Merge branch 'devel' into issue40

CHANGES.txt

@@ -1,4 +1,5 @@
-Jun 11, 2013 - Added reduce=-1 option to get lowest resolution thumbnail
+Jun 11, 2013 - v0.1.8  Added reduce=-1 option to get lowest resolution
+    thumbnail.
 
 Jun 07, 2013 - v0.1.7  Changed Exif dictionary names from ['Exif', 'Photo',
     'Iop', 'GPSInfo'] to ['Image', 'Photo', 'Iop', 'GPSInfo'].  

MANIFEST.in

@@ -1,4 +1,3 @@
 include *.txt *.md
-recursive-include *.txt *.py
 prune build
 exclude readthedocs-pip-requirements.txt

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 = '0.1.7'
+release = '0.1.8'
 
 # The language for content autogenerated by Sphinx. Refer to documentation
 # for a list of supported languages.

docs/source/how_do_i.rst

@@ -7,7 +7,7 @@ Read the lowest resolution thumbnail?
 =====================================
 Printing the Jp2k object should reveal the number of resolutions (look in the
 COD segment section), but you can take a shortcut by supplying -1 as the reduce
-level.
+level. ::
 
     >>> import pkg_resources
     >>> import glymur
@@ -38,7 +38,7 @@ codestream box, only the main header is printed.  It is possible to print
 
 Work with XMP UUIDs?
 ====================
-The example JP2 file shipped with glymur has an XMP UUID::
+The example JP2 file shipped with glymur has an XMP UUID. ::
 
     >>> import pkg_resources
     >>> from glymur import Jp2k

glymur/jp2box.py

@@ -12,6 +12,7 @@ References
 """
 
 import copy
+import datetime
 import math
 import os
 import pprint
@@ -153,9 +154,9 @@ class ColourSpecificationBox(Jp2kBox):
     colorspace : int or None
         Enumerated colorspace, corresponds to one of 'sRGB', 'greyscale', or
         'YCC'.  If not None, then icc_profile must be None.
-    icc_profile : byte array or None
+    icc_profile : _ICCProfile or None
-        ICC profile according to ICC profile specification.  If not None, then
+        ICC profile header according to ICC profile specification.  If not
-        color_space must be None.
+        None, then color_space must be None.
     """
     def __init__(self, **kwargs):
         Jp2kBox.__init__(self, id='', longname='Colour Specification')
@@ -174,8 +175,7 @@ class ColourSpecificationBox(Jp2kBox):
             x = _colorspace_map_display[self.colorspace]
             msg += '\n    Colorspace:  {0}'.format(x)
         else:
-            x = len(self.icc_profile)
+            msg += '\n    ICC Profile:  {0}'.format(self.icc_profile.__str__())
-            msg += '\n    ICC Profile:  {0} bytes'.format(x)
 
         return msg
 
@@ -221,12 +221,169 @@ class ColourSpecificationBox(Jp2kBox):
             # ICC profile
             kwargs['colorspace'] = None
             n = offset + length - f.tell()
-            kwargs['icc_profile'] = f.read(n)
+            if n < 128:
+                msg = "ICC profile header is corrupt, length is "
+                msg += "only {0} instead of 128."
+                warnings.warn(msg.format(n), UserWarning)
+                kwargs['icc_profile'] = None
+            else:
+                icc_profile = _ICCProfile(f.read(n))
+                kwargs['icc_profile'] = icc_profile
 
