Merge branch 'issue86' into devel

CHANGES.txt

@@ -1,3 +1,10 @@
+Jul 23, 2013 - v0.2.5  Fixed inconsistency in XML handling, now all instances
+    are always ElementTree objects (issue82).
+
+Jul 21, 2013 - v0.2.4  Fixed markdown bug for Fedora 17 information, fixed
+    out-of-date windows information (issue79).  Fixed incorrect
+    interpretation of Psot parameter (issue78).
+
 Jul 18, 2013 - v0.2.3  Support for Python 2.6, OpenJPEG 1.4.  Incompatible
     change to ChannelDefinitionBox constructor.  Added RGBA example.
 

README.md

@@ -1,9 +1,9 @@
 glymur: a Python interface for JPEG 2000
 =========================================
 
-**glymur** contains a Python interface to the OpenJPEG library
+**glymur** contains a Python interface to the OpenJPEG library which
-which allows linux and mac users to read and write JPEG 2000 files.  
+allows one to read and write JPEG 2000 files.  **glymur** works on
-**glymur** works on Python 2.6, 2.7 and 3.3.  Python 3.3 is strongly 
+Python 2.6, 2.7 and 3.3.  Python 3.3 is strongly
 recommended.
 
 Please read the docs, https://glymur.readthedocs.org/en/latest/

docs/source/conf.py

@@ -78,7 +78,7 @@ copyright = u'2013, John Evans'
 # The short X.Y version.
 version = '0.1'
 # The full version, including alpha/beta/rc tags.
-release = '0.2.3'
+release = '0.2.5'
 
 # The language for content autogenerated by Sphinx. Refer to documentation
 # for a list of supported languages.

docs/source/detailed_installation.rst

@@ -115,7 +115,7 @@ following RPMs installed.
       * numpy
       * matplotlib (optional)
 
-In addition, you must install contextlib2 and Pillow via pip.
+In addition, you must install contextlib2 and Pillow via pip. ::
 
     $ yum install python-devel # pip needs this in order to compile Pillow
     $ pip-python install Pillow --user
@@ -137,8 +137,17 @@ platforms.
 Testing
 '''''''
 
-If you wish to run the tests (strongly recommended :-), you can either run them
+There are two environment variables you may wish to set before running the
-from within python as follows ... ::
+tests.  
+
+    * **OPJ_DATA_ROOT** - points to directory for OpenJPEG test data
+    * **FORMAT_CORPUS_ROOT** - points to directory for format-corpus repository  (see https://github.com/openplanets/format-corpus)
+
+Setting these two environment variables is not required, as any tests using 
+either of them will be skipped.
+
+In order to run the tests, you can either run them from within
+python as follows ... ::
 
     >>> import glymur
     >>> glymur.runtests()

docs/source/how_do_i.rst

@@ -185,9 +185,8 @@ Work with XMP UUIDs?
 ====================
 The example JP2 file shipped with glymur has an XMP UUID. ::
 
-    >>> from glymur import Jp2k
+    >>> import glymur
-    >>> file = glymur.data.nemo()
+    >>> j = glymur.Jp2k(glymur.data.nemo())
-    >>> j = Jp2k(file)
     >>> print(j.box[4])
     UUID Box (uuid) @ (715, 2412)
         UUID:  be7acfcb-97a9-42e8-9c71-999491e3afac (XMP)
@@ -198,7 +197,7 @@ The example JP2 file shipped with glymur has an XMP UUID. ::
           </rdf:RDF>
         </ns0:xmpmeta>
 
-Since the UUID data in this case is returned as an ElementTree Element, one can
+Since the UUID data in this case is returned as an ElementTree instance, one can
 use ElementTree to access the data.  For example, to extract the 
 **CreatorTool** attribute value, the following would work::
 

docs/source/roadmap.rst

@@ -6,7 +6,6 @@ Here's an incomplete list of what I'd like to focus on in the near future.
 
     * continue to monitor upstream changes in the openjp2 library
     * investigate using CFFI or cython instead of ctypes to wrap openjp2
-    * investigate swapping out ElementTree for LXML
     * eventually expose the openjp2 API
     * investigate JPIP
     

glymur/__init__.py

@@ -6,7 +6,6 @@ from .jp2k import Jp2k
 from .jp2dump import jp2dump
 
 from . import data
-from . import test
 
 
 def runtests():

glymur/codestream.py

@@ -5,7 +5,6 @@ codestreams.
 """
 # pylint: disable=C0302,R0902,R0903,R0913
 
-from itertools import takewhile
 import math
 import struct
 import sys
@@ -43,16 +42,6 @@ for _marker in range(0xff90, 0xff94):
     _VALID_MARKERS.append(_marker)
 
 
-class InconsistentStartOfTileError(IOError):
-    """To be raised if bad SOT segment encountered.
-
-    SOT segment offsets are recorded as encountered.  The offsets should all be
-    different.
-    """
-    def __init__(self, msg):
-        IOError.__init__(self, msg)
-
-
 class Codestream(object):
     """Container for codestream information.
 
