From ad23f203da33b69cd20ba9044bb0b9787156afbb Mon Sep 17 00:00:00 2001
From: Matt McCormick <matt.mccormick@kitware.com>
Date: Sun, 22 Jul 2012 19:36:33 -0400
Subject: [PATCH] ENH: Add SimpleITK IO plugin.

IO plugin for SimpleITK, http://simpleitk.org/

imread and imsave implemented. Tests based off the PIL tests.
---
 skimage/io/_plugins/simpleitk_plugin.ini |  3 +
 skimage/io/_plugins/simpleitk_plugin.py  | 21 ++++++
 skimage/io/tests/test_simpleitk.py       | 93 ++++++++++++++++++++++++
 3 files changed, 117 insertions(+)
 create mode 100644 skimage/io/_plugins/simpleitk_plugin.ini
 create mode 100644 skimage/io/_plugins/simpleitk_plugin.py
 create mode 100644 skimage/io/tests/test_simpleitk.py

diff --git a/skimage/io/_plugins/simpleitk_plugin.ini b/skimage/io/_plugins/simpleitk_plugin.ini
new file mode 100644
index 00000000..75a6d995
--- /dev/null
+++ b/skimage/io/_plugins/simpleitk_plugin.ini
@@ -0,0 +1,3 @@
+[simpleitk]
+description = Image reading and writing via SimpleITK
+provides = imread, imsave
diff --git a/skimage/io/_plugins/simpleitk_plugin.py b/skimage/io/_plugins/simpleitk_plugin.py
new file mode 100644
index 00000000..90f7cbc6
--- /dev/null
+++ b/skimage/io/_plugins/simpleitk_plugin.py
@@ -0,0 +1,21 @@
+__all__ = ['imread', 'imsave']
+
+try:
+    import SimpleITK as sitk
+except ImportError:
+    raise ImportError("SimpleITK could not be found. "
+                      "Please try "
+                      "  easy_install SimpleITK "
+                      "or refer to "
+                      "  http://simpleitk.org/ "
+                      "for further instructions.")
+
+
+def imread(fname):
+    sitk_img = sitk.ReadImage(fname)
+    return sitk.GetArrayFromImage(sitk_img)
+
+
+def imsave(fname, arr):
+    sitk_img = sitk.GetImageFromArray(arr, isVector=True)
+    sitk.WriteImage(sitk_img, fname)
diff --git a/skimage/io/tests/test_simpleitk.py b/skimage/io/tests/test_simpleitk.py
new file mode 100644
index 00000000..4bb2cc23
--- /dev/null
+++ b/skimage/io/tests/test_simpleitk.py
@@ -0,0 +1,93 @@
+import os.path
+import numpy as np
+from numpy.testing import *
+from numpy.testing.decorators import skipif
+
+from tempfile import NamedTemporaryFile
+
+from skimage import data_dir
+from skimage.io import imread, imsave, use_plugin, reset_plugins
+
+try:
+    import SimpleITK as sitk
+    use_plugin('simpleitk')
+except ImportError:
+    sitk_available = False
+else:
+    sitk_available = True
+
+
+def teardown():
+    reset_plugins()
+
+
+def setup_module(self):
+    """The effect of the `plugin.use` call may be overridden by later imports.
+    Call `use_plugin` directly before the tests to ensure that sitk is used.
+
+    """
+    try:
+        use_plugin('simpleitk')
+    except ImportError:
+        pass
+
+
+@skipif(not sitk_available)
+def test_imread_flatten():
+    # a color image is flattened
+    img = imread(os.path.join(data_dir, 'color.png'), flatten=True)
+    assert img.ndim == 2
+    assert img.dtype == np.float64
+    img = imread(os.path.join(data_dir, 'camera.png'), flatten=True)
+    # check that flattening does not occur for an image that is grey already.
+    assert np.sctype2char(img.dtype) in np.typecodes['AllInteger']
+
+
+@skipif(not sitk_available)
+def test_bilevel():
+    expected = np.zeros((10, 10))
+    expected[::2] = 255
+
+    img = imread(os.path.join(data_dir, 'checker_bilevel.png'))
+    assert_array_equal(img, expected)
+
+
+@skipif(not sitk_available)
+def test_imread_uint16():
+    expected = np.load(os.path.join(data_dir, 'chessboard_GRAY_U8.npy'))
+    img = imread(os.path.join(data_dir, 'chessboard_GRAY_U16.tif'))
+    assert np.issubdtype(img.dtype, np.uint16)
+    assert_array_almost_equal(img, expected)
+
+
+@skipif(not sitk_available)
+def test_imread_uint16_big_endian():
+    expected = np.load(os.path.join(data_dir, 'chessboard_GRAY_U8.npy'))
+    img = imread(os.path.join(data_dir, 'chessboard_GRAY_U16B.tif'))
+    assert_array_almost_equal(img, expected)
+
+
+class TestSave:
+    def roundtrip(self, dtype, x):
+        f = NamedTemporaryFile(suffix='.mha')
+        fname = f.name
+        f.close()
+        imsave(fname, x)
+        y = imread(fname)
+
+        assert_array_almost_equal(x, y)
+
+    @skipif(not sitk_available)
+    def test_imsave_roundtrip(self):
+        for shape in [(10, 10), (10, 10, 3), (10, 10, 4)]:
+            for dtype in (np.uint8, np.uint16, np.float32, np.float64):
+                x = np.ones(shape, dtype=dtype) * np.random.random(shape)
+
+                if np.issubdtype(dtype, float):
+                    yield self.roundtrip, dtype, x
+                else:
+                    x = (x * 255).astype(dtype)
+                    yield self.roundtrip, dtype, x
+
+if __name__ == "__main__":
+    run_module_suite()