Glymur 0.13.5__tar.gz → 0.13.7__tar.gz

{glymur-0.13.5 → glymur-0.13.7}/CHANGES.txt

@@ -1,3 +1,14 @@
+Jan 15, 2025 - v0.13.7
+    Qualify on python 3.13
+    Fix test warnings due to scikit-image deprecation.
+    Update CI test matrix, tighten 3rd party library requirements.
+    Add ability to construct XML box from file-like object.
+    Add circle-ci CI.
+    Fix test suite for numpy 2.x printing (thanks to Arne Keller).
+
+Aug 19, 2024 - v0.13.6
+    Fix tiff2jp2 when tile coverage not square.
+
 July 26, 2024 - v0.13.5
     Add support for parsing the CAP segment.
     End official support for OpenJPEG 2.3.x.

{glymur-0.13.5 → glymur-0.13.7}/Glymur.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
-Metadata-Version: 2.1
+Metadata-Version: 2.2
 Name: Glymur
-Version: 0.13.5
+Version: 0.13.7
 Home-page: https://github.com/quintusdias/glymur
 Author: 'John Evans'
 Author-email: "John Evans" <jevans667cc@proton.me>
@@ -9,12 +9,13 @@ Classifier: Programming Language :: Python
 Classifier: Programming Language :: Python :: 3.10
 Classifier: Programming Language :: Python :: 3.11
 Classifier: Programming Language :: Python :: 3.12
+Classifier: Programming Language :: Python :: 3.13
 Classifier: Programming Language :: Python :: Implementation :: CPython
 Classifier: License :: OSI Approved :: MIT License
 Classifier: Intended Audience :: Science/Research
 Classifier: Operating System :: OS Independent
 Classifier: Topic :: Scientific/Engineering
-Requires-Python: >=3.8
+Requires-Python: >=3.9
 Description-Content-Type: text/markdown
 License-File: LICENSE.txt
 Requires-Dist: numpy

{glymur-0.13.5 → glymur-0.13.7}/PKG-INFO

@@ -1,6 +1,6 @@
-Metadata-Version: 2.1
+Metadata-Version: 2.2
 Name: Glymur
-Version: 0.13.5
+Version: 0.13.7
 Home-page: https://github.com/quintusdias/glymur
 Author: 'John Evans'
 Author-email: "John Evans" <jevans667cc@proton.me>
@@ -9,12 +9,13 @@ Classifier: Programming Language :: Python
 Classifier: Programming Language :: Python :: 3.10
 Classifier: Programming Language :: Python :: 3.11
 Classifier: Programming Language :: Python :: 3.12
+Classifier: Programming Language :: Python :: 3.13
 Classifier: Programming Language :: Python :: Implementation :: CPython
 Classifier: License :: OSI Approved :: MIT License
 Classifier: Intended Audience :: Science/Research
 Classifier: Operating System :: OS Independent
 Classifier: Topic :: Scientific/Engineering
-Requires-Python: >=3.8
+Requires-Python: >=3.9
 Description-Content-Type: text/markdown
 License-File: LICENSE.txt
 Requires-Dist: numpy

{glymur-0.13.5 → glymur-0.13.7}/glymur/jp2box.py

@@ -2969,9 +2969,9 @@ class XMLBox(Jp2kBox):
         ----------
         xml : ElementTree
             An ElementTree object already existing in python.
-        filename : str or path
-            File from which to read XML.  If filename is not None, then the xml
-            keyword argument must be None.
+        filename : file, str, or pathlib.Path
+            File to read.  If filename is not None, then the xml keyword
+            argument must be None.
         """
         super().__init__()
         if filename is not None and xml is not None:
@@ -2981,7 +2981,7 @@ class XMLBox(Jp2kBox):
             )
             raise RuntimeError(msg)
         if filename is not None:
-            self.xml = ET.parse(str(filename))
+            self.xml = ET.parse(filename)
         else:
             self.xml = xml
         self.length = length

{glymur-0.13.5 → glymur-0.13.7}/glymur/jp2kr.py

@@ -886,9 +886,9 @@ 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.
+        This differs from the codestream property in that segment
+        metadata that lies past the end of the codestream header
+        can be retrieved.
 
