fixes in grace export and work on fit dialog

doc/source/_templates/autosummary/_class.rst

@@ -1,27 +0,0 @@
-{{ objname | escape | underline}}
-
-Import as {{ fullname }}
-
-.. currentmodule:: {{ module }}
-
-.. autoclass:: {{ objname }}
-
-   {% block methods %}
-   {% if methods %}
-   .. rubric:: {{ _('Methods') }}
-
-   .. autosummary::
-      :toctree:
-
-   {% for item in methods %}
-   {%- if not item.startswith('_') %}
-      ~{{ name }}.{{ item }}
-   {%- endif %}
-   {%- endfor %}
-   {% endif %}
-   {% endblock %}
-   
-.. minigallery:: {{module}}.{{objname}}
-   :add-heading:
-
-

doc/source/_templates/autosummary/class.rst

@@ -1,14 +1,27 @@
-:mod:`{{ module | escape }}`.{{ objname }}
+{{ fullname | escape | underline}}
-{{ underline }}==================
 
 .. currentmodule:: {{ module }}
 
 .. autoclass:: {{ objname }}
-    :members:
-    :inherited-members:
 
-.. include:: {{ fullname }}.examples
+   {% block methods %}
 
-.. raw:: html
+   {% if methods %}
+   .. rubric:: {{ _('Methods') }}
 
-    <div class="clearer"></div>
+   {% for item in methods %}
+   .. automethod:: {{ item }}
+   {%- endfor %}
+   {% endif %}
+   {% endblock %}
+
+   {% block attributes %}
+   {% if attributes %}
+   .. rubric:: {{ _('Attributes') }}
+
+   .. autosummary::
+   {% for item in attributes %}
+      ~{{ name }}.{{ item }}
+   {%- endfor %}
+   {% endif %}
+   {% endblock %}

doc/source/_templates/autosummary/class_with_attributes.rst

@@ -1,33 +0,0 @@
-{{ fullname | escape | underline}}
-
-.. currentmodule:: {{ module }}
-
-.. autoclass:: {{ objname }}
-
-   {%- block methods %}
-   {% if methods %}
-   .. rubric:: {{ _('Methods') }}
-
-   {%- for item in methods %}
-   {% if not item.startswith('_') %}
-   .. automethod:: {{ item }}
-   {%- endif %}
-   {%- endfor %}
-   {%- endif %}
-   {% endblock %}
-
-   {%- block attributes %}
-   {%- if attributes %}
-   .. rubric:: {{ _('Attributes') }}
-
-   {% for item in attributes %}
-   .. autoattribute:: {{ item }}
-   {%- endfor %}
-   {% endif %}
-   {% endblock -%}
-
-.. include:: {{ fullname }}.examples
-
-.. raw:: html
-
-    <div class="clearer"></div>

doc/source/api/distributions.rst

@@ -1,4 +1,5 @@
 .. automodule:: nmreval.distributions
-   :no-members:
+   :members:
-   :no-inherited-members:
+   :inherited-members:
-   :no-special-members:
+   :undoc-members:
+

doc/source/api/models.rst

@@ -1,4 +1,2 @@
 .. automodule:: nmreval.models
-   :no-members:
+   :members:
-   :no-inherited-members:
-   :no-special-members:

doc/source/conf.py

@@ -39,7 +39,6 @@ version = release
 extensions = [
     'sphinx.ext.autodoc',
     'sphinx.ext.autosummary',
-    'sphinx.ext.inheritance_diagram',
     'sphinx.ext.napoleon',
     'sphinx.ext.viewcode',
     'sphinx.ext.intersphinx',
@@ -55,14 +54,13 @@ intersphinx_mapping = {
     'matplotlib': ('https://matplotlib.org/stable', None),
 }
 
-# autodoc options
+# # autodoc options
 autodoc_typehints = 'none'
 autodoc_class_signature = 'separated'
 autoclass_content = 'class'
 autodoc_member_order = 'groupwise'
-# autodoc_default_options = {'members': False, 'inherited-members': False}
+#
-
+# # autosummay options
-# autosummay options
 autosummary_generate = True
 
