Refurbishment (#118)

Update 23 tools and macros * Update 23 tools * Rename tools Change the `Performs` in the name of the two tools - `Performs projective transformation with/without labels` - `Performs projective transformation` to `Perform`, which is more consistent with the name of the other tools (imperative form). * Update projective_transformation.xml * Update projective_transformation_points.xml * Add CONVENTIONS.md * wip * wip * Update CONVENTIONS.md * Update CONVENTIONS.md * Update CONVENTIONS.md * Update CONVENTIONS.md * Update CONVENTIONS.md * Update CONVENTIONS.md * Remove help section * Update CONVENTIONS.md * Update CONVENTIONS.md * Update CONVENTIONS.md * Update * Update test data * Add content assertions * Update pr.yaml * Update * Update pr.yaml * Add `pip install pillow` * Merge CONVENTIONS.md into CONTRIBUTING.md * Temporarilly fix CI * Update `2d_feature_extraction` tool * Update `2d_auto_threshold` tool * Fix `2d_feature_extraction` tests * Fix test data * Fix tool * Start refactoring `2d_simple_filter` tool * Fix `2d_simple_filter` tool * Add more tests * Fix tests * Update * Fix * Update CONTRIBUTING.md * Fix bugs * Update CONTRIBUTING.md * Update CONTRIBUTING.md * Fix linting issues * Update CONTRIBUTING.md * Refactor tests using macros * Update tests * Update CONTRIBUTING.md * Update CONTRIBUTING.md * Update pr.yaml * Update `anisotropic_diffusion` tool * Fix spelling (was BE, using AE is more consistent) * Update `2d_histogram_equalization` tool * Update `colorize_labels` tool * Update `bf2raw` tool * Add `macros/creators.xml` * Update `rfove` tool * Fix `bioformats2raw` and `voronoi_tessellation` tools * Fix labels * Fix `rfove` tool * Update `overlay_images` tool * Add RGB test for `overlay_images` * Update `overlay_images` help * Add image verification support to CI (#117) * Update pr.yaml * Update * Update pr.yaml * Add `pip install pillow` * Temporarilly fix CI * Update pr.yaml * Update ci.yaml * Add test tool from `/test/functional/tools/image_diff.xml` * Update pr.yaml * Add .shed.yml * Add missing test files * Switch CI to galaxy fork `kostrykin/galaxy` branch `galaxy-image-analysis` This is a temporary change to enable the features from: - galaxyproject/galaxy#17556 - galaxyproject/galaxy#17581 * Remove `test` tool * Update CONTRIBUTING.md * Update CONTRIBUTING.md * Update CONTRIBUTING.md * Update test data * Add RGB test for `overlay_images` * Update `anisotropic_diffusion` to medpy 0.4.0 * Update PULL_REQUEST_TEMPLATE.md * Update `projective_transformation_points` tool * Update PULL_REQUEST_TEMPLATE.md * Update `bioformats2raw` * Update `projective_transformation` tool * Update `bfconvert` tool (tests failing) * Update CONTRIBUTING.md * Fix `bfconvert` tests * Fix test data size * Update `projective_transformation_points` tool * Remove spurious files * Update requirements using `@TOOL_VERSION@` macro * Update `segmetrics` tool * Remove spurious sym links * Update `superdsm` tool * Update `scale_image` tool (not finished yet) * Fix tests * Fix `scale_image` tool * Refactor * Fix linting issues * Update tests and help of `2d_simple_filter` tool * Update `scale_image` help * Update CI to use latest version of `galaxy` fork * Fix tests for float TIFF in `scale_image` tool * Add tifffile to CI workflows * Fix tests of `bfconvert` tool * Update `2d_filter_segmentation_by_features` tool * Update `image_math` tool * Update `orientationpy` tool * Update `morphological_operations` tool * Update `split_labelmap` tool * Add float TIFF test for `2d_simple_filter` * Update `slice_image` tool * Add missing macros * Update help of `2d_filter_segmentation_by_features` tool * Update `concat_images` tool * Fix linting issues * Fix file sizes * Fix missing `profile` * Update test macros
BMCV · Apr 4, 2024 · c045f06 · c045f06
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diff --git a/.github/PULL_REQUEST_TEMPLATE.md b/.github/PULL_REQUEST_TEMPLATE.md
@@ -1,12 +1,14 @@
-**For the contributor:**
-* [ ] I have read the [CONTRIBUTING.md](https://github.com/BMCV/galaxy-image-analysis/blob/master/CONTRIBUTING.md) document.
-* [ ] License permits unrestricted use (educational + commercial).
-* [ ] This PR adds or updates a tool or tool collection.
-  * [ ] This PR adds a new tool or tool collection.
-  * [ ] This PR updates an existing tool or tool collection.
-  * [ ] Tools added/updated by this PR comply with the [Naming and Annotation Conventions for Tools in the Image Community in Galaxy](https://github.com/elixir-europe/biohackathon-projects-2023/blob/main/16/paper/paper.md#conventions) (or explain why they do not).
-* [ ] This PR does something else (explain below).
 
