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 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 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 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 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 __call__(self):
self.started.emit()
self.progressSetRange.emit(0, len(self.files))
writer = HdfWriter(self.outfile)
colors = [self.colors[ch] for ch in self.channels.values()]
writer.setupFile(self.metadata.n_images, self.channels, colors)
writer.saveSettings(self.seg_params, self.feature_groups,
self.channels.values(), self.colors)
try:
gsize = self.seg_params.values()[0].gallery_size
for i, (file_, treatment) in enumerate(self.files.iteritems()):
self.progressUpdate.emit(i + 1)
self.interruption_point()
self.thread().msleep(self.PYDELAY)
mp = LsmProcessor(file_, self.seg_params, self.channels, gsize,
treatment)
# first channel for primary segementation
mp.segmentation()
mp.calculateFeatures(self.feature_groups)
objects = mp.objects
# saveData ignores empty objects
image = mp.image[:, :, :, self.channels.keys()]
writer.saveData(objects, image, treatment)
self.contourImage.emit(tuple(mp.iterQImages()),
objects.contours)
self.progressSetRange.emit(0, 0)
self.progressUpdate.emit(-1)
writer.flush()
self.finished.emit()
except AbortQWorker:
pass
except HdfError as e:
self.error.emit(e)
traceback.print_exc()
raise
except Exception as e:
self.error.emit(e)
traceback.print_exc()
raise
finally:
writer.close()
def __call__(self):
self.started.emit()
self.progressSetRange.emit(0, len(self.files))
writer = HdfWriter(self.outfile)
colors = [self.colors[ch] for ch in self.channels.values()]
writer.setupFile(self.metadata.n_images, self.channels, colors)
writer.saveSettings(self.seg_params, self.feature_groups,
self.channels.values(), self.colors)
try:
gsize = self.seg_params.values()[0].gallery_size
for i, (file_, treatment) in enumerate(self.files.iteritems()):
self.progressUpdate.emit(i+1)
self.interruption_point()
self.thread().msleep(self.PYDELAY)
mp = LsmProcessor(file_, self.seg_params, self.channels, gsize,
treatment)
# first channel for primary segementation
mp.segmentation()
mp.calculateFeatures(self.feature_groups)
objects = mp.objects
# saveData ignores empty objects
image = mp.image[:, :, :, self.channels.keys()]
writer.saveData(objects, image, treatment)
self.contourImage.emit(tuple(mp.iterQImages()),
objects.contours)
self.progressSetRange.emit(0, 0)
self.progressUpdate.emit(-1)
writer.flush()
self.finished.emit()
except AbortQWorker:
pass
except HdfError as e:
self.error.emit(e)
traceback.print_exc()
raise
except Exception as e:
self.error.emit(e)
traceback.print_exc()
raise
finally:
writer.close()
