From 2ef6f0ae7353b018bc15a2a34bdf7ae941b38271 Mon Sep 17 00:00:00 2001
From: Stefan van der Walt <stefan@sun.ac.za>
Date: Fri, 28 Jun 2013 10:26:11 -0500
Subject: [PATCH 01/19] Remove 2to3.

---
 setup.py | 5 +----
 1 file changed, 1 insertion(+), 4 deletions(-)

diff --git a/setup.py b/setup.py
index d62a0d86..22db8e75 100644
--- a/setup.py
+++ b/setup.py
@@ -30,10 +30,7 @@ import sys
 import re
 import setuptools
 from numpy.distutils.core import setup
-try:
-    from distutils.command.build_py import build_py_2to3 as build_py
-except ImportError:
-    from distutils.command.build_py import build_py
+from distutils.command.build_py import build_py
 
 
 def configuration(parent_package='', top_path=None):

From 70d21f23a2a4f0984d98559b54dc5e692b0cb9bc Mon Sep 17 00:00:00 2001
From: Stefan van der Walt <stefan@sun.ac.za>
Date: Fri, 28 Jun 2013 11:32:11 -0500
Subject: [PATCH 02/19] Add six compatibility module.

---
 skimage/_shared/six.py | 423 +++++++++++++++++++++++++++++++++++++++++
 1 file changed, 423 insertions(+)
 create mode 100644 skimage/_shared/six.py

