def setupToolbar(self):
self.toolBar = ViewToolBar(self)
self.fileToolBar = FileToolBar(self)
self.fileToolBar.actionOpen.triggered.connect(self.onFileOpen)
self.fileToolBar.actionNew.triggered.connect(self.newDataFile)
self.batchToolBar = BatchToolBar(self)
self.batchToolBar.batchChanged.connect(self.loadItems)
self.batchToolBar.actionReload.triggered.connect(self.loadItems)
self.actionReloadFile.triggered.connect(self.loadItems)
self.sortToolBar = SortToolBar(self)
self.addToolBar(QtCore.Qt.TopToolBarArea, self.fileToolBar)
self.addToolBar(QtCore.Qt.TopToolBarArea, self.toolBar)
self.addToolBar(QtCore.Qt.TopToolBarArea, self.sortToolBar)
self.addToolBar(QtCore.Qt.BottomToolBarArea, self.batchToolBar)
self.navToolBar = NavToolBar(self)
self.addToolBar(QtCore.Qt.BottomToolBarArea, self.navToolBar)
self.navToolBar.coordUpdated.connect(self.loader.setCoordinate)
class AtMainWindow(QtWidgets.QMainWindow):
coordUpdated = QtCore.pyqtSignal("PyQt_PyObject")
abort = QtCore.pyqtSignal()
def __init__(self, file_=None, *args, **kw):
super(AtMainWindow, self).__init__(*args, **kw)
loadUI(splitext(__file__)[0]+'.ui', self)
self.setWindowTitle(version.appstr)
self.setAcceptDrops(True)
self.featuredlg = AtFeatureSelectionDlg(self)
self.featuredlg.hide()
self.loaderThread = AtThread(self)
self.loader = AtLoader()
self._lastdir = expanduser("~")
try:
self.assistant = AtAssistant(MANUAL)
self.assistant.hide()
except IOError:
QMessageBox.information(self, "Information",
"Sorry help files are not installed")
self.setupToolbar()
self.tileview = AtGraphicsView(
parent=self,
gsize=self.navToolBar.galsize)
self.toolBar.valueChanged.connect(self.tileview.zoom)
self.toolBar.flagsChanged.connect(
self.tileview.setViewFlags, Qt.QueuedConnection)
self.setCentralWidget(self.tileview)
self.setupDock()
self.setupProgressBar()
self.loader.fileOpened.connect(self.updateToolbars)
self.loader.progressUpdate.connect(self.updateProgressBar)
self.loader.itemCountChanged.connect(self.batchToolBar.setItemCount)
self.loader.itemLoaded.connect(self.tileview.addItem)
self.abort.connect(self.loader.abort)
self.actionNewFile.triggered.connect(self.newDataFile)
self.actionOpenHdf.triggered.connect(self.onFileOpen)
self.actionCloseHdf.triggered.connect(self.onFileClose)
self.actionPreferences.triggered.connect(self.onPreferences)
# Data Export
self.actionExportViewPanel.triggered.connect(self.saveImage)
self.actionSaveData2Csv.triggered.connect(self.saveData2Csv)
self.actionSaveCountingStats.triggered.connect(self.saveCountingStats)
# Plots
self.actionGroupedByClass.triggered.connect(self.plotGroupedByClass)
self.actionGroupedByTreatment.triggered.connect(
self.plotGroupedByTreatment)
self.actionIntensity.triggered.connect(self.plotIntesity)
self.actionSize.triggered.connect(self.plotSize)
self.actionStdDev.triggered.connect(self.plotStdDev)
self.actionPlotAll.triggered.connect(self.plotAll)
self.actionAboutQt.triggered.connect(self.onAboutQt)
self.actionAboutAnnotationTool.triggered.connect(self.onAbout)
self.actionFeatureSelection.triggered.connect(
self.showFeatureDlg)
self.actionHelpManual.triggered.connect(self.onHelpManual)
self.actionShortcuts.triggered.connect(self.onHelpShortcuts)
self.actionGettingStarted.triggered.connect(self.onHelpGettingStarted)
self.actionRefresh.triggered.connect(self.refresh)
self.actionSelectAll.triggered.connect(
self.tileview.actionSelectAll.trigger)
self.actionInvertSelection.triggered.connect(
self.tileview.actionInvertSelection.trigger)
self.actionSelectByTreatment.triggered.connect(self.selectByTreatment)
