Updated test pararmeters

bgruening · Sep 18, 2024 · 80709fa · 80709fa
1 parent 34aef8f
commit 80709fa
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Showing 14 changed files with 16 additions and 16 deletions.
diff --git a/tools/cellpose/cellpose.xml b/tools/cellpose/cellpose.xml
@@ -1,4 +1,4 @@
-<tool id="cellpose" name="Run generalist cell and nucleus segmentation" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="22.05">
+<tool id="cellpose" name="Run generalist cell and nucleus segmentation" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="23.02">
     <description>with Cellpose</description>
     <macros>
         <token name="@TOOL_VERSION@">3.0.11</token>
@@ -76,66 +76,66 @@
             <param name="model_type" value="cyto"/>
             <param name="chan" value="2"/>
             <param name="chan2" value="3"/>
-            <output name="cp_mask" file="img02_cp_masks_cyto.tif" compare="sim_size" delta_frac="0.1"/>
-            <output name="cp_segm" file="img02_cp_segm_cyto.png" compare="sim_size" delta_frac="0.1"/>
+            <output name="cp_mask" file="img02_cp_masks_cyto.tif" compare="image_diff" metric="mae" eps="0.01"/>
+            <output name="cp_segm" file="img02_cp_segm_cyto.png" compare="image_diff" metric="mae" eps="0.01"/>
         </test>
         <test expect_num_outputs="2">
             <param name="img_in" value="img02.png"/>
             <param name="model_type" value="cyto2"/>
             <param name="chan" value="2"/>
             <param name="chan2" value="3"/>
-            <output name="cp_mask" file="img02_cp_masks_cyto2.tif" compare="sim_size" delta_frac="0.1"/>
-            <output name="cp_segm" file="img02_cp_segm_cyto2.png" compare="sim_size" delta_frac="0.1"/>
+            <output name="cp_mask" file="img02_cp_masks_cyto2.tif" compare="image_diff" metric="mae" eps="0.01"/>
+            <output name="cp_segm" file="img02_cp_segm_cyto2.png" compare="image_diff" metric="mae" eps="0.01"/>
         </test>
         <test expect_num_outputs="2">
             <param name="img_in" value="img02.png"/>
             <param name="model_type" value="cyto3"/>
             <param name="chan" value="2"/>
             <param name="chan2" value="3"/>
-            <output name="cp_mask" file="img02_cp_masks_cyto3.tif" compare="sim_size" delta_frac="0.1"/>
-            <output name="cp_segm" file="img02_cp_segm_cyto3.png" compare="sim_size" delta_frac="0.1"/>
+            <output name="cp_mask" file="img02_cp_masks_cyto3.tif" compare="image_diff" metric="mae" eps="0.01"/>
+            <output name="cp_segm" file="img02_cp_segm_cyto3.png" compare="image_diff" metric="mae" eps="0.01"/>
         </test>
         <test expect_num_outputs="2">
             <param name="img_in" value="img02.png"/>
             <param name="model_type" value="nuclei"/>
             <param name="chan" value="2"/>
             <param name="chan2" value="3"/>
-            <output name="cp_mask" file="img02_cp_masks_nuclei.tif" compare="sim_size" delta_frac="0.1"/>
-            <output name="cp_segm" file="img02_cp_segm_nuclei.png" compare="sim_size" delta_frac="0.1"/>
+            <output name="cp_mask" file="img02_cp_masks_nuclei.tif" compare="image_diff" metric="mae" eps="0.01"/>
+            <output name="cp_segm" file="img02_cp_segm_nuclei.png" compare="image_diff" metric="mae" eps="0.01"/>
         </test>
         <test expect_num_outputs="2">
             <param name="img_in" value="img02.png"/>
             <param name="model_type" value="cyto"/>
             <param name="chan" value="2"/>
             <param name="chan2" value="1"/>
-            <output name="cp_mask" file="img02_cp_masks_chan.tif" compare="sim_size" delta_frac="0.1"/>
-            <output name="cp_segm" file="img02_cp_segm_chan.png" compare="sim_size" delta_frac="0.1"/>
