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Commit message:
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_feature_extraction/ commit bb2d58ed37d8eb09583b86e3cdd9f5d1b56c42a0 |
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2d_feature_extraction.py 2d_feature_extraction.xml |
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test-data/input/README.md test-data/input/input10.zarr/0/c/0/0/0 test-data/input/input10.zarr/0/c/1/0/0 test-data/input/input10.zarr/0/zarr.json test-data/input/input10.zarr/1/c/0/0/0 test-data/input/input10.zarr/1/c/1/0/0 test-data/input/input10.zarr/1/zarr.json test-data/input/input10.zarr/2/c/0/0/0 test-data/input/input10.zarr/2/c/1/0/0 test-data/input/input10.zarr/2/zarr.json test-data/input/input10.zarr/3/c/0/0/0 test-data/input/input10.zarr/3/c/1/0/0 test-data/input/input10.zarr/3/zarr.json test-data/input/input10.zarr/4/c/1/0/0 test-data/input/input10.zarr/4/zarr.json test-data/input/input10.zarr/zarr.json test-data/input/input11.tiff test-data/input/input12.png test-data/input/input13.zarr/0/c/0/0 test-data/input/input13.zarr/0/zarr.json test-data/input/input13.zarr/zarr.json test-data/input/input1_uint8.tiff test-data/input/input3_uint16.tiff test-data/input/input9.zarr/0/c/0/0/0 test-data/input/input9.zarr/0/c/1/0/0 test-data/input/input9.zarr/0/zarr.json test-data/input/input9.zarr/1/c/0/0/0 test-data/input/input9.zarr/1/c/1/0/0 test-data/input/input9.zarr/1/zarr.json test-data/input/input9.zarr/2/c/0/0/0 test-data/input/input9.zarr/2/c/1/0/0 test-data/input/input9.zarr/2/zarr.json test-data/input/input9.zarr/3/c/0/0/0 test-data/input/input9.zarr/3/c/1/0/0 test-data/input/input9.zarr/3/zarr.json test-data/input/input9.zarr/4/c/0/0/0 test-data/input/input9.zarr/4/c/1/0/0 test-data/input/input9.zarr/4/zarr.json test-data/input/input9.zarr/zarr.json test-data/input/ome-zarr-examples/LICENSE test-data/input/ome-zarr-examples/image-03.zarr/.zattrs test-data/input/ome-zarr-examples/image-03.zarr/.zgroup test-data/input/ome-zarr-examples/image-03.zarr/0/.zarray test-data/input/ome-zarr-examples/image-03.zarr/0/0/0/0 test-data/input/ome-zarr-examples/image-03.zarr/0/0/1/0 test-data/input/ome-zarr-examples/image-03.zarr/0/1/0/0 test-data/input/ome-zarr-examples/image-03.zarr/0/1/1/0 test-data/input/ome-zarr-examples/image-03.zarr/labels/.zattrs test-data/input/ome-zarr-examples/image-03.zarr/labels/.zgroup test-data/output/input11.tsv test-data/output/input12.tsv test-data/output/input13-area.tsv test-data/output/input13-area_convex.tsv test-data/output/input13-area_filled.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-eccentricity.tsv test-data/output/input13-equivalent_diameter_area.tsv test-data/output/input13-euler_number.tsv test-data/output/input13-extent.tsv test-data/output/input13-inertia_tensor_eigvals.tsv test-data/output/input13-max_intensity.tsv test-data/output/input13-mean_intensity.tsv test-data/output/input13-min_intensity.tsv test-data/output/input13-moments.tsv test-data/output/input13-moments_hu.tsv test-data/output/input13-orientation.tsv test-data/output/input13-perimeter.tsv test-data/output/input13-solidity.tsv test-data/output/input9.tsv validators.xml |
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test-data/input.tiff test-data/out.tsv |
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| diff -r 6a2b26c297a4 -r 0b5ddf7b2924 2d_feature_extraction.py --- a/2d_feature_extraction.py Wed Dec 17 11:23:18 2025 +0000 +++ b/2d_feature_extraction.py Sun Jan 04 20:56:49 2026 +0000 |
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| b'@@ -1,127 +1,115 @@\n-import argparse\n-\n-import giatools.io\n+import giatools\n import numpy as np\n import pandas as pd\n-import skimage.feature\n+import scipy.ndimage as ndi\n import skimage.measure\n-import skimage.morphology\n-import skimage.segmentation\n+\n+# Fail early if an optional backend is not available\n+giatools.require_backend(\'omezarr\')\n+\n+\n+def surface(labels: np.ndarray, label: int) -> int:\n+ """\n+ Ad-hoc implementation for computation of the "perimeter" of an object in 3D (that is a surface).\n+ """\n+ assert labels.ndim == 3 # sanity check\n+\n+ # Create 3-D structuring element with 4-connectivity\n+ selem = np.zeros((3, 3, 3), bool)\n+ for ijk in np.ndindex(*selem.shape):\n+ if (np.array(ijk) == 1).sum() >= 2:\n+ selem[*ijk] = True # noqa: E999\n+ assert selem.sum() == 7 # sanity check\n+\n+ # Compute the area of the surface\n+ cc = (labels == label)\n+ cc_interior = ndi.binary_erosion(cc, selem)\n+ surface = np.logical_xor(cc, cc_interior)\n+ return surface.sum() # number of voxels on the surface of the object\n+\n+\n+def compute_if_dask(obj):\n+ """\n+ Return the computed object or array if it is a Dask array or deferred computable Dask object.