pymcxray package¶

Subpackages¶

Submodules¶

pymcxray.AnalyzeNumberBackgroundWindows module¶

Analyze the number of background windows on the x-ray spectrum.

class pymcxray.AnalyzeNumberBackgroundWindows.AnalyzeNumberBackgroundWindows[source]¶

Bases: object

plotData()[source]¶

plotDifference()[source]¶

readData()[source]¶

pymcxray.AnalyzeNumberBackgroundWindows.run()[source]¶

pymcxray.AtomData module¶

MCXRay atom data.

pymcxray.AtomData.getAtomSymbol(atomic_number)[source]¶

pymcxray.AtomData.getAtomicNumber(symbol)[source]¶

pymcxray.AtomData.getIonizationEnergy_keV(shell, element)[source]¶

pymcxray.AtomData.getMassDensity_g_cm3(symbol)[source]¶

pymcxray.AtomData.getShellList()[source]¶

pymcxray.AtomData.getXRayEnergy_keV(line, element)[source]¶

pymcxray.AtomData.get_atomic_weight_g_mol(atomic_number)[source]¶

pymcxray.AtomData.run()[source]¶

pymcxray.BatchFile module¶

MCXRay batch file creator.

class pymcxray.BatchFile.BatchFile(name, numberFiles=1)[source]¶

Bases: object

addSimulationName(simulationFilename)[source]¶

removePreviousFiles(path)[source]¶

write(path)[source]¶

pymcxray.BatchFileConsole module¶

MCXRay console batch file creator.

class pymcxray.BatchFileConsole.BatchFileConsole(name, programName, numberFiles=1)[source]¶

Bases: object

The batch file is responsible to create the simulation structure with a copy of mcxray program.

One important parameter to set is the numberFiles, this is the number of batch files generated and that can be run in parallel. For maximum efficiency it should be set as the number of logical processors minus 1 or 2. For example, on a computer with 12 logical processors, the numberFiles should be set at 10.

Parameters:	name (str) – Basename used for the batch files programName (str) – Name of the executable to add in the batch file numberFiles (int) – Number of batch files to generate and possibly to run in parallel

addSimulationName(simulationFilename)[source]¶

Add a simulation in the simulation list.

Parameters:	simulationFilename (str) – File path of the simulation added

write(path)[source]¶

Write the batch files for all simulations in the simulation list.

Parameters:	path (str) – Path where the batch files are written.

pymcxray.ComparisonModels module¶

Comparison of the models used by MCXray.

class pymcxray.ComparisonModels.ComparisonModels(dataPath)[source]¶

Bases: object

graphicsEnergyLoss()[source]¶

graphicsIonizationCrossSection()[source]¶

graphicsXrayCrossSectionBremstrahlung()[source]¶

graphicsXrayMassAbsorptionCoefficient()[source]¶

pymcxray.ComparisonModels.runVersion1_2_3()[source]¶

pymcxray.ComparisonModels.runVersion1_4_0()[source]¶

pymcxray.ComparisonModels.runVersion1_4_1()[source]¶

pymcxray.DebugSimulatedSpectrum module¶

Debug the simulated spectrum implementation in mcxray.

class pymcxray.DebugSimulatedSpectrum.DebugSimulatedSpectrum[source]¶

Bases: object

runRegion()[source]¶

runSpecimen()[source]¶

pymcxray.DebugSimulatedSpectrum.run()[source]¶

pymcxray.ElementProperties module¶

pymcxray.ElementProperties.computeAtomicDensity_atom_cm3(massDensity_g_cm3, atomicMass_g_mol)[source]¶

Compute the atomic density.

\[n_{i} = \frac{N_{A} \rho_{i}}{A_{i}}\]

where

\(n_{i}\) is the atomic density in \(\mathrm{atoms}/cm^{3}\)
\(N_{A}\) is the Avogadro number in \(\mathrm{atoms}/mole\)
\(\rho_{i}\) is the mass density in \(g/cm^{3}\)
\(A_{i}\) is the atomic mass in \(g/mole\)

Parameters:	massDensity_g_cm3 (float) – atomicMass_g_mol (float) –

pymcxray.ElementProperties.g_FermiEnergy = [1.0, 1.0, 4.7, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 3.1, 1.0, 1.0, 0.555, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 7.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 5.5, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 5.5, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 0.0, 1.0, 1.0, 1.0, 1.0]¶

Fermi energy of element in atomic number order.

