Mercurial > repos > imgteam > overlay_images
changeset 3:eb173a1fabc4 draft default tip
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/overlay_images/ commit 574caf027453f080a7f86f80eae9775ed1c8afa0
| author | imgteam |
|---|---|
| date | Mon, 23 Sep 2024 10:26:14 +0000 |
| parents | f42d21fe65d8 |
| children | |
| files | creators.xml overlay_images.py overlay_images.xml test-data/sample1.tif test-data/sample1_uint16.tif test-data/sample1_uint8.tif test-data/sample1_uint8_rgb.png test-data/test3.png test-data/test3.tif test-data/test4.png test-data/test4.tif test-data/test5.png tests.xml |
| diffstat | 13 files changed, 214 insertions(+), 40 deletions(-) [+] |
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--- /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 @@ +<macros> + + <xml name="creators/bmcv"> + <organization name="Biomedical Computer Vision Group, Heidelberg Universtiy" alternateName="BMCV" url="http://www.bioquant.uni-heidelberg.de/research/groups/biomedical_computer_vision.html" /> + <yield /> + </xml> + + <xml name="creators/rmassei"> + <person givenName="Riccardo" familyName="Massei"/> + <yield/> + </xml> + + <xml name="creators/alliecreason"> + <person givenName="Allison" familyName="Creason"/> + <yield/> + </xml> + + <xml name="creators/bugraoezdemir"> + <person givenName="Bugra" familyName="Oezdemir"/> + <yield/> + </xml> + + <xml name="creators/thawn"> + <person givenName="Till" familyName="Korten"/> + <yield/> + </xml> + +</macros>
--- 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')
--- 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 @@ -<tool id="ip_overlay_images" name="Overlay Images" version="0.0.3" profile="20.05"> - <description>for visualization</description> +<tool id="ip_overlay_images" name="Overlay images" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.05"> + <description></description> + <macros> + <import>creators.xml</import> + <import>tests.xml</import> + <token name="@TOOL_VERSION@">0.0.4</token> + <token name="@VERSION_SUFFIX@">4</token> + </macros> + <creator> + <expand macro="creators/bmcv"/> + <expand macro="creators/thawn"/> + </creator> + <edam_operations> + <edam_operation>operation_3443</edam_operation> + </edam_operations> + <xrefs> + <xref type="bio.tools">galaxy_image_analysis</xref> + </xrefs> <requirements> <requirement type="package" version="0.18.1">scikit-image</requirement> <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="1.21">numpy</requirement> + <requirement type="package" version="10.4.0">pillow</requirement> + <requirement type="package" version="0.1">giatools</requirement> </requirements> <command detect_errors="aggressive"> <![CDATA[ python '$__tool_directory__/overlay_images.py' - '$method_option.im1' '$method_option.im2' ./output.tif + '$method_option.im1' '$method_option.im2' + #if $method_option.method == "seg_contour" + ./output.png + #else + ./output.tif + #end if --method $method_option.method #if $method_option.method == "blending" --alpha $method_option.alpha @@ -23,23 +46,23 @@ </command> <inputs> <conditional name="method_option"> - <param name="method" type="select" label="How to visualize the overlay?"