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Extracted bioformats code from CellProfiler
(http:://github.com/CellProfiler/CellProfiler) rev. 5fc781e8d2a1b8abe508e56c60ec50295cd12aef and started documentation
0 parents  commit e673169

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‎.gitignore‎

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*.pyc
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/build
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/docs/_build
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/python_bioformats.egg-info

‎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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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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__version__ = "$Revision$"
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import os.path
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import javabridge
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import formatreader as _formatreader
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import formatwriter as _formatwriter
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_jars_dir = os.path.join(os.path.dirname(__file__), 'jars')
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JARS = javabridge.JARS + [os.path.realpath(os.path.join(_jars_dir, name + '.jar'))
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for name in ['loci_tools']]
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# See http://www.loci.wisc.edu/software/bio-formats
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READABLE_FORMATS = ('al3d', 'am', 'amiramesh', 'apl', 'arf', 'avi', 'bmp',
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'c01', 'cfg', 'cxd', 'dat', 'dcm', 'dicom', 'dm3', 'dv',
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'eps', 'epsi', 'fits', 'flex', 'fli', 'gel', 'gif', 'grey',
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'hdr', 'html', 'hx', 'ics', 'ids', 'img', 'ims', 'ipl',
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'ipm', 'ipw', 'jp2', 'jpeg', 'jpg', 'l2d', 'labels', 'lei',
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'lif', 'liff', 'lim', 'lsm', 'mdb', 'mnc', 'mng', 'mov',
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'mrc', 'mrw', 'mtb', 'naf', 'nd', 'nd2', 'nef', 'nhdr',
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'nrrd', 'obsep', 'oib', 'oif', 'ome', 'ome.tiff', 'pcx',
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'pgm', 'pic', 'pict', 'png', 'ps', 'psd', 'r3d', 'raw',
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'scn', 'sdt', 'seq', 'sld', 'stk', 'svs', 'tif', 'tiff',
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'tnb', 'txt', 'vws', 'xdce', 'xml', 'xv', 'xys', 'zvi')
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WRITABLE_FORMATS = ('avi', 'eps', 'epsi', 'ics', 'ids', 'jp2', 'jpeg', 'jpg',
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'mov', 'ome', 'ome.tiff', 'png', 'ps', 'tif', 'tiff')
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ImageReader = _formatreader.make_image_reader_class()
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FormatTools = _formatreader.make_format_tools_class()
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OMETiffWriter = _formatwriter.make_ome_tiff_writer_class()
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ChannelSeparator = _formatreader.make_reader_wrapper_class(
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"loci/formats/ChannelSeparator")
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from .metadatatools import createOMEXMLMetadata as create_ome_xml_metadata
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from .metadatatools import wrap_imetadata_object
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import metadatatools as _metadatatools
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PixelType = _metadatatools.make_pixel_type_class()
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load_image = _formatreader.load_using_bioformats
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def init_logger():
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javabridge.static_call("org/apache/log4j/BasicConfigurator",
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"configure", "()V")
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log4j_logger = javabridge.static_call("org/apache/log4j/Logger",
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"getRootLogger",
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"()Lorg/apache/log4j/Logger;")
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warn_level = javabridge.get_static_field("org/apache/log4j/Level", "WARN",
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"Lorg/apache/log4j/Level;")
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javabridge.call(log4j_logger, "setLevel", "(Lorg/apache/log4j/Level;)V",
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warn_level)
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if __name__ == "__main__":
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# Handy-dandy PyShell for exploring BioFormats / Rhino / ImageJ
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import wx.py.PyCrust
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wx.py.PyCrust.main()
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J.kill_vm()

‎bioformats/formatreader.py‎

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‎bioformats/formatwriter.py‎

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‎bioformats/jars/loci_tools.jar‎

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‎bioformats/log4j.py‎

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import unittest
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import javabridge
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def basic_config():
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javabridge.static_call("org/apache/log4j/BasicConfigurator",
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"configure", "()V")
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log4j_logger = javabridge.static_call("org/apache/log4j/Logger",
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"getRootLogger",
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"()Lorg/apache/log4j/Logger;")
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warn_level = javabridge.get_static_field("org/apache/log4j/Level","WARN",
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"Lorg/apache/log4j/Level;")
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javabridge.call(log4j_logger, "setLevel", "(Lorg/apache/log4j/Level;)V",
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warn_level)

