diff --git a/doc/source/_templates/autosummary/_class.rst b/doc/source/_templates/autosummary/_class.rst
deleted file mode 100644
index eae2e87..0000000
--- a/doc/source/_templates/autosummary/_class.rst
+++ /dev/null
@@ -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:
-
-
diff --git a/doc/source/_templates/autosummary/class.rst b/doc/source/_templates/autosummary/class.rst
index 4fa8438..4eca388 100644
--- a/doc/source/_templates/autosummary/class.rst
+++ b/doc/source/_templates/autosummary/class.rst
@@ -1,14 +1,27 @@
-:mod:`{{ module | escape }}`.{{ objname }}
-{{ underline }}==================
+{{ fullname | escape | underline}}
.. currentmodule:: {{ module }}
.. autoclass:: {{ objname }}
- :members:
- :inherited-members:
-.. include:: {{ fullname }}.examples
+ {% block methods %}
-.. raw:: html
+ {% if methods %}
+ .. rubric:: {{ _('Methods') }}
-
+ {% 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 %}
diff --git a/doc/source/_templates/autosummary/class_with_attributes.rst b/doc/source/_templates/autosummary/class_with_attributes.rst
deleted file mode 100644
index 272b80d..0000000
--- a/doc/source/_templates/autosummary/class_with_attributes.rst
+++ /dev/null
@@ -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
-
-
diff --git a/doc/source/api/distributions.rst b/doc/source/api/distributions.rst
index c62e52c..c1489a3 100644
--- a/doc/source/api/distributions.rst
+++ b/doc/source/api/distributions.rst
@@ -1,4 +1,5 @@
.. automodule:: nmreval.distributions
- :no-members:
- :no-inherited-members:
- :no-special-members:
+ :members:
+ :inherited-members:
+ :undoc-members:
+
diff --git a/doc/source/api/models.rst b/doc/source/api/models.rst
index 3bcef09..b5c9ad4 100644
--- a/doc/source/api/models.rst
+++ b/doc/source/api/models.rst
@@ -1,4 +1,2 @@
.. automodule:: nmreval.models
- :no-members:
- :no-inherited-members:
- :no-special-members:
+ :members:
diff --git a/doc/source/conf.py b/doc/source/conf.py
index a23eb00..4f0356f 100644
--- a/doc/source/conf.py
+++ b/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
diff --git a/nmreval/gui_qt/_py/fitfunctionwidget.py b/nmreval/gui_qt/_py/fitfunctionwidget.py
index 3035f2f..2d44e05 100644
--- a/nmreval/gui_qt/_py/fitfunctionwidget.py
+++ b/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)
- sizePolicy = QtWidgets.QSizePolicy(QtWidgets.QSizePolicy.MinimumExpanding, QtWidgets.QSizePolicy.Maximum)
+ self.typecomboBox = QtWidgets.QComboBox(Form)
+ sizePolicy = QtWidgets.QSizePolicy(QtWidgets.QSizePolicy.MinimumExpanding, QtWidgets.QSizePolicy.Fixed)
sizePolicy.setHorizontalStretch(0)
sizePolicy.setVerticalStretch(0)
- sizePolicy.setHeightForWidth(self.widget.sizePolicy().hasHeightForWidth())
- self.widget.setSizePolicy(sizePolicy)
- self.widget.setObjectName("widget")
- self.gridLayout.addWidget(self.widget, 4, 0, 1, 2)
+ sizePolicy.setHeightForWidth(self.typecomboBox.sizePolicy().hasHeightForWidth())
+ self.typecomboBox.setSizePolicy(sizePolicy)
+ self.typecomboBox.setObjectName("typecomboBox")
+ 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.use_combobox.setObjectName("use_combobox")
- self.gridLayout.addWidget(self.use_combobox, 6, 0, 1, 2)
+ self.functree = FitModelTree(Form)
+ self.functree.setObjectName("functree")
+ 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
diff --git a/nmreval/gui_qt/data/container.py b/nmreval/gui_qt/data/container.py
index 3aae696..1c188e1 100644
--- a/nmreval/gui_qt/data/container.py
+++ b/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)
- from ..io.exporters import GraceExporter
+ dic = self._manager.graphs[self.graph].get_state()
+ 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)
diff --git a/nmreval/gui_qt/fit/fit_forms.py b/nmreval/gui_qt/fit/fit_forms.py
index 6d8f25d..354d02d 100644
--- a/nmreval/gui_qt/fit/fit_forms.py