@@ -113,7 +102,19 @@ class Codestream(object):
         while True:
 
             read_buffer = fptr.read(2)
-            marker_id, = struct.unpack('>H', read_buffer)
+            try:
+                marker_id, = struct.unpack('>H', read_buffer)
+            except struct.error:
+                # Treat this as a warning.
+                msg = "Marker had length {0} instead of expected length of 2 "
+                msg += "bytes.  Codestream parsing terminated."
+                warnings.warn(msg.format(len(read_buffer)))
+                break
+
+            if marker_id == 0xff90 and header_only:
+                # Start-of-tile (SOT) means that we are out of the main header
+                # and there is no need to go further.
+                break
 
             try:
                 segment = self._process_marker_segment(fptr, marker_id)
@@ -139,12 +140,6 @@ class Codestream(object):
 
                 fptr.seek(self._tile_offset[-1] + self._tile_length[-1])
 
-        if header_only:
-            # start-of-tile (SOT) means we are out of the main header.
-            # No need to go any further.
-            gen = takewhile(lambda s:  s.marker_id != 'SOT', self.segment)
-            self.segment = list(gen)
-
 
     def _process_marker_segment(self, fptr, marker_id):
         """Process and return a segment from the codestream.
@@ -210,19 +205,12 @@ class Codestream(object):
             # we encounter start-of-data marker segments.
 
             segment = _parse_sot_segment(fptr)
-            if segment.offset not in self._tile_offset:
+            self._tile_offset.append(segment.offset)
-                self._tile_offset.append(segment.offset)
+            if segment.psot == 0:
-                if segment.psot == 0:
+                tile_part_length = self.offset + self.length - segment.offset - 2
-                    tile_part_length = self.offset + self.length - segment.offset - 2
-                else:
-                    tile_part_length = segment.psot
-                self._tile_length.append(tile_part_length)
             else:
-                msg = "Inconsistent start-of-tile (SOT) marker segment "
+                tile_part_length = segment.psot
-                msg += "encountered in tile with index {0}.  "
+            self._tile_length.append(tile_part_length)
-                msg += "Codestream parsing terminated."
-                msg = msg.format(segment.isot)
-                raise InconsistentStartOfTileError(msg)
 
         elif marker_id == 0xff93:
             # start of data.  Need to seek past the current tile part.

glymur/jp2box.py

@@ -520,6 +520,195 @@ class ChannelDefinitionBox(Jp2kBox):
         return box
 
 
+class CodestreamHeaderBox(Jp2kBox):
+    """Container for codestream header box information.
+
+    Attributes
+    ----------
+    box_id : str
+        4-character identifier for the box.
+    length : int
+        length of the box in bytes.
+    offset : int
+        offset of the box from the start of the file.
+    longname : str
+        more verbose description of the box.
+    box : list
+        List of boxes contained in this superbox.
+    """
+    def __init__(self, length=0, offset=-1):
+        Jp2kBox.__init__(self, box_id='jpch', longname='Codestream Header')
+        self.length = length
+        self.offset = offset
+        self.box = []
+
+    def __str__(self):
+        msg = Jp2kBox.__str__(self)
+        for box in self.box:
+            boxstr = str(box)
+
+            # Add indentation.
+            strs = [('\n    ' + x) for x in boxstr.split('\n')]
+            msg += ''.join(strs)
+        return msg
+
+    @staticmethod
+    def parse(fptr, offset, length):
+        """Parse codestream header box.
+
+        Parameters
+        ----------
+        fptr : file
+            Open file object.
+        offset : int
+            Start position of box in bytes.
+        length : int
+            Length of the box in bytes.
+
+        Returns
+        -------
+        AssociationBox instance
+        """
+        box = CodestreamHeaderBox(length=length, offset=offset)
+
+        # The codestream header box is a superbox, so go ahead and parse its 
+        # child boxes.
+        box.box = box.parse_superbox(fptr)
+
+        return box
+
+
+class CompositingLayerHeaderBox(Jp2kBox):
+    """Container for compositing layer header box information.
+
+    Attributes
+    ----------
+    box_id : str
+        4-character identifier for the box.
+    length : int
+        length of the box in bytes.
+    offset : int
+        offset of the box from the start of the file.
+    longname : str
+        more verbose description of the box.
+    box : list
+        List of boxes contained in this superbox.
+    """
+    def __init__(self, length=0, offset=-1):
+        Jp2kBox.__init__(self, box_id='jplh',
+                         longname='Compositing Layer Header')
+        self.length = length
+        self.offset = offset
+        self.box = []
+
+    def __str__(self):
+        msg = Jp2kBox.__str__(self)
+        for box in self.box:
+            boxstr = str(box)
+
+            # Add indentation.
+            strs = [('\n    ' + x) for x in boxstr.split('\n')]
+            msg += ''.join(strs)
+        return msg
+
+    @staticmethod
+    def parse(fptr, offset, length):
+        """Parse compositing layer header box.
+
+        Parameters
+        ----------
+        fptr : file
+            Open file object.
+        offset : int
+            Start position of box in bytes.
+        length : int
+            Length of the box in bytes.
+
+        Returns
+        -------
+        AssociationBox instance
+        """
+        box = CompositingLayerHeaderBox(length=length, offset=offset)
+
+        # This box is a superbox, so go ahead and parse its # child boxes.
+        box.box = box.parse_superbox(fptr)
+
+        return box
+
+
+class JP2HeaderBox(Jp2kBox):
+    """Container for JP2 header box information.
+
+    Attributes
+    ----------
+    box_id : str
+        4-character identifier for the box.
+    length : int
+        length of the box in bytes.
+    offset : int
+        offset of the box from the start of the file.
+    longname : str
+        more verbose description of the box.
+    box : list
+        List of boxes contained in this superbox.
+    """
+    def __init__(self, length=0, offset=-1):
+        Jp2kBox.__init__(self, box_id='jp2h', longname='JP2 Header')
+        self.length = length
+        self.offset = offset
+        self.box = []
+
+    def __str__(self):
+        msg = Jp2kBox.__str__(self)
+        for box in self.box:
+            boxstr = str(box)
+
+            # Add indentation.
+            strs = [('\n    ' + x) for x in boxstr.split('\n')]
+            msg += ''.join(strs)
+        return msg
+
+    def write(self, fptr):
+        """Write a JP2 Header box to file.
+        """
+        # Write the contained boxes, then come back and write the length.
+        orig_pos = fptr.tell()
+        fptr.write(struct.pack('>I', 0))
+        fptr.write('jp2h'.encode())
+        for box in self.box:
+            box.write(fptr)
+
+        end_pos = fptr.tell()
+        fptr.seek(orig_pos)
+        fptr.write(struct.pack('>I', end_pos - orig_pos))
+        fptr.seek(end_pos)
+
+    @staticmethod
+    def parse(fptr, offset, length):
+        """Parse JPEG 2000 header box.
+
+        Parameters
+        ----------
+        fptr : file
+            Open file object.
+        offset : int
+            Start position of box in bytes.
+        length : int
+            Length of the box in bytes.
+
+        Returns
+        -------
+        JP2HeaderBox instance
+        """
+        box = JP2HeaderBox(length=length, offset=offset)
+
+        # The JP2 header box is a superbox, so go ahead and parse its child
+        # boxes.
+        box.box = box.parse_superbox(fptr)
+
+        return box
+
+
 class ComponentMappingBox(Jp2kBox):
     """Container for channel identification information.
 
