def __init__(self, *args, **kw):
super(ImportDialog, self).__init__(*args, **kw)
loadUI(splitext(__file__)[0] + '.ui', self)
for name, scn in FileScanner.iterclasses():
self.structType.addItem(scn.icon(), name)
self.structType.setIconSize(QtCore.QSize(48, 24))
self.metadata = None
self._files = None
self.progressBar.hide()
self.segdlg = SegmentationDialog(self)
self.segdlg.hide()
self.thread = AtThread(self)
self.viewer.setSizePolicy(QtWidgets.QSizePolicy.MinimumExpanding,
QtWidgets.QSizePolicy.MinimumExpanding)
self.cbar = ChannelBar(self, self.viewer)
self.cbox.addWidget(self.cbar)
self.cbar.newPixmap.connect(self.viewer.showPixmap,
Qt.DirectConnection)
self.cbar.newContourImage.connect(self.viewer.contourImage)
self.dataFileBtn.clicked.connect(self.onOpenOutFile)
self.imageDirBtn.clicked.connect(self.onOpenImageDir)
self.startBtn.clicked.connect(self.raw2hdf)
self.closeBtn.clicked.connect(self.close)
self.closeBtn.clicked.connect(self.cbar.clear)
self.segmentationBtn.clicked.connect(self.onSegmentationBtn)
self.slider.newValue.connect(self.showObjects)
self.slider.valueChanged.connect(self.showImage)
self.slider.sliderReleased.connect(self.showObjects)
self.slider.sliderPressed.connect(self.cbar.clearContours)
self.contoursCb.stateChanged.connect(self.onContours)
self.showBBoxes.stateChanged.connect(self.onBBoxes)
self.showBBoxes.stateChanged.connect(self.showObjects)
self.segdlg.paramsChanged.connect(self.showObjects)
self.segdlg.refreshBtn.clicked.connect(self.showObjects)
self.segdlg.imageUpdate.connect(self.showImage)
self.segdlg.activateChannels.connect(self.cbar.activateChannels)
self.segdlg.changeColor.connect(self.cbar.setColor)
self.nextBtn.clicked.connect(self.onNextBtn)
self.prevBtn.clicked.connect(self.onPrevBtn)
def __init__(self, *args, **kw):
super(ImportDialog, self).__init__(*args, **kw)
loadUI(splitext(__file__)[0]+'.ui', self)
for name, scn in FileScanner.iterclasses():
self.structType.addItem(scn.icon(), name)
self.structType.setIconSize(QtCore.QSize(48, 24))
self.metadata = None
self._files = None
self.progressBar.hide()
self.segdlg = SegmentationDialog(self)
self.segdlg.hide()
self.thread = AtThread(self)
self.viewer.setSizePolicy(QtWidgets.QSizePolicy.MinimumExpanding,
QtWidgets.QSizePolicy.MinimumExpanding)
self.cbar = ChannelBar(self, self.viewer)
self.cbox.addWidget(self.cbar)
self.cbar.newPixmap.connect(self.viewer.showPixmap,
Qt.DirectConnection)
self.cbar.newContourImage.connect(self.viewer.contourImage)
self.dataFileBtn.clicked.connect(self.onOpenOutFile)
self.imageDirBtn.clicked.connect(self.onOpenImageDir)
self.startBtn.clicked.connect(self.raw2hdf)
self.closeBtn.clicked.connect(self.close)
self.closeBtn.clicked.connect(self.cbar.clear)
self.segmentationBtn.clicked.connect(self.onSegmentationBtn)
self.slider.newValue.connect(self.showObjects)
self.slider.valueChanged.connect(self.showImage)
self.slider.sliderReleased.connect(self.showObjects)
self.slider.sliderPressed.connect(self.cbar.clearContours)
self.contoursCb.stateChanged.connect(self.onContours)
self.showBBoxes.stateChanged.connect(self.onBBoxes)
self.showBBoxes.stateChanged.connect(self.showObjects)
self.segdlg.paramsChanged.connect(self.showObjects)
self.segdlg.refreshBtn.clicked.connect(self.showObjects)
self.segdlg.imageUpdate.connect(self.showImage)
self.segdlg.activateChannels.connect(self.cbar.activateChannels)
self.segdlg.changeColor.connect(self.cbar.setColor)
self.nextBtn.clicked.connect(self.onNextBtn)
self.prevBtn.clicked.connect(self.onPrevBtn)
