How to use the cellprofiler.utilities.jutil.make_method function in CellProfiler

#
    # This uses the writers.txt file from inside the loci_tools.jar
    #
    class_list = jutil.make_instance("loci/formats/ClassList", 
                                     "(Ljava/lang/String;"
                                     "Ljava/lang/Class;" # base
                                     "Ljava/lang/Class;)V", # location in jar
                                     "writers.txt", base_klass, klass)
    class ImageWriter(IFormatWriter):
        new_fn = jutil.make_new(class_name, '(Lloci/formats/ClassList;)V')
        def __init__(self):
            self.new_fn(class_list)
            
        setId = jutil.make_method('setId', '(Ljava/lang/String;)V', 
                                  'Sets the current file name.')
        addStatusListener = jutil.make_method('addStatusListener', '()Lloci/formats/StatusListener;',
                                              'Adds a listener for status update events.')
        close = jutil.make_method('close','()V',
                                  'Closes currently open file(s) and frees allocated memory.')
        getFormat = jutil.make_method('getFormat', '()Ljava/lang/String;', 
                                      'Gets the name of this file format.')
        getNativeDataType = jutil.make_method('getNativeDataType', '()Ljava/lang/Class;',
                                              'Returns the native data type of image planes for this reader, as returned by IFormatReader.openPlane(int, int, int, int, int) or IFormatWriter#saveData.')
        getStatusListeners = jutil.make_method('getStatusListeners', '()[Lloci/formats/StatusListener;',
                                               'Gets a list of all registered status update listeners.')
        getSuffixes = jutil.make_method('getSuffixes', '()Ljava/lang/String;', 
                                        'Gets the default file suffixes for this file format.')
        getWriter = jutil.make_method('getWriter', '()Lloci/formats/IFormatWriter;', 
                                      'Gets the writer used to save the current file.')
#        getWriter = jutil.make_method('getWriter', '(Ljava/lang/Class)Lloci/formats/IFormatWriter;', 
#                                      'Gets the file format writer instance matching the given class.')
#        getWriter = jutil.make_method('getWriter', '(Ljava/lang/String;)Lloci/formats/IFormatWriter;', 

'Return the dimension order as a five-character string, e.g. "XYCZT"')
        getMetadataValue = jutil.make_method('getMetadataValue',
                                             '(Ljava/lang/String;)'
                                             'Ljava/lang/Object;',
                                             'Look up a specific metadata value from the store')
        getSeriesMetadata = jutil.make_method('getSeriesMetadata',
                                              '()Ljava/util/Hashtable;',
                                              'Obtains the hashtable contaning the series metadata field/value pairs')
        getSeriesCount = jutil.make_method('getSeriesCount',
                                           '()I',
                                           'Return the # of image series in the file')
        getSeries = jutil.make_method('getSeries', '()I',
                                      'Return the currently selected image series')
        getImageCount = jutil.make_method('getImageCount',
                                          '()I','Determines the number of images in the current file')
        getIndex = jutil.make_method('getIndex', '(III)I',
                                     'Get the plane index given z, c, t')
        getRGBChannelCount = jutil.make_method('getRGBChannelCount',
                                               '()I','Gets the number of channels per RGB image (if not RGB, this returns 1')
        getSizeC = jutil.make_method('getSizeC', '()I',
                                     'Get the number of color planes')
        getSizeT = jutil.make_method('getSizeT', '()I',
                                     'Get the number of frames in the image')
        getSizeX = jutil.make_method('getSizeX', '()I',
                                     'Get the image width')
        getSizeY = jutil.make_method('getSizeY', '()I',
                                     'Get the image height')
        getSizeZ = jutil.make_method('getSizeZ', '()I',
                                     'Get the image depth')
        getPixelType = jutil.make_method('getPixelType', '()I',
                                         'Get the pixel type: see FormatTools for types')
        isLittleEndian = jutil.make_method('isLittleEndian',

stream - the RandomAccessInputStream to be used to read the file contents
            
            Note that both isThisTypeS and isThisTypeStream must return true
            for the type to truly be handled.''')
        def setId(self, path):
            '''Set the name of the file'''
            jutil.call(self.o, 'setId', 
                       '(Ljava/lang/String;)V',
                       path)
                                            
