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)
finished = QtCore.pyqtSignal()
setProgress = QtCore.pyqtSignal(int)
setProgressRange = QtCore.pyqtSignal(int, int)
def __init__(self, *args, **kw):
super(ImportDialog, self).__init__(*args, **kw)
loadUI(splitext(__file__)[0] + ".ui", self)
self.zsliceMethod.addItems(ZProject.names())
self.zsliceMethod.currentIndexChanged.connect(self.onZSliceMethodChanged)
self.pool = None
self._pool_running = False
for name, scn in FileScanner.iterclasses():
self.structType.addItem(scn.icon(), name)
self.structType.setIconSize(QtCore.QSize(48, 24))
self._files = None
self._regex = None
self.progressBar.hide()
self.segdlg = SegmentationDialog(self)
self.segdlg.hide()
self.zslice.valueChanged.connect(self.segdlg.setZSlice)
self.segdlg.zslice.valueChanged.connect(self.zslice.setValue)
self.zsliceMethod.currentIndexChanged.connect(self.segdlg.zsliceMethod.setCurrentIndex)
self.segdlg.zsliceMethod.currentIndexChanged.connect(self.zsliceMethod.setCurrentIndex)
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.cbar.colorsChanged.connect(self.segdlg.updateRowColors)
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)
self.reloadBtn.clicked.connect(self.onReloadBtn)
self.setProgressRange.connect(self.progressBar.setRange)
self.setProgress.connect(self.progressBar.setValue, Qt.DirectConnection)
def onZSliceMethodChanged(self, index):
if index == ZProject.Select:
self.zslice.show()
else:
self.zslice.hide()
def setMaxZSlice(self, value, block=True):
if value == 0:
self.zstack.hide()
else:
self.zstack.show()
state = self.zslice.blockSignals(block)
self.zslice.setMaximum(value)
self.zslice.setValue(max(0, floor(value / 2.0) - 1))
self.segdlg.setMaxZSlice(value, block)
self.zslice.blockSignals(state)
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 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.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 data as", path, "hdf (*.hdf *.h5)")[0]
self.dataFile.setText(ofile)
def imageDimensionsDlg(self, file_):
"""Pop up dialog to define stack order and image dimensins."""
dlg = ImageDims(self._files)
dlg.exec_()
if dlg.result() > 0:
dims = dlg.dimensionInfo()
self.setMaxZSlice(dims[1])
if dlg.useRegex.isChecked():
self._files = dlg.files
return dims
else:
return None
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
try:
self._dimUpdate(self._files[0].file)
self._initialImage()
except IOError as e:
pass
def onReloadBtn(self):
if self._files is not None:
i = self.slider.value()
try:
self._dimUpdate(self._files[i].file)
self._initialImage(i)
except (IOError, AttributeError) as e:
pass
def _dimUpdate(self, file_):
# ask user for image dims and stack order, tiff file only
mtype = mimetypes.guess_type(file_)[0]
if mtype != "image/lsm":
regex = self.imageDimensionsDlg(file_)
if regex is not None: # in case of cancel button
self._regex = regex
self.setMaxZSlice(self._regex.nzslices)
self.dirinfo.setText("%d images found" % len(self._files))
def _initialImage(self, index=0):
"""Process the first image."""
# don't know nz yet when segmentationParams is called
self.segdlg.setZSlice(0, block=True)
proc = TiffProcessor(
self._files[index], self._regex, self.segdlg.segmentationParams(), self.cbar.checkedChannels()
)
images = 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.setMaxZSlice(proc.zSlices - 1)
self.segdlg.blockSignals(state)
self.slider.setRange(0, len(self._files) - 1)
self.slider.setValue(index)
self.showObjects()
def showImage(self, index=0):
# no image directory yet
if self._files is None:
return
try:
proc = TiffProcessor(
self._files[index], self._regex, self.segdlg.segmentationParams(), self.cbar.checkedChannels()
)
except IndexError:
return
self.viewer.clearPolygons()
self.viewer.clearRects()
images = 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 = TiffProcessor(
self._files[index], self._regex, self.segdlg.segmentationParams(), self.cbar.checkedChannels()
)
# first channel for primary segementation
mp.segmentation()
except Exception as e:
QMessageBox.critical(self, "Error", "%s:%s" % (type(e), str(e)))
finally:
objects = mp.objects()
if not objects:
self.viewer.clearPolygons()
self.viewer.clearRects()
return
if self.contoursCb.isChecked():
self.cbar.setContours(objects.contours)
if self.showBBoxes.isChecked():
self.cbar.drawRectangles(objects.centers.values(), self.segdlg.galSize.value(), isize=mp.size)
def onError(self, exc):
self.pool.terminate()
self.showSlider()
self.startBtn.setText("Start")
self._pool_running = False
QMessageBox.critical(self, "Error", str(exc))
def onFinished(self):
self.saveData()
self.raise_()
self.showSlider()
self._pool_running = False
QMessageBox.information(self, "Informaton", "Image preprocessing successful")
def showSlider(self):
QApplication.restoreOverrideCursor()
self._pool_running = False
self.startBtn.setText("Start")
self.progressBar.hide()
self.sliderframe.show()
# self.setEnabled(True)
def hideSlider(self):
QApplication.setOverrideCursor(QCursor(Qt.WaitCursor))
self.startBtn.setText("Abort")
self._pool_running = True
self.progressBar.show()
self.sliderframe.hide()
# self.setEnabled(False)
# self.startBtn.setEnabled(True)
def raw2hdf(self):
if not self.dataFile.text():
self.onOpenOutFile()
if not self.dataFile.text():
return
if self._pool_running:
self.showSlider()
self.pool.terminate()
return
nfiles = len(self._files)
self.pool = Pool(processes=cpu_count() - 1)
self._pool_running = True
self.hideSlider()
self.progressBar.setRange(0, 2 * nfiles - 1)
self.progressBar.setValue(0)
channels = self.cbar.checkedChannels()
self.results = list()
callback = QCallBack(nfiles)
callback.tick.connect(self.incrementProgress)
callback.finished.connect(self.onFinished)
callback.error.connect(self.onError)
for file_ in self._files:
self.results.append(
self.pool.apply_async(
processBild,
[file_, self._regex, self.segdlg.segmentationParams(), self.segdlg.featureGroups(), channels],
callback=callback,
)
)
def incrementProgress(self, value=None):
if value is None:
value = self.progressBar.value() + 1
self.setProgress.emit(value)
def saveData(self):
# be carefull save Data is runs in a different thread
# (callback of map_async)
self.pool.close()
self.pool.join()
self.parent().onFileClose()
writer = HdfWriter(self.dataFile.text())
try:
channels = self.cbar.checkedChannels()
proc = TiffProcessor(
self._files[0], self._regex, self.segdlg.segmentationParams(), self.cbar.checkedChannels()
)
colors = [self.cbar.colors[ch] for ch in channels.values()]
writer.setupFile(len(self._files), channels, colors)
writer.saveSettings(
self.segdlg.segmentationParams(), self.segdlg.featureGroups(), channels.values(), self.cbar.colors
)
for i, res_ in enumerate(self.results):
res = res_.get()
file_, image, image_objects, feature_names = res
# reconstruct the ObjectDict
objects = ObjectDict("multicolor")
objects.feature_names = feature_names
for obj in image_objects:
objects[obj.label] = obj
writer.saveData(objects, image, None, file_.file)
self.incrementProgress()
writer.flush()
finally:
writer.close()
self.finished.emit()
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")