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.classification.stateChanged.connect(
self.tileview.toggleClassIndicators, Qt.QueuedConnection)
self.toolBar.masking.stateChanged.connect(
self.tileview.toggleMasks, Qt.QueuedConnection)
self.toolBar.outline.stateChanged.connect(
self.tileview.toggleOutlines, Qt.QueuedConnection)
self.toolBar.description.stateChanged.connect(
self.tileview.toggleDescription, Qt.QueuedConnection)
self.setCentralWidget(self.tileview)
self.setupDock()
self.setupProgressBar()
self.loader.fileOpened.connect(self.updateToolbars)
self.loader.progressUpdate.connect(self.updateProgressBar)
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)
self.actionExportViewPanel.triggered.connect(self.saveImage)
self.actionSaveData2Csv.triggered.connect(self.saveData2Csv)
self.actionSaveCountingStats.triggered.connect(self.saveCountingStats)
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.actionRefresh.triggered.connect(self.refresh)
self.actionSelectAll.triggered.connect(
self.tileview.actionSelectAll.trigger)
self.actionInvertSelection.triggered.connect(
self.tileview.actionInvertSelection.trigger)
self.tileview.zoomChanged.connect(self.updateZoomFactor)
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()
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.classification.stateChanged.connect(
self.tileview.toggleClassIndicators, Qt.QueuedConnection)
self.toolBar.masking.stateChanged.connect(
self.tileview.toggleMasks, Qt.QueuedConnection)
self.toolBar.outline.stateChanged.connect(
self.tileview.toggleOutlines, Qt.QueuedConnection)
self.toolBar.description.stateChanged.connect(
self.tileview.toggleDescription, Qt.QueuedConnection)
self.setCentralWidget(self.tileview)
self.setupDock()
self.setupProgressBar()
self.loader.fileOpened.connect(self.updateToolbars)
self.loader.progressUpdate.connect(self.updateProgressBar)
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)
self.actionExportViewPanel.triggered.connect(self.saveImage)
self.actionSaveData2Csv.triggered.connect(self.saveData2Csv)
self.actionSaveCountingStats.triggered.connect(self.saveCountingStats)
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.actionRefresh.triggered.connect(self.refresh)
self.actionSelectAll.triggered.connect(
self.tileview.actionSelectAll.trigger)
self.actionInvertSelection.triggered.connect(
self.tileview.actionInvertSelection.trigger)
self.tileview.zoomChanged.connect(self.updateZoomFactor)
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 onHelpManual(self):
self.assistant.show()
self.assistant.raise_()
def onHelpShortcuts(self):
self.onHelpManual()
self.assistant.openKeyword("Shortcuts")
def refresh(self):
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 _saveSettings(self):
settings = QtCore.QSettings(version.organisation, version.appname)
settings.beginGroup('Gui')
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('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()
def closeEvent(self, event):
self.assistant.close()
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("Annotation", self)
self.annodock.setWidget(self.annotation)
self.annodock.setObjectName("annotation")
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)
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.finished.connect(frame.hide)
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:
features = self.featuredlg.checkedItems()
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 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.addToolBar(QtCore.Qt.TopToolBarArea, self.toolBar)
