Merge branch 'issue103' into devel

docs/source/how_do_i.rst

@@ -3,7 +3,7 @@ How do I...?
 ------------
 
 
-Read the lowest resolution thumbnail?
+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
@@ -14,7 +14,7 @@ resolution level. ::
     >>> j = glymur.Jp2k(file)
     >>> thumbnail = j.read(rlevel=-1)
 
-Display metadata?
+display metadata?
 =================
 There are two ways.  From the unix command line, the script *jp2dump* is
 available. ::
@@ -34,8 +34,41 @@ codestream box, only the main header is printed.  It is possible to print
 
     >>> print(j.get_codestream())
 
-Add XML Metadata?
+add XML metadata?
 =================
+You can append any number of XML boxes to a JP2 file (not to a raw codestream).
+Consider the following XML file `data.xml` : ::
+
+    <?xml version="1.0"?>
+    <info>
+        <locality>
+            <city>Boston</city>
+            <snowfall>24.9 inches</snowfall>
+        </locality>
+        <locality>
+            <city>Portland</city>
+            <snowfall>31.9 inches</snowfall>
+        </locality>
+        <locality>
+            <city>New York City</city>
+            <snowfall>11.4 inches</snowfall>
+        </locality>
+    </info>
+
+The **append** method can add an XML box (only XML boxes are currently
+allowed)::
+
+    >>> import shutil
+    >>> import glymur
+    >>> shutil.copyfile(glymur.data.nemo(), 'myfile.jp2')
+    >>> from xml.etree import cElementTree as ET
+    >>> jp2 = glymur.Jp2k('myfile.jp2')
+    >>> xmlbox = glymur.jp2box.XMLBox(filename='data.xml')
+    >>> jp2.append(xmlbox)
+    >>> print(jp2)
+
+add metadata in a more general fashion?
+=======================================
 An existing raw codestream (or JP2 file) can be wrapped (re-wrapped) in a 
 user-defined set of JP2 boxes.  To get just a minimal JP2 jacket on the 
 codestream provided by `goodstuff.j2k` (a file consisting of a raw codestream),
@@ -87,7 +120,7 @@ though.  Take the following example content in an XML file `favorites.xml` : ::
 and add it after the JP2 header box, but before the codestream box ::
 
     >>> boxes = jp2.box  # The box attribute is the list of JP2 boxes
-    >>> xmlbox = glymur.jp2box.XMLBox(file='favorites.xml')
+    >>> xmlbox = glymur.jp2box.XMLBox(filename='favorites.xml')
     >>> boxes.insert(3, xmlbox)
     >>> jp2_xml = jp2.wrap("newfile_with_xml.jp2", boxes=boxes)
     >>> print(jp2_xml)
@@ -119,7 +152,12 @@ and add it after the JP2 header box, but before the codestream box ::
         . (truncated)
         .
 
-Create an image with an alpha layer?
+As to the question of which method you should use, **append** or **wrap**,
+to add metadata, you should keep in mind that **wrap** produces a new JP2 file,
+while **append** modifies an existing file and is currently limited to XML
+boxes.
+
+create an image with an alpha layer?
 ====================================
 
 OpenJPEG can create JP2 files with more than 3 components (requires
@@ -181,7 +219,7 @@ Here's how the Preview application on the mac shows the RGBA image.
 .. image:: goodstuff_alpha.png
 
     
-Work with XMP UUIDs?
+work with XMP UUIDs?
 ====================
 The example JP2 file shipped with glymur has an XMP UUID. ::
 

glymur/codestream.py

@@ -1308,7 +1308,7 @@ class QCCsegment(Segment):
         self.offset = offset
 
         self.mantissa, self.exponent = parse_quantization(self.spqcc,
-                                                            self.sqcc)
+                                                          self.sqcc)
         self.guard_bits = (self.sqcc & 0xe0) >> 5
 
     def __str__(self):

glymur/jp2k.py

@@ -432,6 +432,42 @@ class Jp2k(Jp2kBox):
         # Refresh the metadata.
         self.parse()
 
+    def append(self, box):
+        """Append a JP2 box to the file in-place.
+
+        Parameters
+        ----------
+        box : Jp2Box
+            Instance of a JP2 box.  Currently only XML boxes are allowed.
+        """
+        if self._codec_format == opj2.CODEC_J2K:
+            msg = "Only JP2 files can currently have boxes appended to them."
+            raise IOError(msg)
+
+        if box.box_id != 'xml ':
+            raise IOError("Only XML boxes can currently be appended.")
+
+        # Check the last box.  If the length field is zero, then rewrite
+        # the length field to reflect the true length of the box.
+        with open(self.filename, 'rb') as ifile:
+            offset = self.box[-1].offset
+            ifile.seek(offset)
+            read_buffer = ifile.read(4)
+            box_length, = struct.unpack('>I', read_buffer)
+            if box_length == 0:
+                # Reopen the file in write mode and rewrite the length field.
+                true_box_length = os.path.getsize(ifile.name) - offset
+                with open(self.filename, 'r+b') as ofile:
+                    ofile.seek(offset)
+                    write_buffer = struct.pack('>I', true_box_length)
+                    ofile.write(write_buffer)
+
+        # Can now safely append the box.
+        with open(self.filename, 'ab') as ofile:
+            box.write(ofile)
+
+        self.parse()
+
     def wrap(self, filename, boxes=None):
         """Write the codestream back out to file, wrapped in new JP2 jacket.
 
