#!/usr/bin/env python
##############################################################################
#
# diffpy.srfit by DANSE Diffraction group
# Simon J. L. Billinge
# (c) 2008 The Trustees of Columbia University
# in the City of New York. All rights reserved.
#
# File coded by: Chris Farrow
#
# See AUTHORS.txt for a list of people who contributed.
# See LICENSE_DANSE.txt for license information.
#
##############################################################################
"""This module contains parsers for SAS data.
SASParser uses the sas DataLoader class to load data.
"""
__all__ = ["SASParser"]
from diffpy.srfit.exceptions import ParseError
from diffpy.srfit.fitbase.profileparser import ProfileParser
[docs]
class SASParser(ProfileParser):
"""Class for parsing a sas profile.
This uses a sas DataLoader to load the data. The DataInfo object it returns
is held in the metadata under the name "datainfo".
Attributes
Attributes
----------
_format
Name of the data format that this parses (string, default
""). The format string is a unique identifier for the data
format handled by the parser.
_banks
The data from each bank. Each bank contains a
(x, y, dx, dy) tuple:
x
A numpy array containing the independent
variable read from the file.
y
A numpy array containing the profile
from the file.
dx
A numpy array containing the uncertainty in x
read from the file. This is 0 if the
uncertainty cannot be read.
dy
A numpy array containing the uncertainty read
from the file. This is 0 if the uncertainty
cannot be read.
_x
Independent variable from the chosen bank
_y
Profile from the chosen bank
_dx
Uncertainty in independent variable from the chosen bank
_dy
Uncertainty in profile from the chosen bank
_meta
A dictionary containing metadata read from the file.
General Metadata
----------------
filename
The name of the file from which data was parsed. This key
will not exist if data was not read from file.
nbanks
The number of banks parsed.
bank
The chosen bank number.
Metadata
--------
datainfo
The DataInfo object used to do the data parsing.
These may appear in the metadata dictionary
"""
_format = "SAS"
[docs]
def parseFile(self, filename):
"""Parse a file and set the _x, _y, _dx, _dy and _meta variables.
This wipes out the currently loaded data and selected bank number.
Parameters
----------
filename
The name of the file to parse
Raises IOError if the file cannot be read
Raises ParseError if the file cannot be parsed
"""
import sasdata.dataloader.loader as sas_dataloader
Loader = sas_dataloader.Loader
loader = Loader()
try:
data = loader.load(str(filename))
except RuntimeError as e:
raise ParseError(e)
except ValueError as e:
raise ParseError(e)
self._banks = []
self._meta = {}
self._meta["filename"] = filename
self._meta["datainfo"] = data
for data_obj in data:
self._banks.append(
[data_obj.x, data_obj.y, data_obj.dx, data_obj.dy]
)
# FIXME: Revisit when we refactor the SAS characteristic functions.
# Why is a list imported but only the first element is taken?
# Is this desired behavior?
self.selectBank(0)
return
[docs]
def parseString(self, patstring):
"""Parse a string and set the _x, _y, _dx, _dy and _meta variables.
When _dx or _dy cannot be obtained in the data format it is set to 0.
This wipes out the currently loaded data and selected bank number.
Parameters
----------
patstring
A string containing the pattern
Raises ParseError if the string cannot be parsed
"""
# This calls on parseFile, as that is how the sas data loader works.
import tempfile
fh, fn = tempfile.mkstemp()
outfile = open(fn, "w")
fn.write(patstring)
outfile.close()
self.parseFile(fn)
del self._metadata["filename"]
# Close the temporary file and delete it
import os
os.close(fh)
os.remove(fn)
return
# End of class SASParser