self.toolBar.actionOpen.triggered.connect(self.onFileOpen)
self.toolBar.actionNew.triggered.connect(self.newDataFile)
self.actionReloadFile.triggered.connect(self.loadItems)
self.navToolBar = NavToolBar(self)
self.addToolBar(QtCore.Qt.BottomToolBarArea, self.navToolBar)
self.navToolBar.coordUpdated.connect(self.loader.setCoordinate)
self.sortToolBar = SortToolBar(self)
self.addToolBar(QtCore.Qt.TopToolBarArea, self.sortToolBar)
def newDataFile(self):
dlg = ImportDialog(self,
Qt.WindowMinMaxButtonsHint|Qt.WindowCloseButtonHint)
dlg.loadData.connect(self._openAndLoad)
dlg.exec_()
def onThrowAnchor(self):
self.sorting.removeAll()
self.sorting.addItems(self.tileview.selectedItems())
self.sorting.applyDefaultSortAlgorithm()
self.sorting.sortAscending()
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._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.tileview.updateRaster(self.navToolBar.galsize)
self.tileview.updateNColumns(self.tileview.size().width())
self.progressbar.setRange(0, self.navToolBar.nitems)
self.loader.setNumberItems(self.navToolBar.nitems)
self.loader.setGallerySize(self.navToolBar.galsize)
self.loaderThread.start(self.loader)
class ImportDialog(QtWidgets.QDialog):
loadData = QtCore.pyqtSignal(str)
def __init__(self, *args, **kw):
super(ImportDialog, self).__init__(*args, **kw)
loadUI(splitext(__file__)[0] + '.ui', self)
for name, scn in FileScanner.iterclasses():
self.structType.addItem(scn.icon(), name)
self.structType.setIconSize(QtCore.QSize(48, 24))
self.metadata = None
self._files = None
self.progressBar.hide()
self.segdlg = SegmentationDialog(self)
self.segdlg.hide()
self.thread = AtThread(self)
self.viewer.setSizePolicy(QtWidgets.QSizePolicy.MinimumExpanding,
QtWidgets.QSizePolicy.MinimumExpanding)
self.cbar = ChannelBar(self, self.viewer)
self.cbox.addWidget(self.cbar)
self.cbar.newPixmap.connect(self.viewer.showPixmap,
Qt.DirectConnection)
self.cbar.newContourImage.connect(self.viewer.contourImage)
self.dataFileBtn.clicked.connect(self.onOpenOutFile)
self.imageDirBtn.clicked.connect(self.onOpenImageDir)
self.startBtn.clicked.connect(self.raw2hdf)
self.closeBtn.clicked.connect(self.close)
self.closeBtn.clicked.connect(self.cbar.clear)
self.segmentationBtn.clicked.connect(self.onSegmentationBtn)
self.slider.newValue.connect(self.showObjects)
self.slider.valueChanged.connect(self.showImage)
self.slider.sliderReleased.connect(self.showObjects)
self.slider.sliderPressed.connect(self.cbar.clearContours)
self.contoursCb.stateChanged.connect(self.onContours)
self.showBBoxes.stateChanged.connect(self.onBBoxes)
self.showBBoxes.stateChanged.connect(self.showObjects)
self.segdlg.paramsChanged.connect(self.showObjects)
self.segdlg.refreshBtn.clicked.connect(self.showObjects)
self.segdlg.imageUpdate.connect(self.showImage)
self.segdlg.activateChannels.connect(self.cbar.activateChannels)
self.segdlg.changeColor.connect(self.cbar.setColor)
self.nextBtn.clicked.connect(self.onNextBtn)
self.prevBtn.clicked.connect(self.onPrevBtn)
def keyPressEvent(self, event):
if event.key() == Qt.Key_F5:
self.showObjects()
def closeEvent(self, event):
super(ImportDialog, self).closeEvent(event)
ofile = self.dataFile.text()
if self.loadOnClose.isChecked() and isfile(ofile):
self.loadData.emit(ofile)
def onNextBtn(self):
self.slider.setValue(self.slider.value() + 1)
self.showObjects()
def onPrevBtn(self):
self.slider.setValue(self.slider.value() - 1)
self.showObjects()
def onContours(self, state):
if state == Qt.Checked:
self.showObjects()
else:
self.cbar.clearContours()
