def _setupLongrunningCalculation(self,msg,numForProgress):
self.setEnabled(False)
QtGui.QApplication.setOverrideCursor(Qt.QCursor(QtCore.Qt.WaitCursor))
# create a progress that is shown in the main stack (where usually the plot is shown)
self.progresswidget=MyProgressWidget(msg,numForProgress)
self.clswidgets.mainstack.addWidget(self.progresswidget)
self.clswidgets.mainstack.setCurrentIndex(1)
self.clswidgets.statusbar.setVisible(False)
class ODMainWindow(QtGui.QMainWindow):
def __init__(self):
super(ODMainWindow, self).__init__()
self.initUI()
def initUI(self):
self.clswidgets=ClsWidgets()
self.clswidgets.statusbar=self.statusBar()
self.newAction = QtGui.QAction('&New', self)
self.newAction.setShortcut(QtGui.QKeySequence.New)
self.newAction.setStatusTip('Create new project from plate files.')
self.newAction.triggered.connect(self.newClsFromPlatefilesChoose)
self.openAction = QtGui.QAction('&Open', self)
self.openAction.setShortcut(QtGui.QKeySequence.Open)
self.openAction.setStatusTip('Open file.')
self.openAction.triggered.connect(self.openSerialisedClsChoose)
self.reloadAction = QtGui.QAction('&Reload', self)
self.reloadAction.setShortcut(QtGui.QKeySequence.Refresh)
self.reloadAction.setStatusTip('Reload plate files.')
self.reloadAction.triggered.connect(self.clswidgets.reload)
self.saveAsAction = QtGui.QAction('Save as', self)
self.saveAsAction.setShortcut(QtGui.QKeySequence.SaveAs)
self.saveAsAction.setStatusTip('Save data.')
self.saveAsAction.triggered.connect(self.saveAs)
self.saveAction = QtGui.QAction('Save', self)
self.saveAction.setShortcut(QtGui.QKeySequence.Save)
self.saveAction.setStatusTip('Save data.')
self.saveAction.triggered.connect(self.save)
self.savePdfAction = QtGui.QAction('Export &figure', self)
self.savePdfAction.setStatusTip('Save a figure of viabilities/survival integrals.')
self.savePdfAction.triggered.connect(self.savePdf)
self.saveCsvAction = QtGui.QAction('Export &properties', self)
self.saveCsvAction.setStatusTip('Save a table containing viabilities/survival integrals.')
self.saveCsvAction.triggered.connect(self.saveCsv)
self.closeAction = QtGui.QAction('&Close', self)
self.closeAction.setShortcut(QtGui.QKeySequence.Close)
self.closeAction.setStatusTip('Close file.')
self.closeAction.triggered.connect(self.close)
self.exitAction = QtGui.QAction('&Exit', self)
self.exitAction.setShortcut(QtGui.QKeySequence.Quit)
self.exitAction.setStatusTip('Exit.')
self.exitAction.triggered.connect(self.quit)
menubar = self.menuBar()
fileMenu = menubar.addMenu('&File')
fileMenu.addAction(self.newAction)
fileMenu.addAction(self.openAction)
fileMenu.addAction(self.reloadAction)
fileMenu.addAction(self.saveAsAction)
fileMenu.addAction(self.saveAction)
fileMenu.addAction(self.saveCsvAction)
fileMenu.addAction(self.savePdfAction)
fileMenu.addAction(self.closeAction)
fileMenu.addAction(self.exitAction)
self.aboutAction = QtGui.QAction('&About', self)
self.aboutAction.triggered.connect(self.showAbout)
helpMenu = menubar.addMenu('&Help')
helpMenu.addAction(self.aboutAction)
self.mainwidget=QtGui.QWidget(self)
mainwidgetLayout=QtGui.QVBoxLayout()
self.mainwidget.setLayout(mainwidgetLayout)
self.setCentralWidget(self.mainwidget)
self.graphsnchooser = QtGui.QSplitter(QtCore.Qt.Horizontal,self.mainwidget)
mainwidgetLayout.addWidget(self.graphsnchooser)
self.graphsnchooser.setSizePolicy(Qt.QSizePolicy.Expanding,
Qt.QSizePolicy.Expanding)
self.graphsnchooser.addWidget(self.clswidgets.clsView)
self.graphsnchooser.addWidget(self.clswidgets.mainstack)
self.graphsnchooser.setStretchFactor(0,1)
self.graphsnchooser.setStretchFactor(1,4)
self.setGeometry(100, 100, 1024, 600)
self.clear()
self.show()
def clear(self):
self.newAction.setEnabled(True)
self.openAction.setEnabled(True)
self.reloadAction.setEnabled(False)
self.saveAsAction.setEnabled(False)
self.saveAction.setEnabled(False)
self.saveCsvAction.setEnabled(False)
self.savePdfAction.setEnabled(False)
self.closeAction.setEnabled(False)
self.exitAction.setEnabled(True)
self.saveFilename=None
self.clswidgets.clear()