         Parameters
         ----------

{glymur-0.13.5 → glymur-0.13.7}/glymur/tiff.py

@@ -862,7 +862,7 @@ class Tiff2Jp2k(object):
         partial_jp2_tile_rows = (self.imageheight / jth) != (self.imageheight // jth)  # noqa : E501
         partial_jp2_tile_cols = (self.imagewidth / jtw) != (self.imagewidth // jtw)  # noqa : E501
 
-        num_jp2k_tile_rows = int(np.ceil(self.imagewidth / jtw))
+        num_jp2k_tile_rows = int(np.ceil(self.imageheight / jth))
         num_jp2k_tile_cols = int(np.ceil(self.imagewidth / jtw))
 
         jp2k_tile_row = int(np.ceil(jp2k_tile_num // num_jp2k_tile_cols))

{glymur-0.13.5 → glymur-0.13.7}/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 = "0.13.5"
+version = "0.13.7"
 
 version_tuple = parse(version).release
 

{glymur-0.13.5 → glymur-0.13.7}/setup.cfg

@@ -1,6 +1,6 @@
 [metadata]
 name = Glymur
-version = 0.13.5
+version = 0.13.7
 author = 'John Evans'
 author_email = "John Evans" <jevans667cc@proton.me>
 license = 'MIT'
@@ -14,6 +14,7 @@ classifiers =
 	Programming Language :: Python :: 3.10
 	Programming Language :: Python :: 3.11
 	Programming Language :: Python :: 3.12
+	Programming Language :: Python :: 3.13
 	Programming Language :: Python :: Implementation :: CPython
 	License :: OSI Approved :: MIT License
 	Intended Audience :: Science/Research
@@ -26,7 +27,7 @@ install_requires =
 	numpy
 	lxml
 	packaging
-python_requires = >=3.8
+python_requires = >=3.9
 include_package_data = True
 zip_safe = False
 

{glymur-0.13.5 → glymur-0.13.7}/tests/test_jp2box_xml.py

@@ -4,8 +4,9 @@ Test suite specifically targeting the JP2 XML box layout.
 """
 # Standard library imports
 import importlib.resources as ir
-from io import BytesIO
+from io import BytesIO, StringIO
 import pathlib
+import shutil
 import struct
 import warnings
 
@@ -30,35 +31,11 @@ class TestXML(fixtures.TestCommon):
     def setUp(self):
         super().setUp()
 
-        raw_xml = b"""<?xml version="1.0"?>
-        <data>
-            <country name="Liechtenstein">
-                <rank>1</rank>
-                <year>2008</year>
-                <gdppc>141100</gdppc>
-                <neighbor name="Austria" direction="E"/>
-                <neighbor name="Switzerland" direction="W"/>
-            </country>
-            <country name="Singapore">
-                <rank>4</rank>
-                <year>2011</year>
-                <gdppc>59900</gdppc>
-                <neighbor name="Malaysia" direction="N"/>
-            </country>
-            <country name="Panama">
-                <rank>68</rank>
-                <year>2011</year>
-                <gdppc>13600</gdppc>
-                <neighbor name="Costa Rica" direction="W"/>
-                <neighbor name="Colombia" direction="E"/>
-            </country>
-        </data>"""
-        path = self.test_dir_path / 'data.xml'
-        with path.open(mode='wb') as tfile:
-            tfile.write(raw_xml)
-            tfile.flush()
-        self.xmlfile_path = path
-        self.xmlfile = str(path)
+        p = ir.files('tests.data').joinpath('countries.xml')
+        dest_path = self.test_dir_path / 'data.xml'
+        shutil.copyfile(p, dest_path)
+        self.xmlfile_path = dest_path
+        self.xmlfile = str(dest_path)
 
         j2k = Jp2k(self.j2kfile)
         codestream = j2k.get_codestream()
@@ -134,6 +111,40 @@ class TestXML(fixtures.TestCommon):
         self.assertEqual(neighbor.attrib['name'], 'Malaysia')
         self.assertEqual(neighbor.attrib['direction'], 'N')
 
+    def test_xml_from_bytesio_object(self):
+        """
+        SCENARIO:  Create an xml box by pointing at a file-like BytesIO object
+
+        EXPECTED RESULT:  The xml box is validated.
+        """
+        btext = self.xmlfile_path.read_bytes()
+        b = BytesIO(btext)
+        box = glymur.jp2box.XMLBox(filename=b)
+
+        elts = box.xml.findall('country')
+        self.assertEqual(len(elts), 3)
+
+        neighbor = elts[1].find('neighbor')
+        self.assertEqual(neighbor.attrib['name'], 'Malaysia')
+        self.assertEqual(neighbor.attrib['direction'], 'N')
+
+    def test_xml_from_stringio_object(self):
+        """
+        SCENARIO:  Create an xml box by pointing at a file-like StringIO object
+
+        EXPECTED RESULT:  The xml box is validated.
+        """
+        text = self.xmlfile_path.read_text()
+        sio = StringIO(text)
+        box = glymur.jp2box.XMLBox(filename=sio)
+
+        elts = box.xml.findall('country')
+        self.assertEqual(len(elts), 3)
+
+        neighbor = elts[1].find('neighbor')
+        self.assertEqual(neighbor.attrib['name'], 'Malaysia')
+        self.assertEqual(neighbor.attrib['direction'], 'N')
+
     def test_utf8_xml_from_xml_file(self):
         """
         XMLBox from an XML file with encoding declaration.

