Source code for xrayutilities.io.rigaku_ras

# This file is part of xrayutilities.
#
# xrayutilities is free software; you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation; either version 2 of the License, or
# (at your option) any later version.
#
# This program is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
# GNU General Public License for more details.
#
# You should have received a copy of the GNU General Public License
# along with this program; if not, see <http://www.gnu.org/licenses/>.
#
# Copyright (C) 2015-2016 Dominik Kriegner <dominik.kriegner@gmail.com>


"""
class for reading data + header information from Rigaku RAS (3-column ASCII)
files

Such datafiles are generated by the Smartlab Guidance software from Rigaku.
"""

import os.path
import re
from itertools import islice

import numpy
import numpy.lib.recfunctions

from .. import config
from ..exception import InputError
# relative imports from xrayutilities
from .helper import xu_open

re_measstart = re.compile(r"^\*RAS_DATA_START")
re_measend = re.compile(r"^\*RAS_DATA_END")
re_headerstart = re.compile(r"^\*RAS_HEADER_START")
re_headerend = re.compile(r"^\*RAS_HEADER_END")
re_datastart = re.compile(r"^\*RAS_INT_START")
re_dataend = re.compile(r"^\*RAS_INT_END")
re_scanaxis = re.compile(r"^\*MEAS_SCAN_AXIS_X_INTERNAL")
re_intstart = re.compile(r"^\*RAS_INT_START")
re_datestart = re.compile(r"^\*MEAS_SCAN_START_TIME")
re_datestop = re.compile(r"^\*MEAS_SCAN_END_TIME")
re_initmoponame = re.compile(r"^\*MEAS_COND_AXIS_NAME_INTERNAL")
re_initmopovalue = re.compile(r"^\*MEAS_COND_AXIS_POSITION")
re_datacount = re.compile(r"^\*MEAS_DATA_COUNT")
re_measspeed = re.compile(r"^\*MEAS_SCAN_SPEED ")
re_measstep = re.compile(r"^\*MEAS_SCAN_STEP ")


