BUGFIX: VFT;

change to src layout

bin/evaluate.py

@@ -2,7 +2,7 @@
 
 import sys
 import pathlib
-sys.path.append(str(pathlib.Path().cwd().parent))
+sys.path.append(str(pathlib.Path(__file__).parent.parent / 'src'))
 
 from nmreval.configs import check_for_config
 
@@ -15,8 +15,8 @@ check_for_config()
 from nmreval.lib.logger import handle_exception
 sys.excepthook = handle_exception
 
-from nmreval.gui_qt import App
+from gui_qt import App
-from nmreval.gui_qt.main.mainwindow import NMRMainWindow
+from gui_qt.main.mainwindow import NMRMainWindow
 
 app = App([])
 

doc/Makefile

@@ -4,7 +4,7 @@
 # You can set these variables from the command line, and also
 # from the environment for the first two.
 SPHINXOPTS    ?=
-SPHINXBUILD   ?= /autohome/dominik/miniconda3/bin/sphinx-build
+SPHINXBUILD   ?= # /autohome/dominik/miniconda3/bin/sphinx-build
 SOURCEDIR     = /autohome/dominik/nmreval/doc/source
 BUILDDIR      = /autohome/dominik/nmreval/doc/_build
 

doc/examples/nmr/plot_RelaxationEvaluation.py

@@ -1,16 +1,9 @@
 """
-==========
+================================
-T1 minimum
+Example of apodization functions
-==========
+================================
 
-``RelaxationEvaluation`` is used to get width parameter from a T1 minimum.
+This file
-As a subclass of ``Relaxation`` it can also be used to calculate Relaxation times.
-The basic steps are:
-
-* Determine a T1 minimum with `nmreval.nmr.RelaxationEvaluation.calculate_t1_min`
-* Calculate width parameter of a spectral density/coupling constants/... with
-  ``RelaxationEvaluation.get_increase``
-* Calculate correlation times from these values with ``RelaxationEvaluation.correlation_from_t1``
 """
 import numpy as np
 import matplotlib.pyplot as plt

doc/source/_templates/autosummary/class.rst

@@ -3,25 +3,36 @@
 .. currentmodule:: {{ module }}
 
 .. autoclass:: {{ objname }}
+   :exclude-members: {% for item in methods %}{%- if not item.startswith('_') or item in ['__call__'] %}{{ item }}, {% endif %}{%- endfor %}
 
-   {% block methods %}
+   {%- block methods %}
-
    {% if methods %}
-   .. rubric:: {{ _('Methods') }}
+   .. rubric:: Methods
-
-   {% for item in methods %}
-   .. automethod:: {{ item }}
-   {%- endfor %}
-   {% endif %}
-   {% endblock %}
-
-   {% block attributes %}
-   {% if attributes %}
-   .. rubric:: {{ _('Attributes') }}
 
    .. autosummary::
-   {% for item in attributes %}
+      :toctree:
-      ~{{ name }}.{{ item }}
+
-   {%- endfor %}
+   {% for item in methods %}
+   {%- if not item.startswith('_') or item in ['__call__'] %}   ~{{ name }}.{{ item }}
    {% endif %}
-   {% endblock %}
+   {%- endfor %}
+   {%- endif %}
+   {%- endblock %}
+
+   {%- block attributes %}
+   {%- if attributes %}
+   .. rubric:: Properties
+
+   .. autosummary::
+      :toctree:
+
+   {% for item in attributes %}
+   {%- if not item.startswith('_') or item in ['__call__'] %}   ~{{ name }}.{{ item }}
+   {% endif %}
+   {%- endfor %}
+   {%- endif %}
+   {%- endblock %}
+
+.. _sphx_glr_backref_{{ fullname }}:
+.. minigallery:: {{ objname }}
+   :add-heading:

doc/source/api/distributions.rst

@@ -1,5 +1,2 @@
 .. automodule:: nmreval.distributions
    :members:
-   :inherited-members:
-   :undoc-members:
-

doc/source/api/index.rst

@@ -11,3 +11,4 @@ Reference
    models
    distributions
    nmr
+   math

doc/source/conf.py

@@ -12,7 +12,7 @@
 #
 import os
 import sys
-sys.path.append('/autohome/dominik/nmreval')
+sys.path.append(os.path.abspath('../../src'))
 import nmreval
 
 
@@ -43,6 +43,9 @@ extensions = [
     'sphinx.ext.viewcode',
     'sphinx.ext.intersphinx',
     'sphinx_gallery.gen_gallery',
+    'sphinx.ext.todo',
+    'sphinx.ext.autosectionlabel',
+    'sphinx.ext.mathjax',
 ]
 
 # configuration for intersphinx
@@ -56,7 +59,7 @@ intersphinx_mapping = {
 
 # # autodoc options
 autodoc_typehints = 'none'
-autodoc_class_signature = 'separated'
+# autodoc_class_signature = 'separated'
 autoclass_content = 'class'
 autodoc_member_order = 'groupwise'
 #
@@ -79,6 +82,7 @@ sphinx_gallery_conf = {
     'min_reported_time': 10000000000,
     'show_memory': False,
     'show_signature': False,
+    'line_numbers': True,
 }
 
 # The suffix(es) of source filenames.
@@ -151,15 +155,23 @@ todo_include_todos = False
 # The theme to use for HTML and HTML Help pages.  See the documentation for
 # a list of builtin themes.
 #
-html_theme = 'pydata_sphinx_theme'
+html_theme = 'sphinx_material'  # 'sphinx_rtd_theme'  # 'pydata_sphinx_theme'
 
 # Theme options are theme-specific and customize the look and feel of a theme
 # further.  For a list of options available for each theme, see the
 # documentation.
 html_theme_options = {
-    'collapse_navigation': False,
+    'nav_title': 'nmreval',
-    'show_prev_next': False,
+    # 'base_url': 'https://chaos3.fkp.physik.tu-darmstadt.de/source/nmreval',
-    'navbar_end': ['navbar-icon-links.html', 'search-field.html'],
+    'repo_url': 'https://chaos3.fkp.physik.tu-darmstadt.de/source/nmreval',
+    'repo_name': 'Repo',
+    'html_minify': True,
+    'css_minify': True,
+    'master_doc': False,
+    'globaltoc_depth': 3,
+    'globaltoc_collapse': True,
+    'globaltoc_includehidden': True,
+    'heroes': {'index': 'Fun for the whole family!!!!'}
 }
 
 # Add any paths that contain custom themes here, relative to this directory.
@@ -183,10 +195,10 @@ html_static_path = ['_static']
 html_logo = '_static/logo.png'
 
 # Custom sidebar templates, maps document names to template names.
-html_sidebars = {'**': ['sidebar-nav-bs.html']}
+html_sidebars = {
-# html_sidebars = {
+    "**": ["logo-text.html", "globaltoc.html", "localtoc.html", "searchbox.html"]
-#     '**': ['localtoc.html', 'relations.html', 'sourcelink.html', 'searchbox.html'],
+}
-# }
+
 
 # If true, links to the reST sources are added to the pages.
 html_show_sourcelink = False
@@ -205,7 +217,7 @@ html_last_updated_fmt = ''
 html_additional_pages = {}
 
 # If false, no module index is generated.
-html_domain_indices = False
+html_domain_indices = True
 
 # If false, no index is generated.
 html_use_index = True
@@ -214,10 +226,10 @@ html_use_index = True
 html_split_index = False
 
 # If true, "Created using Sphinx" is shown in the HTML footer. Default is True.
-# html_show_sphinx = True
+html_show_sphinx = True
 
 # If true, "(C) Copyright ..." is shown in the HTML footer. Default is True.
-# html_show_copyright = True
+html_show_copyright = True
 
 # If true, an OpenSearch description file will be output, and all pages will
 # contain a <link> tag referring to it.  The value of this option must be the

doc/source/index.rst

@@ -10,15 +10,15 @@ NMREval documentation
 .. toctree::
    :maxdepth: 1
 
+   install.rst
    user_guide/index
    gallery/index
    api/index
 
 
 
-Indices and tables
+Indices
-==================
+=======
 
-* :ref:`genindex`
+| :ref:`genindex`
-* :ref:`modindex`
+| :ref:`modindex`
-* :ref:`search`

doc/source/nmr/pake.rst

@@ -11,7 +11,8 @@ In general, time signals are calculated by integration of all orientations (see
 .. math::
    g(t) = \int f[\omega_\text{int}(\theta, \phi)t]\sin\theta\,\mathrm{d}\theta\,\mathrm{d}\phi
 
-with :math:`f(\theta, \phi, t) = \cos[\omega_\text{int}(\theta, \phi) t]` or :math:`\exp[i\omega_\text{int}(\theta) t]` and fourier transform for a spectrum.
+with :math:`f(\theta, \phi, t) = \cos[\omega_\text{int}(\theta, \phi) t]` or :math:`\exp[i\omega_\text{int}(\theta) t]`
+and fourier transform for a spectrum.
 However, summation over :math:`\theta`, :math:`\phi`, and calculating :math:`f(\theta, \phi, t)` for each orientation is time consuming.
 
