2).sum()
with np.errstate(all='ignore'):
res = optimize.minimize(cost, p0, bounds=[(b1, b2) for (b1, b2) in zip(lb, ub)],
method='Nelder-Mead', options={'maxiter': 500 * len(p0)})
method='Nelder-Mead', options={'maxiter': 1000 * len(p0)})
for v, var_pars_k in zip(data, data_pars):
self.make_results(v, res.x, var, var_pars_k, (sum(len(d) for d in data), len(p0)))
@ -398,21 +365,15 @@ class FitRoutine(object):
odr_data = odr.Data(data.x, data.y)
def func(p, _):
self.step += 1
if self._abort:
raise FitAbortException(f'Fit aborted by user')
return _cost_odr(p, data, var_pars, data.para_keys)
return self.__cost_odr(p, data, var_pars, data.para_keys)
odr_model = odr.Model(func)
corr, partial_corr, res = self._odr_fit(odr_data, odr_model, p0)
self.make_results(data, res.beta, var_pars, data.para_keys, (len(data), len(p0)),
err=res.sd_beta, corr=corr, partial_corr=partial_corr)
def _odr_fit(self, odr_data, odr_model, p0):
o = odr.ODR(odr_data, odr_model, beta0=p0)
res = o.run()
corr = res.cov_beta / (res.sd_beta[:, None] * res.sd_beta[None, :]) * res.res_var
try:
corr_inv = np.linalg.inv(corr)
@ -421,14 +382,15 @@ class FitRoutine(object):
partial_corr[np.diag_indices_from(partial_corr)] = 1.
except np.linalg.LinAlgError:
partial_corr = corr
return corr, partial_corr, res
self.make_results(data, res.beta, var_pars, data.para_keys, (len(data), len(p0)),
err=res.sd_beta, corr=corr, partial_corr=partial_corr)
def _odr_global(self, data, p0, var, data_pars):
def func(p, _):
self.step += 1
if self._abort:
raise FitAbortException(f'Fit aborted by user')
return _cost_odr_glob(p, data, var, data_pars)
return self.__cost_odr_glob(p, data, var, data_pars)
x = []
y = []
@ -439,7 +401,17 @@ class FitRoutine(object):
odr_data = odr.Data(x, y)
odr_model = odr.Model(func)
corr, partial_corr, res = self._odr_fit(odr_data, odr_model, p0)
o = odr.ODR(odr_data, odr_model, beta0=p0, ifixb=var)
res = o.run()
corr = res.cov_beta / (res.sd_beta[:, None] * res.sd_beta[None, :]) * res.res_var
try:
corr_inv = np.linalg.inv(corr)
corr_inv_diag = np.diag(np.sqrt(1 / np.diag(corr_inv)))
partial_corr = -1. * np.dot(np.dot(corr_inv_diag, corr_inv), corr_inv_diag) # Partial correlation matrix
partial_corr[np.diag_indices_from(partial_corr)] = 1.
except np.linalg.LinAlgError:
partial_corr = corr
for v, var_pars_k in zip(data, data_pars):
self.make_results(v, res.beta, var, var_pars_k, (sum(len(d) for d in data), len(p0)),
@ -453,17 +425,15 @@ class FitRoutine(object):
# update parameter values
for keys, p_value, err_value in zip(var_pars, p, err):
if keys in data.parameter.keys():
data.parameter[keys].scaled_value = p_value
data.parameter[keys].scaled_error = err_value
data.parameter[keys].namespace[keys] = data.parameter[keys].value
self.parameter[keys].scaled_value = p_value
self.parameter[keys].scaled_error = err_value
combinations = list(product(var_pars, var_pars))
actual_parameters = []
corr_idx = []
for i, p_i in enumerate(used_pars):
actual_parameters.append(data.parameter[p_i])
actual_parameters.append(self.parameter[p_i])
for j, p_j in enumerate(used_pars):
try:
# find the position of the parameter combinations
@ -484,18 +454,9 @@ class FitRoutine(object):
idx = self.data.index(data)
model = data.get_model()
self.result[idx] = FitResultCreator.make_with_model(
model,
data.x,
data.y,
actual_parameters,
data.fun_kwargs,
data.we_string,
data.idx,
*shape,
corr=actual_corr,
pcorr=actual_pcorr,
)
self.result[idx] = FitResultCreator.make_with_model(model, data.x, data.y,
actual_parameters, data.fun_kwargs, data.idx,
*shape, corr=actual_corr, pcorr=actual_pcorr)
return self.result
@ -503,18 +464,11 @@ class FitRoutine(object):
def _calc_error(jac, chi, nobs, nvars):
# copy of scipy.curve_fit to calculate covariance
# noinspection PyTupleAssignmentBalance
try:
_, s, vt = la.svd(jac, full_matrices=False)
except ValueError as e:
# this may be issue #39: On entry to DGESSD parameter had an illegal value
# catch this exception and ignore error calculation
logger.error(f'Error calculation failed with {e.args}')
pcov = None
else:
threshold = EPS * max(jac.shape) * s[0]
s = s[s > threshold]
vt = vt[:s.size]
pcov = np.dot(vt.T / s**2, vt) * chi / (nobs - nvars)
_, s, vt = la.svd(jac, full_matrices=False)
threshold = EPS * max(jac.shape) * s[0]
s = s[s > threshold]
vt = vt[:s.size]
pcov = np.dot(vt.T / s**2, vt) * chi / (nobs - nvars)
if pcov is None:
_err = np.zeros(nvars)
@ -533,4 +487,3 @@ class FitRoutine(object):
partial_corr = corr
return _err, corr, partial_corr

41
src/nmreval/fit/model.py
View File

@ -6,7 +6,7 @@ from typing import Sized
from numpy import inf
from ._meta import MultiModel
from .parameter import Parameters, Parameter
from .parameter import Parameters
class Model(object):
@ -25,6 +25,7 @@ class Model(object):
self.ub = [i if i is not None else inf for i in self.ub]
self.parameter = Parameters()
self.global_parameter = {}
self.is_complex = None
self._complex_part = False
@ -79,33 +80,23 @@ class Model(object):
self.fun_kwargs = {k: v.default for k, v in inspect.signature(model.func).parameters.items()
if v.default is not inspect.Parameter.empty}
def set_global_parameter(self,
key: str | Parameter,
value: float | str = None,
*,
var: bool = None,
