From f6761524481c163ed72e8cbdadec98776192c31f Mon Sep 17 00:00:00 2001
From: wilsaj <wilson.andrew.j+github@gmail.com>
Date: Fri, 20 Jul 2012 15:18:09 -0500
Subject: [PATCH 01/15] add stefan's image class

---
 skimage/io/_io.py | 56 ++++++++++++++++++++++++++++++++++++++++++++++-
 1 file changed, 55 insertions(+), 1 deletion(-)

diff --git a/skimage/io/_io.py b/skimage/io/_io.py
index 477fe8bc..85e5c005 100644
--- a/skimage/io/_io.py
+++ b/skimage/io/_io.py
@@ -5,10 +5,64 @@ from skimage.io._plugins import call as call_plugin
 from skimage.color import rgb2grey
 import numpy as np
 
+
 # Shared image queue
 _image_stack = []
 
 
+class Image(np.ndarray):
+    """Image data with tags."""
+
+    tags = {'filename': '',
+            'EXIF': {},
+            'info': {}}
+
+    def __new__(image_cls, arr, **kwargs):
+        """Set the image data and tags according to given parameters.
+
+        Input:
+        ------
+        `image_cls` : Image class specification
+            This is not normally specified by the user.
+        `arr` : ndarray
+            Image data.
+        ``**kwargs`` : Image tags as keywords
+            Specified in the form ``tag0=value``, ``tag1=value``.
+
+        """
+        x = np.asarray(arr).view(image_cls)
+        for tag, value in Image.tags.items():
+            setattr(x, tag, kwargs.get(tag, getattr(arr, tag, value)))
+        return x
+
+    def __array_finalize__(self, obj):
+        """Copy object tags."""
+        for tag, value in Image.tags.items():
+            setattr(self, tag, getattr(obj, tag, value))
+        return
+
+    def __reduce__(self):
+        object_state = list(np.ndarray.__reduce__(self))
+        subclass_state = {}
+        for tag in self.tags:
+            subclass_state[tag] = getattr(self, tag)
+        object_state[2] = (object_state[2], subclass_state)
+        return tuple(object_state)
+
+    def __setstate__(self, state):
+        nd_state, subclass_state = state
+        np.ndarray.__setstate__(self, nd_state)
+
+        for tag in subclass_state:
+            setattr(self, tag, subclass_state[tag])
+
+    @property
+    def exposure(self):
+        """Return exposure time based on EXIF tag."""
+        exposure = self.EXIF['EXIF ExposureTime'].values[0]
+        return exposure.num / float(exposure.den)
+
+
 def push(img):
     """Push an image onto the shared image stack.
 
@@ -77,7 +131,7 @@ def imread(fname, as_grey=False, plugin=None, flatten=None,
     if as_grey and getattr(img, 'ndim', 0) >= 3:
         img = rgb2grey(img)
 
-    return img
+    return Image(img)
 
 
 def imread_collection(load_pattern, conserve_memory=True,

From d2e04848453696acb68ddfea57ab455b6c8cc9a6 Mon Sep 17 00:00:00 2001
From: wilsaj <wilson.andrew.j+github@gmail.com>
Date: Fri, 20 Jul 2012 15:19:22 -0500
Subject: [PATCH 02/15] add html repr method for Image class

---
 skimage/io/_io.py | 13 +++++++++++++
 1 file changed, 13 insertions(+)

diff --git a/skimage/io/_io.py b/skimage/io/_io.py
index 85e5c005..3e5bb670 100644
--- a/skimage/io/_io.py
+++ b/skimage/io/_io.py
@@ -1,10 +1,17 @@
 __all__ = ['imread', 'imread_collection', 'imsave', 'imshow', 'show',
            'push', 'pop']
 
+import base64
+
 from skimage.io._plugins import call as call_plugin
 from skimage.color import rgb2grey
 import numpy as np
 
+try:
+    import cStringIO as StringIO
+except ImportError:
+    import StringIO
+
 
 # Shared image queue
 _image_stack = []
@@ -49,6 +56,12 @@ class Image(np.ndarray):
         object_state[2] = (object_state[2], subclass_state)
         return tuple(object_state)
 