> + <param name="method" type="select" label="Type of the overlay"> <option value="coloc_vis" selected="True">Colocalization</option> - <option value="blending">Blending</option> - <option value="seg_contour">Segmentation mask over image</option> + <option value="blending">Linear blending</option> + <option value="seg_contour">Segmentation contours over image</option> </param> <when value="coloc_vis"> - <param name="im1" type="data" format="tiff,png" label="Image #1 (red channel)" /> - <param name="im2" type="data" format="tiff,png" label="Image #2 (green channel)" /> + <param name="im1" type="data" format="tiff,png" label="Image 1 (red channel)" /> + <param name="im2" type="data" format="tiff,png" label="Image 2 (green channel)" /> </when> <when value="blending"> - <param name="im1" type="data" format="tiff,png" label="Image #1" /> - <param name="im2" type="data" format="tiff,png" label="Image #2" /> - <param name="alpha" type="float" value="0.5" min="0.0" max="1.0" label="The weight for blending: I_out = (1 - w) * I_1 + w * I_2."/> + <param name="im1" type="data" format="tiff,png" label="Image 1" /> + <param name="im2" type="data" format="tiff,png" label="Image 2" /> + <param name="alpha" type="float" value="0.5" min="0.0" max="1.0" label="The weight for blending: result = (1 - weight) * image1 + weight * image2." /> </when> <when value="seg_contour"> - <param name="im1" type="data" format="tiff,png" label="Image" /> - <param name="im2" type="data" format="tiff,png" label="Label image" /> + <param name="im1" type="data" format="tiff,png" label="Intensity image" /> + <param name="im2" type="data" format="tiff,png" label="Label map" /> <param name="thickness" type="integer" value="2" min="1" label="Contour thickness (in pixels)" /> <param name="color" type="color" value="#ff0000" label="Contour color"/> <param argument="--show_label" type="boolean" checked='false' truevalue="--show_label" falsevalue="" label="Show labels" /> @@ -48,45 +71,70 @@ </conditional> </inputs> <outputs> - <data format="tiff" name="out" from_work_dir="output.tif" /> + <data format="tiff" name="out_tiff" from_work_dir="output.tif" label="${tool.name} on ${on_string} output:tiff"> + <filter>method_option['method'] != 'seg_contour'</filter> + </data> + <data format="png" name="out_png" from_work_dir="output.png" label="${tool.name} on ${on_string} output:png"> + <filter>method_option['method'] == 'seg_contour'</filter> + </data> </outputs> <tests> - <test> + <test expect_num_outputs="1"> <param name="im1" value="mask1.tif"/> <param name="im2" value="mask1r.tif"/> <param name="method" value="coloc_vis"/> - <output name="out" value="test1.tif" ftype="tiff" compare="sim_size" delta_frac="0.1"/> + <expand macro="tests/intensity_image_diff" name="out_tiff" value="test1.tif" ftype="tiff"/> </test> - <test> + <test expect_num_outputs="1"> <param name="im1" value="mask1.tif"/> <param name="im2" value="mask1r.tif"/> <param name="method" value="blending"/> <param name="alpha" value="0.3"/> - <output name="out" value="test2.tif" ftype="tiff" compare="sim_size" delta_frac="0.1"/> + <expand macro="tests/intensity_image_diff" name="out_tiff" value="test2.tif" ftype="tiff"/> </test> - <test> - <param name="im1" value="sample1.tif"/> + <test expect_num_outputs="1"> + <param name="im1" value="sample1_uint8.tif"/> <param name="im2" value="mask1.tif"/> <param name="method" value="seg_contour"/> <param name="thickness" value="2"/> <param name="color" value="#ff0000"/> <param name="show_label" value="--show_label"/> - <output name="out" value="test3.tif" ftype="tiff" compare="sim_size" delta_frac="0.1"/> + <expand macro="tests/intensity_image_diff" name="out_png" value="test3.png" ftype="png"/> </test> - <test> - <param name="im1" value="sample1.tif"/> + <test expect_num_outputs="1"><!-- segmentation overlay, 8bit test --> + <param name="im1" value="sample1_uint8.tif"/> + <param name="im2" value="mask2.tif"/> + <param name="method" value="seg_contour"/> + <param name="thickness" value="2"/> + <param name="color" value="#ff0000"/> + <expand macro="tests/intensity_image_diff" name="out_png" value="test4.png" ftype="png"/> + </test> + <test expect_num_outputs="1"><!