Update args and docs from cellfinder. (#165)

Author: matham

benchmarks/benchmarks/cellfinder.py

@@ -204,29 +204,34 @@ def setup(self):
 
     def time_cellfinder_run(self):
         cellfinder_run(
-            self.signal_array,
-            self.background_array,
-            self.cfg.voxel_sizes,
-            self.cfg.start_plane,
-            self.cfg.end_plane,
-            self.cfg.trained_model,
-            self.cfg.model_weights,
-            self.cfg.model,
-            self.cfg.batch_size,
-            self.cfg.n_free_cpus,
-            self.cfg.network_voxel_sizes,
-            self.cfg.soma_diameter,
-            self.cfg.ball_xy_size,
-            self.cfg.ball_z_size,
-            self.cfg.ball_overlap_fraction,
-            self.cfg.log_sigma_size,
-            self.cfg.n_sds_above_mean_thresh,
-            self.cfg.soma_spread_factor,
-            self.cfg.max_cluster_size,
-            self.cfg.cube_width,
-            self.cfg.cube_height,
-            self.cfg.cube_depth,
-            self.cfg.network_depth,
+            signal_array=self.signal_array,
+            background_array=self.background_array,
+            voxel_sizes=self.cfg.voxel_sizes,
+            start_plane=self.cfg.start_plane,
+            end_plane=self.cfg.end_plane,
+            trained_model=self.cfg.trained_model,
+            model_weights=self.cfg.model_weights,
+            model=self.cfg.model,
+            classification_batch_size=self.cfg.classification_batch_size,
+            n_free_cpus=self.cfg.n_free_cpus,
+            network_voxel_sizes=self.cfg.network_voxel_sizes,
+            soma_diameter=self.cfg.soma_diameter,
+            ball_xy_size=self.cfg.ball_xy_size,
+            ball_z_size=self.cfg.ball_z_size,
+            ball_overlap_fraction=self.cfg.ball_overlap_fraction,
+            log_sigma_size=self.cfg.log_sigma_size,
+            n_sds_above_mean_thresh=self.cfg.n_sds_above_mean_thresh,
+            n_sds_above_mean_tiled_thresh=self.cfg.n_sds_above_mean_tiled_thresh,
+            tiled_thresh_tile_size=self.cfg.tiled_thresh_tile_size,
+            soma_spread_factor=self.cfg.soma_spread_factor,
+            max_cluster_size=self.cfg.max_cluster_size,
+            cube_width=self.cfg.cube_width,
+            cube_height=self.cfg.cube_height,
+            cube_depth=self.cfg.cube_depth,
+            network_depth=self.cfg.network_depth,
+            detection_batch_size=self.cfg.detection_batch_size,
+            torch_device=self.cfg.torch_device,
+            pin_memory=self.cfg.pin_memory,
         )
 
 
@@ -244,29 +249,34 @@ def setup(self):
 