\n+ """\n+ return obj.compute() if hasattr(obj, \'compute\') else obj\n \n \n if __name__ == \'__main__\':\n+ tool = giatools.ToolBaseplate()\n+ tool.add_input_image(\'labels\')\n+ tool.add_input_image(\'intensities\', required=False)\n+ tool.parser.add_argument(\'--output\', type=str)\n+ tool.parse_args()\n \n- parser = argparse.ArgumentParser(description=\'Extract image features\')\n+ # Validate the input image\n+ try:\n+ label_image = tool.args.input_images[\'labels\']\n+ if any(label_image.shape[label_image.axes.index(axis)] > 1 for axis in label_image.axes if axis not in \'ZYX\'):\n+ raise ValueError(f\'This tool is not applicable to images with {label_image.original_axes} axes.\')\n+\n+ # Extract the image features\n+ for section in tool.run(\'ZYX\'): # the validation code above guarantees that we will have only a single iteration\n+ df = pd.DataFrame()\n \n- # TODO create factory for boilerplate code\n- features = parser.add_argument_group(\'compute features\')\n- features.add_argument(\'--all\', dest=\'all_features\', action=\'store_true\')\n- features.add_argument(\'--label\', dest=\'add_label\', action=\'store_true\')\n- features.add_argument(\'--patches\', dest=\'add_roi_patches\', action=\'store_true\')\n- features.add_argument(\'--max_intensity\', dest=\'max_intensity\', action=\'store_true\')\n- features.add_argument(\'--mean_intensity\', dest=\'mean_intensity\', action=\'store_true\')\n- features.add_argument(\'--min_intensity\', dest=\'min_intensity\', action=\'store_true\')\n- features.add_argument(\'--moments_hu\', dest=\'moments_hu\', action=\'store_true\')\n- features.add_argument(\'--centroid\', dest=\'centroid\', action=\'store_true\')\n- features.add_argument(\'--bbox\', dest=\'bbox\', action=\'store_true\')\n- features.add_argument(\'--area\', dest=\'area\', action=\'store_true\')\n- features.add_argument(\'--filled_area\', dest=\'filled_area\', action=\'store_true\')\n- features.add_argument(\'--convex_area\', dest=\'convex_area\', action=\'store_true\')\n- features.add_argument(\'--perimeter\', dest=\'perimeter\', action=\'store_true\')\n- features.add_argument(\'--extent\', dest=\'extent\', action=\'store_true\')\n- features.add_argument(\'--eccentricity\', dest=\'eccentricity\', action=\'store_true\')\n- features.add_argument(\'--equivalent_diameter\', dest=\'equivalent_diameter\', action=\'store_true\')\n- features.add_argument(\'--euler_number\', dest=\'euler_number\', action=\'store_true\')\n- features.add_argument(\'--inertia_tensor_eigvals\', dest=\'inertia_tensor_eigvals\', action=\'store_true\')\n- features.add_argument(\'--major_axis_length\', dest=\'major_axis_length\', action=\'store_true\')\n- features.add_argument(\'--minor_axis_length\', dest=\'minor_axis_length\', action=\'store_true\')\n- features.add_argument(\'--orientati'..b' # Add the object perimeter/surface\n+ elif feature_name == \'perimeter\' and labels_section_data.ndim == 3:\n+ df[\'perimeter\'] = df[\'it\'].map(\n+ lambda ait: surface(labels_section_data, regions[ait].label), # `skimage.measure.regionprops` cannot compute perimeters for 3-D data\n+ )\n \n- if args.centroid or args.all_features:\n- df[\'centroid\'] = df[\'it\'].map(lambda ait: regions[ait].centroid)\n- if args.bbox or args.all_features:\n- df[\'bbox\'] = df[\'it\'].map(lambda ait: regions[ait].bbox)\n- if args.area or args.all_features:\n- df[\'area\'] = df[\'it\'].map(lambda ait: regions[ait].area)\n- if args.filled_area or args.all_features:\n- df[\'filled_area\'] = df[\'it\'].map(lambda ait: regions[ait].filled_area)\n- if args.convex_area or args.all_features:\n- df[\'convex_area\'] = df[\'it\'].map(lambda ait: regions[ait].convex_area)\n- if args.perimeter or args.all_features:\n- df[\'perimeter\'] = df[\'it\'].map(lambda ait: regions[ait].perimeter)\n- if args.extent or args.all_features:\n- df[\'extent\'] = df[\'it\'].map(lambda ait: regions[ait].extent)\n- if args.eccentricity or args.all_features:\n- df[\'eccentricity\'] = df[\'it\'].map(lambda ait: regions[ait].eccentricity)\n- if args.equivalent_diameter or args.all_features:\n- df[\'equivalent_diameter\'] = df[\'it\'].map(lambda ait: regions[ait].equivalent_diameter)\n- if args.euler_number or args.all_features:\n- df[\'euler_number\'] = df[\'it\'].map(lambda