def setCls(self,cls,select={'row0': 0,'row1': None}):
self.cls=cls
self.tableModel=ODplateModel(self.cls)
self.tableModel.dataChanged.connect(self.updatePlateFig)
self.clsView.setModel(self.tableModel)
self.clsView.header().setResizeMode(0, Qt.QHeaderView.ResizeToContents)
self.clsView.header().setResizeMode(1, Qt.QHeaderView.ResizeToContents)
self.clsView.selectionModel().selectionChanged.connect(self.selectionChanged)
self.clsView.setFocus()
self._setSample(self.cls)
if select is not None:
if select['row1'] is None:
selectIndex=self.tableModel.index(select['row0'],0,self.clsView.currentIndex())
else:
parentIndex=self.tableModel.index(select['row0'],0,self.clsView.currentIndex())
selectIndex=self.tableModel.index(select['row1'],0,parentIndex)
self.clsView.setCurrentIndex(selectIndex)
class ClsWidgets(object):
"""
Plot widgets, dialogs an the like needed for Chronological Life Span analysis
"""
def __init__(self):
self.tableModel=None
self.clsView=DeselectableTreeView()
self.mplcnvs=MyMplCanvas()
self.mainstack=QtGui.QStackedWidget()
self.mainstack.addWidget(self.mplcnvs)
self.navigationWidget=QtGui.QWidget()
self.ntb=NavigationToolbar(self.mplcnvs,self.navigationWidget)
self.statusbar=None
self.statusbarWidgets=[]
self.clear()
def clear(self):
self.mplcnvs.fig.clear()
self.mplcnvs.draw()
self.statusToStatusBar(None)
self.clsView.setModel(EmptyModel())
self.tableModel=None
self.platefiles=[]
self.days=[]
self.cls=None
def disconnect(self):
"""
NOTE this cannot be inside clear as disconnect fails if nothing is bound
"""
if self.tableModel is not None:
self.tableModel.dataChanged.disconnect()
def setCls(self,cls,select={'row0': 0,'row1': None}):
self.cls=cls
self.tableModel=ODplateModel(self.cls)
self.tableModel.dataChanged.connect(self.updatePlateFig)
self.clsView.setModel(self.tableModel)
self.clsView.header().setResizeMode(0, Qt.QHeaderView.ResizeToContents)
self.clsView.header().setResizeMode(1, Qt.QHeaderView.ResizeToContents)
self.clsView.selectionModel().selectionChanged.connect(self.selectionChanged)
self.clsView.setFocus()
self._setSample(self.cls)
if select is not None:
if select['row1'] is None:
selectIndex=self.tableModel.index(select['row0'],0,self.clsView.currentIndex())
else:
parentIndex=self.tableModel.index(select['row0'],0,self.clsView.currentIndex())
selectIndex=self.tableModel.index(select['row1'],0,parentIndex)
self.clsView.setCurrentIndex(selectIndex)
def loadSerialisedCls(self,catfilename):
try:
self.cls=Cls(None,None,serialisedFilename=catfilename)
self.platefiles=self.cls.files
self.days=self.cls.days
self.setCls(self.cls)
except Exception as err:
self.cls=None
self.platefiles=None
self.days=None
raise
def loadCls(self,files,days,select={'row0': 0,'row1': None}):
if files is None or days is None:
return
if len(files) != len(days):
QtGui.QMessageBox.warning(Qt.qApp.activeWindow(),'Could not load plates',
'Could not load plates because number of plates does not equal number of days')
else:
self.platefiles=files
self.days=days
self.cls=Cls(files,days)
self.setCls(self.cls,select)
def currentViewSelectionAsDict(self):
sel=self.clsView.selectedIndexes()
select=None
if sel is not None and len(sel) > 0:
if sel[0].parent().isValid():