 ---
 
-<!-- Please describe your PR here -->
+**FOR THE CONTRIBUTOR — Please fill out if applicable**
+
+Please make sure you have read the [CONTRIBUTING.md](https://github.com/BMCV/galaxy-image-analysis/blob/master/CONTRIBUTING.md) document (last updated: 2024/03/18).
+
+* [ ] License permits unrestricted use (educational + commercial).
+
+If this PR adds or updates a tool or tool collection:
+
+* [ ] This PR adds a new tool or tool collection.
+* [ ] This PR updates an existing tool or tool collection.
+* [ ] Tools added/updated by this PR comply with the [Naming and Annotation Conventions for Tools in the Image Community in Galaxy](https://github.com/elixir-europe/biohackathon-projects-2023/blob/main/16/paper/paper.md#conventions) (or explain why they do not).
diff --git a/.github/workflows/ci.yaml b/.github/workflows/ci.yaml
@@ -110,8 +110,8 @@ jobs:
         tool-list: ${{ needs.setup.outputs.tool-list }}
         additional-planemo-options: --biocontainers -s tests,output,inputs,help,general,command,citations,tool_xsd,xml_order,tool_urls,shed_metadata
     - run: |
-        python -m pip install git+https://[email protected]/galaxyproject/galaxy.git@5c1d045ce7b1e45f85608346baed5455324ee967#subdirectory=packages/util
-        python -m pip install git+https://[email protected]/galaxyproject/galaxy.git@5c1d045ce7b1e45f85608346baed5455324ee967#subdirectory=packages/tool_util
+        python -m pip install git+https://[email protected]/kostrykin/galaxy.git@galaxy-image-analysis#subdirectory=packages/util
+        python -m pip install git+https://[email protected]/kostrykin/galaxy.git@galaxy-image-analysis#subdirectory=packages/tool_util
 #
 # ---------------------------------------------------------
 #
@@ -185,9 +185,9 @@ jobs:
         chunk: ${{ matrix.chunk }}
         chunk-count: ${{ needs.setup.outputs.chunk-count }}
     - run: |
-        python -m pip install git+https://[email protected]/galaxyproject/galaxy.git@5c1d045ce7b1e45f85608346baed5455324ee967#subdirectory=packages/util
-        python -m pip install git+https://[email protected]/galaxyproject/galaxy.git@5c1d045ce7b1e45f85608346baed5455324ee967#subdirectory=packages/tool_util
-        python -m pip install pillow
+        python -m pip install git+https://[email protected]/kostrykin/galaxy.git@galaxy-image-analysis#subdirectory=packages/util
+        python -m pip install git+https://[email protected]/kostrykin/galaxy.git@galaxy-image-analysis#subdirectory=packages/tool_util
+        python -m pip install pillow tifffile
 #
 # ---------------------------------------------------------
 #