ait: regions[ait].euler_number)\n- if args.inertia_tensor_eigvals or args.all_features:\n- df[\'inertia_tensor_eigvals\'] = df[\'it\'].map(lambda ait: regions[ait].inertia_tensor_eigvals)\n- if args.major_axis_length or args.all_features:\n- df[\'major_axis_length\'] = df[\'it\'].map(lambda ait: regions[ait].major_axis_length)\n- if args.minor_axis_length or args.all_features:\n- df[\'minor_axis_length\'] = df[\'it\'].map(lambda ait: regions[ait].minor_axis_length)\n- if args.orientation or args.all_features:\n- df[\'orientation\'] = df[\'it\'].map(lambda ait: regions[ait].orientation)\n- if args.solidity or args.all_features:\n- df[\'solidity\'] = df[\'it\'].map(lambda ait: regions[ait].solidity)\n- if args.moments or args.all_features:\n- df[\'moments\'] = df[\'it\'].map(lambda ait: regions[ait].moments)\n- if args.convexity or args.all_features:\n- perimeter = df[\'it\'].map(lambda ait: regions[ait].perimeter)\n- area = df[\'it\'].map(lambda ait: regions[ait].area)\n- df[\'convexity\'] = area / (perimeter * perimeter)\n+ # Skip features that are not available when processing 3-D images\n+ elif feature_name in (\'eccentricity\', \'moments_hu\', \'orientation\') and labels_section_data.ndim == 3:\n+ print(f\'Skip feature that is not available for 3-D images: "{feature_name}"\')\n+\n+ # Add another feature from `regions` that was computed via `skimage.measure.regionprops`\n+ else:\n+ try:\n+ df[feature_name] = df[\'it\'].map(lambda ait: getattr(regions[ait], feature_name))\n+ except TypeError:\n+ raise ValueError(f\'Unknown feature: "{feature_name}"\')\n \n- del df[\'it\']\n- df.to_csv(out_file, sep=\'\\t\', lineterminator=\'\\n\', index=False)\n+ # Resolve any remaining Dask objects to the actual values (e.g., when processing Zarrs)\n+ df = df.map(compute_if_dask)\n+\n+ # Convert lists/tuples/arrays to lists of plain Python numbers (e.g., float instead of np.float64)\n+ df = df.map(\n+ lambda obj: np.asarray(obj).tolist() if type(obj) in (list, tuple, np.ndarray) else obj,\n+ )\n+\n+ del df[\'it\']\n+ df.to_csv(tool.args.raw_args.output, sep=\'\\t\', lineterminator=\'\\n\', index=False)\n+\n+ except ValueError as err:\n+ exit(err.args[0])\n' |
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| diff -r 6a2b26c297a4 -r 0b5ddf7b2924 2d_feature_extraction.xml --- a/2d_feature_extraction.xml Wed Dec 17 11:23:18 2025 +0000 +++ b/2d_feature_extraction.xml Sun Jan 04 20:56:49 2026 +0000 |
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| b'@@ -2,84 +2,122 @@\n <description>with scikit-image</description>\n <macros>\n <import>creators.xml</import>\n- <token name="@TOOL_VERSION@">0.18.1</token>\n+ <import>validators.xml</import>\n+ <token name="@TOOL_VERSION@">0.25.2</token>\n <token name="@VERSION_SUFFIX@">0</token>\n+ <xml name="features">\n+ <param name="features" type="select" label="Available features" multiple="true" display="checkboxes"\n+ help="*) Features marked with an asterisk are only available for 2-D images (not for 3-D images).">\n+ <option value="label" selected="true">Label from the label map</option>\n+ <yield/>\n+ <option value="area">Area</option>\n+ <option value="area_convex">Convex area</option>\n+ <option value="area_filled">Filled area</option>\n+ <option value="axis_major_length">Major axis length</option>\n+ <option value="axis_minor_length">Minor axis length</option>\n+ <option value="bbox">Bounding box</option>\n+ <option value="centroid">Centroid</option>\n+ <option value="eccentricity">Eccentricity*</option>\n+ <option value="equivalent_diameter_area">Equivalent diameter</option>\n+ <option value="euler_number">Euler number</option>\n+ <option value="extent">Extent</option>\n+ <option value="inertia_tensor_eigvals">Inertia tensor eigenvalues</option>\n+ <option value="moments">Moments</option>\n+ <option value="moments_hu">Moments Hu*</option>\n+ <option value="orientation">Orientation*</option>\n+ <option value="perimeter">Perimeter</option>\n+ <option value="solidity">Solidity</option>\n+ </param>\n+ </xml>\n+ <xml name="zarr-isolated-feature-test" tokens="feature">\n+ <test>\n+ <param name="labels" value="input/input13.zarr"/>\n+ <conditional name="setup">\n+ <param name="mode" value="with-intensities"/>\n+ <param name="intensities" value="input/input1_uint8.tiff"/>\n+ <param name="features" value="@FEATURE@"/>\n+ </conditional>\n+ <output name="output" ftype="tabular" value="output/input13-@FEATURE@.tsv"/>\n+ </test>\n+ </xml>\n </macros>\n <creator>\n <expand macro="creators/bmcv"/>\n+ <expand macro="creators/kostrykin"/>\n </creator>\n <edam_operations>\n <edam_operation>operation_3443</edam_operation>\n </edam_operations>\n <xrefs>\n <xref type="bio.tools">scikit-image</xref>\n+ <xref type="bio.tools">giatools</xref>\n+ <xref type="bio.tools">galaxy_image_analysis</xref>\n <xref type="biii">scikit-image</xref>\n </xrefs>\n <requirements>\n <requirement type="package" version="@TOOL_VERSION@">scikit-image</requirement>\n <requirement type="package" version="2.2.2">pandas</requirement>\n- <requirement type="package" version="1.23.3">numpy</requirement>\n- <requirement type="package" version="2020.10.1">tifffile</requirement>\n- <requirement type="package" version="0.1">giatools</requirement>\n+ <requirement type="package" version="0.7.3">giatools</requirement>\n+ <requirement type="package" version="0.12.2">ome-zarr</requirement>\n </requirements>\n- <command detect_errors="aggressive">\n- <![CDATA[\n- python \'$__tool_directory__/2d_feature_extraction.py\'\n- #if $feature_options[\'features\'] == \'all\'\n- --all\n- #else if $feature_options[\'features\'] == \'select\'\n- ${\' \'.join(str( $feature_options[\'selected_features\'] ).split(\',\'))}\n- #end if\n- #if $use_raw_option[\'use_raw\'] == \'raw_image\'\n- --raw \'$input_raw\'\n- #end if\n- \'$input_label\' \'$output\'\n- ]]>\n- </command>\n+ <required_files>\n+ '..b' value="label"/>\n+ </conditional>\n+ <assert_stderr>\n+ <!-- Rejected by validator -->\n+ <has_n_lines n="0"/>\n+ </assert_stderr>\n+ <assert_stdout>\n+ <!-- Rejected by validator -->\n+ <has_n_lines n="0"/>\n+ </assert_stdout>\n+ </test>\n+ <test expect_failure="true">\n+ <param name="labels" value="input/input10.zarr"/>\n+ <conditional name="setup">\n+ <param name="mode" value="without-intensities"/>\n+ <param name="features" value="label"/>\n+ </conditional>\n+ <assert_stderr>\n+ <!-- Rejected by py-script -->\n+ <has_text text="This tool is not applicable to images with CYX axes."/>\n+ </assert_stderr>\n </test>\n </tests>\n <help>\n \n- **Computes features of a label map.**\n+**Computes features of a label map.**\n+\n+The computed features are computed based solely on the properties of the objects in the label map, or, optionally, by also taking the intensities from a corresponding intensity image into account. Labels with value 0 are ignored.\n+\n+Both images must be 2-D or 3-D single-channel images.\n+\n+Supported Features\n+==================\n+\n+**Area:** Area of the region i.e. number of pixels of the region scaled by pixel-area.\n+\n+**Convex area:** Area of the convex hull image, which is the smallest convex polygon that encloses the region.\n+\n+**Filled area:** Area of the region with all the holes filled in.\n+\n+**Major axis length:** The length of the major axis of the ellipse that has the same normalized second central moments as the region.\n+\n+**Minor axis length:** The length of the minor axis of the ellipse that has the same normalized second central moments as the region.\n+\n+**Bounding box:** Bounding box `(min_row, min_col, max_row, max_col)`. Pixels belonging to the bounding box are in the half-open interval `[min_row; max_row)` and `[min_col; max_col)`.\n \n- The computed features are computed based solely on the properties of the labels in the label map,\n- or, optionally, by also taking the intensities from a corresponding intensity image into account.\n+**Centroid:** Centroid coordinate tuple `(row, col)`.\n+\n+**Eccentricity:** Eccentricity of the ellipse that has the same second-moments as the region. The eccentricity is the ratio of the focal distance (distance between focal points) over the major axis length. The value is in the interval [0, 1). When it is 0, the ellipse becomes a circle.\n+\n+**Equivalent diameter:** The diameter of a circle with the same area as the region.\n+\n+**Euler number:** Euler characteristic of the set of non-zero pixels. Computed as number of connected components subtracted by number of holes (input.ndim connectivity). In 3-D, number of connected components plus number of holes subtracted by number of tunnels.\n+\n+**Extent:** Ratio of pixels in the region to pixels in the total bounding box. Computed as `area / (rows * cols)`.\n \n- The label map must be a 2-D or 3-D single-channel image.\n+**Inertia tensor eigenvalues:** The eigenvalues of the inertia tensor in decreasing order.\n+\n+**Moments:** Spatial moments up to 3rd order: `m_ij = sum{ array(row, col) * row^i * col^j }` where the sum is over the row, col coordinates of the region.\n+\n+**Moments Hu:** Hu moments (translation, scale and rotation invariant).\n+\n+**Orientation:** Angle between the vertical axis (rows) and the major axis of the ellipse that has the same second moments as the region, ranging from `-pi/2` to `pi/2` counter-clockwise.\n+\n+**Perimeter:** Perimeter of object which approximates the contour as a line through the centers of border pixels using a 4-connectivity. Generalizes to the surface of an object in 3-D, which uses a different approximation.\n+\n+**Solidity:** Ratio of pixels in the region to pixels of the convex hull image.\n \n </help>\n <citations>\n' |
