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Add point postprocessing #27

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merged 2 commits into from
Jul 16, 2024
Merged

Add point postprocessing #27

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8817cbf
Add point postprocessing
heyufan1995 Jul 16, 2024
a6d8bbf
[pre-commit.ci] auto fixes from pre-commit.com hooks
pre-commit-ci[bot] Jul 16, 2024
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9 changes: 7 additions & 2 deletions scripts/infer.py
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Original file line number Diff line number Diff line change
Expand Up @@ -30,7 +30,7 @@

from .sliding_window import point_based_window_inferer, sliding_window_inference
from .train import CONFIG
from .utils.trans_utils import VistaPostTransform
from .utils.trans_utils import VistaPostTransform, get_largest_connected_component_point

rearrange, _ = optional_import("einops", name="rearrange")
sys.path.insert(0, os.path.abspath(os.path.dirname(__file__)))
Expand Down Expand Up @@ -168,7 +168,8 @@ def infer(
batch_data = self.batch_data
else:
batch_data = self.infer_transforms(image_file)
batch_data["label_prompt"] = label_prompt
if label_prompt is not None:
batch_data["label_prompt"] = label_prompt
batch_data = list_data_collate([batch_data])
self.batch_data = batch_data
if point is not None:
Expand Down Expand Up @@ -231,6 +232,10 @@ def infer(
meta=batch_data["image"].meta,
)
self.prev_mask = batch_data["pred"]
if label_prompt is None and point is not None:
batch_data["pred"] = get_largest_connected_component_point(
batch_data["pred"], point_coords=point, point_labels=point_label
)
batch_data["image"] = batch_data["image"].to("cpu")
batch_data["pred"] = batch_data["pred"].to("cpu")
torch.cuda.empty_cache()
Expand Down
2 changes: 1 addition & 1 deletion scripts/utils/trans_utils.py
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Expand Up @@ -195,7 +195,7 @@ def dilate3d(input_tensor, erosion=3):


def get_largest_connected_component_point(
img: NdarrayTensor, point_coords=None, point_labels=None, post_idx=3
img: NdarrayTensor, point_coords=None, point_labels=None
) -> NdarrayTensor:
"""
Gets the largest connected component mask of an image. img is before post process! And will include NaN values.
Expand Down