Merge pull request #73 from HelmholtzAI-Consultants-Munich/multicellp…

…ose-integration Multicellpose integration
HelmholtzAI-Consultants-Munich · Feb 23, 2024 · a2aaa6c · a2aaa6c
2 parents 4c596c4 + 72397dd
commit a2aaa6c
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Showing 4 changed files with 308 additions and 36 deletions.
diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml
@@ -48,7 +48,7 @@ jobs:
           pip install pytest-qt
           pip install pytest-xvfb
           pip install coverage
-          pip install -e ".[testing]"
+          pip install -e --no-cache-dir ".[testing]"
           pip install matplotlib
         working-directory: src/client
 
@@ -97,7 +97,7 @@ jobs:
           pip install pytest
           pip install wheel
           pip install coverage
-          pip install -e ".[testing]"
+          pip install -e --no-cache-dir ".[testing]"
         working-directory: src/server
 
       - name: Test with pytest

diff --git a/src/client/test/test_app.py b/src/client/test/test_app.py
@@ -68,13 +68,14 @@ def test_run_inference_run(app):
         "--reload",
         "--port=7010",
     ]
-    process = subprocess.Popen(command)
+    process = subprocess.Popen(command, stdin=subprocess.PIPE, shell=False)
     # and wait until it is setup
     if sys.platform == 'win32' or sys.platform == 'cygwin': time.sleep(240) 
     else: time.sleep(60)
     # then do model serving
     message_text, message_title = app.run_inference()
     # and assert returning message
+    print(f"HERE: {message_text, message_title}")
     assert message_text== "Success! Masks generated for all images"
     assert message_title=="Information"
     # finally clean up process

diff --git a/src/server/dcp_server/config.cfg b/src/server/dcp_server/config.cfg
@@ -1,26 +1,27 @@
 {
     "setup": {
         "segmentation": "GeneralSegmentation",
-        "model_to_use": "UNet", 
+        "model_to_use": "CellposeMultichannel", 
         "accepted_types": [".jpg", ".jpeg", ".png", ".tiff", ".tif"],
         "seg_name_string": "_seg"
     },
 
     "service": {
         "runner_name": "bento_runner",
-        "bento_model_path": "unetN",
+        "bento_model_path": "cp-multi",
         "service_name": "data-centric-platform",
         "port": 7010
     },
 
     "model": { 
         "segmentor": {
             "model_type": "cyto"
+
         },
         "classifier":{
             "model_class": "RandomForest",
             "in_channels": 1,
-            "num_classes": 3,
+            "num_classes": 2,
             "features":[64,128,256,512],
             "black_bg": "False",
             "include_mask": "False"
@@ -33,7 +34,7 @@
 
     "train":{
         "segmentor":{
-            "n_epochs": 10,
+            "n_epochs": 5,
             "channels": [0,0],
             "min_train_masks": 1
         },