 Alternatively, if the orientations are equidistant in :math:`\cos\theta`, one can get to the spectrum directly by creating a histogram of :math:`\omega_\text{int}(\theta, \phi)`, thus circumventing a lot of calculations.

doc/source/user_guide/fit.rst

@@ -4,10 +4,6 @@
 Fitting data
 ============
 
-.. image:: ../_static/fit_dialog.png
-    :scale: 80%
-    :align: center
-
 The picture gives an example of dialog to setup and start fits.
 First, there is the possibiity to fit different functions, called models to differentiate from the functions inside each
 model, to different data simultaneously.

doc/source/user_guide/index.rst

@@ -1,11 +1,13 @@
-==========
+**********
 User Guide
-==========
+**********
 
 
 .. toctree::
    :maxdepth: 2
 
-   read
+   gui/index
+   read/index
+   edit_signals
    fit
    shift_scale

doc/source/user_guide/read.rst

@@ -1,19 +0,0 @@
-.. _user_guide.read:
-
-*************
-Reading files
-*************
-
-Supported filetypes are
-
-   * Text files,
-   * DAMARIS HDF5 files,
-   * Grace images.
-   * HP alpha-analyzer EPS files
-   * NTNMR .tnt files
-
-DAMARIS HDF files
-=================
-
-After scanning the selected file the program shows a list of the available data.
-

nmreval/distributions/gengamma.py

@@ -1,111 +0,0 @@
-from typing import Union
-
-import numpy as np
-from scipy.integrate import simps
-from scipy.special import gammaln
-
-from .base import Distribution
-
-
-class GGAlpha(Distribution):
-    name = r'General \Gamma (\alpha-process)'
-    parameter = [r'\alpha', r'\beta']
-
-    @staticmethod
-    def correlation(t, tau0, *args):
-        logtau0 = np.log(tau0)
-        logtau = np.linspace(logtau0-20, logtau0+20, num=4001)
-        taus = np.exp(logtau)
-        gtau = GGAlpha.distribution(taus, tau0, *args)
-        ret_val = np.array([simps(np.exp(-xvals/taus)*gtau, logtau) for xvals in t])
-        return ret_val
-
-    @staticmethod
-    def susceptibility(omega, tau0, *args):
-        logtau0 = np.log(tau0)
-        logtau = np.linspace(logtau0 - 20, logtau0 + 20, num=4001)
-        taus = np.exp(logtau)
-        gtau = GGAlpha.distribution(taus, tau0, *args)
-        ret_val = np.array([simps(1/(1+1j*xvals*taus) * gtau, logtau) for xvals in omega])
-        return ret_val
-
-    @staticmethod
-    def distribution(taus: Union[float, np.ndarray], tau: float, *args) -> Union[float, np.ndarray]:
-        alpha, beta = args
-        b_to_a = beta / alpha
-        norm = np.exp(gammaln(b_to_a) - b_to_a * np.log(b_to_a)) / alpha
-        t_to_t0 = taus / tau
-        ret_val = np.exp(-b_to_a * t_to_t0 ** alpha) * t_to_t0 ** beta
-
-        return ret_val / norm
-
-
-class GGAlphaEW(Distribution):
-    name = r'General \Gamma (\alpha-process + EW)'
-    parameter = [r'\alpha', r'\beta']
-
-    @staticmethod
-    def correlation(t, tau0, *args):
-        logtau0 = np.log(tau0)
-        logtau = np.linspace(logtau0-20, logtau0+20, num=4001)
-        taus = np.exp(logtau)
-        gtau = GGAlphaEW.distribution(taus, tau0, *args)
-        # wir integrieren ueber lntau, nicht tau
-        ret_val = np.array([simps(np.exp(-xvals/taus)*gtau, logtau) for xvals in t])
-        return ret_val
-
-    @staticmethod
-    def susceptibility(omega, tau0, *args):
-        logtau0 = np.log(tau0)
-        logtau = np.linspace(logtau0 - 20, logtau0 + 20, num=4001)
-        taus = np.exp(logtau)
-        gtau = GGAlphaEW.distribution(taus, tau0, *args)
-        ret_val = np.array([simps(1/(1+1j*xvals*taus) * gtau, logtau) for xvals in omega])
-        return ret_val
-
-    @staticmethod
-    def distribution(tau: Union[float, np.ndarray], tau0: float, *args) -> Union[float, np.ndarray]:
-        alpha, beta, sigma, gamma = args
-        if gamma == beta:
-            return GGAlpha.distribution(tau, tau0, alpha, beta)
-        b_to_a = beta / alpha
-        g_to_a = gamma / alpha
-        t_to_t0 = tau / tau0
-        norm = (np.exp(gammaln(b_to_a)) + sigma**(gamma-beta) *
-                np.exp(gammaln(g_to_a) + (b_to_a-g_to_a)*np.log(b_to_a))) / np.exp(b_to_a*np.log(b_to_a)) / alpha
-
-        ret_val = np.exp(-b_to_a * t_to_t0**alpha) * t_to_t0**beta * (1 + (t_to_t0*sigma)**(gamma-beta))
-
-        return ret_val / norm
-
-
-class GGBeta(Distribution):
-    name = r'General \Gamma (\beta-process)'
-    parameter = [r'\alpha', r'\beta']
-
-    @staticmethod
-    def correlation(t, tau0, *args):
-        logtau0 = np.log(tau0)
-        logtau = np.linspace(logtau0-20, logtau0+20, num=4001)
-        taus = np.exp(logtau)
-        gtau = GGBeta.distribution(taus, tau0, *args)
-        # wir integrieren ueber lntau, nicht tau
-        ret_val = np.array([simps(np.exp(-xvals/taus)*gtau, logtau) for xvals in t])
-        return ret_val
-
-    @staticmethod
-    def susceptibility(omega, tau0, *args):
-        logtau0 = np.log(tau0)
-        logtau = np.linspace(logtau0 - 20, logtau0 + 20, num=4001)
-        taus = np.exp(logtau)
-        gtau = GGBeta.distribution(taus, tau0, *args)
-        ret_val = np.array([simps(1/(1+1j*xvals*taus) * gtau, logtau) for xvals in omega])
-        return ret_val
-
-    @staticmethod
-    def distribution(tau: Union[float, np.ndarray], tau0: float, *args) -> Union[float, np.ndarray]:
-        a, b = args
-        norm = a * (1+b) * np.sin(np.pi*b/(1+b)) * b**(b/(1+b)) / np.pi
-        ret_val = b * (tau/tau0)**a + (tau/tau0)**(-a*b)
-
-        return norm / ret_val

