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# -*- coding: utf-8 -*-
# imageio is distributed under the terms of the (new) BSD License.
"""Read/Write images using SimpleITK.
Backend: `Insight Toolkit <https://itk.org/>`_
.. note::
To use this plugin you have to install its backend::
pip install imageio[itk]
The ItkFormat uses the ITK or SimpleITK library to support a range of
ITK-related formats. It also supports a few common formats (e.g. PNG and JPEG).
Parameters
----------
None
"""
from ..core import Format, has_module
_itk = None # Defer loading to load_lib() function.
def load_lib():
global _itk, _read_function, _write_function
try:
import itk as _itk
_read_function = _itk.imread
_write_function = _itk.imwrite
except ImportError:
try:
import SimpleITK as _itk
_read_function = _itk.ReadImage
_write_function = _itk.WriteImage
except ImportError:
raise ImportError(
"itk could not be found. "
"Please try "
" python -m pip install itk "
"or "
" python -m pip install simpleitk "
"or refer to "
" https://itkpythonpackage.readthedocs.io/ "
"for further instructions."
)
return _itk
# Split up in real ITK and all supported formats.
ITK_FORMATS = (
".gipl",
".ipl",
".mha",
".mhd",
".nhdr",
"nia",
"hdr",
".nrrd",
".nii",
".nii.gz",
".img",
".img.gz",
".vtk",
"hdf5",
"lsm",
"mnc",
"mnc2",
"mgh",
"mnc",
"pic",
)
ALL_FORMATS = ITK_FORMATS + (
".bmp",
".jpeg",
".jpg",
".png",
".tiff",
".tif",
".dicom",
".dcm",
".gdcm",
)
class ItkFormat(Format):
"""See :mod:`imageio.plugins.simpleitk`"""
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("itk.ImageIOBase") or 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("itk.ImageIOBase") or has_module("SimpleITK"):
return request.extension in ALL_FORMATS
# -- reader
class Reader(Format.Reader):
def _open(self, pixel_type=None, fallback_only=None, **kwargs):
if not _itk:
load_lib()
args = ()
if pixel_type is not None:
args += (pixel_type,)
if fallback_only is not None:
args += (fallback_only,)
self._img = _read_function(self.request.get_local_filename(), *args)
def _get_length(self):
return 1
def _close(self):
pass
def _get_data(self, index):
# Get data
if index != 0:
error_msg = "Index out of range while reading from itk file"
raise IndexError(error_msg)
# Return array and empty meta data
return _itk.GetArrayFromImage(self._img), {}
def _get_meta_data(self, index):
error_msg = "The itk plugin does not support meta data, currently."
raise RuntimeError(error_msg)
# -- 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)
_write_function(_itk_img, self.request.get_local_filename())
def set_meta_data(self, meta):
error_msg = "The itk plugin does not support meta data, currently."
raise RuntimeError(error_msg)
|
