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#/*##########################################################################
#
# The PyMca X-Ray Fluorescence Toolkit
#
# Copyright (c) 2019 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__ = "Wout De Nolf"
__contact__ = "wout.de_nolf@esrf.eu"
__license__ = "MIT"
__copyright__ = "European Synchrotron Radiation Facility, Grenoble, France"
import unittest
import tempfile
import shutil
import os
import sys
import numpy
from PyMca5.tests import XrfData
try:
from PyMca5.PyMcaIO import HDF5Stack1D
HAS_H5PY = True
except ImportError:
HAS_H5PY = False
class testXrfData(unittest.TestCase):
def setUp(self):
self.path = tempfile.mkdtemp(prefix='pymca')
def tearDown(self):
shutil.rmtree(self.path)
def testSpecMesh(self):
filename = os.path.join(self.path, 'meshscan.dat')
# SpecFileStack: only works with one detector
nDet = 1
info = XrfData.generateSpecMesh(filename, nDet=nDet, same=False)
nDet0, nRows0, nColumns0, nChannels = info['data'].shape
from PyMca5.PyMcaIO import SpecFileStack
stack = SpecFileStack.SpecFileStack(filelist=[filename]).data
self.assertEqual(nDet, nDet0)
self.assertEqual(stack.shape, (1, nRows0*nColumns0, nChannels))
for i in range(nRows0):
for j in range(nColumns0):
for k in range(1):
# C-order (row-major)
mca = stack[k, i*nColumns0+j]
numpy.testing.assert_array_equal(mca, info['data'][k, i, j])
# SpecFileLayer: works with more than one detector
nDet = 2
info = XrfData.generateSpecMesh(filename, nDet=nDet, same=False)
nDet0, nRows0, nColumns0, nChannels = info['data'].shape
nCounters0 = 2
from PyMca5.PyMcaCore import SpecFileLayer
ffile = SpecFileLayer.SpecFileLayer()
ffile.SetSource(filename)
fileinfo = ffile.GetSourceInfo()
scaninfo, counters = ffile.LoadSource('1.1')
scan = ffile.Source.select('1.1')
nCounters, nRows, nColumns = counters.shape
self.assertEqual(scaninfo['NbMcaDet'], nDet)
self.assertEqual(scaninfo['NbMca'], nDet*nColumns*nRows)
self.assertEqual(nColumns, nColumns0)
self.assertEqual(nRows, nRows0)
self.assertEqual(nCounters, nCounters0)
self.assertEqual(nDet, nDet0)
for i in range(nRows):
for j in range(nColumns):
for k in range(nDet):
mca = scan.mca(i*nColumns*nDet+j*nDet+k+1)
# TODO: bug in specfile (reads one channel less)
numpy.testing.assert_array_equal(mca, info['data'][k, i, j])
del ffile.Source
def testEdfMap(self):
filename = os.path.join(self.path, 'xrfmap.edf')
nDet = 2
info = XrfData.generateEdfMap(filename, nDet=nDet, same=False)
nDet0, nRows0, nColumns0, nChannels = info['data'].shape
from PyMca5.PyMcaIO import EDFStack
files = [os.path.join(self.path, 'xrfmap_xia{:02d}_0001_0000_{:04d}.edf'.format(k, i))
for i in range(nRows0)
for k in range(nDet0)]
stack = EDFStack.EDFStack(filelist=sorted(files)).data
self.assertEqual(nDet, nDet0)
self.assertEqual(stack.shape, (nDet0*nRows0, nColumns0, nChannels))
for i in range(nRows0):
for j in range(nColumns0):
for k in range(nDet):
mca = stack[i+k*nRows0, j]
numpy.testing.assert_array_equal(mca, info['data'][k, i, j])
@unittest.skipIf(not HAS_H5PY, "skipped h5py missing")
def testHdf5Map(self):
from PyMca5.PyMcaIO import HDF5Stack1D
filename = os.path.join(self.path, 'xrfmap.h5')
# TODO: only works for 1 detector
nDet = 1
info = XrfData.generateHdf5Map(filename, nDet=nDet, same=False)
nDet0, nRows0, nColumns0, nChannels = info['data'].shape
datasets = ['/xrf/mca{:02d}/data'.format(k) for k in range(nDet)]
selection = {'y': datasets[0]}
stack = HDF5Stack1D.HDF5Stack1D([filename], selection).data
self.assertEqual(stack.shape, (nRows0, nColumns0, nChannels))
for i in range(nRows0):
for j in range(nColumns0):
for k in range(nDet):
numpy.testing.assert_array_equal(stack[i, j], info['data'][k, i, j])
def getSuite(auto=True):
testSuite = unittest.TestSuite()
if auto:
testSuite.addTest(unittest.TestLoader().loadTestsFromTestCase(testXrfData))
else:
# use a predefined order
testSuite.addTest(testXrfData("testSpecMesh"))
testSuite.addTest(testXrfData("testEdfMap"))
testSuite.addTest(testXrfData("testHdf5Map"))
return testSuite
def test(auto=False):
return unittest.TextTestRunner(verbosity=2).run(getSuite(auto=auto))
if __name__ == '__main__':
if len(sys.argv) > 1:
auto = False
else:
auto = True
result = test(auto)
sys.exit(not result.wasSuccessful())
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