         box = ColourSpecificationBox(**kwargs)
         return box
 
 
+class _ICCProfile:
+    """
+    """
+    profile_class = {b'scnr': 'input device profile',
+                     b'mntr': 'display device profile',
+                     b'prtr': 'output device profile',
+                     b'link': 'devicelink profile',
+                     b'spac': 'colorspace conversion profile',
+                     b'abst': 'abstract profile',
+                     b'nmcl': 'name colour profile'}
+
+    colour_space_dict = {b'XYZ ': 'XYZ',
+                         b'Lab ': 'Lab',
+                         b'Luv ': 'Luv',
+                         b'YCbr': 'YCbCr',
+                         b'Yxy ': 'Yxy',
+                         b'RGB ': 'RGB',
+                         b'GRAY': 'gray',
+                         b'HSV ': 'hsv',
+                         b'HLS ': 'hls',
+                         b'CMYK': 'CMYK',
+                         b'CMY ': 'cmy',
+                         b'2CLR': '2colour',
+                         b'3CLR': '3colour',
+                         b'4CLR': '4colour',
+                         b'5CLR': '5colour',
+                         b'6CLR': '6colour',
+                         b'7CLR': '7colour',
+                         b'8CLR': '8colour',
+                         b'9CLR': '9colour',
+                         b'ACLR': '10colour',
+                         b'BCLR': '11colour',
+                         b'CCLR': '12colour',
+                         b'DCLR': '13colour',
+                         b'ECLR': '14colour',
+                         b'FCLR': '15colour'}
+
+    rendering_intent_dict = {0: 'perceptual',
+                             1: 'media-relative colorimetric',
+                             2: 'saturation',
+                             3: 'ICC-absolute colorimetric'}
+
+    def __init__(self, buffer):
+        self._raw_buffer = buffer
+
+        self.size, = struct.unpack('>I', self._raw_buffer[0:4])
+        self.preferred_cmm_type, = struct.unpack('>I', self._raw_buffer[4:8])
+
+        data = struct.unpack('>BB', self._raw_buffer[8:10])
+        major = data[0]
+        minor = (data[1] & 0xf0) >> 4
+        bugfix = (data[1] & 0x0f)
+        self.version = '{0}.{1}.{2}'.format(major, minor, bugfix)
+
+        self.device_class = self.profile_class[self._raw_buffer[12:16]]
+        self.colour_space = self.colour_space_dict[self._raw_buffer[16:20]]
+        self.connection_space = self.colour_space_dict[self._raw_buffer[20:24]]
+
+        data = struct.unpack('>HHHHHH', self._raw_buffer[24:36])
+        self.datetime = datetime.datetime(*data)
+        self.file_signature = buffer[36:40].decode('utf-8')
+        if buffer[40:44] == b'\x00\x00\x00\x00':
+            self.platform = 'unrecognized'
+        else:
+            self.platform = buffer[40:44].decode('utf-8')
+
+        self.flags, = struct.unpack('>I', buffer[44:48])
+
+        self.device_manufacturer = buffer[48:52].decode('utf-8')
+        if buffer[52:56] == b'\x00\x00\x00\x00':
+            self.device_model = ''
+        else:
+            self.device_model = buffer[52:56].decode('utf-8')
+        self.device_attributes, = struct.unpack('>Q', buffer[56:64])
+        self.rendering_intent, = struct.unpack('>I', buffer[64:68])
+
+        data = struct.unpack('>iii', buffer[68:80])
+        self.illuminant = np.array(data, dtype=np.float64) / 65536
+
+        if buffer[80:84] == b'\x00\x00\x00\x00':
+            self.creator = 'unrecognized'
+        else:
+            self.creator = buffer[80:84].decode('utf-8')
+
+        self.profile_id = buffer[84:100]
+        self.reserved = buffer[100:127]
+
+    def __str__(self):
+        msg = "\n        Size:  {0}"
+        msg += "\n        Preferred CMM type:  {1:x}"
+        msg += "\n        Version:  {2}"
+        msg += "\n        Device class signature:  {3}"
+        msg += "\n        Color space:  {4}"
+        msg += "\n        Connection space:  {5}"
+        msg += "\n        Creation time:  {6}"
+        msg += "\n        File signature:  {7}"
+        msg += "\n        Platform:  {8}"
+        msg += "\n        Flags:  {9}"
+        msg += "\n        Device manufacturer:  {10}"
+        msg += "\n        Device model:  {11}"
+        msg += "\n        Device attributes:  {12}"
+        msg += "\n        Rendering intent:  {13}"
+        msg += "\n        Illuminant:  {14}"
+        msg += "\n        Creator signature:  {15}"
+
+        if self.flags & 0x01:
+            flag_string = 'embedded, '
+        else:
+            flag_string = 'not embedded, '
+        if self.flags & 0x02:
+            flag_string += 'cannot be used independently'
+        else:
+            flag_string += 'can be used independently'
+
+        if self.device_attributes & 0x01:
+            attr_string = 'transparency, '
+        else:
+            attr_string = 'reflective, '
+        if self.device_attributes & 0x02:
+            attr_string += 'matte, '
+        else:
+            attr_string += 'glossy, '
+        if self.device_attributes & 0x04:
+            attr_string += 'negative media polarity, '
+        else:
+            attr_string += 'positive media polarity, '
+        if self.device_attributes & 0x08:
+            attr_string += 'black and white media'
+        else:
+            attr_string += 'color media'
+
+        msg = msg.format(self.size,
+                         self.preferred_cmm_type,
+                         self.version,
+                         self.device_class,
+                         self.colour_space,
+                         self.connection_space,
+                         self.datetime,
+                         self.file_signature,
+                         self.platform,
+                         flag_string,
+                         self.device_manufacturer,
+                         self.device_model,
+                         attr_string,
+                         self.rendering_intent_dict[self.rendering_intent],
+                         self.illuminant,
+                         self.creator)
+        return(msg)
+
+
 class ComponentDefinitionBox(Jp2kBox):
     """Container for component definition box information.
 

