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 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 _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 processBild(file_, regex, segparams, feature_groups, channels):
try:
gsize = segparams.values()[0].gallery_size
mp = TiffProcessor(file_, regex, segparams, channels, gsize)
mp.segmentation()
mp.calculateFeatures(feature_groups)
image = mp.image[:, :, :, channels.keys()]
objects = mp.objects()
# cannot return OrderedDict from multiprocessing, so I split the dict
# and reconstruct it in the main process
except Exception as e:
return e
else:
return file_, image, objects.values(), objects.feature_names