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#/*##########################################################################
#
# The PyMca X-Ray Fluorescence Toolkit
#
# Copyright (c) 2020 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 os
import sys
import numpy
import gc
import shutil
import tempfile
try:
import h5py
HAS_H5PY = True
except:
HAS_H5PY = None
DEBUG = 0
class testMcaStackExport(unittest.TestCase):
def setUp(self):
"""
Get the data directory
"""
self._importSuccess = False
self._outputDir = None
self._h5File = None
try:
from PyMca5 import PyMcaDataDir
self._importSuccess = True
self.dataDir = PyMcaDataDir.PYMCA_DATA_DIR
except:
self.dataDir = None
def tearDown(self):
gc.collect()
if self._h5File is not None:
fileName = self._h5File
if os.path.exists(fileName):
os.remove(fileName)
if self._outputDir is not None:
shutil.rmtree(self._outputDir, ignore_errors=True)
if os.path.exists(self._outputDir):
raise IOError("Directory <%s> not deleted" % self._outputDir)
@unittest.skipIf(not HAS_H5PY, "skipped h5py missing")
def testSingleStackExport(self):
from PyMca5 import PyMcaDataDir
from PyMca5.PyMcaIO import specfilewrapper as specfile
from PyMca5.PyMcaIO import ConfigDict
from PyMca5.PyMcaCore import DataObject
from PyMca5.PyMcaCore import StackBase
from PyMca5.PyMcaCore import McaStackExport
spe = os.path.join(self.dataDir, "Steel.spe")
cfg = os.path.join(self.dataDir, "Steel.cfg")
sf = specfile.Specfile(spe)
self.assertTrue(len(sf) == 1, "File %s cannot be read" % spe)
self.assertTrue(sf[0].nbmca() == 1,
"Spe file should contain MCA data")
y = counts = sf[0].mca(1)
x = channels = numpy.arange(y.size).astype(numpy.float64)
sf = None
configuration = ConfigDict.ConfigDict()
configuration.read(cfg)
calibration = configuration["detector"]["zero"], \
configuration["detector"]["gain"], 0.0
initialTime = configuration["concentrations"]["time"]
# create the data
nRows = 5
nColumns = 10
nTimes = 3
data = numpy.zeros((nRows, nColumns, counts.size), dtype = numpy.float64)
live_time = numpy.zeros((nRows * nColumns), dtype=numpy.float64)
xpos = 10 + numpy.zeros((nRows * nColumns), dtype=numpy.float64)
ypos = 100 + numpy.zeros((nRows * nColumns), dtype=numpy.float64)
mcaIndex = 0
for i in range(nRows):
for j in range(nColumns):
data[i, j] = counts
live_time[i * nColumns + j] = initialTime * \
(1 + mcaIndex % nTimes)
xpos[mcaIndex] += j
ypos[mcaIndex] += i
mcaIndex += 1
# create the stack data object
stack = DataObject.DataObject()
stack.data = data
stack.info = {}
stack.info["McaCalib"] = calibration
stack.info["McaLiveTime"] = live_time
stack.x = [channels]
stack.info["positioners"] = {"x": xpos,
"y": ypos}
tmpDir = tempfile.gettempdir()
self._h5File = os.path.join(tmpDir, "SteelStack.h5")
if os.path.exists(self._h5File):
os.remove(self._h5File)
McaStackExport.exportStackList(stack, self._h5File)
# read back the stack
from PyMca5.PyMcaIO import HDF5Stack1D
stackRead = HDF5Stack1D.HDF5Stack1D([self._h5File],
{"y":"/measurement/detector_00"})
# let's play
sb = StackBase.StackBase()
sb.setStack(stackRead)
# positioners
data = stackRead.info["positioners"]["x"]
self.assertTrue(numpy.allclose(data, xpos),
"Incorrect readout of x positions")
data = stackRead.info["positioners"]["y"]
self.assertTrue(numpy.allclose(data, ypos),
"Incorrect readout of y positions")
# calibration and live time
x, y, legend, info = sb.getStackOriginalCurve()
readCalib = info["McaCalib"]
readLiveTime = info["McaLiveTime"]
self.assertTrue(abs(readCalib[0] - calibration[0]) < 1.0e-10,
"Calibration zero. Expected %f got %f" % \
(calibration[0], readCalib[0]))
self.assertTrue(abs(readCalib[1] - calibration[1]) < 1.0e-10,
"Calibration gain. Expected %f got %f" % \
(calibration[1], readCalib[0]))
self.assertTrue(abs(readCalib[2] - calibration[2]) < 1.0e-10,
"Calibration 2nd order. Expected %f got %f" % \
(calibration[2], readCalib[2]))
self.assertTrue(abs(live_time.sum() - readLiveTime) < 1.0e-5,
"Incorrect sum of live time data")
@unittest.skipIf(not HAS_H5PY, "skipped h5py missing")
def testSingleArrayExport(self):
from PyMca5.PyMcaCore import StackBase
from PyMca5.PyMcaCore import McaStackExport
tmpDir = tempfile.gettempdir()
self._h5File = os.path.join(tmpDir, "Array.h5")
data = numpy.arange(3*1024).reshape(3, 1024)
McaStackExport.exportStackList([data], self._h5File)
# read back the stack
from PyMca5.PyMcaIO import HDF5Stack1D
stackRead = HDF5Stack1D.HDF5Stack1D([self._h5File],
{"y":"/measurement/detector_00"})
# let's play
sb = StackBase.StackBase()
sb.setStack(stackRead)
# check the data
self.assertTrue(numpy.allclose(data, stackRead.data),
"Incorrect data readout")
def getSuite(auto=True):
testSuite = unittest.TestSuite()
if auto:
testSuite.addTest(unittest.TestLoader().loadTestsFromTestCase(\
testMcaStackExport))
else:
# use a predefined order
testSuite.addTest(testMcaStackExport("testSingleStackExport"))
testSuite.addTest(testMcaStackExport("testSingleArrayExport"))
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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