nmreval/gui_qt/_py/fitcreationdialog.py

@@ -1,189 +0,0 @@
-# -*- coding: utf-8 -*-
-
-# Form implementation generated from reading ui file 'resources/_ui/fitcreationdialog.ui'
-#
-# Created by: PyQt5 UI code generator 5.12.3
-#
-# 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(614, 776)
-        self.verticalLayout_5 = QtWidgets.QVBoxLayout(Dialog)
-        self.verticalLayout_5.setContentsMargins(3, 3, 3, 3)
-        self.verticalLayout_5.setSpacing(3)
-        self.verticalLayout_5.setObjectName("verticalLayout_5")
-        self.groupBox = QtWidgets.QGroupBox(Dialog)
-        self.groupBox.setCheckable(True)
-        self.groupBox.setChecked(False)
-        self.groupBox.setObjectName("groupBox")
-        self.verticalLayout_7 = QtWidgets.QVBoxLayout(self.groupBox)
-        self.verticalLayout_7.setContentsMargins(3, 3, 3, 3)
-        self.verticalLayout_7.setSpacing(3)
-        self.verticalLayout_7.setObjectName("verticalLayout_7")
-        self.widget_2 = QtWidgets.QWidget(self.groupBox)
-        self.widget_2.setObjectName("widget_2")
-        self.gridLayout_2 = QtWidgets.QGridLayout(self.widget_2)
-        self.gridLayout_2.setContentsMargins(0, 0, 0, 0)
-        self.gridLayout_2.setSpacing(3)
-        self.gridLayout_2.setObjectName("gridLayout_2")
-        self.name_lineedit = QtWidgets.QLineEdit(self.widget_2)
-        self.name_lineedit.setObjectName("name_lineedit")
-        self.gridLayout_2.addWidget(self.name_lineedit, 0, 1, 1, 1)
-        self.group_lineedit = QtWidgets.QLineEdit(self.widget_2)
-        self.group_lineedit.setObjectName("group_lineedit")
-        self.gridLayout_2.addWidget(self.group_lineedit, 1, 1, 1, 1)
-        self.group_label = QtWidgets.QLabel(self.widget_2)
-        self.group_label.setObjectName("group_label")
-        self.gridLayout_2.addWidget(self.group_label, 1, 0, 1, 1)
-        self.name_label = QtWidgets.QLabel(self.widget_2)
-        self.name_label.setObjectName("name_label")
-        self.gridLayout_2.addWidget(self.name_label, 0, 0, 1, 1)
-        self.lineEdit = QtWidgets.QLineEdit(self.widget_2)
-        self.lineEdit.setObjectName("lineEdit")
-        self.gridLayout_2.addWidget(self.lineEdit, 2, 1, 1, 1)
-        self.label_2 = QtWidgets.QLabel(self.widget_2)
-        self.label_2.setObjectName("label_2")
-        self.gridLayout_2.addWidget(self.label_2, 2, 0, 1, 1)
-        self.verticalLayout_7.addWidget(self.widget_2)
-        self.verticalLayout_5.addWidget(self.groupBox)
-        self.groupBox_2 = QtWidgets.QGroupBox(Dialog)
-        self.groupBox_2.setCheckable(True)
-        self.groupBox_2.setChecked(False)
-        self.groupBox_2.setObjectName("groupBox_2")
-        self.verticalLayout_2 = QtWidgets.QVBoxLayout(self.groupBox_2)
-        self.verticalLayout_2.setContentsMargins(3, 3, 3, 3)
-        self.verticalLayout_2.setSpacing(3)
-        self.verticalLayout_2.setObjectName("verticalLayout_2")
-        self.widget_3 = QtWidgets.QWidget(self.groupBox_2)
-        self.widget_3.setObjectName("widget_3")
-        self.verticalLayout_8 = QtWidgets.QVBoxLayout(self.widget_3)
-        self.verticalLayout_8.setContentsMargins(0, 0, 0, 0)
-        self.verticalLayout_8.setSpacing(3)
-        self.verticalLayout_8.setObjectName("verticalLayout_8")
-        self.tableWidget = QtWidgets.QTableWidget(self.widget_3)
-        sizePolicy = QtWidgets.QSizePolicy(QtWidgets.QSizePolicy.Expanding, QtWidgets.QSizePolicy.Expanding)
-        sizePolicy.setHorizontalStretch(0)
-        sizePolicy.setVerticalStretch(0)
-        sizePolicy.setHeightForWidth(self.tableWidget.sizePolicy().hasHeightForWidth())
-        self.tableWidget.setSizePolicy(sizePolicy)
-        self.tableWidget.setSelectionMode(QtWidgets.QAbstractItemView.SingleSelection)
-        self.tableWidget.setSelectionBehavior(QtWidgets.QAbstractItemView.SelectRows)
-        self.tableWidget.setColumnCount(4)
-        self.tableWidget.setObjectName("tableWidget")
-        self.tableWidget.setRowCount(0)
-        item = QtWidgets.QTableWidgetItem()
-        self.tableWidget.setHorizontalHeaderItem(0, item)
-        item = QtWidgets.QTableWidgetItem()
-        self.tableWidget.setHorizontalHeaderItem(1, item)
-        item = QtWidgets.QTableWidgetItem()
-        self.tableWidget.setHorizontalHeaderItem(2, item)
-        item = QtWidgets.QTableWidgetItem()
-        self.tableWidget.setHorizontalHeaderItem(3, item)
-        self.verticalLayout_8.addWidget(self.tableWidget)
-        self.parameter_button = QtWidgets.QToolButton(self.widget_3)
-        self.parameter_button.setToolButtonStyle(QtCore.Qt.ToolButtonTextBesideIcon)
-        self.parameter_button.setAutoRaise(False)
-        self.parameter_button.setArrowType(QtCore.Qt.RightArrow)
-        self.parameter_button.setObjectName("parameter_button")
-        self.verticalLayout_8.addWidget(self.parameter_button)
-        self.verticalLayout_2.addWidget(self.widget_3)
-        self.verticalLayout_5.addWidget(self.groupBox_2)
-        self.groupBox_3 = QtWidgets.QGroupBox(Dialog)
-        self.groupBox_3.setCheckable(True)
-        self.groupBox_3.setChecked(False)
-        self.groupBox_3.setObjectName("groupBox_3")
-        self.verticalLayout_3 = QtWidgets.QVBoxLayout(self.groupBox_3)
-        self.verticalLayout_3.setContentsMargins(3, 3, 3, 3)
-        self.verticalLayout_3.setSpacing(3)
-        self.verticalLayout_3.setObjectName("verticalLayout_3")
-        self.widget = QtWidgets.QWidget(self.groupBox_3)
-        self.widget.setObjectName("widget")
-        self.verticalLayout_6 = QtWidgets.QVBoxLayout(self.widget)
-        self.verticalLayout_6.setContentsMargins(0, 0, 0, 0)
-        self.verticalLayout_6.setSpacing(3)
-        self.verticalLayout_6.setObjectName("verticalLayout_6")
-        self.use_nuclei = QtWidgets.QCheckBox(self.widget)
-        self.use_nuclei.setObjectName("use_nuclei")
-        self.verticalLayout_6.addWidget(self.use_nuclei)
-        self.tabWidget = QtWidgets.QTabWidget(self.widget)
-        self.tabWidget.setTabPosition(QtWidgets.QTabWidget.West)
-        self.tabWidget.setTabsClosable(True)
-        self.tabWidget.setObjectName("tabWidget")
-        self.verticalLayout_6.addWidget(self.tabWidget)
-        self.selection_button = QtWidgets.QToolButton(self.widget)
-        self.selection_button.setToolButtonStyle(QtCore.Qt.ToolButtonTextBesideIcon)
-        self.selection_button.setArrowType(QtCore.Qt.RightArrow)
-        self.selection_button.setObjectName("selection_button")
-        self.verticalLayout_6.addWidget(self.selection_button)
-        self.verticalLayout_3.addWidget(self.widget)
-        self.verticalLayout_5.addWidget(self.groupBox_3)
-        self.groupBox_4 = QtWidgets.QGroupBox(Dialog)
-        self.groupBox_4.setCheckable(True)
-        self.groupBox_4.setChecked(False)
-        self.groupBox_4.setObjectName("groupBox_4")
-        self.verticalLayout = QtWidgets.QVBoxLayout(self.groupBox_4)
-        self.verticalLayout.setObjectName("verticalLayout")
-        self.namespace_widget = QNamespaceWidget(self.groupBox_4)
-        sizePolicy = QtWidgets.QSizePolicy(QtWidgets.QSizePolicy.MinimumExpanding, QtWidgets.QSizePolicy.Preferred)
-        sizePolicy.setHorizontalStretch(0)
-        sizePolicy.setVerticalStretch(0)
-        sizePolicy.setHeightForWidth(self.namespace_widget.sizePolicy().hasHeightForWidth())
-        self.namespace_widget.setSizePolicy(sizePolicy)
-        self.namespace_widget.setObjectName("namespace_widget")
-        self.verticalLayout.addWidget(self.namespace_widget)
-        self.verticalLayout_5.addWidget(self.groupBox_4)
-        self.frame_4 = QtWidgets.QFrame(Dialog)
-        self.frame_4.setObjectName("frame_4")
-        self.verticalLayout_4 = QtWidgets.QVBoxLayout(self.frame_4)
-        self.verticalLayout_4.setContentsMargins(3, 3, 3, 3)
-        self.verticalLayout_4.setSpacing(3)
-        self.verticalLayout_4.setObjectName("verticalLayout_4")
-        self.label = QtWidgets.QLabel(self.frame_4)
-        self.label.setObjectName("label")
-        self.verticalLayout_4.addWidget(self.label)
-        self.plainTextEdit = CodeEditor(self.frame_4)
-        self.plainTextEdit.setObjectName("plainTextEdit")
-        self.verticalLayout_4.addWidget(self.plainTextEdit)
-        self.verticalLayout_5.addWidget(self.frame_4)
-        self.buttonBox = QtWidgets.QDialogButtonBox(Dialog)
-        self.buttonBox.setOrientation(QtCore.Qt.Horizontal)
-        self.buttonBox.setStandardButtons(QtWidgets.QDialogButtonBox.Cancel|QtWidgets.QDialogButtonBox.Ok)
-        self.buttonBox.setObjectName("buttonBox")
-        self.verticalLayout_5.addWidget(self.buttonBox)
-        self.name_label.setBuddy(self.name_lineedit)
-
-        self.retranslateUi(Dialog)
-        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", "Dialog"))
-        self.groupBox.setTitle(_translate("Dialog", "Description"))
-        self.group_label.setText(_translate("Dialog", "Group"))
-        self.name_label.setText(_translate("Dialog", "Name"))
-        self.label_2.setText(_translate("Dialog", "Equation"))
-        self.groupBox_2.setTitle(_translate("Dialog", "Variables"))
-        item = self.tableWidget.horizontalHeaderItem(0)
-        item.setText(_translate("Dialog", "Variable"))
-        item = self.tableWidget.horizontalHeaderItem(1)
-        item.setText(_translate("Dialog", "Name"))
-        item = self.tableWidget.horizontalHeaderItem(2)
-        item.setText(_translate("Dialog", "Lower bound"))
-        item = self.tableWidget.horizontalHeaderItem(3)
-        item.setText(_translate("Dialog", "Upper bound"))
-        self.parameter_button.setText(_translate("Dialog", "Add parameter"))
-        self.groupBox_3.setTitle(_translate("Dialog", "Multiple choice part"))
-        self.use_nuclei.setText(_translate("Dialog", "Add gyromagnetic ratios"))
-        self.selection_button.setText(_translate("Dialog", "Add selection"))
-        self.groupBox_4.setTitle(_translate("Dialog", "Available namespace"))
-        self.label.setText(_translate("Dialog", "Function y = func(x)"))
-from ..lib.codeeditor import CodeEditor
-from ..lib.namespace import QNamespaceWidget

