# -*- coding: UTF-8 -*-
"""Module containing functions enabling to read, make and
write ITK images.
"""
__version__ = "0.2"
__author__ = "Esther Alberts"
import os
import numpy as np
import SimpleITK as itk
def reduce_arr_dtype(arr, verbose=False):
"""Change arr.dtype to a more memory-efficient dtype, without changing
any element in arr."""
if np.all(arr - np.asarray(arr, "uint8") == 0):
if arr.dtype != "uint8":
if verbose:
print("Converting " + str(arr.dtype) + " to uint8 np.ndarray")
arr = np.asarray(arr, dtype="uint8")
elif np.all(arr - np.asarray(arr, "int8") == 0):
if arr.dtype != "int8":
if verbose:
print("Converting " + str(arr.dtype) + " to int8 np.ndarray")
arr = np.asarray(arr, dtype="int8")
elif np.all(arr - np.asarray(arr, "uint16") == 0):
if arr.dtype != "uint16":
if verbose:
print("Converting " + str(arr.dtype) + " to uint16 np.ndarray")
arr = np.asarray(arr, dtype="uint16")
elif np.all(arr - np.asarray(arr, "int16") == 0):
if arr.dtype != "int16":
if verbose:
print("Converting " + str(arr.dtype) + " to int16 np.ndarray")
arr = np.asarray(arr, dtype="int16")
return arr
def make_itk_image(arr, proto_image=None, verbose=True):
"""Create an itk image given an image array.
Parameters
----------
arr : ndarray
Array to create an itk image with.
proto_image : itk image, optional
Proto itk image to provide Origin, Spacing and Direction.
Returns
-------
image : itk image
The itk image containing the input array `arr`.
"""
arr = reduce_arr_dtype(arr, verbose=verbose)
image = itk.GetImageFromArray(arr)
if proto_image != None:
image.CopyInformation(proto_image)
return image
def write_itk_image(image, path):
"""Write an itk image to a path.
Parameters
----------
image : itk image or np.ndarray
Image to be written.
path : str
Path where the image should be written to.
"""
if isinstance(image, np.ndarray):
image = make_itk_image(image)
writer = itk.ImageFileWriter()
writer.SetFileName(path)
if os.path.splitext(path)[1] == ".nii":
Warning("You are converting nii, " + "be careful with type conversions")
writer.Execute(image)
def get_itk_image(path_or_image):
"""Get an itk image given a path.
Parameters
----------
path : str or itk.Image
Path pointing to an image file with extension among
*TIFF, JPEG, PNG, BMP, DICOM, GIPL, Bio-Rad, LSM, Nifti (.nii and .nii.gz),
Analyze, SDT/SPR (Stimulate), Nrrd or VTK images*.
Returns
-------
image : itk image
The itk image.
"""
if isinstance(path_or_image, itk.Image):
return path_or_image
if not os.path.exists(path_or_image):
err = path_or_image + " doesnt exist"
raise AttributeError(err)
reader = itk.ImageFileReader()
reader.SetFileName(path_or_image)
image = reader.Execute()
return image
def get_itk_array(path_or_image):
"""Get an image array given a path or itk image.
Parameters
----------
path_or_image : str or itk image
Path pointing to an image file with extension among
*TIFF, JPEG, PNG, BMP, DICOM, GIPL, Bio-Rad, LSM, Nifti (.nii and .nii.gz),
Analyze, SDT/SPR (Stimulate), Nrrd or VTK images* or an itk image.
Returns
-------
arr : ndarray
Image ndarray contained in the given path or the itk image.
"""
if isinstance(path_or_image, np.ndarray):
return path_or_image
elif isinstance(path_or_image, str):
image = get_itk_image(path_or_image)
elif isinstance(path_or_image, itk.Image):
image = path_or_image
else:
err = "Image type not recognized: " + str(type(path_or_image))
raise RuntimeError(err)
arr = itk.GetArrayFromImage(image)
return arr
def copy_image_info(input_path, ref_path):
"""Copy origin, direction and spacing information from ref_path
into the header in input_path."""
print("OVerwriting " + input_path[-50:])
ref_im = get_itk_image(ref_path)
im = get_itk_image(input_path)
dim = im.GetSize()
if dim != ref_im.GetSize():
err = "Images are not of same dimension, I will not copy image info!"
raise RuntimeError(err)
im.SetOrigin(ref_im.GetOrigin())
im.SetDirection(ref_im.GetDirection())
im.SetSpacing(ref_im.GetSpacing())
if im.GetSize() != dim:
err = "Dimension changed during copying image info: aborting"
raise RuntimeError(err)
write_itk_image(im, input_path)
def load_arr_from_paths(paths):
"""For every str in paths (paths can consis of nested lists),
load the image at this path. If any str is not a path, an error
is thrown. All other objects are preserved."""
if isinstance(paths, str):
im_arrs = get_itk_array(paths)
elif isinstance(paths, (list, tuple)):
for i, sub_paths in enumerate(paths):
paths[i] = load_arr_from_paths(sub_paths)
im_arrs = paths
else:
im_arrs = paths
return im_arrs
def get_itk_data(path_or_image, verbose=False):
"""Get the image array, image size and pixel dimensions given an itk
image or a path.
Parameters
----------
path_or_image : str or itk image
Path pointing to an image file with extension among
*TIFF, JPEG, PNG, BMP, DICOM, GIPL, Bio-Rad, LSM, Nifti (.nii and .nii.gz),
Analyze, SDT/SPR (Stimulate), Nrrd or VTK images* or an itk image.
verbose : boolean, optional
If true, print image shape, spacing and data type of the image
corresponding to `path_or_image.`
Returns
-------
arr : ndarray
Image array contained in the given path or the itk image.
shape : tuple
Shape of the image array contained in the given path or the itk
image.
spacing : tuple
Pixel spacing (resolution) of the image array contained in the
given path or the itk image.
"""
if isinstance(path_or_image, np.ndarray):
arr = path_or_image
spacing = None
else:
if isinstance(path_or_image, str):
image = get_itk_image(path_or_image)
else:
image = path_or_image
arr = itk.GetArrayFromImage(image)
spacing = image.GetSpacing()[::-1]
shape = arr.shape
data_type = arr.dtype
if verbose:
print("\t image shape: " + str(shape))
print("\t image spacing: " + str(spacing))
print("\t image data type: " + str(data_type))
return arr, shape, spacing
def read_dicom(source_path, verbose=True):
"""Reads dicom series into an itk image.
Parameters
----------
source_path : string
path to directory containing dicom series.
verbose : boolean
print out all series file names.
Returns
-------
image : itk image
image volume.
"""
reader = itk.ImageSeriesReader()
names = reader.GetGDCMSeriesFileNames(source_path)
if len(names) < 1:
raise IOError("No Series can be found at the specified path!")
elif verbose:
print(
"image series with %d dicom files found in : %s"
% (len(names), source_path[-50:])
)
reader.SetFileNames(names)
image = reader.Execute()
if verbose:
get_itk_data(image, verbose=True)
return image
