| Previous changeset 8:0b5ddf7b2924 (2026-01-04) Next changeset 10:519fad2c552a (2026-01-06) |
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Commit message:
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_feature_extraction/ commit 5bf032c4908e344099fba24e914bd26367d24a90 |
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modified:
2d_feature_extraction.xml test-data/output/input11.tsv test-data/output/input12.tsv test-data/output/input13-axis_major_length.tsv test-data/output/input13-axis_minor_length.tsv test-data/output/input13-bbox.tsv test-data/output/input13-centroid.tsv test-data/output/input13-equivalent_diameter_area.tsv test-data/output/input13-inertia_tensor_eigvals.tsv test-data/output/input13-moments.tsv test-data/output/input13-moments_hu.tsv test-data/output/input13-orientation.tsv test-data/output/input9.tsv |
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| diff -r 0b5ddf7b2924 -r 45076fd788c9 2d_feature_extraction.xml --- a/2d_feature_extraction.xml Sun Jan 04 20:56:49 2026 +0000 +++ b/2d_feature_extraction.xml Mon Jan 05 14:36:17 2026 +0000 |
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| @@ -37,7 +37,7 @@ <param name="intensities" value="input/input1_uint8.tiff"/> <param name="features" value="@FEATURE@"/> </conditional> - <output name="output" ftype="tabular" value="output/input13-@FEATURE@.tsv"/> + <output name="output" ftype="tabular" value="output/input13-@FEATURE@.tsv" compare="re_match"/> </test> </xml> </macros> @@ -132,7 +132,7 @@ <param name="mode" value="without-intensities"/> <param name="features" value="label,area,area_convex,solidity"/> </conditional> - <output name="output" ftype="tabular" value="output/input12.tsv"/> + <output name="output" ftype="tabular" value="output/input12.tsv" compare="re_match"/> </test> <test> <param name="labels" value="input/input11.tiff"/> @@ -141,7 +141,7 @@ <param name="intensities" value="input/input1_uint8.tiff"/> <param name="features" value="area,mean_intensity,perimeter"/> </conditional> - <output name="output" ftype="tabular" value="output/input11.tsv"/> + <output name="output" ftype="tabular" value="output/input11.tsv" compare="re_match"/> </test> <!-- Single-channel 2-D Zarr (isolated features, verify that Dask arrays are converted to NumPy arrays whenever necessary) --> <expand macro="zarr-isolated-feature-test" feature="area"/> @@ -172,7 +172,7 @@ <param name="intensities" value="input/input8_zyx.zarr"/> <param name="features" value="area,area_convex,area_filled,axis_major_length,axis_minor_length,bbox,centroid,eccentricity,equivalent_diameter_area,euler_number,extent,inertia_tensor_eigvals,moments,moments_hu,orientation,perimeter,solidity,max_intensity,mean_intensity,min_intensity"/> </conditional> - <output name="output" ftype="tabular" value="output/input9.tsv"/> + <output name="output" ftype="tabular" value="output/input9.tsv" compare="re_match"/> <assert_stdout> <has_line line='Skip feature that is not available for 3-D images: "eccentricity"'/> <has_line line='Skip feature that is not available for 3-D images: "moments_hu"'/> |