{glymur-0.13.5 → glymur-0.13.7}/tests/test_printing.py

@@ -1074,7 +1074,8 @@ class TestPrinting(fixtures.TestCommon):
                 "array([ 0, 10, 20, ..., 70, 80, 90], dtype=uint32)),\n"
                 "                    ('ExifTag', OrderedDict([('Make', 'HTC')]))])"  # noqa : E501
             )
-        self.assertEqual(actual, expected)
+        # Numpy 2.x adds shape to string representation
+        self.assertEqual(actual.replace("shape=(10,), ", ""), expected)
 
     def test_crg(self):
         """verify printing of CRG segment"""

{glymur-0.13.5 → glymur-0.13.7}/tests/test_tiff2jp2.py

@@ -12,6 +12,7 @@ from uuid import UUID
 import warnings
 
 # 3rd party library imports
+from PIL import Image
 import numpy as np
 import skimage
 
@@ -43,6 +44,7 @@ class TestSuite(fixtures.TestCommon):
         cls.ycbcr_bg = root.joinpath('ycbcr_bg.tif')
         cls.ycbcr_stripped = root.joinpath('ycbcr_stripped.tif')
         cls.stripped = root.joinpath('stripped.tif')
+        cls.moon63 = root.joinpath('moon63.tif')
 
         test_tiff_dir = tempfile.mkdtemp()
         cls.test_tiff_path = pathlib.Path(test_tiff_dir)
@@ -192,6 +194,17 @@ class TestSuite(fixtures.TestCommon):
 
         cls.exif = path
 
+    def _imread(self, path, mode=None):
+
+        with Image.open(path) as img:
+
+            if mode is not None:
+                img = img.convert(mode)
+
+            imagedata = np.array(img)
+
+        return imagedata
+
     def test_smoke(self):
         """
         SCENARIO:  Convert TIFF file to JP2
@@ -354,7 +367,7 @@ class TestSuite(fixtures.TestCommon):
             j.layer = layer
             d[layer] = j[:]
 
-        truth = skimage.io.imread(self.moon)
+        truth = self._imread(self.moon)
 
         with warnings.catch_warnings():
             # MSE is zero for that first image, resulting in a divide-by-zero
@@ -393,7 +406,7 @@ class TestSuite(fixtures.TestCommon):
             j.layer = layer
             d[layer] = j[:]
 
-        truth = skimage.io.imread(self.moon)
+        truth = self._imread(self.moon)
 
         with warnings.catch_warnings():
             # MSE is zero for that first image, resulting in a divide-by-zero
@@ -631,9 +644,7 @@ class TestSuite(fixtures.TestCommon):
 
         jp2 = Jp2k(self.temp_jp2_filename)
         actual = jp2[:]
-        expected = skimage.io.imread(
-            self.moon3_partial_last_strip, plugin='pil'
-        )
+        expected = self._imread(self.moon3_partial_last_strip)
         np.testing.assert_array_equal(actual, expected)
 
         c = jp2.get_codestream()
@@ -659,9 +670,8 @@ class TestSuite(fixtures.TestCommon):
         jp2 = Jp2k(self.temp_jp2_filename)
         actual = jp2[:]
 
-        expected = skimage.io.imread(
-            self.moon3_partial_last_strip, plugin='pil'
-        )
+        expected = self._imread(self.moon3_partial_last_strip)
+
         np.testing.assert_array_equal(actual, expected)
 
         c = jp2.get_codestream()
@@ -812,7 +822,7 @@ class TestSuite(fixtures.TestCommon):
 
         jp2 = Jp2k(self.temp_jp2_filename)
         actual = jp2[:]
-        expected = skimage.io.imread(self.ycbcr_stripped, plugin='pil')
+        expected = self._imread(self.ycbcr_stripped)
         np.testing.assert_array_equal(actual, expected)
 
         c = jp2.get_codestream()
@@ -835,7 +845,7 @@ class TestSuite(fixtures.TestCommon):
 