+    def _repr_html_(self):
+        str_buffer = StringIO.StringIO()
+        imsave(str_buffer, self, format_str='png')
+        base64_str = base64.b64encode(str_buffer.getvalue())
+        return '<img src="data:image/png;base64,%s">' % base64_str
+
     def __setstate__(self, state):
         nd_state, subclass_state = state
         np.ndarray.__setstate__(self, nd_state)

From 605a4e2cd73e4ec1e2ff49ccd18625f06a93b1e5 Mon Sep 17 00:00:00 2001
From: wilsaj <wilson.andrew.j+github@gmail.com>
Date: Fri, 20 Jul 2012 15:22:53 -0500
Subject: [PATCH 03/15] add support for serializing to file-like objects (e.g.
 StringIO) to PIL plugin

---
 skimage/io/_plugins/pil_plugin.py | 14 +++++++++++---
 1 file changed, 11 insertions(+), 3 deletions(-)

diff --git a/skimage/io/_plugins/pil_plugin.py b/skimage/io/_plugins/pil_plugin.py
index 96106c5c..f42efe89 100644
--- a/skimage/io/_plugins/pil_plugin.py
+++ b/skimage/io/_plugins/pil_plugin.py
@@ -59,17 +59,21 @@ def _palette_is_grayscale(pil_image):
     return np.allclose(np.diff(valid_palette), 0)
 
 
-def imsave(fname, arr):
+def imsave(fname, arr, format_str=None):
     """Save an image to disk.
 
     Parameters
     ----------
-    fname : str
+    fname : str or file-like object
         Name of destination file.
     arr : ndarray of uint8 or float
         Array (image) to save.  Arrays of data-type uint8 should have
         values in [0, 255], whereas floating-point arrays must be
         in [0, 1].
+    format_str: str
+        Format to save as, this is required if using a file-like object;
+        this is optional if fname is a string and the format can be
+        derived from the extension.
 
     Notes
     -----
@@ -101,7 +105,11 @@ def imsave(fname, arr):
         arr = arr.astype(np.uint8)
 
     img = Image.fromstring(mode, (arr.shape[1], arr.shape[0]), arr.tostring())
-    img.save(fname)
+
+    if isinstance(fname, basestring):
+        img.save(fname, format=format_str)
+    elif callable(getattr(fname, 'write', None)):
+        img.save(fname, format=format_str)
 
 
 def imshow(arr):

From 70cf6cfba0040dc347a31c75de4b0b06a2bd7bd0 Mon Sep 17 00:00:00 2001
From: wilsaj <wilson.andrew.j+github@gmail.com>
Date: Fri, 20 Jul 2012 15:39:50 -0500
Subject: [PATCH 04/15] fix test so it looks for new Image class

---
 skimage/io/_io.py                   | 2 +-
 skimage/io/tests/test_collection.py | 3 ++-
 2 files changed, 3 insertions(+), 2 deletions(-)

diff --git a/skimage/io/_io.py b/skimage/io/_io.py
index 3e5bb670..f3184588 100644
--- a/skimage/io/_io.py
+++ b/skimage/io/_io.py
@@ -1,4 +1,4 @@
-__all__ = ['imread', 'imread_collection', 'imsave', 'imshow', 'show',
+__all__ = ['Image', 'imread', 'imread_collection', 'imsave', 'imshow', 'show',
            'push', 'pop']
 
 import base64
diff --git a/skimage/io/tests/test_collection.py b/skimage/io/tests/test_collection.py
index 0d420ae7..bf183f2b 100644
--- a/skimage/io/tests/test_collection.py
+++ b/skimage/io/tests/test_collection.py
@@ -7,6 +7,7 @@ from numpy.testing.decorators import skipif
 
 from skimage import data_dir
 from skimage.io import ImageCollection, MultiImage
+from skimage.io import Image as ioImage
 
 
 try:
@@ -33,7 +34,7 @@ class TestImageCollection():
     def test_getitem(self):
         num = len(self.collection)
         for i in range(-num, num):
-            assert type(self.collection[i]) is np.ndarray
+            assert type(self.collection[i]) is ioImage
         assert_array_almost_equal(self.collection[0],
                                   self.collection[-num])
 

From 32d3e1b161a12c46fa5c52a66c4bccd705c572b3 Mon Sep 17 00:00:00 2001
From: wilsaj <wilson.andrew.j+github@gmail.com>
Date: Fri, 20 Jul 2012 16:44:05 -0500
Subject: [PATCH 05/15] use repr_png and repr_jpeg hooks rather than repr_html
 these will work in the ipython qtconsole as well!