+++ b/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)
diff --git a/nmreval/gui_qt/fit/fitfunction.py b/nmreval/gui_qt/fit/fitfunction.py
index 32612b3..0d98c4b 100644
--- a/nmreval/gui_qt/fit/fitfunction.py
+++ b/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):
- return self.use_combobox.count()
+ def __len__(self) -> int:
+ 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')
- def show_parameter(self, idx: int):
- if self.use_combobox.count():
- self.showFunction.emit(self.use_combobox.itemData(idx, QtCore.Qt.UserRole))
+ @QtCore.pyqtSlot(QtWidgets.QTreeWidgetItem, int, name='on_functree_itemClicked')
+ def show_parameter(self, item: QtWidgets.QTreeWidgetItem, _: int):
+ self.showFunction.emit(item.data(0, self.functree.counterRole))
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()
diff --git a/nmreval/gui_qt/graphs/graphwindow.py b/nmreval/gui_qt/graphs/graphwindow.py
index c4da8ed..ef79125 100644
--- a/nmreval/gui_qt/graphs/graphwindow.py
+++ b/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 \
- (item in self.graphic.items() or other_item in self.graphic.items()):
- self.legend.addItem(item, convert(item.opts.get('name', ''), old='tex', new='html'))
+ if self.listWidget.item(i).checkState():
+ if item in self.graphic.items():
+ 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:
diff --git a/nmreval/gui_qt/io/exporters.py b/nmreval/gui_qt/io/exporters.py
index b031d68..8dec1ed 100644
--- a/nmreval/gui_qt/io/exporters.py
+++ b/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
diff --git a/nmreval/gui_qt/lib/gol.py b/nmreval/gui_qt/lib/gol.py
index 603d56a..6974b03 100644
--- a/nmreval/gui_qt/lib/gol.py
+++ b/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]
diff --git a/nmreval/gui_qt/lib/pg_objects.py b/nmreval/gui_qt/lib/pg_objects.py
index 52f3955..99559a5 100644
--- a/nmreval/gui_qt/lib/pg_objects.py
+++ b/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['symbolcolor'] = Colors.Black
+ self.opts['linecolor'] = (0, 0, 0)
+ 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']
diff --git a/nmreval/gui_qt/lib/stuff.py b/nmreval/gui_qt/lib/stuff.py
index 9af81bb..e0454cd 100644
--- a/nmreval/gui_qt/lib/stuff.py
+++ b/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]:
diff --git a/nmreval/io/graceeditor.py b/nmreval/io/graceeditor.py
index b5776db..3949929 100644
--- a/nmreval/io/graceeditor.py
+++ b/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:
- kwargs['xaxes scale'] = 'Logarithmic' if x else 'Normal'
- if y is not None:
- kwargs['yaxes scale'] = 'Logarithmic' if y else 'Normal'
+ for ax, label in [(x, 'x'), (y, 'y')]:
+ if ax is not None:
+ if ax:
+ 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)
diff --git a/nmreval/models/__init__.py b/nmreval/models/__init__.py
index 68c2498..2a1aa1e 100755
--- a/nmreval/models/__init__.py
+++ b/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
diff --git a/nmreval/models/basic.py b/nmreval/models/basic.py
index c7bc0c0..6ce6c3b 100644
--- a/nmreval/models/basic.py
+++ b/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`
-
- .. 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
-
+ Crossover between power laws
"""
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
-
- .. math::
- y = C\sin(a x - \phi)
-
- Args:
- x (array_like): Input values
- c (float): Prefactor
- a (float): frequency
- phi (float): shift
-
+ Wavy sine function
"""
-
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)
diff --git a/nmreval/models/diffusion.py b/nmreval/models/diffusion.py
index 359fdd1..4e03f92 100644
--- a/nmreval/models/diffusion.py
+++ b/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))
diff --git a/nmreval/models/relaxation.py b/nmreval/models/relaxation.py
index ccd8314..ca4230b 100644
--- a/nmreval/models/relaxation.py