self.tileview.zoomChanged.connect(self.updateZoomFactor)
self.tileview.quickSort.connect(self.sortToolBar.quickSortBtn.toggle)
self.tileview.quickSort.connect(self.onQuickSort)
self.featuredlg.selectionChanged.connect(
self.annotation.predictionInvalid)
self.loader.started.connect(self.onLoadingStarted)
self.zoom = QtWidgets.QLabel('100%')
self.statusbar.insertPermanentWidget(0, self.zoom)
self.statusbar.insertPermanentWidget(1,
QtWidgets.QLabel('Number of items:'))
self.nitems = QtWidgets.QLabel('0')
self.statusbar.insertPermanentWidget(2, self.nitems)
self._restoreSettings()
self.navToolBar.hide()
self.show()
if file_ is not None:
self.loader.openFile(file_)
self.loadItems()
def updateProgressBar(self, value):
if value < 0:
self.progressbar.setRange(0, 0)
self.progressbar.setValue(value)
def updateZoomFactor(self, factor):
self.zoom.setText("%d%s" %(round(100*factor, 0), "%"))
def dragEnterEvent(self, event):
event.acceptProposedAction()
def dragMoveEvent(self, event):
event.acceptProposedAction()
def dropEvent(self, event):
mimeData = event.mimeData()
if mimeData.hasUrls():
if len(mimeData.urls()) == 1:
self.abort.emit()
self.loaderThread.wait()
self.loader.close()
self.onDropEvent(fix_path(mimeData.urls()[0].path()))
event.acceptProposedAction()
def dragLeaveEvent(self, event):
event.accept()
def onInitalStartup(self):
self.onHelpGettingStarted()
def onHelpManual(self):
self.assistant.show()
self.assistant.raise_()
self.assistant.openKeyword('Shortcuts')
def onHelpShortcuts(self):
self.onHelpManual()
self.assistant.openKeyword("Shortcuts")
def onHelpGettingStarted(self):
self.onHelpManual()
self.assistant.openKeyword("Getting started")
def refresh(self):
if self.loader.file is None:
return
self.tileview.actionRefresh.trigger()
self.contrast.enhanceContrast()
def showFeatureDlg(self):
self.featuredlg.show()
self.featuredlg.raise_()
def onPreferences(self):
dlg = AtPreferencesDialog(self)
dlg.exec_()
def onAboutQt(self):
QMessageBox.aboutQt(self, "about Qt")
def onAbout(self):
dlg = AtAboutDialog(self)
dlg.exec_()
def resetCursor(self):
QApplication.restoreOverrideCursor()
def setWaitingCursor(self):
QApplication.setOverrideCursor(QCursor(Qt.WaitCursor))
def _saveSettings(self):
settings = QtCore.QSettings(version.organisation, version.appname)
settings.beginGroup('Gui')
settings.setValue('config', version.config)
settings.setValue('state', self.saveState())
settings.setValue('geometry', self.saveGeometry())
settings.setValue('classifier',
self.annotation.classifiers.currentText())
settings.endGroup()
AtConfig().saveSettings()
def _restoreSettings(self):
settings = QtCore.QSettings(version.organisation, version.appname)
settings.beginGroup('Gui')
if settings.contains('config'):
if version.config != settings.value('config'):
# FIXME - helpengine needs to be delayed for unknown reason
QtCore.QTimer.singleShot(500, self.onInitalStartup)
return
else:
QtCore.QTimer.singleShot(500, self.onInitalStartup)
if settings.contains('geometry'):
geometry = settings.value('geometry')
self.restoreGeometry(geometry)
if settings.contains('state'):
state = settings.value('state')
self.restoreState(state)
if settings.contains('classifier'):
clfname = settings.value("classifier")
self.annotation.setCurrentClassifier(clfname)
AtConfig().restoreSettings()
settings.endGroup()
self.batchToolBar.setBatchSize(AtConfig().batch_size)
def closeEvent(self, event):
if self.annotation.isModified():
msg = "The classifier has not been saved. Close program anyway?"