glymur/jp2k.py

@@ -138,7 +138,7 @@ class Jp2k(Jp2kBox):
             f.seek(0)
             self.box = self._parse_superbox(f)
 
-    def write(self, data, cratios=None, eph=False, psnr=None, numres=None,
+    def write(self, img_array, cratios=None, eph=False, psnr=None, numres=None,
               cbsize=None, psizes=None, grid_offset=None, sop=False,
               subsam=None, tilesize=None, prog=None, modesw=None,
               colorspace=None, verbose=False):
@@ -150,7 +150,7 @@ class Jp2k(Jp2kBox):
 
         Parameters
         ----------
-        data : array
+        img_array : ndarray
             Image data to be written to file.
         callbacks : bool, optional
             If true, enable default info handler such that INFO messages
@@ -307,19 +307,19 @@ class Jp2k(Jp2kBox):
             msg = "Cannot specify cratios and psnr together."
             raise RuntimeError(msg)
 
-        if data.ndim == 2:
+        if img_array.ndim == 2:
-            numrows, numcols = data.shape
+            numrows, numcols = img_array.shape
-            data = data.reshape(numrows, numcols, 1)
+            img_array = img_array.reshape(numrows, numcols, 1)
-        elif data.ndim == 3:
+        elif img_array.ndim == 3:
             pass
         else:
-            msg = "{0}D imagery is not allowed.".format(data.ndim)
+            msg = "{0}D imagery is not allowed.".format(img_array.ndim)
             raise IOError(msg)
 
-        numrows, numcols, num_comps = data.shape
+        numrows, numcols, num_comps = img_array.shape
 
         if colorspace is None:
-            if data.shape[2] == 1 or data.shape[2] == 2:
+            if img_array.shape[2] == 1 or img_array.shape[2] == 2:
                 colorspace = opj2._CLRSPC_GRAY
             else:
                 # No YCC unless specifically told to do so.
@@ -331,15 +331,15 @@ class Jp2k(Jp2kBox):
             if colorspace not in ('rgb', 'grey', 'gray'):
                 msg = 'Invalid colorspace "{0}"'.format(colorspace)
                 raise IOError(msg)
-            elif colorspace == 'rgb' and data.shape[2] < 3:
+            elif colorspace == 'rgb' and img_array.shape[2] < 3:
                 msg = 'RGB colorspace requires at least 3 components.'
                 raise IOError(msg)
             else:
                 colorspace = _cspace_map[colorspace]
 
