add load_image param
Browse filesSigned-off-by: binliu <[email protected]>
- vista3d_pipeline.py +7 -3
vista3d_pipeline.py
CHANGED
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@@ -52,6 +52,7 @@ class VISTA3DPipeline(Pipeline):
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"image_key",
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"resample_spacing",
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"metadata_path",
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]
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INFERENCE_EXTRA_ARGS = [
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"mode",
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@@ -105,6 +106,7 @@ class VISTA3DPipeline(Pipeline):
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image_key: str = "image",
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resample_spacing: Sequence = (1.5, 1.5, 1.5),
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metadata_path: str = os.path.join(FILE_PATH, "metadata.json"),
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):
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device = self.device
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subclass = {
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@@ -114,8 +116,7 @@ class VISTA3DPipeline(Pipeline):
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}
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metadata = json.loads(pathlib.Path(metadata_path).read_text())
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labels_dict = metadata["network_data_format"]["outputs"]["pred"]["channel_def"]
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-
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-
[
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LoadImaged(keys=image_key, image_only=True),
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EnsureChannelFirstd(keys=image_key),
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EnsureTyped(keys=image_key, device=device, track_meta=True),
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@@ -137,7 +138,10 @@ class VISTA3DPipeline(Pipeline):
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Orientationd(keys=image_key, axcodes="RAS"),
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CastToTyped(keys=image_key, dtype=torch.float32),
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]
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-
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return preprocessing_transforms
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def _init_postprocessing_transforms(
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"image_key",
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"resample_spacing",
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"metadata_path",
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+
"load_image",
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]
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INFERENCE_EXTRA_ARGS = [
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"mode",
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image_key: str = "image",
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resample_spacing: Sequence = (1.5, 1.5, 1.5),
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metadata_path: str = os.path.join(FILE_PATH, "metadata.json"),
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+
load_image: bool = True,
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):
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device = self.device
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subclass = {
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}
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metadata = json.loads(pathlib.Path(metadata_path).read_text())
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labels_dict = metadata["network_data_format"]["outputs"]["pred"]["channel_def"]
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+
preprocessing_list = [
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LoadImaged(keys=image_key, image_only=True),
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EnsureChannelFirstd(keys=image_key),
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EnsureTyped(keys=image_key, device=device, track_meta=True),
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Orientationd(keys=image_key, axcodes="RAS"),
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CastToTyped(keys=image_key, dtype=torch.float32),
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]
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+
if not load_image:
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+
preprocessing_list.pop(0)
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+
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+
preprocessing_transforms = Compose(preprocessing_list)
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return preprocessing_transforms
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def _init_postprocessing_transforms(
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