merge branch 'release-0.8.0rc2'

The test requirement for six was problematic, as some versions cause
problems with assertWarns and some do not.  We are already filtering
out versions that we know cause problems and it can unintentionally
cause an upgrade superceding the system version if it remains as a
"test_requires" option, so best to get rid of it.  Additionally, the
"test_requires" option was entirely removed as pip doesn't recognize it
upon install, so "mock" would not be installed on Python2.7 via pip.

The doctest fix was the real fix for #316, not sure why this did
not show up when testing on linux mint

CHANGES.txt

@@ -1,3 +1,8 @@
+Jan 10, 2015 - v0.8.0  Reduced number of steps required for writing
+    images.  Deprecated old read and write methods in favor of
+    array-style slicing.  Added ignore_pclr_cmap_cdef, verbose,
+    shape, codestream, layer properties.
+
 Oct 06, 2014 - v0.7.2  Added ellipsis support in array-style slicing.
 
 Oct 02, 2014 - v0.7.1  Fixed README to mention Python 3.4

docs/source/api.rst

@@ -1,116 +0,0 @@
----
-API
----
-
-Jp2k
-----
-.. autoclass:: glymur.Jp2k
-   :members: read, write, wrap, read_bands, get_codestream
-
-Individual Boxes
-----------------
-Jp2kbox
-'''''''
-.. autoclass:: glymur.jp2box.Jp2kBox
-   :members:
-
-AssociationBox
-''''''''''''''
-.. autoclass:: glymur.jp2box.AssociationBox
-   :members:
-
-ColourSpecificationBox
-''''''''''''''''''''''
-.. autoclass:: glymur.jp2box.ColourSpecificationBox
-   :members:
-
-ChannelDefinitionBox
-''''''''''''''''''''''
-.. autoclass:: glymur.jp2box.ChannelDefinitionBox
-   :members:
-
-ComponentMappingBox
-'''''''''''''''''''
-.. autoclass:: glymur.jp2box.ComponentMappingBox
-   :members:
-
-ContiguousCodestreamBox
-'''''''''''''''''''''''
-.. autoclass:: glymur.jp2box.ContiguousCodestreamBox
-   :members:
-
-DataEntryURLBox
-'''''''''''''''
-.. autoclass:: glymur.jp2box.DataEntryURLBox
-   :members:
-
-FileTypeBox
-'''''''''''
-.. autoclass:: glymur.jp2box.FileTypeBox
-   :members:
-
-ImageHeaderBox
-''''''''''''''
-.. autoclass:: glymur.jp2box.ImageHeaderBox
-   :members:
-
-JP2HeaderBox
-''''''''''''
-.. autoclass:: glymur.jp2box.JP2HeaderBox
-   :members:
-
-JPEG2000SignatureBox
-''''''''''''''''''''
-.. autoclass:: glymur.jp2box.JPEG2000SignatureBox
-   :members:
-
-LabelBox
-''''''''
-.. autoclass:: glymur.jp2box.LabelBox
-   :members:
-
-PaletteBox
-''''''''''
-.. autoclass:: glymur.jp2box.PaletteBox
-   :members:
-
-ReaderRequirementsBox
-'''''''''''''''''''''
-.. autoclass:: glymur.jp2box.ReaderRequirementsBox
-   :members:
-
-ResolutionBox
-'''''''''''''
-.. autoclass:: glymur.jp2box.ResolutionBox
-   :members:
-
-CaptureResolutionBox
-''''''''''''''''''''
-.. autoclass:: glymur.jp2box.CaptureResolutionBox
-   :members:
-
-DisplayResolutionBox
-''''''''''''''''''''
-.. autoclass:: glymur.jp2box.DisplayResolutionBox
-   :members:
-
-UUIDBox
-'''''''
-.. autoclass:: glymur.jp2box.UUIDBox
-   :members:
-
-UUIDInfoBox
-'''''''''''
-.. autoclass:: glymur.jp2box.UUIDInfoBox
-   :members:
-
-UUIDListBox
-'''''''''''
-.. autoclass:: glymur.jp2box.UUIDListBox
-   :members:
-
-XMLBox
-''''''
-.. autoclass:: glymur.jp2box.XMLBox
-   :members:
-

docs/source/conf.py

@@ -75,9 +75,9 @@ copyright = u'2013, John Evans'
 # built documents.
 #
 # The short X.Y version.
-version = '0.7'
+version = '0.8'
 # The full version, including alpha/beta/rc tags.
-release = '0.7.2'
+release = '0.8.0'
 