nmreval/gui_qt/fit/function_creation_dialog.py

@@ -1,238 +0,0 @@
-import re
-
-import numexpr as ne
-import numpy as np
-
-from ..Qt import QtCore, QtWidgets
-from .._py.fitcreationdialog import Ui_Dialog
-
-
-_numexpr_funcs = []
-for k, _ in ne.expressions.functions.items():
-    pat = k + r'\('
-    _numexpr_funcs.append((re.compile(pat), 'np.' + k + '('))
-
-
-class QUserFitCreator(QtWidgets.QDialog, Ui_Dialog):
-    classCreated = QtCore.pyqtSignal(object)
-
-    def __init__(self, parent=None):
-        super().__init__(parent=parent)
-        self.setupUi(self)
-
-        self.namespace_widget.make_namespace()
-
-        self.tableWidget.itemChanged.connect(self.update_function)
-
-        self.groupBox.toggled.connect(self.change_visibility)
-        self.groupBox_2.toggled.connect(self.change_visibility)
-        self.groupBox_3.toggled.connect(self.change_visibility)
-        self.groupBox_4.toggled.connect(self.change_visibility)
-
-        self.groupBox.setChecked(True)
-
-    def __call__(self, *args, **kwargs):
-        for w in [self.lineEdit_4, self.lineEdit, self.lineEdit_3, self.lineEdit_2,
-                  self.parameterLineEdit, self.externalParametersLineEdit]:
-            w.clear()
-
-    def check(self):
-        self.name = self.name_lineedit.text()
-        self.group = self.group_lineedit.text()
-        self.eq = str(self.lineEdit.text())
-        self.p = str(self.parameterLineEdit.text()).split()
-        self.func = str(self.lineEdit_4.text())
-        self._func_string = ''
-
-        error = []
-        for k, v in [('Name', self.name), ('Group', self.group), ('Parameters', self.p), ('Function', self.func)]:
-            if not v:
-                error.append('Empty ' + str(k))
-        if self.name:
-            if self.name[0].isdigit():
-                error.append('Name starts with digit')
-        if self.p:
-            if set(self.p) & set(self.ext_p):
-                error.append('Duplicate entries: {}'.format(list(set(self.p) & set(self.ext_p))))
-        if self.p and self.func:
-            p_test = np.ones((len(self.p)+len(self.ext_p)))
-            _x = np.arange(2)
-            namespace = {'x': _x}
-            for i, pp in enumerate(p_test):
-                namespace[f'p_{i}'] = pp
-            self._func_string = self.func + ''
-            self._func_string = self._func_string.replace('[', '_').replace(']', '')
-            try:
-                ne.evaluate(self._func_string, local_dict=namespace)
-            except KeyError:
-                error.append(f'Incorrect evaluation {self.func}')
-
-        if error:
-            QtWidgets.QMessageBox().warning(self, 'Invalid entries', '\n'.join(error))
-        else:
-            return True
-
-    def accept(self):
-        self.confirm()
-        super().accept()
-
-    def confirm(self):
-        print(f'    name = {self.name_lineedit.text()}')
-        group_type = self.group_lineedit.text()
-        if group_type:
-            print(f'    group = "{group_type}"')
-        else:
-            print('    group = "User-defined"')
-        var = []
-        for row in range(self.tableWidget.rowCount()):
-            var.append(self.tableWidget.item(row, 1).text())
-        if var:
-            print('    params = [r"', end='')
-            print('", r"'.join(var) + '"]')
-        else:
-            print('    params = []')
-
-        print('\n@staticmethod')
-        print(self.label.text())
-        import inspect
-        for k, v in self.namespace_widget.namespace.flatten().items():
-            if inspect.isfunction(v):
-                print(k, inspect.getmodule(v))
-                print(k, [cc[1] for cc in inspect.getmembers(v) if cc[0] == '__qualname__'])
-            else:
-                print(k, v)
-        print(self.plainTextEdit.toPlainText())
-
-    @QtCore.pyqtSlot(name='on_parameter_button_clicked')
-    def add_variable(self):
-        self.tableWidget.blockSignals(True)
-        row = self.tableWidget.rowCount()
-        self.tableWidget.setRowCount(row+1)
-
-        self.tableWidget.setItem(row, 0, QtWidgets.QTableWidgetItem('p'+str(row)))
-        self.tableWidget.setItem(row, 1, QtWidgets.QTableWidgetItem('p_{'+str(row)+'}'))
-        self.tableWidget.setItem(row, 2, QtWidgets.QTableWidgetItem('--'))
-        self.tableWidget.setItem(row, 3, QtWidgets.QTableWidgetItem('--'))
-        self.tableWidget.blockSignals(False)
-        self.update_function(None)
-
-    @QtCore.pyqtSlot(name='on_selection_button_clicked')
-    def add_choice(self):
-        cnt = self.tabWidget.count()
-        self.tabWidget.addTab(ChoiceWidget(self), 'choice' + str(cnt))
-        self.tabWidget.setCurrentIndex(cnt)
-
-    def register(self):
-        i = 0
-        basename = self.name.replace(' ', '')
-        classname = basename
-        # while classname in _userfits:
-        #     classname = basename + '_' + str(i)
-        #     i += 1
-        c = register_class(classname, self.name, self.group, self.p, self.eq, self._func_string)
-        self.classCreated.emit(c)
-        return classname, c
-
-    def save(self, cname):
-        t = '\n# Created automatically\n' \
-            'class {cname:}(object):\n'\
-            '    name = "{name:}"\n' \
-            '    type = "{group:}"\n'\
-            '    equation = "{eq:}"\n'\
-            '    params = {p:}\n' \
-            '    ext_params = {ep:}\n\n' \
-            '    @staticmethod\n' \
-            '    def func(p, x):\n' \
-            '        return {func:}\n'
-        f_string = self.func
-        for pat, repl in _numexpr_funcs:
-            f_string = re.sub(pat, repl, f_string)
-
-    @QtCore.pyqtSlot(QtWidgets.QTableWidgetItem)
-    @QtCore.pyqtSlot(str)
-    def update_function(self, _):
-        var = []
-        for row in range(self.tableWidget.rowCount()):
-            var.append(self.tableWidget.item(row, 0).text())
-
-        if self.use_nuclei.isChecked():
-            var.append('nucleus=2.67522128e8')
-
-        # for row in range(self.selection_combobox.count()):
-        #     var.append(self.selection_combobox.itemText(row) + '=')
-
-        self.label.setText('def func(x, ' + ', '.join(var) + '):')
-
-    def change_visibility(self):
-        sender = self.sender()
-
-        for gb in [self.groupBox, self.groupBox_2, self.groupBox_3, self.groupBox_4]:
-            gb.blockSignals(True)
-            gb.setChecked(sender == gb)
-            gb.blockSignals(False)
-
-        self.widget_2.setVisible(sender == self.groupBox)
-        self.widget_3.setVisible(sender == self.groupBox_2)
-        self.widget.setVisible(sender == self.groupBox_3)
-        self.namespace_widget.setVisible(sender == self.groupBox_4)
-
-
-class ChoiceWidget(QtWidgets.QWidget):
-    def __init__(self, parent=None):
-        super().__init__(parent=parent)
-
-        self._init_ui()
-
-    def _init_ui(self):
-        layout = QtWidgets.QGridLayout()
-        layout.setContentsMargins(3, 3, 3, 3)
-        layout.setHorizontalSpacing(6)
-
-        self.label = QtWidgets.QLabel('Name', parent=self)
-        layout.addWidget(self.label, 0, 0)
-        self.name_line = QtWidgets.QLineEdit(self)
-        layout.addWidget(self.name_line, 0, 1)
-
-        self.label_2 = QtWidgets.QLabel('Displayed name', parent=self)
-        layout.addWidget(self.label_2, 0, 2)
-        self.display_line = QtWidgets.QLineEdit(self)
-        layout.addWidget(self.display_line, 0, 3)
-
-        self.label_3 = QtWidgets.QLabel('Type', parent=self)
-        layout.addWidget(self.label_3)
-        self.types = QtWidgets.QComboBox(self)
-        self.types.addItems(['str', 'int', 'float'])
-        layout.addWidget(self.types)
-
-        self.add_button = QtWidgets.QPushButton('Add option')
-        layout.addWidget(self.add_button)
-
-        self.table = QtWidgets.QTableWidget(self)
-        self.table.setColumnCount(2)
-        self.table.setHorizontalHeaderLabels(['Name', 'Value'])
-        layout.addWidget(self.table, 2, 0, 1, 4)
-
-        self.setLayout(layout)
-
-
-def register_class(cname, name, group, p, eq, func):
-    c = type(cname, (), {})
-    c.name = name
-    c.type = group
-    c.params = p
-    c.equation = eq
-    c.func = func_decorator(func)
-
-    return c
-
-
-def func_decorator(f_string):
-    # we need this decorator because the result is used in a class
-
-    def wrapped_f(*args):
-        namespace = {'x': args[1]}
-        for i, pp in enumerate(args[0]):
-            namespace['p_{}'.format(i)] = pp
-        return ne.evaluate(f_string, local_dict=namespace)
-
-    return wrapped_f