lb: float = None,
ub: float = None,
default_bounds: bool = False,
) -> Parameter:
def set_global_parameter(self, idx, p, var=None, lb=None, ub=None, default_bounds=False):
if idx is None:
self.parameter = Parameters()
self.global_parameter = {}
return
if isinstance(key, Parameter):
p = key
key = f'p{next(Parameters.parameter_counter)}'
self.parameter.add_parameter(key, p)
if default_bounds:
if lb is None:
lb = [self.lb[i] for i in idx]
if ub is None:
ub = [self.lb[i] for i in idx]
else:
idx = [self.params.index(key)]
if default_bounds:
if lb is None:
lb = [self.lb[i] for i in idx]
if ub is None:
ub = [self.lb[i] for i in idx]
gp = self.parameter.add_parameter(p, var=var, lb=lb, ub=ub)
for k, v in zip(idx, gp):
self.global_parameter[k] = v
p = self.parameter.add(key, value, var=var, lb=lb, ub=ub)
p.is_global = True
return p
return gp
@staticmethod
def _prep(param_len, val):

385
src/nmreval/fit/parameter.py
View File

@ -1,268 +1,123 @@
from __future__ import annotations
import ast
import re
from numbers import Number
from itertools import count
from io import StringIO
import numpy as np
class Parameters(dict):
parameter_counter = count()
# is one global namespace a good idea?
namespace: dict = {}
count = count()
def __init__(self):
super().__init__()
self._mapping: dict = {}
def __str__(self):
return 'Parameters:\n' + '\n'.join([str(k)+': '+str(v) for k, v in self.items()])
def __str__(self) -> str:
return 'Parameters:\n' + '\n'.join([f'{k}: {v}' for k, v in self.items()])
def __getitem__(self, item) -> Parameter:
if item in self._mapping:
return super().__getitem__(self._mapping[item])
def __getitem__(self, item):
if isinstance(item, (list, tuple, np.ndarray)):
values = []
for item_i in item:
values.append(super().__getitem__(item_i))
return values
else:
return super().__getitem__(item)
def __setitem__(self, key, value):
self.add_parameter(key, value)
def __contains__(self, item):
for v in self.values():
if item == v.name:
return True
return False
def add(self,
name: str,
value: str | float | int = None,
*,
var: bool = True,
lb: str | float = -np.inf,
ub: str | float = np.inf) -> Parameter:
par = Parameter(name=name, value=value, var=var, lb=lb, ub=ub)
key = f'_p{next(Parameters.parameter_counter)}'
self.add_parameter(key, par)
return par
def add_parameter(self, key: str, parameter: Parameter):
self._mapping[parameter.name] = key
super().__setitem__(key, parameter)
parameter.eval_allowed = False
self.namespace[key] = parameter.value
parameter.namespace = self.namespace
parameter.eval_allowed = True
self.update_namespace()
def replace_parameter(self, key_out: str, key_in: str, parameter: Parameter):
self.add_parameter(key_in, parameter)
for k, v in self._mapping.items():
if v == key_out:
self._mapping[k] = key_in
break
if key_out in self.namespace:
del self.namespace[key_out]
def fix(self):
for v in self.keys():
v._value = v.value
v.namespace = {}
@staticmethod
def reset():
Parameters.namespace = {}
def _prep_bounds(val, p_len: int) -> list:
# helper function to ensure that bounds and variable are of parameter shape
if isinstance(val, (Number, bool)) or val is None:
return [val] * p_len
def get_key(self, name: str) -> str | None:
elif len(val) == p_len:
return val
elif len(val) == 1:
return [val[0]] * p_len
else:
raise ValueError('Input {} has wrong dimensions'.format(val))
def add_parameter(self, param, var=None, lb=None, ub=None):
if isinstance(param, Number):
param = [param]
p_len = len(param)
# make list if only single value is given
var = self._prep_bounds(var, p_len)
lb = self._prep_bounds(lb, p_len)
ub = self._prep_bounds(ub, p_len)
new_keys = []
for i in range(p_len):
new_idx = next(self.count)
new_keys.append(new_idx)
self[new_idx] = Parameter(param[i], var=var[i], lb=lb[i], ub=ub[i])
return new_keys
def copy(self):
p = Parameters()
for k, v in self.items():
if name == v.name:
return k
p[k] = Parameter(v.value, var=v.var, lb=v.lb, ub=v.ub)
return
if len(p) == 0:
return p
max_k = max(p.keys())
c = next(p.count)
while c < max_k:
c = next(p.count)
return p
def get_state(self):
return {k: v.get_state() for k, v in self.items()}
def update_namespace(self):
for p in self.values():
try:
p.value
except NameError:
expression = p._expr_disp
for n, k in self._mapping.items():
expression, num_replaced = re.subn(re.escape(n), k, expression)
p._expr = expression
def prepare_bounds(self):
print('prepare_bounds')
original_values = list(self.values())
for param in original_values:
already_with_expression = False
for mode, value in (('lower', param.lb), ('upper', param.ub)):
print(mode, value)
if already_with_expression:
raise ValueError('Only one boundary can be an expression')
already_with_expression = self.parse(param, value, bnd=mode)
def parse(self, parameter, expression: str, bnd: str = 'lower') -> bool:
try:
float(expression)
return False
except ValueError:
pp = ast.parse(expression)
expr_syms = pp.body[0].value
if isinstance(expr_syms, ast.BinOp):
left, op, right = expr_syms.left, expr_syms.op, expr_syms.right
# check for sign in numerator
sign = 1
if isinstance(left, ast.UnaryOp):
if isinstance(left.op, (ast.Not, ast.Invert)):
raise ValueError('Only `+` and `-` are supported for signs')
if isinstance(left.op, ast.USub):
