def test_getIntensity(self):
"""
Tests for method `getIntensity`.
"""
phirhozThinFilm = PhirhozGeneratedCharacteristicThinFilm.PhirhozGeneratedCharacteristicThinFilm(
)
phirhozThinFilm.path = get_current_module_path(
__file__, "../../../test_data/results")
phirhozThinFilm.basename = "SimulationMCXrayPhirhozTestCases_Cu_E500d0keV_N100000e"
phirhozThinFilm.read()
self.assertEquals(1, phirhozThinFilm.numberRegions)
regionID = 0
atomicSymbol = "Cu"
intensity = phirhozThinFilm.getIntensity(
regionID, atomicSymbol,
PhirhozGeneratedCharacteristicThinFilm.SUBSHELL_K)
self.assertAlmostEquals(390.159, intensity, 6)
intensity = phirhozThinFilm.getIntensity(
regionID, atomicSymbol,
PhirhozGeneratedCharacteristicThinFilm.SUBSHELL_L)
self.assertAlmostEquals(13367.3, intensity, 6)
intensity = phirhozThinFilm.getIntensity(
regionID, atomicSymbol,
PhirhozGeneratedCharacteristicThinFilm.SUBSHELL_M)
self.assertAlmostEquals(0.0, intensity, 6)
def test_isOlderThan(self):
filename = "empty"
filepathRef = get_current_module_path(
__file__, "../../test_data/serialization/")
filepathRef = os.path.join(filepathRef, filename + '.ser')
if not os.path.isfile(filepathRef):
raise SkipTest
filepath1 = os.path.join(self.tempPath, filename + '_1' + '.ser')
time.sleep(1.0)
shutil.copy(filepathRef, filepath1)
filepath2 = os.path.join(self.tempPath, filename + '_2' + '.ser')
time.sleep(1.0)
shutil.copy(filepathRef, filepath2)
filepath3 = os.path.join(self.tempPath, filename + '_3' + '.ser')
time.sleep(1.0)
shutil.copy(filepathRef, filepath3)
self.serialization.setFilepath(filepath2)
self.assertFalse(self.serialization.isOlderThan(filepath1))
self.assertFalse(self.serialization.isOlderThan(filepath2))
self.assertTrue(self.serialization.isOlderThan(filepath3))
filepath = "/casd/csadf/asdfsdaf/sadfsdaf.ser"
self.assertFalse(self.serialization.isOlderThan(filepath))
filepath = "/casd/csadf/asdfsdaf/sadfsdaf.ser"
self.serialization.setFilepath(filepath)
self.assertTrue(self.serialization.isOlderThan(filepath3))
def test_read(self):
"""
Tests for method `read`.
"""
phirhozThinFilm = PhirhozGeneratedCharacteristicThinFilm.PhirhozGeneratedCharacteristicThinFilm(
)
phirhozThinFilm.path = get_current_module_path(
__file__, "../../../test_data/results")
phirhozThinFilm.basename = "SimulationMCXrayPhirhozTestCases_Cu_E500d0keV_N100000e"
phirhozThinFilm.read()
self.assertEquals(1, phirhozThinFilm.numberRegions)
intensity = phirhozThinFilm.intensities[0]
self.assertEquals(
"0",
intensity[PhirhozGeneratedCharacteristicThinFilm.INDEX_REGION])
self.assertEquals(
"Cu",
intensity[PhirhozGeneratedCharacteristicThinFilm.ATOM_SYMBOL])
self.assertEquals(
"390.159",
intensity[PhirhozGeneratedCharacteristicThinFilm.SUBSHELL_K])
self.assertEquals(
"13367.3",
intensity[PhirhozGeneratedCharacteristicThinFilm.SUBSHELL_L])
self.assertEquals(
"0", intensity[PhirhozGeneratedCharacteristicThinFilm.SUBSHELL_M])
def setUp(self):
"""
Setup method.
