# 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) 2013-2021, 2023 Dominik Kriegner <dominik.kriegner@gmail.com>
"""
class for reading data + header information from tty08 data files
tty08 is a system used at beamline P08 at Hasylab Hamburg and creates simple
ASCII files to save the data. Information is easily read from the multicolumn
data file. the functions below enable also to parse the information of the
header
"""
import glob
import os.path
import re
import numpy
import numpy.lib.recfunctions
from ..exception import InputError
# relative imports from xrayutilities
from .helper import xu_open
re_columns = re.compile(r"/\*H")
re_command = re.compile(r"^/\*C command")
re_comment = re.compile(r"^/\*")
re_date = re.compile(r"^/\*D date")
re_epoch = re.compile(r"^/\*T epoch")
re_initmopo = re.compile(r"^/\*M")
[docs]
class tty08File:
"""
Represents a tty08 data file. The file is read during the
Constructor call. This class should work for data stored at
beamline P08 using the tty08 acquisition system.
Parameters
----------
filename : str
tty08-filename
mcadir : str, optional
directory name of MCA files
"""
[docs]
def __init__(self, filename, path=None, mcadir=None):
self.filename = filename
if path is None:
self.full_filename = self.filename
else:
self.full_filename = os.path.join(path, self.filename)
self.Read()
if mcadir is not None:
self.mca_directory = mcadir
self.mca_files = sorted(glob.glob(
os.path.join(self.mca_directory, '*')))
if self.mca_files:
self.ReadMCA()
[docs]
def ReadMCA(self):
self.mca = numpy.empty((len(self.mca_files),
numpy.loadtxt(self.mca_files[0]).shape[0]),
dtype=float)
for i in range(len(self.mca_files)):
mcadata = numpy.loadtxt(self.mca_files[i])
self.mca[i, :] = mcadata[:, 1]
if i == 0:
if len(mcadata.shape) == 2:
self.mca_channels = mcadata[:, 0]
else:
self.mca_channels = numpy.arange(0, mcadata.shape[0])
mcatemp = self.mca.view([('MCA',
(self.mca.dtype, self.mca.shape[1]))])
self.data = numpy.lib.recfunctions.merge_arrays([self.data, mcatemp],
flatten=True)
[docs]
def Read(self):
"""
Read the data from the file
"""
with xu_open(self.full_filename) as fid:
# read header
self.init_mopo = {}
for line in fid:
line = line.decode('ascii')
if re_command.match(line):
m = line.split(':')
self.scan_command = m[1].strip()
if re_date.match(line):
m = line.split(':', 1)
self.scan_date = m[1].strip()
if re_epoch.match(line):
m = line.split(':', 1)
self.epoch = float(m[1])
if re_initmopo.match(line):
m = line[3:]
m = m.split(';')
for e in m:
e = e.split('=')
self.init_mopo[e[0].strip()] = float(e[1])
if re_columns.match(line):
self.columns = tuple(line.split()[1:])
# here all necessary information is read and we can start
# reading the data
break
self.data = numpy.loadtxt(fid, comments="/")
self.data = numpy.rec.fromrecords(self.data, names=self.columns)
[docs]
def gettty08_scan(scanname, scannumbers, *args, **keyargs):
"""
function to obtain the angular cooridinates as well as intensity values
saved in TTY08 datafiles. Especially usefull 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`: the name of the omega motor (or its equivalent)
- `ttname`: the name of the two theta motor (or its equivalent)
keyargs : dict, optional
keyword arguments are passed on to tty08File
Returns
-------
[ang1, ang2, ...] : list, optional
angular positions of the center channel of the position sensitive
detector (numpy.ndarray 1D), omitted if no `args` are given
MAP : ndarray
All the data values as stored in the data file (includes the
intensities e.g. MAP['MCA']).
Examples
--------
>>> [om, tt], MAP = xu.io.gettty08_scan('text%05d.dat', 36, 'omega',
... 'gamma') # doctest: +SKIP
"""
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:
scan = tty08File(scanname % nr, **keyargs)
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
if len(args) == 1:
return retval[0], MAP
return retval, MAP