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#/*##########################################################################
#
# The PyMca X-Ray Fluorescence Toolkit
#
# Copyright (c) 2004-2017 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 os
import sys
import numpy
import mmap
import re
from PyMca5.PyMcaIO import JcampReader
from PyMca5.PyMcaIO import SpecFileAbstractClass
if sys.version < "3":
from StringIO import StringIO
else:
from io import StringIO
DEBUG = 0
if DEBUG:
import time
class JcampFileParser(SpecFileAbstractClass.SpecFileAbstractClass):
def __init__(self, filename, single=False):
# get the number of entries in the file
self.__lastEntryData = -1
if DEBUG:
t0 = time.time()
if sys.maxsize > 2**32:
self._useMMap = True
else:
self._useMMap = False
if DEBUG:
print("USING MMPA = ", self._useMMap)
if self._useMMap:
# 64-bit supported
f = open(filename, "rb")
mm = mmap.mmap(f.fileno(), 0, access=mmap.ACCESS_READ)
a = [x.start() for x in re.finditer("##TITLE".encode("utf-8"), mm)]
b = [x.end() for x in re.finditer("##END.*\n".encode("utf-8"), mm)]
mm = None
f.close()
# we can have twice the TITLE before the first data block
# we get rid of the second to have also the file header
if len(a) > 1:
if a[1] < b[0]:
del a[1]
self._scanLimits = [(start, end) for start, end in zip(a, b)]
else:
# 32-bit
self._scanLimits = []
f = open(filename, "rb")
entryStarted = False
current = f.tell()
line = f.readline()
nLines = 0
while len(line):
if entryStarted:
if line.startswith("##END=".encode("utf-8")):
lineEnd = nLines
self._scanLimits.append((start, f.tell(), lineStart, lineEnd))
entryStarted = False
if single:
break
elif line.startswith("##TITLE".encode("utf-8")):
start = current
lineStart = nLines
entryStarted = True
nLines += 1
current = f.tell()
line = f.readline()
f.close()
if DEBUG:
print("Elapsed CURRENT = ", time.time() - t0)
self._filename = os.path.abspath(filename)
if DEBUG:
print("PARSING FIRST ")
t0 = time.time()
self._parseEntryData(0)
if DEBUG:
elapsed = time.time() - t0
print("ELAPSED PER SCAN = ", elapsed)
print("N SCANS = ", self.scanno())
print("EXPECTED = ", elapsed * self.scanno())
def _parseEntryData(self, idx):
if idx == self.__lastEntryData:
# nothing to be done
return
if (idx < 0) or (idx >= len(self._scanLimits)):
raise IndexError("Only %d entries in file. Requested %d" % (len(self._scanLimits), idx))
start, end = self._scanLimits[idx][0:2]
if self._useMMap:
#get the relevant file section
f = open(self._filename, "rb")
scanBuffer = mmap.mmap(f.fileno(), 0, access=mmap.ACCESS_READ)[start:end]
f.close()
# the Reader expects to work with strings and not with bytes
scanBuffer = scanBuffer.decode("utf-8")
fileBlock = True
else:
#get the relevant file section
f = open(self._filename, "r")
start, end = self._scanLimits[idx][0:2]
f.seek(start)
scanBuffer = StringIO(f.read(1 + end - start))
f.close()
fileBlock = False
instance = JcampReader.JcampReader(scanBuffer, block=fileBlock)
info = instance.info
jcampDict = info
x, y = instance.data
title = jcampDict.get('TITLE', "Unknown scan")
xLabel = jcampDict.get('XUNITS', 'channel')
yLabel = jcampDict.get('YUNITS', 'counts')
try:
fileheader = instance._header
except:
print("JCampFileParser cannot access '_header' attribute")
fileheader=None
data = numpy.zeros((x.size, 2), numpy.float32)
data[:, 0] = x
data[:, 1] = y
self.scandata = []
scanheader = ["#S %d %s" % (2*idx + 1, title),
"#N 2",
"#L %s %s" % (xLabel, yLabel)]
scanData = JCAMPFileScan(data,
scantype="SCAN",
scanheader=scanheader,
labels=[xLabel, yLabel],
fileheader=fileheader)
self.scandata.append(scanData)
scanheader = ["#S %d %s" % (2*idx + 2, title)]
if jcampDict['XYDATA'].upper() == '(X++(Y..Y))':
# we can deal with the X axis via its calibration
scanheader.append("#@CHANN %d %d %d 1" % (len(x), 0, len(x) - 1))
scanheader.append("#@CALIB %f %f 0" % (x[0], x[1] - x[0]))
scantype = "MCA"
scanData = JCAMPFileScan(data, scantype="MCA",
scanheader=scanheader,
#labels=[xLabel, yLabel],
fileheader=fileheader)
self.scandata.append(scanData)
self.__lastEntryData = idx
def __getitem__(self, item):
if item < 0:
item = self.scanno() - item
idx = item // 2
self._parseEntryData(idx)
return self.scandata[item % 2]
def list(self):
return '1:%d' % self.scanno()
def scanno(self):
return len(self.scandata) * len(self._scanLimits)
class JCAMPFileScan(SpecFileAbstractClass.SpecFileAbstractScan):
def __init__(self, data, scantype="SCAN",
scanheader=None, labels=None, fileheader=None):
SpecFileAbstractClass.SpecFileAbstractScan.__init__(self, data,
scantype=scantype, scanheader=scanheader,
labels=labels)
self._data = data
self._fileHeader = fileheader
def fileheader(self, key=''):
return self._fileHeader
def nbmca(self):
if self.scantype == 'SCAN':
return 0
else:
return 1
def mca(self, number):
if number not in [1]:
raise ValueError("Specfile mca numberig starts at 1")
return self._data[:, number]
def isJcampFile(filename):
return JcampReader.isJcampFile(filename)
if __name__ == "__main__":
if len(sys.argv) < 2:
print("Usage: python JCAMPFileParser.py filename")
sys.exit(0)
print(" isJCAMPFile = ", isJcampFile(sys.argv[1]))
sf = JcampFileParser(sys.argv[1])
print("nscans = ", sf.scanno())
print("list = ", sf.list())
print("select = ", sf.select(sf.list()[0]))
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