Merge branch 'release-0.2.4'

CHANGES.txt

@@ -1,3 +1,7 @@
+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+    out-of-date windows information (issue79).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 = '0.2.4'
 
 # 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
@@ -126,8 +126,11 @@ Windows
 -------
 The only configuration I've tested is Python(xy), which uses Python 2.7.  
 Python(xy) already comes with numpy, but you will have to install pip and then
-contextlib2 and mock as well.  Both 1.5.1 and the svn development versions of
+contextlib2 and mock as well.  Glymur seems to work with both 1.5.1 and the 
-openjpeg work.
+svn development versions of openjpeg.
+
+Glymur has been tested **far less** extensively on Windows than on the other 
+platforms.  
 
 
 '''''''

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

@@ -57,7 +57,12 @@ class Codestream(object):
 
     Attributes
     ----------
-    segment : list of marker segments
+    segment : iterable
+        list of marker segments
+    offset : int
+        Offset of the codestream from start of the file in bytes.
+    length : int
+        Length of the codestream in bytes.
 
     Raises
     ------
@@ -70,17 +75,22 @@ class Codestream(object):
        15444-1:2004 - Information technology -- JPEG 2000 image coding system:
        Core coding system
     """
-    def __init__(self, fptr, header_only=True):
+    def __init__(self, fptr, length, header_only=True):
         """
         Parameters
         ----------
         fptr : file
             Open file object.
+        length : int
+            Length of the codestream in bytes.
         header_only : bool, optional
             If True, only marker segments in the main header are parsed.
             Supplying False may impose a large performance penalty.
         """
 
+        self.offset = fptr.tell()
+        self.length = length
+
         # Number of components.  Must be kept track of for the processing of
         # many segments.
         self._csiz = -1
@@ -111,9 +121,9 @@ class Codestream(object):
 
             try:
                 segment = self._process_marker_segment(fptr, marker_id)
-            except InconsistentStartOfTileError as isote:
+            except Exception as error:
                 # Treat this as a warning.
-                msg = str(isote)
+                msg = str(error)
                 warnings.warn(msg)
                 break
 
@@ -199,7 +209,11 @@ class Codestream(object):
             segment = _parse_sot_segment(fptr)
             if segment.offset not in self._tile_offset:
                 self._tile_offset.append(segment.offset)
-                self._tile_length.append(segment.psot)
+                if segment.psot == 0:
+                    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 "
                 msg += "encountered in tile with index {0}.  "

glymur/jp2box.py

@@ -644,7 +644,7 @@ class ContiguousCodestreamBox(Jp2kBox):
         -------
         ContiguousCodestreamBox instance
         """
-        main_header = Codestream(fptr, header_only=True)
+        main_header = Codestream(fptr, length, header_only=True)
         box = ContiguousCodestreamBox(main_header, length=length,
                                       offset=offset)
         return box

glymur/jp2k.py

@@ -1033,7 +1033,8 @@ class Jp2k(Jp2kBox):
         """
         with open(self.filename, 'rb') as fptr:
             if self._codec_format == _opj2.CODEC_J2K:
-                codestream = Codestream(fptr, header_only=header_only)
+                codestream = Codestream(fptr, self.length,
+                                        header_only=header_only)
             else:
                 box = [x for x in self.box if x.box_id == 'jp2c']
                 if len(box) != 1:
@@ -1042,9 +1043,15 @@ class Jp2k(Jp2kBox):
                 fptr.seek(box[0].offset)
                 read_buffer = fptr.read(8)
                 (box_length, _) = struct.unpack('>I4s', read_buffer)
-                if box_length == 1:
+                if box_length == 0:
+                    # The length of the box is presumed to last until the end
+                    # of the file.  Compute the effective length of the box.
+                    box_length = os.path.getsize(fptr.name) - fptr.tell() + 8
+                elif box_length == 1:
                     # Seek past the XL field.
                     read_buffer = fptr.read(8)
-                codestream = Codestream(fptr, header_only=header_only)
+                    box_length, = struct.unpack('>Q', read_buffer)
+                codestream = Codestream(fptr, box_length - 8,
+                                        header_only=header_only)
 
             return codestream

glymur/test/test_codestream.py

@@ -28,8 +28,7 @@ except:
 class TestCodestream(unittest.TestCase):
 
     def setUp(self):
-        self.jp2file = pkg_resources.resource_filename(glymur.__name__,
+        self.jp2file = glymur.data.nemo()
-                                                       "data/nemo.jp2")
 
     def tearDown(self):
         pass
@@ -95,5 +94,16 @@ class TestCodestream(unittest.TestCase):
             self.assertEqual(c.segment[2].length, 3)
             self.assertEqual(c.segment[2]._data, b'\x00')
 
