# HG changeset patch
# User bgruening
# Date 1742059435 0
# Node ID e5370bb716333da60736b28dabd734834b9a6e00
# Parent  1857781df226105cd906b6852adae28e62eac0a1
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/cellpose commit 5846f23282167df28e6cc00e1bda31523b66b5b4

diff -r 1857781df226 -r e5370bb71633 cellpose.xml
--- a/cellpose.xml	Tue Feb 11 14:47:54 2025 +0000
+++ b/cellpose.xml	Sat Mar 15 17:23:55 2025 +0000
@@ -2,7 +2,7 @@
     <description>with Cellpose</description>
     <macros>
         <token name="@TOOL_VERSION@">3.1.0</token>
-        <token name="@VERSION_SUFFIX@">0</token>
+        <token name="@VERSION_SUFFIX@">1</token>
         <xml name="channel">
             <option value="0" selected="true">grayscale/None</option>
             <option value="1">red</option>
@@ -19,6 +19,7 @@
     <version_command>echo "@VERSION@"</version_command>
     <command detect_errors="exit_code">
          <![CDATA[
+        export MKL_NUM_THREADS=1 &&
         export CELLPOSE_LOCAL_MODELS_PATH='cellpose_models' &&
         mkdir -p segmentation &&
         ln -s '${img_in}' ./image.${img_in.ext} &&
@@ -34,7 +35,7 @@
         <inputs name="inputs" />
     </configfiles>
     <inputs>
-        <param name="img_in" type="data" format="ome.tiff,tiff,jpeg,png" label="Choose the image file for segmention (usually after registration)"/>
+        <param name="img_in" type="data" format="ome.tiff,tiff,jpg,png" label="Choose the image file for segmention (usually after registration)"/>
         <param name="model_type" type="select" label="Choose the pre-trained model type">
             <option value="nuclei" selected="true">nuclei</option>
             <option value="cyto">cyto</option>
@@ -115,7 +116,9 @@
             <param name="model_type" value="cyto"/>
             <param name="chan" value="2"/>
             <param name="chan2" value="3"/>
-            <param name="diameter" value="50"/>
+            <section name="options">
+                <param name="diameter" value="50"/>
+            </section>
             <output name="cp_mask" file="img02_cp_masks_diameter.tif" compare="image_diff"/>
             <output name="cp_segm" file="img02_cp_segm_diameter.png" compare="image_diff"/>
         </test>
diff -r 1857781df226 -r e5370bb71633 cp_segmentation.py
--- a/cp_segmentation.py	Tue Feb 11 14:47:54 2025 +0000
+++ b/cp_segmentation.py	Sat Mar 15 17:23:55 2025 +0000
@@ -3,11 +3,24 @@
 import os
 import warnings
 
+# Make sure, that `MKL_NUM_THREADS` is set to 1, to ensure reproducibility:
+# https://forum.image.sc/t/reproducibility-how-we-spent-years-building-containers-and-then-mkl-decided-to-screw-our-results/109599
+if str(os.environ['MKL_NUM_THREADS']) != '1':
+    warnings.warn('MKL_NUM_THREADS must be set to 1 to ensure reproducibility, and will be adjusted accordingly for now.')
+    os.environ['MKL_NUM_THREADS'] = '1'
+
+# Load the remaining packages *after* adjusting `MKL_NUM_THREADS` (this likely necessary for it to take effect)
 import matplotlib.pyplot as plt
 import numpy as np
 import skimage.io
+import torch
 from cellpose import models, plot, transforms
 
+# Apply PyTorch guidelines for reproducibility
+torch.backends.cudnn.benchmark = True
+torch.backends.cudnn.deterministic = True
+torch.manual_seed(0)
+
 
 def main(inputs, img_path, img_format, output_dir):
     """
diff -r 1857781df226 -r e5370bb71633 test-data/img02_cp_masks_rescale.tif
Binary file test-data/img02_cp_masks_rescale.tif has changed
diff -r 1857781df226 -r e5370bb71633 test-data/img02_cp_segm_cyto.png
Binary file test-data/img02_cp_segm_cyto.png has changed
diff -r 1857781df226 -r e5370bb71633 test-data/img02_cp_segm_diameter.png
Binary file test-data/img02_cp_segm_diameter.png has changed
diff -r 1857781df226 -r e5370bb71633 test-data/img02_cp_segm_gpu.png
Binary file test-data/img02_cp_segm_gpu.png has changed