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| diff -r 0b5ddf7b2924 -r 45076fd788c9 test-data/output/input11.tsv --- a/test-data/output/input11.tsv Sun Jan 04 20:56:49 2026 +0000 +++ b/test-data/output/input11.tsv Mon Jan 05 14:36:17 2026 +0000 |
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| @@ -1,2 +1,2 @@ area mean_intensity perimeter -20825.0 129.36364945978391 590.399061660723 +20825.0 129.3636[0-9]+ 590.3990[0-9]+ |
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| diff -r 0b5ddf7b2924 -r 45076fd788c9 test-data/output/input12.tsv --- a/test-data/output/input12.tsv Sun Jan 04 20:56:49 2026 +0000 +++ b/test-data/output/input12.tsv Mon Jan 05 14:36:17 2026 +0000 |
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| @@ -1,24 +1,24 @@ label area area_convex solidity -1 28.0 29.0 0.9655172413793104 +1 28.0 29.0 0.9655[0-9]+ 2 17.0 17.0 1.0 3 9.0 9.0 1.0 4 15.0 15.0 1.0 -5 23.0 26.0 0.8846153846153846 +5 23.0 26.0 0.8846[0-9]+ 6 21.0 21.0 1.0 7 11.0 11.0 1.0 8 60.0 80.0 0.75 -9 58.0 86.0 0.6744186046511628 +9 58.0 86.0 0.6744[0-9]+ 10 22.0 22.0 1.0 11 2.0 2.0 1.0 -12 41.0 42.0 0.9761904761904762 -13 74.0 102.0 0.7254901960784313 +12 41.0 42.0 0.9761[0-9]+ +13 74.0 102.0 0.7254[0-9]+ 14 9.0 9.0 1.0 15 8.0 8.0 1.0 -16 27.0 28.0 0.9642857142857143 +16 27.0 28.0 0.9642[0-9]+ 17 6.0 6.0 1.0 -18 61.0 73.0 0.8356164383561644 -19 55.0 72.0 0.7638888888888888 -20 18.0 23.0 0.782608695652174 +18 61.0 73.0 0.8356[0-9]+ +19 55.0 72.0 0.7638[0-9]+ +20 18.0 23.0 0.7826[0-9]+ 21 1.0 1.0 1.0 22 4.0 4.0 1.0 23 10.0 10.0 1.0 |
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| diff -r 0b5ddf7b2924 -r 45076fd788c9 test-data/output/input13-axis_major_length.tsv --- a/test-data/output/input13-axis_major_length.tsv Sun Jan 04 20:56:49 2026 +0000 +++ b/test-data/output/input13-axis_major_length.tsv Mon Jan 05 14:36:17 2026 +0000 |
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| @@ -1,3 +1,3 @@ axis_major_length -57.723478758647246 -57.723478758647246 +57.7234[0-9]+ +57.7234[0-9]+ |
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| diff -r 0b5ddf7b2924 -r 45076fd788c9 test-data/output/input13-axis_minor_length.tsv --- a/test-data/output/input13-axis_minor_length.tsv Sun Jan 04 20:56:49 2026 +0000 +++ b/test-data/output/input13-axis_minor_length.tsv Mon Jan 05 14:36:17 2026 +0000 |
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| @@ -1,3 +1,3 @@ axis_minor_length -57.723478758647246 -57.723478758647246 +57.7234[0-9]+ +57.7234[0-9]+ |
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| diff -r 0b5ddf7b2924 -r 45076fd788c9 test-data/output/input13-bbox.tsv --- a/test-data/output/input13-bbox.tsv Sun Jan 04 20:56:49 2026 +0000 +++ b/test-data/output/input13-bbox.tsv Mon Jan 05 14:36:17 2026 +0000 |
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| @@ -1,3 +1,3 @@ bbox -[50, 60, 100, 110] -[150, 160, 200, 210] +\[50, 60, 100, 110\] +\[150, 160, 200, 210\] |
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| diff -r 0b5ddf7b2924 -r 45076fd788c9 test-data/output/input13-centroid.tsv --- a/test-data/output/input13-centroid.tsv Sun Jan 04 20:56:49 2026 +0000 +++ b/test-data/output/input13-centroid.tsv Mon Jan 05 14:36:17 2026 +0000 |
