def get_enhance_bounds(chf_fpaths, low_theshold, high_threshold):
# initialize the pixels array
pix = []
# open 100 images max (time consuming)
if len(chf_fpaths) > 100:
chf_fpaths = random.sample(chf_fpaths, 100)
# create a for loop here
counter = 1
for image_path in chf_fpaths:
# open the image
print "Getting pixels in Image " + image_path
print str(counter) + " / " + str(len(chf_fpaths))
counter += 1
imp_orig = Opener().openImage(image_path)
# get the pixel values
image_pix = list(imp_orig.getProcessor().getPixels())
imp_orig.close()
imp_orig.flush()
# select randomly 10% of the pixels (maybe memory issues)
image_pix_sel = random.sample(image_pix, int(len(image_pix) * 0.1))
pix = pix + image_pix_sel
# get the percentile values to threshold
IJ.log('Quantifying pixel values for contrast enhancement...')
low_pix = percentile(pix, low_theshold)
high_pix = percentile(pix, high_threshold)
return low_pix, high_pix
for channel in range(1, (number_of_channels_in_mouse + 1)):
channel_files = getChannelFiles(MouseIDFiles, channel)
# get the full path
chf_fpaths = [path.join(In_dir, x) for x in channel_files]
# get the minimum and maximum pixel value
min_pixval, max_pixval = get_enhance_bounds(
chf_fpaths, low_theshold, high_threshold)
IJ.log("Found pixel bounds " + str(min_pixval) + " and " +
str(max_pixval) + " for channel " + str(channel))
counter = 1
for chfile in chf_fpaths:
# open file
ch_img = Opener().openImage(chfile)
ch_tit = ch_img.getTitle()
# adjust contrast
ch_img.getProcessor().setMinAndMax(min_pixval, max_pixval)
# convert to 8-bit (which also applies the contrast)
ImageConverter(ch_img).convertToGray8()
# save
IJ.saveAsTiff(ch_img, path.join(Out_dir, ch_tit))
# close and flush
ch_img.close()
ch_img.flush()
print("Image " + str(counter) + " of " + str(len(chf_fpaths)) +
" processed")
counter += 1
IJ.log('Mouse ' + MouseID + ' processed')
print("DONE, find your results in " + Out_dir)
