#/*##########################################################################
#
# 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("\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 ThermoEMSFileParser(object):
def __init__(self, filename):
if not os.path.exists(filename):
raise IOError("File %s does not exists" % filename)
_fileObject = BufferedFile(filename)
#Only one measurement per file
header = []
ddict = {}
line = _fileObject.readline()
ok = False
if filename.lower().endswith(".ems"):
if line.startswith("#FORMAT") or \
(("EMSA" in line) and ("Spectral" in line)):
ok = True
if not ok:
raise IOError("This does look as a Thermo EMS file")
while not line.startswith("#SPECTRUM"):
splitLine = line.split(":")
if len(splitLine) == 2:
ddict[splitLine[0][1:].strip()] = splitLine[1]
header.append(line)
line = _fileObject.readline()
header.append(line)
line = _fileObject.readline().strip()
line = line.replace(','," ")
splitLine = line.split()
data = []
while(len(splitLine)):
if len(splitLine[0]):
try:
data.append([float(x) for x in splitLine if len(x) > 0])
except ValueError:
break
else:
break
line = _fileObject.readline().strip()
line = line.replace(','," ")
splitLine = line.split()
_fileObject.close()
data = numpy.array(data, dtype=numpy.float)
ddict["data"] = data
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):
if item >= self.scanno():
raise IndexError("Only %d scans in file" % self.scanno)
motorValues = []
for key in self._motorNames:
motorValues.append(float(self._data[key][item]))
return ThermoEMSScan(self._data, item, motorValues=motorValues)
[docs] def scanno(self):
"""
Gives back the number of scans in the file
"""
return 1
[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 ThermoEMSScan(object):
def __init__(self, data, number, motorValues=None):
if motorValues is None:
motorValues = []
self._data = data
self._number = number
self._motorValues = motorValues
self._scanHeader = ["#S %d %s" % (number + 1,self._data['TITLE'])]
if ("DATE" in self._data) and ("TIME" in self._data):
self._scanHeader.append("#D %s %s" % \
(self._data["DATE"], self._data["TIME"]))
#return the life time, the preset the elapsed?
# to be safe, I return the LiveTime
if "LIVETIME -s" in self._data:
if "REALTIME -s" in self._data:
self._scanHeader.append("#@CTIME %s %s %s" % (self._data["REALTIME -s"],
self._data["LIVETIME -s"],
self._data["LIVETIME -s"]))
else:
self._scanHeader.append("#@CTIME %s %s %s" % (self._data["LIVETIME -s"],
self._data["LIVETIME -s"],
self._data["LIVETIME -s"]))
if ("CHOFFSET" in self._data) and ("NPOINTS" in self._data):
self._scanHeader.append("#@CHANN %d %d %d 1" % (int(float(self._data["NPOINTS"])),
int(float(self._data["CHOFFSET"])),
int(float(self._data["NPOINTS"])-1)))
else:
self._scanHeader.append("#@CHANN %d 0 %d 1" % (self._data["data"].shape[0],
self._data["data"].shape[0]-1))
if "OFFSET" in self._data:
if "XPERCHAN" in self._data:
self._scanHeader.append("#@CALIB %s %s 0.0" % \
(self._data["OFFSET"],
self._data["XPERCHAN"]))
[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'][:, 1]
[docs] def alllabels(self):
return []
[docs] def allmotorpos(self):
return self._motorValues
[docs] def command(self):
return self._data['TITLE']
[docs] def date(self):
return self._data["DATE"] + " " + self._data["TIME"]
#a = "#S %d %s" % (self._number + 1, self.command())
#return [a]
[docs] def order(self):
return 1
[docs] def number(self):
return self._number + 1
[docs] def lines(self):
return 0
[docs]def isThermoEMSFile(filename):
f = open(filename, 'r')
try:
line = f.readline()
except:
f.close()
return False
try:
if filename.lower().endswith(".ems"):
if line.startswith("#FORMAT") or \
(("EMSA" in line) and ("Spectral" in line)):
return True
except:
pass
return False
[docs]def test(filename):
if isThermoEMSFile(filename):
sf=ThermoEMSFileParser(filename)
else:
print("Not a Thermo EMS File")
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])