+    def test_psot_is_zero(self):
+        # Psot=0 in SOT is perfectly legal.  Issue #78.
+        filename = os.path.join(data_root,
+                                'input/nonregression/123.j2c')
+        j = Jp2k(filename)
+        c = j.get_codestream(header_only=False)
+
+        # The codestream is valid, so we should be able to get the entire
+        # codestream, so the last one is EOC.
+        self.assertEqual(c.segment[-1].marker_id, 'EOC')
+
 if __name__ == "__main__":
     unittest.main()

glymur/test/test_opj_suite.py

@@ -823,12 +823,16 @@ class TestSuite(unittest.TestCase):
         self.assertTrue(True)
 
     def test_NR_DEC_broken2_jp2_5_decode(self):
-        jfile = os.path.join(data_root,
+        # Null pointer access
-                             'input/nonregression/broken2.jp2')
+        jfile = os.path.join(data_root, 'input/nonregression/broken2.jp2')
         with self.assertRaises(IOError):
-            data = Jp2k(jfile).read()
+            with warnings.catch_warnings():
+                # Library warning, invalid number of subbands.
+                warnings.simplefilter("ignore")
+                data = Jp2k(jfile).read()
         self.assertTrue(True)
 
+
     @unittest.skipIf(sys.hexversion < 0x03020000,
                      "Uses features introduced in 3.2.")
     def test_NR_DEC_broken3_jp2_6_decode(self):
@@ -845,7 +849,10 @@ class TestSuite(unittest.TestCase):
         jfile = os.path.join(data_root,
                              'input/nonregression/broken4.jp2')
         with self.assertRaises(IOError):
-            data = Jp2k(jfile).read()
+            with warnings.catch_warnings():
+                # Library warning, invalid number of subbands.
+                warnings.simplefilter("ignore")
+                data = Jp2k(jfile).read()
         self.assertTrue(True)
 
     @unittest.skip("fprintf stderr output in r2343.")
@@ -6003,13 +6010,16 @@ class TestSuiteDump(unittest.TestCase):
         self.assertEqual(c.segment[6]._exponent,
                          [8] + [9, 9, 10] * 5)
 
+    @unittest.skipIf(sys.hexversion < 0x03020000,
+                     "Uses features introduced in 3.2, 'assertWarns'.")
     def test_NR_broken2_jp2_dump(self):
         # Invalid marker ID on codestream.
-        jfile = os.path.join(data_root,
+        jfile = os.path.join(data_root, 'input/nonregression/broken2.jp2')
-                             'input/nonregression/broken2.jp2')
+        with self.assertWarns(UserWarning):
-        with self.assertRaises(IOError):
             jp2 = Jp2k(jfile)
 
+        self.assertEqual(jp2.box[-1].main_header.segment[-1].marker_id, 'QCC')
+
     @unittest.skipIf(sys.hexversion < 0x03020000,
                      "Uses features introduced in 3.2.")
     def test_NR_broken3_jp2_dump(self):
@@ -6137,12 +6147,16 @@ class TestSuiteDump(unittest.TestCase):
         self.assertEqual(c.segment[6]._exponent,
                          [8] + [9, 9, 10] * 5)
 
+    @unittest.skipIf(sys.hexversion < 0x03020000,
+                     "Uses features introduced in 3.2, 'assertWarns'")
     def test_NR_broken4_jp2_dump(self):
-        jfile = os.path.join(data_root,
+        # Has an invalid marker in the main header
-                             'input/nonregression/broken4.jp2')
+        jfile = os.path.join(data_root, 'input/nonregression/broken4.jp2')
-        with self.assertRaises(IOError):
+        with self.assertWarns(UserWarning):
             jp2 = Jp2k(jfile)
 
+        self.assertEqual(jp2.box[-1].main_header.segment[-1].marker_id, 'QCC')
+
     def test_NR_file409752(self):
         jfile = os.path.join(data_root,
                              'input/nonregression/file409752.jp2')
@@ -7799,18 +7813,22 @@ 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):
-        jfile = os.path.join(data_root,
+        # Null pointer access
-                             'input/nonregression/broken2.jp2')
+        jfile = os.path.join(data_root, 'input/nonregression/broken2.jp2')
-        with self.assertRaises(IOError):
+        with self.assertRaises(ValueError):
-            data = Jp2k(jfile).read()
+            with warnings.catch_warnings():
+                # Library warning, invalid number of subbands.
+                warnings.simplefilter("ignore")
+                data = Jp2k(jfile).read()
         self.assertTrue(True)
 
