added test for image component parameters type

CHANGES.txt

@@ -1,8 +1,3 @@
-Jan 10, 2015 - v0.8.0  Reduced number of steps required for writing
-    images.  Deprecated old read and write methods in favor of
-    array-style slicing.  Added ignore_pclr_cmap_cdef, verbose,
-    shape, codestream, layer properties.
-
 Oct 06, 2014 - v0.7.2  Added ellipsis support in array-style slicing.
 
 Oct 02, 2014 - v0.7.1  Fixed README to mention Python 3.4

docs/source/api.rst

@@ -0,0 +1,116 @@
+---
+API
+---
+
+Jp2k
+----
+.. autoclass:: glymur.Jp2k
+   :members: read, write, wrap, read_bands, get_codestream
+
+Individual Boxes
+----------------
+Jp2kbox
+'''''''
+.. autoclass:: glymur.jp2box.Jp2kBox
+   :members:
+
+AssociationBox
+''''''''''''''
+.. autoclass:: glymur.jp2box.AssociationBox
+   :members:
+
+ColourSpecificationBox
+''''''''''''''''''''''
+.. autoclass:: glymur.jp2box.ColourSpecificationBox
+   :members:
+
+ChannelDefinitionBox
+''''''''''''''''''''''
+.. autoclass:: glymur.jp2box.ChannelDefinitionBox
+   :members:
+
+ComponentMappingBox
+'''''''''''''''''''
+.. autoclass:: glymur.jp2box.ComponentMappingBox
+   :members:
+
+ContiguousCodestreamBox
+'''''''''''''''''''''''
+.. autoclass:: glymur.jp2box.ContiguousCodestreamBox
+   :members:
+
+DataEntryURLBox
+'''''''''''''''
+.. autoclass:: glymur.jp2box.DataEntryURLBox
+   :members:
+
+FileTypeBox
+'''''''''''
+.. autoclass:: glymur.jp2box.FileTypeBox
+   :members:
+
+ImageHeaderBox
+''''''''''''''
+.. autoclass:: glymur.jp2box.ImageHeaderBox
+   :members:
+
+JP2HeaderBox
+''''''''''''
+.. autoclass:: glymur.jp2box.JP2HeaderBox
+   :members:
+
+JPEG2000SignatureBox
+''''''''''''''''''''
+.. autoclass:: glymur.jp2box.JPEG2000SignatureBox
+   :members:
+
+LabelBox
+''''''''
+.. autoclass:: glymur.jp2box.LabelBox
+   :members:
+
+PaletteBox
+''''''''''
+.. autoclass:: glymur.jp2box.PaletteBox
+   :members:
+
+ReaderRequirementsBox
+'''''''''''''''''''''
+.. autoclass:: glymur.jp2box.ReaderRequirementsBox
+   :members:
+
+ResolutionBox
+'''''''''''''
+.. autoclass:: glymur.jp2box.ResolutionBox
+   :members:
+
+CaptureResolutionBox
+''''''''''''''''''''
+.. autoclass:: glymur.jp2box.CaptureResolutionBox
+   :members:
+
+DisplayResolutionBox
+''''''''''''''''''''
+.. autoclass:: glymur.jp2box.DisplayResolutionBox
+   :members:
+
+UUIDBox
+'''''''
+.. autoclass:: glymur.jp2box.UUIDBox
+   :members:
+
+UUIDInfoBox
+'''''''''''
+.. autoclass:: glymur.jp2box.UUIDInfoBox
+   :members:
+
+UUIDListBox
+'''''''''''
+.. autoclass:: glymur.jp2box.UUIDListBox
+   :members:
+
+XMLBox
+''''''
+.. autoclass:: glymur.jp2box.XMLBox
+   :members:
+

docs/source/conf.py

@@ -13,6 +13,7 @@
 # serve to show the default.
 
 import sys
+import os
 
 
 class Mock(object):
@@ -41,12 +42,12 @@ for mod_name in MOCK_MODULES:
 # If extensions (or modules to document with autodoc) are in another directory,
 # add these directories to sys.path here. If the directory is relative to the
 # documentation root, use os.path.abspath to make it absolute, like shown here.
-# sys.path.insert(0, os.path.abspath('.'))
+#sys.path.insert(0, os.path.abspath('.'))
 
 # -- General configuration ----------------------------------------------------
 
 # If your documentation needs a minimal Sphinx version, state it here.
-# needs_sphinx = '1.0'
+#needs_sphinx = '1.0'
 
 # Add any Sphinx extension module names here, as strings. They can be
 # extensions coming with Sphinx (named 'sphinx.ext.*') or your custom ones.
@@ -61,7 +62,7 @@ templates_path = ['_templates']
 source_suffix = '.rst'
 
 # The encoding of source files.
-# source_encoding = 'utf-8-sig'
+#source_encoding = 'utf-8-sig'
 
 # The master toctree document.
 master_doc = 'index'
@@ -75,19 +76,19 @@ copyright = u'2013, John Evans'
 # built documents.
 #
 # The short X.Y version.
-version = '0.8'
+version = '0.7'
 # The full version, including alpha/beta/rc tags.
-release = '0.8.0'
+release = '0.7.2'
 
 # The language for content autogenerated by Sphinx. Refer to documentation
 # for a list of supported languages.
-# language = None
+#language = None
 
 # There are two options for replacing |today|: either, you set today to some
 # non-false value, then it is used:
-# today = ''
+#today = ''
 # Else, today_fmt is used as the format for a strftime call.
-# today_fmt = '%B %d, %Y'
+#today_fmt = '%B %d, %Y'
 
 # List of patterns, relative to source directory, that match files and
 # directories to ignore when looking for source files.
@@ -95,24 +96,24 @@ exclude_patterns = []
 
 # The reST default role (used for this markup: `text`) to use for all
 # documents.
-# default_role = None
+#default_role = None
 
 # If true, '()' will be appended to :func: etc. cross-reference text.
-# add_function_parentheses = True
+#add_function_parentheses = True
 
 # If true, the current module name will be prepended to all description
 # unit titles (such as .. function::).
-# add_module_names = True
+#add_module_names = True
 
 # If true, sectionauthor and moduleauthor directives will be shown in the
 # output. They are ignored by default.
-# show_authors = False
+#show_authors = False
 
 # The name of the Pygments (syntax highlighting) style to use.
 pygments_style = 'sphinx'
 
 # A list of ignored prefixes for module index sorting.
-# modindex_common_prefix = []
+#modindex_common_prefix = []
 
 
 # -- Options for HTML output --------------------------------------------------
@@ -124,26 +125,26 @@ html_theme = 'default'
 # Theme options are theme-specific and customize the look and feel of a theme
 # further.  For a list of options available for each theme, see the
 # documentation.
-# html_theme_options = {}
+#html_theme_options = {}
 
 # Add any paths that contain custom themes here, relative to this directory.
-# html_theme_path = []
+#html_theme_path = []
 
 # The name for this set of Sphinx documents.  If None, it defaults to
 # "<project> v<release> documentation".
-# html_title = None
+#html_title = None
 
 # A shorter title for the navigation bar.  Default is the same as html_title.
-# html_short_title = None
+#html_short_title = None
 
 # The name of an image file (relative to this directory) to place at the top
 # of the sidebar.
-# html_logo = None
+#html_logo = None
 
 # The name of an image file (within the static path) to use as favicon of the
 # docs.  This file should be a Windows icon file (.ico) being 16x16 or 32x32
 # pixels large.
-# html_favicon = None
+#html_favicon = None
 
 # Add any paths that contain custom static files (such as style sheets) here,
 # relative to this directory. They are copied after the builtin static files,
@@ -152,44 +153,44 @@ html_static_path = ['_static']
 
 # If not '', a 'Last updated on:' timestamp is inserted at every page bottom,
 # using the given strftime format.
-# html_last_updated_fmt = '%b %d, %Y'
+#html_last_updated_fmt = '%b %d, %Y'
 
 # If true, SmartyPants will be used to convert quotes and dashes to
 # typographically correct entities.
-# html_use_smartypants = True
+#html_use_smartypants = True
 
 # Custom sidebar templates, maps document names to template names.
-# html_sidebars = {}
+#html_sidebars = {}
 
 # Additional templates that should be rendered to pages, maps page names to
 # template names.
-# html_additional_pages = {}
+#html_additional_pages = {}
 
 # If false, no module index is generated.
-# html_domain_indices = True
+#html_domain_indices = True
 
 # If false, no index is generated.
-# html_use_index = True
+#html_use_index = True
 
 # If true, the index is split into individual pages for each letter.
-# html_split_index = False
+#html_split_index = False
 
 # If true, links to the reST sources are added to the pages.
 html_show_sourcelink = True
 
 # If true, "Created using Sphinx" is shown in the HTML footer. Default is True.
-# html_show_sphinx = True
+#html_show_sphinx = True
 
 # If true, "(C) Copyright ..." is shown in the HTML footer. Default is True.
-# html_show_copyright = True
+#html_show_copyright = True
 
 # If true, an OpenSearch description file will be output, and all pages will
 # contain a <link> tag referring to it.  The value of this option must be the
 # base URL from which the finished HTML is served.
-# html_use_opensearch = ''
+#html_use_opensearch = ''
 
 # This is the file name suffix for HTML files (e.g. ".xhtml").
-# html_file_suffix = None
+#html_file_suffix = None
 
 # Output file base name for HTML help builder.
 htmlhelp_basename = 'glymurdoc'
@@ -198,13 +199,13 @@ htmlhelp_basename = 'glymurdoc'
 # -- Options for LaTeX output -------------------------------------------------
 
 # The paper size ('letterpaper' or 'a4paper').
-# 'papersize': 'letterpaper',
+#'papersize': 'letterpaper',
 
 # The font size ('10pt', '11pt' or '12pt').
-# 'pointsize': '10pt',
+#'pointsize': '10pt',
 
 # Additional stuff for the LaTeX preamble.
-# 'preamble': '',
+#'preamble': '',
 latex_elements = {}
 
 # Grouping the document tree into LaTeX files. List of tuples
@@ -215,23 +216,23 @@ latex_documents = [('index', 'glymur.tex', u'glymur Documentation',
 
 # The name of an image file (relative to this directory) to place at the top of
 # the title page.
-# latex_logo = None
+#latex_logo = None
 
 # For "manual" documents, if this is true, then toplevel headings are parts,
 # not chapters.
-# latex_use_parts = False
+#latex_use_parts = False
 
 # If true, show page references after internal links.
-# latex_show_pagerefs = False
+#latex_show_pagerefs = False
 
 # If true, show URL addresses after external links.
-# latex_show_urls = False
+#latex_show_urls = False
 
 # Documents to append as an appendix to all manuals.
-# latex_appendices = []
+#latex_appendices = []
 
 # If false, no module index is generated.
-# latex_domain_indices = True
+#latex_domain_indices = True
 
 
 # -- Options for manual page output -------------------------------------------
@@ -244,7 +245,7 @@ man_pages = [
 ]
 
 # If true, show URL addresses after external links.
-# man_show_urls = False
+#man_show_urls = False
 
 
 # -- Options for Texinfo output -----------------------------------------------
@@ -257,13 +258,13 @@ texinfo_documents = [('index', 'glymur', u'glymur Documentation',
                       'One line description of project.', 'Miscellaneous'), ]
 
 # Documents to append as an appendix to all manuals.
-# texinfo_appendices = []
+#texinfo_appendices = []
 
 # If false, no module index is generated.
-# texinfo_domain_indices = True
+#texinfo_domain_indices = True
 
 # How to display URL addresses: 'footnote', 'no', or 'inline'.
-# texinfo_show_urls = 'footnote'
+#texinfo_show_urls = 'footnote'
 
 
 # Example configuration for intersphinx: refer to the Python standard library.

docs/source/detailed_installation.rst

@@ -15,7 +15,7 @@ or if you use windows, then read on.
 
 Glymur uses ctypes to access the openjp2/openjpeg libraries, and
 because ctypes accesses libraries in a platform-dependent manner,
-it is recommended that **if** you compile and install OpenJPEG into a
+it is recommended that if you compile and install OpenJPEG into a
 non-standard location, you should then create a configuration file
 to help Glymur properly find the openjpeg or openjp2 libraries
 (linux users or macports users don’t need to bother with this if
@@ -50,9 +50,6 @@ installed in a non-standard place, i.e. ::
     [library]
     openjpeg: /somewhere/lib/libopenjpeg.so
 
-Once again, you should not have to bother with a configuration file if you use
-mac or linux and OpenJPEG is provided by your package manager.
-
 '''''''
 Testing
 '''''''

docs/source/how_do_i.rst

@@ -14,22 +14,27 @@ 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[:]
-    >>> fullres.shape
+    >>> print(fullres.shape)
     (1456, 2592, 3)
     >>> thumbnail = jp2[::2, ::2]
-    >>> thumbnail.shape
+    >>> print(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
+So long as the image data can fit entirely into memory, array-style slicing may
-constructor.
+also be used to write JPEG 2000 files.
     
     >>> import glymur, numpy as np
-    >>> jp2 = glymur.Jp2k('zeros.jp2', data=np.zeros((640, 480), dtype=np.uint8)
+    >>> jp2 = glymur.Jp2k('zeros.jp2', mode='wb')
+    >>> jp2[:] = np.zeros((640, 480), dtype=np.uint8)
 
-You must have OpenJPEG version 1.5 or more recent in order to write JPEG 2000
+The :py:meth:`write` method exposes many more options for other JPEG 2000
-images with glymur.
+features.  You should have OpenJPEG version 1.5 or more recent before writing
+JPEG 2000 images.
 
 ... display metadata?
 =====================
@@ -214,9 +219,9 @@ making use of the :py:meth:`set_printoptions` function::
         UUID:  be7acfcb-97a9-42e8-9c71-999491e3afac (XMP)
     Contiguous Codestream Box (jp2c) @ (3223, 1132296)
 
-It is possible to easily print the codestream header details as well, i.e. ::
+It is possible to print all the gory codestream details as well, i.e. ::
 
-    >>> print(j.codestream)   # details not show
+    >>> print(j.get_codestream())   # details not shown
 
 ... add XML metadata?
 =====================
@@ -349,14 +354,15 @@ image isn't square. ::
     >>> import numpy as np
     >>> import glymur
     >>> from glymur import Jp2k
-    >>> rgb = Jp2k(glymur.data.goodstuff())[:]
+    >>> rgb = Jp2k(glymur.data.goodstuff()).read()
     >>> 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', data=rgba)
+    >>> jp2 = Jp2k('tmp.jp2', 'wb')
+    >>> 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
@@ -442,7 +448,7 @@ following
     'Google'
 
 But that would be painful.  A better solution is to install the Python XMP
-Toolkit (make sure it is at least version 2.0)::
+Toolkit (make sure it is version 2.0)::
 
     >>> from libxmp import XMPMeta
     >>> from libxmp.consts import XMP_NS_XMP as NS_XAP
@@ -459,7 +465,8 @@ 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', data=image)
+    >>> jp2 = Jp2k('PIA17145.jp2', 'wb')
+    >>> jp2[:] = image
 
 Next you can extract the XMP metadata.
 

docs/source/index.rst

@@ -17,6 +17,7 @@ Contents:
    how_do_i
    whatsnew/index
    roadmap
+   api
 
 ------------------
 Indices and tables

docs/source/roadmap.rst

@@ -1,3 +1,12 @@
+-------------------------------------
+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

@@ -2,26 +2,10 @@
 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
+      attributes (see issue 248)

docs/source/whatsnew/0.8.rst

@@ -1,24 +0,0 @@
-=====================
-Changes in glymur 0.8
-=====================
-
-Changes in 0.8.0
-=================
-
-    * Simplified writing images by moving data and options into the
-      constructor.
-    * Deprecated :py:meth:`read` method in favor of array-style slicing.
-      In order to retain certain functionality, the following parameters 
-      to the :py:meth:`read` method have become top-level properties
-
-      * verbose
-      * layer
-      * ignore_pclr_cmap_cdef
-
-    * Two additional properties were introduced.
-
-      * codestream
-      * shape
-
-      
- 

docs/source/whatsnew/index.rst

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

glymur/__init__.py

@@ -1,25 +1,21 @@
 """glymur - read, write, and interrogate JPEG 2000 files
 """
+import sys
 import unittest
 
 from glymur import version
 __version__ = version.version
 
 from .jp2k import Jp2k
-from .jp2box import (get_printoptions,
+from .jp2box import (
-                     set_printoptions,
+        get_printoptions, set_printoptions,
-                     get_parseoptions,
+        get_parseoptions, set_parseoptions
-                     set_parseoptions)
+)
 
 from . import data
 
-
 def runtests():
     """Discover and run all tests for the glymur package.
     """
     suite = unittest.defaultTestLoader.discover(__path__[0])
     unittest.TextTestRunner(verbosity=2).run(suite)
-
-
-__all__ = [__version__, Jp2k, get_printoptions, set_printoptions,
-           get_parseoptions, set_parseoptions, data, runtests]

glymur/_uuid_io.py

@@ -3,13 +3,14 @@
 Part of glymur.
 """
 from collections import OrderedDict
+import pprint
+import re
 import struct
 import sys
 import warnings
 
 import lxml.etree as ET
 
-
 def xml(raw_data):
     """
     XMP data to be parsed as XML.
@@ -22,7 +23,6 @@ def xml(raw_data):
 
     return ET.ElementTree(elt)
 
-
 def tiff_header(read_buffer):
     """
     Interpret the uuid raw data as a tiff header.
@@ -37,8 +37,8 @@ def tiff_header(read_buffer):
         # big endian
         endian = '>'
     else:
-        msg = "The byte order indication in the TIFF header ({0}) is "
+        msg = "The byte order indication in the TIFF header ({0}) is invalid.  "
-        msg += "invalid.  It should be either {1} or {2}."
+        msg += "It should be either {1} or {2}."
         msg = msg.format(read_buffer[6:8], bytes([73, 73]), bytes([77, 77]))
         raise IOError(msg)
 
@@ -503,3 +503,6 @@ class _ExifInteroperabilityIfd(_Ifd):
     def __init__(self, endian, read_buffer, offset):
         _Ifd.__init__(self, endian, read_buffer, offset)
         self.post_process(self.tagnum2name)
+
+
+

glymur/codestream.py

@@ -6,13 +6,16 @@ codestreams.
 
 # The number of lines in the module is long and that's ok.  It would not help
 # matters to move anything out to another file.
+# pylint: disable=C0302
 
 # "Too many instance attributes", "Too many arguments"
 # Some segments just have a lot of information.
 # It doesn't make sense to subclass just for that.
+# pylint: disable=R0902,R0913
 
 # "Too few public methods"  Some segments don't define any new methods from
 # the base Segment class.
+# pylint: disable=R0903
 
 import math
 import struct
@@ -21,22 +24,24 @@ import warnings
 
 import numpy as np
 
-from .core import (LRCP, RLCP, RPCL, PCRL, CPRL,
+from .core import (
-                   WAVELET_XFORM_9X7_IRREVERSIBLE,
+        LRCP, RLCP, RPCL, PCRL, CPRL,
-                   WAVELET_XFORM_5X3_REVERSIBLE,
+        WAVELET_XFORM_9X7_IRREVERSIBLE, WAVELET_XFORM_5X3_REVERSIBLE,
-                   _Keydefaultdict)
+        _Keydefaultdict
+)
 from .lib import openjp2 as opj2
 
 _factory = lambda x:  '{0} (invalid)'.format(x)
-_PROGRESSION_ORDER_DISPLAY = _Keydefaultdict(_factory, {LRCP: 'LRCP',
+_PROGRESSION_ORDER_DISPLAY = _Keydefaultdict(_factory,
-                                                        RLCP: 'RLCP',
+        { LRCP: 'LRCP',
-                                                        RPCL: 'RPCL',
+          RLCP: 'RLCP',
-                                                        PCRL: 'PCRL',
+          RPCL: 'RPCL',
-                                                        CPRL: 'CPRL'})
+          PCRL: 'PCRL',
+          CPRL: 'CPRL'})
 
-_keysvalues = {WAVELET_XFORM_9X7_IRREVERSIBLE: '9-7 irreversible',
+_WAVELET_TRANSFORM_DISPLAY = _Keydefaultdict(_factory,
-               WAVELET_XFORM_5X3_REVERSIBLE: '5-3 reversible'}
+        { WAVELET_XFORM_9X7_IRREVERSIBLE: '9-7 irreversible',
-_WAVELET_TRANSFORM_DISPLAY = _Keydefaultdict(_factory, _keysvalues)
+          WAVELET_XFORM_5X3_REVERSIBLE: '5-3 reversible'})
 
 _NO_PROFILE = 0
 _PROFILE_0 = 1
@@ -47,11 +52,12 @@ _PROFILE_4 = 4
 _KNOWN_PROFILES = [_NO_PROFILE, _PROFILE_0, _PROFILE_1, _PROFILE_3, _PROFILE_4]
 
 # How to display the codestream profile.
-_CAPABILITIES_DISPLAY = _Keydefaultdict(_factory, {_NO_PROFILE: 'no profile',
+_CAPABILITIES_DISPLAY = _Keydefaultdict(_factory,
-                                                   _PROFILE_0: '0',
+        { _NO_PROFILE: 'no profile',
-                                                   _PROFILE_1: '1',
+          _PROFILE_0: '0',
-                                                   _PROFILE_3: 'Cinema 2K',
+          _PROFILE_1: '1',
-                                                   _PROFILE_4: 'Cinema 4K'})
+          _PROFILE_3: 'Cinema 2K',
+          _PROFILE_4: 'Cinema 4K'} )
 
 # Need a catch-all list of valid markers.
 # See table A-1 in ISO/IEC FCD15444-1.
@@ -293,6 +299,7 @@ class Codestream(object):
             msg += ''.join(strs)
         return msg
 
+    # pylint: disable=R0201
     def _parse_cme_segment(self, fptr):
         """Parse the CME marker segment.
 
@@ -688,7 +695,7 @@ class Codestream(object):
         try:
             num_tiles_x = (xysiz[0] - xyosiz[0]) / (xytsiz[0] - xytosiz[0])
             num_tiles_y = (xysiz[1] - xyosiz[1]) / (xytsiz[1] - xytosiz[1])
-        except ZeroDivisionError:
+        except ZeroDivisionError as err:
             warnings.warn("Invalid tile dimensions.")
         else:
             numtiles = math.ceil(num_tiles_x) * math.ceil(num_tiles_y)
@@ -696,6 +703,7 @@ class Codestream(object):
                 msg = "Invalid number of tiles ({0}).".format(numtiles)
                 warnings.warn(msg)
 
+
         kwargs = {'rsiz': rsiz,
                   'xysiz': xysiz,
                   'xyosiz': xyosiz,
@@ -822,6 +830,7 @@ class Codestream(object):
 
         return TLMsegment(length, offset, ztlm, ttlm, ptlm)
 
+    # pylint: disable=W0613
     def _parse_reserved_marker(self, fptr):
         """Marker range between 0xff30 and 0xff39.
         """
@@ -1605,7 +1614,6 @@ class SOCsegment(Segment):
         msg = "glymur.codestream.SOCsegment()"
         return msg
 
-
 class SODsegment(Segment):
     """Container for Start of Data (SOD) segment information.
 

glymur/command_line.py

@@ -2,36 +2,32 @@
 Entry point for console script jp2dump.
 """
 import argparse
-import os
+import sys
 import warnings
-
+from . import Jp2k, set_printoptions
-from . import Jp2k, set_printoptions, set_parseoptions, lib
-
 
 def main():
     """
     Entry point for console script jp2dump.
     """
 
-    kwargs = {'description': 'Print JPEG2000 metadata.',
+    description='Print JPEG2000 metadata.'
-              'formatter_class': argparse.ArgumentDefaultsHelpFormatter}
+    parser = argparse.ArgumentParser(description=description)
-    parser = argparse.ArgumentParser(**kwargs)
 
     parser.add_argument('-x', '--noxml',
-                        help='suppress XML',
+            help='Suppress XML.',
-                        action='store_true')
+            action='store_true')
     parser.add_argument('-s', '--short',
-                        help='only print box id, offset, and length',
+            help='Only print box id, offset, and length.',
-                        action='store_true')
+            action='store_true')
 
-    chelp = 'Level of codestream information.  0 suppresses all details, '
+    chelp = 'Level of codestream information.  0 suppressed all details, '
-    chelp += '1 prints the main header, 2 prints the full codestream.'
+    chelp += '1 prints headers, 2 prints the full codestream'
     parser.add_argument('-c', '--codestream',
-                        help=chelp,
+            help=chelp,
-                        metavar='LEVEL',
+            nargs=1,
-                        nargs=1,
+            type=int,
-                        type=int,
+            default=[0])
-                        default=[1])
 
     parser.add_argument('filename')
 
@@ -40,33 +36,30 @@ def main():
         set_printoptions(xml=False)
     if args.short:
         set_printoptions(short=True)
-
+    
     codestream_level = args.codestream[0]
     if codestream_level not in [0, 1, 2]:
         raise ValueError("Invalid level of codestream information specified.")
 
     if codestream_level == 0:
         set_printoptions(codestream=False)
-    elif codestream_level == 2:
+        print_full_codestream = False
-        set_parseoptions(full_codestream=True)
+    elif codestream_level == 1:
-
+        print_full_codestream = False
+    else:
+        print_full_codestream = True
+    
     filename = args.filename
-
+    
     with warnings.catch_warnings(record=True) as wctx:
 
         # JP2 metadata can be extensive, so don't print any warnings until we
         # are done with the metadata.
-        jp2 = Jp2k(filename)
+        j = Jp2k(filename)
-        if jp2._codec_format == lib.openjp2.CODEC_J2K:
+        if print_full_codestream:
-            if codestream_level == 0:
+            print(j.get_codestream(header_only=False))
-                print('File:  {0}'.format(os.path.basename(filename)))
-            elif codestream_level == 1:
-                print(jp2)
-            elif codestream_level == 2:
-                print('File:  {0}'.format(os.path.basename(filename)))
-                print(jp2.get_codestream(header_only=False))
         else:
-            print(jp2)
+            print(j)
 
         # Re-emit any warnings that may have been suppressed.
         if len(wctx) > 0:

glymur/core.py

@@ -1,7 +1,8 @@
 """Core definitions to be shared amongst the modules.
 """
 import collections
-
+import copy
+import lxml.etree as ET
 
 class _Keydefaultdict(collections.defaultdict):
     """Unlisted keys help form their own error message.
@@ -120,12 +121,12 @@ ROMM_RGB = 21
 
 _factory = lambda x:  '{0} (unrecognized)'.format(x)
 _COLORSPACE_MAP_DISPLAY = _Keydefaultdict(_factory,
-                                          {CMYK:  'CMYK',
+        { CMYK:  'CMYK',
-                                           SRGB:  'sRGB',
+          SRGB:  'sRGB',
-                                           GREYSCALE:  'greyscale',
+          GREYSCALE:  'greyscale',
-                                           YCC:  'YCC',
+          YCC:  'YCC',
-                                           E_SRGB:  'e-sRGB',
+          E_SRGB:  'e-sRGB',
-                                           ROMM_RGB:  'ROMM-RGB'})
+          ROMM_RGB:  'ROMM-RGB'} )
 
 # enumerated color channel types
 COLOR = 0
@@ -133,11 +134,11 @@ OPACITY = 1
 PRE_MULTIPLIED_OPACITY = 2
 _UNSPECIFIED = 65535
 _factory = lambda x:  '{0} (invalid)'.format(x)
-_dict = {COLOR:  'color',
+_COLOR_TYPE_MAP_DISPLAY = _Keydefaultdict(_factory,
-         OPACITY:  'opacity',
+        { COLOR:  'color',
-         PRE_MULTIPLIED_OPACITY: 'pre-multiplied opacity',
+          OPACITY:  'opacity',
-         _UNSPECIFIED:  'unspecified'}
+          PRE_MULTIPLIED_OPACITY:  'pre-multiplied opacity',
-_COLOR_TYPE_MAP_DISPLAY = _Keydefaultdict(_factory, _dict)
+          _UNSPECIFIED:  'unspecified'})
 
 # color channel definitions.
 RED = 1
@@ -152,3 +153,4 @@ _COLORSPACE = {SRGB: {"R": 1, "G": 2, "B": 3},
                YCC: {"Y": 1, "Cb": 2, "Cr": 3},
                E_SRGB: {"R": 1, "G": 2, "B": 3},
                ROMM_RGB: {"R": 1, "G": 2, "B": 3}}
+

glymur/data/__init__.py

@@ -43,3 +43,4 @@ def jpxfile():
     """
     filename = pkg_resources.resource_filename(__name__, "heliov.jpx")
     return filename
+

glymur/jp2box.py

@@ -11,6 +11,8 @@ References
    Extensions
 """
 
+# pylint: disable=C0302,R0903,R0913,W0142
+
 from collections import OrderedDict
 import datetime
 import io
@@ -20,37 +22,35 @@ import pprint
 import struct
 import sys
 import textwrap
-from uuid import UUID
+import uuid
 import warnings
 
 import lxml.etree as ET
 import numpy as np
 
 from .codestream import Codestream
-from .core import (_COLORSPACE_MAP_DISPLAY, _COLOR_TYPE_MAP_DISPLAY,
+from .core import (
-                   SRGB, GREYSCALE, YCC,
+        _COLORSPACE_MAP_DISPLAY, _COLOR_TYPE_MAP_DISPLAY,
-                   ENUMERATED_COLORSPACE, RESTRICTED_ICC_PROFILE,
+        SRGB, GREYSCALE, YCC,
-                   ANY_ICC_PROFILE, VENDOR_COLOR_METHOD,
+        ENUMERATED_COLORSPACE, RESTRICTED_ICC_PROFILE,
-                   _Keydefaultdict)
+        ANY_ICC_PROFILE, VENDOR_COLOR_METHOD,
+        _Keydefaultdict
+)
 
 from . import _uuid_io
 
-_factory = lambda x: '{0} (invalid)'.format(x)
+_METHOD_DISPLAY = {
-_keysvalues = {ENUMERATED_COLORSPACE: 'enumerated colorspace',
+    ENUMERATED_COLORSPACE: 'enumerated colorspace',
-               RESTRICTED_ICC_PROFILE: 'restricted ICC profile',
+    RESTRICTED_ICC_PROFILE: 'restricted ICC profile',
-               ANY_ICC_PROFILE: 'any ICC profile',
+    ANY_ICC_PROFILE: 'any ICC profile',
-               VENDOR_COLOR_METHOD: 'vendor color method'}
+    VENDOR_COLOR_METHOD: 'vendor color method'}
-_METHOD_DISPLAY = _Keydefaultdict(_factory, _keysvalues)
 
 _factory = lambda x: '{0} (invalid)'.format(x)
-_keysvalues = {1: 'accurately represents correct colorspace definition',
+_APPROX_DISPLAY = _Keydefaultdict(_factory,
-               2: ('approximates correct colorspace definition, '
+        {1: 'accurately represents correct colorspace definition',
-                   'exceptional quality'),
+         2: 'approximates correct colorspace definition, exceptional quality',
-               3: ('approximates correct colorspace definition, '
+         3: 'approximates correct colorspace definition, reasonable quality',
-                   'reasonable quality'),
+         4: 'approximates correct colorspace definition, poor quality'})
-               4: 'approximates correct colorspace definition, poor quality'}
-_APPROX_DISPLAY = _Keydefaultdict(_factory, _keysvalues)
-
 
 class Jp2kBox(object):
     """Superclass for JPEG 2000 boxes.
@@ -109,6 +109,7 @@ class Jp2kBox(object):
             msg += '\n' + self._indent(boxstr)
         return msg
 
+
     def _indent(self, textstr, indent_level=4):
         """
         Indent a string.
@@ -134,6 +135,7 @@ class Jp2kBox(object):
             lst = [(' ' * indent_level + x) for x in textstr.split('\n')]
             return '\n'.join(lst)
 
+
     def _write_superbox(self, fptr, box_id):
         """Write a superbox.
 
