Replace test-data and fix test for preprocessor

goeckslab · Aug 15, 2024 · ebacfef · ebacfef
1 parent 248e106
commit ebacfef
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Showing 12 changed files with 54 additions and 37 deletions.
diff --git a/tools/visinity/test-data/celltypes.csv b/tools/visinity/test-data/celltypes.csv
@@ -1,5 +1,5 @@
-phenotypeID,phenotype
-0,epithelial
-1,tcell
-2,bcell
-3,macrophage
+phenotypeID,phenotype
+0,epithelial
+1,tcell
+2,bcell
+3,macrophage
diff --git a/tools/visinity/test-data/dataset_names.csv b/tools/visinity/test-data/dataset_names.csv
@@ -1,3 +1,2 @@
-names
-img_1
-img_2
+names
+img_1
diff --git a/tools/visinity/test-data/img_1.ome.tiff b/tools/visinity/test-data/img_1.ome.tiff
diff --git a/tools/visinity/test-data/img_2.ome.tiff b/tools/visinity/test-data/img_2.ome.tiff
diff --git a/tools/visinity/test-data/mask_1.tiff b/tools/visinity/test-data/mask_1.tiff
diff --git a/tools/visinity/test-data/mask_2.tiff b/tools/visinity/test-data/mask_2.tiff
diff --git a/tools/visinity/test-data/quant_1.csv b/tools/visinity/test-data/quant_1.csv
diff --git a/tools/visinity/test-data/quant_2.csv b/tools/visinity/test-data/quant_2.csv
diff --git a/tools/visinity/test-data/test_image.ome.tiff b/tools/visinity/test-data/test_image.ome.tiff
diff --git a/tools/visinity/test-data/test_mask.tiff b/tools/visinity/test-data/test_mask.tiff
diff --git a/tools/visinity/test-data/test_quant.csv b/tools/visinity/test-data/test_quant.csv
@@ -0,0 +1,41 @@
+CellID,CHAN_0,CHAN_1,X_centroid,Y_centroid,Area,MajorAxisLength,MinorAxisLength,Eccentricity,Solidity,Extent,Orientation,phenotype
+1,51.14091983548991,2.290488748001694,1275.204120950442,1094.3768565455614,146374,2281.259866065922,1725.3575809195545,0.6542043213246477,0.051162046,0.047094427,-0.168143532,0
+2,72.73037051491572,2.271715003536844,1269.4086518525746,1041.6905871161305,81994,2340.824450942512,1704.9999369166883,0.6851778308365126,0.028878245,0.026567878769026585,-0.117566742,0
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+36,108.42250922509226,2.263837638376384,1241.7343173431734,2016.7564575645756,542,2084.227657055674,105.61011791566496,0.9987153944664529,0.002292705,0.001944555,-1.569710217,3
+37,102.45038167938931,2.5114503816793894,1202.2824427480916,2017.2213740458014,131,2082.377100579906,96.76338950178457,0.99891979,0.000814368,0.000656194,1.5679661674945196,3
+38,97.29850746268657,2.2686567164179103,1284.7611940298507,2012.955223880597,67,2156.725360764424,97.29765365095275,0.9989818630700821,0.000402736,0.000337967,-1.567633091,3
+39,92.75,3.875,1186.75,2025.5,8,2204.4711436093553,69.06502004388332,0.9995091101407876,0.000165347,7.931550717309619e-05,-1.556173619,3
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diff --git a/tools/visinity/vis-preprocess.xml b/tools/visinity/vis-preprocess.xml
@@ -34,31 +34,26 @@
             <param name="dataset_names" value="dataset_names.csv" />
             <param name="channel_files">
                 <collection type="list">
-                    <element name="i1" value="img_1.ome.tiff" />
-                    <element name="i2" value="img_2.ome.tiff" />
+                    <element name="i1" value="test_image.ome.tiff" />
                 </collection>
             </param>
             <param name="label_files">
                 <collection type="list">
-                    <element name="m1" value="mask_1.tiff" />
-                    <element name="m2" value="mask_2.tiff" />
+                    <element name="m1" value="test_mask.tiff" />
                 </collection>
             </param>
             <param name="quant_csvs">
                 <collection type="list">
-                    <element name="q1" value="quant_1.csv" />
-                    <element name="q2" value="quant_2.csv" />
+                    <element name="q1" value="test_quant.csv" />
                 </collection>
             </param>
             <param name="celltype_csv" value="celltypes.csv" />
-            <output name="out_archive" file="test_visinity_archive.zip" compare="sim_size" />
+            <output name="out_archive" file="output_archive.zip" compare="sim_size" />
             <!-- FIXME: replace with chunk below once CI is upgraded to Galaxy v24 -->
             <!-- <output name="out_archive">
                 <has_archive_member path="./config.json"/>
-                <has_archive_member path="./img_1/embedding.npy"/>
-                <has_archive_member path="./img_2/embedding.npy"/>
-                <has_archive_member path="./img_1/neighborhood.npy"/>
-                <has_archive_member path="./img_2/neighborhood.npy"/>
+                <has_archive_member path="./test_image/embedding.npy"/>
+                <has_archive_member path="./test_image/neighborhood.npy"/>
             </output> -->
         </test>
     </tests>