bug-fixer (#40)

fixes #32, #34, #39

Co-authored-by: Dominik Demuth <dominik.demuth@physik.tu-darmstadt.de>
Reviewed-on: IPKM/nmreval#40

.gitignore

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

src/gui_qt/_py/eval_expr_dialog.py

@@ -1,10 +1,11 @@
 # -*- coding: utf-8 -*-
 
-# Form implementation generated from reading ui file 'resources/_ui/eval_expr_dialog.ui'
+# Form implementation generated from reading ui file 'src/resources/_ui/eval_expr_dialog.ui'
 #
-# Created by: PyQt5 UI code generator 5.12.3
+# Created by: PyQt5 UI code generator 5.15.9
 #
-# WARNING! All changes made in this file will be lost!
+# WARNING: Any manual changes made to this file will be lost when pyuic5 is
+# run again.  Do not edit this file unless you know what you are doing.
 
 
 from PyQt5 import QtCore, QtGui, QtWidgets
@@ -36,14 +37,14 @@ class Ui_CalcDialog(object):
         self.label_2 = QtWidgets.QLabel(self.page)
         self.label_2.setObjectName("label_2")
         self.verticalLayout_2.addWidget(self.label_2)
-        self.listWidget = QtWidgets.QListWidget(self.page)
+        self.listWidget = QListWidgetSelect(self.page)
         sizePolicy = QtWidgets.QSizePolicy(QtWidgets.QSizePolicy.Preferred, QtWidgets.QSizePolicy.MinimumExpanding)
         sizePolicy.setHorizontalStretch(0)
         sizePolicy.setVerticalStretch(0)
         sizePolicy.setHeightForWidth(self.listWidget.sizePolicy().hasHeightForWidth())
         self.listWidget.setSizePolicy(sizePolicy)
         self.listWidget.setEditTriggers(QtWidgets.QAbstractItemView.NoEditTriggers)
-        self.listWidget.setSelectionMode(QtWidgets.QAbstractItemView.SingleSelection)
+        self.listWidget.setSelectionMode(QtWidgets.QAbstractItemView.ExtendedSelection)
         self.listWidget.setObjectName("listWidget")
         self.verticalLayout_2.addWidget(self.listWidget)
         self.overwrite_checkbox = QtWidgets.QCheckBox(self.page)
@@ -202,7 +203,7 @@ class Ui_CalcDialog(object):
         self.label_8.setBuddy(self.line_doubleSpinBox)
 
         self.retranslateUi(CalcDialog)
-        self.stackedWidget.setCurrentIndex(2)
+        self.stackedWidget.setCurrentIndex(0)
         QtCore.QMetaObject.connectSlotsByName(CalcDialog)
         CalcDialog.setTabOrder(self.calc_edit, self.listWidget)
         CalcDialog.setTabOrder(self.listWidget, self.overwrite_checkbox)
@@ -237,4 +238,5 @@ class Ui_CalcDialog(object):
         self.label_11.setText(_translate("CalcDialog", "Style"))
         self.label.setText(_translate("CalcDialog", "Expressions are evaluated line by line and change previous values"))
 from ..lib.delegates import ColorListEditor, LineStyleEditor, SymbolStyleEditor
+from ..lib.listwidget import QListWidgetSelect
 from ..lib.namespace import QNamespaceWidget

src/gui_qt/data/signaledit/editsignalwidget.py

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

src/gui_qt/lib/listwidget.py

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

src/gui_qt/main/mainwindow.py

@@ -76,8 +76,8 @@ class NMRMainWindow(QtWidgets.QMainWindow, Ui_BaseWindow):
                 self.look_for_update()
 
         self.__timer = QtCore.QTimer()
-        self.__savepath = config_paths() / f'{datetime.datetime.now().strftime("%Y-%m-%d_%H%M%S")}.nmr'
+        self.__backup_path = config_paths() / f'{datetime.datetime.now().strftime("%Y-%m-%d_%H%M%S")}.nmr'
-        self.__timer.start(0.2*60*1000)  # every three minutese
+        self.__timer.start(3*60*1000)  # every three minutese
         self.__timer.timeout.connect(self._autosave)
 
     def _init_gui(self):
@@ -146,7 +146,7 @@ class NMRMainWindow(QtWidgets.QMainWindow, Ui_BaseWindow):
         self.actionUndo.setIcon(icon)
         self.menuData.insertAction(self.actionRedo, self.actionUndo)
 
-        # # self.actionSave.triggered.connect(lambda: self.management.save('/autohome/dominik/nmreval/testdata/test.nmr', ''))
+        # self.actionSave.triggered.connect(lambda: self.management.save('/autohome/dominik/nmreval/testdata/test.nmr', ''))
         # self.actionSave.triggered.connect(self.save)
         self.action_save_fit_parameter.triggered.connect(self.save_fit_parameter)
         self.ac_group2.triggered.connect(self.change_fit_limits)
@@ -269,6 +269,7 @@ class NMRMainWindow(QtWidgets.QMainWindow, Ui_BaseWindow):
             selected_filter = save_dialog.selectedNameFilter()
 
             if savefile is not None:
+                self.path = savefile.parent
                 use_underscore = save_dialog.checkBox.isChecked()
                 self.management.save(savefile, selected_filter, strip_spaces=use_underscore)
 
@@ -1028,7 +1029,7 @@ class NMRMainWindow(QtWidgets.QMainWindow, Ui_BaseWindow):
         write_state({'History': {'recent path': str(self.path)}})
 
         # remove backup file when closing
-        self.__savepath.unlink(missing_ok=True)
+        self.__backup_path.unlink(missing_ok=True)
 
         super().close()
 
@@ -1056,5 +1057,5 @@ class NMRMainWindow(QtWidgets.QMainWindow, Ui_BaseWindow):
     def _autosave(self):
         # TODO better separate thread may it takes some time to save
         self.status.setText('Autosave...')
-        NMRWriter(self.management.graphs, self.management.data).export(self.__savepath)
+        NMRWriter(self.management.graphs, self.management.data).export(self.__backup_path)
         self.status.setText('')

src/nmreval/fit/minimizer.py

@@ -14,6 +14,8 @@ from .result import FitResultCreator
 
 __all__ = ['FitRoutine', 'FitAbortException']
 
+from ..lib.logger import logger
+
 
 class FitAbortException(Exception):
     pass
@@ -464,11 +466,18 @@ class FitRoutine(object):
     def _calc_error(jac, chi, nobs, nvars):
         # copy of scipy.curve_fit to calculate covariance
         # noinspection PyTupleAssignmentBalance
-        _, s, vt = la.svd(jac, full_matrices=False)
+        try:
-        threshold = EPS * max(jac.shape) * s[0]
+            _, s, vt = la.svd(jac, full_matrices=False)
-        s = s[s > threshold]
+        except ValueError as e:
-        vt = vt[:s.size]
+            # this may be issue #39: On entry to DGESSD parameter had an illegal value
-        pcov = np.dot(vt.T / s**2, vt) * chi / (nobs - nvars)
+            # catch this exception and ignore error calculation
+            logger.error(f'Error calculation failed with {e.args}')
+            pcov = None
+        else:
+            threshold = EPS * max(jac.shape) * s[0]
+            s = s[s > threshold]
+            vt = vt[:s.size]
+            pcov = np.dot(vt.T / s**2, vt) * chi / (nobs - nvars)
 
         if pcov is None:
             _err = np.zeros(nvars)

src/resources/_ui/eval_expr_dialog.ui

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