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ljosaljosa
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Change license to GPL. Resolves CellProfiler#3.
The license of python-bioformats as a whole has to be GPL because loci_tools.jar is GPL licensed. The python files remain under the more permissive BSD license.
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‎COPYING

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‎README.rst

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@@ -15,7 +15,8 @@ GitHub repository: https://github.com/CellProfiler/python-bioformats
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Report bugs here: https://github.com/CellProfiler/python-bioformats/issues
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python-bioformats is licensed under the BSD license. See the
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accompanying file LICENSE for details.
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python-bioformats is licensed under the GNU General Public License
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(GPL). Many files are licensed under the more permissive BSD license.
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See the accompanying files COPYING and LICENSE for details.
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Copyright (c) 2009-2014 Broad Institute. All rights reserved.

‎bioformats/__init__.py

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'''Bioformats package - wrapper for loci.bioformats java code
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CellProfiler is distributed under the GNU General Public License,
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but this file is licensed under the more permissive BSD license.
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See the accompanying file LICENSE for details.
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# Python-bioformats is distributed under the GNU General Public
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# License, but this file is licensed under the more permissive BSD
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# license. See the accompanying file LICENSE for details.
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#
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# Copyright (c) 2009-2014 Broad Institute
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# All rights reserved.
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Copyright (c) 2003-2009 Massachusetts Institute of Technology
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Copyright (c) 2009-2013 Broad Institute
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All rights reserved.
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Please see the AUTHORS file for credits.
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'''Bioformats package - wrapper for loci.bioformats java code
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Website: http://www.cellprofiler.org
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'''
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__version__ = "$Revision$"
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‎bioformats/formatreader.py

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# Python-bioformats is distributed under the GNU General Public
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# License, but this file is licensed under the more permissive BSD
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# license. See the accompanying file LICENSE for details.
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#
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# Copyright (c) 2009-2014 Broad Institute
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# All rights reserved.
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'''formatreader.py - mechanism to wrap a bioformats ReaderWrapper and ImageReader
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Example:
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my_red_image, my_green_image, my_blue_image = \
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[cs.open_bytes(cs.getIndex(0,i,0)) for i in range(3)]
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CellProfiler is distributed under the GNU General Public License,
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but this file is licensed under the more permissive BSD license.
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See the accompanying file LICENSE for details.
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Copyright (c) 2003-2009 Massachusetts Institute of Technology
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Copyright (c) 2009-2014 Broad Institute
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All rights reserved.
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Please see the AUTHORS file for credits.
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Website: http://www.cellprofiler.org'
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'''
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__version__ = "$Revision$"

‎bioformats/formatwriter.py

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# Python-bioformats is distributed under the GNU General Public
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# License, but this file is licensed under the more permissive BSD
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# license. See the accompanying file LICENSE for details.
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#
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# Copyright (c) 2009-2014 Broad Institute
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# All rights reserved.
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'''formatwriter.py - mechanism to wrap a bioformats WriterWrapper and ImageWriter
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The following file formats can be written using Bio-Formats:
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and is especially useful for formats that do not support multiple images per
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file.
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CellProfiler is distributed under the GNU General Public License,
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but this file is licensed under the more permissive BSD license.
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See the accompanying file LICENSE for details.
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Copyright (c) 2003-2009 Massachusetts Institute of Technology
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Copyright (c) 2009-2014 Broad Institute
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All rights reserved.
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Please see the AUTHORS file for credits.
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Website: http://www.cellprofiler.org
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'''
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__version__ = "$Revision$"

‎bioformats/log4j.py

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# Python-bioformats is distributed under the GNU General Public
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# License, but this file is licensed under the more permissive BSD
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# license. See the accompanying file LICENSE for details.
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#
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# Copyright (c) 2009-2014 Broad Institute
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# All rights reserved.
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import unittest
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import javabridge
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‎bioformats/metadatatools.py

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''' metadatatools.py - mechanism to wrap some bioformats metadata classes
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CellProfiler is distributed under the GNU General Public License,
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but this file is licensed under the more permissive BSD license.
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See the accompanying file LICENSE for details.
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# Python-bioformats is distributed under the GNU General Public
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# License, but this file is licensed under the more permissive BSD
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# license. See the accompanying file LICENSE for details.
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#
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# Copyright (c) 2009-2014 Broad Institute
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# All rights reserved.
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Copyright (c) 2003-2009 Massachusetts Institute of Technology
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Copyright (c) 2009-2014 Broad Institute
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All rights reserved.
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Please see the AUTHORS file for credits.
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''' metadatatools.py - mechanism to wrap some bioformats metadata classes
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Website: http://www.cellprofiler.org
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'''
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__version__ = "$Revision$"

‎bioformats/noseplugin.py

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# CellProfiler is distributed under the GNU General Public License.
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# See the accompanying file LICENSE for details.
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# Python-bioformats is distributed under the GNU General Public
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# License, but this file is licensed under the more permissive BSD
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# license. See the accompanying file LICENSE for details.
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#
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# Copyright (c) 2003-2009 Massachusetts Institute of Technology
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# Copyright (c) 2009-2013 Broad Institute
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#
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# Please see the AUTHORS file for credits.
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#
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# Website: http://www.cellprofiler.org
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# Copyright (c) 2009-2014 Broad Institute
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# All rights reserved.
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import logging
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from nose.plugins import Plugin

