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bug-fixer (#40)

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fixes #32, #34, #39

Co-authored-by: Dominik Demuth <dominik.demuth@physik.tu-darmstadt.de>
Reviewed-on: IPKM/nmreval#40
This commit is contained in:
Dominik Demuth 2023-04-07 13:45:28 +00:00
parent 43285b4bd5
commit 6b71de8265
7 changed files with 58 additions and 20 deletions
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1
.gitignore vendored
View File

@ -5,3 +5,4 @@ AppDir
NMReval*.zsync
.idea
*.zs-old
docs

14
src/gui_qt/_py/eval_expr_dialog.py
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@ -1,10 +1,11 @@
# -*- coding: utf-8 -*-
# Form implementation generated from reading ui file 'resources/_ui/eval_expr_dialog.ui'
# Form implementation generated from reading ui file 'src/resources/_ui/eval_expr_dialog.ui'
#
# Created by: PyQt5 UI code generator 5.12.3
# Created by: PyQt5 UI code generator 5.15.9
#
# WARNING! All changes made in this file will be lost!
# 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
@ -36,14 +37,14 @@ 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 = QtWidgets.QListWidget(self.page)
self.listWidget = QListWidgetSelect(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.SingleSelection)
self.listWidget.setSelectionMode(QtWidgets.QAbstractItemView.ExtendedSelection)
self.listWidget.setObjectName("listWidget")
self.verticalLayout_2.addWidget(self.listWidget)
self.overwrite_checkbox = QtWidgets.QCheckBox(self.page)
@ -202,7 +203,7 @@ class Ui_CalcDialog(object):
self.label_8.setBuddy(self.line_doubleSpinBox)
self.retranslateUi(CalcDialog)
self.stackedWidget.setCurrentIndex(2)
self.stackedWidget.setCurrentIndex(0)
QtCore.QMetaObject.connectSlotsByName(CalcDialog)
CalcDialog.setTabOrder(self.calc_edit, self.listWidget)
CalcDialog.setTabOrder(self.listWidget, self.overwrite_checkbox)
@ -237,4 +238,5 @@ 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

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

@ -46,7 +46,7 @@ class EditSignalWidget(QtWidgets.QWidget, Ui_Form):
stype = 'pts'
else:
try:
_nop = float(self.lineEdit.text())
_nop = float(self.ls_lineEdit.text())
except ValueError:
_nop = 0.0
stype = 'time'

20
src/gui_qt/lib/listwidget.py Normal file
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@ -0,0 +1,20 @@
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)

11
src/gui_qt/main/mainwindow.py
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@ -76,8 +76,8 @@ class NMRMainWindow(QtWidgets.QMainWindow, Ui_BaseWindow):
self.look_for_update()
self.__timer = QtCore.QTimer()
self.__savepath = config_paths() / f'{datetime.datetime.now().strftime("%Y-%m-%d_%H%M%S")}.nmr'
self.__timer.start(0.2*60*1000) # every three minutese
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 minutese
self.__timer.timeout.connect(self._autosave)
def _init_gui(self):
@ -146,7 +146,7 @@ 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(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)
@ -269,6 +269,7 @@ 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)
@ -1028,7 +1029,7 @@ class NMRMainWindow(QtWidgets.QMainWindow, Ui_BaseWindow):
write_state({'History': {'recent path': str(self.path)}})
# remove backup file when closing
self.__savepath.unlink(missing_ok=True)
self.__backup_path.unlink(missing_ok=True)
super().close()
@ -1056,5 +1057,5 @@ class NMRMainWindow(QtWidgets.QMainWindow, Ui_BaseWindow):
def _autosave(self):
# TODO better separate thread may it takes some time to save
self.status.setText('Autosave...')
NMRWriter(self.management.graphs, self.management.data).export(self.__savepath)
NMRWriter(self.management.graphs, self.management.data).export(self.__backup_path)
self.status.setText('')

19
src/nmreval/fit/minimizer.py
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@ -14,6 +14,8 @@ from .result import FitResultCreator
__all__ = ['FitRoutine', 'FitAbortException']
from ..lib.logger import logger
class FitAbortException(Exception):
pass
@ -464,11 +466,18 @@ class FitRoutine(object):
def _calc_error(jac, chi, nobs, nvars):
# copy of scipy.curve_fit to calculate covariance
# noinspection PyTupleAssignmentBalance
_, 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)
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)
if pcov is None:
_err = np.zeros(nvars)

11
src/resources/_ui/eval_expr_dialog.ui
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@ -27,7 +27,7 @@
<item>
<widget class="QStackedWidget" name="stackedWidget">
<property name="currentIndex">
<number>2</number>
<number>0</number>
</property>
<widget class="QWidget" name="page">
<layout class="QVBoxLayout" name="verticalLayout_2">
@ -54,7 +54,7 @@
</widget>
</item>
<item>
<widget class="QListWidget" name="listWidget">
<widget class="QListWidgetSelect" name="listWidget">
<property name="sizePolicy">
<sizepolicy hsizetype="Preferred" vsizetype="MinimumExpanding">
<horstretch>0</horstretch>
@ -65,7 +65,7 @@
<set>QAbstractItemView::NoEditTriggers</set>
</property>
<property name="selectionMode">
<enum>QAbstractItemView::SingleSelection</enum>
<enum>QAbstractItemView::ExtendedSelection</enum>
</property>
</widget>
</item>
@ -414,6 +414,11 @@
<header>..lib.namespace</header>
<container>1</container>
</customwidget>
<customwidget>
<class>QListWidgetSelect</class>
<extends>QListWidget</extends>
<header>..lib.listwidget</header>
</customwidget>
</customwidgets>
<tabstops>
<tabstop>calc_edit</tabstop>