        getMetadataStore = jutil.make_method('getMetadataStore', '()Lloci/formats/meta/MetadataStore;',
                                             'Retrieves the current metadata store for this reader.')
        get8BitLookupTable = jutil.make_method(
            'get8BitLookupTable',
            '()[[B', 'Get a lookup table for 8-bit indexed images')
        get16BitLookupTable = jutil.make_method(
            'get16BitLookupTable',
            '()[[S', 'Get a lookup table for 16-bit indexed images')
        def get_class_name(self):
            return jutil.call(jutil.call(self.o, 'getClass', '()Ljava/lang/Class;'),
                              'getName', '()Ljava/lang/String;')
        
        @property
        def suffixNecessary(self):
            if self.get_class_name() == 'loci.formats.in.JPKReader':
                return True;
            env = jutil.get_env()
            klass = env.get_object_class(self.o)
            field_id = env.get_field_id(klass, "suffixNecessary", "Z")
            if field_id is None:
                return None
            return env.get_boolean_field(self.o, field_id)

setSeries = jutil.make_method('setSeries','(I)V','Set the currently selected image series')
        setGroupFiles = jutil.make_method('setGroupFiles', '(Z)V', 
                                          'Force reader to group or not to group files in a multi-file set')
        setMetadataStore = jutil.make_method('setMetadataStore',
                                             '(Lloci/formats/meta/MetadataStore;)V',
                                             'Sets the default metadata store for this reader.')
        setMetadataOptions = jutil.make_method('setMetadataOptions',
                                               '(Lloci/formats/in/MetadataOptions;)V',
                                               'Sets the metadata options used when reading metadata')
        setOriginalMetadataPopulated = jutil.make_method(
            'setOriginalMetadataPopulated', '(Z)V')
        isThisTypeS = jutil.make_method(
            'isThisType',
            '(Ljava/lang/String;)Z',
            'Return true if the filename might be handled by this reader')
        isThisTypeSZ = jutil.make_method(
            'isThisType',
            '(Ljava/lang/String;Z)Z',
            '''Return true if the named file is handled by this reader.
            
            filename - name of file
            
            allowOpen - True if the reader is allowed to open files
                        when making its determination
            ''')
        isThisTypeStream = jutil.make_method(
            'isThisType',
            '(Lloci/common/RandomAccessInputStream;)Z',
            '''Return true if the stream might be parseable by this reader.
            
            stream - the RandomAccessInputStream to be used to read the file contents

def get_parameter_wrapper(parameter):
    '''wrap the imagej.plugin.Parameter class'''
    class Parameter(object):
        def __init__(self):
            self.o = parameter
        label = J.make_method('label', '()Ljava/lang/String;',
                              'Label to display in editor')
        digits = J.make_method('digits', '()I',
                               'Number of digits to display to right of decimal point')
        columns = J.make_method('columns', '()I',
                                'Number of columns in edit box')
        units = J.make_method('units', '()Ljava/lang/String;',
                              'Units to display to right of edit box')
        widget = J.make_method('widget', '()Ljava/lang/String;',
                             'Name of display widget')
        required = J.make_method('required', '()Z',
                                 'True if required, False if default available')
        persist = J.make_method('persist', '()Ljava/lang/String;',
                                'Key to use when persisting field value')
        output = J.make_method('output', '()Z',
                               'True if field is an output parameter, '
                               'False if field is an input parameter')
    return Parameter()

