From 98d01c39b47d88ea4eeae20f2f6adacadd9e2b3d Mon Sep 17 00:00:00 2001
From: Pavankumar Videm <pavanvidem@gmail.com>
Date: Mon, 7 Apr 2025 14:34:06 +0200
Subject: [PATCH] bioimage_inference change output format from tif to tiff

---
 tools/bioimaging/bioimage_inference.xml | 16 ++++++++--------
 tools/bioimaging/main.py                |  2 +-
 2 files changed, 9 insertions(+), 9 deletions(-)

diff --git a/tools/bioimaging/bioimage_inference.xml b/tools/bioimaging/bioimage_inference.xml
index da673b1db5..291f04b3e1 100644
--- a/tools/bioimaging/bioimage_inference.xml
+++ b/tools/bioimaging/bioimage_inference.xml
@@ -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/" />
@@ -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>
@@ -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>
@@ -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>
@@ -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>
@@ -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>
@@ -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>
@@ -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>
diff --git a/tools/bioimaging/main.py b/tools/bioimaging/main.py
index 68399e5bf9..4c31fefeb0 100644
--- a/tools/bioimaging/main.py
+++ b/tools/bioimaging/main.py
@@ -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")