@@ -1608,7 +1797,7 @@ class XMLBox(Jp2kBox):
         offset of the box from the start of the file.
     longname : str
         more verbose description of the box.
-    xml : ElementTree.Element
+    xml : ElementTree object
         XML section.
     """
     def __init__(self, xml=None, filename=None, length=0, offset=-1):
@@ -1636,10 +1825,7 @@ class XMLBox(Jp2kBox):
         msg = Jp2kBox.__str__(self)
         xml = self.xml
         if self.xml is not None:
-            try:
+            msg += _pretty_print_xml(self.xml)
-                msg += _pretty_print_xml(self.xml)
-            except TypeError:
-                msg += _pretty_print_xml(self.xml.getroot())
         else:
             msg += '\n    {0}'.format(xml)
         return msg
@@ -1682,7 +1868,8 @@ class XMLBox(Jp2kBox):
         text = text.rstrip('\0')
 
         try:
-            xml = ET.fromstring(text)
+            elt = ET.fromstring(text)
+            xml = ET.ElementTree(elt)
         except ParseError as parse_error:
             msg = 'A problem was encountered while parsing an XML box:  "{0}"'
             msg = msg.format(str(parse_error))
@@ -1926,13 +2113,11 @@ class UUIDBox(Jp2kBox):
             # XMP data.  Parse as XML.  Seems to be a difference between
             # ElementTree in version 2.7 and 3.3.
             if sys.hexversion < 0x03000000:
-                #parser = ET.XMLParser(encoding='utf-8')
+                elt = ET.fromstring(raw_data)
-                #import pdb; pdb.set_trace()
-                #self.data = ET.fromstringlist(raw_data, parser=parser)
-                self.data = ET.fromstring(raw_data)
             else:
                 text = raw_data.decode('utf-8')
-                self.data = ET.fromstring(text)
+                elt = ET.fromstring(text)
+            self.data = ET.ElementTree(elt)
         elif the_uuid.bytes == b'JpgTiffExif->JP2':
             exif_obj = Exif(raw_data)
             ifds = OrderedDict()
@@ -2513,11 +2698,13 @@ _BOX_WITH_ID = {
     'cdef': ChannelDefinitionBox,
     'cmap': ComponentMappingBox,
     'colr': ColourSpecificationBox,
-    'jP  ': JPEG2000SignatureBox,
     'ftyp': FileTypeBox,
     'ihdr': ImageHeaderBox,
-    'jp2h': JP2HeaderBox,
+    'jP  ': JPEG2000SignatureBox,
+    'jpch': CodestreamHeaderBox,
+    'jplh': CompositingLayerHeaderBox,
     'jp2c': ContiguousCodestreamBox,
+    'jp2h': JP2HeaderBox,
     'lbl ': LabelBox,
     'pclr': PaletteBox,
     'res ': ResolutionBox,
@@ -2555,8 +2742,8 @@ def _pretty_print_xml(xml, level=0):
     """Pretty print XML data.
     """
     xml = copy.deepcopy(xml)
-    _indent(xml, level=level)
+    _indent(xml.getroot(), level=level)
-    xmltext = ET.tostring(xml).decode('utf-8')
+    xmltext = ET.tostring(xml.getroot()).decode('utf-8')
 
