# 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) 2015-2019, 2023 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 generate_filenames, 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:
"""
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
"""
[docs]
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(f"XU.io.RASFile: {t}: '{line}'")
if re_measstart.match(line):
continue
if 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:
"""
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
"""
[docs]
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(f"XU.io.RASScan: {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:
try:
self.init_mopo[keys[k]] = position[k]
except KeyError:
# in case of missing position entry in the datafile header
self.init_mopo[keys[k]] = None
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 = sum(len(line) for line in lines)
if config.VERBOSITY >= config.DEBUG:
print(f"XU.io.RASScan: offset {offset}; data-length {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 or list
name of the scans, for multiple scans this can be a template string or
a list of filenames. See
:func:`~xrayutilities.io.helper.generate_filenames` for details and
examples.
scannumbers : int, tuple or list or None
List of scan numbers or generally replacement values for the template
string given as scanname. Set to None if not needed.
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 = getras_scan('text%05d.ras', 36, 'Omega',
... 'TwoTheta') # doctest: +SKIP
"""
filenames = generate_filenames(scanname, 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 fn in filenames:
rasfile = RASFile(fn, **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 motname in args:
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
if len(args) == 1:
return retval[0], MAP
return retval, MAP