Merge branch 'issue77' into devel

CHANGES.txt

@@ -1,3 +1,6 @@
+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     out-of-date windows information (issue79).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).

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 = '0.2.4'
+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

@@ -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::
 

glymur/__init__.py

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

glymur/codestream.py

@@ -102,7 +102,14 @@ 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

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/test/test_conformance.py

@@ -0,0 +1,133 @@
+"""
+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
+except:
+    raise
+
+try:
+    opj_data_root = os.environ['OPJ_DATA_ROOT']
+except KeyError:
+    opj_data_root = None
+except:
+    raise
+
+
+@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_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):
@@ -7260,7 +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',

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',

setup.py

@@ -2,7 +2,7 @@ from setuptools import setup, find_packages
 import sys
 
 kwargs = {'name': 'Glymur',
-          'version': '0.2.4',
+          'version': '0.2.5',
           'description': 'Tools for accessing JPEG2000 files',
           'long_description': open('README.md').read(),
           'author': 'John Evans',