# HG changeset patch
# User imgteam
# Date 1727087174 0
# Node ID eb173a1fabc4ebfe74c661a5103bbd97519fef0b
# Parent f42d21fe65d8769c12762208c77f731dd96cb5af
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/overlay_images/ commit 574caf027453f080a7f86f80eae9775ed1c8afa0
diff -r f42d21fe65d8 -r eb173a1fabc4 creators.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/creators.xml Mon Sep 23 10:26:14 2024 +0000
@@ -0,0 +1,28 @@
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diff -r f42d21fe65d8 -r eb173a1fabc4 overlay_images.py
--- a/overlay_images.py Thu Aug 10 07:29:24 2023 +0000
+++ b/overlay_images.py Mon Sep 23 10:26:14 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]:
@@ -33,15 +34,17 @@
img = np.squeeze(img)
assert img.ndim == 2 or (img.ndim == 3 and img.shape[-1] in (3, 4))
if str(img.dtype).startswith('float'):
- img = np.round(img * 255).astype('uint8')
- elif img.dtype == 'uint16':
- img = img // 256
- elif img.dtype != 'uint8':
+ img = np.round(img * 255).astype(np.uint8)
+ elif img.dtype == np.uint16:
+ img = (img // 256).astype(np.uint8)
+ elif img.dtype != np.uint8:
raise ValueError(f'unknown dtype: {img.dtype}')
if img.ndim == 2:
- return np.dstack([img] * 3).copy()
+ result = np.dstack([img] * 3).copy()
else:
- return img[:, :, :3].copy()
+ result = img[:, :, :3].copy()
+ assert result.dtype == np.uint8, result.dtype
+ return result
def coloc_vis(in_red_fn, in_green_fn, out_fn):
@@ -59,8 +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:
@@ -70,8 +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')
diff -r f42d21fe65d8 -r eb173a1fabc4 overlay_images.xml
--- a/overlay_images.xml Thu Aug 10 07:29:24 2023 +0000
+++ b/overlay_images.xml Mon Sep 23 10:26:14 2024 +0000
@@ -1,15 +1,38 @@
-
- for visualization
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+ creators.xml
+ tests.xml
+ 0.0.4
+ 4
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+ operation_3443
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+ galaxy_image_analysis
+
scikit-image
matplotlib
tifffile
- numpy
+ numpy
+ pillow
+ giatools
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@@ -48,45 +71,70 @@
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+ method_option['method'] != 'seg_contour'
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+ method_option['method'] == 'seg_contour'
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- **What it does**
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+ This tool overlays two image to visualize *linear image blending*, *colocalization*, or *segmentation contours*
+ over an intensity image. For *image blending* and *colocalization*, the input images must be single-channel 2-D
+ images. For *segmentation contours*, the intensity must be a 2-D single-channel or 2-D RGB image.
+
+ ]]>
10.1016/j.jbiotec.2017.07.019
diff -r f42d21fe65d8 -r eb173a1fabc4 test-data/sample1.tif
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diff -r f42d21fe65d8 -r eb173a1fabc4 test-data/sample1_uint16.tif
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diff -r f42d21fe65d8 -r eb173a1fabc4 test-data/sample1_uint8.tif
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diff -r f42d21fe65d8 -r eb173a1fabc4 test-data/sample1_uint8_rgb.png
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diff -r f42d21fe65d8 -r eb173a1fabc4 test-data/test3.png
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diff -r f42d21fe65d8 -r eb173a1fabc4 test-data/test3.tif
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diff -r f42d21fe65d8 -r eb173a1fabc4 test-data/test4.png
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diff -r f42d21fe65d8 -r eb173a1fabc4 test-data/test4.tif
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diff -r f42d21fe65d8 -r eb173a1fabc4 test-data/test5.png
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diff -r f42d21fe65d8 -r eb173a1fabc4 tests.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/tests.xml Mon Sep 23 10:26:14 2024 +0000
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