@@ -1133,6 +1169,7 @@ def _unpack_colorspace(colorspace, img_array, cparams):
 
     return colorspace
 
+
 def _populate_comptparms(img_array, cparams):
     """Instantiate and populate comptparms structure.
 
@@ -1171,6 +1208,7 @@ def _populate_comptparms(img_array, cparams):
 
     return comptparms
 
+
 def _populate_image_struct(cparams, image, imgdata):
     """Populates image struct needed for compression.
 
@@ -1203,6 +1241,7 @@ def _populate_image_struct(cparams, image, imgdata):
 
     return image
 
+
 def _validate_compression_params(img_array, cparams):
     """Check that the compression parameters are valid.
 
@@ -1313,4 +1352,3 @@ class LibraryNotFoundError(IOError):
     """
     def __init__(self, msg):
         IOError.__init__(self, msg)
-

glymur/test/fixtures.py

@@ -30,7 +30,7 @@ NO_READ_BACKEND_MSG += "order to run the tests in this suite."
 try:
     from matplotlib.pyplot import imread
 
-    # The whole point of trying to import PIL is to determine if it's there 
+    # The whole point of trying to import PIL is to determine if it's there
     # or not.  We won't use it directly.
     # pylint:  disable=F0401,W0611
     import PIL

glymur/test/test_callbacks.py

@@ -91,7 +91,7 @@ class TestCallbacks15(unittest.TestCase):
 
     def test_info_callbacks_on_read(self):
         """Verify stdout when reading.
-        
+
         Verify that we get the expected stdio output when our internal info
         callback handler is enabled.
         """

glymur/test/test_codestream.py

@@ -5,7 +5,7 @@ Test suite for codestream parsing.
 # unittest doesn't work well with R0904.
 # pylint: disable=R0904
 
-# tempfile.TemporaryDirectory, unittest.assertWarns introduced in 3.2 
+# tempfile.TemporaryDirectory, unittest.assertWarns introduced in 3.2
 # pylint: disable=E1101
 
 # unittest2 is python2.6 only (pylint/python-2.7)

glymur/test/test_config.py

@@ -4,7 +4,7 @@ OPENJP2 may be present in some form or other.
 # unittest doesn't work well with R0904.
 # pylint: disable=R0904
 
-# tempfile.TemporaryDirectory, unittest.assertWarns introduced in 3.2 
+# tempfile.TemporaryDirectory, unittest.assertWarns introduced in 3.2
 # pylint: disable=E1101
 
 # unittest.mock only in Python 3.3 (python2.7/pylint import issue)

glymur/test/test_jp2box.py

@@ -18,8 +18,11 @@ Test suite specifically targeting JP2 box layout.
 
 import doctest
 import os
+import shutil
+import struct
 import sys
 import tempfile
+import uuid
 import xml.etree.cElementTree as ET
 
 if sys.hexversion < 0x02070000:
@@ -502,6 +505,100 @@ class TestColourSpecificationBox(unittest.TestCase):
                                                  approximation=approx)
 
