#/*########################################################################## # # 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 from PyMca5.PyMcaIO import SpecFileAbstractClass DEBUG = 0 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 def readline(self): if self.__currentLine >= len(self.__buffer): return "" line = self.__buffer[self.__currentLine] self.__currentLine += 1 return line def close(self): self.__buffer = [""] self.__currentLine = 0 return class BAXSCSVFileParser(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() if not (line.startswith("Bruker AXS") or \ (("KTI" in line) and ("Spectrum" in line))): raise IOError("This does look as a Bruker AXS Handheld CSV file") while not line.startswith("Channel#"): header.append(line) line = _fileObject.readline() header.append(line) line = _fileObject.readline() 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() line = line.replace('"',"") splitLine = line.split(",") _fileObject.close() dataColumnNames = [x for x in header[-1].split(",") if len(x) > 0] data = numpy.array(data, dtype=numpy.float) #print(header) #print(data) labels=[] #create an abstract scan object self._scan = [BAXSCSVScan(data, scantype='MCA', scanheader=header, #labels=labels, #motor_values=self.motorValues, point=False)] def __getitem__(self, item): return self._scan[item] def scanno(self): """ Gives back the number of scans in the file """ return len(self_scan) def list(self): return "1:1" 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) def allmotors(self): if DEBUG: print("BAXCSVFileParser allmotors called") return [] class BAXSCSVScan(SpecFileAbstractClass.SpecFileAbstractScan): def __init__(self, data, scantype='MCA', identification="1.1", scanheader=None, labels=None, motor_values=None, point=False): SpecFileAbstractClass.SpecFileAbstractScan.__init__(self, data, scantype=scantype, identification=identification, scanheader=scanheader, labels=labels, point=point) self._data = data def nbmca(self): return 1 def mca(self, number): # it gives the last column (some files have three columns) # corresponding to channels, counts and (probably) corrected counts # this seems to be confirmed by the fact the Live Time is 0.0 in those # files if number <= 0: raise IndexError("Mca numbering starts at 1") elif number > self.nbmca(): raise IndexError("Only %d MCA's" % number) return self._data[:, -1] def header(self, key): if key == "@CALIB": gain = 1.0 offset = 0.0 for item in self.scanheader: if item.startswith("eV per channel,"): gain = 0.001 * float(item.split(",")[-1]) return ["#@CALIB %f %f %f" % (offset, gain, 0.0)] elif key == "@CTIME": preset = -1 live = -1 duration = -1 for item in self.scanheader: if item.startswith("Duration Time,"): duration = float(item.split(",")[-1]) elif item.startswith("Live Time,"): live = float(item.split(",")[-1]) if self._data.shape[1] == 3: # counts are already corrected live = duration if (preset > 0) and (duration > 0) and (live > 0): return ["#CTIME %f %f %f" % (preset, live, duration)] elif (duration > 0) and (live > 0): return ["#CTIME %f %f %f" % (duration, live, duration)] elif (live > 0): return ["#CTIME %f %f %f" % (live, live, live)] elif (duration > 0): return ["#CTIME %f %f %f" % (duration, duration, duration)] else: return [] else: return super(BAXSCSVScan, self).header(key) def isBAXSCSVFile(filename): f = open(filename, 'r') try: line = f.readline() except: f.close() return False try: if filename.lower().endswith(".csv"): if line.startswith("Bruker AXS") or \ (("KTI" in line) and ("Spectrum" in line)): return True except: pass return False def test(filename): if isBAXSCSVFile(filename): sf=BAXSCSVFileParser(filename) else: print("Not a Bruker AXS 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])