progress

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
+It's pretty simple, just supply the image data as the 2nd argument to the Jp2k
-also be used to write JPEG 2000 files.
+constructor.
     
     >>> import glymur, numpy as np
-    >>> jp2 = glymur.Jp2k('zeros.jp2', mode='wb')
+    >>> data = np.zeros((640, 480), dtype=np.uint8)
-    >>> jp2[:] = 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
+You should have OpenJPEG version 1.5 or more recent before writing JPEG 2000 images.
-features.  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 = Jp2k('tmp.jp2', data=rgba)
-    >>> jp2[:] = 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 = Jp2k('PIA17145.jp2', data=image)
-    >>> jp2[:] = image
 
 Next you can extract the XMP metadata.
 

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
 ------------

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

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.

docs/source/whatsnew/index.rst

@@ -8,6 +8,7 @@ These document the changes between minor (or major) versions of glymur.
 
 .. toctree::
 
-    0.5
+    0.8
-    0.6
     0.7
+    0.6
+    0.5

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:

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 = Jp2k(tfile.name, shape=expected.shape)
-            j[...] = self.j2k_data
+            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.

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 = Jp2k(jfile)[:]
-        d = j.read()
         self.assertTrue(True)
 
     def test_NR_broken4_jp2_dump(self):

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))