[docs]class RASFile(object): """ Represents a RAS data file. The file is read during the constructor call Parameters ---------- filename : str name of the ras-file path : str, optional path to the data file """ def __init__(self, filename, path=None): self.filename = filename if path is None: self.full_filename = self.filename else: self.full_filename = os.path.join(path, self.filename) self.scans = [] self.Read()
[docs] def Read(self): """ Read the data from the file """ with xu_open(self.full_filename) as fid: while True: t = fid.tell() line = fid.readline() line = line.decode('ascii', 'ignore') if config.VERBOSITY >= config.DEBUG: print("XU.io.RASFile: %d: '%s'" % (t, line)) if re_measstart.match(line): continue elif re_headerstart.match(line): s = RASScan(self.full_filename, t) self.scans.append(s) fid.seek(s.fidend) # set handle to after scan elif re_measend.match(line) or line in (None, ''): break else: continue if len(self.scans) > 0: self.scan = self.scans[0]
[docs]class RASScan(object): """ Represents a single Scan portion of a RAS data file. The scan is parsed during the constructor call Parameters ---------- filename : str file name of the data file pos : int seek position of the 'RAS_HEADER_START' line """ def __init__(self, filename, pos): self.filename = filename self.fidpos = pos self.fidend = pos with xu_open(self.filename) as self.fid: self.fid.seek(self.fidpos) self._parse_header() self._parse_data() self.fidend = self.fid.tell() def _parse_header(self): """ Read the data from the file """ # read header self.header = [] keys = {} position = {} offset = self.fid.tell() for line in self.fid: offset += len(line) line = line.decode('ascii', 'ignore') self.header.append(line) if config.VERBOSITY >= config.DEBUG: print("XU.io.RASScan: %d: '%s'" % (offset, line)) if re_datestart.match(line): m = line.split(' ', 1)[-1].strip() self.scan_start = m.strip('"') elif re_datestop.match(line): m = line.split(' ', 1)[-1].strip() self.scan_stop = m.strip('"') elif re_initmoponame.match(line): idx = int(line.split('-', 1)[-1].split()[0]) moname = line.split(' ', 1)[-1].strip().strip('"') keys[idx] = moname elif re_initmopovalue.match(line): idx = int(line.split('-', 1)[-1].split()[0]) mopos = line.split(' ', 1)[-1].strip().strip('"') try: mopos = float(mopos) except ValueError: pass position[idx] = mopos elif re_scanaxis.match(line): self.scan_axis = line.split(' ', 1)[-1].strip().strip('"') elif re_datacount.match(line): length = line.split(' ', 1)[-1].strip().strip('"') self.length = int(float(length)) elif re_measspeed.match(line): speed = line.split(' ', 1)[-1].strip().strip('"') self.meas_speed = float(speed) elif re_measstep.match(line): step = line.split(' ', 1)[-1].strip().strip('"') self.meas_step = float(step) elif re_headerend.match(line): break # generate header dictionary self.init_mopo = {} for k in keys: self.init_mopo[keys[k]] = position[k] self.fid.seek(offset) def _parse_data(self): line = self.fid.readline().decode('ascii', 'ignore') offset = self.fid.tell() if re_datastart.match(line): lines = islice(self.fid, self.length) self.data = numpy.genfromtxt(lines) self.data = numpy.rec.fromrecords(self.data, names=[self.scan_axis, 'int', 'att']) self.fid.seek(offset) lines = islice(self.fid, self.length) dlength = numpy.sum([len(line) for line in lines]) if config.VERBOSITY >= config.DEBUG: print("XU.io.RASScan: offset %d; data-length %d" % (offset, dlength)) self.fid.seek(offset + dlength) else: raise IOError('File handle at wrong position to read data!')
[docs]def getras_scan(scanname, scannumbers, *args, **kwargs): """ function to obtain the angular cooridinates as well as intensity values saved in RAS datafiles. Especially useful for reciprocal space map measurements, and to combine date from several scans further more it is possible to obtain even more positions from the data file if more than two string arguments with its names are given Parameters ---------- scanname : str name of the scans, for multiple scans this needs to be a template string scannumbers : int, tuple or list number of the scans of the reciprocal space map args : str, optional names of the motors. to read reciprocal space maps measured in coplanar diffraction give: - omname: name of the omega motor (or its equivalent) - ttname: name of the two theta motor (or its equivalent) kwargs : dict keyword arguments forwarded to RASFile function Returns ------- [ang1, ang2, ...] : list angular positions are extracted from the respective scan header, or motor positions during the scan. this is omitted if no `args` are given rasdata : ndarray the data values (includes the intensities e.g. rasdata['int']). Examples -------- >>> [om, tt], MAP = xu.io.getras_scan('text%05d.ras', 36, 'Omega', >>> 'TwoTheta') """ if isinstance(scannumbers, (list, tuple)): scanlist = scannumbers else: scanlist = list([scannumbers]) angles = dict.fromkeys(args) for key in angles: if not isinstance(key, str): raise InputError("*arg values need to be strings with motornames") angles[key] = numpy.zeros(0) buf = numpy.zeros(0) MAP = numpy.zeros(0) for nr in scanlist: rasfile = RASFile(scanname % nr, **kwargs) for scan in rasfile.scans: sdata = scan.data if MAP.dtype == numpy.float64: MAP.dtype = sdata.dtype # append scan data to MAP, where all data are stored MAP = numpy.append(MAP, sdata) # check type of scan for i in range(len(args)): motname = args[i] scanlength = len(sdata) try: buf = sdata[motname] except ValueError: buf = scan.init_mopo[motname] * numpy.ones(scanlength) angles[motname] = numpy.concatenate((angles[motname], buf)) retval = [] for motname in args: # create return values in correct order retval.append(angles[motname]) if not args: return MAP elif len(args) == 1: return retval[0], MAP else: return retval, MAP