     # Indent it a bit.
     lst = [('    ' + x) for x in xmltext.split('\n')]

glymur/jp2k.py

@@ -22,6 +22,7 @@ from .codestream import Codestream
 from .core import SRGB
 from .core import GREYSCALE
 from .core import PROGRESSION_ORDER
+from .core import ENUMERATED_COLORSPACE, RESTRICTED_ICC_PROFILE
 from .jp2box import Jp2kBox
 from .jp2box import JPEG2000SignatureBox
 from .jp2box import FileTypeBox
@@ -159,6 +160,24 @@ class Jp2k(Jp2kBox):
             # boxes) here.
             fptr.seek(0)
             self.box = self.parse_superbox(fptr)
+            self._validate()
+
+    def _validate(self):
+        """Validate the JPEG 2000 outermost superbox.
+        """
+        # A jp2-branded file cannot contain an "any ICC profile
+        ftyp = self.box[1]
+        if ftyp.brand == 'jp2 ':
+            jp2h = [box for box in self.box if box.box_id == 'jp2h'][0]
+            colrs = [box for box in jp2h.box if box.box_id == 'colr']
+            for colr in colrs: 
+                if colr.method not in (ENUMERATED_COLORSPACE,
+                                       RESTRICTED_ICC_PROFILE):
+                    msg = "Color Specification box method must specify either "
+                    msg += "an enumerated colorspace or a restricted ICC "
+                    msg += "profile if the file type box brand is 'jp2 '."
+                    warnings.warn(msg)
+
 
     # pylint:  disable-msg=W0221
     def write(self, img_array, cratios=None, eph=False, psnr=None, numres=None,

glymur/lib/config.py

@@ -35,9 +35,6 @@ def glymurrc_fname():
         fname = os.path.join(confdir, 'glymurrc')
         if os.path.exists(fname):
             return fname
-        else:
-            msg = "Configuration directory '{0}' does not exist.".format(fname)
-            warnings.warn(msg)
 
     # didn't find a configuration file.
     return None

glymur/test/__init__.py

@@ -1,11 +0,0 @@
-from .test_callbacks import TestCallbacks as callbacks
-from .test_codestream import TestCodestream as codestream
-from .test_config import TestSuite as config
-from .test_jp2k import TestJp2k as jp2k
-from .test_icc import TestICC as icc
-from .test_printing import TestPrinting as printing
-from .test_opj_suite import TestSuite as suite
-from .test_opj_suite import TestSuiteDump as suitedump
-from .test_opj_suite_write import TestSuiteWrite as suitew
-from .test_opj_suite_neg import TestSuiteNegative as suiteneg
-from .test_jp2box import TestJp2Boxes as box

glymur/test/test_config.py

@@ -81,40 +81,5 @@ class TestSuite(unittest.TestCase):
                         with self.assertWarns(UserWarning) as cw:
                             imp.reload(glymur.lib.openjp2)
 
-    def test_missing_config_file_via_environ(self):
-        # Verify that we error out properly if the configuration file
-        # specified via environment variable is not found.
-        with tempfile.TemporaryDirectory() as tdir:
-            with patch.dict('os.environ', {'XDG_CONFIG_HOME': tdir}):
-                # Misconfigured new configuration file should
-                # be rejected.
-                with self.assertWarns(UserWarning) as cw:
-                    imp.reload(glymur.lib.openjp2)
-
-    def test_home_dir_missing_config_dir(self):
-        # Verify no exception is raised if $HOME is missing .config directory.
-        with tempfile.TemporaryDirectory() as tdir:
-            with patch.dict('os.environ', {'HOME': tdir}):
-                # Misconfigured new configuration file should
-                # be rejected.
-                with self.assertWarns(UserWarning) as cw:
-                    imp.reload(glymur.lib.openjp2)
-
-    def test_home_dir_missing_glymur_rc_dir(self):
-        # Should warn but not error if $HOME/.config but no glymurrc dir.
-        with tempfile.TemporaryDirectory() as tdir:
-            # We need the subdirectory to be specifically named as ".config"
-            # in order for this test to work.  A specifically-named temporary
-            # directory does not seem to be possible, so try to symlink it.
-            # Supposedly the symlink gets cleaned up with tdir gets cleaned up.
-            with tempfile.TemporaryDirectory(suffix=".config", dir=tdir) \
-                    as tdir_config:
-                os.symlink(tdir_config, os.path.join(tdir, '.config'))
-                with patch.dict('os.environ', {'HOME': tdir}):
-                    # Misconfigured new configuration file should
-                    # be rejected.
-                    with self.assertWarns(UserWarning) as cw:
-                        imp.reload(glymur.lib.openjp2)
-
 if __name__ == "__main__":
     unittest.main()