nmreval/math/wideline.py

@@ -1,357 +0,0 @@
-import numpy as np
-from scipy.integrate import trapz
-
-from .orientations import zcw_spherical as crystallites
-
-
-class Powder(object):
-    def __init__(self, n=100):
-        self.alpha, self.beta, self.wt = crystallites(n)
-
-
-class Pake(object):
-    parameter = {'delta': 0., 'eta': 0., 'w_iso': 0.,
-                 'x': None, 'y': None, 'half': False}
-
-    def __init__(self, samples=10000):
-        self.powder = Powder(n=samples)
-        self.dw = None
-        self.parameter = {}
-        self.GB = 1000
-        self.pw = 1e-6
-        self.legendre = 0
-        self.axial = 0
-        self.calc_prefactor()
-
-    def calc_prefactor(self):
-        """
-        Calculates angular dependencies
-        Returns
-        -------
-
-        """
-        self.legendre = 3 * np.square(np.cos(self.powder.beta)) - 1
-        self.axial = np.square(np.sin(self.powder.beta)) * np.cos(2 * self.powder.alpha)
-
-    def set_parameter(self, p, dw=None):
-        self.parameter['delta'] = p[0] * 1e3
-        self.parameter['eta'] = p[1]
-        self.GB = p[2] * 1e3
-        self.pw = p[3] * 1e-6
-        if len(p) == 5:
-            self.parameter['w_iso'] = p[4] * 1e3
-        if dw is not None:
-            self.dw = dw
-
-    @staticmethod
-    def _check_old_data(x, d, e, w, h):
-        if Pake.parameter['x'] is None:
-            return False
-        if Pake.parameter['w_iso'] == w and Pake.parameter['delta'] == d and \
-                        Pake.parameter['eta'] == e and Pake.parameter['half'] == h and \
-                        Pake.parameter['x'][0] == x[0] and Pake.parameter['x'][1] == x[1]:
-            return True
-        return False
-
-    def calc_timesignal(self, tt, p, half=False):
-        """
-        Calculate time signal of pake spectrum
-        Parameters
-        ----------
-        tt: time array
-        p: list of parameters [delta, eta, GB, omega_iso]
-        half: if False, Pake spectrum will be calculated, if True, chemical shift spectrum will be calculated
-
-        Returns
-        -------
-        timesignal
-        """
-        _delta, _eta, _wiso = p
-        omega = 0.5 * _delta * (self.legendre - _eta * self.axial)
-        if half:
-            omega += _wiso
-        weight = self.powder.wt
-        if half:
-            fid_real = np.zeros_like(tt, dtype=float)
-            fid_imag = np.zeros_like(tt, dtype=float)
-            for k, v in zip(omega, weight):
-                pha = 2 * np.pi * k * tt
-                fid_real += (np.cos(pha)) * v
-                fid_imag += (np.sin(pha)) * v
-            fid = 1j * fid_imag
-            fid += fid_real
-        else:
-            fid = np.zeros_like(tt, dtype=float)
-            for k, v in zip(omega, weight):
-                fid += np.cos(2 * np.pi * k * tt) * v
-        return fid
-
-    @staticmethod
-    def calc_pulse(pw, f):
-        _phi = 2 * np.pi * f * pw
-        pulse = ((0.5 * np.pi * np.sin(np.sqrt(0.25 * np.pi ** 2 + 0.5 * _phi ** 2))) /
-                 np.sqrt(0.25 * np.pi ** 2 + 0.25 * _phi ** 2)) ** 1
-
-        return pulse
-
-    def pake_spectrum(self, x, p=None, half=False):
-        if p is None:
-            _gb = self.GB
-            _pw = self.pw
-            try:
-                _delta = self.parameter['delta']
-                _eta = self.parameter['eta']
-                _wiso = self.parameter['w_iso']
-            except KeyError:
-                _delta = Pake.parameter['delta']
-                _eta = Pake.parameter['eta']
-                _wiso = Pake.parameter['w_iso']
-        else:
-            _delta = p[0] * 1e3
-            _eta = p[1]
-            _gb = p[2] * 1e3
-            _pw = p[3] * 1e-6
-            _wiso = p[4] * 1e3
-
-        # x is time
-        if abs(x[1] - x[0]) < 1:
-            if self.dw is None:
-                self.dw = x[1] - x[0]
-            t = x
-            nop = len(x)
-            isfreq = False
-        # x is frequency
-        else:
-            df = (x[1] - x[0])
-            if self.dw is None:
-                self.dw = 1 / (df * len(x))
-            if len(x) != 1 / (self.dw * df):
-                nop = int(1 / (self.dw * df))
-            else:
-                nop = len(x)
-
-            # avoid calculation for to much points
-            t = np.arange(0, min(8192, nop)) * self.dw
-            isfreq = True
-
-        new_data = self._check_old_data((nop, self.dw), _delta, _eta, _wiso, half)
-
-        if new_data:
-            fid = Pake.parameter['y'] + 0
-            Pake.parameter['delta'] = _delta
-            Pake.parameter['eta'] = _eta
-            Pake.parameter['w_iso'] = _wiso
-            Pake.parameter['x'] = (nop, self.dw)
-            Pake.parameter['half'] = half
-            self.GB = _gb
-            self.pw = _pw
-            fid = self.calc_timesignal(t, [_delta, _eta, _wiso], half=half)
-            Pake.parameter['y'] = fid + 0
-
-
-        fid *= np.exp(-(_gb * t) ** 2)
-
-        # add zeros to get desired signal length
-        if len(fid) != nop:
-            fid = np.append(fid, np.zeros((nop - len(fid))), axis=0)
-
-        spec = np.fft.fftshift(np.fft.fft(fid))
-        spec -= np.mean(spec[:10])
-        _f = np.fft.fftshift(np.fft.fftfreq(nop, d=self.dw))
-
-        # take finite pulse length into account
-        if _pw != 0:
-            pulse = self.calc_pulse(_pw, _f)
-            spec *= pulse
-
-        # shift pake spectrum by isotropic shift
-        if not half:
-            spec = np.roll(spec, int(self.dw * _wiso * nop))
-
-        # cut to original frequency range
-        if isfreq:
-            # mask = np.ma.masked_inside(_f, min(x), max(x)).mask
-            # spec = spec[mask]
-            spec = np.interp(x, _f, spec.real)
-
-        spec.real -= np.mean(spec.real[:10])
-
-        return spec.real / max(spec.real)
-
-    def pake(self, x, p=None):
-        return self.pake_spectrum(x, p=p)
-
-    def halfpake(self, x, p=None):
-        return self.pake_spectrum(x, p=p, half=True)
-
-
-class SecondOrder(object):
-    parameter = {'c_q': 1e6, 'eta': 0.,
-                 'x': None, 'y': None}
-
-    def __init__(self, samples=200000):
-        self.powder = Powder(n=samples)
-        self.dw = None
-        self.parameter = {}
-        self.GB = 1000
-        self.pw = 1e-6
-        self.legendre = 0
-        self.axial = 0
-        self.coupling = 1
-        self.larmor = 2 * np.pi * 100e6
-
-    def set_parameter(self, p, dw=None, larmor=None, spin=2.5):
-        self.parameter['c_q'] = 2 * np.pi * p[0] * 1e6
-        self.parameter['eta'] = p[1]
-        self.GB = p[2] * 1e3
-        if dw is not None:
-            self.dw = dw
-        if larmor is not None:
-            self.larmor = 2 * np.pi * larmor
-        self._calc_coupling(2 * np.pi * p[0] * 1e6, spin=spin)
-
-    def _calc_coupling(self, c_q, spin=2.5):
-        omega_q = c_q / (2 * spin * (2 * spin - 1))
-        self.coupling = 1.5 * omega_q ** 2 / self.larmor * (spin * (spin + 1) - 0.75)
-
-    def calc_omega(self, eta, delta):
-        self._calc_coupling(delta)
-        cos2phi = np.cos(2 * self.powder.alpha)
-        cos_theta_square = 0.5 + 0.5 * np.cos(2 * self.powder.beta)
-        prefactor_a = -3.375 + 2.25 * eta * cos2phi - 0.375 * (eta * cos2phi) ** 2
-        prefactor_b = 3.75 - 0.5 * eta ** 2 - 2 * eta * cos2phi + 0.75 * (eta * cos2phi) ** 2
-        prefactor_c = -0.375 + (eta ** 2) / 3. - 0.25 * eta * cos2phi - 0.375 * (eta * cos2phi) ** 2
-        ret_val = np.zeros_like(cos2phi)
-        ret_val += prefactor_a * cos_theta_square ** 2
-        ret_val += prefactor_b * cos_theta_square
-        ret_val += prefactor_c
-        return self.coupling * ret_val
-
-    def calc_timesignal(self, tt, p):
-        delta, eta = p
-        omega = self.calc_omega(eta, delta)
-        weight = self.powder.wt
-        fid_real = np.zeros_like(tt, dtype=float)
-        fid_imag = np.zeros_like(tt, dtype=float)
-
-        for o, w in zip(omega, weight):
-            pha = o * tt
-            co_pha = np.cos(pha)
-            si_pha = np.sin(pha)
-            fid_real += co_pha * w
-            fid_imag += si_pha * w
-
-        fid = 1j * fid_imag
-        fid += fid_real
-        return fid
-
-    def spectrum(self, x, p=None):
-        if p is None:
-            p = [self.parameter['c_q'], self.parameter['eta'], self.GB]
-        if abs(x[1] - x[0]) < 1:
-            if self.dw is None:
-                self.dw = x[1] - x[0]
-            t = x
-            nop = len(x)
-            isfreq = False
-        else:
-            df = (x[1] - x[0])
-            if self.dw is None:
-                self.dw = 1 / (df * len(x))
-            if len(x) != 1 / (self.dw * df):
-                nop = int(1 / (self.dw * df))
-            else:
-                nop = len(x)
-            t = np.arange(0, min(8192, nop)) * self.dw
-            isfreq = True
-
-        fid = self.calc_timesignal(t, p[:-1])
-        fid *= np.exp(-(p[-1] * t) ** 2)
-
-        if len(fid) != nop:
-            fid = np.append(fid, np.zeros((nop - len(fid))), axis=0)
-
-        spec = np.fft.fftshift(np.fft.fft(fid))
-        _f = np.fft.fftshift(np.fft.fftfreq(nop, d=self.dw))
-
-        if isfreq:
-            mask = np.ma.masked_inside(_f, min(x), max(x)).mask
-            spec = spec[mask]
-
-        return spec.real - np.mean(spec.real[:10])
-
-
-def csa(x: np.ndarray, delta: float, eta: float, wiso: float, gb: float, sw: float):
-    dw = 1 / sw
-    a, b, _ = crystallites(200000)
-    bins = 0.5 * (x[1:] + x[:-1])
-    bins = np.hstack((np.array([0.5 * (-x[1] + 3 * x[0])]), bins, np.array([0.5 * (3 * x[-1] - x[-2])])))
-
-    omega = wiso + delta * 0.5 * (3 * np.cos(b) ** 2 - 1 - eta * np.square(np.sin(b)) * np.cos(2 * a))
-
-    s_left = np.histogram(omega, bins=bins)[0]
-    s = s_left
-
-    if gb != 0:
-        apd = np.exp(-4 * np.log(2) * (np.fft.fftshift(np.fft.fftfreq(len(x), d=dw)) / sw) ** 2) * \
-              2 * np.sqrt(np.log(2) / np.pi) / gb
-        ret_val = np.convolve(s, apd, mode='same')
-    else:
-        ret_val = s
-
-    return ret_val / trapz(ret_val, x)
-
-
-def pake(p, x):
-    dw = 1/p[-1]
-    a, b, _ = crystallites(200000)
-    bins = 0.5 * (x[1:] + x[:-1])
-    bins = np.hstack((np.array([0.5 * (-x[1] + 3 * x[0])]), bins, np.array([0.5 * (3 * x[-1] - x[-2])])))
-
-    omega = p[0] * 0.5 * (3*np.cos(b)**2 - 1 - p[1] * np.square(np.sin(b)) * np.cos(2 * a))
-
-    s_left = np.histogram(omega, bins=bins)[0]
-    s_right = np.histogram(-omega, bins=bins)[0]
-    s = s_left + s_right
-
-    if p[2] != 0:
-        apd = np.exp(-4 * np.log(2) * (np.fft.fftshift(np.fft.fftfreq(len(x), d=dw)) / p[2]) ** 2) * \
-              2 * np.sqrt(np.log(2) / np.pi) / p[2]
-        ret_val = np.convolve(s, apd, mode='same')
-    else:
-        ret_val = s
-
-    return ret_val/trapz(ret_val, x)
-
-
-def sec_order(p, x, spin=2.5):
-    dw = 1/p[-1]
-    a, b, _ = crystallites(200000)
-    bins = 0.5 * (x[1:] + x[:-1])
-    bins = np.hstack((np.array([0.5 * (-x[1] + 3 * x[0])]), bins, np.array([0.5 * (3 * x[-1] - x[-2])])))
-
-    omega_q = 2 * np.pi * p[0] / (2*spin * (2*spin - 1))
-    coupling = 1.5 * (omega_q**2 / (2 * np.pi *p[3])) * (spin*(spin + 1) - 0.75)
-
-    cos2phi = np.cos(2 * a)
-    cos_theta_square = 0.5+0.5*np.cos(2*b)
-    prefactor_a = -3.375 + 2.25*p[1] * cos2phi - 0.375 * (p[1] * cos2phi)**2
-    prefactor_b = 3.75 - 0.5 * p[1]**2 - 2*p[1]*cos2phi + 0.75 * (p[1]*cos2phi)**2
-    prefactor_c = -0.375 + (p[1]**2)/3. - 0.25*p[1]*cos2phi - 0.375 * (p[1]*cos2phi)**2
-    orient = np.zeros_like(cos2phi)
-    orient += prefactor_a * cos_theta_square ** 2
-    orient += prefactor_b * cos_theta_square
-    orient += prefactor_c
-
-    omega = coupling * orient
-
-    s = np.histogram(omega/(2*np.pi), bins=bins)[0]
-
-    if p[2] != 0:
-        apd = np.exp(-4 * np.log(2) * (np.fft.fftshift(np.fft.fftfreq(len(x), d=dw)) / p[2]) ** 2) * \
-              2 * np.sqrt(np.log(2) / np.pi) / p[2]
-        ret_val = np.convolve(s, apd, mode='same')
-    else:
-        ret_val = s
-
-    return ret_val / trapz(ret_val, x)

