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#/*##########################################################################
#
# 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. Armando Sole - ESRF Data Analysis"
__contact__ = "sole@esrf.fr"
__license__ = "MIT"
__copyright__ = "European Synchrotron Radiation Facility, Grenoble, France"
import unittest
import numpy
class DummyArray(object):
def __init__(self, data):
"""
This class forces ROI and spectra calculation to be performed as
it is made for a dynamically loaded array.
This allows detection of the PyMca bug track issue 3544665
"""
self.data = numpy.array(data, copy=False)
def __getitem__(self, *var):
if len(var) == 1:
return self.data[var[0]]
elif len(var) == 2:
return self.data[var[0], var[1]]
elif len(var) == 3:
return self.data[var[0], var[1], var[2]]
def getShape(self):
return self.data.shape
def getDType(self):
return self.data.dtype
def getSize(self):
s = 1
for item in self.__shape:
s *= item
return s
shape = property(getShape)
dtype = property(getDType)
size = property(getSize)
class testStackBase(unittest.TestCase):
def testStackBaseImport(self):
from PyMca5.PyMcaCore import StackBase
def testStackBaseStack1DDataHandling(self):
from PyMca5.PyMcaCore import StackBase
nrows = 50
ncolumns = 100
nchannels = 500
a = numpy.ones((nrows, ncolumns), numpy.float)
referenceData = numpy.zeros((nrows, ncolumns, nchannels),
numpy.float)
for i in range(nchannels):
referenceData[:, :, i] = a * i
a = None
mask = numpy.zeros((nrows, ncolumns), numpy.uint8)
mask[20:30, 15:50] = 1
dummyArray = DummyArray(referenceData)
defaultMca = referenceData.sum(axis=0, dtype=numpy.float64).sum(axis=0)
maskedMca = referenceData[mask>0, :].sum(axis=0)
for fileindex in [0, 1]:
#usually only one file index case is used but
#we test both to have a better coverage
j = 0
for data in [referenceData, dummyArray]:
if j == 0:
dynamic = ""
j = 1
else:
dynamic = "dynamic "
stackBase = StackBase.StackBase()
stackBase.setStack(data, mcaindex=2, fileindex=fileindex)
channels, counts = stackBase.getActiveCurve()[0:2]
self.assertTrue(numpy.allclose(defaultMca, counts),
"Incorrect %sdefault mca" % dynamic)
# set mask
stackBase.setSelectionMask(mask)
self.assertTrue(numpy.allclose(stackBase.getSelectionMask(), mask),
"Incorrect mask set and get")
# get mca from mask
mcaDataObject = stackBase.calculateMcaDataObject()
self.assertTrue(numpy.allclose(mcaDataObject.y[0], maskedMca),
"Incorrect %smca from mask calculation" % dynamic)
#get image from roi
i0 = 100
imiddle = 200
i1 = 400
# calculate
imageDict = stackBase.calculateROIImages(i0, i1, imiddle=imiddle)
self.assertTrue(numpy.allclose(imageDict['ROI'], data[:,:,i0:i1].sum(axis=-1)),
"Incorrect ROI image from %sROI calculation" % dynamic)
self.assertTrue(numpy.allclose(imageDict['Left'], data[:,:,i0]),
"Incorrect Left image from %sROI calculation" % dynamic)
self.assertTrue(numpy.allclose(imageDict['Right'], data[:,:,i1-1]),
"Incorrect Right image from %sROI calculation" % dynamic)
self.assertTrue(numpy.allclose(imageDict['Middle'], data[:,:,imiddle]),
"Incorrect Middle image from %sROI calculation" % dynamic)
stackBase = None
data = None
dummyArray = None
referenceData = None
def testStackBaseStack2DDataHandling(self):
from PyMca5.PyMcaCore import StackBase
nrows = 50
ncolumns = 100
nchannels = 500
a = numpy.ones((nrows, ncolumns), numpy.float)
referenceData = numpy.zeros((nchannels, nrows, ncolumns),
numpy.float)
for i in range(nchannels):
referenceData[i] = a * i
a = None
mask = numpy.zeros((nrows, ncolumns), numpy.uint8)
mask[20:30, 15:50] = 1
dummyArray = DummyArray(referenceData)
defaultMca = referenceData.sum(axis=2, dtype=numpy.float64).sum(axis=1)
maskedMca = referenceData[:,mask>0].sum(axis=1)
for fileindex in [1, 2]:
#usually only one file index case is used but
#we test both to have a better coverage
j = 0
for data in [referenceData, dummyArray]:
if j == 0:
dynamic = ""
j = 1
else:
dynamic = "dynamic "
stackBase = StackBase.StackBase()
stackBase.setStack(data, mcaindex=0, fileindex=fileindex)
channels, counts = stackBase.getActiveCurve()[0:2]
self.assertTrue(numpy.allclose(defaultMca, counts),
"Incorrect %sdefault mca" % dynamic)
# set mask
stackBase.setSelectionMask(mask)
self.assertTrue(numpy.allclose(stackBase.getSelectionMask(), mask),
"Incorrect mask set and get")
# get mca from mask
mcaDataObject = stackBase.calculateMcaDataObject()
self.assertTrue(numpy.allclose(mcaDataObject.y[0], maskedMca),
"Incorrect %smca from mask calculation" % dynamic)
#get image from roi
i0 = 100
imiddle = 200
i1 = 400
# calculate
imageDict = stackBase.calculateROIImages(i0, i1, imiddle=imiddle)
self.assertTrue(numpy.allclose(imageDict['ROI'], data[i0:i1, :,:].sum(axis=0)),
"Incorrect ROI image from %sROI calculation" % dynamic)
self.assertTrue(numpy.allclose(imageDict['Left'], data[i0,:,:]),
"Incorrect Left image from %sROI calculation" % dynamic)
self.assertTrue(numpy.allclose(imageDict['Right'], data[i1-1,:,:]),
"Incorrect Right image from %sROI calculation" % dynamic)
self.assertTrue(numpy.allclose(imageDict['Middle'], data[imiddle,:,:]),
"Incorrect Middle image from %sROI calculation" % dynamic)
stackBase = None
data = None
dummyArray = None
referenceData = None
def getSuite(auto=True):
testSuite = unittest.TestSuite()
if auto:
testSuite.addTest(\
unittest.TestLoader().loadTestsFromTestCase(testStackBase))
else:
# use a predefined order
testSuite.addTest(testStackBase("testStackBaseImport"))
testSuite.addTest(testStackBase("testStackBaseStack1DDataHandling"))
testSuite.addTest(testStackBase("testStackBaseStack2DDataHandling"))
return testSuite
def test(auto=False):
unittest.TextTestRunner(verbosity=2).run(getSuite(auto=auto))
if __name__ == '__main__':
test()
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