+++ b/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))
diff --git a/nmreval/models/user_models.py b/nmreval/models/user_models.py
deleted file mode 100644
index 5f98df4..0000000
--- a/nmreval/models/user_models.py
+++ /dev/null
@@ -1,3 +0,0 @@
-from ..configs import config_paths
-
-print(config_paths() / 'usermodels.py')
diff --git a/pyproject.toml b/pyproject.toml
new file mode 100644
index 0000000..ff2d408
--- /dev/null
+++ b/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
+
+
+
+
+
diff --git a/resources/_rc/__init__.py b/resources/_rc/__init__.py
deleted file mode 100644
index e69de29..0000000
diff --git a/resources/_ui/fitfunctionwidget.ui b/resources/_ui/fitfunctionwidget.ui
index 345ac8c..124e5b2 100644
--- a/resources/_ui/fitfunctionwidget.ui
+++ b/resources/_ui/fitfunctionwidget.ui
@@ -6,8 +6,8 @@
0
0
- 314
- 232
+ 382
+ 375
@@ -35,17 +35,17 @@
3
- -
-
+
-
+
-
+
0
0
- -
+
-
@@ -102,6 +102,16 @@
+ -
+
+
+
+ 0
+ 0
+
+
+
+
-
@@ -124,42 +134,6 @@
- -
-
-
-
- 0
- 0
-
-
-
-
- -
-
-
-
- 0
- 0
-
-
-
-
- -
-
-
-
- 0
- 0
-
-
-
- Equation
-
-
- true
-
-
-
-
@@ -190,17 +164,38 @@
- -
-
+
-
+
+
+
+ 1
+
+
+
+
+ -
+
+
+
+ 0
+ 0
+
+
+
+ Equation
+
+
+ true
+
+
- ExpandableWidget
- QWidget
-
- 1
+ FitModelTree
+ QTreeWidget
+
diff --git a/setup.cfg b/setup.cfg
new file mode 100644
index 0000000..9eb7cc4
--- /dev/null
+++ b/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
+
+
+
+
+
diff --git a/setup.py b/setup.py
index 072b099..e730e9c 100755
--- a/setup.py
+++ b/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
- # package, this name will be registered for you. It will determine how
- # users can install this project, e.g.:
+ # name='nmreval', # Required
+ # version='0.1', # Required
+ # 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
- #
- # And where it will live on PyPI: https://pypi.org/project/sampleproject/
- #
- # There are some restrictions on what makes a valid project name
- # specification here:
- # https://packaging.python.org/specifications/core-metadata/#name
- name='nmreval', # Required
-
- # Versions should comply with PEP 440:
- # https://www.python.org/dev/peps/pep-0440/
- #
- # For a discussion on single-sourcing the version across setup.py and the
- # project code, see
- # https://packaging.python.org/guides/single-sourcing-package-version/
- version='0.1', # Required
-
- # This is a one-line description or tagline of what your project does. This
- # corresponds to the "Summary" metadata field:
- # https://packaging.python.org/specifications/core-metadata/#summary
- description='A sample Python project', # Optional
-
- # This is an optional longer description of your project that represents
- # the body of text which users will see when they visit PyPI.
- #
- # 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'],
+ # keywords='nmr, physics, science', # Optional
+ # package_dir={'': '.'}, # Optional
+ # packages=find_packages(where='.'), # Required
+ # include_package_data=True,
+ # python_requires='>=3.7',
+ # install_requires=[
+ # 'numpy',
+ # 'scipy',
+ # 'matplotlib',
+ # 'bsddb3',
+ # 'pyqtgraph',
+ # 'pyqt',
+ # 'h5py'
+ # ], # Optional
+ # # extras_require={ # Optional
+ # # 'dev': ['check-manifest'],
+ # # 'test': ['coverage'],
+ # # },
+ # package_data={ # Optional
+ # 'sample': ['package_data.dat'],
+ # },
+ # data_files=[('my_data', ['data/data_file'])], # Optional
+ # entry_points={ # Optional
+ # 'console_scripts': [
+ # 'evaluate=bin:evaluate',
+ # ],
# },
-
- # 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 '/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',
- # 'Funding': 'https://donate.pypi.org',
- # 'Say Thanks!': 'http://saythanks.io/to/example',
- # 'Source': 'https://github.com/pypa/sampleproject/',
+ # 'Source': 'https://chaos3.fkp.physik.tu-darmstadt.de/source/nmreval/',
# },
)