 # spinx-gallery

nmreval/gui_qt/_py/fitfunctionwidget.py

@@ -13,7 +13,7 @@ from PyQt5 import QtCore, QtGui, QtWidgets
 class Ui_Form(object):
     def setupUi(self, Form):
         Form.setObjectName("Form")
-        Form.resize(314, 232)
+        Form.resize(382, 375)
         sizePolicy = QtWidgets.QSizePolicy(QtWidgets.QSizePolicy.Preferred, QtWidgets.QSizePolicy.Maximum)
         sizePolicy.setHorizontalStretch(0)
         sizePolicy.setVerticalStretch(0)
@@ -23,14 +23,14 @@ class Ui_Form(object):
         self.gridLayout.setContentsMargins(0, 0, 0, 0)
         self.gridLayout.setSpacing(3)
         self.gridLayout.setObjectName("gridLayout")
-        self.widget = ExpandableWidget(Form)
+        self.typecomboBox = QtWidgets.QComboBox(Form)
-        sizePolicy = QtWidgets.QSizePolicy(QtWidgets.QSizePolicy.MinimumExpanding, QtWidgets.QSizePolicy.Maximum)
+        sizePolicy = QtWidgets.QSizePolicy(QtWidgets.QSizePolicy.MinimumExpanding, QtWidgets.QSizePolicy.Fixed)
         sizePolicy.setHorizontalStretch(0)
         sizePolicy.setVerticalStretch(0)
-        sizePolicy.setHeightForWidth(self.widget.sizePolicy().hasHeightForWidth())
+        sizePolicy.setHeightForWidth(self.typecomboBox.sizePolicy().hasHeightForWidth())
-        self.widget.setSizePolicy(sizePolicy)
+        self.typecomboBox.setSizePolicy(sizePolicy)
-        self.widget.setObjectName("widget")
+        self.typecomboBox.setObjectName("typecomboBox")
-        self.gridLayout.addWidget(self.widget, 4, 0, 1, 2)
+        self.gridLayout.addWidget(self.typecomboBox, 0, 0, 1, 2)
         self.complex_widget = QtWidgets.QWidget(Form)
         self.complex_widget.setObjectName("complex_widget")
         self.gridLayout_2 = QtWidgets.QGridLayout(self.complex_widget)
@@ -53,7 +53,15 @@ class Ui_Form(object):
         self.label.setSizePolicy(sizePolicy)
         self.label.setObjectName("label")
         self.gridLayout_2.addWidget(self.label, 0, 0, 1, 2)
-        self.gridLayout.addWidget(self.complex_widget, 5, 0, 1, 2)
+        self.gridLayout.addWidget(self.complex_widget, 6, 0, 1, 2)
+        self.fitcomboBox = QtWidgets.QComboBox(Form)
+        sizePolicy = QtWidgets.QSizePolicy(QtWidgets.QSizePolicy.MinimumExpanding, QtWidgets.QSizePolicy.Fixed)
+        sizePolicy.setHorizontalStretch(0)
+        sizePolicy.setVerticalStretch(0)
+        sizePolicy.setHeightForWidth(self.fitcomboBox.sizePolicy().hasHeightForWidth())
+        self.fitcomboBox.setSizePolicy(sizePolicy)
+        self.fitcomboBox.setObjectName("fitcomboBox")
+        self.gridLayout.addWidget(self.fitcomboBox, 1, 0, 1, 2)
         self.use_function_button = QtWidgets.QToolButton(Form)
         sizePolicy = QtWidgets.QSizePolicy(QtWidgets.QSizePolicy.MinimumExpanding, QtWidgets.QSizePolicy.Maximum)
         sizePolicy.setHorizontalStretch(0)
@@ -65,31 +73,6 @@ class Ui_Form(object):
         self.use_function_button.setArrowType(QtCore.Qt.RightArrow)
         self.use_function_button.setObjectName("use_function_button")
         self.gridLayout.addWidget(self.use_function_button, 3, 1, 1, 1)
-        self.fitcomboBox = QtWidgets.QComboBox(Form)
-        sizePolicy = QtWidgets.QSizePolicy(QtWidgets.QSizePolicy.MinimumExpanding, QtWidgets.QSizePolicy.Fixed)
-        sizePolicy.setHorizontalStretch(0)
-        sizePolicy.setVerticalStretch(0)
-        sizePolicy.setHeightForWidth(self.fitcomboBox.sizePolicy().hasHeightForWidth())
-        self.fitcomboBox.setSizePolicy(sizePolicy)
-        self.fitcomboBox.setObjectName("fitcomboBox")
-        self.gridLayout.addWidget(self.fitcomboBox, 1, 0, 1, 2)
-        self.typecomboBox = QtWidgets.QComboBox(Form)
-        sizePolicy = QtWidgets.QSizePolicy(QtWidgets.QSizePolicy.MinimumExpanding, QtWidgets.QSizePolicy.Fixed)
-        sizePolicy.setHorizontalStretch(0)
-        sizePolicy.setVerticalStretch(0)
-        sizePolicy.setHeightForWidth(self.typecomboBox.sizePolicy().hasHeightForWidth())
-        self.typecomboBox.setSizePolicy(sizePolicy)
-        self.typecomboBox.setObjectName("typecomboBox")
-        self.gridLayout.addWidget(self.typecomboBox, 0, 0, 1, 2)
-        self.fitequation = QtWidgets.QLabel(Form)
-        sizePolicy = QtWidgets.QSizePolicy(QtWidgets.QSizePolicy.MinimumExpanding, QtWidgets.QSizePolicy.Fixed)
-        sizePolicy.setHorizontalStretch(0)
-        sizePolicy.setVerticalStretch(0)
-        sizePolicy.setHeightForWidth(self.fitequation.sizePolicy().hasHeightForWidth())
-        self.fitequation.setSizePolicy(sizePolicy)
-        self.fitequation.setWordWrap(True)
-        self.fitequation.setObjectName("fitequation")
-        self.gridLayout.addWidget(self.fitequation, 2, 0, 1, 2)
         self.operator_combobox = QtWidgets.QComboBox(Form)
         self.operator_combobox.setSizeAdjustPolicy(QtWidgets.QComboBox.AdjustToContents)
         self.operator_combobox.setFrame(True)
@@ -99,9 +82,19 @@ class Ui_Form(object):
         self.operator_combobox.addItem("")
         self.operator_combobox.addItem("")
         self.gridLayout.addWidget(self.operator_combobox, 3, 0, 1, 1)
-        self.use_combobox = QtWidgets.QComboBox(Form)
+        self.functree = FitModelTree(Form)
-        self.use_combobox.setObjectName("use_combobox")
+        self.functree.setObjectName("functree")
-        self.gridLayout.addWidget(self.use_combobox, 6, 0, 1, 2)
+        self.functree.headerItem().setText(0, "1")
+        self.gridLayout.addWidget(self.functree, 5, 0, 1, 2)
+        self.fitequation = QtWidgets.QLabel(Form)
+        sizePolicy = QtWidgets.QSizePolicy(QtWidgets.QSizePolicy.MinimumExpanding, QtWidgets.QSizePolicy.Fixed)
+        sizePolicy.setHorizontalStretch(0)
+        sizePolicy.setVerticalStretch(0)
+        sizePolicy.setHeightForWidth(self.fitequation.sizePolicy().hasHeightForWidth())
+        self.fitequation.setSizePolicy(sizePolicy)
+        self.fitequation.setWordWrap(True)
+        self.fitequation.setObjectName("fitequation")
+        self.gridLayout.addWidget(self.fitequation, 2, 0, 1, 2)
 
