soorena62
40 lines
1.2 KiB
Python
40 lines
1.2 KiB
Python
import os
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import json
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import numpy as np
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import SimpleITK as sitk
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def run_pysera(image_path: str, mask_path: str):
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# Read image and mask from file paths
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image = sitk.ReadImage(str(image_path))
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mask = sitk.ReadImage(str(mask_path))
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# Ensure mask is binary {0,1} and integer typed
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mask = sitk.Cast(mask, sitk.sitkUInt8)
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# Treat any non-zero voxel as 1
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mask = sitk.BinaryThreshold(
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mask,
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lowerThreshold=1,
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upperThreshold=1_000_000,
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insideValue=1,
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outsideValue=0,
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)
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# Use proper radius vector for BinaryErode based on image dimension
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dim = image.GetDimension()
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radius = [1] * dim # e.g., [1,1,1] for 3D or [1,1] for 2D
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# Safe morphological operation on the binary mask
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eroded = sitk.BinaryErode(mask, radius)
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mask_array = sitk.GetArrayFromImage(mask)
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eroded_array = sitk.GetArrayFromImage(eroded)
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mask_border = np.logical_xor(mask_array, eroded_array)
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# Example features (replace with your real extraction pipeline)
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features = {
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"voxel_spacing": tuple(image.GetSpacing()),
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"mask_voxels": int(np.sum(mask_array)),
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"mask_border_voxels": int(np.sum(mask_border)),
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}
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return features
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