Glymur 0.13.3__tar.gz → 0.13.5__tar.gz

{glymur-0.13.3 → glymur-0.13.5}/CHANGES.txt

@@ -1,3 +1,12 @@
+July 26, 2024 - v0.13.5
+    Add support for parsing the CAP segment.
+    End official support for OpenJPEG 2.3.x.
+    Fix issue preventing API docs from building.
+
+July 4, 2024 - v0.13.4
+    Don't reset openjpeg codec in Jp2k if already set in Jp2kr.
+    Update CI configuration to specify openjpeg versions.
+    
 June 30, 2024 - v0.13.3
     Refactor parsing errors and warnings.
     Update CI configuration for numpy 2.0.

{glymur-0.13.3 → glymur-0.13.5}/Glymur.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: Glymur
-Version: 0.13.3
+Version: 0.13.5
 Home-page: https://github.com/quintusdias/glymur
 Author: 'John Evans'
 Author-email: "John Evans" <jevans667cc@proton.me>

{glymur-0.13.3 → glymur-0.13.5}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: Glymur
-Version: 0.13.3
+Version: 0.13.5
 Home-page: https://github.com/quintusdias/glymur
 Author: 'John Evans'
 Author-email: "John Evans" <jevans667cc@proton.me>

{glymur-0.13.3 → glymur-0.13.5}/glymur/codestream.py

@@ -189,7 +189,7 @@ class Codestream(object):
             0xff3f: self._parse_reserved_marker,
 
             # 0xff4f:  SOC (already encountered by the time we get here)
-            0xff50: self._parse_reserved_segment,
+            0xff50: self._parse_cap_segment,
             0xff51: self._parse_siz_segment,
             0xff52: self._parse_cod_segment,
             0xff53: self._parse_coc_segment,
@@ -713,6 +713,37 @@ class Codestream(object):
 
         return RGNsegment(crgn, srgn, sprgn, length, offset)
 
+    @classmethod
+    def _parse_cap_segment(cls, fptr):
+        """Parse the SIZ segment.
+
+        Parameters
+        ----------
+        fptr : file
+            Open file object.
+
+        Returns
+        -------
+        SIZSegment
+            The current SIZ segment.
+        """
+        offset = fptr.tell() - 2
+
+        read_buffer = fptr.read(2)
+        length, = struct.unpack('>H', read_buffer)
+        read_buffer = fptr.read(length - 2)
+
+        pcap, = struct.unpack('>I', read_buffer[:4])
+
+        n = (length - 6) // 2
+        ccap = struct.unpack('>' + 'H' * n, read_buffer[4:])
+
+        segment = CAPsegment(
+            pcap=pcap, ccap=ccap, length=length, offset=offset,
+        )
+
+        return segment
+
     @classmethod
     def _parse_siz_segment(cls, fptr):
         """Parse the SIZ segment.
@@ -736,7 +767,9 @@ class Codestream(object):
         data = struct.unpack_from('>HIIIIIIIIH', read_buffer)
 
         rsiz = data[0]
-        if rsiz not in _KNOWN_PROFILES:
+
+        # Bit 14 (16384) signifies HTJ2K (JPH)
+        if rsiz not in _KNOWN_PROFILES and not np.bitwise_and(rsiz, 16384):
             msg = f"Invalid profile: (Rsiz={rsiz})."
             warnings.warn(msg, UserWarning)
 