self._setWindowTitle()
def enDisableActionsAfterLoading(self):
self.newAction.setEnabled(False)
self.openAction.setEnabled(False)
self.reloadAction.setEnabled(True)
self.saveAsAction.setEnabled(True)
self.saveAction.setEnabled(True)
self.saveCsvAction.setEnabled(True)
self.savePdfAction.setEnabled(True)
self.closeAction.setEnabled(True)
self.exitAction.setEnabled(True)
def _setWindowTitle(self):
wtitle=''
if self.clswidgets.cls is not None:
if self.saveFilename is not None:
wtitle=os.path.basename(self.saveFilename)+' - '
elif (self.clswidgets.platefiles is not None and len(self.clswidgets.platefiles)
and self.clswidgets.days is not None and len(self.clswidgets.days)):
wtitle=os.path.basename(self.clswidgets.platefiles[0])+' day '+'{:g}'.format(self.clswidgets.days[0])+', ... - '
self.setWindowTitle(wtitle+'Chronological life span Analysis Tool (CATHODE)')
def newClsFromPlatefilesChoose(self):
dialog=ClsWidgets.ClsFromPlateFilesDialog(self.clswidgets,self.clswidgets.platefiles,self.clswidgets.days)
if dialog.exec_() == QtGui.QDialog.Accepted:
self.newClsFromPlatefiles(dialog.platefiles,dialog.days)
def newClsFromPlatefiles(self,platefiles,days):
try:
self.clswidgets.loadCls(platefiles,days)
self.enDisableActionsAfterLoading()
except Cls.Error as err:
QtGui.QMessageBox.warning(self,'Error loading file',str(err))
return
except Exception as err:
msg=str(err)+"\n"
if msg is None:
msg=''
exc_type, exc_value, exc_tb = sys.exc_info()
for line in traceback.format_exception(exc_type, exc_value, exc_tb):
msg+=line
QtGui.QMessageBox.warning(self,'Unknown error',msg)
self._setWindowTitle()
def openSerialisedClsChoose(self):
self.close()
fname = QtGui.QFileDialog.getOpenFileName(self, 'Open file', '', 'Cls data (*.cat)')
if len(fname) == 0:
return
condition=""
self.openSerialisedCls(str(fname))
def openSerialisedCls(self,catfilename):
self.close()
if not os.path.exists(catfilename):
QtGui.QMessageBox.warning(self,'Error loading file',catfilename+' does not exist.')
self.clear()
return
try:
self.clswidgets.loadSerialisedCls(catfilename)
self.saveFilename=catfilename
self.enDisableActionsAfterLoading()
except (Cls.Error, Plate.Error) as err:
QtGui.QMessageBox.warning(self,'Error loading file',str(err))
return
except Exception as err:
msg=str(err)+"\n"
if msg is None:
msg=''
exc_type, exc_value, exc_tb = sys.exc_info()
for line in traceback.format_exception(exc_type, exc_value, exc_tb):
msg+=line
QtGui.QMessageBox.warning(self,'Unknown error',msg)
self._setWindowTitle()
def saveAs(self):
if self.clswidgets.cls is None:
return
fname = str(getSaveFileNameDialogWithDefaultSuffix(self, 'Save file', '', 'CLS data (*.cat)', 'cat'))
if len(fname) == 0:
return
self.saveFilename=fname
self.saveAction.setEnabled(True)
self._setWindowTitle()
return self._save()
def save(self):
if self.saveFilename is None:
return self.saveAs()
else:
return self._save()
def _save(self):
try:
savestatus=self.clswidgets.cls.saveLightweight(self.saveFilename)
if savestatus is not None:
QtGui.QMessageBox.warning(self,savestatus.messageType(),savestatus.longmessage())
return True
except (Cls.Error, Plate.Error) as err:
QtGui.QMessageBox.warning(self,'Error saving datafile',str(err))
odplate_=None
except Exception as err:
msg=str(err)+"\n"
if msg is None:
msg=''
exc_type, exc_value, exc_tb = sys.exc_info()
for line in traceback.format_exception(exc_type, exc_value, exc_tb):
msg+=line
QtGui.QMessageBox.warning(self,'Unknown error',msg)
odplate_=None
return False
def close(self):
if self.clswidgets.cls is not None and self.clswidgets.cls.modified:
ret=QtGui.QMessageBox.question(self,"CLS Analysis Tool (CATHODE)",
"The document has been modified.\n"
+"Do you want to save your changes?",
QtGui.QMessageBox.Save | QtGui.QMessageBox.Discard | QtGui.QMessageBox.Cancel,
QtGui.QMessageBox.Save)
if ret == QtGui.QMessageBox.Save:
if not self.save():
return False
elif ret == QtGui.QMessageBox.Cancel:
return False
#elif ret == QtGui.QMessageBox.Discard:
self.clear()
return True
def quit(self):
if self.close():
QtGui.qApp.quit()
def saveCsv(self):