-        if data.dtype == np.uint8:
+        if img_array.dtype == np.uint8:
             comp_prec = 8
-        elif data.dtype == np.uint16:
+        elif img_array.dtype == np.uint16:
             comp_prec = 16
         else:
             raise RuntimeError("unhandled datatype")
@@ -368,7 +368,7 @@ class Jp2k(Jp2kBox):
 
         # Stage the image data to the openjpeg data structure.
         for k in range(0, num_comps):
-            layer = np.ascontiguousarray(data[:, :, k], dtype=np.int32)
+            layer = np.ascontiguousarray(img_array[:, :, k], dtype=np.int32)
             dest = image.contents.comps[k].data
             src = layer.ctypes.data
             ctypes.memmove(dest, src, layer.nbytes)
@@ -419,7 +419,7 @@ class Jp2k(Jp2kBox):
 
         Returns
         -------
-        result : array
+        img_array : ndarray
             The image data.
 
         Raises
@@ -451,18 +451,18 @@ class Jp2k(Jp2kBox):
             msg = "Components must all have the same subsampling factors."
             raise IOError(msg)
 
-        data = self._read_common(reduce=reduce,
+        img_array = self._read_common(reduce=reduce,
-                                 layer=layer,
+                                      layer=layer,
-                                 area=area,
+                                      area=area,
-                                 tile=tile,
+                                      tile=tile,
-                                 verbose=verbose,
+                                      verbose=verbose,
-                                 as_bands=False)
+                                      as_bands=False)
 
-        if data.shape[2] == 1:
+        if img_array.shape[2] == 1:
-            data = data.view()
+            img_array = img_array.view()
-            data.shape = data.shape[0:2]
+            img_array.shape = img_array.shape[0:2]
 
-        return data
+        return img_array
 
     def _read_common(self, reduce=0, layer=0, area=None, tile=None,
                      verbose=False, as_bands=False):
@@ -486,7 +486,7 @@ class Jp2k(Jp2kBox):
 
         Returns
         -------
-        data : list or array
+        img_array : ndarray
             The individual image components or a single array.
         """
         dparam = opj2._set_default_decoder_parameters()

glymur/test/__init__.py

@@ -1,6 +1,7 @@
 from .test_callbacks import TestCallbacks as callbacks
 from .test_codestream import TestCodestream as codestream
 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_write import TestSuiteWrite as suitew

glymur/test/test_icc.py

@@ -0,0 +1,74 @@
+import datetime
+import os
+import struct
+import sys
+import tempfile
+import unittest
+import warnings
+from xml.etree import cElementTree as ET
+
+import numpy as np
+import pkg_resources
+
+from glymur import Jp2k
+import glymur
+
+try:
+    data_root = os.environ['OPJ_DATA_ROOT']
+except KeyError:
+    data_root = None
+except:
+    raise
+
+
+@unittest.skipIf(data_root is None,
+                 "OPJ_DATA_ROOT environment variable not set")
+class TestICC(unittest.TestCase):
+
+    def setUp(self):
+        pass
+
+    def tearDown(self):
+        pass
+
+    def test_file5(self):
+        filename = os.path.join(data_root, 'input/conformance/file5.jp2')
+        j = Jp2k(filename)
+        profile = j.box[3].box[1].icc_profile
+        self.assertEqual(profile.size, 546)
+        self.assertEqual(profile.preferred_cmm_type, 0)
+        self.assertEqual(profile.version, '2.2.0')
+        self.assertEqual(profile.device_class, 'input device profile')
+        self.assertEqual(profile.colour_space, 'RGB')
+        self.assertEqual(profile.datetime,
+                         datetime.datetime(2001, 8, 30, 13, 32, 37))
+        self.assertEqual(profile.file_signature, 'acsp')
+        self.assertEqual(profile.platform, 'unrecognized')
+        self.assertTrue(profile.flags & 0x01)  # embedded
+        self.assertFalse(profile.flags & 0x02)  # use anywhere
+
+        self.assertEqual(profile.device_manufacturer, 'KODA')
+        self.assertEqual(profile.device_model, 'ROMM')
+
+        self.assertFalse(profile.device_attributes & 0x01)  # reflective
+        self.assertFalse(profile.device_attributes & 0x02)  # glossy
+        self.assertFalse(profile.device_attributes & 0x04)  # positive
+        self.assertFalse(profile.device_attributes & 0x08)  # colour
+        self.assertEqual(profile.rendering_intent & 0x00ff, 0)  # perceptual
+
+        np.testing.assert_almost_equal(profile.illuminant,
+                                       (0.964203, 1.000000, 0.824905),
+                                       decimal=6)
+
+        self.assertEqual(profile.creator, 'JPEG')
+
+    @unittest.skipIf(sys.hexversion < 0x03020000,
+                     "Uses features introduced in 3.2.")
+    def test_invalid_profile_header(self):
+        jfile = os.path.join(data_root,
+                             'input/nonregression/orb-blue10-lin-jp2.jp2')
+        with self.assertWarns(UserWarning) as cw:
+            data = Jp2k(jfile).read()
+
+if __name__ == "__main__":
+    unittest.main()