         self.retranslateUi(Form)
         QtCore.QMetaObject.connectSlotsByName(Form)
@@ -115,9 +108,9 @@ class Ui_Form(object):
         self.complex_comboBox.setItemText(2, _translate("Form", "Imaginary"))
         self.label.setText(_translate("Form", "Complex function found"))
         self.use_function_button.setText(_translate("Form", "Use"))
-        self.fitequation.setText(_translate("Form", "Equation"))
         self.operator_combobox.setItemText(0, _translate("Form", "Add"))
         self.operator_combobox.setItemText(1, _translate("Form", "Multiply"))
         self.operator_combobox.setItemText(2, _translate("Form", "Subtract"))
         self.operator_combobox.setItemText(3, _translate("Form", "Divide by"))
-from ..lib.expandablewidget import ExpandableWidget
+        self.fitequation.setText(_translate("Form", "Equation"))
+from ..fit.fit_forms import FitModelTree

nmreval/gui_qt/data/container.py

@@ -15,7 +15,7 @@ from ...lib.symbols import SymbolStyle, symbolcycle
 from ...data.nmr import Spectrum, FID
 
 from ..Qt import QtCore
-from ..io.exporters import pgitem_to_dic
+from ..io.exporters import GraceExporter
 from ..lib.decorators import plot_update
 from ..lib.pg_objects import ErrorBars, PlotItem
 
@@ -33,6 +33,7 @@ class ExperimentContainer(QtCore.QObject):
         self._fits = []
         self._data = data
         self._manager = kwargs.get('manager')
+        self.graph = ''
 
         self.mode = 'point'
         self.plot_real = None
@@ -374,10 +375,12 @@ class ExperimentContainer(QtCore.QObject):
     def save(self, fname):
         ext = fname.suffix
         if ext == '.agr':
-            real_dic = pgitem_to_dic(self.plot_real)
+            dic = self._manager.graphs[self.graph].get_state()
-            from ..io.exporters import GraceExporter
+            dic['items'] = [self.plot_real.get_data_opts()]
+            if self.plot_imag is not None:
+                dic['items'].append(self.plot_imag.get_data_opts())
 
-            GraceExporter(real_dic).export(fname)
+            GraceExporter(dic).export(fname)
 
         elif ext in ['.dat', '.txt']:
             self._data.savetxt(fname, err=True)

nmreval/gui_qt/fit/fit_forms.py

@@ -409,6 +409,9 @@ class FitTableWidget(QtWidgets.QTableWidget):
         while self.rowCount():
             self.removeRow(0)
 
+        self.setColumnCount(2)
+        self.hideColumn(1)
+
         for (sid, name) in set_ids:
             item = QtWidgets.QTableWidgetItem(name)
             item.setCheckState(QtCore.Qt.Checked)
@@ -419,7 +422,7 @@ class FitTableWidget(QtWidgets.QTableWidget):
 
             item2 = QtWidgets.QTableWidgetItem('')
             self.setItem(row, 1, item2)
-            cb = QtWidgets.QComboBox()
+            cb = QtWidgets.QComboBox(parent=self)
             cb.addItem('Default')
             self.setCellWidget(row, 1, cb)
 

nmreval/gui_qt/fit/fitfunction.py

@@ -1,7 +1,6 @@
 from itertools import cycle, count
 from typing import List, Tuple, Union
 
-from .fit_forms import FitModelTree
 from ..lib import get_icon
 from .._py.fitfunctionwidget import Ui_Form
 from ..Qt import QtWidgets, QtCore, QtGui
@@ -26,9 +25,6 @@ class QFunctionWidget(QtWidgets.QWidget, Ui_Form):
         super().__init__(parent=parent)
 
         self.setupUi(self)
-        self.functree = FitModelTree()
-        self.widget.setText('Model structure')
-        self.widget.addWidget(self.functree)
 
         self._types = []
         self.functions = find_models(models)
@@ -57,8 +53,14 @@ class QFunctionWidget(QtWidgets.QWidget, Ui_Form):
         for i, op_icon in enumerate(self.op_names):
             self.operator_combobox.setItemIcon(i, get_icon(op_icon))
 
-    def __len__(self):
+    def __len__(self) -> int:
-        return self.use_combobox.count()
+        num = 0
+        iterator = QtWidgets.QTreeWidgetItemIterator(self.functree)
+        while iterator.value():
+            num += 1
+            iterator += 1
+
+        return num
 
     @QtCore.pyqtSlot(int, name='on_typecomboBox_currentIndexChanged')
     def change_group(self, idx: int):
@@ -114,11 +116,6 @@ class QFunctionWidget(QtWidgets.QWidget, Ui_Form):
             qcolor = QtGui.QColor(color)
         self.functree.add_function(idx, cnt, op, name, qcolor, **kwargs)
 
-        self.use_combobox.addItem(name, userData=cnt)
-
-        self.use_combobox.setItemData(self.use_combobox.count()-1, color, QtCore.Qt.DecorationRole)
-        self.use_combobox.setCurrentIndex(self.use_combobox.count() - 1)
-
         f = self.functions[idx]
         if hasattr(f, 'iscomplex') and f.iscomplex:
             self.iscomplex = True
@@ -138,17 +135,11 @@ class QFunctionWidget(QtWidgets.QWidget, Ui_Form):
             iterator += 1
         self.complex_widget.setVisible(self.iscomplex)
 
-        for i in range(self.use_combobox.count()):
-            if idx == self.use_combobox.itemData(i):
-                self.use_combobox.removeItem(i)
-                break
-
         self.itemRemoved.emit(idx)
 
-    @QtCore.pyqtSlot(int, name='on_use_combobox_currentIndexChanged')
+    @QtCore.pyqtSlot(QtWidgets.QTreeWidgetItem, int, name='on_functree_itemClicked')
-    def show_parameter(self, idx: int):
+    def show_parameter(self, item: QtWidgets.QTreeWidgetItem, _: int):
-        if self.use_combobox.count():
+        self.showFunction.emit(item.data(0, self.functree.counterRole))
-            self.showFunction.emit(self.use_combobox.itemData(idx, QtCore.Qt.UserRole))
 
     def get_selected(self):
         function_nr, idx = self.functree.get_selected()
@@ -217,9 +208,5 @@ class QFunctionWidget(QtWidgets.QWidget, Ui_Form):
         self.functree.clear()
         self.functree.blockSignals(False)
 