 
+@unittest.skipIf(glymur.lib.openjp2.OPENJP2 is None,
+                 "Missing openjp2 library.")
+class TestAppend(unittest.TestCase):
+    """Tests for append method."""
+
+    def setUp(self):
+        self.j2kfile = glymur.data.goodstuff()
+        self.jp2file = glymur.data.nemo()
+
+    def tearDown(self):
+        pass
+
+    def test_append_xml(self):
+        """Should be able to append an XML box."""
+        with tempfile.NamedTemporaryFile(suffix=".jp2") as tfile:
+            shutil.copyfile(self.jp2file, tfile.name)
+
+            jp2 = Jp2k(tfile.name)
+            the_xml = ET.fromstring('<?xml version="1.0"?><data>0</data>')
+            xmlbox = glymur.jp2box.XMLBox(xml=the_xml)
+            jp2.append(xmlbox)
+
+            # The sequence of box IDs should be the same as before, but with an
+            # xml box at the end.
+            box_ids = [box.box_id for box in jp2.box]
+            expected = ['jP  ', 'ftyp', 'jp2h', 'uuid', 'uuid', 'jp2c', 'xml ']
+            self.assertEqual(box_ids, expected)
+            self.assertEqual(ET.tostring(jp2.box[-1].xml.getroot()),
+                             b'<data>0</data>')
+
+    def test_only_jp2_allowed_to_append(self):
+        """Only JP2 files are allowed to be appended."""
+        with tempfile.NamedTemporaryFile(suffix=".j2k") as tfile:
+            shutil.copyfile(self.j2kfile, tfile.name)
+
+            jp2 = Jp2k(tfile.name)
+
+            # Make a UUID box.
+            uuid_instance = uuid.UUID('00000000-0000-0000-0000-000000000000')
+            data = b'0123456789'
+            uuidbox = glymur.jp2box.UUIDBox(uuid_instance, data)
+            with self.assertRaises(IOError):
+                jp2.append(uuidbox)
+
+    def test_length_field_is_zero(self):
+        """L=0 (length field in box header) is handled.
+
+        L=0 implies that the containing box is the last box.  If this is not
+        handled properly, the appended box is never seen.
+        """
+        baseline_jp2 = Jp2k(self.jp2file)
+        with tempfile.NamedTemporaryFile(suffix='.jp2') as tfile:
+            with open(self.jp2file, 'rb') as ifile:
+                # Everything up until the jp2c box.
+                offset = baseline_jp2.box[-1].offset
+                tfile.write(ifile.read(offset))
+
+                # Write the L, T fields of the jp2c box such that L == 0
+                write_buffer = struct.pack('>I4s', int(0), b'jp2c')
+                tfile.write(write_buffer)
+
+                # Write out the rest of the codestream.
+                ifile.seek(offset+8)
+                tfile.write(ifile.read())
+                tfile.flush()
+
+            jp2 = Jp2k(tfile.name)
+            the_xml = ET.fromstring('<?xml version="1.0"?><data>0</data>')
+            xmlbox = glymur.jp2box.XMLBox(xml=the_xml)
+            jp2.append(xmlbox)
+
+            # The sequence of box IDs should be the same as before, but with an
+            # xml box at the end.
+            box_ids = [box.box_id for box in jp2.box]
+            expected = ['jP  ', 'ftyp', 'jp2h', 'uuid', 'uuid', 'jp2c', 'xml ']
+            self.assertEqual(box_ids, expected)
+            self.assertEqual(ET.tostring(jp2.box[-1].xml.getroot()),
+                             b'<data>0</data>')
+
+    def test_only_xml_allowed_to_append(self):
+        """Only XML boxes are allowed to be appended."""
+        with tempfile.NamedTemporaryFile(suffix=".jp2") as tfile:
+            shutil.copyfile(self.jp2file, tfile.name)
+
+            jp2 = Jp2k(tfile.name)
+
+            # Make a UUID box.
+            uuid_instance = uuid.UUID('00000000-0000-0000-0000-000000000000')
+            data = b'0123456789'
+            uuidbox = glymur.jp2box.UUIDBox(uuid_instance, data)
+            with self.assertRaises(IOError):
+                jp2.append(uuidbox)
+
+
 @unittest.skipIf(glymur.lib.openjp2.OPENJP2 is None,
                  "Missing openjp2 library.")
 class TestWrap(unittest.TestCase):
@@ -703,7 +800,7 @@ class TestJp2Boxes(unittest.TestCase):
     def test_default_ihdr(self):
         """Should be able to instantiate an image header box."""
         ihdr = glymur.jp2box.ImageHeaderBox(height=512, width=256,
-                                         num_components=3)
+                                            num_components=3)
         self.assertEqual(ihdr.height,  512)
         self.assertEqual(ihdr.width,  256)
         self.assertEqual(ihdr.num_components,  3)
@@ -715,7 +812,7 @@ class TestJp2Boxes(unittest.TestCase):
         """Should be able to set jp2h boxes."""
         box = JP2HeaderBox()
         box.box = [ImageHeaderBox(height=512, width=256),
-                  ColourSpecificationBox(colorspace=glymur.core.GREYSCALE)]
+                   ColourSpecificationBox(colorspace=glymur.core.GREYSCALE)]
         self.assertTrue(True)
 
     def test_default_ccodestreambox(self):

glymur/test/test_opj_suite.py

@@ -17,7 +17,7 @@ suite.
 # unittest fools pylint with "too many public methods"
 # pylint: disable=R0904
 
-# Some tests use numpy test infrastructure, which means the tests never 
+# Some tests use numpy test infrastructure, which means the tests never
 # reference "self", so pylint claims it should be a function.  No, no, no.
 # pylint: disable=R0201
 

glymur/test/test_opj_suite_write.py

@@ -441,7 +441,8 @@ class TestSuiteWrite(unittest.TestCase):
             self.assertEqual(len(codestream.segment[2].spcod), 9)
 
             # 18 SOP segments.
-            nsops = [x.nsop for x in codestream.segment if x.marker_id == 'SOP']
+            nsops = [x.nsop for x in codestream.segment
+                     if x.marker_id == 'SOP']
             self.assertEqual(nsops, list(range(18)))
 
     def test_NR_ENC_Bretagne2_ppm_7_encode(self):