glymur/test/test_conformance.py

@@ -0,0 +1,129 @@
+"""
+These tests deal with JPX/JP2/J2K images in the format-corpus repository.
+"""
+#pylint:  disable-all
+
+import os
+import sys
+
+if sys.hexversion < 0x02070000:
+    import unittest2 as unittest
+else:
+    import unittest
+
+import warnings
+
+from glymur import Jp2k
+import glymur
+
+try:
+    format_corpus_data_root = os.environ['FORMAT_CORPUS_DATA_ROOT']
+except KeyError:
+    format_corpus_data_root = None
+
+try:
+    opj_data_root = os.environ['OPJ_DATA_ROOT']
+except KeyError:
+    opj_data_root = None
+
+
+@unittest.skipIf(format_corpus_data_root is None,
+                 "FORMAT_CORPUS_DATA_ROOT environment variable not set")
+@unittest.skipIf(sys.hexversion < 0x03020000,
+                 "Requires features introduced in 3.2 (assertWarns)")
+class TestSuiteFormatCorpus(unittest.TestCase):
+
+    def setUp(self):
+        pass
+
+    def tearDown(self):
+        pass
+
+    def test_balloon_trunc1(self):
+        # Has one byte shaved off of EOC marker.
+        jfile = os.path.join(format_corpus_data_root,
+                             'jp2k-test/byteCorruption/balloon_trunc1.jp2')
+        j2k = Jp2k(jfile)
+        with self.assertWarns(UserWarning):
+            c = j2k.get_codestream(header_only=False)
+        
+        # The last segment is truncated, so there should not be an EOC marker.
+        self.assertNotEqual(c.segment[-1].marker_id, 'EOC')
+
+        # The codestream is not as long as claimed.
+        with self.assertRaises(OSError):
+            j2k.read(rlevel=-1)
+
+    def test_balloon_trunc2(self):
+        # Shortened by 5000 bytes.
+        jfile = os.path.join(format_corpus_data_root,
+                             'jp2k-test/byteCorruption/balloon_trunc2.jp2')
+        j2k = Jp2k(jfile)
+        with self.assertWarns(UserWarning):
+            c = j2k.get_codestream(header_only=False)
+        
+        # The last segment is truncated, so there should not be an EOC marker.
+        self.assertNotEqual(c.segment[-1].marker_id, 'EOC')
+
+        # The codestream is not as long as claimed.
+        with self.assertRaises(OSError):
+            j2k.read(rlevel=-1)
+
+    def test_balloon_trunc3(self):
+        # Most of last tile is missing.
+        jfile = os.path.join(format_corpus_data_root,
+                             'jp2k-test/byteCorruption/balloon_trunc3.jp2')
+        j2k = Jp2k(jfile)
+        with self.assertWarns(UserWarning):
+            c = j2k.get_codestream(header_only=False)
+        
+        # The last segment is truncated, so there should not be an EOC marker.
+        self.assertNotEqual(c.segment[-1].marker_id, 'EOC')
+
+        # Should error out, it does not.
+        #with self.assertRaises(OSError):
+        #    j2k.read(rlevel=-1)
+
+    def test_jp2_brand_vs_any_icc_profile(self):
+        # If 'jp2 ', then the method cannot be any icc profile.
+        jfile = os.path.join(format_corpus_data_root,
+                             'jp2k-test', 'icc',
+                             'balloon_eciRGBv2_ps_adobeplugin.jpf')
+        with self.assertWarns(UserWarning):
+            j2k = Jp2k(jfile)
+        
+    def test_jp2_brand_vs_any_icc_profile_multiple_colr(self):
+        # Has colr box, one that conforms, one that does not.
+
+        # Wrong 'brand' field; contains two versions of ICC profile: one
+        # embedded using "Any ICC" method; other embedded using "Restricted
+        # ICC" method, with description ("Modified eciRGB v2") and profileClass
+        # ("Input Device") changed relative to original profile.
+        lst = [format_corpus_data_root, 'jp2k-test', 'icc',
+               'balloon_eciRGBv2_ps_adobeplugin_jp2compatible.jpf']
+        jfile = os.path.join(*lst)
+        with self.assertWarns(UserWarning):
+            j2k = Jp2k(jfile)
+        
+
+@unittest.skipIf(opj_data_root is None,
+                 "OPJ_DATA_ROOT environment variable not set")
+@unittest.skipIf(sys.hexversion < 0x03020000,
+                 "Requires features introduced in 3.2 (assertWarns)")
+class TestSuiteOpj(unittest.TestCase):
+
+    def setUp(self):
+        pass
+
+    def tearDown(self):
+        pass
+
+    def test_jp2_brand_vs_any_icc_profile(self):
+        # If 'jp2 ', then the method cannot be any icc profile.
+        filename = os.path.join(opj_data_root,
+                                'input/nonregression/text_GBR.jp2')
+        with self.assertWarns(UserWarning):
+            j2k = Jp2k(filename)
+        
+if __name__ == "__main__":
+    unittest.main()

glymur/test/test_jp2box.py

@@ -19,6 +19,11 @@ from glymur.jp2box import *
 from glymur.core import COLOR, OPACITY
 from glymur.core import RED, GREEN, BLUE, GREY, WHOLE_IMAGE
 
+try:
+    format_corpus_data_root = os.environ['FORMAT_CORPUS_DATA_ROOT']
+except KeyError:
+    format_corpus_data_root = None
+
 
 # Doc tests should be run as well.
 def load_tests(loader, tests, ignore):
@@ -365,7 +370,7 @@ class TestXML(unittest.TestCase):
             j2k.wrap(tfile.name, boxes=boxes)
             jp2 = Jp2k(tfile.name)
             self.assertEqual(jp2.box[3].box_id, 'xml ')
-            self.assertEqual(ET.tostring(jp2.box[3].xml),
+            self.assertEqual(ET.tostring(jp2.box[3].xml.getroot()),
                              b'<data>0</data>')
 
     @unittest.skipIf(os.name == "nt",
@@ -467,7 +472,7 @@ class TestColourSpecificationBox(unittest.TestCase):
 