nmreval/models/gengamma.py

@@ -1,268 +0,0 @@
-import numpy as np
-from scipy.special import gammaln
-from ..math.logfourier import logft
-
-stepsize = 0.2  # 0.05
-span1 = 20
-span2 = 30
-
-
-class GeneralGamma(object):
-    lower_b = 20
-    upper_b = 20
-    dx = 0.2
-
-    @staticmethod
-    def gga_dist(tau, tau0, alpha, beta):
-        b_to_a = beta / alpha
-        norm = np.exp(gammaln(b_to_a) - b_to_a * np.log(b_to_a)) / alpha
-        t_to_t0 = tau / tau0
-        ret_val = np.exp(-b_to_a * t_to_t0 ** alpha) * t_to_t0 ** beta
-
-        return ret_val / norm
-
-    @staticmethod
-    def gga_ew_dist(tau, tau0, alpha, beta, sigma, gamma):
-        if gamma == beta:
-            return GeneralGamma.gga_dist(tau, tau0, alpha, beta)
-        b_to_a = beta / alpha
-        g_to_a = gamma / alpha
-        t_to_t0 = tau / tau0
-        norm = (np.exp(gammaln(b_to_a)) + sigma**(gamma-beta) * np.exp(gammaln(g_to_a) + (b_to_a-g_to_a)*np.log(b_to_a))) / np.exp(b_to_a*np.log(b_to_a)) / alpha
-
-        ret_val = np.exp(-b_to_a * t_to_t0**alpha) * t_to_t0**beta * (1 + (t_to_t0*sigma)**(gamma-beta))
-
-        return ret_val / norm
-
-    @staticmethod
-    def ggb_dist(tau, tau0, a, b):
-        norm = a * (1+b) * np.sin(np.pi*b/(1+b)) * b**(b/(1+b)) / np.pi
-        ret_val = b * (tau/tau0)**a + (tau/tau0)**(-a*b)
-
-        return norm / ret_val
-
-    @staticmethod
-    def _gg_time(t, tau0, *args, **kwargs):
-        logtau = np.log(tau0)
-        steps = np.arange(logtau - GeneralGamma.lower_b, logtau + GeneralGamma.upper_b, GeneralGamma.dx)
-        taus = np.exp(steps)
-        ret_val = np.zeros_like(t)
-        dist = {'gga': GeneralGamma.gga_dist,
-                'gga_ew': GeneralGamma.gga_ew_dist,
-                'ggb': GeneralGamma.ggb_dist}[kwargs.pop('mode', 'gga')]
-        gtau = dist(taus, tau0, *args)
-        for i, xval in enumerate(t):
-            y = np.exp(- xval / taus)
-            y *= gtau
-            y = y[1:] + y[:-1]
-            ret_val[i] = np.sum(y) * GeneralGamma.dx / 2
-        return ret_val
-
-    @staticmethod
-    def ggaew_b_freq(f, tau0, alpha, beta, sigma, gamma, tau1, a, b, r, dec=5):
-        t = np.logspace(np.log10(1 / max(f)) - dec, np.log10(1 / min(f)) + dec, num=int(len(f) * (0.5 * dec)))
-        phi_a = GeneralGamma.ggaew(t, tau0, alpha, beta, sigma, gamma)
-        phi_b = GeneralGamma.ggb(t, tau1, a, b)
-        temp = phi_a * (1 - r + r * phi_b)
-
-        ret_val = logft(t, temp, new_x=2 * np.pi * f)[1].y
-
-        return ret_val * f * 2 * np.pi
-
-    @staticmethod
-    def gga_b_freq(f, tau0, alpha, beta, tau1, a, b, r, dec=5):
-        t = np.logspace(np.log10(1 / max(f)) - dec, np.log10(1 / min(f)) + dec, num=int(len(f) * (0.5 * dec)))
-        phi_a = GeneralGamma.gga(t, tau0, alpha, beta)
-        phi_b = GeneralGamma.ggb(t, tau1, a, b)
-        temp = phi_a * (1 - r + r * phi_b)
-
-        ret_val = logft(t, temp, new_x=2 * np.pi * f)[1].y
-
-        return ret_val * f * 2 * np.pi
-
-    @staticmethod
-    def gga(t, tau0, alpha, beta):
-        return GeneralGamma._gg_time(t, tau0, alpha, beta, mode='gga')
-
-    @staticmethod
-    def ggaew(t, tau0, alpha, beta, sigma, gamma):
-        return GeneralGamma._gg_time(t, tau0, alpha, beta, sigma, gamma, mode='gga_ew')
-
-    @staticmethod
-    def ggb(t, tau0, a, b):
-        return GeneralGamma._gg_time(t, tau0, a, b, mode='ggb')
-
-    @staticmethod
-    def ggaew_b(t, tau0, alpha, beta, sigma, gamma, tau1, a, b, r):
-        phi_a = GeneralGamma.ggaew(t, tau0, alpha, beta, sigma, gamma)
-        phi_b = GeneralGamma.ggb(t, tau1, a, b)
-        ret_val = phi_a * (1 - r + r * phi_b)
-        return ret_val
-
-    @staticmethod
-    def gga_b(t, tau0, alpha, beta, tau1, a, b, r):
-        phi_a = GeneralGamma.gga(t, tau0, alpha, beta)
-        phi_b = GeneralGamma.ggb(t, tau1, a, b)
-        ret_val = phi_a * (1 - r + r * phi_b)
-        return ret_val
-
-
-class FitGG(object):
-    name = 'Alpha + Beta + EW'
-    type = 'Gamma-Functions'
-    equation = r'A*\Phi_{\alpha,EW} * [1 - C + C*\Phi_{\beta}] + B'
-    params = ['A', 'B',
-              r'\tau_{\alpha}', r'\alpha', r'\beta', '\sigma', '\gamma',
-              r'\tau_{\beta}', 'a', 'b', 'C']
-
-    @staticmethod
-    def func(p, x):
-        amp, base, tau0, alpha, beta, sigma, gamma, tau1, a, b, c = p
-        phi_a = GeneralGamma.ggaew(x, tau0, alpha, beta, sigma, gamma)
-        phi_b = GeneralGamma.ggb(x, tau1, a, b)
-        ret_val = amp * phi_a * (1 - c + c * phi_b) + base
-        return ret_val
-
-
-# Definiere Funktionen #
-def glntau1_td(ttime, tau, alpha, beta):
-    lnx = np.log(tau) + span1
-    intmin = np.log(tau) - span2
-    steps = np.arange(lnx, intmin, -stepsize)
-    explnx = np.exp(steps)
-    betatoalpha = beta / alpha
-    logtau = np.log(tau)
-    if betatoalpha > 80:
-        norm = np.exp(.5 * np.log(2 * np.pi / betatoalpha) - betatoalpha) / alpha
-    else:
-        norm = np.exp(gammaln(betatoalpha)) / alpha / np.power(betatoalpha, betatoalpha)
-    y = np.exp(-np.exp((steps - logtau) * alpha) * betatoalpha) * np.power(explnx / tau, beta) * np.exp(-ttime / explnx)
-    y = y[1:] + y[:-1]
-    intval = np.sum(y) / 2
-    intval = intval * stepsize / norm
-    return intval
-
-
-def gga(t, tau0, alpha, beta):
-    logtau = np.log(tau0)
-    stepsize = 0.2
-    steps = np.arange(logtau - 20, logtau + 20, stepsize)
-    taus = np.exp(steps)/tau0
-    betatoalpha = beta / alpha
-    norm = np.exp(gammaln(betatoalpha) - betatoalpha*np.log(betatoalpha)) / alpha
-    ret_val = np.zeros_like(t)
-    gtau = np.exp(-taus ** alpha * betatoalpha) * taus ** beta
-    for i, xval in enumerate(t):
-        # exponent = -taus**alpha * betatoalpha - xval/taus/tau0
-        y = np.exp(- xval/taus/tau0)
-        y *= gtau
-        y = y[1:] + y[:-1]
-        ret_val[i] = np.sum(y) * stepsize / norm / 2
-    return ret_val
-
-
-def ggaew(t, tau0, alpha, beta, sigma, gamma):
-    logtau = np.log(tau0)
-    stepsize = 0.2
-    steps = np.arange(logtau - 20, logtau + 20, stepsize)
-    taus = np.exp(steps) / tau0
-    q1 = beta / alpha
-    q2 = gamma / alpha
-    norm = (np.exp(gammaln(q1)) + sigma**(gamma-beta) * np.exp((q1-q2)*np.log(q1)) * np.exp(gammaln(q2))) / alpha / np.exp(q1*np.log(q1))
-    ret_val = np.empty_like(t)
-    gtau = np.exp(-taus**alpha * q1) * taus**beta * (1 + (taus*sigma)**(gamma-beta))
-    for i, xval in enumerate(t):
-        y = np.exp(-xval/taus/tau0)
-        y *= gtau
-        y = y[1:] + y[:-1]
-        ret_val[i] = np.sum(y) * stepsize / norm / 2
-    return ret_val
-
-
-def ggaew_b(t, tau0, alpha, beta, sigma, gamma, tau1, a, b, r):
-    phi_a = ggaew(t, tau0, alpha, beta,sigma, gamma)
-    phi_b = ggb(t, tau1, a, b)
-    ret_val = phi_a * (1-r + r*phi_b)
-    return ret_val
-
-
-def ggb(t, tau0, a, b):
-    logtau = np.log(tau0)
-    stepsize = 0.2
-    steps = np.arange(logtau - 20, logtau + 20, stepsize)
-    taus = np.exp(steps) / tau0
-    norm = np.pi / (a*(1+b)) / b**(b/(1+b)) / np.sin(np.pi*b / (1+b))
-    ret_val = np.empty_like(t)
-    gtau = 1. / (b * taus**a + taus**(-b*a))
-    for i, xval in enumerate(t):
-        y = np.exp(-xval / taus / tau0)
-        y *= gtau
-        y = y[1:] + y[:-1]
-        ret_val[i] = np.sum(y) * stepsize / norm / 2
-    return ret_val
-
-
-def glntau2_td(ttime, tau, alpha, beta, sigma, gam):
-    intval = 0
-    lnx = np.log(tau) + span1
-    intmin = np.log(tau) - span2
-    steps = np.arange(lnx, intmin, -stepsize)
-    explnx = np.exp(steps)
-    logtau = np.log(tau)
-    q1 = beta / alpha
-    q2 = gam / alpha
-
-    if q2 > 80:
-        norm = (np.exp(.5 * np.log(2 * np.pi / q1) - q1) + np.power(sigma, alpha * (q2 - q1)) * np.power(q2 / q1,
-                                                                                                      -q2) * np.exp(
-            .5 * np.log(2 * np.PI / q2) - q2)) / alpha
-    elif q1 > 80:
-        norm = (np.exp(.5 * np.log(2 * np.pi / q1) - q1) + np.power(sigma, alpha * (q2 - q1)) * np.power(q2 / q1,
-                                                                                                    -q2) * np.exp(
-            gammaln(q2)) * np.power(q1, -q1)) / alpha
-    else:
-        norm = (np.exp(gammaln(q1)) + np.power(sigma, gam - beta) * np.power(q1, q1 - q2) * np.exp(gammaln(q2))) / (
-                alpha * np.power(q1, q1))
-    y = np.exp(-np.exp((steps - logtau) * alpha) * q1) * np.power(explnx / tau, beta) * (
-            1 + np.power(explnx * sigma / tau, gam - beta)) * np.exp(-ttime / explnx)
-    y = y[1:] + y[:-1]
-    intval = np.sum(y) / 2
-    intval = intval * stepsize / norm
-    return intval
-
-
-def glnbeta_td(ttime, tau, a, b):
-    intval = 0
-    lnx = np.log(tau) + span1
-    intmin = np.log(tau) - span2
-    steps = np.arange(lnx, intmin, -stepsize)
-    explnx = np.exp(steps)
-    norm = np.pi / (a * (1 + b)) / np.power(b, b / (1. + b)) / np.sin(np.pi * b / (1. + b))
-    y = 1. / (b * np.power(explnx / tau, a) + np.power(explnx / tau, -(b * a))) * np.exp(-ttime / explnx)
-    y = y[1:] + y[:-1]
-    intval = np.sum(y) / 2
-
-    intval = intval * stepsize / norm
-    return intval
-
-
-def g2(p, x):
-    ret_val = np.empty(np.shape(x))
-    for i, xval in enumerate(x):
-        # fkt1 = glntau2_td(xval, p[1], p[2], p[3], p[4], p[5])
-        # fkt1 = glntau1_td(xval, p[1], p[2], p[3])
-        fkt1 = glntau2_td(xval, p[1], p[2], p[3], p[4], p[5])
-        fkt2 = glnbeta_td(xval, p[6], p[7], p[8])
-        # ret_val[i] = (fkt1 * ((1 - p[4]) + p[4] * fkt2) * p[0]) + np.abs(p[9]) * np.exp(-(xval/p[10])**p[11]) + p[8]
-        ret_val[i] = fkt1 * (1-p[0] + p[0]*fkt2)
-    return ret_val
-
-
-def g1(p, x):
-    ret_val = np.empty(np.shape(x))
-    for i, xval in enumerate(x):
-        #        fkt1 = glntau1_td(xval,p[1],p[2],p[3])
-        fkt1 = glntau2_td(xval, p[1], p[2], p[3], p[11], p[12])
-        fkt2 = glnbeta_td(xval, p[5], p[6], p[7])
-        ret_val[i] = p[0] * (fkt1 * ((1 - p[4]) + p[4] * fkt2)) + np.abs(p[8]) * np.exp(-(xval / p[9]) ** p[10])
-    return ret_val

