Customizable resolution for object measures

Author: schilling40

flamingo_tools/measurements.py

@@ -25,7 +25,7 @@
 
 def _measure_volume_and_surface(mask, resolution):
     # Use marching_cubes for 3D data
-    verts, faces, normals, _ = marching_cubes(mask, spacing=(resolution,) * 3)
+    verts, faces, normals, _ = marching_cubes(mask, spacing=resolution)
 
     mesh = trimesh.Trimesh(vertices=verts, faces=faces, vertex_normals=normals)
     surface = mesh.area
@@ -61,9 +61,9 @@ def _get_bounding_box_and_center(table, seg_id, resolution, shape, dilation):
     )
 
     center = (
-        int(row.anchor_z.item() / resolution),
-        int(row.anchor_y.item() / resolution),
-        int(row.anchor_x.item() / resolution),
+        int(row.anchor_z.item() / resolution[0]),
+        int(row.anchor_y.item() / resolution[1]),
+        int(row.anchor_x.item() / resolution[2]),
     )
 
     return bb, center
@@ -236,7 +236,7 @@ def compute_object_measures_impl(
     image: np.typing.ArrayLike,
     segmentation: np.typing.ArrayLike,
     n_threads: Optional[int] = None,
-    resolution: float = 0.38,
+    resolution: Optional[Tuple[float, float, float]] = (0.38, 0.38, 0.38),
     table: Optional[pd.DataFrame] = None,
     feature_set: str = "default",
     background_mask: Optional[np.typing.ArrayLike] = None,
@@ -307,7 +307,7 @@ def compute_object_measures(
     image_key: Optional[str] = None,
     segmentation_key: Optional[str] = None,
     n_threads: Optional[int] = None,
-    resolution: float = 0.38,
+    resolution: Optional[Tuple[float, float, float]] = (0.38, 0.38, 0.38),
     force: bool = False,
     feature_set: str = "default",
     s3_flag: bool = False,

reproducibility/object_measures/repro_object_measures.py

@@ -4,6 +4,7 @@
 from multiprocessing import cpu_count
 from typing import Optional
 
+import numpy as np
 import flamingo_tools.s3_utils as s3_utils
 from flamingo_tools.measurements import compute_object_measures, compute_sgn_background_mask
 
@@ -18,6 +19,7 @@ def repro_object_measures(
 ):
     s3_flag = True
     input_key = "s0"
+    default_resolution = 0.38
     default_component_list = [1]
     default_bg_mask = None
 
@@ -29,10 +31,15 @@ def repro_object_measures(
         cochlea = dic["cochlea"]
         image_channels = dic["image_channel"] if isinstance(dic["image_channel"], list) else [dic["image_channel"]]
         seg_channel = dic["segmentation_channel"]
+        resolution = tuple(dic["resolution"]) if "resolution" in dic else default_resolution
         component_list = dic["component_list"] if "component_list" in dic else default_component_list
         bg_mask = dic["background_mask"] if "background_mask" in dic else default_bg_mask
         print(f"Processing cochlea {cochlea}")
 
+        if not isinstance(resolution, float):
+            assert len(resolution) == 3
+            resolution = np.array(resolution)[::-1]
+
         for img_channel in image_channels:
 
             print(f"Processing image channel {img_channel}")
@@ -88,6 +95,7 @@ def repro_object_measures(
                     median_only=median_only,
                     background_mask=bg_mask,
                     n_threads=n_threads,
+                    resolution=resolution,
                 )