def test_read(self):
"""
Tests for method `read`.
"""
for title in testUtilities.getSimulationTitles():
logging.info(title)
specimen = Specimen.Specimen()
filepath = os.path.abspath(os.path.join(self.testDataPath, "%s/%s.sam" % (title, title)))
specimen.read(filepath)
self.assertEquals(Version.VERSION_1_1_1.major, specimen.version.major)
self.assertEquals(Version.VERSION_1_1_1.minor, specimen.version.minor)
self.assertEquals(Version.VERSION_1_1_1.revision, specimen.version.revision)
self.assertEquals(Version.VERSION_1_1_1, specimen.version)
specimenRef = self.getSpecimenReference(title)
self.assertEquals(specimenRef.version.major, specimen.version.major)
self.assertEquals(specimenRef.version.minor, specimen.version.minor, title)
self.assertEquals(specimenRef.version.revision, specimen.version.revision)
self.assertEquals(specimenRef.version, specimen.version)
self.assertEquals(specimenRef.numberRegions, specimen.numberRegions)
def test_write(self):
"""
Tests for method `write`.
"""
raise SkipTest
self.maxDiff = None
for title in testUtilities.getSimulationTitles():
logging.info(title)
specimenRef = self.getSpecimenReference(title)
filepathReference = os.path.abspath(os.path.join(self.testDataPath, "%s/%s.sam" % (title, title)))
filepath = os.path.join(self.tempDataPath, "%s.sam" % (title))
specimen = Specimen.Specimen()
specimen = specimenRef
specimen.write(filepath)
linesRef = open(filepathReference, 'r').readlines()
lines = open(filepath, 'r').readlines()
for index in range(len(linesRef)):
lineRef = linesRef[index]
line = lines[index]
message = "%i:\n%s\n%s" % (index, lineRef, line)
self.assertEquals(lineRef, line, message)
self.assertListEqual(linesRef, lines)
def getSpecimenReference(self, title):
specimen = Specimen.Specimen()
if title == "AuBC cyl":
specimen.numberRegions = 4
specimen.version = Version.Version(1, 1, 1)
region = Region.Region()
region.numberElements = 1
element = Element.Element(6)
region.elements.append(element)
region.regionType = RegionType.REGION_TYPE_BOX
parameters = [-10000000000.0, 10000000000.0, -10000000000.0, 10000000000.0, 0.0, 20000000000.0]
region.regionDimensions = RegionDimensions.RegionDimensionsBox(parameters)
specimen.regions.append(region)
region = Region.Region()
region.numberElements = 1
element = Element.Element(79)
region.elements.append(element)
region.regionType = RegionType.REGION_TYPE_BOX
parameters = [0.0, 10000000000.0, -10000000000.0, 10000000000.0, 0.0, 20000000000.0]
region.regionDimensions = RegionDimensions.RegionDimensionsBox(parameters)
specimen.regions.append(region)
region = Region.Region()
region.numberElements = 1
element = Element.Element(5)
region.elements.append(element)
region.regionType = RegionType.REGION_TYPE_CYLINDER
parameters = [-500.0, -500.0, 300.0, 0.0, 1.0, 0.35, 1000.0, 300.0]
region.regionDimensions = RegionDimensions.RegionDimensionsCylinder(parameters)
specimen.regions.append(region)
region = Region.Region()
region.numberElements = 1
element = Element.Element(5)
region.elements.append(element)
region.regionType = RegionType.REGION_TYPE_CYLINDER
parameters = [500.0, 500.0, 300.0, 0.0, -1.0, 0.35, 1000.0, 300.0]
region.regionDimensions = RegionDimensions.RegionDimensionsCylinder(parameters)
specimen.regions.append(region)
elif title == "BioRitchieNew111017":
specimen.numberRegions = 7
specimen.version = Version.Version(1, 1, 1)
region = Region.Region()
region.numberElements = 3
element = Element.Element(6, 0.7)
region.elements.append(element)
element = Element.Element(8, 0.28)
region.elements.append(element)
element = Element.Element(17, 0.02)
region.elements.append(element)
region.regionMassDensity_g_cm3 = 1.14
region.regionType = RegionType.REGION_TYPE_BOX
parameters = [-10000000000.0, 10000000000.0, -10000000000.0, 10000000000.0, 0.0, 20000000000.0]
