Source code for PyMca5.PyMcaIO.OlympusCSVFileParser

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# The PyMca X-Ray Fluorescence Toolkit
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# Copyright (c) 2004-2014 European Synchrotron Radiation Facility
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__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
[docs] def mca(self, number):
# 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 fileheader(self): a = "#S %d %s" % (self._number + 1, self.command()) return [a]
[docs] def header(self,key): if DEBUG: print("Requested key = ", key) if key in ['S', '#S']: return self.fileheader()[0] elif key == 'N': return [] elif key == 'L': return [] elif key in ['D', '@CTIME', '@CALIB', '@CHANN']: for item in self._scanHeader: if item.startswith("#" + key): return [item] return [] elif key == "" or key == " ": return self._scanHeader else: return []
[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])