sign = -1
left = left.operand
# is expression number / parameter?
if not (isinstance(left, ast.Constant) and isinstance(op, ast.Div) and isinstance(right, ast.Name)):
raise ValueError('Only simple division `const/parameter` are possible')
result = self.make_proxy_div(parameter, left.value*sign, right.id, bnd=bnd)
return result
else:
raise ValueError('I cannot work under these conditions')
def make_proxy_div(self, param, num: str | float, denom: str | float, bnd: str = 'upper') -> bool:
other_param = self[denom]
other_lb, other_ub = other_param.lb, other_param.ub
proxy = {'name': f'{param.name}*{other_param.name}', 'value': other_param.value*param.value, 'lb': None, 'ub': None}
# switching signs is bad for inequalities
if other_lb < 0 < other_ub:
raise ValueError('Parameter in expression changes sign')
if bnd == 'upper':
# this whole schlamassel is only working for some values as lower bound
if param.lb not in [-np.inf, 0]:
raise ValueError('Invalid lower bounds')
if other_ub < 0 or num < 0:
# upper bound is always negative, switch boundaries
proxy['lb'] = num
proxy['ub'] = param.lb if param.lb == 0 else np.inf
else:
# upper bound is always positive
proxy['lb'] = param.lb
proxy['ub'] = num
elif bnd == 'lower':
if param.ub not in [np.inf, 0]:
raise ValueError('Invalid upper bound')
if other_ub <= 0 or num < 0:
proxy['lb'] = param.lb if param.lb == 0 else np.inf
proxy['ub'] = num
else:
proxy['lb'] = num
proxy['ub'] = param.ub
else:
raise ValueError(f'unknown bound {bnd!r}, use `upper`or `lower`')
param.set_expression(f'{num}/{denom}')
self.add(**proxy)
self.update_namespace()
return True
class Parameter:
"""
Container for one parameter
"""
__slots__ = ['name', 'value', 'error', 'init_val', 'var', 'lb', 'ub', 'scale', 'function']
# TODO Parameter should know its own key
def __init__(self,
name: str,
value: float | str,
var: bool = True,
lb: str | float = -np.inf,
ub: str | float = np.inf,
):
self._value: float | None = None
self.var: bool = bool(var) if var is not None else True
self.error: None | float = None if self.var is False else 0.0
self.name: str = name
self.function: str = ""
def __init__(self, value: float, var: bool = True, lb: float = -np.inf, ub: float = np.inf):
self.lb = lb if lb is not None else -np.inf
self.ub = ub if ub is not None else np.inf
self.lb: str | None | float = lb if lb is not None else -np.inf
self.ub: str | float | None = ub if ub is not None else np.inf
self.namespace: dict = {}
self.eval_allowed: bool = True
self._expr: None | str = None
self._expr_disp: None | str = None
self.is_global = False
if isinstance(value, str):
self._expr_disp = value
self._expr = value
self.var = False
if self.lb <= value <= self.ub:
self.value = value
else:
if isinstance(self.lb, (int, float)) and isinstance(self.ub, (int, float)):
if (self.lb <= value <= self.ub) or (not self.var):
self._value = value
else:
raise ValueError('Value of parameter is outside bounds')
else:
self._value = value
raise ValueError('Value of parameter is outside bounds')
self.init_val = value
self.init_val = value
with np.errstate(divide='ignore'):
# throws RuntimeWarning for zeros
self.scale = 10**(np.floor(np.log10(np.abs(self.value))))
with np.errstate(divide='ignore'):
# throws RuntimeWarning for zeros
self.scale = 10**(np.floor(np.log10(np.abs(self.value))))
if self.scale == 0:
self.scale = 1.
if self.scale == 0:
self.scale = 1.