‎bioformats/omexml.py

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# Python-bioformats is distributed under the GNU General Public
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# License, but this file is licensed under the more permissive BSD
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# license. See the accompanying file LICENSE for details.
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#
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# Copyright (c) 2009-2014 Broad Institute
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# All rights reserved.
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"""omexml.py read and write OME xml
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"""
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# CellProfiler is distributed under the GNU General Public License.
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# See the accompanying file LICENSE for details.
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#
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# Developed by the Broad Institute
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#
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# Copyright (c) 2003-2009 Massachusetts Institute of Technology
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# Copyright (c) 2003-2013 Broad Institute
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# All rights reserved.
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#
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# Please see the AUTHORS file for credits.
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#
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# Website: http://www.cellprofiler.org
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#
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import xml.etree.ElementTree
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from xml.etree import cElementTree as ElementTree
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from cStringIO import StringIO

‎bioformats/tests/__init__.py

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'''
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CellProfiler is distributed under the GNU General Public License,
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but this file is licensed under the more permissive BSD license.
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See the accompanying file LICENSE for details.
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Copyright (c) 2003-2009 Massachusetts Institute of Technology
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Copyright (c) 2009-2013 Broad Institute
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All rights reserved.
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Please see the AUTHORS file for credits.
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Website: http://www.cellprofiler.org
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'''
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‎bioformats/tests/test_formatreader.py

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'''test_formatreader.py - test the Bioformats format reader wrapper
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CellProfiler is distributed under the GNU General Public License,
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but this file is licensed under the more permissive BSD license.
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See the accompanying file LICENSE for details.
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# Python-bioformats is distributed under the GNU General Public
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# License, but this file is licensed under the more permissive BSD
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# license. See the accompanying file LICENSE for details.
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#
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# Copyright (c) 2009-2014 Broad Institute
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# All rights reserved.
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Copyright (c) 2003-2009 Massachusetts Institute of Technology
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Copyright (c) 2009-2014 Broad Institute
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All rights reserved.
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Please see the AUTHORS file for credits.
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'''test_formatreader.py - test the Bioformats format reader wrapper
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Website: http://www.cellprofiler.org
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'''
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import numpy as np

‎bioformats/tests/test_formatwriter.py

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'''test_formatwriter.py - test the Bioformats format reader wrapper
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CellProfiler is distributed under the GNU General Public License,
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but this file is licensed under the more permissive BSD license.
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See the accompanying file LICENSE for details.
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Copyright (c) 2003-2009 Massachusetts Institute of Technology
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Copyright (c) 2009-2014 Broad Institute
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All rights reserved.
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# Python-bioformats is distributed under the GNU General Public
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# License, but this file is licensed under the more permissive BSD
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# license. See the accompanying file LICENSE for details.
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#
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# Copyright (c) 2009-2014 Broad Institute
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# All rights reserved.
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Please see the AUTHORS file for credits.
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'''test_formatwriter.py - test the Bioformats format reader wrapper
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Website: http://www.cellprofiler.org
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'''
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import numpy as np
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for i in range(img.shape[0]):
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result = load_using_bioformats(path, t=i, rescale = False)
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np.testing.assert_array_equal(img[i], result)
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‎bioformats/tests/test_load_using_bioformats.py

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#!/usr/bin/env python
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# Python-bioformats is distributed under the GNU General Public
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# License, but this file is licensed under the more permissive BSD
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# license. See the accompanying file LICENSE for details.
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#
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# Copyright (c) 2009-2014 Broad Institute
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# All rights reserved.
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import os
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import unittest

‎bioformats/tests/test_omexml.py

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# Python-bioformats is distributed under the GNU General Public
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# License, but this file is licensed under the more permissive BSD
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# license. See the accompanying file LICENSE for details.
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#
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# Copyright (c) 2009-2014 Broad Institute
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# All rights reserved.
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"""test_omexml.py read and write OME xml
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"""
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# CellProfiler is distributed under the GNU General Public License.
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# See the accompanying file LICENSE for details.
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#
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# Developed by the Broad Institute
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#
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# Copyright (c) 2003-2009 Massachusetts Institute of Technology
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# Copyright (c) 2003-2013 Broad Institute
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# All rights reserved.
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#
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# Please see the AUTHORS file for credits.
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#
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# Website: http://www.cellprofiler.org
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#
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import datetime
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import os
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import unittest
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</Value>
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</XMLAnnotation>
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</StructuredAnnotations>
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</OME>"""
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</OME>"""

‎docs/index.rst

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used by the cell image analysis software CellProfiler
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(cellprofiler.org).
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python-bioformats is licensed under the GNU General Public License
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(GPL). Many files are licensed under the more permissive BSD license.
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Installation and testing
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========================

‎setup.py

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url="http://github.com/CellProfiler/python-bioformats/",
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packages=['bioformats'],
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classifiers=['Development Status :: 5 - Production/Stable',
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'License :: OSI Approved :: BSD License',
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'License :: OSI Approved :: GPL License',
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'Programming Language :: Java',
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'Topic :: Scientific/Engineering :: Bio-Informatics',
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'Topic :: Multimedia :: Graphics :: Graphics Conversion'
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],
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license='BSD License',
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license='GPL License',
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package_data={'bioformats': ['jars/*.jar']},
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install_requires=['javabridge>=1.0']
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)

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