Consolidated more parameters into pydantic models

extensions/chaeo/zmask.py

@@ -9,7 +9,7 @@ from sklearn.linear_model import LinearRegression
 
 from extensions.chaeo.annotators import draw_boxes_on_3d_image
 from extensions.chaeo.products import export_patches_from_zstack, export_multichannel_patches_from_zstack, export_patch_masks_from_zstack, get_patches_from_zmask_meta, get_patch_masks_from_zmask_meta
-from extensions.chaeo.params import AnnotatedZStackParams, PatchParams, RoiFilter, RoiSetMetaParams, RoiSetExportParams
+from extensions.chaeo.params import RoiFilter, RoiSetMetaParams, RoiSetExportParams
 from extensions.chaeo.process import mask_largest_object
 from model_server.accessors import GenericImageDataAccessor, InMemoryDataAccessor, write_accessor_data_to_file
 from model_server.models import InstanceSegmentationModel
@@ -26,9 +26,10 @@ class RoiSet(object):
         self.zmask, self.zmask_meta, self.df, self.interm = build_zmask_from_object_mask(
             acc_mask,
             acc_raw,
-            filters=params.filters,
-            mask_type=params.mask_type,
-            expand_box_by=params.expand_box_by
+            params=params,
+            # filters=params.filters,
+            # mask_type=params.mask_type,
+            # expand_box_by=params.expand_box_by
         )
 
         self.acc_raw = acc_raw
@@ -138,9 +139,7 @@ class RoiSet(object):
 def build_zmask_from_object_mask(
         obmask: GenericImageDataAccessor,
         zstack: GenericImageDataAccessor,
-        filters=None,
-        mask_type='contours',
-        expand_box_by=(0, 0),
+        params: RoiSetMetaParams,
 ):
     """
     Given a 2D mask of objects, build a 3D mask, where each object's z-position is determined by the index of
@@ -164,7 +163,9 @@ def build_zmask_from_object_mask(
             label_map: np.ndarray (h x w) where each unique object has an integer label
             argmax: np.ndarray (h x w x 1 x 1) z-index of highest intensity in zstack
     """
-
+    filters = params.filters
+    mask_type = params.mask_type
+    expand_box_by = params.expand_box_by
     # validate inputs
     # assert zstack.chroma == 1
     assert mask_type in ('contours', 'boxes'), mask_type