162 lines
4.2 KiB
Python
162 lines
4.2 KiB
Python
# -*- coding: utf-8 -*-
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# imageio is distributed under the terms of the (new) BSD License.
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""" Storage of image data in multiple formats.
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"""
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from .. import formats
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from ..core import Format, has_module
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_itk = None # Defer loading to load_lib() function.
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def load_lib():
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global _itk, _read_function, _write_function
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try:
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import itk as _itk
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_read_function = _itk.imread
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_write_function = _itk.imwrite
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except ImportError:
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try:
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import SimpleITK as _itk
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_read_function = _itk.ReadImage
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_write_function = _itk.WriteImage
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except ImportError:
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raise ImportError(
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"itk could not be found. "
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"Please try "
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" python -m pip install itk "
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"or "
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" python -m pip install simpleitk "
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"or refer to "
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" https://itkpythonpackage.readthedocs.io/ "
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"for further instructions."
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)
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return _itk
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# Split up in real ITK and all supported formats.
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ITK_FORMATS = (
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".gipl",
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".ipl",
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".mha",
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".mhd",
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".nhdr",
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"nia",
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"hdr",
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".nrrd",
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".nii",
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".nii.gz",
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".img",
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".img.gz",
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".vtk",
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"hdf5",
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"lsm",
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"mnc",
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"mnc2",
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"mgh",
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"mnc",
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"pic",
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)
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ALL_FORMATS = ITK_FORMATS + (
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".bmp",
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".jpeg",
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".jpg",
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".png",
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".tiff",
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".tif",
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".dicom",
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".dcm",
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".gdcm",
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)
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class ItkFormat(Format):
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""" The ItkFormat uses the ITK or SimpleITK library to support a range of
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ITK-related formats. It also supports a few common formats that are
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also supported by the freeimage plugin (e.g. PNG and JPEG).
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This format requires the ``itk`` or ``SimpleITK`` package.
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Parameters for reading
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----------------------
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None.
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Parameters for saving
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---------------------
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None.
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"""
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def _can_read(self, request):
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# If the request is a format that only this plugin can handle,
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# we report that we can do it; a useful error will be raised
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# when simpleitk is not installed. For the more common formats
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# we only report that we can read if the library is installed.
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if request.extension in ITK_FORMATS:
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return True
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if has_module("itk.ImageIOBase") or has_module("SimpleITK"):
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return request.extension in ALL_FORMATS
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def _can_write(self, request):
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if request.extension in ITK_FORMATS:
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return True
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if has_module("itk.ImageIOBase") or has_module("SimpleITK"):
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return request.extension in ALL_FORMATS
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# -- reader
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class Reader(Format.Reader):
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def _open(self, pixel_type=None, fallback_only=None, **kwargs):
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if not _itk:
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load_lib()
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args = ()
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if pixel_type is not None:
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args += (pixel_type,)
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if fallback_only is not None:
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args += (fallback_only,)
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self._img = _read_function(self.request.get_local_filename(), *args)
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def _get_length(self):
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return 1
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def _close(self):
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pass
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def _get_data(self, index):
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# Get data
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if index != 0:
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error_msg = "Index out of range while reading from itk file"
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raise IndexError(error_msg)
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# Return array and empty meta data
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return _itk.GetArrayFromImage(self._img), {}
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def _get_meta_data(self, index):
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error_msg = "The itk plugin does not support meta data, currently."
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raise RuntimeError(error_msg)
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# -- writer
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class Writer(Format.Writer):
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def _open(self):
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if not _itk:
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load_lib()
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def _close(self):
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pass
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def _append_data(self, im, meta):
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_itk_img = _itk.GetImageFromArray(im)
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_write_function(_itk_img, self.request.get_local_filename())
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def set_meta_data(self, meta):
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error_msg = "The itk plugin does not support meta data, currently."
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raise RuntimeError(error_msg)
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# Register
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title = "Insight Segmentation and Registration Toolkit (ITK) format"
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format = ItkFormat("itk", title, " ".join(ALL_FORMATS), "iIvV")
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formats.add_format(format)
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