From 89a1b0bb1c6b812f82805a3bb3488051ec40045f Mon Sep 17 00:00:00 2001
From: John Evans <john.g.evans@noaa.gov>
Date: Tue, 11 Nov 2014 10:46:59 -0500
Subject: [PATCH 01/23] progress, working on rlevel

---
 glymur/jp2k.py           | 52 ++++++++++++++++++++++++++++------------
 glymur/test/test_jp2k.py | 46 ++++++++++++++++++++---------------
 2 files changed, 64 insertions(+), 34 deletions(-)

diff --git a/glymur/jp2k.py b/glymur/jp2k.py
index f36b75e..25efacd 100644
--- a/glymur/jp2k.py
+++ b/glymur/jp2k.py
@@ -60,6 +60,23 @@ class Jp2k(Jp2kBox):
         List of top-level boxes in the file.  Each box may in turn contain
         its own list of boxes.  Will be empty if the file consists only of a
         raw codestream.
+
+    Examples
+    --------
+    >>> import glymur
+    >>> 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)
     """
 
     def __init__(self, filename, mode='rb'):
@@ -957,6 +974,25 @@ class Jp2k(Jp2kBox):
         return data[:, :, bands]
 
 
+    def _read(self):
+        """Read a JPEG 2000 image.
+
+        Returns
+        -------
+        img_array : ndarray
+            The image data.
+
+        Raises
+        ------
+        IOError
+            If the image has differing subsample factors.
+        """
+        if version.openjpeg_version_tuple[0] < 2:
+            img = self._read_openjpeg(**kwargs)
+        else:
+            img = self._read_openjp2(**kwargs)
+        return img
+
     def read(self, **kwargs):
         """Read a JPEG 2000 image.
 
@@ -988,22 +1024,8 @@ class Jp2k(Jp2kBox):
         ------
         IOError
             If the image has differing subsample factors.
-
-        Examples
-        --------
-        >>> import glymur
-        >>> jfile = glymur.data.nemo()
-        >>> jp = glymur.Jp2k(jfile)
-        >>> image = jp.read()
-        >>> image.shape
-        (1456, 2592, 3)
-
-        Read the lowest resolution thumbnail.
-
-        >>> thumbnail = jp.read(rlevel=-1)
-        >>> thumbnail.shape
-        (728, 1296, 3)
         """
+        warnings.warn("Use array-style slicing instead.", DeprecationWarning)
         if version.openjpeg_version_tuple[0] < 2:
             img = self._read_openjpeg(**kwargs)
         else:
diff --git a/glymur/test/test_jp2k.py b/glymur/test/test_jp2k.py
index 9a9fb72..4933777 100644
--- a/glymur/test/test_jp2k.py
+++ b/glymur/test/test_jp2k.py
@@ -67,11 +67,13 @@ class SliceProtocolBase(unittest.TestCase):
     def setUpClass(self):
 
         self.jp2 = Jp2k(glymur.data.nemo())
-        self.jp2_data = self.jp2.read()
+        self.jp2_data = self.jp2[:]
+        self.jp2_data_r1 = self.jp2[::2, ::2]
 
         self.j2k = Jp2k(glymur.data.goodstuff())
-        self.j2k_data = self.j2k.read()
+        self.j2k_data = self.j2k[:]
 
+        self.j2k_data_r1 = self.j2k[::2, ::2]
 
 @unittest.skipIf(os.name == "nt", fixtures.WINDOWS_TMP_FILE_MSG)
 class TestSliceProtocolBaseWrite(SliceProtocolBase):
@@ -82,7 +84,7 @@ class TestSliceProtocolBaseWrite(SliceProtocolBase):
         with tempfile.NamedTemporaryFile(suffix='.j2k') as tfile:
             j = Jp2k(tfile.name, 'wb')
             j[...] = self.j2k_data
-            actual = j.read()
+            actual = j[:]
 
         np.testing.assert_array_equal(actual, expected)
 
@@ -92,7 +94,7 @@ class TestSliceProtocolBaseWrite(SliceProtocolBase):
         with tempfile.NamedTemporaryFile(suffix='.j2k') as tfile:
             j = Jp2k(tfile.name, 'wb')
             j[:] = self.j2k_data
-            actual = j.read()
+            actual = j[:]
 
         np.testing.assert_array_equal(actual, expected)
 
@@ -167,9 +169,9 @@ class TestSliceProtocolRead(SliceProtocolBase):
         np.testing.assert_array_equal(actual, expected)
 
     def test_reduce_resolution_and_slice_in_third_dimension(self):
-        d = self.j2k[::2, ::2, 1:3]
-        all = self.j2k.read(rlevel=1)
-        np.testing.assert_array_equal(all[:,:,1:3], d)
+        actual = self.j2k[::2, ::2, 1:3]
+        expected = self.j2k_data_r1[:, :, 1:3]
+        np.testing.assert_array_equal(actual, expected)
 
     def test_retrieve_single_row(self):
         actual = self.jp2[0]
@@ -231,24 +233,24 @@ class TestSliceProtocolRead(SliceProtocolBase):
         expected = self.jp2_data[728:, :]
         np.testing.assert_array_equal(actual, expected)
 
-    def test_region_rlevel1(self):
+    def test_region_rlevel1_odd(self):
         actual = self.jp2[0:201:2, 0:201:2]
-        expected = self.jp2.read(area=(0, 0, 201, 201), rlevel=1)
+        expected = self.jp2_data_r1[:101, :101, :]
+        np.testing.assert_array_equal(actual, expected)
+
+    def test_region_rlevel1_even(self):
+        actual = self.jp2[0:202:2, 0:202:2]
+        expected = self.jp2_data_r1[:101, :101, :]
         np.testing.assert_array_equal(actual, expected)
 
     def test_region_rlevel1_slice_start_is_none(self):
         actual = self.jp2[:201:2, :201:2]
-        expected = self.jp2.read(area=(0, 0, 201, 201), rlevel=1)
+        expected = self.jp2_data_r1[:101, :101, :]
         np.testing.assert_array_equal(actual, expected)
 
     def test_region_rlevel1_slice_stop_is_none(self):
         actual = self.jp2[201::2, 201::2]
-        expected = self.jp2.read(area=(201, 201, 1456, 2592), rlevel=1)
-        np.testing.assert_array_equal(actual, expected)
-
-    def test_region_rlevel1(self):
-        actual = self.jp2[0:202:2, 0:202:2]
-        expected = self.jp2.read(area=(0, 0, 202, 202), rlevel=1)
+        expected = self.jp2_data_r1[101:, 101:, :]
         np.testing.assert_array_equal(actual, expected)
 
     def test_ellipsis_full_read(self):
@@ -476,6 +478,12 @@ class TestJp2k(unittest.TestCase):
     def tearDown(self):
         pass
 
+    @unittest.skipIf(WARNING_INFRASTRUCTURE_ISSUE, WARNING_INFRASTRUCTURE_MSG)
+    def test_warn_if_using_read_method(self):
+        """Should warn if read method is called"""
+        with self.assertWarns(DeprecationWarning):
+            Jp2k(self.jp2file).read()
+
     def test_shape_jp2(self):
         """verify shape attribute for JP2 file
         """
@@ -519,7 +527,7 @@ class TestJp2k(unittest.TestCase):
     def test_irreversible(self):
         """Irreversible"""
         j = Jp2k(self.jp2file)
-        expdata = j.read()
+        expdata = j[:]
         with tempfile.NamedTemporaryFile(suffix='.j2k') as tfile:
             j2 = Jp2k(tfile.name, 'wb')
             j2.write(expdata, irreversible=True)
@@ -528,7 +536,7 @@ class TestJp2k(unittest.TestCase):
             self.assertEqual(codestream.segment[2].spcod[8],
                              glymur.core.WAVELET_XFORM_9X7_IRREVERSIBLE)
 
-            actdata = j2.read()
+            actdata = j2[:]
             self.assertTrue(fixtures.mse(actdata[0], expdata[0]) < 0.38)
 
     @unittest.skipIf(re.match('1.[0-4]', openjpeg_version) is not None,
@@ -538,7 +546,7 @@ class TestJp2k(unittest.TestCase):
     def test_no_cxform_pclr_jpx(self):
         """Indices for pclr jpxfile if no color transform"""
         j = Jp2k(self.jpxfile)
-        rgb = j.read()
+        rgb = j[:]
         idx = j.read(ignore_pclr_cmap_cdef=True)
         nr, nc = 1024, 1024
         self.assertEqual(rgb.shape, (nr, nc, 3))

From a1413b0f15c7e40d1fd86312a0a7b563c5219989 Mon Sep 17 00:00:00 2001
From: John Evans <john.g.evans@noaa.gov>
Date: Wed, 12 Nov 2014 17:30:43 -0500
Subject: [PATCH 02/23] progress

---
 glymur/test/test_jp2k.py      | 49 ++++++++++---------
 glymur/test/test_opj_suite.py | 90 +++++++++++++++++------------------
 2 files changed, 69 insertions(+), 70 deletions(-)

diff --git a/glymur/test/test_jp2k.py b/glymur/test/test_jp2k.py
index 4933777..5e28db0 100644
--- a/glymur/test/test_jp2k.py
+++ b/glymur/test/test_jp2k.py
@@ -74,6 +74,7 @@ class SliceProtocolBase(unittest.TestCase):
         self.j2k_data = self.j2k[:]
 
         self.j2k_data_r1 = self.j2k[::2, ::2]
+        self.j2k_data_r5 = self.j2k[::32, ::32]
 
 @unittest.skipIf(os.name == "nt", fixtures.WINDOWS_TMP_FILE_MSG)
 class TestSliceProtocolBaseWrite(SliceProtocolBase):
@@ -313,7 +314,7 @@ class TestSliceProtocolRead(SliceProtocolBase):
 
     def test_region_rlevel5(self):
         actual = self.j2k[5:533:32, 27:423:32]
-        expected = self.j2k.read(area=(5, 27, 533, 423), rlevel=5)
+        expected = self.j2k_data_r5[1:17, 1:14]
         np.testing.assert_array_equal(actual, expected)
 
 @unittest.skipIf(OPJ_DATA_ROOT is None,
@@ -480,7 +481,7 @@ class TestJp2k(unittest.TestCase):
 
     @unittest.skipIf(WARNING_INFRASTRUCTURE_ISSUE, WARNING_INFRASTRUCTURE_MSG)
     def test_warn_if_using_read_method(self):
-        """Should warn if read method is called"""
+        """Should warn if deprecated read method is called"""
         with self.assertWarns(DeprecationWarning):
             Jp2k(self.jp2file).read()
 
@@ -575,7 +576,7 @@ class TestJp2k(unittest.TestCase):
         """Verify that rlevel=-1 gets us the lowest resolution image"""
         j = Jp2k(self.j2kfile)
         thumbnail1 = j.read(rlevel=-1)
-        thumbnail2 = j.read(rlevel=5)
+        thumbnail2 = j[::32, ::32]
         np.testing.assert_array_equal(thumbnail1, thumbnail2)
         self.assertEqual(thumbnail1.shape, (25, 15, 3))
 
@@ -734,7 +735,7 @@ class TestJp2k(unittest.TestCase):
         """Just a very basic test that reading a JP2 file does not error out.
         """
         j2k = Jp2k(self.jp2file)
-        j2k.read(rlevel=1)
+        j2k[::2, ::2]
 
     def test_basic_j2k(self):
         """This test is only useful when openjp2 is not available
@@ -742,7 +743,7 @@ class TestJp2k(unittest.TestCase):
         working J2K test.
         """
         j2k = Jp2k(self.j2kfile)
-        j2k.read()
+        j2k[:]
 
     def test_empty_box_with_j2k(self):
         """Verify that the list of boxes in a J2C/J2K file is present, but
@@ -867,7 +868,7 @@ class TestJp2k(unittest.TestCase):
         """Read JPX codestream when jp2-compatible."""
         # The file in question has multiple codestreams.
         jpx = Jp2k(self.jpxfile)
-        data = jpx.read()
+        data = jpx[:]
         self.assertEqual(data.shape, (1024, 1024, 3))
 
     def test_read_bands_without_openjp2(self):
@@ -1021,21 +1022,21 @@ class TestJp2k_write(unittest.TestCase):
     def test_write_with_jp2_in_caps(self):
         """should be able to write with JP2 suffix."""
         j2k = Jp2k(self.j2kfile)
-        expdata = j2k.read()
+        expdata = j2k[:]
         with tempfile.NamedTemporaryFile(suffix='.JP2') as tfile:
             ofile = Jp2k(tfile.name, 'wb')
-            ofile.write(expdata)
-            actdata = ofile.read()
+            ofile[:] = expdata
+            actdata = ofile[:]
             np.testing.assert_array_equal(actdata, expdata)
 
     def test_write_srgb_without_mct(self):
         """should be able to write RGB without specifying mct"""
         j2k = Jp2k(self.j2kfile)
-        expdata = j2k.read()
+        expdata = j2k[:]
         with tempfile.NamedTemporaryFile(suffix='.jp2') as tfile:
             ofile = Jp2k(tfile.name, 'wb')
             ofile.write(expdata, mct=False)
-            actdata = ofile.read()
+            actdata = ofile[:]
             np.testing.assert_array_equal(actdata, expdata)
 
             codestream = ofile.get_codestream()
@@ -1044,7 +1045,7 @@ class TestJp2k_write(unittest.TestCase):
     def test_write_grayscale_with_mct(self):
         """MCT usage makes no sense for grayscale images."""
         j2k = Jp2k(self.j2kfile)
-        expdata = j2k.read()
+        expdata = j2k[:]
         with tempfile.NamedTemporaryFile(suffix='.jp2') as tfile:
             ofile = Jp2k(tfile.name, 'wb')
             with self.assertRaises(IOError):
@@ -1054,11 +1055,11 @@ class TestJp2k_write(unittest.TestCase):
         """Must be able to write a CPRL progression order file"""
         # Issue 17
         j = Jp2k(self.jp2file)
-        expdata = j.read(rlevel=1)
+        expdata = j[::2, ::2]
         with tempfile.NamedTemporaryFile(suffix='.jp2') as tfile:
             ofile = Jp2k(tfile.name, 'wb')
             ofile.write(expdata, prog='CPRL')
-            actdata = ofile.read()
+            actdata = ofile[:]
             np.testing.assert_array_equal(actdata, expdata)
 
             codestream = ofile.get_codestream()
@@ -1145,7 +1146,7 @@ class TestJp2k_2_0(unittest.TestCase):
         """Test asoc and label box"""
         # Construct a fake file with an asoc and a label box, as
         # OpenJPEG doesn't have such a file.
-        data = Jp2k(self.jp2file).read(rlevel=1)
+        data = Jp2k(self.jp2file)[::2, ::2]
         with tempfile.NamedTemporaryFile(suffix='.jp2') as tfile:
             j = Jp2k(tfile.name, 'wb')
             j.write(data)
@@ -1246,11 +1247,9 @@ class TestJp2k_2_1(unittest.TestCase):
                 tfile.write(data[offset+53:offset+55])
                 tfile.write(b'\x00')
                 tfile.write(data[offset+57:offset+59])
-                #tfile.write(data[3184:3186])
                 tfile.write(b'\x00')
 
                 tfile.write(data[offset+59:])
-                #tfile.write(data[3186:])
                 tfile.flush()
                 with warnings.catch_warnings():
                     warnings.simplefilter('ignore')
@@ -1260,10 +1259,10 @@ class TestJp2k_2_1(unittest.TestCase):
                                             :\sdx=1\sdy=0''', re.VERBOSE)
                     if sys.hexversion < 0x03020000:
                         with self.assertRaisesRegexp((IOError, OSError), regexp):
-                            j.read(rlevel=1)
+                            j[::2, ::2]
                     else:
                         with self.assertRaisesRegex((IOError, OSError), regexp):
-                            j.read(rlevel=1)
+                            j[::2, ::2]
 
 @unittest.skipIf(OPJ_DATA_ROOT is None,
                  "OPJ_DATA_ROOT environment variable not set")
@@ -1364,7 +1363,7 @@ class TestJp2kOpjDataRoot(unittest.TestCase):
             self.assertEqual(codestream.segment[2].spcod[8],
                              glymur.core.WAVELET_XFORM_9X7_IRREVERSIBLE)
 
-            actdata = j.read()
+            actdata = j[:]
             self.assertTrue(fixtures.mse(actdata, expdata) < 250)
 
     @unittest.skipIf(WARNING_INFRASTRUCTURE_ISSUE, WARNING_INFRASTRUCTURE_MSG)
@@ -1372,9 +1371,9 @@ class TestJp2kOpjDataRoot(unittest.TestCase):
         """Indices for pclr jpxfile if no color transform"""
         filename = opj_data_file('input/conformance/file9.jp2')
         with self.assertWarns(UserWarning):
-            j = Jp2k(filename)
-        rgb = j.read()
-        idx = j.read(ignore_pclr_cmap_cdef=True)
+            jp2 = Jp2k(filename)
+        rgb = jp2[:]
+        idx = jp2.read(ignore_pclr_cmap_cdef=True)
         self.assertEqual(rgb.shape, (512, 768, 3))
         self.assertEqual(idx.shape, (512, 768))
 
@@ -1396,7 +1395,7 @@ class TestJp2kOpjDataRoot(unittest.TestCase):
         filename = opj_data_file('input/conformance/p0_05.j2k')
         j = Jp2k(filename)
         with self.assertRaises(RuntimeError):
-            j.read()
+            j[:]
         
     @unittest.skipIf(WARNING_INFRASTRUCTURE_ISSUE, WARNING_INFRASTRUCTURE_MSG)
     def test_no_cxform_cmap(self):
@@ -1407,7 +1406,7 @@ class TestJp2kOpjDataRoot(unittest.TestCase):
         with self.assertWarns(UserWarning):
             # The file has a bad compatibility list entry.  Not important here.
             j = Jp2k(filename)
-        ycbcr = j.read()
+        ycbcr = j[:]
         crcby = j.read(ignore_pclr_cmap_cdef=True)
 
         expected = np.zeros(ycbcr.shape, ycbcr.dtype)
diff --git a/glymur/test/test_opj_suite.py b/glymur/test/test_opj_suite.py
index a033aae..a10185b 100644
--- a/glymur/test/test_opj_suite.py
+++ b/glymur/test/test_opj_suite.py
@@ -57,7 +57,7 @@ class TestSuite(unittest.TestCase):
     def test_ETS_C1P0_p0_01_j2k(self):
         jfile = opj_data_file('input/conformance/p0_01.j2k')
         jp2k = Jp2k(jfile)
-        jpdata = jp2k.read(rlevel=0)
+        jpdata = jp2k[:]
 
         pgxfile = opj_data_file('baseline/conformance/c1p0_01_0.pgx')
         pgxdata = read_pgx(pgxfile)
@@ -67,7 +67,7 @@ class TestSuite(unittest.TestCase):
     def test_ETS_C1P0_p0_03_j2k(self):
         jfile = opj_data_file('input/conformance/p0_03.j2k')
         jp2k = Jp2k(jfile)
-        jpdata = jp2k.read(rlevel=0)
+        jpdata = jp2k[:]
 
         pgxfile = opj_data_file('baseline/conformance/c1p0_03_0.pgx')
         pgxdata = read_pgx(pgxfile)
@@ -77,7 +77,7 @@ class TestSuite(unittest.TestCase):
     def test_ETS_C1P0_p0_04_j2k(self):
         jfile = opj_data_file('input/conformance/p0_04.j2k')
         jp2k = Jp2k(jfile)
-        jpdata = jp2k.read(rlevel=0)
+        jpdata = jp2k[:]
 
         pgxfile = opj_data_file('baseline/conformance/c1p0_04_0.pgx')
         pgxdata = read_pgx(pgxfile)
@@ -97,7 +97,7 @@ class TestSuite(unittest.TestCase):
     def test_ETS_C1P0_p0_08_j2k(self):
         jfile = opj_data_file('input/conformance/p0_08.j2k')
         jp2k = Jp2k(jfile)
-        jpdata = jp2k.read(rlevel=1)
+        jpdata = jp2k[::2, ::2]
 
         pgxfile = opj_data_file('baseline/conformance/c1p0_08_0.pgx')
         pgxdata = read_pgx(pgxfile)
@@ -114,7 +114,7 @@ class TestSuite(unittest.TestCase):
     def test_ETS_C1P0_p0_09_j2k(self):
         jfile = opj_data_file('input/conformance/p0_09.j2k')
         jp2k = Jp2k(jfile)
-        jpdata = jp2k.read(rlevel=0)
+        jpdata = jp2k[:]
 
         pgxfile = opj_data_file('baseline/conformance/c1p0_09_0.pgx')
         pgxdata = read_pgx(pgxfile)
@@ -123,7 +123,7 @@ class TestSuite(unittest.TestCase):
     def test_ETS_C1P0_p0_11_j2k(self):
         jfile = opj_data_file('input/conformance/p0_11.j2k')
         jp2k = Jp2k(jfile)
-        jpdata = jp2k.read(rlevel=0)
+        jpdata = jp2k[:]
 
         pgxfile = opj_data_file('baseline/conformance/c1p0_11_0.pgx')
         pgxdata = read_pgx(pgxfile)
@@ -132,7 +132,7 @@ class TestSuite(unittest.TestCase):
     def test_ETS_C1P0_p0_14_j2k(self):
         jfile = opj_data_file('input/conformance/p0_14.j2k')
         jp2k = Jp2k(jfile)
-        jpdata = jp2k.read(rlevel=0)
+        jpdata = jp2k[:]
 
         pgxfile = opj_data_file('baseline/conformance/c1p0_14_0.pgx')
         pgxdata = read_pgx(pgxfile)
@@ -149,7 +149,7 @@ class TestSuite(unittest.TestCase):
     def test_ETS_C1P0_p0_15_j2k(self):
         jfile = opj_data_file('input/conformance/p0_15.j2k')
         jp2k = Jp2k(jfile)
-        jpdata = jp2k.read(rlevel=0)
+        jpdata = jp2k[:]
 
         pgxfile = opj_data_file('baseline/conformance/c1p0_15_0.pgx')
         pgxdata = read_pgx(pgxfile)
@@ -158,7 +158,7 @@ class TestSuite(unittest.TestCase):
     def test_ETS_C1P0_p0_16_j2k(self):
         jfile = opj_data_file('input/conformance/p0_16.j2k')
         jp2k = Jp2k(jfile)
-        jpdata = jp2k.read(rlevel=0)
+        jpdata = jp2k[:]
 
         pgxfile = opj_data_file('baseline/conformance/c1p0_16_0.pgx')
         pgxdata = read_pgx(pgxfile)
@@ -167,7 +167,7 @@ class TestSuite(unittest.TestCase):
     def test_ETS_C1P1_p1_01_j2k(self):
         jfile = opj_data_file('input/conformance/p1_01.j2k')
         jp2k = Jp2k(jfile)
-        jpdata = jp2k.read(rlevel=0)
+        jpdata = jp2k[:]
 
         pgxfile = opj_data_file('baseline/conformance/c1p1_01_0.pgx')
         pgxdata = read_pgx(pgxfile)
@@ -176,7 +176,7 @@ class TestSuite(unittest.TestCase):
     def test_ETS_C1P1_p1_02_j2k(self):
         jfile = opj_data_file('input/conformance/p1_02.j2k')
         jp2k = Jp2k(jfile)
-        jpdata = jp2k.read(rlevel=0)
+        jpdata = jp2k[:]
 
         pgxfile = opj_data_file('baseline/conformance/c1p1_02_0.pgx')
         pgxdata = read_pgx(pgxfile)
@@ -196,7 +196,7 @@ class TestSuite(unittest.TestCase):
     def test_ETS_C1P1_p1_04_j2k(self):
         jfile = opj_data_file('input/conformance/p1_04.j2k')
         jp2k = Jp2k(jfile)
-        jpdata = jp2k.read()
+        jpdata = jp2k[:]
 
         pgxfile = opj_data_file('baseline/conformance/c1p1_04_0.pgx')
         pgxdata = read_pgx(pgxfile)
@@ -206,95 +206,95 @@ class TestSuite(unittest.TestCase):
     def test_NR_DEC_Bretagne2_j2k_1_decode(self):
         jfile = opj_data_file('input/nonregression/Bretagne2.j2k')
         jp2 = Jp2k(jfile)
-        jp2.read()
+        jp2[:]
         self.assertTrue(True)
 
     def test_NR_DEC__00042_j2k_2_decode(self):
         jfile = opj_data_file('input/nonregression/_00042.j2k')
         jp2 = Jp2k(jfile)
-        jp2.read()
+        jp2[:]
         self.assertTrue(True)
 
     def test_NR_DEC_buxI_j2k_9_decode(self):
         jfile = opj_data_file('input/nonregression/buxI.j2k')
-        Jp2k(jfile).read()
+        Jp2k(jfile)[:]
         self.assertTrue(True)
 
     def test_NR_DEC_buxR_j2k_10_decode(self):
         jfile = opj_data_file('input/nonregression/buxR.j2k')
-        Jp2k(jfile).read()
+        Jp2k(jfile)[:]
         self.assertTrue(True)
 
     def test_NR_DEC_Cannotreaddatawithnosizeknown_j2k_11_decode(self):
         relpath = 'input/nonregression/Cannotreaddatawithnosizeknown.j2k'
         jfile = opj_data_file(relpath)
-        Jp2k(jfile).read()
+        Jp2k(jfile)[:]
         self.assertTrue(True)
 
     def test_NR_DEC_cthead1_j2k_12_decode(self):
         jfile = opj_data_file('input/nonregression/cthead1.j2k')
-        Jp2k(jfile).read()
+        Jp2k(jfile)[:]
         self.assertTrue(True)
 
     def test_NR_DEC_CT_Phillips_JPEG2K_Decompr_Problem_j2k_13_decode(self):
         relpath = 'input/nonregression/CT_Phillips_JPEG2K_Decompr_Problem.j2k'
         jfile = opj_data_file(relpath)
-        Jp2k(jfile).read()
+        Jp2k(jfile)[:]
         self.assertTrue(True)
 
     def test_NR_DEC_j2k32_j2k_15_decode(self):
         jfile = opj_data_file('input/nonregression/j2k32.j2k')
-        Jp2k(jfile).read()
+        Jp2k(jfile)[:]
         self.assertTrue(True)
 
     def test_NR_DEC_MarkerIsNotCompliant_j2k_17_decode(self):
         jfile = opj_data_file('input/nonregression/MarkerIsNotCompliant.j2k')
-        Jp2k(jfile).read()
+        Jp2k(jfile)[:]
         self.assertTrue(True)
 
     def test_NR_DEC_Marrin_jp2_18_decode(self):
         jfile = opj_data_file('input/nonregression/Marrin.jp2')
-        Jp2k(jfile).read()
+        Jp2k(jfile)[:]
         self.assertTrue(True)
 
     def test_NR_DEC_movie_00000_j2k_20_decode(self):
         jfile = opj_data_file('input/nonregression/movie_00000.j2k')
-        Jp2k(jfile).read()
+        Jp2k(jfile)[:]
         self.assertTrue(True)
 
     def test_NR_DEC_movie_00001_j2k_21_decode(self):
         jfile = opj_data_file('input/nonregression/movie_00001.j2k')
-        Jp2k(jfile).read()
+        Jp2k(jfile)[:]
         self.assertTrue(True)
 
     def test_NR_DEC_movie_00002_j2k_22_decode(self):
         jfile = opj_data_file('input/nonregression/movie_00002.j2k')
-        Jp2k(jfile).read()
+        Jp2k(jfile)[:]
         self.assertTrue(True)
 
     def test_NR_DEC_orb_blue_lin_j2k_j2k_23_decode(self):
         jfile = opj_data_file('input/nonregression/orb-blue10-lin-j2k.j2k')
-        Jp2k(jfile).read()
+        Jp2k(jfile)[:]
         self.assertTrue(True)
 
     def test_NR_DEC_orb_blue_win_j2k_j2k_24_decode(self):
         jfile = opj_data_file('input/nonregression/orb-blue10-win-j2k.j2k')
-        Jp2k(jfile).read()
+        Jp2k(jfile)[:]
         self.assertTrue(True)
 
     def test_NR_DEC_relax_jp2_27_decode(self):
         jfile = opj_data_file('input/nonregression/relax.jp2')
-        Jp2k(jfile).read()
+        Jp2k(jfile)[:]
         self.assertTrue(True)
 
     def test_NR_DEC_test_lossless_j2k_28_decode(self):
         jfile = opj_data_file('input/nonregression/test_lossless.j2k')
-        Jp2k(jfile).read()
+        Jp2k(jfile)[:]
         self.assertTrue(True)
 
     def test_NR_DEC_pacs_ge_j2k_30_decode(self):
         jfile = opj_data_file('input/nonregression/pacs.ge.j2k')
-        Jp2k(jfile).read()
+        Jp2k(jfile)[:]
         self.assertTrue(True)
 
 
@@ -317,14 +317,14 @@ class TestSuiteWarns(MetadataBase):
         with self.assertWarns(UserWarning):
             # Bad compatibility list item.
             jp2k = Jp2k(jfile)
-        jpdata = jp2k.read()
+        jpdata = jp2k[:]
         self.assertEqual(jpdata.shape, (512, 768, 3))
 
     def test_ETS_JP2_file2(self):
         jfile = opj_data_file('input/conformance/file2.jp2')
         with self.assertWarns(UserWarning):
             jp2k = Jp2k(jfile)
-        jpdata = jp2k.read()
+        jpdata = jp2k[:]
         self.assertEqual(jpdata.shape, (640, 480, 3))
 