-        self.use_combobox.blockSignals(True)
-        self.use_combobox.clear()
-        self.use_combobox.blockSignals(False)
-
         self.complex_comboBox.setCurrentIndex(0)
         self.complex_widget.hide()

nmreval/gui_qt/graphs/graphwindow.py

@@ -511,9 +511,11 @@ class QGraphWindow(QtWidgets.QGraphicsView, Ui_GraphWindow):
             item = self.real_plots[sid]
             other_item = self.imag_plots[sid]
             # should legend be visible? is either real part or imaginary part shown?
-            if self.listWidget.item(i).checkState() and \
+            if self.listWidget.item(i).checkState():
-                    (item in self.graphic.items() or other_item in self.graphic.items()):
+                if item in self.graphic.items():
-                self.legend.addItem(item, convert(item.opts.get('name', ''), old='tex', new='html'))
+                    self.legend.addItem(item, convert(item.opts.get('name', ''), old='tex', new='html'))
+                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):
         filters = 'All files (*.*);;AGR (*.agr);;SVG (*.svg);;PDF (*.pdf)'
@@ -580,12 +582,21 @@ class QGraphWindow(QtWidgets.QGraphicsView, Ui_GraphWindow):
 
                 self.set_color(foreground=fg_color, background=bg_color)
 
-    def export_graphics(self):
+    def export_graphics(self) -> dict:
         dic = self.get_state()
         dic['items'] = []
 
+        in_legend = []
+
         for item in self.curves():
-            item_dic = item[0].get_data_opts()
+            plot_item = item[0]
+            legend_shown = False
+            for sample, _ in self.legend.items:
+                if sample.item is plot_item:
+                    legend_shown = True
+                    break
+            in_legend.append(legend_shown)
+            item_dic = plot_item.get_data_opts()
             if len(item) == 2:
                 # plot can show errorbars
                 item_dic['yerr'] = item[1].opts['topData']
@@ -593,6 +604,8 @@ class QGraphWindow(QtWidgets.QGraphicsView, Ui_GraphWindow):
             if item_dic:
                 dic['items'].append(item_dic)
 
+        dic['in_legend'] = in_legend
+
         return dic
 
     def get_state(self) -> dict:

nmreval/gui_qt/io/exporters.py

@@ -1,9 +1,8 @@
+from __future__ import annotations
+
 from numpy import c_
 
 from ...io.graceeditor import GraceEditor
-from ...lib.colors import Colors
-from ...lib.lines import LineStyle
-from ...lib.symbols import SymbolStyle
 from ...utils.text import convert
 
 from ..Qt import QtGui, QtCore, QtPrintSupport
@@ -14,7 +13,7 @@ class GraceExporter:
         self.__agr = None
         self.__opts = kwargs
 
-    def export(self, outfile: str, mode: (int, str) = 'w'):
+    def export(self, outfile: str, mode: int | str = 'w'):
         if mode == 'w':
             self.__agr = GraceEditor()
         else:
@@ -27,7 +26,7 @@ class GraceExporter:
             new_g.set_log(x=self.__opts['log'][0], y=self.__opts['log'][1])
 
             new_g.set_onoff('legend', self.__opts['legend'])
-            new_g.set_property(**{'title': '"' + convert(self.__opts['labels'][2], old="html", new="agr") + '"',
+            new_g.set_property(**{'title': f'"{convert(self.__opts["labels"][2], old="html", new="agr")}"',
                                   'legend loctype': 'view',
                                   'legend': ', '.join(str(i) for i in new_g.world_to_view(self.__opts['legend_pos']))})
 
@@ -43,7 +42,7 @@ class GraceExporter:
         colors = self.__agr.colors
 
         new_colors = []
-        for item in self.__opts['items']:
+        for plot_label, item in zip(self.__opts['in_legend'], self.__opts['items']):
             new_s = self.__agr.new_set(g_idx)
 
             sc = item['symbolcolor']
@@ -75,7 +74,12 @@ class GraceExporter:
 
             new_s.set_line(**{'color': c_num, 'linewidth': item['linewidth'],
                               'linestyle': item['linestyle'].to_agr()})
-            new_s.set_property(comment='"' + item['name'] + '"', legend='"' + item['name'] + '"')
+
+            if plot_label:
+                new_s.set_property(comment=f'"{item["name"]}"',
+                                   legend=f'"{convert(item["name"], old="tex", new="agr")}"')
+            else:
+                new_s.set_property(comment=f'"{item["name"]}"')
 
             data = self.__agr.dataset(g_idx, new_s.idx)
             if 'yerr' in item:
@@ -108,36 +112,3 @@ class PDFPrintExporter:
         painter = QtGui.QPainter(printer)
         self.graphic.render(painter)
         painter.end()
-
-
-def pgitem_to_dic(item):
-    x, y = item.xData, item.yData
-    if (x is None) or (len(x) == 0):
-        return
-
-    opts = item.opts
-    item_dic = {
-        'x': x, 'y': y,
-        'name': opts['name'],
-        'symbolsize': opts['symbolSize']
-    }
-
-    if opts['symbol'] is None:
-        item_dic['symbol'] = SymbolStyle.No
-        item_dic['symbolcolor'] = Colors.Black
-    else:
-        item_dic['symbol'] = SymbolStyle.from_str(opts['symbol'])
-        item_dic['symbolcolor'] = Colors.from_rgb(*opts['symbolBrush'].color().getRgbF()[:3], normed=True)
-
-    pen = opts['pen']
-
-    if pen is not None:
-        item_dic['linestyle'] = LineStyle(pen.style())
-        item_dic['linecolor'] = Colors.from_rgb(*pen.color().getRgbF()[:3], normed=True)
-        item_dic['linewidth'] = pen.widthF()
-    else:
-        item_dic['linestyle'] = LineStyle.No
-        item_dic['linecolor'] = item_dic['symbolcolor']
-        item_dic['linewidth'] = 0.0
-
-    return item_dic

nmreval/gui_qt/lib/gol.py

@@ -35,8 +35,6 @@ def diamond(a):
         y = a-x
         pxl.extend([[x, y], [-x, y], [x, -y], [-x, -y]])
 
