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from __future__ import print_function
#
# This file is part of Mantis, a Multivariate ANalysis Tool for Spectromicroscopy.
#
# Copyright (C) 2011 Mirna Lerotic, 2nd Look
# http://2ndlookconsulting.com
# License: GNU GPL v3
#
# Mantis is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# any later version.
#
# Mantis is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
# GNU General Public License for more details <http://www.gnu.org/licenses/>.
import numpy
import os
title = 'text table'
extension = ['*.csv','*.txt','*.xas']
read_types = ['spectrum','stack']
write_types = ['spectrum','stack']
def identify(filename):
try:
with open(filename, 'tr') as check_file: # try open file in text mode and read a single line
check_file.readline()
return True
except:
return False
def GetFileStructure(FileName):
return None
#----------------------------------------------------------------------
def read(filename, self, selection=None, *args, **kwargs):
with open(str(filename),'r') as f:
Line = f.readline().split()
if Line == ['#X', '#Y', '#Wave', '#Intensity']:
read_stack(filename, self, **kwargs)
else:
read_spectrum(filename, self, **kwargs)
return
def read_stack(filename, self, selection=None, *args, **kwargs):
"""
This reads the text version of an SPC hyperspectral map from a Raman measurement.
"""
f = open(str(filename),'r')
xlist = []
ylist = []
wlist = []
ilist = []
for line in f:
if line.startswith(("*","%","#")):
pass
else:
x, y, w, i = [float (x) for x in line.split()]
xlist.append(x)
ylist.append(y)
wlist.append(w)
ilist.append(i)
self.x_dist = numpy.unique(xlist)
self.y_dist = numpy.unique(ylist)
self.ev = numpy.unique(wlist)
self.n_cols = len(self.x_dist)
self.n_rows = len(self.y_dist)
self.n_ev = len(self.ev)
self.data_dwell = numpy.ones((self.n_ev))*1.0
self.absdata = numpy.empty((self.n_cols,self.n_rows, self.n_ev))
self.absdata = numpy.flip(numpy.transpose(numpy.reshape(ilist, (self.n_rows, self.n_cols, self.n_ev), order='C'), axes=[1,0,2]), axis=2)
self.fill_h5_struct_from_stk()
return
def read_spectrum(filename, self, selection=None, *args, **kwargs):
f = open(str(filename),'r')
elist = []
ilist = []
for line in f:
if line.startswith(("*","%","#")):
pass
else:
e, i = [float (x) for x in line.split(',')]
elist.append(e)
ilist.append(i)
self.evi0 = numpy.array(elist)
self.i0data = numpy.array(ilist)
f.close()
self.i0_dwell = None
return
#----------------------------------------------------------------------
def write(filename, data_object, data_type):
"""Switchyard for writing different types of data."""
if data_type in ['spectrum']:
write_spectrum(filename, data_object.absdata, data_object.ev)
elif data_type in ['stack']:
write_spectrum(filename, numpy.average(data_object.absdata,axis=(0,1)), energies=data_object.ev, title='I0 Spectrum')
#----------------------------------------------------------------------
def write_spectrum(filename, data, energies, title=None ):
if title is None:
title = 'Spectrum'
with open(filename, 'w') as f:
print('********************* '+title+' ********************', file=f)
print('*', file=f)
print('* ev, intensity', file=f)
for ie in range(len(energies)):
print('{0:06.2f}, {1:06f}'.format(energies[ie], data[ie]), file=f)
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