def __str__(self) -> str:
start = StringIO()
self.var = bool(var) if var is not None else True
self.error = None if self.var is False else 0.0
self.name = ''
self.function = ''
def __str__(self):
start = ''
if self.name:
if self.function:
start.write(f"{self.name} ({self.function})")
start = f'{self.name} ({self.function}): '
else:
start.write(self.name)
if self.is_global:
start.write("*")
start.write(": ")
start = self.name + ': '
if self.var:
start.write(f"{self.value:.4g} +/- {self.error:.4g}, init={self.init_val}")
return start + f'{self.value:.4g} +/- {self.error:.4g}, init={self.init_val}'
else:
start.write(f"{self.value:.4g}")
if self._expr is None:
start.write(" (fixed)")
else:
start.write(f" (calc: {self._expr_disp})")
return start + f'{self.value:} (fixed)'
return start.getvalue()
def __add__(self, other: Parameter | float | int) -> float:
def __add__(self, other: Parameter | float) -> float:
if isinstance(other, (float, int)):
return self.value + other
elif isinstance(other, Parameter):
@ -272,88 +127,40 @@ class Parameter:
return self.__add__(other)
@property
def scaled_value(self) -> float:
def scaled_value(self):
return self.value / self.scale
@scaled_value.setter
def scaled_value(self, value: float) -> None:
self._value = value * self.scale
def scaled_value(self, value):
self.value = value * self.scale
@property
def value(self) -> float | None:
if self._value is not None:
return self._value
if self._expr is not None and self.eval_allowed:
return eval(self._expr, {}, self.namespace)
return
def set_expression(self, expr: str):
self._value = None
self._expr_disp = expr
self._expr = expr
self.var = False
@property
def scaled_error(self) -> None | float:
if self.error is not None:
def scaled_error(self):
if self.error is None:
return self.error
else:
return self.error / self.scale
return
@scaled_error.setter
def scaled_error(self, value) -> None:
def scaled_error(self, value):
self.error = value * self.scale
def get_state(self) -> dict:
state_dict = {
'name': self.name,
'value': self._value,
'error': self.error,
'init_val': self.init_val,
'var': self.var,
'lb': self.lb,
'ub': self.ub,
'scale': self.scale,
'function': self.function,
'_expr': self._expr,
'_expr_disp': self._expr_disp,
'is_global': self.is_global,
}
return state_dict
def get_state(self):
return {slot: getattr(self, slot) for slot in self.__slots__}
@staticmethod
def set_state(state: dict) -> Parameter:
par = Parameter(state.get('name'), state.pop('value'))
def set_state(state: dict):
par = Parameter(state.pop('value'))
for k, v in state.items():
setattr(par, k, v)
return par
@property
def full_name(self) -> str:
def full_name(self):
name = self.name
if self.function:
name += f" ({self.function})"
name += ' (' + self.function + ')'
return name
def copy(self) -> Parameter:
if self._expr:
val = self._expr_disp
else:
val = self._value
para_copy = Parameter(name=self.name, value=val, var=self.var, lb=self.lb, ub=self.ub)
para_copy._expr = self._expr
para_copy.namespace = self.namespace
para_copy.is_global = self.is_global
para_copy.error = self.error
para_copy.function = self.function
return para_copy
def fix(self):
self._value = self.value
self.namespace = {}

176
src/nmreval/fit/result.py
View File

@ -2,7 +2,6 @@ from __future__ import annotations
import re
from collections import OrderedDict
from io import StringIO
from pathlib import Path
from typing import Any
@ -42,19 +41,7 @@ class FitResultCreator:
kwargs['name'], stats, idx)
@staticmethod
def make_with_model(
model: 'Model',
x_orig: np.ndarray,
y_orig: np.ndarray,
p: 'Parameters',
fun_kwargs: dict,
we: str,
idx: str | None,
nobs: int,
nvar: int,
corr: np.ndarray,
pcorr: np.ndarray,
) -> FitResult:
def make_with_model(model, x_orig, y_orig, p, fun_kwargs, idx, nobs, nvar, corr, pcorr) -> FitResult:
if np.all(x_orig > 0) and (np.max(x_orig) > 100 * np.min(x_orig)):
islog = True
else:
@ -76,22 +63,8 @@ class FitResultCreator:
parameters = OrderedDict([(k, v) for k, v in zip(pnames, p)])
p_final = [p.value for p in parameters.values()]
resid = model.func(p_final, x_orig, **fun_kwargs) - y_orig
actual_mode = -1
if 'complex_mode' in fun_kwargs:
actual_mode = fun_kwargs['complex_mode']