reply = QMessageBox.question(
self, 'Warning', msg, QMessageBox.Yes, QMessageBox.No)
if reply == QMessageBox.Yes:
event.accept()
else:
event.ignore()
return
self._saveSettings()
try:
self.abort.emit()
self.loaderThread.wait()
self.loader.close()
if self.assistant is not None:
self.assistant.close()
except AttributeError:
pass
def setupDock(self):
self.contrast = AtContrastWidget(self, self.tileview)
self.sorting = AtSortWidget(self, self.tileview, self.featuredlg)
self.annotation = AtAnnotationWidget(
self, self.tileview, self.featuredlg)
self.contrastdock = QtWidgets.QDockWidget("Contrast", self)
self.contrastdock.setWidget(self.contrast)
self.contrastdock.setObjectName("contrast")
self.addDockWidget(Qt.LeftDockWidgetArea, self.contrastdock)
self.sortdock = QtWidgets.QDockWidget("Sorting", self)
self.sortdock.setWidget(self.sorting)
self.sortdock.setObjectName("sorting")
self.addDockWidget(Qt.RightDockWidgetArea, self.sortdock)
self.annodock = QtWidgets.QDockWidget("Training", self)
self.annodock.setWidget(self.annotation)
self.annodock.setObjectName("training")
self.addDockWidget(Qt.RightDockWidgetArea, self.annodock)
self.tabifyDockWidget(self.sortdock, self.annodock)
# add action to the view menu
sort_action = self.sortdock.toggleViewAction()
sort_action.setShortcuts(QKeySequence(Qt.ALT + Qt.SHIFT + Qt.Key_S))
self.menuView.addAction(sort_action)
anno_action = self.annodock.toggleViewAction()
anno_action.setShortcuts(QKeySequence(Qt.ALT + Qt.SHIFT + Qt.Key_A))
self.menuView.addAction(anno_action)
contrast_action = self.contrastdock.toggleViewAction()
contrast_action.setShortcuts(
QKeySequence(Qt.ALT + Qt.SHIFT + Qt.Key_C))
self.menuView.addAction(contrast_action)
# crosslink sorter dock and sorter toolbar
self.sortToolBar.sortAlgorithm.currentIndexChanged.connect(
self.sorting.sortAlgorithm.setCurrentIndex)
self.sorting.sortAlgorithm.currentIndexChanged.connect(
self.sortToolBar.sortAlgorithm.setCurrentIndex)
self.sortToolBar.sortAscendingBtn.clicked.connect(
self.sorting.sortAscending)
self.sortToolBar.sortDescendingBtn.clicked.connect(
self.sorting.sortDescending)
self.sortToolBar.quickSortBtn.toggled.connect(
self.tileview.setQuickSortMode)
def setupProgressBar(self):
frame = QtWidgets.QFrame(self)
self.progressbar = QtWidgets.QProgressBar(frame)
self.progressbar.setMaximumHeight(15)
self.abortBtn = QtWidgets.QPushButton('abort', self)
self.abortBtn.clicked.connect(self.abort.emit)
self.abortBtn.setMaximumHeight(20)
hbox = QtWidgets.QHBoxLayout(frame)
hbox.addWidget(self.progressbar)
hbox.addWidget(self.abortBtn)
hbox.setContentsMargins(0, 0, 0, 0)
self.loaderThread.started.connect(frame.show)
self.loaderThread.started.connect(self.setWaitingCursor)
self.loaderThread.finished.connect(frame.hide)
self.loaderThread.finished.connect(self.resetCursor)
frame.hide()
self.statusBar().addPermanentWidget(frame)
def saveImage(self):
filename = QFileDialog.getSaveFileName(
self, "Save image as ...",
self._lastdir.replace('.hdf', '.png'),
"png - Image (*.png)")[0]
if filename:
scene = self.tileview.scene()
size = scene.sceneRect().size().toSize()
image = QtGui.QImage(size, QtGui.QImage.Format_RGB32)
painter = QtGui.QPainter(image)
image.fill(QtCore.Qt.white)
scene.render(painter)
painter.end()
image.save(filename)
self.statusBar().showMessage("Image saved to %s" %filename)
def saveData2Csv(self):
filename = QFileDialog.getSaveFileName(
self, "Save csv-file as ...",