‎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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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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__version__ = "$Revision$"
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from javabridge import jutil
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import bioformats
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def createOMEXMLMetadata():
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'''Creates an OME-XML metadata object using reflection, to avoid direct
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dependencies on the optional loci.formats.ome package.
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'''
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return jutil.static_call('loci/formats/MetadataTools', 'createOMEXMLMetadata', '()Lloci/formats/meta/IMetadata;')
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class MetadataStore(object):
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''' '''
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def __init__(self, o):
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self.o = o
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createRoot = jutil.make_method('createRoot', '()V', '')
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def setPixelsBigEndian(self, bigEndian, imageIndex, binDataIndex):
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'''Set the endianness for a particular image
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bigEndian - True for big-endian, False for little-endian
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imageIndex - index of the image in question from IFormatReader.get_index?
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binDataIndex - ???
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'''
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# Post loci_tools 4.2
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try:
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jutil.call(self.o, 'setPixelsBinDataBigEndian',
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'(Ljava/lang/Boolean;II)V',
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bigEndian, imageIndex, binDataIndex)
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except jutil.JavaException:
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jutil.call(self.o, 'setPixelsBigEndian', '(Ljava/lang/Boolean;II)V',
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bigEndian, imageIndex, binDataIndex)
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def setPixelsDimensionOrder(self, dimension_order, imageIndex, binDataIndex):
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'''Set the dimension order for a series'''
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# Post loci_tools 4.2 - use ome.xml.model.DimensionOrder
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try:
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jdimension_order = jutil.static_call(
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'ome/xml/model/enums/DimensionOrder', 'fromString',
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'(Ljava/lang/String;)Lome/xml/model/enums/DimensionOrder;',
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dimension_order)
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jutil.call(self.o, 'setPixelsDimensionOrder',
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'(Lome/xml/model/enums/DimensionOrder;I)V',
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jdimension_order, imageIndex)
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except jutil.JavaException:
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jutil.call(self.o, 'setPixelsDimensionOrder',
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'(Ljava/lang/String;II)V',
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dimension_order, imageIndex, binDataIndex)
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setPixelsPixelType = jutil.make_method(
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'setPixelsPixelType', '(Ljava/lang/String;II)V',
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'''Sets the pixel storage type
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pixel_type - text representation of the type, e.g. "uint8"
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imageIndex - ?
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binDataIndex - ?
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WARNING: only available in BioFormats < 4.2
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''')
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setPixelsType = jutil.make_method(
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'setPixelsType', '(Lome/xml/model/enums/PixelType;I)V',
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'''Set the pixel storage type
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pixel_type - one of the enumerated values from PixelType.
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imageIndex - ?
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See the ome.xml.model.enums.PixelType and make_pixel_type_class's
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PixelType for possible values.
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''')
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def setPixelsSizeX(self, x, imageIndex, binDataIndex):
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try:
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jutil.call(self.o, 'setPixelsSizeX',
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'(Lome/xml/model/primitives/PositiveInteger;I)V',
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PositiveInteger(x), imageIndex)
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except jutil.JavaException:
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jutil.call(self.o, 'setPixelsSizeX',
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'(Ljava/lang/Integer;II)V', x, imageIndex, binDataIndex)
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def setPixelsSizeY(self, y, imageIndex, binDataIndex):
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try:
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jutil.call(self.o, 'setPixelsSizeY',
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'(Lome/xml/model/primitives/PositiveInteger;I)V',
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PositiveInteger(y), imageIndex)
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except jutil.JavaException:
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jutil.call(self.o, 'setPixelsSizeY',
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'(Ljava/lang/Integer;II)V', y, imageIndex, binDataIndex)
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def setPixelsSizeZ(self, z, imageIndex, binDataIndex):
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try:
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jutil.call(self.o, 'setPixelsSizeZ',
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'(Lome/xml/model/primitives/PositiveInteger;I)V',
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PositiveInteger(z), imageIndex)
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except jutil.JavaException:
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jutil.call(self.o, 'setPixelsSizeZ',
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'(Ljava/lang/Integer;II)V', z, imageIndex, binDataIndex)