For element H to Lr (1-103). From: CASINO source code, DOS version.

Todo

Add units.

pymcxray.ElementProperties.g_atomicMass_g_mol = [1.0079, 4.0026, 6.941, 9.01218, 10.81, 12.011, 14.0067, 15.9994, 18.998403, 20.179, 22.98977, 24.305, 26.98154, 28.0855, 30.97376, 32.06, 35.453, 39.948, 39.0983, 40.08, 44.9559, 47.9, 50.9415, 51.996, 54.938, 55.847, 58.9332, 58.7, 63.546, 65.38, 69.72, 72.59, 74.9216, 78.96, 79.904, 83.8, 85.4678, 87.62, 88.9056, 91.22, 92.9064, 95.94, 98.0, 101.07, 102.9055, 106.4, 107.868, 112.41, 114.82, 118.69, 121.75, 127.6, 126.9045, 131.3, 132.9054, 137.33, 138.9055, 140.12, 140.9077, 144.24, 145.0, 150.4, 151.96, 157.25, 158.9254, 162.5, 164.9304, 167.26, 168.9342, 173.04, 174.967, 178.49, 180.9479, 183.85, 186.207, 190.2, 192.22, 195.09, 196.9665, 200.59, 204.37, 207.2, 208.9804, 209.0, 210.0, 222.0, 223.0, 226.0254, 227.0278, 232.0381, 231.0359, 238.029, 237.0482, 244.0, 243.0, 247.0, 247.0, 251.0, 252.0, 257.0, 258.0, 259.0, 260.0, 261.0, 262.0, 263.0]¶

Atomic weight of element in atomic number order.

For element H to Sg (1-106).

Unit \(g/mole\).

From: Tableau periodique des elements, Sargent-Welch scientifique Canada Limitee.

pymcxray.ElementProperties.g_kFermi = [70000000.0, 70000000.0, 110000000.0, 70000000.0, 70000000.0, 70000000.0, 70000000.0, 70000000.0, 70000000.0, 70000000.0, 90000000.0, 70000000.0, 70000000.0, 40000000.0, 70000000.0, 70000000.0, 70000000.0, 70000000.0, 70000000.0, 70000000.0, 70000000.0, 70000000.0, 70000000.0, 70000000.0, 70000000.0, 70000000.0, 70000000.0, 70000000.0, 135000000.0, 70000000.0, 70000000.0, 70000000.0, 70000000.0, 70000000.0, 70000000.0, 70000000.0, 70000000.0, 70000000.0, 70000000.0, 70000000.0, 70000000.0, 70000000.0, 70000000.0, 70000000.0, 70000000.0, 70000000.0, 119000000.0, 70000000.0, 70000000.0, 70000000.0, 70000000.0, 70000000.0, 70000000.0, 70000000.0, 70000000.0, 70000000.0, 70000000.0, 70000000.0, 70000000.0, 70000000.0, 70000000.0, 70000000.0, 70000000.0, 70000000.0, 70000000.0, 70000000.0, 70000000.0, 70000000.0, 70000000.0, 70000000.0, 70000000.0, 70000000.0, 70000000.0, 70000000.0, 70000000.0, 70000000.0, 70000000.0, 70000000.0, 119000000.0, 70000000.0, 70000000.0, 70000000.0, 70000000.0, 70000000.0, 70000000.0, 70000000.0, 70000000.0, 70000000.0, 70000000.0, 70000000.0, 70000000.0, 70000000.0, 70000000.0, 70000000.0, 70000000.0, 70000000.0, 70000000.0, 70000000.0, 0.0, 70000000.0, 70000000.0, 70000000.0, 70000000.0]¶

Fermi wavelength of element in atomic number order.

