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Bugfix postprocess #61

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Bugfix postprocess #61

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ff42665
Fixed error if no cells detected, return type more consistent
MSt-10 Mar 31, 2025
04f9563
Merge branch 'vanvalenlab:master' into bugfix-no-cells
MSt-10 Apr 2, 2025
3cd21a4
Fixed bug in postprocess_predictions
MSt-10 Apr 2, 2025
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10 changes: 5 additions & 5 deletions cellSAM/model.py
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Original file line number Diff line number Diff line change
Expand Up @@ -144,9 +144,9 @@ def segment_cellular_image(
model, img = model.to(device), img.to(device)

preds = model.predict(img, x=None, boxes_per_heatmap=bounding_boxes, device=device, fast=fast)
if preds is None:
if preds[0] is None:
warn("No cells detected in the image.")
return np.zeros(img.shape[1:], dtype=np.int32), None, None
return np.zeros(img.shape[-2:], dtype=np.uint8), None, torch.empty((1, 4))

segmentation_predictions, _, x, bounding_boxes = preds

Expand All @@ -160,12 +160,12 @@ def segment_cellular_image(
return mask, x.cpu().numpy(), bounding_boxes


def postprocess_predictions(mask: np.ndarray):
mask_values = np.unique(mask)
def postprocess_predictions(masks: np.ndarray):
mask_values = np.unique(masks)
new_masks = []
selem = disk(2)
for mask_value in mask_values[1:]:
mask = mask == mask_value
mask = masks == mask_value
mask, _ = remove_small_regions(mask, 20, mode="holes")
mask, _ = remove_small_regions(mask, 20, mode="islands")
opened_mask = binary_opening(mask, selem)
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