     @unittest.skipIf(glymur.version.openjpeg_version_tuple[0] < 2,
@@ -342,7 +342,7 @@ class TestSuiteWarns(MetadataBase):
         jfile = opj_data_file('input/conformance/file4.jp2')
         with self.assertWarns(UserWarning):
             jp2k = Jp2k(jfile)
-        jpdata = jp2k.read()
+        jpdata = jp2k[:]
         self.assertEqual(jpdata.shape, (512, 768))
 
     def test_ETS_JP2_file5(self):
@@ -351,35 +351,35 @@ class TestSuiteWarns(MetadataBase):
             # There's a warning for an unknown compatibility entry.
             # Ignore it here.
             jp2k = Jp2k(jfile)
-        jpdata = jp2k.read()
+        jpdata = jp2k[:]
         self.assertEqual(jpdata.shape, (512, 768, 3))
 
     def test_ETS_JP2_file6(self):
         jfile = opj_data_file('input/conformance/file6.jp2')
         with self.assertWarns(UserWarning):
             jp2k = Jp2k(jfile)
-        jpdata = jp2k.read()
+        jpdata = jp2k[:]
         self.assertEqual(jpdata.shape, (512, 768))
 
     def test_ETS_JP2_file7(self):
         jfile = opj_data_file('input/conformance/file7.jp2')
         with self.assertWarns(UserWarning):
             jp2k = Jp2k(jfile)
-        jpdata = jp2k.read()
+        jpdata = jp2k[:]
         self.assertEqual(jpdata.shape, (640, 480, 3))
 
     def test_ETS_JP2_file8(self):
         jfile = opj_data_file('input/conformance/file8.jp2')
         with self.assertWarns(UserWarning):
             jp2k = Jp2k(jfile)
-        jpdata = jp2k.read()
+        jpdata = jp2k[:]
         self.assertEqual(jpdata.shape, (400, 700))
 
     def test_ETS_JP2_file9(self):
         jfile = opj_data_file('input/conformance/file9.jp2')
         with self.assertWarns(UserWarning):
             jp2k = Jp2k(jfile)
-        jpdata = jp2k.read()
+        jpdata = jp2k[:]
         self.assertEqual(jpdata.shape, (512, 768, 3))
 
     def test_NR_broken_jp2_dump(self):
@@ -469,13 +469,13 @@ class TestSuiteWarns(MetadataBase):
         jfile = opj_data_file('input/nonregression/orb-blue10-lin-jp2.jp2')
         with self.assertWarns(UserWarning):
             # This file has an invalid ICC profile
-            Jp2k(jfile).read()
+            Jp2k(jfile)[:]
         self.assertTrue(True)
 
     def test_NR_DEC_orb_blue_win_jp2_26_decode(self):
         jfile = opj_data_file('input/nonregression/orb-blue10-win-jp2.jp2')
         with self.assertWarns(UserWarning):
-            Jp2k(jfile).read()
+            Jp2k(jfile)[:]
         self.assertTrue(True)
 
 
@@ -590,7 +590,7 @@ class TestSuite2point0(unittest.TestCase):
     def test_ETS_C1P0_p0_10_j2k(self):
         jfile = opj_data_file('input/conformance/p0_10.j2k')
         jp2k = Jp2k(jfile)
-        jpdata = jp2k.read(rlevel=0)
+        jpdata = jp2k[:]
 
         pgxfile = opj_data_file('baseline/conformance/c1p0_10_0.pgx')
         pgxdata = read_pgx(pgxfile)
@@ -611,7 +611,7 @@ class TestSuite2point0(unittest.TestCase):
         with self.assertRaises(IOError):
             with self.assertWarns(UserWarning):
                 # Invalid marker ID.
-                Jp2k(jfile).read()
+                Jp2k(jfile)[:]
         self.assertTrue(True)
 
     @unittest.skipIf(WARNING_INFRASTRUCTURE_ISSUE, WARNING_INFRASTRUCTURE_MSG)
@@ -620,7 +620,7 @@ class TestSuite2point0(unittest.TestCase):
         with self.assertRaises(IOError):
             with self.assertWarns(UserWarning):
                 # invalid number of subbands, bad marker ID
-                Jp2k(jfile).read()
+                Jp2k(jfile)[:]
         self.assertTrue(True)
 
     @unittest.skipIf(WARNING_INFRASTRUCTURE_ISSUE, WARNING_INFRASTRUCTURE_MSG)
@@ -632,9 +632,9 @@ class TestSuite2point0(unittest.TestCase):
         if glymur.version.openjpeg_version_tuple[0] < 2:
             with self.assertWarns(UserWarning):
                 # Incorrect warning issued about tile parts.
-                Jp2k(jfile).read()
+                Jp2k(jfile)[:]
         else:
-            Jp2k(jfile).read()
+            Jp2k(jfile)[:]
         self.assertTrue(True)
 
 

From c15fe52f82e11d83264068edd55ab93daf2bf0ad Mon Sep 17 00:00:00 2001
From: jevans <john.g.evans.ne@gmail.com>
Date: Wed, 12 Nov 2014 20:53:13 -0500
Subject: [PATCH 03/23] progress

---
 glymur/test/test_opj_suite_neg.py | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/glymur/test/test_opj_suite_neg.py b/glymur/test/test_opj_suite_neg.py
index 058be42..440ebaa 100644
--- a/glymur/test/test_opj_suite_neg.py
+++ b/glymur/test/test_opj_suite_neg.py
@@ -121,7 +121,7 @@ class TestSuiteNegative(unittest.TestCase):
     def test_precinct_size_not_p2(self):
         """precinct sizes should be powers of two."""
         ifile = Jp2k(self.j2kfile)
-        data = ifile.read(rlevel=2)
+        data = ifile[::4, ::4]
         with tempfile.NamedTemporaryFile(suffix='.jp2') as tfile:
             ofile = Jp2k(tfile.name, 'wb')
             with self.assertRaises(IOError):
@@ -131,7 +131,7 @@ class TestSuiteNegative(unittest.TestCase):
     def test_cblk_size_not_power_of_two(self):
         """code block sizes should be powers of two."""
         ifile = Jp2k(self.j2kfile)
-        data = ifile.read(rlevel=2)
+        data = ifile[::4, ::4]
         with tempfile.NamedTemporaryFile(suffix='.jp2') as tfile:
             ofile = Jp2k(tfile.name, 'wb')
             with self.assertRaises(IOError):
@@ -141,7 +141,7 @@ class TestSuiteNegative(unittest.TestCase):
     def test_cblk_size_precinct_size(self):
         """code block sizes should never exceed half that of precinct size."""
         ifile = Jp2k(self.j2kfile)
-        data = ifile.read(rlevel=2)
+        data = ifile[::4, ::4]
         with tempfile.NamedTemporaryFile(suffix='.jp2') as tfile:
             ofile = Jp2k(tfile.name, 'wb')
             with self.assertRaises(IOError):

From 82a9edae6246c2703b12887f85af01e606039de6 Mon Sep 17 00:00:00 2001
From: jevans <john.g.evans.ne@gmail.com>
Date: Wed, 12 Nov 2014 21:09:09 -0500
Subject: [PATCH 04/23] progress

---
 glymur/jp2k.py           | 4 ++--
 glymur/test/test_jp2k.py | 2 +-
 2 files changed, 3 insertions(+), 3 deletions(-)

diff --git a/glymur/jp2k.py b/glymur/jp2k.py
index 25efacd..a33d466 100644
--- a/glymur/jp2k.py
+++ b/glymur/jp2k.py
@@ -966,7 +966,7 @@ class Jp2k(Jp2kBox):
                 numrows if rows.stop is None else rows.stop,
                 numcols if cols.stop is None else cols.stop
                 )
-        data = self.read(area=area, rlevel=rlevel)
+        data = self._read(area=area, rlevel=rlevel)
         if len(pargs) == 2:
             return data
 
@@ -974,7 +974,7 @@ class Jp2k(Jp2kBox):
         return data[:, :, bands]
 
 
-    def _read(self):
+    def _read(self, **kwargs):
         """Read a JPEG 2000 image.
 
         Returns
diff --git a/glymur/test/test_jp2k.py b/glymur/test/test_jp2k.py
index 5e28db0..dda8161 100644
--- a/glymur/test/test_jp2k.py
+++ b/glymur/test/test_jp2k.py
@@ -1379,7 +1379,7 @@ class TestJp2kOpjDataRoot(unittest.TestCase):
 
         # Should be able to manually reconstruct the RGB image from the palette
         # and indices.
-        palette = j.box[2].box[1].palette
+        palette = jp2.box[2].box[1].palette
         rgb_from_idx = np.zeros(rgb.shape, dtype=np.uint8)
         for r in np.arange(rgb.shape[0]):
             for c in np.arange(rgb.shape[1]):

From 4f2a896eff2a0707b494fb8db95fa09b1be9dd19 Mon Sep 17 00:00:00 2001
From: jevans <john.g.evans.ne@gmail.com>
Date: Thu, 13 Nov 2014 13:39:36 -0500
Subject: [PATCH 05/23] ignore_pclr_cmap_cdef is now a property

---
 glymur/jp2k.py                    | 49 ++++++++++++++++++-------------
 glymur/test/test_jp2k.py          |  9 ++++--
 glymur/test/test_opj_suite_2p1.py |  4 +--
 glymur/test/test_printing.py      |  2 +-
 4 files changed, 37 insertions(+), 27 deletions(-)

diff --git a/glymur/jp2k.py b/glymur/jp2k.py
index a33d466..f7271dd 100644
--- a/glymur/jp2k.py
+++ b/glymur/jp2k.py
@@ -60,6 +60,11 @@ class Jp2k(Jp2kBox):
         List of top-level boxes in the file.  Each box may in turn contain
         its own list of boxes.  Will be empty if the file consists only of a
         raw codestream.
+    shape : tuple
+        Size of the image.
+    ignore_pclr_cmap_cdef : bool
+        Whether or not to ignore the pclr, cmap, or cdef boxes during any
+        color transformation.  Defaults to False.
 
     Examples
     --------
@@ -95,11 +100,20 @@ class Jp2k(Jp2kBox):
         self._codec_format = None
         self._colorspace = None
         self._shape = None
+        self._ignore_pclr_cmap_cdef = False
 
         # Parse the file for JP2/JPX contents only if we are reading it.
         if mode == 'rb':
             self.parse()
 
+    @property
+    def ignore_pclr_cmap_cdef(self):
+        return self._ignore_pclr_cmap_cdef
+
+    @ignore_pclr_cmap_cdef.setter
+    def ignore_pclr_cmap_cdef(self, ignore_pclr_cmap_cdef):
+        self._ignore_pclr_cmap_cdef = ignore_pclr_cmap_cdef
+
     @property
     def shape(self):
         if self._shape is not None:
@@ -1009,9 +1023,6 @@ class Jp2k(Jp2kBox):
             (first_row, first_col, last_row, last_col)
         tile : int, optional
             Number of tile to decode.
-        ignore_pclr_cmap_cdef : bool
-            Whether or not to ignore the pclr, cmap, or cdef boxes during any
-            color transformation.  Defaults to False.
         verbose : bool, optional
             Print informational messages produced by the OpenJPEG library.
 
@@ -1025,6 +1036,8 @@ class Jp2k(Jp2kBox):
         IOError
             If the image has differing subsample factors.
         """
+        if 'ignore_pclr_cmap_cdef' in kwargs:
+            self.ignore_pclr_cmap_cdef = kwargs['ignore_pclr_cmap_cdef']
         warnings.warn("Use array-style slicing instead.", DeprecationWarning)
         if version.openjpeg_version_tuple[0] < 2:
             img = self._read_openjpeg(**kwargs)
@@ -1044,8 +1057,7 @@ class Jp2k(Jp2kBox):
             msg += "the read_bands method instead."
             raise RuntimeError(msg)
 
-    def _read_openjpeg(self, rlevel=0, ignore_pclr_cmap_cdef=False,
-                       verbose=False, area=None):
+    def _read_openjpeg(self, rlevel=0, verbose=False, area=None):
         """Read a JPEG 2000 image using libopenjpeg.
 
         Parameters
@@ -1053,9 +1065,6 @@ class Jp2k(Jp2kBox):
         rlevel : int, optional
             Factor by which to rlevel output resolution.  Use -1 to get the
             lowest resolution thumbnail.
-        ignore_pclr_cmap_cdef : bool
-            Whether or not to ignore the pclr, cmap, or cdef boxes during any
-            color transformation.  Defaults to False.
         verbose : bool, optional
             Print informational messages produced by the OpenJPEG library.
         area : tuple, optional
@@ -1074,7 +1083,7 @@ class Jp2k(Jp2kBox):
         """
         self._subsampling_sanity_check()
 
-        self._populate_dparams(rlevel, ignore_pclr_cmap_cdef)
+        self._populate_dparams(rlevel)
 
         with ExitStack() as stack:
             try:
@@ -1127,8 +1136,7 @@ class Jp2k(Jp2kBox):
 
         return data
 
-    def _read_openjp2(self, rlevel=0, layer=0, area=None, tile=None,
-                      verbose=False, ignore_pclr_cmap_cdef=False):
+    def _read_openjp2(self, rlevel=0, layer=0, area=None, tile=None, verbose=False):
         """Read a JPEG 2000 image using libopenjp2.
 
         Parameters
@@ -1158,8 +1166,7 @@ class Jp2k(Jp2kBox):
         """
         self._subsampling_sanity_check()
 
-        self._populate_dparams(rlevel, ignore_pclr_cmap_cdef,
-                               layer=layer, tile=tile, area=area)
+        self._populate_dparams(rlevel, layer=layer, tile=tile, area=area)
 
         with ExitStack() as stack:
             if re.match("2.1", version.openjpeg_version):
@@ -1203,8 +1210,7 @@ class Jp2k(Jp2kBox):
 
         return img_array
 
-    def _populate_dparams(self, rlevel, ignore_pclr_cmap_cdef, tile=None,
-                          layer=None, area=None):
+    def _populate_dparams(self, rlevel, tile=None, layer=None, area=None):
         """Populate decompression structure with appropriate input parameters.
 
         Parameters
@@ -1218,9 +1224,6 @@ class Jp2k(Jp2kBox):
             (first_row, first_col, last_row, last_col)
         tile : int
             Number of tile to decode.
-        ignore_pclr_cmap_cdef : bool
-            Whether or not to ignore the pclr, cmap, or cdef boxes during any
-            color transformation.  Defaults to False.
         """
         if opj2.OPENJP2 is not None:
             dparam = opj2.set_default_decoder_parameters()
@@ -1233,6 +1236,10 @@ class Jp2k(Jp2kBox):
         infile += b'0' * nelts
         dparam.infile = infile
 
+        if self.ignore_pclr_cmap_cdef:
+            # Return raw codestream components.
+            dparam.flags |= 1
+
         dparam.decod_format = self._codec_format
 
         if layer is not None:
@@ -1267,7 +1274,7 @@ class Jp2k(Jp2kBox):
             dparam.tile_index = tile
             dparam.nb_tile_to_decode = 1
 
-        if ignore_pclr_cmap_cdef is True:
+        if self.ignore_pclr_cmap_cdef:
             # Return raw codestream components.
             dparam.flags |= 1
 
@@ -1319,8 +1326,8 @@ class Jp2k(Jp2kBox):
                                "OpenJPEG installed before using this "
                                "functionality.")
 
-        self._populate_dparams(rlevel, ignore_pclr_cmap_cdef,
-                               layer=layer, tile=tile, area=area)
+        self.ignore_pclr_cmap_cdef = ignore_pclr_cmap_cdef
+        self._populate_dparams(rlevel, layer=layer, tile=tile, area=area)
 
         with ExitStack() as stack:
             if re.match("2.1", version.openjpeg_version):
diff --git a/glymur/test/test_jp2k.py b/glymur/test/test_jp2k.py
index dda8161..f615cc4 100644
--- a/glymur/test/test_jp2k.py
+++ b/glymur/test/test_jp2k.py
@@ -548,7 +548,8 @@ class TestJp2k(unittest.TestCase):
         """Indices for pclr jpxfile if no color transform"""
         j = Jp2k(self.jpxfile)
         rgb = j[:]
-        idx = j.read(ignore_pclr_cmap_cdef=True)
+        j.ignore_pclr_cmap_cdef = True
+        idx = j[:]
         nr, nc = 1024, 1024
         self.assertEqual(rgb.shape, (nr, nc, 3))
         self.assertEqual(idx.shape, (nr, nc))
@@ -1373,7 +1374,8 @@ class TestJp2kOpjDataRoot(unittest.TestCase):
         with self.assertWarns(UserWarning):
             jp2 = Jp2k(filename)
         rgb = jp2[:]
-        idx = jp2.read(ignore_pclr_cmap_cdef=True)
+        jp2.ignore_pclr_cmap_cdef = True
+        idx = jp2[:]
         self.assertEqual(rgb.shape, (512, 768, 3))
         self.assertEqual(idx.shape, (512, 768))
 
@@ -1407,7 +1409,8 @@ class TestJp2kOpjDataRoot(unittest.TestCase):
             # The file has a bad compatibility list entry.  Not important here.
             j = Jp2k(filename)
         ycbcr = j[:]
-        crcby = j.read(ignore_pclr_cmap_cdef=True)
+        j.ignore_pclr_cmap_cdef = True
+        crcby = j[:]
 
         expected = np.zeros(ycbcr.shape, ycbcr.dtype)
         for k in range(crcby.shape[2]):
diff --git a/glymur/test/test_opj_suite_2p1.py b/glymur/test/test_opj_suite_2p1.py
index addc48b..b151842 100644
--- a/glymur/test/test_opj_suite_2p1.py
+++ b/glymur/test/test_opj_suite_2p1.py
@@ -134,7 +134,7 @@ class TestSuite2point1(unittest.TestCase):
         jfile = opj_data_file('input/conformance/p1_04.j2k')
         jp2k = Jp2k(jfile)
         tdata = jp2k.read(tile=63, rlevel=2)  # last tile
-        odata = jp2k.read(rlevel=2)
+        odata = jp2k[::4, ::4]
         np.testing.assert_array_equal(tdata, odata[224:256, 224:256])
 
     def test_NR_DEC_p1_04_j2k_59_decode(self):
@@ -148,7 +148,7 @@ class TestSuite2point1(unittest.TestCase):
         jfile = opj_data_file('input/conformance/p1_04.j2k')
         jp2k = Jp2k(jfile)
         tdata = jp2k.read(tile=12, rlevel=1)  # 2nd row, 5th column
-        odata = jp2k.read(rlevel=1)
+        odata = jp2k[::2, ::2]
         np.testing.assert_array_equal(tdata, odata[64:128, 256:320])
 
     @unittest.skipIf(WARNING_INFRASTRUCTURE_ISSUE, WARNING_INFRASTRUCTURE_MSG)
diff --git a/glymur/test/test_printing.py b/glymur/test/test_printing.py
index 7a5f9b9..5c09c81 100644
--- a/glymur/test/test_printing.py
+++ b/glymur/test/test_printing.py
@@ -111,7 +111,7 @@ class TestPrinting(unittest.TestCase):
         """verify printing of asoc, label boxes"""
         # Construct a fake file with an asoc and a label box, as
         # OpenJPEG doesn't have such a file.
-        data = glymur.Jp2k(self.jp2file).read(rlevel=1)
+        data = glymur.Jp2k(self.jp2file)[::2, ::2]
         with tempfile.NamedTemporaryFile(suffix='.jp2') as tfile:
             j = glymur.Jp2k(tfile.name, 'wb')
             j.write(data)

From 4f1c34991fc4de349495280d8af51f5cdfa2c15c Mon Sep 17 00:00:00 2001
From: jevans <john.g.evans.ne@gmail.com>
Date: Mon, 17 Nov 2014 07:33:43 -0500
Subject: [PATCH 06/23] replacing more uses of read function with array-style
 slicing

---
 glymur/jp2k.py                    |  4 +-
 glymur/test/test_opj_suite_2p1.py | 96 +++++++++++++++----------------
 2 files changed, 50 insertions(+), 50 deletions(-)

diff --git a/glymur/jp2k.py b/glymur/jp2k.py
index f7271dd..a45f9e2 100644
--- a/glymur/jp2k.py
+++ b/glymur/jp2k.py
@@ -894,7 +894,7 @@ class Jp2k(Jp2kBox):
             # This retrieves a single row.
             row = pargs
             area = (row, 0, row + 1, numcols)
-            return self.read(area=area).squeeze()
+            return self._read(area=area).squeeze()
 
         if pargs is Ellipsis:
             # Case of jp2[...]
@@ -903,7 +903,7 @@ class Jp2k(Jp2kBox):
         if isinstance(pargs, slice):
             if pargs.start is None and pargs.stop is None and pargs.step is None:
                 # Case of jp2[:]
-                return self.read()
+                return self._read()
 
             # Corner case of jp2[x] where x is a slice object with non-null
             # members.  Just augment it with an ellipsis and let the code 
diff --git a/glymur/test/test_opj_suite_2p1.py b/glymur/test/test_opj_suite_2p1.py
index b151842..0fec986 100644
--- a/glymur/test/test_opj_suite_2p1.py
+++ b/glymur/test/test_opj_suite_2p1.py
@@ -61,27 +61,27 @@ class TestSuite2point1(unittest.TestCase):
         with self.assertWarns(UserWarning):
             # brand is 'jp2 ', but has any icc profile.
             jp2 = Jp2k(jfile)
-        jp2.read()
+        jp2[:]
         self.assertTrue(True)
 
     def test_NR_DEC_kodak_2layers_lrcp_j2c_31_decode(self):
         jfile = opj_data_file('input/nonregression/kodak_2layers_lrcp.j2c')
-        Jp2k(jfile).read()
+        Jp2k(jfile)[:]
         self.assertTrue(True)
 
     def test_NR_DEC_kodak_2layers_lrcp_j2c_32_decode(self):
         jfile = opj_data_file('input/nonregression/kodak_2layers_lrcp.j2c')
-        Jp2k(jfile).read(layer=2)
+        Jp2k(jfile)[::4, ::4]
         self.assertTrue(True)
 
     def test_NR_DEC_issue104_jpxstream_jp2_33_decode(self):
         jfile = opj_data_file('input/nonregression/issue104_jpxstream.jp2')
-        Jp2k(jfile).read()
+        Jp2k(jfile)[:]
         self.assertTrue(True)
 
     def test_NR_DEC_mem_b2b86b74_2753_jp2_35_decode(self):
         jfile = opj_data_file('input/nonregression/mem-b2b86b74-2753.jp2')
-        Jp2k(jfile).read()
+        Jp2k(jfile)[:]
         self.assertTrue(True)
 
     @unittest.skipIf(WARNING_INFRASTRUCTURE_ISSUE, WARNING_INFRASTRUCTURE_MSG)
@@ -92,7 +92,7 @@ class TestSuite2point1(unittest.TestCase):
             # Invalid number of resolutions.
             j = Jp2k(jfile)
             with self.assertRaises(IOError):
-                j.read()
+                j[:]
 
     @unittest.skipIf(WARNING_INFRASTRUCTURE_ISSUE, WARNING_INFRASTRUCTURE_MSG)
     def test_NR_DEC_gdal_fuzzer_check_number_of_tiles_jp2_38_decode(self):
@@ -102,7 +102,7 @@ class TestSuite2point1(unittest.TestCase):
             # Invalid number of tiles.
             j = Jp2k(jfile)
             with self.assertRaises(IOError):
-                j.read()
+                j[:]
 
     @unittest.skipIf(WARNING_INFRASTRUCTURE_ISSUE, WARNING_INFRASTRUCTURE_MSG)
     def test_NR_DEC_gdal_fuzzer_check_comp_dx_dy_jp2_39_decode(self):
@@ -111,23 +111,23 @@ class TestSuite2point1(unittest.TestCase):
         with self.assertWarns(UserWarning):
             # Invalid subsampling value
             with self.assertRaises(IOError):
-                Jp2k(jfile).read()
+                Jp2k(jfile)[:]
 
     def test_NR_DEC_file_409752_jp2_40_decode(self):
         jfile = opj_data_file('input/nonregression/file409752.jp2')
         with self.assertRaises(RuntimeError):
-            Jp2k(jfile).read()
+            Jp2k(jfile)[:]
 
     def test_NR_DEC_issue206_image_000_jp2_42_decode(self):
         jfile = opj_data_file('input/nonregression/issue206_image-000.jp2')
-        Jp2k(jfile).read()
+        Jp2k(jfile)[:]
         self.assertTrue(True)
 
     def test_NR_DEC_p1_04_j2k_57_decode(self):
         jfile = opj_data_file('input/conformance/p1_04.j2k')
         jp2k = Jp2k(jfile)
         tdata = jp2k.read(tile=63)  # last tile
-        odata = jp2k.read()
+        odata = jp2k[:]
         np.testing.assert_array_equal(tdata, odata[896:1024, 896:1024])
 
     def test_NR_DEC_p1_04_j2k_58_decode(self):
@@ -141,7 +141,7 @@ class TestSuite2point1(unittest.TestCase):
         jfile = opj_data_file('input/conformance/p1_04.j2k')
         jp2k = Jp2k(jfile)
         tdata = jp2k.read(tile=12)  # 2nd row, 5th column
-        odata = jp2k.read()
+        odata = jp2k[:]
         np.testing.assert_array_equal(tdata, odata[128:256, 512:640])
 
     def test_NR_DEC_p1_04_j2k_60_decode(self):
@@ -161,7 +161,7 @@ class TestSuite2point1(unittest.TestCase):
             # Invalid component number.
             j = Jp2k(jfile)
             with self.assertRaises(IOError):
-                j.read()
+                j[:]
 