requirements.txt

@@ -1,8 +1,8 @@
 matplotlib
 numpy
 scipy
+pyqt
+h5py
 pyqtgraph
 bsddb3
-h5py
-pyqt
 

resources/_ui/fitcreationdialog.ui

@@ -1,419 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<ui version="4.0">
- <class>Dialog</class>
- <widget class="QDialog" name="Dialog">
-  <property name="geometry">
-   <rect>
-    <x>0</x>
-    <y>0</y>
-    <width>614</width>
-    <height>776</height>
-   </rect>
-  </property>
-  <property name="windowTitle">
-   <string>Dialog</string>
-  </property>
-  <layout class="QVBoxLayout" name="verticalLayout_5">
-   <property name="spacing">
-    <number>3</number>
-   </property>
-   <property name="leftMargin">
-    <number>3</number>
-   </property>
-   <property name="topMargin">
-    <number>3</number>
-   </property>
-   <property name="rightMargin">
-    <number>3</number>
-   </property>
-   <property name="bottomMargin">
-    <number>3</number>
-   </property>
-   <item>
-    <widget class="QGroupBox" name="groupBox">
-     <property name="title">
-      <string>Description</string>
-     </property>
-     <property name="checkable">
-      <bool>true</bool>
-     </property>
-     <property name="checked">
-      <bool>false</bool>
-     </property>
-     <layout class="QVBoxLayout" name="verticalLayout_7">
-      <property name="spacing">
-       <number>3</number>
-      </property>
-      <property name="leftMargin">
-       <number>3</number>
-      </property>
-      <property name="topMargin">
-       <number>3</number>
-      </property>
-      <property name="rightMargin">
-       <number>3</number>
-      </property>
-      <property name="bottomMargin">
-       <number>3</number>
-      </property>
-      <item>
-       <widget class="QWidget" name="widget_2" native="true">
-        <layout class="QGridLayout" name="gridLayout_2">
-         <property name="leftMargin">
-          <number>0</number>
-         </property>
-         <property name="topMargin">
-          <number>0</number>
-         </property>
-         <property name="rightMargin">
-          <number>0</number>
-         </property>
-         <property name="bottomMargin">
-          <number>0</number>
-         </property>
-         <property name="spacing">
-          <number>3</number>
-         </property>
-         <item row="0" column="1">
-          <widget class="QLineEdit" name="name_lineedit"/>
-         </item>
-         <item row="1" column="1">
-          <widget class="QLineEdit" name="group_lineedit"/>
-         </item>
-         <item row="1" column="0">
-          <widget class="QLabel" name="group_label">
-           <property name="text">
-            <string>Group</string>
-           </property>
-          </widget>
-         </item>
-         <item row="0" column="0">
-          <widget class="QLabel" name="name_label">
-           <property name="text">
-            <string>Name</string>
-           </property>
-           <property name="buddy">
-            <cstring>name_lineedit</cstring>
-           </property>
-          </widget>
-         </item>
-         <item row="2" column="1">
-          <widget class="QLineEdit" name="lineEdit"/>
-         </item>
-         <item row="2" column="0">
-          <widget class="QLabel" name="label_2">
-           <property name="text">
-            <string>Equation</string>
-           </property>
-          </widget>
-         </item>
-        </layout>
-       </widget>
-      </item>
-     </layout>
-    </widget>
-   </item>
-   <item>
-    <widget class="QGroupBox" name="groupBox_2">
-     <property name="title">
-      <string>Variables</string>
-     </property>
-     <property name="checkable">
-      <bool>true</bool>
-     </property>
-     <property name="checked">
-      <bool>false</bool>
-     </property>
-     <layout class="QVBoxLayout" name="verticalLayout_2">
-      <property name="spacing">
-       <number>3</number>
-      </property>
-      <property name="leftMargin">
-       <number>3</number>
-      </property>
-      <property name="topMargin">
-       <number>3</number>
-      </property>
-      <property name="rightMargin">
-       <number>3</number>
-      </property>
-      <property name="bottomMargin">
-       <number>3</number>
-      </property>
-      <item>
-       <widget class="QWidget" name="widget_3" native="true">
-        <layout class="QVBoxLayout" name="verticalLayout_8">
-         <property name="spacing">
-          <number>3</number>
-         </property>
-         <property name="leftMargin">
-          <number>0</number>
-         </property>
-         <property name="topMargin">
-          <number>0</number>
-         </property>
-         <property name="rightMargin">
-          <number>0</number>
-         </property>
-         <property name="bottomMargin">
-          <number>0</number>
-         </property>
-         <item>
-          <widget class="QTableWidget" name="tableWidget">
-           <property name="sizePolicy">
-            <sizepolicy hsizetype="Expanding" vsizetype="Expanding">
-             <horstretch>0</horstretch>
-             <verstretch>0</verstretch>
-            </sizepolicy>
-           </property>
-           <property name="selectionMode">
-            <enum>QAbstractItemView::SingleSelection</enum>
-           </property>
-           <property name="selectionBehavior">
-            <enum>QAbstractItemView::SelectRows</enum>
-           </property>
-           <property name="columnCount">
-            <number>4</number>
-           </property>
-           <column>
-            <property name="text">
-             <string>Variable</string>
-            </property>
-           </column>
-           <column>
-            <property name="text">
-             <string>Name</string>
-            </property>
-           </column>
-           <column>
-            <property name="text">
-             <string>Lower bound</string>
-            </property>
-           </column>
-           <column>
-            <property name="text">
-             <string>Upper bound</string>
-            </property>
-           </column>
-          </widget>
-         </item>
-         <item>
-          <widget class="QToolButton" name="parameter_button">
-           <property name="text">
-            <string>Add parameter</string>
-           </property>
-           <property name="toolButtonStyle">
-            <enum>Qt::ToolButtonTextBesideIcon</enum>
-           </property>
-           <property name="autoRaise">
-            <bool>false</bool>
-           </property>
-           <property name="arrowType">
-            <enum>Qt::RightArrow</enum>
-           </property>
-          </widget>
-         </item>
-        </layout>
-       </widget>
-      </item>
-     </layout>
-    </widget>
-   </item>
-   <item>
-    <widget class="QGroupBox" name="groupBox_3">
-     <property name="title">
-      <string>Multiple choice part</string>
-     </property>
-     <property name="checkable">
-      <bool>true</bool>
-     </property>
-     <property name="checked">
-      <bool>false</bool>
-     </property>
-     <layout class="QVBoxLayout" name="verticalLayout_3">
-      <property name="spacing">
-       <number>3</number>
-      </property>
-      <property name="leftMargin">
-       <number>3</number>
-      </property>
-      <property name="topMargin">
-       <number>3</number>
-      </property>
-      <property name="rightMargin">
-       <number>3</number>
-      </property>
-      <property name="bottomMargin">
-       <number>3</number>
-      </property>
-      <item>
-       <widget class="QWidget" name="widget" native="true">
-        <layout class="QVBoxLayout" name="verticalLayout_6">
-         <property name="spacing">
-          <number>3</number>
-         </property>
-         <property name="leftMargin">
-          <number>0</number>
-         </property>
-         <property name="topMargin">
-          <number>0</number>
-         </property>
-         <property name="rightMargin">
-          <number>0</number>
-         </property>
-         <property name="bottomMargin">
-          <number>0</number>
-         </property>
-         <item>
-          <widget class="QCheckBox" name="use_nuclei">
-           <property name="text">
-            <string>Add gyromagnetic ratios</string>
-           </property>
-          </widget>
-         </item>
-         <item>
-          <widget class="QTabWidget" name="tabWidget">
-           <property name="tabPosition">
-            <enum>QTabWidget::West</enum>
-           </property>
-           <property name="tabsClosable">
-            <bool>true</bool>
-           </property>
-          </widget>
-         </item>
-         <item>
-          <widget class="QToolButton" name="selection_button">
-           <property name="text">
-            <string>Add selection</string>
-           </property>
-           <property name="toolButtonStyle">
-            <enum>Qt::ToolButtonTextBesideIcon</enum>
-           </property>
-           <property name="arrowType">
-            <enum>Qt::RightArrow</enum>
-           </property>
-          </widget>
-         </item>
-        </layout>
-       </widget>
-      </item>
-     </layout>
-    </widget>
-   </item>
-   <item>
-    <widget class="QGroupBox" name="groupBox_4">
-     <property name="title">
-      <string>Available namespace</string>
-     </property>
-     <property name="checkable">
-      <bool>true</bool>
-     </property>
-     <property name="checked">
-      <bool>false</bool>
-     </property>
-     <layout class="QVBoxLayout" name="verticalLayout">
-      <item>
-       <widget class="QNamespaceWidget" name="namespace_widget" native="true">
-        <property name="sizePolicy">
-         <sizepolicy hsizetype="MinimumExpanding" vsizetype="Preferred">
-          <horstretch>0</horstretch>
-          <verstretch>0</verstretch>
-         </sizepolicy>
-        </property>
-       </widget>
-      </item>
-     </layout>
-    </widget>
-   </item>
-   <item>
-    <widget class="QFrame" name="frame_4">
-     <layout class="QVBoxLayout" name="verticalLayout_4">
-      <property name="spacing">
-       <number>3</number>
-      </property>
-      <property name="leftMargin">
-       <number>3</number>
-      </property>
-      <property name="topMargin">
-       <number>3</number>
-      </property>
-      <property name="rightMargin">
-       <number>3</number>
-      </property>
-      <property name="bottomMargin">
-       <number>3</number>
-      </property>
-      <item>
-       <widget class="QLabel" name="label">
-        <property name="text">
-         <string>Function y = func(x)</string>
-        </property>
-       </widget>
-      </item>
-      <item>
-       <widget class="CodeEditor" name="plainTextEdit"/>
-      </item>
-     </layout>
-    </widget>
-   </item>
-   <item>
-    <widget class="QDialogButtonBox" name="buttonBox">
-     <property name="orientation">
-      <enum>Qt::Horizontal</enum>
-     </property>
-     <property name="standardButtons">
-      <set>QDialogButtonBox::Cancel|QDialogButtonBox::Ok</set>
-     </property>
-    </widget>
-   </item>
-  </layout>
- </widget>
- <customwidgets>
-  <customwidget>
-   <class>QNamespaceWidget</class>
-   <extends>QWidget</extends>
-   <header>..lib.namespace</header>
-   <container>1</container>
-  </customwidget>
-  <customwidget>
-   <class>CodeEditor</class>
-   <extends>QPlainTextEdit</extends>
-   <header>..lib.codeeditor</header>
-  </customwidget>
- </customwidgets>
- <resources/>
- <connections>
-  <connection>
-   <sender>buttonBox</sender>
-   <signal>accepted()</signal>
-   <receiver>Dialog</receiver>
-   <slot>accept()</slot>
-   <hints>
-    <hint type="sourcelabel">
-     <x>248</x>
-     <y>254</y>
-    </hint>
-    <hint type="destinationlabel">
-     <x>157</x>
-     <y>274</y>
-    </hint>
-   </hints>
-  </connection>
-  <connection>
-   <sender>buttonBox</sender>
-   <signal>rejected()</signal>
-   <receiver>Dialog</receiver>
-   <slot>reject()</slot>
-   <hints>
-    <hint type="sourcelabel">
-     <x>316</x>
-     <y>260</y>
-    </hint>
-    <hint type="destinationlabel">
-     <x>286</x>
-     <y>274</y>
-    </hint>
-   </hints>
-  </connection>
- </connections>
-</ui>