diff --git a/skimage/_shared/six.py b/skimage/_shared/six.py
new file mode 100644
index 00000000..8a877b17
--- /dev/null
+++ b/skimage/_shared/six.py
@@ -0,0 +1,423 @@
+"""Utilities for writing code that runs on Python 2 and 3"""
+
+# Copyright (c) 2010-2013 Benjamin Peterson
+#
+# Permission is hereby granted, free of charge, to any person obtaining a copy
+# of this software and associated documentation files (the "Software"), to deal
+# in the Software without restriction, including without limitation the rights
+# to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+# copies of the Software, and to permit persons to whom the Software is
+# furnished to do so, subject to the following conditions:
+#
+# The above copyright notice and this permission notice shall be included in all
+# copies or substantial portions of the Software.
+#
+# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+# IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+# FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+# AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+# LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+# OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+# SOFTWARE.
+
+import operator
+import sys
+import types
+
+__author__ = "Benjamin Peterson <benjamin@python.org>"
+__version__ = "1.3.0"
+
+
+# Useful for very coarse version differentiation.
+PY2 = sys.version_info[0] == 2
+PY3 = sys.version_info[0] == 3
+
+if PY3:
+    string_types = str,
+    integer_types = int,
+    class_types = type,
+    text_type = str
+    binary_type = bytes
+
+    MAXSIZE = sys.maxsize
+else:
+    string_types = basestring,
+    integer_types = (int, long)
+    class_types = (type, types.ClassType)
+    text_type = unicode
+    binary_type = str
+
+    if sys.platform.startswith("java"):
+        # Jython always uses 32 bits.
+        MAXSIZE = int((1 << 31) - 1)
+    else:
+        # It's possible to have sizeof(long) != sizeof(Py_ssize_t).
+        class X(object):
+            def __len__(self):
+                return 1 << 31
+        try:
+            len(X())
+        except OverflowError:
+            # 32-bit
+            MAXSIZE = int((1 << 31) - 1)
+        else:
+            # 64-bit
+            MAXSIZE = int((1 << 63) - 1)
+        del X
+
+
+def _add_doc(func, doc):
+    """Add documentation to a function."""
+    func.__doc__ = doc
+
+
+def _import_module(name):
+    """Import module, returning the module after the last dot."""
+    __import__(name)
+    return sys.modules[name]
+
+
+class _LazyDescr(object):
+
+    def __init__(self, name):
+        self.name = name
+
+    def __get__(self, obj, tp):
+        result = self._resolve()
+        setattr(obj, self.name, result)
+        # This is a bit ugly, but it avoids running this again.
+        delattr(tp, self.name)
+        return result
+
+
+class MovedModule(_LazyDescr):
+
+    def __init__(self, name, old, new=None):
+        super(MovedModule, self).__init__(name)
+        if PY3:
+            if new is None:
+                new = name
+            self.mod = new
+        else:
+            self.mod = old
+
+    def _resolve(self):
+        return _import_module(self.mod)
+
+
+class MovedAttribute(_LazyDescr):
+
+    def __init__(self, name, old_mod, new_mod, old_attr=None, new_attr=None):
+        super(MovedAttribute, self).__init__(name)
+        if PY3:
+            if new_mod is None:
+                new_mod = name
+            self.mod = new_mod
+            if new_attr is None:
+                if old_attr is None:
+                    new_attr = name
+                else:
+                    new_attr = old_attr
+            self.attr = new_attr
+        else:
+            self.mod = old_mod
+            if old_attr is None:
+                old_attr = name
+            self.attr = old_attr
+
+    def _resolve(self):
+        module = _import_module(self.mod)
+        return getattr(module, self.attr)
+
+
+
+class _MovedItems(types.ModuleType):
+    """Lazy loading of moved objects"""
+
+
+_moved_attributes = [
+    MovedAttribute("cStringIO", "cStringIO", "io", "StringIO"),
+    MovedAttribute("filter", "itertools", "builtins", "ifilter", "filter"),
+    MovedAttribute("input", "__builtin__", "builtins", "raw_input", "input"),
+    MovedAttribute("map", "itertools", "builtins", "imap", "map"),
+    MovedAttribute("range", "__builtin__", "builtins", "xrange", "range"),
+    MovedAttribute("reload_module", "__builtin__", "imp", "reload"),
+    MovedAttribute("reduce", "__builtin__", "functools"),
+    MovedAttribute("StringIO", "StringIO", "io"),
+    MovedAttribute("xrange", "__builtin__", "builtins", "xrange", "range"),
+    MovedAttribute("zip", "itertools", "builtins", "izip", "zip"),
+
+    MovedModule("builtins", "__builtin__"),
+    MovedModule("configparser", "ConfigParser"),
+    MovedModule("copyreg", "copy_reg"),
+    MovedModule("http_cookiejar", "cookielib", "http.cookiejar"),
+    MovedModule("http_cookies", "Cookie", "http.cookies"),
+    MovedModule("html_entities", "htmlentitydefs", "html.entities"),
+    MovedModule("html_parser", "HTMLParser", "html.parser"),
+    MovedModule("http_client", "httplib", "http.client"),
+    MovedModule("email_mime_multipart", "email.MIMEMultipart", "email.mime.multipart"),
+    MovedModule("email_mime_text", "email.MIMEText", "email.mime.text"),
+    MovedModule("email_mime_base", "email.MIMEBase", "email.mime.base"),
+    MovedModule("BaseHTTPServer", "BaseHTTPServer", "http.server"),
+    MovedModule("CGIHTTPServer", "CGIHTTPServer", "http.server"),
+    MovedModule("SimpleHTTPServer", "SimpleHTTPServer", "http.server"),
+    MovedModule("cPickle", "cPickle", "pickle"),
+    MovedModule("queue", "Queue"),
+    MovedModule("reprlib", "repr"),
+    MovedModule("socketserver", "SocketServer"),
+    MovedModule("tkinter", "Tkinter"),
+    MovedModule("tkinter_dialog", "Dialog", "tkinter.dialog"),
+    MovedModule("tkinter_filedialog", "FileDialog", "tkinter.filedialog"),
+    MovedModule("tkinter_scrolledtext", "ScrolledText", "tkinter.scrolledtext"),
+    MovedModule("tkinter_simpledialog", "SimpleDialog", "tkinter.simpledialog"),
+    MovedModule("tkinter_tix", "Tix", "tkinter.tix"),
+    MovedModule("tkinter_constants", "Tkconstants", "tkinter.constants"),
+    MovedModule("tkinter_dnd", "Tkdnd", "tkinter.dnd"),
+    MovedModule("tkinter_colorchooser", "tkColorChooser",
+                "tkinter.colorchooser"),
+    MovedModule("tkinter_commondialog", "tkCommonDialog",
+                "tkinter.commondialog"),
+    MovedModule("tkinter_tkfiledialog", "tkFileDialog", "tkinter.filedialog"),
+    MovedModule("tkinter_font", "tkFont", "tkinter.font"),
+    MovedModule("tkinter_messagebox", "tkMessageBox", "tkinter.messagebox"),
+    MovedModule("tkinter_tksimpledialog", "tkSimpleDialog",
+                "tkinter.simpledialog"),
+    MovedModule("urllib_robotparser", "robotparser", "urllib.robotparser"),
+    MovedModule("winreg", "_winreg"),
+]
+for attr in _moved_attributes:
+    setattr(_MovedItems, attr.name, attr)
+del attr
+
+moves = sys.modules[__name__ + ".moves"] = _MovedItems("moves")
+
+
+def add_move(move):
+    """Add an item to six.moves."""
+    setattr(_MovedItems, move.name, move)
+
+
+def remove_move(name):
+    """Remove item from six.moves."""
+    try:
+        delattr(_MovedItems, name)
+    except AttributeError:
+        try:
+            del moves.__dict__[name]
+        except KeyError:
+            raise AttributeError("no such move, %r" % (name,))
+
+
+if PY3:
+    _meth_func = "__func__"
+    _meth_self = "__self__"
+
+    _func_closure = "__closure__"
+    _func_code = "__code__"
+    _func_defaults = "__defaults__"
+    _func_globals = "__globals__"
+
+    _iterkeys = "keys"
+    _itervalues = "values"
+    _iteritems = "items"
+    _iterlists = "lists"
+else:
+    _meth_func = "im_func"
+    _meth_self = "im_self"
+
+    _func_closure = "func_closure"
+    _func_code = "func_code"
+    _func_defaults = "func_defaults"
+    _func_globals = "func_globals"
+
+    _iterkeys = "iterkeys"
+    _itervalues = "itervalues"
+    _iteritems = "iteritems"
+    _iterlists = "iterlists"
+
+
+try:
+    advance_iterator = next
+except NameError:
+    def advance_iterator(it):
+        return it.next()
+next = advance_iterator
+
+
+try:
+    callable = callable
+except NameError:
+    def callable(obj):
+        return any("__call__" in klass.__dict__ for klass in type(obj).__mro__)
+
+
+if PY3:
+    def get_unbound_function(unbound):
+        return unbound
+
+    create_bound_method = types.MethodType
+
+    Iterator = object
+else:
+    def get_unbound_function(unbound):
+        return unbound.im_func
+
+    def create_bound_method(func, obj):
+        return types.MethodType(func, obj, obj.__class__)
+
+    class Iterator(object):
+
+        def next(self):
+            return type(self).__next__(self)
+
+    callable = callable
+_add_doc(get_unbound_function,
+         """Get the function out of a possibly unbound function""")
+
+
+get_method_function = operator.attrgetter(_meth_func)
+get_method_self = operator.attrgetter(_meth_self)
+get_function_closure = operator.attrgetter(_func_closure)
+get_function_code = operator.attrgetter(_func_code)
+get_function_defaults = operator.attrgetter(_func_defaults)
+get_function_globals = operator.attrgetter(_func_globals)
+
+
+def iterkeys(d, **kw):
+    """Return an iterator over the keys of a dictionary."""
+    return iter(getattr(d, _iterkeys)(**kw))
+
+def itervalues(d, **kw):
+    """Return an iterator over the values of a dictionary."""
+    return iter(getattr(d, _itervalues)(**kw))
+
+def iteritems(d, **kw):
+    """Return an iterator over the (key, value) pairs of a dictionary."""
+    return iter(getattr(d, _iteritems)(**kw))
+
+def iterlists(d, **kw):
+    """Return an iterator over the (key, [values]) pairs of a dictionary."""
+    return iter(getattr(d, _iterlists)(**kw))
+
+
+if PY3:
+    def b(s):
+        return s.encode("latin-1")
+    def u(s):
+        return s
+    unichr = chr
+    if sys.version_info[1] <= 1:
+        def int2byte(i):
+            return bytes((i,))
+    else:
+        # This is about 2x faster than the implementation above on 3.2+
+        int2byte = operator.methodcaller("to_bytes", 1, "big")
+    byte2int = operator.itemgetter(0)
+    indexbytes = operator.getitem
+    iterbytes = iter
+    import io
+    StringIO = io.StringIO
+    BytesIO = io.BytesIO
+else:
+    def b(s):
+        return s
+    def u(s):
+        return unicode(s, "unicode_escape")
+    unichr = unichr
+    int2byte = chr
+    def byte2int(bs):
+        return ord(bs[0])
+    def indexbytes(buf, i):
+        return ord(buf[i])
+    def iterbytes(buf):
+        return (ord(byte) for byte in buf)
+    import StringIO
+    StringIO = BytesIO = StringIO.StringIO
+_add_doc(b, """Byte literal""")
+_add_doc(u, """Text literal""")
+
+
+if PY3:
+    import builtins
+    exec_ = getattr(builtins, "exec")
+
+
+    def reraise(tp, value, tb=None):
+        if value.__traceback__ is not tb:
+            raise value.with_traceback(tb)
+        raise value
+
+
+    print_ = getattr(builtins, "print")
+    del builtins
+
+else:
+    def exec_(_code_, _globs_=None, _locs_=None):
+        """Execute code in a namespace."""
+        if _globs_ is None:
+            frame = sys._getframe(1)
+            _globs_ = frame.f_globals
+            if _locs_ is None:
+                _locs_ = frame.f_locals
+            del frame
+        elif _locs_ is None:
+            _locs_ = _globs_
+        exec("""exec _code_ in _globs_, _locs_""")
+
+
+    exec_("""def reraise(tp, value, tb=None):
+    raise tp, value, tb
+""")
+
+
+    def print_(*args, **kwargs):
+        """The new-style print function."""
+        fp = kwargs.pop("file", sys.stdout)
+        if fp is None:
+            return
+        def write(data):
+            if not isinstance(data, basestring):
+                data = str(data)
+            fp.write(data)
+        want_unicode = False
+        sep = kwargs.pop("sep", None)
+        if sep is not None:
+            if isinstance(sep, unicode):
+                want_unicode = True
+            elif not isinstance(sep, str):
+                raise TypeError("sep must be None or a string")
+        end = kwargs.pop("end", None)
+        if end is not None:
+            if isinstance(end, unicode):
+                want_unicode = True
+            elif not isinstance(end, str):
+                raise TypeError("end must be None or a string")
+        if kwargs:
+            raise TypeError("invalid keyword arguments to print()")
+        if not want_unicode:
+            for arg in args:
+                if isinstance(arg, unicode):
+                    want_unicode = True
+                    break
+        if want_unicode:
+            newline = unicode("\n")
+            space = unicode(" ")
+        else:
+            newline = "\n"
+            space = " "
+        if sep is None:
+            sep = space
+        if end is None:
+            end = newline
+        for i, arg in enumerate(args):
+            if i:
+                write(sep)
+            write(arg)
+        write(end)
+
+_add_doc(reraise, """Reraise an exception.""")
+
+
+def with_metaclass(meta, *bases):
+    """Create a base class with a metaclass."""
+    return meta("NewBase", bases, {})