---
 skimage/io/_io.py | 10 +++++++---
 1 file changed, 7 insertions(+), 3 deletions(-)

diff --git a/skimage/io/_io.py b/skimage/io/_io.py
index f3184588..c271f25b 100644
--- a/skimage/io/_io.py
+++ b/skimage/io/_io.py
@@ -56,11 +56,15 @@ class Image(np.ndarray):
         object_state[2] = (object_state[2], subclass_state)
         return tuple(object_state)
 
-    def _repr_html_(self):
+    def _repr_png_(self):
         str_buffer = StringIO.StringIO()
         imsave(str_buffer, self, format_str='png')
-        base64_str = base64.b64encode(str_buffer.getvalue())
-        return '<img src="data:image/png;base64,%s">' % base64_str
+        return str_buffer.getvalue()
+
+    def _repr_jpeg_(self):
+        str_buffer = StringIO.StringIO()
+        imsave(str_buffer, self, format_str='jpeg')
+        return str_buffer.getvalue()
 
     def __setstate__(self, state):
         nd_state, subclass_state = state

From 74cde286b405a06480efba046242e79f92b20882 Mon Sep 17 00:00:00 2001
From: wilsaj <wilson.andrew.j+github@gmail.com>
Date: Fri, 20 Jul 2012 20:33:25 -0500
Subject: [PATCH 06/15] allow qt_plugin imsave() function to write to file-like
 objects

---
 skimage/io/_plugins/qt_plugin.py | 21 +++++++++++++++++----
 1 file changed, 17 insertions(+), 4 deletions(-)

diff --git a/skimage/io/_plugins/qt_plugin.py b/skimage/io/_plugins/qt_plugin.py
index dd4e4a8f..401589a9 100644
--- a/skimage/io/_plugins/qt_plugin.py
+++ b/skimage/io/_plugins/qt_plugin.py
@@ -7,8 +7,8 @@ import sys
 window_manager.acquire('qt')
 
 try:
-    from PyQt4.QtGui import (QApplication, QMainWindow, QImage, QPixmap,
-                             QLabel, QWidget)
+    from PyQt4.QtGui import (QApplication, QImage,
+                             QLabel, QMainWindow, QPixmap, QWidget)
     from PyQt4 import QtCore, QtGui
     import sip
     import warnings
@@ -148,12 +148,21 @@ def _app_show():
         print 'No images to show.  See `imshow`.'
 
 
-def imsave(filename, img):
+def imsave(filename, img, format_str=None):
     # we can add support for other than 3D uint8 here...
     img = prepare_for_display(img)
     qimg = QImage(img.data, img.shape[1], img.shape[0],
                           img.strides[0], QImage.Format_RGB888)
-    saved = qimg.save(filename)
+    if _is_filelike(filename):
+        byte_array = QtCore.QByteArray()
+        qbuffer = QtCore.QBuffer()
+        qbuffer.open(QtCore.QIODevice.ReadWrite)
+        saved = qimg.save(qbuffer, format_str.upper())
+        qbuffer.seek(0)
+        filename.write(qbuffer.readAll())
+        qbuffer.close()
+    else:
+        saved = qimg.save(filename)
     if not saved:
         from textwrap import dedent
         msg = dedent(
@@ -161,3 +170,7 @@ def imsave(filename, img):
             for the QT imsave plugin are:
             BMP, JPG, JPEG, PNG, PPM, TIFF, XBM, XPM''')
         raise RuntimeError(msg)
+
+
+def _is_filelike(possible_filelike):
+    return callable(getattr(possible_filelike, 'write', None))