@@ -189,14 +191,13 @@ class Jp2kBox(object):
         try:
             box = parser(fptr, start, num_bytes)
         except ValueError as err:
-            msg = "Encountered an unrecoverable ValueError while parsing a "
+            msg = "Encountered an unrecoverable ValueError while parsing a {0} "
-            msg += "{0} box at byte offset {1}.  The original error message "
+            msg += "box at byte offset {1}.  The original error message was "
-            msg += "was \"{2}\""
+            msg += "\"{2}\""
             msg = msg.format(_BOX_WITH_ID[box_id].longname, start, str(err))
             warnings.warn(msg, UserWarning)
             box = UnknownBox(box_id.decode('utf-8'),
-                             length=num_bytes,
+                             length=num_bytes, offset=start, longname='Unknown')
-                             offset=start, longname='Unknown')
 
         return box
 
@@ -298,7 +299,6 @@ class ColourSpecificationBox(Jp2kBox):
     """
     longname = 'Colour Specification'
     box_id = 'colr'
-
     def __init__(self, method=ENUMERATED_COLORSPACE, precedence=0,
                  approximation=0, colorspace=None, icc_profile=None,
                  length=0, offset=-1):
@@ -337,16 +337,16 @@ class ColourSpecificationBox(Jp2kBox):
 
         if self.icc_profile is None:
             if self.colorspace not in [SRGB, GREYSCALE, YCC]:
-                msg = "Colorspace should correspond to one of SRGB, "
+                msg = "Colorspace should correspond to one of SRGB, GREYSCALE, "
-                msg += "GREYSCALE, or YCC."
+                msg += "or YCC."
                 self._dispatch_validation_error(msg, writing=True)
 
         self._validate(writing=True)
 
+
     def __repr__(self):
         msg = "glymur.jp2box.ColourSpecificationBox("
-        msg += "method={0}, precedence={1}, approximation={2}, "
+        msg += "method={0}, precedence={1}, approximation={2}, colorspace={3}, "
-        msg += "colorspace={3}, "
         msg += "icc_profile={4})"
         msg = msg.format(self.method,
                          self.precedence,
@@ -357,7 +357,7 @@ class ColourSpecificationBox(Jp2kBox):
 
     def __str__(self):
         msg = Jp2kBox.__str__(self)
-        if _printoptions['short'] is True:
+        if _printoptions['short'] == True:
             return msg
 
         msg += '\n    Method:  {0}'.format(_METHOD_DISPLAY[self.method])
@@ -619,9 +619,10 @@ class ChannelDefinitionBox(Jp2kBox):
             msg += "    65535 - unspecified"
             self._dispatch_validation_error(msg, writing=writing)
 
+
     def __str__(self):
         msg = Jp2kBox.__str__(self)
-        if _printoptions['short'] is True:
+        if _printoptions['short'] == True:
             return msg
 
         for j in range(len(self.association)):
@@ -841,7 +842,7 @@ class CompositingLayerHeaderBox(Jp2kBox):
         List of boxes contained in this superbox.
     """
     box_id = 'jplh'
-    longname = 'Compositing Layer Header'
+    longname='Compositing Layer Header'
 
     def __init__(self, box=None, length=0, offset=-1):
         Jp2kBox.__init__(self)
@@ -930,7 +931,7 @@ class ComponentMappingBox(Jp2kBox):
 
     def __str__(self):
         msg = Jp2kBox.__str__(self)
-        if _printoptions['short'] is True:
+        if _printoptions['short'] == True:
             return msg
 
         for k in range(len(self.component_index)):
@@ -1001,19 +1002,18 @@ class ContiguousCodestreamBox(Jp2kBox):
         offset of the box from the start of the file.
     longname : str
         more verbose description of the box.
-    codestream : Codestream object
+    main_header : Codestream object
-        Contains list of codestream marker/segments.  By default, only the main
+        contains list of main header marker/segments
-        header is retrieved.
     main_header_offset : int
         offset of main header from start of file
     """
     box_id = 'jp2c'
     longname = 'Contiguous Codestream'
 
-    def __init__(self, codestream=None, main_header_offset=None, length=0,
+    def __init__(self, main_header=None, main_header_offset=None, length=0,
                  offset=-1):
         Jp2kBox.__init__(self)
-        self._codestream = codestream
+        self._main_header = main_header
         self.length = length
         self.offset = offset
         self.main_header_offset = main_header_offset
@@ -1022,33 +1022,29 @@ class ContiguousCodestreamBox(Jp2kBox):
         self._filename = None
 
     @property
-    def codestream(self):
+    def main_header(self):
-        if _parseoptions['full_codestream'] is True:
+        if self._main_header is None:
-            header_only = False
-        else:
-            header_only = True
-        if self._codestream is None:
             if self._filename is not None:
                 with open(self._filename, 'rb') as fptr:
                     fptr.seek(self.main_header_offset)
-                    codestream = Codestream(fptr, self._length,
+                    main_header = Codestream(fptr, self._length, header_only=True)
-                                            header_only=header_only)
+                    self._main_header = main_header
-                    self._codestream = codestream
+        return self._main_header
-        return self._codestream
 
     def __repr__(self):
-        msg = "glymur.jp2box.ContiguousCodeStreamBox(codestream={0})"
+        msg = "glymur.jp2box.ContiguousCodeStreamBox(main_header={0})"
-        return msg.format(repr(self.codestream))
+        return msg.format(repr(self.main_header))
 
     def __str__(self):
         msg = Jp2kBox.__str__(self)
-        if _printoptions['short'] is True:
+        if _printoptions['short'] == True:
             return msg
-        if _printoptions['codestream'] is False:
+        if _printoptions['codestream'] == False:
             return msg
 
-        for segment in self.codestream.segment:
+        msg += '\n    Main header:'
-            msg += '\n' + self._indent(str(segment), indent_level=4)
+        for segment in self.main_header.segment:
+            msg += '\n' + self._indent(str(segment), indent_level=8)
 
         return msg
 
@@ -1070,11 +1066,11 @@ class ContiguousCodestreamBox(Jp2kBox):
         ContiguousCodestreamBox instance
         """
         main_header_offset = fptr.tell()
-        if _parseoptions['full_codestream'] is True:
+        if _parseoptions['codestream'] is True:
-            codestream = Codestream(fptr, length, header_only=False)
+            main_header = Codestream(fptr, length, header_only=True)
         else:
-            codestream = None
+            main_header = None
-        box = cls(codestream, main_header_offset=main_header_offset,
+        box = cls(main_header, main_header_offset=main_header_offset,
                   length=length, offset=offset)
         box._filename = fptr.name
         box._length = length
@@ -1122,8 +1118,7 @@ class DataReferenceBox(Jp2kBox):
         """Verify that the box obeys the specifications for writing.
         """
         if len(self.DR) == 0:
-            msg = "A data reference box cannot be empty when written to a "
+            msg = "A data reference box cannot be empty when written to a file."
-            msg += "file."
             self._dispatch_validation_error(msg, writing=True)
         self._validate(writing=True)
 
@@ -1150,7 +1145,7 @@ class DataReferenceBox(Jp2kBox):
 
     def __str__(self):
         msg = Jp2kBox.__str__(self)
-        if _printoptions['short'] is True:
+        if _printoptions['short'] == True:
             return msg
 
         for box in self.DR:
@@ -1253,7 +1248,7 @@ class FileTypeBox(Jp2kBox):
 
     def __str__(self):
         msg = Jp2kBox.__str__(self)
-        if _printoptions['short'] is True:
+        if _printoptions['short'] == True:
             return msg
 
         lst = [msg,
@@ -1316,18 +1311,12 @@ class FileTypeBox(Jp2kBox):
             brand = brand.decode('utf-8')
 
         # Extract the compatibility list.  Each entry has 4 bytes.
-        num_entries = int((length - 16) / 4)
+        num_entries = int((length - 16)/ 4)
         compatibility_list = []
         for j in range(int(num_entries)):
             entry, = struct.unpack_from('>4s', read_buffer, 8 + j * 4)
             if sys.hexversion >= 0x03000000:
-                try:
+                entry = entry.decode('utf-8')
-                    entry = entry.decode('utf-8')
-                except UnicodeDecodeError:
-                    # The entry is invalid, but we've got code to catch this
-                    # later on.
-                    pass
-
             compatibility_list.append(entry)
 
         return cls(brand=brand, minor_version=minor_version,
@@ -1385,7 +1374,7 @@ class FragmentListBox(Jp2kBox):
 
     def __str__(self):
         msg = Jp2kBox.__str__(self)
-        if _printoptions['short'] is True:
+        if _printoptions['short'] == True:
             return msg
 
         for j in range(len(self.fragment_offset)):
@@ -1469,10 +1458,7 @@ class FragmentTableBox(Jp2kBox):
 
     def __repr__(self):
         msg = "glymur.jp2box.FragmentTableBox(box={0})"
-        if len(self.box) == 0:
+        msg = msg.format(None) if (len(self.box) == 0) else msg.format(self.box)
-            msg = msg.format(None)
-        else:
-            msg = msg.format(self.box)
         return msg
 
     def __str__(self):
@@ -1519,6 +1505,7 @@ class FragmentTableBox(Jp2kBox):
         self._write_superbox(fptr, b'ftbl')
 
 
+
 class FreeBox(Jp2kBox):
     """Container for JPX free box information.
 
@@ -1547,7 +1534,7 @@ class FreeBox(Jp2kBox):
 
     def __str__(self):
         msg = Jp2kBox.__str__(self)
-        if _printoptions['short'] is True:
+        if _printoptions['short'] == True:
             return msg
 
         return msg
@@ -1643,7 +1630,7 @@ class ImageHeaderBox(Jp2kBox):
 
     def __str__(self):
         msg = Jp2kBox.__str__(self)
-        if _printoptions['short'] is True:
+        if _printoptions['short'] == True:
             return msg
 
         msg = "{0}"
@@ -1874,7 +1861,7 @@ class JPEG2000SignatureBox(Jp2kBox):
 
     def __str__(self):
         msg = Jp2kBox.__str__(self)
-        if _printoptions['short'] is True:
+        if _printoptions['short'] == True:
             return msg
 
         msg += '\n    Signature:  {0:02x}{1:02x}{2:02x}{3:02x}'
@@ -1963,7 +1950,7 @@ class PaletteBox(Jp2kBox):
 
     def __str__(self):
         msg = Jp2kBox.__str__(self)
-        if _printoptions['short'] is True:
+        if _printoptions['short'] == True:
             return msg
 
         msg += '\n    Size:  ({0} x {1})'.format(*self.palette.shape)
@@ -1993,6 +1980,7 @@ class PaletteBox(Jp2kBox):
                                    *bps_signed)
         fptr.write(write_buffer)
 
+        bps = self.bits_per_component
         # All components are the same.  Writing is straightforward.
         if self.bits_per_component[0] <= 8:
             write_buffer = memoryview(self.palette.astype(np.uint8))
@@ -2032,10 +2020,13 @@ class PaletteBox(Jp2kBox):
             # Ok the palette has the same datatype for all columns.  We should
             # be able to efficiently read it.
             if bps[0] <= 8:
+                nbytes_per_row = ncols
                 dtype = np.uint8
             elif bps[0] <= 16:
+                nbytes_per_row = 2 * ncols
                 dtype = np.uint16
             elif bps[0] <= 32:
+                nbytes_per_row = 3 * ncols
                 dtype = np.uint32
 
             palette = np.frombuffer(read_buffer[3 + ncols:], dtype=dtype)
@@ -2079,80 +2070,80 @@ _READER_REQUIREMENTS_DISPLAY = {
     7:  'JPEG codestream as defined in ISO/IEC 10918-1',
     8:  'Deprecated - does not contain opacity',
     9:  'Non-premultiplied opacity channel',
-    10: 'Premultiplied opacity channel',
+    10:  'Premultiplied opacity channel',
-    11: 'Chroma-key based opacity',
+    11:  'Chroma-key based opacity',
-    12: 'Deprecated - codestream is contiguous',
+    12:  'Deprecated - codestream is contiguous',
-    13: 'Fragmented codestream where all fragments are in file and in order',
+    13:  'Fragmented codestream where all fragments are in file and in order',
-    14: ('Fragmented codestream where all fragments are in file '
+    14:  'Fragmented codestream where all fragments are in file '
-         'but are out of order'),
+         + 'but are out of order',
-    15: ('Fragmented codestream where not all fragments are within the file '
+    15:  'Fragmented codestream where not all fragments are within the file '
-         'but are all in locally accessible files'),
+         + 'but are all in locally accessible files',
-    16: ('Fragmented codestream where some fragments may be accessible '
+    16:  'Fragmented codestream where some fragments may be accessible '
-         'only through a URL specified network connection'),
+         + 'only through a URL specified network connection',
-    17: ('Compositing required to produce rendered result from multiple '
+    17:  'Compositing required to produce rendered result from multiple '
-         'compositing layers'),
+         + 'compositing layers',
-    18: 'Deprecated - support for compositing is not required',
+    18:  'Deprecated - support for compositing is not required',
-    19: ('Deprecated - contains multiple, discrete layers that should not '
+    19:  'Deprecated - contains multiple, discrete layers that should not '
-         'be combined through either animation or compositing'),
+         + 'be combined through either animation or compositing',
-    20: ('Deprecated - compositing layers each contain only a single '
+    20:  'Deprecated - compositing layers each contain only a single '
-         'codestream'),
+         + 'codestream',
-    21: 'At least one compositing layer consists of multiple codestreams',
+    21:  'At least one compositing layer consists of multiple codestreams',
-    22: 'Deprecated - all compositing layers are in the same colourspace',
+    22:  'Deprecated - all compositing layers are in the same colourspace',
-    23: ('Colourspace transformations are required to combine compositing '
+    23:  'Colourspace transformations are required to combine compositing '
-         'layers; not all compositing layers are in the same colourspace'),
+         + 'layers; not all compositing layers are in the same colourspace',
-    24: 'Deprecated - rendered result created without using animation',
+    24:  'Deprecated - rendered result created without using animation',
-    25: ('Deprecated - animated, but first layer covers entire area and is '
+    25:  'Deprecated - animated, but first layer covers entire area and is '
-         'opaque'),
+         + 'opaque',
-    26: 'First animation layer does not cover entire rendered result',
+    26:  'First animation layer does not cover entire rendered result',
-    27: 'Deprecated - animated, and no layer is reused',
+    27:  'Deprecated - animated, and no layer is reused',
-    28: 'Reuse of animation layers',
+    28:  'Reuse of animation layers',
-    29: 'Deprecated - animated, but layers are reused',
+    29:  'Deprecated - animated, but layers are reused',
-    30: 'Some animated frames are non-persistent',
+    30:  'Some animated frames are non-persistent',
-    31: 'Deprecated - rendered result created without using scaling',
+    31:  'Deprecated - rendered result created without using scaling',
-    32: 'Rendered result involves scaling within a layer',
+    32:  'Rendered result involves scaling within a layer',
-    33: 'Rendered result involves scaling between layers',
+    33:  'Rendered result involves scaling between layers',
-    34: 'ROI metadata',
+    34:  'ROI metadata',
-    35: 'IPR metadata',
+    35:  'IPR metadata',
-    36: 'Content metadata',
+    36:  'Content metadata',
-    37: 'History metadata',
+    37:  'History metadata',
-    38: 'Creation metadata',
+    38:  'Creation metadata',
-    39: 'JPX digital signatures',
+    39:  'JPX digital signatures',
-    40: 'JPX checksums',
+    40:  'JPX checksums',
-    41: 'Desires Graphics Arts Reproduction specified',
+    41:  'Desires Graphics Arts Reproduction specified',
-    42: 'Deprecated - compositing layer uses palettized colour',
+    42:  'Deprecated - compositing layer uses palettized colour',
-    43: 'Deprecated - compositing layer uses restricted ICC profile',
+    43:  'Deprecated - compositing layer uses restricted ICC profile',
-    44: 'Compositing layer uses Any ICC profile',
+    44:  'Compositing layer uses Any ICC profile',
-    45: 'Deprecated - compositing layer uses sRGB enumerated colourspace',
+    45:  'Deprecated - compositing layer uses sRGB enumerated colourspace',
-    46: 'Deprecated - compositing layer uses sRGB-grey enumerated colourspace',
+    46:  'Deprecated - compositing layer uses sRGB-grey enumerated colourspace',
-    47: 'BiLevel 1 enumerated colourspace',
+    47:  'BiLevel 1 enumerated colourspace',
-    48: 'BiLevel 2 enumerated colourspace',
+    48:  'BiLevel 2 enumerated colourspace',
-    49: 'YCbCr 1 enumerated colourspace',
+    49:  'YCbCr 1 enumerated colourspace',
-    50: 'YCbCr 2 enumerated colourspace',
+    50:  'YCbCr 2 enumerated colourspace',
-    51: 'YCbCr 3 enumerated colourspace',
+    51:  'YCbCr 3 enumerated colourspace',
-    52: 'PhotoYCC enumerated colourspace',
+    52:  'PhotoYCC enumerated colourspace',
-    53: 'YCCK enumerated colourspace',
+    53:  'YCCK enumerated colourspace',
-    54: 'CMY enumerated colourspace',
+    54:  'CMY enumerated colourspace',
-    55: 'CMYK enumerated colorspace',
+    55:  'CMYK enumerated colorspace',
-    56: 'CIELab enumerated colourspace with default parameters',
+    56:  'CIELab enumerated colourspace with default parameters',
-    57: 'CIELab enumerated colourspace with non-default parameters',
+    57:  'CIELab enumerated colourspace with non-default parameters',
-    58: 'CIEJab enumerated colourspace with default parameters',
+    58:  'CIEJab enumerated colourspace with default parameters',
-    59: 'CIEJab enumerated colourspace with non-default parameters',
+    59:  'CIEJab enumerated colourspace with non-default parameters',
-    60: 'e-sRGB enumerated colorspace',
+    60:  'e-sRGB enumerated colorspace',
-    61: 'ROMM_RGB enumerated colorspace',
+    61:  'ROMM_RGB enumerated colorspace',
-    62: 'Non-square samples',
+    62:  'Non-square samples',
-    63: 'Deprecated - compositing layers have labels',
+    63:  'Deprecated - compositing layers have labels',
-    64: 'Deprecated - codestreams have labels',
+    64:  'Deprecated - codestreams have labels',
-    65: 'Deprecated - compositing layers have different colour spaces',
+    65:  'Deprecated - compositing layers have different colour spaces',
-    66: 'Deprecated - compositing layers have different metadata',
+    66:  'Deprecated - compositing layers have different metadata',
-    67: 'GIS metadata XML box',
+    67:  'GIS metadata XML box',
-    68: 'JPSEC extensions in codestream as specified by ISO/IEC 15444-8',
+    68:  'JPSEC extensions in codestream as specified by ISO/IEC 15444-8',
-    69: 'JP3D extensions in codestream as specified by ISO/IEC 15444-10',
+    69:  'JP3D extensions in codestream as specified by ISO/IEC 15444-10',
-    70: 'Deprecated - compositing layer uses sYCC enumerated colour space',
+    70:  'Deprecated - compositing layer uses sYCC enumerated colour space',
-    71: 'e-sYCC enumerated colourspace',
+    71:  'e-sYCC enumerated colourspace',
-    72: ('JPEG 2000 Part 2 codestream as restricted by baseline conformance '
+    72:  'JPEG 2000 Part 2 codestream as restricted by baseline conformance '
-         'requirements in M.9.2.3'),
+         + 'requirements in M.9.2.3',
-    73: 'YPbPr(1125/60) enumerated colourspace',
+    73:  'YPbPr(1125/60) enumerated colourspace',
-    74: 'YPbPr(1250/50) enumerated colourspace'}
+    74:  'YPbPr(1250/50) enumerated colourspace'}
 
 
 class ReaderRequirementsBox(Jp2kBox):
@@ -2212,11 +2203,10 @@ class ReaderRequirementsBox(Jp2kBox):
 
     def __str__(self):
         msg = Jp2kBox.__str__(self)
-        if _printoptions['short'] is True:
+        if _printoptions['short'] == True:
             return msg
 
-        msg += '\n    Fully Understands Aspect Mask:  0x{0:x}'
+        msg += '\n    Fully Understands Aspect Mask:  0x{0:x}'.format(self.fuam)
-        msg = msg.format(self.fuam)
         msg += '\n    Display Completely Mask:  0x{0:x}'.format(self.dcm)
 
         msg += '\n    Standard Features and Masks:'
@@ -2272,8 +2262,7 @@ class ReaderRequirementsBox(Jp2kBox):
             standard_flag, standard_mask = data
 
             nflags = len(standard_flag)
-            vendor_offset = (1 + 2 * mask_length + 2
+            vendor_offset = 1 + 2 * mask_length + 2 + (2 + mask_length) * nflags
-                             + (2 + mask_length) * nflags)
             data = _parse_vendor_features(read_buffer[vendor_offset:],
                                           mask_length)
             vendor_feature, vendor_mask = data
@@ -2330,8 +2319,8 @@ def _parse_rreq3(read_buffer, length, offset):
     read_buffer = read_buffer[9 + num_standard_features * 10:]
     for j in range(num_vendor_features):
         uslice = slice(j * entry_length, (j + 1) * entry_length)
-        ubuffer = read_buffer[uslice]
+        ubuffer = read_buffer[slice]
-        vendor_feature.append(UUID(bytes=ubuffer[0:16]))
+        vendor_feature.append(uuid.UUID(bytes=ubuffer[0:16]))
 
         lst = struct.unpack('>BBB', ubuffer[16:])
         vmask = lst[0] << 16 | lst[1] << 8 | lst[2]
@@ -2359,11 +2348,14 @@ def _parse_standard_flag(read_buffer, mask_length):
     # from the buffer read from file.
     mask_format = {1: 'B', 2: 'H', 4: 'I'}[mask_length]
 
+    #read_buffer = fptr.read(2)
     num_standard_flags, = struct.unpack_from('>H', read_buffer, offset=0)
 
     # Read in standard flags and standard masks.  Each standard flag should
     # be two bytes, but the standard mask flag is as long as specified by
     # the mask length.
+    #read_buffer = fptr.read(num_standard_flags * (2 + mask_length))
+
     fmt = '>' + ('H' + mask_format) * num_standard_flags
     data = struct.unpack_from(fmt, read_buffer, offset=2)
 
@@ -2394,12 +2386,13 @@ def _parse_vendor_features(read_buffer, mask_length):
     # Each vendor feature consists of a 16-byte UUID plus a mask whose
     # length is specified by, you guessed it, "mask_length".
     entry_length = 16 + mask_length
+    #read_buffer = fptr.read(num_vendor_features * entry_length)
     vendor_feature = []
     vendor_mask = []
     for j in range(num_vendor_features):
         uslice = slice(2 + j * entry_length, 2 + (j + 1) * entry_length)
         ubuffer = read_buffer[uslice]
-        vendor_feature.append(UUID(bytes=ubuffer[0:16]))
+        vendor_feature.append(uuid.UUID(bytes=ubuffer[0:16]))
 
         vmask = struct.unpack('>' + mask_format, ubuffer[16:])
         vendor_mask.append(vmask)
@@ -2501,7 +2494,7 @@ class CaptureResolutionBox(Jp2kBox):
 
     def __str__(self):
         msg = Jp2kBox.__str__(self)
-        if _printoptions['short'] is True:
+        if _printoptions['short'] == True:
             return msg
 
         msg += '\n    VCR:  {0}'.format(self.vertical_resolution)
@@ -2567,7 +2560,7 @@ class DisplayResolutionBox(Jp2kBox):
 
     def __str__(self):
         msg = Jp2kBox.__str__(self)
-        if _printoptions['short'] is True:
+        if _printoptions['short'] == True:
             return msg
 
         msg += '\n    VDR:  {0}'.format(self.vertical_resolution)
@@ -2627,7 +2620,7 @@ class LabelBox(Jp2kBox):
 
     def __str__(self):
         msg = Jp2kBox.__str__(self)
-        if _printoptions['short'] is True:
+        if _printoptions['short'] == True:
             return msg
 
         msg += '\n    Label:  {0}'.format(self.label)
@@ -2695,7 +2688,7 @@ class NumberListBox(Jp2kBox):
 
     def __str__(self):
         msg = Jp2kBox.__str__(self)
-        if _printoptions['short'] is True:
+        if _printoptions['short'] == True:
             return msg
 
         for j, association in enumerate(self.associations):
@@ -2745,8 +2738,7 @@ class NumberListBox(Jp2kBox):
     def write(self, fptr):
         """Write a NumberList box to file.
         """
-        fptr.write(struct.pack('>I4s',
+        fptr.write(struct.pack('>I4s', len(self.associations) * 4 + 8, b'nlst'))
-                               len(self.associations) * 4 + 8, b'nlst'))
 
         fmt = '>' + 'I' * len(self.associations)
         write_buffer = struct.pack(fmt, *self.associations)
@@ -2798,9 +2790,9 @@ class XMLBox(Jp2kBox):
 
     def __str__(self):
         msg = Jp2kBox.__str__(self)
-        if _printoptions['short'] is True:
+        if _printoptions['short'] == True:
             return msg
-        if _printoptions['xml'] is False:
+        if _printoptions['xml'] == False:
             return msg
 
         msg += '\n'
@@ -2919,7 +2911,7 @@ class UUIDListBox(Jp2kBox):
 
     def __str__(self):
         msg = Jp2kBox.__str__(self)
-        if _printoptions['short'] is True:
+        if _printoptions['short'] == True:
             return msg
 
         for j, uuid_item in enumerate(self.ulst):
@@ -2950,8 +2942,8 @@ class UUIDListBox(Jp2kBox):
 
         ulst = []
         for j in range(num_uuids):
-            uuid_buffer = read_buffer[2 + j * 16:2 + (j + 1) * 16]
+            uuid_buffer = read_buffer[2 + j * 16 : 2 + (j + 1) * 16]
-            ulst.append(UUID(bytes=uuid_buffer))
+            ulst.append(uuid.UUID(bytes=uuid_buffer))
 
         return cls(ulst, length=length, offset=offset)
 
@@ -3064,6 +3056,7 @@ class DataEntryURLBox(Jp2kBox):
         fptr.write(write_buffer)
         fptr.write(url)
 
+
     def __repr__(self):
         msg = "glymur.jp2box.DataEntryURLBox({0}, {1}, '{2}')"
         msg = msg.format(self.version, self.flag, self.url)
@@ -3071,7 +3064,7 @@ class DataEntryURLBox(Jp2kBox):
 
     def __str__(self):
         msg = Jp2kBox.__str__(self)
-        if _printoptions['short'] is True:
+        if _printoptions['short'] == True:
             return msg
 
         msg += '\n    '
@@ -3209,7 +3202,7 @@ class UUIDBox(Jp2kBox):
         """
         Private function for parsing UUID payloads if possible.
         """
-        if self.uuid == UUID('be7acfcb-97a9-42e8-9c71-999491e3afac'):
+        if self.uuid == uuid.UUID('be7acfcb-97a9-42e8-9c71-999491e3afac'):
             self.data = _uuid_io.xml(self.raw_data)
         elif self.uuid.bytes == b'JpgTiffExif->JP2':
             self.data = _uuid_io.tiff_header(self.raw_data)
@@ -3223,23 +3216,23 @@ class UUIDBox(Jp2kBox):
 
     def __str__(self):
         msg = Jp2kBox.__str__(self)
-        if _printoptions['short'] is True:
+        if _printoptions['short'] == True:
             return msg
 
         msg = '{0}\n    UUID:  {1}'.format(msg, self.uuid)
-        if self.uuid == UUID('be7acfcb-97a9-42e8-9c71-999491e3afac'):
+        if self.uuid == uuid.UUID('be7acfcb-97a9-42e8-9c71-999491e3afac'):
             msg += ' (XMP)'
         elif self.uuid.bytes == b'JpgTiffExif->JP2':
             msg += ' (EXIF)'
         else:
             msg += ' (unknown)'
 
-        if (((_printoptions['xml'] is False) and
+        if (((_printoptions['xml'] == False) and
-             (self.uuid == UUID('be7acfcb-97a9-42e8-9c71-999491e3afac')))):
+             (self.uuid == uuid.UUID('be7acfcb-97a9-42e8-9c71-999491e3afac')))):
             # If it's an XMP UUID, don't print the XML contents.
             return msg
 
-        if self.uuid == UUID('be7acfcb-97a9-42e8-9c71-999491e3afac'):
+        if self.uuid == uuid.UUID('be7acfcb-97a9-42e8-9c71-999491e3afac'):
             line = '\n    UUID Data:\n{0}'
             xmlstring = ET.tostring(self.data,
                                     encoding='utf-8',
@@ -3282,7 +3275,7 @@ class UUIDBox(Jp2kBox):
         """
         num_bytes = offset + length - fptr.tell()
         read_buffer = fptr.read(num_bytes)
-        the_uuid = UUID(bytes=read_buffer[0:16])
+        the_uuid = uuid.UUID(bytes=read_buffer[0:16])
         return cls(the_uuid, read_buffer[16:], length=length, offset=offset)
 
 
@@ -3317,20 +3310,18 @@ _BOX_WITH_ID = {
     b'uuid': UUIDBox,
     b'xml ': XMLBox}
 
-_parseoptions = {'full_codestream': False}
+_parseoptions = {'codestream': True}
 
-
+def set_parseoptions(codestream=True):
-def set_parseoptions(full_codestream=True):
     """Set parsing options.
 
     These options determine the way JPEG 2000 boxes are parsed.
 
     Parameters
     ----------
-    full_codestream : bool, defaults to True
+    codestream : bool, defaults to True
-        When False, only the codestream header is parsed for metadata.  This
+        When False, the codestream header is only parsed when accessed.  This
-        can results in faster JP2/JPX parsing.  When True, the entire
+        can results in faster JP2/JPX parsing.
-        codestream is parsed for metadata.
 
     See also
     --------
@@ -3341,10 +3332,9 @@ def set_parseoptions(full_codestream=True):
     To put back the default options, you can use:
 
     >>> import glymur
-    >>> glymur.set_parseoptions(full_codestream=True)
+    >>> glymur.set_parseoptions(codestream=True)
     """
-    _parseoptions['full_codestream'] = full_codestream
+    _parseoptions['codestream'] = codestream
-
 
 def get_parseoptions():
     """Return the current parsing options.
@@ -3366,7 +3356,6 @@ def get_parseoptions():
 
 _printoptions = {'short': False, 'xml': True, 'codestream': True}
 
-
 def set_printoptions(**kwargs):
     """Set printing options.
 