-- segmentation overlay, 16bit test --> + <param name="im1" value="sample1_uint16.tif"/> <param name="im2" value="mask2.tif"/> <param name="method" value="seg_contour"/> <param name="thickness" value="2"/> <param name="color" value="#ff0000"/> - <output name="out" value="test4.tif" ftype="tiff" compare="sim_size" delta_frac="0.1"/> + <expand macro="tests/intensity_image_diff" name="out_png" value="test4.png" ftype="png" eps="1"/> + </test> + <test expect_num_outputs="1"><!-- segmentation overlay, 8bit RGB test --> + <param name="im1" value="sample1_uint8_rgb.png"/> + <param name="im2" value="mask2.tif"/> + <param name="method" value="seg_contour"/> + <param name="thickness" value="2"/> + <param name="color" value="#ff0000"/> + <expand macro="tests/intensity_image_diff" name="out_png" value="test5.png" ftype="png"/> </test> </tests> - <help> - **What it does** + <help><![CDATA[ + + **Overlays two images for visualization.** - This tool overlays two image to visualize 1) image blending, 2) colocalization, or 3) a segmentation mask over an image. - </help> + 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. + + ]]></help> <citations> <citation type="doi">10.1016/j.jbiotec.2017.07.019</citation> </citations>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tests.xml Mon Sep 23 10:26:14 2024 +0000 @@ -0,0 +1,95 @@ +<macros> + + <!-- Macros for verification of image outputs --> + + <xml + name="tests/binary_image_diff" + tokens="name,value,ftype,metric,eps" + token_metric="mae" + token_eps="0.01"> + + <output name="@NAME@" value="@VALUE@" ftype="@FTYPE@" compare="image_diff" metric="@METRIC@" eps="@EPS@" pin_labels="0"> + <assert_contents> + <has_image_n_labels n="2"/> + <yield/> + </assert_contents> + </output> + + </xml> + + <xml + name="tests/label_image_diff" + tokens="name,value,ftype,metric,eps,pin_labels" + token_metric="iou" + token_eps="0.01" + token_pin_labels="0"> + + <output name="@NAME@" value="@VALUE@" ftype="@FTYPE@" compare="image_diff" metric="@METRIC@" eps="@EPS@" pin_labels="@PIN_LABELS@"> + <assert_contents> + <yield/> + </assert_contents> + </output> + + </xml> + + <xml + name="tests/intensity_image_diff" + tokens="name,value,ftype,metric,eps" + token_metric="rms" + token_eps="0.01"> + + <output name="@NAME@" value="@VALUE@" ftype="@FTYPE@" compare="image_diff" metric="@METRIC@" eps="@EPS@"> + <assert_contents> + <yield/> + </assert_contents> + </output> + + </xml> + + <!-- Variants of the above for verification of collection elements --> + + <xml + name="tests/binary_image_diff/element" + tokens="name,value,ftype,metric,eps" + token_metric="mae" + token_eps="0.01"> + + <element name="@NAME@" value="@VALUE@" ftype="@FTYPE@" compare="image_diff" metric="@METRIC@" eps="@EPS@" pin_labels="0"> + <assert_contents> + <has_image_n_labels n="2"/> + <yield/> + </assert_contents> + </element> + + </xml> + + <xml + name="tests/label_image_diff/element" + tokens="name,value,ftype,metric,eps" + token_metric="iou" + token_eps="0.01" + token_pin_labels="0"> + + <element name="@NAME@" value="@VALUE@" ftype="@FTYPE@" compare="image_diff" metric="@METRIC@" eps="@EPS@" pin_labels="@PIN_LABELS@"> + <assert_contents> + <yield/> + </assert_contents> + </element> + + </xml> + + <xml + name="tests/intensity_image_diff/element" + tokens="name,value,ftype,metric,eps" + token_metric="rms" + token_eps="0.01"> + + <element name="@NAME@" value="@VALUE@" ftype="@FTYPE@" compare="image_diff" metric="@METRIC@" eps="@EPS@"> + <assert_contents> + <yield/> + </assert_contents> + </element> + + </xml> + +</macros>