def save(self):
ref = sitk.GetImageFromArray(self.ct_array)
SaveArrayToNiiByRef(os.path.join(self.case_path, "result_ct.nii.gz"),
np.transpose(self.ct_array, (1, 2, 0)), ref)
SaveArrayToNiiByRef(os.path.join(self.case_path, "result_pet.nii.gz"),
np.transpose(self.pet_array, (1, 2, 0)), ref)
SaveArrayToNiiByRef(os.path.join(self.case_path, "result_cp.nii.gz"),
np.transpose(self.cp_array, (1, 2, 0)), ref)
SaveArrayToNiiByRef(os.path.join(self.case_path, "result_roi.nii.gz"),
np.transpose(self.roi_array, (1, 2, 0)), ref)
def get_nii(self):
reader = sitk.ImageSeriesReader()
dcm_names = reader.GetGDCMSeriesFileNames(self.dicom_path)
reader.SetFileNames(dcm_names)
dcm_image_all = reader.Execute()
dcm_image_array = sitk.GetArrayFromImage(dcm_image_all)
dcm_image_array = np.transpose(dcm_image_array, (1, 2, 0))
try:
SaveArrayToNiiByRef(store_path=os.path.join(
self.store_path, "ct.nii"),
array=dcm_image_array,
ref_image=self.roi)
except:
pass
def get_ROI(self, value, store_name): # value用来选择
ruangu_roi = os.path.join(self.case_path, "roi.nii.gz") # 软骨路径
xiagu_roi = os.path.join(self.case_path,
"moved_new_roi.nii.gz") # 下骨路径
data_path = os.path.join(self.case_path, "data_1.nii")
data_array = standard(np.flipud(get_array_from_path(data_path)))
data = sitk.ReadImage(data_path)
ruangu_roi_array = get_array_from_path(ruangu_roi)
single_ruangu_array = np.where(ruangu_roi_array == value, 1, 0) # 软骨
xiagu_roi_array = get_array_from_path(xiagu_roi)
single_xiagu_array = np.where(xiagu_roi_array == value, 1, 0) # 下骨
# 显示检查
# Imshow3DArray(data_array, [single_ruangu_array, single_xiagu_array])
SaveArrayToNiiByRef(
os.path.join(self.case_path, "ruan_gu_" + store_name + ".nii"),
single_ruangu_array, data)
SaveArrayToNiiByRef(
os.path.join(self.case_path, "xia_gu_" + store_name + ".nii"),
single_xiagu_array, data)
def get_result(self):
for folder in os.listdir(self.root_path):
folder_path = os.path.join(self.root_path, folder)
for case in os.listdir(folder_path):
case_path = os.path.join(folder_path, case)
ct_path = os.path.join(case_path, "croped_ct.npy")
pet_path = os.path.join(case_path, "croped_pet.npy")
roi_path = os.path.join(case_path, "pred_roi.npy")
ct_array = np.load(ct_path)
pet_array = np.load(pet_path)
roi_array = np.load(roi_path)
pet_ct_array = pet_array + ct_array
#############
# 显示结果
#############
roi = sitk.GetImageFromArray(roi_array)
pet_array = np.transpose(pet_array, (1, 2, 0))
ct_array = np.transpose(ct_array, (1, 2, 0))
pet_ct_array = np.transpose(pet_ct_array, (1, 2, 0))
roi_array = np.transpose(roi_array, (1, 2, 0))
SaveArrayToNiiByRef(store_path=os.path.join(
case_path, "result_ct.nii"),
array=ct_array,
ref_image=roi)
SaveArrayToNiiByRef(store_path=os.path.join(
case_path, "result_pet.nii"),
array=pet_array,
ref_image=roi)
SaveArrayToNiiByRef(store_path=os.path.join(
case_path, "result_ct_pet.nii"),
array=pet_ct_array,
ref_image=roi)
SaveArrayToNiiByRef(store_path=os.path.join(
case_path, "result_roi.nii"),
array=roi_array,
ref_image=roi)
print("Case {} is finished!".format(case))
def flup_pet():
"""将pet的数据进行上下颠倒"""
root_path = r"Y:\DYB\PETCT_EGFR"
for folder in os.listdir(root_path):
folder_path = os.path.join(root_path, folder)
for case in os.listdir(folder_path):
case_path = os.path.join(folder_path, case)
pet_path = os.path.join(case_path, "pet_Resize.nii")
pet_array = get_array_from_path(pet_path)
pet_array = np.flipud(pet_array)
pet = sitk.ReadImage(pet_path)
SaveArrayToNiiByRef(store_path=os.path.join(case_path, "new_pet_resize.nii"),
array=pet_array,
ref_image=pet)
print("case {} is finished!".format(case))
def get_new_t2(root_path):
"""对图像进行平滑"""
for case in os.listdir(root_path):
t2_path = os.path.join(root_path, case, "T2.nii")
t2_array = get_array_from_path(t2_path)
# roi_array = get_array_from_path(os.path.join(root_path, case, "ruan_gu_up_1.nii"))
new_t2_array = cv2.blur(t2_array, (5, 5))
new_t2_array = new_t2_array.astype(np.int64)
t2 = sitk.ReadImage(t2_path)
SaveArrayToNiiByRef(store_path=os.path.join(root_path, case,
"new_T2.nii"),
array=new_t2_array,
ref_image=t2)
print("Case {} is finished!".format(case))
def get_data_roi():
root_path = r"Y:\DYB\PETCT_EGFR"
for folder in os.listdir(root_path):
folder_path = os.path.join(root_path, folder)
for case in os.listdir(folder_path):
case_path = os.path.join(folder_path, case)
ct_path = os.path.join(case_path, "ct.nii")
roi_path = os.path.join(case_path, "no_name.nii")
data = sitk.ReadImage(ct_path)
ct_array = get_array_from_path(ct_path)
roi_array = get_array_from_path(roi_path)
roi_array = np.flipud(roi_array)
SaveArrayToNiiByRef(store_path=os.path.join(
case_path, "ct_roi.nii"),
array=roi_array,
ref_image=data)
print(case)