For element H to Lr (1–103). From: CASINO source code, DOS version.

Todo

Add units.

pymcxray.ElementProperties.g_massDensity_g_cm3 = [0.0899, 0.1787, 0.53, 1.85, 2.34, 2.62, 1.251, 1.429, 1.696, 0.901, 0.97, 1.74, 2.7, 2.33, 1.82, 2.07, 3.17, 1.784, 0.86, 1.55, 3.0, 4.5, 5.8, 7.19, 7.43, 7.86, 8.9, 8.9, 8.96, 7.14, 5.91, 5.32, 5.72, 4.8, 3.12, 3.74, 1.53, 2.6, 4.5, 6.49, 8.55, 10.2, 11.5, 12.2, 12.4, 12.0, 10.5, 8.65, 7.31, 7.3, 6.68, 6.24, 4.92, 5.89, 1.87, 3.5, 6.7, 6.78, 6.77, 7.0, 6.475, 7.54, 5.26, 7.89, 8.27, 8.54, 8.8, 9.05, 9.33, 6.98, 9.84, 13.1, 16.6, 19.3, 21.0, 22.4, 22.5, 21.4, 19.3, 13.53, 11.85, 11.4, 9.8, 9.4, 1.0, 9.91, 1.0, 5.0, 10.07, 11.7, 15.4, 18.9, 20.4, 19.8, 13.6, 13.511]¶

Mass density of element in atomic number order.

For element H to Cm (1-96).

In \(g/cm{3}\).

From: Tableau periodique des elements, Sargent-Welch scientifique Canada Limitee.

Note

Element Z = 85 and 87 set to 1 for the calculation.

pymcxray.ElementProperties.g_plasmonEnergy = [15.0, 15.0, 7.1, 18.7, 22.7, 15.0, 15.0, 15.0, 15.0, 15.0, 5.7, 10.3, 15.0, 16.7, 15.0, 15.0, 15.0, 15.0, 3.7, 8.8, 14.0, 17.9, 21.8, 24.9, 21.6, 23.0, 20.9, 20.7, 19.3, 17.2, 13.8, 16.2, 15.0, 15.0, 15.0, 15.0, 3.41, 8.0, 12.5, 15.0, 15.0, 15.0, 15.0, 15.0, 15.0, 15.0, 15.0, 19.2, 15.0, 13.4, 15.2, 17.0, 11.4, 15.0, 2.9, 7.2, 15.0, 15.0, 15.0, 15.0, 15.0, 15.0, 15.0, 15.0, 13.3, 15.0, 15.0, 14.0, 15.0, 15.0, 15.0, 15.0, 15.0, 15.0, 15.0, 15.0, 15.0, 35.0, 15.0, 15.0, 15.0, 13.0, 14.2, 15.0, 15.0, 15.0, 15.0, 15.0, 25.0, 15.0, 15.0, 15.0, 15.0, 15.0, 15.0, 15.0, 15.0, 15.0, 15.0, 15.0, 15.0, 15.0, 15.0]¶

Plasmon energy of element in atomic number order.

For element H to Lr (1-103). From: CASINO source code, DOS version.

Todo

Add units.

pymcxray.ElementProperties.getAtomicMass_g_mol(atomicNumber)[source]¶

pymcxray.ElementProperties.getAtomicNumber(atomicNumber=None, name=None, symbol=None)[source]¶

pymcxray.ElementProperties.getAtomicNumberByName(name)[source]¶

pymcxray.ElementProperties.getAtomicNumberBySymbol(symbol)[source]¶

pymcxray.ElementProperties.getFermiEnergy_eV(atomicNumber)[source]¶

pymcxray.ElementProperties.getKFermi_eV(atomicNumber)[source]¶

pymcxray.ElementProperties.getKRatioCorrection(atomicNumber)[source]¶

Get the constant k ratio correction needed by the mean ionization potential from the atomic number.