 @unittest.skipIf(OPJ_DATA_ROOT is None,
                  "OPJ_DATA_ROOT environment variable not set")
@@ -179,164 +179,164 @@ class TestReadArea(unittest.TestCase):
 
         jfile = opj_data_file('input/conformance/p1_04.j2k')
         self.j2k = Jp2k(jfile)
-        self.j2k_data = self.j2k.read()
-        self.j2k_half_data = self.j2k.read(rlevel=1)
-        self.j2k_quarter_data = self.j2k.read(rlevel=2)
+        self.j2k_data = self.j2k[:]
+        self.j2k_half_data = self.j2k[::2, ::2]
+        self.j2k_quarter_data = self.j2k[::4, ::4]
 
         jfile = opj_data_file('input/conformance/p1_06.j2k')
         self.j2k_p1_06 = Jp2k(jfile)
 
     def test_NR_DEC_p1_04_j2k_43_decode(self):
-        actual = self.j2k.read(area=(0, 0, 1024, 1024))
+        actual = self.j2k[:1024, :1024]
         expected = self.j2k_data
         np.testing.assert_array_equal(actual, expected)
 
     def test_NR_DEC_p1_04_j2k_44_decode(self):
-        actual = self.j2k.read(area=(640, 512, 768, 640))
+        actual = self.j2k[640:768, 512:640]
         expected = self.j2k_data[640:768, 512:640]
         np.testing.assert_array_equal(actual, expected)
 
     def test_NR_DEC_p1_04_j2k_45_decode(self):
-        actual = self.j2k.read(area=(896, 896, 1024, 1024))
+        actual = self.j2k[896:1024, 896:1024]
         expected = self.j2k_data[896:1024, 896:1024]
         np.testing.assert_array_equal(actual, expected)
 
     def test_NR_DEC_p1_04_j2k_46_decode(self):
-        actual = self.j2k.read(area=(500, 100, 800, 300))
+        actual = self.j2k[500:800, 100:300]
         expected = self.j2k_data[500:800, 100:300]
         np.testing.assert_array_equal(actual, expected)
 
     def test_NR_DEC_p1_04_j2k_47_decode(self):
-        actual = self.j2k.read(area=(520, 260, 600, 360))
+        actual = self.j2k[520:600, 260:360]
         expected = self.j2k_data[520:600, 260:360]
         np.testing.assert_array_equal(actual, expected)
 
     def test_NR_DEC_p1_04_j2k_48_decode(self):
-        actual = self.j2k.read(area=(520, 260, 660, 360))
+        actual = self.j2k[520:660, 260:360]
         expected = self.j2k_data[520:660, 260:360]
         np.testing.assert_array_equal(actual, expected)
 
     def test_NR_DEC_p1_04_j2k_49_decode(self):
-        actual = self.j2k.read(area=(520, 360, 600, 400))
+        actual = self.j2k[520:600, 360:400]
         expected = self.j2k_data[520:600, 360:400]
         np.testing.assert_array_equal(actual, expected)
 
     def test_NR_DEC_p1_04_j2k_50_decode(self):
-        actual = self.j2k.read(area=(0, 0, 1024, 1024), rlevel=2)
+        actual = self.j2k[:1024:4, :1024:4]
         expected = self.j2k_quarter_data
         np.testing.assert_array_equal(actual, expected)
 
     def test_NR_DEC_p1_04_j2k_51_decode(self):
-        actual = self.j2k.read(area=(640, 512, 768, 640), rlevel=2)
+        actual = self.j2k[640:768:4, 512:640:4]
         expected = self.j2k_quarter_data[160:192, 128:160]
         np.testing.assert_array_equal(actual, expected)
 
     def test_NR_DEC_p1_04_j2k_52_decode(self):
-        actual = self.j2k.read(area=(896, 896, 1024, 1024), rlevel=2)
+        actual = self.j2k[896:1024:4, 896:1024:4]
         expected = self.j2k_quarter_data[224:352, 224:352]
         np.testing.assert_array_equal(actual, expected)
 
     def test_NR_DEC_p1_04_j2k_53_decode(self):
-        actual = self.j2k.read(area=(500, 100, 800, 300), rlevel=2)
+        actual = self.j2k[500:800:4, 100:300:4]
         expected = self.j2k_quarter_data[125:200, 25:75]
         np.testing.assert_array_equal(actual, expected)
 
     def test_NR_DEC_p1_04_j2k_54_decode(self):
-        actual = self.j2k.read(area=(520, 260, 600, 360), rlevel=2)
+        actual = self.j2k[520:600:4, 260:360:4]
         expected = self.j2k_quarter_data[130:150, 65:90]
         np.testing.assert_array_equal(actual, expected)
 
     def test_NR_DEC_p1_04_j2k_55_decode(self):
-        actual = self.j2k.read(area=(520, 260, 660, 360), rlevel=2)
+        actual = self.j2k[520:660:4, 260:360:4]
         expected = self.j2k_quarter_data[130:165, 65:90]
         np.testing.assert_array_equal(actual, expected)
 
     def test_NR_DEC_p1_04_j2k_56_decode(self):
-        actual = self.j2k.read(area=(520, 360, 600, 400), rlevel=2)
+        actual = self.j2k[520:600:4, 360:400:4]
         expected = self.j2k_quarter_data[130:150, 90:100]
         np.testing.assert_array_equal(actual, expected)
 
     def test_NR_DEC_p1_06_j2k_70_decode(self):
-        actual = self.j2k_p1_06.read(area=(9, 9, 12, 12), rlevel=1)
+        actual = self.j2k_p1_06[9:12:2, 9:12:2]
         self.assertEqual(actual.shape, (1, 1, 3))
 
     def test_NR_DEC_p1_06_j2k_71_decode(self):
-        actual = self.j2k_p1_06.read(area=(10, 4, 12, 10), rlevel=1)
+        actual = self.j2k_p1_06[10:12:2, 4:10:2]
         self.assertEqual(actual.shape, (1, 3, 3))
 
     def test_NR_DEC_p1_06_j2k_72_decode(self):
-        ssdata = self.j2k_p1_06.read(area=(3, 3, 9, 9), rlevel=1)
+        ssdata = self.j2k_p1_06[3:9:2, 3:9:2]
         self.assertEqual(ssdata.shape, (3, 3, 3))
 
     def test_NR_DEC_p1_06_j2k_73_decode(self):
-        ssdata = self.j2k_p1_06.read(area=(4, 4, 7, 7), rlevel=1)
+        ssdata = self.j2k_p1_06[4:7:2, 4:7:2]
         self.assertEqual(ssdata.shape, (2, 2, 3))
 
     def test_NR_DEC_p1_06_j2k_74_decode(self):
-        ssdata = self.j2k_p1_06.read(area=(4, 4, 5, 5), rlevel=1)
+        ssdata = self.j2k_p1_06[4:5:2, 4:5:2]
         self.assertEqual(ssdata.shape, (1, 1, 3))
 
     def test_NR_DEC_p1_06_j2k_75_decode(self):
         # Image size would be 0 x 0.
         with self.assertRaises((IOError, OSError)):
-            self.j2k_p1_06.read(area=(9, 9, 12, 12), rlevel=2)
+            self.j2k_p1_06[9:12:4, 9:12:4]
 
     def test_NR_DEC_p0_04_j2k_85_decode(self):
-        actual = self.j2k.read(area=(0, 0, 256, 256))
+        actual = self.j2k[:256, :256]
         expected = self.j2k_data[:256, :256]
         np.testing.assert_array_equal(actual, expected)
 
     def test_NR_DEC_p0_04_j2k_86_decode(self):
-        actual = self.j2k.read(area=(0, 128, 128, 256))
+        actual = self.j2k[:128, 128:256]
         expected = self.j2k_data[:128, 128:256]
         np.testing.assert_array_equal(actual, expected)
 
     def test_NR_DEC_p0_04_j2k_87_decode(self):
-        actual = self.j2k.read(area=(10, 50, 200, 120))
+        actual = self.j2k[10:200, 50:120]
         expected = self.j2k_data[10:200, 50:120]
         np.testing.assert_array_equal(actual, expected)
 
     def test_NR_DEC_p0_04_j2k_88_decode(self):
-        actual = self.j2k.read(area=(150, 10, 210, 190))
+        actual = self.j2k[150:210, 10:190]
         expected = self.j2k_data[150:210, 10:190]
         np.testing.assert_array_equal(actual, expected)
 
     def test_NR_DEC_p0_04_j2k_89_decode(self):
-        actual = self.j2k.read(area=(80, 100, 150, 200))
+        actual = self.j2k[80:150, 100:200]
         expected = self.j2k_data[80:150, 100:200]
         np.testing.assert_array_equal(actual, expected)
 
     def test_NR_DEC_p0_04_j2k_90_decode(self):
-        actual = self.j2k.read(area=(20, 150, 50, 200))
+        actual = self.j2k[20:50, 150:200]
         expected = self.j2k_data[20:50, 150:200]
         np.testing.assert_array_equal(actual, expected)
 
     def test_NR_DEC_p0_04_j2k_91_decode(self):
-        actual = self.j2k.read(area=(0, 0, 256, 256), rlevel=2)
+        actual = self.j2k[:256:4, :256:4]
         expected = self.j2k_quarter_data[0:64, 0:64]
         np.testing.assert_array_equal(actual, expected)
 
     def test_NR_DEC_p0_04_j2k_92_decode(self):
-        actual = self.j2k.read(area=(0, 128, 128, 256), rlevel=2)
+        actual = self.j2k[:128:4, 128:256:4]
         expected = self.j2k_quarter_data[:32, 32:64]
         np.testing.assert_array_equal(actual, expected)
 
     def test_NR_DEC_p0_04_j2k_93_decode(self):
-        actual = self.j2k.read(area=(10, 50, 200, 120), rlevel=2)
+        actual = self.j2k[10:200:4, 50:120:4]
         expected = self.j2k_quarter_data[3:50, 13:30]
         np.testing.assert_array_equal(actual, expected)
 
     def test_NR_DEC_p0_04_j2k_94_decode(self):
-        actual = self.j2k.read(area=(150, 10, 210, 190), rlevel=2)
+        actual = self.j2k[150:210:4, 10:190:4]
         expected = self.j2k_quarter_data[38:53, 3:48]
         np.testing.assert_array_equal(actual, expected)
 
     def test_NR_DEC_p0_04_j2k_95_decode(self):
-        actual = self.j2k.read(area=(80, 100, 150, 200), rlevel=2)
+        actual = self.j2k[80:150:4, 100:200:4]
         expected = self.j2k_quarter_data[20:38, 25:50]
         np.testing.assert_array_equal(actual, expected)
 
     def test_NR_DEC_p0_04_j2k_96_decode(self):
-        actual = self.j2k.read(area=(20, 150, 50, 200), rlevel=2)
+        actual = self.j2k[20:50:4, 150:200:4]
         expected = self.j2k_quarter_data[5:13, 38:50]
         np.testing.assert_array_equal(actual, expected)

From 63d6a2f1e18e7d3adfbda0a14776e62c3c6a2753 Mon Sep 17 00:00:00 2001
From: jevans <john.g.evans.ne@gmail.com>
Date: Mon, 17 Nov 2014 18:17:47 -0500
Subject: [PATCH 07/23] progress

---
 glymur/test/test_opj_suite_2p1.py | 60 ++++++++++++++++++++++++++++---
 1 file changed, 56 insertions(+), 4 deletions(-)

diff --git a/glymur/test/test_opj_suite_2p1.py b/glymur/test/test_opj_suite_2p1.py
index 0fec986..12bffcf 100644
--- a/glymur/test/test_opj_suite_2p1.py
+++ b/glymur/test/test_opj_suite_2p1.py
@@ -30,6 +30,7 @@ suite.
 import re
 import sys
 import unittest
+import warnings
 
 import numpy as np
 
@@ -41,6 +42,24 @@ from .fixtures import WARNING_INFRASTRUCTURE_ISSUE, WARNING_INFRASTRUCTURE_MSG
 from .fixtures import mse, peak_tolerance, read_pgx, opj_data_file
 
 
+@unittest.skipIf(OPJ_DATA_ROOT is None,
+                 "OPJ_DATA_ROOT environment variable not set")
+@unittest.skipIf(re.match(r'''(1|2.0.0)''',
+                          glymur.version.openjpeg_version) is not None,
+                 "Only supported in 2.0.1 or higher")
+#class TestVersion0p7BackwardsCompatibility(unittest.TestSuite):
+class TestBlah(unittest.TestSuite):
+    """
+    Tests for backwards compatibility with version 0.7.
+    """
+
+    def test_blah_NR_DEC_p1_04_j2k_57_decode(self):
+        jfile = opj_data_file('input/conformance/p1_04.j2k')
+        jp2k = Jp2k(jfile)
+        tdata = jp2k.read(tile=63)  # last tile
+        odata = jp2k[:]
+        np.testing.assert_array_equal(tdata, odata[896:1024, 896:1024])
+
 @unittest.skipIf(OPJ_DATA_ROOT is None,
                  "OPJ_DATA_ROOT environment variable not set")
 @unittest.skipIf(re.match(r'''(1|2.0.0)''',
@@ -126,28 +145,61 @@ class TestSuite2point1(unittest.TestCase):
     def test_NR_DEC_p1_04_j2k_57_decode(self):
         jfile = opj_data_file('input/conformance/p1_04.j2k')
         jp2k = Jp2k(jfile)
-        tdata = jp2k.read(tile=63)  # last tile
+        tdata = jp2k[896:1024, 896:1024] # last tile
         odata = jp2k[:]
         np.testing.assert_array_equal(tdata, odata[896:1024, 896:1024])
 
+    def test_NR_DEC_p1_04_j2k_57_decode_0p7_backwards_compatibility(self):
+        """
+        0.7.x usage deprecated
+        """
+        jfile = opj_data_file('input/conformance/p1_04.j2k')
+        jp2k = Jp2k(jfile)
+        if sys.hexversion < 0x03000000:
+            with warnings.catch_warnings():
+                # Suppress a warning due to deprecated syntax
+                warnings.simplefilter("ignore")
+                tdata = jp2k.read(tile=63)  # last tile
+        else:
+            with self.assertWarns(DeprecationWarning):
+                tdata = jp2k.read(tile=63)  # last tile
+        odata = jp2k[:]
+        np.testing.assert_array_equal(tdata, odata[896:1024, 896:1024])
+
+    def test_NR_DEC_p1_04_j2k_58_decode_0p7_backwards_compatibility(self):
+        """
+        0.7.x usage deprecated
+        """
+        jfile = opj_data_file('input/conformance/p1_04.j2k')
+        jp2k = Jp2k(jfile)
+        if sys.hexversion < 0x03000000:
+            with warnings.catch_warnings():
+                # Suppress a warning due to deprecated syntax
+                tdata = jp2k.read(tile=63, rlevel=2)  # last tile
+        else:
+            with self.assertWarns(DeprecationWarning):
+                tdata = jp2k.read(tile=63, rlevel=2)  # last tile
+        odata = jp2k[::4, ::4]
+        np.testing.assert_array_equal(tdata, odata[224:256, 224:256])
+
     def test_NR_DEC_p1_04_j2k_58_decode(self):
         jfile = opj_data_file('input/conformance/p1_04.j2k')
         jp2k = Jp2k(jfile)
-        tdata = jp2k.read(tile=63, rlevel=2)  # last tile
+        tdata = jp2k[896:1024:4, 896:1024:4]  # last tile
         odata = jp2k[::4, ::4]
         np.testing.assert_array_equal(tdata, odata[224:256, 224:256])
 
     def test_NR_DEC_p1_04_j2k_59_decode(self):
         jfile = opj_data_file('input/conformance/p1_04.j2k')
         jp2k = Jp2k(jfile)
-        tdata = jp2k.read(tile=12)  # 2nd row, 5th column
+        tdata = jp2k[128:256, 512:640]  # 2nd row, 5th column
         odata = jp2k[:]
         np.testing.assert_array_equal(tdata, odata[128:256, 512:640])
 
     def test_NR_DEC_p1_04_j2k_60_decode(self):
         jfile = opj_data_file('input/conformance/p1_04.j2k')
         jp2k = Jp2k(jfile)
-        tdata = jp2k.read(tile=12, rlevel=1)  # 2nd row, 5th column
+        tdata = jp2k[128:256:2, 512:640:2]  # 2nd row, 5th column
         odata = jp2k[::2, ::2]
         np.testing.assert_array_equal(tdata, odata[64:128, 256:320])
 

From 2a3128e983c23422bc4f5c857f1c4c05b63061d6 Mon Sep 17 00:00:00 2001
From: jevans <john.g.evans.ne@gmail.com>
Date: Mon, 17 Nov 2014 22:27:52 -0500
Subject: [PATCH 08/23] subsumed test_opj_suite_2p1 ito test_opj_suite

---
 glymur/test/test_opj_suite.py     | 334 ++++++++++++++++++++++++-
 glymur/test/test_opj_suite_2p1.py | 394 ------------------------------
 2 files changed, 332 insertions(+), 396 deletions(-)
 delete mode 100644 glymur/test/test_opj_suite_2p1.py

diff --git a/glymur/test/test_opj_suite.py b/glymur/test/test_opj_suite.py
index a10185b..1dd4026 100644
--- a/glymur/test/test_opj_suite.py
+++ b/glymur/test/test_opj_suite.py
@@ -638,5 +638,335 @@ class TestSuite2point0(unittest.TestCase):
         self.assertTrue(True)
 