glymur/test/test_opj_suite.py

@@ -3579,7 +3579,7 @@ class TestSuite(unittest.TestCase):
         self.assertEqual(jp2.box[3].box[1].method, 2)  # enumerated
         self.assertEqual(jp2.box[3].box[1].precedence, 0)
         self.assertEqual(jp2.box[3].box[1].approximation, 1)  # JPX exact
-        self.assertEqual(len(jp2.box[3].box[1].icc_profile), 546)
+        self.assertEqual(jp2.box[3].box[1].icc_profile.size, 546)
         self.assertIsNone(jp2.box[3].box[1].colorspace)
 
         # Jp2 Header
@@ -3674,7 +3674,7 @@ class TestSuite(unittest.TestCase):
         self.assertEqual(jp2.box[3].box[1].method, 2)
         self.assertEqual(jp2.box[3].box[1].precedence, 0)
         self.assertEqual(jp2.box[3].box[1].approximation, 1)  # JPX exact
-        self.assertEqual(len(jp2.box[3].box[1].icc_profile), 13332)
+        self.assertEqual(jp2.box[3].box[1].icc_profile.size, 13332)
         self.assertIsNone(jp2.box[3].box[1].colorspace)
 
         # Jp2 Header
@@ -3723,7 +3723,7 @@ class TestSuite(unittest.TestCase):
         self.assertEqual(jp2.box[2].box[1].method, 2)  # enumerated
         self.assertEqual(jp2.box[2].box[1].precedence, 0)
         self.assertEqual(jp2.box[2].box[1].approximation, 1)  # JPX exact
-        self.assertEqual(len(jp2.box[2].box[1].icc_profile), 414)
+        self.assertEqual(jp2.box[2].box[1].icc_profile.size, 414)
         self.assertIsNone(jp2.box[2].box[1].colorspace)
 
         # XML box
@@ -6394,7 +6394,10 @@ class TestSuite(unittest.TestCase):
     def test_NR_orb_blue10_lin_jp2_dump(self):
         jfile = os.path.join(data_root,
                              'input/nonregression/orb-blue10-lin-jp2.jp2')
-        jp2 = Jp2k(jfile)
+        with warnings.catch_warnings():
+            # This file has an invalid ICC profile
+            warnings.simplefilter("ignore")
+            jp2 = Jp2k(jfile)
 
         ids = [box.id for box in jp2.box]
         self.assertEqual(ids, ['jP  ', 'ftyp', 'jp2h', 'jp2c'])
@@ -6426,7 +6429,7 @@ class TestSuite(unittest.TestCase):
         self.assertEqual(jp2.box[2].box[1].method, 2)  # res icc
         self.assertEqual(jp2.box[2].box[1].precedence, 0)
         self.assertEqual(jp2.box[2].box[1].approximation, 0)  # JP2
-        self.assertEqual(len(jp2.box[2].box[1].icc_profile), 1)
+        self.assertIsNone(jp2.box[2].box[1].icc_profile)
         self.assertIsNone(jp2.box[2].box[1].colorspace)
 