-    print(np.array(pxl).shape)
-
     return np.array(pxl)
 
 
@@ -100,7 +98,6 @@ class GameOfLife:
         self.fill = np.zeros(self.populations)
         self._populate(fill, pattern)
 
-        print(rules)
         if isinstance(rules, str):
             try:
                 b_rule, s_rule = predefined_rules[rules]

nmreval/gui_qt/lib/pg_objects.py

@@ -165,8 +165,8 @@ class PlotItem(PlotDataItem):
     def __init__(self, *args, **kwargs):
         super().__init__(*args, **kwargs)
 
-        self.opts['linecolor'] = Colors.Black
+        self.opts['linecolor'] = (0, 0, 0)
-        self.opts['symbolcolor'] = Colors.Black
+        self.opts['symbolcolor'] = (0, 0, 0)
 
         if self.opts['pen'] is not None:
             pen = self.opts['pen']
@@ -251,7 +251,6 @@ class PlotItem(PlotDataItem):
             x = []
         if y is None:
             y = []
-        # scatterArgs['mask'] = self.dataMask
 
         if curveArgs['pen'] is not None or (curveArgs['brush'] is not None and curveArgs['fillLevel'] is not None):
             is_finite = np.isfinite(x) & np.isfinite(y)
@@ -347,7 +346,6 @@ class PlotItem(PlotDataItem):
             item_dic['symbolcolor'] = opts['symbolcolor']
 
         pen = opts['pen']
-
         if pen is not None:
             item_dic['linestyle'] = LineStyle(pen.style())
             item_dic['linecolor'] = opts['linecolor']

nmreval/gui_qt/lib/stuff.py

@@ -180,7 +180,6 @@ class SnakeBoard(Board):
         self.update()
 
     def snake_move(self):
-        print(self.next_direction)
         if self.next_direction:
             turn = self.next_direction.pop()
             if self.direction != self._direction_pairs[turn]:

nmreval/io/graceeditor.py

@@ -463,10 +463,16 @@ class GraceGraph(GraceProperties):
 
     def set_log(self, x=None, y=None):
         kwargs = {}
-        if x is not None:
+        for ax, label in [(x, 'x'), (y, 'y')]:
-            kwargs['xaxes scale'] = 'Logarithmic' if x else 'Normal'
+            if ax is not None:
-        if y is not None:
+                if ax:
-            kwargs['yaxes scale'] = 'Logarithmic' if y else 'Normal'
+                    kwargs[label + 'axes scale'] = 'Logarithmic'
+                    kwargs[label + 'axis  ticklabel format'] = 'power'
+                    kwargs[label + 'axis  ticklabel prec'] = '0'
+                else:
+                    kwargs[label + 'axes scale'] = 'Normal'
+                    kwargs[label + 'axis  ticklabel format'] = 'general'
+                    kwargs[label + 'axis  ticklabel prec'] = '5'
 
         for i, line in enumerate(self):
             m = self._RE_ENTRY.match(line)

nmreval/models/__init__.py

@@ -1,14 +1,14 @@
 """
-=============
+=====================================
-Fit functions
+Fit functions (:mod:`nmreval.models`)
-=============
+=====================================
 
 .. currentmodule:: nmreval.models
 
 .. autosummary::
     :toctree: generated
     :nosignatures:
-    :template: autosummary/class_with_attributes.rst
+    :recursive:
 
     Constant
     Linear

nmreval/models/basic.py

@@ -3,7 +3,7 @@
 Basic functions
 ***************
 
-Simple basic functions
+Simple functions
 """
 
 import numpy as np
@@ -27,7 +27,7 @@ class Constant:
         Constant
 
         .. math::
-            y = c \cdot x
+            y = c
 
         Args:
             x (array-like): Input values
@@ -135,22 +135,7 @@ class Parabola:
 
 class PowerLawCross:
     """
-    Crossover between to power laws at position :math:`x_0`
+    Crossover between power laws
-
-    .. math::
-        y \\propto
-        \\begin{cases}
-            x^{b_1}, & x \le x_0 \\\\
-            x^{b_2}, & x > x_0
-        \\end{cases}
-
-    Args:
-        x (array_like): Input values
-        c (float): Prefactor
-        b1 (float): Exponent of first power law
-        b2 (float): Exponent of second power law
-        x0 (float): x position of crossover
-
     """
     type = 'Basic'
     name = 'Crossing Power Laws'
@@ -158,6 +143,23 @@ class PowerLawCross:
 
     @staticmethod
     def func(x, c, b1, b2, x0):
+        """
+        Crossover between to power laws at position :math:`x_0`
+
+        .. math::
+            y \\propto
+            \\begin{cases}
+                x^{b_1}, & x \le x_0 \\\\
+                x^{b_2}, & x > x_0
+            \\end{cases}
+
+        Args:
+            x (array_like): Input values
+            c (float): Prefactor
+            b1 (float): Exponent of first power law
+            b2 (float): Exponent of second power law
+            x0 (float): x position of crossover
+        """
         mas = np.nonzero(x > x0)
         ret_val = c * x**b1
         c2 = c * x0**(b1-b2)
@@ -167,19 +169,8 @@ class PowerLawCross:
 
 class Sine:
     """
-    Sine function
+    Wavy sine function
-
-    .. math::
-        y = C\sin(a x - \phi)
-
-    Args:
-        x (array_like): Input values
-        c (float): Prefactor
-        a (float): frequency
-        phi (float): shift
-
     """
-
     type = 'Basic'
     name = 'Sine'
     equation = r'C*sin(a*x-\phi)'
@@ -187,6 +178,19 @@ class Sine:
 
     @staticmethod
     def func(x, c: float, a: float, phi: float):
+        """
+        Calculate sine function
+
+        .. math::
+            y = C\sin(a x - \phi)
+
+        Args:
+            x (array_like): Input values
+            c (float): Prefactor
+            a (float): frequency
+            phi (float): shift
+
+        """
         return c*np.sin(a*x-phi)
 