diff --git a/.github/workflows/pr.yaml b/.github/workflows/pr.yaml
@@ -140,8 +140,8 @@ jobs:
 # - https://github.com/galaxyproject/galaxy/pull/17581
 #
     - run: |
-        python -m pip install --no-dependencies git+https://[email protected]/galaxyproject/galaxy.git@5c1d045ce7b1e45f85608346baed5455324ee967#subdirectory=packages/util
-        python -m pip install --no-dependencies git+https://[email protected]/galaxyproject/galaxy.git@5c1d045ce7b1e45f85608346baed5455324ee967#subdirectory=packages/tool_util
+        python -m pip install --no-dependencies git+https://[email protected]/kostrykin/galaxy.git@galaxy-image-analysis#subdirectory=packages/util
+        python -m pip install --no-dependencies git+https://[email protected]/kostrykin/galaxy.git@galaxy-image-analysis#subdirectory=packages/tool_util
 #
 # ---------------------------------------------------------
 #
@@ -311,9 +311,9 @@ jobs:
 # - https://github.com/galaxyproject/galaxy/pull/17581
 #
     - run: |
-        python -m pip install --no-dependencies git+https://[email protected]/galaxyproject/galaxy.git@5c1d045ce7b1e45f85608346baed5455324ee967#subdirectory=packages/util
-        python -m pip install --no-dependencies git+https://[email protected]/galaxyproject/galaxy.git@5c1d045ce7b1e45f85608346baed5455324ee967#subdirectory=packages/tool_util
-        python -m pip install pillow
+        python -m pip install --no-dependencies git+https://[email protected]/kostrykin/galaxy.git@galaxy-image-analysis#subdirectory=packages/util
+        python -m pip install --no-dependencies git+https://[email protected]/kostrykin/galaxy.git@galaxy-image-analysis#subdirectory=packages/tool_util
+        python -m pip install pillow tifffile
 #
 # ---------------------------------------------------------
 #

diff --git a/CONTRIBUTING.md b/CONTRIBUTING.md
@@ -1,36 +1,98 @@
 # Contributing
 
-This document describes how to contribute to this repository. Pull
-requests containing bug fixes, updates, and extensions to the existing
-tools and tool suites in this repository will be considered for
-inclusion.
+This document is the attempt to collect some rough rules for tools to follow in this repository, to facilitate their consistency and interoperability. This document is an extension to the [Naming and Annotation Conventions for Tools in the Image Community in Galaxy](https://github.com/elixir-europe/biohackathon-projects-2023/blob/main/16/paper/paper.md#conventions) and compatibility should be maintained. This document is work in progress.
 
-## How to Contribute
+**How to Contribute:**
 
 * Make sure you have a [GitHub account](https://github.com/signup/free)
 * Make sure you have git [installed](https://help.github.com/articles/set-up-git)
 * Fork the repository on [GitHub](https://github.com/BMCV/galaxy-image-analysis/fork)
 * Make the desired modifications - consider using a [feature branch](https://github.com/Kunena/Kunena-Forum/wiki/Create-a-new-branch-with-git-and-manage-branches).
-* Try to stick to the [Conventions for Tools in the Image Community](https://github.com/elixir-europe/biohackathon-projects-2023/blob/main/16/conventions.md) and the [IUC standards](http://galaxy-iuc-standards.readthedocs.org/en/latest/) whenever you can
+* Try to stick to the [Conventions for Tools in the Image Community](https://github.com/elixir-europe/biohackathon-projects-2023/blob/main/16/paper/paper.md#conventions) and the [IUC standards](http://galaxy-iuc-standards.readthedocs.org/en/latest/) whenever you can
 * Make sure you have added the necessary tests for your changes and they pass.
 * Open a [pull request](https://help.github.com/articles/using-pull-requests) with these changes.
 