         jp2 = Jp2k(self.temp_jp2_filename)
         actual = jp2[:]
-        expected = skimage.io.imread(self.ycbcr_bg, plugin='pil')
+        expected = self._imread(self.ycbcr_bg)
         np.testing.assert_array_equal(actual, expected)
 
         c = jp2.get_codestream()
@@ -882,9 +892,8 @@ class TestSuite(fixtures.TestCommon):
 
         jp2 = Jp2k(self.temp_jp2_filename)
         actual = jp2[:]
-        expected = skimage.io.imread(
-            self.astronaut_ycbcr_jpeg_tiled, plugin='pil'
-        )
+        expected = self._imread(self.astronaut_ycbcr_jpeg_tiled)
+
         np.testing.assert_array_equal(actual, expected)
 
         c = jp2.get_codestream()
@@ -908,9 +917,7 @@ class TestSuite(fixtures.TestCommon):
 
         jp2 = Jp2k(self.temp_jp2_filename)
         actual = jp2[:]
-        expected = skimage.io.imread(
-            self.astronaut_ycbcr_jpeg_tiled, plugin='pil'
-        )
+        expected = self._imread(self.astronaut_ycbcr_jpeg_tiled)
         np.testing.assert_array_equal(actual, expected)
 
         c = jp2.get_codestream()
@@ -933,9 +940,7 @@ class TestSuite(fixtures.TestCommon):
 
         jp2 = Jp2k(self.temp_jp2_filename)
         actual = jp2[:]
-        expected = skimage.io.imread(
-            self.astronaut_ycbcr_jpeg_tiled, plugin='pil'
-        )
+        expected = self._imread(self.astronaut_ycbcr_jpeg_tiled)
         np.testing.assert_array_equal(actual, expected)
 
         c = jp2.get_codestream()
@@ -1835,9 +1840,7 @@ class TestSuite(fixtures.TestCommon):
         # Read in the image (as expected on little-endian), flip it
         # around, prepend an alpha layer, then get rid of the last layer
         # to simulate what would have happened on big-endian.
-        expected = skimage.io.imread(
-            self.astronaut_ycbcr_jpeg_tiled, plugin='pil'
-        )
+        expected = self._imread(self.astronaut_ycbcr_jpeg_tiled)
         h, w, _ = expected.shape
         expected = np.flip(expected, axis=2)
         A = np.ones((h, w, 1), dtype=np.uint8) * 255
@@ -1873,9 +1876,7 @@ class TestSuite(fixtures.TestCommon):
         # Read in the image (as expected on little-endian), flip it
         # around, prepend an alpha layer, then get rid of the last layer
         # to simulate what would have happened on big-endian.
-        expected = skimage.io.imread(
-            self.astronaut_ycbcr_jpeg_tiled, plugin='pil'
-        )
+        expected = self._imread(self.astronaut_ycbcr_jpeg_tiled)
         h, w, _ = expected.shape
         expected = np.flip(expected, axis=2)
         A = np.ones((h, w, 1), dtype=np.uint8) * 255
@@ -1911,7 +1912,7 @@ class TestSuite(fixtures.TestCommon):
         # Read in the image (as expected on little-endian), flip it
         # around, prepend an alpha layer, then get rid of the last layer
         # to simulate what would have happened on big-endian.
-        expected = skimage.io.imread(self.ycbcr_stripped, plugin='pil')
+        expected = self._imread(self.ycbcr_stripped)
         h, w, _ = expected.shape
         expected = np.flip(expected, axis=2)
         A = np.ones((h, w, 1), dtype=np.uint8) * 255
@@ -1919,3 +1920,26 @@ class TestSuite(fixtures.TestCommon):
         expected = expected[:, :, :3]
 
         np.testing.assert_array_equal(actual, expected)
+
+    def test_unevenly_tiled(self):
+        """
+        SCENARIO:  Convert monochromatic TIFF file to JP2.  The TIFF is tiled
+        2x3, and the 2nd row of tiles consists of partial tiles.
+
+        EXPECTED RESULT:  The JP2 file validates
+        """
+        with Tiff2Jp2k(
+            self.moon63, self.temp_jp2_filename, tilesize=(32, 32)
+        ) as j:
+            j.run()
+
+        jp2 = Jp2k(self.temp_jp2_filename)
+        actual = jp2[:]
+        expected = self._imread(self.moon63)
+        np.testing.assert_array_equal(actual, expected)
+
+        c = jp2.get_codestream()
+        self.assertEqual(c.segment[1].xsiz, 96)
+        self.assertEqual(c.segment[1].ysiz, 63)
+        self.assertEqual(c.segment[1].xtsiz, 32)
+        self.assertEqual(c.segment[1].ytsiz, 32)