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:
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()
# 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)
# Set the size of the memory allocation pool used by the JVM.
memory_size = imagej2_base_utils.get_max_heap_size_value(args.max_heap_size_type, args.max_heap_size)
# 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(memory_size, 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 += " %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:
error_message = imagej2_base_utils.get_stderr_exception(tmp_err, tmp_stderr, tmp_out, tmp_stdout)
imagej2_base_utils.stop_err(error_message)
# Handle processing errors.
if os.path.getsize(error_log) > 0:
