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app.py
CHANGED
@@ -1,16 +1,13 @@
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import gradio as gr
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import nibabel as nib
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import pydicom
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import os
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import dicom2nifti
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def convert(input):
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# if linux
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path = input.name
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print("Zip file path:", path)
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assert path.endswith('.zip'), 'File must be a zip file'
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-
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os.system(f'unzip -q "{path}" -d "{path[:-4]}"')
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path = path[:-4]
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files = os.listdir(path)
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@@ -19,19 +16,18 @@ def convert(input):
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print("Dicom folder path:", path)
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dicom_files = os.listdir(path)
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assert [f.endswith('.dcm') for f in dicom_files], 'Dicom folder must contain only .dcm files'
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print("This is the list of files in the folder:", os.listdir(path))
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# create an output file that has the same name as the input file but with a .nii.gz extension
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output_file = os.path.join(path, os.path.basename(path) + '.nii.gz')
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dicom2nifti.dicom_series_to_nifti(path, output_file, reorient_nifti=True)
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print("Nifti file path:", output_file)
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-
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return output_file
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gr.Interface(
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fn=convert,
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inputs=gr.File(type="file", label="Dicom folder (.zip)", file_types=["zip"]),
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outputs="file",
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title="Convert a Dicom folder to a Nifti (.nii.gz) file",
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)
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import gradio as gr
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# import nibabel as nib
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# import pydicom
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import os
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import dicom2nifti
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def convert(input):
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path = input.name
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print("Zip file path:", path)
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assert path.endswith('.zip'), 'File must be a zip file'
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os.system(f'unzip -q "{path}" -d "{path[:-4]}"')
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path = path[:-4]
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files = os.listdir(path)
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print("Dicom folder path:", path)
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dicom_files = os.listdir(path)
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assert [f.endswith('.dcm') for f in dicom_files], 'Dicom folder must contain only .dcm files'
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output_file = os.path.join(path, os.path.basename(path) + '.nii.gz')
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dicom2nifti.dicom_series_to_nifti(path, output_file, reorient_nifti=True)
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print("Nifti file path:", output_file)
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return output_file
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app = gr.Interface(
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fn=convert,
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inputs=gr.File(type="file", label="Dicom folder (.zip)", file_types=["zip"]),
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outputs="file",
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title="Convert a Dicom folder to a Nifti (.nii.gz) file",
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)
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app.queue(concurrency_count=1)
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app.launch()
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