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 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)
parser = argparse.ArgumentParser() parser.add_argument( '--input', dest='input', help='Path to the input file' ) parser.add_argument( '--input_datatype', dest='input_datatype', help='Datatype of the input image' ) parser.add_argument( '--threshold_min', dest='threshold_min', type=float, help='Minimum threshold value' ) parser.add_argument( '--threshold_max', dest='threshold_max', type=float, help='Maximum threshold value' ) parser.add_argument( '--method', dest='method', help='Threshold method' ) parser.add_argument( '--display', dest='display', help='Display mode' ) parser.add_argument( '--black_background', dest='black_background', help='Black background' ) parser.add_argument( '--stack_histogram', dest='stack_histogram', help='Stack histogram' ) parser.add_argument( '--jython_script', dest='jython_script', help='Path to the Jython script' ) parser.add_argument( '--output', dest='output', help='Path to the output file' ) parser.add_argument( '--output_datatype', dest='output_datatype', help='Datatype of the output image' ) args = parser.parse_args() tmp_dir = imagej2_base_utils.get_temp_dir() # ImageJ expects valid image file extensions, so the Galaxy .dat extension does not # work for some features. The following creates a symlink with an appropriate file # extension that points to the Galaxy dataset. This symlink is used by ImageJ. tmp_input_path = imagej2_base_utils.get_input_image_path( tmp_dir, args.input, args.input_datatype ) tmp_output_path = imagej2_base_utils.get_temporary_image_path( tmp_dir, args.output_datatype ) # Define command response buffers. tmp_out = tempfile.NamedTemporaryFile().name tmp_stdout = open( tmp_out, 'wb' ) tmp_err = tempfile.NamedTemporaryFile().name tmp_stderr = open( tmp_err, 'wb' ) # Java writes a lot of stuff to stderr, so we'll specify a file for handling actual errors. error_log = tempfile.NamedTemporaryFile( delete=False ).name # Build the command line. cmd = imagej2_base_utils.get_base_command_imagej2( None, jython_script=args.jython_script ) if cmd is None:
