54 lines
1.5 KiB
Python
54 lines
1.5 KiB
Python
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import SimpleITK as sitk
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from rt_utils import RTStructBuilder
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import numpy as np
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DCM_CT = '/nn/3378417/20241112/CT/8'
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NII_CT = "/nn/3378417/20241112/nii/8_1.1_CyberKnife_head(MAR)_20241112110016_4.nii.gz"
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label_file = "/nn/3378417/20241112/nii/8_1.1_CyberKnife_head(MAR)_20241112110016.label.nii.gz"
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rtss_file = '/nn/3378417/20241112/CT/8-rtss.dcm'
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# reg_transform(NII_CT, NII_MR, output_file, label_file)
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reader = sitk.ImageSeriesReader()
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dicom_names = reader.GetGDCMSeriesFileNames(DCM_CT)
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reader.SetFileNames(dicom_names)
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# reader.SetFileNames(sorted(dicom_names))
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reader.MetaDataDictionaryArrayUpdateOn()
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reader.LoadPrivateTagsOn()
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image = reader.Execute()
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sitk.WriteImage(image, '0/image.nii.gz')
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nnU = sitk.ReadImage(label_file)
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nnU = sitk.Resample(nnU, image, sitk.Transform(), sitk.sitkNearestNeighbor)
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sitk.WriteImage(nnU, '0/nnU.nii.gz')
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ccfilter = sitk.ConnectedComponentImageFilter ()
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nnUCC = ccfilter.Execute(nnU)
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ObjectCount1 = ccfilter.GetObjectCount()
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rtstruct = RTStructBuilder.create_new(dicom_series_path=DCM_CT)
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print(ObjectCount1)
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for j1 in range(ObjectCount1):
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label1 = sitk.BinaryThreshold(nnUCC, j1+1, j1+1)
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# label1 = sitk.AntiAliasBinary(label1)
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mask = sitk.GetArrayFromImage(label1).astype(bool)
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mask = np.transpose(mask, (1, 2, 0))
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# continue
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if mask.any():
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print(j1)
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rtstruct.add_roi(
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mask=mask,
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# use_pin_hole=True,
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# name="n%d"%n,
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)
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print(rtss_file)
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rtstruct.save(rtss_file)
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# return rtss_file
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