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#!/usr/bin/env python
#/*##########################################################################
#
# 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 os
import numpy
import logging
from PyMca5.PyMcaIO import EdfFile
_logger = logging.getLogger(__name__)
class PyMcaBatchBuildOutput(object):
def __init__(self, inputdir=None, outputdir=None):
self.inputDir = inputdir
self.outputDir = outputdir
def buildOutput(self, inputdir=None, outputdir=None, delete=None):
if inputdir is None:inputdir = self.inputDir
if inputdir is None:inputdir = os.getcwd()
if outputdir is None: outputdir = self.outputDir
if outputdir is None: outputdir = inputdir
if delete is None:
if outputdir == inputdir:
delete = True
_logger.debug("delete option = %s", delete)
allfiles = os.listdir(inputdir)
partialedflist = []
partialdatlist = []
partialconlist = []
for filename in allfiles:
if filename.endswith('000000_partial.edf'):partialedflist.append(filename)
elif filename.endswith('000000_partial.dat'):partialdatlist.append(filename)
elif filename.endswith('000000_partial_concentrations.txt'):partialconlist.append(filename)
#IMAGES
edfoutlist = []
for filename in partialedflist:
_logger.debug("Dealing with filename %s", filename)
edflist = self.getIndexedFileList(os.path.join(inputdir, filename))
i = 0
for edfname in edflist:
edf = EdfFile.EdfFile(edfname, access='rb', fastedf = 0)
nImages = edf.GetNumImages()
#get always the last image
data0 = edf.GetData(nImages-1)
data0[data0<0] = 0
if i == 0:
header = edf.GetHeader(0)
data = data0.copy()
else:
data += data0
del edf
i += 1
edfname = filename.replace('_000000_partial.edf',".edf")
edfoutname = os.path.join(outputdir, edfname)
_logger.debug("Dealing with output filename %s", edfoutname)
if os.path.exists(edfoutname):
_logger.debug("Output file already exists, trying to delete it")
os.remove(edfoutname)
edfout = EdfFile.EdfFile(edfoutname, access="wb")
edfout.WriteImage (header , data, Append=0)
del edfout
edfoutlist.append(edfoutname)
if delete:
for filename in edflist:
try:
os.remove(filename)
except:
_logger.warning("Cannot delete file %s" % filename)
#DAT IMAGES
datoutlist = []
for filename in partialdatlist:
edflist = self.getIndexedFileList(os.path.join(inputdir, filename))
first = True
for edfname in edflist:
f = open(edfname)
lines = f.readlines()
f.close()
j = 1
while (not len( lines[-j].replace("\n",""))):
j += 1
if first:
first = False
labels = lines[0].replace("\n","").split(" ")
nlabels = len(labels)
nrows = len(lines) - j
data = numpy.zeros((nrows, nlabels), numpy.double)
inputdata = numpy.zeros((nrows, nlabels), numpy.double)
chisqIndex = labels.index('chisq')
for i in range(nrows):
inputdata[i, :] = [float(x) for x in lines[i+1].split()]
if inputdata[i, chisqIndex] < 0.0:
inputdata[i, chisqIndex] = 0.0
data += inputdata
outfilename = os.path.join(outputdir, filename.replace("_000000_partial",""))
if os.path.exists(outfilename):
os.remove(outfilename)
outfile=open(outfilename,'w+')
outfile.write('%s' % lines[0])
line=""
for row in range(nrows):
#line = "%d" % inputdata[row, 0]
for col in range(nlabels):
if col == 0 : line += "%d" % inputdata[row, col]
elif col == 1 : line += " %d" % inputdata[row, col]
else: line += " %g" % data[row, col]
line += "\n"
outfile.write("%s" % line)
line =""
outfile.write("\n")
outfile.close()
datoutlist.append(outfilename)
if delete:
for filename in edflist:
os.remove(filename)
#CONCENTRATIONS
outconlist = []
for filename in partialconlist:
edflist = self.getIndexedFileList(os.path.join(inputdir, filename))
i = 0
for edfname in edflist:
edf = open(edfname, 'rb')
if i == 0:
outfilename = os.path.join(outputdir, filename.replace("_000000_partial",""))
if os.path.exists(outfilename):
os.remove(outfilename)
outfile = open(outfilename,'wb')
lines = edf.readlines()
for line in lines:
outfile.write(line)
edf.close()
i += 1
outfile.close()
outconlist.append(outfilename)
if delete:
for filename in edflist:
os.remove(filename)
return edfoutlist, datoutlist, outconlist
def getIndexedFileList(self, filename, begin=None,end=None, skip = None, fileindex=0):
name = os.path.basename(filename)
n = len(name)
i = 1
numbers = ['0', '1', '2', '3', '4', '5',
'6', '7', '8','9']
while (i <= n):
c = name[n-i:n-i+1]
if c in ['0', '1', '2',
'3', '4', '5',
'6', '7', '8',
'9']:
break
i += 1
suffix = name[n-i+1:]
if len(name) == len(suffix):
#just one file, one should use standard widget
#and not this one.
self.loadFileList(filename, fileindex=fileindex)
else:
nchain = []
while (i<=n):
c = name[n-i:n-i+1]
if c not in ['0', '1', '2',
'3', '4', '5',
'6', '7', '8',
'9']:
break
else:
nchain.append(c)
i += 1
number = ""
nchain.reverse()
for c in nchain:
number += c
fformat = "%" + "0%dd" % len(number)
if (len(number) + len(suffix)) == len(name):
prefix = ""
else:
prefix = name[0:n-i+1]
prefix = os.path.join(os.path.dirname(filename),prefix)
if not os.path.exists(prefix + number + suffix):
_logger.error("Internal error in EDFStack")
_logger.error("file should exist: %s " % (prefix + number + suffix))
return
i = 0
if begin is None:
begin = 0
testname = prefix+fformat % begin+suffix
while not os.path.exists(prefix+ fformat % begin+suffix):
begin += 1
testname = prefix+fformat % begin+suffix
if len(testname) > len(filename):break
i = begin
else:
i = begin
if not os.path.exists(prefix+fformat % i+suffix):
raise ValueError("Invalid start index file = %s" % \
(prefix+fformat % i+suffix))
f = prefix+fformat % i+suffix
filelist = []
while os.path.exists(f):
filelist.append(f)
i += 1
if end is not None:
if i > end:
break
f = prefix+fformat % i+suffix
return filelist
if __name__ == "__main__":
import sys
if len(sys.argv) < 2:
print("Usage:")
print("python PyMcaBatchBuildOutput.py directory")
sys.exit(0)
directory = sys.argv[1]
w = PyMcaBatchBuildOutput(directory)
w.buildOutput()
"""
allfiles = os.listdir(directory)
edflist = []
datlist = []
for filename in allfiles:
if filename.endswith('000000_partial.edf'):edflist.append(filename)
elif filename.endswith('000000_partial.dat'):datlist.append(filename)
for filename in edflist:
print w.getIndexedFileList(os.path.join(directory, filename))
"""
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