+            <output name="cp_mask" file="img02_cp_masks_chan.tif" compare="image_diff" metric="mae" eps="0.01"/>
+            <output name="cp_segm" file="img02_cp_segm_chan.png" compare="image_diff" metric="mae" eps="0.01"/>
         </test>
         <test expect_num_outputs="2">
             <param name="img_in" value="img02.png"/>
             <param name="model_type" value="cyto"/>
             <param name="chan" value="2"/>
             <param name="chan2" value="3"/>
             <param name="diameter" value="50"/>
-            <output name="cp_mask" file="img02_cp_masks_diameter.tif" compare="sim_size" delta_frac="0.1"/>
-            <output name="cp_segm" file="img02_cp_segm_diameter.png" compare="sim_size" delta_frac="0.1"/>
+            <output name="cp_mask" file="img02_cp_masks_diameter.tif" compare="image_diff" metric="mae" eps="0.01"/>
+            <output name="cp_segm" file="img02_cp_segm_diameter.png" compare="image_diff" metric="mae" eps="0.01"/>
         </test>
         <test expect_num_outputs="2">
             <param name="img_in" value="img02.png"/>
             <param name="use_gpu" value="true"/>
             <param name="model_type" value="cyto"/>
             <param name="chan" value="2"/>
             <param name="chan2" value="3"/>
-            <output name="cp_mask" file="img02_cp_masks_gpu.tif" compare="sim_size" delta_frac="0.1"/>
-            <output name="cp_segm" file="img02_cp_segm_gpu.png" compare="sim_size" delta_frac="0.1"/>
+            <output name="cp_mask" file="img02_cp_masks_gpu.tif" compare="image_diff" metric="mae" eps="0.01"/>
+            <output name="cp_segm" file="img02_cp_segm_gpu.png" compare="image_diff" metric="mae" eps="0.01"/>
         </test>
         <test expect_num_outputs="1">
             <param name="img_in" value="img02.png"/>
             <param name="model_type" value="cyto"/>
             <param name="chan" value="2"/>
             <param name="chan2" value="3"/>
             <param name="show_segmentation" value="false"/>
-            <output name="cp_mask" file="img02_cp_masks_cyto.tif" compare="sim_size" delta_frac="0.1"/>
+            <output name="cp_mask" file="img02_cp_masks_cyto.tif" compare="image_diff" metric="mae" eps="0.01"/>
         </test>
     </tests>
     <help>

diff --git a/tools/cellpose/test-data/img02_cp_masks_chan.tif b/tools/cellpose/test-data/img02_cp_masks_chan.tif
diff --git a/tools/cellpose/test-data/img02_cp_masks_cyto.tif b/tools/cellpose/test-data/img02_cp_masks_cyto.tif
diff --git a/tools/cellpose/test-data/img02_cp_masks_cyto2.tif b/tools/cellpose/test-data/img02_cp_masks_cyto2.tif
diff --git a/tools/cellpose/test-data/img02_cp_masks_diameter.tif b/tools/cellpose/test-data/img02_cp_masks_diameter.tif
diff --git a/tools/cellpose/test-data/img02_cp_masks_gpu.tif b/tools/cellpose/test-data/img02_cp_masks_gpu.tif
diff --git a/tools/cellpose/test-data/img02_cp_masks_nuclei.tif b/tools/cellpose/test-data/img02_cp_masks_nuclei.tif
diff --git a/tools/cellpose/test-data/img02_cp_segm_chan.png b/tools/cellpose/test-data/img02_cp_segm_chan.png
diff --git a/tools/cellpose/test-data/img02_cp_segm_cyto.png b/tools/cellpose/test-data/img02_cp_segm_cyto.png
diff --git a/tools/cellpose/test-data/img02_cp_segm_cyto2.png b/tools/cellpose/test-data/img02_cp_segm_cyto2.png
diff --git a/tools/cellpose/test-data/img02_cp_segm_cyto3.png b/tools/cellpose/test-data/img02_cp_segm_cyto3.png
diff --git a/tools/cellpose/test-data/img02_cp_segm_diameter.png b/tools/cellpose/test-data/img02_cp_segm_diameter.png
diff --git a/tools/cellpose/test-data/img02_cp_segm_gpu.png b/tools/cellpose/test-data/img02_cp_segm_gpu.png
diff --git a/tools/cellpose/test-data/img02_cp_segm_nuclei.png b/tools/cellpose/test-data/img02_cp_segm_nuclei.png