"""
unittest.TestCase.setUp(self)
self.filepath = get_current_module_path(
__file__,
"../../../../test_data/exportedFiles/CNTsFePt_30keV_100e_100pixels_BF.txt"
)
def test_isFile(self):
filepathRef = "/casd/csadf/asdfsdaf/sadfsdaf.ser"
self.serialization.setFilepath(filepathRef)
self.assertFalse(self.serialization.isFile())
filepathRef = get_current_module_path(
__file__, "../../test_data/serialization/empty.ser")
if not os.path.isfile(filepathRef):
raise SkipTest
self.serialization.setFilepath(filepathRef)
self.assertTrue(self.serialization.isFile())
def test_getIntensity(self):
"""
Tests for method `getIntensity`.
"""
phirhozThinFilm = PhirhozEmittedCharacteristicThinFilm.PhirhozEmittedCharacteristicThinFilm(
)
phirhozThinFilm.path = get_current_module_path(
__file__, "../../../test_data/results")
phirhozThinFilm.basename = "SimulationMCXrayPhirhozTestCases_Cu_E500d0keV_N100000e"
phirhozThinFilm.read()
self.assertEquals(1, phirhozThinFilm.numberRegions)
regionID = 0
atomicSymbol = "Cu"
intensity = phirhozThinFilm.getIntensity(
regionID, atomicSymbol,
PhirhozEmittedCharacteristicThinFilm.LINE_KA1)
self.assertAlmostEquals(0.00194507, intensity, 6)
intensity = phirhozThinFilm.getIntensity(
regionID, atomicSymbol,
PhirhozEmittedCharacteristicThinFilm.LINE_KA2)
self.assertAlmostEquals(0.00179503, intensity, 6)
intensity = phirhozThinFilm.getIntensity(
regionID, atomicSymbol,
PhirhozEmittedCharacteristicThinFilm.LINE_KB1)
self.assertAlmostEquals(0.0337762, intensity, 6)
intensity = phirhozThinFilm.getIntensity(
regionID, atomicSymbol,
PhirhozEmittedCharacteristicThinFilm.LINE_KB2)
self.assertAlmostEquals(0.0, intensity, 6)
intensity = phirhozThinFilm.getIntensity(
regionID, atomicSymbol,
PhirhozEmittedCharacteristicThinFilm.LINE_LA)
self.assertAlmostEquals(8.20759E-158, intensity, 6)
intensity = phirhozThinFilm.getIntensity(
regionID, atomicSymbol,
PhirhozEmittedCharacteristicThinFilm.LINE_LB1)
self.assertAlmostEquals(0.0, intensity, 6)
intensity = phirhozThinFilm.getIntensity(
regionID, atomicSymbol,
PhirhozEmittedCharacteristicThinFilm.LINE_LB2)
self.assertAlmostEquals(0.0, intensity, 6)
intensity = phirhozThinFilm.getIntensity(
regionID, atomicSymbol,
PhirhozEmittedCharacteristicThinFilm.LINE_LG)
self.assertAlmostEquals(0.0, intensity, 6)
intensity = phirhozThinFilm.getIntensity(
regionID, atomicSymbol,
PhirhozEmittedCharacteristicThinFilm.LINE_MA)
self.assertAlmostEquals(0.0, intensity, 6)
def run():
from pymcxray import get_current_module_path
filepath = get_current_module_path(
__file__,
"../../../../test_data/exportedFiles/CNTsFePt_30keV_100e_100pixels_BF.txt"
)
dataMap = DataMap(filepath)
dataMap.read()
dataMap.showImage()
dataMap.saveImage()
def test_read(self):
"""
Tests for method `read`.
"""
spectrumFile = XraySimulatedSpectraSpecimen.XraySimulatedSpectraSpecimen()
spectrumFile.path = get_current_module_path(__file__, "../../../test_data/results")
spectrumFile.basename = "testC_10e_10kp"
spectrumFile.read()
self.assertEquals(1024, len(spectrumFile.energies_keV))
self.assertEquals(1024, len(spectrumFile.totals))
def test_read(self):
"""
Tests for method `read`.