 # The language for content autogenerated by Sphinx. Refer to documentation
 # for a list of supported languages.

docs/source/detailed_installation.rst

@@ -15,7 +15,7 @@ or if you use windows, then read on.
 
 Glymur uses ctypes to access the openjp2/openjpeg libraries, and
 because ctypes accesses libraries in a platform-dependent manner,
-it is recommended that if you compile and install OpenJPEG into a
+it is recommended that **if** you compile and install OpenJPEG into a
 non-standard location, you should then create a configuration file
 to help Glymur properly find the openjpeg or openjp2 libraries
 (linux users or macports users don’t need to bother with this if
@@ -50,6 +50,9 @@ installed in a non-standard place, i.e. ::
     [library]
     openjpeg: /somewhere/lib/libopenjpeg.so
 
+Once again, you should not have to bother with a configuration file if you use
+mac or linux and OpenJPEG is provided by your package manager.
+
 '''''''
 Testing
 '''''''

docs/source/how_do_i.rst

@@ -26,10 +26,10 @@ It's pretty simple, just supply the image data as the 2nd argument to the Jp2k
 constructor.
     
     >>> import glymur, numpy as np
-    >>> data = np.zeros((640, 480), dtype=np.uint8)
-    >>> jp2 = glymur.Jp2k('zeros.jp2', data=data)
+    >>> jp2 = glymur.Jp2k('zeros.jp2', data=np.zeros((640, 480), dtype=np.uint8)
 
-You should have OpenJPEG version 1.5 or more recent before writing JPEG 2000 images.
+You must have OpenJPEG version 1.5 or more recent in order to write JPEG 2000
+images with glymur.
 
 ... display metadata?
 =====================
@@ -442,7 +442,7 @@ following
     'Google'
 
 But that would be painful.  A better solution is to install the Python XMP
-Toolkit (make sure it is version 2.0)::
+Toolkit (make sure it is at least version 2.0)::
 
     >>> from libxmp import XMPMeta
     >>> from libxmp.consts import XMP_NS_XMP as NS_XAP

docs/source/index.rst

@@ -17,7 +17,6 @@ Contents:
    how_do_i
    whatsnew/index
    roadmap
-   api
 
 ------------------
 Indices and tables

docs/source/whatsnew/0.8.rst

@@ -7,6 +7,18 @@ Changes in 0.8.0
 
     * Simplified writing images by moving data and options into the
       constructor.
-    * The main_header attribute of the ContiguousCodestream class is now called
-      codestream.
     * Deprecated :py:meth:`read` method in favor of array-style slicing.
+      In order to retain certain functionality, the following parameters 
+      to the :py:meth:`read` method have become top-level properties
+
+      * verbose
+      * layer
+      * ignore_pclr_cmap_cdef
+
+    * Two additional properties were introduced.
+
+      * codestream
+      * shape
+
+      
+ 

glymur/jp2box.py

@@ -1032,7 +1032,7 @@ class ContiguousCodestreamBox(Jp2kBox):
                 with open(self._filename, 'rb') as fptr:
                     fptr.seek(self.main_header_offset)
                     codestream = Codestream(fptr, self._length,
-                                             header_only=header_only)
+                                            header_only=header_only)
                     self._codestream = codestream
         return self._codestream
 

glymur/jp2k.py

@@ -205,28 +205,30 @@ class Jp2k(Jp2kBox):
         if self._shape is not None:
             return self._shape
 