@@ -3376,15 +3365,12 @@ def set_printoptions(**kwargs):
     ----------
     short : bool, optional
         When True, only the box ID, offset, and length are displayed.  Useful
-        for displaying only the basic structure or skeleton of a JPEG 2000
+        for displaying only the basic structure or skeleton of a JPEG 2000 file.
-        file.
     xml : bool, optional
         When False, printing of the XML contents of any XML boxes or UUID XMP
         boxes is suppressed.
     codestream : bool, optional
-        When False, only the codestream header is printed.  When True, the
+        When False, printing of the codestream contents is suppressed.
-        entire codestream is printed.  This option has no effect when the
-        'short' option is set to True.
 
     See also
     --------
@@ -3402,7 +3388,6 @@ def set_printoptions(**kwargs):
             raise TypeError('"{0}" not a valid keyword parameter.'.format(key))
         _printoptions[key] = value
 
-
 def get_printoptions():
     """Return the current print options.
 
@@ -3422,3 +3407,5 @@ def get_printoptions():
     set_printoptions
     """
     return _printoptions
+
+

glymur/jp2k.py

@@ -10,12 +10,13 @@ License:  MIT
 import sys
 
 # Exitstack not found in contextlib in 2.7
+# pylint: disable=E0611
 if sys.hexversion >= 0x03030000:
     from contextlib import ExitStack
-    from itertools import filterfalse
+    from itertools import compress, filterfalse
 else:
     from contextlib2 import ExitStack
-    from itertools import ifilterfalse as filterfalse
+    from itertools import compress, ifilterfalse as filterfalse
 
 from collections import Counter
 import ctypes
@@ -30,11 +31,21 @@ import numpy as np
 
 from .codestream import Codestream
 from . import core, version
-from .jp2box import (Jp2kBox, JPEG2000SignatureBox, FileTypeBox,
+from .jp2box import (
-                     JP2HeaderBox, ColourSpecificationBox,
+        Jp2kBox, JPEG2000SignatureBox, FileTypeBox, JP2HeaderBox,
-                     ContiguousCodestreamBox, ImageHeaderBox)
+        ColourSpecificationBox, ContiguousCodestreamBox, ImageHeaderBox
+)
 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.
@@ -43,200 +54,33 @@ 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
         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.
-    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
-    codestream : object
-        JP2 or J2K codestream object
-
-    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, data=None, shape=None, **kwargs):
+    def __init__(self, filename, mode='rb'):
         """
-        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
+        mode : str, optional
-            image data to be written
+            The mode used to open the file.
-        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
-
+        self.mode = mode
         self.box = []
         self._codec_format = None
         self._colorspace = None
-        self._layer = 0
-        self._codestream = None
-        if data is not None:
-            self._shape = data.shape
-        else:
-            self._shape = shape
-
-        self._ignore_pclr_cmap_cdef = False
-        self._verbose = False
 
         # Parse the file for JP2/JPX contents only if we are reading it.
-        if data is None and shape is None:
+        if mode == 'rb':
             self.parse()
-        elif data is not None:
-            self._write(data, **kwargs)
-
-    @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 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 "
-            msg += "OpenJPEG is 2.0 or higher."
-            raise RuntimeError(msg)
-        self._layer = layer
-
-    @property
-    def codestream(self):
-        if self._codestream is None:
-            self._codestream = self.get_codestream(header_only=True)
-        return self._codestream
-
-    @codestream.setter
-    def codestream(self, the_codestream):
-        self._codestream = the_codestream
-
-    @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:
-            return self._shape
-
-        if self._codec_format == opj2.CODEC_J2K:
-            # get the image size from the codestream
-            cstr = self.codestream
-            height = cstr.segment[1].ysiz
-            width = cstr.segment[1].xsiz
-            num_components = len(cstr.segment[1].xrsiz)
-        else:
-            # try to get the image size from the IHDR box
-            jp2h = [box for box in self.box if box.box_id == 'jp2h'][0]
-            ihdr = [box for box in jp2h.box if box.box_id == 'ihdr'][0]
-
-            height, width = ihdr.height, ihdr.width
-            num_components = ihdr.num_components
-
-            if num_components == 1:
-                # but if there is a PCLR box, then we need to check that as
-                # well, as that turns a single-channel image into a
-                # multi-channel image
-                pclr = [box for box in jp2h.box if box.box_id == 'pclr']
-                if len(pclr) > 0:
-                    num_components = len(pclr[0].signed)
-
-        if num_components == 1:
-            self.shape = (height, width)
-        else:
-            self.shape = (height, width, num_components)
-
-        return self._shape
-
-    @shape.setter
-    def shape(self, shape):
-        self._shape = shape
 
     def __repr__(self):
         msg = "glymur.Jp2k('{0}')".format(self.filename)
@@ -248,7 +92,8 @@ class Jp2k(Jp2kBox):
             for box in self.box:
                 metadata.append(str(box))
         else:
-            metadata.append(str(self.codestream))
+            codestream = self.get_codestream()
+            metadata.append(str(codestream))
         return '\n'.join(metadata)
 
     def parse(self):
@@ -373,8 +218,8 @@ class Jp2k(Jp2kBox):
         kwargs : dictionary
             non-image keyword inputs provided to write method
         """
-        if ((('cinema2k' in kwargs or 'cinema4k' in kwargs) and
+        if (('cinema2k' in kwargs or 'cinema4k' in kwargs)  and
-             (len(set(kwargs)) > 1))):
+                (len(set(kwargs)) > 1)):
             msg = "Cannot specify cinema2k/cinema4k along with other options."
             raise IOError(msg)
 
@@ -489,19 +334,79 @@ class Jp2k(Jp2kBox):
 
         self._cparams = cparams
 
-    def _write(self, img_array, verbose=False, **kwargs):
+    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.
-        """
-        if re.match("0|1.[0-4]", version.openjpeg_version) is not None:
-            msg = "You must have at least version 1.5 of OpenJPEG "
-            msg += "in order to write images."
-            raise RuntimeError(msg)
 
-        self._determine_colorspace(**kwargs)
+        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.
+
+        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 "
+                               "in order to write images.")
+
+        self._determine_colorspace(img_array, **kwargs)
         self._populate_cparams(img_array, **kwargs)
 
         if opj2.OPENJP2 is not None:
@@ -530,12 +435,10 @@ class Jp2k(Jp2kBox):
             # set image offset and reference grid
             image.contents.x0 = self._cparams.image_offset_x0
             image.contents.y0 = self._cparams.image_offset_y0
-            image.contents.x1 = (image.contents.x0
+            image.contents.x1 = image.contents.x0 \
-                                 + (numcols - 1) * self._cparams.subsampling_dx
+                              + (numcols - 1) * self._cparams.subsampling_dx + 1
-                                 + 1)
+            image.contents.y1 = image.contents.y0 \
-            image.contents.y1 = (image.contents.y0
+                              + (numrows - 1) * self._cparams.subsampling_dy + 1
-                                 + (numrows - 1) * self._cparams.subsampling_dy
-                                 + 1)
 
             # Stage the image data to the openjpeg data structure.
             for k in range(0, numlayers):
@@ -642,24 +545,25 @@ class Jp2k(Jp2kBox):
                 raise IOError(msg)
 
         if img_array.dtype != np.uint8 and img_array.dtype != np.uint16:
-            msg = "Only uint8 and uint16 datatypes are currently supported "
+            msg = "Only uint8 and uint16 images are currently supported."
-            msg += "when writing."
             raise RuntimeError(msg)
 
-    def _determine_colorspace(self, colorspace=None, **kwargs):
+    def _determine_colorspace(self, img_array, colorspace=None, **kwargs):
         """Determine the colorspace from the supplied inputs.
-
+    
         Parameters
         ----------
+        img_array : ndarray
+            Image data to be written to file.
         colorspace : str, optional
             Either 'rgb' or 'gray'.
         """
         if colorspace is None:
             # Must infer the colorspace from the image dimensions.
-            if len(self.shape) < 3:
+            if img_array.ndim < 3:
                 # A single channel image is grayscale.
                 self._colorspace = opj2.CLRSPC_GRAY
-            elif self.shape[2] == 1 or self.shape[2] == 2:
+            elif img_array.shape[2] == 1 or img_array.shape[2] == 2:
                 # A single channel image or an image with two channels is going
                 # to be greyscale.
                 self._colorspace = opj2.CLRSPC_GRAY
@@ -670,19 +574,15 @@ class Jp2k(Jp2kBox):
             if colorspace.lower() not in ('rgb', 'grey', 'gray'):
                 msg = 'Invalid colorspace "{0}"'.format(colorspace)
                 raise IOError(msg)
-            elif colorspace.lower() == 'rgb' and self.shape[2] < 3:
+            elif colorspace.lower() == 'rgb' and img_array.shape[2] < 3:
                 msg = 'RGB colorspace requires at least 3 components.'
                 raise IOError(msg)
-
+    
             # Turn the colorspace from a string to the enumerated value that
             # the library expects.
-            COLORSPACE_MAP = {'rgb': opj2.CLRSPC_SRGB,
+            self._colorspace = _COLORSPACE_MAP[colorspace.lower()]
-                              '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):
         """
         Write JPEG 2000 file using OpenJPEG 2.x interface.
@@ -703,11 +603,7 @@ class Jp2k(Jp2kBox):
             codec = opj2.create_compress(self._cparams.codec_fmt)
             stack.callback(opj2.destroy_codec, codec)
 
-            if self._verbose or verbose:
+            info_handler = _INFO_CALLBACK if verbose else None
-                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)
@@ -748,8 +644,7 @@ class Jp2k(Jp2kBox):
         if not ((box.box_id == 'xml ') or
                 (box.box_id == 'uuid' and
                  box.uuid == UUID('be7acfcb-97a9-42e8-9c71-999491e3afac'))):
-            msg = "Only XML boxes and XMP UUID boxes can currently be "
+            msg = "Only XML boxes and XMP UUID boxes can currently be appended."
-            msg += "appended."
             raise IOError(msg)
 
         # Check the last box.  If the length field is zero, then rewrite
@@ -845,7 +740,7 @@ class Jp2k(Jp2kBox):
                 raise IOError(msg)
 
             # Find the first codestream in the file.
-            jp2c = [_box for _box in self.box if _box.box_id == 'jp2c']
+            jp2c = [box for box in self.box if box.box_id == 'jp2c']
             offset = jp2c[0].offset
 
         # Ready to write the codestream.
@@ -879,9 +774,10 @@ class Jp2k(Jp2kBox):
                  FileTypeBox(),
                  JP2HeaderBox(),
                  ContiguousCodestreamBox()]
-        height = self.codestream.segment[1].ysiz
+        codestream = self.get_codestream()
-        width = self.codestream.segment[1].xsiz
+        height = codestream.segment[1].ysiz
-        num_components = len(self.codestream.segment[1].xrsiz)
+        width = codestream.segment[1].xsiz
+        num_components = len(codestream.segment[1].xrsiz)
         if num_components < 3:
             colorspace = core.GREYSCALE
         else:
@@ -905,13 +801,13 @@ class Jp2k(Jp2kBox):
         Slicing protocol.
         """
         if ((isinstance(index, slice) and
-            (index.start is None and
+            (index.start == None and
-                index.stop is None and
+                index.stop == None and
-                index.step is None)) or (index is Ellipsis)):
+                index.step == None)) or (index is Ellipsis)):
             # 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)
@@ -920,32 +816,29 @@ class Jp2k(Jp2kBox):
         """
         Slicing protocol.
         """
-        if len(self.shape) == 2:
+        codestream = self.get_codestream(header_only=True)
-            numrows, numcols = self.shape
+        numrows = codestream.segment[1].ysiz
-            numbands = 1
+        numcols = codestream.segment[1].xsiz
-        else:
+        numbands = codestream.segment[1].Csiz
-            numrows, numcols, numbands = self.shape
 
         if isinstance(pargs, int):
             # Not a very good use of this protocol, but technically legal.
             # 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[...]
-            return self._read()
+            return self.read()
 
         if isinstance(pargs, slice):
-            if (((pargs.start is None) and
+            if pargs.start is None and pargs.stop is None and pargs.step is None:
-                 (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
+            # members.  Just augment it with an ellipsis and let the code 
             # below handle it.
             pargs = (pargs, Ellipsis)
 
@@ -988,7 +881,8 @@ class Jp2k(Jp2kBox):
             # Reduce dimensionality in the scalar dimension.
             return np.squeeze(data, axis=idx)
 
-        # Assuming pargs is a tuple of slices from now on.
+
+        # Assuming pargs is a tuple of slices from now on.  
         rows = pargs[0]
         cols = pargs[1]
         if len(pargs) == 2:
@@ -1005,28 +899,49 @@ class Jp2k(Jp2kBox):
         # Ok, reduce layer step is the same in both xy directions, so just take
         # one of them.
         step = rows_step
-
+    
         # Check if the step size is a power of 2.
         if np.abs(np.log2(step) - np.round(np.log2(step))) > 1e-6:
             msg = "Row and column strides must be powers of 2."
             raise IndexError(msg)
         rlevel = np.int(np.round(np.log2(step)))
 
-        area = (0 if rows.start is None else rows.start,
+        area = (
+                0 if rows.start is None else rows.start,
                 0 if cols.start is None else cols.start,
                 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
 
         # Ok, 3 arguments in pargs.
         return data[:, :, bands]
 
-    def _read(self, **kwargs):
+
+    def read(self, **kwargs):
         """Read a JPEG 2000 image.
 
+        Parameters
+        ----------
+        rlevel : int, optional
+            Factor by which to rlevel output resolution.  Use -1 to get the
+            lowest resolution thumbnail.  This is the only keyword option
+            available to use when the OpenJPEG version is 1.5 or earlier.
+        layer : int, optional
+            Number of quality layer to decode.
+        area : tuple, optional
+            Specifies decoding image area,
+            (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.
+
         Returns
         -------
         img_array : ndarray
@@ -1036,65 +951,42 @@ class Jp2k(Jp2kBox):
         ------
         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):
+        Examples
-        """
+        --------
-        """
+        >>> import glymur
-        # Read a JPEG 2000 image.
+        >>> jfile = glymur.data.nemo()
-        #
+        >>> jp = glymur.Jp2k(jfile)
-        # Parameters
+        >>> image = jp.read()
-        # ----------
+        >>> image.shape
-        # rlevel : int, optional
+        (1456, 2592, 3)
-        #     Factor by which to rlevel output resolution.  Use -1 to get the
-        #     lowest resolution thumbnail.  This is the only keyword option
-        #     available to use when the OpenJPEG version is 1.5 or earlier.
-        # layer : int, optional
-        #     Number of quality layer to decode.
-        # area : tuple, optional
-        #     Specifies decoding image area,
-        #     (first_row, first_col, last_row, last_col)
-        # tile : int, optional
-        #     Number of tile to decode.
-        # verbose : bool, optional
-        #     Print informational messages produced by the OpenJPEG library.
-        #
-        # Returns
-        # -------
-        # img_array : ndarray
-        #     The image data.
-        #
-        # Raises
-        # ------
-        # IOError
-        #     If the image has differing subsample factors.
 
-        if 'ignore_pclr_cmap_cdef' in kwargs:
+        Read the lowest resolution thumbnail.
-            self.ignore_pclr_cmap_cdef = kwargs['ignore_pclr_cmap_cdef']
+
-        warnings.warn("Use array-style slicing instead.", DeprecationWarning)
+        >>> thumbnail = jp.read(rlevel=-1)
-        if version.openjpeg_version_tuple[0] < 2:
+        >>> thumbnail.shape
-            img = self._read_openjpeg(**kwargs)
+        (728, 1296, 3)
-        else:
+        """
+        if opj2.OPENJP2 is not None:
             img = self._read_openjp2(**kwargs)
+        else:
+            img = self._read_openjpeg(**kwargs)
         return img
 
     def _subsampling_sanity_check(self):
         """Check for differing subsample factors.
         """
-        dxs = np.array(self.codestream.segment[1].xrsiz)
+        codestream = self.get_codestream(header_only=True)
-        dys = np.array(self.codestream.segment[1].yrsiz)
+        dxs = np.array(codestream.segment[1].xrsiz)
+        dys = np.array(codestream.segment[1].yrsiz)
         if np.any(dxs - dxs[0]) or np.any(dys - dys[0]):
             msg = "Components must all have the same subsampling factors "
             msg += "to use this method.  Please consider using OPENJP2 and "
             msg += "the read_bands method instead."
             raise RuntimeError(msg)
 
-    def _read_openjpeg(self, rlevel=0, verbose=False, area=None):
+    def _read_openjpeg(self, rlevel=0, ignore_pclr_cmap_cdef=False,
+                       verbose=False, area=None):
         """Read a JPEG 2000 image using libopenjpeg.
 
         Parameters
@@ -1102,6 +994,9 @@ 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
@@ -1120,7 +1015,7 @@ class Jp2k(Jp2kBox):
         """
         self._subsampling_sanity_check()
 
-        self._populate_dparams(rlevel)
+        self._populate_dparams(rlevel, ignore_pclr_cmap_cdef)
 
         with ExitStack() as stack:
             try:
@@ -1130,10 +1025,7 @@ class Jp2k(Jp2kBox):
 
                 event_mgr = opj.EventMgrType()
                 info_handler = ctypes.cast(_INFO_CALLBACK, ctypes.c_void_p)
-                if verbose or self._verbose:
+                event_mgr.info_handler = info_handler if verbose else None
-                    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,
@@ -1176,8 +1068,8 @@ class Jp2k(Jp2kBox):
 
         return data
 
-    def _read_openjp2(self, rlevel=0, layer=None, area=None, tile=None,
+    def _read_openjp2(self, rlevel=0, layer=0, area=None, tile=None,
-                      verbose=False):
+                      verbose=False, ignore_pclr_cmap_cdef=False):
         """Read a JPEG 2000 image using libopenjp2.
 
         Parameters
@@ -1205,12 +1097,10 @@ 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, tile=tile, area=area)
+        self._populate_dparams(rlevel, ignore_pclr_cmap_cdef,
+                               layer=layer, tile=tile, area=area)
 
         with ExitStack() as stack:
             if re.match("2.1", version.openjpeg_version):
@@ -1227,8 +1117,7 @@ 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)
@@ -1245,8 +1134,7 @@ class Jp2k(Jp2kBox):
                                      self._dparams.DA_x0, self._dparams.DA_y0,
                                      self._dparams.DA_x1, self._dparams.DA_y1)
                 opj2.decode(codec, stream, image)
-
+                opj2.end_decompress(codec, stream)
-            opj2.end_decompress(codec, stream)
 
             img_array = extract_image_cube(image)
 
@@ -1255,11 +1143,14 @@ class Jp2k(Jp2kBox):
 
         return img_array
 
-    def _populate_dparams(self, rlevel, tile=None, area=None):
+    def _populate_dparams(self, rlevel, ignore_pclr_cmap_cdef, tile=None,
+                          layer=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
@@ -1267,6 +1158,9 @@ 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()
@@ -1279,18 +1173,16 @@ 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
 
-        dparam.cp_layer = self._layer
+        if layer is not None:
+            dparam.cp_layer = layer
 
         # Must check the specified rlevel against the maximum.
         if rlevel != 0:
             # Must check the specified rlevel against the maximum.
-            max_rlevel = self.codestream.segment[2].spcod[4]
+            codestream = self.get_codestream()
+            max_rlevel = codestream.segment[2].spcod[4]
             if rlevel == -1:
                 # -1 is shorthand for the largest rlevel
                 rlevel = max_rlevel
@@ -1315,13 +1207,13 @@ class Jp2k(Jp2kBox):
             dparam.tile_index = tile
             dparam.nb_tile_to_decode = 1
 
-        if self.ignore_pclr_cmap_cdef:
+        if ignore_pclr_cmap_cdef is True:
             # Return raw codestream components.
             dparam.flags |= 1
 
         self._dparams = dparam
 
-    def read_bands(self, rlevel=0, layer=None, area=None, tile=None,
+    def read_bands(self, rlevel=0, layer=0, area=None, tile=None,
                    verbose=False, ignore_pclr_cmap_cdef=False):
         """Read a JPEG 2000 image.
 
@@ -1367,10 +1259,8 @@ class Jp2k(Jp2kBox):
                                "OpenJPEG installed before using this "
                                "functionality.")
 
-        self.ignore_pclr_cmap_cdef = ignore_pclr_cmap_cdef
+        self._populate_dparams(rlevel, ignore_pclr_cmap_cdef,
-        if layer is not None:
+                               layer=layer, tile=tile, area=area)
-            self._layer = layer
-        self._populate_dparams(rlevel, tile=tile, area=area)
 
         with ExitStack() as stack:
             if re.match("2.1", version.openjpeg_version):
@@ -1446,6 +1336,7 @@ class Jp2k(Jp2kBox):
                 codestream = Codestream(fptr, self.length,
                                         header_only=header_only)
             else:
+                ftyp = self.box[1]
                 box = [x for x in self.box if x.box_id == 'jp2c']
                 fptr.seek(box[0].offset)
                 read_buffer = fptr.read(8)
@@ -1465,7 +1356,7 @@ class Jp2k(Jp2kBox):
 
     def _populate_image_struct(self, image, imgdata):
         """Populates image struct needed for compression.
-
+    
         Parameters
         ----------
         image : ImageType(ctypes.Structure)
@@ -1473,9 +1364,9 @@ class Jp2k(Jp2kBox):
         img_array : ndarray
             Image data to be written to file.
         """
-
+    
         numrows, numcols, num_comps = imgdata.shape
-
+    
         # set image offset and reference grid
         image.contents.x0 = self._cparams.image_offset_x0
         image.contents.y0 = self._cparams.image_offset_y0
@@ -1483,7 +1374,7 @@ class Jp2k(Jp2kBox):
                              (numcols - 1) * self._cparams.subsampling_dx + 1)
         image.contents.y1 = (image.contents.y0 +
                              (numrows - 1) * self._cparams.subsampling_dy + 1)
-
+    
         # Stage the image data to the openjpeg data structure.
         for k in range(0, num_comps):
             if re.match("2.0", version.openjpeg_version) is not None:
@@ -1497,19 +1388,19 @@ class Jp2k(Jp2kBox):
                                           core.OPJ_PROFILE_CINEMA_4K):
                     image.contents.comps[k].prec = 12
                     image.contents.comps[k].bpp = 12
-
+    
             layer = np.ascontiguousarray(imgdata[:, :, k], dtype=np.int32)
             dest = image.contents.comps[k].data
             src = layer.ctypes.data
             ctypes.memmove(dest, src, layer.nbytes)
-
+    
         return image
-
+    
     def _populate_comptparms(self, img_array):
         """Instantiate and populate comptparms structure.
-
+    
         This structure defines the image components.
-
+    
         Parameters
         ----------
         img_array : ndarray
@@ -1538,8 +1429,8 @@ class Jp2k(Jp2kBox):
             comptparms[j].sgnd = 0
 
         self._comptparms = comptparms
-
+    
-
+    
 def _component2dtype(component):
     """Take an OpenJPEG component structure and determine the numpy datatype.
 
@@ -1585,7 +1476,6 @@ JP2_IDS = ['colr', 'cdef', 'cmap', 'jp2c', 'ftyp', 'ihdr', 'jp2h', 'jP  ',
            'pclr', 'res ', 'resc', 'resd', 'xml ', 'ulst', 'uinf', 'url ',
            'uuid']
 
-
 def _validate_jp2_box_sequence(boxes):
     """Run through series of tests for JP2 box legality.
 
@@ -1601,13 +1491,12 @@ def _validate_jp2_box_sequence(boxes):
         count = _collect_box_count(boxes)
         for box_id in count.keys():
             if box_id not in JP2_IDS:
-                msg = "The presence of a '{0}' box requires that the file "
+                msg = "The presence of a '{0}' box requires that the file type "
-                msg += "type brand be set to 'jpx '."
+                msg += "brand be set to 'jpx '."
                 raise IOError(msg.format(box_id))
 
         _validate_jp2_colr(boxes)
 
-
 def _validate_jp2_colr(boxes):
     """
     Validate JP2 requirements on colour specification boxes.
@@ -1619,7 +1508,6 @@ def _validate_jp2_colr(boxes):
             msg = "A JP2 colr box cannot have a non-zero approximation field."
             raise IOError(msg)
 
-
 def _validate_jpx_box_sequence(boxes):
     """Run through series of tests for JPX box legality."""
     _validate_label(boxes)
@@ -1628,7 +1516,6 @@ def _validate_jpx_box_sequence(boxes):
     _validate_singletons(boxes)
     _validate_top_level(boxes)
 
-
 def _validate_signature_compatibility(boxes):
     """Validate the file signature and compatibility status."""
     # Check for a bad sequence of boxes.
@@ -1716,8 +1603,6 @@ def _validate_channel_definition(jp2h, colr):
 
 
 JP2H_CHILDREN = set(['bpcc', 'cdef', 'cmap', 'ihdr', 'pclr'])
-
-
 def _check_jp2h_child_boxes(boxes, parent_box_name):
     """Certain boxes can only reside in the JP2 header."""
     box_ids = set([box.box_id for box in boxes])
@@ -1745,7 +1630,6 @@ def _collect_box_count(boxes):
 
 TOP_LEVEL_ONLY_BOXES = set(['dtbl'])
 
-
 def _check_superbox_for_top_levels(boxes):
     """Several boxes can only occur at the top level."""
     # We are only looking at the boxes contained in a superbox, so if any of
@@ -1761,7 +1645,6 @@ def _check_superbox_for_top_levels(boxes):
         if hasattr(box, 'box'):
             _check_superbox_for_top_levels(box.box)
 
-
 def _validate_top_level(boxes):
     """Several boxes can only occur at the top level."""
     # Add the counts in the superboxes.
@@ -1781,7 +1664,6 @@ def _validate_top_level(boxes):
         msg += 'a fragment table box as well.'
         raise IOError(msg)
 
-
 def _validate_singletons(boxes):
     """Several boxes can only occur once."""
     count = _collect_box_count(boxes)
@@ -1790,9 +1672,6 @@ 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 '.
@@ -1807,7 +1686,6 @@ def _validate_jpx_brand(boxes, brand):
             # Same set of checks on any child boxes.
             _validate_jpx_brand(box.box, brand)
 
-
 def _validate_jpx_compatibility(boxes, compatibility_list):
     """
     If there is a JPX box then the compatibility list must also contain 'jpx '.
@@ -1823,7 +1701,6 @@ def _validate_jpx_compatibility(boxes, compatibility_list):
             # Same set of checks on any child boxes.
             _validate_jpx_compatibility(box.box, compatibility_list)
 
-
 def _validate_label(boxes):
     """
     Label boxes can only be inside association, codestream headers, or
@@ -1840,7 +1717,6 @@ def _validate_label(boxes):
                 # Same set of checks on any child boxes.
                 _validate_label(box.box)
 
-
 def extract_image_cube(image):
     """Extract 3D image from openjpeg data structure.
     """
@@ -1896,6 +1772,7 @@ def extract_image_bands(image):
     return data
 
 
+
 # Setup the default callback handlers.  See the callback functions subsection
 # in the ctypes section of the Python documentation for a solid explanation of
 # what's going on here.

glymur/lib/__init__.py

@@ -2,5 +2,3 @@
 from . import openjp2 as openjp2
 from . import openjpeg as openjpeg
 from . import c
-
-__all__ = [openjp2, openjpeg, c]

glymur/lib/config.py

@@ -1,6 +1,9 @@
 """
 Configure glymur to use installed libraries if possible.
 """
+# configparser is new in python3 (pylint/python-2.7)
+# pylint: disable=F0401
+
 import ctypes
 from ctypes.util import find_library
 import os
@@ -16,21 +19,18 @@ else:
     from configparser import NoOptionError
 
 # default library locations for MacPorts
-_macports_default_location = {'openjp2': '/opt/local/lib/libopenjp2.dylib',
+_macports_default_location = {
-                              'openjpeg': '/opt/local/lib/libopenjpeg.dylib'}
+        'openjp2': '/opt/local/lib/libopenjp2.dylib',
+        'openjpeg': '/opt/local/lib/libopenjpeg.dylib'
+}
 
 # default library locations on Windows
-_windows_default_location = {'openjp2': os.path.join('C:\\',
+_windows_default_location = {
-                                                     'Program files',
+        'openjp2': os.path.join('C:\\', 'Program files', 'OpenJPEG 2.0',
-                                                     'OpenJPEG 2.0',
+                                'bin', 'openjp2.dll'),
-                                                     'bin',
+        'openjpeg': os.path.join('C:\\', 'Program files', 'OpenJPEG 1.5',
-                                                     'openjp2.dll'),
+                                 'bin', 'openjpeg.dll')
-                             'openjpeg': os.path.join('C:\\',
+}
-                                                      'Program files',
-                                                      'OpenJPEG 1.5',
-                                                      'bin',
-                                                      'openjpeg.dll')}
-
 
 def glymurrc_fname():
     """Return the path to the configuration file.
@@ -55,9 +55,8 @@ def glymurrc_fname():
     # didn't find a configuration file.
     return None
 
-
 def load_openjpeg_library(libname):
-
+    
     path = read_config_file(libname)
     if path is not None:
         return load_library_handle(path)
@@ -80,15 +79,13 @@ def load_openjpeg_library(libname):
 
     return load_library_handle(path)
 
-
 def load_library_handle(path):
     """Load the library, return the ctypes handle."""
 
     if path is None or path in ['None', 'none']:
-        # Either could not find a library via ctypes or
+        # Either could not find a library via ctypes or user-configuration-file,
-        # user-configuration-file, or we could not find it in any of the
+        # or we could not find it in any of the default locations.
-        # default locations, or possibly the user intentionally does not want
+        # This is probably a very old linux.
-        # one of the libraries to load.
         return None
 
     try:
@@ -97,10 +94,10 @@ def load_library_handle(path):
         else:
             opj_lib = ctypes.CDLL(path)
     except (TypeError, OSError):
-        msg = 'The library specified by configuration file at {0} could not '
+       msg = '"Library {0}" could not be loaded.  Operating in degraded mode.'
-        msg += 'be loaded.'
+       msg = msg.format(path)
-        warnings.warn(msg.format(path), UserWarning)
+       warnings.warn(msg, UserWarning)
-        opj_lib = None
+       opj_lib = None
 
     return opj_lib
 
@@ -133,7 +130,6 @@ def read_config_file(libname):
         path = None
     return path
 
-
 def glymur_config():
     """
     Try to ascertain locations of openjp2, openjpeg libraries.
@@ -148,10 +144,9 @@ def glymur_config():
         lst.append(load_openjpeg_library(libname))
     if all(handle is None for handle in lst):
         msg = "Neither the openjp2 nor the openjpeg library could be loaded.  "
-        warnings.warn(msg)
+        raise IOError(msg)
     return tuple(lst)
 
-
 def get_configdir():
     """Return string representing the configuration directory.
 

glymur/lib/openjp2.py

@@ -2,6 +2,8 @@
 Wraps individual functions in openjp2 library.
 """
 
+# pylint: disable=C0302,R0903,W0201
+
 import ctypes
 import re
 import sys
@@ -11,7 +13,6 @@ from .config import glymur_config
 
 OPENJP2, OPENJPEG = glymur_config()
 
-
 def version():
     """Wrapper for opj_version library routine."""
     try:
@@ -49,6 +50,13 @@ JPWL_MAX_NO_TILESPECS = 16
 TRUE = 1
 FALSE = 0
 
+#PROFILE = {'none': 0,        # No profile
+#        0: 1,                # Profile 0
+#        1: 2,                # Profile 1
+#        'part2': 0x8000,     # At least one extension
+#        'Cinema2K': 0x0003,  # 2K cinema profile
+#        'Cinema4K': 0x0004,  # 4K cinema profile
+
 # supported color spaces
 CLRSPC_UNKNOWN = -1
 CLRSPC_UNSPECIFIED = 0
@@ -408,6 +416,7 @@ class CompressionParametersType(ctypes.Structure):
                 for j in range(self.numpocs):
                     msg += "        [#{0}]:".format(j)
                     msg += "            {0}".format(str(self.poc[j]))
+                    msg += textwrap.indent(textstr, ' ' * 12)
 
             elif field_name in ['tcp_rates', 'tcp_distoratio']:
                 lst = []
@@ -480,14 +489,6 @@ class ImageCompType(ctypes.Structure):
     if _MINOR == '1':
         _fields_.append(("alpha",               ctypes.c_uint16))
 
-    def __str__(self):
-        msg = "{0}:\n".format(self.__class__)
-        for field_name, _ in self._fields_:
-            msg += "    {0}: {1}\n".format(
-                field_name, getattr(self, field_name))
-        return msg
-
-
 class ImageType(ctypes.Structure):
     """Defines image data and characteristics.
 