"""
intensitiesFile = XrayIntensities.XrayIntensities()
intensitiesFile.path = get_current_module_path(
__file__, "../../../test_data/results")
intensitiesFile.basename = "SimulationsFRatio_Al0d200000Cu0d800000_E5d0keV"
intensitiesFile.read()
self.assertEquals(5, intensitiesFile.numberIntensities)
def _createIgnoredItems(sectionName, configurationFile):
configurationFilepath = get_current_module_path(__file__,
configurationFile)
values = read_value_from_configuration_file(configurationFilepath,
"Testings",
sectionName,
default="")
names = []
for item in values.split(','):
names.append(item.strip())
return names
def run():
path = get_current_module_path(__file__, "../../../test_data/version1.2")
filepath = os.path.join(
path,
"SimulationsComplexPhiRhoZ_Cr_T5nm_Z0nm_Al_E10d0keV_ElectronTrajectoriesResults.csv"
)
#filepath = os.path.join(path, "SimulationsComplexPhiRhoZ_Cr100T50A_IsolatedLayer_E10d0keV_ElectronTrajectoriesResults.csv")
electronTrajectoriesResults = ElectronTrajectoriesResults(filepath)
electronTrajectoriesResults.drawXZ()
electronTrajectoriesResults.drawXY()
electronTrajectoriesResults.drawYZ()
plt.show()
def test_deleteFile(self):
filename = "empty.ser"
filepathRef = get_current_module_path(
__file__, "../../test_data/serialization/")
filepathRef = os.path.join(filepathRef, filename)
if not os.path.isfile(filepathRef):
raise SkipTest
filepath = os.path.join(self.tempPath, filename)
shutil.copy2(filepathRef, filepath)
self.serialization.setFilepath(filepath)
self.assertTrue(os.path.isfile(filepath))
self.serialization.deleteFile()
self.assertFalse(os.path.isfile(filepath))
def test_read(self):
"""
Tests for method `read`.
"""
spectrumFile = XraySpectraSpecimen.XraySpectraSpecimen()
spectrumFile.path = get_current_module_path(
__file__, "../../../test_data/results")
spectrumFile.basename = "ExperimentalSpectraMCXRay_Au100T250000A_E200d0keV_N1000e_N21000000X_t600s_w20eV_N64W"
spectrumFile.read()
self.assertEquals(40000, len(spectrumFile.energies_keV))
self.assertEquals(40000, len(spectrumFile.totals))
self.assertEquals(40000, len(spectrumFile.characteristics))
self.assertEquals(40000, len(spectrumFile.backgrounds))
def test_read(self):
"""
Tests for method `read`.
"""
spectrumFile = XraySpectraSpecimenEmittedDetected.XraySpectraSpecimenEmittedDetected(
)
spectrumFile.path = get_current_module_path(
__file__, "../../../test_data/results")
spectrumFile.basename = "SimulationsAuNPonC_Au_d100A_C_E10d0keV_N10000e_N1000000X"
spectrumFile.read()
self.assertEquals(2000, len(spectrumFile.energies_keV))
self.assertEquals(2000, len(spectrumFile.totals))
self.assertEquals(2000, len(spectrumFile.characteristics))
self.assertEquals(2000, len(spectrumFile.backgrounds))
def test_read(self):
"""
Tests for method `read`.
"""
#PhirhozMCXRay_Ag_E5d0keV_N10000e_tB0d0deg_TOA45d0deg_PhirhozEmittedCharacteristic_Region0.csv
spectrumFile = PhirhozEmittedCharacteristic.PhirhozEmittedCharacteristic()
spectrumFile.path = get_current_module_path(__file__, "../../../test_data/results")
spectrumFile.basename = "PhirhozMCXRay_Ag_E5d0keV_N10000e_tB0d0deg_TOA45d0deg"
regionID = 0
spectrumFile.read(regionID)
self.assertEquals(5, len(spectrumFile.fieldNames))
self.assertEquals(128, len(spectrumFile.depth_A))
self.assertEquals(4, len(spectrumFile.phirhozs))
self.assertEquals(128, len(spectrumFile.phirhozs[("Ag", "La")]))
def run():
import pymcxray.BatchFileConsole as BatchFileConsole
configurationFilepath = get_current_module_path(__file__,
"../../MCXRay_latest.cfg")
programName = get_mcxray_program_name(configurationFilepath)
batchFile = BatchFileConsole.BatchFileConsole(
"BatchSimulationTestLinescansMM2017", programName, numberFiles=10)
analyze = SimulationTestLinescansMM2017(
relativePath=r"mcxray/SimulationTestLinescansMM2017",
configurationFilepath=configurationFilepath)
analyze.overwrite = False
analyze.run(batchFile)
plt.show()
def run():