 

nmreval/models/diffusion.py

@@ -116,15 +116,16 @@ class Peschier:
     name = 'Diffusion + Cross-Relaxation'
     type = 'Diffusion'
     equation = r'Diffusion with cross-relax f(ast) \rightarrow s(low)'
-    params = ['M_{0}', 'D', 'T_{1,f}', 'T_{1,s}', 'k_{f}', 'k_{s}', 't_{ev}', 'g']
+    params = ['M_{0}', 'D', 'T_{1,f}', 'T_{1,s}', 'k', 'p_{f}', 't_{ev}', 'g']
     bounds = [(0, None), (0, None), (0, None), (0, None), (0, None), (0, None)]
     choices = [(r'\gamma', 'nucleus', gamma)]
 
     @staticmethod
-    def func(x, m0, d, t1f, t1s, kf, ks, tp, g, nucleus=2.67522128e8):
+    def func(x, m0, d, t1f, t1s, k, pf, tp, g, nucleus: float = 2.67522128e8):
         q = nucleus*g*tp
 
         r1s, r1f = 1 / t1s, 1 / t1f
+        kf, ks = pf*k, (1-pf)*k
         a_plus = 0.5 * (d*q*q + kf + ks + r1f + r1s + np.sqrt((d*q*q + kf + r1f - ks - r1s)**2 + 4*kf*ks))
         a_minu = 0.5 * (d*q*q + kf + ks + r1f + r1s - np.sqrt((d*q*q + kf + r1f - ks - r1s)**2 + 4*kf*ks))
 

nmreval/models/relaxation.py

@@ -119,20 +119,3 @@ class SatRecMLF:
         if kind == 'inv':
             a = 2
         return dm * (1 - a * mlf(-(x/t1)**alpha, alpha)) + m0
-
-
-class PeschierHomogeneous:
-    name = 'Cross-Relaxation (g=0)'
-    type = 'Relaxation'
-    equation = r'Cross-Relaxation f(ast) \rightarrow s(low) (m_{s}(0)=0)'
-    params = ['M_{0}', 'k_{s}', 'k_{f}', 'T_{1,s}', 'T_{1,f}']
-    bounds = [(0, None), (0, None), (0, None), (0, None), (0, None)]
-
-    @staticmethod
-    def func(x, m, ks, kf, t1s, t1f):
-        r1f, r1s = 1/t1f, 1/t1s
-        a_plus = 0.5*((kf + ks + r1f + r1s) + np.sqrt((kf + r1f - ks - r1s)**2 + 4*kf*ks))
-        a_minu = 0.5*((kf + ks + r1f + r1s) - np.sqrt((kf + r1f - ks - r1s)**2 + 4*kf*ks))
-
-        return m*((a_plus - ks - r1s) / (a_plus - a_minu) * np.exp(-a_plus * x) -
-                  (a_minu - ks - r1s) / (a_plus - a_minu) * np.exp(-a_minu * x))

nmreval/models/user_models.py

@@ -1,3 +0,0 @@
-from ..configs import config_paths
-
-print(config_paths() / 'usermodels.py')

pyproject.toml

@@ -0,0 +1,53 @@
+[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',
+]
+keywords = ['nmr', 'physics', 'science']
+classifiers = [
+   '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"}
+
+[tool.setuptools]
+include_package_data = true
+
+
+[tool.setuptools.packages]
+find = {}
+scripts = bin/evaluate.py
+
+[tool.setuptools.packages.find]
+include =[
+   'nmreval*',
+   'resources*',
+]
+
+[tool.setuptools.package_data]
+* = *.txt, *.npz, *.png, *.json
+
+
+
+
+

resources/_ui/fitfunctionwidget.ui

@@ -6,8 +6,8 @@
    <rect>
     <x>0</x>
     <y>0</y>
-    <width>314</width>
+    <width>382</width>
-    <height>232</height>
+    <height>375</height>
    </rect>
   </property>
   <property name="sizePolicy">
@@ -35,17 +35,17 @@
    <property name="spacing">
     <number>3</number>
    </property>
-   <item row="4" column="0" colspan="2">
+   <item row="0" column="0" colspan="2">
-    <widget class="ExpandableWidget" name="widget" native="true">
+    <widget class="QComboBox" name="typecomboBox">
      <property name="sizePolicy">
-      <sizepolicy hsizetype="MinimumExpanding" vsizetype="Maximum">
+      <sizepolicy hsizetype="MinimumExpanding" vsizetype="Fixed">
        <horstretch>0</horstretch>
        <verstretch>0</verstretch>
       </sizepolicy>
      </property>
     </widget>
    </item>
-   <item row="5" column="0" colspan="2">
+   <item row="6" column="0" colspan="2">
     <widget class="QWidget" name="complex_widget" native="true">
      <layout class="QGridLayout" name="gridLayout_2">
       <property name="leftMargin">
@@ -102,6 +102,16 @@
      </layout>
     </widget>
    </item>
+   <item row="1" column="0" colspan="2">
+    <widget class="QComboBox" name="fitcomboBox">
+     <property name="sizePolicy">
+      <sizepolicy hsizetype="MinimumExpanding" vsizetype="Fixed">
+       <horstretch>0</horstretch>
+       <verstretch>0</verstretch>
+      </sizepolicy>
+     </property>
+    </widget>
+   </item>
    <item row="3" column="1">
     <widget class="QToolButton" name="use_function_button">
      <property name="sizePolicy">
@@ -124,42 +134,6 @@
      </property>
     </widget>
    </item>
-   <item row="1" column="0" colspan="2">
-    <widget class="QComboBox" name="fitcomboBox">
-     <property name="sizePolicy">
-      <sizepolicy hsizetype="MinimumExpanding" vsizetype="Fixed">
-       <horstretch>0</horstretch>
-       <verstretch>0</verstretch>
-      </sizepolicy>
-     </property>
-    </widget>
-   </item>
-   <item row="0" column="0" colspan="2">
-    <widget class="QComboBox" name="typecomboBox">
-     <property name="sizePolicy">
-      <sizepolicy hsizetype="MinimumExpanding" vsizetype="Fixed">
-       <horstretch>0</horstretch>
-       <verstretch>0</verstretch>
-      </sizepolicy>
-     </property>
-    </widget>
-   </item>
-   <item row="2" column="0" colspan="2">
-    <widget class="QLabel" name="fitequation">
-     <property name="sizePolicy">
-      <sizepolicy hsizetype="MinimumExpanding" vsizetype="Fixed">
-       <horstretch>0</horstretch>
-       <verstretch>0</verstretch>
-      </sizepolicy>
-     </property>
-     <property name="text">
-      <string>Equation</string>
-     </property>
-     <property name="wordWrap">
-      <bool>true</bool>
-     </property>
-    </widget>
-   </item>
    <item row="3" column="0">
     <widget class="QComboBox" name="operator_combobox">
      <property name="sizeAdjustPolicy">
@@ -190,17 +164,38 @@
      </item>
     </widget>
    </item>
-   <item row="6" column="0" colspan="2">
+   <item row="5" column="0" colspan="2">
-    <widget class="QComboBox" name="use_combobox"/>
+    <widget class="FitModelTree" name="functree">
+     <column>
+      <property name="text">
+       <string notr="true">1</string>
+      </property>
+     </column>
+    </widget>
+   </item>
+   <item row="2" column="0" colspan="2">
+    <widget class="QLabel" name="fitequation">
+     <property name="sizePolicy">
+      <sizepolicy hsizetype="MinimumExpanding" vsizetype="Fixed">
+       <horstretch>0</horstretch>
+       <verstretch>0</verstretch>
+      </sizepolicy>
+     </property>
+     <property name="text">
+      <string>Equation</string>
+     </property>
+     <property name="wordWrap">
+      <bool>true</bool>
+     </property>
+    </widget>
    </item>
   </layout>
  </widget>
  <customwidgets>
   <customwidget>
-   <class>ExpandableWidget</class>
+   <class>FitModelTree</class>
-   <extends>QWidget</extends>
+   <extends>QTreeWidget</extends>
-   <header>..lib.expandablewidget</header>
+   <header>..fit.fit_forms</header>
-   <container>1</container>
   </customwidget>
  </customwidgets>
  <resources/>