Parameters:	atomic_number (int) – Atomic number

pymcxray.ElementProperties.getKRatioCorrectionMonsel(atomicNumber, workFunction_keV)[source]¶: /// K value as defined by Monsel. /// Used in DE/DS calculation. Casino uses K Gauvin,but for low energy, /// JR Lowney says that this one is more appropriate (and by experience, /// it is effectively better for the secondary yield). /// <p> NOTE : Depends on J (ionisation potential). So it must already be calculated before. /// @param element Element for whom we want to calculate the K value. /// @return The K value of the element passed in argument

pymcxray.ElementProperties.getMassDensity_g_cm3(atomicNumber)[source]¶

pymcxray.ElementProperties.getMeanIonizationEnergy_eV(atomic_number)[source]¶

Get the mean ionization potential from the atomic number.

In \(eV\).

Parameters:	atomic_number (int) – Atomic number

pymcxray.ElementProperties.getName(atomicNumber)[source]¶

pymcxray.ElementProperties.getPlasmonEnergy_eV(atomicNumber)[source]¶

pymcxray.ElementProperties.getSymbol(atomicNumber)[source]¶

pymcxray.ElementProperties.run()[source]¶

pymcxray.ElementProperties.runAtomicNumberSymbol()[source]¶

pymcxray.Simulation module¶

MCXRay simulation parameters.

class pymcxray.Simulation.Layer(elements, thickness_nm, mass_density_g_cm3=None)[source]¶: Bases: object

class pymcxray.Simulation.Simulation(overwrite=True)[source]¶

Bases: object

basename¶

beamDiameter_nm¶

beamPosition_nm¶

beamTilt_deg¶

createSimulationFiles(path, simulationPath, hdf5_group)[source]¶

current_A¶

detectorAzimuthalAngle_deg¶

detectorChannelWidth_eV¶

detectorCrystalDistance_cm¶

detectorCrystalRadius_cm¶

detectorCrystalThickness_cm¶

detectorNoise_eV¶

elasticCrossSectionScalingFactor¶

energyLossScalingFactor¶

energy_keV¶

filename¶

generateBaseFilename()[source]¶

getFilenameSuffixes()[source]¶

getParameters()[source]¶

getProgramVersionFilepath(simulationPath)[source]¶

isDone(simulationPath, hdf5_group=None)[source]¶

modelXrayBremsstrahlung¶

name¶

numberContinuumWindows¶

numberElectrons¶

numberEnergyWindows¶

numberLayersX¶

numberLayersY¶

numberLayersZ¶

numberPhotons¶

removeInputsFiles()[source]¶

resultsBasename¶

setParameters(parameters)[source]¶

solidAngle_sr¶

spectrumInterpolationModel¶

takeOffAngle_deg¶

time_s¶

pymcxray.Simulation.computeWeightFraction(atomicNumberRef, atomicWeights)[source]¶

pymcxray.Simulation.createAlloyBoxInSubstrate(elementsParticle, elementsSubstrate, boxParameters_nm)[source]¶

pymcxray.Simulation.createAlloyBoxInThinFilm(elementsParticle, atomicNumberSubstrate, boxParameters_nm, filmThickness_nm)[source]¶

pymcxray.Simulation.createAlloyBoxInVaccuum(elements, boxParameters_nm)[source]¶

pymcxray.Simulation.createAlloyBulkSample(elements, sampleName=None)[source]¶

pymcxray.Simulation.createAlloyFilmOverSubstrate(film_elements, substrate_elements, film_thickness_nm=10.0, film_mass_density_g_cm3=None, substrate_mass_density_g_cm3=None)[source]¶

pymcxray.Simulation.createAlloyMultiVerticalLayer(elementsLayers, layerWidths_nm)[source]¶

pymcxray.Simulation.createAlloyParticleInSubstrate(elementsParticle, atomicNumberSubstrate, particleRadius_nm, particlePositionZ_nm=None)[source]¶

pymcxray.Simulation.createAlloyParticleInThinFilm(elementsParticle, atomicNumberSubstrate, particleRadius_nm, filmThickness_nm, particlePositionZ_nm=None)[source]¶