From fbb2ec3afab89c0d3866edcae7f636df32bdd9bd Mon Sep 17 00:00:00 2001
From: wilsaj <wilson.andrew.j+github@gmail.com>
Date: Fri, 20 Jul 2012 20:34:12 -0500
Subject: [PATCH 07/15] close temp StringIO buffers when we're done with them

---
 skimage/io/_io.py | 8 ++++++--
 1 file changed, 6 insertions(+), 2 deletions(-)

diff --git a/skimage/io/_io.py b/skimage/io/_io.py
index c271f25b..514b828c 100644
--- a/skimage/io/_io.py
+++ b/skimage/io/_io.py
@@ -59,12 +59,16 @@ class Image(np.ndarray):
     def _repr_png_(self):
         str_buffer = StringIO.StringIO()
         imsave(str_buffer, self, format_str='png')
-        return str_buffer.getvalue()
+        return_str = str_buffer.getvalue()
+        str_buffer.close()
+        return return_str
 
     def _repr_jpeg_(self):
         str_buffer = StringIO.StringIO()
         imsave(str_buffer, self, format_str='jpeg')
-        return str_buffer.getvalue()
+        return_str = str_buffer.getvalue()
+        str_buffer.close()
+        return return_str
 
     def __setstate__(self, state):
         nd_state, subclass_state = state

From dcb7dacc6c5f37e9ab534a7e289044db4c77c010 Mon Sep 17 00:00:00 2001
From: wilsaj <wilson.andrew.j+github@gmail.com>
Date: Sat, 21 Jul 2012 10:23:20 -0500
Subject: [PATCH 08/15] open buffer on on byte_array

---
 skimage/io/_plugins/qt_plugin.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/skimage/io/_plugins/qt_plugin.py b/skimage/io/_plugins/qt_plugin.py
index 401589a9..bb4cf232 100644
--- a/skimage/io/_plugins/qt_plugin.py
+++ b/skimage/io/_plugins/qt_plugin.py
@@ -155,7 +155,7 @@ def imsave(filename, img, format_str=None):
                           img.strides[0], QImage.Format_RGB888)
     if _is_filelike(filename):
         byte_array = QtCore.QByteArray()
-        qbuffer = QtCore.QBuffer()
+        qbuffer = QtCore.QBuffer(byte_array)
         qbuffer.open(QtCore.QIODevice.ReadWrite)
         saved = qimg.save(qbuffer, format_str.upper())
         qbuffer.seek(0)

From a31e0d9eeb83f03d113c254bd12df9d9bcf721e9 Mon Sep 17 00:00:00 2001
From: wilsaj <wilson.andrew.j+github@gmail.com>
Date: Tue, 24 Jul 2012 23:01:51 -0500
Subject: [PATCH 09/15] remove superfluous conditional logic

---
 skimage/io/_plugins/pil_plugin.py | 6 +-----
 1 file changed, 1 insertion(+), 5 deletions(-)

diff --git a/skimage/io/_plugins/pil_plugin.py b/skimage/io/_plugins/pil_plugin.py
index f42efe89..2247f3a1 100644
--- a/skimage/io/_plugins/pil_plugin.py
+++ b/skimage/io/_plugins/pil_plugin.py
@@ -105,11 +105,7 @@ def imsave(fname, arr, format_str=None):
         arr = arr.astype(np.uint8)
 
     img = Image.fromstring(mode, (arr.shape[1], arr.shape[0]), arr.tostring())
-
-    if isinstance(fname, basestring):
-        img.save(fname, format=format_str)
-    elif callable(getattr(fname, 'write', None)):
-        img.save(fname, format=format_str)
+    img.save(fname, format=format_str)
 
 
 def imshow(arr):

From 7368332df97f94b67b625a0837c4164122f879d4 Mon Sep 17 00:00:00 2001
From: wilsaj <wilson.andrew.j+github@gmail.com>
Date: Tue, 24 Jul 2012 23:07:44 -0500
Subject: [PATCH 10/15] remove unused import