-## Using the new image-based verifications for tool testing
+## Terminology
 
-The new image-based verifications for Galaxy tool tests https://github.com/galaxyproject/galaxy/pull/17556 and https://github.com/galaxyproject/galaxy/pull/17581 won't be available in Galaxy before 24.1 is released.
+**Label maps** are images with pixel-level annotations, usually corresponding to distinct image regions (e.g., objects). We avoid the terms *label image* and *labeled image*, since these can be easily confused with image-level annotations (instead of pixel-level). The labels (pixel values) must uniquely identify the labeled image regions (i.e. labels must be unique, even for non-adjacent image regions). If a label semantically corresponds to the image background, that label should be 0.
+
+**Binary images** are a special case of label maps with only two labels (e.g., image background and image foreground). To facilitate visual perception, the foreground label should correspond to white (value 255 for `uint8` images and value 65535 for `uint16` images), since background corresponds to the label 0, which is black.
+
+**Intensity images** are images which are *not* label maps (and thus neither binary images).
+
+## File types
+
+If a tool wrapper only supports single-channel 2-D images and uses a Python script, the structure of the input should be verified right after loading the image:
+
+```python
+im = skimage.io.imread(args.input)
+im = np.squeeze(im)  # remove axes with length 1
+assert im.ndim == 2
+```
+
+Tools with **label map inputs** should accept PNG and TIFF files. Tools with **label map outputs** should produce either `uint16` single-channel PNG or `uint16` single-channel TIFF. Using `uint8` instead of `uint16` is also acceptable, if there definetely are no more than 256 different labels. Using `uint8` should be preferred for binary images.
+
+> [!NOTE]  
+> It is a common misconception that PNG files must be RGB or RGBA, and that only `uint8` pixel values are supported. For example, the `cv2` module (OpenCV) can be used to create single-channel PNG files, or PNG files with `uint16` pixel values. Such files can then be read by `skimage.io.imread` without issues (however, `skimage.io.imwrite` seems not to be able to write such PNG files).
+
+Tools with **intensity image inputs** should accept PNG and TIFF files. Tools with **intensity image outputs** can be any data type and either PNG or TIFF. Image outputs meant for visualization (e.g., segmentation overlays, charts) should be PNG.
+
+## Testing
+
+### Testing infrastructure
+
+The support for the new [`image_diff` output verification method](https://docs.galaxyproject.org/en/latest/dev/schema.html#tool-tests-test-output) and [assertions for image data](https://docs.galaxyproject.org/en/latest/dev/schema.html#assertions-for-image-data) for Galaxy tool testing probably won't be available in Galaxy before 24.1 is released.
 
 Meanwhile, they are already available in the CI of the **galaxy-image-analyis** repostiroy! 🎉 https://github.com/BMCV/galaxy-image-analysis/pull/117
 
-To also use them locally, you need to install the development versions of two Galaxy packages:
+To also use them locally, you need to install the development versions of two Galaxy packages, pillow, and tifffile:
 ```python
-python -m pip install git+https://git@github.com/galaxyproject/galaxy.git@5c1d045ce7b1e45f85608346baed5455324ee967#subdirectory=packages/util
-python -m pip install git+https://git@github.com/galaxyproject/galaxy.git@5c1d045ce7b1e45f85608346baed5455324ee967#subdirectory=packages/tool_util
+python -m pip install git+https://git@github.com/kostrykin/galaxy.git@galaxy-image-analysis#subdirectory=packages/util
+python -m pip install git+https://git@github.com/kostrykin/galaxy.git@galaxy-image-analysis#subdirectory=packages/tool_util
+python -m pip install pillow tifffile
 ```
 
-The commit [`5c1d045ce7b1e45f85608346baed5455324ee967`](https://github.com/galaxyproject/galaxy/commit/5c1d045ce7b1e45f85608346baed5455324ee967) corresponds to the latest merged bug fixes.
+The [galaxy-image-analysis branch](https://github.com/kostrykin/galaxy/tree/galaxy-image-analysis) of the <https://github.com/kostrykin/galaxy> fork is the same as the [23.1 release of Galaxy](https://github.com/galaxyproject/galaxy/tree/release_23.1), plus the support for the image-based verification extensions.
 
