Merge pull request #149 from zachrahan/tifffile-plugin

ENH: add tifffile plugin, tifffile tests, beef up freeimage tests

skimage/io/_plugins/tifffile_plugin.ini

@@ -0,0 +1,3 @@
+[tifffile]
+description = Open and save TIFF and TIFF-based (LSM, STK, etc.) images using tifffile.py
+provides = imread, imsave

skimage/io/_plugins/tifffile_plugin.py

@@ -0,0 +1,6 @@
+try:
+    from tifffile import imread, imsave
+except ImportError:
+    raise ImportError("The tifffile module could not be found.\n"
+        "It can be obtained at "
+        "<http://www.lfd.uci.edu/~gohlke/code/tifffile.py.html>\n")

skimage/io/tests/test_freeimage.py

@@ -1,23 +1,66 @@
 import os
 import skimage as si
 import skimage.io as sio
+import numpy as np
 
 from numpy.testing import *
 from numpy.testing.decorators import skipif
+from tempfile import NamedTemporaryFile
 
 try:
     import skimage.io._plugins.freeimage_plugin as fi
     FI_available = True
+    sio.use_plugin('freeimage')
 except OSError:
     FI_available = False
 
 @skipif(not FI_available)
-def test_read():
-    sio.use_plugin('freeimage', 'imread')
+def test_imread():
     img = sio.imread(os.path.join(si.data_dir, 'color.png'))
     assert img.shape == (370, 371, 3)
     assert all(img[274,135] == [0, 130, 253])
 
+@skipif(not FI_available)
+def test_imread_uint16():
+    expected = np.load(os.path.join(si.data_dir, 'chessboard_GRAY_U8.npy'))
+    img = sio.imread(os.path.join(si.data_dir, 'chessboard_GRAY_U16.tif'))
+    assert img.dtype == np.uint16
+    assert_array_almost_equal(img, expected)
+
+@skipif(not FI_available)
+def test_imread_uint16_big_endian():
+    expected = np.load(os.path.join(si.data_dir, 'chessboard_GRAY_U8.npy'))
+    img = sio.imread(os.path.join(si.data_dir, 'chessboard_GRAY_U16B.tif'))
+    assert img.dtype == np.uint16
+    assert_array_almost_equal(img, expected)
+
+
+class TestSave:
+    def roundtrip(self, dtype, x, suffix):
+        print dtype, x.shape, suffix
+        f = NamedTemporaryFile(suffix='.'+suffix)
+        fname = f.name
+        f.close()
+        sio.imsave(fname, x)
+        y = sio.imread(fname)
+        assert_array_equal(x, y)
+
+    @skipif(not FI_available)
+    def test_imsave_roundtrip(self):
+        for shape, dtype, format in [
+              [(10, 10), (np.uint8, np.uint16), ('tif', 'png')], 
+              [(10, 10), (np.float32,), ('tif',)], 
+              [(10, 10, 3), (np.uint8,), ('png',)], 
+              [(10, 10, 4), (np.uint8,), ('png',)]
+            ]:
+            tests = [(d,f) for d in dtype for f in format]
+            for d, f in tests:
+                x = np.ones(shape, dtype=d) * np.random.random(shape)
+                if not np.issubdtype(d, float):
+                    x = (x * 255).astype(d)
+                yield self.roundtrip, d, x, f
+
+
 @skipif(not FI_available)
 def test_metadata():
     meta = fi.read_metadata(os.path.join(si.data_dir, 'multipage.tif'))

skimage/io/tests/test_tifffile.py

@@ -0,0 +1,53 @@
+import os
+import skimage as si
+import skimage.io as sio
+import numpy as np
+
+from numpy.testing import *
+from numpy.testing.decorators import skipif
+from tempfile import NamedTemporaryFile
+
+try:
+    import skimage.io._plugins.tifffile_plugin as tf
+    TF_available = True
+    sio.use_plugin('tifffile')
+except OSError:
+    TF_available = False
+
+@skipif(not TF_available)
+def test_imread_uint16():
+    expected = np.load(os.path.join(si.data_dir, 'chessboard_GRAY_U8.npy'))
+    img = sio.imread(os.path.join(si.data_dir, 'chessboard_GRAY_U16.tif'))
+    assert img.dtype == np.uint16
+    assert_array_almost_equal(img, expected)
+
+@skipif(not TF_available)
+def test_imread_uint16_big_endian():
+    expected = np.load(os.path.join(si.data_dir, 'chessboard_GRAY_U8.npy'))
+    img = sio.imread(os.path.join(si.data_dir, 'chessboard_GRAY_U16B.tif'))
+    assert img.dtype == np.uint16
+    assert_array_almost_equal(img, expected)
+
+
+class TestSave:
+    def roundtrip(self, dtype, x):
+        f = NamedTemporaryFile(suffix='.tif')
+        fname = f.name
+        f.close()
+        sio.imsave(fname, x)
+        y = sio.imread(fname)
+        assert_array_equal(x, y)
+
+    @skipif(not TF_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 not np.issubdtype(dtype, float):
+                    x = (x * 255).astype(dtype)
+                yield self.roundtrip, dtype, x
+
+
+if __name__ == "__main__":
+    run_module_suite()