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| diff -r 6a2b26c297a4 -r 0b5ddf7b2924 test-data/input/README.md --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/input/README.md Sun Jan 04 20:56:49 2026 +0000 |
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| @@ -0,0 +1,73 @@ +# Overview of the test images + +## Label maps + +### `input9.zarr`: + +- axes: `ZYX` +- resolution: `(2, 100, 100)` +- dtype: `bool` +- binary image +- metadata: + - resolution: `(1.0, 1.0)` + - z-spacing: `1.0` + - unit: `um` + +### `input11.tiff` + +- axes: `YX` +- resolution: `(265, 329)` +- dtype: `uint16` +- binary image + +### `input12.png` + +- axes: `YX` +- resolution: `(58, 64)` +- dtype: `uint8` +- labels: `0...24` + +### `input13.zarr` + +- axes: `YX` +- resolution: `(265, 329)` +- dtype: `uint8` +- labels: `0...2` + +## Intensity images + +### `input1_uint8.tiff`: + +- axes: `YX` +- resolution: `(265, 329)` +- dtype: `uint8` +- metadata: none + +### `input3_uint16.tiff`: + +- axes: `YXC` +- resolution: `(58, 64, 3)` +- dtype: `uint16` +- metadata: + - resolution: `(2.0, 1.0)` + - unit: `mm` + +### `input8_zyx.zarr`: + +- axes: `ZYX` +- resolution: `(2, 100, 100)` +- dtype: `float64` +- metadata: + - resolution: `(1.0, 1.0)` + - z-spacing: `1.0` + - unit: `um` + +### `input10.zarr`: + +- axes: `CYX` +- resolution: `(2, 64, 64)` +- dtype: `uint8` +- metadata: + - resolution: `(1.0, 1.0)` + - z-spacing: `1.0` + - unit: `um` |
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| @@ -0,0 +1,46 @@ +{ + "shape": [ + 2, + 64, + 64 + ], + "data_type": "uint8", + "chunk_grid": { + "name": "regular", + "configuration": { + "chunk_shape": [ + 1, + 100, + 100 + ] + } + }, + "chunk_key_encoding": { + "name": "default", + "configuration": { + "separator": "/" + } + }, + "fill_value": 0, + "codecs": [ + { + "name": "bytes" + }, + { + "name": "zstd", + "configuration": { + "level": 0, + "checksum": false + } + } + ], + "attributes": {}, + "dimension_names": [ + "c", + "y", + "x" + ], + "zarr_format": 3, + "node_type": "array", + "storage_transformers": [] +} \ No newline at end of file |
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| diff -r 6a2b26c297a4 -r 0b5ddf7b2924 test-data/input/input13.zarr/0/zarr.json --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/input/input13.zarr/0/zarr.json Sun Jan 04 20:56:49 2026 +0000 |
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| diff -r 6a2b26c297a4 -r 0b5ddf7b2924 test-data/input/input13.zarr/zarr.json --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/input/input13.zarr/zarr.json Sun Jan 04 20:56:49 2026 +0000 |
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| [ |
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| diff -r 6a2b26c297a4 -r 0b5ddf7b2924 test-data/input/input9.zarr/3/zarr.json --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/input/input9.zarr/3/zarr.json Sun Jan 04 20:56:49 2026 +0000 |
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| diff -r 6a2b26c297a4 -r 0b5ddf7b2924 test-data/input/input9.zarr/4/zarr.json --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/input/input9.zarr/4/zarr.json Sun Jan 04 20:56:49 2026 +0000 |
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| diff -r 6a2b26c297a4 -r 0b5ddf7b2924 test-data/input/input9.zarr/zarr.json --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/input/input9.zarr/zarr.json Sun Jan 04 20:56:49 2026 +0000 |
| [ |
