Mercurial > repos > imgteam > overlay_images
changeset 4:37662cbf44b8 draft
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/overlay_images/ commit 85185439087caafebf1c75dc78b61a2a1f181225
| author | imgteam |
|---|---|
| date | Fri, 17 Nov 2023 23:34:57 +0000 |
| parents | 22ff7c705a83 |
| children | 002f7bad3e82 |
| files | overlay_images.py overlay_images.xml test-data/sample1.tif test-data/sample1_uint16.tif test-data/sample1_uint8.tif test-data/test4.png |
| diffstat | 6 files changed, 27 insertions(+), 13 deletions(-) [+] |
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--- a/overlay_images.py Wed Nov 08 19:57:15 2023 +0000 +++ b/overlay_images.py Fri Nov 17 23:34:57 2023 +0000 @@ -33,15 +33,17 @@ 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):
--- a/overlay_images.xml Wed Nov 08 19:57:15 2023 +0000 +++ b/overlay_images.xml Fri Nov 17 23:34:57 2023 +0000 @@ -1,5 +1,9 @@ -<tool id="ip_overlay_images" name="Overlay images" version="0.0.3-3" profile="20.05"> +<tool id="ip_overlay_images" name="Overlay images" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.05"> <description></description> + <macros> + <token name="@TOOL_VERSION@">0.0.4</token> + <token name="@VERSION_SUFFIX@">0</token> + </macros> <edam_operations> <edam_operation>operation_3443</edam_operation> </edam_operations> @@ -81,7 +85,7 @@ <output name="out_tiff" value="test2.tif" ftype="tiff" compare="sim_size" delta_frac="0.1"/> </test> <test expect_num_outputs="1"> - <param name="im1" value="sample1.tif"/> + <param name="im1" value="sample1_uint8.tif"/> <param name="im2" value="mask1.tif"/> <param name="method" value="seg_contour"/> <param name="thickness" value="2"/> @@ -89,8 +93,16 @@ <param name="show_label" value="--show_label"/> <output name="out_png" value="test3.png" ftype="png" compare="sim_size" delta_frac="0.1"/> </test> - <test expect_num_outputs="1"> - <param name="im1" value="sample1.tif"/> + <test expect_num_outputs="1"><!-- segemtation 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"/> + <output name="out_png" value="test4.png" ftype="png" compare="sim_size" delta_frac="0.1"/> + </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"/> @@ -99,9 +111,9 @@ </test> </tests> <help> - **What it does** - - This tool overlays two image to visualize 1) image blending, 2) colocalization, or 3) a segmentation mask over an image. + <![CDATA[ + This tool overlays two image to visualize 1) image blending, 2) colocalization, or 3) a segmentation mask over an image. + ]]> </help> <citations> <citation type="doi">10.1016/j.jbiotec.2017.07.019</citation>