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| @@ -1,3 +1,3 @@ centroid -[74.5, 84.5] -[174.5, 184.5] +\[74.5, 84.5\] +\[174.5, 184.5\] |
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| diff -r 0b5ddf7b2924 -r 45076fd788c9 test-data/output/input13-equivalent_diameter_area.tsv --- a/test-data/output/input13-equivalent_diameter_area.tsv Sun Jan 04 20:56:49 2026 +0000 +++ b/test-data/output/input13-equivalent_diameter_area.tsv Mon Jan 05 14:36:17 2026 +0000 |
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| @@ -1,3 +1,3 @@ equivalent_diameter_area -56.41895835477563 -56.41895835477563 +56.4189[0-9]+ +56.4189[0-9]+ |
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| diff -r 0b5ddf7b2924 -r 45076fd788c9 test-data/output/input13-inertia_tensor_eigvals.tsv --- a/test-data/output/input13-inertia_tensor_eigvals.tsv Sun Jan 04 20:56:49 2026 +0000 +++ b/test-data/output/input13-inertia_tensor_eigvals.tsv Mon Jan 05 14:36:17 2026 +0000 |
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| @@ -1,3 +1,3 @@ inertia_tensor_eigvals -[208.25, 208.25] -[208.25, 208.25] +\[208.25, 208.25\] +\[208.25, 208.25\] |
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| diff -r 0b5ddf7b2924 -r 45076fd788c9 test-data/output/input13-moments.tsv --- a/test-data/output/input13-moments.tsv Sun Jan 04 20:56:49 2026 +0000 +++ b/test-data/output/input13-moments.tsv Mon Jan 05 14:36:17 2026 +0000 |
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| @@ -1,3 +1,3 @@ moments -[[2500.0, 61250.0, 2021250.0, 75031250.0], [61250.0, 1500625.0, 49520625.0, 1838265625.0], [2021250.0, 49520625.0, 1634180625.0, 60662765625.0], [75031250.0, 1838265625.0, 60662765625.0, 2251875390625.0]] -[[2500.0, 61250.0, 2021250.0, 75031250.0], [61250.0, 1500625.0, 49520625.0, 1838265625.0], [2021250.0, 49520625.0, 1634180625.0, 60662765625.0], [75031250.0, 1838265625.0, 60662765625.0, 2251875390625.0]] +\[\[2500.0, 61250.0, 2021250.0, 75031250.0\], \[61250.0, 1500625.0, 49520625.0, 1838265625.0\], \[2021250.0, 49520625.0, 1634180625.0, 60662765625.0\], \[75031250.0, 1838265625.0, 60662765625.0, 2251875390625.0\]\] +\[\[2500.0, 61250.0, 2021250.0, 75031250.0\], \[61250.0, 1500625.0, 49520625.0, 1838265625.0\], \[2021250.0, 49520625.0, 1634180625.0, 60662765625.0\], \[75031250.0, 1838265625.0, 60662765625.0, 2251875390625.0\]\] |
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| diff -r 0b5ddf7b2924 -r 45076fd788c9 test-data/output/input13-moments_hu.tsv --- a/test-data/output/input13-moments_hu.tsv Sun Jan 04 20:56:49 2026 +0000 +++ b/test-data/output/input13-moments_hu.tsv Mon Jan 05 14:36:17 2026 +0000 |
| [ |
| @@ -1,3 +1,3 @@ moments_hu -[0.1666, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0] -[0.1666, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0] +\[0.1666, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0\] +\[0.1666, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0\] |
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| diff -r 0b5ddf7b2924 -r 45076fd788c9 test-data/output/input13-orientation.tsv --- a/test-data/output/input13-orientation.tsv Sun Jan 04 20:56:49 2026 +0000 +++ b/test-data/output/input13-orientation.tsv Mon Jan 05 14:36:17 2026 +0000 |