fun_kwargs['complex_mode'] = 0
_y = model.func(p_final, _x, **fun_kwargs)
if not actual_mode < 0:
if actual_mode == 1:
_y.imag = 0
elif actual_mode == 2:
_y.real = 0
fun_kwargs['complex_mode'] = actual_mode
resid = model.func(p_final, x_orig, **fun_kwargs) - y_orig
stats = FitResultCreator.calc_statistics(_y, resid, nobs, nvar)
varied = [p.var for p in parameters.values()]
@ -116,25 +89,10 @@ class FitResultCreator:
correlation = corr
partial_correlation = pcorr
return FitResult(
x=_x,
y=_y,
x_data=x_orig,
y_data=y_orig,
params=parameters,
fun_kwargs=fun_kwargs,
resid=resid,
nobs=nobs,
nvar=nvar,
we=we,
name=model.name,
stats=stats,
idx=idx,
corr=correlation,
pcorr=partial_correlation,
islog=islog,
func=model,
)
return FitResult(_x, _y, x_orig, y_orig, parameters, fun_kwargs, resid,
nobs, nvar, model.name, stats,
idx=idx, corr=correlation, pcorr=partial_correlation,
islog=islog, func=model)
@staticmethod
def calc_statistics(y, residual, nobs=None, nvar=None):
@ -172,38 +130,22 @@ class FitResultCreator:
class FitResult(Points):
def __init__(
self: FitResult,
x: np.ndarray,
y: np.ndarray,
x_data: np.ndarray,
y_data: np.ndarray,
params: dict,
fun_kwargs: dict,
resid: np.ndarray,
nobs: int,
nvar: int,
we: str,
name: str,
stats: dict,
idx: int = None,
corr: np.ndarray = None,
pcorr: np.ndarray = None,
islog: bool = False,
func=None,
**kwargs
):
def __init__(self, x: np.ndarray, y: np.ndarray,
x_data: np.ndarray, y_data: np.ndarray,
params: dict, fun_kwargs: dict,
resid: np.ndarray, nobs: int, nvar: int, name: str, stats: dict,
idx=None, corr=None, pcorr=None, islog=False, func=None,
**kwargs):
self.parameter, name = self._prepare_names(params, name)
label = kwargs.get('label', name)
super().__init__(x=x, y=y, name=label, **kwargs)
super().__init__(x=x, y=y, name=name, **kwargs)
self.residual = resid
self.idx = idx
self.statistics = stats
self.nobs = nobs
self.nvar = nvar
self.we = we
self.fun_kwargs = fun_kwargs
self.correlation = corr
self.partial_correlation = pcorr
@ -230,7 +172,7 @@ class FitResult(Points):
nice_name = m.group(1)
if func_number in split_funcs:
nice_func = split_funcs[func_number]
pvalue.fix()
pvalue.name = nice_name
pvalue.function = nice_func
parameter_dic[pname] = pvalue
@ -267,31 +209,27 @@ class FitResult(Points):
return self.nobs-self.nvar
def pprint(self, statistics=True, correlations=True):
s = StringIO()
s.write('Fit result:\n')
s.write(f' model : {self.name}\n')
s.write(f' #data : {self.nobs}\n')
s.write(f' #var : {self.nvar}\n')
s.write(f' #weight: {self.we}\n')
s.write('\nParameter\n')
s.write(self.parameter_string())
print('Fit result:')
print(' model :', self.name)
print(' #data :', self.nobs)
print(' #var :', self.nvar)
print('\nParameter')
print(self._parameter_string())
if statistics:
s.write('\nStatistics\n')
print('Statistics')
for k, v in self.statistics.items():
s.write(f' {k} : {v:.4f}\n')
print(f' {k} : {v:.4f}')
if correlations and self.correlation is not None:
s.write('\nCorrelation (partial corr.)\n')
s.write(self._correlation_string())
s.write('\n')
print('\nCorrelation (partial corr.)')
print(self._correlation_string())
print()
print(s.getvalue())
def parameter_string(self):
def _parameter_string(self):
ret_val = ''
for pkey, pval in self.parameter.items():
for pval in self.parameter.values():
ret_val += convert(str(pval), old='tex', new='str') + '\n'
if self.fun_kwargs:
@ -303,7 +241,9 @@ class FitResult(Points):
def _correlation_string(self):
ret_val = ''
for p_i, p_j, corr_ij, pcorr_ij in self.correlation_list():
ret_val += f" {convert(p_i, old='tex', new='str')} / {convert(p_j, old='tex', new='str')} : {corr_ij:.4f} ({pcorr_ij:.4f})\n"
ret_val += ' {} / {} : {:.4f} ({:.4f})\n'.format(convert(p_i, old='tex', new='str'),
convert(p_j, old='tex', new='str'),
corr_ij, pcorr_ij)
return ret_val
def correlation_list(self, limit=0.1):
@ -352,7 +292,7 @@ class FitResult(Points):
with path.open(writemode) as f:
if overwrite or not path.exists():
f.write('# xvalue(1)\t')
f.write('# label(1)\t')
for i, pname in enumerate(self.parameter.keys()):
raw_name = convert(pname, old='tex', new='str')
f.write(f'{raw_name}({2*i+2})\t{raw_name}_err({2*i+3})\t')
@ -366,15 +306,10 @@ class FitResult(Points):
err = 0.