'()Ljava/util/Hashtable;',
                                              'Obtains the hashtable contaning the series metadata field/value pairs')
        getSeriesCount = jutil.make_method('getSeriesCount',
                                           '()I',
                                           'Return the # of image series in the file')
        getSeries = jutil.make_method('getSeries', '()I',
                                      'Return the currently selected image series')
        getImageCount = jutil.make_method('getImageCount',
                                          '()I','Determines the number of images in the current file')
        getIndex = jutil.make_method('getIndex', '(III)I',
                                     'Get the plane index given z, c, t')
        getRGBChannelCount = jutil.make_method('getRGBChannelCount',
                                               '()I','Gets the number of channels per RGB image (if not RGB, this returns 1')
        getSizeC = jutil.make_method('getSizeC', '()I',
                                     'Get the number of color planes')
        getSizeT = jutil.make_method('getSizeT', '()I',
                                     'Get the number of frames in the image')
        getSizeX = jutil.make_method('getSizeX', '()I',
                                     'Get the image width')
        getSizeY = jutil.make_method('getSizeY', '()I',
                                     'Get the image height')
        getSizeZ = jutil.make_method('getSizeZ', '()I',
                                     'Get the image depth')
        getPixelType = jutil.make_method('getPixelType', '()I',
                                         'Get the pixel type: see FormatTools for types')
        isLittleEndian = jutil.make_method('isLittleEndian',
                                           '()Z','Return True if the data is in little endian order')
        isRGB = jutil.make_method('isRGB', '()Z',
                                  'Return True if images in the file are RGB')
        isInterleaved = jutil.make_method('isInterleaved', '()Z',
                                          'Return True if image colors are interleaved within a plane')
        isIndexed = jutil.make_method('isIndexed', '()Z',

'Gets whether or not the channels in an image are interleaved.')
        isSupportedType = jutil.make_method('isSupportedType', '(I)Z', 
                                            'Checks if the given pixel type is supported.')
#        saveBytes = jutil.make_method('saveBytes', '([BZ)V', 
#                                      'Saves the given byte array to the current file.')
        saveBytes = jutil.make_method('saveBytes', '([BIZZ)V', 
                                      'Saves the given byte array to the given series in the current file.')
        savePlane = jutil.make_method('savePlane', '(Ljava/lang/Object;Z)V', 
                                      'Saves the given image plane to the current file.')
#        savePlane = jutil.make_method('savePlane', '(Ljava/lang/Object;IZZ)V', 
#                                      'Saves the given image plane to the given series in the current file.')
        setColorModel = jutil.make_method('setColorModel', '(Ljava/awt/image/ColorModel;)V', 
                                          'Sets the color model.')
        setCompression = jutil.make_method('setCompression', '(Ljava/lang/String;)V', 
                                           'Sets the current compression type.')
        setFramesPerSecond = jutil.make_method('setFramesPerSecond', '(I)V', 
                                               'Sets the frames per second to use when writing.')
        setInterleaved = jutil.make_method('setInterleaved', '(Z)V', 
                                           'Sets whether or not the channels in an image are interleaved.')
        setMetadataRetrieve = jutil.make_method('setMetadataRetrieve', '(Lloci/formats/meta/MetadataRetrieve;)V', 
                                                'Sets the metadata retrieval object from which to retrieve standardized metadata.')
    return IFormatWriter

def wrap_data_view(view):
    class DataView(object):
        def __init__(self, o=view):
            self.o = o
        isCompatible = J.make_method("isCompatible", "(Limagej/data/Data;)Z")
        initialize = J.make_method("initialize", "(Limagej/data/Data;)V")
        getData = J.make_method("getData", "()Limagej/data/Data;")
        getPlanePosition = J.make_method(
            "getPlanePosition", "()Limagej/data/Position;")
        setSelected = J.make_method("setSelected", "(Z)V")
        isSelected = J.make_method("isSelected", "()Z")
        getPreferredWidth = J.make_method("getPreferredWidth", "()I")
        getPreferredHeight = J.make_method("getPreferredHeight", "()I")
        update = make_invoke_method("update")
        rebuild = make_invoke_method("rebuild")
        dispose = make_invoke_method("dispose")
    return DataView()

def get_parameter_wrapper(parameter):
    '''wrap the imagej.plugin.Parameter class'''
    class Parameter(object):
        def __init__(self):
            self.o = parameter
        label = J.make_method('label', '()Ljava/lang/String;',
                              'Label to display in editor')
        digits = J.make_method('digits', '()I',
                               'Number of digits to display to right of decimal point')
        columns = J.make_method('columns', '()I',
                                'Number of columns in edit box')
        units = J.make_method('units', '()Ljava/lang/String;',
                              'Units to display to right of edit box')
        widget = J.make_method('widget', '()Ljava/lang/String;',
                             'Name of display widget')
        required = J.make_method('required', '()Z',
                                 'True if required, False if default available')
        persist = J.make_method('persist', '()Ljava/lang/String;',
                                'Key to use when persisting field value')
        output = J.make_method('output', '()Z',
                               'True if field is an output parameter, '
                               'False if field is an input parameter')