 @unittest.skipIf(glymur.lib.openjp2.OPENJP2 is None,
                  "Missing openjp2 library.")
-class TestJp2Boxes(unittest.TestCase):
+class TestWrap(unittest.TestCase):
 
     def setUp(self):
         self.j2kfile = glymur.data.goodstuff()
@@ -476,39 +481,6 @@ class TestJp2Boxes(unittest.TestCase):
     def tearDown(self):
         pass
 
-    def test_default_JPEG2000SignatureBox(self):
-        # Should be able to instantiate a JPEG2000SignatureBox
-        b = glymur.jp2box.JPEG2000SignatureBox()
-        self.assertEqual(b.signature, (13, 10, 135, 10))
-
-    def test_default_FileTypeBox(self):
-        # Should be able to instantiate a FileTypeBox
-        b = glymur.jp2box.FileTypeBox()
-        self.assertEqual(b.brand, 'jp2 ')
-        self.assertEqual(b.minor_version, 0)
-        self.assertEqual(b.compatibility_list, ['jp2 '])
-
-    def test_default_ImageHeaderBox(self):
-        # Should be able to instantiate an image header box.
-        b = glymur.jp2box.ImageHeaderBox(height=512, width=256,
-                                         num_components=3)
-        self.assertEqual(b.height,  512)
-        self.assertEqual(b.width,  256)
-        self.assertEqual(b.num_components,  3)
-        self.assertEqual(b.bits_per_component, 8)
-        self.assertFalse(b.signed)
-        self.assertFalse(b.colorspace_unknown)
-
-    def test_default_JP2HeaderBox(self):
-        b1 = JP2HeaderBox()
-        b1.box = [ImageHeaderBox(height=512, width=256),
-                  ColourSpecificationBox(colorspace=glymur.core.GREYSCALE)]
-
-    def test_default_ContiguousCodestreamBox(self):
-        b = ContiguousCodestreamBox()
-        self.assertEqual(b.box_id, 'jp2c')
-        self.assertIsNone(b.main_header)
-
     def verify_wrapped_raw(self, jp2file):
         # Shared method by at least two tests.
         jp2 = Jp2k(jp2file)
@@ -673,5 +645,75 @@ class TestJp2Boxes(unittest.TestCase):
             with self.assertRaises(IOError):
                 j2k.wrap(tfile.name, boxes=boxes)
 
+
+class TestJp2Boxes(unittest.TestCase):
+
+    def test_default_JPEG2000SignatureBox(self):
+        # Should be able to instantiate a JPEG2000SignatureBox
+        b = glymur.jp2box.JPEG2000SignatureBox()
+        self.assertEqual(b.signature, (13, 10, 135, 10))
+
+    def test_default_FileTypeBox(self):
+        # Should be able to instantiate a FileTypeBox
+        b = glymur.jp2box.FileTypeBox()
+        self.assertEqual(b.brand, 'jp2 ')
+        self.assertEqual(b.minor_version, 0)
+        self.assertEqual(b.compatibility_list, ['jp2 '])
+
+    def test_default_ImageHeaderBox(self):
+        # Should be able to instantiate an image header box.
+        b = glymur.jp2box.ImageHeaderBox(height=512, width=256,
+                                         num_components=3)
+        self.assertEqual(b.height,  512)
+        self.assertEqual(b.width,  256)
+        self.assertEqual(b.num_components,  3)
+        self.assertEqual(b.bits_per_component, 8)
+        self.assertFalse(b.signed)
+        self.assertFalse(b.colorspace_unknown)
+
+    def test_default_JP2HeaderBox(self):
+        b1 = JP2HeaderBox()
+        b1.box = [ImageHeaderBox(height=512, width=256),
+                  ColourSpecificationBox(colorspace=glymur.core.GREYSCALE)]
+
+    def test_default_ContiguousCodestreamBox(self):
+        b = ContiguousCodestreamBox()
+        self.assertEqual(b.box_id, 'jp2c')
+        self.assertIsNone(b.main_header)
+
+
+class TestJpxBoxes(unittest.TestCase):
+
+    def setUp(self):
+        pass
+
+    def tearDown(self):
+        pass
+
+    @unittest.skipIf(format_corpus_data_root is None,
+                     "FORMAT_CORPUS_DATA_ROOT environment variable not set")
+    def test_codestream_header(self):
+        # Should recognize codestream header box.
+        jfile = os.path.join(format_corpus_data_root,
+                             'jp2k-formats/balloon.jpf')
+        jpx = Jp2k(jfile)
+
+        # This superbox just happens to be empty.
+        self.assertEqual(jpx.box[4].box_id, 'jpch')
+        self.assertEqual(len(jpx.box[4].box), 0)
+
+    @unittest.skipIf(format_corpus_data_root is None,
+                     "FORMAT_CORPUS_DATA_ROOT environment variable not set")
+    def test_compositing_layer_header(self):
+        # Should recognize compositing layer header box.
+        jfile = os.path.join(format_corpus_data_root,
+                             'jp2k-formats/balloon.jpf')
+        jpx = Jp2k(jfile)
+
+        # This superbox just happens to be empty.
+        self.assertEqual(jpx.box[5].box_id, 'jplh')
+        self.assertEqual(len(jpx.box[5].box), 0)
+
+
 if __name__ == "__main__":
     unittest.main()

