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# -*- coding: utf-8 -*-
# imageio is distributed under the terms of the (new) BSD License.
""" Storage of image data in tiff format.
"""
from __future__ import absolute_import, print_function, division
from .. import formats
from ..core import Format, has_module
_itk = None # Defer loading to load_lib() function.
def load_lib():
global _itk
try:
import SimpleITK as _itk
except ImportError:
raise ImportError(
"SimpleITK could not be found. "
"Please try "
" easy_install SimpleITK "
"or refer to "
" http://simpleitk.org/ "
"for further instructions."
)
return _itk
# Split up in real ITK and all supported formats.
ITK_FORMATS = (".gipl", ".ipl", ".mha", ".mhd", ".nhdr", ".nii", ".nrrd", ".vtk")
ALL_FORMATS = ITK_FORMATS + (
".bmp",
".jpeg",
".jpg",
".png",
".tiff",
".tif",
".dicom",
".gdcm",
)
class ItkFormat(Format):
""" The ItkFormat uses the simpleITK library to support a range of
ITK-related formats. It also supports a few common formats that are
also supported by the freeimage plugin (e.g. PNG and JPEG).
This format requires the ``simpleITK`` package.
Parameters for reading
----------------------
None.
Parameters for saving
---------------------
None.
"""
def _can_read(self, request):
# If the request is a format that only this plugin can handle,
# we report that we can do it; a useful error will be raised
# when simpleitk is not installed. For the more common formats
# we only report that we can read if the library is installed.
if request.extension in ITK_FORMATS:
return True
if has_module("SimpleITK"):
return request.extension in ALL_FORMATS
def _can_write(self, request):
if request.extension in ITK_FORMATS:
return True
if has_module("SimpleITK"):
return request.extension in ALL_FORMATS
# -- reader
class Reader(Format.Reader):
def _open(self, **kwargs):
if not _itk:
load_lib()
self._img = _itk.ReadImage(self.request.get_local_filename())
def _get_length(self):
return 1
def _close(self):
pass
def _get_data(self, index):
# Get data
if index != 0:
raise IndexError("Index out of range while reading from itk file")
# Return array and empty meta data
return _itk.GetArrayFromImage(self._img), {}
def _get_meta_data(self, index):
raise RuntimeError("The itk format does not support " " meta data.")
# -- writer
class Writer(Format.Writer):
def _open(self):
if not _itk:
load_lib()
def _close(self):
pass
def _append_data(self, im, meta):
_itk_img = _itk.GetImageFromArray(im, isVector=True)
_itk.WriteImage(_itk_img, self.request.get_local_filename())
def set_meta_data(self, meta):
raise RuntimeError("The itk format does not support " " meta data.")
# Register
title = "Insight Segmentation and Registration Toolkit (ITK) format"
format = ItkFormat("itk", title, " ".join(ALL_FORMATS), "iIvV")
formats.add_format(format)
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