# import the batch file class.
from pymcxray.BatchFileConsole import BatchFileConsole
# Find the configuration file path
configuration_file_path = get_current_module_path(__file__,
"MCXRay_latest.cfg")
program_name = get_mcxray_program_name(configuration_file_path)
# Create the batch file object.
batch_file = BatchFileConsole("BatchSimulationTestMapsMM2017",
program_name,
numberFiles=6)
# Create the simulation object and add the batch file object to it.
analyze = SimulationTestMapsMM2017(
relativePath=r"mcxray/SimulationTestMapsMM2017",
configurationFilepath=configuration_file_path)
analyze.run(batch_file)
def test_read(self):
"""
Tests for method `read`.
"""
phirhozThinFilm = PhirhozEmittedCharacteristicThinFilm.PhirhozEmittedCharacteristicThinFilm(
)
phirhozThinFilm.path = get_current_module_path(
__file__, "../../../test_data/results")
phirhozThinFilm.basename = "SimulationMCXrayPhirhozTestCases_Cu_E500d0keV_N100000e"
phirhozThinFilm.read()
self.assertEquals(1, phirhozThinFilm.numberRegions)
intensity = phirhozThinFilm.intensities[0]
self.assertEquals(
"0", intensity[PhirhozEmittedCharacteristicThinFilm.INDEX_REGION])
self.assertEquals(
"Cu", intensity[PhirhozEmittedCharacteristicThinFilm.ATOM_SYMBOL])
self.assertEquals(
"0.00194507",
intensity[PhirhozEmittedCharacteristicThinFilm.LINE_KA1])
self.assertEquals(
"0.00179503",
intensity[PhirhozEmittedCharacteristicThinFilm.LINE_KA2])
self.assertEquals(
"0.0337762",
intensity[PhirhozEmittedCharacteristicThinFilm.LINE_KB1])
self.assertEquals(
"0", intensity[PhirhozEmittedCharacteristicThinFilm.LINE_KB2])
self.assertEquals(
"8.20759e-158",
intensity[PhirhozEmittedCharacteristicThinFilm.LINE_LA])
self.assertEquals(
"0", intensity[PhirhozEmittedCharacteristicThinFilm.LINE_LB1])
self.assertEquals(
"0", intensity[PhirhozEmittedCharacteristicThinFilm.LINE_LB2])
self.assertEquals(
"0", intensity[PhirhozEmittedCharacteristicThinFilm.LINE_LG])
self.assertEquals(
"0", intensity[PhirhozEmittedCharacteristicThinFilm.LINE_MA])
def test_read(self):
"""
Tests for method `read`.
"""
spectrumFile = XraySimulatedSpectraRegion.XraySimulatedSpectraRegion()
spectrumFile.path = get_current_module_path(
__file__, "../../../test_data/results")
spectrumFile.basename = "testC_10e_10kp"
spectrumFile.read()
self.assertEquals(1024, len(spectrumFile.channelNumbers))
self.assertEquals(1024, len(spectrumFile.energiesReference_keV))
self.assertEquals(1024, len(spectrumFile.energies_keV))
self.assertEquals(1024, len(spectrumFile.simulatedIntensities))
self.assertEquals(1024, len(spectrumFile.detectedIntensities))
self.assertEquals(1024, len(spectrumFile.eNetPeak[0]))
self.assertEquals(1024, len(spectrumFile.peakToBackgrpound))
self.assertEquals(1024, len(spectrumFile.peakToBackgrpoundAverage))
def test_read(self):
"""
Tests for method `read`.