self._lastdir.replace(".hdf", ".csv"),
"Comma separated values (*.csv)")[0]
if filename:
if AtConfig().only_classifier_features:
features = self.featuredlg.checkedItems()
else:
features = self.featuredlg.allItems()
exporter = CsvExporter(filename, self.tileview.items,
features)
exporter.save()
self.statusBar().showMessage("Image saved to %s" %filename)
def saveCountingStats(self):
filename = QFileDialog.getSaveFileName(
self, "Save csv-file as ...",
self._lastdir.replace(".hdf", "_statistics.csv"),
"Comma separated values (*.csv)")[0]
if filename:
features = self.featuredlg.checkedItems()
exporter = StatsExporter(filename, self.tileview.items,
features)
exporter.save()
self.statusBar().showMessage("Image saved to %s" %filename)
def _validPlotData(self):
flag = False
if not self.tileview.items:
QMessageBox.information(self, "Nothing to plot!",
"No data file is opened")
elif not self.annotation.hasValidClassifier():
QMessageBox.information(self, "Nothing to plot!",
"No valid classifier trained or loaded")
elif not self.annotation.hasValidPrediction():
QMessageBox.information(self, "Nothing to plot!",
"Press 'Predict' before plotting")
else:
flag = True
return flag
def plotGroupedByTreatment(self, pos=False):
if self._validPlotData():
classes = self.annotation.currentClassifier().classes
barplot = plots.BarGraph(self.tileview.items, classes,
self.actionExcludeTrainingData.isChecked(), self)
self.actionCloseAll.triggered.connect(barplot.close)
if pos:
barplot.move(pos)
barplot.show()
else:
barplot.exec_()
def plotGroupedByClass(self, pos=False):
if self._validPlotData():
classes = self.annotation.currentClassifier().classes
barplot = plots.BarGraph2(self.tileview.items, classes,
self.actionExcludeTrainingData.isChecked(), self)
self.actionCloseAll.triggered.connect(barplot.close)
if pos:
barplot.move(pos)
barplot.show()
else:
barplot.exec_()
def plotIntesity(self, pos=False):
if self._validPlotData():
indices = self.featuredlg.indexByName(CoreFeatures.Intensity)
classes = self.annotation.currentClassifier().classes
boxplot = plots.BoxPlot(
self.tileview.items, indices, classes, "Intensity",
self.actionExcludeTrainingData.isChecked(), self)
self.actionCloseAll.triggered.connect(boxplot.close)
if pos:
boxplot.move(pos)
boxplot.show()
else:
boxplot.exec_()
def plotSize(self, pos=False):
if self._validPlotData():
indices = self.featuredlg.indexByName(CoreFeatures.Size)
classes = self.annotation.currentClassifier().classes
boxplot = plots.BoxPlot(
self.tileview.items, indices, classes, "Size",
self.actionExcludeTrainingData.isChecked(),
self)
self.actionCloseAll.triggered.connect(boxplot.close)
if pos:
boxplot.move(pos)
boxplot.show()
else:
boxplot.exec_()
def plotStdDev(self, pos=False):
if self._validPlotData():
indices = self.featuredlg.indexByName(CoreFeatures.StdDev)
classes = self.annotation.currentClassifier().classes
boxplot = plots.BoxPlot(
self.tileview.items, indices, classes,
"Standard Deviation",
self.actionExcludeTrainingData.isChecked(),
self)
self.actionCloseAll.triggered.connect(boxplot.close)
if pos:
boxplot.move(pos)
boxplot.show()
else:
boxplot.exec_()
def plotAll(self):
"""Plot everything for people who don't know what do"""
if self._validPlotData():
shift = QtCore.QPoint(20, 20)
pos = self.pos() + 4*shift
pos = [pos + i*shift for i in xrange(5)]
self.plotGroupedByClass(pos[0])
self.plotGroupedByTreatment(pos[1])
self.plotIntesity(pos[2])