     @unittest.skipIf(sys.hexversion < 0x03020000,
                      "Uses features introduced in 3.2.")
     def test_NR_DEC_broken3_jp2_6_decode(self):
-        jfile = os.path.join(data_root,
+        jfile = os.path.join(data_root, 'input/nonregression/broken3.jp2')
-                             'input/nonregression/broken3.jp2')
         with self.assertWarns(UserWarning) as cw:
             # colr box has bad length.
             j = Jp2k(jfile)
@@ -7818,11 +7836,16 @@ 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):
-        jfile = os.path.join(data_root,
+        # Null pointer access
-                             'input/nonregression/broken4.jp2')
+        jfile = os.path.join(data_root, 'input/nonregression/broken4.jp2')
-        with self.assertRaises(IOError):
+        with self.assertRaises(ValueError):
-            data = Jp2k(jfile).read()
+            with warnings.catch_warnings():
+                # Library warning, invalid number of subbands.
+                warnings.simplefilter("ignore")
+                data = Jp2k(jfile).read()
         self.assertTrue(True)
 
     @unittest.skip("fprintf stderr output in r2343.")

glymur/test/test_opj_suite_neg.py

@@ -73,25 +73,16 @@ class TestSuiteNegative(unittest.TestCase):
             with self.assertRaises(RuntimeError):
                 j.write(data, psnr=[30, 35, 40], cratios=[2, 3, 4])
 
-    @unittest.skipIf(sys.hexversion < 0x03020000,
-                     "Uses features introduced in 3.2.")
     def test_NR_MarkerIsNotCompliant_j2k_dump(self):
-        # SOT marker gives bad offset.
         relpath = 'input/nonregression/MarkerIsNotCompliant.j2k'
         jfile = os.path.join(data_root, relpath)
         jp2k = Jp2k(jfile)
-        with self.assertWarns(UserWarning) as cw:
+        c = jp2k.get_codestream(header_only=False)
-            c = jp2k.get_codestream(header_only=False)
-
-        # Verify that the last segment returned in the codestream is SOD,
-        # not EOC.  Codestream parsing should stop when we try to jump to
-        # the end of SOT.
-        self.assertEqual(c.segment[-1].marker_id, 'SOD')
 
     @unittest.skipIf(sys.hexversion < 0x03020000,
                      "Uses features introduced in 3.2.")
     def test_NR_illegalcolortransform_dump(self):
-        # SOT marker gives bad offset.
+        # EOC marker is bad
         relpath = 'input/nonregression/illegalcolortransform.j2k'
         jfile = os.path.join(data_root, relpath)
         jp2k = Jp2k(jfile)
@@ -103,20 +94,11 @@ class TestSuiteNegative(unittest.TestCase):
         # the end of SOT.
         self.assertEqual(c.segment[-1].marker_id, 'SOD')
 
-    @unittest.skipIf(sys.hexversion < 0x03020000,
-                     "Uses features introduced in 3.2.")
     def test_NR_Cannotreaddatawithnosizeknown_j2k(self):
-        # SOT marker gives bad offset.
         relpath = 'input/nonregression/Cannotreaddatawithnosizeknown.j2k'
         jfile = os.path.join(data_root, relpath)
         jp2k = Jp2k(jfile)
-        with self.assertWarns(UserWarning) as cw:
+        c = jp2k.get_codestream(header_only=False)
-            c = jp2k.get_codestream(header_only=False)
-
-        # Verify that the last segment returned in the codestream is SOD,
-        # not EOC.  Codestream parsing should stop when we try to jump to
-        # the end of SOT.
-        self.assertEqual(c.segment[-1].marker_id, 'SOD')
 
     @unittest.skipIf(os.name == "nt", "Temporary file issue on window.")
     def test_code_block_dimensions(self):

release.txt

@@ -6,34 +6,38 @@
 |           |        |        |        | 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  |        |        |        |                                      |
 +-----------+--------+--------+--------+--------------------------------------+
 
+Make release branch, qualify on all platforms.
 Pylint on entire package should exceed 0.95.
 pep8 should be pass cleanly.
 Coverage should exceed 95%.
+Make release candidate, push to Pypi, qualify in virtual environment.
+Merge release branch to master, tag, push to master, push to Pypi.
+

setup.py

@@ -2,7 +2,7 @@ from setuptools import setup, find_packages
 import sys
 
 kwargs = {'name': 'Glymur',
-          'version': '0.2.3',
+          'version': '0.2.4',
           'description': 'Tools for accessing JPEG2000 files',
           'long_description': open('README.md').read(),
           'author': 'John Evans',