update

.CondaPkg/env/Lib/site-packages/imageio/plugins/simpleitk.py

@@ -0,0 +1,156 @@
+# -*- 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)