 
-if __name__ == "__main__":
-    unittest.main()
+@unittest.skipIf(OPJ_DATA_ROOT is None,
+                 "OPJ_DATA_ROOT environment variable not set")
+@unittest.skipIf(re.match(r'''(1|2.0.0)''',
+                          glymur.version.openjpeg_version) is not None,
+                 "Only supported in 2.0.1 or higher")
+class TestSuite2point1(unittest.TestCase):
+    """Runs tests introduced in version 2.0+ or that pass only in 2.0+"""
+
+    def setUp(self):
+        pass
+
+    def tearDown(self):
+        pass
+
+    @unittest.skipIf(WARNING_INFRASTRUCTURE_ISSUE, WARNING_INFRASTRUCTURE_MSG)
+    def test_NR_DEC_text_GBR_jp2_29_decode(self):
+        jfile = opj_data_file('input/nonregression/text_GBR.jp2')
+        with self.assertWarns(UserWarning):
+            # brand is 'jp2 ', but has any icc profile.
+            jp2 = Jp2k(jfile)
+        jp2[:]
+        self.assertTrue(True)
+
+    def test_NR_DEC_kodak_2layers_lrcp_j2c_31_decode(self):
+        jfile = opj_data_file('input/nonregression/kodak_2layers_lrcp.j2c')
+        Jp2k(jfile)[:]
+        self.assertTrue(True)
+
+    def test_NR_DEC_kodak_2layers_lrcp_j2c_32_decode(self):
+        jfile = opj_data_file('input/nonregression/kodak_2layers_lrcp.j2c')
+        Jp2k(jfile)[::4, ::4]
+        self.assertTrue(True)
+
+    def test_NR_DEC_issue104_jpxstream_jp2_33_decode(self):
+        jfile = opj_data_file('input/nonregression/issue104_jpxstream.jp2')
+        Jp2k(jfile)[:]
+        self.assertTrue(True)
+
+    def test_NR_DEC_mem_b2b86b74_2753_jp2_35_decode(self):
+        jfile = opj_data_file('input/nonregression/mem-b2b86b74-2753.jp2')
+        Jp2k(jfile)[:]
+        self.assertTrue(True)
+
+    @unittest.skipIf(WARNING_INFRASTRUCTURE_ISSUE, WARNING_INFRASTRUCTURE_MSG)
+    def test_NR_DEC_gdal_fuzzer_unchecked_num_resolutions_jp2_36_decode(self):
+        f = 'input/nonregression/gdal_fuzzer_unchecked_numresolutions.jp2'
+        jfile = opj_data_file(f)
+        with self.assertWarns(UserWarning):
+            # Invalid number of resolutions.
+            j = Jp2k(jfile)
+            with self.assertRaises(IOError):
+                j[:]
+
+    @unittest.skipIf(WARNING_INFRASTRUCTURE_ISSUE, WARNING_INFRASTRUCTURE_MSG)
+    def test_NR_DEC_gdal_fuzzer_check_number_of_tiles_jp2_38_decode(self):
+        relpath = 'input/nonregression/gdal_fuzzer_check_number_of_tiles.jp2'
+        jfile = opj_data_file(relpath)
+        with self.assertWarns(UserWarning):
+            # Invalid number of tiles.
+            j = Jp2k(jfile)
+            with self.assertRaises(IOError):
+                j[:]
+
+    @unittest.skipIf(WARNING_INFRASTRUCTURE_ISSUE, WARNING_INFRASTRUCTURE_MSG)
+    def test_NR_DEC_gdal_fuzzer_check_comp_dx_dy_jp2_39_decode(self):
+        relpath = 'input/nonregression/gdal_fuzzer_check_comp_dx_dy.jp2'
+        jfile = opj_data_file(relpath)
+        with self.assertWarns(UserWarning):
+            # Invalid subsampling value
+            with self.assertRaises(IOError):
+                Jp2k(jfile)[:]
+
+    def test_NR_DEC_file_409752_jp2_40_decode(self):
+        jfile = opj_data_file('input/nonregression/file409752.jp2')
+        with self.assertRaises(RuntimeError):
+            Jp2k(jfile)[:]
+
+    def test_NR_DEC_issue206_image_000_jp2_42_decode(self):
+        jfile = opj_data_file('input/nonregression/issue206_image-000.jp2')
+        Jp2k(jfile)[:]
+        self.assertTrue(True)
+
+    def test_NR_DEC_p1_04_j2k_57_decode(self):
+        jfile = opj_data_file('input/conformance/p1_04.j2k')
+        jp2k = Jp2k(jfile)
+        tdata = jp2k[896:1024, 896:1024] # last tile
+        odata = jp2k[:]
+        np.testing.assert_array_equal(tdata, odata[896:1024, 896:1024])
+
+    def test_NR_DEC_p1_04_j2k_57_decode_0p7_backwards_compatibility(self):
+        """
+        0.7.x usage deprecated
+        """
+        jfile = opj_data_file('input/conformance/p1_04.j2k')
+        jp2k = Jp2k(jfile)
+        if sys.hexversion < 0x03000000:
+            with warnings.catch_warnings():
+                # Suppress a warning due to deprecated syntax
+                warnings.simplefilter("ignore")
+                tdata = jp2k.read(tile=63)  # last tile
+        else:
+            with self.assertWarns(DeprecationWarning):
+                tdata = jp2k.read(tile=63)  # last tile
+        odata = jp2k[:]
+        np.testing.assert_array_equal(tdata, odata[896:1024, 896:1024])
+
+    def test_NR_DEC_p1_04_j2k_58_decode_0p7_backwards_compatibility(self):
+        """
+        0.7.x usage deprecated
+        """
+        jfile = opj_data_file('input/conformance/p1_04.j2k')
+        jp2k = Jp2k(jfile)
+        if sys.hexversion < 0x03000000:
+            with warnings.catch_warnings():
+                # Suppress a warning due to deprecated syntax
+                tdata = jp2k.read(tile=63, rlevel=2)  # last tile
+        else:
+            with self.assertWarns(DeprecationWarning):
+                tdata = jp2k.read(tile=63, rlevel=2)  # last tile
+        odata = jp2k[::4, ::4]
+        np.testing.assert_array_equal(tdata, odata[224:256, 224:256])
+
+    def test_NR_DEC_p1_04_j2k_58_decode(self):
+        jfile = opj_data_file('input/conformance/p1_04.j2k')
+        jp2k = Jp2k(jfile)
+        tdata = jp2k[896:1024:4, 896:1024:4]  # last tile
+        odata = jp2k[::4, ::4]
+        np.testing.assert_array_equal(tdata, odata[224:256, 224:256])
+
+    def test_NR_DEC_p1_04_j2k_59_decode(self):
+        jfile = opj_data_file('input/conformance/p1_04.j2k')
+        jp2k = Jp2k(jfile)
+        tdata = jp2k[128:256, 512:640]  # 2nd row, 5th column
+        odata = jp2k[:]
+        np.testing.assert_array_equal(tdata, odata[128:256, 512:640])
+
+    def test_NR_DEC_p1_04_j2k_60_decode(self):
+        jfile = opj_data_file('input/conformance/p1_04.j2k')
+        jp2k = Jp2k(jfile)
+        tdata = jp2k[128:256:2, 512:640:2]  # 2nd row, 5th column
+        odata = jp2k[::2, ::2]
+        np.testing.assert_array_equal(tdata, odata[64:128, 256:320])
+
+    @unittest.skipIf(WARNING_INFRASTRUCTURE_ISSUE, WARNING_INFRASTRUCTURE_MSG)
+    def test_NR_DEC_jp2_36_decode(self):
+        lst = ('input',
+               'nonregression',
+               'gdal_fuzzer_assert_in_opj_j2k_read_SQcd_SQcc.patch.jp2')
+        jfile = opj_data_file('/'.join(lst))
+        with self.assertWarns(UserWarning):
+            # Invalid component number.
+            j = Jp2k(jfile)
+            with self.assertRaises(IOError):
+                j[:]
+
+@unittest.skipIf(OPJ_DATA_ROOT is None,
+                 "OPJ_DATA_ROOT environment variable not set")
+@unittest.skipIf(re.match(r'''(1|2.0.0)''',
+                          glymur.version.openjpeg_version) is not None,
+                 "Only supported in 2.0.1 or higher")
+class TestReadArea(unittest.TestCase):
+    """
+    Runs tests introduced in version 2.0+ or that pass only in 2.0+
+    
+    Specifically for read method with area parameter.
+    """
+    @classmethod
+    def setUpClass(self):
+
+        jfile = opj_data_file('input/conformance/p1_04.j2k')
+        self.j2k = Jp2k(jfile)
+        self.j2k_data = self.j2k[:]
+        self.j2k_half_data = self.j2k[::2, ::2]
+        self.j2k_quarter_data = self.j2k[::4, ::4]
+
+        jfile = opj_data_file('input/conformance/p1_06.j2k')
+        self.j2k_p1_06 = Jp2k(jfile)
+
+    def test_NR_DEC_p1_04_j2k_43_decode(self):
+        actual = self.j2k[:1024, :1024]
+        expected = self.j2k_data
+        np.testing.assert_array_equal(actual, expected)
+
+    def test_NR_DEC_p1_04_j2k_44_decode(self):
+        actual = self.j2k[640:768, 512:640]
+        expected = self.j2k_data[640:768, 512:640]
+        np.testing.assert_array_equal(actual, expected)
+
+    def test_NR_DEC_p1_04_j2k_45_decode(self):
+        actual = self.j2k[896:1024, 896:1024]
+        expected = self.j2k_data[896:1024, 896:1024]
+        np.testing.assert_array_equal(actual, expected)
+
+    def test_NR_DEC_p1_04_j2k_46_decode(self):
+        actual = self.j2k[500:800, 100:300]
+        expected = self.j2k_data[500:800, 100:300]
+        np.testing.assert_array_equal(actual, expected)
+
+    def test_NR_DEC_p1_04_j2k_47_decode(self):
+        actual = self.j2k[520:600, 260:360]
+        expected = self.j2k_data[520:600, 260:360]
+        np.testing.assert_array_equal(actual, expected)
+
+    def test_NR_DEC_p1_04_j2k_48_decode(self):
+        actual = self.j2k[520:660, 260:360]
+        expected = self.j2k_data[520:660, 260:360]
+        np.testing.assert_array_equal(actual, expected)
+
+    def test_NR_DEC_p1_04_j2k_49_decode(self):
+        actual = self.j2k[520:600, 360:400]
+        expected = self.j2k_data[520:600, 360:400]
+        np.testing.assert_array_equal(actual, expected)
+
+    def test_NR_DEC_p1_04_j2k_50_decode(self):
+        actual = self.j2k[:1024:4, :1024:4]
+        expected = self.j2k_quarter_data
+        np.testing.assert_array_equal(actual, expected)
+
+    def test_NR_DEC_p1_04_j2k_51_decode(self):
+        actual = self.j2k[640:768:4, 512:640:4]
+        expected = self.j2k_quarter_data[160:192, 128:160]
+        np.testing.assert_array_equal(actual, expected)
+
+    def test_NR_DEC_p1_04_j2k_52_decode(self):
+        actual = self.j2k[896:1024:4, 896:1024:4]
+        expected = self.j2k_quarter_data[224:352, 224:352]
+        np.testing.assert_array_equal(actual, expected)
+
+    def test_NR_DEC_p1_04_j2k_53_decode(self):
+        actual = self.j2k[500:800:4, 100:300:4]
+        expected = self.j2k_quarter_data[125:200, 25:75]
+        np.testing.assert_array_equal(actual, expected)
+
+    def test_NR_DEC_p1_04_j2k_54_decode(self):
+        actual = self.j2k[520:600:4, 260:360:4]
+        expected = self.j2k_quarter_data[130:150, 65:90]
+        np.testing.assert_array_equal(actual, expected)
+
+    def test_NR_DEC_p1_04_j2k_55_decode(self):
+        actual = self.j2k[520:660:4, 260:360:4]
+        expected = self.j2k_quarter_data[130:165, 65:90]
+        np.testing.assert_array_equal(actual, expected)
+
+    def test_NR_DEC_p1_04_j2k_56_decode(self):
+        actual = self.j2k[520:600:4, 360:400:4]
+        expected = self.j2k_quarter_data[130:150, 90:100]
+        np.testing.assert_array_equal(actual, expected)
+
+    def test_NR_DEC_p1_06_j2k_70_decode(self):
+        actual = self.j2k_p1_06[9:12:2, 9:12:2]
+        self.assertEqual(actual.shape, (1, 1, 3))
+
+    def test_NR_DEC_p1_06_j2k_71_decode(self):
+        actual = self.j2k_p1_06[10:12:2, 4:10:2]
+        self.assertEqual(actual.shape, (1, 3, 3))
+
+    def test_NR_DEC_p1_06_j2k_72_decode(self):
+        ssdata = self.j2k_p1_06[3:9:2, 3:9:2]
+        self.assertEqual(ssdata.shape, (3, 3, 3))
+
+    def test_NR_DEC_p1_06_j2k_73_decode(self):
+        ssdata = self.j2k_p1_06[4:7:2, 4:7:2]
+        self.assertEqual(ssdata.shape, (2, 2, 3))
+
+    def test_NR_DEC_p1_06_j2k_74_decode(self):
+        ssdata = self.j2k_p1_06[4:5:2, 4:5:2]
+        self.assertEqual(ssdata.shape, (1, 1, 3))
+
+    def test_NR_DEC_p1_06_j2k_75_decode(self):
+        # Image size would be 0 x 0.
+        with self.assertRaises((IOError, OSError)):
+            self.j2k_p1_06[9:12:4, 9:12:4]
+
+    def test_NR_DEC_p0_04_j2k_85_decode(self):
+        actual = self.j2k[:256, :256]
+        expected = self.j2k_data[:256, :256]
+        np.testing.assert_array_equal(actual, expected)
+
+    def test_NR_DEC_p0_04_j2k_86_decode(self):
+        actual = self.j2k[:128, 128:256]
+        expected = self.j2k_data[:128, 128:256]
+        np.testing.assert_array_equal(actual, expected)
+
+    def test_NR_DEC_p0_04_j2k_87_decode(self):
+        actual = self.j2k[10:200, 50:120]
+        expected = self.j2k_data[10:200, 50:120]
+        np.testing.assert_array_equal(actual, expected)
+
+    def test_NR_DEC_p0_04_j2k_88_decode(self):
+        actual = self.j2k[150:210, 10:190]
+        expected = self.j2k_data[150:210, 10:190]
+        np.testing.assert_array_equal(actual, expected)
+
+    def test_NR_DEC_p0_04_j2k_89_decode(self):
+        actual = self.j2k[80:150, 100:200]
+        expected = self.j2k_data[80:150, 100:200]
+        np.testing.assert_array_equal(actual, expected)
+
+    def test_NR_DEC_p0_04_j2k_90_decode(self):
+        actual = self.j2k[20:50, 150:200]
+        expected = self.j2k_data[20:50, 150:200]
+        np.testing.assert_array_equal(actual, expected)
+
+    def test_NR_DEC_p0_04_j2k_91_decode(self):
+        actual = self.j2k[:256:4, :256:4]
+        expected = self.j2k_quarter_data[0:64, 0:64]
+        np.testing.assert_array_equal(actual, expected)
+
+    def test_NR_DEC_p0_04_j2k_92_decode(self):
+        actual = self.j2k[:128:4, 128:256:4]
+        expected = self.j2k_quarter_data[:32, 32:64]
+        np.testing.assert_array_equal(actual, expected)
+
+    def test_NR_DEC_p0_04_j2k_93_decode(self):
+        actual = self.j2k[10:200:4, 50:120:4]
+        expected = self.j2k_quarter_data[3:50, 13:30]
+        np.testing.assert_array_equal(actual, expected)
+
+    def test_NR_DEC_p0_04_j2k_94_decode(self):
+        actual = self.j2k[150:210:4, 10:190:4]
+        expected = self.j2k_quarter_data[38:53, 3:48]
+        np.testing.assert_array_equal(actual, expected)
+
+    def test_NR_DEC_p0_04_j2k_95_decode(self):
+        actual = self.j2k[80:150:4, 100:200:4]
+        expected = self.j2k_quarter_data[20:38, 25:50]
+        np.testing.assert_array_equal(actual, expected)
+
+    def test_NR_DEC_p0_04_j2k_96_decode(self):
+        actual = self.j2k[20:50:4, 150:200:4]
+        expected = self.j2k_quarter_data[5:13, 38:50]
+        np.testing.assert_array_equal(actual, expected)
diff --git a/glymur/test/test_opj_suite_2p1.py b/glymur/test/test_opj_suite_2p1.py
deleted file mode 100644
index 12bffcf..0000000
--- a/glymur/test/test_opj_suite_2p1.py
+++ /dev/null
@@ -1,394 +0,0 @@
-"""
-The tests defined here roughly correspond to what is in the OpenJPEG test
-suite.
-"""
-
-# Some test names correspond with openjpeg tests.  Long names are ok in this
-# case.
-# pylint: disable=C0103
-
-# All of these tests correspond to tests in openjpeg, so no docstring is really
-# needed.
-# pylint: disable=C0111
-
-# This module is very long, cannot be helped.
-# pylint: disable=C0302
-
-# unittest fools pylint with "too many public methods"
-# pylint: disable=R0904
-
-# 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
-
-# Many tests are pretty long and that can't be helped.
-# pylint:  disable=R0915
-
-# asserWarns introduced in python 3.2 (python2.7/pylint issue)
-# pylint: disable=E1101
-
-import re
-import sys
-import unittest
-import warnings
-
-import numpy as np
-
-from glymur import Jp2k
-import glymur
-
-from .fixtures import OPJ_DATA_ROOT
-from .fixtures import WARNING_INFRASTRUCTURE_ISSUE, WARNING_INFRASTRUCTURE_MSG
-from .fixtures import mse, peak_tolerance, read_pgx, opj_data_file
-
-
-@unittest.skipIf(OPJ_DATA_ROOT is None,
-                 "OPJ_DATA_ROOT environment variable not set")
-@unittest.skipIf(re.match(r'''(1|2.0.0)''',
-                          glymur.version.openjpeg_version) is not None,
-                 "Only supported in 2.0.1 or higher")
-#class TestVersion0p7BackwardsCompatibility(unittest.TestSuite):
-class TestBlah(unittest.TestSuite):
-    """
-    Tests for backwards compatibility with version 0.7.
-    """
-
-    def test_blah_NR_DEC_p1_04_j2k_57_decode(self):
-        jfile = opj_data_file('input/conformance/p1_04.j2k')
-        jp2k = Jp2k(jfile)
-        tdata = jp2k.read(tile=63)  # last tile
-        odata = jp2k[:]
-        np.testing.assert_array_equal(tdata, odata[896:1024, 896:1024])
-
-@unittest.skipIf(OPJ_DATA_ROOT is None,
-                 "OPJ_DATA_ROOT environment variable not set")
-@unittest.skipIf(re.match(r'''(1|2.0.0)''',
-                          glymur.version.openjpeg_version) is not None,
-                 "Only supported in 2.0.1 or higher")
-class TestSuite2point1(unittest.TestCase):
-    """Runs tests introduced in version 2.0+ or that pass only in 2.0+"""
-
-    def setUp(self):
-        pass
-
-    def tearDown(self):
-        pass
-
-    @unittest.skipIf(WARNING_INFRASTRUCTURE_ISSUE, WARNING_INFRASTRUCTURE_MSG)
-    def test_NR_DEC_text_GBR_jp2_29_decode(self):
-        jfile = opj_data_file('input/nonregression/text_GBR.jp2')
-        with self.assertWarns(UserWarning):
-            # brand is 'jp2 ', but has any icc profile.
-            jp2 = Jp2k(jfile)
-        jp2[:]
-        self.assertTrue(True)
-
-    def test_NR_DEC_kodak_2layers_lrcp_j2c_31_decode(self):
-        jfile = opj_data_file('input/nonregression/kodak_2layers_lrcp.j2c')
-        Jp2k(jfile)[:]
-        self.assertTrue(True)
-
-    def test_NR_DEC_kodak_2layers_lrcp_j2c_32_decode(self):
-        jfile = opj_data_file('input/nonregression/kodak_2layers_lrcp.j2c')
-        Jp2k(jfile)[::4, ::4]
-        self.assertTrue(True)
-
-    def test_NR_DEC_issue104_jpxstream_jp2_33_decode(self):
-        jfile = opj_data_file('input/nonregression/issue104_jpxstream.jp2')
-        Jp2k(jfile)[:]
-        self.assertTrue(True)
-
-    def test_NR_DEC_mem_b2b86b74_2753_jp2_35_decode(self):
-        jfile = opj_data_file('input/nonregression/mem-b2b86b74-2753.jp2')
-        Jp2k(jfile)[:]
-        self.assertTrue(True)
-
-    @unittest.skipIf(WARNING_INFRASTRUCTURE_ISSUE, WARNING_INFRASTRUCTURE_MSG)
-    def test_NR_DEC_gdal_fuzzer_unchecked_num_resolutions_jp2_36_decode(self):
-        f = 'input/nonregression/gdal_fuzzer_unchecked_numresolutions.jp2'
-        jfile = opj_data_file(f)
-        with self.assertWarns(UserWarning):
-            # Invalid number of resolutions.
-            j = Jp2k(jfile)
-            with self.assertRaises(IOError):
-                j[:]
-
-    @unittest.skipIf(WARNING_INFRASTRUCTURE_ISSUE, WARNING_INFRASTRUCTURE_MSG)
-    def test_NR_DEC_gdal_fuzzer_check_number_of_tiles_jp2_38_decode(self):
-        relpath = 'input/nonregression/gdal_fuzzer_check_number_of_tiles.jp2'
-        jfile = opj_data_file(relpath)
-        with self.assertWarns(UserWarning):
-            # Invalid number of tiles.
-            j = Jp2k(jfile)
-            with self.assertRaises(IOError):
-                j[:]
-
-    @unittest.skipIf(WARNING_INFRASTRUCTURE_ISSUE, WARNING_INFRASTRUCTURE_MSG)
-    def test_NR_DEC_gdal_fuzzer_check_comp_dx_dy_jp2_39_decode(self):
-        relpath = 'input/nonregression/gdal_fuzzer_check_comp_dx_dy.jp2'
-        jfile = opj_data_file(relpath)
-        with self.assertWarns(UserWarning):
-            # Invalid subsampling value
-            with self.assertRaises(IOError):
-                Jp2k(jfile)[:]
-
-    def test_NR_DEC_file_409752_jp2_40_decode(self):
-        jfile = opj_data_file('input/nonregression/file409752.jp2')
-        with self.assertRaises(RuntimeError):
-            Jp2k(jfile)[:]
-
-    def test_NR_DEC_issue206_image_000_jp2_42_decode(self):
-        jfile = opj_data_file('input/nonregression/issue206_image-000.jp2')
-        Jp2k(jfile)[:]
-        self.assertTrue(True)
-
-    def test_NR_DEC_p1_04_j2k_57_decode(self):
-        jfile = opj_data_file('input/conformance/p1_04.j2k')
-        jp2k = Jp2k(jfile)
-        tdata = jp2k[896:1024, 896:1024] # last tile
-        odata = jp2k[:]
-        np.testing.assert_array_equal(tdata, odata[896:1024, 896:1024])
-
-    def test_NR_DEC_p1_04_j2k_57_decode_0p7_backwards_compatibility(self):
-        """
-        0.7.x usage deprecated
-        """
-        jfile = opj_data_file('input/conformance/p1_04.j2k')
-        jp2k = Jp2k(jfile)
-        if sys.hexversion < 0x03000000:
-            with warnings.catch_warnings():
-                # Suppress a warning due to deprecated syntax
-                warnings.simplefilter("ignore")
-                tdata = jp2k.read(tile=63)  # last tile
-        else:
-            with self.assertWarns(DeprecationWarning):
-                tdata = jp2k.read(tile=63)  # last tile
-        odata = jp2k[:]
-        np.testing.assert_array_equal(tdata, odata[896:1024, 896:1024])
-
-    def test_NR_DEC_p1_04_j2k_58_decode_0p7_backwards_compatibility(self):
-        """
-        0.7.x usage deprecated
-        """
-        jfile = opj_data_file('input/conformance/p1_04.j2k')
-        jp2k = Jp2k(jfile)
-        if sys.hexversion < 0x03000000:
-            with warnings.catch_warnings():
-                # Suppress a warning due to deprecated syntax
-                tdata = jp2k.read(tile=63, rlevel=2)  # last tile
-        else:
-            with self.assertWarns(DeprecationWarning):
-                tdata = jp2k.read(tile=63, rlevel=2)  # last tile
-        odata = jp2k[::4, ::4]
-        np.testing.assert_array_equal(tdata, odata[224:256, 224:256])
-
-    def test_NR_DEC_p1_04_j2k_58_decode(self):
-        jfile = opj_data_file('input/conformance/p1_04.j2k')
-        jp2k = Jp2k(jfile)
-        tdata = jp2k[896:1024:4, 896:1024:4]  # last tile
-        odata = jp2k[::4, ::4]
-        np.testing.assert_array_equal(tdata, odata[224:256, 224:256])
-
-    def test_NR_DEC_p1_04_j2k_59_decode(self):
-        jfile = opj_data_file('input/conformance/p1_04.j2k')
-        jp2k = Jp2k(jfile)
-        tdata = jp2k[128:256, 512:640]  # 2nd row, 5th column
-        odata = jp2k[:]
-        np.testing.assert_array_equal(tdata, odata[128:256, 512:640])
-
-    def test_NR_DEC_p1_04_j2k_60_decode(self):
-        jfile = opj_data_file('input/conformance/p1_04.j2k')
-        jp2k = Jp2k(jfile)
-        tdata = jp2k[128:256:2, 512:640:2]  # 2nd row, 5th column
-        odata = jp2k[::2, ::2]
-        np.testing.assert_array_equal(tdata, odata[64:128, 256:320])
-
-    @unittest.skipIf(WARNING_INFRASTRUCTURE_ISSUE, WARNING_INFRASTRUCTURE_MSG)
-    def test_NR_DEC_jp2_36_decode(self):
-        lst = ('input',
-               'nonregression',
-               'gdal_fuzzer_assert_in_opj_j2k_read_SQcd_SQcc.patch.jp2')
-        jfile = opj_data_file('/'.join(lst))
-        with self.assertWarns(UserWarning):
-            # Invalid component number.
-            j = Jp2k(jfile)
-            with self.assertRaises(IOError):
-                j[:]
-
-@unittest.skipIf(OPJ_DATA_ROOT is None,
-                 "OPJ_DATA_ROOT environment variable not set")
-@unittest.skipIf(re.match(r'''(1|2.0.0)''',
-                          glymur.version.openjpeg_version) is not None,
-                 "Only supported in 2.0.1 or higher")
-class TestReadArea(unittest.TestCase):
-    """
-    Runs tests introduced in version 2.0+ or that pass only in 2.0+
-    
-    Specifically for read method with area parameter.
-    """
-    @classmethod
-    def setUpClass(self):
-
-        jfile = opj_data_file('input/conformance/p1_04.j2k')
-        self.j2k = Jp2k(jfile)
-        self.j2k_data = self.j2k[:]
-        self.j2k_half_data = self.j2k[::2, ::2]
-        self.j2k_quarter_data = self.j2k[::4, ::4]
-
-        jfile = opj_data_file('input/conformance/p1_06.j2k')
-        self.j2k_p1_06 = Jp2k(jfile)
-
-    def test_NR_DEC_p1_04_j2k_43_decode(self):
-        actual = self.j2k[:1024, :1024]
-        expected = self.j2k_data
-        np.testing.assert_array_equal(actual, expected)
-
-    def test_NR_DEC_p1_04_j2k_44_decode(self):
-        actual = self.j2k[640:768, 512:640]
-        expected = self.j2k_data[640:768, 512:640]
-        np.testing.assert_array_equal(actual, expected)
-
-    def test_NR_DEC_p1_04_j2k_45_decode(self):
-        actual = self.j2k[896:1024, 896:1024]
-        expected = self.j2k_data[896:1024, 896:1024]
-        np.testing.assert_array_equal(actual, expected)
-
-    def test_NR_DEC_p1_04_j2k_46_decode(self):
-        actual = self.j2k[500:800, 100:300]
-        expected = self.j2k_data[500:800, 100:300]
-        np.testing.assert_array_equal(actual, expected)
-
-    def test_NR_DEC_p1_04_j2k_47_decode(self):
-        actual = self.j2k[520:600, 260:360]
-        expected = self.j2k_data[520:600, 260:360]
-        np.testing.assert_array_equal(actual, expected)
-
-    def test_NR_DEC_p1_04_j2k_48_decode(self):
-        actual = self.j2k[520:660, 260:360]
-        expected = self.j2k_data[520:660, 260:360]
-        np.testing.assert_array_equal(actual, expected)
-
-    def test_NR_DEC_p1_04_j2k_49_decode(self):
-        actual = self.j2k[520:600, 360:400]
-        expected = self.j2k_data[520:600, 360:400]
-        np.testing.assert_array_equal(actual, expected)
-
-    def test_NR_DEC_p1_04_j2k_50_decode(self):
-        actual = self.j2k[:1024:4, :1024:4]
-        expected = self.j2k_quarter_data
-        np.testing.assert_array_equal(actual, expected)
-
-    def test_NR_DEC_p1_04_j2k_51_decode(self):
-        actual = self.j2k[640:768:4, 512:640:4]
-        expected = self.j2k_quarter_data[160:192, 128:160]
-        np.testing.assert_array_equal(actual, expected)
-
-    def test_NR_DEC_p1_04_j2k_52_decode(self):
-        actual = self.j2k[896:1024:4, 896:1024:4]
-        expected = self.j2k_quarter_data[224:352, 224:352]
-        np.testing.assert_array_equal(actual, expected)
-
-    def test_NR_DEC_p1_04_j2k_53_decode(self):
-        actual = self.j2k[500:800:4, 100:300:4]
-        expected = self.j2k_quarter_data[125:200, 25:75]
-        np.testing.assert_array_equal(actual, expected)
-
-    def test_NR_DEC_p1_04_j2k_54_decode(self):
-        actual = self.j2k[520:600:4, 260:360:4]
-        expected = self.j2k_quarter_data[130:150, 65:90]
-        np.testing.assert_array_equal(actual, expected)
-
-    def test_NR_DEC_p1_04_j2k_55_decode(self):
-        actual = self.j2k[520:660:4, 260:360:4]
-        expected = self.j2k_quarter_data[130:165, 65:90]
-        np.testing.assert_array_equal(actual, expected)
-
-    def test_NR_DEC_p1_04_j2k_56_decode(self):
-        actual = self.j2k[520:600:4, 360:400:4]
-        expected = self.j2k_quarter_data[130:150, 90:100]
-        np.testing.assert_array_equal(actual, expected)
-
-    def test_NR_DEC_p1_06_j2k_70_decode(self):
-        actual = self.j2k_p1_06[9:12:2, 9:12:2]
-        self.assertEqual(actual.shape, (1, 1, 3))
-
-    def test_NR_DEC_p1_06_j2k_71_decode(self):
-        actual = self.j2k_p1_06[10:12:2, 4:10:2]
-        self.assertEqual(actual.shape, (1, 3, 3))
-
-    def test_NR_DEC_p1_06_j2k_72_decode(self):
-        ssdata = self.j2k_p1_06[3:9:2, 3:9:2]
-        self.assertEqual(ssdata.shape, (3, 3, 3))
-
-    def test_NR_DEC_p1_06_j2k_73_decode(self):
-        ssdata = self.j2k_p1_06[4:7:2, 4:7:2]
-        self.assertEqual(ssdata.shape, (2, 2, 3))
-
-    def test_NR_DEC_p1_06_j2k_74_decode(self):
-        ssdata = self.j2k_p1_06[4:5:2, 4:5:2]
-        self.assertEqual(ssdata.shape, (1, 1, 3))
-
-    def test_NR_DEC_p1_06_j2k_75_decode(self):
-        # Image size would be 0 x 0.
-        with self.assertRaises((IOError, OSError)):
-            self.j2k_p1_06[9:12:4, 9:12:4]
-
-    def test_NR_DEC_p0_04_j2k_85_decode(self):
-        actual = self.j2k[:256, :256]
-        expected = self.j2k_data[:256, :256]
-        np.testing.assert_array_equal(actual, expected)
-
-    def test_NR_DEC_p0_04_j2k_86_decode(self):
-        actual = self.j2k[:128, 128:256]
-        expected = self.j2k_data[:128, 128:256]
-        np.testing.assert_array_equal(actual, expected)
-
-    def test_NR_DEC_p0_04_j2k_87_decode(self):
-        actual = self.j2k[10:200, 50:120]
-        expected = self.j2k_data[10:200, 50:120]
-        np.testing.assert_array_equal(actual, expected)
-
-    def test_NR_DEC_p0_04_j2k_88_decode(self):
-        actual = self.j2k[150:210, 10:190]
-        expected = self.j2k_data[150:210, 10:190]
-        np.testing.assert_array_equal(actual, expected)
-
-    def test_NR_DEC_p0_04_j2k_89_decode(self):
-        actual = self.j2k[80:150, 100:200]
-        expected = self.j2k_data[80:150, 100:200]
-        np.testing.assert_array_equal(actual, expected)
-
-    def test_NR_DEC_p0_04_j2k_90_decode(self):
-        actual = self.j2k[20:50, 150:200]
-        expected = self.j2k_data[20:50, 150:200]
-        np.testing.assert_array_equal(actual, expected)
-
-    def test_NR_DEC_p0_04_j2k_91_decode(self):
-        actual = self.j2k[:256:4, :256:4]
-        expected = self.j2k_quarter_data[0:64, 0:64]
-        np.testing.assert_array_equal(actual, expected)
-
-    def test_NR_DEC_p0_04_j2k_92_decode(self):
-        actual = self.j2k[:128:4, 128:256:4]
-        expected = self.j2k_quarter_data[:32, 32:64]
-        np.testing.assert_array_equal(actual, expected)
-
-    def test_NR_DEC_p0_04_j2k_93_decode(self):
-        actual = self.j2k[10:200:4, 50:120:4]
-        expected = self.j2k_quarter_data[3:50, 13:30]
-        np.testing.assert_array_equal(actual, expected)
-
-    def test_NR_DEC_p0_04_j2k_94_decode(self):
-        actual = self.j2k[150:210:4, 10:190:4]
-        expected = self.j2k_quarter_data[38:53, 3:48]
-        np.testing.assert_array_equal(actual, expected)
-
-    def test_NR_DEC_p0_04_j2k_95_decode(self):
-        actual = self.j2k[80:150:4, 100:200:4]
-        expected = self.j2k_quarter_data[20:38, 25:50]
-        np.testing.assert_array_equal(actual, expected)
-
-    def test_NR_DEC_p0_04_j2k_96_decode(self):
-        actual = self.j2k[20:50:4, 150:200:4]
-        expected = self.j2k_quarter_data[5:13, 38:50]
-        np.testing.assert_array_equal(actual, expected)

From a35ebe18369e3892d6ca1713a76ecfdacbccd428 Mon Sep 17 00:00:00 2001
From: John Evans <john.g.evans@noaa.gov>
Date: Tue, 18 Nov 2014 08:03:34 -0500
Subject: [PATCH 09/23] backwards compatibility tests need to be filtered out
 on some platforms

The need to verify the warning means that the python-six issue applies.
---
 glymur/test/test_opj_suite.py | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/glymur/test/test_opj_suite.py b/glymur/test/test_opj_suite.py
index 1dd4026..cf44eaa 100644
--- a/glymur/test/test_opj_suite.py
+++ b/glymur/test/test_opj_suite.py
@@ -30,6 +30,7 @@ suite.
 import re
 import sys
 import unittest
+import warnings
 
 import numpy as np
 
@@ -727,6 +728,7 @@ class TestSuite2point1(unittest.TestCase):
         odata = jp2k[:]
         np.testing.assert_array_equal(tdata, odata[896:1024, 896:1024])
 
+    @unittest.skipIf(WARNING_INFRASTRUCTURE_ISSUE, WARNING_INFRASTRUCTURE_MSG)
     def test_NR_DEC_p1_04_j2k_57_decode_0p7_backwards_compatibility(self):
         """
         0.7.x usage deprecated
@@ -744,6 +746,7 @@ class TestSuite2point1(unittest.TestCase):
         odata = jp2k[:]
         np.testing.assert_array_equal(tdata, odata[896:1024, 896:1024])
 
+    @unittest.skipIf(WARNING_INFRASTRUCTURE_ISSUE, WARNING_INFRASTRUCTURE_MSG)
     def test_NR_DEC_p1_04_j2k_58_decode_0p7_backwards_compatibility(self):
         """
         0.7.x usage deprecated

From 036b14cc2b671ce375c32bf99677e8acc546556e Mon Sep 17 00:00:00 2001
From: John Evans <john.g.evans.ne@gmail.com>
Date: Tue, 18 Nov 2014 09:48:19 -0500
Subject: [PATCH 10/23] filter out write tests that should not run on openjpeg
 1.3

---
 glymur/test/test_jp2box.py   | 2 ++
 glymur/test/test_jp2k.py     | 4 ++++
 glymur/test/test_printing.py | 2 ++
 3 files changed, 8 insertions(+)

diff --git a/glymur/test/test_jp2box.py b/glymur/test/test_jp2box.py
index 72daf17..b8ad2ec 100644
--- a/glymur/test/test_jp2box.py
+++ b/glymur/test/test_jp2box.py
@@ -54,6 +54,8 @@ class TestDataEntryURL(unittest.TestCase):
     def setUp(self):
         self.jp2file = glymur.data.nemo()
 
+    @unittest.skipIf(re.match("1.5|2", glymur.version.openjpeg_version) is None,
+                     "Must have openjpeg 1.5 or higher to run")
     def test_wrap_greyscale(self):
         """A single component should be wrapped as GREYSCALE."""
         j = Jp2k(self.jp2file)
diff --git a/glymur/test/test_jp2k.py b/glymur/test/test_jp2k.py
index f615cc4..73315bc 100644
--- a/glymur/test/test_jp2k.py
+++ b/glymur/test/test_jp2k.py
@@ -76,6 +76,8 @@ class SliceProtocolBase(unittest.TestCase):
         self.j2k_data_r1 = self.j2k[::2, ::2]
         self.j2k_data_r5 = self.j2k[::32, ::32]
 
+@unittest.skipIf(re.match("1.5|2", glymur.version.openjpeg_version) is None,
+                 "Must have openjpeg 1.5 or higher to run")
 @unittest.skipIf(os.name == "nt", fixtures.WINDOWS_TMP_FILE_MSG)
 class TestSliceProtocolBaseWrite(SliceProtocolBase):
 
@@ -524,6 +526,8 @@ class TestJp2k(unittest.TestCase):
         jpx = Jp2k(self.jpxfile)
         self.assertEqual(jpx.shape, (1024, 1024, 3))
 
+    @unittest.skipIf(re.match("1.5|2", glymur.version.openjpeg_version) is None,
+                     "Must have openjpeg 1.5 or higher to run")
     @unittest.skipIf(os.name == "nt", "Unexplained failure on windows")
     def test_irreversible(self):
         """Irreversible"""
diff --git a/glymur/test/test_printing.py b/glymur/test/test_printing.py
index 5c09c81..5dae016 100644
--- a/glymur/test/test_printing.py
+++ b/glymur/test/test_printing.py
@@ -107,6 +107,8 @@ class TestPrinting(unittest.TestCase):
         with self.assertRaises(TypeError):
             glymur.set_printoptions(hi='low')
 
+    @unittest.skipIf(re.match("1.5|2", glymur.version.openjpeg_version) is None,
+                     "Must have openjpeg 1.5 or higher to run")
     def test_asoc_label_box(self):
         """verify printing of asoc, label boxes"""
         # Construct a fake file with an asoc and a label box, as

From 117b7d1bbe71ac9b3bd26d866e6fce94dcf6116e Mon Sep 17 00:00:00 2001
From: John Evans <john.g.evans@noaa.gov>
Date: Tue, 18 Nov 2014 10:06:52 -0500
Subject: [PATCH 11/23] refactored, skipping tests not to be run on openjpeg
 1.3

---
 glymur/test/test_opj_suite_neg.py | 77 +++++++++++++++++--------------
 1 file changed, 43 insertions(+), 34 deletions(-)

diff --git a/glymur/test/test_opj_suite_neg.py b/glymur/test/test_opj_suite_neg.py
index 440ebaa..350b7a5 100644
--- a/glymur/test/test_opj_suite_neg.py
+++ b/glymur/test/test_opj_suite_neg.py
@@ -24,6 +24,7 @@ from .fixtures import OPJ_DATA_ROOT, opj_data_file, read_image
 from .fixtures import NO_READ_BACKEND, NO_READ_BACKEND_MSG
 from .fixtures import NO_SKIMAGE_FREEIMAGE_SUPPORT
 from .fixtures import WARNING_INFRASTRUCTURE_ISSUE, WARNING_INFRASTRUCTURE_MSG
+from . import fixtures
 
 from glymur import Jp2k
 import glymur
@@ -31,7 +32,7 @@ import glymur
 
 @unittest.skipIf(OPJ_DATA_ROOT is None,
                  "OPJ_OPJ_DATA_ROOT environment variable not set")
-class TestSuiteNegative(unittest.TestCase):
+class TestSuiteNegativeRead(unittest.TestCase):
     """Test suite for certain negative tests from openjpeg suite."""
 
     def setUp(self):
@@ -41,33 +42,6 @@ class TestSuiteNegative(unittest.TestCase):
     def tearDown(self):
         pass
 
-
-    @unittest.skipIf(NO_SKIMAGE_FREEIMAGE_SUPPORT,
-                     "Cannot read input image without scikit-image/freeimage")
-    @unittest.skipIf(os.name == "nt", "Temporary file issue on window.")
-    def test_cinema2K_bad_frame_rate(self):
-        """Cinema2k frame rate must be either 24 or 48."""
-        relfile = 'input/nonregression/X_5_2K_24_235_CBR_STEM24_000.tif'
-        infile = opj_data_file(relfile)
-        data = skimage.io.imread(infile)
-        with tempfile.NamedTemporaryFile(suffix='.j2k') as tfile:
-            j = Jp2k(tfile.name, 'wb')
-            with self.assertRaises(IOError):
-                j.write(data, cinema2k=36)
-
-
-    @unittest.skipIf(NO_READ_BACKEND, NO_READ_BACKEND_MSG)
-    @unittest.skipIf(os.name == "nt", "Temporary file issue on window.")
-    def test_psnr_with_cratios(self):
-        """Using psnr with cratios options is not allowed."""
-        # Not an OpenJPEG test, but close.
-        infile = opj_data_file('input/nonregression/Bretagne1.ppm')
-        data = read_image(infile)
-        with tempfile.NamedTemporaryFile(suffix='.j2k') as tfile:
-            j = Jp2k(tfile.name, 'wb')
-            with self.assertRaises(IOError):
-                j.write(data, psnr=[30, 35, 40], cratios=[2, 3, 4])
-
     def test_nr_marker_not_compliant(self):
         """non-compliant marker, should still be able to read"""
         relpath = 'input/nonregression/MarkerIsNotCompliant.j2k'
@@ -98,7 +72,47 @@ class TestSuiteNegative(unittest.TestCase):
         jp2k.get_codestream(header_only=False)
         self.assertTrue(True)
 
-    @unittest.skipIf(os.name == "nt", "Temporary file issue on window.")
+
+@unittest.skipIf(re.match("1.5|2", glymur.version.openjpeg_version) is None,
+                 "Must have openjpeg 1.5 or higher to run")
+@unittest.skipIf(os.name == "nt", fixtures.WINDOWS_TMP_FILE_MSG)
+@unittest.skipIf(OPJ_DATA_ROOT is None,
+                 "OPJ_OPJ_DATA_ROOT environment variable not set")
+class TestSuiteNegativeWrite(unittest.TestCase):
+    """Test suite for certain negative tests from openjpeg suite."""
+
+    def setUp(self):
+        self.jp2file = glymur.data.nemo()
+        self.j2kfile = glymur.data.goodstuff()
+
+    def tearDown(self):
+        pass
+
+
+    @unittest.skipIf(NO_SKIMAGE_FREEIMAGE_SUPPORT,
+                     "Cannot read input image without scikit-image/freeimage")
+    def test_cinema2K_bad_frame_rate(self):
+        """Cinema2k frame rate must be either 24 or 48."""
+        relfile = 'input/nonregression/X_5_2K_24_235_CBR_STEM24_000.tif'
+        infile = opj_data_file(relfile)
+        data = skimage.io.imread(infile)
+        with tempfile.NamedTemporaryFile(suffix='.j2k') as tfile:
+            j = Jp2k(tfile.name, 'wb')
+            with self.assertRaises(IOError):
+                j.write(data, cinema2k=36)
+
+
+    @unittest.skipIf(NO_READ_BACKEND, NO_READ_BACKEND_MSG)
+    def test_psnr_with_cratios(self):
+        """Using psnr with cratios options is not allowed."""
+        # Not an OpenJPEG test, but close.
+        infile = opj_data_file('input/nonregression/Bretagne1.ppm')
+        data = read_image(infile)
+        with tempfile.NamedTemporaryFile(suffix='.j2k') as tfile:
+            j = Jp2k(tfile.name, 'wb')
+            with self.assertRaises(IOError):
+                j.write(data, psnr=[30, 35, 40], cratios=[2, 3, 4])
+
     def test_code_block_dimensions(self):
         """don't allow extreme codeblock sizes"""
         # opj_compress doesn't allow the dimensions of a codeblock
@@ -117,7 +131,6 @@ class TestSuiteNegative(unittest.TestCase):
             with self.assertRaises(IOError):
                 j.write(data, cbsize=(2, 2048))
 
-    @unittest.skipIf(os.name == "nt", "Temporary file issue on window.")
     def test_precinct_size_not_p2(self):
         """precinct sizes should be powers of two."""
         ifile = Jp2k(self.j2kfile)
@@ -127,7 +140,6 @@ class TestSuiteNegative(unittest.TestCase):
             with self.assertRaises(IOError):
                 ofile.write(data, psizes=[(13, 13)])
 
-    @unittest.skipIf(os.name == "nt", "Temporary file issue on window.")
     def test_cblk_size_not_power_of_two(self):
         """code block sizes should be powers of two."""
         ifile = Jp2k(self.j2kfile)
@@ -137,7 +149,6 @@ class TestSuiteNegative(unittest.TestCase):
             with self.assertRaises(IOError):
                 ofile.write(data, cbsize=(13, 12))
 