"""
#SimulationsAuNPonCExperimental_Au_d61A_C_E5d0keV_N10000e_N1000X_SpectraAtomEmittedDetectedLines_Region1.csv
spectrumFile = XraySpectraAtomEmittedDetectedLines.XraySpectraAtomEmittedDetectedLines(
)
spectrumFile.path = get_current_module_path(
__file__, "../../../test_data/results")
spectrumFile.basename = "SimulationsAuNPonCExperimental_Au_d61A_C_E5d0keV_N10000e_N1000X"
regionID = 1
spectrumFile.read(regionID)
self.assertEquals(0.0025, spectrumFile.energies_keV[0])
self.assertEquals(4.9975, spectrumFile.energies_keV[-1])
self.assertEquals(1000, len(spectrumFile.energies_keV))
self.assertEquals(1, len(spectrumFile.characteristics))
self.assertEquals(1000, len(spectrumFile.characteristics['Au']))
def __init__(self, simulationPath=None, basepath=None, relativePath=None, configurationFilepath=None):
if configurationFilepath is None:
self._configurationFilepath = get_current_module_path(__file__, "../../pyMcGill.cfg")
else:
self._configurationFilepath = configurationFilepath
self._output = None
self.overwrite = True
self.resetCache = False
self.useSerialization = True
self.verbose = True
self.createBackup = True
self.use_hdf5 = False
self.delete_result_files = False
self.read_interval_h = 1
self.read_interval_m = None
if simulationPath is not None:
self._simulationPath = os.path.normpath(simulationPath)
else:
self._simulationPath = None
if basepath is not None:
self._basepath = os.path.normpath(basepath)
else:
self._basepath = None
if relativePath is not None:
self._relativePath = os.path.normpath(relativePath)
else:
self._relativePath = None
self._createAllFolders(self.getSimulationPath())
self._simulationResultsList = {}
self._serializationExtension = '.ser'
self.format_digit = {}
def run():
simulation_name = "SimulationTrainingMapsMM2017_Fe075"
elements = [(26, 0.75), (27, 0.25)]
# import the batch file class.
from pymcxray.BatchFileConsole import BatchFileConsole
# Find the configuration file path
configuration_file_path = get_current_module_path(__file__,
"MCXRay_latest.cfg")
program_name = get_mcxray_program_name(configuration_file_path)
# Create the batch file object.
batch_file = BatchFileConsole("BatchSimulationTrainingMapsMM2017",
program_name,
numberFiles=10)
# Create the simulation object and add the batch file object to it.
analyze = SimulationTrainingMapsMM2017(
simulation_name,
elements,
relativePath=r"mcxray/SimulationTrainingMapsMM2017",
configurationFilepath=configuration_file_path)
analyze.run(batch_file)
def test_read(self):
"""
Tests for method `read`.
"""
electronResults = ElectronResults.ElectronResults()
electronResults.path = get_current_module_path(
__file__, "../../../test_data/results")
electronResults.basename = "SimulationKalefEzra1982_Al100T10000A_E300d0keV_N100000e"
electronResults.read()
self.assertEquals(100000, electronResults.numberSimulatedElectrons)
self.assertEquals(0, electronResults.numberInternalElectrons)
self.assertEquals(43, electronResults.numberBackscatteredElectrons)
self.assertEquals(99956, electronResults.numberTransmittedElectrons)
self.assertEquals(0, electronResults.numberSkirtedElectrons)
self.assertEquals(458571, electronResults.numberElectronCollisions)
self.assertEquals(0, electronResults.fractionInternalElectrons)
self.assertEquals(0.00043,
electronResults.fractionBackscatteredElectrons)
self.assertEquals(0.99956,
electronResults.fractionTransmittedElectrons)
self.assertEquals(0, electronResults.fractionSkirtedElectrons)