-        cstr = self.codestream
-        height = cstr.segment[1].ysiz
-        width = cstr.segment[1].xsiz
-        num_components = len(cstr.segment[1].xrsiz)
+        if self._codec_format == opj2.CODEC_J2K:
+            # get the image size from the codestream
+            cstr = self.codestream
+            height = cstr.segment[1].ysiz
+            width = cstr.segment[1].xsiz
+            num_components = len(cstr.segment[1].xrsiz)
+        else:
+            # try to get the image size from the IHDR box
+            jp2h = [box for box in self.box if box.box_id == 'jp2h'][0]
+            ihdr = [box for box in jp2h.box if box.box_id == 'ihdr'][0]
 
-        # If JP2 and a palette box is present, then determine the shape from
-        # that.
-        if num_components == 1:
-            if self._codec_format == opj2.CODEC_J2K:
-                # There's no palette box or component mapping in a J2K file.
-                # The 3rd component in the shape would then be 1, but we'll
-                # ignore that.
-                self.shape = (height, width)
-            else:
-                jp2h = [box for box in self.box if box.box_id == 'jp2h'][0]
+            height, width = ihdr.height, ihdr.width
+            num_components = ihdr.num_components
+
+            if num_components == 1:
+                # but if there is a PCLR box, then we need to check that as
+                # well, as that turns a single-channel image into a
+                # multi-channel image
                 pclr = [box for box in jp2h.box if box.box_id == 'pclr']
-                if len(pclr) == 0:
-                    # No palette box, so just one component, which we will
-                    # ignore.
-                    self.shape = (height, width)
-                else:
-                    self.shape = (height, width, len(pclr[0].signed))
+                if len(pclr) > 0:
+                    num_components = len(pclr[0].signed)
+
+        if num_components == 1:
+            self.shape = (height, width)
         else:
             self.shape = (height, width, num_components)
 
@@ -918,9 +920,11 @@ class Jp2k(Jp2kBox):
         """
         Slicing protocol.
         """
-        numrows = self.codestream.segment[1].ysiz
-        numcols = self.codestream.segment[1].xsiz
-        numbands = self.codestream.segment[1].Csiz
+        if len(self.shape) == 2:
+            numrows, numcols = self.shape
+            numbands = 1
+        else:
+            numrows, numcols, numbands = self.shape
 
         if isinstance(pargs, int):
             # Not a very good use of this protocol, but technically legal.

glymur/test/fixtures.py

@@ -2,7 +2,6 @@
 Test fixtures common to more than one test point.
 """
 import os
-import platform
 import re
 import sys
 import textwrap
@@ -34,14 +33,6 @@ elif re.match('1.[0-6]', six.__version__) is not None:
     WARNING_INFRASTRUCTURE_ISSUE = True
     msg = "Cannot run test with version {0} of python-six"
     WARNING_INFRASTRUCTURE_MSG = msg.format(six.__version__)
-elif ((re.match('1.8', six.__version__) is not None) and 
-      (sys.platform.startswith('linux')) and 
-      (platform.linux_distribution() == ('LinuxMint', '17', 'qiana'))):
-    WARNING_INFRASTRUCTURE_ISSUE = True
-    linux_distribution = platform.linux_distribution()
-    msg = "Cannot run test with version {0} of python-six on {1}"
-    WARNING_INFRASTRUCTURE_MSG = msg.format(six.__version__,
-                                            platform.linux_distribution)
 
 # Cannot reopen a named temporary file in windows.
 WINDOWS_TMP_FILE_MSG = "cannot use NamedTemporaryFile like this in windows"
@@ -554,7 +545,7 @@ text_gbr_34 = """Colour Specification Box (colr) @ (179, 1339)
 dump = r'''JPEG 2000 Signature Box (jP  ) @ (0, 12)
     Signature:  0d0a870a
 File Type Box (ftyp) @ (12, 20)
-    Brand:  jp2 
+    Brand:  jp2
     Compatibility:  ['jp2 ']
 JP2 Header Box (jp2h) @ (32, 45)
     Image Header Box (ihdr) @ (40, 22)
@@ -678,7 +669,7 @@ Contiguous Codestream Box (jp2c) @ (3223, 1132296)
 dump = r"""JPEG 2000 Signature Box (jP  ) @ (0, 12)
     Signature:  0d0a870a
 File Type Box (ftyp) @ (12, 20)
-    Brand:  jp2 
+    Brand:  jp2
     Compatibility:  ['jp2 ']
 JP2 Header Box (jp2h) @ (32, 45)
     Image Header Box (ihdr) @ (40, 22)
@@ -701,7 +692,7 @@ nemo_dump_no_codestream = dump.format(_indent(nemo_xmp))
 nemo_dump_no_codestream_no_xml = r"""JPEG 2000 Signature Box (jP  ) @ (0, 12)
     Signature:  0d0a870a
 File Type Box (ftyp) @ (12, 20)
-    Brand:  jp2 
+    Brand:  jp2
     Compatibility:  ['jp2 ']
 JP2 Header Box (jp2h) @ (32, 45)
     Image Header Box (ihdr) @ (40, 22)