setup.cfg

@@ -0,0 +1,47 @@
+[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
+keywords = nmr, physics, science
+classifiers =
+   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 = BSD 3-Clause License
+
+[options]
+include_package_data = True
+packages = find:
+scripts = bin/evaluate.py
+
+[options.packages.find]
+include =
+   nmreval*
+   resources*
+
+[options.package_data]
+* = *.txt, *.npz, *.png, *.json
+
+
+
+
+

setup.py

@@ -1,11 +1,3 @@
-from setuptools import setup
-
-setup(
-    name='nmreval',
-    version='0.1',
-    packages=['.nmreval']
-)
-
 """A setuptools based setup module.
 
 See:
@@ -26,193 +18,57 @@ long_description = (here / 'README.md').read_text(encoding='utf-8')
 # Fields marked as "Optional" may be commented out.
 
 setup(
-    # This is the name of your project. The first time you publish this
+    # name='nmreval',  # Required
-    # package, this name will be registered for you. It will determine how
+    # version='0.1',  # Required
-    # users can install this project, e.g.:
+    # description='A sample Python project',  # Optional
+    # long_description=long_description,  # Optional
+    # long_description_content_type='text/markdown',  # Optional (see note above)
+    # url='https://chaos3.fkp.physik.tu-darmstadt.de/source/nmreval/', # Optional
+    # author='Dominik Demuth',  # Optional
+    # author_email='dominik.demuth@physik.tu-darmstadt.de',  # Optional
+    # classifiers=[  # Optional
+    #     'Development Status :: 3 - Alpha',
+    #     'Intended Audience :: End Users/Desktop',
+    #     'Intended Audience :: Science/Research',
+    #     'Topic :: Scientific/Engineering :: Physics',
+    #     'Topic :: Scientific/Engineering :: Visualization',
+    #     'License :: OSI Approved :: BSD 3-Clause 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 :: Only',
+    # ],
     #
-    # $ pip install sampleproject
+    # keywords='nmr, physics, science',  # Optional
-    #
+    # package_dir={'': '.'},  # Optional
-    # And where it will live on PyPI: https://pypi.org/project/sampleproject/
+    # packages=find_packages(where='.'),  # Required
-    #
+    # include_package_data=True,
-    # There are some restrictions on what makes a valid project name
+    # python_requires='>=3.7',
-    # specification here:
+    # install_requires=[
-    # https://packaging.python.org/specifications/core-metadata/#name
+    #     'numpy',
-    name='nmreval',  # Required
+    #     'scipy',
-
+    #     'matplotlib',
-    # Versions should comply with PEP 440:
+    #     'bsddb3',
-    # https://www.python.org/dev/peps/pep-0440/
+    #     'pyqtgraph',
-    #
+    #     'pyqt',
-    # For a discussion on single-sourcing the version across setup.py and the
+    #     'h5py'
-    # project code, see
+    # ],  # Optional
-    # https://packaging.python.org/guides/single-sourcing-package-version/
+    # # extras_require={  # Optional
-    version='0.1',  # Required
+    # #     'dev': ['check-manifest'],
-
+    # #     'test': ['coverage'],
-    # This is a one-line description or tagline of what your project does. This
+    # # },
-    # corresponds to the "Summary" metadata field:
+    # package_data={  # Optional
-    # https://packaging.python.org/specifications/core-metadata/#summary
+    #     'sample': ['package_data.dat'],
-    description='A sample Python project',  # Optional
+    # },
-
+    # data_files=[('my_data', ['data/data_file'])],  # Optional
-    # This is an optional longer description of your project that represents
+    # entry_points={  # Optional
-    # the body of text which users will see when they visit PyPI.
+    #     'console_scripts': [
-    #
+    #         'evaluate=bin:evaluate',
-    # Often, this is the same as your README, so you can just read it in from
+    #     ],
-    # that file directly (as we have already done above)
-    #
-    # This field corresponds to the "Description" metadata field:
-    # https://packaging.python.org/specifications/core-metadata/#description-optional
-    long_description=long_description,  # Optional
-
-    # Denotes that our long_description is in Markdown; valid values are
-    # text/plain, text/x-rst, and text/markdown
-    #
-    # Optional if long_description is written in reStructuredText (rst) but
-    # required for plain-text or Markdown; if unspecified, "applications should
-    # attempt to render [the long_description] as text/x-rst; charset=UTF-8 and
-    # fall back to text/plain if it is not valid rst" (see link below)
-    #
-    # This field corresponds to the "Description-Content-Type" metadata field:
-    # https://packaging.python.org/specifications/core-metadata/#description-content-type-optional
-    long_description_content_type='text/x-rst',  # Optional (see note above)
-
-    # This should be a valid link to your project's main homepage.
-    #
-    # This field corresponds to the "Home-Page" metadata field:
-    # https://packaging.python.org/specifications/core-metadata/#home-page-optional
-    url='https://github.com/pypa/sampleproject',  # Optional
-
-    # This should be your name or the name of the organization which owns the
-    # project.
-    author='Dominik Demuth',  # Optional
-
-    # This should be a valid email address corresponding to the author listed
-    # above.