From 9a38a59a258e50b3076fbb05e4d6ee1df2a7fc06 Mon Sep 17 00:00:00 2001
From: Stefan van der Walt <stefan@sun.ac.za>
Date: Fri, 28 Jun 2013 11:33:36 -0500
Subject: [PATCH 03/19] Remove is_str and replace by isinstance(...,
 six.string_types).

---
 skimage/_shared/utils.py    | 13 +------------
 skimage/color/colorlabel.py |  4 ++--
 2 files changed, 3 insertions(+), 14 deletions(-)

diff --git a/skimage/_shared/utils.py b/skimage/_shared/utils.py
index e1642102..aad9220d 100644
--- a/skimage/_shared/utils.py
+++ b/skimage/_shared/utils.py
@@ -2,18 +2,7 @@ import warnings
 import functools
 
 
-__all__ = ['deprecated', 'is_str']
-
-
-try:
-    isinstance("", basestring)
-    def is_str(s):
-        """Return True if `s` is a string. Safe for Python 2 and 3."""
-        return isinstance(s, basestring)
-except NameError:
-    def is_str(s):
-        """Return True if `s` is a string. Safe for Python 2 and 3."""
-        return isinstance(s, str)
+__all__ = ['deprecated']
 
 
 class deprecated(object):
diff --git a/skimage/color/colorlabel.py b/skimage/color/colorlabel.py
index f1c91d67..41974f38 100644
--- a/skimage/color/colorlabel.py
+++ b/skimage/color/colorlabel.py
@@ -4,7 +4,7 @@ import itertools
 import numpy as np
 
 from skimage import img_as_float
-from skimage._shared.utils import is_str
+from skimage._shared import six
 from .colorconv import rgb2gray, gray2rgb
 from . import rgb_colors
 
@@ -30,7 +30,7 @@ def _rgb_vector(color):
     color : str or array
         Color name in `color_dict` or RGB float values between [0, 1].
     """
-    if is_str(color):
+    if isinstance(color, six.string_types):
         color = color_dict[color]
     # slice to handle RGBA colors
     return np.array(color[:3]).reshape(1, 3)

From a1adfa8d549121950303629881bffcbbcf04961e Mon Sep 17 00:00:00 2001
From: Stefan van der Walt <stefan@sun.ac.za>
Date: Fri, 28 Jun 2013 11:37:08 -0500
Subject: [PATCH 04/19] Correctly check for string type.