@@ -932,6 +965,49 @@ class Segment(object):
         return msg
 
 
+class CAPsegment(Segment):
+    """CAP (Extended Capabilities) segment information.
+
+    Attributes
+    ----------
+    marker_id : str
+        Identifier for the segment.
+    offset : int
+        Offset of marker segment in bytes from beginning of file.
+    length : int
+        Length of marker segment in bytes.  This number does not include the
+        two bytes constituting the marker.
+    pcap : 32-bit unsigned int
+        bitmask where the kth 1 represents use of capabilities in Part k of
+        ISO/IEC 15444-k.
+    ccap : 16-bit unsigned int
+        The precise meaning depends on the related parts of ISO/IEC 15444-k.
+    """
+    def __init__(self, pcap, ccap, length, offset):
+        super().__init__(marker_id='CAP')
+        self.pcap = pcap
+        self.ccap = ccap
+        self.length = length
+        self.offset = offset
+
+    def __str__(self):
+        msg = Segment.__str__(self)
+
+        msg += '\n'
+
+        # have to cast to uint64 because, you know, stupid windows
+        parts = [
+            k for k in range(32)
+            if np.bitwise_and(np.uint64(self.pcap), np.uint64(1 << (32 - k)))
+        ]
+
+        for b in parts:
+            msg += f'    Pcap:  Part {b} (ISO/IEC 15444-{b})\n'
+        msg += f'    Ccap:  {self.ccap}'
+
+        return msg
+
+
 class COCsegment(Segment):
     """COC (Coding style Component) segment information.
 
@@ -1666,7 +1742,12 @@ class SIZsegment(Segment):
         try:
             profile = _CAPABILITIES_DISPLAY[self.rsiz]
         except KeyError:
-            profile = f'{self.rsiz} (invalid)'
+            if np.bitwise_and(self.rsiz, 16384):
+                # HTJ2K profile that is uninterpreted
+                profile = f'{self.rsiz}'
+            else:
+                # profile unknown
+                profile = f'{self.rsiz} (invalid)'
         msg = msg.format(
             profile=profile,
             height=self.ysiz, width=self.xsiz,

{glymur-0.13.3 → glymur-0.13.5}/glymur/jp2box.py

@@ -1259,7 +1259,7 @@ class FileTypeBox(Jp2kBox):
     """
     box_id = 'ftyp'
     longname = 'File Type'
-    _valid_cls = ['jp2 ', 'jpx ', 'jpxb']
+    _valid_cls = ['jp2 ', 'jph ', 'jpx ', 'jpxb']
 
     def __init__(
         self, brand='jp2 ', minor_version=0, compatibility_list=None,
@@ -1304,16 +1304,19 @@ class FileTypeBox(Jp2kBox):
         return text
 
     def _validate(self, writing=False):
-        """Validate the box before writing to file."""
-        if self.brand not in ['jp2 ', 'jpx ']:
+        """
+        Validate the box before writing to file.
+        """
+        if self.brand not in ['jp2 ', 'jpx ', 'jph ']:
             msg = (
                 f"The file type brand was '{self.brand}'.  "
-                f"It should be either 'jp2 ' or 'jpx '."
+                f"It should be either 'jp2 ', 'jpx ', or 'jph '."
             )
             if writing:
                 raise InvalidJp2kError(msg)
             else:
                 warnings.warn(msg, UserWarning)
+
         for item in self.compatibility_list:
             if item not in self._valid_cls:
                 msg = (

{glymur-0.13.3 → glymur-0.13.5}/glymur/jp2k.py

@@ -34,13 +34,12 @@ from .lib import openjp2 as opj2
 
 
 class Jp2k(Jp2kr):
-    """Write JPEG 2000 files.
+    """Write JPEG 2000 files (and optionally read them as well).
 
     Parameters
     ----------
     filename : str or path
-        The path to JPEG 2000 file.  If you are only reading JPEG 2000 files,
-        this is the only argument you need to supply.
+        The path to JPEG 2000 file.
     data : np.ndarray, optional
         Image data to be written to file.
     shape : Tuple[int, int, ...], optional
@@ -105,35 +104,6 @@ class Jp2k(Jp2kr):
     verbose : bool, optional
         Print informational messages produced by the OpenJPEG library.
 