src/gui_qt/Qt.py

@@ -1,7 +1,7 @@
 
 from PyQt5 import QtCore, QtGui, QtWidgets, QtPrintSupport
 
-# from PySide2 import QtCore, QtGui, QtWidgets
+# from PySide2 import QtCore, QtGui, QtWidgets, QtPrintSupport
 # QtCore.pyqtSignal = QtCore.Signal
 # QtCore.pyqtProperty = QtCore.Property
 # QtCore.pyqtSlot = QtCore.Slot

src/gui_qt/__init__.py

@@ -1,6 +1,7 @@
+from nmreval.configs import read_configuration
+
 from .Qt import QtWidgets
 from .lib.styles import MyProxyStyle
-from ..configs import read_configuration
 
 
 class App(QtWidgets.QApplication):

src/gui_qt/_py/fitcreationdialog.py

@@ -0,0 +1,77 @@
+# -*- coding: utf-8 -*-
+
+# Form implementation generated from reading ui file 'resources/_ui/fitcreationdialog.ui'
+#
+# 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.
+
+
+from PyQt5 import QtCore, QtGui, QtWidgets
+
+
+class Ui_Dialog(object):
+    def setupUi(self, Dialog):
+        Dialog.setObjectName("Dialog")
+        Dialog.resize(773, 633)
+        sizePolicy = QtWidgets.QSizePolicy(QtWidgets.QSizePolicy.Preferred, QtWidgets.QSizePolicy.MinimumExpanding)
+        sizePolicy.setHorizontalStretch(0)
+        sizePolicy.setVerticalStretch(0)
+        sizePolicy.setHeightForWidth(Dialog.sizePolicy().hasHeightForWidth())
+        Dialog.setSizePolicy(sizePolicy)
+        self.verticalLayout = QtWidgets.QVBoxLayout(Dialog)
+        self.verticalLayout.setObjectName("verticalLayout")
+        self.splitter = QtWidgets.QSplitter(Dialog)
+        self.splitter.setOrientation(QtCore.Qt.Vertical)
+        self.splitter.setObjectName("splitter")
+        self.tabWidget = QtWidgets.QTabWidget(self.splitter)
+        self.tabWidget.setObjectName("tabWidget")
+        self.description_box = QtWidgets.QWidget()
+        self.description_box.setObjectName("description_box")
+        self.verticalLayout_2 = QtWidgets.QVBoxLayout(self.description_box)
+        self.verticalLayout_2.setContentsMargins(3, 3, 3, 3)
+        self.verticalLayout_2.setSpacing(0)
+        self.verticalLayout_2.setObjectName("verticalLayout_2")
+        self.tabWidget.addTab(self.description_box, "")
+        self.args_box = QtWidgets.QWidget()
+        self.args_box.setObjectName("args_box")
+        self.verticalLayout_3 = QtWidgets.QVBoxLayout(self.args_box)
+        self.verticalLayout_3.setContentsMargins(3, 3, 3, 3)
+        self.verticalLayout_3.setSpacing(0)
+        self.verticalLayout_3.setObjectName("verticalLayout_3")
+        self.tabWidget.addTab(self.args_box, "")
+        self.kwargs_box = QtWidgets.QWidget()
+        self.kwargs_box.setObjectName("kwargs_box")
+        self.verticalLayout_5 = QtWidgets.QVBoxLayout(self.kwargs_box)
+        self.verticalLayout_5.setObjectName("verticalLayout_5")
+        self.tabWidget.addTab(self.kwargs_box, "")
+        self.namespace_box = QtWidgets.QWidget()
+        self.namespace_box.setObjectName("namespace_box")
+        self.verticalLayout_6 = QtWidgets.QVBoxLayout(self.namespace_box)
+        self.verticalLayout_6.setObjectName("verticalLayout_6")
+        self.tabWidget.addTab(self.namespace_box, "")
+        self.plainTextEdit = CodeEditor(self.splitter)
+        self.plainTextEdit.setEnabled(True)
+        self.plainTextEdit.setObjectName("plainTextEdit")
+        self.verticalLayout.addWidget(self.splitter)
+        self.buttonBox = QtWidgets.QDialogButtonBox(Dialog)
+        self.buttonBox.setOrientation(QtCore.Qt.Horizontal)
+        self.buttonBox.setStandardButtons(QtWidgets.QDialogButtonBox.Cancel|QtWidgets.QDialogButtonBox.Ok)
+        self.buttonBox.setObjectName("buttonBox")
+        self.verticalLayout.addWidget(self.buttonBox)
+
+        self.retranslateUi(Dialog)
+        self.tabWidget.setCurrentIndex(0)
+        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", "Create fit function"))
+        self.tabWidget.setTabText(self.tabWidget.indexOf(self.description_box), _translate("Dialog", "Description"))
+        self.tabWidget.setTabText(self.tabWidget.indexOf(self.args_box), _translate("Dialog", "Variables"))
+        self.tabWidget.setTabText(self.tabWidget.indexOf(self.kwargs_box), _translate("Dialog", "Multiple choice"))
+        self.tabWidget.setTabText(self.tabWidget.indexOf(self.namespace_box), _translate("Dialog", "Available Functions"))
+from ..lib.codeeditor import CodeEditor

src/gui_qt/_py/shift_scale_dialog.py

@@ -310,5 +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.utils import SciSpinBox
+from ..lib.spinboxes import SciSpinBox
 from pyqtgraph import PlotWidget

src/gui_qt/data/container.py

@@ -1,3 +1,4 @@
+from __future__ import annotations
 from collections import OrderedDict
 from itertools import cycle
 from typing import Any
@@ -5,14 +6,14 @@ from typing import Any
 import numpy as np
 from pyqtgraph import mkPen
 
-from ...data.points import Points
+from nmreval.data.points import Points
-from ...data.signals import Signal
+from nmreval.data.signals import Signal
-from ...utils.text import convert
+from nmreval.utils.text import convert
-from ...data.bds import BDS
+from nmreval.data.bds import BDS
-from ...lib.colors import BaseColor, TUColors
+from nmreval.lib.colors import BaseColor, TUColors
-from ...lib.lines import LineStyle
+from nmreval.lib.lines import LineStyle
-from ...lib.symbols import SymbolStyle, symbolcycle
+from nmreval.lib.symbols import SymbolStyle, symbolcycle
-from ...data.nmr import Spectrum, FID
+from nmreval.data.nmr import Spectrum, FID
 
 from ..Qt import QtCore, QtGui
 from ..io.exporters import GraceExporter
@@ -254,7 +255,7 @@ class ExperimentContainer(QtCore.QObject):
     def has_fits(self):
         return len(self._fits) != 0
 
-    def set_fits(self, value: str or list, replace: bool = False):
+    def set_fits(self, value: str | list, replace: bool = False):
         if isinstance(value, str):
             value = [value]