Updated references to testing fixtures; chaeo tests failing but suspect this was the case before

extensions/chaeo/batch_jobs/proj0004-exp0038-fixed.py

@@ -11,7 +11,7 @@ if __name__ == '__main__':
         'batch-output'
     )
 
-    px_ilp = Path.home() / 'model-server' / 'ilastik' / 'AF405-bodies_boundaries.ilp'
+    px_ilp = Path.home() / 'model_server' / 'ilastik' / 'AF405-bodies_boundaries.ilp'
 
     params = {
         'pxmap_threshold': 0.25,

extensions/chaeo/conf/testing.py

 from pathlib import Path
 
-root = Path.home() / 'model-server'
+root = Path.home() / 'model_server'
 
 multichannel_zstack = {
     'path': root / 'testing' / 'zmask-test-stack-chlorophyl.tif',
@@ -11,12 +11,12 @@ multichannel_zstack = {
 }
 
 pixel_classifier = {
-    'path': root / 'ilastik' / 'AF405-bodies_boundaries.ilp'
+    'path': root / 'testing' / 'zmask' / 'AF405-bodies_boundaries.ilp'
 }
 
 pipeline_params = {
     'threshold': 0.6,
 }
 
-output_path = root / 'testing_output' / 'chaeo'
+output_path = root / 'testing' / 'output' / 'chaeo'
 output_path.mkdir(parents=True, exist_ok=True)
\ No newline at end of file

extensions/chaeo/examples/batch_obj_cla.py

@@ -15,8 +15,8 @@ if __name__ == '__main__':
         'zmask_to_automic',
     )
 
-    px_ilp = Path.home() / 'model-server' / 'testing' / 'zmask' / 'AF405-bodies_boundaries.ilp'
-    ob_ilp = Path.home() / 'model-server' / 'testing' / 'zmask' / 'auto_obj_after.ilp'
+    px_ilp = Path.home() / 'model_server' / 'testing' / 'zmask' / 'AF405-bodies_boundaries.ilp'
+    ob_ilp = Path.home() / 'model_server' / 'testing' / 'zmask' / 'auto_obj_after.ilp'
 
     params = {
         'pxmap_threshold': 0.25,

extensions/chaeo/examples/export_patch_focus_metrics.py

@@ -112,7 +112,7 @@ if __name__ == '__main__':
     )
 
     csv_args = {'mode': 'w', 'header': True} # when creating file
-    px_ilp = Path.home() / 'model-server' / 'ilastik' / 'AF405-bodies_boundaries.ilp'
+    px_ilp = Path.home() / 'model_server' / 'ilastik' / 'AF405-bodies_boundaries.ilp'
 
     for ff in where_czi.iterdir():
         if ff.stem != 'Selection--W0000--P0009-T0001':