self.viewer.clearPolygons()
def onBBoxes(self, state):
if state == Qt.Checked:
self.showObjects()
else:
self.viewer.clearRects()
def onSegmentationBtn(self):
self.segdlg.show()
self.segdlg.raise_()
def onOpenOutFile(self):
ofile = self.dataFile.text()
idir = self.imageDir.text()
if isfile(ofile):
path = dirname(ofile)
elif isdir(idir):
path = dirname(idir)
else:
path = expanduser("~")
ofile = QFileDialog.getSaveFileName(self, "save to hdf file", path,
"hdf (*.hdf *.h5)")[0]
self.dataFile.setText(ofile)
def onOpenImageDir(self):
self.cbar.clearContours()
self.viewer.clearRects()
self.viewer.clearPolygons()
idir = self.imageDir.text()
ofile = self.dataFile.text()
if isdir(idir):
path = dirname(idir)
elif isfile(ofile):
path = dirname(ofile)
else:
path = expanduser("~")
# TODO use getOpenFileNames instead
idir = QFileDialog.getExistingDirectory(self,
"Select an image directory",
path)
# cancel button
if not idir:
return
self.imageDir.setText(idir)
scanner = FileScanner(self.structType.currentText(), idir)
self._files = scanner()
if not self._files:
QMessageBox.warning(self, "Error", "No files found")
return
self.dirinfo.setText("%d images found" % len(self._files))
proc = LsmProcessor(self._files.keys()[0],
self.segdlg.segmentationParams(),
self.cbar.checkedChannels(),
treatment=self._files.values()[0])
self.metadata = proc.metadata
self.metadata.n_images = len(self._files)
images = list(proc.iterQImages())
props = list(proc.iterprops())
self.cbar.addChannels(len(images))
self.cbar.setImages(images, list(proc.iterprops()))
state = self.segdlg.blockSignals(True)
self.segdlg.setRegions(self.cbar.allChannels(), props)
self.segdlg.setMaxZSlice(self.metadata.n_zslices - 1)
self.segdlg.blockSignals(state)
self.slider.setRange(0, self.metadata.n_images - 1)
self.slider.setValue(0)
self.showObjects()
def showImage(self, index=0):
# no image directory yet
if self._files is None:
return
try:
proc = LsmProcessor(self._files.keys()[index],
self.segdlg.segmentationParams(),
self.cbar.checkedChannels(),
treatment=self._files.values()[index])
except IndexError:
return
self.viewer.clearPolygons()
self.viewer.clearRects()
images = list(proc.iterQImages())
self.cbar.setImages(images, list(proc.iterprops()))
def showObjects(self):
if not (self.contoursCb.isChecked() or \
self.showBBoxes.isChecked()) or \
self._files is None:
return
index = self.slider.value()
try:
mp = LsmProcessor(self._files.keys()[index],
self.segdlg.segmentationParams(),
self.cbar.checkedChannels(),
treatment=self._files.values()[index])
# first channel for primary segementation
mp.segmentation()
except Exception as e:
QMessageBox.critical(self, "Error", "%s:%s" % (type(e), str(e)))
finally:
if not mp.objects:
return
if self.contoursCb.isChecked():
self.cbar.setContours(mp.objects.contours)
if self.showBBoxes.isChecked():
self.cbar.drawRectangles(mp.objects.centers.values(),
self.segdlg.galSize.value(),
isize=self.metadata.size)
def onError(self, exc):
self.startBtn.setText("Start")
QMessageBox.critical(self, "Error", str(exc))
def onFinished(self):
self.raise_()
self.startBtn.setText("Start")
QMessageBox.information(self, "finished", "training set saved")
def showSlider(self):
self.progressBar.hide()
self.sliderframe.show()
def hideSlider(self):
self.progressBar.show()
self.sliderframe.hide()
def raw2hdf(self):
if self.thread.isRunning():
self.startBtn.setText("Start")
self.thread.worker.abort()
else:
self.viewer.clearPolygons()
self.viewer.clearRects()
try:
worker = AtImporter(self._files, self.metadata,
self.dataFile.text(),