@@ -518,26 +519,6 @@ class ImageType(ctypes.Structure):
         # restricted ICC profile buffer length
         ("icc_profile_len",     ctypes.c_uint32)]
 
-    def __str__(self):
-        msg = "{0}:\n".format(self.__class__)
-        for field_name, _ in self._fields_:
-
-            if field_name == "numcomps":
-                msg += "    numcomps: {0}\n".format(self.numcomps)
-                for j in range(self.numcomps):
-                    msg += "        comps[#{0}]:\n".format(j)
-                    msg += textwrap.indent(str(self.comps[j]), ' ' * 12)
-
-            elif field_name == "comps":
-                # handled above
-                pass
-
-            else:
-                msg += "    {0}: {1}\n".format(
-                    field_name, getattr(self, field_name))
-
-        return msg
-
 
 class ImageComptParmType(ctypes.Structure):
     """Component parameters structure used by image_create function.
@@ -575,6 +556,107 @@ class ImageComptParmType(ctypes.Structure):
         return msg
 
 
+class TccpInfo(ctypes.Structure):
+    """Tile-component coding parameters information.
+
+    Corresponds to tccp_info_t type in openjp2 header file.
+    """
+    _fields_ = [
+        # component index
+        ("compno",          ctypes.c_uint32),
+
+        # coding style
+        ("csty",            ctypes.c_uint32),
+
+        # number of resolutions
+        ("numresolutions",  ctypes.c_uint32),
+
+        # code-blocks width
+        ("cblkw",           ctypes.c_uint32),
+
+        # code-blocks height
+        ("cblkh",           ctypes.c_uint32),
+
+        # code-block coding style
+        ("cblksty",         ctypes.c_uint32),
+
+        # discrete wavelet transform identifier
+        ("qmfbid",          ctypes.c_uint32),
+
+        # quantization style
+        ("qntsty",          ctypes.c_uint32),
+
+        # stepsizes used for quantization
+        ("stepsizes_mant",  ctypes.c_uint32 * J2K_MAXBANDS),
+        ("stepsizes_expn",  ctypes.c_uint32 * J2K_MAXBANDS),
+
+        # stepsizes used for quantization
+        ("numgbits",        ctypes.c_uint32),
+
+        # region of interest shift
+        ("roishift",        ctypes.c_int32),
+
+        # precinct width
+        ("prcw",            ctypes.c_uint32 * J2K_MAXRLVLS),
+
+        # precinct width
+        ("prch",            ctypes.c_uint32 * J2K_MAXRLVLS)]
+
+
+class TileInfoV2(ctypes.Structure):
+    """Tile coding parameters information
+
+    Corresponds to tile_info_v2_t type in openjp2 headers.
+    """
+    _fields_ = [
+        # number (index) of tile
+        ("tileno",          ctypes.c_int32),
+
+        # coding style
+        ("csty",            ctypes.c_uint32),
+
+        # progression order
+        ("prg",             PROG_ORDER_TYPE),
+
+        # number of layers
+        ("numlayers",       ctypes.c_uint32),
+
+        # multi-component transform identifier
+        ("mct",             ctypes.c_uint32),
+
+        # information concerning tile component parameters
+        ("tccp_info",       ctypes.POINTER(TccpInfo))]
+
+
+class CodestreamInfoV2(ctypes.Structure):
+    """information about the codestream.
+
+    Corresponds to codestream_info_v2_t type in openjp2 header files.
+    """
+    _fields_ = [
+        # tile info
+        # tile origin in x, y (XTOsiz, YTOsiz)
+        ("tx0",       ctypes.c_uint32),
+        ("ty0",       ctypes.c_uint32),
+
+        # tile size in x, y = XTsiz, YTsiz
+        ("tdx",       ctypes.c_uint32),
+        ("tdy",       ctypes.c_uint32),
+
+        # number of tiles in X, Y
+        ("tw",        ctypes.c_uint32),
+        ("th",        ctypes.c_uint32),
+
+        # number of components
+        ("nbcomps",   ctypes.c_uint32),
+
+        # default information regarding tiles inside of image
+        ("m_default_tile_info",   TileInfoV2),
+
+        # information regarding tiles inside of image
+        ("tile_info",             ctypes.POINTER(TileInfoV2))]
+
+
 def check_error(status):
     """Set a generic function as the restype attribute of all OpenJPEG
     functions that return a BOOL_TYPE value.  This way we do not have to check
@@ -737,6 +819,28 @@ def encode(codec, stream):
     OPENJP2.opj_encode(codec, stream)
 
 
+def get_cstr_info(codec):
+    """get the codestream information from the codec
+
+    Wraps the openjp2 library function opj_get_cstr_info.
+
+    Parameters
+    ----------
+    codec : CODEC_TYPE
+        The jpeg2000 codec.
+
+    Returns
+    -------
+    cstr_info_p : CodestreamInfoV2
+        Reference to codestream information.
+    """
+    OPENJP2.opj_get_cstr_info.argtypes = [CODEC_TYPE]
+    OPENJP2.opj_get_cstr_info.restype = ctypes.POINTER(CodestreamInfoV2)
+
+    cstr_info_p = OPENJP2.opj_get_cstr_info(codec)
+    return cstr_info_p
+
+
 def get_decoded_tile(codec, stream, imagep, tile_index):
     """get the decoded tile from the codec
 
@@ -767,6 +871,23 @@ def get_decoded_tile(codec, stream, imagep, tile_index):
     OPENJP2.opj_get_decoded_tile(codec, stream, imagep, tile_index)
 
 
+def destroy_cstr_info(cstr_info_p):
+    """destroy codestream information after compression or decompression
+
+    Wraps the openjp2 library function opj_destroy_cstr_info.
+
+    Parameters
+    ----------
+    cstr_info_p : CodestreamInfoV2 pointer
+        Pointer to codestream info structure.
+    """
+    ARGTYPES = [ctypes.POINTER(ctypes.POINTER(CodestreamInfoV2))]
+    OPENJP2.opj_destroy_cstr_info.argtypes = ARGTYPES
+    OPENJP2.opj_destroy_cstr_info.restype = ctypes.c_void_p
+
+    OPENJP2.opj_destroy_cstr_info(ctypes.byref(cstr_info_p))
+
+
 def end_compress(codec, stream):
     """End of compressing the current image.
 
@@ -909,7 +1030,7 @@ def read_header(stream, codec):
     ARGTYPES = [STREAM_TYPE_P, CODEC_TYPE,
                 ctypes.POINTER(ctypes.POINTER(ImageType))]
     OPENJP2.opj_read_header.argtypes = ARGTYPES
-    OPENJP2.opj_read_header.restype = check_error
+    OPENJP2.opj_read_header.restype = check_error 
 
     imagep = ctypes.POINTER(ImageType)()
     OPENJP2.opj_read_header(stream, codec, ctypes.byref(imagep))
@@ -1268,7 +1389,6 @@ def _stream_create_default_file_stream_2p0(fptr, isa_read_stream):
     stream = OPENJP2.opj_stream_create_default_file_stream(fptr, read_stream)
     return stream
 
-
 def _stream_create_default_file_stream_2p1(fname, isa_read_stream):
     """Wraps openjp2 library function opj_stream_create_default_vile_stream.
 
@@ -1295,7 +1415,7 @@ def _stream_create_default_file_stream_2p1(fname, isa_read_stream):
     stream = OPENJP2.opj_stream_create_default_file_stream(file_argument,
                                                            read_stream)
     return stream
-
+    
 if re.match(r'''2.0''', version()):
     stream_create_default_file_stream = _stream_create_default_file_stream_2p0
 else:

glymur/lib/openjpeg.py

@@ -1,9 +1,13 @@
 """Wraps library calls to openjpeg.
 """
 
+# pylint: disable=R0903
+
 import ctypes
 import sys
 
+import numpy as np
+
 from .config import glymur_config
 
 _, OPENJPEG = glymur_config()
@@ -55,10 +59,8 @@ class CommonStructType(ctypes.Structure):
                 ("mj2_handle", ctypes.c_void_p)]
 
 
-STREAM_READ = 0x0001  # The stream was opened for reading.
+STREAM_READ  = 0x0001 # The stream was opened for reading.
-STREAM_WRITE = 0x0002  # The stream was opened for writing.
+STREAM_WRITE = 0x0002 # The stream was opened for writing.
-
-
 class CioType(ctypes.Structure):
     """Byte input-output stream (CIO)
 
@@ -89,57 +91,70 @@ class CompressionInfoType(CommonStructType):
 class PocType(ctypes.Structure):
     """Progression order changes."""
     _fields_ = [("resno", ctypes.c_int),
-                # Resolution num start, Component num start, given by POC
+            # Resolution num start, Component num start, given by POC
-                ("compno0", ctypes.c_int),
+            ("compno0", ctypes.c_int),
 
-                # Layer num end,Resolution num end, Component num end, given
+            # Layer num end,Resolution num end, Component num end, given by POC
-                # by POC
+            ("layno1", ctypes.c_int),
-                ("layno1", ctypes.c_int),
+            ("resno1", ctypes.c_int),
-                ("resno1", ctypes.c_int),
+            ("compno1", ctypes.c_int),
-                ("compno1", ctypes.c_int),
 
-                # Layer num start,Precinct num start, Precinct num end
+            # Layer num start,Precinct num start, Precinct num end
-                ("layno0", ctypes.c_int),
+            ("layno0", ctypes.c_int),
-                ("precno0", ctypes.c_int),
+            ("precno0", ctypes.c_int),
-                ("precno1", ctypes.c_int),
+            ("precno1", ctypes.c_int),
 
-                # Progression order enum
+            # Progression order enum
-                # OPJ_PROG_ORDER prg1,prg;
+            # OPJ_PROG_ORDER prg1,prg;
-                ("prg1", ctypes.c_int),
+            ("prg1", ctypes.c_int),
-                ("prg", ctypes.c_int),
+            ("prg", ctypes.c_int),
 
-                # Progression order string
+            # Progression order string
-                # char progorder[5];
+            # char progorder[5];
-                ("progorder",            ctypes.c_char * 5),
+            ("progorder",            ctypes.c_char * 5),
 
-                # Tile number
+            # Tile number
-                # int tile;
+            # int tile;
-                ("tile", ctypes.c_int),
+            ("tile", ctypes.c_int),
 
-                ("tx0", ctypes.c_int),
+            # /** Start and end values for Tile width and height*/
-                ("tx1", ctypes.c_int),
+            # int tx0,tx1,ty0,ty1;
-                ("ty0", ctypes.c_int),
+            ("tx0", ctypes.c_int),
-                ("ty1", ctypes.c_int),
+            ("tx1", ctypes.c_int),
-                ("layS", ctypes.c_int),
+            ("ty0", ctypes.c_int),
-                ("resS", ctypes.c_int),
+            ("ty1", ctypes.c_int),
-                ("compS", ctypes.c_int),
+
-                ("prcS", ctypes.c_int),
+            # /** Start value, initialised in pi_initialise_encode*/
-                ("layE", ctypes.c_int),
+            # int layS, resS, compS, prcS;
-                ("resE", ctypes.c_int),
+            ("layS", ctypes.c_int),
-                ("compE", ctypes.c_int),
+            ("resS", ctypes.c_int),
-                ("prcE", ctypes.c_int),
+            ("compS", ctypes.c_int),
-                ("txS", ctypes.c_int),
+            ("prcS", ctypes.c_int),
-                ("txE", ctypes.c_int),
+
-                ("tyS", ctypes.c_int),
+            # /** End value, initialised in pi_initialise_encode */
-                ("tyE", ctypes.c_int),
+            # int layE, resE, compE, prcE;
-                ("dx", ctypes.c_int),
+            ("layE", ctypes.c_int),
-                ("dy", ctypes.c_int),
+            ("resE", ctypes.c_int),
-                ("lay_t", ctypes.c_int),
+            ("compE", ctypes.c_int),
-                ("res_t", ctypes.c_int),
+            ("prcE", ctypes.c_int),
-                ("comp_t", ctypes.c_int),
+
-                ("prc_t", ctypes.c_int),
+            # Start and end values of Tile width and height, initialised in
-                ("tx0_t", ctypes.c_int),
+            # pi_initialise_encode int txS,txE,tyS,tyE,dx,dy;
-                ("ty0_t", ctypes.c_int)]
+            ("txS", ctypes.c_int),
+            ("txE", ctypes.c_int),
+            ("tyS", ctypes.c_int),
+            ("tyE", ctypes.c_int),
+            ("dx", ctypes.c_int),
+            ("dy", ctypes.c_int),
+
+            # Temporary values for Tile parts, initialised in pi_create_encode
+            # int lay_t, res_t, comp_t, prc_t,tx0_t,ty0_t;
+            ("lay_t", ctypes.c_int),
+            ("res_t", ctypes.c_int),
+            ("comp_t", ctypes.c_int),
+            ("prc_t", ctypes.c_int),
+            ("tx0_t", ctypes.c_int),
+            ("ty0_t", ctypes.c_int)]
 
 
 class CompressionParametersType(ctypes.Structure):
@@ -360,47 +375,48 @@ class DecompressionParametersType(ctypes.Structure):
 class ImageComptParmType(ctypes.Structure):
     """Component parameters structure used by the opj_image_create function.
     """
-    _fields_ = [("dx", ctypes.c_int),
+    _fields_ = [
-                # XRsiz: horizontal separation of a sample of ith component
+            # XRsiz: horizontal separation of a sample of ith component with
-                # with respect to the reference grid
+            # respect to the reference grid
+            ("dx", ctypes.c_int),
 
-                # YRsiz: vertical separation of a sample of ith component with
+            # YRsiz: vertical separation of a sample of ith component with
-                # respect to the reference grid */
+            # respect to the reference grid */
-                ("dy", ctypes.c_int),
+            ("dy", ctypes.c_int),
 
-                # data width, height
+            # data width, height
-                ("w", ctypes.c_int),
+            ("w", ctypes.c_int),
-                ("h", ctypes.c_int),
+            ("h", ctypes.c_int),
 
-                # x component offset compared to the whole image
+            # x component offset compared to the whole image
-                # y component offset compared to the whole image
+            # y component offset compared to the whole image
-                ("x0", ctypes.c_int),
+            ("x0", ctypes.c_int),
-                ("y0", ctypes.c_int),
+            ("y0", ctypes.c_int),
 
-                # precision
+            # precision
-                ('prec', ctypes.c_int),
+            ('prec', ctypes.c_int),
 
-                # image depth in bits
+            # image depth in bits
-                ('bpp', ctypes.c_int),
+            ('bpp', ctypes.c_int),
 
-                # signed (1) / unsigned (0)
+            # signed (1) / unsigned (0)
-                ('sgnd', ctypes.c_int)]
+            ('sgnd', ctypes.c_int)]
 
 
 class ImageCompType(ctypes.Structure):
     """Defines a single image component. """
     _fields_ = [("dx",        ctypes.c_int),
-                ("dy",            ctypes.c_int),
+            ("dy",            ctypes.c_int),
-                ("w",             ctypes.c_int),
+            ("w",             ctypes.c_int),
-                ("h",             ctypes.c_int),
+            ("h",             ctypes.c_int),
-                ("x0",            ctypes.c_int),
+            ("x0",            ctypes.c_int),
-                ("y0",            ctypes.c_int),
+            ("y0",            ctypes.c_int),
-                ("prec",          ctypes.c_int),
+            ("prec",          ctypes.c_int),
-                ("bpp",           ctypes.c_int),
+            ("bpp",           ctypes.c_int),
-                ("sgnd",          ctypes.c_int),
+            ("sgnd",          ctypes.c_int),
-                ("resno_decoded", ctypes.c_int),
+            ("resno_decoded", ctypes.c_int),
-                ("factor",        ctypes.c_int),
+            ("factor",        ctypes.c_int),
-                ("data",          ctypes.POINTER(ctypes.c_int))]
+            ("data",          ctypes.POINTER(ctypes.c_int))]
 
 
 class ImageType(ctypes.Structure):
@@ -452,7 +468,6 @@ def cio_tell(cio):
     pos = OPENJPEG.cio_tell(cio)
     return pos
 
-
 def create_compress(fmt):
     """Wrapper for openjpeg library function opj_create_compress.
 
@@ -523,11 +538,56 @@ def destroy_decompress(dinfo):
     OPENJPEG.opj_destroy_decompress(dinfo)
 
 
+def image_cmptparm_t_from_np(np_image):
+    """Return appropriate image_cmptparm_t based on given numpy array.
+    """
+    try:
+        num_comps = np_image.shape[2]
+    except IndexError:
+        num_comps = 1
+
+    cmpt_parm_array_t = ImageCmptparmType * num_comps
+    tarr = cmpt_parm_array_t()
+
+    if np_image.dtype == np.uint8:
+        prec = 8
+        bpp = 8
+        sgnd = 0
+    elif np_image.dtype == np.int8:
+        prec = 8
+        bpp = 8
+        sgnd = 1
+    elif np_image.dtype == np.uint16:
+        prec = 16
+        bpp = 16
+        sgnd = 0
+    elif np_image.dtype == np.int16:
+        prec = 16
+        bpp = 16
+        sgnd = 1
+    else:
+        raise(TypeError("unhandled"))
+
+    for j in range(0, num_comps):
+        tarr[j].dx = 1
+        tarr[j].dy = 1
+        tarr[j].w = np_image.shape[1]
+        tarr[j].h = np_image.shape[0]
+        tarr[j].x0 = 0
+        tarr[j].y0 = 0
+        tarr[j].prec = prec
+        tarr[j].bpp = bpp
+        tarr[j].sgnd = sgnd
+
+    return(tarr)
+
+
 def image_create(cmptparms, cspace):
     """Wrapper for openjpeg library function opj_image_create.
     """
-    lst = [ctypes.c_int, ctypes.POINTER(ImageComptParmType), ctypes.c_int]
+    OPENJPEG.opj_image_create.argtypes = [ctypes.c_int,
-    OPENJPEG.opj_image_create.argtypes = lst
+            ctypes.POINTER(ImageComptParmType),
+            ctypes.c_int]
     OPENJPEG.opj_image_create.restype = ctypes.POINTER(ImageType)
 
     image = OPENJPEG.opj_image_create(len(cmptparms), cmptparms, cspace)

glymur/lib/test/fixtures.py

@@ -127,18 +127,3 @@ default_image_component_parameters = """<class 'glymur.lib.openjp2.ImageComptPar
     prec: 0
     bpp: 0
     sgnd: 0"""
-
-# The "icc_profile_buf" field is problematic as it is a pointer value, i.e.
-#
-#     icc_profile_buf: <glymur.lib.openjp2.LP_c_ubyte object at 0x7f28cd5d5d90>
-#
-# Have to treat it as a regular expression.
-default_image_type = """<class 'glymur.lib.openjp2.ImageType'>:
-    x0: 0
-    y0: 0
-    x1: 0
-    y1: 0
-    numcomps: 0
-    color_space: 0
-    icc_profile_buf: <glymur.lib.openjp2.LP_c_ubyte object at 0x[0-9A-Fa-f]*>
-    icc_profile_len: 0"""

glymur/lib/test/test_openjp2.py

@@ -1,8 +1,13 @@
 """
 Tests for libopenjp2 wrapping functions.
 """
+# R0904:  Seems like pylint is fooled in this situation
+# W0142:  using kwargs is ok in this context
+# pylint: disable=R0904,W0142
+
 import os
 import re
+import sys
 import tempfile
 import unittest
 
@@ -16,8 +21,8 @@ from glymur.lib import openjp2
 @unittest.skipIf(openjp2.OPENJP2 is None,
                  "Missing openjp2 library.")
 @unittest.skipIf(re.match(r'''(1|2.0)''',
-                          glymur.version.openjpeg_version) is not None,
+                              glymur.version.openjpeg_version) is not None,
-                 "Not to be run until 2.1.0")
+                     "Not to be run until 2.1.0")
 class TestOpenJP2(unittest.TestCase):
     """Test openjp2 library functionality.
 
@@ -51,6 +56,53 @@ class TestOpenJP2(unittest.TestCase):
         self.assertEqual(dparams.DA_x1, 0)
         self.assertEqual(dparams.DA_y1, 0)
 
+    def tile_macro(self, codec, stream, imagep, tidx):
+        """called only by j2k_random_tile_access"""
+        openjp2.get_decoded_tile(codec, stream, imagep, tidx)
+        for j in range(imagep.contents.numcomps):
+            self.assertIsNotNone(imagep.contents.comps[j].data)
+
+    def j2k_random_tile_access(self, filename, codec_format=None):
+        """fixture called by the test_rtaX methods"""
+        dparam = openjp2.set_default_decoder_parameters()
+
+        infile = filename.encode()
+        nelts = openjp2.PATH_LEN - len(infile)
+        infile += b'0' * nelts
+        dparam.infile = infile
+
+        dparam.decod_format = codec_format
+
+        codec = openjp2.create_decompress(codec_format)
+
+        openjp2.set_info_handler(codec, None)
+        openjp2.set_warning_handler(codec, None)
+        openjp2.set_error_handler(codec, None)
+
+        stream = openjp2.stream_create_default_file_stream(filename, True)
+
+        openjp2.setup_decoder(codec, dparam)
+        image = openjp2.read_header(stream, codec)
+
+        cstr_info = openjp2.get_cstr_info(codec)
+
+        tile_ul = 0
+        tile_ur = cstr_info.contents.tw - 1
+        tile_lr = cstr_info.contents.tw * cstr_info.contents.th - 1
+        tile_ll = tile_lr - cstr_info.contents.tw
+
+        self.tile_macro(codec, stream, image, tile_ul)
+        self.tile_macro(codec, stream, image, tile_ur)
+        self.tile_macro(codec, stream, image, tile_lr)
+        self.tile_macro(codec, stream, image, tile_ll)
+
+        openjp2.destroy_cstr_info(cstr_info)
+
+        openjp2.end_decompress(codec, stream)
+        openjp2.destroy_codec(codec)
+        openjp2.stream_destroy(stream)
+        openjp2.image_destroy(image)
+
     def test_tte0(self):
         """Runs test designated tte0 in OpenJPEG test suite."""
         with tempfile.NamedTemporaryFile(suffix=".j2k") as tfile:
@@ -108,6 +160,15 @@ class TestOpenJP2(unittest.TestCase):
             tile_decoder(**kwargs)
         self.assertTrue(True)
 
+    def test_rta1(self):
+        """Runs test designated rta1 in OpenJPEG test suite."""
+        with tempfile.NamedTemporaryFile(suffix=".j2k") as tfile:
+            self.xtx1_setup(tfile.name)
+
+            codec_format = openjp2.CODEC_J2K
+            self.j2k_random_tile_access(tfile.name, codec_format)
+        self.assertTrue(True)
+
     def test_tte2(self):
         """Runs test designated tte2 in OpenJPEG test suite."""
         with tempfile.NamedTemporaryFile(suffix=".jp2") as tfile:
@@ -129,25 +190,62 @@ class TestOpenJP2(unittest.TestCase):
             tile_decoder(**kwargs)
         self.assertTrue(True)
 
+    def test_rta2(self):
+        """Runs test designated rta2 in OpenJPEG test suite."""
+        with tempfile.NamedTemporaryFile(suffix=".jp2") as tfile:
+            xtx2_setup(tfile.name)
+
+            codec_format = openjp2.CODEC_JP2
+            self.j2k_random_tile_access(tfile.name, codec_format)
+
     def test_tte3(self):
         """Runs test designated tte3 in OpenJPEG test suite."""
         with tempfile.NamedTemporaryFile(suffix=".j2k") as tfile:
             xtx3_setup(tfile.name)
         self.assertTrue(True)
 
+    def test_rta3(self):
+        """Runs test designated rta3 in OpenJPEG test suite."""
+        with tempfile.NamedTemporaryFile(suffix=".j2k") as tfile:
+            xtx3_setup(tfile.name)
+
+            codec_format = openjp2.CODEC_J2K
+            self.j2k_random_tile_access(tfile.name, codec_format)
+        self.assertTrue(True)
+
     def test_tte4(self):
         """Runs test designated tte4 in OpenJPEG test suite."""
         with tempfile.NamedTemporaryFile(suffix=".j2k") as tfile:
             xtx4_setup(tfile.name)
         self.assertTrue(True)
 
+    def test_rta4(self):
+        """Runs test designated rta4 in OpenJPEG test suite."""
+        with tempfile.NamedTemporaryFile(suffix=".j2k") as tfile:
+            xtx4_setup(tfile.name)
+
+            codec_format = openjp2.CODEC_J2K
+            self.j2k_random_tile_access(tfile.name, codec_format)
+
     def test_tte5(self):
         """Runs test designated tte5 in OpenJPEG test suite."""
         with tempfile.NamedTemporaryFile(suffix=".j2k") as tfile:
             xtx5_setup(tfile.name)
         self.assertTrue(True)
 
+    def test_rta5(self):
+        """Runs test designated rta5 in OpenJPEG test suite."""
+        with tempfile.NamedTemporaryFile(suffix=".j2k") as tfile:
+            xtx5_setup(tfile.name)
 
+            codec_format = openjp2.CODEC_J2K
+            self.j2k_random_tile_access(tfile.name, codec_format)
+
+
+#def tile_encoder(num_comps=None, tile_width=None, tile_height=None,
+#                 filename=None, codec=None, comp_prec=None,
+#                 image_width=None, image_height=None,
+#                 irreversible=None):
 def tile_encoder(**kwargs):
     """Fixture used by many tests."""
     num_tiles = ((kwargs['image_width'] / kwargs['tile_width']) *
@@ -211,7 +309,7 @@ def tile_encoder(**kwargs):
     openjp2.setup_encoder(codec, l_param, l_image)
 
     stream = openjp2.stream_create_default_file_stream(kwargs['filename'],
-                                                       False)
+                                                          False)
     openjp2.start_compress(codec, l_image, stream)
 
     for j in np.arange(num_tiles):
@@ -222,14 +320,13 @@ def tile_encoder(**kwargs):
     openjp2.destroy_codec(codec)
     openjp2.image_destroy(l_image)
 
-
 def tile_decoder(**kwargs):
     """Fixture called with various configurations by many tests.
 
