Merge branch 'issue179' into devel

Conflicts:
	glymur/test/test_jp2k.py
	glymur/test/test_opj_suite_write.py

glymur/jp2k.py

@@ -696,8 +696,9 @@ class Jp2k(Jp2kBox):
             (first_row, first_col, last_row, last_col)
         tile : int, optional
             Number of tile to decode.
-        no_cxform : bool
+        ignore_pclr_cmap_cdef : bool
-            Whether or not to apply intended color transforms.
+            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.
 
@@ -752,7 +753,7 @@ class Jp2k(Jp2kBox):
             msg += "the read_bands method instead."
             raise RuntimeError(msg)
 
-    def _read_openjpeg(self, rlevel=0, no_cxform=False, verbose=False):
+    def _read_openjpeg(self, rlevel=0, ignore_pclr_cmap_cdef=False, verbose=False):
         """Read a JPEG 2000 image using libopenjpeg.
 
         Parameters
@@ -760,8 +761,9 @@ class Jp2k(Jp2kBox):
         rlevel : int, optional
             Factor by which to rlevel output resolution.  Use -1 to get the
             lowest resolution thumbnail.
-        no_cxform : bool
+        ignore_pclr_cmap_cdef : bool
-            Whether or not to apply intended color transforms.
+            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.
 
@@ -797,7 +799,7 @@ class Jp2k(Jp2kBox):
                 dparameters = opj.DecompressionParametersType()
                 opj.set_default_decoder_parameters(ctypes.byref(dparameters))
 
-                if no_cxform is True:
+                if ignore_pclr_cmap_cdef is True:
                     # Return raw codestream components.
                     dparameters.flags |= 1
 
@@ -845,7 +847,7 @@ class Jp2k(Jp2kBox):
         return data
 
     def _read_openjp2(self, rlevel=0, layer=0, area=None, tile=None,
-                      verbose=False, no_cxform=False):
+                      verbose=False, ignore_pclr_cmap_cdef=False):
         """Read a JPEG 2000 image using libopenjp2.
 
         Parameters
@@ -875,7 +877,8 @@ class Jp2k(Jp2kBox):
         """
         self._subsampling_sanity_check()
 
-        dparam = self._populate_dparam(layer, rlevel, area, tile, no_cxform)
+        dparam = self._populate_dparam(layer, rlevel, area, tile,
+                                       ignore_pclr_cmap_cdef)
 
         with ExitStack() as stack:
             if hasattr(opj2.OPENJP2,
@@ -919,7 +922,7 @@ class Jp2k(Jp2kBox):
 
         return img_array
 
-    def _populate_dparam(self, layer, rlevel, area, tile, no_cxform):
+    def _populate_dparam(self, layer, rlevel, area, tile, ignore_pclr_cmap_cdef):
         """Populate decompression structure with appropriate input parameters.
 
         Parameters
@@ -933,8 +936,9 @@ class Jp2k(Jp2kBox):
             (first_row, first_col, last_row, last_col)
         tile : int
             Number of tile to decode.
-        no_cxform : bool
+        ignore_pclr_cmap_cdef : bool
-            Whether or not to apply intended color transforms.
+            Whether or not to ignore the pclr, cmap, or cdef boxes during any
+            color transformation.  Defaults to False.
 
         Returns
         -------
@@ -972,14 +976,14 @@ class Jp2k(Jp2kBox):
             dparam.tile_index = tile
             dparam.nb_tile_to_decode = 1
 
-        if no_cxform is True:
+        if ignore_pclr_cmap_cdef is True:
             # Return raw codestream components.
             dparam.flags |= 1
 
         return dparam
 
     def read_bands(self, rlevel=0, layer=0, area=None, tile=None,
-                   verbose=False, no_cxform=False):
+                   verbose=False, ignore_pclr_cmap_cdef=False):
         """Read a JPEG 2000 image.
 
         The only time you should use this method is when the image has
@@ -997,8 +1001,9 @@ class Jp2k(Jp2kBox):
             (first_row, first_col, last_row, last_col)
         tile : int, optional
             Number of tile to decode.
-        no_cxform : bool
+        ignore_pclr_cmap_cdef : bool
-            Whether or not to apply intended color transforms.
+            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.
 
@@ -1028,7 +1033,7 @@ class Jp2k(Jp2kBox):
                                        "of OpenJP2 installed before using "
                                        "this functionality.")
 
-        dparam = self._populate_dparam(layer, rlevel, area, tile, no_cxform)
+        dparam = self._populate_dparam(layer, rlevel, area, tile, ignore_pclr_cmap_cdef)
 
         with ExitStack() as stack:
             if hasattr(opj2.OPENJP2,

glymur/test/test_jp2k.py

@@ -96,7 +96,7 @@ class TestJp2k(unittest.TestCase):
         """Indices for pclr jpxfile if no color transform"""
         j = Jp2k(self.jpxfile)
         rgb = j.read()
-        idx = j.read(no_cxform=True)
+        idx = j.read(ignore_pclr_cmap_cdef=True)
         self.assertEqual(rgb.shape, (1024, 1024, 3))
         self.assertEqual(idx.shape, (1024, 1024))
 
@@ -109,6 +109,21 @@ class TestJp2k(unittest.TestCase):
                 rgb_from_idx[r, c] = palette[idx[r, c]]
         np.testing.assert_array_equal(rgb, rgb_from_idx)
 
+    def test_no_cxform_cmap(self):
+        """Bands as physically ordered, not as physically intended"""
+        # This file has the components physically reversed.  The cmap box
+        # tells the decoder how to order them, but this flag prevents that.
+        filename = opj_data_file('input/conformance/file2.jp2')
+        j = Jp2k(filename)
+        ycbcr = j.read()
+        crcby = j.read(ignore_pclr_cmap_cdef=True)
+
+        expected = np.zeros(ycbcr.shape, ycbcr.dtype)
+        for k in range(crcby.shape[2]):
+            expected[:,:,crcby.shape[2] - k - 1] = crcby[:,:,k]
+
+        np.testing.assert_array_equal(ycbcr, expected)
+
     def test_file_not_present(self):
         """Should error out if reading from a file that does not exist"""
         # Verify that we error out appropriately if not given an existing file
@@ -763,7 +778,7 @@ class TestJp2kOpjDataRoot(unittest.TestCase):
         filename = opj_data_file('input/conformance/file9.jp2')
         j = Jp2k(filename)
         rgb = j.read()
-        idx = j.read(no_cxform=True)
+        idx = j.read(ignore_pclr_cmap_cdef=True)
         self.assertEqual(rgb.shape, (512, 768, 3))
         self.assertEqual(idx.shape, (512, 768))
 
@@ -805,7 +820,7 @@ class TestJp2kOpjDataRoot(unittest.TestCase):
         filename = opj_data_file('input/conformance/file2.jp2')
         j = Jp2k(filename)
         ycbcr = j.read()
-        crcby = j.read(no_cxform=True)
+        crcby = j.read(ignore_pclr_cmap_cdef=True)
 
         expected = np.zeros(ycbcr.shape, ycbcr.dtype)
         for k in range(crcby.shape[2]):