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)
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")