select={ 'row0': sel[0].parent().row(), 'row1': sel[0].row()}
else:
select={ 'row0': sel[0].row(), 'row1': None}
return select
def reload(self):
# let mouse cursor appear busy
QtGui.QApplication.setOverrideCursor(Qt.QCursor(QtCore.Qt.WaitCursor))
# store selection of QTreeView
select=self.currentViewSelectionAsDict()
self.disconnect()
# store state of QTreeView
expState=storeViewExpandState(self.clsView,self.tableModel)
# reload and restore selection
self.cls.reload()
self.setCls(self.cls,select)
# restore state of QTreeView
restoreViewExpandState(self.clsView,self.tableModel,expState)
# mouse cursor should not be busy anymore
QtGui.QApplication.restoreOverrideCursor()
def selectionChanged(self,selected,deselected):
"""
the model view selection changed
"""
if len(selected.indexes()):
selindex=selected.indexes()[0]
tc=selindex.internalPointer()._itemData
self._setSample(tc)
else:
self._setSample(self.cls)
def _setSample(self,tc):
self.selectedClsObject=tc
self.updatePlateFig()
def statusToStatusBar(self,status):
if self.statusbar is None:
return
# clear previous statuses
for st in self.statusbarWidgets:
self.statusbar.removeWidget(st)
self.statusbarWidgets=[]
if status is None:
return
type2status=status.type2status()
thekeys=list(type2status.keys())
thekeys.sort()
for sttype in thekeys:
if type2status[sttype].severity() is Severity.warning:
continue # handled below
ql=QtGui.QLabel()
ql.setText(type2status[sttype].shortmessage())
ql.setToolTip(type2status[sttype].longmessage())
self.statusbar.addPermanentWidget(ql)
self.statusbarWidgets.append(ql)
for sttype in thekeys:
if type2status[sttype].severity() is not Severity.warning:
continue # handled above
ql=QtGui.QLabel()
ql.setText(type2status[sttype].shortmessage())
ql.setToolTip(type2status[sttype].longmessage())
ql.setStyleSheet("color: red")
self.statusbar.addPermanentWidget(ql)
self.statusbarWidgets.append(ql)
def updatePlateFig(self):
self.mplcnvs.fig.clear()
self.statusToStatusBar(None)
if self.selectedClsObject is None:
return
QtGui.QApplication.setOverrideCursor(Qt.QCursor(QtCore.Qt.WaitCursor))
try:
status=StatusMessage()
if isinstance(self.selectedClsObject, ClsReplicate):
status=platereader.clsplot.viabilityToMatplotlib(self.selectedClsObject,self.mplcnvs.fig)
self.mplcnvs.fig.tight_layout()
self.mplcnvs.draw()
self.statusToStatusBar(status)
QtGui.QApplication.restoreOverrideCursor()
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
self.mplcnvs.fig.clear()
self.mplcnvs.draw()
self.statusToStatusBar(None)
QtGui.QApplication.restoreOverrideCursor()
QtGui.QMessageBox.warning(self.mainstack,'Unknown error',msg)
return
class ClsFromPlateFilesDialog(QtGui.QDialog):
def __init__(self,clswidgets,files=[],days=[]):
super(ClsWidgets.ClsFromPlateFilesDialog, self).__init__()
self.setWindowTitle('CLS files and days')
self.clswidgets=clswidgets
self.platefiles=files
self.days=days
self.lastSelectedDirectory=RememberLastVisistedDirectory('')
#
self.tableOfFileNDayLayout=QtGui.QVBoxLayout()
self.setupTableOfFiles()
self.addButtonLayout=QtGui.QHBoxLayout()
self.addButton=QtGui.QPushButton("+")
self.addButton.setMinimumWidth(40)
self.addButton.setMinimumWidth(40)
self.addButton.clicked.connect(self.addFileDay)
