Adjust block_shape based on input dimensions

constantinpape · web-flow · commit 92303d7c8c68 · 2025-12-01T19:33:24.000+01:00
diff --git a/flamingo_tools/segmentation/synapse_detection.py b/flamingo_tools/segmentation/synapse_detection.py
@@ -182,8 +182,8 @@ def marker_detection(
         )
 
     if not os.path.exists(detection_path):
-        block_shape = (64, 256, 256)
         input_ = zarr.open(output_path, "r")[prediction_key]
+        block_shape = (min(64, input_.shape[0]), min(input_.shape[1], 256), min(input_.shape[2], 256))
         detections = find_local_maxima(
             input_, block_shape=block_shape, min_distance=2, threshold_abs=0.5, verbose=True, n_threads=16,
         )

Original file line number	Diff line number	Diff line change
`@@ -182,8 +182,8 @@ def marker_detection(`
`182`	`182`	`)`
`183`	`183`
`184`	`184`	`if not os.path.exists(detection_path):`
`185`		`- block_shape = (64, 256, 256)`
`186`	`185`	`input_ = zarr.open(output_path, "r")[prediction_key]`
	`186`	`+ block_shape = (min(64, input_.shape[0]), min(input_.shape[1], 256), min(input_.shape[2], 256))`
`187`	`187`	`detections = find_local_maxima(`
`188`	`188`	`input_, block_shape=block_shape, min_distance=2, threshold_abs=0.5, verbose=True, n_threads=16,`
`189`	`189`	`)`