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 += ' %s' % args.operation # Handle the expression, which must be enclosed in " if not None. if args.expression in [None, 'None']: cmd += ' None' else: cmd += ' "%s"' % args.expression cmd += imagej2_base_utils.handle_none_type(args.bin_constant, val_type='int') cmd += imagej2_base_utils.handle_none_type(args.float_constant) 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)
# 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 += ' %s' % args.operation # Handle the expression, which must be enclosed in " if not None. if args.expression in [ None, 'None' ]: cmd += ' None' else: cmd += ' "%s"' % args.expression cmd += imagej2_base_utils.handle_none_type( args.bin_constant, val_type='int' ) cmd += imagej2_base_utils.handle_none_type( args.float_constant ) 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:
# 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' % args.input_datatype cmd += ' %s ' % args.noise cmd += imagej2_base_utils.handle_none_type( args.standard_deviation ) cmd += imagej2_base_utils.handle_none_type( args.radius ) cmd += imagej2_base_utils.handle_none_type( args.threshold ) cmd += ' %s' % args.which_outliers cmd += ' %s' % args.randomj cmd += imagej2_base_utils.handle_none_type( args.trials ) cmd += imagej2_base_utils.handle_none_type( args.probability ) cmd += imagej2_base_utils.handle_none_type( args.lammbda ) cmd += imagej2_base_utils.handle_none_type( args.order, val_type='int' ) cmd += imagej2_base_utils.handle_none_type( args.mean ) cmd += imagej2_base_utils.handle_none_type( args.sigma ) cmd += imagej2_base_utils.handle_none_type( args.min ) cmd += imagej2_base_utils.handle_none_type( args.max ) cmd += ' %s' % args.insertion cmd += ' %s' % tmp_output_path
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 += ' %s' % args.size cmd += ' %.3f' % args.circularity_min cmd += ' %.3f' % args.circularity_max cmd += ' %s' % args.show cmd += ' %s' % args.display_results cmd += '%s' % imagej2_base_utils.handle_none_type( args.all_results, val_type='str' ) cmd += ' %s' % args.exclude_edges cmd += ' %s' % args.include_holes cmd += '%s' % imagej2_base_utils.handle_none_type( tmp_output_path, val_type='str' ) cmd += ' %s' % args.output_datatype cmd += '%s' % imagej2_base_utils.handle_none_type( args.results, val_type='str' ) # 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 )
# 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 += " %s" % args.black_background cmd += " %s" % args.size cmd += " %.3f" % args.circularity_min cmd += " %.3f" % args.circularity_max cmd += " %s" % args.show cmd += " %s" % args.display_results cmd += "%s" % imagej2_base_utils.handle_none_type(args.all_results, val_type="str") cmd += " %s" % args.exclude_edges cmd += " %s" % args.include_holes cmd += "%s" % imagej2_base_utils.handle_none_type(tmp_output_path, val_type="str") cmd += " %s" % args.output_datatype cmd += "%s" % imagej2_base_utils.handle_none_type(args.results, val_type="str") # 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)
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 += ' %s' % args.black_background cmd += ' %s' % args.size cmd += ' %.3f' % args.circularity_min cmd += ' %.3f' % args.circularity_max cmd += ' %s' % args.show cmd += ' %s' % args.display_results cmd += '%s' % imagej2_base_utils.handle_none_type(args.all_results, val_type='str') cmd += ' %s' % args.exclude_edges cmd += ' %s' % args.include_holes cmd += '%s' % imagej2_base_utils.handle_none_type(tmp_output_path, val_type='str') cmd += ' %s' % args.output_datatype cmd += '%s' % imagej2_base_utils.handle_none_type(args.results, val_type='str') # Run the command. proc = subprocess.Popen(args=cmd, stderr=tmp_stderr, stdout=tmp_stdout, shell=True) rc = proc.wait() # Handle execution errors.
# 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 += ' %s' % args.equalize_histogram cmd += imagej2_base_utils.handle_none_type( args.saturated_pixels ) cmd += ' %s' % args.normalize 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:
# 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 += ' %s' % args.input_datatype cmd += ' %s ' % args.noise cmd += imagej2_base_utils.handle_none_type( args.standard_deviation ) cmd += imagej2_base_utils.handle_none_type( args.radius ) cmd += imagej2_base_utils.handle_none_type( args.threshold ) cmd += ' %s' % args.which_outliers cmd += ' %s' % args.randomj cmd += imagej2_base_utils.handle_none_type( args.trials ) cmd += imagej2_base_utils.handle_none_type( args.probability ) cmd += imagej2_base_utils.handle_none_type( args.lammbda ) cmd += imagej2_base_utils.handle_none_type( args.order, val_type='int' ) cmd += imagej2_base_utils.handle_none_type( args.mean ) cmd += imagej2_base_utils.handle_none_type( args.sigma ) cmd += imagej2_base_utils.handle_none_type( args.min ) cmd += imagej2_base_utils.handle_none_type( args.max ) cmd += ' %s' % args.insertion cmd += ' %s' % tmp_output_path
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 += ' %s' % args.equalize_histogram cmd += imagej2_base_utils.handle_none_type(args.saturated_pixels) cmd += ' %s' % args.normalize 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)