---
 skimage/io/_io.py                       | 5 +++--
 skimage/io/collection.py                | 3 ++-
 skimage/io/tests/test_collection.py     | 5 ++---
 skimage/viewer/plugins/overlayplugin.py | 4 +++-
 4 files changed, 10 insertions(+), 7 deletions(-)

diff --git a/skimage/io/_io.py b/skimage/io/_io.py
index 7b21b2b8..63d3d7e4 100644
--- a/skimage/io/_io.py
+++ b/skimage/io/_io.py
@@ -15,6 +15,7 @@ import numpy as np
 
 from skimage.io._plugins import call as call_plugin
 from skimage.color import rgb2grey
+from skimage._shared import six
 
 
 # Shared image queue
@@ -25,7 +26,7 @@ URL_REGEX = re.compile(r'http://|https://|ftp://|file://|file:\\')
 
 def is_url(filename):
     """Return True if string is an http or ftp path."""
-    return (isinstance(filename, basestring) and
+    return (isinstance(filename, six.string_types) and
             URL_REGEX.match(filename) is not None)
 
 
@@ -220,7 +221,7 @@ def imshow(arr, plugin=None, **plugin_args):
         Passed to the given plugin.
 
     """
-    if isinstance(arr, basestring):
+    if isinstance(arr, six.string_types):
         arr = call_plugin('imread', arr, plugin=plugin)
     return call_plugin('imshow', arr, plugin=plugin, **plugin_args)
 
diff --git a/skimage/io/collection.py b/skimage/io/collection.py
index 7c3f739b..96855dbd 100644
--- a/skimage/io/collection.py
+++ b/skimage/io/collection.py
@@ -10,6 +10,7 @@ from copy import copy
 
 import numpy as np
 from ._io import imread
+from .._shared import six
 
 
 def concatenate_images(ic):
@@ -296,7 +297,7 @@ class ImageCollection(object):
     """
     def __init__(self, load_pattern, conserve_memory=True, load_func=None):
         """Load and manage a collection of images."""
-        if isinstance(load_pattern, basestring):
+        if isinstance(load_pattern, six.string_types):
             load_pattern = load_pattern.split(':')
             self._files = []
             for pattern in load_pattern:
diff --git a/skimage/io/tests/test_collection.py b/skimage/io/tests/test_collection.py
index f650daeb..25cd1152 100644
--- a/skimage/io/tests/test_collection.py
+++ b/skimage/io/tests/test_collection.py
@@ -12,6 +12,7 @@ from skimage import data_dir
 from skimage.io import ImageCollection, MultiImage
 from skimage.io.collection import alphanumeric_key
 from skimage.io import Image as ioImage
+from skimage._shared import six
 
 
 try:
@@ -21,8 +22,6 @@ except ImportError:
 else:
     PIL_available = True
 
-if sys.version_info[0] > 2:
-    basestring = str
 
 class TestAlphanumericKey():
     def setUp(self):
@@ -129,7 +128,7 @@ class TestMultiImage():
 
     @skipif(not PIL_available)
     def test_files_property(self):
-        assert isinstance(self.img.filename, basestring)
+        assert isinstance(self.img.filename, six.string_types)
 
         def set_filename(f):
             self.img.filename = f
diff --git a/skimage/viewer/plugins/overlayplugin.py b/skimage/viewer/plugins/overlayplugin.py
index 25ea3b00..dc5ca060 100644
--- a/skimage/viewer/plugins/overlayplugin.py
+++ b/skimage/viewer/plugins/overlayplugin.py
@@ -3,6 +3,7 @@ from warnings import warn
 from skimage.util.dtype import dtype_range
 from .base import Plugin
 from ..utils import ClearColormap, update_axes_image
+from skimage._shared import six
 
 
 __all__ = ['OverlayPlugin']
@@ -77,7 +78,8 @@ class OverlayPlugin(Plugin):
     @color.setter
     def color(self, index):
         # Update colormap whenever color is changed.
-        if isinstance(index, basestring) and index not in self.color_names:
+        if isinstance(index, six.string_types) and \
+           index not in self.color_names:
             raise ValueError("%s not defined in OverlayPlugin.colors" % index)
         else:
             name = self.color_names[index]

From b04c3282bf1f718a6c93454a4bec66eb0a88b559 Mon Sep 17 00:00:00 2001
From: Stefan van der Walt <stefan@sun.ac.za>
Date: Fri, 28 Jun 2013 14:56:01 -0500
Subject: [PATCH 05/19] Fix zip.

---
 skimage/color/colorlabel.py | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/skimage/color/colorlabel.py b/skimage/color/colorlabel.py
index 41974f38..d6379037 100644
--- a/skimage/color/colorlabel.py
+++ b/skimage/color/colorlabel.py
@@ -5,6 +5,7 @@ import numpy as np
 
 from skimage import img_as_float
 from skimage._shared import six
+from skimage._shared.six.moves import zip
 from .colorconv import rgb2gray, gray2rgb
 from . import rgb_colors
 
@@ -88,7 +89,7 @@ def label2rgb(label, image=None, colors=None, alpha=0.3,
             bg_color = _rgb_vector(bg_color)
             color_cycle = itertools.chain(bg_color, color_cycle)
 
-    for c, i in itertools.izip(color_cycle, labels):
+    for c, i in zip(color_cycle, labels):
         mask = (label == i)
         colorized[mask] = c * alpha + colorized[mask] * (1 - alpha)
 

From 84615478e43e992fdf8a0e44942e60122aa2cfab Mon Sep 17 00:00:00 2001
From: Stefan van der Walt <stefan@sun.ac.za>
Date: Fri, 28 Jun 2013 15:09:58 -0500
Subject: [PATCH 06/19] Fix function code.