glymur/test/test_opj_suite.py

@@ -990,7 +990,11 @@ class TestSuite(unittest.TestCase):
     def test_NR_DEC_text_GBR_jp2_29_decode(self):
         jfile = os.path.join(data_root,
                              'input/nonregression/text_GBR.jp2')
-        data = Jp2k(jfile).read()
+        with warnings.catch_warnings():
+            # brand is 'jp2 ', but has any icc profile.
+            warnings.simplefilter("ignore")
+            jp2 = Jp2k(jfile)
+        data = jp2.read()
         self.assertTrue(True)
 
     def test_NR_DEC_pacs_ge_j2k_30_decode(self):
@@ -4021,7 +4025,7 @@ class TestSuiteDump(unittest.TestCase):
         self.assertEqual(jp2.box[1].compatibility_list[1], 'jp2 ')
 
         # XML box
-        tags = [x.tag for x in jp2.box[2].xml]
+        tags = [x.tag for x in jp2.box[2].xml.getroot()]
         self.assertEqual(tags,
                          ['{http://www.jpeg.org/jpx/1.0/xml}'
                           + 'GENERAL_CREATION_INFO'])
@@ -4046,7 +4050,7 @@ class TestSuiteDump(unittest.TestCase):
         self.assertEqual(jp2.box[3].box[1].colorspace, glymur.core.SRGB)
 
         # XML box
-        tags = [x.tag for x in jp2.box[4].xml]
+        tags = [x.tag for x in jp2.box[4].xml.getroot()]
         self.assertEqual(tags, ['{http://www.jpeg.org/jpx/1.0/xml}CAPTION',
                                 '{http://www.jpeg.org/jpx/1.0/xml}LOCATION',
                                 '{http://www.jpeg.org/jpx/1.0/xml}EVENT'])
@@ -4376,13 +4380,13 @@ class TestSuiteDump(unittest.TestCase):
         self.assertIsNone(jp2.box[2].box[1].colorspace)
 
         # XML box
-        tags = [x.tag for x in jp2.box[3].xml]
+        tags = [x.tag for x in jp2.box[3].xml.getroot()]
         self.assertEqual(tags,
                          ['{http://www.jpeg.org/jpx/1.0/xml}'
                           + 'GENERAL_CREATION_INFO'])
 
         # XML box
-        tags = [x.tag for x in jp2.box[5].xml]
+        tags = [x.tag for x in jp2.box[5].xml.getroot()]
         self.assertEqual(tags,
                          ['{http://www.jpeg.org/jpx/1.0/xml}CAPTION',
                           '{http://www.jpeg.org/jpx/1.0/xml}LOCATION',
@@ -6954,8 +6958,7 @@ class TestSuiteDump(unittest.TestCase):
         self.assertEqual(c.segment[3]._exponent, [4] + [5, 5, 6] * 5)
 
     def test_NR_merged_dump(self):
-        jfile = os.path.join(data_root,
+        jfile = os.path.join(data_root, 'input/nonregression/merged.jp2')
-                             'input/nonregression/merged.jp2')
         jp2 = Jp2k(jfile)
 
         ids = [box.box_id for box in jp2.box]
@@ -7261,7 +7264,10 @@ class TestSuiteDump(unittest.TestCase):
     def test_NR_text_GBR_dump(self):
         jfile = os.path.join(data_root,
                              'input/nonregression/text_GBR.jp2')
-        jp2 = Jp2k(jfile)
+        with warnings.catch_warnings():
+            # brand is 'jp2 ', but has any icc profile.
+            warnings.simplefilter("ignore")
+            jp2 = Jp2k(jfile)
 
         ids = [box.box_id for box in jp2.box]
         lst = ['jP  ', 'ftyp', 'rreq', 'jp2h',
@@ -7813,6 +7819,8 @@ class TestSuite15(unittest.TestCase):
             data = jp2.read()
         self.assertTrue(True)
 
+    @unittest.skipIf(int(glymur.lib.openjpeg.version().split('.')[1]) < 5,
+                     "Segfaults openjpeg 1.4 and earlier.")
     def test_NR_DEC_broken2_jp2_5_decode(self):
         # Null pointer access
         jfile = os.path.join(data_root, 'input/nonregression/broken2.jp2')
@@ -7834,6 +7842,8 @@ class TestSuite15(unittest.TestCase):
         with self.assertRaises(ValueError) as ce:
             d = j.read()
 
+    @unittest.skipIf(int(glymur.lib.openjpeg.version().split('.')[1]) < 5,
+                     "Segfaults openjpeg 1.4 and earlier.")
     def test_NR_DEC_broken4_jp2_7_decode(self):
         # Null pointer access
         jfile = os.path.join(data_root, 'input/nonregression/broken4.jp2')

glymur/test/test_printing.py

@@ -4,6 +4,7 @@ import pkg_resources
 import struct
 import sys
 import tempfile
+import warnings
 