-    @unittest.skipIf(os.name == "nt", "Temporary file issue on window.")
     def test_cblk_size_precinct_size(self):
         """code block sizes should never exceed half that of precinct size."""
         ifile = Jp2k(self.j2kfile)
@@ -149,5 +160,3 @@ class TestSuiteNegative(unittest.TestCase):
                             cbsize=(64, 64),
                             psizes=[(64, 64)])
 
-if __name__ == "__main__":
-    unittest.main()

From 373afb692e3f90a2f5896f3edfd372e0c659eb41 Mon Sep 17 00:00:00 2001
From: jevans <john.g.evans.ne@gmail.com>
Date: Tue, 18 Nov 2014 20:45:25 -0500
Subject: [PATCH 12/23] progress

---
 glymur/jp2k.py                | 29 +++++++++++++++++++++++++----
 glymur/test/test_callbacks.py | 25 +++++++++++++++++++++----
 2 files changed, 46 insertions(+), 8 deletions(-)

diff --git a/glymur/jp2k.py b/glymur/jp2k.py
index a45f9e2..8d8ffd4 100644
--- a/glymur/jp2k.py
+++ b/glymur/jp2k.py
@@ -62,9 +62,15 @@ class Jp2k(Jp2kBox):
         raw codestream.
     shape : tuple
         Size of the image.
+
+    Properties
+    ----------
     ignore_pclr_cmap_cdef : bool
-        Whether or not to ignore the pclr, cmap, or cdef boxes during any
-        color transformation.  Defaults to False.
+        whether or not to ignore the pclr, cmap, or cdef boxes during any
+        color transformation, defaults to False.
+    verbose : bool
+        whether or not to print informational messages produced by the
+        OpenJPEG library, defaults to false
 
     Examples
     --------
@@ -100,7 +106,9 @@ class Jp2k(Jp2kBox):
         self._codec_format = None
         self._colorspace = None
         self._shape = None
+
         self._ignore_pclr_cmap_cdef = False
+        self._verbose = False
 
         # Parse the file for JP2/JPX contents only if we are reading it.
         if mode == 'rb':
@@ -114,6 +122,14 @@ class Jp2k(Jp2kBox):
     def ignore_pclr_cmap_cdef(self, ignore_pclr_cmap_cdef):
         self._ignore_pclr_cmap_cdef = ignore_pclr_cmap_cdef
 
+    @property
+    def verbose(self):
+        return self._verbose
+
+    @verbose.setter
+    def verbose(self, verbose):
+        self._verbose = verbose
+
     @property
     def shape(self):
         if self._shape is not None:
@@ -671,7 +687,11 @@ class Jp2k(Jp2kBox):
             codec = opj2.create_compress(self._cparams.codec_fmt)
             stack.callback(opj2.destroy_codec, codec)
 
-            info_handler = _INFO_CALLBACK if verbose else None
+            if self._verbose or verbose:
+                info_handler = _INFO_CALLBACK
+            else:
+                info_handler = None
+
             opj2.set_info_handler(codec, info_handler)
             opj2.set_warning_handler(codec, _WARNING_CALLBACK)
             opj2.set_error_handler(codec, _ERROR_CALLBACK)
@@ -1183,7 +1203,8 @@ class Jp2k(Jp2kBox):
 
             opj2.set_error_handler(codec, _ERROR_CALLBACK)
             opj2.set_warning_handler(codec, _WARNING_CALLBACK)
-            if verbose:
+
+            if self._verbose or verbose:
                 opj2.set_info_handler(codec, _INFO_CALLBACK)
             else:
                 opj2.set_info_handler(codec, None)
diff --git a/glymur/test/test_callbacks.py b/glymur/test/test_callbacks.py
index ce3bb8c..a58cfeb 100644
--- a/glymur/test/test_callbacks.py
+++ b/glymur/test/test_callbacks.py
@@ -39,7 +39,7 @@ class TestCallbacks(unittest.TestCase):
                      "Missing openjp2 library.")
     @unittest.skipIf(WARNING_INFRASTRUCTURE_ISSUE, WARNING_INFRASTRUCTURE_MSG)
     @unittest.skipIf(os.name == "nt", "Temporary file issue on window.")
-    def test_info_callback_on_write(self):
+    def test_info_callback_on_write_backwards_compatibility(self):
         """Verify messages printed when writing an image in verbose mode."""
         j = glymur.Jp2k(self.jp2file)
         with self.assertWarns(UserWarning):
@@ -52,20 +52,37 @@ class TestCallbacks(unittest.TestCase):
         expected = '[INFO] tile number 1 / 1'
         self.assertEqual(actual, expected)
 
+    @unittest.skipIf(glymur.version.openjpeg_version[0] != '2',
+                     "Missing openjp2 library.")
+    @unittest.skipIf(os.name == "nt", "Temporary file issue on window.")
+    def test_info_callback_on_write(self):
+        """Verify messages printed when writing an image in verbose mode."""
+        j = glymur.Jp2k(self.jp2file)
+        tiledata = j[:]
+        with tempfile.NamedTemporaryFile(suffix='.jp2') as tfile:
+            jp2 = glymur.Jp2k(tfile.name, 'wb')
+            with patch('sys.stdout', new=StringIO()) as fake_out:
+                jp2.verbose = True
+                jp2[:] = tiledata
+                actual = fake_out.getvalue().strip()
+        expected = '[INFO] tile number 1 / 1'
+        self.assertEqual(actual, expected)
+
     def test_info_callbacks_on_read(self):
         """stdio output when info callback handler is enabled"""
 
         # Verify that we get the expected stdio output when our internal info
         # callback handler is enabled.
-        j = glymur.Jp2k(self.j2kfile)
+        jp2 = glymur.Jp2k(self.j2kfile)
         with patch('sys.stdout', new=StringIO()) as fake_out:
-            j.read(rlevel=1, verbose=True)
+            jp2.verbose = True
+            jp2[::2, ::2]
             actual = fake_out.getvalue().strip()
 
         if glymur.version.openjpeg_version[0] == '2':
             lines = ['[INFO] Start to read j2k main header (0).',
                      '[INFO] Main header has been correctly decoded.',
-                     '[INFO] No decoded area parameters, set the decoded area to the whole image',
+                     '[INFO] Setting decoding area to 0,0,480,800',
                      '[INFO] Header of tile 0 / 0 has been read.',
                      '[INFO] Tile 1/1 has been decoded.',
                      '[INFO] Image data has been updated with tile 1.']

From 9025bb3ec3ee3ae6cb2b8efb01d39cbe08216b4c Mon Sep 17 00:00:00 2001
From: jevans <john.g.evans.ne@gmail.com>
Date: Tue, 18 Nov 2014 23:15:09 -0500
Subject: [PATCH 13/23] layer is now a property

---
 glymur/jp2k.py           | 35 ++++++++++++++++++++++++++---------
 glymur/test/test_jp2k.py |  4 ++--
 2 files changed, 28 insertions(+), 11 deletions(-)

diff --git a/glymur/jp2k.py b/glymur/jp2k.py
index 8d8ffd4..2ea9588 100644
--- a/glymur/jp2k.py
+++ b/glymur/jp2k.py
@@ -68,6 +68,8 @@ class Jp2k(Jp2kBox):
     ignore_pclr_cmap_cdef : bool
         whether or not to ignore the pclr, cmap, or cdef boxes during any
         color transformation, defaults to False.
+    layer : int
+        zero-based number of quality layer to decode
     verbose : bool
         whether or not to print informational messages produced by the
         OpenJPEG library, defaults to false
@@ -106,6 +108,7 @@ class Jp2k(Jp2kBox):
         self._codec_format = None
         self._colorspace = None
         self._shape = None
+        self._layer = 0
 
         self._ignore_pclr_cmap_cdef = False
         self._verbose = False
@@ -122,6 +125,18 @@ class Jp2k(Jp2kBox):
     def ignore_pclr_cmap_cdef(self, ignore_pclr_cmap_cdef):
         self._ignore_pclr_cmap_cdef = ignore_pclr_cmap_cdef
 
+    @property
+    def layer(self):
+        return self._layer
+
+    @layer.setter
+    def layer(self, layer):
+        if version.openjpeg_version_tuple[0] < 2:
+            msg = "Layer property not supported unless the version of OpenJPEG "
+            msg += "is 2.0 or higher."
+            raise RuntimeError(msg)
+        self._layer = layer
+
     @property
     def verbose(self):
         return self._verbose
@@ -1156,7 +1171,7 @@ class Jp2k(Jp2kBox):
 
         return data
 
-    def _read_openjp2(self, rlevel=0, layer=0, area=None, tile=None, verbose=False):
+    def _read_openjp2(self, rlevel=0, layer=None, area=None, tile=None, verbose=False):
         """Read a JPEG 2000 image using libopenjp2.
 
         Parameters
@@ -1184,9 +1199,12 @@ class Jp2k(Jp2kBox):
         RuntimeError
             If the image has differing subsample factors.
         """
+        if layer is not None:
+            self._layer = layer
+
         self._subsampling_sanity_check()
 
-        self._populate_dparams(rlevel, layer=layer, tile=tile, area=area)
+        self._populate_dparams(rlevel, tile=tile, area=area)
 
         with ExitStack() as stack:
             if re.match("2.1", version.openjpeg_version):
@@ -1231,13 +1249,11 @@ class Jp2k(Jp2kBox):
 
         return img_array
 
-    def _populate_dparams(self, rlevel, tile=None, layer=None, area=None):
+    def _populate_dparams(self, rlevel, tile=None, area=None):
         """Populate decompression structure with appropriate input parameters.
 
         Parameters
         ----------
-        layer : int
-            Number of quality layer to decode.
         rlevel : int
             Factor by which to rlevel output resolution.
         area : tuple
@@ -1263,8 +1279,7 @@ class Jp2k(Jp2kBox):
 
         dparam.decod_format = self._codec_format
 
-        if layer is not None:
-            dparam.cp_layer = layer
+        dparam.cp_layer = self._layer
 
         # Must check the specified rlevel against the maximum.
         if rlevel != 0:
@@ -1301,7 +1316,7 @@ class Jp2k(Jp2kBox):
 
         self._dparams = dparam
 
-    def read_bands(self, rlevel=0, layer=0, area=None, tile=None,
+    def read_bands(self, rlevel=0, layer=None, area=None, tile=None,
                    verbose=False, ignore_pclr_cmap_cdef=False):
         """Read a JPEG 2000 image.
 
@@ -1348,7 +1363,9 @@ class Jp2k(Jp2kBox):
                                "functionality.")
 
         self.ignore_pclr_cmap_cdef = ignore_pclr_cmap_cdef
-        self._populate_dparams(rlevel, layer=layer, tile=tile, area=area)
+        if layer is not None:
+            self._layer = layer
+        self._populate_dparams(rlevel, tile=tile, area=area)
 
         with ExitStack() as stack:
             if re.match("2.1", version.openjpeg_version):
diff --git a/glymur/test/test_jp2k.py b/glymur/test/test_jp2k.py
index 73315bc..55cea0e 100644
--- a/glymur/test/test_jp2k.py
+++ b/glymur/test/test_jp2k.py
@@ -1094,8 +1094,8 @@ class TestJp2k_1_x(unittest.TestCase):
         """
         with patch('glymur.version.openjpeg_version_tuple', new=(1, 5, 0)):
             j2k = Jp2k(self.j2kfile)
-            with self.assertRaises(TypeError):
-                j2k.read(layer=1)
+            with self.assertRaises(RuntimeError):
+                j2k.layer = 1
 
 
 @unittest.skipIf(os.name == "nt", fixtures.WINDOWS_TMP_FILE_MSG)

From e2059d59e8a15196fd142870172cead1ef85e54b Mon Sep 17 00:00:00 2001
From: jevans <john.g.evans.ne@gmail.com>
Date: Wed, 19 Nov 2014 07:24:47 -0500
Subject: [PATCH 14/23] removed repeated array-style slicing tests

---
 glymur/test/test_codestream.py | 149 ----------
 glymur/test/test_jp2k.py       | 495 +++++++++++++++++----------------
 2 files changed, 255 insertions(+), 389 deletions(-)
 delete mode 100644 glymur/test/test_codestream.py

diff --git a/glymur/test/test_codestream.py b/glymur/test/test_codestream.py
deleted file mode 100644
index e520713..0000000
--- a/glymur/test/test_codestream.py
+++ /dev/null
@@ -1,149 +0,0 @@
-"""
-Test suite for codestream parsing.
-"""
-
-# unittest doesn't work well with R0904.
-# pylint: disable=R0904
-
-import os
-import struct
-import sys
-import tempfile
-import unittest
-
-from glymur import Jp2k
-import glymur
-
-from .fixtures import opj_data_file, OPJ_DATA_ROOT
-
-class TestCodestream(unittest.TestCase):
-    """Test suite for unusual codestream cases."""
-
-    def setUp(self):
-        self.jp2file = glymur.data.nemo()
-
-    def tearDown(self):
-        pass
-
-    def test_siz_segment_ssiz_unsigned(self):
-        """ssiz attribute to be removed in future release"""
-        j = Jp2k(self.jp2file)
-        codestream = j.get_codestream()
-
-        # The ssiz attribute was simply a tuple of raw bytes.
-        # The first 7 bits are interpreted as the bitdepth, the MSB determines
-        # whether or not it is signed.
-        self.assertEqual(codestream.segment[1].ssiz, (7, 7, 7))
-
-
-@unittest.skipIf(OPJ_DATA_ROOT is None,
-                 "OPJ_DATA_ROOT environment variable not set")
-class TestCodestreamOpjData(unittest.TestCase):
-    """Test suite for unusual codestream cases.  Uses OPJ_DATA_ROOT"""
-
-    def setUp(self):
-        self.jp2file = glymur.data.nemo()
-
-    def tearDown(self):
-        pass
-
-    @unittest.skipIf(os.name == "nt", "Temporary file issue on window.")
-    def test_reserved_marker_segment(self):
-        """Reserved marker segments are ok."""
-
-        # Some marker segments were reserved in FCD15444-1.  Since that
-        # standard is old, some of them may have come into use.
-        #
-        # Let's inject a reserved marker segment into a file that
-        # we know something about to make sure we can still parse it.
-        filename = os.path.join(OPJ_DATA_ROOT, 'input/conformance/p0_01.j2k')
-        with tempfile.NamedTemporaryFile(suffix='.j2k') as tfile:
-            with open(filename, 'rb') as ifile:
-                # Everything up until the first QCD marker.
-                read_buffer = ifile.read(45)
-                tfile.write(read_buffer)
-
-                # Write the new marker segment, 0xff6f = 65391
-                read_buffer = struct.pack('>HHB', int(65391), int(3), int(0))
-                tfile.write(read_buffer)
-
-                # Get the rest of the input file.
-                read_buffer = ifile.read()
-                tfile.write(read_buffer)
-                tfile.flush()
-
-            codestream = Jp2k(tfile.name).get_codestream()
-
-            self.assertEqual(codestream.segment[2].marker_id, '0xff6f')
-            self.assertEqual(codestream.segment[2].length, 3)
-            self.assertEqual(codestream.segment[2].data, b'\x00')
-
-    def test_psot_is_zero(self):
-        """Psot=0 in SOT is perfectly legal.  Issue #78."""
-        filename = os.path.join(OPJ_DATA_ROOT,
-                                'input/nonregression/123.j2c')
-        j = Jp2k(filename)
-        codestream = 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(codestream.segment[-1].marker_id, 'EOC')
-
-
-    def test_siz_segment_ssiz_signed(self):
-        """ssiz attribute to be removed in future release"""
-        filename = os.path.join(OPJ_DATA_ROOT, 'input/conformance/p0_03.j2k')
-        j = Jp2k(filename)
-        codestream = j.get_codestream()
-
-        # The ssiz attribute was simply a tuple of raw bytes.
-        # The first 7 bits are interpreted as the bitdepth, the MSB determines
-        # whether or not it is signed.
-        self.assertEqual(codestream.segment[1].ssiz, (131,))
-
-
-class TestCodestreamRepr(unittest.TestCase):
-
-    def setUp(self):
-        self.jp2file = glymur.data.nemo()
-
-    def tearDown(self):
-        pass
-
-    def test_soc(self):
-        """Test SOC segment repr"""
-        segment = glymur.codestream.SOCsegment()
-        newseg = eval(repr(segment))
-        self.assertEqual(newseg.marker_id, 'SOC')
-
-    def test_siz(self):
-        """Test SIZ segment repr"""
-        kwargs = {'rsiz': 0,
-                  'xysiz': (2592, 1456),
-                  'xyosiz': (0, 0),
-                  'xytsiz': (2592, 1456),
-                  'xytosiz': (0, 0),
-                  'Csiz': 3,
-                  'bitdepth': (8, 8, 8),
-                  'signed':  (False, False, False),
-                  'xyrsiz': ((1, 1, 1), (1, 1, 1))}
-        segment = glymur.codestream.SIZsegment(**kwargs)
-        newseg = eval(repr(segment))
-        self.assertEqual(newseg.marker_id, 'SIZ')
-        self.assertEqual(newseg.xsiz, 2592)
-        self.assertEqual(newseg.ysiz, 1456)
-        self.assertEqual(newseg.xosiz, 0)
-        self.assertEqual(newseg.yosiz, 0)
-        self.assertEqual(newseg.xtsiz, 2592)
-        self.assertEqual(newseg.ytsiz, 1456)
-        self.assertEqual(newseg.xtosiz, 0)
-        self.assertEqual(newseg.ytosiz, 0)
-
-        self.assertEqual(newseg.xrsiz, (1, 1, 1))
-        self.assertEqual(newseg.yrsiz, (1, 1, 1))
-        self.assertEqual(newseg.bitdepth, (8, 8, 8))
-        self.assertEqual(newseg.signed, (False, False, False))
-
-
-if __name__ == "__main__":
-    unittest.main()
diff --git a/glymur/test/test_jp2k.py b/glymur/test/test_jp2k.py
index 55cea0e..7e8c067 100644
--- a/glymur/test/test_jp2k.py
+++ b/glymur/test/test_jp2k.py
@@ -191,71 +191,6 @@ class TestSliceProtocolRead(SliceProtocolBase):
         expected = self.jp2_data[20, 20, 2]
         np.testing.assert_array_equal(actual, expected)
 
-    def test_full_resolution_slicing_by_quarters_upper_left(self):
-        actual = self.jp2[:728, :1296]
-        expected = self.jp2_data[:728, :1296]
-        np.testing.assert_array_equal(actual, expected)
-
-    def test_full_resolution_slicing_by_quarters_lower_left(self):
-        actual = self.jp2[728:, :1296]
-        expected = self.jp2_data[728:, :1296]
-        np.testing.assert_array_equal(actual, expected)
-
-    def test_full_resolution_slicing_by_quarters_upper_right(self):
-        actual = self.jp2[:728, 1296:]
-        expected = self.jp2_data[:728, 1296:]
-        np.testing.assert_array_equal(actual, expected)
-
-    def test_full_resolution_slicing_by_quarters_lower_right(self):
-        actual = self.jp2[728:, 1296:]
-        expected = self.jp2_data[728:, 1296:]
-        np.testing.assert_array_equal(actual, expected)
-
-    def test_full_resolution_slicing_by_quarters_center(self):
-        actual = self.jp2[364:1092, 648:1942]
-        expected = self.jp2_data[364:1092, 648:1942]
-        np.testing.assert_array_equal(actual, expected)
-
-    def test_full_resolution_slicing_by_halves_left(self):
-        actual = self.jp2[:, :1296]
-        expected = self.jp2_data[:, :1296]
-        np.testing.assert_array_equal(actual, expected)
-
-    def test_full_resolution_slicing_by_right_half(self):
-        actual = self.jp2[:, 1296:]
-        expected = self.jp2_data[:, 1296:]
-        np.testing.assert_array_equal(actual, expected)
-
-    def test_full_resolution_slicing_by_top_half(self):
-        actual = self.jp2[:728, :]
-        expected = self.jp2_data[:728, :]
-        np.testing.assert_array_equal(actual, expected)
-
-    def test_full_resolution_slicing_by_bottom_half(self):
-        actual = self.jp2[728:, :]
-        expected = self.jp2_data[728:, :]
-        np.testing.assert_array_equal(actual, expected)
-
-    def test_region_rlevel1_odd(self):
-        actual = self.jp2[0:201:2, 0:201:2]
-        expected = self.jp2_data_r1[:101, :101, :]
-        np.testing.assert_array_equal(actual, expected)
-
-    def test_region_rlevel1_even(self):
-        actual = self.jp2[0:202:2, 0:202:2]
-        expected = self.jp2_data_r1[:101, :101, :]
-        np.testing.assert_array_equal(actual, expected)
-
-    def test_region_rlevel1_slice_start_is_none(self):
-        actual = self.jp2[:201:2, :201:2]
-        expected = self.jp2_data_r1[:101, :101, :]
-        np.testing.assert_array_equal(actual, expected)
-
-    def test_region_rlevel1_slice_stop_is_none(self):
-        actual = self.jp2[201::2, 201::2]
-        expected = self.jp2_data_r1[101:, 101:, :]
-        np.testing.assert_array_equal(actual, expected)
-
     def test_ellipsis_full_read(self):
         actual = self.j2k[...]
         expected = self.j2k_data
@@ -292,184 +227,11 @@ class TestSliceProtocolRead(SliceProtocolBase):
         expected = self.j2k_data[3:8, :,:]
         np.testing.assert_array_equal(actual, expected)
 
-    def test_slice_protocol_2d_reduce_resolution(self):
-        d = self.j2k[:]
-        self.assertEqual(d.shape, (800, 480, 3))
-
-        d = self.j2k[::1, ::1]
-        self.assertEqual(d.shape, (800, 480, 3))
-
-        d = self.j2k[::2, ::2]
-        self.assertEqual(d.shape, (400, 240, 3))
-
-        d = self.j2k[::4, ::4]
-        self.assertEqual(d.shape, (200, 120, 3))
-
-        d = self.j2k[::8, ::8]
-        self.assertEqual(d.shape, (100, 60, 3))
-
-        d = self.j2k[::16, ::16]
-        self.assertEqual(d.shape, (50, 30, 3))
-
-        d = self.j2k[::32, ::32]
-        self.assertEqual(d.shape, (25, 15, 3))
-
     def test_region_rlevel5(self):
         actual = self.j2k[5:533:32, 27:423:32]
         expected = self.j2k_data_r5[1:17, 1:14]
         np.testing.assert_array_equal(actual, expected)
 
-@unittest.skipIf(OPJ_DATA_ROOT is None,
-                 "OPJ_DATA_ROOT environment variable not set")
-class TestSliceProtocolOpjData(unittest.TestCase):
-    """
-    Test slice protocol, i.e. when using [ ] to read image data.
-    These correspond to tests for the read method with the area parameter.
-    """
-    @classmethod
-    def setUpClass(self):
-
-        jfile = opj_data_file('input/conformance/p1_04.j2k')
-        self.j2k = Jp2k(jfile)
-        self.j2k_data = self.j2k.read()
-        self.j2k_half_data = self.j2k.read(rlevel=1)
-        self.j2k_quarter_data = self.j2k.read(rlevel=2)
-
-    def test_NR_DEC_p1_04_j2k_43_decode(self):
-        actual = self.j2k[:1024, :1024]
-        expected = self.j2k_data
-        np.testing.assert_array_equal(actual, expected)
-
-    def test_NR_DEC_p1_04_j2k_44_decode(self):
-        actual = self.j2k[640:768, 512:640]
-        expected = self.j2k_data[640:768, 512:640]
-        np.testing.assert_array_equal(actual, expected)
-
-    def test_NR_DEC_p1_04_j2k_45_decode(self):
-        actual = self.j2k[896:1024, 896:1024]
-        expected = self.j2k_data[896:1024, 896:1024]
-        np.testing.assert_array_equal(actual, expected)
-
-    def test_NR_DEC_p1_04_j2k_46_decode(self):
-        actual = self.j2k[500:800, 100:300]
-        expected = self.j2k_data[500:800, 100:300]
-        np.testing.assert_array_equal(actual, expected)
-
-    def test_NR_DEC_p1_04_j2k_47_decode(self):
-        actual = self.j2k[520:600, 260:360]
-        expected = self.j2k_data[520:600, 260:360]
-        np.testing.assert_array_equal(actual, expected)
-
-    def test_NR_DEC_p1_04_j2k_48_decode(self):
-        actual = self.j2k[520:660, 260:360]
-        expected = self.j2k_data[520:660, 260:360]
-        np.testing.assert_array_equal(actual, expected)
-
-    def test_NR_DEC_p1_04_j2k_49_decode(self):
-        actual = self.j2k[520:600, 360:400]
-        expected = self.j2k_data[520:600, 360:400]
-        np.testing.assert_array_equal(actual, expected)
-
-    def test_NR_DEC_p1_04_j2k_50_decode(self):
-        actual = self.j2k[:1024:4, :1024:4]
-        expected = self.j2k_quarter_data[:256, :256]
-        np.testing.assert_array_equal(actual, expected)
-
-    def test_NR_DEC_p1_04_j2k_51_decode(self):
-        actual = self.j2k[640:768:4, 512:640:4]
-        expected = self.j2k_quarter_data[160:192, 128:160]
-        np.testing.assert_array_equal(actual, expected)
-
-    def test_NR_DEC_p1_04_j2k_52_decode(self):
-        actual = self.j2k[896:1024:4, 896:1024:4]
-        expected = self.j2k_quarter_data[224:352, 224:352]
-        np.testing.assert_array_equal(actual, expected)
-
-    def test_NR_DEC_p1_04_j2k_53_decode(self):
-        actual = self.j2k[500:800:4, 100:300:4]
-        expected = self.j2k_quarter_data[125:200, 25:75]
-        np.testing.assert_array_equal(actual, expected)
-
-    def test_NR_DEC_p1_04_j2k_54_decode(self):
-        actual = self.j2k[520:600:4, 260:360:4]
-        expected = self.j2k_quarter_data[130:150, 65:90]
-        np.testing.assert_array_equal(actual, expected)
-
-    def test_NR_DEC_p1_04_j2k_55_decode(self):
-        actual = self.j2k[520:660:4, 260:360:4]
-        expected = self.j2k_quarter_data[130:165, 65:90]
-        np.testing.assert_array_equal(actual, expected)
-
-    def test_NR_DEC_p1_04_j2k_56_decode(self):
-        actual = self.j2k[520:600:4, 360:400:4]
-        expected = self.j2k_quarter_data[130:150, 90:100]
-        np.testing.assert_array_equal(actual, expected)
-
-    def test_NR_DEC_p1_06_j2k_75_decode(self):
-        # Image size would be 0 x 0.
-        with self.assertRaises((IOError, OSError)):
-            self.j2k[9:12:4, 9:12:4]
-
-    def test_NR_DEC_p0_04_j2k_85_decode(self):
-        actual = self.j2k[:256, :256]
-        expected = self.j2k_data[:256, :256]
-        np.testing.assert_array_equal(actual, expected)
-
-    def test_NR_DEC_p0_04_j2k_86_decode(self):
-        actual = self.j2k[:128, 128:256]
-        expected = self.j2k_data[:128, 128:256]
-        np.testing.assert_array_equal(actual, expected)
-
-    def test_NR_DEC_p0_04_j2k_87_decode(self):
-        actual = self.j2k[10:200, 50:120]
-        expected = self.j2k_data[10:200, 50:120]
-        np.testing.assert_array_equal(actual, expected)
-
-    def test_NR_DEC_p0_04_j2k_88_decode(self):
-        actual = self.j2k[150:210, 10:190]
-        expected = self.j2k_data[150:210, 10:190]
-        np.testing.assert_array_equal(actual, expected)
-
-    def test_NR_DEC_p0_04_j2k_89_decode(self):
-        actual = self.j2k[80:150, 100:200]
-        expected = self.j2k_data[80:150, 100:200]
-        np.testing.assert_array_equal(actual, expected)
-
-    def test_NR_DEC_p0_04_j2k_90_decode(self):
-        actual = self.j2k[20:50, 150:200]
-        expected = self.j2k_data[20:50, 150:200]
-        np.testing.assert_array_equal(actual, expected)
-
-    def test_NR_DEC_p0_04_j2k_91_decode(self):
-        actual = self.j2k[:256:4, :256:4]
-        expected = self.j2k_quarter_data[0:64, 0:64]
-        np.testing.assert_array_equal(actual, expected)
-
-    def test_NR_DEC_p0_04_j2k_92_decode(self):
-        actual = self.j2k[:128:4, 128:256:4]
-        expected = self.j2k_quarter_data[:32, 32:64]
-        np.testing.assert_array_equal(actual, expected)
-
-    def test_NR_DEC_p0_04_j2k_93_decode(self):
-        actual = self.j2k[10:200:4, 50:120:4]
-        expected = self.j2k_quarter_data[3:50, 13:30]
-        np.testing.assert_array_equal(actual, expected)
-
-    def test_NR_DEC_p0_04_j2k_94_decode(self):
-        actual = self.j2k[150:210:4, 10:190:4]
-        expected = self.j2k_quarter_data[38:53, 3:48]
-        np.testing.assert_array_equal(actual, expected)
-
-    def test_NR_DEC_p0_04_j2k_95_decode(self):
-        actual = self.j2k[80:150:4, 100:200:4]
-        expected = self.j2k_quarter_data[20:38, 25:50]
-        np.testing.assert_array_equal(actual, expected)
-
-    def test_NR_DEC_p0_04_j2k_96_decode(self):
-        actual = self.j2k[20:50:4, 150:200:4]
-        expected = self.j2k_quarter_data[5:13, 38:50]
-        np.testing.assert_array_equal(actual, expected)
-
 class TestJp2k(unittest.TestCase):
     """These tests should be run by just about all configuration."""
 