---
 skimage/_shared/utils.py | 7 +++++--
 1 file changed, 5 insertions(+), 2 deletions(-)

diff --git a/skimage/_shared/utils.py b/skimage/_shared/utils.py
index aad9220d..fb9376ab 100644
--- a/skimage/_shared/utils.py
+++ b/skimage/_shared/utils.py
@@ -1,6 +1,8 @@
 import warnings
 import functools
 
+from . import six
+
 
 __all__ = ['deprecated']
 
@@ -35,10 +37,11 @@ class deprecated(object):
         @functools.wraps(func)
         def wrapped(*args, **kwargs):
             if self.behavior == 'warn':
+                func_code = six.get_function_code(func)
                 warnings.warn_explicit(msg,
                     category=DeprecationWarning,
-                    filename=func.func_code.co_filename,
-                    lineno=func.func_code.co_firstlineno + 1)
+                    filename=func_code.co_filename,
+                    lineno=func_code.co_firstlineno + 1)
             elif self.behavior == 'raise':
                 raise DeprecationWarning(msg)
             return func(*args, **kwargs)

From 504ad94dc69c4cd1231e3df8446cc33a84153b87 Mon Sep 17 00:00:00 2001
From: Stefan van der Walt <stefan@sun.ac.za>
Date: Fri, 28 Jun 2013 15:16:46 -0500
Subject: [PATCH 07/19] Fix iterator.

---
 skimage/measure/find_contours.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/skimage/measure/find_contours.py b/skimage/measure/find_contours.py
index 68e471ac..298c09de 100755
--- a/skimage/measure/find_contours.py
+++ b/skimage/measure/find_contours.py
@@ -126,8 +126,8 @@ def find_contours(array, level,
 def _take_2(seq):
     iterator = iter(seq)
     while(True):
-        n1 = iterator.next()
-        n2 = iterator.next()
+        n1 = next(iterator)
+        n2 = next(iterator)
         yield (n1, n2)
 
 

From eb66e343514b891ea34b5e5236ae6eb0f5cbca40 Mon Sep 17 00:00:00 2001
From: Stefan van der Walt <stefan@sun.ac.za>
Date: Fri, 28 Jun 2013 16:19:49 -0500
Subject: [PATCH 08/19] Fix label casting for numpy 1.7.

---
 skimage/morphology/misc.py | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/skimage/morphology/misc.py b/skimage/morphology/misc.py
index 820ce4a1..4e71b224 100644
--- a/skimage/morphology/misc.py
+++ b/skimage/morphology/misc.py
@@ -66,7 +66,8 @@ def remove_small_objects(ar, min_size=64, connectivity=1, in_place=False):
 
     if out.dtype == bool:
         selem = nd.generate_binary_structure(ar.ndim, connectivity)
-        ccs = nd.label(ar, selem)[0]
+        ccs = np.zeros_like(ar, dtype=np.int)
+        nd.label(ar, selem, output=ccs)
     else:
         ccs = out
 

From 227b2097200e4bbb17da5686d0603bdfeb2a63bc Mon Sep 17 00:00:00 2001
From: Adam Wisniewski <adamw@tbcn.ca>
Date: Fri, 28 Jun 2013 18:09:27 -0400
Subject: [PATCH 09/19] fix arraypad

---
 skimage/util/arraypad.py | 6 ++++--
 1 file changed, 4 insertions(+), 2 deletions(-)

diff --git a/skimage/util/arraypad.py b/skimage/util/arraypad.py
index 52a2e3e5..acc89b7b 100644
--- a/skimage/util/arraypad.py
+++ b/skimage/util/arraypad.py
@@ -4,8 +4,10 @@ of an n-dimensional array.
 
 """
 from __future__ import division, absolute_import, print_function
+from skimage._shared.six import integer_types
 
 import numpy as np
+
 try:
     # Available on 2.x at base, Py3 requires this compatibility import.
     # Later versions of NumPy have this for 2.x as well.
@@ -1036,11 +1038,11 @@ def _normalize_shape(narray, shape):
                 fmt = "Unable to create correctly shaped tuple from %s"
                 raise ValueError(fmt % (normshp,))
     elif (isinstance(shape, (tuple, list))
-            and isinstance(shape[0], (int, float, long))
+            and isinstance(shape[0], integer_types + (float,))
             and len(shape) == 1):
         normshp = ((shape[0], shape[0]), ) * shapelen
     elif (isinstance(shape, (tuple, list))
-            and isinstance(shape[0], (int, float, long))
+            and isinstance(shape[0], integer_types + (float,))
             and len(shape) == 2):
         normshp = (shape, ) * shapelen
     if normshp is None:

From 81519b7863f636a758ac0e00d8b1c2296e3c5696 Mon Sep 17 00:00:00 2001
From: Adam Wisniewski <adamw@tbcn.ca>
Date: Fri, 28 Jun 2013 18:14:46 -0400
Subject: [PATCH 10/19] adding main to run tests