-    Examples
-    --------
-    >>> jfile = glymur.data.nemo()
-    >>> jp2 = glymur.Jp2k(jfile)
-    >>> jp2.shape
-    (1456, 2592, 3)
-    >>> image = jp2[:]
-    >>> image.shape
-    (1456, 2592, 3)
-
-    Read a lower resolution thumbnail.
-
-    >>> thumbnail = jp2[::2, ::2]
-    >>> thumbnail.shape
-    (728, 1296, 3)
-
-    Make use of OpenJPEG's thread support
-
-    >>> import time
-    >>> if glymur.version.openjpeg_version >= '2.2.0':
-    ...     jp2file = glymur.data.nemo()
-    ...     jp2 = glymur.Jp2k(jp2file)
-    ...     t0 = time.time(); data = jp2[:]; t1 = time.time()
-    ...     t1 - t0 #doctest: +SKIP
-    0.9024193286895752
-    ...     glymur.set_options('lib.num_threads', 4)
-    ...     t0 = time.time(); data = jp2[:]; t1 = time.time()
-    ...     t1 - t0 #doctest: +SKIP
-    0.4060473537445068
     """
 
     def __init__(
@@ -206,13 +176,13 @@ class Jp2k(Jp2kr):
             # Must be determined when writing.
             self._shape = None
 
-        # If there already was a shape attribute, then don't mess with it,
-        # it was set by the reader superclass.
-
-        if self.filename[-4:].endswith(('.jp2', '.JP2', '.jpx', 'JPX')):
-            self._codec_format = opj2.CODEC_JP2
-        else:
-            self._codec_format = opj2.CODEC_J2K
+        if not hasattr(self, '_codec_format'):
+            # Only set codec format if the superclass has not done so, i.e.
+            # we are writing instead of reading.
+            if self.filename[-4:].endswith(('.jp2', '.JP2', '.jpx', 'JPX')):
+                self._codec_format = opj2.CODEC_JP2
+            else:
+                self._codec_format = opj2.CODEC_J2K
 
         self._validate_kwargs()
 
@@ -800,12 +770,6 @@ class Jp2k(Jp2kr):
         -------
         Jp2k
             Newly wrapped Jp2k object.
-
-        Examples
-        --------
-        >>> jfile = glymur.data.goodstuff()
-        >>> j2k = glymur.Jp2k(jfile)
-        >>> jp2 = j2k.wrap('jp2_from_j2k.jp2')
         """
         if boxes is None:
             boxes = self._get_default_jp2_boxes()

{glymur-0.13.3 → glymur-0.13.5}/glymur/jp2kr.py

@@ -55,6 +55,19 @@ class Jp2kr(Jp2kBox):
     >>> thumbnail = jp2[::2, ::2]
     >>> thumbnail.shape
     (728, 1296, 3)
+
+    Make use of OpenJPEG's thread support
+
+    >>> import time
+    >>> jp2file = glymur.data.nemo()
+    >>> jp2 = glymur.Jp2k(jp2file)
+    >>> t0 = time.time(); data = jp2[:]; t1 = time.time()
+    >>> t1 - t0 #doctest: +SKIP
+    0.9024193286895752
+    >>> glymur.set_option('lib.num_threads', 4)
+    >>> t0 = time.time(); data = jp2[:]; t1 = time.time()
+    >>> t1 - t0 #doctest: +SKIP
+    0.4060473537445068
     """
 
     def __init__(
@@ -233,7 +246,7 @@ class Jp2kr(Jp2kBox):
 
     @property
     def codestream(self):
-        """Metadata for JP2 or J2K codestream (header only)."""
+        """Metadata for JP2 or J2K codestream header."""
         if self._codestream is None:
             self._codestream = self.get_codestream(header_only=True)
         return self._codestream
@@ -523,6 +536,9 @@ class Jp2kr(Jp2kBox):
     def read(self, **kwargs):
         """Read a JPEG 2000 image.
 
+        .. deprecated:: 0.13.5
+           Use numpy-style slicing instead.
+
         Returns
         -------
         img_array : ndarray
@@ -724,7 +740,7 @@ class Jp2kr(Jp2kBox):
                    verbose=False, ignore_pclr_cmap_cdef=False):
         """Read a JPEG 2000 image.
 
-        The only time you should use this method is when the image has
+        The only time you should ever use this method is when the image has
         different subsampling factors across components.  Otherwise you should
         use the read method.
 
@@ -870,6 +886,10 @@ class Jp2kr(Jp2kBox):
     def get_codestream(self, header_only=True):
         """Retrieve codestream.
 