| @@ -0,0 +1,98 @@ +{ + "attributes": { + "ome": { + "version": "0.5", + "multiscales": [ + { + "datasets": [ + { + "path": "0", + "coordinateTransformations": [ + { + "type": "scale", + "scale": [ + 1.0, + 1.0, + 1.0 + ] + } + ] + }, + { + "path": "1", + "coordinateTransformations": [ + { + "type": "scale", + "scale": [ + 1.0, + 2.0, + 2.0 + ] + } + ] + }, + { + "path": "2", + "coordinateTransformations": [ + { + "type": "scale", + "scale": [ + 1.0, + 4.0, + 4.0 + ] + } + ] + }, + { + "path": "3", + "coordinateTransformations": [ + { + "type": "scale", + "scale": [ + 1.0, + 8.333333333333334, + 8.333333333333334 + ] + } + ] + }, + { + "path": "4", + "coordinateTransformations": [ + { + "type": "scale", + "scale": [ + 1.0, + 16.666666666666668, + 16.666666666666668 + ] + } + ] + } + ], + "name": "/", + "axes": [ + { + "name": "z", + "type": "space", + "unit": "micrometer" + }, + { + "name": "y", + "type": "space", + "unit": "micrometer" + }, + { + "name": "x", + "type": "space", + "unit": "micrometer" + } + ] + } + ] + } + }, + "zarr_format": 3, + "node_type": "group" +} |
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| diff -r 6a2b26c297a4 -r 0b5ddf7b2924 test-data/input/ome-zarr-examples/LICENSE --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/input/ome-zarr-examples/LICENSE Sun Jan 04 20:56:49 2026 +0000 |
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| @@ -0,0 +1,28 @@ +BSD 3-Clause License + +Copyright (c) 2023, Tommaso Comparin + +Redistribution and use in source and binary forms, with or without +modification, are permitted provided that the following conditions are met: + +1. Redistributions of source code must retain the above copyright notice, this + list of conditions and the following disclaimer. + +2. Redistributions in binary form must reproduce the above copyright notice, + this list of conditions and the following disclaimer in the documentation + and/or other materials provided with the distribution. + +3. Neither the name of the copyright holder nor the names of its + contributors may be used to endorse or promote products derived from + this software without specific prior written permission. + +THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" +AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE +IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE +DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE +FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL +DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR +SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER +CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, +OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE +OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. |
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| diff -r 6a2b26c297a4 -r 0b5ddf7b2924 test-data/input/ome-zarr-examples/image-03.zarr/.zattrs --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/input/ome-zarr-examples/image-03.zarr/.zattrs Sun Jan 04 20:56:49 2026 +0000 |
| [ |
| @@ -0,0 +1,40 @@ +{ + "multiscales": [ + { + "axes": [ + { + "name": "z", + "type": "space", + "unit": "micrometer" + }, + { + "name": "y", + "type": "space", + "unit": "micrometer" + }, + { + "name": "x", + "type": "space", + "unit": "micrometer" + } + ], + "datasets": [ + { + "coordinateTransformations": [ + { + "scale": [ + 1.0, + 1.0, + 1.0 + ], + "type": "scale" + } + ], + "path": "0" + } + ], + "version": "0.4" + } + ], + "version": "0.4" +} \ No newline at end of file |
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| diff -r 6a2b26c297a4 -r 0b5ddf7b2924 test-data/input/ome-zarr-examples/image-03.zarr/.zgroup --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/input/ome-zarr-examples/image-03.zarr/.zgroup Sun Jan 04 20:56:49 2026 +0000 |
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| @@ -0,0 +1,3 @@ +{ + "zarr_format": 2 +} \ No newline at end of file |
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| diff -r 6a2b26c297a4 -r 0b5ddf7b2924 test-data/input/ome-zarr-examples/image-03.zarr/0/.zarray --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/input/ome-zarr-examples/image-03.zarr/0/.zarray Sun Jan 04 20:56:49 2026 +0000 |
| [ |
| @@ -0,0 +1,25 @@ +{ + "chunks": [ + 1, + 50, + 100 + ], + "compressor": { + "blocksize": 0, + "clevel": 5, + "cname": "lz4", + "id": "blosc", + "shuffle": 1 + }, + "dimension_separator": "/", + "dtype": "<f8", + "fill_value": 0.0, + "filters": null, + "order": "C", + "shape": [ + 2, + 100, + 100 + ], + "zarr_format": 2 +} \ No newline at end of file |
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| @@ -0,0 +1,3 @@ +{ + "labels": [] +} \ No newline at end of file |
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| diff -r 6a2b26c297a4 -r 0b5ddf7b2924 test-data/input/ome-zarr-examples/image-03.zarr/labels/.zgroup --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/input/ome-zarr-examples/image-03.zarr/labels/.zgroup Sun Jan 04 20:56:49 2026 +0000 |
