Working on JSON dump of run data

extensions/chaeo/examples/batch_run_patches.py

+import json
 from pathlib import Path
 import re
 from time import localtime, strftime
@@ -41,18 +42,33 @@ if __name__ == '__main__':
             continue
 
 
-        result = export_patches_from_multichannel_zstack(
-            input_zstack_path=where_czi/ff,
-            px_model=px_model,
-            pxmap_threshold=0.25,
-            pixel_class=0,
-            zmask_channel=0,
-            patches_channel=4,
-            where_output=where_output,
-            mask_type='boxes',
-            zmask_filters={'area': (1e3, 1e8)},
-            zmask_expand_box_by=(128, 0),
-        )
+        export_kwargs = {
+            'input_zstack_path': (where_czi / ff).__str__(),
+            'px_model': px_model.model_id,
+            'pxmap_threshold': 0.25,
+            'pixel_class': 0,
+            'zmask_channel': 0,
+            'patches_channel': 4,
+            'where_output': where_output.__str__(),
+            'mask_type': 'boxes',
+            'zmask_filters': {'area': (1e3, 1e8)},
+            'zmask_expand_box_by': (128, 0),
+        }
+
+        # result = export_patches_from_multichannel_zstack(
+        #     input_zstack_path=where_czi / ff,
+        #     px_model=px_model,
+        #     pxmap_threshold=0.25,
+        #     pixel_class=0,
+        #     zmask_channel=0,
+        #     patches_channel=4,
+        #     where_output=where_output,
+        #     mask_type='boxes',
+        #     zmask_filters={'area': (1e3, 1e8)},
+        #     zmask_expand_box_by=(128, 0),
+        # )
+
+        result = export_patches_from_multichannel_zstack(**export_kwargs)
 
         # parse and record results
         df = result['dataframe']
@@ -66,4 +82,5 @@ if __name__ == '__main__':
             write_accessor_data_to_file(
                 where_output / k / (ff.stem + '.tif'),
                 InMemoryDataAccessor(result['interm'][k])
-                )
\ No newline at end of file
+                )
+

extensions/chaeo/workflows.py

@@ -12,21 +12,21 @@ from model_server.accessors import generate_file_accessor, InMemoryDataAccessor,
 from model_server.workflows import Timer
 
 def export_patches_from_multichannel_zstack(
-        input_zstack_path: Path,
-        px_model: IlastikPixelClassifierModel,
+        input_zstack_path: str,
+        px_model_id: str,
         pxmap_threshold: float,
         pixel_class: int,
         zmask_channel: int,
         patches_channel: int,
-        where_output: Path,
+        where_output: str,
         mask_type: str = 'boxes',
         zmask_filters: Dict = None,
         zmask_expand_box_by: int = None,
 ) -> Dict:
 
     ti = Timer()
-    stack = generate_file_accessor(input_zstack_path)
-    fstem = input_zstack_path.stem
+    stack = generate_file_accessor(Path(input_zstack_path))
+    fstem = Path(input_zstack_path).stem
     ti.click('file_input')
     assert stack.nz > 1, 'Expecting z-stack'
 
@@ -34,11 +34,12 @@ def export_patches_from_multichannel_zstack(
     mip = InMemoryDataAccessor(
         stack.get_one_channel_data(channel=0).data.max(axis=-1, keepdims=True)
     )
+    # px_model =
     pxmap, _ = px_model.infer(mip)
     ti.click('infer_pixel_probability')
 
     write_accessor_data_to_file(
-        where_output / 'pixel_probabilities' / (fstem + '.tif'),
+        Path(where_output) / 'pixel_probabilities' / (fstem + '.tif'),
         pxmap
     )
     ti.click('export_pixel_probability')
@@ -61,7 +62,7 @@ def export_patches_from_multichannel_zstack(
 
     # export patches
     files = export_patches_from_zstack(
-        where_output / '2d_patches',
+        Path(where_output) / '2d_patches',
         stack.get_one_channel_data(patches_channel),
         zmask_meta,
         prefix=fstem,
@@ -78,14 +79,14 @@ def export_patches_from_multichannel_zstack(
         )
     )
     write_accessor_data_to_file(
-        where_output / 'annotated_zstacks' / (fstem + '.tif'),
+        Path(where_output) / 'annotated_zstacks' / (fstem + '.tif'),
         annotated
     )
     ti.click('export_annotated_zstack')
 
     return {
         'pixel_model_id': px_model.model_id,
-        'input_filepath': str(input_zstack_path),
+        'input_filepath': input_zstack_path,
         'number_of_objects': len(zmask_meta),
         'success': True,
         'timer_results': ti.events,