region.regionDimensions = RegionDimensions.RegionDimensionsBox(parameters)
specimen.regions.append(region)
region = Region.Region()
region.numberElements = 2
element = Element.Element(8, 0.53)
region.elements.append(element)
element = Element.Element(14, 0.47)
region.elements.append(element)
region.regionMassDensity_g_cm3 = 2.2
region.regionType = RegionType.REGION_TYPE_CYLINDER
parameters = [-20000.0, 0.0, 30000.0, 1.0, 0.0, 0.0, 40000.0, 30000.0]
region.regionDimensions = RegionDimensions.RegionDimensionsCylinder(parameters)
specimen.regions.append(region)
region = Region.Region()
region.numberElements = 3
element = Element.Element(6, 0.7)
region.elements.append(element)
element = Element.Element(8, 0.28)
region.elements.append(element)
element = Element.Element(17, 0.02)
region.elements.append(element)
region.regionMassDensity_g_cm3 = 1.14
region.regionType = RegionType.REGION_TYPE_CYLINDER
parameters = [-20000.0, 0.0, 30000.0, 1.0, 0.0, 0.0, 40000.0, 29500.0]
region.regionDimensions = RegionDimensions.RegionDimensionsCylinder(parameters)
specimen.regions.append(region)
region = Region.Region()
region.numberElements = 7
region.elements.append(Element.Element(1, 0.071))
region.elements.append(Element.Element(6, 0.414))
region.elements.append(Element.Element(7, 0.168))
region.elements.append(Element.Element(8, 0.285))
region.elements.append(Element.Element(15, 0.036))
region.elements.append(Element.Element(16, 0.006))
region.elements.append(Element.Element(76, 0.02))
region.regionMassDensity_g_cm3 = 1.32
region.regionType = RegionType.REGION_TYPE_SPHERE
parameters = [12000.0, 10000.0, 10000.0, 8000.0]
region.regionDimensions = RegionDimensions.RegionDimensionsSphere(parameters)
specimen.regions.append(region)
region = Region.Region()
region.numberElements = 9
region.elements.append(Element.Element(1, 0.11))
region.elements.append(Element.Element(6, 0.49))
region.elements.append(Element.Element(7, 0.12))
region.elements.append(Element.Element(8, 0.25))
region.elements.append(Element.Element(12, 0.003))
region.elements.append(Element.Element(15, 0.003))
region.elements.append(Element.Element(16, 0.003))
region.elements.append(Element.Element(25, 0.001))
region.elements.append(Element.Element(76, 0.02))
region.regionMassDensity_g_cm3 = 1.24
region.regionType = RegionType.REGION_TYPE_SPHERE
parameters = [-10000.0, 0.0, 20000.0, 15000.0]
region.regionDimensions = RegionDimensions.RegionDimensionsSphere(parameters)
specimen.regions.append(region)
region = Region.Region()
region.numberElements = 9
region.elements.append(Element.Element(1, 0.11))
region.elements.append(Element.Element(6, 0.49))
region.elements.append(Element.Element(7, 0.12))
region.elements.append(Element.Element(8, 0.25))
region.elements.append(Element.Element(12, 0.003))
region.elements.append(Element.Element(15, 0.003))
region.elements.append(Element.Element(16, 0.003))
region.elements.append(Element.Element(25, 0.001))
region.elements.append(Element.Element(76, 0.02))
region.regionMassDensity_g_cm3 = 1.24
region.regionType = RegionType.REGION_TYPE_SPHERE
parameters = [10000.0, -5000.0, 25000.0, 6000.0]
region.regionDimensions = RegionDimensions.RegionDimensionsSphere(parameters)
specimen.regions.append(region)
region = Region.Region()
region.numberElements = 7
region.elements.append(Element.Element(1, 0.077))
region.elements.append(Element.Element(6, 0.497))
region.elements.append(Element.Element(7, 0.11))
region.elements.append(Element.Element(8, 0.259))
region.elements.append(Element.Element(15, 0.031))
region.elements.append(Element.Element(16, 0.006))
region.elements.append(Element.Element(76, 0.02))
region.regionMassDensity_g_cm3 = 1.18
region.regionType = RegionType.REGION_TYPE_SPHERE