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def setPixelsSizeC(self, c, imageIndex, binDataIndex):
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try:
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jutil.call(self.o, 'setPixelsSizeC',
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'(Lome/xml/model/primitives/PositiveInteger;I)V',
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PositiveInteger(c), imageIndex)
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except jutil.JavaException:
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jutil.call(self.o, 'setPixelsSizeC',
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'(Ljava/lang/Integer;II)V', c, imageIndex, binDataIndex)
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def setPixelsSizeT(self, t, imageIndex, binDataIndex):
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try:
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jutil.call(self.o, 'setPixelsSizeT',
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'(Lome/xml/model/primitives/PositiveInteger;I)V',
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PositiveInteger(t), imageIndex)
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except jutil.JavaException:
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jutil.call(self.o, 'setPixelsSizeT',
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'(Ljava/lang/Integer;II)V', t, imageIndex, binDataIndex)
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def setLogicalChannelSamplesPerPixel(self, samplesPerPixel, imageIndex, channelIndex):
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'For a particular LogicalChannel, sets number of channel components in the logical channel.'
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try:
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jutil.call(self.o, 'setChannelSamplesPerPixel',
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'(Lome/xml/model/primitives/PositiveInteger;II)V',
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PositiveInteger(samplesPerPixel),
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imageIndex, channelIndex)
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except jutil.JavaException:
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jutil.call(self.o, 'setLogicalChannelSamplesPerPixel',
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'(Ljava/lang/Integer;II)V', samplesPerPixel,
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imageIndex, channelIndex)
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setImageID = jutil.make_method(
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'setImageID', '(Ljava/lang/String;I)V',
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'''Tag the indexed image with a name
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id - the name, for instance Image:0
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imageIndex - the index of the image (series???)
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''')
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setPixelsID = jutil.make_method(
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'setPixelsID', '(Ljava/lang/String;I)V',
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'''Tag the pixels with a name (???)
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id - the name, for instance Pixels:0
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imageIndex - the index of the image (???)
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''')
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setChannelID = jutil.make_method(
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'setChannelID', '(Ljava/lang/String;II)V',
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'''Give an ID name to the given channel
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id - the name of the channel
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imageIndex - (???)
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channelIndex - index of the channel to be ID'ed''')
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class MetadataRetrieve(object):
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''' '''
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def __init__(self, o):
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self.o = o
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getPixelsBigEndian = jutil.make_method('getPixelsBigEndian', '(II)Ljava/lang/Boolean;',
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'For a particular Pixels, gets endianness of the pixels set.')
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getPixelsDimensionOrder = jutil.make_method('getPixelsDimensionOrder', '(II)Ljava/lang/String;',
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'For a particular Pixels, gets the dimension order of the pixels set.')
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getPixelsPixelType = jutil.make_method('getPixelsPixelType', '(II)Ljava/lang/String;',
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'For a particular Pixels, gets the pixel type.')
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getPixelsSizeX = jutil.make_method('getPixelsSizeX', '(II)Ljava/lang/Integer;',
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'For a particular Pixels, gets The size of an individual plane or section\'s X axis (width).')
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getPixelsSizeY = jutil.make_method('getPixelsSizeY', '(II)Ljava/lang/Integer;',
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'For a particular Pixels, gets The size of an individual plane or section\'s Y axis (height).')
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getPixelsSizeZ = jutil.make_method('getPixelsSizeZ', '(II)Ljava/lang/Integer;',
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'For a particular Pixels, gets number of optical sections per stack.')
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getPixelsSizeC = jutil.make_method('getPixelsSizeC', '(II)Ljava/lang/Integer;',
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'For a particular Pixels, gets number of channels per timepoint.')
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getPixelsSizeT = jutil.make_method('getPixelsSizeT', '(II)Ljava/lang/Integer;',
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'For a particular Pixels, gets number of timepoints.')
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getLogicalChannelSamplesPerPixel = jutil.make_method('getLogicalChannelSamplesPerPixel', '(II)Ljava/lang/Integer;',
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'For a particular LogicalChannel, gets number of channel components in the logical channel.')
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getChannelName = jutil.make_method('getChannelName',
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'(II)Ljava/lang/String;',
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'''Get the name for a particular channel.
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imageIndex - image # to query (use C = 0)
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channelIndex - channel # to query''')
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getChannelID = jutil.make_method('getChannelID',
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'(II)Ljava/lang/String;',
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'''Get the OME channel ID for a particular channel.
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imageIndex - image # to query (use C = 0)
