From 6ebc43bad8e1e94660ab7978cdd51098d125bb91 Mon Sep 17 00:00:00 2001
From: Luis Pedro Coelho <luis@luispedro.org>
Date: Mon, 5 Nov 2012 22:17:42 +0000
Subject: [PATCH 1/4] ENH Add imread io plugin

This relies on imread (https://github.com/luispedro/imread) which
supports a few microscopy formats otherwise hard to read (LSM and
MetaMorph STK) as well as basic ones.
---
 skimage/io/_plugins/imread_plugin.ini |  3 +
 skimage/io/_plugins/imread_plugin.py  | 43 ++++++++++++++
 skimage/io/tests/test_imread.py       | 85 +++++++++++++++++++++++++++
 3 files changed, 131 insertions(+)
 create mode 100644 skimage/io/_plugins/imread_plugin.ini
 create mode 100644 skimage/io/_plugins/imread_plugin.py
 create mode 100644 skimage/io/tests/test_imread.py

diff --git a/skimage/io/_plugins/imread_plugin.ini b/skimage/io/_plugins/imread_plugin.ini
new file mode 100644
index 00000000..a6a5ddb1
--- /dev/null
+++ b/skimage/io/_plugins/imread_plugin.ini
@@ -0,0 +1,3 @@
+[imread]
+description = Image reading and writing via imread
+provides = imread, imsave
diff --git a/skimage/io/_plugins/imread_plugin.py b/skimage/io/_plugins/imread_plugin.py
new file mode 100644
index 00000000..7e7681b0
--- /dev/null
+++ b/skimage/io/_plugins/imread_plugin.py
@@ -0,0 +1,43 @@
+__all__ = ['imread', 'imsave']
+
+import numpy as np
+
+try:
+    import imread as _imread
+except ImportError:
+    raise ImportError("Imread could not be found"
+                      "Please refer to http://pypi.python.org/pypi/imread/ "
+                      "for further instructions.")
+
+def imread(fname, dtype=None):
+    """Load an image from file.
+
+    Parameters
+    ----------
+    fname : str
+        Name of input file
+
+    """
+    im = _imread.imread(fname)
+    if dtype is not None:
+        im = im.asdtype(dtype)
+    return im
+
+def imsave(fname, arr, format_str=None):
+    """Save an image to disk.
+
+    Parameters
+    ----------
+    fname : str
+        Name of destination file.
+    arr : ndarray of uint8 or uint16
+        Array (image) to save.
+    format_str: str,optional
+        Format to save as. 
+
+    Notes
+    -----
+    Currently, only 8-bit precision is supported.
+    """
+    return _imread.imsave(fname, arr, formatstr=format_str)
+
diff --git a/skimage/io/tests/test_imread.py b/skimage/io/tests/test_imread.py
new file mode 100644
index 00000000..8dd6ea6f
--- /dev/null
+++ b/skimage/io/tests/test_imread.py
@@ -0,0 +1,85 @@
+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 imread as _imread
+    use_plugin('imread')
+except ImportError:
+    imread_available = False
+else:
+    imread_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 imread is used.
+
+    """
+    try:
+        use_plugin('imread')
+    except ImportError:
+        pass
+
+
+
+@skipif(not imread_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 imread_available)
+def test_imread_palette():
+    img = imread(os.path.join(data_dir, 'palette_color.png'))
+    assert img.ndim == 3
+
+
+@skipif(not imread_available)
+def test_bilevel():
+    expected = np.zeros((10, 10), bool)
+    expected[::2] = 1
+
+    img = imread(os.path.join(data_dir, 'checker_bilevel.png'))
+    assert_array_equal(img, expected)
+
+
+class TestSave:
+    def roundtrip(self, x, scaling=1):
+        f = NamedTemporaryFile(suffix='.png')
+        fname = f.name
+        f.close()
+        imsave(fname, x)
+        y = imread(fname)
+
+        assert_array_almost_equal((x * scaling).astype(np.int32), y)
+
+    @skipif(not imread_available)
+    def test_imsave_roundtrip(self):
+        dtype = np.uint8
+        for shape in [(10, 10), (10, 10, 3), (10, 10, 4)]:
+            x = np.ones(shape, dtype=dtype) * np.random.random(shape)
+
+            if np.issubdtype(dtype, float):
+                yield self.roundtrip, x, 255
+            else:
+                x = (x * 255).astype(dtype)
+                yield self.roundtrip, x
+
+if __name__ == "__main__":
+    run_module_suite()

From 10ce9b89abaf7f2d9bb914771bb77d7f1ded55f5 Mon Sep 17 00:00:00 2001
From: Luis Pedro Coelho <luis@luispedro.org>
Date: Mon, 5 Nov 2012 22:32:43 +0000
Subject: [PATCH 2/4] RFCT Use `skimage.utils.convert` for type conversion

---
 skimage/io/_plugins/imread_plugin.py | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/skimage/io/_plugins/imread_plugin.py b/skimage/io/_plugins/imread_plugin.py
index 7e7681b0..323fbec8 100644
--- a/skimage/io/_plugins/imread_plugin.py
+++ b/skimage/io/_plugins/imread_plugin.py
@@ -1,6 +1,7 @@
 __all__ = ['imread', 'imsave']
 
 import numpy as np
+from skimage.utils.dtype import convert
 
 try:
     import imread as _imread
@@ -20,7 +21,7 @@ def imread(fname, dtype=None):
     """
     im = _imread.imread(fname)
     if dtype is not None:
-        im = im.asdtype(dtype)
+        im = convert(im, dtype)
     return im
 
 def imsave(fname, arr, format_str=None):

From 1f84c5e35fb6bc981af7c2938e3a997e2d965b6c Mon Sep 17 00:00:00 2001
From: Luis Pedro Coelho <luis@luispedro.org>
Date: Mon, 5 Nov 2012 22:33:40 +0000
Subject: [PATCH 3/4] DOC Add myself to CONTRIBUTORS.txt

---
 CONTRIBUTORS.txt | 5 ++++-
 1 file changed, 4 insertions(+), 1 deletion(-)

diff --git a/CONTRIBUTORS.txt b/CONTRIBUTORS.txt
index 8ba62e0b..012fd53d 100644
--- a/CONTRIBUTORS.txt
+++ b/CONTRIBUTORS.txt
@@ -119,4 +119,7 @@
   Perimeter calculation in regionprops.
 
 - Olivier Debeir
-  Rank filters (8- and 16-bits) using sliding window.
\ No newline at end of file
+  Rank filters (8- and 16-bits) using sliding window.
+
+- Luis Pedro Coelho
+  imread plugin

From 38f699471eab29259a075bcc52fef4514aed81d7 Mon Sep 17 00:00:00 2001
From: Luis Pedro Coelho <luis@luispedro.org>
Date: Sat, 24 Nov 2012 11:12:17 +0000
Subject: [PATCH 4/4] TST Remove unneeded test

Per stefanv's comment on github, this was testing functionality higher
up in skimage.io
---
 skimage/io/tests/test_imread.py | 12 ------------
 1 file changed, 12 deletions(-)

diff --git a/skimage/io/tests/test_imread.py b/skimage/io/tests/test_imread.py
index 8dd6ea6f..afb9eac9 100644
--- a/skimage/io/tests/test_imread.py
+++ b/skimage/io/tests/test_imread.py
@@ -21,18 +21,6 @@ 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 imread is used.
-
-    """
-    try:
-        use_plugin('imread')
-    except ImportError:
-        pass
-
-
-
 @skipif(not imread_available)
 def test_imread_flatten():
     # a color image is flattened