+	    This differs from the codestream property in that segment
+    	metadata that lies past the end of the codestream header
+    	can be retrieved.
+
         Parameters
         ----------
         header_only : bool, optional

{glymur-0.13.3 → glymur-0.13.5}/glymur/version.py

@@ -20,7 +20,7 @@ from .lib import tiff
 
 # Do not change the format of this next line!  Doing so risks breaking
 # setup.py
-version = "0.13.3"
+version = "0.13.5"
 
 version_tuple = parse(version).release
 

{glymur-0.13.3 → glymur-0.13.5}/setup.cfg

@@ -1,6 +1,6 @@
 [metadata]
 name = Glymur
-version = 0.13.3
+version = 0.13.5
 author = 'John Evans'
 author_email = "John Evans" <jevans667cc@proton.me>
 license = 'MIT'

{glymur-0.13.3 → glymur-0.13.5}/tests/test_codestream.py

@@ -30,6 +30,19 @@ class TestSuite(fixtures.TestCommon):
         self.p1_06 = ir.files('tests.data').joinpath('p1_06.j2k')
         self.issue142 = ir.files('tests.data').joinpath('issue142.j2k')
         self.edf_c2_1178956 = ir.files('tests.data').joinpath('edf_c2_1178956.jp2')  # noqa : E501
+        self.htj2k = ir.files('tests.data').joinpath('oj-ht-byte.jph')
+
+    def test_cap_marker_segment(self):
+        """
+        SCENARIO:  the file has a CAP marker segment for the 3rd segment
+
+        EXPECTED RESULT:  the segment metadata is verified
+        """
+        j = Jp2k(self.htj2k)
+        cap = j.codestream.segment[2]
+
+        self.assertEqual(cap.pcap, 131072)
+        self.assertEqual(cap.ccap, (3,))
 
     def test_unrecognized_marker(self):
         """

{glymur-0.13.3 → glymur-0.13.5}/tests/test_jp2box.py

@@ -20,7 +20,7 @@ import numpy as np
 
 # Local imports ...
 import glymur
-from glymur import Jp2k
+from glymur import Jp2k, Jp2kr
 from glymur.jp2box import (
     ColourSpecificationBox, ContiguousCodestreamBox, FileTypeBox,
     ImageHeaderBox, JP2HeaderBox, JPEG2000SignatureBox, BitsPerComponentBox,
@@ -356,6 +356,16 @@ class TestChannelDefinition(fixtures.TestCommon):
 class TestFileTypeBox(fixtures.TestCommon):
     """Test suite for ftyp box issues."""
 
+    def test_jph(self):
+        """
+        SCENARIO:  JPH box
+
+        EXPECTED RESULT:  The brand is verified.
+        """
+        path = ir.files('tests.data').joinpath('oj-ht-byte.jph')
+        j = Jp2kr(path)
+        self.assertEqual(j.box[1].brand, 'jph ')
+
     def test_bad_brand_on_parse(self):
         """
         SCENARIO:  The JP2 file file type box does not contain a valid brand.

{glymur-0.13.3 → glymur-0.13.5}/tests/test_jp2k.py

@@ -29,8 +29,8 @@ from . import fixtures
 
 
 @unittest.skipIf(OPENJPEG_NOT_AVAILABLE, OPENJPEG_NOT_AVAILABLE_MSG)
-@unittest.skipIf(glymur.version.openjpeg_version < '2.3.0',
-                 "Requires as least v2.3.0")
+@unittest.skipIf(glymur.version.openjpeg_version < '2.4.0',
+                 "Requires as least v2.4.0")
 class TestJp2k(fixtures.TestCommon):
     """These tests should be run by just about all configuration."""
 
