#/*########################################################################## # Copyright (C) 2004-2012 European Synchrotron Radiation Facility # # This file is part of the PyMca X-ray Fluorescence Toolkit developed at # the ESRF by the Software group. # # This file is free software; you can redistribute it and/or modify it # under the terms of the GNU Lesser General Public License as published by the # Free Software Foundation; either version 2 of the License, or (at your option) # any later version. # # This file 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 Lesser General Public License for more # details. # #############################################################################*/ __author__ = "V.A. Sole - ESRF Data Analysis" 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 PyMca import StackBase def testStackBaseStack1DDataHandling(self): from PyMca 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 PyMca 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()