pymcxray.Simulation.createAlloyThinFilm(elements, filmThickness_nm)[source]¶

pymcxray.Simulation.createAlloyThinFilm2(elements, filmThickness_nm)[source]¶

pymcxray.Simulation.createBoxFeatureInSubstrate(feature_elements, substrate_elements, depth_nm, width_nm)[source]¶

pymcxray.Simulation.createFilmInSubstrate(atomicNumberFilm, atomicNumberSubstrate, filmThickness_nm, filmTopPositionZ_nm)[source]¶

pymcxray.Simulation.createFilmOverSubstrate(atomicNumberFilm, atomicNumberSubstrate, filmThickness_nm=10.0)[source]¶

pymcxray.Simulation.createParticleInSubstrate(atomicNumberParticle, atomicNumberSubstrate, particleRadius_nm, particlePositionZ_nm=None)[source]¶

pymcxray.Simulation.createParticleOnFilm(atomicNumberParticle, atomicNumberSubstrate, particleDiameter_nm, filmThiskness_nm)[source]¶

pymcxray.Simulation.createParticleOnSubstrate(atomicNumberParticle, atomicNumberSubstrate, particleDiameter_nm)[source]¶

pymcxray.Simulation.createPhirhozSpecimens(atomicNumberTracer, atomicNumberMatrix, tracerThickness_nm, maximumThickness_nm)[source]¶

pymcxray.Simulation.createPureBulkSample(atomic_number)[source]¶

pymcxray.Simulation.create_cnt_sample(body_elements, cnt_length_nm=1000.0, cnt_outside_diameter_nm=100.0, cnt_inside_diameter_nm=50.0, particle_diameter_nm=5.0)[source]¶

pymcxray.Simulation.create_multi_horizontal_layer(substrate_elements, layers, substrate_mass_density_g_cm3=None)[source]¶

Create a horizontal multi layer sample.

The substrate is the first region created. The other region are each of the element in the layers.

Parameters:	substrate_elements – list of atomic number and weight fraction pair for the composition of the substrate layers – substrate_mass_density_g_cm3 –
Returns:

pymcxray.Simulation.create_weight_fractions(weight_fraction_step, number_elements)[source]¶

pymcxray.Simulation.create_weight_fractions_trace(weight_fraction_step, number_elements, min_weight_fraction, max_weight_fraction)[source]¶

pymcxray.SimulationsParameters module¶

Simulations parameters

class pymcxray.SimulationsParameters.SimulationsParameters[source]¶

Bases: dict

addCompute(parameterKey)[source]¶

addFixed(parameterKey, value)[source]¶

addVaried(parameterKey, values)[source]¶

computeNumberXrays(experiment)[source]¶

computeNumberXraysFilepath¶

fixedParameters¶

getAllSimulationParameters()[source]¶

getVariedParameterLabels()[source]¶

variedParameters¶

class pymcxray.SimulationsParameters.SimulationsParametersFixed[source]¶

Bases: object

addExperiment(experiment)[source]¶

getAllSimulationParameters()[source]¶

pymcxray.Testings module¶

pymcxray.mcxray module¶

Base module to create and analuyze MCXRay simulations.

pymcxray.multipleloop module¶

This module provides a tool for handling computer experiments with of a set of input parameters, where each input parameter is varied in a prescribed fashion.

In short, the parameters are held in a dictionary where the keys are the names of the parameters and the values are the numerical, string or other values of the parameters. The value can take on multiple values: e.g., an integer parameter ‘a’ can have values -1, 1 and 10. Similarly, a string parameter ‘method’ can have values ‘Newton’ and ‘Bisection’. The module will generate all combination of all parameters and values, which in the mentioned example will be (-1, ‘Newton’), (1, ‘Newton’), (10, ‘Newton’), (-1, ‘Bisection’), (1, ‘Bisection’), and (10, ‘Bisection’). Particular combination of values can easily be removed.

