annotate jython_utils.py @ 0:f6df6830d5ec draft

"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"

import imagej2_base_utils
from ij import IJ

IMAGE_PLUS_IMAGE_TYPE_FIELD_VALUES = { '0':'GRAY8', '1':'GRAY16', '2':'GRAY32',
                                       '3':'COLOR_256', '4':'COLOR_RGB' }

def asbool( val ):
    return str( val ).lower() in [ 'yes', 'true' ]

def convert_before_saving_as_tiff( image_plus ):
    # The bUnwarpJ plug-in produces TIFF image stacks consisting of 3
    # slices which can be viewed in ImageJ.  The 3 slices are: 1) the
    # registered image, 2) the target image and 3) the black/white warp
    # image.  When running bUnwarpJ from the command line (as these
    # Galaxy wrappers do) the initial call to IJ.openImage() (to open the
    # registered source and target images produced by bUnwarpJ) in the
    # tool's jython_script.py returns an ImagePlus object with a single
    # slice which is the "generally undesired" slice 3 discussed above.
    # However, a call to IJ.saveAs() will convert the single-slice TIFF
    # into a 3-slice TIFF image stack (as described above) if the selected
    # format for saving is TIFF.  Galaxy supports only single-layered
    # images, so to work around this behavior, we have to convert the
    # image to something other than TIFF so that slices are eliminated.
    # We can then convert back to TIFF for saving.  There might be a way
    # to do this without converting twice, but I spent a lot of time looking
    # and I have yet to discover it.
    tmp_dir = imagej2_base_utils.get_temp_dir()
    tmp_out_png_path = imagej2_base_utils.get_temporary_image_path( tmp_dir, 'png' )
    IJ.saveAs( image_plus, 'png', tmp_out_png_path )
    return IJ.openImage( tmp_out_png_path )

def get_binary_options( black_background, iterations=1, count=1, pad_edges_when_eroding='no' ):
    options = [ 'edm=Overwrite', 'iterations=%d' % iterations, 'count=%d' % count ]
    if asbool( pad_edges_when_eroding ):
        options.append( 'pad' )
    if asbool( black_background ):
        options.append( "black" )
    return " ".join( options )

def get_display_image_type( image_type ):
    return IMAGE_PLUS_IMAGE_TYPE_FIELD_VALUES.get( str( image_type ), None )

def handle_error( error_log, msg ):
    # Java writes a lot of stuff to stderr, so the received error_log 
    # will log actual errors.
    elh = open( error_log, 'wb' )
    elh.write( msg )
    elh.close()