---
 skimage/io/_io.py | 2 --
 1 file changed, 2 deletions(-)

diff --git a/skimage/io/_io.py b/skimage/io/_io.py
index 514b828c..29076433 100644
--- a/skimage/io/_io.py
+++ b/skimage/io/_io.py
@@ -1,8 +1,6 @@
 __all__ = ['Image', 'imread', 'imread_collection', 'imsave', 'imshow', 'show',
            'push', 'pop']
 
-import base64
-
 from skimage.io._plugins import call as call_plugin
 from skimage.color import rgb2grey
 import numpy as np

From b9d468b6686eb40af29ad5c24b2dd6afa3e06542 Mon Sep 17 00:00:00 2001
From: wilsaj <wilson.andrew.j+github@gmail.com>
Date: Tue, 24 Jul 2012 23:20:22 -0500
Subject: [PATCH 11/15] use standard conventions for Image.__new__() cls
 attribute and docstring

---
 skimage/io/_io.py | 10 ++++------
 1 file changed, 4 insertions(+), 6 deletions(-)

diff --git a/skimage/io/_io.py b/skimage/io/_io.py
index 29076433..8320ef9f 100644
--- a/skimage/io/_io.py
+++ b/skimage/io/_io.py
@@ -22,20 +22,18 @@ class Image(np.ndarray):
             'EXIF': {},
             'info': {}}
 
-    def __new__(image_cls, arr, **kwargs):
+    def __new__(cls, arr, **kwargs):
         """Set the image data and tags according to given parameters.
 
         Input:
         ------
-        `image_cls` : Image class specification
-            This is not normally specified by the user.
-        `arr` : ndarray
+        arr : ndarray
             Image data.
-        ``**kwargs`` : Image tags as keywords
+        kwargs : Image tags as keywords
             Specified in the form ``tag0=value``, ``tag1=value``.
 
         """
-        x = np.asarray(arr).view(image_cls)
+        x = np.asarray(arr).view(cls)
         for tag, value in Image.tags.items():
             setattr(x, tag, kwargs.get(tag, getattr(arr, tag, value)))
         return x

From 2b66f0c30314a8043efe0b8d5c9374b1468a3689 Mon Sep 17 00:00:00 2001
From: wilsaj <wilson.andrew.j+github@gmail.com>
Date: Tue, 24 Jul 2012 23:21:42 -0500
Subject: [PATCH 12/15] role duplicate logic for Image._repr_png_() and
 Image._repr_jpeg_() into a common method

---
 skimage/io/_io.py | 11 +++++------
 1 file changed, 5 insertions(+), 6 deletions(-)

diff --git a/skimage/io/_io.py b/skimage/io/_io.py
index 8320ef9f..95cb5abc 100644
--- a/skimage/io/_io.py
+++ b/skimage/io/_io.py
@@ -53,15 +53,14 @@ class Image(np.ndarray):
         return tuple(object_state)
 
     def _repr_png_(self):
-        str_buffer = StringIO.StringIO()
-        imsave(str_buffer, self, format_str='png')
-        return_str = str_buffer.getvalue()
-        str_buffer.close()
-        return return_str
+        return self._repr_image_format('png')
 
     def _repr_jpeg_(self):
+        return self._repr_image_format('jpeg')
+
+    def _repr_image_format(self, format_str):
         str_buffer = StringIO.StringIO()
-        imsave(str_buffer, self, format_str='jpeg')
+        imsave(str_buffer, self, format_str=format_str)
         return_str = str_buffer.getvalue()
         str_buffer.close()
         return return_str

From 9bd445700a059b5b861f10d7ff78a2cf0bd0ed75 Mon Sep 17 00:00:00 2001
From: wilsaj <wilson.andrew.j+github@gmail.com>
Date: Sun, 12 Aug 2012 18:20:58 -0500
Subject: [PATCH 13/15] add note about to display protocol to Image docstring