self.cbar.checkedChannels(),
self.cbar.colors(),
self.segdlg.segmentationParams(),
self.segdlg.featureGroups())
except Exception as e:
QMessageBox.critical(self, str(e), traceback.format_exc())
return
worker.connetToProgressBar(self.progressBar, Qt.QueuedConnection)
worker.started.connect(self.hideSlider)
worker.finished.connect(self.showSlider)
worker.finished.connect(self.onFinished, Qt.QueuedConnection)
worker.error.connect(self.onError, Qt.QueuedConnection)
worker.contourImage.connect(self.cbar.contourImage,
Qt.QueuedConnection)
self.thread.start(worker)
self.startBtn.setText("Abort")
class ImportDialog(QtWidgets.QDialog):
loadData = QtCore.pyqtSignal(str)
def __init__(self, *args, **kw):
super(ImportDialog, self).__init__(*args, **kw)
loadUI(splitext(__file__)[0]+'.ui', self)
for name, scn in FileScanner.iterclasses():
self.structType.addItem(scn.icon(), name)
self.structType.setIconSize(QtCore.QSize(48, 24))
self.metadata = None
self._files = None
self.progressBar.hide()
self.segdlg = SegmentationDialog(self)
self.segdlg.hide()
self.thread = AtThread(self)
self.viewer.setSizePolicy(QtWidgets.QSizePolicy.MinimumExpanding,
QtWidgets.QSizePolicy.MinimumExpanding)
self.cbar = ChannelBar(self, self.viewer)
self.cbox.addWidget(self.cbar)
self.cbar.newPixmap.connect(self.viewer.showPixmap,
Qt.DirectConnection)
self.cbar.newContourImage.connect(self.viewer.contourImage)
self.dataFileBtn.clicked.connect(self.onOpenOutFile)
self.imageDirBtn.clicked.connect(self.onOpenImageDir)
self.startBtn.clicked.connect(self.raw2hdf)
self.closeBtn.clicked.connect(self.close)
self.closeBtn.clicked.connect(self.cbar.clear)
self.segmentationBtn.clicked.connect(self.onSegmentationBtn)
self.slider.newValue.connect(self.showObjects)
self.slider.valueChanged.connect(self.showImage)
self.slider.sliderReleased.connect(self.showObjects)
self.slider.sliderPressed.connect(self.cbar.clearContours)
self.contoursCb.stateChanged.connect(self.onContours)
self.showBBoxes.stateChanged.connect(self.onBBoxes)
self.showBBoxes.stateChanged.connect(self.showObjects)
self.segdlg.paramsChanged.connect(self.showObjects)
self.segdlg.refreshBtn.clicked.connect(self.showObjects)
self.segdlg.imageUpdate.connect(self.showImage)
self.segdlg.activateChannels.connect(self.cbar.activateChannels)
self.segdlg.changeColor.connect(self.cbar.setColor)
self.nextBtn.clicked.connect(self.onNextBtn)
self.prevBtn.clicked.connect(self.onPrevBtn)
def keyPressEvent(self, event):
if event.key() == Qt.Key_F5:
self.showObjects()
def closeEvent(self, event):
super(ImportDialog, self).closeEvent(event)
ofile = self.dataFile.text()
if self.loadOnClose.isChecked() and isfile(ofile):
self.loadData.emit(ofile)
def onNextBtn(self):
self.slider.setValue(self.slider.value()+1)
self.showObjects()
def onPrevBtn(self):
self.slider.setValue(self.slider.value()-1)
self.showObjects()
def onContours(self, state):
if state == Qt.Checked:
self.showObjects()
else:
self.cbar.clearContours()
self.viewer.clearPolygons()
def onBBoxes(self, state):
if state == Qt.Checked:
self.showObjects()
else:
self.viewer.clearRects()
def onSegmentationBtn(self):
self.segdlg.show()
self.segdlg.raise_()
def onOpenOutFile(self):
ofile = self.dataFile.text()
idir = self.imageDir.text()
if isfile(ofile):
path = dirname(ofile)
elif isdir(idir):
path = dirname(idir)
else:
path = expanduser("~")
ofile = QFileDialog.getSaveFileName(self, "save to hdf file",
path,
"hdf (*.hdf *.h5)")[0]
self.dataFile.setText(ofile)
def onOpenImageDir(self):
self.cbar.clearContours()
self.viewer.clearRects()