---
 skimage/util/tests/test_montage.py | 3 +++
 skimage/util/tests/test_shape.py   | 3 +++
 2 files changed, 6 insertions(+)

diff --git a/skimage/util/tests/test_montage.py b/skimage/util/tests/test_montage.py
index 47e5426d..bc5f2176 100644
--- a/skimage/util/tests/test_montage.py
+++ b/skimage/util/tests/test_montage.py
@@ -79,3 +79,6 @@ def test_rescale_intensity():
 def test_error_ndim():
     arr_error = np.random.randn(1, 2, 3, 4)
     montage2d(arr_error)
+
+if __name__ == '__main__':
+    np.testing.run_module_suite()
diff --git a/skimage/util/tests/test_shape.py b/skimage/util/tests/test_shape.py
index 3b5f8d41..33e3b638 100644
--- a/skimage/util/tests/test_shape.py
+++ b/skimage/util/tests/test_shape.py
@@ -139,3 +139,6 @@ def test_view_as_windows_2D():
                                 [9, 10, 11],
                                 [13, 14, 15],
                                 [17, 18, 19]]]]))
+
+if __name__ == '__main__':
+    np.testing.run_module_suite()

From 9d1907a21178ff841a77da7098ade16af9db544f Mon Sep 17 00:00:00 2001
From: Stefan van der Walt <stefan@sun.ac.za>
Date: Fri, 28 Jun 2013 17:16:13 -0500
Subject: [PATCH 11/19] Fix im_class access in Python 3.

---
 skimage/_shared/utils.py        | 8 ++++++++
 skimage/transform/_geometric.py | 5 +++--
 2 files changed, 11 insertions(+), 2 deletions(-)

diff --git a/skimage/_shared/utils.py b/skimage/_shared/utils.py
index fb9376ab..8ba67ec5 100644
--- a/skimage/_shared/utils.py
+++ b/skimage/_shared/utils.py
@@ -1,5 +1,6 @@
 import warnings
 import functools
+import sys
 
 from . import six
 
@@ -54,3 +55,10 @@ class deprecated(object):
             wrapped.__doc__ = doc + '\n\n    ' + wrapped.__doc__
 
         return wrapped
+
+
+def get_bound_method_class(m):
+    """Return the class for a bound method.
+
+    """
+    return m.im_class if sys.version < '3' else m.__self__.__class__
diff --git a/skimage/transform/_geometric.py b/skimage/transform/_geometric.py
index 58109224..f4920f46 100644
--- a/skimage/transform/_geometric.py
+++ b/skimage/transform/_geometric.py
@@ -4,6 +4,7 @@ from scipy import ndimage, spatial
 from skimage.util import img_as_float
 from ._warps_cy import _warp_fast
 
+from skimage._shared.utils import get_bound_method_class
 
 class GeometricTransform(object):
     """Perform geometric transformations on a set of coordinates.
@@ -1009,8 +1010,8 @@ def warp(image, inverse_map=None, map_args={}, output_shape=None, order=1,
         if inverse_map in HOMOGRAPHY_TRANSFORMS:
             matrix = inverse_map._matrix
         elif hasattr(inverse_map, '__name__') \
-                and inverse_map.__name__ == 'inverse' \
-                and inverse_map.im_class in HOMOGRAPHY_TRANSFORMS:
+             and inverse_map.__name__ == 'inverse' \
+             and get_bound_method_class(inverse_map) in HOMOGRAPHY_TRANSFORMS:
             matrix = np.linalg.inv(inverse_map.im_self._matrix)
         if matrix is not None:
             # transform all bands

From 558298f426ed66ef5ca49d34a4faa85f0635b9a2 Mon Sep 17 00:00:00 2001
From: Stefan van der Walt <stefan@sun.ac.za>
Date: Fri, 28 Jun 2013 17:18:55 -0500
Subject: [PATCH 12/19] Fix im_self access in Python 3.

---
 skimage/transform/_geometric.py | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/skimage/transform/_geometric.py b/skimage/transform/_geometric.py
index f4920f46..32857893 100644
--- a/skimage/transform/_geometric.py
+++ b/skimage/transform/_geometric.py
@@ -5,6 +5,8 @@ from skimage.util import img_as_float
 from ._warps_cy import _warp_fast
 
 from skimage._shared.utils import get_bound_method_class
+from skimage._shared import six
+
 
 class GeometricTransform(object):
     """Perform geometric transformations on a set of coordinates.
@@ -1012,7 +1014,7 @@ def warp(image, inverse_map=None, map_args={}, output_shape=None, order=1,
         elif hasattr(inverse_map, '__name__') \
              and inverse_map.__name__ == 'inverse' \
              and get_bound_method_class(inverse_map) in HOMOGRAPHY_TRANSFORMS:
-            matrix = np.linalg.inv(inverse_map.im_self._matrix)
+            matrix = np.linalg.inv(six.get_method_self(inverse_map)._matrix)
         if matrix is not None:
             # transform all bands
             dims = []

From f0506f1293bc77544f5dd406c56981beeba8dcc9 Mon Sep 17 00:00:00 2001
From: Stefan van der Walt <stefan@sun.ac.za>
Date: Fri, 28 Jun 2013 17:24:46 -0500
Subject: [PATCH 13/19] Fix imports under Python 3.

---
 skimage/viewer/canvastools/__init__.py  | 6 +++---
 skimage/viewer/canvastools/linetool.py  | 2 +-
 skimage/viewer/canvastools/painttool.py | 2 +-
 skimage/viewer/utils/__init__.py        | 2 +-
 skimage/viewer/widgets/__init__.py      | 4 ++--
 5 files changed, 8 insertions(+), 8 deletions(-)

diff --git a/skimage/viewer/canvastools/__init__.py b/skimage/viewer/canvastools/__init__.py
index 22a2d205..f5b89e2c 100644
--- a/skimage/viewer/canvastools/__init__.py
+++ b/skimage/viewer/canvastools/__init__.py
@@ -1,3 +1,3 @@
-from linetool import LineTool, ThickLineTool
-from recttool import RectangleTool
-from painttool import PaintTool
+from .linetool import LineTool, ThickLineTool
+from .recttool import RectangleTool
+from .painttool import PaintTool
diff --git a/skimage/viewer/canvastools/linetool.py b/skimage/viewer/canvastools/linetool.py
index 7a459401..0b1d3b0c 100644
--- a/skimage/viewer/canvastools/linetool.py
+++ b/skimage/viewer/canvastools/linetool.py
@@ -5,7 +5,7 @@ try:
 except ImportError:
     print("Could not import matplotlib -- skimage.viewer not available.")
 