| b |
| @@ -0,0 +1,3 @@ +{ + "zarr_format": 2 +} \ No newline at end of file |
| b |
| diff -r 6a2b26c297a4 -r 0b5ddf7b2924 test-data/out.tsv --- a/test-data/out.tsv Wed Dec 17 11:23:18 2025 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,3 +0,0 @@ -label area -1 8 -2 9 |
| b |
| diff -r 6a2b26c297a4 -r 0b5ddf7b2924 test-data/output/input11.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/output/input11.tsv Sun Jan 04 20:56:49 2026 +0000 |
| b |
| @@ -0,0 +1,2 @@ +area mean_intensity perimeter +20825.0 129.36364945978391 590.399061660723 |
| b |
| diff -r 6a2b26c297a4 -r 0b5ddf7b2924 test-data/output/input12.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/output/input12.tsv Sun Jan 04 20:56:49 2026 +0000 |
| b |
| @@ -0,0 +1,25 @@ +label area area_convex solidity +1 28.0 29.0 0.9655172413793104 +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 +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 +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 +14 9.0 9.0 1.0 +15 8.0 8.0 1.0 +16 27.0 28.0 0.9642857142857143 +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 +21 1.0 1.0 1.0 +22 4.0 4.0 1.0 +23 10.0 10.0 1.0 +24 8.0 8.0 1.0 |
| b |
| diff -r 6a2b26c297a4 -r 0b5ddf7b2924 test-data/output/input13-area.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/output/input13-area.tsv Sun Jan 04 20:56:49 2026 +0000 |
| b |
| @@ -0,0 +1,3 @@ +area +2500.0 +2500.0 |
| b |
| diff -r 6a2b26c297a4 -r 0b5ddf7b2924 test-data/output/input13-area_convex.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/output/input13-area_convex.tsv Sun Jan 04 20:56:49 2026 +0000 |
| b |
| @@ -0,0 +1,3 @@ +area_convex +2500.0 +2500.0 |
| b |
| diff -r 6a2b26c297a4 -r 0b5ddf7b2924 test-data/output/input13-area_filled.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/output/input13-area_filled.tsv Sun Jan 04 20:56:49 2026 +0000 |
| b |
| @@ -0,0 +1,3 @@ +area_filled +2500.0 +2500.0 |
| b |
| diff -r 6a2b26c297a4 -r 0b5ddf7b2924 test-data/output/input13-axis_major_length.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/output/input13-axis_major_length.tsv Sun Jan 04 20:56:49 2026 +0000 |
| b |
| @@ -0,0 +1,3 @@ +axis_major_length +57.723478758647246 +57.723478758647246 |
| b |
| diff -r 6a2b26c297a4 -r 0b5ddf7b2924 test-data/output/input13-axis_minor_length.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/output/input13-axis_minor_length.tsv Sun Jan 04 20:56:49 2026 +0000 |
| b |
| @@ -0,0 +1,3 @@ +axis_minor_length +57.723478758647246 +57.723478758647246 |
| b |
| diff -r 6a2b26c297a4 -r 0b5ddf7b2924 test-data/output/input13-bbox.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/output/input13-bbox.tsv Sun Jan 04 20:56:49 2026 +0000 |
| [ |
| @@ -0,0 +1,3 @@ +bbox +[50, 60, 100, 110] +[150, 160, 200, 210] |
| b |
| diff -r 6a2b26c297a4 -r 0b5ddf7b2924 test-data/output/input13-centroid.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/output/input13-centroid.tsv Sun Jan 04 20:56:49 2026 +0000 |
| [ |
| @@ -0,0 +1,3 @@ +centroid +[74.5, 84.5] +[174.5, 184.5] |
| b |
| diff -r 6a2b26c297a4 -r 0b5ddf7b2924 test-data/output/input13-eccentricity.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/output/input13-eccentricity.tsv Sun Jan 04 20:56:49 2026 +0000 |
| b |
| @@ -0,0 +1,3 @@ +eccentricity +0.0 +0.0 |
| b |
| diff -r 6a2b26c297a4 -r 0b5ddf7b2924 test-data/output/input13-equivalent_diameter_area.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/output/input13-equivalent_diameter_area.tsv Sun Jan 04 20:56:49 2026 +0000 |
| b |
| @@ -0,0 +1,3 @@ +equivalent_diameter_area +56.41895835477563 +56.41895835477563 |
| b |
| diff -r 6a2b26c297a4 -r 0b5ddf7b2924 test-data/output/input13-euler_number.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/output/input13-euler_number.tsv Sun Jan 04 20:56:49 2026 +0000 |
| b |
| @@ -0,0 +1,3 @@ +euler_number +1 +1 |
| b |
| diff -r 6a2b26c297a4 -r 0b5ddf7b2924 test-data/output/input13-extent.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/output/input13-extent.tsv Sun Jan 04 20:56:49 2026 +0000 |
| b |
| @@ -0,0 +1,3 @@ +extent +1.0 +1.0 |
| b |
| diff -r 6a2b26c297a4 -r 0b5ddf7b2924 test-data/output/input13-inertia_tensor_eigvals.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/output/input13-inertia_tensor_eigvals.tsv Sun Jan 04 20:56:49 2026 +0000 |
| [ |
| @@ -0,0 +1,3 @@ +inertia_tensor_eigvals +[208.25, 208.25] +[208.25, 208.25] |
| b |
| diff -r 6a2b26c297a4 -r 0b5ddf7b2924 test-data/output/input13-max_intensity.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/output/input13-max_intensity.tsv Sun Jan 04 20:56:49 2026 +0000 |