---
 skimage/io/_io.py | 6 +++++-
 1 file changed, 5 insertions(+), 1 deletion(-)

diff --git a/skimage/io/_io.py b/skimage/io/_io.py
index 95cb5abc..20337797 100644
--- a/skimage/io/_io.py
+++ b/skimage/io/_io.py
@@ -16,7 +16,11 @@ _image_stack = []
 
 
 class Image(np.ndarray):
-    """Image data with tags."""
+    """Class representing Image data.
+
+    These objects have tags for image metadata and IPython display protocol
+    methods for image display.
+    """
 
     tags = {'filename': '',
             'EXIF': {},

From fabedb58ec4bcdb24dd816c3a405779adff7cf22 Mon Sep 17 00:00:00 2001
From: wilsaj <wilson.andrew.j+github@gmail.com>
Date: Sun, 12 Aug 2012 18:54:43 -0500
Subject: [PATCH 14/15] add unit test for Image._repr_png_() with PIL plugin

---
 skimage/io/tests/test_pil.py | 15 +++++++++++++++
 1 file changed, 15 insertions(+)

diff --git a/skimage/io/tests/test_pil.py b/skimage/io/tests/test_pil.py
index e442c856..fa62e1dd 100644
--- a/skimage/io/tests/test_pil.py
+++ b/skimage/io/tests/test_pil.py
@@ -33,6 +33,7 @@ def setup_module(self):
         pass
 
 
+
 @skipif(not PIL_available)
 def test_imread_flatten():
     # a color image is flattened
@@ -78,6 +79,20 @@ def test_imread_uint16():
     assert_array_almost_equal(img, expected)
 
 
+@skipif(not PIL_available)
+def test_repr_png():
+    img_path = os.path.join(data_dir, 'camera.png')
+    original_img = imread(img_path)
+    original_img_str = original_img._repr_png_()
+
+    with NamedTemporaryFile(suffix='.png', mode='r+') as temp_png:
+        temp_png.write(original_img_str)
+        temp_png.seek(0)
+        round_trip = imread(temp_png)
+
+    assert np.all(original_img == round_trip)
+
+
 # Big endian images not correctly loaded for PIL < 1.1.7
 # Renable test when PIL 1.1.7 is more common.
 @skipif(True)

From 38a96b9ac9af7c65b2ac1bf33f28daccaa5c4e23 Mon Sep 17 00:00:00 2001
From: wilsaj <wilson.andrew.j+github@gmail.com>
Date: Tue, 21 Aug 2012 20:50:52 -0500
Subject: [PATCH 15/15] Remove tag metadata-related fucntions from Image class

---
 skimage/io/_io.py | 27 ---------------------------
 1 file changed, 27 deletions(-)

diff --git a/skimage/io/_io.py b/skimage/io/_io.py
index 20337797..71002395 100644
--- a/skimage/io/_io.py
+++ b/skimage/io/_io.py
@@ -42,20 +42,6 @@ class Image(np.ndarray):
             setattr(x, tag, kwargs.get(tag, getattr(arr, tag, value)))
         return x
 
-    def __array_finalize__(self, obj):
-        """Copy object tags."""
-        for tag, value in Image.tags.items():
-            setattr(self, tag, getattr(obj, tag, value))
-        return
-
-    def __reduce__(self):
-        object_state = list(np.ndarray.__reduce__(self))
-        subclass_state = {}
-        for tag in self.tags:
-            subclass_state[tag] = getattr(self, tag)
-        object_state[2] = (object_state[2], subclass_state)
-        return tuple(object_state)
-
     def _repr_png_(self):
         return self._repr_image_format('png')
 
@@ -69,19 +55,6 @@ class Image(np.ndarray):
         str_buffer.close()
         return return_str
 
-    def __setstate__(self, state):
-        nd_state, subclass_state = state
-        np.ndarray.__setstate__(self, nd_state)
-
-        for tag in subclass_state:
-            setattr(self, tag, subclass_state[tag])
-
-    @property
-    def exposure(self):
-        """Return exposure time based on EXIF tag."""
-        exposure = self.EXIF['EXIF ExposureTime'].values[0]
-        return exposure.num / float(exposure.den)
-
 
 def push(img):
     """Push an image onto the shared image stack.