-from base import CanvasToolBase, ToolHandles
+from .base import CanvasToolBase, ToolHandles
 
 
 __all__ = ['LineTool', 'ThickLineTool']
diff --git a/skimage/viewer/canvastools/painttool.py b/skimage/viewer/canvastools/painttool.py
index 3fbab153..b5d67229 100644
--- a/skimage/viewer/canvastools/painttool.py
+++ b/skimage/viewer/canvastools/painttool.py
@@ -8,7 +8,7 @@ try:
 except ImportError:
     print("Could not import matplotlib -- skimage.viewer not available.")
 
-from base import CanvasToolBase
+from .base import CanvasToolBase
 
 
 __all__ = ['PaintTool']
diff --git a/skimage/viewer/utils/__init__.py b/skimage/viewer/utils/__init__.py
index 5af24064..bb67a43f 100644
--- a/skimage/viewer/utils/__init__.py
+++ b/skimage/viewer/utils/__init__.py
@@ -1 +1 @@
-from core import *
+from .core import *
diff --git a/skimage/viewer/widgets/__init__.py b/skimage/viewer/widgets/__init__.py
index 6552a313..efa9fe9d 100644
--- a/skimage/viewer/widgets/__init__.py
+++ b/skimage/viewer/widgets/__init__.py
@@ -1,2 +1,2 @@
-from core import *
-from history import *
+from .core import *
+from .history import *

From 0286d2d30fcc59045711f6200158864b98ea33fc Mon Sep 17 00:00:00 2001
From: Stefan van der Walt <stefan@sun.ac.za>
Date: Fri, 28 Jun 2013 17:47:21 -0500
Subject: [PATCH 14/19] Use int32 for labelling.

---
 skimage/morphology/misc.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/skimage/morphology/misc.py b/skimage/morphology/misc.py
index 4e71b224..88770371 100644
--- a/skimage/morphology/misc.py
+++ b/skimage/morphology/misc.py
@@ -66,7 +66,7 @@ def remove_small_objects(ar, min_size=64, connectivity=1, in_place=False):
 
     if out.dtype == bool:
         selem = nd.generate_binary_structure(ar.ndim, connectivity)
-        ccs = np.zeros_like(ar, dtype=np.int)
+        ccs = np.zeros_like(ar, dtype=np.int32)
         nd.label(ar, selem, output=ccs)
     else:
         ccs = out

From 39e66c022903bf53c5d5ad6f1463b569569af849 Mon Sep 17 00:00:00 2001
From: Stefan van der Walt <stefan@sun.ac.za>
Date: Sat, 29 Jun 2013 10:18:43 -0500
Subject: [PATCH 15/19] Add  to public API.

---
 skimage/_shared/utils.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/skimage/_shared/utils.py b/skimage/_shared/utils.py
index 8ba67ec5..ea631716 100644
--- a/skimage/_shared/utils.py
+++ b/skimage/_shared/utils.py
@@ -5,7 +5,7 @@ import sys
 from . import six
 
 
-__all__ = ['deprecated']
+__all__ = ['deprecated', 'get_bound_method_class']
 
 
 class deprecated(object):

From 25661719293b95413e3e13cfab78a1b2ad76e709 Mon Sep 17 00:00:00 2001
From: Stefan van der Walt <stefan@sun.ac.za>
Date: Sat, 29 Jun 2013 10:40:49 -0500
Subject: [PATCH 16/19] Space code more readably in transform.

---
 skimage/transform/_geometric.py | 4 ++++
 1 file changed, 4 insertions(+)

diff --git a/skimage/transform/_geometric.py b/skimage/transform/_geometric.py
index 32857893..4153b5bd 100644
--- a/skimage/transform/_geometric.py
+++ b/skimage/transform/_geometric.py
@@ -1009,12 +1009,16 @@ def warp(image, inverse_map=None, map_args={}, output_shape=None, order=1,
     # use fast Cython version for specific interpolation orders
     if order in range(4) and not map_args:
         matrix = None
+
         if inverse_map in HOMOGRAPHY_TRANSFORMS:
             matrix = inverse_map._matrix
+
         elif hasattr(inverse_map, '__name__') \
              and inverse_map.__name__ == 'inverse' \
              and get_bound_method_class(inverse_map) in HOMOGRAPHY_TRANSFORMS:
+
             matrix = np.linalg.inv(six.get_method_self(inverse_map)._matrix)
+
         if matrix is not None:
             # transform all bands
             dims = []

From 6cef8727a0c06fcc97f6d18b0d11ca4733bb7d7d Mon Sep 17 00:00:00 2001
From: Tony S Yu <tsyu80@gmail.com>
Date: Sat, 29 Jun 2013 10:56:03 -0500
Subject: [PATCH 17/19] Minor fixes