     Reads a tile.  That's all it does.
     """
     stream = openjp2.stream_create_default_file_stream(kwargs['filename'],
-                                                       True)
+                                                          True)
     dparam = openjp2.set_default_decoder_parameters()
 
     dparam.decod_format = kwargs['codec_format']
@@ -267,7 +364,6 @@ def tile_decoder(**kwargs):
     openjp2.stream_destroy(stream)
     openjp2.image_destroy(image)
 
-
 def ttx0_setup(filename):
     """Runs tests tte0, tte0."""
     kwargs = {'filename': filename,
@@ -281,7 +377,6 @@ def ttx0_setup(filename):
               'tile_width': 100}
     tile_encoder(**kwargs)
 
-
 def xtx2_setup(filename):
     """Runs tests rta2, tte2, ttd2."""
     kwargs = {'filename': filename,
@@ -295,7 +390,6 @@ def xtx2_setup(filename):
               'tile_width': 128}
     tile_encoder(**kwargs)
 
-
 def xtx3_setup(filename):
     """Runs tests tte3, rta3."""
     kwargs = {'filename': filename,
@@ -309,7 +403,6 @@ def xtx3_setup(filename):
               'tile_width': 128}
     tile_encoder(**kwargs)
 
-
 def xtx4_setup(filename):
     """Runs tests rta4, tte4."""
     kwargs = {'filename': filename,
@@ -323,7 +416,6 @@ def xtx4_setup(filename):
               'tile_width': 128}
     tile_encoder(**kwargs)
 
-
 def xtx5_setup(filename):
     """Runs tests rta5, tte5."""
     kwargs = {'filename': filename,
@@ -336,3 +428,6 @@ def xtx5_setup(filename):
               'tile_height': 256,
               'tile_width': 256}
     tile_encoder(**kwargs)
+
+if __name__ == "__main__":
+    unittest.main()

glymur/lib/test/test_openjpeg.py

@@ -1,6 +1,8 @@
 """
 Tests for OpenJPEG module.
 """
+# pylint: disable=E1101,R0904
+
 import ctypes
 import re
 import sys
@@ -8,7 +10,6 @@ import unittest
 
 import glymur
 
-
 @unittest.skipIf(glymur.lib.openjpeg.OPENJPEG is None,
                  "Missing openjpeg library.")
 class TestOpenJPEG(unittest.TestCase):

glymur/lib/test/test_printing.py

@@ -16,9 +16,8 @@ else:
 import glymur
 from . import fixtures
 
-
 @unittest.skipIf(sys.hexversion < 0x03000000, "do not care about 2.7 here")
-@unittest.skipIf(re.match('0|1|2.0', glymur.version.openjpeg_version),
+@unittest.skipIf(re.match('1|2.0', glymur.version.openjpeg_version),
                  "Requires openjpeg 2.1.0 or higher")
 class TestPrintingOpenjp2(unittest.TestCase):
     """Tests for verifying how printing works on openjp2 library structures."""
@@ -64,12 +63,5 @@ class TestPrintingOpenjp2(unittest.TestCase):
         expected = fixtures.default_image_component_parameters
         self.assertEqual(actual, expected)
 
-    def test_default_image_type(self):
-        """printing default image type"""
-        it = glymur.lib.openjp2.ImageType()
-        with patch('sys.stdout', new=StringIO()) as fake_out:
-            print(it)
-            actual = fake_out.getvalue().strip()
 
-        expected = fixtures.default_image_type
+
-        self.assertRegex(actual, expected)

glymur/test/fixtures.py

@@ -13,14 +13,6 @@ import six
 
 import glymur
 
-# If openjpeg is not installed, many tests cannot be run.
-if glymur.version.openjpeg_version == '0.0.0':
-    OPENJPEG_NOT_AVAILABLE = True
-    OPENJPEG_NOT_AVAILABLE_MSG = 'OpenJPEG library not installed'
-else:
-    OPENJPEG_NOT_AVAILABLE = False
-    OPENJPEG_NOT_AVAILABLE_MSG = None
-
 # Some versions of "six" on python3 cause problems when verifying warnings.
 # Only use when the version is 1.7 or higher.
 # And moreover, we only test using the 3.x infrastructure, never on 2.x.
@@ -37,7 +29,6 @@ elif re.match('1.[0-6]', six.__version__) is not None:
 # Cannot reopen a named temporary file in windows.
 WINDOWS_TMP_FILE_MSG = "cannot use NamedTemporaryFile like this in windows"
 
-
 class MetadataBase(unittest.TestCase):
     """
     Base class for testing metadata.
@@ -102,8 +93,8 @@ class MetadataBase(unittest.TestCase):
         """
         verify the fields of a RGN segment
         """
-        self.assertEqual(actual.crgn, expected.crgn)  # 0 = component
+        self.assertEqual(actual.crgn, expected.crgn) # 0 = component
-        self.assertEqual(actual.srgn, expected.srgn)  # 0 = implicit
+        self.assertEqual(actual.srgn, expected.srgn) # 0 = implicit
         self.assertEqual(actual.sprgn, expected.sprgn)
 
     def verifySOTsegment(self, actual, expected):
@@ -126,9 +117,8 @@ class MetadataBase(unittest.TestCase):
         """
         Verify the fields of the SIZ segment.
         """
-        for field in ['rsiz', 'xsiz', 'ysiz', 'xosiz', 'yosiz', 'xtsiz',
+        for field in ['rsiz', 'xsiz', 'ysiz', 'xosiz', 'yosiz', 'xtsiz', 
-                      'ytsiz', 'xtosiz', 'ytosiz', 'bitdepth',
+                'ytsiz', 'xtosiz', 'ytosiz', 'bitdepth', 'xrsiz', 'yrsiz']:
-                      'xrsiz', 'yrsiz']:
             self.assertEqual(getattr(actual, field), getattr(expected, field))
 
     def verifyImageHeaderBox(self, box1, box2):
@@ -155,7 +145,7 @@ class MetadataBase(unittest.TestCase):
         else:
             self.assertEqual(actual.colorspace, expected.colorspace)
             self.assertIsNone(actual.icc_profile)
-
+        
 
 # The Python XMP Toolkit may be used for XMP UUIDs, but only if available and
 # if the version is at least 2.0.0.
@@ -185,7 +175,7 @@ except:
 # The Cinema2K/4K tests seem to need the freeimage backend to skimage.io
 # in order to work.  Unfortunately, scikit-image/freeimage is about as wonky as
 # it gets.  Anaconda can get totally weirded out on versions up through 3.6.4
-# on Python3 with scikit-image up through version 0.10.0.
+# on Python3 with scikit-image up through version 0.10.0.  
 NO_SKIMAGE_FREEIMAGE_SUPPORT = False
 try:
     import skimage
@@ -213,7 +203,7 @@ def _indent(textstr):
         String to be indented.
     indent_level : str
         Number of spaces of indentation to add.
-
+    
     Returns
     -------
     indented_string : str
@@ -236,6 +226,7 @@ try:
 
     # The whole point of trying to import PIL is to determine if it's there
     # or not.  We won't use it directly.
+    # pylint:  disable=F0401,W0611
     import PIL
 
     NO_READ_BACKEND = False
@@ -545,7 +536,7 @@ text_gbr_34 = """Colour Specification Box (colr) @ (179, 1339)
 dump = r'''JPEG 2000 Signature Box (jP  ) @ (0, 12)
     Signature:  0d0a870a
 File Type Box (ftyp) @ (12, 20)
-    Brand:  jp2
+    Brand:  jp2 
     Compatibility:  ['jp2 ']
 JP2 Header Box (jp2h) @ (32, 45)
     Image Header Box (ihdr) @ (40, 22)
@@ -601,6 +592,7 @@ Contiguous Codestream Box (jp2c) @ (3223, 1132296)
             "Created by OpenJPEG version 2.0.0"'''
 
 nemo_with_codestream_header = dump.format(_indent(nemo_xmp))
+#nemo_dump_full = dump.format(_indent(nemo_xmp))
 
 nemo_dump_short = r"""JPEG 2000 Signature Box (jP  ) @ (0, 12)
 File Type Box (ftyp) @ (12, 20)
@@ -613,7 +605,7 @@ Contiguous Codestream Box (jp2c) @ (3223, 1132296)"""
 nemo_dump_no_xml = '''JPEG 2000 Signature Box (jP  ) @ (0, 12)
     Signature:  0d0a870a
 File Type Box (ftyp) @ (12, 20)
-    Brand:  jp2
+    Brand:  jp2 
     Compatibility:  ['jp2 ']
 JP2 Header Box (jp2h) @ (32, 45)
     Image Header Box (ihdr) @ (40, 22)
@@ -669,7 +661,7 @@ Contiguous Codestream Box (jp2c) @ (3223, 1132296)
 dump = r"""JPEG 2000 Signature Box (jP  ) @ (0, 12)
     Signature:  0d0a870a
 File Type Box (ftyp) @ (12, 20)
-    Brand:  jp2
+    Brand:  jp2 
     Compatibility:  ['jp2 ']
 JP2 Header Box (jp2h) @ (32, 45)
     Image Header Box (ihdr) @ (40, 22)
@@ -691,26 +683,6 @@ nemo_dump_no_codestream = dump.format(_indent(nemo_xmp))
 
 nemo_dump_no_codestream_no_xml = r"""JPEG 2000 Signature Box (jP  ) @ (0, 12)
     Signature:  0d0a870a
-File Type Box (ftyp) @ (12, 20)
-    Brand:  jp2
-    Compatibility:  ['jp2 ']
-JP2 Header Box (jp2h) @ (32, 45)
-    Image Header Box (ihdr) @ (40, 22)
-        Size:  [1456 2592 3]
-        Bitdepth:  8
-        Signed:  False
-        Compression:  wavelet
-        Colorspace Unknown:  False
-    Colour Specification Box (colr) @ (62, 15)
-        Method:  enumerated colorspace
-        Precedence:  0
-        Colorspace:  sRGB
-UUID Box (uuid) @ (77, 3146)
-    UUID:  be7acfcb-97a9-42e8-9c71-999491e3afac (XMP)
-Contiguous Codestream Box (jp2c) @ (3223, 1132296)"""
-
-nemo = """JPEG 2000 Signature Box (jP  ) @ (0, 12)
-    Signature:  0d0a870a
 File Type Box (ftyp) @ (12, 20)
     Brand:  jp2 
     Compatibility:  ['jp2 ']
@@ -727,171 +699,7 @@ JP2 Header Box (jp2h) @ (32, 45)
         Colorspace:  sRGB
 UUID Box (uuid) @ (77, 3146)
     UUID:  be7acfcb-97a9-42e8-9c71-999491e3afac (XMP)
-    UUID Data:
+Contiguous Codestream Box (jp2c) @ (3223, 1132296)"""
-    <?xpacket begin="" id="W5M0MpCehiHzreSzNTczkc9d"?>
-    <ns0:xmpmeta xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:ns0="adobe:ns:meta/" xmlns:ns2="http://ns.adobe.com/xap/1.0/" xmlns:ns3="http://ns.adobe.com/tiff/1.0/" xmlns:ns4="http://ns.adobe.com/exif/1.0/" xmlns:ns5="http://ns.adobe.com/photoshop/1.0/" xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" ns0:xmptk="Exempi + XMP Core 5.1.2">
-     <rdf:RDF>
-      <rdf:Description rdf:about="">
-       <ns2:CreatorTool>Google</ns2:CreatorTool>
-       <ns2:CreateDate>2013-02-09T14:47:53</ns2:CreateDate>
-      </rdf:Description>
-      <rdf:Description rdf:about="">
-       <ns3:YCbCrPositioning>1</ns3:YCbCrPositioning>
-       <ns3:XResolution>72/1</ns3:XResolution>
-       <ns3:YResolution>72/1</ns3:YResolution>
-       <ns3:ResolutionUnit>2</ns3:ResolutionUnit>
-       <ns3:Make>HTC</ns3:Make>
-       <ns3:Model>HTC Glacier</ns3:Model>
-       <ns3:ImageWidth>2592</ns3:ImageWidth>
-       <ns3:ImageLength>1456</ns3:ImageLength>
-       <ns3:BitsPerSample>
-        <rdf:Seq>
-         <rdf:li>8</rdf:li>
-         <rdf:li>8</rdf:li>
-         <rdf:li>8</rdf:li>
-        </rdf:Seq>
-       </ns3:BitsPerSample>
-       <ns3:PhotometricInterpretation>2</ns3:PhotometricInterpretation>
-       <ns3:SamplesPerPixel>3</ns3:SamplesPerPixel>
-       <ns3:WhitePoint>
-        <rdf:Seq>
-         <rdf:li>1343036288/4294967295</rdf:li>
-         <rdf:li>1413044224/4294967295</rdf:li>
-        </rdf:Seq>
-       </ns3:WhitePoint>
-       <ns3:PrimaryChromaticities>
-        <rdf:Seq>
-         <rdf:li>2748779008/4294967295</rdf:li>
-         <rdf:li>1417339264/4294967295</rdf:li>
-         <rdf:li>1288490240/4294967295</rdf:li>
-         <rdf:li>2576980480/4294967295</rdf:li>
-         <rdf:li>644245120/4294967295</rdf:li>
-         <rdf:li>257698032/4294967295</rdf:li>
-        </rdf:Seq>
-       </ns3:PrimaryChromaticities>
-      </rdf:Description>
-      <rdf:Description rdf:about="">
-       <ns4:ColorSpace>1</ns4:ColorSpace>
-       <ns4:PixelXDimension>2528</ns4:PixelXDimension>
-       <ns4:PixelYDimension>1424</ns4:PixelYDimension>
-       <ns4:FocalLength>353/100</ns4:FocalLength>
-       <ns4:GPSAltitudeRef>0</ns4:GPSAltitudeRef>
-       <ns4:GPSAltitude>0/1</ns4:GPSAltitude>
-       <ns4:GPSMapDatum>WGS-84</ns4:GPSMapDatum>
-       <ns4:DateTimeOriginal>2013-02-09T14:47:53</ns4:DateTimeOriginal>
-       <ns4:ISOSpeedRatings>
-        <rdf:Seq>
-         <rdf:li>76</rdf:li>
-        </rdf:Seq>
-       </ns4:ISOSpeedRatings>
-       <ns4:ExifVersion>0220</ns4:ExifVersion>
-       <ns4:FlashpixVersion>0100</ns4:FlashpixVersion>
-       <ns4:ComponentsConfiguration>
-        <rdf:Seq>
-         <rdf:li>1</rdf:li>
-         <rdf:li>2</rdf:li>
-         <rdf:li>3</rdf:li>
-         <rdf:li>0</rdf:li>
-        </rdf:Seq>
-       </ns4:ComponentsConfiguration>
-       <ns4:GPSLatitude>42,20.56N</ns4:GPSLatitude>
-       <ns4:GPSLongitude>71,5.29W</ns4:GPSLongitude>
-       <ns4:GPSTimeStamp>2013-02-09T19:47:53Z</ns4:GPSTimeStamp>
-       <ns4:GPSProcessingMethod>NETWORK</ns4:GPSProcessingMethod>
-      </rdf:Description>
-      <rdf:Description rdf:about="">
-       <ns5:DateCreated>2013-02-09T14:47:53</ns5:DateCreated>
-      </rdf:Description>
-      <rdf:Description rdf:about="">
-       <dc:Creator>
-        <rdf:Seq>
-         <rdf:li>Glymur</rdf:li>
-         <rdf:li>Python XMP Toolkit</rdf:li>
-        </rdf:Seq>
-       </dc:Creator>
-      </rdf:Description>
-     </rdf:RDF>
-    </ns0:xmpmeta>
-    <?xpacket end="w"?>
-Contiguous Codestream Box (jp2c) @ (3223, 1132296)
-    SOC marker segment @ (3231, 0)
-    SIZ marker segment @ (3233, 47)
-        Profile:  no profile
-        Reference Grid Height, Width:  (1456 x 2592)
-        Vertical, Horizontal Reference Grid Offset:  (0 x 0)
-        Reference Tile Height, Width:  (1456 x 2592)
-        Vertical, Horizontal Reference Tile Offset:  (0 x 0)
-        Bitdepth:  (8, 8, 8)
-        Signed:  (False, False, False)
-        Vertical, Horizontal Subsampling:  ((1, 1), (1, 1), (1, 1))
-    COD marker segment @ (3282, 12)
-        Coding style:
-            Entropy coder, without partitions
-            SOP marker segments:  False
-            EPH marker segments:  False
-        Coding style parameters:
-            Progression order:  LRCP
-            Number of layers:  2
-            Multiple component transformation usage:  reversible
-            Number of resolutions:  2
-            Code block height, width:  (64 x 64)
-            Wavelet transform:  5-3 reversible
-            Precinct size:  default, 2^15 x 2^15
-            Code block context:
-                Selective arithmetic coding bypass:  False
-                Reset context probabilities on coding pass boundaries:  False
-                Termination on each coding pass:  False
-                Vertically stripe causal context:  False
-                Predictable termination:  False
-                Segmentation symbols:  False
-    QCD marker segment @ (3296, 7)
-        Quantization style:  no quantization, 2 guard bits
-        Step size:  [(0, 8), (0, 9), (0, 9), (0, 10)]
-    CME marker segment @ (3305, 37)
-        "Created by OpenJPEG version 2.0.0"
-    SOT marker segment @ (3344, 10)
-        Tile part index:  0
-        Tile part length:  1132173
-        Tile part instance:  0
-        Number of tile parts:  1
-    COC marker segment @ (3356, 9)
-        Associated component:  1
-        Coding style for this component:  Entropy coder, PARTITION = 0
-        Coding style parameters:
-            Number of resolutions:  2
-            Code block height, width:  (64 x 64)
-            Wavelet transform:  5-3 reversible
-            Code block context:
-                Selective arithmetic coding bypass:  False
-                Reset context probabilities on coding pass boundaries:  False
-                Termination on each coding pass:  False
-                Vertically stripe causal context:  False
-                Predictable termination:  False
-                Segmentation symbols:  False
-    QCC marker segment @ (3367, 8)
-        Associated Component:  1
-        Quantization style:  no quantization, 2 guard bits
-        Step size:  [(0, 8), (0, 9), (0, 9), (0, 10)]
-    COC marker segment @ (3377, 9)
-        Associated component:  2
-        Coding style for this component:  Entropy coder, PARTITION = 0
-        Coding style parameters:
-            Number of resolutions:  2
-            Code block height, width:  (64 x 64)
-            Wavelet transform:  5-3 reversible
-            Code block context:
-                Selective arithmetic coding bypass:  False
-                Reset context probabilities on coding pass boundaries:  False
-                Termination on each coding pass:  False
-                Vertically stripe causal context:  False
-                Predictable termination:  False
-                Segmentation symbols:  False
-    QCC marker segment @ (3388, 8)
-        Associated Component:  2
-        Quantization style:  no quantization, 2 guard bits
-        Step size:  [(0, 8), (0, 9), (0, 9), (0, 10)]
-    SOD marker segment @ (3398, 0)
-    EOC marker segment @ (1135517, 0)"""
 
 # Output of reader requirements printing for text_GBR.jp2
 text_GBR_rreq = r"""Reader Requirements Box (rreq) @ (40, 109)
@@ -927,7 +735,7 @@ issue_183_colr = """Colour Specification Box (colr) @ (62, 12)
     Method:  restricted ICC profile
     Precedence:  0
     ICC Profile:  None"""
-
+        
 
 # Progression order is invalid.
 issue_186_progression_order = """COD marker segment @ (174, 12)
@@ -1092,3 +900,4 @@ goodstuff_with_full_header = r"""Codestream:
         Step size:  [(0, 8), (0, 9), (0, 9), (0, 10), (0, 9), (0, 9), (0, 10), (0, 9), (0, 9), (0, 10), (0, 9), (0, 9), (0, 10), (0, 9), (0, 9), (0, 10)]
     SOD marker segment @ (164, 0)
     EOC marker segment @ (115218, 0)"""
+

glymur/test/test_callbacks.py

@@ -1,6 +1,12 @@
 """
 Test suite for openjpeg's callback functions.
 """
+# R0904:  Seems like pylint is fooled in this situation
+# pylint: disable=R0904
+
+# 'mock' most certainly is in unittest (Python 3.3)
+# pylint: disable=E0611,F0401
+
 import os
 import re
 import sys
@@ -19,7 +25,8 @@ import glymur
 
 from .fixtures import WARNING_INFRASTRUCTURE_ISSUE, WARNING_INFRASTRUCTURE_MSG
 
-
+@unittest.skipIf(glymur.lib.openjp2.OPENJP2 is None,
+                 "Missing openjp2 library.")
 class TestCallbacks(unittest.TestCase):
     """Test suite for callbacks."""
 
@@ -30,60 +37,68 @@ class TestCallbacks(unittest.TestCase):
     def tearDown(self):
         pass
 
-    @unittest.skipIf(glymur.version.openjpeg_version[0] != '2',
-                     "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_backwards_compatibility(self):
+    def test_info_callback_on_write(self):
         """Verify messages printed when writing an image in verbose mode."""
         j = glymur.Jp2k(self.jp2file)
         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:
-                glymur.Jp2k(tfile.name, data=tiledata, verbose=True)
+                j.write(tiledata, verbose=True)
-            actual = fake_out.getvalue().strip()
-        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:
-            with patch('sys.stdout', new=StringIO()) as fake_out:
-                glymur.Jp2k(tfile.name, data=tiledata, verbose=True)
                 actual = fake_out.getvalue().strip()
         expected = '[INFO] tile number 1 / 1'
         self.assertEqual(actual, expected)
 
-    @unittest.skipIf(glymur.version.openjpeg_version[0] == '0',
-                     "Missing openjpeg/openjp2 library.")
     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.
-        jp2 = glymur.Jp2k(self.j2kfile)
+        j = glymur.Jp2k(self.j2kfile)
         with patch('sys.stdout', new=StringIO()) as fake_out:
-            jp2.verbose = True
+            j.read(rlevel=1, verbose=True, area=(0, 0, 200, 150))
-            jp2[::2, ::2]
             actual = fake_out.getvalue().strip()
 
-        if glymur.version.openjpeg_version[0] == '2':
+        lines = ['[INFO] Start to read j2k main header (0).',
-            lines = ['[INFO] Start to read j2k main header (0).',
+                 '[INFO] Main header has been correctly decoded.',
-                     '[INFO] Main header has been correctly decoded.',
+                 '[INFO] Setting decoding area to 0,0,150,200',
-                     '[INFO] Setting decoding area to 0,0,480,800',
+                 '[INFO] Header of tile 0 / 0 has been read.',
-                     '[INFO] Header of tile 0 / 0 has been read.',
+                 '[INFO] Tile 1/1 has been decoded.',
-                     '[INFO] Tile 1/1 has been decoded.',
+                 '[INFO] Image data has been updated with tile 1.']
-                     '[INFO] Image data has been updated with tile 1.']
+
+        expected = '\n'.join(lines)
+        self.assertEqual(actual, expected)
+
+
+@unittest.skipIf(glymur.lib.openjpeg.OPENJPEG is None,
+                 "Missing openjpeg library.")
+class TestCallbacks15(unittest.TestCase):
+    """This test suite is for OpenJPEG 1.5.1 properties.
+    """
+
+    def setUp(self):
+        self.jp2file = glymur.data.nemo()
+        self.j2kfile = glymur.data.goodstuff()
+
+    def tearDown(self):
+        pass
+
+    def test_info_callbacks_on_read(self):
+        """Verify stdout when reading.
+
+        Verify that we get the expected stdio output when our internal info
+        callback handler is enabled.
+        """
+        with patch('glymur.lib.openjp2.OPENJP2', new=None):
+            # Force to use OPENJPEG instead of OPENJP2.
+            j = glymur.Jp2k(self.j2kfile)
+            with patch('sys.stdout', new=StringIO()) as fake_out:
+                j.read(rlevel=1, verbose=True)
+                actual = fake_out.getvalue().strip()
 
-            expected = '\n'.join(lines)
-            self.assertEqual(actual, expected)
-        else:
             regex = re.compile(r"""\[INFO\]\stile\s1\sof\s1\s+
                                    \[INFO\]\s-\stiers-1\stook\s
                                            [0-9]+\.[0-9]+\ss\s+
@@ -93,7 +108,13 @@ class TestCallbacks(unittest.TestCase):
                                            [0-9]+\.[0-9]+\ss""",
                                re.VERBOSE)
 
+            # assertRegex in Python 3.3 (python2.7/pylint issue)
+            # pylint: disable=E1101
             if sys.hexversion <= 0x03020000:
                 self.assertRegexpMatches(actual, regex)
             else:
                 self.assertRegex(actual, regex)
+
+
+if __name__ == "__main__":
+    unittest.main()

glymur/test/test_codestream.py

@@ -0,0 +1,149 @@
+"""
+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()

glymur/test/test_config.py

@@ -1,8 +1,16 @@
 """These tests are for edge cases where OPENJPEG does not exist, but
 OPENJP2 may be present in some form or other.
 """
-import contextlib
+# unittest doesn't work well with R0904.
-import ctypes
+# pylint: disable=R0904
+
+# tempfile.TemporaryDirectory, unittest.assertWarns introduced in 3.2
+# pylint: disable=E1101
+
+# unittest.mock only in Python 3.3 (python2.7/pylint import issue)
+# pylint:  disable=E0611,F0401
+
+
 import imp
 import os
 import sys
@@ -17,42 +25,10 @@ else:
 import glymur
 from glymur import Jp2k
 
-from .fixtures import (WARNING_INFRASTRUCTURE_ISSUE,
+from .fixtures import (
-                       WARNING_INFRASTRUCTURE_MSG,
+        WARNING_INFRASTRUCTURE_ISSUE, WARNING_INFRASTRUCTURE_MSG,
-                       WINDOWS_TMP_FILE_MSG)
+        WINDOWS_TMP_FILE_MSG
-
+)
-
-def openjpeg_not_found_by_ctypes():
-    """
-    Need to know if openjpeg library can be picked right up by ctypes for one
-    of the tests.
-    """
-    with patch.dict('os.environ',
-                    {'DYLD_FALLBACK_LIBRARY_PATH': '/opt/local/lib'}):
-        if ctypes.util.find_library('openjpeg') is None:
-            return True
-        else:
-            return False
-
-
-@contextlib.contextmanager
-def chdir(dirname=None):
-    """
-    This context manager restores the value of the current working directory
-    (cwd) after the enclosed code block completes or raises an exception.  If a
-    directory name is supplied to the context manager then the cwd is changed
-    prior to running the code block.
-
-    Shamelessly lifted from
-    http://www.astropython.org/snippet/2009/10/chdir-context-manager
-    """
-    curdir = os.getcwd()
-    try:
-        if dirname is not None:
-            os.chdir(dirname)
-        yield
-    finally:
-        os.chdir(curdir)
 
 
 @unittest.skipIf(sys.hexversion < 0x03020000,
@@ -89,6 +65,7 @@ class TestSuite(unittest.TestCase):
 
                 # Need to reliably recover the location of the openjp2 library,
                 # so using '_name' appears to be the only way to do it.
+                # pylint:  disable=W0212
                 libloc = glymur.lib.openjp2.OPENJP2._name
                 line = 'openjp2: {0}\n'.format(libloc)
                 tfile.write(line)
@@ -117,56 +94,17 @@ class TestSuite(unittest.TestCase):
                         with self.assertWarnsRegex(UserWarning, regex):
                             imp.reload(glymur.lib.openjp2)
 
-    @unittest.skipIf(glymur.lib.openjp2.OPENJPEG is None,
-                     "Needs openjp2 and openjpeg before this test make sense.")
-    @unittest.skipIf(os.name == "nt", WINDOWS_TMP_FILE_MSG)
-    def test_library_specified_as_None(self):
-        """Verify that we can stop library from being loaded by using None."""
-        with tempfile.TemporaryDirectory() as tdir:
-            configdir = os.path.join(tdir, 'glymur')
-            os.mkdir(configdir)
-            fname = os.path.join(configdir, 'glymurrc')
-            with open(fname, 'w') as fptr:
-                # Essentially comment out openjp2 and preferentially load
-                # openjpeg instead.
-                fptr.write('[library]\n')
-                fptr.write('openjp2: None\n')
-                msg = 'openjpeg: {0}\n'
-                msg = msg.format(glymur.lib.openjp2.OPENJPEG._name)
-                fptr.write(msg)
-                fptr.flush()
-                with patch.dict('os.environ', {'XDG_CONFIG_HOME': tdir}):
-                    imp.reload(glymur.lib.openjp2)
-                    self.assertIsNone(glymur.lib.openjp2.OPENJP2)
-                    self.assertIsNotNone(glymur.lib.openjp2.OPENJPEG)
 
-    @unittest.skipIf(glymur.lib.openjp2.OPENJPEG is None,
+@unittest.skipIf(glymur.lib.openjp2.OPENJP2 is None and
-                     "Needs openjpeg before this test make sense.")
+                 glymur.lib.openjpeg.OPENJPEG is None,
-    @unittest.skipIf(openjpeg_not_found_by_ctypes(),
+                 "Missing openjp2 library.")
-                     "OpenJPEG must be found before this test can work.")
+class TestConfig(unittest.TestCase):
-    @unittest.skipIf(os.name == "nt", WINDOWS_TMP_FILE_MSG)
+    """Test suite for reading without proper library in place."""
-    def test_config_dir_but_no_config_file(self):
 
-        with tempfile.TemporaryDirectory() as tdir:
+    def setUp(self):
-            configdir = os.path.join(tdir, 'glymur')
+        self.jp2file = glymur.data.nemo()
-            os.mkdir(configdir)
+        self.j2kfile = glymur.data.goodstuff()
-            with patch.dict('os.environ', {'XDG_CONFIG_HOME': tdir}):
+
-                # Should still be able to load openjpeg, despite the
+    def tearDown(self):
-                # configuration file not being there
+        pass
-                imp.reload(glymur.lib.openjpeg)
-                self.assertIsNotNone(glymur.lib.openjp2.OPENJPEG)
 
-    @unittest.skipIf(os.name == "nt", WINDOWS_TMP_FILE_MSG)
-    def test_config_file_in_current_directory(self):
-        """A configuration file in the current directory should be honored."""
-        libloc = glymur.lib.openjp2.OPENJP2._name
-        with tempfile.TemporaryDirectory() as tdir1:
-            fname = os.path.join(tdir1, 'glymurrc')
-            with open(fname, 'w') as fptr:
-                fptr.write('[library]\n')
-                fptr.write('openjp2: {0}\n'.format(libloc))
-                fptr.flush()
-                with chdir(tdir1):
-                    # Should be able to load openjp2 as before.
-                    imp.reload(glymur.lib.openjp2)
-                    self.assertEqual(glymur.lib.openjp2.OPENJP2._name, libloc)

glymur/test/test_glymur_warnings.py

@@ -1,32 +1,34 @@
 """
 Test suite for warnings issued by glymur.
 """
+
+# unittest doesn't work well with R0904.
+# pylint: disable=R0904
+
+import platform
 import os
 import re
 import struct
+import sys
 import tempfile
 import unittest
 
+import six
+
 from glymur import Jp2k
 import glymur
 
 from .fixtures import opj_data_file, OPJ_DATA_ROOT
 from .fixtures import WARNING_INFRASTRUCTURE_ISSUE, WARNING_INFRASTRUCTURE_MSG
 
-
+@unittest.skipIf(sys.hexversion < 0x03040000 and platform.system() == 'Linux',
+                 "inexplicable failures on 3.3 and linux")
 @unittest.skipIf(OPJ_DATA_ROOT is None,
                  "OPJ_DATA_ROOT environment variable not set")
 @unittest.skipIf(WARNING_INFRASTRUCTURE_ISSUE, WARNING_INFRASTRUCTURE_MSG)
 class TestWarnings(unittest.TestCase):
     """Test suite for warnings issued by glymur."""
 