glymur/test/test_jp2box.py

@@ -27,12 +27,17 @@ from .fixtures import (WARNING_INFRASTRUCTURE_ISSUE,
                        WINDOWS_TMP_FILE_MSG, MetadataBase)
 
 
+def docTearDown(doctest_obj):
+    glymur.set_parseoptions(full_codestream=False)
+
+
 def load_tests(loader, tests, ignore):
     """Run doc tests as well."""
     if os.name == "nt":
         # Can't do it on windows, temporary file issue.
         return tests
-    tests.addTests(doctest.DocTestSuite('glymur.jp2box'))
+    tests.addTests(doctest.DocTestSuite('glymur.jp2box',
+                                        tearDown=docTearDown))
     return tests
 
 

glymur/test/test_jp2k.py

@@ -39,6 +39,7 @@ from . import fixtures
 def docTearDown(doctest_obj):
     glymur.set_parseoptions(full_codestream=False)
 
+
 # Doc tests should be run as well.
 def load_tests(loader, tests, ignore):
     """Should run doc tests as well"""
@@ -1079,9 +1080,6 @@ class TestParsing(unittest.TestCase):
 class TestJp2kOpjDataRootWarnings(unittest.TestCase):
     """These tests should be run by just about all configuration."""
 
-    def tearDown(self):
-        glymur.set_parseoptions(full_codestream=False)
-
     def test_undecodeable_box_id(self):
         """Should warn in case of undecodeable box ID but not error out."""
         filename = opj_data_file('input/nonregression/edf_c2_1013627.jp2')

glymur/test/test_printing.py

@@ -1065,12 +1065,14 @@ class TestJp2dump(unittest.TestCase):
         expected = '\n'.join(expected)
         self.assertEqual(actual, expected)
 
-    @unittest.skipIf(sys.hexversion < 0x03000000, "assertRegex not in 2.7")
     def test_jp2_codestream_0(self):
         """Verify dumping with -c 0, supressing all codestream details."""
         actual = self.run_jp2dump(['', '-c', '0', self.jp2file])
 
-        expected = fixtures.nemo_dump_no_codestream
+        # shave off the codestream details
+        lines = fixtures.nemo.split('\n')
+        expected = lines[0:105]
+        expected = '\n'.join(expected)
         self.assertEqual(actual, expected)
 
     def test_jp2_codestream_1(self):

glymur/version.py

@@ -18,7 +18,7 @@ from .lib import openjpeg as opj, openjp2 as opj2
 
 # Do not change the format of this next line!  Doing so risks breaking
 # setup.py
-version = "0.7.2"
+version = "0.8.0"
 _sv = LooseVersion(version)
 version_tuple = _sv.version
 

setup.py

@@ -21,12 +21,10 @@ kwargs = {'name': 'Glymur',
           'test_suite': 'glymur.test'}
 
 install_requires = ['numpy>=1.7.0', 'lxml>=3.0.0']
-test_requires = ['six>=1.7.0']
 if sys.hexversion < 0x03030000:
     install_requires.append('contextlib2>=0.4')
-    test_requires.append('mock>=1.0.1')
+    install_requires.append('mock>=1.0.1')
 kwargs['install_requires'] = install_requires
-kwargs['test_requires'] = test_requires
 
 clssfrs = ["Programming Language :: Python",
            "Programming Language :: Python :: 2.7",