f.write(f'{p.value:.8e}\t{err:.8e}\t')
f.write('# ')
if self.fun_kwargs:
f.write('# ')
for k, v in self.fun_kwargs.items():
f.write(f"{convert(k, old='tex', new='str')}: {convert(str(v), old='tex', new='str')}\t")
f.write(f'weight: {self.we}\t')
f.write('\n')
f.write(f'# line above from: {self.name} (model: {self.model_name})')
f.write('\n')
def f_test(self, chi2: float, dof: float):
@ -382,13 +317,7 @@ class FitResult(Points):
f_value = 1e318
else:
f_value = (chi2-self.statistics['chi^2']) / (dof-self.dof) / self.statistics['red. chi^2']
try:
prob_f = 1-fdist.cdf(f_value, dof-self.dof, self.dof)
except:
prob_f = 0
return f_value, prob_f
return f_value, 1-fdist.cdf(f_value, dof-self.dof, self.dof)
def get_state(self):
state = super().get_state()
@ -398,7 +327,6 @@ class FitResult(Points):
state[attr] = getattr(self, attr)
state['name'] = self._model_name
state['label'] = self.name
state['corr'] = self.correlation
state['pcorr'] = self.partial_correlation
state['stats'] = self.statistics
@ -418,47 +346,21 @@ class FitResult(Points):
def with_new_x(self, x_values):
if self.func is None:
raise ValueError('no fit function available to calculate new y values')
actual_mode = -1
if 'complex_mode' in self.fun_kwargs:
actual_mode = self.fun_kwargs['complex_mode']
self.fun_kwargs['complex_mode'] = 0
raise ValueError('no fit function available to calcualate new y values')
new_fit = self.copy()
y_values = self.func.func(self.p_final, x_values, **self.fun_kwargs)
if not actual_mode < 0:
if actual_mode == 1:
y_values.imag = 0
elif actual_mode == 2:
y_values.real = 0
self.fun_kwargs['complex_mode'] = actual_mode
new_fit.set_data(x_values, y_values, y_err=0.0)
new_fit.set_data(x_values, y_values)
return new_fit
def sub(self, x_values):
part_functions = []
actual_mode = -1
if 'complex_mode' in self.fun_kwargs:
actual_mode = self.fun_kwargs['complex_mode']
self.fun_kwargs['complex_mode'] = 0
for sub_name, sub_y in zip(self.func.sub_name(), self.func.sub(self.p_final, x_values, **self.fun_kwargs)):
if not actual_mode < 0:
if actual_mode == 1:
sub_y.imag = 0
elif actual_mode == 2:
sub_y.real = 0
if np.iscomplexobj(sub_y):
part_functions.append(Signal(x_values, sub_y, name=sub_name))
else:
part_functions.append(Points(x_values, sub_y, name=sub_name))
if actual_mode > 0:
self.fun_kwargs['complex_mode'] = actual_mode
return part_functions
return part_functions

105
src/nmreval/io/asciireader.py
View File

@ -1,5 +1,3 @@
from __future__ import annotations
import pathlib
import re
from io import BytesIO
@ -9,18 +7,18 @@ import numpy as np
from ..data.points import Points
from ..data.nmr import FID, Spectrum
from ..data.bds import BDS
from ..data.dsc import DSC
from ..utils.utils import staggered_range
NUMBERRE = re.compile(r'[0-9]\.*[0-9]*[Ee]*[+-]*[0-9]*')
class AsciiReader:
# delimiters = ['\t', ' ', ',']
delimiters = ['\t', ' ', ',']
def __init__(self, fname):
self.fname = None
self.header = []
self.lines = []
self.data = []
self.delays = None
self.width = []
self.line_comment = []
@ -42,16 +40,15 @@ class AsciiReader:
break
def make_preview(self, num_lines: int):
if num_lines <= len(self.lines):
return self.lines[:num_lines], max(self.width[:num_lines]), self.line_comment
if num_lines <= len(self.data):
return self.data[:num_lines], max(self.width[:num_lines])
num_lines += len(self.header)
with self.fname.open('r') as f:
for i, line in enumerate(islice(f, len(self.header)+len(self.lines), num_lines)):
line = line.strip('\n\t\r, ')
line = re.sub(r'[\t ;,] *', ';', line)
line = line.split(';')
for i, line in enumerate(islice(f, len(self.header)+len(self.data), num_lines)):
line = line.rstrip('\n\t\r, ')
line = re.split('[\s,;]', line)
try:
comment_start = line.index('#')
self.line_comment.append(' '.join(line[comment_start:]))
@ -59,15 +56,10 @@ class AsciiReader:
except ValueError:
self.line_comment.append('')
is_empty = len(line) == 0
self.width.append(len(line))
self.data.append(line)
if not is_empty:
self.lines.append(line)
self.width.append(len(line))
else:
self.lines.append('')
return self.lines, max(self.width), self.line_comment
return self.data, max(self.width)
def look_for_delay(self, fname=None):
if fname is None:
@ -87,49 +79,34 @@ class AsciiReader:
if stagg:
self.delays = staggered_range(self.delays, stepsize=stag_size)
def export(
self: 'AsciiReader',
x: int | str = None,
y: list = None,
yerr: list = None,
mode: str = 'points',
col_names=None,
num_value: float = None,
) -> list:
mode = mode.lower()
if mode not in ['points', 'fid', 'spectrum', 'dsc', 'bds']:
raise ValueError(f'Unknown mode {mode!r} as selected class')
def export(self, x: int = None, y: list = None, yerr: list = None,
mode: str = 'Points', col_names=None) -> list:
if yerr is None:
yerr = []
elif y is None:
raise ValueError('y is None and yerr is not None')
# if (x is None) ^ (y is None):
# raise ValueError(f'x is {type(x)} and y is {type(y)}, should be both None or both defined')
if (x is None) ^ (y is None):
raise ValueError(f'x is {type(x)} and y is {type(y)}, should be both None or both defined')
if x is None:
x = [0]
elif isinstance(x, int):
x = [x]
elif isinstance(x, str) and x == 'index':
x = []
else:
raise ValueError(f'type of x is {type(x)} not `int` or `str`')
raise ValueError(f'x is {type(x)} not int')
if y is None:
y = list(range(int(len(x) != 0), max(self.width)))
y = list(range(1, max(self.width)))
cols = x + y + yerr
with self.fname.open('rb') as fh:
tmp_ = re.sub(b'[;,]', b' ', fh.read())
raw_data = np.genfromtxt(BytesIO(tmp_), usecols=cols, missing_values='--')
del tmp_
if raw_data.ndim == 1:
# only one row or column
if len(self.lines) == 1:
if len(self.data) == 1:
# one row
raw_data = raw_data.reshape(1, -1)
else:
@ -142,45 +119,33 @@ class AsciiReader:
else:
raw_data = raw_data.reshape((1, *raw_data.shape))
if len(x) == 0 or raw_data.shape[2] == 1:
_temp = np.zeros((raw_data.shape[0], raw_data.shape[1], raw_data.shape[2]+1))
_temp[:, :, 0] = np.arange(raw_data.shape[1])
_temp[:, :, 1:] = raw_data
raw_data = _temp
if y:
y = [i+1 for i in y]
else:
y = [1]
filename = self.fname.stem
if self.delays:
delay_names = self.delays
else:
delay_names = [num_value]
delay_names = [filename]
imported_sets = []
for i, value in enumerate(delay_names):
kwargs = {
'value': value,
'filename': self.fname,
'name': filename,
'group': filename,
'y_err': None
}
kwargs = {'value': value, 'filename': self.fname, 'name': filename, 'group': filename, 'y_err': None}
num_y = len(y)
single_len = 1
stepsize = 1
if mode in ['spectrum', 'fid', 'bds']:
# complex data types
if mode == 'Points':
single_len = 1
cls = Points
stepsize = 1
elif mode == 'FID':
cls = FID
single_len = 2
stepsize = 2
cls = {'points': Points, 'fid': FID, 'spectrum': Spectrum, 'bds': BDS, 'dsc': DSC}[mode]
elif mode == 'Spectrum':
cls = Spectrum
single_len = 2
stepsize = 2
else:
raise ValueError(f'Unknown mode {mode}, mot ´Points´, ´FID´ or ´Spectrum´.')