-    def test_invalid_compatibility_list_entry(self):
-        """should not error out with invalid compatibility list entry"""
-        filename = opj_data_file('input/nonregression/issue397.jp2')
-        with self.assertWarns(UserWarning):
-            Jp2k(filename)
-        self.assertTrue(True)
-
     def test_exceeded_box_length(self):
         """
         should warn if reading past end of a box
@@ -53,11 +55,12 @@ class TestWarnings(unittest.TestCase):
         """
         relpath = 'input/nonregression/issue188_beach_64bitsbox.jp2'
         jfile = opj_data_file(relpath)
-        pattern = r"""Unrecognized\sbox\s\(b'XML\s'\)\sencountered."""
+        regex = re.compile(r"""Unrecognized\sbox\s\(b'XML\s'\)\sencountered.""",
-        regex = re.compile(pattern, re.VERBOSE)
+                           re.VERBOSE)
         with self.assertWarnsRegex(UserWarning, regex):
             Jp2k(jfile)
 
+
     def test_NR_gdal_fuzzer_unchecked_numresolutions_dump(self):
         """
         Has an invalid number of resolutions.
@@ -69,7 +72,7 @@ class TestWarnings(unittest.TestCase):
                                \(\d+\)\.""",
                            re.VERBOSE)
         with self.assertWarnsRegex(UserWarning, regex):
-            Jp2k(jfile).get_codestream()
+            Jp2k(jfile)
 
     @unittest.skipIf(re.match("1.5|2.0.0", glymur.version.openjpeg_version),
                      "Test not passing on 1.5.x, not introduced until 2.x")
@@ -84,7 +87,7 @@ class TestWarnings(unittest.TestCase):
                                \(\d+\)\.""",
                            re.VERBOSE)
         with self.assertWarnsRegex(UserWarning, regex):
-            Jp2k(jfile).get_codestream()
+            Jp2k(jfile)
 
     def test_NR_gdal_fuzzer_check_comp_dx_dy_jp2_dump(self):
         """
@@ -97,7 +100,7 @@ class TestWarnings(unittest.TestCase):
                                dx=\d+,\s*dy=\d+""",
                            re.VERBOSE)
         with self.assertWarnsRegex(UserWarning, regex):
-            Jp2k(jfile).get_codestream()
+            Jp2k(jfile)
 
     def test_NR_gdal_fuzzer_assert_in_opj_j2k_read_SQcd_SQcc_patch_jp2(self):
         lst = ['input', 'nonregression',
@@ -107,32 +110,53 @@ class TestWarnings(unittest.TestCase):
                                number\sof\scomponents\sis\sonly\s\d+""",
                            re.VERBOSE)
         with self.assertWarnsRegex(UserWarning, regex):
-            Jp2k(jfile).get_codestream()
+            Jp2k(jfile)
+
+    def test_NR_broken_jp2_dump(self):
+        """
+        The colr box has a ridiculously incorrect box length.
+        """
+        jfile = opj_data_file('input/nonregression/broken.jp2')
+        regex = re.compile(r'''b'colr'\sbox\shas\sincorrect\sbox\slength\s
+                               \(\d+\)''',
+                           re.VERBOSE)
+        with self.assertWarnsRegex(UserWarning, regex):
+            jp2 = Jp2k(jfile)
+
+    def test_NR_broken2_jp2_dump(self):
+        """
+        Invalid marker ID on codestream.
+        """
+        jfile = opj_data_file('input/nonregression/broken2.jp2')
+        regex = re.compile(r'''Invalid\smarker\sid\sencountered\sat\sbyte\s
+                               \d+\sin\scodestream:\s*"0x[a-fA-F0-9]{4}"''', 
+                           re.VERBOSE)
+        with self.assertWarnsRegex(UserWarning, regex):
+            Jp2k(jfile)
 
     def test_bad_rsiz(self):
         """Should warn if RSIZ is bad.  Issue196"""
         filename = opj_data_file('input/nonregression/edf_c2_1002767.jp2')
         with self.assertWarnsRegex(UserWarning, 'Invalid profile'):
-            Jp2k(filename).get_codestream()
+            Jp2k(filename)
 
     def test_bad_wavelet_transform(self):
         """Should warn if wavelet transform is bad.  Issue195"""
         filename = opj_data_file('input/nonregression/edf_c2_10025.jp2')
         with self.assertWarnsRegex(UserWarning, 'Invalid wavelet transform'):
-            Jp2k(filename).get_codestream()
+            Jp2k(filename)
 
     def test_invalid_progression_order(self):
         """Should still be able to parse even if prog order is invalid."""
         jfile = opj_data_file('input/nonregression/2977.pdf.asan.67.2198.jp2')
         with self.assertWarnsRegex(UserWarning, 'Invalid progression order'):
-            Jp2k(jfile).get_codestream()
+            Jp2k(jfile)
 
     def test_tile_height_is_zero(self):
         """Zero tile height should not cause an exception."""
-        filename = 'input/nonregression/2539.pdf.SIGFPE.706.1712.jp2'
+        filename = opj_data_file('input/nonregression/2539.pdf.SIGFPE.706.1712.jp2')
-        filename = opj_data_file(filename)
         with self.assertWarnsRegex(UserWarning, 'Invalid tile dimensions'):
-            Jp2k(filename).get_codestream()
+            Jp2k(filename)
 
     @unittest.skipIf(os.name == "nt", "Temporary file issue on window.")
     def test_unknown_marker_segment(self):
@@ -155,9 +179,9 @@ class TestWarnings(unittest.TestCase):
                 read_buffer = ifile.read()
                 tfile.write(read_buffer)
                 tfile.flush()
-
+ 
                 with self.assertWarnsRegex(UserWarning, 'Unrecognized marker'):
-                    Jp2k(tfile.name).get_codestream()
+                    codestream = Jp2k(tfile.name).get_codestream()
 
 
 if __name__ == "__main__":

glymur/test/test_icc.py

@@ -1,7 +1,13 @@
 """
 ICC profile tests.
 """
+
+# unittest doesn't work well with R0904.
+# pylint: disable=R0904
+
 import datetime
+import os
+import sys
 import unittest
 
 import numpy as np
@@ -60,6 +66,11 @@ class TestICC(unittest.TestCase):
         """invalid ICC header data should cause UserWarning"""
         jfile = opj_data_file('input/nonregression/orb-blue10-lin-jp2.jp2')
 
+        # assertWarns in Python 3.3 (python2.7/pylint issue)
+        # pylint: disable=E1101
         regex = 'ICC profile header is corrupt'
         with self.assertWarnsRegex(UserWarning, regex):
             Jp2k(jfile)
+
+if __name__ == "__main__":
+    unittest.main()

glymur/test/test_jp2box.py

@@ -1,6 +1,18 @@
 """
 Test suite specifically targeting JP2 box layout.
 """
+# E1103:  return value from read may be list or np array
+# pylint: disable=E1103
+
+# R0902:  More than 7 instance attributes are just fine for testing.
+# pylint: disable=R0902
+
+# R0904:  Seems like pylint is fooled in this situation
+# pylint: disable=R0904
+
+# W0613:  load_tests doesn't need to use ignore or loader arguments.
+# pylint: disable=W0613
+
 import doctest
 import os
 import re
@@ -8,6 +20,7 @@ import shutil
 import struct
 import sys
 import tempfile
+import uuid
 from uuid import UUID
 import unittest
 
@@ -22,13 +35,15 @@ from glymur.jp2box import JPEG2000SignatureBox
 from glymur.core import COLOR, OPACITY
 from glymur.core import RED, GREEN, BLUE, GREY, WHOLE_IMAGE
 
-from .fixtures import (WARNING_INFRASTRUCTURE_ISSUE,
+from .fixtures import (
-                       WARNING_INFRASTRUCTURE_MSG,
+        WARNING_INFRASTRUCTURE_ISSUE, WARNING_INFRASTRUCTURE_MSG,
-                       WINDOWS_TMP_FILE_MSG, MetadataBase)
+        WINDOWS_TMP_FILE_MSG, MetadataBase
+)
 
-
+try:
-def docTearDown(doctest_obj):
+    FORMAT_CORPUS_DATA_ROOT = os.environ['FORMAT_CORPUS_DATA_ROOT']
-    glymur.set_parseoptions(full_codestream=False)
+except KeyError:
+    FORMAT_CORPUS_DATA_ROOT = None
 
 
 def load_tests(loader, tests, ignore):
@@ -36,35 +51,31 @@ def load_tests(loader, tests, ignore):
     if os.name == "nt":
         # Can't do it on windows, temporary file issue.
         return tests
-    tests.addTests(doctest.DocTestSuite('glymur.jp2box',
+    tests.addTests(doctest.DocTestSuite('glymur.jp2box'))
-                                        tearDown=docTearDown))
     return tests
 
-
 @unittest.skipIf(os.name == "nt", WINDOWS_TMP_FILE_MSG)
 class TestDataEntryURL(unittest.TestCase):
     """Test suite for DataEntryURL boxes."""
     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)
-        data = j[:]
+        data = j.read()
         red = data[:, :, 0]
 
         # Write it back out as a raw codestream.
         with tempfile.NamedTemporaryFile(suffix=".j2k") as tfile1:
-            j2k = glymur.Jp2k(tfile1.name, data=red)
+            j2k = glymur.Jp2k(tfile1.name, 'wb')
+            j2k.write(data[:, :, 0])
 
             # Ok, now rewrap it as JP2.  The colorspace should be GREYSCALE.
             with tempfile.NamedTemporaryFile(suffix=".jp2") as tfile2:
                 jp2 = j2k.wrap(tfile2.name)
                 self.assertEqual(jp2.box[2].box[1].colorspace,
-                                 glymur.core.GREYSCALE)
+                        glymur.core.GREYSCALE)
 
     def test_basic_url(self):
         """Just your most basic URL box."""
@@ -86,7 +97,7 @@ class TestDataEntryURL(unittest.TestCase):
         self.assertEqual(jp22.box[4].url, url)
 
     def test_null_termination(self):
-        """I.9.3.2 specifies that location field must be null terminated."""
+        """I.9.3.2 specifies that the location field must be null terminated."""
         jp2 = Jp2k(self.jp2file)
 
         url = 'http://glymur.readthedocs.org'
@@ -97,21 +108,18 @@ class TestDataEntryURL(unittest.TestCase):
             jp22 = jp2.wrap(tfile.name, boxes=boxes)
 
             self.assertEqual(jp22.box[-1].length, 42)
-
+    
-            # Go to the last box.  Seek past the L, T, version,
+            # Go to the last box.  Seek past the L, T, version, and flag fields.
-            # and flag fields.
             with open(tfile.name, 'rb') as fptr:
                 fptr.seek(jp22.box[-1].offset + 4 + 4 + 1 + 3)
-
+    
-                nbytes = (jp22.box[-1].offset +
+                nbytes = jp22.box[-1].offset + jp22.box[-1].length - fptr.tell()
-                          jp22.box[-1].length -
-                          fptr.tell())
                 read_buffer = fptr.read(nbytes)
                 read_url = read_buffer.decode('utf-8')
                 self.assertEqual(url + chr(0), read_url)
 
 
-@unittest.skipIf(re.match(r'''0|1|2.0.0''',
+@unittest.skipIf(re.match(r'''(1|2.0.0)''',
                           glymur.version.openjpeg_version) is not None,
                  "Not supported until 2.1")
 @unittest.skipIf(os.name == "nt", WINDOWS_TMP_FILE_MSG)
@@ -122,21 +130,24 @@ class TestChannelDefinition(unittest.TestCase):
     def setUpClass(cls):
         """Need a one_plane plane image for greyscale testing."""
         j2k = Jp2k(glymur.data.goodstuff())
-        data = j2k[:]
+        data = j2k.read()
         # Write the first component back out to file.
         with tempfile.NamedTemporaryFile(suffix=".j2k", delete=False) as tfile:
-            Jp2k(tfile.name, data=data[:, :, 0])
+            grey_j2k = Jp2k(tfile.name, 'wb')
+            grey_j2k.write(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:
-            Jp2k(tfile.name, data=data[:, :, 0:1])
+            grey_j2k = Jp2k(tfile.name, 'wb')
+            grey_j2k.write(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)
-            Jp2k(tfile.name, data=data4)
+            rgba_jp2.write(data4)
             cls.four_planes = tfile.name
 
     @classmethod
@@ -389,7 +400,7 @@ class TestFileTypeBox(unittest.TestCase):
             ftyp = glymur.jp2box.FileTypeBox(brand='jp3')
         with self.assertRaises(IOError):
             with tempfile.TemporaryFile() as tfile:
-                ftyp.write(tfile)
+                ftyp.write(tfile) 
 
     @unittest.skipIf(WARNING_INFRASTRUCTURE_ISSUE, WARNING_INFRASTRUCTURE_MSG)
     def test_cl_entry_unknown(self):
@@ -399,8 +410,7 @@ class TestFileTypeBox(unittest.TestCase):
             ftyp = glymur.jp2box.FileTypeBox(compatibility_list=['jp3'])
         with self.assertRaises(IOError):
             with tempfile.TemporaryFile() as tfile:
-                ftyp.write(tfile)
+                ftyp.write(tfile) 
-
 
 class TestColourSpecificationBox(unittest.TestCase):
     """Test suite for colr box instantiation."""
@@ -523,8 +533,8 @@ class TestPaletteBox(unittest.TestCase):
         bps = (8, 8, 8)
         signed = (False, False)
         with self.assertWarns(UserWarning):
-            glymur.jp2box.PaletteBox(palette, bits_per_component=bps,
+            pclr = glymur.jp2box.PaletteBox(palette, bits_per_component=bps,
-                                     signed=signed)
+                                            signed=signed)
 
     @unittest.skipIf(WARNING_INFRASTRUCTURE_ISSUE, WARNING_INFRASTRUCTURE_MSG)
     def test_mismatched_signed_palette(self):
@@ -533,8 +543,8 @@ class TestPaletteBox(unittest.TestCase):
         bps = (8, 8, 8, 8)
         signed = (False, False, False, False)
         with self.assertWarns(UserWarning):
-            glymur.jp2box.PaletteBox(palette, bits_per_component=bps,
+            pclr = glymur.jp2box.PaletteBox(palette, bits_per_component=bps,
-                                     signed=signed)
+                                            signed=signed)
 
     def test_writing_with_different_bitdepths(self):
         """Bitdepths must be the same when writing."""
@@ -634,7 +644,7 @@ class TestAppend(unittest.TestCase):
             jp2 = Jp2k(tfile.name)
 
             # Make a UUID box.  Only XMP UUID boxes can currently be appended.
-            uuid_instance = UUID('00000000-0000-0000-0000-000000000000')
+            uuid_instance = uuid.UUID('00000000-0000-0000-0000-000000000000')
             data = b'0123456789'
             uuidbox = glymur.jp2box.UUIDBox(uuid_instance, data)
             with self.assertRaises(IOError):
@@ -790,7 +800,7 @@ class TestWrap(unittest.TestCase):
             # list to trigger the error.
             boxes[2].box = []
             with self.assertRaises(IOError):
-                jp2.wrap(tfile.name, boxes=boxes)
+                jp22 = jp2.wrap(tfile.name, boxes=boxes)
 
     def test_default_layout_with_boxes(self):
         """basic test for rewrapping a jp2 file, boxes specified"""
@@ -855,8 +865,8 @@ class TestWrap(unittest.TestCase):
         """A palette box must reside in a JP2 header box."""
         palette = np.array([[255, 0, 255], [0, 255, 0]], dtype=np.int32)
         bps = (8, 8, 8)
-        pclr = glymur.jp2box.PaletteBox(palette=palette,
+        signed = (True, False, True)
-                                        bits_per_component=bps,
+        pclr = glymur.jp2box.PaletteBox(palette=palette, bits_per_component=bps,
                                         signed=(True, False, True))
 
         j2k = Jp2k(self.j2kfile)
@@ -968,8 +978,7 @@ class TestWrap(unittest.TestCase):
         """Rewrap a jpx file."""
         with tempfile.NamedTemporaryFile(suffix='.jp2') as tfile1:
             jpx = Jp2k(self.jpxfile)
-            idx = (list(range(5)) +
+            idx = list(range(5)) + list(range(9, 12)) + list(range(6, 9)) + [12]
-                   list(range(9, 12)) + list(range(6, 9))) + [12]
             boxes = [jpx.box[j] for j in idx]
             jpx2 = jpx.wrap(tfile1.name, boxes=boxes)
             exp_ids = [box.box_id for box in boxes]
@@ -1021,11 +1030,11 @@ class TestJp2Boxes(unittest.TestCase):
         """Raw instantiation should not produce a main_header."""
         box = ContiguousCodestreamBox()
         self.assertEqual(box.box_id, 'jp2c')
-        self.assertIsNone(box.codestream)
+        self.assertIsNone(box.main_header)
 
     def test_codestream_main_header_offset(self):
         """main_header_offset is an attribute of the CCS box"""
-        j = Jp2k(self.jpxfile)
+        j = Jp2k(self.jpxfile);
         self.assertEqual(j.box[5].main_header_offset,
                          j.box[5].offset + 8)
 
@@ -1226,8 +1235,8 @@ class TestRepr(MetadataBase):
 
     def test_uuidlist_box(self):
         """Verify __repr__ method on ulst box."""
-        uuid1 = UUID('00000000-0000-0000-0000-000000000001')
+        uuid1 = uuid.UUID('00000000-0000-0000-0000-000000000001')
-        uuid2 = UUID('00000000-0000-0000-0000-000000000002')
+        uuid2 = uuid.UUID('00000000-0000-0000-0000-000000000002')
         uuids = [uuid1, uuid2]
         ulst = glymur.jp2box.UUIDListBox(ulst=uuids)
         newbox = eval(repr(ulst))
@@ -1239,6 +1248,7 @@ class TestRepr(MetadataBase):
         """Verify Palette box repr."""
         palette = np.array([[255, 0, 1000], [0, 255, 0]], dtype=np.int32)
         bps = (8, 8, 16)
+        signed = (True, False, True)
         box = glymur.jp2box.PaletteBox(palette=palette, bits_per_component=bps,
                                        signed=(True, False, True))
 
@@ -1281,15 +1291,14 @@ class TestRepr(MetadataBase):
 
     def test_uuid_box_generic(self):
         """Verify uuid repr method."""
-        uuid_instance = UUID('00000000-0000-0000-0000-000000000000')
+        uuid_instance = uuid.UUID('00000000-0000-0000-0000-000000000000')
         data = b'0123456789'
         box = glymur.jp2box.UUIDBox(the_uuid=uuid_instance, raw_data=data)
 
         # Since the raw_data parameter is a sequence of bytes which could be
         # quite long, don't bother trying to make it conform to eval(repr()).
         regexp = r"""glymur.jp2box.UUIDBox\("""
-        regexp += """the_uuid="""
+        regexp += """the_uuid=UUID\('00000000-0000-0000-0000-000000000000'\),\s"""
-        regexp += """UUID\('00000000-0000-0000-0000-000000000000'\),\s"""
         regexp += """raw_data=<byte\sarray\s10\selements>\)"""
 
         if sys.hexversion < 0x03000000:
@@ -1306,8 +1315,7 @@ class TestRepr(MetadataBase):
         # Since the raw_data parameter is a sequence of bytes which could be
         # quite long, don't bother trying to make it conform to eval(repr()).
         regexp = r"""glymur.jp2box.UUIDBox\("""
-        regexp += """the_uuid="""
+        regexp += """the_uuid=UUID\('be7acfcb-97a9-42e8-9c71-999491e3afac'\),\s"""
-        regexp += """UUID\('be7acfcb-97a9-42e8-9c71-999491e3afac'\),\s"""
         regexp += """raw_data=<byte\sarray\s3122\selements>\)"""
 
         if sys.hexversion < 0x03000000:
@@ -1323,10 +1331,49 @@ class TestRepr(MetadataBase):
 
         # Difficult to eval(repr()) this, so just match the general pattern.
         regexp = "glymur.jp2box.ContiguousCodeStreamBox"
-        regexp += "[(]codestream=<glymur.codestream.Codestream\sobject\s"
+        regexp += "[(]main_header=<glymur.codestream.Codestream\sobject\s"
         regexp += "at\s0x([a-fA-F0-9]*)>[)]"
 
         if sys.hexversion < 0x03000000:
             self.assertRegexpMatches(repr(box), regexp)
         else:
             self.assertRegex(repr(box), regexp)
+
+
+
+class TestJpxBoxes(unittest.TestCase):
+    """Tests for JPX boxes."""
+
+    def setUp(self):
+        pass
+
+    def tearDown(self):
+        pass
+
+    @unittest.skipIf(FORMAT_CORPUS_DATA_ROOT is None,
+                     "FORMAT_CORPUS_DATA_ROOT environment variable not set")
+    def test_codestream_header(self):
+        """Should recognize codestream header box."""
+        jfile = os.path.join(FORMAT_CORPUS_DATA_ROOT,
+                             'jp2k-formats/balloon.jpf')
+        jpx = Jp2k(jfile)
+
+        # This superbox just happens to be empty.
+        self.assertEqual(jpx.box[4].box_id, 'jpch')
+        self.assertEqual(len(jpx.box[4].box), 0)
+
+    @unittest.skipIf(FORMAT_CORPUS_DATA_ROOT is None,
+                     "FORMAT_CORPUS_DATA_ROOT environment variable not set")
+    def test_compositing_layer_header(self):
+        """Should recognize compositing layer header box."""
+        jfile = os.path.join(FORMAT_CORPUS_DATA_ROOT,
+                             'jp2k-formats/balloon.jpf')
+        jpx = Jp2k(jfile)
+
+        # This superbox just happens to be empty.
+        self.assertEqual(jpx.box[5].box_id, 'jplh')
+        self.assertEqual(len(jpx.box[5].box), 0)
+
+
+if __name__ == "__main__":
+    unittest.main()

glymur/test/test_jp2box_jpx.py

@@ -6,6 +6,7 @@ Test suite specifically targeting JPX box layout.
 import ctypes
 import os
 import struct
+import sys
 import tempfile
 import unittest
 
@@ -19,7 +20,6 @@ from glymur.jp2box import ColourSpecificationBox
 
 from .fixtures import WARNING_INFRASTRUCTURE_ISSUE, WARNING_INFRASTRUCTURE_MSG
 
-
 @unittest.skipIf(os.name == "nt", "Temporary file issue on window.")
 class TestJPXWrap(unittest.TestCase):
     """Test suite for wrapping JPX files."""
@@ -184,7 +184,7 @@ class TestJPXWrap(unittest.TestCase):
 
         with tempfile.NamedTemporaryFile(suffix=".jpx") as tfile:
             with self.assertRaises(IOError):
-                jp2.wrap(tfile.name, boxes=boxes)
+                jpx = jp2.wrap(tfile.name, boxes=boxes)
 
     def test_cgrp_neg(self):
         """Can't write a cgrp with anything but colr sub boxes"""
@@ -204,7 +204,7 @@ class TestJPXWrap(unittest.TestCase):
 
         with tempfile.NamedTemporaryFile(suffix=".jpx") as tfile:
             with self.assertRaises(IOError):
-                jp2.wrap(tfile.name, boxes=boxes)
+                jpx = jp2.wrap(tfile.name, boxes=boxes)
 
     def test_ftbl(self):
         """Write a fragment table box."""
@@ -484,7 +484,7 @@ class TestJPX(unittest.TestCase):
                 ftbl.write(tfile)
 
     def test_data_reference_requires_dtbl(self):
-        """The existance of data reference box requires a ftbl box as well."""
+        """The existance of a data reference box requires a ftbl box as well."""
         flag = 0
         version = (0, 0, 0)
         url1 = 'file:////usr/local/bin'
@@ -574,7 +574,7 @@ class TestJPX(unittest.TestCase):
                           131072, 65536, 32768, 16384, 8192]
         for j in range(len(standard_flags)):
             mask = (standard_masks[j] >> 16,
-                    standard_masks[j] & 0x0000ffff >> 8,
+                    standard_masks[j] & 0x0000ffff>> 8,
                     standard_masks[j] & 0x000000ff)
             struct.pack_into('>HBBB', rreq_buffer, 17 + j * 5,
                              standard_flags[j], *mask)
@@ -599,6 +599,7 @@ class TestJPX(unittest.TestCase):
         self.assertEqual(jpx.box[2].standard_flag,
                          (5, 42, 45, 2, 18, 19, 1, 8, 12, 31, 20))
 
+
     def test_nlst(self):
         """Verify that we can handle a number list box."""
         j = Jp2k(self.jpxfile)

glymur/test/test_jp2box_uuid.py

@@ -1,7 +1,17 @@
 # -*- coding:  utf-8 -*-
 """Test suite for printing.
 """
+# C0302:  don't care too much about having too many lines in a test module
+# pylint: disable=C0302
+
+# E061:  unittest.mock introduced in 3.3 (python-2.7/pylint issue)
+# pylint: disable=E0611,F0401
+
+# R0904:  Not too many methods in unittest.
+# pylint: disable=R0904
+
 import os
+import re
 import shutil
 import struct
 import sys
@@ -13,18 +23,30 @@ if sys.hexversion < 0x02070000:
 else:
     import unittest
 
+if sys.hexversion < 0x03000000:
+    from StringIO import StringIO
+else:
+    from io import StringIO
+
+if sys.hexversion <= 0x03030000:
+    from mock import patch
+else:
+    from unittest.mock import patch
+
 import lxml.etree
 
-from .fixtures import (WARNING_INFRASTRUCTURE_ISSUE,
+from .fixtures import HAS_PYTHON_XMP_TOOLKIT, OPJ_DATA_ROOT
-                       WARNING_INFRASTRUCTURE_MSG,
+from .fixtures import WARNING_INFRASTRUCTURE_ISSUE, WARNING_INFRASTRUCTURE_MSG
-                       WINDOWS_TMP_FILE_MSG)
+
+if HAS_PYTHON_XMP_TOOLKIT:
+    from libxmp import XMPMeta
 
 import glymur
 from glymur import Jp2k
-from .fixtures import SimpleRDF
+from .fixtures import OPJ_DATA_ROOT, opj_data_file, SimpleRDF
 
 
-@unittest.skipIf(os.name == "nt", WINDOWS_TMP_FILE_MSG)
+@unittest.skipIf(os.name == "nt", "Unexplained failure on windows")
 class TestSuite(unittest.TestCase):
     """Tests for XMP, Exif UUIDs."""
 
@@ -79,9 +101,8 @@ class TestSuite(unittest.TestCase):
             jp2 = glymur.Jp2k(tfile.name)
             self.assertEqual(jp2.box[-1].data['Make'], "HTC")
 
-
 @unittest.skipIf(WARNING_INFRASTRUCTURE_ISSUE, WARNING_INFRASTRUCTURE_MSG)
-@unittest.skipIf(os.name == "nt", WINDOWS_TMP_FILE_MSG)
+@unittest.skipIf(os.name == "nt", "Unexplained failure on windows")
 class TestSuiteWarns(unittest.TestCase):
     """Tests for XMP, Exif UUIDs, issues warnings."""
 
@@ -90,7 +111,7 @@ class TestSuiteWarns(unittest.TestCase):
 
     def tearDown(self):
         pass
-
+        
     def test_unrecognized_exif_tag(self):
         """Verify warning in case of unrecognized tag."""
         with tempfile.NamedTemporaryFile(suffix='.jp2', mode='wb') as tfile:
@@ -114,7 +135,7 @@ class TestSuiteWarns(unittest.TestCase):
             tfile.flush()
 
             with self.assertWarnsRegex(UserWarning, 'Unrecognized Exif tag'):
-                glymur.Jp2k(tfile.name)
+                j = glymur.Jp2k(tfile.name)
 
     def test_bad_tag_datatype(self):
         """Only certain datatypes are allowable"""
@@ -170,3 +191,6 @@ class TestSuiteWarns(unittest.TestCase):
                 jp2 = glymur.Jp2k(tfile.name)
 
             self.assertEqual(jp2.box[-1].box_id, 'uuid')
+
+if __name__ == "__main__":
+    unittest.main()

glymur/test/test_jp2box_xml.py

@@ -2,12 +2,35 @@
 """
 Test suite specifically targeting JP2 box layout.
 """
+# E1103:  return value from read may be list or np array
+# pylint: disable=E1103
+
+# R0902:  More than 7 instance attributes are just fine for testing.
+# pylint: disable=R0902
+
+# R0904:  Seems like pylint is fooled in this situation
+# pylint: disable=R0904
+
+# W0613:  load_tests doesn't need to use ignore or loader arguments.
+# pylint: disable=W0613
+
 import os
 import re
 import struct
+import sys
 import tempfile
 import unittest
 
+if sys.hexversion < 0x03000000:
+    from StringIO import StringIO
+else:
+    from io import StringIO
+
+if sys.hexversion <= 0x03030000:
+    from mock import patch
+else:
+    from unittest.mock import patch
+
 import lxml.etree as ET
 
 import glymur
@@ -20,7 +43,6 @@ from .fixtures import OPJ_DATA_ROOT, opj_data_file
 from .fixtures import WARNING_INFRASTRUCTURE_ISSUE, WARNING_INFRASTRUCTURE_MSG
 from . import fixtures
 
-
 @unittest.skipIf(os.name == "nt", fixtures.WINDOWS_TMP_FILE_MSG)
 class TestXML(unittest.TestCase):
     """Test suite for XML boxes."""
@@ -145,6 +167,7 @@ class TestXML(unittest.TestCase):
                                  u'<country>Россия</country>')
 
 
+
 class TestJp2kBadXmlFile(unittest.TestCase):
     """Test suite for bad XML box situations"""
 
@@ -270,19 +293,22 @@ class TestXML_OpjDataRoot(unittest.TestCase):
                                               'nonregression',
                                               'issue171.jp2'))
         msg = 'An illegal BOM \(byte order marker\) was detected and removed '
-        msg += 'from the XML contents in the box starting at byte offset \d+'
+        msg += 'from the XML contents in the box starting at byte offset \d+' 
         with self.assertWarnsRegex(UserWarning, re.compile(msg)):
             jp2 = Jp2k(filename)
 
         self.assertIsNotNone(jp2.box[3].xml)
+            
 
     def test_invalid_utf8(self):
         """Bad byte sequence that cannot be parsed."""
-        relname = '26ccf3651020967f7778238ef5af08af.SIGFPE.d25.527.jp2'
         filename = opj_data_file(os.path.join('input',
                                               'nonregression',
-                                              relname))
+                                              '26ccf3651020967f7778238ef5af08af.SIGFPE.d25.527.jp2'))
         with self.assertWarns((UserWarning, UserWarning)):
             jp2 = Jp2k(filename)
 
         self.assertIsNone(jp2.box[3].box[1].box[1].xml)
+            
+
+

glymur/test/test_opj_suite.py

@@ -2,10 +2,34 @@
 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
 
@@ -13,14 +37,13 @@ import glymur
 from glymur import Jp2k
 from glymur.jp2box import FileTypeBox, ImageHeaderBox, ColourSpecificationBox
 
-from .fixtures import (OPJ_DATA_ROOT, MetadataBase,
+from .fixtures import (
-                       WARNING_INFRASTRUCTURE_ISSUE,
+        OPJ_DATA_ROOT, MetadataBase,
-                       WARNING_INFRASTRUCTURE_MSG,
+        WARNING_INFRASTRUCTURE_ISSUE, WARNING_INFRASTRUCTURE_MSG,
-                       mse, peak_tolerance, read_pgx, opj_data_file,
+        mse, peak_tolerance, read_pgx, opj_data_file
-                       OPENJPEG_NOT_AVAILABLE, OPENJPEG_NOT_AVAILABLE_MSG)
+)
 