self.viewer.clearPolygons()
idir = self.imageDir.text()
ofile = self.dataFile.text()
if isdir(idir):
path = dirname(idir)
elif isfile(ofile):
path = dirname(ofile)
else:
path = expanduser("~")
# TODO use getOpenFileNames instead
idir = QFileDialog.getExistingDirectory(self,
"Select an image directory",
path)
# cancel button
if not idir:
return
self.imageDir.setText(idir)
scanner = FileScanner(self.structType.currentText(), idir)
self._files = scanner()
if not self._files:
QMessageBox.warning(self, "Error", "No files found")
return
self.dirinfo.setText("%d images found" %len(self._files))
proc = LsmProcessor(self._files.keys()[0],
self.segdlg.segmentationParams(),
self.cbar.checkedChannels(),
treatment=self._files.values()[0])
self.metadata = proc.metadata
self.metadata.n_images = len(self._files)
images = list(proc.iterQImages())
props = list(proc.iterprops())
self.cbar.addChannels(len(images))
self.cbar.setImages(images, list(proc.iterprops()))
state = self.segdlg.blockSignals(True)
self.segdlg.setRegions(self.cbar.allChannels(), props)
self.segdlg.setMaxZSlice(self.metadata.n_zslices-1)
self.segdlg.blockSignals(state)
self.slider.setRange(0, self.metadata.n_images-1)
self.slider.setValue(0)
self.showObjects()
def showImage(self, index=0):
# no image directory yet
if self._files is None:
return
try:
proc = LsmProcessor(self._files.keys()[index],
self.segdlg.segmentationParams(),
self.cbar.checkedChannels(),
treatment=self._files.values()[index])
except IndexError:
return
self.viewer.clearPolygons()
self.viewer.clearRects()
images = list(proc.iterQImages())
self.cbar.setImages(images, list(proc.iterprops()))
def showObjects(self):
if not (self.contoursCb.isChecked() or \
self.showBBoxes.isChecked()) or \
self._files is None:
return
index = self.slider.value()
try:
mp = LsmProcessor(self._files.keys()[index],
self.segdlg.segmentationParams(),
self.cbar.checkedChannels(),
treatment=self._files.values()[index])
# first channel for primary segementation
mp.segmentation()
except Exception as e:
QMessageBox.critical(self, "Error", "%s:%s" %(type(e), str(e)))
finally:
if not mp.objects:
return
if self.contoursCb.isChecked():
self.cbar.setContours(mp.objects.contours)
if self.showBBoxes.isChecked():
self.cbar.drawRectangles(mp.objects.centers.values(),
self.segdlg.galSize.value(),
isize=self.metadata.size)
def onError(self, exc):
self.startBtn.setText("Start")
QMessageBox.critical(self, "Error", str(exc))
def onFinished(self):
self.raise_()
self.startBtn.setText("Start")
QMessageBox.information(self, "finished", "training set saved")
def showSlider(self):
self.progressBar.hide()
self.sliderframe.show()
def hideSlider(self):
self.progressBar.show()
self.sliderframe.hide()
def raw2hdf(self):
if self.thread.isRunning():
self.startBtn.setText("Start")
self.thread.worker.abort()
else:
self.viewer.clearPolygons()
self.viewer.clearRects()
try:
worker = AtImporter(self._files,
self.metadata,
self.dataFile.text(),
self.cbar.checkedChannels(),
self.cbar.colors(),
self.segdlg.segmentationParams(),
self.segdlg.featureGroups())
except Exception as e:
QMessageBox.critical(self, str(e), traceback.format_exc())
return
worker.connetToProgressBar(self.progressBar, Qt.QueuedConnection)
worker.started.connect(self.hideSlider)
worker.finished.connect(self.showSlider)
worker.finished.connect(self.onFinished, Qt.QueuedConnection)
worker.error.connect(self.onError, Qt.QueuedConnection)
worker.contourImage.connect(self.cbar.contourImage,
Qt.QueuedConnection)
self.thread.start(worker)
self.startBtn.setText("Abort")