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stack_channels.py
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stack_channels.py
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#!/usr/bin/env python
### This script takes a list of images and stacks them into a single image stack using Dask
import numpy as np
import argparse
import tifffile
from aicsimageio.writers import OmeTiffWriter
from aicsimageio import aics_image as AI
import aicsimageio
import dask
import dask.array as da
def main():
parser = argparse.ArgumentParser()
parser.add_argument(
"-i",
"--input",
nargs="+",
help="List of images to stack"
)
parser.add_argument(
"-o",
"--output",
dest="output",
type=str,
)
parser.add_argument(
"--num-channels",
dest="num_channels",
type=int
)
args = parser.parse_args()
channel_counter = 0
img = AI.AICSImage(args.input[0]).get_image_dask_data("CYX")
out = da.empty(shape = [args.num_channels,
img[0].shape[0],
img[0].shape[1]])
print(out.shape)
if img.shape[0]>1:
for channel in range(img.shape[0]):
out[channel_counter] = img[channel]
channel_counter += 1
else:
out[channel_counter] = img[0]
channel_counter += 1
if len(args.input)>1:
for i in range(len(args.input[1:])):
img = AI.AICSImage(args.input[1+i]).get_image_dask_data("CYX")
if img.shape[0]>1:
for channel in range(img.shape[0]):
out[channel_counter] = img[channel]
channel_counter += 1
else:
out[channel_counter] = img[0]
channel_counter += 1
OmeTiffWriter.save(out,
args.output,
dim_order = "CYX")
if __name__ == "__main__":
main()