@@ -1423,6 +1185,259 @@ class TestJp2kOpjDataRoot(unittest.TestCase):
         np.testing.assert_array_equal(ycbcr, expected)
 
 
+class TestCodestream(unittest.TestCase):
+    """Test suite for unusual codestream cases."""
 
-if __name__ == "__main__":
-    unittest.main()
+    def setUp(self):
+        self.jp2file = glymur.data.nemo()
+
+    def tearDown(self):
+        pass
+
+    def test_siz_segment_ssiz_unsigned(self):
+        """ssiz attribute to be removed in future release"""
+        j = Jp2k(self.jp2file)
+        codestream = j.get_codestream()
+
+        # The ssiz attribute was simply a tuple of raw bytes.
+        # The first 7 bits are interpreted as the bitdepth, the MSB determines
+        # whether or not it is signed.
+        self.assertEqual(codestream.segment[1].ssiz, (7, 7, 7))
+
+
+@unittest.skipIf(OPJ_DATA_ROOT is None,
+                 "OPJ_DATA_ROOT environment variable not set")
+class TestCodestreamOpjData(unittest.TestCase):
+    """Test suite for unusual codestream cases.  Uses OPJ_DATA_ROOT"""
+
+    def setUp(self):
+        self.jp2file = glymur.data.nemo()
+
+    def tearDown(self):
+        pass
+
+    @unittest.skipIf(os.name == "nt", "Temporary file issue on window.")
+    def test_reserved_marker_segment(self):
+        """Reserved marker segments are ok."""
+
+        # Some marker segments were reserved in FCD15444-1.  Since that
+        # standard is old, some of them may have come into use.
+        #
+        # Let's inject a reserved marker segment into a file that
+        # we know something about to make sure we can still parse it.
+        filename = os.path.join(OPJ_DATA_ROOT, 'input/conformance/p0_01.j2k')
+        with tempfile.NamedTemporaryFile(suffix='.j2k') as tfile:
+            with open(filename, 'rb') as ifile:
+                # Everything up until the first QCD marker.
+                read_buffer = ifile.read(45)
+                tfile.write(read_buffer)
+
+                # Write the new marker segment, 0xff6f = 65391
+                read_buffer = struct.pack('>HHB', int(65391), int(3), int(0))
+                tfile.write(read_buffer)
+
+                # Get the rest of the input file.
+                read_buffer = ifile.read()
+                tfile.write(read_buffer)
+                tfile.flush()
+
+            codestream = Jp2k(tfile.name).get_codestream()
+
+            self.assertEqual(codestream.segment[2].marker_id, '0xff6f')
+            self.assertEqual(codestream.segment[2].length, 3)
+            self.assertEqual(codestream.segment[2].data, b'\x00')
+
+    def test_psot_is_zero(self):
+        """Psot=0 in SOT is perfectly legal.  Issue #78."""
+        filename = os.path.join(OPJ_DATA_ROOT,
+                                'input/nonregression/123.j2c')
+        j = Jp2k(filename)
+        codestream = 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(codestream.segment[-1].marker_id, 'EOC')
+
+
+    def test_siz_segment_ssiz_signed(self):
+        """ssiz attribute to be removed in future release"""
+        filename = os.path.join(OPJ_DATA_ROOT, 'input/conformance/p0_03.j2k')
+        j = Jp2k(filename)
+        codestream = j.get_codestream()
+
+        # The ssiz attribute was simply a tuple of raw bytes.
+        # The first 7 bits are interpreted as the bitdepth, the MSB determines
+        # whether or not it is signed.
+        self.assertEqual(codestream.segment[1].ssiz, (131,))
+
+
+class TestCodestreamRepr(unittest.TestCase):
+
+    def setUp(self):
+        self.jp2file = glymur.data.nemo()
+
+    def tearDown(self):
+        pass
+
+    def test_soc(self):
+        """Test SOC segment repr"""
+        segment = glymur.codestream.SOCsegment()
+        newseg = eval(repr(segment))
+        self.assertEqual(newseg.marker_id, 'SOC')
+
+    def test_siz(self):
+        """Test SIZ segment repr"""
+        kwargs = {'rsiz': 0,
+                  'xysiz': (2592, 1456),
+                  'xyosiz': (0, 0),
+                  'xytsiz': (2592, 1456),
+                  'xytosiz': (0, 0),
+                  'Csiz': 3,
+                  'bitdepth': (8, 8, 8),
+                  'signed':  (False, False, False),
+                  'xyrsiz': ((1, 1, 1), (1, 1, 1))}
+        segment = glymur.codestream.SIZsegment(**kwargs)
+        newseg = eval(repr(segment))
+        self.assertEqual(newseg.marker_id, 'SIZ')
+        self.assertEqual(newseg.xsiz, 2592)
+        self.assertEqual(newseg.ysiz, 1456)
+        self.assertEqual(newseg.xosiz, 0)
+        self.assertEqual(newseg.yosiz, 0)
+        self.assertEqual(newseg.xtsiz, 2592)
+        self.assertEqual(newseg.ytsiz, 1456)
+        self.assertEqual(newseg.xtosiz, 0)
+        self.assertEqual(newseg.ytosiz, 0)
+
+        self.assertEqual(newseg.xrsiz, (1, 1, 1))
+        self.assertEqual(newseg.yrsiz, (1, 1, 1))
+        self.assertEqual(newseg.bitdepth, (8, 8, 8))
+        self.assertEqual(newseg.signed, (False, False, False))
+
+
+class TestCodestream(unittest.TestCase):
+    """Test suite for unusual codestream cases."""
+
+    def setUp(self):
+        self.jp2file = glymur.data.nemo()
+
+    def tearDown(self):
+        pass
+
+    def test_siz_segment_ssiz_unsigned(self):
+        """ssiz attribute to be removed in future release"""
+        j = Jp2k(self.jp2file)
+        codestream = j.get_codestream()
+
+        # The ssiz attribute was simply a tuple of raw bytes.
+        # The first 7 bits are interpreted as the bitdepth, the MSB determines
+        # whether or not it is signed.
+        self.assertEqual(codestream.segment[1].ssiz, (7, 7, 7))
+
+
+@unittest.skipIf(OPJ_DATA_ROOT is None,
+                 "OPJ_DATA_ROOT environment variable not set")
+class TestCodestreamOpjData(unittest.TestCase):
+    """Test suite for unusual codestream cases.  Uses OPJ_DATA_ROOT"""
+
+    def setUp(self):
+        self.jp2file = glymur.data.nemo()
+
+    def tearDown(self):
+        pass
+
+    @unittest.skipIf(os.name == "nt", "Temporary file issue on window.")
+    def test_reserved_marker_segment(self):
+        """Reserved marker segments are ok."""
+
+        # Some marker segments were reserved in FCD15444-1.  Since that
+        # standard is old, some of them may have come into use.
+        #
+        # Let's inject a reserved marker segment into a file that
+        # we know something about to make sure we can still parse it.
+        filename = os.path.join(OPJ_DATA_ROOT, 'input/conformance/p0_01.j2k')
+        with tempfile.NamedTemporaryFile(suffix='.j2k') as tfile:
+            with open(filename, 'rb') as ifile:
+                # Everything up until the first QCD marker.
+                read_buffer = ifile.read(45)
+                tfile.write(read_buffer)
+
+                # Write the new marker segment, 0xff6f = 65391
+                read_buffer = struct.pack('>HHB', int(65391), int(3), int(0))
+                tfile.write(read_buffer)
+
+                # Get the rest of the input file.
+                read_buffer = ifile.read()
+                tfile.write(read_buffer)
+                tfile.flush()
+
+            codestream = Jp2k(tfile.name).get_codestream()
+
+            self.assertEqual(codestream.segment[2].marker_id, '0xff6f')
+            self.assertEqual(codestream.segment[2].length, 3)
+            self.assertEqual(codestream.segment[2].data, b'\x00')
+
+    def test_psot_is_zero(self):
+        """Psot=0 in SOT is perfectly legal.  Issue #78."""
+        filename = os.path.join(OPJ_DATA_ROOT,
+                                'input/nonregression/123.j2c')
+        j = Jp2k(filename)
+        codestream = 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(codestream.segment[-1].marker_id, 'EOC')
+
+
+    def test_siz_segment_ssiz_signed(self):
+        """ssiz attribute to be removed in future release"""
+        filename = os.path.join(OPJ_DATA_ROOT, 'input/conformance/p0_03.j2k')
+        j = Jp2k(filename)
+        codestream = j.get_codestream()
+
+        # The ssiz attribute was simply a tuple of raw bytes.
+        # The first 7 bits are interpreted as the bitdepth, the MSB determines
+        # whether or not it is signed.
+        self.assertEqual(codestream.segment[1].ssiz, (131,))
+
+
+class TestCodestreamRepr(unittest.TestCase):
+
+    def setUp(self):
+        self.jp2file = glymur.data.nemo()
+
+    def tearDown(self):
+        pass
+
+    def test_soc(self):
+        """Test SOC segment repr"""
+        segment = glymur.codestream.SOCsegment()
+        newseg = eval(repr(segment))
+        self.assertEqual(newseg.marker_id, 'SOC')
+
+    def test_siz(self):
+        """Test SIZ segment repr"""
+        kwargs = {'rsiz': 0,
+                  'xysiz': (2592, 1456),
+                  'xyosiz': (0, 0),
+                  'xytsiz': (2592, 1456),
+                  'xytosiz': (0, 0),
+                  'Csiz': 3,
+                  'bitdepth': (8, 8, 8),
+                  'signed':  (False, False, False),
+                  'xyrsiz': ((1, 1, 1), (1, 1, 1))}
+        segment = glymur.codestream.SIZsegment(**kwargs)
+        newseg = eval(repr(segment))
+        self.assertEqual(newseg.marker_id, 'SIZ')
+        self.assertEqual(newseg.xsiz, 2592)
+        self.assertEqual(newseg.ysiz, 1456)
+        self.assertEqual(newseg.xosiz, 0)
+        self.assertEqual(newseg.yosiz, 0)
+        self.assertEqual(newseg.xtsiz, 2592)
+        self.assertEqual(newseg.ytsiz, 1456)
+        self.assertEqual(newseg.xtosiz, 0)
+        self.assertEqual(newseg.ytosiz, 0)
+
+        self.assertEqual(newseg.xrsiz, (1, 1, 1))
+        self.assertEqual(newseg.yrsiz, (1, 1, 1))
+        self.assertEqual(newseg.bitdepth, (8, 8, 8))
+        self.assertEqual(newseg.signed, (False, False, False))

From 3ebb708e115842f581c2fdcf5952d68341e74822 Mon Sep 17 00:00:00 2001
From: John Evans <john.g.evans@noaa.gov>
Date: Wed, 19 Nov 2014 07:59:05 -0500
Subject: [PATCH 15/23] progress

---
 glymur/jp2k.py           | 5 ++++-
 glymur/test/test_jp2k.py | 5 ++++-
 2 files changed, 8 insertions(+), 2 deletions(-)

diff --git a/glymur/jp2k.py b/glymur/jp2k.py
index 2ea9588..9e2e120 100644
--- a/glymur/jp2k.py
+++ b/glymur/jp2k.py
@@ -1128,7 +1128,10 @@ class Jp2k(Jp2kBox):
 
                 event_mgr = opj.EventMgrType()
                 info_handler = ctypes.cast(_INFO_CALLBACK, ctypes.c_void_p)
-                event_mgr.info_handler = info_handler if verbose else None
+                if verbose or self._verbose:
+                    event_mgr.info_handler = info_handler
+                else:
+                    event_mgr.info_handler = None
                 event_mgr.warning_handler = ctypes.cast(_WARNING_CALLBACK,
                                                         ctypes.c_void_p)
                 event_mgr.error_handler = ctypes.cast(_ERROR_CALLBACK,
diff --git a/glymur/test/test_jp2k.py b/glymur/test/test_jp2k.py
index 7e8c067..553a07e 100644
--- a/glymur/test/test_jp2k.py
+++ b/glymur/test/test_jp2k.py
@@ -227,6 +227,7 @@ class TestSliceProtocolRead(SliceProtocolBase):
         expected = self.j2k_data[3:8, :,:]
         np.testing.assert_array_equal(actual, expected)
 
+    @unittest.skip('see issue 301')
     def test_region_rlevel5(self):
         actual = self.j2k[5:533:32, 27:423:32]
         expected = self.j2k_data_r5[1:17, 1:14]
@@ -288,7 +289,7 @@ class TestJp2k(unittest.TestCase):
         jpx = Jp2k(self.jpxfile)
         self.assertEqual(jpx.shape, (1024, 1024, 3))
 
-    @unittest.skipIf(re.match("1.5|2", glymur.version.openjpeg_version) is None,
+    @unittest.skipIf(re.match("0|1.[0-4]", glymur.version.openjpeg_version),
                      "Must have openjpeg 1.5 or higher to run")
     @unittest.skipIf(os.name == "nt", "Unexplained failure on windows")
     def test_irreversible(self):
@@ -1116,6 +1117,8 @@ class TestJp2kOpjDataRootWarnings(unittest.TestCase):
 class TestJp2kOpjDataRoot(unittest.TestCase):
     """These tests should be run by just about all configuration."""
 
+    @unittest.skipIf(re.match("0|1.[0-4]", glymur.version.openjpeg_version),
+                     "Must have openjpeg 1.5 or higher to run")
     @unittest.skipIf(os.name == "nt", fixtures.WINDOWS_TMP_FILE_MSG)
     def test_irreversible(self):
         """Irreversible"""

From 3c7341509059e083231bd15198b2a28243958bbd Mon Sep 17 00:00:00 2001
From: John Evans <john.g.evans@noaa.gov>
Date: Wed, 19 Nov 2014 09:22:40 -0500
Subject: [PATCH 16/23] progress, no more deprecation warnings?

---
 glymur/test/test_jp2k.py | 10 +++++++---
 1 file changed, 7 insertions(+), 3 deletions(-)

diff --git a/glymur/test/test_jp2k.py b/glymur/test/test_jp2k.py
index 553a07e..5158520 100644
--- a/glymur/test/test_jp2k.py
+++ b/glymur/test/test_jp2k.py
@@ -340,6 +340,7 @@ class TestJp2k(unittest.TestCase):
         self.assertEqual(newjp2.mode, 'rb')
         self.assertEqual(len(newjp2.box), 0)
 
+    @unittest.skip("see issue 302")
     def test_rlevel_max(self):
         """Verify that rlevel=-1 gets us the lowest resolution image"""
         j = Jp2k(self.j2kfile)
@@ -352,7 +353,7 @@ class TestJp2k(unittest.TestCase):
         """Should error out appropriately if reduce level too high"""
         j = Jp2k(self.jp2file)
         with self.assertRaises(IOError):
-            j.read(rlevel=6)
+            j[::64, ::64]
 
     def test_not_jpeg2000(self):
         """Should error out appropriately if not given a JPEG 2000 file."""
@@ -849,8 +850,11 @@ class TestJp2k_1_x(unittest.TestCase):
         """
         with patch('glymur.version.openjpeg_version_tuple', new=(1, 5, 0)):
             j2k = Jp2k(self.j2kfile)
-            with self.assertRaises(TypeError):
-                j2k.read(tile=0)
+            with warnings.catch_warnings():
+                # The tile keyword is deprecated, so suppress the warning.
+                warnings.simplefilter('ignore')
+                with self.assertRaises(TypeError):
+                    j2k.read(tile=0)
 
     def test_layer(self):
         """layer option not allowed for 1.x.

From 6e1637e470b245a2bbf3b74d2dc95c49359e4838 Mon Sep 17 00:00:00 2001
From: John Evans <john.g.evans@noaa.gov>
Date: Wed, 19 Nov 2014 14:25:44 -0500
Subject: [PATCH 17/23] starting on incompatible changes to writing

---
 glymur/jp2k.py                      | 112 +++++++++++++++++++++-------
 glymur/test/test_jp2k.py            | 103 +++++++++++--------------
 glymur/test/test_opj_suite_write.py |   3 +-
 3 files changed, 128 insertions(+), 90 deletions(-)

diff --git a/glymur/jp2k.py b/glymur/jp2k.py
index 9e2e120..2126d89 100644
--- a/glymur/jp2k.py
+++ b/glymur/jp2k.py
@@ -37,16 +37,6 @@ from .jp2box import (
 )
 from .lib import openjpeg as opj, openjp2 as opj2, c as libc
 
-JP2_IDS = ['colr', 'cdef', 'cmap', 'jp2c', 'ftyp', 'ihdr', 'jp2h', 'jP  ',
-           'pclr', 'res ', 'resc', 'resd', 'xml ', 'ulst', 'uinf', 'url ',
-           'uuid']
-JPX_IDS = ['asoc', 'nlst']
-
-_COLORSPACE_MAP = {'rgb': opj2.CLRSPC_SRGB,
-                   'gray': opj2.CLRSPC_GRAY,
-                   'grey': opj2.CLRSPC_GRAY,
-                   'ycc': opj2.CLRSPC_YCC}
-
 class Jp2k(Jp2kBox):
     """JPEG 2000 file.
 
@@ -54,8 +44,6 @@ class Jp2k(Jp2kBox):
     ----------
     filename : str
         The path to the JPEG 2000 file.
-    mode : str
-        The mode used to open the file.
     box : sequence
         List of top-level boxes in the file.  Each box may in turn contain
         its own list of boxes.  Will be empty if the file consists only of a
@@ -92,18 +80,16 @@ class Jp2k(Jp2kBox):
     (728, 1296, 3)
     """
 
-    def __init__(self, filename, mode='rb'):
+    def __init__(self, filename, data=None, shape=None, **kwargs):
         """
         Parameters
         ----------
         filename : str or file
             The path to JPEG 2000 file.
-        mode : str, optional
-            The mode used to open the file.
         """
         Jp2kBox.__init__(self)
         self.filename = filename
-        self.mode = mode
+
         self.box = []
         self._codec_format = None
         self._colorspace = None
@@ -114,8 +100,10 @@ class Jp2k(Jp2kBox):
         self._verbose = False
 
         # Parse the file for JP2/JPX contents only if we are reading it.
-        if mode == 'rb':
+        if data is None and shape is None:
             self.parse()
+        else:
+            self._write(data, **kwargs)
 
     @property
     def ignore_pclr_cmap_cdef(self):
@@ -433,6 +421,77 @@ class Jp2k(Jp2kBox):
 
         self._cparams = cparams
 
+    def _write(self, img_array, verbose=False, **kwargs):
+        """Write image data to a JP2/JPX/J2k file.  Intended usage of the
+        various parameters follows that of OpenJPEG's opj_compress utility.
+
+        This method can only be used to create JPEG 2000 images that can fit
+        in memory.
+
+        Parameters
+        ----------
+        img_array : ndarray
+            Image data to be written to file.
+        cbsize : tuple, optional
+            Code block size (DY, DX).
+        cinema2k : int, optional
+            frames per second, either 24 or 48
+        cinema4k : bool, optional
+            Set to True to specify Cinema4K mode, defaults to false.
+        colorspace : str, optional
+            Either 'rgb' or 'gray'.
+        cratios : iterable
+            Compression ratios for successive layers.
+        eph : bool, optional
+            If true, write SOP marker after each header packet.
+        grid_offset : tuple, optional
+            Offset (DY, DX) of the origin of the image in the reference grid.
+        irreversible : bool, optional
+            If true, use the irreversible DWT 9-7 transform. 
+        mct : bool, optional
+            Specifies usage of the multi component transform.  If not
+            specified, defaults to True if the colorspace is RGB.
+        modesw : int, optional
+            Mode switch.
+                1 = BYPASS(LAZY)
+                2 = RESET
+                4 = RESTART(TERMALL)
+                8 = VSC
+                16 = ERTERM(SEGTERM)
+                32 = SEGMARK(SEGSYM)
+        numres : int, optional
+            Number of resolutions.
+        prog : str, optional
+            Progression order, one of "LRCP" "RLCP", "RPCL", "PCRL", "CPRL".
+        psnr : iterable, optional
+            Different PSNR for successive layers.
+        psizes : list, optional
+            List of precinct sizes.  Each precinct size tuple is defined in
+            (height x width).
+        sop : bool, optional
+            If true, write SOP marker before each packet.
+        subsam : tuple, optional
+            Subsampling factors (dy, dx).
+        tilesize : tuple, optional
+            Numeric tuple specifying tile size in terms of (numrows, numcols),
+            not (X, Y).
+        verbose : bool, optional
+            Print informational messages produced by the OpenJPEG library.
+
+        """
+        if re.match("1.[0-4]", version.openjpeg_version) is not None:
+            raise RuntimeError("You must have at least version 1.5 of OpenJPEG "
+                               "in order to write images.")
+
+        self._shape = img_array.shape
+        self._determine_colorspace(**kwargs)
+        self._populate_cparams(img_array, **kwargs)
+
+        if opj2.OPENJP2 is not None:
+            self._write_openjp2(img_array, verbose=verbose)
+        else:
+            self._write_openjpeg(img_array, verbose=verbose)
+
     def write(self, img_array, verbose=False, **kwargs):
         """Write image data to a JP2/JPX/J2k file.  Intended usage of the
         various parameters follows that of OpenJPEG's opj_compress utility.
@@ -490,16 +549,6 @@ class Jp2k(Jp2kBox):
         verbose : bool, optional
             Print informational messages produced by the OpenJPEG library.
 
-        Examples
-        --------
-        >>> import glymur
-        >>> jfile = glymur.data.nemo()
-        >>> jp2 = glymur.Jp2k(jfile)
-        >>> data = jp2.read(rlevel=1)
-        >>> from tempfile import NamedTemporaryFile
-        >>> tfile = NamedTemporaryFile(suffix='.jp2', delete=False)
-        >>> j = Jp2k(tfile.name, mode='wb')
-        >>> j.write(data.astype(np.uint8))
         """
         if re.match("1.[0-4]", version.openjpeg_version) is not None:
             raise RuntimeError("You must have at least version 1.5 of OpenJPEG "
@@ -679,7 +728,12 @@ class Jp2k(Jp2kBox):
     
             # Turn the colorspace from a string to the enumerated value that
             # the library expects.
-            self._colorspace = _COLORSPACE_MAP[colorspace.lower()]
+            COLORSPACE_MAP = {'rgb': opj2.CLRSPC_SRGB,
+                              'gray': opj2.CLRSPC_GRAY,
+                              'grey': opj2.CLRSPC_GRAY,
+                              'ycc': opj2.CLRSPC_YCC}
+
+            self._colorspace = COLORSPACE_MAP[colorspace.lower()]
     
     
     def _write_openjp2(self, img_array, verbose=False):
@@ -1780,6 +1834,8 @@ def _validate_singletons(boxes):
     if 'dtbl' in multiples:
         raise IOError('There can only be one dtbl box in a file.')
 
+JPX_IDS = ['asoc', 'nlst']
+
 def _validate_jpx_brand(boxes, brand):
     """
     If there is a JPX box then the brand must be 'jpx '.
diff --git a/glymur/test/test_jp2k.py b/glymur/test/test_jp2k.py
index 5158520..257688f 100644
--- a/glymur/test/test_jp2k.py
+++ b/glymur/test/test_jp2k.py
@@ -81,6 +81,7 @@ class SliceProtocolBase(unittest.TestCase):
 @unittest.skipIf(os.name == "nt", fixtures.WINDOWS_TMP_FILE_MSG)
 class TestSliceProtocolBaseWrite(SliceProtocolBase):
 
+    @unittest.skip('requires shape implementation')
     def test_write_ellipsis(self):
         expected = self.j2k_data
 
@@ -95,12 +96,12 @@ class TestSliceProtocolBaseWrite(SliceProtocolBase):
         expected = self.j2k_data
 
         with tempfile.NamedTemporaryFile(suffix='.j2k') as tfile:
-            j = Jp2k(tfile.name, 'wb')
-            j[:] = self.j2k_data
+            j = Jp2k(tfile.name, data=self.j2k_data)
             actual = j[:]
 
         np.testing.assert_array_equal(actual, expected)
 
+    @unittest.skip('requires shape implementation')
     def test_cannot_write_with_non_default_single_slice(self):
         with tempfile.NamedTemporaryFile(suffix='.j2k') as tfile:
             j = Jp2k(tfile.name, 'wb')
@@ -113,30 +114,35 @@ class TestSliceProtocolBaseWrite(SliceProtocolBase):
             with self.assertRaises(TypeError):
                 j[slice(0, 640)] = self.j2k_data
 
+    @unittest.skip('requires shape implementation')
     def test_cannot_write_a_row(self):
         with tempfile.NamedTemporaryFile(suffix='.j2k') as tfile:
             j = Jp2k(tfile.name, 'wb')
             with self.assertRaises(TypeError):
                 j[5] = self.j2k_data
 
+    @unittest.skip('requires shape implementation')
     def test_cannot_write_a_pixel(self):
         with tempfile.NamedTemporaryFile(suffix='.j2k') as tfile:
             j = Jp2k(tfile.name, 'wb')
             with self.assertRaises(TypeError):
                 j[25, 35] = self.j2k_data[25, 35]
 
+    @unittest.skip('requires shape implementation')
     def test_cannot_write_a_column(self):
         with tempfile.NamedTemporaryFile(suffix='.j2k') as tfile:
             j = Jp2k(tfile.name, 'wb')
             with self.assertRaises(TypeError):
                 j[:, 25, :] = self.j2k_data[:, :25, :]
 
+    @unittest.skip('requires shape implementation')
     def test_cannot_write_a_band(self):
         with tempfile.NamedTemporaryFile(suffix='.j2k') as tfile:
             j = Jp2k(tfile.name, 'wb')
             with self.assertRaises(TypeError):
                 j[:, :, 0] = self.j2k_data[:, :, 0]
 
+    @unittest.skip('requires shape implementation')
     def test_cannot_write_a_subarray(self):
         with tempfile.NamedTemporaryFile(suffix='.j2k') as tfile:
             j = Jp2k(tfile.name, 'wb')
@@ -297,8 +303,7 @@ class TestJp2k(unittest.TestCase):
         j = Jp2k(self.jp2file)
         expdata = j[:]
         with tempfile.NamedTemporaryFile(suffix='.j2k') as tfile:
-            j2 = Jp2k(tfile.name, 'wb')
-            j2.write(expdata, irreversible=True)
+            j2 = Jp2k(tfile.name, data=expdata, irreversible=True)
 
             codestream = j2.get_codestream()
             self.assertEqual(codestream.segment[2].spcod[8],
@@ -337,7 +342,6 @@ class TestJp2k(unittest.TestCase):
         newjp2 = eval(repr(j))
 
         self.assertEqual(newjp2.filename, self.j2kfile)
-        self.assertEqual(newjp2.mode, 'rb')
         self.assertEqual(len(newjp2.box), 0)
 
     @unittest.skip("see issue 302")
@@ -664,32 +668,30 @@ class TestJp2k_write(unittest.TestCase):
         data = np.zeros((640, 480), dtype=np.uint8)
         with tempfile.NamedTemporaryFile(suffix='.j2k') as tfile:
             with self.assertRaises(IOError):
-                j = Jp2k(tfile.name, 'wb')
-                j.write(data, cbsize=(16, 16), psizes=[(16, 16)])
+                j = Jp2k(tfile.name, data=data,
+                        cbsize=(16, 16), psizes=[(16, 16)])
 
     def test_precinct_size_not_power_of_two(self):
         """must be power of two"""
         data = np.zeros((640, 480), dtype=np.uint8)
         with tempfile.NamedTemporaryFile(suffix='.j2k') as tfile:
             with self.assertRaises(IOError):
-                j = Jp2k(tfile.name, 'wb')
-                j.write(data, cbsize=(16, 16), psizes=[(48, 48)])
+                j = Jp2k(tfile.name, data=data,
+                        cbsize=(16, 16), psizes=[(48, 48)])
 
     def test_unsupported_int32(self):
         """Should raise a runtime error if trying to write int32"""
         data = np.zeros((128, 128), dtype=np.int32)
         with tempfile.NamedTemporaryFile(suffix='.j2k') as tfile:
             with self.assertRaises(RuntimeError):
-                j = Jp2k(tfile.name, 'wb')
-                j.write(data)
+                j = Jp2k(tfile.name, data=data)
 
     def test_unsupported_uint32(self):
         """Should raise a runtime error if trying to write uint32"""
         data = np.zeros((128, 128), dtype=np.uint32)
         with tempfile.NamedTemporaryFile(suffix='.j2k') as tfile:
             with self.assertRaises(RuntimeError):
-                j = Jp2k(tfile.name, 'wb')
-                j.write(data)
+                j = Jp2k(tfile.name, data=data)
 
     def test_write_with_version_too_early(self):
         """Should raise a runtime error if trying to write with version 1.3"""
@@ -699,8 +701,7 @@ class TestJp2k_write(unittest.TestCase):
             with patch('glymur.version.openjpeg_version', new=version):
                 with tempfile.NamedTemporaryFile(suffix='.j2k') as tfile:
                     with self.assertRaises(RuntimeError):
-                        j = Jp2k(tfile.name, 'wb')
-                        j.write(data)
+                        j = Jp2k(tfile.name, data=data)
 
     def test_cblkh_different_than_width(self):
         """Verify that we can set a code block size where height does not equal
@@ -708,11 +709,8 @@ class TestJp2k_write(unittest.TestCase):
         """
         data = np.zeros((128, 128), dtype=np.uint8)
         with tempfile.NamedTemporaryFile(suffix='.j2k') as tfile:
-            j = Jp2k(tfile.name, 'wb')
-
             # The code block dimensions are given as rows x columns.
-            j.write(data, cbsize=(16, 32))
-
+            j = Jp2k(tfile.name, data=data, cbsize=(16, 32))
             codestream = j.get_codestream()
 
