def slice_by_label():
'''
:return:
'''
files = glob.glob("../datasets/myo_data/train25_myops_gd_convert/*.nii.gz")
output_lab_dir = "../datasets/myo_data/train25_myops_gd_crop/"
output_img_dir = "../datasets/myo_data/train25_myops_crop/"
mkdir_if_not_exist(output_lab_dir)
for i in files:
lab = sitk.ReadImage(i)
#先转化成统一space,保证crop的大小一致
lab = sitkResample3DV2(lab, sitk.sitkNearestNeighbor, [1, 1, 1])
bbox = get_bounding_boxV2(sitk.GetArrayFromImage(lab), padding=10)
##extend bbox
crop_lab = crop_by_bbox(lab, bbox)
crop_lab = sitkResize3DV2(crop_lab,
[256, 256, crop_lab.GetSize()[-1]],
sitk.sitkNearestNeighbor)
sitk_write_image(crop_lab[:, :, crop_lab.GetSize()[-1] // 2],
dir=output_lab_dir,
name=os.path.basename(i))
img_file = glob.glob(
"../datasets/myo_data/train25_convert/*%s*.nii.gz" %
(os.path.basename(i).split("_")[2]))
for j in img_file:
img = sitk.ReadImage(j)
img = sitkResample3DV2(img, sitk.sitkLinear, [1, 1, 1])
crop_img = crop_by_bbox(img, bbox)
crop_img = sitkResize3DV2(
crop_img, [256, 256, crop_img.GetSize()[-1]], sitk.sitkLinear)
sitk_write_image(crop_img[:, :, crop_lab.GetSize()[-1] // 2],
dir=output_img_dir,
name=os.path.basename(j))
def __sitkresize(self, img, lab, size):
img = sitkResize3DV2(img, size, sitk.sitkLinear)
# img=sitkResize3D(img,size)
lab = sitkResize3DV2(lab, size, sitk.sitkNearestNeighbor)
# lab=sitkResize3D(lab,size)
return img, lab
def resize_img_lab(imgs,labs,output_img,output_lab,zscore):
for p_img,p_lab in zip(imgs,labs):
img_obj=sitk.ReadImage(p_img)
lab_obj=sitk.ReadImage(p_lab)
resize_lab = sitkResize3DV2(lab_obj, [96, 96, 96], sitk.sitkNearestNeighbor)
sitk_write_image(resize_lab, dir=output_lab, name=os.path.basename(p_lab))
resize_img = sitkResize3DV2(img_obj, [96, 96, 96], sitk.sitkLinear)
if zscore:
resize_img=sitk.RescaleIntensity(resize_img)
resize_img=sitk.Normalize(resize_img)
sitk_write_image(resize_img, dir=output_img, name=os.path.basename(p_img))
def de_resize(refs, tgts, output_dir):
for r, t in zip(refs, tgts):
ref = sitk.ReadImage(r)
lab = sitk.ReadImage(t)
lab = sitkResize3DV2(lab, ref.GetSize(), sitk.sitkNearestNeighbor)
sitk_write_image(lab, dir=output_dir, name=os.path.basename(t))
def preprocess_mannul_itk_img(self, structure=420):
for i in range(self.img.num_data):
print("process image %d" % (i + 1))
image = self.img.get_file_obj(i)
print("original size: ", image.GetSize())
image = sitkResize3DV2(image, [96, 96, 96], sitk.sitkLinear)
print("image size: ", image.GetSize())
# image=self.__reset_space(image)
self.__itksave_single_img(image, i, tag='resize')
def de_resize(self, structure):
self.structure = structure
save_dir = self.target_labels.dir_name + "_deResize"
for i in range(self.target_labels.num_data):
print("process image %d" % (i + 1))
ref = self.references.get_file_obj(i)
lab = self.target_labels.get_file_obj(i)
lab = sitkResize3DV2(lab, ref.GetSize(), sitk.sitkNearestNeighbor)
self.__itksave_label(lab, i, save_dir)
return save_dir