-    author_email='dominik.demuth@physik.tu-darmstadt.de',  # Optional
-
-    # Classifiers help users find your project by categorizing it.
-    #
-    # For a list of valid classifiers, see https://pypi.org/classifiers/
-    classifiers=[  # Optional
-        # How mature is this project? Common values are
-        #   3 - Alpha
-        #   4 - Beta
-        #   5 - Production/Stable
-        'Development Status :: 3 - Alpha',
-
-        # Indicate who your project is intended for
-        'Intended Audience :: Developers',
-        'Topic :: Software Development :: Build Tools',
-
-        # Pick your license as you wish
-        'License :: OSI Approved :: MIT License',
-
-        # Specify the Python versions you support here. In particular, ensure
-        # that you indicate you support Python 3. These classifiers are *not*
-        # checked by 'pip install'. See instead 'python_requires' below.
-        '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',
-    ],
-
-    # This field adds keywords for your project which will appear on the
-    # project page. What does your project relate to?
-    #
-    # Note that this is a list of additional keywords, separated
-    # by commas, to be used to assist searching for the distribution in a
-    # larger catalog.
-    keywords='sample, setuptools, development',  # Optional
-
-    # When your source code is in a subdirectory under the project root, e.g.
-    # `src/`, it is necessary to specify the `package_dir` argument.
-    package_dir={'': 'src'},  # Optional
-
-    # You can just specify package directories manually here if your project is
-    # simple. Or you can use find_packages().
-    #
-    # Alternatively, if you just want to distribute a single Python file, use
-    # the `py_modules` argument instead as follows, which will expect a file
-    # called `my_module.py` to exist:
-    #
-    #   py_modules=["my_module"],
-    #
-    packages=find_packages(where='src'),  # Required
-
-    # Specify which Python versions you support. In contrast to the
-    # 'Programming Language' classifiers above, 'pip install' will check this
-    # and refuse to install the project if the version does not match. See
-    # https://packaging.python.org/guides/distributing-packages-using-setuptools/#python-requires
-    python_requires='>=3.7, <4',
-
-    # This field lists other packages that your project depends on to run.
-    # Any package you put here will be installed by pip when your project is
-    # installed, so they must be valid existing projects.
-    #
-    # For an analysis of "install_requires" vs pip's requirements files see:
-    # https://packaging.python.org/discussions/install-requires-vs-requirements/
-    install_requires=[
-        'numpy',
-        'scipy',
-        'matplotlib',
-        'bsddb3',
-        'pyqtgraph',
-        'PyQt4',
-        'h5py'
-    ],  # Optional
-
-    # List additional groups of dependencies here (e.g. development
-    # dependencies). Users will be able to install these using the "extras"
-    # syntax, for example:
-    #
-    #   $ pip install sampleproject[dev]
-    #
-    # Similar to `install_requires` above, these must be valid existing
-    # projects.
-    # extras_require={  # Optional
-    #     'dev': ['check-manifest'],
-    #     'test': ['coverage'],
     # },
-
-    # If there are data files included in your packages that need to be
-    # installed, specify them here.
-    package_data={  # Optional
-        'sample': ['package_data.dat'],
-    },
-
-    # Although 'package_data' is the preferred approach, in some case you may
-    # need to place data files outside of your packages. See:
-    # http://docs.python.org/distutils/setupscript.html#installing-additional-files
-    #
-    # In this case, 'data_file' will be installed into '<sys.prefix>/my_data'
-    data_files=[('my_data', ['data/data_file'])],  # Optional
-
-    # To provide executable scripts, use entry points in preference to the
-    # "scripts" keyword. Entry points provide cross-platform support and allow
-    # `pip` to create the appropriate form of executable for the target
-    # platform.
-    #
-    # For example, the following would provide a command called `sample` which
-    # executes the function `main` from this package when invoked:
-    entry_points={  # Optional
-        'console_scripts': [
-            'sample=bin:main',
-        ],
-    },
-
-    # List additional URLs that are relevant to your project as a dict.
-    #
-    # This field corresponds to the "Project-URL" metadata fields:
-    # https://packaging.python.org/specifications/core-metadata/#project-url-multiple-use
-    #
-    # Examples listed include a pattern for specifying where the package tracks
-    # issues, where the source is hosted, where to say thanks to the package
-    # maintainers, and where to support the project financially. The key is
-    # what's used to render the link text on PyPI.
     # project_urls={  # Optional
-    #     'Bug Reports': 'https://github.com/pypa/sampleproject/issues',
+    #     'Source': 'https://chaos3.fkp.physik.tu-darmstadt.de/source/nmreval/',
-    #     'Funding': 'https://donate.pypi.org',
-    #     'Say Thanks!': 'http://saythanks.io/to/example',
-    #     'Source': 'https://github.com/pypa/sampleproject/',
     # },
 )