#/*##########################################################################
#
# The PyMca X-Ray Fluorescence Toolkit
#
# Copyright (c) 2004-2014 European Synchrotron Radiation Facility
#
# This file is part of the PyMca X-ray Fluorescence Toolkit developed at
# the ESRF by the Software group.
#
# Permission is hereby granted, free of charge, to any person obtaining a copy
# of this software and associated documentation files (the "Software"), to deal
# in the Software without restriction, including without limitation the rights
# to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
# copies of the Software, and to permit persons to whom the Software is
# furnished to do so, subject to the following conditions:
#
# The above copyright notice and this permission notice shall be included in
# all copies or substantial portions of the Software.
#
# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
# IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
# FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
# AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
# LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
# OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
# THE SOFTWARE.
#
#############################################################################*/
__author__ = "V.A. Sole - ESRF Data Analysis"
__contact__ = "sole@esrf.fr"
__license__ = "MIT"
__copyright__ = "European Synchrotron Radiation Facility, Grenoble, France"
import sys
import os
import numpy
DEBUG = 0
[docs]class BufferedFile(object):
def __init__(self, filename):
f = open(filename, 'r')
self.__buffer = f.read()
f.close()
self.__buffer = self.__buffer.replace("\x00", "")
self.__buffer = self.__buffer.replace("\r", "\n")
self.__buffer = self.__buffer.replace("\n\n", "\n")
self.__buffer = self.__buffer.split("\n")
self.__currentLine = 0
[docs] def readline(self):
if self.__currentLine >= len(self.__buffer):
return ""
line = self.__buffer[self.__currentLine]
self.__currentLine += 1
return line
[docs] def close(self):
self.__buffer = [""]
self.__currentLine = 0
return
[docs]class OlympusCSVFileParser(object):
def __init__(self, filename):
if not os.path.exists(filename):
raise IOError("File %s does not exists" % filename)
_fileObject = BufferedFile(filename)
#Several measurement per file
ddict = {}
line = _fileObject.readline()
if not line.startswith("\xff\xfeTestID"):
raise IOError("This does not look an Olympus CSV file")
splitLine = line[2:].split("\t")
nSpectra = len(splitLine) - 1
channel = 0
while(len(splitLine) > 1):
key = splitLine[0]
if len(key):
ddict[key] = splitLine[1:]
if key == "NumData":
nChannels = int(splitLine[1])
ddict['data'] = numpy.zeros((nSpectra, nChannels), numpy.float)
else:
ddict['data'][:, channel] = [float(x) for x in splitLine[1:]]
channel += 1
line = _fileObject.readline()
splitLine = line.split("\t")
_fileObject.close()
interestingMotors = ["VacPressure",
"TubeVoltageSet",
"AmbientPressure",
"Realtime",
"Livetime",
"FilterPosition",
"TubeCurrentMon",
"TubeVoltageMon",
"ExposureNum",
"TubeCurrentSet"]
self._motorNames = []
for key in ddict.keys():
#print("Key = ", key, "ken = ", len(ddict[key]))
if key in interestingMotors:
self._motorNames.append(key)
self._data = ddict
def __getitem__(self, item):
motorValues = []
for key in self._motorNames:
motorValues.append(float(self._data[key][item]))
return OlympusCSVScan(self._data, item, motorValues=motorValues)
[docs] def scanno(self):
"""
Gives back the number of scans in the file
"""
return self._data['data'].shape[0]
[docs] def list(self):
return "1:%d" % self.scanno()
[docs] def select(self, key):
"""
key is of the from s.o
scan number, scan order
"""
n = key.split(".")
return self.__getitem__(int(n[0])-1)
[docs] def allmotors(self):
return self._motorNames
[docs]class OlympusCSVScan(object):
def __init__(self, data, number, motorValues=None):
if motorValues is None:
motorValues = []
self._data = data
self._number = number
self._motorValues = motorValues
self._scanHeader = [self.fileheader()[0]]
if "TimeStamp" in self._data:
self._scanHeader.append("#D %s" % \
self._data["TimeStamp"][self._number])
#return the life time, the preset the elapsed?
# to be safe, I return the LiveTime
if "Livetime" in self._data:
self._scanHeader.append("#@CTIME %s %s %s" % (self._data["Livetime"][self._number],
self._data["Livetime"][self._number],
self._data["Livetime"][self._number]))
self._scanHeader.append("#@CHANN %d 0 %d 1" % (self._data["data"].shape[1],
self._data["data"].shape[1]-1))
if "Offset" in self._data:
if "Slope" in self._data:
self._scanHeader.append("#@CALIB %s %s 0.0" % \
(self._data["Offset"][self._number],
self._data["Slope"][self._number]))
[docs] def nbmca(self):
return 1
# it gives the last column (some files have three columns)
# corresponding to channels, counts and (probably) corrected counts
if number <= 0:
raise IndexError("Mca numbering starts at 1")
elif number > self.nbmca():
raise IndexError("Only %d MCA's" % number)
return self._data['data'][self._number]
[docs] def alllabels(self):
return []
[docs] def allmotorpos(self):
return self._motorValues
[docs] def command(self):
return self._data['TestID'][self._number]
[docs] def date(self):
return self._data["TimeStamp"][self._number]
[docs] def order(self):
return 1
[docs] def number(self):
return self._number + 1
[docs] def lines(self):
return 0
[docs]def isOlympusCSVFile(filename):
f = open(filename, 'r')
try:
line = f.readline()
except:
f.close()
return False
line = line.replace("\x00","")
try:
if filename.lower().endswith(".csv"):
if line[2:].startswith("TestID"):
return True
except:
pass
return False
[docs]def test(filename):
if isOlympusCSVFile(filename):
sf=OlympusCSVFileParser(filename)
else:
print("Not an Olympus CSV File")
return
print(sf[0].header('S'))
print(sf[0].header('D'))
print(sf[0].alllabels())
#print(sf[0].allmotorsvalues())
print(sf[0].nbmca())
print(sf[0].mca(1))
if __name__ == "__main__":
test(sys.argv[1])