self.plotSize(pos[3])
self.plotStdDev(pos[4])
def updateToolbars(self, props):
# in case of cellh5 file
if props.gal_settings_mutable:
self.navToolBar.show()
self.navToolBar.updateToolbar(props)
self.contrast.setChannelNames(props.channel_names, props.colors)
self.nitems.setText(str(props.n_items))
def setupToolbar(self):
self.toolBar = ViewToolBar(self)
self.fileToolBar = FileToolBar(self)
self.fileToolBar.actionOpen.triggered.connect(self.onFileOpen)
self.fileToolBar.actionNew.triggered.connect(self.newDataFile)
self.batchToolBar = BatchToolBar(self)
self.batchToolBar.batchChanged.connect(self.loadItems)
self.batchToolBar.actionReload.triggered.connect(self.loadItems)
self.actionReloadFile.triggered.connect(self.loadItems)
self.sortToolBar = SortToolBar(self)
self.addToolBar(QtCore.Qt.TopToolBarArea, self.fileToolBar)
self.addToolBar(QtCore.Qt.TopToolBarArea, self.toolBar)
self.addToolBar(QtCore.Qt.TopToolBarArea, self.sortToolBar)
self.addToolBar(QtCore.Qt.BottomToolBarArea, self.batchToolBar)
self.navToolBar = NavToolBar(self)
self.addToolBar(QtCore.Qt.BottomToolBarArea, self.navToolBar)
self.navToolBar.coordUpdated.connect(self.loader.setCoordinate)
def newDataFile(self):
try:
dlg = ImportDialog(
self, Qt.WindowMinMaxButtonsHint|Qt.WindowCloseButtonHint)
dlg.loadData.connect(self._openAndLoad)
dlg.exec_()
except Exception as e:
QMessageBox.critical(None, "Error", str(e))
def onQuickSort(self):
self.sorting.removeAll()
items = self.tileview.selectedItems()
self.sorting.addItems(items)
self.sorting.applyDefaultSortAlgorithm()
self.sorting.sortAscending()
self.tileview.centerOn(items[0])
def selectByTreatment(self):
label, flag = QInputDialog.getItem(self, "Select a Treatment",
"Treatment", self.tileview.treatments, editable=False)
if flag:
self.tileview.selectByTreatment(label)
def addToSortPanel(self):
self.sorting.addItems(self.tileview.selectedItems())
def onFileClose(self):
self.loader.close()
self.tileview.clear()
self.featuredlg.clear()
self.sorting.clear()
def onFileOpen(self):
file_ = QFileDialog.getOpenFileName(
self, "Open hdf5 file", self._lastdir,
"Hdf files (*.hdf5 *.ch5 *.hdf *.h5)")[0]
if bool(file_):
self.tileview.zoom(1.0)
self._fileOpen(file_)
self.loadItems()
def _fileOpen(self, file_):
self._lastdir = abspath(file_)
try:
self.loader.openFile(file_)
except Exception as e:
self.statusBar().showMessage(str(e))
msg = "Could not open file\n %s" %str(e)
QMessageBox.critical(self, "Error", msg)
else:
self.statusBar().showMessage(basename(file_))
def _openAndLoad(self, file_):
self.onFileClose()
self._fileOpen(file_)
self.loadItems()
def onLoadingStarted(self):
self.annotation.setFeatureNames(self.loader.featureNames)
try:
self.featuredlg.setFeatureGroups(self.loader.featureGroups)
self.sorting.setFeatureGroups(self.loader.featureGroups)
except RuntimeError as e:
pass
def onDropEvent(self, path):
self._fileOpen(path)
self.loadItems()
def loadItems(self):
self.abort.emit()
self.loaderThread.wait()
self.tileview.setViewFlags(self.toolBar.viewFlags())
self.tileview.clear()
self.progressbar.setValue(0)
self.tileview.updateRaster(self.navToolBar.galsize)
self.tileview.updateNColumns(self.tileview.size().width())
idx = self.batchToolBar.indices()
self.nitems.setText("%d/%d" %(len(idx), self.batchToolBar.count))
self.progressbar.setRange(0, len(idx))
self.loader.setBatch(idx)
self.loader.setGallerySize(self.navToolBar.galsize)
self.loaderThread.start(self.loader)