         # detect cells
         self.detected_cells = cellfinder_run(
-            self.signal_array,
-            self.background_array,
-            self.cfg.voxel_sizes,
-            self.cfg.start_plane,
-            self.cfg.end_plane,
-            self.cfg.trained_model,
-            self.cfg.model_weights,
-            self.cfg.model,
-            self.cfg.batch_size,
-            self.cfg.n_free_cpus,
-            self.cfg.network_voxel_sizes,
-            self.cfg.soma_diameter,
-            self.cfg.ball_xy_size,
-            self.cfg.ball_z_size,
-            self.cfg.ball_overlap_fraction,
-            self.cfg.log_sigma_size,
-            self.cfg.n_sds_above_mean_thresh,
-            self.cfg.soma_spread_factor,
-            self.cfg.max_cluster_size,
-            self.cfg.cube_width,
-            self.cfg.cube_height,
-            self.cfg.cube_depth,
-            self.cfg.network_depth,
+            signal_array=self.signal_array,
+            background_array=self.background_array,
+            voxel_sizes=self.cfg.voxel_sizes,
+            start_plane=self.cfg.start_plane,
+            end_plane=self.cfg.end_plane,
+            trained_model=self.cfg.trained_model,
+            model_weights=self.cfg.model_weights,
+            model=self.cfg.model,
+            classification_batch_size=self.cfg.classification_batch_size,
+            n_free_cpus=self.cfg.n_free_cpus,
+            network_voxel_sizes=self.cfg.network_voxel_sizes,
+            soma_diameter=self.cfg.soma_diameter,
+            ball_xy_size=self.cfg.ball_xy_size,
+            ball_z_size=self.cfg.ball_z_size,
+            ball_overlap_fraction=self.cfg.ball_overlap_fraction,
+            log_sigma_size=self.cfg.log_sigma_size,
+            n_sds_above_mean_thresh=self.cfg.n_sds_above_mean_thresh,
+            n_sds_above_mean_tiled_thresh=self.cfg.n_sds_above_mean_tiled_thresh,
+            tiled_thresh_tile_size=self.cfg.tiled_thresh_tile_size,
+            soma_spread_factor=self.cfg.soma_spread_factor,
+            max_cluster_size=self.cfg.max_cluster_size,
+            cube_width=self.cfg.cube_width,
+            cube_height=self.cfg.cube_height,
+            cube_depth=self.cfg.cube_depth,
+            network_depth=self.cfg.network_depth,
+            detection_batch_size=self.cfg.detection_batch_size,
+            torch_device=self.cfg.torch_device,
+            pin_memory=self.cfg.pin_memory,
         )
 
     def time_save_cells(self):

brainglobe_workflows/brainmapper/main.py

@@ -120,21 +120,26 @@ def run_all(args, what_to_run, atlas):
         )
 
         points = detect.main(
-            signal_array,
-            args.start_plane,
-            args.end_plane,
-            args.voxel_sizes,
-            args.soma_diameter,
-            args.max_cluster_size,
-            args.ball_xy_size,
-            args.ball_z_size,
-            args.ball_overlap_fraction,
-            args.soma_spread_factor,
-            args.n_free_cpus,
-            args.log_sigma_size,
-            args.n_sds_above_mean_thresh,
+            signal_array=signal_array,
+            start_plane=args.start_plane,
+            end_plane=args.end_plane,
+            voxel_sizes=args.voxel_sizes,
+            soma_diameter=args.soma_diameter,
+            max_cluster_size=args.max_cluster_size,
+            ball_xy_size=args.ball_xy_size,
+            ball_z_size=args.ball_z_size,
+            ball_overlap_fraction=args.ball_overlap_fraction,
+            soma_spread_factor=args.soma_spread_factor,
+            n_free_cpus=args.n_free_cpus,
+            log_sigma_size=args.log_sigma_size,
+            n_sds_above_mean_thresh=args.n_sds_above_mean_thresh,
+            n_sds_above_mean_tiled_thresh=args.n_sds_above_mean_tiled_thresh,
+            tiled_thresh_tile_size=args.tiled_thresh_tile_size,
             save_planes=args.save_planes,
             plane_directory=args.plane_directory,
+            batch_size=args.detection_batch_size,
+            torch_device=args.torch_device,
+            pin_memory=args.pin_memory,
         )
         ensure_directory_exists(args.paths.points_directory)
 
@@ -166,19 +171,20 @@ def run_all(args, what_to_run, atlas):
             background_array = read_z_stack(args.background_planes_path[0])
 
             points = classify.main(
-                points,
-                signal_array,
-                background_array,
-                args.n_free_cpus,
-                args.voxel_sizes,
-                args.network_voxel_sizes,
-                args.batch_size,
-                args.cube_height,
-                args.cube_width,
-                args.cube_depth,
-                args.trained_model,
-                model_weights,
-                args.network_depth,
+                points=points,
+                signal_array=signal_array,
+                background_array=background_array,
+                n_free_cpus=args.n_free_cpus,
+                voxel_sizes=args.voxel_sizes,
+                network_voxel_sizes=args.network_voxel_sizes,
+                batch_size=args.classification_batch_size,
+                cube_height=args.cube_height,
+                cube_width=args.cube_width,
+                cube_depth=args.cube_depth,
+                trained_model=args.trained_model,
+                model_weights=model_weights,
+                network_depth=args.network_depth,
+                pin_memory=args.pin_memory,
             )
             save_cells(
                 points,