 In addition, instead of running `planemo test`, you should use:
 ```python
 planemo test --galaxy_source https://github.com/kostrykin/galaxy --galaxy_branch galaxy-image-analysis
 ```
-The [galaxy-image-analysis branch](https://github.com/kostrykin/galaxy/tree/galaxy-image-analysis) of the <https://github.com/kostrykin/galaxy> fork is the same as the [23.1 release of Galaxy](https://github.com/galaxyproject/galaxy/tree/release_23.1), plus the support for the image-based verification extensions.
+Linting with `planemo lint` works as usual.
+
+### Writing tests
+
+We recommend using macros for verification of image outputs. The macros are loaded as follows:
+```xml
+<macros>
+    <import>tests.xml</import>
+</macros>
+```
+
+For testing of **binary image outputs** we recommend using the `mae` metric (mean absolute error). With the default value of `eps` of 0.01, this asserts that at most 1% of the image pixels are labeled differently:
+```xml
+<expand macro="tests/binary_image_diff" name="output" value="output.tif" ftype="tiff"/>
+```
+The macro also ensures that the image contains two distinct label values, which are not interchangable.
+
+For testing of non-binary **label map outputs** with interchangeable labels, we recommend using the `iou` metric (one minus the *intersection over the union*). With the default value of `eps` of 0.01, this asserts that there is no labeled image region with an *intersection over the union* of less than 99%:
+```xml
+<expand macro="tests/label_image_diff" name="output" value="output.tif" ftype="tiff"/>
+```
+Label 0 is commonly connotated as the image background, and is not interchangable by default. Use `pin_labels=""` to make it interchangable.
+
+For testing of **intensity image outputs** we recommend the `rms` metric (root mean square), because it is very sensitive to large pixel value differences, but tolerates smaller differences:
+```xml
+<expand macro="tests/intensity_image_diff" name="output" value="output.tif" ftype="tiff"/>
+```
+For `uint8` and `uint16` images, increasing the default value of `eps` to `1.0` should be tolerable, if required.
+
+## Future extensions
+
+Below is a list of open questions:
+
+- **How do we want to cope with multi-channel label maps?** For example, do or can we distinguish RGB labels from multi-channel binary masks, which are sometimes used to represent overlapping objects?
+
+- How can we distinguish multi-channel 2-D images from single-channel 3-D images?
+
+- How can we make clear to the user, whether a tool requires a 2-D image or also supports 3-D?
diff --git a/README.md b/README.md
@@ -25,7 +25,7 @@ If Galaxy Image Analysis helped with the analysis of your data, please do not fo
 - [Process images using arithmetic expressions](https://usegalaxy.eu/root?tool_id=toolshed.g2.bx.psu.edu/repos/imgteam/image_math/image_math) with NumPy
 - [Scale image](https://usegalaxy.eu/root?tool_id=toolshed.g2.bx.psu.edu/repos/imgteam/scale_image/ip_scale_image) with scikit-image
 - [Show image info](https://usegalaxy.eu/root?tool_id=toolshed.g2.bx.psu.edu/repos/imgteam/image_info/ip_imageinfo) with Bioformats
-- [Slice image](https://usegalaxy.eu/root?tool_id=toolshed.g2.bx.psu.edu/repos/imgteam/slice_image/ip_slice_image)
+- [Slice image into patches](https://usegalaxy.eu/root?tool_id=toolshed.g2.bx.psu.edu/repos/imgteam/slice_image/ip_slice_image)
 - [Switch axis coordinates](https://usegalaxy.eu/root?tool_id=toolshed.g2.bx.psu.edu/repos/imgteam/imagecoordinates_flipaxis/imagecoordinates_flipaxis)
 
 ### Image conversion

diff --git a/macros/creators.xml b/macros/creators.xml
@@ -0,0 +1,23 @@
+<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/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>
diff --git a/macros/creators/bmcv.xml b/macros/creators/bmcv.xml
diff --git a/macros/tests.xml b/macros/tests.xml
@@ -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>