def displayImage(self, imp, show = True): imp.setDisplayMode(IJ.COMPOSITE) enhancer = ContrastEnhancer() enhancer.setUseStackHistogram(True) splitter = ChannelSplitter() for c in range(1, imp.getNChannels() + 1): imp.c = c enhancer.stretchHistogram(imp, 0.35) if show: imp.show()
pixel_size = 1.0
files = glob.glob(input_dir + "*.tif")
files.sort()
frame_i = 1
for file in files:
print("Processing frame \033[1m" + str(frame_i) + "\033[0m")
frame = IJ.openImage(file) # ImagePlus
# Get just the signal channel
frame_stack = channel_splitter.getChannel(frame, channel) # ImageStack
frame = ImagePlus("Channel " + str(channel), frame_stack)
# Map signal to entire 16-bit range
contrast_enhancer.stretchHistogram(frame, 0.01)
processor = frame.getProcessor()
if(processor.getBitDepth() == 32):
processor.setMinAndMax(0, 1.0)
else:
processor.setMinAndMax(0, processor.maxValue())
frame = ImagePlus("Frame " + str(frame_i), processor)
# Convert to 8-bit, grayscale
converter = ImageConverter(frame)
converter.convertToGray8()
# Perform median filtering
processor = frame.getProcessor()