The usage and implementation of the module are documented in the book “Python Scripting for Computational Science” (H. P. Langtangen, Springer, 2009), Chapter 12.1.

pymcxray.multipleloop.combine(prm_values)[source]¶

Compute the combination of all parameter values in the prm_values (nested) list. Main function in this module.

param prm_values: nested list (parameter_name, list_of_parameter_values) or dictionary prm_values[parameter_name] = list_of_parameter_values. return: (all, names, varied) where

all contains all combinations (experiments) all[i] is the list of individual parameter values in experiment no i

names contains a list of all parameter names

varied holds a list of parameter names that are varied (i.e. where there is more than one value of the parameter, the rest of the parameters have fixed values)

Code example:

>>> dx = array([1.0/2**k for k in range(2,5)])
>>> dt = 3*dx;  dt = dt[:-1]
>>> p = {'dx': dx, 'dt': dt}
>>> p
{'dt': [ 0.75 , 0.375,], 'dx': [ 0.25  , 0.125 , 0.0625,]}
>>> all, names, varied = combine(p)
>>> all
[[0.75, 0.25], [0.375, 0.25], [0.75, 0.125], [0.375, 0.125],
 [0.75, 0.0625], [0.375, 0.0625]]

pymcxray.pymcxray module¶

pymcxray.test_AtomData module¶

Tests for the module AtomData.

class pymcxray.test_AtomData.TestAtomData(methodName='runTest')[source]¶

Bases: unittest.case.TestCase

TestCase class for the module AtomData.

Create an instance of the class that will use the named test method when executed. Raises a ValueError if the instance does not have a method with the specified name.

setUp()[source]¶: Setup method.

tearDown()[source]¶: Teardown method.

testConstants()[source]¶: First test to check if the testcase is working with the testing framework.

testSkeleton()[source]¶: First test to check if the testcase is working with the testing framework.

pymcxray.test_BatchFileConsole module¶

Tests for the module BatchFileConsole.

class pymcxray.test_BatchFileConsole.TestBatchFileConsole(methodName='runTest')[source]¶

Bases: unittest.case.TestCase

TestCase class for the module BatchFileConsole.

Create an instance of the class that will use the named test method when executed. Raises a ValueError if the instance does not have a method with the specified name.

setUp()[source]¶: Setup method.

tearDown()[source]¶: Teardown method.

testSkeleton()[source]¶: First test to check if the testcase is working with the testing framework.

pymcxray.test_ComparisonModels module¶

Tests for the module ComparisonModels.

class pymcxray.test_ComparisonModels.TestComparisonModels(methodName='runTest')[source]¶

Bases: unittest.case.TestCase

TestCase class for the module ComparisonModels.

Create an instance of the class that will use the named test method when executed. Raises a ValueError if the instance does not have a method with the specified name.

setUp()[source]¶: Setup method.

tearDown()[source]¶: Teardown method.

testSkeleton()[source]¶: First test to check if the testcase is working with the testing framework.

pymcxray.test_Simulation module¶

Tests for the module Simulation.

class pymcxray.test_Simulation.TestSimulation(methodName='runTest')[source]¶

Bases: unittest.case.TestCase

TestCase class for the module Simulation.

Create an instance of the class that will use the named test method when executed. Raises a ValueError if the instance does not have a method with the specified name.

setUp()[source]¶: Setup method.

tearDown()[source]¶: Teardown method.

testSkeleton()[source]¶: First test to check if the testcase is working with the testing framework.

test_create_multi_horizontal_layer()[source]¶: Test the create_multi_horizontal_layer method.

test_create_weight_fractions()[source]¶

test_create_weight_fractions_trace()[source]¶

test_create_weight_fractions_trace_speed_test_three_elements()[source]¶

test_create_weight_fractions_trace_speed_test_two_elements()[source]¶

pymcxray.test_SimulationsParameters module¶

Tests for the module SimulationsParameters.

class pymcxray.test_SimulationsParameters.TestSimulationsParameters(methodName='runTest')[source]¶

Bases: unittest.case.TestCase

TestCase class for the module SimulationsParameters.