| b |
| @@ -0,0 +1,3 @@ +max_intensity +205.0 +195.0 |
| b |
| diff -r 6a2b26c297a4 -r 0b5ddf7b2924 test-data/output/input13-mean_intensity.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/output/input13-mean_intensity.tsv Sun Jan 04 20:56:49 2026 +0000 |
| b |
| @@ -0,0 +1,3 @@ +mean_intensity +130.1204 +131.9028 |
| b |
| diff -r 6a2b26c297a4 -r 0b5ddf7b2924 test-data/output/input13-min_intensity.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/output/input13-min_intensity.tsv Sun Jan 04 20:56:49 2026 +0000 |
| b |
| @@ -0,0 +1,3 @@ +min_intensity +27.0 +26.0 |
| b |
| diff -r 6a2b26c297a4 -r 0b5ddf7b2924 test-data/output/input13-moments.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/output/input13-moments.tsv Sun Jan 04 20:56:49 2026 +0000 |
| [ |
| @@ -0,0 +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]] |
| b |
| diff -r 6a2b26c297a4 -r 0b5ddf7b2924 test-data/output/input13-moments_hu.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/output/input13-moments_hu.tsv Sun Jan 04 20:56:49 2026 +0000 |
| [ |
| @@ -0,0 +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] |
| b |
| diff -r 6a2b26c297a4 -r 0b5ddf7b2924 test-data/output/input13-orientation.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/output/input13-orientation.tsv Sun Jan 04 20:56:49 2026 +0000 |
| b |
| @@ -0,0 +1,3 @@ +orientation +-0.7853981633974483 +-0.7853981633974483 |
| b |
| diff -r 6a2b26c297a4 -r 0b5ddf7b2924 test-data/output/input13-perimeter.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/output/input13-perimeter.tsv Sun Jan 04 20:56:49 2026 +0000 |
| b |
| @@ -0,0 +1,3 @@ +perimeter +196.0 +196.0 |
| b |
| diff -r 6a2b26c297a4 -r 0b5ddf7b2924 test-data/output/input13-solidity.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/output/input13-solidity.tsv Sun Jan 04 20:56:49 2026 +0000 |
| b |
| @@ -0,0 +1,3 @@ +solidity +1.0 +1.0 |
| b |
| diff -r 6a2b26c297a4 -r 0b5ddf7b2924 test-data/output/input9.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/output/input9.tsv Sun Jan 04 20:56:49 2026 +0000 |
| [ |
| @@ -0,0 +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 |
| b |
| diff -r 6a2b26c297a4 -r 0b5ddf7b2924 validators.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/validators.xml Sun Jan 04 20:56:49 2026 +0000 |
| [ |
| @@ -0,0 +1,45 @@ +<macros> + + <!-- Macros for validation of inputs --> + + <xml name="validators/is_single_channel"> + <!-- + The OME-Zarr datatype in Galaxy is currently not derived from the Image datatype, and it does + hence not inherit the metadata fields like `channels`. To cope with that, we allow all datasets + except those where we *know* that they are *not* single-channel. + --> + <validator type="expression" message="Dataset is a multi-channel image" + ><![CDATA[getattr(value.metadata, "channels", None) in (None, '') or int(value.metadata.channels) < 2]]></validator> + </xml> + + <xml name="validators/is_single_frame"> + <!-- + The OME-Zarr datatype in Galaxy is currently not derived from the Image datatype, and it does + hence not inherit the metadata fields like `frames`. To cope with that, we allow all datasets + except those where we *know* that they are *not* single-frame. + --> + <validator type="expression" message="Dataset is a multi-frame image" + ><![CDATA[getattr(value.metadata, "frames", None) in (None, '') or int(value.metadata.frames) < 2]]></validator> + </xml> + + <xml name="validators/is_2d"> + <!-- + The OME-Zarr datatype in Galaxy is currently not derived from the Image datatype, and it does + hence not inherit the metadata fields like `depth`. To cope with that, we allow all datasets + except those where we *know* that they are *not* 2-D. + --> + <validator type="expression" message="Dataset is a 3-D image" + ><![CDATA[getattr(value.metadata, "depth", None) in (None, '') or int(value.metadata.depth) < 2]]></validator> + </xml> + + <xml name="validators/is_binary"> + <!-- + The OME-Zarr datatype in Galaxy is currently not derived from the Image datatype, and it does + hence not inherit the metadata fields like `num_unique_values`. To cope with that, we allow all + datasets except those where we *know* that they are *not* binary. + --> + <validator type="expression" message="Dataset is not a binary image" + ><![CDATA[getattr(value.metadata, "num_unique_values", None) in (None, '') or int(value.metadata.num_unique_values) <= 2]]></validator> + </xml> + +</macros> |