             # Code block size is reported as XY in the codestream.
@@ -721,59 +719,55 @@ class TestJp2k_write(unittest.TestCase):
     def test_too_many_dimensions(self):
         """OpenJP2 only allows 2D or 3D images."""
         with tempfile.NamedTemporaryFile(suffix='.j2k') as tfile:
-            j = Jp2k(tfile.name, 'wb')
             with self.assertRaises(IOError):
-                data = np.zeros((128, 128, 2, 2), dtype=np.uint8)
-                j.write(data)
+                j = Jp2k(tfile.name,
+                        data=np.zeros((128, 128, 2, 2), dtype=np.uint8))
 
     def test_2d_rgb(self):
         """RGB must have at least 3 components."""
         with tempfile.NamedTemporaryFile(suffix='.jp2') as tfile:
-            j = Jp2k(tfile.name, 'wb')
             with self.assertRaises(IOError):
-                data = np.zeros((128, 128, 2), dtype=np.uint8)
-                j.write(data, colorspace='rgb')
+                j = Jp2k(tfile.name,
+                    data=np.zeros((128, 128, 2), dtype=np.uint8),
+                    colorspace='rgb')
 
     def test_colorspace_with_j2k(self):
         """Specifying a colorspace with J2K does not make sense"""
         with tempfile.NamedTemporaryFile(suffix='.j2k') as tfile:
-            j = Jp2k(tfile.name, 'wb')
             with self.assertRaises(IOError):
-                data = np.zeros((128, 128, 3), dtype=np.uint8)
-                j.write(data, colorspace='rgb')
+                j = Jp2k(tfile.name,
+                    data=np.zeros((128, 128, 3), dtype=np.uint8),
+                    colorspace='rgb')
 
     def test_specify_rgb(self):
         """specify RGB explicitly"""
         with tempfile.NamedTemporaryFile(suffix='.jp2') as tfile:
-            j = Jp2k(tfile.name, 'wb')
-            data = np.zeros((128, 128, 3), dtype=np.uint8)
-            j.write(data, colorspace='rgb')
+            j = Jp2k(tfile.name,
+                data=np.zeros((128, 128, 3), dtype=np.uint8),
+                colorspace='rgb')
             self.assertEqual(j.box[2].box[1].colorspace, glymur.core.SRGB)
 
     def test_specify_gray(self):
         """test gray explicitly specified (that's GRAY, not GREY)"""
         with tempfile.NamedTemporaryFile(suffix='.jp2') as tfile:
-            j = Jp2k(tfile.name, 'wb')
             data = np.zeros((128, 128), dtype=np.uint8)
-            j.write(data, colorspace='gray')
+            j = Jp2k(tfile.name, data=data, colorspace='gray')
             self.assertEqual(j.box[2].box[1].colorspace,
                              glymur.core.GREYSCALE)
 
     def test_specify_grey(self):
         """test grey explicitly specified"""
         with tempfile.NamedTemporaryFile(suffix='.jp2') as tfile:
-            j = Jp2k(tfile.name, 'wb')
             data = np.zeros((128, 128), dtype=np.uint8)
-            j.write(data, colorspace='grey')
+            j = Jp2k(tfile.name, data=data, colorspace='grey')
             self.assertEqual(j.box[2].box[1].colorspace,
                              glymur.core.GREYSCALE)
 
     def test_grey_with_two_extra_comps(self):
         """should be able to write gray + two extra components"""
         with tempfile.NamedTemporaryFile(suffix='.jp2') as tfile:
-            j = Jp2k(tfile.name, 'wb')
             data = np.zeros((128, 128, 3), dtype=np.uint8)
-            j.write(data, colorspace='gray')
+            j = Jp2k(tfile.name, data=data, colorspace='gray')
             self.assertEqual(j.box[2].box[0].height, 128)
             self.assertEqual(j.box[2].box[0].width, 128)
             self.assertEqual(j.box[2].box[0].num_components, 3)
@@ -783,18 +777,16 @@ class TestJp2k_write(unittest.TestCase):
     def test_specify_ycc(self):
         """Should reject YCC"""
         with tempfile.NamedTemporaryFile(suffix='.jp2') as tfile:
-            j = Jp2k(tfile.name, 'wb')
             with self.assertRaises(IOError):
                 data = np.zeros((128, 128, 3), dtype=np.uint8)
-                j.write(data, colorspace='ycc')
+                j = Jp2k(tfile.name, data=data, colorspace='ycc')
 
     def test_write_with_jp2_in_caps(self):
         """should be able to write with JP2 suffix."""
         j2k = Jp2k(self.j2kfile)
         expdata = j2k[:]
         with tempfile.NamedTemporaryFile(suffix='.JP2') as tfile:
-            ofile = Jp2k(tfile.name, 'wb')
-            ofile[:] = expdata
+            ofile = Jp2k(tfile.name, data=expdata)
             actdata = ofile[:]
             np.testing.assert_array_equal(actdata, expdata)
 
@@ -803,8 +795,7 @@ class TestJp2k_write(unittest.TestCase):
         j2k = Jp2k(self.j2kfile)
         expdata = j2k[:]
         with tempfile.NamedTemporaryFile(suffix='.jp2') as tfile:
-            ofile = Jp2k(tfile.name, 'wb')
-            ofile.write(expdata, mct=False)
+            ofile = Jp2k(tfile.name, data=expdata, mct=False)
             actdata = ofile[:]
             np.testing.assert_array_equal(actdata, expdata)
 
@@ -816,9 +807,8 @@ class TestJp2k_write(unittest.TestCase):
         j2k = Jp2k(self.j2kfile)
         expdata = j2k[:]
         with tempfile.NamedTemporaryFile(suffix='.jp2') as tfile:
-            ofile = Jp2k(tfile.name, 'wb')
             with self.assertRaises(IOError):
-                ofile.write(expdata[:, :, 0], mct=True)
+                ofile = Jp2k(tfile.name, data=expdata[:, :, 0], mct=True)
 
     def test_write_cprl(self):
         """Must be able to write a CPRL progression order file"""
@@ -826,8 +816,7 @@ class TestJp2k_write(unittest.TestCase):
         j = Jp2k(self.jp2file)
         expdata = j[::2, ::2]
         with tempfile.NamedTemporaryFile(suffix='.jp2') as tfile:
-            ofile = Jp2k(tfile.name, 'wb')
-            ofile.write(expdata, prog='CPRL')
+            ofile = Jp2k(tfile.name, data=expdata, prog='CPRL')
             actdata = ofile[:]
             np.testing.assert_array_equal(actdata, expdata)
 
@@ -873,10 +862,9 @@ class Test_2p0_official(unittest.TestCase):
         """Can only write 4 components on 2.0+, should error out otherwise."""
         with patch('glymur.version.openjpeg_version', new="2.0.0"):
             with tempfile.NamedTemporaryFile(suffix='.jp2') as tfile:
-                j = Jp2k(tfile.name, 'wb')
                 data = np.zeros((128, 128, 4), dtype=np.uint8)
                 with self.assertRaises(IOError):
-                    j.write(data)
+                    Jp2k(tfile.name, data=data)
 
 
 @unittest.skipIf(glymur.version.openjpeg_version_tuple[0] < 2,
@@ -908,10 +896,9 @@ class TestJp2k_2_0(unittest.TestCase):
     def test_unrecognized_jp2_clrspace(self):
         """We only allow RGB and GRAYSCALE.  Should error out with others"""
         with tempfile.NamedTemporaryFile(suffix='.jp2') as tfile:
-            j = Jp2k(tfile.name, 'wb')
+            data = np.zeros((128, 128, 3), dtype=np.uint8)
             with self.assertRaises(IOError):
-                data = np.zeros((128, 128, 3), dtype=np.uint8)
-                j.write(data, colorspace='cmyk')
+                j = Jp2k(tfile.name, data=data, colorspace='cmyk')
 
     @unittest.skipIf(os.name == "nt", fixtures.WINDOWS_TMP_FILE_MSG)
     def test_asoc_label_box(self):
@@ -920,8 +907,7 @@ class TestJp2k_2_0(unittest.TestCase):
         # OpenJPEG doesn't have such a file.
         data = Jp2k(self.jp2file)[::2, ::2]
         with tempfile.NamedTemporaryFile(suffix='.jp2') as tfile:
-            j = Jp2k(tfile.name, 'wb')
-            j.write(data)
+            j = Jp2k(tfile.name, data=data)
 
             with tempfile.NamedTemporaryFile(suffix='.jp2') as tfile2:
 
@@ -979,9 +965,8 @@ class TestJp2k_2_1(unittest.TestCase):
     def test_grey_with_extra_component(self):
         """version 2.0 cannot write gray + extra"""
         with tempfile.NamedTemporaryFile(suffix='.jp2') as tfile:
-            j = Jp2k(tfile.name, 'wb')
             data = np.zeros((128, 128, 2), dtype=np.uint8)
-            j.write(data)
+            j = Jp2k(tfile.name, data=data)
             self.assertEqual(j.box[2].box[0].height, 128)
             self.assertEqual(j.box[2].box[0].width, 128)
             self.assertEqual(j.box[2].box[0].num_components, 2)
@@ -992,9 +977,8 @@ class TestJp2k_2_1(unittest.TestCase):
     def test_rgb_with_extra_component(self):
         """v2.0+ should be able to write extra components"""
         with tempfile.NamedTemporaryFile(suffix='.jp2') as tfile:
-            j = Jp2k(tfile.name, 'wb')
             data = np.zeros((128, 128, 4), dtype=np.uint8)
-            j.write(data)
+            j = Jp2k(tfile.name, data=data)
             self.assertEqual(j.box[2].box[0].height, 128)
             self.assertEqual(j.box[2].box[0].width, 128)
             self.assertEqual(j.box[2].box[0].num_components, 4)
@@ -1130,8 +1114,7 @@ class TestJp2kOpjDataRoot(unittest.TestCase):
         expdata = np.fromfile(filename, dtype=np.uint16)
         expdata.resize((2816, 2048))
         with tempfile.NamedTemporaryFile(suffix='.j2k') as tfile:
-            j = Jp2k(tfile.name, 'wb')
-            j.write(expdata, irreversible=True)
+            j = Jp2k(tfile.name, data=expdata, irreversible=True)
 
             codestream = j.get_codestream()
             self.assertEqual(codestream.segment[2].spcod[8],
diff --git a/glymur/test/test_opj_suite_write.py b/glymur/test/test_opj_suite_write.py
index 8be1cef..b394d72 100644
--- a/glymur/test/test_opj_suite_write.py
+++ b/glymur/test/test_opj_suite_write.py
@@ -221,9 +221,8 @@ class TestNegative2pointzero(unittest.TestCase):
         for version in versions:
             with patch('glymur.version.openjpeg_version', new=version):
                 with tempfile.NamedTemporaryFile(suffix='.j2k') as tfile:
-                    j = Jp2k(tfile.name, 'wb')
                     with self.assertRaises(IOError):
-                        j.write(data, cinema2k=48)
+                        j = Jp2k(tfile.name, data=data, cinema2k=48)
 
 
 @unittest.skipIf(re.match(r'''1.[0-4]''', openjpeg_version) is not None,

From 8f8e9eff852d7f064c713983c9f64fb590212ba7 Mon Sep 17 00:00:00 2001
From: John Evans <john.g.evans@noaa.gov>
Date: Wed, 19 Nov 2014 14:49:15 -0500
Subject: [PATCH 18/23] get write tests passing on travis

---
 glymur/test/test_jp2box.py   | 16 ++++++----------
 glymur/test/test_printing.py |  3 +--
 2 files changed, 7 insertions(+), 12 deletions(-)

diff --git a/glymur/test/test_jp2box.py b/glymur/test/test_jp2box.py
index b8ad2ec..9d1f9cf 100644
--- a/glymur/test/test_jp2box.py
+++ b/glymur/test/test_jp2box.py
@@ -59,13 +59,12 @@ class TestDataEntryURL(unittest.TestCase):
     def test_wrap_greyscale(self):
         """A single component should be wrapped as GREYSCALE."""
         j = Jp2k(self.jp2file)
-        data = j.read()
+        data = j[:]
         red = data[:, :, 0]
 
         # Write it back out as a raw codestream.
         with tempfile.NamedTemporaryFile(suffix=".j2k") as tfile1:
-            j2k = glymur.Jp2k(tfile1.name, 'wb')
-            j2k.write(data[:, :, 0])
+            j2k = glymur.Jp2k(tfile1.name, data=red)
 
             # Ok, now rewrap it as JP2.  The colorspace should be GREYSCALE.
             with tempfile.NamedTemporaryFile(suffix=".jp2") as tfile2:
@@ -126,24 +125,21 @@ class TestChannelDefinition(unittest.TestCase):
     def setUpClass(cls):
         """Need a one_plane plane image for greyscale testing."""
         j2k = Jp2k(glymur.data.goodstuff())
-        data = j2k.read()
+        data = j2k[:]
         # Write the first component back out to file.
         with tempfile.NamedTemporaryFile(suffix=".j2k", delete=False) as tfile:
-            grey_j2k = Jp2k(tfile.name, 'wb')
-            grey_j2k.write(data[:, :, 0])
+            grey_j2k = Jp2k(tfile.name, data=data[:, :, 0])
             cls.one_plane = tfile.name
         # Write the first two components back out to file.
         with tempfile.NamedTemporaryFile(suffix=".j2k", delete=False) as tfile:
-            grey_j2k = Jp2k(tfile.name, 'wb')
-            grey_j2k.write(data[:, :, 0:1])
+            grey_j2k = Jp2k(tfile.name, data=data[:, :, 0:1])
             cls.two_planes = tfile.name
         # Write four components back out to file.
         with tempfile.NamedTemporaryFile(suffix=".j2k", delete=False) as tfile:
-            rgba_jp2 = Jp2k(tfile.name, 'wb')
             shape = (data.shape[0], data.shape[1], 1)
             alpha = np.zeros((shape), dtype=data.dtype)
             data4 = np.concatenate((data, alpha), axis=2)
-            rgba_jp2.write(data4)
+            rgba_jp2 = Jp2k(tfile.name, data=data4)
             cls.four_planes = tfile.name
 
     @classmethod
diff --git a/glymur/test/test_printing.py b/glymur/test/test_printing.py
index 5dae016..5eedfe5 100644
--- a/glymur/test/test_printing.py
+++ b/glymur/test/test_printing.py
@@ -115,8 +115,7 @@ class TestPrinting(unittest.TestCase):
         # OpenJPEG doesn't have such a file.
         data = glymur.Jp2k(self.jp2file)[::2, ::2]
         with tempfile.NamedTemporaryFile(suffix='.jp2') as tfile:
-            j = glymur.Jp2k(tfile.name, 'wb')
-            j.write(data)
+            j = glymur.Jp2k(tfile.name, data=data)
 
             with tempfile.NamedTemporaryFile(suffix='.jp2') as tfile2:
 

From e1846c31e0cb2bfab24456eb26c4b6f3ed539fa6 Mon Sep 17 00:00:00 2001
From: John Evans <john.g.evans@noaa.gov>
Date: Wed, 19 Nov 2014 15:34:03 -0500
Subject: [PATCH 19/23] progress on write

---
 glymur/test/test_callbacks.py       |  4 +--
 glymur/test/test_opj_suite_neg.py   | 27 ++++++---------
 glymur/test/test_opj_suite_write.py | 53 ++++++++++++-----------------
 3 files changed, 33 insertions(+), 51 deletions(-)

diff --git a/glymur/test/test_callbacks.py b/glymur/test/test_callbacks.py
index a58cfeb..d8fc28e 100644
--- a/glymur/test/test_callbacks.py
+++ b/glymur/test/test_callbacks.py
@@ -60,10 +60,8 @@ class TestCallbacks(unittest.TestCase):
         j = glymur.Jp2k(self.jp2file)
         tiledata = j[:]
         with tempfile.NamedTemporaryFile(suffix='.jp2') as tfile:
-            jp2 = glymur.Jp2k(tfile.name, 'wb')
             with patch('sys.stdout', new=StringIO()) as fake_out:
-                jp2.verbose = True
-                jp2[:] = tiledata
+                jp2 = glymur.Jp2k(tfile.name, data=tiledata, verbose=True)
                 actual = fake_out.getvalue().strip()
         expected = '[INFO] tile number 1 / 1'
         self.assertEqual(actual, expected)
diff --git a/glymur/test/test_opj_suite_neg.py b/glymur/test/test_opj_suite_neg.py
index 350b7a5..c7e31e5 100644
--- a/glymur/test/test_opj_suite_neg.py
+++ b/glymur/test/test_opj_suite_neg.py
@@ -97,9 +97,8 @@ class TestSuiteNegativeWrite(unittest.TestCase):
         infile = opj_data_file(relfile)
         data = skimage.io.imread(infile)
         with tempfile.NamedTemporaryFile(suffix='.j2k') as tfile:
-            j = Jp2k(tfile.name, 'wb')
             with self.assertRaises(IOError):
-                j.write(data, cinema2k=36)
+                j = Jp2k(tfile.name, data=data, cinema2k=36)
 
 
     @unittest.skipIf(NO_READ_BACKEND, NO_READ_BACKEND_MSG)
@@ -109,9 +108,9 @@ class TestSuiteNegativeWrite(unittest.TestCase):
         infile = opj_data_file('input/nonregression/Bretagne1.ppm')
         data = read_image(infile)
         with tempfile.NamedTemporaryFile(suffix='.j2k') as tfile:
-            j = Jp2k(tfile.name, 'wb')
             with self.assertRaises(IOError):
-                j.write(data, psnr=[30, 35, 40], cratios=[2, 3, 4])
+                j = Jp2k(tfile.name, 
+                        data=data, psnr=[30, 35, 40], cratios=[2, 3, 4])
 
     def test_code_block_dimensions(self):
         """don't allow extreme codeblock sizes"""
@@ -119,44 +118,38 @@ class TestSuiteNegativeWrite(unittest.TestCase):
         # to be too small or too big, so neither will we.
         data = np.zeros((256, 256), dtype=np.uint8)
         with tempfile.NamedTemporaryFile(suffix='.j2k') as tfile:
-            j = Jp2k(tfile.name, 'wb')
-
             # opj_compress doesn't allow code block area to exceed 4096.
             with self.assertRaises(IOError):
-                j.write(data, cbsize=(256, 256))
+                j = Jp2k(tfile.name, data=data, cbsize=(256, 256))
 
             # opj_compress doesn't allow either dimension to be less than 4.
             with self.assertRaises(IOError):
-                j.write(data, cbsize=(2048, 2))
+                j = Jp2k(tfile.name, data=data, cbsize=(2048, 2))
             with self.assertRaises(IOError):
-                j.write(data, cbsize=(2, 2048))
+                j = Jp2k(tfile.name, data=data, cbsize=(2, 2048))
 
     def test_precinct_size_not_p2(self):
         """precinct sizes should be powers of two."""
         ifile = Jp2k(self.j2kfile)
         data = ifile[::4, ::4]
         with tempfile.NamedTemporaryFile(suffix='.jp2') as tfile:
-            ofile = Jp2k(tfile.name, 'wb')
             with self.assertRaises(IOError):
-                ofile.write(data, psizes=[(13, 13)])
+                ofile = Jp2k(tfile.name, data=data, psizes=[(13, 13)])
 
     def test_cblk_size_not_power_of_two(self):
         """code block sizes should be powers of two."""
         ifile = Jp2k(self.j2kfile)
         data = ifile[::4, ::4]
         with tempfile.NamedTemporaryFile(suffix='.jp2') as tfile:
-            ofile = Jp2k(tfile.name, 'wb')
             with self.assertRaises(IOError):
-                ofile.write(data, cbsize=(13, 12))
+                ofile = Jp2k(tfile.name, data=data, cbsize=(13, 12))
 
     def test_cblk_size_precinct_size(self):
         """code block sizes should never exceed half that of precinct size."""
         ifile = Jp2k(self.j2kfile)
         data = ifile[::4, ::4]
         with tempfile.NamedTemporaryFile(suffix='.jp2') as tfile:
-            ofile = Jp2k(tfile.name, 'wb')
             with self.assertRaises(IOError):
-                ofile.write(data,
-                            cbsize=(64, 64),
-                            psizes=[(64, 64)])
+                ofile = Jp2k(tfile.name, 
+                        data=data, cbsize=(64, 64), psizes=[(64, 64)])
 
diff --git a/glymur/test/test_opj_suite_write.py b/glymur/test/test_opj_suite_write.py
index b394d72..9d8f5b7 100644
--- a/glymur/test/test_opj_suite_write.py
+++ b/glymur/test/test_opj_suite_write.py
@@ -87,9 +87,9 @@ class WriteCinema(CinemaBase):
         infile = opj_data_file(relfile)
         data = skimage.io.imread(infile)
         with tempfile.NamedTemporaryFile(suffix='.j2k') as tfile:
-            j = Jp2k(tfile.name, 'wb')
             with self.assertRaises(IOError):
-                j.write(data, cinema2k=48, cratios=[200, 100, 50])
+                j = Jp2k(tfile.name, data=data,
+                        cinema2k=48, cratios=[200, 100, 50])
 
     def test_cinema4K_with_others(self):
         """Can't specify cinema4k with any other options."""
@@ -97,9 +97,9 @@ class WriteCinema(CinemaBase):
         infile = opj_data_file(relfile)
         data = skimage.io.imread(infile)
         with tempfile.NamedTemporaryFile(suffix='.j2k') as tfile:
-            j = Jp2k(tfile.name, 'wb')
             with self.assertRaises(IOError):
-                j.write(data, cinema4k=True, cratios=[200, 100, 50])
+                j = Jp2k(tfile.name, data=data,
+                        cinema4k=True, cratios=[200, 100, 50])
 
 
 @unittest.skipIf(WARNING_INFRASTRUCTURE_ISSUE, WARNING_INFRASTRUCTURE_MSG)
@@ -248,8 +248,7 @@ class TestSuiteWrite(fixtures.MetadataBase):
         expdata = np.fromfile(filename, dtype=np.uint16)
         expdata.resize((2816, 2048))
         with tempfile.NamedTemporaryFile(suffix='.j2k') as tfile:
-            j = Jp2k(tfile.name, 'wb')
-            j.write(expdata, irreversible=True)
+            j = Jp2k(tfile.name, data=expdata, irreversible=True)
 
             codestream = j.get_codestream()
             self.assertEqual(codestream.segment[2].spcod[8],
@@ -261,8 +260,7 @@ class TestSuiteWrite(fixtures.MetadataBase):
         infile = opj_data_file('input/nonregression/Bretagne1.ppm')
         data = read_image(infile)
         with tempfile.NamedTemporaryFile(suffix='.j2k') as tfile:
-            j = Jp2k(tfile.name, 'wb')
-            j.write(data, cratios=[200, 100, 50])
+            j = Jp2k(tfile.name, data=data, cratios=[200, 100, 50])
 
             # Should be three layers.
             c = j.get_codestream()
@@ -293,8 +291,7 @@ class TestSuiteWrite(fixtures.MetadataBase):
         infile = opj_data_file('input/nonregression/Bretagne1.ppm')
         data = read_image(infile)
         with tempfile.NamedTemporaryFile(suffix='.j2k') as tfile:
-            j = Jp2k(tfile.name, 'wb')
-            j.write(data, psnr=[30, 35, 40], numres=2)
+            j = Jp2k(tfile.name, data=data, psnr=[30, 35, 40], numres=2)
 
             # Should be three layers.
             codestream = j.get_codestream()
@@ -325,9 +322,9 @@ class TestSuiteWrite(fixtures.MetadataBase):
         infile = opj_data_file('input/nonregression/Bretagne1.ppm')
         data = read_image(infile)
         with tempfile.NamedTemporaryFile(suffix='.j2k') as tfile:
-            j = Jp2k(tfile.name, 'wb')
-            j.write(data, psnr=[30, 35, 40], cbsize=(16, 16),
-                    psizes=[(64, 64)])
+            j = Jp2k(tfile.name, 
+                    data=data,
+                    psnr=[30, 35, 40], cbsize=(16, 16), psizes=[(64, 64)])
 
             # Should be three layers.
             codestream = j.get_codestream()
@@ -360,8 +357,8 @@ class TestSuiteWrite(fixtures.MetadataBase):
         infile = opj_data_file('input/nonregression/Bretagne2.ppm')
         data = read_image(infile)
         with tempfile.NamedTemporaryFile(suffix='.j2k') as tfile:
-            j = Jp2k(tfile.name, 'wb')
-            j.write(data,
+            j = Jp2k(tfile.name,
+                    data=data,
                     psizes=[(128, 128)] * 3,
                     cratios=[100, 20, 2],
                     tilesize=(480, 640),
@@ -397,8 +394,7 @@ class TestSuiteWrite(fixtures.MetadataBase):
         infile = opj_data_file('input/nonregression/Bretagne2.ppm')
         data = read_image(infile)
         with tempfile.NamedTemporaryFile(suffix='.j2k') as tfile:
-            j = Jp2k(tfile.name, 'wb')
-            j.write(data, tilesize=(127, 127), prog="PCRL")
+            j = Jp2k(tfile.name, data=data, tilesize=(127, 127), prog="PCRL")
 
             codestream = j.get_codestream()
 
@@ -428,8 +424,7 @@ class TestSuiteWrite(fixtures.MetadataBase):
         infile = opj_data_file('input/nonregression/Bretagne2.ppm')
         data = read_image(infile)
         with tempfile.NamedTemporaryFile(suffix='.j2k') as tfile:
-            j = Jp2k(tfile.name, 'wb')
-            j.write(data, subsam=(2, 2), sop=True)
+            j = Jp2k(tfile.name, data=data, subsam=(2, 2), sop=True)
 
             codestream = j.get_codestream(header_only=False)
 
@@ -464,8 +459,7 @@ class TestSuiteWrite(fixtures.MetadataBase):
         infile = opj_data_file('input/nonregression/Bretagne2.ppm')
         data = read_image(infile)
         with tempfile.NamedTemporaryFile(suffix='.j2k') as tfile:
-            j = Jp2k(tfile.name, 'wb')
-            j.write(data, modesw=38, eph=True)
+            j = Jp2k(tfile.name, data=data, modesw=38, eph=True)
 
             codestream = j.get_codestream(header_only=False)
 
@@ -499,8 +493,8 @@ class TestSuiteWrite(fixtures.MetadataBase):
         infile = opj_data_file('input/nonregression/Bretagne2.ppm')
         data = read_image(infile)
         with tempfile.NamedTemporaryFile(suffix='.j2k') as tfile:
-            j = Jp2k(tfile.name, 'wb')
-            j.write(data, grid_offset=[300, 150], cratios=[800])
+            j = Jp2k(tfile.name,
+                    data=data, grid_offset=[300, 150], cratios=[800])
 
             codestream = j.get_codestream(header_only=False)
 
@@ -530,8 +524,7 @@ class TestSuiteWrite(fixtures.MetadataBase):
         infile = opj_data_file('input/nonregression/Cevennes1.bmp')
         data = read_image(infile)
         with tempfile.NamedTemporaryFile(suffix='.j2k') as tfile:
-            j = Jp2k(tfile.name, 'wb')
-            j.write(data, cratios=[800])
+            j = Jp2k(tfile.name, data=data, cratios=[800])
 
             codestream = j.get_codestream(header_only=False)
 
@@ -561,8 +554,7 @@ class TestSuiteWrite(fixtures.MetadataBase):
         infile = opj_data_file('input/nonregression/Cevennes2.ppm')
         data = read_image(infile)
         with tempfile.NamedTemporaryFile(suffix='.j2k') as tfile:
-            j = Jp2k(tfile.name, 'wb')
-            j.write(data, cratios=[50])
+            j = Jp2k(tfile.name, data=data, cratios=[50])
 
             codestream = j.get_codestream(header_only=False)
 
@@ -591,8 +583,8 @@ class TestSuiteWrite(fixtures.MetadataBase):
         """NR-ENC-Rome.bmp-11-encode"""
         data = read_image(opj_data_file('input/nonregression/Rome.bmp'))
         with tempfile.NamedTemporaryFile(suffix='.jp2') as tfile:
-            jp2 = Jp2k(tfile.name, 'wb')
-            jp2.write(data, psnr=[30, 35, 50], prog='LRCP', numres=3)
+            jp2 = Jp2k(tfile.name,
+                    data=data, psnr=[30, 35, 50], prog='LRCP', numres=3)
 
             ids = [box.box_id for box in jp2.box]
             self.assertEqual(ids, ['jP  ', 'ftyp', 'jp2h', 'jp2c'])
@@ -657,8 +649,7 @@ class TestSuiteWrite(fixtures.MetadataBase):
         infile = opj_data_file('input/nonregression/random-issue-0005.tif')
         data = read_image(infile)
         with tempfile.NamedTemporaryFile(suffix='.j2k') as tfile:
-            j = Jp2k(tfile.name, 'wb')
-            j.write(data)
+            j = Jp2k(tfile.name, data=data)
 
             codestream = j.get_codestream(header_only=False)
 

From 5e8a66c38e80c1476cd5518e00a42a223f54644e Mon Sep 17 00:00:00 2001
From: John Evans <john.g.evans.ne@gmail.com>
Date: Wed, 19 Nov 2014 17:08:29 -0500
Subject: [PATCH 20/23] fix tab error

---
 glymur/test/test_callbacks.py | 5 ++---
 1 file changed, 2 insertions(+), 3 deletions(-)

diff --git a/glymur/test/test_callbacks.py b/glymur/test/test_callbacks.py
index d8fc28e..c29f816 100644
--- a/glymur/test/test_callbacks.py
+++ b/glymur/test/test_callbacks.py
@@ -45,10 +45,9 @@ class TestCallbacks(unittest.TestCase):
         with self.assertWarns(UserWarning):
             tiledata = j.read(tile=0)
         with tempfile.NamedTemporaryFile(suffix='.jp2') as tfile:
-            j = glymur.Jp2k(tfile.name, 'wb')
             with patch('sys.stdout', new=StringIO()) as fake_out:
-                j.write(tiledata, verbose=True)
-                actual = fake_out.getvalue().strip()
+            	j = glymur.Jp2k(tfile.name, data=tiledata, verbose=True)
+            actual = fake_out.getvalue().strip()
         expected = '[INFO] tile number 1 / 1'
         self.assertEqual(actual, expected)
 

From 3f7c08739c7c28a381e8fa4a217a0f3b60eb9c0d Mon Sep 17 00:00:00 2001
From: jevans <john.g.evans.ne@gmail.com>
Date: Wed, 19 Nov 2014 23:09:12 -0500
Subject: [PATCH 21/23] progress

---
 docs/source/how_do_i.rst            |  20 ++-
 docs/source/roadmap.rst             |   9 --
 docs/source/whatsnew/0.7.rst        |  18 ++-
 docs/source/whatsnew/0.8.rst        |  10 ++
 docs/source/whatsnew/index.rst      |   5 +-
 glymur/jp2k.py                      | 189 +++++++++-------------------
 glymur/test/test_jp2k.py            |  30 ++---
 glymur/test/test_opj_suite_dump.py  |   3 +-
 glymur/test/test_opj_suite_write.py |  18 +--
 9 files changed, 117 insertions(+), 185 deletions(-)
 create mode 100644 docs/source/whatsnew/0.8.rst

diff --git a/docs/source/how_do_i.rst b/docs/source/how_do_i.rst
index 5d11d67..65647fa 100644
--- a/docs/source/how_do_i.rst
+++ b/docs/source/how_do_i.rst
@@ -25,16 +25,14 @@ features such as quality layers.
 
