Mercurial > repos > imgteam > colocalization_viz
changeset 1:fc85eb253163 draft
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/colocalization_viz/ commit 1453917dfaf4c0922aec82c400015ff7e13ab737
| author | imgteam |
|---|---|
| date | Mon, 22 Jul 2019 07:08:46 -0400 |
| parents | 9ddb11b272ee |
| children | c73332d5c3bb |
| files | colocalization_viz.py colocalization_viz.xml test-data/out.png |
| diffstat | 3 files changed, 22 insertions(+), 14 deletions(-) [+] |
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--- a/colocalization_viz.py Sat Feb 09 14:32:01 2019 -0500 +++ b/colocalization_viz.py Mon Jul 22 07:08:46 2019 -0400 @@ -1,25 +1,31 @@ import skimage.io import skimage.color +from skimage import img_as_uint +from skimage.exposure import equalize_adapthist import numpy as np -import os +import argparse import sys -import warnings -#TODO make importable by python script -args = sys.argv - +# TODO make importable by python script def readImg(path): img = skimage.io.imread(path) + if len(img.shape) > 2: img = skimage.color.rgb2gray(img) - img = np.expand_dims(img > 0, 3) + img = equalize_adapthist(img, clip_limit=0.03) + img = img_as_uint(img) + img = np.reshape(img, [img.shape[0], img.shape[1], 1]) return img -im1 = readImg(args[1]) -im2 = readImg(args[2]) -res = np.concatenate((im1, im2, np.zeros_like(im1)), axis=2) * 1.0 -with warnings.catch_warnings(): - warnings.simplefilter("ignore") - skimage.io.imsave(args[3], res) +parser = argparse.ArgumentParser() +parser.add_argument('input_file1', type=argparse.FileType('r'), default=sys.stdin, help='input file (red)') +parser.add_argument('input_file2', type=argparse.FileType('r'), default=sys.stdin, help='input file (green)') +parser.add_argument('out_file', type=argparse.FileType('w'), default=sys.stdin, help='out file (TIFF)') +args = parser.parse_args() + +im1 = readImg(args.input_file1.name) +im2 = readImg(args.input_file2.name) +res = np.concatenate((im1, im2, np.zeros_like(im1)), axis=-1) +skimage.io.imsave(args.out_file.name, res)
--- a/colocalization_viz.xml Sat Feb 09 14:32:01 2019 -0500 +++ b/colocalization_viz.xml Mon Jul 22 07:08:46 2019 -0400 @@ -1,13 +1,15 @@ -<tool id="ip_colocalization" name="Colocalization" version="0.0.6"> +<tool id="ip_colocalization" name="Colocalization" version="0.0.8"> <description>of two segmentation maps</description> <requirements> <requirement type="package" version="0.14.2">scikit-image</requirement> <requirement type="package" version="1.15.4">numpy</requirement> + <requirement type="package" version="5.3.0">pillow</requirement> + <requirement type="package" version="0.15.1">tifffile</requirement> </requirements> <command detect_errors="aggressive"> <![CDATA[ python '$__tool_directory__/colocalization_viz.py' '$input_mask1' '$input_mask2' ./out.png - ]]> + ]]> </command> <inputs> <param name="input_mask1" type="data" format="tiff" label="Mask1 Source File" />