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channelIndex - channel # to query''')
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def wrap_imetadata_object(o):
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''' Returns a python object wrapping the functionality of the given
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IMetaData object (as returned by createOMEXMLMetadata) '''
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class IMetadata(MetadataStore, MetadataRetrieve):
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''' '''
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def __init__(self, o):
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MetadataStore.__init__(self, o)
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MetadataRetrieve.__init__(self, o)
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self.o = o
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return IMetadata(o)
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__pixel_type_class = None
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def make_pixel_type_class():
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'''The class, ome.xml.model.enums.PixelType
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The Java class has enumerations for the various image data types
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such as UINT8 or DOUBLE
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'''
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global __pixel_type_class
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if __pixel_type_class is None:
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class PixelType(object):
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'''Provide enums from ome.xml.model.enums.PixelType'''
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klass = jutil.get_env().find_class('ome/xml/model/enums/PixelType')
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INT8 = jutil.get_static_field(klass, 'INT8', 'Lome/xml/model/enums/PixelType;')
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INT16 = jutil.get_static_field(klass, 'INT16', 'Lome/xml/model/enums/PixelType;')
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INT32 = jutil.get_static_field(klass, 'INT32', 'Lome/xml/model/enums/PixelType;')
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UINT8 = jutil.get_static_field(klass, 'UINT8', 'Lome/xml/model/enums/PixelType;')
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UINT16 = jutil.get_static_field(klass, 'UINT16', 'Lome/xml/model/enums/PixelType;')
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UINT32 = jutil.get_static_field(klass, 'UINT32', 'Lome/xml/model/enums/PixelType;')
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FLOAT = jutil.get_static_field(klass, 'FLOAT', 'Lome/xml/model/enums/PixelType;')
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BIT = jutil.get_static_field(klass, 'BIT', 'Lome/xml/model/enums/PixelType;')
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DOUBLE = jutil.get_static_field(klass, 'DOUBLE', 'Lome/xml/model/enums/PixelType;')
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COMPLEX = jutil.get_static_field(klass, 'COMPLEX', 'Lome/xml/model/enums/PixelType;')
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DOUBLECOMPLEX = jutil.get_static_field(klass, 'DOUBLECOMPLEX', 'Lome/xml/model/enums/PixelType;')
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__pixel_type_class = PixelType()
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return __pixel_type_class
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MINIMUM = 'MINIMUM'
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NO_OVERLAYS = 'NO_OVERLAYS'
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ALL = 'ALL'
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def get_metadata_options(level):
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'''Get an instance of the MetadataOptions interface
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level - MINIMUM, NO_OVERLAYS or ALL to set the metadata retrieval level
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The object returned can be used in setMetadataOptions in a format reader.
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'''
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jlevel = jutil.get_static_field('loci/formats/in/MetadataLevel', level,
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'Lloci/formats/in/MetadataLevel;')
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return jutil.make_instance('loci/formats/in/DefaultMetadataOptions',
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'(Lloci/formats/in/MetadataLevel;)V',
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jlevel)
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def PositiveInteger(some_number):
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'''Return an instance of ome.xml.model.primitives.PositiveInteger
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some_number - the number to be wrapped up in the class
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'''
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return jutil.make_instance('ome/xml/model/primitives/PositiveInteger',
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'(Ljava/lang/Integer;)V', some_number)
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‎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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#
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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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import logging
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from nose.plugins import Plugin
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import javabridge
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log = logging.getLogger(__name__)
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class Log4JPlugin(Plugin):
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'''
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Plugin that initializes Log4J in order to avoid Bioformats error
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messages.
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'''
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enabled = False
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name = "log4j"
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score = 90 # Less than the score of javabridge.nosetests.JavaBridgePlugin
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def begin(self):
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javabridge.static_call("org/apache/log4j/BasicConfigurator",
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"configure", "()V")
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log4j_logger = javabridge.static_call("org/apache/log4j/Logger",
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"getRootLogger",
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"()Lorg/apache/log4j/Logger;")
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warn_level = javabridge.get_static_field("org/apache/log4j/Level","WARN",
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"Lorg/apache/log4j/Level;")
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javabridge.call(log4j_logger, "setLevel", "(Lorg/apache/log4j/Level;)V",
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warn_level)

‎bioformats/tests/Channel1-01-A-01.tif‎

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