# 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:
imagej2_base_utils.stop_err( "ImageJ not found!" )
cmd += ' %s' % error_log
cmd += ' %s' % tmp_input_path
cmd += ' %.3f' % args.threshold_min
cmd += ' %.3f' % args.threshold_max
cmd += ' %s' % args.method
cmd += ' %s' % args.display
cmd += ' %s' % args.black_background
cmd += ' %s' % args.stack_histogram
cmd += ' %s' % tmp_output_path
cmd += ' %s' % args.output_datatype
# Run the command.
proc = subprocess.Popen( args=cmd, stderr=tmp_stderr, stdout=tmp_stdout, shell=True )
rc = proc.wait()
# Handle execution errors.
if rc != 0:
tmp_dir = imagej2_base_utils.get_temp_dir()
source_image_path = imagej2_base_utils.get_input_image_path( tmp_dir, args.source_image, args.source_image_format )
target_image_path = imagej2_base_utils.get_input_image_path( tmp_dir, args.target_image, args.target_image_format )
source_elastic_transformation_path = imagej2_base_utils.get_input_image_path( tmp_dir, args.source_elastic_transformation, 'txt' )
target_raw_transformation_path = imagej2_base_utils.get_input_image_path( tmp_dir, args.target_raw_transformation, 'txt' )
# 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' )
# Build the command line to compose the raw and elastic transformations.
cmd = imagej2_base_utils.get_base_cmd_bunwarpj( None )
if cmd is None:
imagej2_base_utils.stop_err( "bUnwarpJ not found!" )
cmd += ' -compose_raw_elastic'
# Target is sent before source.
cmd += ' %s' % target_image_path
cmd += ' %s' % source_image_path
cmd += ' %s' % target_raw_transformation_path
cmd += ' %s' % source_elastic_transformation_path
cmd += ' %s' % args.output
# Compose the raw and elastic transformations into another raw transformation using bUnwarpJ.
proc = subprocess.Popen( args=cmd, stderr=subprocess.PIPE, stdout=subprocess.PIPE, shell=True )
rc = proc.wait()
if rc != 0:
error_message = imagej2_base_utils.get_stderr_exception( tmp_err, tmp_stderr, tmp_out, tmp_stdout )
imagej2_base_utils.stop_err( error_message )
#!/usr/bin/env python
import argparse
import imagej2_base_utils
import imagej2_utils
if __name__=="__main__":
# Parse Command Line.
parser = argparse.ArgumentParser()
parser.add_argument( '--in_fname', dest='in_fname', help='Path to the input file' )
parser.add_argument( '--input_datatype', dest='input_datatype', help='Input image datatype' )
parser.add_argument( '--output_datatype', dest='output_datatype', help='Output image datatype' )
parser.add_argument( '--out_fname', help='Path to the output file' )
args = parser.parse_args()
# Start the JVM via the Javabridge.
imagej2_utils.start_vm( args=None, class_path=None, max_heap_size=None, run_headless=True )
try:
tmp_dir = imagej2_base_utils.get_temp_dir()
in_image_path = imagej2_base_utils.get_input_image_path( tmp_dir, args.in_fname, args.input_datatype )
# Load the input image.
image, scale = imagej2_utils.load_image( in_image_path, rescale=False, wants_max_intensity=True )
# Write the output image.
out_image_path = imagej2_base_utils.get_temporary_image_path( tmp_dir, args.output_datatype )
imagej2_utils.write_image( image_path=out_image_path, pixels=image, pixel_type=str( image.dtype ), move_to=args.out_fname )
except Exception, e:
imagej2_base_utils.stop_err( str( e ) )
finally:
imagej2_utils.kill_vm()
imagej2_base_utils.cleanup_before_exit( tmp_dir )
dest='output_datatype',
help='Output image datatype')
parser.add_argument('--out_fname', help='Path to the output file')
args = parser.parse_args()
# Start the JVM via the Javabridge.
imagej2_utils.start_vm(args=None,
class_path=None,
max_heap_size=None,
run_headless=True)
try:
tmp_dir = imagej2_base_utils.get_temp_dir()
in_image_path = imagej2_base_utils.get_input_image_path(
tmp_dir, args.in_fname, args.input_datatype)
# Load the input image.
image, scale = imagej2_utils.load_image(in_image_path,
rescale=False,
wants_max_intensity=True)
# Write the output image.
out_image_path = imagej2_base_utils.get_temporary_image_path(
tmp_dir, args.output_datatype)
imagej2_utils.write_image(image_path=out_image_path,
pixels=image,
pixel_type=str(image.dtype),
move_to=args.out_fname)
except Exception, e:
imagej2_base_utils.stop_err(str(e))
finally:
imagej2_utils.kill_vm()
imagej2_base_utils.cleanup_before_exit(tmp_dir)