if self.clswidgets.cls is None:
return
fname = str(getSaveFileNameDialogWithDefaultSuffix(self, 'Save file', '', 'csv (*.csv)', 'csv'))
if len(fname) == 0:
return
# create progress bar, do not allow to press buttons, etc
self._setupLongrunningCalculation('Saving table',len(self.clswidgets.cls.clsReplicateGroups))
# run the real calculation
try:
self.clswidgets.cls.survivalToCsv(fname,progressCall=self._updateProgress)
except Exception as err:
exc_type, exc_value, exc_tb = sys.exc_info()
msg=str(err)+"\n"
if msg is None:
msg=''
for line in traceback.format_exception(exc_type, exc_value, exc_tb):
msg+=line
QtGui.QMessageBox.warning(self,'An error occurred',msg)
# clean up: remove progress bar, enable buttons etc
self._longrunningCalculationFinished()
def savePdf(self):
if self.clswidgets.cls is None:
return
# ask what to export: currently selected one or all CLS replicate groups
dialog=ClsWidgets.PdfDialog()
dialog.show()
if not dialog.exec_():
return
# ask for filename
fname = str(getSaveFileNameDialogWithDefaultSuffix(self, 'Save file', '', 'pdf (*.pdf)', 'pdf'))
if len(fname) == 0:
return
if dialog.currentOrAllRadios.checkedId() == 0:
# currently selected
elementaryIndices=[]
replicateGroupIndices=[]
select=self.clswidgets.currentViewSelectionAsDict()
addWellIdsToTitle=False
if select['row1'] is None:
replicateGroupIndices=[select['row0']]
else:
elementaryIndices=[self.clswidgets.cls.clsReplicateGroups[select['row0']].childWellIndices()[select['row1']]]
addWellIdsToTitle=True
platereader.clsplot.viabilitiesToPdf(self.clswidgets.cls,
fname,
showTitle=dialog.showTitle.checkState(),
addWellIdsToTitle=addWellIdsToTitle,
creator=os.path.basename(sys.argv[0]),
replicateGroupIndices=replicateGroupIndices,
elementaryIndices=elementaryIndices)
elif dialog.currentOrAllRadios.checkedId() == 1:
# all replicates
# create progress bar, do not allow to press buttons, etc
self._setupLongrunningCalculation('Saving figures',self.clswidgets.cls.numberOfNonBackgroundCls())
try:
platereader.clsplot.viabilitiesToPdf(self.clswidgets.cls,
fname,
showTitle=dialog.showTitle.checkState(),
creator=os.path.basename(sys.argv[0]),
replicateGroupIndices=[],
addWellIdsToTitle=False,progressCall=self._updateProgress)
except Exception as err:
exc_type, exc_value, exc_tb = sys.exc_info()
msg=str(err)+"\n"
if msg is None:
msg=''
for line in traceback.format_exception(exc_type, exc_value, exc_tb):
msg+=line
QtGui.QMessageBox.warning(self,'An error occurred',msg)
# clean up: remove progress bar, enable buttons etc
self._longrunningCalculationFinished()
else:
raise RuntimeError('PdfDialog: unknown selection')
def _setupLongrunningCalculation(self,msg,numForProgress):
self.setEnabled(False)
QtGui.QApplication.setOverrideCursor(Qt.QCursor(QtCore.Qt.WaitCursor))
# create a progress that is shown in the main stack (where usually the plot is shown)
self.progresswidget=MyProgressWidget(msg,numForProgress)
self.clswidgets.mainstack.addWidget(self.progresswidget)
self.clswidgets.mainstack.setCurrentIndex(1)
self.clswidgets.statusbar.setVisible(False)
def _longrunningCalculationFinished(self):
self.clswidgets.statusbar.setVisible(True)
self.clswidgets.mainstack.setCurrentIndex(0)
self.clswidgets.mainstack.removeWidget(self.progresswidget)
self.progresswidget=None
self.setEnabled(True)
self.enDisableActionsAfterLoading()
QtGui.QApplication.restoreOverrideCursor()
def _updateProgress(self,intval):
self.progresswidget.updateProgress(intval)
QtGui.QApplication.processEvents()
def showAbout(self):
agpllicense=("This program is free software: you can redistribute it and/or modify "
+"it under the terms of the GNU Affero General Public License as "
+"published by the Free Software Foundation, either version 3 of the "
+"License, or (at your option) any later version.")
msgBox=QtGui.QMessageBox.about(self,'Chronological life span Analysis Tool (CATHODE)',
'Chronological life span Analysis Tool for High-throughput Optical Density Experiments (CATHODE)\nversion '
+__version__
+'\nCopyright (C) 2014 Nils Christian\n'+
agpllicense)