 
-@unittest.skipIf(OPENJPEG_NOT_AVAILABLE, OPENJPEG_NOT_AVAILABLE_MSG)
 @unittest.skipIf(OPJ_DATA_ROOT is None,
                  "OPJ_DATA_ROOT environment variable not set")
 class TestSuite(unittest.TestCase):
@@ -34,7 +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[:]
+        jpdata = jp2k.read(rlevel=0)
 
         pgxfile = opj_data_file('baseline/conformance/c1p0_01_0.pgx')
         pgxdata = read_pgx(pgxfile)
@@ -44,7 +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[:]
+        jpdata = jp2k.read(rlevel=0)
 
         pgxfile = opj_data_file('baseline/conformance/c1p0_03_0.pgx')
         pgxdata = read_pgx(pgxfile)
@@ -54,7 +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[:]
+        jpdata = jp2k.read(rlevel=0)
 
         pgxfile = opj_data_file('baseline/conformance/c1p0_04_0.pgx')
         pgxdata = read_pgx(pgxfile)
@@ -74,7 +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[::2, ::2]
+        jpdata = jp2k.read(rlevel=1)
 
         pgxfile = opj_data_file('baseline/conformance/c1p0_08_0.pgx')
         pgxdata = read_pgx(pgxfile)
@@ -91,7 +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[:]
+        jpdata = jp2k.read(rlevel=0)
 
         pgxfile = opj_data_file('baseline/conformance/c1p0_09_0.pgx')
         pgxdata = read_pgx(pgxfile)
@@ -100,7 +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[:]
+        jpdata = jp2k.read(rlevel=0)
 
         pgxfile = opj_data_file('baseline/conformance/c1p0_11_0.pgx')
         pgxdata = read_pgx(pgxfile)
@@ -109,7 +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[:]
+        jpdata = jp2k.read(rlevel=0)
 
         pgxfile = opj_data_file('baseline/conformance/c1p0_14_0.pgx')
         pgxdata = read_pgx(pgxfile)
@@ -126,7 +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[:]
+        jpdata = jp2k.read(rlevel=0)
 
         pgxfile = opj_data_file('baseline/conformance/c1p0_15_0.pgx')
         pgxdata = read_pgx(pgxfile)
@@ -135,7 +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[:]
+        jpdata = jp2k.read(rlevel=0)
 
         pgxfile = opj_data_file('baseline/conformance/c1p0_16_0.pgx')
         pgxdata = read_pgx(pgxfile)
@@ -144,7 +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[:]
+        jpdata = jp2k.read(rlevel=0)
 
         pgxfile = opj_data_file('baseline/conformance/c1p1_01_0.pgx')
         pgxdata = read_pgx(pgxfile)
@@ -153,7 +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[:]
+        jpdata = jp2k.read(rlevel=0)
 
         pgxfile = opj_data_file('baseline/conformance/c1p1_02_0.pgx')
         pgxdata = read_pgx(pgxfile)
@@ -173,7 +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[:]
+        jpdata = jp2k.read()
 
         pgxfile = opj_data_file('baseline/conformance/c1p1_04_0.pgx')
         pgxdata = read_pgx(pgxfile)
@@ -183,95 +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[:]
+        jp2.read()
         self.assertTrue(True)
 
     def test_NR_DEC__00042_j2k_2_decode(self):
         jfile = opj_data_file('input/nonregression/_00042.j2k')
         jp2 = Jp2k(jfile)
-        jp2[:]
+        jp2.read()
         self.assertTrue(True)
 
     def test_NR_DEC_buxI_j2k_9_decode(self):
         jfile = opj_data_file('input/nonregression/buxI.j2k')
-        Jp2k(jfile)[:]
+        Jp2k(jfile).read()
         self.assertTrue(True)
 
     def test_NR_DEC_buxR_j2k_10_decode(self):
         jfile = opj_data_file('input/nonregression/buxR.j2k')
-        Jp2k(jfile)[:]
+        Jp2k(jfile).read()
         self.assertTrue(True)
 
     def test_NR_DEC_Cannotreaddatawithnosizeknown_j2k_11_decode(self):
         relpath = 'input/nonregression/Cannotreaddatawithnosizeknown.j2k'
         jfile = opj_data_file(relpath)
-        Jp2k(jfile)[:]
+        Jp2k(jfile).read()
         self.assertTrue(True)
 
     def test_NR_DEC_cthead1_j2k_12_decode(self):
         jfile = opj_data_file('input/nonregression/cthead1.j2k')
-        Jp2k(jfile)[:]
+        Jp2k(jfile).read()
         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)[:]
+        Jp2k(jfile).read()
         self.assertTrue(True)
 
     def test_NR_DEC_j2k32_j2k_15_decode(self):
         jfile = opj_data_file('input/nonregression/j2k32.j2k')
-        Jp2k(jfile)[:]
+        Jp2k(jfile).read()
         self.assertTrue(True)
 
     def test_NR_DEC_MarkerIsNotCompliant_j2k_17_decode(self):
         jfile = opj_data_file('input/nonregression/MarkerIsNotCompliant.j2k')
-        Jp2k(jfile)[:]
+        Jp2k(jfile).read()
         self.assertTrue(True)
 
     def test_NR_DEC_Marrin_jp2_18_decode(self):
         jfile = opj_data_file('input/nonregression/Marrin.jp2')
-        Jp2k(jfile)[:]
+        Jp2k(jfile).read()
         self.assertTrue(True)
 
     def test_NR_DEC_movie_00000_j2k_20_decode(self):
         jfile = opj_data_file('input/nonregression/movie_00000.j2k')
-        Jp2k(jfile)[:]
+        Jp2k(jfile).read()
         self.assertTrue(True)
 
     def test_NR_DEC_movie_00001_j2k_21_decode(self):
         jfile = opj_data_file('input/nonregression/movie_00001.j2k')
-        Jp2k(jfile)[:]
+        Jp2k(jfile).read()
         self.assertTrue(True)
 
     def test_NR_DEC_movie_00002_j2k_22_decode(self):
         jfile = opj_data_file('input/nonregression/movie_00002.j2k')
-        Jp2k(jfile)[:]
+        Jp2k(jfile).read()
         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)[:]
+        Jp2k(jfile).read()
         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)[:]
+        Jp2k(jfile).read()
         self.assertTrue(True)
 
     def test_NR_DEC_relax_jp2_27_decode(self):
         jfile = opj_data_file('input/nonregression/relax.jp2')
-        Jp2k(jfile)[:]
+        Jp2k(jfile).read()
         self.assertTrue(True)
 
     def test_NR_DEC_test_lossless_j2k_28_decode(self):
         jfile = opj_data_file('input/nonregression/test_lossless.j2k')
-        Jp2k(jfile)[:]
+        Jp2k(jfile).read()
         self.assertTrue(True)
 
     def test_NR_DEC_pacs_ge_j2k_30_decode(self):
         jfile = opj_data_file('input/nonregression/pacs.ge.j2k')
-        Jp2k(jfile)[:]
+        Jp2k(jfile).read()
         self.assertTrue(True)
 
 
@@ -294,14 +317,14 @@ class TestSuiteWarns(MetadataBase):
         with self.assertWarns(UserWarning):
             # Bad compatibility list item.
             jp2k = Jp2k(jfile)
-        jpdata = jp2k[:]
+        jpdata = jp2k.read()
         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[:]
+        jpdata = jp2k.read()
         self.assertEqual(jpdata.shape, (640, 480, 3))
 
     @unittest.skipIf(glymur.version.openjpeg_version_tuple[0] < 2,
@@ -319,7 +342,7 @@ class TestSuiteWarns(MetadataBase):
         jfile = opj_data_file('input/conformance/file4.jp2')
         with self.assertWarns(UserWarning):
             jp2k = Jp2k(jfile)
-        jpdata = jp2k[:]
+        jpdata = jp2k.read()
         self.assertEqual(jpdata.shape, (512, 768))
 
     def test_ETS_JP2_file5(self):
@@ -328,45 +351,42 @@ class TestSuiteWarns(MetadataBase):
             # There's a warning for an unknown compatibility entry.
             # Ignore it here.
             jp2k = Jp2k(jfile)
-        jpdata = jp2k[:]
+        jpdata = jp2k.read()
         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[:]
+        jpdata = jp2k.read()
         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[:]
+        jpdata = jp2k.read()
         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[:]
+        jpdata = jp2k.read()
         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[:]
+        jpdata = jp2k.read()
         self.assertEqual(jpdata.shape, (512, 768, 3))
 
-    def test_NR_broken1_jp2_dump(self):
+    def test_NR_broken_jp2_dump(self):
-        jfile = opj_data_file('input/nonregression/broken1.jp2')
+        jfile = opj_data_file('input/nonregression/broken.jp2')
 
-        # The colr box has a ridiculously incorrect box length.
+        with self.assertWarns(UserWarning):
-        regex = re.compile(r'''b'colr'\sbox\shas\sincorrect\sbox\slength\s
+            # colr box has bad length.
-                               \(\d+\)''',
-                           re.VERBOSE)
-        with self.assertWarnsRegex(UserWarning, regex):
             jp2 = Jp2k(jfile)
 
         ids = [box.box_id for box in jp2.box]
@@ -385,24 +405,23 @@ class TestSuiteWarns(MetadataBase):
         expected = ColourSpecificationBox(colorspace=glymur.core.SRGB)
         self.verifyColourSpecificationBox(jp2.box[2].box[1], expected)
 
-        c = jp2.box[3].codestream
+        c = jp2.box[3].main_header
 
         ids = [x.marker_id for x in c.segment]
         expected = ['SOC', 'SIZ', 'CME', 'COD', 'QCD', 'QCC', 'QCC']
         self.assertEqual(ids, expected)
 
         kwargs = {'rsiz': 0, 'xysiz': (203, 152), 'xyosiz': (0, 0),
-                  'xytsiz': (203, 152), 'xytosiz': (0, 0),
+                'xytsiz': (203, 152), 'xytosiz': (0, 0), 'bitdepth': (8, 8, 8),
-                  'bitdepth': (8, 8, 8),
+                'signed': (False, False, False),
-                  'signed': (False, False, False),
+                'xyrsiz': [(1, 1, 1), (1, 1, 1)]}
-                  'xyrsiz': [(1, 1, 1), (1, 1, 1)]}
         self.verifySizSegment(c.segment[1],
-                              glymur.codestream.SIZsegment(**kwargs))
+                glymur.codestream.SIZsegment(**kwargs))
 
         pargs = (glymur.core.RCME_ISO_8859_1,
-                 "Creator: JasPer Version 1.701.0".encode())
+                "Creator: JasPer Version 1.701.0".encode())
         self.verifyCMEsegment(c.segment[2],
-                              glymur.codestream.CMEsegment(*pargs))
+                glymur.codestream.CMEsegment(*pargs))
 
         # COD: Coding style default
         self.assertFalse(c.segment[3].scod & 2)  # no sop
@@ -414,7 +433,7 @@ class TestSuiteWarns(MetadataBase):
         self.assertEqual(tuple(c.segment[3].code_block_size),
                          (64, 64))  # cblk
         self.verify_codeblock_style(c.segment[3].spcod[7],
-                                    [False, False, False, False, False, False])
+                [False, False, False, False, False, False])
         self.assertEqual(c.segment[3].spcod[8],
                          glymur.core.WAVELET_XFORM_5X3_REVERSIBLE)
         self.assertEqual(len(c.segment[3].spcod), 9)
@@ -450,19 +469,19 @@ 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)[:]
+            Jp2k(jfile).read()
         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)[:]
+            Jp2k(jfile).read()
         self.assertTrue(True)
 
 
 @unittest.skipIf(OPJ_DATA_ROOT is None,
                  "OPJ_DATA_ROOT environment variable not set")
-@unittest.skipIf(glymur.version.openjpeg_version_tuple[0] != 2,
+@unittest.skipIf(glymur.version.openjpeg_version_tuple[0] == 1,
                  "Feature not supported in glymur until openjpeg 2.0")
 class TestSuiteBands(unittest.TestCase):
     """
@@ -557,7 +576,7 @@ class TestSuiteBands(unittest.TestCase):
 
 @unittest.skipIf(OPJ_DATA_ROOT is None,
                  "OPJ_DATA_ROOT environment variable not set")
-@unittest.skipIf(glymur.version.openjpeg_version_tuple[0] < 2,
+@unittest.skipIf(glymur.version.openjpeg_version_tuple[0] == 1,
                  "Tests not passing until 2.0")
 class TestSuite2point0(unittest.TestCase):
     """Runs tests introduced in version 2.0 or that pass only in 2.0"""
@@ -571,7 +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[:]
+        jpdata = jp2k.read(rlevel=0)
 
         pgxfile = opj_data_file('baseline/conformance/c1p0_10_0.pgx')
         pgxdata = read_pgx(pgxfile)
@@ -587,16 +606,13 @@ class TestSuite2point0(unittest.TestCase):
 
     @unittest.skipIf(WARNING_INFRASTRUCTURE_ISSUE, WARNING_INFRASTRUCTURE_MSG)
     def test_NR_DEC_broken2_jp2_5_decode(self):
-        """
+        # Null pointer access
-        Invalid marker ID on codestream, Null pointer access upon read.
-        """
         jfile = opj_data_file('input/nonregression/broken2.jp2')
-        regex = re.compile(r'''Invalid\smarker\sid\sencountered\sat\sbyte\s
-                               \d+\sin\scodestream:\s*"0x[a-fA-F0-9]{4}"''',
-                           re.VERBOSE)
         with self.assertRaises(IOError):
-            with self.assertWarnsRegex(UserWarning, regex):
+            with self.assertWarns(UserWarning):
-                Jp2k(jfile)[:]
+                # Invalid marker ID.
+                Jp2k(jfile).read()
+        self.assertTrue(True)
 
     @unittest.skipIf(WARNING_INFRASTRUCTURE_ISSUE, WARNING_INFRASTRUCTURE_MSG)
     def test_NR_DEC_broken4_jp2_7_decode(self):
@@ -604,7 +620,7 @@ class TestSuite2point0(unittest.TestCase):
         with self.assertRaises(IOError):
             with self.assertWarns(UserWarning):
                 # invalid number of subbands, bad marker ID
-                Jp2k(jfile)[:]
+                Jp2k(jfile).read()
         self.assertTrue(True)
 
     @unittest.skipIf(WARNING_INFRASTRUCTURE_ISSUE, WARNING_INFRASTRUCTURE_MSG)
@@ -616,344 +632,11 @@ class TestSuite2point0(unittest.TestCase):
         if glymur.version.openjpeg_version_tuple[0] < 2:
             with self.assertWarns(UserWarning):
                 # Incorrect warning issued about tile parts.
-                Jp2k(jfile)[:]
+                Jp2k(jfile).read()
         else:
-            Jp2k(jfile)[:]
+            Jp2k(jfile).read()
         self.assertTrue(True)
 
 
-@unittest.skipIf(OPJ_DATA_ROOT is None,
+if __name__ == "__main__":
-                 "OPJ_DATA_ROOT environment variable not set")
+    unittest.main()
-@unittest.skipIf(re.match(r'''0|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])
-
-    @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
-        """
-        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])
-
-    @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
-        """
-        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'''0|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)

glymur/test/test_opj_suite_2p1.py

@@ -0,0 +1,342 @@
+"""
+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 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 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.read()
+        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()
+        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)
+        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()
+        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()
+        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.read()
+
+    @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.read()
+
+    @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).read()
+
+    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()
+
+    def test_NR_DEC_issue206_image_000_jp2_42_decode(self):
+        jfile = opj_data_file('input/nonregression/issue206_image-000.jp2')
+        Jp2k(jfile).read()
+        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()
+        np.testing.assert_array_equal(tdata, odata[896:1024, 896:1024])
+
+    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
+        odata = jp2k.read(rlevel=2)
+        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
+        odata = jp2k.read()
+        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
+        odata = jp2k.read(rlevel=1)
+        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.read()
+
+@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.read()
+        self.j2k_half_data = self.j2k.read(rlevel=1)
+        self.j2k_quarter_data = self.j2k.read(rlevel=2)
+
+        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))
+        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))
+        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))
+        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))
+        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))
+        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))
+        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))
+        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)
+        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)
+        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)
+        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)
+        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)
+        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)
+        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)
+        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)
+        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)
+        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)
+        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)
+        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)
+        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)
+
+    def test_NR_DEC_p0_04_j2k_85_decode(self):
+        actual = self.j2k.read(area=(0, 0, 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))
+        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))
+        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))
+        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))
+        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))
+        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)
+        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)
+        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)
+        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)
+        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)
+        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)
+        expected = self.j2k_quarter_data[5:13, 38:50]
+        np.testing.assert_array_equal(actual, expected)

glymur/test/test_opj_suite_neg.py

@@ -2,8 +2,15 @@
 The tests here do not correspond directly to the OpenJPEG test suite, but
 seem like logical negative tests to add.
 """
+# E1101:  assertWarns introduced in python 3.2
+# pylint: disable=E1101
+
+# R0904:  Not too many methods in unittest.
+# pylint: disable=R0904
+
 import os
 import re
+import sys
 import tempfile
 import unittest
 
@@ -17,7 +24,6 @@ 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
@@ -25,7 +31,7 @@ import glymur
 
 @unittest.skipIf(OPJ_DATA_ROOT is None,
                  "OPJ_OPJ_DATA_ROOT environment variable not set")
-class TestSuiteNegativeRead(unittest.TestCase):
+class TestSuiteNegative(unittest.TestCase):
     """Test suite for certain negative tests from openjpeg suite."""
 
     def setUp(self):
@@ -35,6 +41,33 @@ class TestSuiteNegativeRead(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'
@@ -65,80 +98,56 @@ class TestSuiteNegativeRead(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:
-            with self.assertRaises(IOError):
-                Jp2k(tfile.name, data=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:
-            with self.assertRaises(IOError):
-                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"""
         # opj_compress doesn't allow the dimensions of a codeblock
         # 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):
-                Jp2k(tfile.name, data=data, cbsize=(256, 256))
+                j.write(data, cbsize=(256, 256))
 
             # opj_compress doesn't allow either dimension to be less than 4.
             with self.assertRaises(IOError):
-                Jp2k(tfile.name, data=data, cbsize=(2048, 2))
+                j.write(data, cbsize=(2048, 2))
             with self.assertRaises(IOError):
-                Jp2k(tfile.name, data=data, cbsize=(2, 2048))
+                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)
-        data = ifile[::4, ::4]
+        data = ifile.read(rlevel=2)
         with tempfile.NamedTemporaryFile(suffix='.jp2') as tfile:
+            ofile = Jp2k(tfile.name, 'wb')
             with self.assertRaises(IOError):
-                Jp2k(tfile.name, data=data, psizes=[(13, 13)])
+                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)
-        data = ifile[::4, ::4]
+        data = ifile.read(rlevel=2)
         with tempfile.NamedTemporaryFile(suffix='.jp2') as tfile:
+            ofile = Jp2k(tfile.name, 'wb')
             with self.assertRaises(IOError):
-                Jp2k(tfile.name, data=data, cbsize=(13, 12))
+                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)
-        data = ifile[::4, ::4]
+        data = ifile.read(rlevel=2)
         with tempfile.NamedTemporaryFile(suffix='.jp2') as tfile:
+            ofile = Jp2k(tfile.name, 'wb')
             with self.assertRaises(IOError):
-                Jp2k(tfile.name, data=data, cbsize=(64, 64), psizes=[(64, 64)])
+                ofile.write(data,
+                            cbsize=(64, 64),
+                            psizes=[(64, 64)])
+
+if __name__ == "__main__":
+    unittest.main()

glymur/test/test_opj_suite_write.py

@@ -2,17 +2,16 @@
 The tests defined here roughly correspond to what is in the OpenJPEG test
 suite.
 """
+# C0103:  method names longer that 30 chars are ok in tests, IMHO
+# R0904:  Seems like pylint is fooled in this situation
+# pylint: disable=R0904,C0103
+
 import os
 import re
 import sys
 import tempfile
 import unittest
 
-if sys.hexversion <= 0x03030000:
-    from mock import patch
-else:
-    from unittest.mock import patch
-
 import numpy as np
 try:
     import skimage.io
@@ -30,7 +29,6 @@ from glymur import Jp2k
 from glymur.codestream import SIZsegment
 from glymur.version import openjpeg_version
 
-
 class CinemaBase(fixtures.MetadataBase):
 
     def verify_cinema_cod(self, cod_segment):
@@ -41,14 +39,14 @@ class CinemaBase(fixtures.MetadataBase):
         self.assertEqual(cod_segment.layers, 1)
         self.assertEqual(cod_segment.spcod[3], 1)  # mct
         self.assertEqual(cod_segment.spcod[4], 5)  # levels
-        self.assertEqual(tuple(cod_segment.code_block_size), (32, 32))
+        self.assertEqual(tuple(cod_segment.code_block_size), (32, 32))  # cblksz
 
     def check_cinema4k_codestream(self, codestream, image_size):
 
         kwargs = {'rsiz': 4, 'xysiz': image_size, 'xyosiz': (0, 0),
-                  'xytsiz': image_size, 'xytosiz': (0, 0),
+                'xytsiz': image_size, 'xytosiz': (0, 0),
-                  'bitdepth': (12, 12, 12), 'signed': (False, False, False),
+                'bitdepth': (12, 12, 12), 'signed': (False, False, False),
-                  'xyrsiz': [(1, 1, 1), (1, 1, 1)]}
+                'xyrsiz': [(1, 1, 1), (1, 1, 1)]}
         self.verifySizSegment(codestream.segment[1], SIZsegment(**kwargs))
 
         self.verify_cinema_cod(codestream.segment[2])
@@ -56,9 +54,9 @@ class CinemaBase(fixtures.MetadataBase):
     def check_cinema2k_codestream(self, codestream, image_size):
 
         kwargs = {'rsiz': 3, 'xysiz': image_size, 'xyosiz': (0, 0),
-                  'xytsiz': image_size, 'xytosiz': (0, 0),
+                'xytsiz': image_size, 'xytosiz': (0, 0),
-                  'bitdepth': (12, 12, 12), 'signed': (False, False, False),
+                'bitdepth': (12, 12, 12), 'signed': (False, False, False),
-                  'xyrsiz': [(1, 1, 1), (1, 1, 1)]}
+                'xyrsiz': [(1, 1, 1), (1, 1, 1)]}
         self.verifySizSegment(codestream.segment[1], SIZsegment(**kwargs))
 
         self.verify_cinema_cod(codestream.segment[2])
@@ -84,9 +82,9 @@ 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):
-                Jp2k(tfile.name, data=data,
+                j.write(data, cinema2k=48, cratios=[200, 100, 50])
-                     cinema2k=48, cratios=[200, 100, 50])
 
     def test_cinema4K_with_others(self):
         """Can't specify cinema4k with any other options."""
@@ -94,9 +92,9 @@ 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):
-                Jp2k(tfile.name, data=data,
+                j.write(data, cinema4k=True, cratios=[200, 100, 50])
-                     cinema4k=True, cratios=[200, 100, 50])
 
 
 @unittest.skipIf(WARNING_INFRASTRUCTURE_ISSUE, WARNING_INFRASTRUCTURE_MSG)
@@ -120,9 +118,10 @@ 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')
             regex = 'OpenJPEG library warning:.*'
             with self.assertWarnsRegex(UserWarning, re.compile(regex)):
-                j = Jp2k(tfile.name, data=data, cinema4k=True)
+                j.write(data, cinema4k=True)
 
             codestream = j.get_codestream()
             self.check_cinema4k_codestream(codestream, (4096, 2160))
@@ -132,9 +131,9 @@ class WriteCinemaWarns(CinemaBase):
         infile = opj_data_file(relfile)
         data = skimage.io.imread(infile)
         with tempfile.NamedTemporaryFile(suffix='.j2k') as tfile:
-            with self.assertWarnsRegex(UserWarning,
+            j = Jp2k(tfile.name, 'wb')
-                                       'OpenJPEG library warning'):
+            with self.assertWarnsRegex(UserWarning, 'OpenJPEG library warning'):
-                j = Jp2k(tfile.name, data=data, cinema2k=48)
+                j.write(data, cinema2k=48)
 
             codestream = j.get_codestream()
             self.check_cinema2k_codestream(codestream, (2048, 857))
@@ -144,9 +143,9 @@ class WriteCinemaWarns(CinemaBase):
         infile = opj_data_file(relfile)
         data = skimage.io.imread(infile)
         with tempfile.NamedTemporaryFile(suffix='.j2k') as tfile:
-            with self.assertWarnsRegex(UserWarning,
+            j = Jp2k(tfile.name, 'wb')
-                                       'OpenJPEG library warning'):
+            with self.assertWarnsRegex(UserWarning, 'OpenJPEG library warning'):
-                j = Jp2k(tfile.name, data=data, cinema2k=48)
+                j.write(data, cinema2k=48)
 
             codestream = j.get_codestream()
             self.check_cinema2k_codestream(codestream, (2048, 1080))
@@ -156,9 +155,9 @@ class WriteCinemaWarns(CinemaBase):
         infile = opj_data_file(relfile)
         data = skimage.io.imread(infile)
         with tempfile.NamedTemporaryFile(suffix='.j2k') as tfile:
-            with self.assertWarnsRegex(UserWarning,
+            j = Jp2k(tfile.name, 'wb')
-                                       'OpenJPEG library warning'):
+            with self.assertWarnsRegex(UserWarning, 'OpenJPEG library warning'):
-                j = Jp2k(tfile.name, data=data, cinema2k=24)
+                j.write(data, cinema2k=24)
 
             codestream = j.get_codestream()
             self.check_cinema2k_codestream(codestream, (2048, 1080))
@@ -168,11 +167,11 @@ class WriteCinemaWarns(CinemaBase):
         infile = opj_data_file(relfile)
         data = skimage.io.imread(infile)
         with tempfile.NamedTemporaryFile(suffix='.j2k') as tfile:
-            with self.assertWarnsRegex(UserWarning,
+            j = Jp2k(tfile.name, 'wb')
-                                       'OpenJPEG library warning'):
+            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 = Jp2k(tfile.name, data=data, cinema2k=24)
+                j.write(data, cinema2k=24)
 
             codestream = j.get_codestream()
             self.check_cinema2k_codestream(codestream, (2048, 857))
@@ -182,11 +181,12 @@ 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 = Jp2k(tfile.name, data=data, cinema2k=48)
+                j.write(data, cinema2k=48)
 
             codestream = j.get_codestream()
             self.check_cinema2k_codestream(codestream, (1998, 1080))
@@ -195,10 +195,12 @@ class WriteCinemaWarns(CinemaBase):
 @unittest.skipIf(NO_SKIMAGE_FREEIMAGE_SUPPORT,
                  "Cannot read input image without scikit-image/freeimage")
 @unittest.skipIf(os.name == "nt", fixtures.WINDOWS_TMP_FILE_MSG)
+@unittest.skipIf(not re.match("(1.5|2.0.0)", glymur.version.openjpeg_version),
+                 "Functionality implemented for 2.0.1")
 @unittest.skipIf(OPJ_DATA_ROOT is None,
                  "OPJ_OPJ_DATA_ROOT environment variable not set")
-class TestNegative2pointzero(unittest.TestCase):
+class TestSuiteNegative2pointzero(unittest.TestCase):
-    """Feature set not supported for versions less than 2.0.1"""
+    """Feature set not supported for versions less than 2.0"""
 
     def setUp(self):
         self.jp2file = glymur.data.nemo()
@@ -208,16 +210,13 @@ class TestNegative2pointzero(unittest.TestCase):
         pass
 
     def test_cinema_mode(self):
-        """Cinema mode not allowed for anything less than 2.0.1"""
         relfile = 'input/nonregression/X_4_2K_24_185_CBR_WB_000.tif'
         infile = opj_data_file(relfile)
         data = skimage.io.imread(infile)
-        versions = ["1.5.0", "2.0.0"]
+        with tempfile.NamedTemporaryFile(suffix='.j2k') as tfile:
-        for version in versions:
+            j = Jp2k(tfile.name, 'wb')
-            with patch('glymur.version.openjpeg_version', new=version):
+            with self.assertRaises(IOError):
-                with tempfile.NamedTemporaryFile(suffix='.j2k') as tfile:
+                j.write(data, cinema2k=48)
-                    with self.assertRaises(IOError):
-                        Jp2k(tfile.name, data=data, cinema2k=48)
 
 
 @unittest.skipIf(re.match(r'''1.[0-4]''', openjpeg_version) is not None,
@@ -243,28 +242,30 @@ 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, data=expdata, irreversible=True)
+            j = Jp2k(tfile.name, 'wb')
+            j.write(expdata, irreversible=True)
 
             codestream = j.get_codestream()
             self.assertEqual(codestream.segment[2].spcod[8],
                              glymur.core.WAVELET_XFORM_9X7_IRREVERSIBLE)
 
+
     def test_NR_ENC_Bretagne1_ppm_1_encode(self):
         """NR-ENC-Bretagne1.ppm-1-encode"""
         infile = opj_data_file('input/nonregression/Bretagne1.ppm')
         data = read_image(infile)
         with tempfile.NamedTemporaryFile(suffix='.j2k') as tfile:
-            j = Jp2k(tfile.name, data=data, cratios=[200, 100, 50])
+            j = Jp2k(tfile.name, 'wb')
+            j.write(data, cratios=[200, 100, 50])
 
             # Should be three layers.
             c = j.get_codestream()
 
         kwargs = {'rsiz': 0, 'xysiz': (640, 480), 'xyosiz': (0, 0),
-                  'xytsiz': (640, 480), 'xytosiz': (0, 0),
+                'xytsiz': (640, 480), 'xytosiz': (0, 0),
-                  'bitdepth': (8, 8, 8), 'signed': (False, False, False),
+                'bitdepth': (8, 8, 8), 'signed': (False, False, False),
-                  'xyrsiz': [(1, 1, 1), (1, 1, 1)]}
+                'xyrsiz': [(1, 1, 1), (1, 1, 1)]}
-        self.verifySizSegment(c.segment[1],
+        self.verifySizSegment(c.segment[1], glymur.codestream.SIZsegment(**kwargs))
-                              glymur.codestream.SIZsegment(**kwargs))
 
         # COD: Coding style default
         self.assertFalse(c.segment[2].scod & 2)  # no sop
@@ -276,7 +277,7 @@ class TestSuiteWrite(fixtures.MetadataBase):
         self.assertEqual(tuple(c.segment[2].code_block_size),
                          (64, 64))  # cblksz
         self.verify_codeblock_style(c.segment[2].spcod[7],
-                                    [False, False, False, False, False, False])
+                [False, False, False, False, False, False])
         self.assertEqual(c.segment[2].spcod[8],
                          glymur.core.WAVELET_XFORM_5X3_REVERSIBLE)
         self.assertEqual(len(c.segment[2].spcod), 9)
@@ -286,17 +287,17 @@ 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, data=data, psnr=[30, 35, 40], numres=2)
+            j = Jp2k(tfile.name, 'wb')
+            j.write(data, psnr=[30, 35, 40], numres=2)
 
             # Should be three layers.
             codestream = j.get_codestream()
 
             kwargs = {'rsiz': 0, 'xysiz': (640, 480), 'xyosiz': (0, 0),
-                      'xytsiz': (640, 480), 'xytosiz': (0, 0),
+                    'xytsiz': (640, 480), 'xytosiz': (0, 0),
-                      'bitdepth': (8, 8, 8), 'signed': (False, False, False),
+                    'bitdepth': (8, 8, 8), 'signed': (False, False, False),
-                      'xyrsiz': [(1, 1, 1), (1, 1, 1)]}
+                    'xyrsiz': [(1, 1, 1), (1, 1, 1)]}
-            self.verifySizSegment(codestream.segment[1],
+            self.verifySizSegment(codestream.segment[1], glymur.codestream.SIZsegment(**kwargs))
-                                  glymur.codestream.SIZsegment(**kwargs))
 
             # COD: Coding style default
             self.assertFalse(codestream.segment[2].scod & 2)  # no sop
@@ -308,8 +309,7 @@ class TestSuiteWrite(fixtures.MetadataBase):
             self.assertEqual(tuple(codestream.segment[2].code_block_size),
                              (64, 64))  # cblksz
             self.verify_codeblock_style(codestream.segment[2].spcod[7],
-                                        [False, False,
+                    [False, False, False, False, False, False])
-                                         False, False, False, False])
             self.assertEqual(codestream.segment[2].spcod[8],
                              glymur.core.WAVELET_XFORM_5X3_REVERSIBLE)
             self.assertEqual(len(codestream.segment[2].spcod), 9)
@@ -319,19 +319,18 @@ 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,
+            j = Jp2k(tfile.name, 'wb')
-                     data=data,
+            j.write(data, psnr=[30, 35, 40], cbsize=(16, 16),
-                     psnr=[30, 35, 40], cbsize=(16, 16), psizes=[(64, 64)])
+                    psizes=[(64, 64)])
 