 ... write images?
 =================
-So long as the image data can fit entirely into memory, array-style slicing may
-also be used to write JPEG 2000 files.
+It's pretty simple, just supply the image data as the 2nd argument to the Jp2k
+constructor.
     
     >>> import glymur, numpy as np
-    >>> jp2 = glymur.Jp2k('zeros.jp2', mode='wb')
-    >>> jp2[:] = np.zeros((640, 480), dtype=np.uint8)
+    >>> data = np.zeros((640, 480), dtype=np.uint8)
+    >>> jp2 = glymur.Jp2k('zeros.jp2', data=data)
 
-The :py:meth:`write` method exposes many more options for other JPEG 2000
-features.  You should have OpenJPEG version 1.5 or more recent before writing
-JPEG 2000 images.
+You should have OpenJPEG version 1.5 or more recent before writing JPEG 2000 images.
 
 ... display metadata?
 =====================
@@ -354,15 +352,14 @@ image isn't square. ::
     >>> import numpy as np
     >>> import glymur
     >>> from glymur import Jp2k
-    >>> rgb = Jp2k(glymur.data.goodstuff()).read()
+    >>> rgb = Jp2k(glymur.data.goodstuff())[:]
     >>> lx, ly = rgb.shape[0:2]
     >>> X, Y = np.ogrid[0:lx, 0:ly]
     >>> mask = ly**2*(X - lx / 2) ** 2 + lx**2*(Y - ly / 2) ** 2 > (lx * ly / 2)**2
     >>> alpha = 255 * np.ones((lx, ly, 1), dtype=np.uint8)
     >>> alpha[mask] = 0
     >>> rgba = np.concatenate((rgb, alpha), axis=2)
-    >>> jp2 = Jp2k('tmp.jp2', 'wb')
-    >>> jp2[:] = rgba
+    >>> jp2 = Jp2k('tmp.jp2', data=rgba)
 
 Next we need to specify what types of channels we have.
 The first three channels are color channels, but we identify the fourth as
@@ -465,8 +462,7 @@ http://photojournal.jpl.nasa.gov/tiff/PIA17145.tif info JPEG 2000::
     >>> import skimage.io
     >>> image = skimage.io.imread('PIA17145.tif')
     >>> from glymur import Jp2k
-    >>> jp2 = Jp2k('PIA17145.jp2', 'wb')
-    >>> jp2[:] = image
+    >>> jp2 = Jp2k('PIA17145.jp2', data=image)
 
 Next you can extract the XMP metadata.
 
diff --git a/docs/source/roadmap.rst b/docs/source/roadmap.rst
index 503fbc4..f0d7017 100644
--- a/docs/source/roadmap.rst
+++ b/docs/source/roadmap.rst
@@ -1,12 +1,3 @@
--------------------------------------
-Platforms Tested (0.7.0 release only)
--------------------------------------
-    * Linux Mint 17 / Python 3.4.0 and 2.7.6 / OpenJPEG 2.1.0 and 1.3.0
-    * MacOS 10.6.8 / MacPorts Python 3.4.1, 3.3.5,and 2.7.8 / OpenJPEG 2.1.0
-    * CentOS 6.5 / Anaconda Python 3.4.1 / OpenJPEG 1.3.0
-    * Fedora 20 i386 / Python 2.7.5 and 3.3.2 / OpenJPEG 1.5.1
-    * Windows 7 32bit / Anaconda Python 2.7.6 and 3.4.1 / OpenJPEG 2.1.0
-
 ------------
 Known Issues
 ------------
diff --git a/docs/source/whatsnew/0.7.rst b/docs/source/whatsnew/0.7.rst
index 0a21d9b..3ed7715 100644
--- a/docs/source/whatsnew/0.7.rst
+++ b/docs/source/whatsnew/0.7.rst
@@ -2,10 +2,26 @@
 Changes in glymur 0.7
 =====================
 
+Changes in 0.7.3
+=================
+    
+    * added read support back for metadata only when the OpenJPEG library is
+      not installed
+
+Changes in 0.7.2
+=================
+
+    * added ellipsis support in array-style slicing
+
+Changes in 0.7.1
+=================
+
+    * fixed release notes regarding Python 3.4
+
 Changes in 0.7.0
 =================
 
     * implemented :py:meth:`__getitem__`, :py:meth:`__setitem__` support
     * added back windows support
     * box_id and longname are class attributes now instead of instance
-      attributes (see issue 248)
+      attributes
diff --git a/docs/source/whatsnew/0.8.rst b/docs/source/whatsnew/0.8.rst
new file mode 100644
index 0000000..f36b593
--- /dev/null
+++ b/docs/source/whatsnew/0.8.rst
@@ -0,0 +1,10 @@
+=====================
+Changes in glymur 0.8
+=====================
+
+Changes in 0.8.0
+=================
+
+    * Simplified writing images by moving data and options into the
+      constructor.  This is backwards-incompatible with 0.7.x.
+    * Deprecated :py:meth:`read` method in favor of array-style slicing.
diff --git a/docs/source/whatsnew/index.rst b/docs/source/whatsnew/index.rst
index 2d69949..4569abd 100644
--- a/docs/source/whatsnew/index.rst
+++ b/docs/source/whatsnew/index.rst
@@ -8,6 +8,7 @@ These document the changes between minor (or major) versions of glymur.
 
 .. toctree::
 
-    0.5
-    0.6
+    0.8
     0.7
+    0.6
+    0.5
diff --git a/glymur/jp2k.py b/glymur/jp2k.py
index 2126d89..d7e04bb 100644
--- a/glymur/jp2k.py
+++ b/glymur/jp2k.py
@@ -82,10 +82,63 @@ class Jp2k(Jp2kBox):
 
     def __init__(self, filename, data=None, shape=None, **kwargs):
         """
+        Only the filename parameter is required in order to read a JPEG 2000
+        file.
+
         Parameters
         ----------
         filename : str or file
-            The path to JPEG 2000 file.
+            the path to JPEG 2000 file
+        image_data : ndarray, optional
+            image data to be written
+        shape : tuple
+            size of image data, only required when image_data is not provided
+        cbsize : tuple, optional
+            code block size (DY, DX)
+        cinema2k : int, optional
+            frames per second, either 24 or 48
+        cinema4k : bool, optional
+            set to True to specify Cinema4K mode, defaults to false
+        colorspace : str, optional
+            either 'rgb' or 'gray'
+        cratios : iterable
+            compression ratios for successive layers
+        eph : bool, optional
+            if true, write SOP marker after each header packet
+        grid_offset : tuple, optional
+            offset (DY, DX) of the origin of the image in the reference grid
+        irreversible : bool, optional
+            if true, use the irreversible DWT 9-7 transform
+        mct : bool, optional
+            specifies usage of the multi component transform, if not
+            specified, defaults to True if the colorspace is RGB
+        modesw : int, optional
+            mode switch
+                1 = BYPASS(LAZY)
+                2 = RESET
+                4 = RESTART(TERMALL)
+                8 = VSC
+                16 = ERTERM(SEGTERM)
+                32 = SEGMARK(SEGSYM)
+        numres : int, optional
+            number of resolutions
+        prog : str, optional
+            progression order, one of "LRCP" "RLCP", "RPCL", "PCRL", "CPRL"
+        psnr : iterable, optional
+            different PSNR for successive layers
+        psizes : list, optional
+            list of precinct sizes, each precinct size tuple is defined in
+            (height x width)
+        sop : bool, optional
+            if true, write SOP marker before each packet
+        subsam : tuple, optional
+            subsampling factors (dy, dx)
+        tilesize : tuple, optional
+            numeric tuple specifying tile size in terms of (numrows, numcols),
+            not (X, Y)
+        verbose : bool, optional
+            print informational messages produced by the OpenJPEG library
+            
         """
         Jp2kBox.__init__(self)
         self.filename = filename
@@ -93,8 +146,11 @@ class Jp2k(Jp2kBox):
         self.box = []
         self._codec_format = None
         self._colorspace = None
-        self._shape = None
         self._layer = 0
+        if data is not None:
+            self._shape = data.shape
+        else:
+            self._shape = shape
 
         self._ignore_pclr_cmap_cdef = False
         self._verbose = False
@@ -102,7 +158,7 @@ class Jp2k(Jp2kBox):
         # Parse the file for JP2/JPX contents only if we are reading it.
         if data is None and shape is None:
             self.parse()
-        else:
+        elif data is not None:
             self._write(data, **kwargs)
 
     @property
@@ -427,134 +483,11 @@ class Jp2k(Jp2kBox):
 
         This method can only be used to create JPEG 2000 images that can fit
         in memory.
-
-        Parameters
-        ----------
-        img_array : ndarray
-            Image data to be written to file.
-        cbsize : tuple, optional
-            Code block size (DY, DX).
-        cinema2k : int, optional
-            frames per second, either 24 or 48
-        cinema4k : bool, optional
-            Set to True to specify Cinema4K mode, defaults to false.
-        colorspace : str, optional
-            Either 'rgb' or 'gray'.
-        cratios : iterable
-            Compression ratios for successive layers.
-        eph : bool, optional
-            If true, write SOP marker after each header packet.
-        grid_offset : tuple, optional
-            Offset (DY, DX) of the origin of the image in the reference grid.
-        irreversible : bool, optional
-            If true, use the irreversible DWT 9-7 transform. 
-        mct : bool, optional
-            Specifies usage of the multi component transform.  If not
-            specified, defaults to True if the colorspace is RGB.
-        modesw : int, optional
-            Mode switch.
-                1 = BYPASS(LAZY)
-                2 = RESET
-                4 = RESTART(TERMALL)
-                8 = VSC
-                16 = ERTERM(SEGTERM)
-                32 = SEGMARK(SEGSYM)
-        numres : int, optional
-            Number of resolutions.
-        prog : str, optional
-            Progression order, one of "LRCP" "RLCP", "RPCL", "PCRL", "CPRL".
-        psnr : iterable, optional
-            Different PSNR for successive layers.
-        psizes : list, optional
-            List of precinct sizes.  Each precinct size tuple is defined in
-            (height x width).
-        sop : bool, optional
-            If true, write SOP marker before each packet.
-        subsam : tuple, optional
-            Subsampling factors (dy, dx).
-        tilesize : tuple, optional
-            Numeric tuple specifying tile size in terms of (numrows, numcols),
-            not (X, Y).
-        verbose : bool, optional
-            Print informational messages produced by the OpenJPEG library.
-
         """
         if re.match("1.[0-4]", version.openjpeg_version) is not None:
             raise RuntimeError("You must have at least version 1.5 of OpenJPEG "
                                "in order to write images.")
 
-        self._shape = img_array.shape
-        self._determine_colorspace(**kwargs)
-        self._populate_cparams(img_array, **kwargs)
-
-        if opj2.OPENJP2 is not None:
-            self._write_openjp2(img_array, verbose=verbose)
-        else:
-            self._write_openjpeg(img_array, verbose=verbose)
-
-    def write(self, img_array, verbose=False, **kwargs):
-        """Write image data to a JP2/JPX/J2k file.  Intended usage of the
-        various parameters follows that of OpenJPEG's opj_compress utility.
-
-        This method can only be used to create JPEG 2000 images that can fit
-        in memory.
-
-        Parameters
-        ----------
-        img_array : ndarray
-            Image data to be written to file.
-        cbsize : tuple, optional
-            Code block size (DY, DX).
-        cinema2k : int, optional
-            frames per second, either 24 or 48
-        cinema4k : bool, optional
-            Set to True to specify Cinema4K mode, defaults to false.
-        colorspace : str, optional
-            Either 'rgb' or 'gray'.
-        cratios : iterable
-            Compression ratios for successive layers.
-        eph : bool, optional
-            If true, write SOP marker after each header packet.
-        grid_offset : tuple, optional
-            Offset (DY, DX) of the origin of the image in the reference grid.
-        irreversible : bool, optional
-            If true, use the irreversible DWT 9-7 transform. 
-        mct : bool, optional
-            Specifies usage of the multi component transform.  If not
-            specified, defaults to True if the colorspace is RGB.
-        modesw : int, optional
-            Mode switch.
-                1 = BYPASS(LAZY)
-                2 = RESET
-                4 = RESTART(TERMALL)
-                8 = VSC
-                16 = ERTERM(SEGTERM)
-                32 = SEGMARK(SEGSYM)
-        numres : int, optional
-            Number of resolutions.
-        prog : str, optional
-            Progression order, one of "LRCP" "RLCP", "RPCL", "PCRL", "CPRL".
-        psnr : iterable, optional
-            Different PSNR for successive layers.
-        psizes : list, optional
-            List of precinct sizes.  Each precinct size tuple is defined in
-            (height x width).
-        sop : bool, optional
-            If true, write SOP marker before each packet.
-        subsam : tuple, optional
-            Subsampling factors (dy, dx).
-        tilesize : tuple, optional
-            Numeric tuple specifying tile size in terms of (numrows, numcols),
-            not (X, Y).
-        verbose : bool, optional
-            Print informational messages produced by the OpenJPEG library.
-
-        """
-        if re.match("1.[0-4]", version.openjpeg_version) is not None:
-            raise RuntimeError("You must have at least version 1.5 of OpenJPEG "
-                               "in order to write images.")
-
-        self._shape = img_array.shape
         self._determine_colorspace(**kwargs)
         self._populate_cparams(img_array, **kwargs)
 
@@ -964,7 +897,7 @@ class Jp2k(Jp2kBox):
             # Case of jp2[:] = data, i.e. write the entire image.
             #
             # Should have a slice object where start = stop = step = None
-            self.write(data)
+            self._write(data)
         else:
             msg = "Partial write operations are currently not allowed."
             raise TypeError(msg)
@@ -987,7 +920,7 @@ class Jp2k(Jp2kBox):
 
         if pargs is Ellipsis:
             # Case of jp2[...]
-            return self.read()
+            return self._read()
 
         if isinstance(pargs, slice):
             if pargs.start is None and pargs.stop is None and pargs.step is None:
diff --git a/glymur/test/test_jp2k.py b/glymur/test/test_jp2k.py
index 257688f..8eaf82a 100644
--- a/glymur/test/test_jp2k.py
+++ b/glymur/test/test_jp2k.py
@@ -81,13 +81,12 @@ class SliceProtocolBase(unittest.TestCase):
 @unittest.skipIf(os.name == "nt", fixtures.WINDOWS_TMP_FILE_MSG)
 class TestSliceProtocolBaseWrite(SliceProtocolBase):
 
-    @unittest.skip('requires shape implementation')
     def test_write_ellipsis(self):
         expected = self.j2k_data
 
         with tempfile.NamedTemporaryFile(suffix='.j2k') as tfile:
-            j = Jp2k(tfile.name, 'wb')
-            j[...] = self.j2k_data
+            j = Jp2k(tfile.name, shape=expected.shape)
+            j[...] = expected
             actual = j[:]
 
         np.testing.assert_array_equal(actual, expected)
@@ -101,10 +100,9 @@ class TestSliceProtocolBaseWrite(SliceProtocolBase):
 
         np.testing.assert_array_equal(actual, expected)
 
-    @unittest.skip('requires shape implementation')
     def test_cannot_write_with_non_default_single_slice(self):
         with tempfile.NamedTemporaryFile(suffix='.j2k') as tfile:
-            j = Jp2k(tfile.name, 'wb')
+            j = Jp2k(tfile.name, shape=self.j2k_data.shape)
             with self.assertRaises(TypeError):
                 j[slice(None, 0)] = self.j2k_data
             with self.assertRaises(TypeError):
@@ -114,38 +112,33 @@ class TestSliceProtocolBaseWrite(SliceProtocolBase):
             with self.assertRaises(TypeError):
                 j[slice(0, 640)] = self.j2k_data
 
-    @unittest.skip('requires shape implementation')
     def test_cannot_write_a_row(self):
         with tempfile.NamedTemporaryFile(suffix='.j2k') as tfile:
-            j = Jp2k(tfile.name, 'wb')
+            j = Jp2k(tfile.name, shape=self.j2k_data.shape)
             with self.assertRaises(TypeError):
                 j[5] = self.j2k_data
 
-    @unittest.skip('requires shape implementation')
     def test_cannot_write_a_pixel(self):
         with tempfile.NamedTemporaryFile(suffix='.j2k') as tfile:
-            j = Jp2k(tfile.name, 'wb')
+            j = Jp2k(tfile.name, shape=self.j2k_data.shape)
             with self.assertRaises(TypeError):
                 j[25, 35] = self.j2k_data[25, 35]
 
-    @unittest.skip('requires shape implementation')
     def test_cannot_write_a_column(self):
         with tempfile.NamedTemporaryFile(suffix='.j2k') as tfile:
-            j = Jp2k(tfile.name, 'wb')
+            j = Jp2k(tfile.name, shape=self.j2k_data.shape)
             with self.assertRaises(TypeError):
                 j[:, 25, :] = self.j2k_data[:, :25, :]
 
-    @unittest.skip('requires shape implementation')
     def test_cannot_write_a_band(self):
         with tempfile.NamedTemporaryFile(suffix='.j2k') as tfile:
-            j = Jp2k(tfile.name, 'wb')
+            j = Jp2k(tfile.name, shape=self.j2k_data.shape)
             with self.assertRaises(TypeError):
                 j[:, :, 0] = self.j2k_data[:, :, 0]
 
-    @unittest.skip('requires shape implementation')
     def test_cannot_write_a_subarray(self):
         with tempfile.NamedTemporaryFile(suffix='.j2k') as tfile:
-            j = Jp2k(tfile.name, 'wb')
+            j = Jp2k(tfile.name, shape=self.j2k_data.shape)
             with self.assertRaises(TypeError):
                 j[:25, :45, :] = self.j2k_data[:25, :25, :]
 
@@ -884,13 +877,13 @@ class TestJp2k_2_0(unittest.TestCase):
         j = Jp2k(self.jp2file)
         with self.assertRaises(IOError):
             # Start corner must be >= 0
-            j.read(area=(-1, -1, 1, 1))
+            j[-1:1, -1:1]
         with self.assertRaises(IOError):
             # End corner must be > 0
-            j.read(area=(10, 10, 0, 0))
+            j[10:0, 10:0]
         with self.assertRaises(IOError):
             # End corner must be >= start corner
-            j.read(area=(10, 10, 8, 8))
+            j[10:8, 10:8]
 
     @unittest.skipIf(os.name == "nt", fixtures.WINDOWS_TMP_FILE_MSG)
     def test_unrecognized_jp2_clrspace(self):
@@ -1043,7 +1036,6 @@ class TestParsing(unittest.TestCase):
         with self.assertWarnsRegex(UserWarning, 'Invalid profile'):
             jp2 = Jp2k(filename)
 
-    #@unittest.skip('trouble is a brewing...')
     def test_main_header(self):
         """Verify that the main header is not loaded when parsing turned off."""
         # The hidden _main_header attribute should show up after accessing it.
diff --git a/glymur/test/test_opj_suite_dump.py b/glymur/test/test_opj_suite_dump.py
index 8201c9f..ee1838b 100644
--- a/glymur/test/test_opj_suite_dump.py
+++ b/glymur/test/test_opj_suite_dump.py
@@ -2847,8 +2847,7 @@ class TestSuiteWarns(MetadataBase):
         relpath = 'input/nonregression/issue188_beach_64bitsbox.jp2'
         jfile = opj_data_file(relpath)
         with self.assertWarns(UserWarning):
-            j = Jp2k(jfile)
-        d = j.read()
+            d = Jp2k(jfile)[:]
         self.assertTrue(True)
 
     def test_NR_broken4_jp2_dump(self):
diff --git a/glymur/test/test_opj_suite_write.py b/glymur/test/test_opj_suite_write.py
index 9d8f5b7..ecb7a7d 100644
--- a/glymur/test/test_opj_suite_write.py
+++ b/glymur/test/test_opj_suite_write.py
@@ -123,10 +123,9 @@ class WriteCinemaWarns(CinemaBase):
         infile = opj_data_file(relfile)
         data = skimage.io.imread(infile)
         with tempfile.NamedTemporaryFile(suffix='.j2k') as tfile:
-            j = Jp2k(tfile.name, 'wb')
             regex = 'OpenJPEG library warning:.*'
             with self.assertWarnsRegex(UserWarning, re.compile(regex)):
-                j.write(data, cinema4k=True)
+                j = Jp2k(tfile.name, data=data, cinema4k=True)
 
             codestream = j.get_codestream()
             self.check_cinema4k_codestream(codestream, (4096, 2160))
@@ -136,9 +135,8 @@ class WriteCinemaWarns(CinemaBase):
         infile = opj_data_file(relfile)
         data = skimage.io.imread(infile)
         with tempfile.NamedTemporaryFile(suffix='.j2k') as tfile:
-            j = Jp2k(tfile.name, 'wb')
             with self.assertWarnsRegex(UserWarning, 'OpenJPEG library warning'):
-                j.write(data, cinema2k=48)
+                j = Jp2k(tfile.name, data=data, cinema2k=48)
 
             codestream = j.get_codestream()
             self.check_cinema2k_codestream(codestream, (2048, 857))
@@ -148,9 +146,8 @@ class WriteCinemaWarns(CinemaBase):
         infile = opj_data_file(relfile)
         data = skimage.io.imread(infile)
         with tempfile.NamedTemporaryFile(suffix='.j2k') as tfile:
-            j = Jp2k(tfile.name, 'wb')
             with self.assertWarnsRegex(UserWarning, 'OpenJPEG library warning'):
-                j.write(data, cinema2k=48)
+                j = Jp2k(tfile.name, data=data, cinema2k=48)
 
             codestream = j.get_codestream()
             self.check_cinema2k_codestream(codestream, (2048, 1080))
@@ -160,9 +157,8 @@ class WriteCinemaWarns(CinemaBase):
         infile = opj_data_file(relfile)
         data = skimage.io.imread(infile)
         with tempfile.NamedTemporaryFile(suffix='.j2k') as tfile:
-            j = Jp2k(tfile.name, 'wb')
             with self.assertWarnsRegex(UserWarning, 'OpenJPEG library warning'):
-                j.write(data, cinema2k=24)
+                j = Jp2k(tfile.name, data=data, cinema2k=24)
 
             codestream = j.get_codestream()
             self.check_cinema2k_codestream(codestream, (2048, 1080))
@@ -172,11 +168,10 @@ class WriteCinemaWarns(CinemaBase):
         infile = opj_data_file(relfile)
         data = skimage.io.imread(infile)
         with tempfile.NamedTemporaryFile(suffix='.j2k') as tfile:
-            j = Jp2k(tfile.name, 'wb')
             with self.assertWarnsRegex(UserWarning, 'OpenJPEG library warning'):
                 # OpenJPEG library warning:  The desired maximum codestream
                 # size has limited at least one of the desired quality layers
-                j.write(data, cinema2k=24)
+                j = Jp2k(tfile.name, data=data, cinema2k=24)
 
             codestream = j.get_codestream()
             self.check_cinema2k_codestream(codestream, (2048, 857))
@@ -186,12 +181,11 @@ class WriteCinemaWarns(CinemaBase):
         infile = opj_data_file(relfile)
         data = skimage.io.imread(infile)
         with tempfile.NamedTemporaryFile(suffix='.j2k') as tfile:
-            j = Jp2k(tfile.name, 'wb')
             regex = 'OpenJPEG library warning'
             with self.assertWarnsRegex(UserWarning, regex):
                 # OpenJPEG library warning:  The desired maximum codestream
                 # size has limited at least one of the desired quality layers
-                j.write(data, cinema2k=48)
+                j = Jp2k(tfile.name, data=data, cinema2k=48)
 
             codestream = j.get_codestream()
             self.check_cinema2k_codestream(codestream, (1998, 1080))

From e446cb15771202899c30918ad50aff5e6cd5f88f Mon Sep 17 00:00:00 2001
From: John Evans <john.g.evans@noaa.gov>
Date: Thu, 20 Nov 2014 10:32:43 -0500
Subject: [PATCH 22/23] filter out max rlevel test on version 1.x of openjpeg,
 closes #301

there's nothing that can be done about it, it's behavior in the library
---
 glymur/test/test_jp2k.py | 10 +++++++++-
 1 file changed, 9 insertions(+), 1 deletion(-)

diff --git a/glymur/test/test_jp2k.py b/glymur/test/test_jp2k.py
index 8eaf82a..99e655f 100644
--- a/glymur/test/test_jp2k.py
+++ b/glymur/test/test_jp2k.py
@@ -226,8 +226,16 @@ class TestSliceProtocolRead(SliceProtocolBase):
         expected = self.j2k_data[3:8, :,:]
         np.testing.assert_array_equal(actual, expected)
 
-    @unittest.skip('see issue 301')
+    @unittest.skipIf(re.match("0|1", glymur.version.openjpeg_version),
+                     "Must have openjpeg 2 or higher to run")
     def test_region_rlevel5(self):
+        """
+        maximim rlevel
+
+        There seems to be a difference between version of openjpeg, as 
+        openjp2 produces an image of size (16, 13, 3) and openjpeg produced
+        (17, 12, 3).
+        """
         actual = self.j2k[5:533:32, 27:423:32]
         expected = self.j2k_data_r5[1:17, 1:14]
         np.testing.assert_array_equal(actual, expected)

From e165edbe53be3fb2024d33a739fb641bfe56b01e Mon Sep 17 00:00:00 2001
From: John Evans <john.g.evans@noaa.gov>
Date: Fri, 21 Nov 2014 10:21:55 -0500
Subject: [PATCH 23/23] progress

---
 docs/source/how_do_i.rst |  7 ++-----
 glymur/test/test_jp2k.py | 21 +++++++++++++++++----
 2 files changed, 19 insertions(+), 9 deletions(-)

diff --git a/docs/source/how_do_i.rst b/docs/source/how_do_i.rst
index 65647fa..8a62b32 100644
--- a/docs/source/how_do_i.rst
+++ b/docs/source/how_do_i.rst
@@ -14,15 +14,12 @@ retrieve a full resolution and first lower-resolution image ::
     >>> jp2file = glymur.data.nemo() # just a path to a JPEG2000 file
     >>> jp2 = glymur.Jp2k(jp2file)
     >>> fullres = jp2[:]
-    >>> print(fullres.shape)
+    >>> fullres.shape
     (1456, 2592, 3)
     >>> thumbnail = jp2[::2, ::2]
-    >>> print(thumbnail.shape)
+    >>> thumbnail.shape
     (728, 1296, 3)
 
-The :py:meth:`read` method exposes many more options for other JPEG 2000
-features such as quality layers.
-
 ... write images?
 =================
 It's pretty simple, just supply the image data as the 2nd argument to the Jp2k
diff --git a/glymur/test/test_jp2k.py b/glymur/test/test_jp2k.py
index 99e655f..b903dda 100644
--- a/glymur/test/test_jp2k.py
+++ b/glymur/test/test_jp2k.py
@@ -345,11 +345,24 @@ class TestJp2k(unittest.TestCase):
         self.assertEqual(newjp2.filename, self.j2kfile)
         self.assertEqual(len(newjp2.box), 0)
 
-    @unittest.skip("see issue 302")
-    def test_rlevel_max(self):
-        """Verify that rlevel=-1 gets us the lowest resolution image"""
+    @unittest.skipIf(WARNING_INFRASTRUCTURE_ISSUE, WARNING_INFRASTRUCTURE_MSG)
+    def test_rlevel_max_backwards_compatibility(self):
+        """
+        Verify that rlevel=-1 gets us the lowest resolution image
+
+        This is an old option only available via the read method, not via
+        array-style slicing.
+        """
         j = Jp2k(self.j2kfile)
-        thumbnail1 = j.read(rlevel=-1)
+        if sys.hexversion < 0x03000000:
+            with warnings.catch_warnings():
+                # Suppress a warning due to deprecated syntax
+                # Not as easy to verify the warning under python2.
+                warnings.simplefilter("ignore")
+                thumbnail1 = j.read(rlevel=-1)
+        else:
+            with self.assertWarns(DeprecationWarning):
+                thumbnail1 = j.read(rlevel=-1)
         thumbnail2 = j[::32, ::32]
         np.testing.assert_array_equal(thumbnail1, thumbnail2)
         self.assertEqual(thumbnail1.shape, (25, 15, 3))