- Use absolute imports so __main__ examples work
- PEP8: 2 blank lines
---
 skimage/util/tests/test_montage.py      | 1 +
 skimage/util/tests/test_shape.py        | 1 +
 skimage/viewer/canvastools/linetool.py  | 2 +-
 skimage/viewer/canvastools/painttool.py | 2 +-
 4 files changed, 4 insertions(+), 2 deletions(-)

diff --git a/skimage/util/tests/test_montage.py b/skimage/util/tests/test_montage.py
index bc5f2176..a25a6ee4 100644
--- a/skimage/util/tests/test_montage.py
+++ b/skimage/util/tests/test_montage.py
@@ -80,5 +80,6 @@ def test_error_ndim():
     arr_error = np.random.randn(1, 2, 3, 4)
     montage2d(arr_error)
 
+
 if __name__ == '__main__':
     np.testing.run_module_suite()
diff --git a/skimage/util/tests/test_shape.py b/skimage/util/tests/test_shape.py
index 33e3b638..8c62a191 100644
--- a/skimage/util/tests/test_shape.py
+++ b/skimage/util/tests/test_shape.py
@@ -140,5 +140,6 @@ def test_view_as_windows_2D():
                                 [13, 14, 15],
                                 [17, 18, 19]]]]))
 
+
 if __name__ == '__main__':
     np.testing.run_module_suite()
diff --git a/skimage/viewer/canvastools/linetool.py b/skimage/viewer/canvastools/linetool.py
index 0b1d3b0c..c32d0ea7 100644
--- a/skimage/viewer/canvastools/linetool.py
+++ b/skimage/viewer/canvastools/linetool.py
@@ -5,7 +5,7 @@ try:
 except ImportError:
     print("Could not import matplotlib -- skimage.viewer not available.")
 
-from .base import CanvasToolBase, ToolHandles
+from skimage.viewer.canvastools.base import CanvasToolBase, ToolHandles
 
 
 __all__ = ['LineTool', 'ThickLineTool']
diff --git a/skimage/viewer/canvastools/painttool.py b/skimage/viewer/canvastools/painttool.py
index b5d67229..0678c460 100644
--- a/skimage/viewer/canvastools/painttool.py
+++ b/skimage/viewer/canvastools/painttool.py
@@ -8,7 +8,7 @@ try:
 except ImportError:
     print("Could not import matplotlib -- skimage.viewer not available.")
 
-from .base import CanvasToolBase
+from skimage.viewer.canvastools.base import CanvasToolBase
 
 
 __all__ = ['PaintTool']

From f429b5abad906bf115e0e4ddc846c066204b28b5 Mon Sep 17 00:00:00 2001
From: Stefan van der Walt <stefan@sun.ac.za>
Date: Sat, 29 Jun 2013 11:00:55 -0500
Subject: [PATCH 18/19] Ensure PIL tests run with PIL.

---
 skimage/io/tests/test_io.py  | 18 +-----------------
 skimage/io/tests/test_pil.py | 19 +++++++++++++++++++
 2 files changed, 20 insertions(+), 17 deletions(-)

diff --git a/skimage/io/tests/test_io.py b/skimage/io/tests/test_io.py
index 6643e82e..8049860a 100644
--- a/skimage/io/tests/test_io.py
+++ b/skimage/io/tests/test_io.py
@@ -1,8 +1,7 @@
 import os
 
-from numpy.testing import *
+from numpy.testing import assert_array_equal, raises, run_module_suite
 import numpy as np
-from StringIO import StringIO
 
 import skimage.io as io
 from skimage import data_dir
@@ -29,20 +28,5 @@ def test_imread_url():
     assert image.shape == (512, 512)
 
 
-def test_imsave_filelike():
-    shape = (2, 2)
-    image = np.zeros(shape)
-    s = StringIO()
-
-    # save to file-like object
-    io.imsave(s, image)
-
-    # read from file-like object
-    s.seek(0)
-    out = io.imread(s)
-    assert out.shape == shape
-    np.testing.assert_allclose(out, image)
-
-
 if __name__ == "__main__":
     run_module_suite()
diff --git a/skimage/io/tests/test_pil.py b/skimage/io/tests/test_pil.py
index 3e2f3dde..664bcf4d 100644
--- a/skimage/io/tests/test_pil.py
+++ b/skimage/io/tests/test_pil.py
@@ -7,6 +7,8 @@ from tempfile import NamedTemporaryFile
 
 from skimage import data_dir
 from skimage.io import imread, imsave, use_plugin, reset_plugins
+from skimage._shared.six.moves import StringIO
+
 
 try:
     from PIL import Image
@@ -124,5 +126,22 @@ class TestSave:
                     x = (x * 255).astype(dtype)
                     yield self.roundtrip, dtype, x
 
+
+@skipif(not PIL_available)
+def test_imsave_filelike():
+    shape = (2, 2)
+    image = np.zeros(shape)
+    s = StringIO()
+
+    # save to file-like object
+    imsave(s, image)
+
+    # read from file-like object
+    s.seek(0)
+    out = imread(s)
+    assert out.shape == shape
+    assert_allclose(out, image)
+
+
 if __name__ == "__main__":
     run_module_suite()

From 9ed26136e2e6db48c2efaf6cf66e67381b5e4589 Mon Sep 17 00:00:00 2001
From: Stefan van der Walt <stefan@sun.ac.za>
Date: Sat, 29 Jun 2013 11:16:10 -0500
Subject: [PATCH 19/19] Do not run flakes on test files -- we have too many
 custom formatted array.

---
 .travis.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.travis.yml b/.travis.yml
index a47dae84..b0e7a494 100644
--- a/.travis.yml
+++ b/.travis.yml
@@ -35,4 +35,4 @@ script:
     # Change back to repository root directory and run all doc examples
     - cd ..
     - for f in doc/examples/*.py; do $PYTHON "$f"; if [ $? -ne 0 ]; then exit 1; fi done
-    - flake8 --exit-zero skimage doc/examples viewer_examples
+    - flake8 --exit-zero --exclude=test_*,six.py skimage doc/examples viewer_examples