             # Should be three layers.
             codestream = j.get_codestream()
 
             kwargs = {'rsiz': 0, 'xysiz': (640, 480), 'xyosiz': (0, 0),
-                      'xytsiz': (640, 480), 'xytosiz': (0, 0),
+                    'xytsiz': (640, 480), 'xytosiz': (0, 0),
-                      'bitdepth': (8, 8, 8), 'signed': (False, False, False),
+                    'bitdepth': (8, 8, 8), 'signed': (False, False, False),
-                      'xyrsiz': [(1, 1, 1), (1, 1, 1)]}
+                    'xyrsiz': [(1, 1, 1), (1, 1, 1)]}
-            self.verifySizSegment(codestream.segment[1],
+            self.verifySizSegment(codestream.segment[1], glymur.codestream.SIZsegment(**kwargs))
-                                  glymur.codestream.SIZsegment(**kwargs))
 
             # COD: Coding style default
             self.assertFalse(codestream.segment[2].scod & 2)  # no sop
@@ -343,8 +342,7 @@ class TestSuiteWrite(fixtures.MetadataBase):
             self.assertEqual(tuple(codestream.segment[2].code_block_size),
                              (16, 16))  # cblksz
             self.verify_codeblock_style(codestream.segment[2].spcod[7],
-                                        [False, False,
+                    [False, False, False, False, False, False])
-                                         False, False, False, False])
             self.assertEqual(codestream.segment[2].spcod[8],
                              glymur.core.WAVELET_XFORM_5X3_REVERSIBLE)
             self.assertEqual(codestream.segment[2].precinct_size,
@@ -356,22 +354,21 @@ 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,
+            j = Jp2k(tfile.name, 'wb')
-                     data=data,
+            j.write(data,
-                     psizes=[(128, 128)] * 3,
+                    psizes=[(128, 128)] * 3,
-                     cratios=[100, 20, 2],
+                    cratios=[100, 20, 2],
-                     tilesize=(480, 640),
+                    tilesize=(480, 640),
-                     cbsize=(32, 32))
+                    cbsize=(32, 32))
 
             # Should be three layers.
             codestream = j.get_codestream()
 
             kwargs = {'rsiz': 0, 'xysiz': (2592, 1944), 'xyosiz': (0, 0),
-                      'xytsiz': (640, 480), 'xytosiz': (0, 0),
+                    'xytsiz': (640, 480), 'xytosiz': (0, 0),
-                      'bitdepth': (8, 8, 8), 'signed': (False, False, False),
+                    'bitdepth': (8, 8, 8), 'signed': (False, False, False),
-                      'xyrsiz': [(1, 1, 1), (1, 1, 1)]}
+                    'xyrsiz': [(1, 1, 1), (1, 1, 1)]}
-            self.verifySizSegment(codestream.segment[1],
+            self.verifySizSegment(codestream.segment[1], glymur.codestream.SIZsegment(**kwargs))
-                                  glymur.codestream.SIZsegment(**kwargs))
 
             # COD: Coding style default
             self.assertFalse(codestream.segment[2].scod & 2)  # no sop
@@ -383,8 +380,7 @@ class TestSuiteWrite(fixtures.MetadataBase):
             self.assertEqual(tuple(codestream.segment[2].code_block_size),
                              (32, 32))  # cblksz
             self.verify_codeblock_style(codestream.segment[2].spcod[7],
-                                        [False, False,
+                    [False, False, False, False, False, False])
-                                         False, False, False, False])
             self.assertEqual(codestream.segment[2].spcod[8],
                              glymur.core.WAVELET_XFORM_5X3_REVERSIBLE)
             self.assertEqual(codestream.segment[2].precinct_size,
@@ -395,16 +391,16 @@ 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, data=data, tilesize=(127, 127), prog="PCRL")
+            j = Jp2k(tfile.name, 'wb')
+            j.write(data, tilesize=(127, 127), prog="PCRL")
 
             codestream = j.get_codestream()
 
             kwargs = {'rsiz': 0, 'xysiz': (2592, 1944), 'xyosiz': (0, 0),
-                      'xytsiz': (127, 127), 'xytosiz': (0, 0),
+                    'xytsiz': (127, 127), 'xytosiz': (0, 0),
-                      'bitdepth': (8, 8, 8), 'signed': (False, False, False),
+                    'bitdepth': (8, 8, 8), 'signed': (False, False, False),
-                      'xyrsiz': [(1, 1, 1), (1, 1, 1)]}
+                    'xyrsiz': [(1, 1, 1), (1, 1, 1)]}
-            self.verifySizSegment(codestream.segment[1],
+            self.verifySizSegment(codestream.segment[1], glymur.codestream.SIZsegment(**kwargs))
-                                  glymur.codestream.SIZsegment(**kwargs))
 
             # COD: Coding style default
             self.assertFalse(codestream.segment[2].scod & 2)  # no sop
@@ -416,8 +412,7 @@ class TestSuiteWrite(fixtures.MetadataBase):
             self.assertEqual(tuple(codestream.segment[2].code_block_size),
                              (64, 64))  # cblksz
             self.verify_codeblock_style(codestream.segment[2].spcod[7],
-                                        [False, False,
+                    [False, False, False, False, False, False])
-                                         False, False, False, False])
             self.assertEqual(codestream.segment[2].spcod[8],
                              glymur.core.WAVELET_XFORM_5X3_REVERSIBLE)
             self.assertEqual(len(codestream.segment[2].spcod), 9)
@@ -427,16 +422,16 @@ 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, data=data, subsam=(2, 2), sop=True)
+            j = Jp2k(tfile.name, 'wb')
+            j.write(data, subsam=(2, 2), sop=True)
 
             codestream = j.get_codestream(header_only=False)
 
             kwargs = {'rsiz': 0, 'xysiz': (5183, 3887), 'xyosiz': (0, 0),
-                      'xytsiz': (5183, 3887), 'xytosiz': (0, 0),
+                    'xytsiz': (5183, 3887), 'xytosiz': (0, 0),
-                      'bitdepth': (8, 8, 8), 'signed': (False, False, False),
+                    'bitdepth': (8, 8, 8), 'signed': (False, False, False),
-                      'xyrsiz': [(2, 2, 2), (2, 2, 2)]}
+                    'xyrsiz': [(2, 2, 2), (2, 2, 2)]}
-            self.verifySizSegment(codestream.segment[1],
+            self.verifySizSegment(codestream.segment[1], glymur.codestream.SIZsegment(**kwargs))
-                                  glymur.codestream.SIZsegment(**kwargs))
 
             # COD: Coding style default
             self.assertTrue(codestream.segment[2].scod & 2)  # sop
@@ -448,8 +443,7 @@ class TestSuiteWrite(fixtures.MetadataBase):
             self.assertEqual(tuple(codestream.segment[2].code_block_size),
                              (64, 64))  # cblksz
             self.verify_codeblock_style(codestream.segment[2].spcod[7],
-                                        [False, False, False,
+                    [False, False, False, False, False, False])
-                                         False, False, False])
             self.assertEqual(codestream.segment[2].spcod[8],
                              glymur.core.WAVELET_XFORM_5X3_REVERSIBLE)
             self.assertEqual(len(codestream.segment[2].spcod), 9)
@@ -464,16 +458,16 @@ 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, data=data, modesw=38, eph=True)
+            j = Jp2k(tfile.name, 'wb')
+            j.write(data, modesw=38, eph=True)
 
             codestream = j.get_codestream(header_only=False)
 
             kwargs = {'rsiz': 0, 'xysiz': (2592, 1944), 'xyosiz': (0, 0),
-                      'xytsiz': (2592, 1944), 'xytosiz': (0, 0),
+                    'xytsiz': (2592, 1944), 'xytosiz': (0, 0),
-                      'bitdepth': (8, 8, 8), 'signed': (False, False, False),
+                    'bitdepth': (8, 8, 8), 'signed': (False, False, False),
-                      'xyrsiz': [(1, 1, 1), (1, 1, 1)]}
+                    'xyrsiz': [(1, 1, 1), (1, 1, 1)]}
-            self.verifySizSegment(codestream.segment[1],
+            self.verifySizSegment(codestream.segment[1], glymur.codestream.SIZsegment(**kwargs))
-                                  glymur.codestream.SIZsegment(**kwargs))
 
             # COD: Coding style default
             self.assertFalse(codestream.segment[2].scod & 2)  # no sop
@@ -483,10 +477,9 @@ class TestSuiteWrite(fixtures.MetadataBase):
             self.assertEqual(codestream.segment[2].spcod[3], 1)  # mct
             self.assertEqual(codestream.segment[2].spcod[4], 5)  # levels
             self.assertEqual(tuple(codestream.segment[2].code_block_size),
-                             (64, 64))  # cblksz
+                            (64, 64))  # cblksz
             self.verify_codeblock_style(codestream.segment[2].spcod[7],
-                                        [False, True, True,
+                    [False, True, True, False, False, True])
-                                         False, False, True])
             self.assertEqual(codestream.segment[2].spcod[8],
                              glymur.core.WAVELET_XFORM_5X3_REVERSIBLE)
             self.assertEqual(len(codestream.segment[2].spcod), 9)
@@ -500,17 +493,16 @@ 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,
+            j = Jp2k(tfile.name, 'wb')
-                     data=data, grid_offset=[300, 150], cratios=[800])
+            j.write(data, grid_offset=[300, 150], cratios=[800])
 
             codestream = j.get_codestream(header_only=False)
 
             kwargs = {'rsiz': 0, 'xysiz': (2742, 2244), 'xyosiz': (150, 300),
-                      'xytsiz': (2742, 2244), 'xytosiz': (0, 0),
+                    'xytsiz': (2742, 2244), 'xytosiz': (0, 0),
-                      'bitdepth': (8, 8, 8), 'signed': (False, False, False),
+                    'bitdepth': (8, 8, 8), 'signed': (False, False, False),
-                      'xyrsiz': [(1, 1, 1), (1, 1, 1)]}
+                    'xyrsiz': [(1, 1, 1), (1, 1, 1)]}
-            self.verifySizSegment(codestream.segment[1],
+            self.verifySizSegment(codestream.segment[1], glymur.codestream.SIZsegment(**kwargs))
-                                  glymur.codestream.SIZsegment(**kwargs))
 
             # COD: Coding style default
             self.assertFalse(codestream.segment[2].scod & 2)  # no sop
@@ -522,8 +514,7 @@ class TestSuiteWrite(fixtures.MetadataBase):
             self.assertEqual(tuple(codestream.segment[2].code_block_size),
                              (64, 64))  # cblksz
             self.verify_codeblock_style(codestream.segment[2].spcod[7],
-                                        [False, False, False,
+                    [False, False, False, False, False, False])
-                                         False, False, False])
             self.assertEqual(codestream.segment[2].spcod[8],
                              glymur.core.WAVELET_XFORM_5X3_REVERSIBLE)
             self.assertEqual(len(codestream.segment[2].spcod), 9)
@@ -533,16 +524,16 @@ 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, data=data, cratios=[800])
+            j = Jp2k(tfile.name, 'wb')
+            j.write(data, cratios=[800])
 
             codestream = j.get_codestream(header_only=False)
 
             kwargs = {'rsiz': 0, 'xysiz': (2592, 1944), 'xyosiz': (0, 0),
-                      'xytsiz': (2592, 1944), 'xytosiz': (0, 0),
+                    'xytsiz': (2592, 1944), 'xytosiz': (0, 0),
-                      'bitdepth': (8, 8, 8), 'signed': (False, False, False),
+                    'bitdepth': (8, 8, 8), 'signed': (False, False, False),
-                      'xyrsiz': [(1, 1, 1), (1, 1, 1)]}
+                    'xyrsiz': [(1, 1, 1), (1, 1, 1)]}
-            self.verifySizSegment(codestream.segment[1],
+            self.verifySizSegment(codestream.segment[1], glymur.codestream.SIZsegment(**kwargs))
-                                  glymur.codestream.SIZsegment(**kwargs))
 
             # COD: Coding style default
             self.assertFalse(codestream.segment[2].scod & 2)  # no sop
@@ -554,8 +545,7 @@ class TestSuiteWrite(fixtures.MetadataBase):
             self.assertEqual(tuple(codestream.segment[2].code_block_size),
                              (64, 64))  # cblksz
             self.verify_codeblock_style(codestream.segment[2].spcod[7],
-                                        [False, False, False,
+                    [False, False, False, False, False, False])
-                                         False, False, False])
             self.assertEqual(codestream.segment[2].spcod[8],
                              glymur.core.WAVELET_XFORM_5X3_REVERSIBLE)
             self.assertEqual(len(codestream.segment[2].spcod), 9)
@@ -565,16 +555,16 @@ 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, data=data, cratios=[50])
+            j = Jp2k(tfile.name, 'wb')
+            j.write(data, cratios=[50])
 
             codestream = j.get_codestream(header_only=False)
 
             kwargs = {'rsiz': 0, 'xysiz': (640, 480), 'xyosiz': (0, 0),
-                      'xytsiz': (640, 480), 'xytosiz': (0, 0),
+                    'xytsiz': (640, 480), 'xytosiz': (0, 0),
-                      'bitdepth': (8, 8, 8), 'signed': (False, False, False),
+                    'bitdepth': (8, 8, 8), 'signed': (False, False, False),
-                      'xyrsiz': [(1, 1, 1), (1, 1, 1)]}
+                    'xyrsiz': [(1, 1, 1), (1, 1, 1)]}
-            self.verifySizSegment(codestream.segment[1],
+            self.verifySizSegment(codestream.segment[1], glymur.codestream.SIZsegment(**kwargs))
-                                  glymur.codestream.SIZsegment(**kwargs))
 
             # COD: Coding style default
             self.assertFalse(codestream.segment[2].scod & 2)  # no sop
@@ -586,8 +576,7 @@ class TestSuiteWrite(fixtures.MetadataBase):
             self.assertEqual(tuple(codestream.segment[2].code_block_size),
                              (64, 64))  # cblksz
             self.verify_codeblock_style(codestream.segment[2].spcod[7],
-                                        [False, False, False,
+                    [False, False, False, False, False, False])
-                                         False, False, False])
             self.assertEqual(codestream.segment[2].spcod[8],
                              glymur.core.WAVELET_XFORM_5X3_REVERSIBLE)
             self.assertEqual(len(codestream.segment[2].spcod), 9)
@@ -596,8 +585,8 @@ 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,
+            jp2 = Jp2k(tfile.name, 'wb')
-                       data=data, psnr=[30, 35, 50], prog='LRCP', numres=3)
+            jp2.write(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'])
@@ -632,14 +621,13 @@ class TestSuiteWrite(fixtures.MetadataBase):
             self.assertIsNone(jp2.box[2].box[1].icc_profile)
             self.assertEqual(jp2.box[2].box[1].colorspace, glymur.core.SRGB)
 
-            codestream = jp2.box[3].codestream
+            codestream = jp2.box[3].main_header
 
             kwargs = {'rsiz': 0, 'xysiz': (640, 480), 'xyosiz': (0, 0),
-                      'xytsiz': (640, 480), 'xytosiz': (0, 0),
+                    'xytsiz': (640, 480), 'xytosiz': (0, 0),
-                      'bitdepth': (8, 8, 8), 'signed': (False, False, False),
+                    'bitdepth': (8, 8, 8), 'signed': (False, False, False),
-                      'xyrsiz': [(1, 1, 1), (1, 1, 1)]}
+                    'xyrsiz': [(1, 1, 1), (1, 1, 1)]}
-            self.verifySizSegment(codestream.segment[1],
+            self.verifySizSegment(codestream.segment[1], glymur.codestream.SIZsegment(**kwargs))
-                                  glymur.codestream.SIZsegment(**kwargs))
 
             # COD: Coding style default
             self.assertFalse(codestream.segment[2].scod & 2)  # no sop
@@ -651,8 +639,7 @@ class TestSuiteWrite(fixtures.MetadataBase):
             self.assertEqual(tuple(codestream.segment[2].code_block_size),
                              (64, 64))  # cblksz
             self.verify_codeblock_style(codestream.segment[2].spcod[7],
-                                        [False, False, False,
+                    [False, False, False, False, False, False])
-                                         False, False, False])
             self.assertEqual(codestream.segment[2].spcod[8],
                              glymur.core.WAVELET_XFORM_5X3_REVERSIBLE)
             self.assertEqual(len(codestream.segment[2].spcod), 9)
@@ -664,16 +651,16 @@ 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, data=data)
+            j = Jp2k(tfile.name, 'wb')
+            j.write(data)
 
             codestream = j.get_codestream(header_only=False)
 
             kwargs = {'rsiz': 0, 'xysiz': (1024, 1024), 'xyosiz': (0, 0),
-                      'xytsiz': (1024, 1024), 'xytosiz': (0, 0),
+                    'xytsiz': (1024, 1024), 'xytosiz': (0, 0),
-                      'bitdepth': (16,), 'signed': (False,),
+                    'bitdepth': (16,), 'signed': (False,),
-                      'xyrsiz': [(1,), (1,)]}
+                    'xyrsiz': [(1,), (1,)]}
-            self.verifySizSegment(codestream.segment[1],
+            self.verifySizSegment(codestream.segment[1], glymur.codestream.SIZsegment(**kwargs))
-                                  glymur.codestream.SIZsegment(**kwargs))
 
             # COD: Coding style default
             self.assertFalse(codestream.segment[2].scod & 2)  # no sop
@@ -685,8 +672,7 @@ class TestSuiteWrite(fixtures.MetadataBase):
             self.assertEqual(tuple(codestream.segment[2].code_block_size),
                              (64, 64))  # cblksz
             self.verify_codeblock_style(codestream.segment[2].spcod[7],
-                                        [False, False, False,
+                    [False, False, False, False, False, False])
-                                         False, False, False])
             self.assertEqual(codestream.segment[2].spcod[8],
                              glymur.core.WAVELET_XFORM_5X3_REVERSIBLE)
             self.assertEqual(len(codestream.segment[2].spcod), 9)

glymur/test/test_printing.py

@@ -1,6 +1,15 @@
 # -*- coding:  utf-8 -*-
 """Test suite for printing.
 """
+# C0302:  don't care too much about having too many lines in a test module
+# pylint: disable=C0302
+
+# E061:  unittest.mock introduced in 3.3 (python-2.7/pylint issue)
+# pylint: disable=E0611,F0401
+
+# R0904:  Not too many methods in unittest.
+# pylint: disable=R0904
+
 import os
 import re
 import struct
@@ -23,12 +32,11 @@ import lxml.etree as ET
 import glymur
 from glymur import Jp2k, command_line
 from . import fixtures
-from .fixtures import (OPJ_DATA_ROOT, opj_data_file,
+from .fixtures import (
-                       WARNING_INFRASTRUCTURE_ISSUE,
+        OPJ_DATA_ROOT, opj_data_file,
-                       WARNING_INFRASTRUCTURE_MSG,
+        WARNING_INFRASTRUCTURE_ISSUE, WARNING_INFRASTRUCTURE_MSG,
-                       WINDOWS_TMP_FILE_MSG,
+        WINDOWS_TMP_FILE_MSG, text_gbr_27, text_gbr_33, text_gbr_34
-                       text_gbr_27, text_gbr_33, text_gbr_34)
+)
-
 
 @unittest.skipIf(os.name == "nt", WINDOWS_TMP_FILE_MSG)
 class TestPrinting(unittest.TestCase):
@@ -42,13 +50,25 @@ class TestPrinting(unittest.TestCase):
         glymur.set_printoptions(short=False, xml=True, codestream=True)
 
     def tearDown(self):
-        glymur.set_parseoptions(full_codestream=False)
+        pass
+
+    def test_codestream(self):
+        """Should be able to print a raw codestream."""
+        j = glymur.Jp2k(self.j2kfile)
+        with patch('sys.stdout', new=StringIO()) as fake_out:
+            print(j)
+            actual = fake_out.getvalue().strip()
+            # Remove the file line, as that is filesystem-dependent.
+            lines = actual.split('\n')
+            actual = '\n'.join(lines[1:])
+
+        self.assertEqual(actual, fixtures.codestream)
 
     def test_version_info(self):
         """Should be able to print(glymur.version.info)"""
         with patch('sys.stdout', new=StringIO()) as fake_out:
             print(glymur.version.info)
-            fake_out.getvalue().strip()
+            actual = fake_out.getvalue().strip()
 
         self.assertTrue(True)
 
@@ -58,7 +78,7 @@ class TestPrinting(unittest.TestCase):
         with tempfile.NamedTemporaryFile(suffix='.jpx') as tfile:
             with open(self.jpxfile, 'rb') as ifile:
                 tfile.write(ifile.read())
-
+            
             # Add the header for an unknown superbox.
             write_buffer = struct.pack('>I4s', 20, 'grp '.encode())
             tfile.write(write_buffer)
@@ -87,17 +107,16 @@ 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
         # OpenJPEG doesn't have such a file.
-        data = glymur.Jp2k(self.jp2file)[::2, ::2]
+        data = glymur.Jp2k(self.jp2file).read(rlevel=1)
         with tempfile.NamedTemporaryFile(suffix='.jp2') as tfile:
+            j = glymur.Jp2k(tfile.name, 'wb')
+            j.write(data)
+
             with tempfile.NamedTemporaryFile(suffix='.jp2') as tfile2:
-                glymur.Jp2k(tfile.name, data=data)
 
                 # Offset of the codestream is where we start.
                 wbuffer = tfile.read(77)
@@ -399,7 +418,7 @@ class TestPrinting(unittest.TestCase):
     @unittest.skipIf(sys.hexversion < 0x03000000,
                      "Only trusting python3 for printing non-ascii chars")
     def test_xml_cyrrilic(self):
-        """Should be able to print XMLBox with utf-8 encoding (cyrrillic)."""
+        """Should be able to print an XMLBox with utf-8 encoding (cyrrillic)."""
         # Seems to be inconsistencies between different versions of python2.x
         # as to what gets printed.
         #
@@ -417,8 +436,7 @@ class TestPrinting(unittest.TestCase):
             actual = fake_out.getvalue().strip()
             if sys.hexversion < 0x03000000:
                 lines = ["XML Box (xml ) @ (-1, 0)",
-                         ("    <country>&#1056;&#1086;&#1089;&#1089;",
+                         "    <country>&#1056;&#1086;&#1089;&#1089;&#1080;&#1103;</country>"]
-                          "&#1080;&#1103;</country>")]
             else:
                 lines = ["XML Box (xml ) @ (-1, 0)",
                          "    <country>Россия</country>"]
@@ -594,14 +612,12 @@ class TestPrinting(unittest.TestCase):
 
         lines = ["UUID Box (uuid) @ (1135519, 76)",
                  "    UUID:  4a706754-6966-6645-7869-662d3e4a5032 (EXIF)",
-                 ("    UUID Data:  OrderedDict([('ImageWidth', 256),"
+                 "    UUID Data:  OrderedDict([('ImageWidth', 256), ('ImageLength', 512), ('Make', 'HTC')])"]
-                  " ('ImageLength', 512), ('Make', 'HTC')])")]
 
         expected = '\n'.join(lines)
 
         self.assertEqual(actual, expected)
 
-
 @unittest.skipIf(OPJ_DATA_ROOT is None,
                  "OPJ_DATA_ROOT environment variable not set")
 @unittest.skipIf(os.name == "nt", "Temporary file issue on window.")
@@ -809,7 +825,6 @@ class TestPrintingOpjDataRoot(unittest.TestCase):
         expected = '\n'.join(lines)
         self.assertEqual(actual, expected)
 
-
 @unittest.skipIf(OPJ_DATA_ROOT is None,
                  "OPJ_DATA_ROOT environment variable not set")
 @unittest.skipIf(os.name == "nt", "Temporary file issue on window.")
@@ -831,31 +846,20 @@ class TestPrintingOpjDataRootWarns(unittest.TestCase):
     def tearDown(self):
         pass
 
-    def test_invalid_colour_specification_method(self):
-        """should not error out with invalid colour specification method"""
-        # Don't care so much about what the output looks like, just that we
-        # do not error out.
-        filename = opj_data_file('input/nonregression/issue397.jp2')
-        with self.assertWarns(UserWarning):
-            jp2 = Jp2k(filename)
-        with patch('sys.stdout', new=StringIO()):
-            print(jp2)
-        self.assertTrue(True)
-
     def test_invalid_colorspace(self):
         """An invalid colorspace shouldn't cause an error."""
         filename = opj_data_file('input/nonregression/edf_c2_1103421.jp2')
         with self.assertWarns(UserWarning):
             jp2 = Jp2k(filename)
-        with patch('sys.stdout', new=StringIO()):
+        with patch('sys.stdout', new=StringIO()) as fake_out:
             print(jp2)
 
     def test_bad_rsiz(self):
         """Should still be able to print if rsiz is bad, issue196"""
         filename = opj_data_file('input/nonregression/edf_c2_1002767.jp2')
         with self.assertWarns(UserWarning):
-            j = Jp2k(filename).get_codestream()
+            j = Jp2k(filename)
-        with patch('sys.stdout', new=StringIO()):
+        with patch('sys.stdout', new=StringIO()) as fake_out:
             print(j)
 
     def test_bad_wavelet_transform(self):
@@ -863,7 +867,7 @@ class TestPrintingOpjDataRootWarns(unittest.TestCase):
         filename = opj_data_file('input/nonregression/edf_c2_10025.jp2')
         with self.assertWarns(UserWarning):
             jp2 = Jp2k(filename)
-            with patch('sys.stdout', new=StringIO()):
+            with patch('sys.stdout', new=StringIO()) as fake_out:
                 print(jp2)
 
     def test_invalid_progression_order(self):
@@ -1024,7 +1028,7 @@ class TestPrintingOpjDataRootWarns(unittest.TestCase):
                                               'issue171.jp2'))
         with self.assertWarns(UserWarning):
             jp2 = Jp2k(filename)
-            with patch('sys.stdout', new=StringIO()):
+            with patch('sys.stdout', new=StringIO()) as fake_out:
                 # No need to verify, it's enough that we don't error out.
                 print(jp2)
 
@@ -1040,10 +1044,9 @@ class TestJp2dump(unittest.TestCase):
 
         # Reset printoptions for every test.
         glymur.set_printoptions(short=False, xml=True, codestream=True)
-        glymur.set_parseoptions(full_codestream=False)
 
     def tearDown(self):
-        glymur.set_parseoptions(full_codestream=False)
+        pass
 
     def run_jp2dump(self, args):
         sys.argv = args
@@ -1056,53 +1059,24 @@ class TestJp2dump(unittest.TestCase):
         return actual
 
     def test_default_nemo(self):
-        """by default one should get the main header"""
+        """Should be able to dump a JP2 file's metadata with no codestream."""
         actual = self.run_jp2dump(['', self.jp2file])
 
-        # shave off the  non-main-header segments
+        self.assertEqual(actual, fixtures.nemo_dump_no_codestream)
-        lines = fixtures.nemo.split('\n')
-        expected = lines[0:140]
-        expected = '\n'.join(expected)
-        self.assertEqual(actual, expected)
 
-    def test_jp2_codestream_0(self):
+    def test_codestream_0(self):
         """Verify dumping with -c 0, supressing all codestream details."""
         actual = self.run_jp2dump(['', '-c', '0', self.jp2file])
 
-        # shave off the codestream details
+        self.assertEqual(actual, fixtures.nemo_dump_no_codestream)
-        lines = fixtures.nemo.split('\n')
-        expected = lines[0:105]
-        expected = '\n'.join(expected)
-        self.assertEqual(actual, expected)
 
-    def test_jp2_codestream_1(self):
+    def test_codestream_1(self):
         """Verify dumping with -c 1, print just the header."""
         actual = self.run_jp2dump(['', '-c', '1', self.jp2file])
 
-        # shave off the  non-main-header segments
+        self.assertEqual(actual, fixtures.nemo_with_codestream_header)
-        lines = fixtures.nemo.split('\n')
-        expected = lines[0:140]
-        expected = '\n'.join(expected)
-        self.assertEqual(actual, expected)
 
-    def test_jp2_codestream_2(self):
+    def test_codestream_2(self):
-        """Verify dumping with -c 2, print entire jp2 jacket, codestream."""
-        actual = self.run_jp2dump(['', '-c', '2', self.jp2file])
-
-        # shave off the  non-main-header segments
-        expected = fixtures.nemo
-        self.assertEqual(actual, expected)
-
-    @unittest.skipIf(sys.hexversion < 0x03000000, "assertRegex not in 2.7")
-    def test_j2k_codestream_0(self):
-        """-c 0 should print just a single line when used on a codestream."""
-        sys.argv = ['', '-c', '0', self.j2kfile]
-        with patch('sys.stdout', new=StringIO()) as fake_out:
-            command_line.main()
-            actual = fake_out.getvalue().strip()
-        self.assertRegex(actual, "File:  .*")
-
-    def test_j2k_codestream_2(self):
         """Verify dumping with -c 2, full details."""
         with patch('sys.stdout', new=StringIO()) as fake_out:
             sys.argv = ['', '-c', '2', self.j2kfile]
@@ -1127,9 +1101,4 @@ class TestJp2dump(unittest.TestCase):
         """Verify dumping with -x, suppress XML."""
         actual = self.run_jp2dump(['', '-x', self.jp2file])
 
-        # shave off the XML and non-main-header segments
+        self.assertEqual(actual, fixtures.nemo_dump_no_codestream_no_xml)
-        lines = fixtures.nemo.split('\n')
-        expected = lines[0:18]
-        expected.extend(lines[104:140])
-        expected = '\n'.join(expected)
-        self.assertEqual(actual, expected)

glymur/version.py

@@ -18,7 +18,7 @@ from .lib import openjpeg as opj, openjp2 as opj2
 
 # Do not change the format of this next line!  Doing so risks breaking
 # setup.py
-version = "0.8.0"
+version = "0.7.2"
 _sv = LooseVersion(version)
 version_tuple = _sv.version
 

setup.py

@@ -1,4 +1,4 @@
-from setuptools import setup
+from setuptools import setup, find_packages
 import os
 import re
 import sys
@@ -11,20 +11,18 @@ kwargs = {'name': 'Glymur',
           'url': 'https://github.com/quintusdias/glymur',
           'packages': ['glymur', 'glymur.data', 'glymur.test', 'glymur.lib',
                        'glymur.lib.test'],
-          'package_data': {'glymur': ['data/*.jp2',
+          'package_data': {'glymur': ['data/*.jp2', 'data/*.j2k', 'data/*.jpx']},
-                                      'data/*.j2k',
-                                      'data/*.jpx']},
           'entry_points': {
               'console_scripts': ['jp2dump=glymur.command_line:main'],
               },
           'license': 'MIT',
           'test_suite': 'glymur.test'}
 
-install_requires = ['numpy>=1.7.0', 'lxml>=3.0.0']
+instllrqrs = ['numpy>=1.4.1', 'lxml>=2.3.2']
 if sys.hexversion < 0x03030000:
-    install_requires.append('contextlib2>=0.4')
+    instllrqrs.append('contextlib2>=0.4')
-    install_requires.append('mock>=1.0.1')
+    instllrqrs.append('mock>=1.0.1')
-kwargs['install_requires'] = install_requires
+kwargs['install_requires'] = instllrqrs
 
 clssfrs = ["Programming Language :: Python",
            "Programming Language :: Python :: 2.7",