Mercurial > repos > imgteam > overlay_images
changeset 6:2495f8b2aefd draft
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/overlay_images/ commit c86a1b93cb7732f7331a981d13465653cc1a2790
| author | imgteam |
|---|---|
| date | Wed, 24 Apr 2024 08:12:55 +0000 |
| parents | 002f7bad3e82 |
| children | 8dc02c854048 |
| files | overlay_images.py overlay_images.xml |
| diffstat | 2 files changed, 8 insertions(+), 6 deletions(-) [+] |
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--- a/overlay_images.py Thu Apr 04 15:25:58 2024 +0000 +++ b/overlay_images.py Wed Apr 24 08:12:55 2024 +0000 @@ -7,6 +7,7 @@ import argparse +import giatools.io import matplotlib.colors import matplotlib.pyplot as plt import numpy as np @@ -18,7 +19,7 @@ def read_im_gray(fn): - img = skimage.io.imread(fn) + img = giatools.io.imread(fn) nDims = len(img.shape) assert nDims in [2, 3], 'this tool only supports single 2D images' if nDims == 3 and img.shape[-1] in [3, 4]: @@ -61,8 +62,8 @@ def blending(im1_fn, im2_fn, out_fn, alpha=0.5): - im1 = skimage.io.imread(im1_fn) - im2 = skimage.io.imread(im2_fn) + im1 = giatools.io.imread(im1_fn) + im2 = giatools.io.imread(im2_fn) assert im1.shape == im2.shape, 'Two images should have the same dimension' out_im = (1 - alpha) * im1 + alpha * im2 if len(im1.shape) > 3: @@ -72,8 +73,8 @@ def seg_contour(im1_fn, im2_fn, out_fn, linewidth, color='#ff0000', show_label=False, label_color='#ffff00'): - img = skimage.io.imread(im1_fn) - labels = skimage.io.imread(im2_fn) + img = giatools.io.imread(im1_fn) + labels = giatools.io.imread(im2_fn) result = get_rgb8_copy(img) cp = ContourPaint(labels, linewidth, where='center')
--- a/overlay_images.xml Thu Apr 04 15:25:58 2024 +0000 +++ b/overlay_images.xml Wed Apr 24 08:12:55 2024 +0000 @@ -4,7 +4,7 @@ <import>creators.xml</import> <import>tests.xml</import> <token name="@TOOL_VERSION@">0.0.4</token> - <token name="@VERSION_SUFFIX@">1</token> + <token name="@VERSION_SUFFIX@">2</token> </macros> <creator> <expand macro="creators/bmcv"/> @@ -21,6 +21,7 @@ <requirement type="package" version="3.3.4">matplotlib</requirement> <requirement type="package" version="2020.10.1">tifffile</requirement> <requirement type="package" version="1.20.2">numpy</requirement> + <requirement type="package" version="0.1">giatools</requirement> </requirements> <command detect_errors="aggressive"> <![CDATA[