self.addButtonLayout.addWidget(self.addButton)
self.addButtonLayout.addStretch()
self.cancelButton=QtGui.QPushButton("Cancel")
self.okButton=QtGui.QPushButton("Ok")
self.cancelButton.setMinimumWidth(80)
self.cancelButton.setMaximumWidth(80)
self.okButton.setMinimumWidth(80)
self.okButton.setMaximumWidth(80)
self.cancelButton.clicked.connect(self.close)
self.okButton.clicked.connect(self.saveSettingsAndClose)
self.okCancelLayout=QtGui.QHBoxLayout()
self.okCancelLayout.addStretch()
self.okCancelLayout.addWidget(self.cancelButton)
self.okCancelLayout.addWidget(self.okButton)
self.mainlayout=QtGui.QVBoxLayout()
self.mainlayout.addLayout(self.tableOfFileNDayLayout)
self.mainlayout.addLayout(self.addButtonLayout)
self.mainlayout.addLayout(self.okCancelLayout)
self.setLayout(self.mainlayout)
def setupTableOfFiles(self):
if self.platefiles is not None and self.days is not None and len(self.platefiles) == len(self.days):
for idx in range(0,len(self.platefiles)):
self.tableOfFileNDayLayout.addLayout(FileLineEditChooserNDayEdit(self.lastSelectedDirectory,
self.platefiles[idx],
str(self.days[idx])))
if os.path.exists(self.platefiles[idx]):
self.lastSelectedDirectory.setDir(os.path.dirname(self.platefiles[idx]))
self.tableOfFileNDayLayout.addLayout(FileLineEditChooserNDayEdit(self.lastSelectedDirectory))
def addFileDay(self):
self.tableOfFileNDayLayout.addLayout(FileLineEditChooserNDayEdit(self.lastSelectedDirectory))
def saveSettingsAndClose(self):
self.platefiles=[]
self.days=[]
for i in range(0,self.tableOfFileNDayLayout.count()):
filename=str(self.tableOfFileNDayLayout.itemAt(i).fileLineEdit.existingFilename())
day, ok=self.tableOfFileNDayLayout.itemAt(i).dayEdit.text().toDouble()
if filename is not None and ok:
self.platefiles.append(filename)
self.days.append(day)
self.accept()
class PdfDialog(QtGui.QDialog):
def __init__(self):
super(ClsWidgets.PdfDialog, self).__init__()
self.setWindowTitle('Save pdf options')
self.currentOrAllRadios=QtGui.QButtonGroup()
r1=QtGui.QRadioButton('Current selection')
r2=QtGui.QRadioButton('All')
r1.setChecked(True)
self.currentOrAllRadios.addButton(r1)
self.currentOrAllRadios.addButton(r2)
self.currentOrAllRadios.setId(r1,0)
self.currentOrAllRadios.setId(r2,1)
currentOrAllGroupbox=QtGui.QGroupBox('CLS to export')
grly=QtGui.QVBoxLayout()
grly.addWidget(r1)
grly.addWidget(r2)
currentOrAllGroupbox.setLayout(grly)
self.showTitle=QtGui.QCheckBox("Add title")
self.showTitle.setToolTip("Add a title consisting of 'sample-condition' to figures.")
showLayout=QtGui.QVBoxLayout()
showLayout.addWidget(self.showTitle)
showGroup=QtGui.QGroupBox('Figure options')
showGroup.setLayout(showLayout)
allLayout=QtGui.QHBoxLayout()
allLayout.addWidget(currentOrAllGroupbox)
allLayout.addWidget(showGroup)
allGroup=QtGui.QGroupBox('')
allGroup.setLayout(allLayout)
buttonlayout=QtGui.QHBoxLayout()
okButton=QtGui.QPushButton("Ok")
okButton.setDefault(True)
cancelButton=QtGui.QPushButton("Cancel")
buttonlayout.addWidget(cancelButton)
buttonlayout.addWidget(okButton)
cancelButton.clicked.connect(self.reject)
okButton.clicked.connect(self.accept)
self.mainlayout=QtGui.QVBoxLayout()
self.mainlayout.addWidget(allGroup)
self.mainlayout.addLayout(buttonlayout)
self.setLayout(self.mainlayout)