 if sys.hexversion < 0x02070000:
     import unittest2 as unittest
@@ -277,9 +278,12 @@ class TestPrinting(unittest.TestCase):
                      "OPJ_DATA_ROOT environment variable not set")
     def test_icc_profile(self):
         filename = os.path.join(data_root, 'input/nonregression/text_GBR.jp2')
-        j = glymur.Jp2k(filename)
+        with warnings.catch_warnings():
+            # brand is 'jp2 ', but has any icc profile.
+            warnings.simplefilter("ignore")
+            jp2 = Jp2k(filename)
         with patch('sys.stdout', new=StringIO()) as fake_out:
-            print(j.box[3].box[1])
+            print(jp2.box[3].box[1])
             actual = fake_out.getvalue().strip()
         lin27 = ["Colour Specification Box (colr) @ (179, 1339)",
                  "    Method:  any ICC profile",
@@ -902,10 +906,13 @@ class TestPrinting(unittest.TestCase):
         # ICC profiles may be used in JP2, but the approximation field should
         # be zero unless we have jpx.  This file does both.
         filename = os.path.join(data_root, 'input/nonregression/text_GBR.jp2')
-        j = glymur.Jp2k(filename)
+        with warnings.catch_warnings():
+            # brand is 'jp2 ', but has any icc profile.
+            warnings.simplefilter("ignore")
+            jp2 = Jp2k(filename)
 
         with patch('sys.stdout', new=StringIO()) as fake_out:
-            print(j.box[3].box[1])
+            print(jp2.box[3].box[1])
             actual = fake_out.getvalue().strip()
         lines = ["Colour Specification Box (colr) @ (179, 1339)",
                  "    Method:  any ICC profile",
@@ -942,10 +949,13 @@ class TestPrinting(unittest.TestCase):
     def test_uuid(self):
         # UUID box
         filename = os.path.join(data_root, 'input/nonregression/text_GBR.jp2')
-        j = glymur.Jp2k(filename)
+        with warnings.catch_warnings():
+            # brand is 'jp2 ', but has any icc profile.
+            warnings.simplefilter("ignore")
+            jp2 = Jp2k(filename)
 
         with patch('sys.stdout', new=StringIO()) as fake_out:
-            print(j.box[4])
+            print(jp2.box[4])
             actual = fake_out.getvalue().strip()
         lines = ['UUID Box (uuid) @ (1544, 25)',
                  '    UUID:  3a0d0218-0ae9-4115-b376-4bca41ce0e71',

release.txt

@@ -6,30 +6,30 @@
 |           |        |        |        | pass.                                |
 +-----------+--------+--------+--------+--------------------------------------+
 | Mac       |   X    |        |        | MacPorts with both OpenJPEG 1.5.1    |
-| 10.6.8    |        |        |        | and OpenJPEG svn.  353 of 449 tests  |
+| 10.6.8    |        |        |        | and OpenJPEG svn.  352 of 450 tests  |
 |           |        |        |        | should pass.                         |
 +-----------+--------+--------+--------+--------------------------------------+
 | Mac       |        |   X    |        | MacPorts with both OpenJPEG 1.5.1    |
-| 10.6.8    |        |        |        | and OpenJPEG svn.  376 of 454 tests  |
+| 10.6.8    |        |        |        | and OpenJPEG svn.  377 of 455 tests  |
 |           |        |        |        | should pass.                         |
 +-----------+--------+--------+--------+--------------------------------------+
 | Mac       |        |        |   X    | MacPorts with both OpenJPEG 1.5.1    |
-| 10.6.8    |        |        |        | and OpenJPEG svn.  401 of 454        |
+| 10.6.8    |        |        |        | and OpenJPEG svn.  402 of 455        |
 |           |        |        |        | tests should pass.                   |
 +-----------+--------+--------+-----------------------------------------------+
 | Fedora 19 |        |        |   X    | Ships with 1.5.1, openjp2 built too. |
-|           |        |        |        | 401 of 454 tests should pass.        |
+|           |        |        |        | 402 of 455 tests should pass.        |
 +-----------+--------+--------+--------+--------------------------------------+
 | Fedora 18 |        |        |   X    | Ships with 1.5.1.  169 of 449 tests  |
 |           |        |        |        | should pass.                         |
 +-----------+--------+--------+--------+--------------------------------------+
-| Fedora 17 |        |   X    |        | Ships with 1.4.0.  169 of 449 tests  |
+| Fedora 17 |        |   X    |        | Ships with 1.4.0.  166 of 450 tests  |
 |           |        |        |        | should pass.                         |
 +-----------+--------+--------+--------+--------------------------------------+
-| CentOS    |   X    |        |        | Ships with 1.3.0.  167 of 449 tests  |
+| CentOS    |   X    |        |        | Ships with 1.3.0.  164 of 450 tests  |
 |   6.3     |        |        |        | should pass.                         |
 +-----------+--------+--------+--------+--------------------------------------+
-| Raspberry |        |   X    |        | Ships with 1.3.0.  169 of 449 tests  |
+| Raspberry |        |   X    |        | Ships with 1.3.0.  166 of 450 tests  |
 |    Pi     |        |        |        | should pass.                         |
 | Debian 7  |        |        |        |                                      |
 +-----------+--------+--------+--------+--------------------------------------+

setup.py

@@ -2,7 +2,7 @@ from setuptools import setup, find_packages
 import sys
 
 kwargs = {'name': 'Glymur',
-          'version': '0.2.3',
+          'version': '0.2.5',
           'description': 'Tools for accessing JPEG2000 files',
           'long_description': open('README.md').read(),
           'author': 'John Evans',