#!/usr/bin/env libtbx.python # # iotbx.xds.xds_inp.py # # James Parkhurst, Richard Gildea, Diamond Light Source, 2014 # # Class to read all the data from a XDS.INP file # from __future__ import absolute_import, division, print_function class reader: """A class to read the XDS.INP file used in XDS""" def __init__(self): pass @staticmethod def is_xds_inp_file(filename): """Check if the given file is an XDS.INP file. Params: filename The XDS.INP filename Returns: True/False the file is a XDS.INP file """ import os return os.path.basename(filename) == 'XDS.INP' def read_file(self, filename, check_filename = True): """Read the XDS.INP file. See http://xds.mpimf-heidelberg.mpg.de/html_doc/xds_files.html for more information about the file format. Param: filename The path to the file """ # defaults self.unit_cell_constants = None self.minimum_valid_pixel_value = 0 self.corrections = None self.trusted_region = None self.maximum_number_of_processor = 32 self.fraction_of_polarization = 0.5 self.polarization_plane_normal = None self.starting_angle = 0.0 self.oscillation_range = None #STARTING_FRAME=first data image (as specified by DATA_RANGE=) self.starting_frame = None self.include_resolution_range = [20.0, 0.0] self.space_group_number = 1 self.max_fac_rmeas = 2.0 self.data_range = None self.sensor_thickness = 0 self.silicon = None self.num_segments = 0 self.segment_orgx = [] self.segment_orgy = [] self.direction_of_segment_x_axis = [] self.direction_of_segment_y_axis = [] self.segment_distance = [] self.segment = [] # Check and read file if reader.is_xds_inp_file(filename): with open(filename, 'r') as fh: lines = fh.readlines() else: raise IOError("{0} is not a XDS.INP file".format(filename)) # Parse the tokens self.parse_lines(lines) def parse_lines(self, lines): """Parse the lines Param: tokens The list of lines """ import re parameters = [] self.untrusted_rectangle = [] for record in lines: comment_char = record.find("!") if comment_char > -1: record = record[0:comment_char] record = record.strip() tok = [c for c in re.split(r' |\t', record) if c != ''] tokens = [] for t in tok: i = t.find('=') if i > -1: tokens.append(t[:i+1]) if (i+1) < len(t): tokens.append(t[i+1:]) else: tokens.append(t) while len(tokens): if len(tokens) == 1: assert tokens[0].find('=') > -1 parameters.append(tokens) break for i_tok, t in enumerate(tokens): if i_tok == 0: assert t.find('=') > -1 elif i_tok > 0 and t.find('=') > -1: parameters.append((tokens[0:i_tok])) tokens = tokens[i_tok:] break elif (i_tok+1) == len(tokens): parameters.append(tokens) tokens = [] break for parameter in parameters: name = parameter[0] if name == 'DETECTOR=': self.detector = " ".join(parameter[1:]) elif name == 'MINIMUM_VALID_PIXEL_VALUE=': self.minimum_valid_pixel_value = float(parameter[1]) elif name == 'OVERLOAD=': self.overload = int(parameter[1]) elif name == 'CORRECTIONS=': if len(parameter) == 1: self.corrections = None else: self.corrections = parameter[1] elif name == 'DIRECTION_OF_DETECTOR_X-AXIS=': self.direction_of_detector_x_axis = [float(_p) for _p in parameter[-3:]] elif name == 'DIRECTION_OF_DETECTOR_Y-AXIS=': self.direction_of_detector_y_axis = [float(_p) for _p in parameter[-3:]] elif name == 'TRUSTED_REGION=': self.trusted_region = [float(_p) for _p in parameter[-2:]] elif name == 'SENSOR_THICKNESS=': self.sensor_thickness = float(parameter[1]) elif name == 'SILICON=': self.silicon = float(parameter[1]) elif name == 'UNTRUSTED_RECTANGLE=': self.untrusted_rectangle.append( [int(_p) for _p in parameter[-4:]]) elif name == 'MAXIMUM_NUMBER_OF_PROCESSORS=': self.maximum_number_of_processor = int(parameter[1]) elif name == 'NX=': self.nx = int(parameter[1]) elif name == 'NY=': self.ny = int(parameter[1]) elif name == 'QX=': self.px = float(parameter[1]) elif name == 'QY=': self.py = float(parameter[1]) elif name == 'ORGX=': self.orgx = float(parameter[1]) elif name == 'ORGY=': self.orgy = float(parameter[1]) elif name == 'ROTATION_AXIS=': self.rotation_axis = [float(_p) for _p in parameter[-3:]] elif name == 'DETECTOR_DISTANCE=': self.detector_distance = float(parameter[1]) elif name == 'X-RAY_WAVELENGTH=': self.xray_wavelength = float(parameter[1]) elif name == 'INCIDENT_BEAM_DIRECTION=': self.incident_beam_direction = [float(_p) for _p in parameter[-3:]] elif name == 'FRACTION_OF_POLARIZATION=': self.fraction_of_polarization = float(parameter[-1]) elif name == 'POLARIZATION_PLANE_NORMAL=': self.polarization_plane_normal = [float(_p) for _p in parameter[-3:]] elif name == 'FRIEDEL\'S_LAW=': self.friedels_law = bool(parameter[-1]) elif name == 'NAME_TEMPLATE_OF_DATA_FRAMES=': self.name_template_of_data_frames = parameter[1:] elif name == 'STARTING_ANGLE=': self.starting_angle = float(parameter[1]) elif name == 'STARTING_FRAME=': self.starting_frame = float(parameter[1]) elif name == 'OSCILLATION_RANGE=': self.oscillation_range = float(parameter[1]) elif name == 'INCLUDE_RESOLUTION_RANGE=': self.include_resolution_range = [float(_p) for _p in parameter[-2:]] elif name == 'UNIT_CELL_CONSTANTS=': self.unit_cell_constants = [float(_p) for _p in parameter[-6:]] elif name == 'SPACE_GROUP_NUMBER=': self.space_group_number = int(parameter[-1]) elif name == 'MAX_FAC_Rmeas=': self.max_fac_rmeas = float(parameter[-1]) elif name == 'DATA_RANGE=': self.data_range = [int(_p) for _p in parameter[-2:]] elif name == 'SEGMENT=': self.num_segments += 1 self.segment.append( [int(_p) for _p in parameter[-4:]]) elif name == 'DIRECTION_OF_SEGMENT_X-AXIS=': self.direction_of_segment_x_axis.append([float(_p) for _p in parameter[-3:]]) elif name == 'DIRECTION_OF_SEGMENT_Y-AXIS=': self.direction_of_segment_y_axis.append([float(_p) for _p in parameter[-3:]]) elif name == 'SEGMENT_DISTANCE=': self.segment_distance.append(float(parameter[-1])) elif name == 'SEGMENT_ORGX=': self.segment_orgx.append(float(parameter[-1])) elif name == 'SEGMENT_ORGY=': self.segment_orgy.append(float(parameter[-1]))