for j in range(1, num_y+1, stepsize):
if col_names is not None:
@ -190,8 +155,8 @@ class AsciiReader:
# more than one axis, append column number
kwargs['name'] = filename + '_' + str(y[j-1])
if j+num_y < raw_data.shape[2]:
kwargs['y_err'] = raw_data[i, :, j+num_y]
if j+num_y+1 < raw_data.shape[2]:
kwargs['y_err'] = raw_data[i, j+num_y+1]
imported_sets.append(cls(x=raw_data[i, :, 0], y=raw_data[i, :, j:j+single_len].T, **kwargs))

118
src/nmreval/io/dsc.py
View File

@ -5,8 +5,6 @@ import re
from collections import namedtuple
import numpy as np
from scipy.stats import linregress
try:
from scipy.integrate import simpson
except ImportError:
@ -35,7 +33,7 @@ class DSCSample:
self.read_file(fname)
def read_file(self, fname: str | Path) -> None:
def read_file(self, fname: str | Path):
fname = Path(fname)
# file contains weird deg C character in stupiod ISO encoding
@ -46,9 +44,11 @@ class DSCSample:
if 'Heat from' in line:
match = DSCSample.NUMBER_RE.findall(line)
self.steps.append(('h', float(match[3]), float(match[1])+273.15, float(match[2])+273.15))
elif 'Cool from' in line:
match = DSCSample.NUMBER_RE.findall(line)
self.steps.append(('c', float(match[3]), float(match[1])+273.15, float(match[2])+273.15))
elif 'Hold for' in line:
match = DSCSample.NUMBER_RE.findall(line)
self.steps.append(('i', float(match[2])+273.15, float(match[1])*60))
@ -141,7 +141,7 @@ class DSCCalibrator:
def __init__(self):
self.sample = None
self.empty = None
self.reference = []
self.reference =[]
self.ref_list = []
def set_measurement(self,
@ -193,30 +193,43 @@ class DSCCalibrator:
for trans_temp, enthalpy in ref_value.transitions:
real_tm.append(trans_temp)
t_low_lim, t_high_lim = trans_temp - 10, trans_temp + np.clip(rate, 20, 35)
t_low_lim, t_high_lim = trans_temp - 10, trans_temp + 20
low_border = np.argmin(np.abs(measurement[0] - t_low_lim))
high_border = np.argmin(np.abs(measurement[0] - t_high_lim))
ref_zoom = measurement[:, low_border:high_border]
x_val = np.array([[ref_zoom[0, 0], 1], [ref_zoom[0, -1], 1]])
y_val = np.array([ref_zoom[1, 0], ref_zoom[1, -1]])
sol = np.linalg.solve(x_val, y_val)
ref_zoom[1] -= (ref_zoom[0] * sol[0] + sol[1])
peak_max = ref_zoom[:, np.argmax(ref_zoom[1])]
integ_limit = (np.argmin(np.abs(ref_zoom[0] - peak_max[0] + 3)),
np.argmin(np.abs(ref_zoom[0] - peak_max[0] - 3)))
# substract baseline around reference peaks
x_val = np.array([[ref_zoom[0, integ_limit[0]], 1], [ref_zoom[0, integ_limit[1]], 1]])
y_val = np.array([ref_zoom[1, integ_limit[0]], ref_zoom[1, integ_limit[1]]])
sol = np.linalg.solve(x_val, y_val)
ref_zoom[1] -= (ref_zoom[0] * sol[0] + sol[1])
# calculate onset slope (use points at position of maximum gradient - 100/rate (+50/rate))
ref_grad = np.gradient(ref_zoom[1])
max_grad = np.argmax(ref_grad)
grad_pos = max_grad-int(50 / rate), max_grad
x_val = np.array([[ref_zoom[0, grad_pos[0]], 1],
[ref_zoom[0, grad_pos[1]], 1]])
y_val = np.array([ref_zoom[1, grad_pos[0]],
ref_zoom[1,grad_pos[1]]])
sol = np.linalg.solve(x_val, y_val)
onset = sol[0] * ref_zoom[0] + sol[1]
melts.append(-sol[1] / sol[0])
if enthalpy is not None:
x_val = np.array([[ref_zoom[0, 0], 1], [ref_zoom[0, -1], 1]])
y_val = np.array([ref_zoom[1, 0], ref_zoom[1, -1]])
sol = np.linalg.solve(x_val, y_val)
ref_zoom[1] -= (ref_zoom[0] * sol[0] + sol[1])
ref_grad = np.gradient(ref_zoom[1])
crossing = np.where(np.diff(np.sign(np.abs(ref_grad)-0.001)))[0]
almost_flat = np.sort(crossing-np.argmax(ref_zoom[1]))
integ_limit = (almost_flat[np.where((almost_flat < -40))[0][-1]]+np.argmax(ref_zoom[1]),
almost_flat[np.where((almost_flat > 40))[0][0]]+np.argmax(ref_zoom[1]))
# subtract baseline around reference peak
sol = self.solve_linear_eq(integ_limit, ref_zoom)