| [ |
| @@ -1,3 +1,3 @@ orientation --0.7853981633974483 --0.7853981633974483 +-0.7853[0-9]+ +-0.7853[0-9]+ |
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| diff -r 0b5ddf7b2924 -r 45076fd788c9 test-data/output/input9.tsv --- a/test-data/output/input9.tsv Sun Jan 04 20:56:49 2026 +0000 +++ b/test-data/output/input9.tsv Mon Jan 05 14:36:17 2026 +0000 |
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| @@ -1,2 +1,2 @@ area area_convex area_filled axis_major_length axis_minor_length bbox centroid equivalent_diameter_area euler_number extent inertia_tensor_eigvals moments perimeter solidity max_intensity mean_intensity min_intensity -10076.0 19452.0 10076.0 141.5372589111894 2.2275554354875524 [0, 0, 0, 2, 100, 100] [0.4791583961889639, 51.02153632393807, 55.51121476776498] 26.797637758267182 -1 0.5038 [1633.5242978752312, 1001.887883165562, 632.1326150314862] [[[10076.0, 559331.0, 39680985.0, 3075710795.0], [514093.0, 26719026.0, 1828782204.0, 137703070104.0], [34057349.0, 1680671976.0, 112117199682.0, 8307987945522.0], [2545051621.0, 120295106826.0, 7853098605480.0, 574813269790152.0]], [[4828.0, 278845.0, 20126387.0, 1574048161.0], [246982.0, 13386366.0, 940613844.0, 72136219614.0], [16531236.0, 855530424.0, 59225271630.0, 4513705336536.0], [1248767206.0, 62249971170.0, 4259056106556.0, 323493844156146.0]], [[4828.0, 278845.0, 20126387.0, 1574048161.0], [246982.0, 13386366.0, 940613844.0, 72136219614.0], [16531236.0, 855530424.0, 59225271630.0, 4513705336536.0], [1248767206.0, 62249971170.0, 4259056106556.0, 323493844156146.0]], [[4828.0, 278845.0, 20126387.0, 1574048161.0], [246982.0, 13386366.0, 940613844.0, 72136219614.0], [16531236.0, 855530424.0, 59225271630.0, 4513705336536.0], [1248767206.0, 62249971170.0, 4259056106556.0, 323493844156146.0]]] 10076 0.5179930084310097 999.8037382034536 523.4422397609023 0.11458563869848337 +10076.0 19452.0 10076.0 141.5372[0-9]+ 2.2275[0-9]+ \[0, 0, 0, 2, 100, 100\] \[0.4791[0-9]+, 51.0215[0-9]+, 55.5112[0-9]+\] 26.7976[0-9]+ -1 0.5038 \[1633.5242[0-9]+, 1001.8878[0-9]+, 632.1326[0-9]+\] \[\[\[10076.0, 559331.0, 39680985.0, 3075710795.0\], \[514093.0, 26719026.0, 1828782204.0, 137703070104.0\], \[34057349.0, 1680671976.0, 112117199682.0, 8307987945522.0\], \[2545051621.0, 120295106826.0, 7853098605480.0, 574813269790152.0\]\], \[\[4828.0, 278845.0, 20126387.0, 1574048161.0\], \[246982.0, 13386366.0, 940613844.0, 72136219614.0\], \[16531236.0, 855530424.0, 59225271630.0, 4513705336536.0\], \[1248767206.0, 62249971170.0, 4259056106556.0, 323493844156146.0\]\], \[\[4828.0, 278845.0, 20126387.0, 1574048161.0\], \[246982.0, 13386366.0, 940613844.0, 72136219614.0\], \[16531236.0, 855530424.0, 59225271630.0, 4513705336536.0\], \[1248767206.0, 62249971170.0, 4259056106556.0, 323493844156146.0\]\], \[\[4828.0, 278845.0, 20126387.0, 1574048161.0\], \[246982.0, 13386366.0, 940613844.0, 72136219614.0\], \[16531236.0, 855530424.0, 59225271630.0, 4513705336536.0\], \[1248767206.0, 62249971170.0, 4259056106556.0, 323493844156146.0\]\]\] 10076 0.5179[0-9]+ 999.8037[0-9]+ 523.4422[0-9]+ 0.1145[0-9]+ |