Create an instance of the class that will use the named test method when executed. Raises a ValueError if the instance does not have a method with the specified name.

setUp()[source]¶: Setup method.

tearDown()[source]¶: Teardown method.

testSkeleton()[source]¶: First test to check if the testcase is working with the testing framework.

pymcxray.test_mcxray module¶

Tests for the module mcxray.

class pymcxray.test_mcxray.Testmcxray(methodName='runTest')[source]¶

Bases: unittest.case.TestCase

TestCase class for the module mcxray.

Create an instance of the class that will use the named test method when executed. Raises a ValueError if the instance does not have a method with the specified name.

setUp()[source]¶: Setup method.

tearDown()[source]¶: Teardown method.

testSkeleton()[source]¶: First test to check if the testcase is working with the testing framework.

pymcxray.tests module¶

Module contents¶

pymcxray.create_path(path)[source]¶

Create a path from the input string if does not exists.

Does not try to distinct between file and directory in the input string. path = “dir1/filename.ext” => “dir1/filename.ext/” where the new directory “filename.ext” is created.

Parameters:	path (str) – The path input string.
Returns:	The path with the path separator at the end
Return type:	str

pymcxray.find_all_files(root, patterns='*', ignore_path_patterns='', ignore_name_patterns='', single_level=False, yield_folders=False)[source]¶

Find all files in a root folder.

From Python Cookbook section 2.16 pages 88–90

Parameters:	root – patterns – ignore_path_patterns – ignore_name_patterns – single_level – yield_folders –
Returns:

pymcxray.get_current_module_path(module_path, relative_path='')[source]¶

Extract the current module path and combine it with the relative path and return it.

Parameters:	module_path (str) – Pass the __FILE__ python keyword for this parameter relative_path (str) – The relative path to combine with the module path
Returns:	The path obtained when combine the module path and relative path
Return type:	str

pymcxray.get_mcxray_archive_name(configuration_file_path, default=None)[source]¶

Read the MCXRay archive name in the configuration file. This option allows to choose which version of MCXRay to use for the simulations.

The configuration file need to have this entry in the section [Paths]:

[Paths]
mcxrayArchiveName=2016-04-11_11h41m28s_MCXRay_v1.6.6.0.zip

Parameters:	configuration_file_path (str) – The file path of the configuration file default (str) – Default value to use if the entry is not found
Returns:	The MCXRay archive name
Return type:	str

pymcxray.get_mcxray_archive_path(configuration_file_path, relative_path='')[source]¶

Read the MCXRay archive path in the configuration file.

The configuration file need to have this entry in the section [Paths]:

[Paths]
mcxrayArchivePath=D:\Dropbox\hdemers\professional\softwareRelease\mcxray

Parameters:	configuration_file_path (str) – The file path of the configuration file relative_path (str) – Relative path to add to the path read in the configuration file
Returns:	Path where the mcxray archive can be found.
Return type:	str

pymcxray.get_mcxray_program_name(configuration_file_path, default=None)[source]¶

Read the MCXRay program name in the configuration file.

This option specify which executable to use in the script. The console_mcxray_x64.exe should be OK for most situation. If you have a 32-bit system, you have to use console_mcxray.exe (32-bit version).

The configuration file need to have this entry in the section [Paths]:

[Paths]
mcxrayProgramName=console_mcxray_x64.exe

Parameters:	configuration_file_path (str) – The fule path of the configuration file default (str) – Default value to use if the entry is not found
Returns:	The MCXRay program name
Return type:	str

pymcxray.get_mcxray_program_path(configuration_file_path, relative_path='')[source]¶

Read the MCXRay program path in the configuration file.

The configuration file need to have this entry in the section [Paths]:

[Paths]
mcxrayProgramPath=C:\hdemers\codings\devcasino

Parameters:	configuration_file_path (str) – The file path of the configuration file relative_path (str) – Relative path to add to the path read in the configuration file
Returns:	Path where the mcxray program can be found.
Return type:	str

Deprecated since version 0.1.