ref_zoom[1] -= (ref_zoom[0] * sol[0] + sol[1])
# integrate over peak to calibrate y axis
# delta H in J/g: Integrate Peak over time and divide by weight
area = simpson(ref_zoom[1, integ_limit[0]:integ_limit[1]],
@ -224,23 +237,6 @@ class DSCCalibrator:
even='avg') * 1e-3
calib_y.append(enthalpy / (area / data.weight))
else:
ref_grad = np.gradient(ref_zoom[1])
res = linregress(ref_zoom[0, :len(ref_grad)//5], ref_zoom[1, :len(ref_grad)//5])
ref_zoom[1] -= (res.slope*ref_zoom[0] + res.intercept)
# calculate onset slope (use points at position of maximum gradient - 100/rate (+50/rate))
ref_grad = np.gradient(ref_zoom[1])
max_grad = np.argmax(ref_grad)
grad_pos = max_grad - max(1, int(160 / rate)), max_grad
sol = self.solve_linear_eq(grad_pos, ref_zoom)
onset = sol[0] * ref_zoom[0] + sol[1]
melts.append(-sol[1] / sol[0])
results.append([ref_zoom, onset, ref_zoom[:, grad_pos]])
if len(melts) > 1:
@ -258,15 +254,7 @@ class DSCCalibrator:
return calib_x, calib_y, results
@staticmethod
def solve_linear_eq(limits: tuple, ref_zoom: np.ndarray) -> np.ndarray:
x_val = np.array([[ref_zoom[0, limits[0]], 1], [ref_zoom[0, limits[1]], 1]])
y_val = np.array([ref_zoom[1, limits[0]], ref_zoom[1, limits[1]]])
sol = np.linalg.solve(x_val, y_val)
return sol
def get_data(self, idx: int, slope: str = 'iso', limits: tuple[float, float] = None):
def get_data(self, idx, slope='iso'):
if self.sample.steps[idx][0] == 'i':
raise ValueError('baseline correction is not implemented for isotherms')
@ -292,11 +280,10 @@ class DSCCalibrator:
empty_y = empty_data[1]
if self.sample.length(idx) != self.empty.length(idx_empty):
with np.errstate(all='ignore'):
empty_y = interp1d(empty_data[2]-empty_data[2, 0], empty_data[1], fill_value='extrapolate')(sample_data[2, 0])
empty_y = interp1d(empty_data[0], empty_data[1], fill_value='extrapolate')(sample_data[0])
sample_data[1] -= empty_y
drift_value = sample_data.copy()[(2, 1), :]
sample_data = sample_data[:, np.isfinite(sample_data[1, :])]
mean_isotherms = []
for offset in [-1, 1]:
@ -316,39 +303,20 @@ class DSCCalibrator:
drift_value = np.c_[drift_value, isotherm_sample]
if slope is not None:
if slope == 'iso':
# calculate slope from difference between isotherms
m = (mean_isotherms[1] - mean_isotherms[0]) / (sample_data[2, -1] - sample_data[2, 0])
region = sample_data[1:, 200:201]
offset = sample_data[1, 200]
else:
# calculate mean slope of heat flow from points in the beginning
region = None
if limits is not None:
if len(limits) != 2:
raise ValueError(f'limits must be tuple of len 2, not {limits!r}')
min_lim, max_lim = min(limits), max(limits)
window = (sample_data[2, :] >= min_lim) * (sample_data[2, :] <= max_lim)
region = sample_data[1:, window]
if region.shape[1] <= 2:
# raise ValueError(f'No data inside selected time window {min_lim/60} min and {max_lim/60} min')
region = None
if region is None:
# if no limits, use all
region = sample_data[1:, 200:-200]
grad = np.gradient(region[0, :], region[1, :])
grad = grad[~np.isnan(grad)]
offset = sample_data[1, 200]
grad = np.gradient(sample_data[1, :], sample_data[2, :])
m = grad[(grad < grad.mean()+grad.std()/5)*(grad > grad.mean()-grad.std()/5)].mean()
offset = region[0, 0]
sample_data[1] -= m * (sample_data[2] - region[1, 0]) + offset
sample_data[1] -= m * (sample_data[2] - sample_data[2, 200]) + offset
line = np.array([[sample_data[2, 0], sample_data[2, -1]],
[m * (sample_data[2, 0] - region[1, 0]) + offset,
m * (sample_data[2, -1] - region[1, 0]) + offset]])
[m * (sample_data[2, 200] - sample_data[2, 200]) + offset,
m * (sample_data[2, -1] - sample_data[2, 200]) + offset]])
else:
line = np.array([[sample_data[2, 0], sample_data[2, -1]], [0, 0]])

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