SimpleITK

00_readme.md

This repository describe 'SimpleITK' which python module is inheritence by 3D voxel image processing module 'ITK'

01_resampleImage.py

def resampleImage(img, new_spacing, image=True):
    '''Spacing幅を変えるときのコード
        img:sitk.Image
        new_spacing: tuple(x,y,z)
        image: image or label. if label, image=False
        sitk.SetSpacingだけではnumpy.shapeは変更されないので注意。
    '''
    def calc_new_size():
        np_size = np.array(img.GetSize())
        np_cur_spacing = np.array(img.GetSpacing())
        np_new_spacing = np.array(new_spacing)

        np_new_size = np_size * np_cur_spacing / new_spacing
        return np_new_size.astype(int).tolist()

    origin = img.GetOrigin()
    size = img.GetSize()
    cur_spacing = img.GetSpacing()
    direction = img.GetDirection()

    new_size = calc_new_size()
    transform = sitk.Transform()                # default is 'IdentityTransform'
    # interpolator = sitk.sitkNearestNeighbor
    interpolator = sitk.sitkBSpline if image else sitk.sitkNearestNeighbor
    return sitk.Resample(img, new_size, transform, interpolator,
                         origin, new_spacing, direction, 0.0, img.GetPixelIDValue())

02_save_niigz.py

def save_niigz(save_path: Path, array: np.array, spacing:tuple):
	# (z,x,y)の方向になるようにする。
	DIRECTION = (1.0, 0.0, 0.0, 0.0, 1.0, 0.0, 0.0, 0.0, -1.0)
	array = array.astype(np.int16)
	save_image = sitk.GetImageFromArray(array)
	save_image.SetSpacing(spacing)
	save_image.SetDirection(DIRECTION)
	if not save_path.parent.is_dir():
			save_path.parent.mkdir()
			print(save_path)
	sitk.WriteImage(save_image, str(save_path), True)

03_get_data.py

from pathlib import Path
def get_data(path: str, spacing:tuple, image=True):
    """pathからスペーシング幅を決めて画像とarrayを返す"""
    if Path(path).is_file():
        img = sitk.ReadImage(str(path))
        # boolを渡して、interpolatorを変更している
        img = self.resampleImage(img, spacing, image=image)
        img_array = sitk.GetArrayFromImage(img)
        return img_array
    else:
        print(f'{path} is not exist.')
        return False

04_resample_whole.py

def resampleImage(img, new_spacing, image=True):
    '''Spacing幅を変えるときのコード
        img:sitk.Image
        new_spacing: tuple(x,y,z)
        image: image or label. if label, image=False
        sitk.SetSpacingだけではnumpy.shapeは変更されないので注意。
    '''
    def calc_new_size():
        np_size = np.array(img.GetSize())
        np_cur_spacing = np.array(img.GetSpacing())
        np_new_spacing = np.array(new_spacing)

        np_new_size = np_size * np_cur_spacing / new_spacing
        return np_new_size.astype(int).tolist()

    origin = img.GetOrigin()
    size = img.GetSize()
    cur_spacing = img.GetSpacing()
    direction = img.GetDirection()

    new_size = calc_new_size()
    transform = sitk.Transform()                # default is 'IdentityTransform'
    # interpolator = sitk.sitkNearestNeighbor
    interpolator = sitk.sitkBSpline if image else sitk.sitkNearestNeighbor
    return sitk.Resample(img, new_size, transform, interpolator,
                         origin, new_spacing, direction, 0.0, img.GetPixelIDValue())

def spacing_changer(impath,sepath,save_impath,save_sepath,spacing,z_pad_size=3):
    def get_data(path: str, spacing=False, image=True):
        """pathからスペーシング幅を決めて画像とarrayを返す"""
        if Path(path).is_file():
            img = sitk.ReadImage(str(path))
            img_array = sitk.GetArrayFromImage(img)
            direction = img.GetDirection()
            spacing = img.GetSpacing()
            
            print('spacing:',img.GetSpacing())
            print('shape:',img.GetSize())
            return img,img_array,direction,spacing
        else:
            print(f'{path} is not exist.')
            return False
    
    im,im_arr,im_direction,im_spacing = get_data(impath,image=True)
    se,se_arr,se_direction,se_spacing = get_data(sepath,image=False)
    
    #ガンがある領域だけ
    z_indexes = np.argwhere(np.sum(np.where(se_arr==2,se_arr,0),axis=(0,1))!=0)
    # z_indexes = np.argwhere(np.sum(se_arr,axis=(0,1))!=0)

    z_top = np.squeeze(z_indexes)[0]
    z_end = np.squeeze(z_indexes)[-1]
    
    new_se_arr = se_arr[...,z_top-5:z_end+5].astype(np.int16)
    new_im_arr = im_arr[...,z_top-5:z_end+5].astype(np.int16)
    

    save_image = sitk.GetImageFromArray(new_im_arr)
    save_segmentation = sitk.GetImageFromArray(new_se_arr)
    
    save_image.SetSpacing(im_spacing)
    save_image.SetDirection(im_direction)
    save_segmentation.SetSpacing(se_spacing)
    save_segmentation.SetDirection(im_direction)


    save_image = resampleImage(save_image, spacing, image=True)
    save_segmentation = resampleImage(save_segmentation, spacing, image=False)
    
    save_image.SetSpacing(spacing)
    save_segmentation.SetSpacing(spacing)
    
    save_segmentation = resampleImage(save_segmentation, spacing, image=False)
    print('resampled shape:', save_image.GetSize(), save_segmentation.GetSize())


    sitk.WriteImage(save_image, str(save_impath), True)
    sitk.WriteImage(save_segmentation, str(save_sepath), True)
    

impaths = sorted(glob.glob('/home/higuchi/ssd2/kits19/data/case_00*/imaging.nii.gz'))
sepaths = sorted(glob.glob('/home/higuchi/ssd2/kits19/data/case_00*/segmentation.nii.gz'))
save_impaths = [re.sub('imaging','imaging_078_078_1',path) for path in impaths]
save_sepaths = [re.sub('imaging','imaging_078_078_1',path) for path in sepaths]

spacing = (1.0, 0.781624972820282, 0.781624972820282)
for impath,sepath,save_impath,save_sepath in zip(impaths,sepaths,save_impaths,save_sepaths):
    try:
        spacing_changer(impath,sepath,save_impath,save_sepath,spacing,z_pad_size=5)
    except:
        print(impath)