@@ -38,6 +38,20 @@ class TestJp2k(fixtures.TestCommon):
         super().setUp()
         glymur.reset_option('all')
 
+    @unittest.skipIf(
+        glymur.version.openjpeg_version < '2.5.0', "Requires as least v2.5.0"
+    )
+    def test_read_htj2k(self):
+        """
+        Scenario:  read an HTJ2K (JPH) file using Jp2k
+
+        Expected response:  The size of the image read is verified.
+        """
+        path = ir.files('tests.data').joinpath('oj-ht-byte.jph')
+        j = Jp2k(path)
+        d = j[:]
+        self.assertEqual(d.shape, (20, 20))
+
     def test_repr(self):
         """
         Scenario:  run repr on Jp2k object

{glymur-0.13.3 → glymur-0.13.5}/tests/test_jp2kr.py

@@ -29,8 +29,8 @@ from . import fixtures
 
 
 @unittest.skipIf(OPENJPEG_NOT_AVAILABLE, OPENJPEG_NOT_AVAILABLE_MSG)
-@unittest.skipIf(glymur.version.openjpeg_version < '2.3.0',
-                 "Requires as least v2.3.0")
+@unittest.skipIf(glymur.version.openjpeg_version < '2.4.0',
+                 "Requires as least v2.4.0")
 class TestJp2kr(fixtures.TestCommon):
     """These tests should be run by just about all configuration."""
 

{glymur-0.13.3 → glymur-0.13.5}/tests/test_printing.py

@@ -42,6 +42,22 @@ class TestPrinting(fixtures.TestCommon):
         super().tearDown()
         glymur.reset_option('all')
 
+    def test_cap_segment(self):
+        """
+        Scenario:  Print a CAP segment
+
+        Expected Result:  segment is verified
+        """
+        htj2k_file = ir.files('tests.data').joinpath('oj-ht-byte.jph')
+        j = glymur.Jp2kr(htj2k_file)
+        actual = str(j.codestream.segment[2])
+        expected = (
+            'CAP marker segment @ (467, 8)\n'
+            '    Pcap:  Part 15 (ISO/IEC 15444-15)\n'
+            '    Ccap:  (3,)'
+        )
+        self.assertEqual(actual, expected)
+
     def test_empty_file(self):
         """
         SCENARIO:  Print the file after with object is constructed, but
@@ -1607,6 +1623,27 @@ class TestPrinting(fixtures.TestCommon):
         )
         self.assertEqual(actual, expected)
 
+    def test_jph_rsiz(self):
+        """
+        Scenario:  parse a JPH file, print the SIZ segment
+
+        Expected result:  no warnings, the output is verified
+        """
+        path = ir.files('tests.data').joinpath('oj-ht-byte.jph')
+
+        with warnings.catch_warnings():
+            warnings.simplefilter('error')
+            j = Jp2k(path)
+            actual = str(j.codestream.segment[1])
+
+        expected = (
+            ir.files('tests.data')
+              .joinpath('jph_siz.txt')
+              .read_text()
+              .rstrip()
+        )
+        self.assertEqual(actual, expected)
+
 
 class TestJp2dump(fixtures.TestCommon):
     """Tests for verifying how jp2dump console script works."""

{glymur-0.13.3 → glymur-0.13.5}/tests/test_threading.py

@@ -22,8 +22,8 @@ from . import fixtures
 
 @unittest.skipIf(os.cpu_count() < 2, "makes no sense if 2 cores not there")
 @unittest.skipIf(OPENJPEG_NOT_AVAILABLE, OPENJPEG_NOT_AVAILABLE_MSG)
-@unittest.skipIf(glymur.version.openjpeg_version < '2.3.0',
-                 "Requires as least v2.3.0")
+@unittest.skipIf(glymur.version.openjpeg_version < '2.4.0',
+                 "Requires as least v2.4.0")
 class TestSuite(fixtures.TestCommon):
     """Test behavior when multiple threads are possible."""
 
@@ -79,7 +79,7 @@ class TestSuite(fixtures.TestCommon):
                 glymur.set_option('lib.num_threads', 2)
 
     @unittest.skipIf(
-        glymur.version.openjpeg_version < '2.4.0', "Requires as least v2.3.0"
+        glymur.version.openjpeg_version < '2.4.0', "Requires as least v2.4.0"
     )
     def test_threads_write_support__ge_2p4(self):
         """