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import numpy as np
import scipy.misc
import h5py
import random
import sys
import argparse
def main(h5_filename, output_dir, color_style, key, im_limit=1000, sideways=False):
image_stack = read_h5_image_stack(h5_filename, key)
if sideways:image_stack = np.transpose(image_stack,(1,0,2))
if im_limit < image_stack.shape[0]: image_stack = image_stack[:im_limit,:,:]
color_map = build_color_map(image_stack, color_style)
output_pngs(image_stack, color_map, output_dir)
def output_pngs(image_stack, color_map, output_dir, channel_id=""):
print "Handling image_stack with shape %s" % (str(image_stack.shape))
if image_stack.ndim > 3:
for jj in range(image_stack.shape[image_stack.ndim-1]):
output_pngs(image_stack[..., jj], color_map, output_dir, "-"+str(jj))
print "Printing pngs to %s" % (output_dir)
(image_count, width, height) = image_stack.shape
for ii in xrange(image_count):
labels = image_stack[ii, ...]
output = np.zeros((width, height, 3))
for w in xrange(width):
for h in xrange(height):
colors = color_map[labels[w,h]]
for channel, intensity in enumerate(colors):
output[w, h, channel] = intensity
save_png(output, str(ii)+channel_id, output_dir)
def save_png(image_matrix, identifier, output_dir):
filename = output_dir + str(identifier) + ".png"
scipy.misc.imsave(filename, image_matrix)
def read_h5_image_stack(h5_filename, key):
f = h5py.File(h5_filename, "r")
return np.array(f[key])
def build_color_map(image_stack, color_style):
if color_style == "random": return build_random_color_map(image_stack)
elif color_style == "grayscale": return build_grayscale_color_map(image_stack)
else: raise NameError("color_style must be 'random' or 'grayscale'")
def build_grayscale_color_map(image_stack):
color_map = {}
uniques = np.unique(image_stack)
max_val = float(np.max(image_stack))
for pixel_value in uniques:
luminance = int(255 * pixel_value / max_val)
color_map[pixel_value] = [luminance, luminance, luminance]
return color_map
def build_random_color_map(image_stack):
color_map = {}
uniques = np.unique(image_stack)
for label in uniques:
color_map[label] = pick_random_color()
return color_map
def pick_random_color():
r = random.randint(0, 255)
g = random.randint(0, 255)
b = random.randint(0, 255)
return [r,g,b]
if __name__ == '__main__':
parser = argparse.ArgumentParser()
parser.add_argument("h5_path", type=str,
help="Path to the target h5")
parser.add_argument("out_path", type=str,
help="Path and prefix of pngs")
parser.add_argument("--side-view", action="store_true",
help="output lateral cross-sections instead of frontals")
parser.add_argument("--random-colors", action="store_true",
help="output with radnom colormap")
parser.add_argument("--im-limit", type=int, default=1000,
help="limit of images to output")
parser.add_argument("--h5-key", type=str, default="stack",
help="path to")
args = parser.parse_args()
if args.random_colors: color = "random"
else: color="grayscale"
main(args.h5_path, args.out_path, color, args.h5_key, im_limit=args.im_limit, sideways=args.side_view)
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