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bioimage_inference change output format from tif to tiff #1603

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Merged
bgruening merged 1 commit into from
Apr 7, 2025
Merged

bioimage_inference change output format from tif to tiff #1603

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16 changes: 8 additions & 8 deletions tools/bioimaging/bioimage_inference.xml
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Original file line number Diff line number Diff line change
Expand Up @@ -2,7 +2,7 @@
<description>with PyTorch</description>
<macros>
<token name="@TOOL_VERSION@">2.4.1</token>
<token name="@VERSION_SUFFIX@">1</token>
<token name="@VERSION_SUFFIX@">2</token>
</macros>
<creator>
<organization name="European Galaxy Team" url="https://galaxyproject.org/eu/" />
Expand Down Expand Up @@ -44,7 +44,7 @@
</param>
</inputs>
<outputs>
<data format="tif" name="output_predicted_image" from_work_dir="output_predicted_image.tif" label="Predicted image"></data>
<data format="tiff" name="output_predicted_image" from_work_dir="output_predicted_image.tiff" label="Predicted image"></data>
<data format="npy" name="output_predicted_image_matrix" from_work_dir="output_predicted_image_matrix.npy" label="Predicted image tensor"></data>
</outputs>
<tests>
Expand All @@ -53,7 +53,7 @@
<param name="input_image_file" value="input_image_file.tif" location="https://zenodo.org/api/records/6647674/files/sample_input_0.tif/content"/>
<param name="input_image_input_size" value="256,256,1,1"/>
<param name="input_image_input_axes" value="bcyx"/>
<output name="output_predicted_image" ftype="tif">
<output name="output_predicted_image" ftype="tiff">
<assert_contents>
<has_size size="524846" delta="110" />
</assert_contents>
Expand All @@ -69,7 +69,7 @@
<param name="input_image_file" value="input_nucleisegboundarymodel.png"/>
<param name="input_image_input_size" value="256,256,1,1"/>
<param name="input_image_input_axes" value="bcyx"/>
<output name="output_predicted_image" ftype="tif">
<output name="output_predicted_image" ftype="tiff">
<assert_contents>
<has_size size="524846" delta="110" />
</assert_contents>
Expand All @@ -85,7 +85,7 @@
<param name="input_image_file" value="input_image_file.tif" location="https://uk1s3.embassy.ebi.ac.uk/public-datasets/bioimage.io/emotional-cricket/1.1/files/sample_input_0.tif"/>
<param name="input_image_input_size" value="128,128,100,1"/>
<param name="input_image_input_axes" value="bczyx"/>
<output name="output_predicted_image" ftype="tif">
<output name="output_predicted_image" ftype="tiff">
<assert_contents>
<has_size size="6572778" delta="100" />
</assert_contents>
Expand All @@ -101,7 +101,7 @@
<param name="input_image_file" value="input_3d-unet-arabidopsis-apical-stem-cells.png" location="https://uk1s3.embassy.ebi.ac.uk/public-datasets/bioimage.io/emotional-cricket/1.1/files/raw.png"/>
<param name="input_image_input_size" value="128,128,100,1"/>
<param name="input_image_input_axes" value="bczyx"/>
<output name="output_predicted_image" ftype="tif">
<output name="output_predicted_image" ftype="tiff">
<assert_contents>
<has_size size="6572778" delta="100" />
</assert_contents>
Expand All @@ -117,7 +117,7 @@
<param name="input_image_file" value="input_platynereisemnucleisegmentationboundarymodel.tif" location="https://uk1s3.embassy.ebi.ac.uk/public-datasets/bioimage.io/organized-badger/1/files/sample_input_0.tif"/>
<param name="input_image_input_size" value="256,256,32,1"/>
<param name="input_image_input_axes" value="bczyx"/>
<output name="output_predicted_image" ftype="tif">
<output name="output_predicted_image" ftype="tiff">
<assert_contents>
<has_size size="16789714" delta="100" />
</assert_contents>
Expand All @@ -133,7 +133,7 @@
<param name="input_image_file" value="input_3d-unet-lateral-root-primordia-cells.tif" location="https://uk1s3.embassy.ebi.ac.uk/public-datasets/bioimage.io/thoughtful-turtle/1/files/sample_input_0.tif"/>
<param name="input_image_input_size" value="128,128,100,1"/>
<param name="input_image_input_axes" value="bczyx"/>
<output name="output_predicted_image" ftype="tif">
<output name="output_predicted_image" ftype="tiff">
<assert_contents>
<has_size size="6572778" delta="100" />
</assert_contents>
Expand Down
2 changes: 1 addition & 1 deletion tools/bioimaging/main.py
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Original file line number Diff line number Diff line change
Expand Up @@ -141,4 +141,4 @@ def dynamic_resize(image: torch.Tensor, target_shape: tuple):
pred_numpy = pred_data.detach().numpy()

# write predicted TIF image to file
imageio.v3.imwrite("output_predicted_image.tif", pred_numpy, extension=".tif")
imageio.v3.imwrite("output_predicted_image.tiff", pred_numpy, extension=".tiff")