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tonpy.py
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tonpy.py
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import pydicom
import os
import SimpleITK as sitk
import numpy as np
from scipy.ndimage import zoom
import pandas as pd
def tonpy(root, save_root, csv_root):
df = pd.read_csv(csv_root)
for i, row in df.iterrows():
if not pd.isna(row).all():
patient = str(row['patient'])
T1_COR = str(row['T1_COR'])
T1_SAG = str(row['T1_SAG'])
T1_TRA = str(row['T1_TRA'])
T2_COR = str(row['T2_COR'])
T2_TRA = str(row['T2_TRA'])
if not os.path.isdir(os.path.join(save_root, patient)):
os.makedirs(os.path.join(save_root, patient))
T1COR_path = os.path.join(save_root, patient, 'T1_COR.npy')
if not os.path.isfile(T1COR_path):
if os.path.isdir(os.path.join(root, patient, T1_COR)):
reader = sitk.ImageSeriesReader()
dicom_names = reader.GetGDCMSeriesFileNames(
os.path.join(root, patient, T1_COR))
reader.SetFileNames(dicom_names)
image = reader.Execute()
image_array = sitk.GetArrayFromImage(image) # z, y, x
origin = image.GetOrigin() # x, y, z
spacing = image.GetSpacing() # x, y, z
print(image_array.shape)
image_array = zoom(image_array,
(140 / image_array.shape[0], 384 / image_array.shape[1], 384 / image_array.shape[2]),
order=1)
image_array = (image_array - image_array.mean()) / image_array.std()
np.save(T1COR_path, image_array)
else:
print(patient,'T1_COR')
T1SAG_path = os.path.join(save_root, patient, 'T1_SAG.npy')
if not os.path.isfile(T1SAG_path):
if os.path.isdir(os.path.join(root, patient, T1_SAG)):
reader = sitk.ImageSeriesReader()
dicom_names = reader.GetGDCMSeriesFileNames(
os.path.join(root, patient, T1_SAG))
reader.SetFileNames(dicom_names)
image = reader.Execute()
image_array = sitk.GetArrayFromImage(image) # z, y, x
print(image_array.shape)
image_array = zoom(image_array,
(140 / image_array.shape[0], 384 / image_array.shape[1], 384 / image_array.shape[2]),
order=1)
image_array = (image_array - image_array.mean()) / image_array.std()
np.save(T1SAG_path, image_array)
else:
print(patient,'T1_SAG')
T1TRA_path = os.path.join(save_root, patient, 'T1_TRA.npy')
if not os.path.isfile(T1TRA_path):
if os.path.isdir(os.path.join(root, patient, T1_TRA)):
reader = sitk.ImageSeriesReader()
dicom_names = reader.GetGDCMSeriesFileNames(
os.path.join(root, patient, T1_TRA))
reader.SetFileNames(dicom_names)
image = reader.Execute()
image_array = sitk.GetArrayFromImage(image) # z, y, x
print(image_array.shape)
image_array = zoom(image_array,
(140 / image_array.shape[0], 384 / image_array.shape[1], 384 / image_array.shape[2]),
order=1)
image_array = (image_array - image_array.mean()) / image_array.std()
np.save(T1TRA_path, image_array)
else:
print(patient,'T1_TRA')
T2COR_path = os.path.join(save_root, patient, 'T2_COR.npy')
if not os.path.isfile(T2COR_path):
if os.path.isdir(os.path.join(root, patient, T2_COR)):
reader = sitk.ImageSeriesReader()
dicom_names = reader.GetGDCMSeriesFileNames(
os.path.join(root, patient, T2_COR))
reader.SetFileNames(dicom_names)
image = reader.Execute()
image_array = sitk.GetArrayFromImage(image) # z, y, x
print(image_array.shape)
image_array = zoom(image_array,
(140 / image_array.shape[0], 384 / image_array.shape[1], 384 / image_array.shape[2]),
order=1)
image_array = (image_array - image_array.mean()) / image_array.std()
np.save(T2COR_path, image_array)
else:
print(patient,'T2_COR')
T2TRA_path = os.path.join(save_root, patient, 'T2_TRA.npy')
if not os.path.isfile(T2TRA_path):
if os.path.isdir(os.path.join(root, patient, T2_TRA)):
reader = sitk.ImageSeriesReader()
dicom_names = reader.GetGDCMSeriesFileNames(
os.path.join(root, patient, T2_TRA))
reader.SetFileNames(dicom_names)
image = reader.Execute()
image_array = sitk.GetArrayFromImage(image) # z, y, x
print(image_array.shape)
image_array = zoom(image_array,
(140 / image_array.shape[0], 384 / image_array.shape[1], 384 / image_array.shape[2]),
order=1)
image_array = (image_array - image_array.mean()) / image_array.std()
np.save(T2TRA_path, image_array)
else:
print(patient,'T2_TRA')
root = '/jhcnas1/xinyi/zhongshan_380/before/before'
save_root = '/jhcnas1/xinyi/zhongshan_380/before/npy'
csv_root = '/jhcnas1/xinyi/zhongshan_380/before.csv'
tonpy(root, save_root, csv_root)
root = '/jhcnas1/xinyi/zhongshan_380/after/after'
save_root = '/jhcnas1/xinyi/zhongshan_380/after/npy'
csv_root = '/jhcnas1/xinyi/zhongshan_380/after.csv'
tonpy(root, save_root, csv_root)