         c = jp2.box[3].main_header
@@ -6490,7 +6493,10 @@ class TestSuite(unittest.TestCase):
     def test_NR_orb_blue10_win_jp2_dump(self):
         jfile = os.path.join(data_root,
                              'input/nonregression/orb-blue10-win-jp2.jp2')
-        jp2 = Jp2k(jfile)
+        with warnings.catch_warnings():
+            # This file has an invalid ICC profile
+            warnings.simplefilter("ignore")
+            jp2 = Jp2k(jfile)
 
         ids = [box.id for box in jp2.box]
         self.assertEqual(ids, ['jP  ', 'ftyp', 'jp2h', 'jp2c'])
@@ -6522,7 +6528,7 @@ class TestSuite(unittest.TestCase):
         self.assertEqual(jp2.box[2].box[1].method, 2)  # restricted icc
         self.assertEqual(jp2.box[2].box[1].precedence, 0)
         self.assertEqual(jp2.box[2].box[1].approximation, 0)  # JP2
-        self.assertEqual(len(jp2.box[2].box[1].icc_profile), 1)
+        self.assertIsNone(jp2.box[2].box[1].icc_profile)
         self.assertIsNone(jp2.box[2].box[1].colorspace)
 
         c = jp2.box[3].main_header
@@ -6624,7 +6630,7 @@ class TestSuite(unittest.TestCase):
         self.assertEqual(jp2.box[3].box[1].method, 3)  # any icc
         self.assertEqual(jp2.box[3].box[1].precedence, 2)
         self.assertEqual(jp2.box[3].box[1].approximation, 1)  # JPX exact
-        self.assertEqual(len(jp2.box[3].box[1].icc_profile), 1328)
+        self.assertEqual(jp2.box[3].box[1].icc_profile.size, 1328)
         self.assertIsNone(jp2.box[3].box[1].colorspace)
 
         # UUID boxes.  All mentioned in the RREQ box.
@@ -6859,7 +6865,10 @@ class TestSuite(unittest.TestCase):
     def test_NR_DEC_orb_blue_lin_jp2_25_decode(self):
         jfile = os.path.join(data_root,
                              'input/nonregression/orb-blue10-lin-jp2.jp2')
-        data = Jp2k(jfile).read()
+        with warnings.catch_warnings():
+            # This file has an invalid ICC profile
+            warnings.simplefilter("ignore")
+            data = Jp2k(jfile).read()
         self.assertTrue(True)
 
     def test_NR_DEC_orb_blue_win_jp2_26_decode(self):

glymur/test/test_printing.py

@@ -790,7 +790,24 @@ class TestPrinting(unittest.TestCase):
                  '    Precedence:  2',
                  '    Approximation:  accurately represents '
                  + 'correct colorspace definition',
-                 '    ICC Profile:  1328 bytes']
+                 '    ICC Profile:  ',
+                 '        Size:  1328',
+                 '        Preferred CMM type:  6170706c',
+                 '        Version:  2.2.0',
+                 '        Device class signature:  display device profile',
+                 '        Color space:  RGB',
+                 '        Connection space:  XYZ',
+                 '        Creation time:  2009-02-25 11:26:11',
+                 '        File signature:  acsp',
+                 '        Platform:  APPL',
+                 '        Flags:  not embedded, can be used independently',
+                 '        Device manufacturer:  appl',
+                 '        Device model:  ',
+                 '        Device attributes:  '
+                 + 'reflective, glossy, positive media polarity, color media',
+                 '        Rendering intent:  perceptual',
+                 '        Illuminant:  [ 0.96420288  1.          0.8249054 ]',
+                 '        Creator signature:  appl']
 
         expected = '\n'.join(lines)
         self.assertEqual(actual, expected)

setup.py

@@ -1,7 +1,7 @@
 from distutils.core import setup
 
 kwargs = {'name': 'Glymur',
-          'version': '0.1.7',
+          'version': '0.1.8',
           'description': 'Tools for accessing JPEG2000 files',
           'long_description': open('README.md').read(),
           'author': 'John Evans',