parameters = [-23000.0, 4000.0, 33500.0, 2000.0]
region.regionDimensions = RegionDimensions.RegionDimensionsSphere(parameters)
specimen.regions.append(region)
specimen._shortHeader = True
elif title == "Bug Al Zr Sphere":
specimen.numberRegions = 2
specimen.version = Version.Version(1, 1, 1)
region = Region.Region()
region.numberElements = 1
element = Element.Element(13)
region.elements.append(element)
region.regionType = RegionType.REGION_TYPE_BOX
parameters = [-10000000000.0, 10000000000.0, -10000000000.0, 10000000000.0, 0.0, 1000.0]
region.regionDimensions = RegionDimensions.RegionDimensionsBox(parameters)
specimen.regions.append(region)
region = Region.Region()
region.numberElements = 1
element = Element.Element(40)
region.elements.append(element)
region.regionType = RegionType.REGION_TYPE_SPHERE
parameters = [0.0, 0.0, 500.0, 499.9]
region.regionDimensions = RegionDimensions.RegionDimensionsSphere(parameters)
specimen.regions.append(region)
elif title == "Mg2SiAlCube3kev":
specimen.numberRegions = 2
specimen.version = Version.Version(1, 1, 1)
region = Region.Region()
region.numberElements = 2
element = Element.Element(12, 0.5)
region.elements.append(element)
element = Element.Element(13, 0.5)
region.elements.append(element)
region.regionType = RegionType.REGION_TYPE_BOX
parameters = [-10000000000.0, 10000000000.0, -10000000000.0, 10000000000.0, 0.0, 20000000000.0]
region.regionDimensions = RegionDimensions.RegionDimensionsBox(parameters)
specimen.regions.append(region)
region = Region.Region()
region.numberElements = 1
element = Element.Element(6)
region.elements.append(element)
region.regionType = RegionType.REGION_TYPE_BOX
parameters = (-10.0, 10.0, -10.0, 10.0, 0.0, 20.0)
region.regionDimensions = RegionDimensions.RegionDimensionsBox(parameters)
specimen.regions.append(region)
elif title == "AlMgBulk5keV_version_1_1_1":
specimen.numberRegions = 3
specimen.version = Version.Version(1, 1, 1)
region = Region.Region()
region.numberElements = 2
element = Element.Element(12, 0.5)
region.elements.append(element)
element = Element.Element(13, 0.5)
region.elements.append(element)
region.regionType = RegionType.REGION_TYPE_BOX
parameters = [-10000000000.0, 10000000000.0, -10000000000.0, 10000000000.0, 0.0, 20000000000.0]
region.regionDimensions = RegionDimensions.RegionDimensionsBox(parameters)
specimen.regions.append(region)
region = Region.Region()
region.numberElements = 1
element = Element.Element(6)
region.elements.append(element)
region.regionType = RegionType.REGION_TYPE_CYLINDER
parameters = [0.0, -5000.0, 0.0, 0.0, 1.0, -0.7, 10000.0, 100.0]
region.regionDimensions = RegionDimensions.RegionDimensionsCylinder(parameters)
specimen.regions.append(region)
region = Region.Region()
region.numberElements = 1
element = Element.Element(79)
region.elements.append(element)
region.regionType = RegionType.REGION_TYPE_SPHERE
parameters = [0.0, 0.0, 101.0, 100.0]
region.regionDimensions = RegionDimensions.RegionDimensionsSphere(parameters)
specimen.regions.append(region)
elif title == "AlMgBulk5keV_version_1_2_0":
specimen.numberRegions = 3
specimen.version = Version.Version(1, 2, 0)
region = Region.Region()
region.numberElements = 2
element = Element.Element(14, 0.4)
region.elements.append(element)
element = Element.Element(15, 0.6)
region.elements.append(element)
region.regionMassDensity_g_cm3 = 23.0
region.regionType = RegionType.REGION_TYPE_BOX
parameters = [-2000000000.0, 6000000000.0, -4000000000.0, 5000000000.0, 0.8, 70000.0]
region.regionDimensions = RegionDimensions.RegionDimensionsBox(parameters)
specimen.regions.append(region)
region = Region.Region()
region.numberElements = 1
element = Element.Element(7)
region.elements.append(element)
region.regionType = RegionType.REGION_TYPE_CYLINDER
parameters = [0.4, -8000.0, 0.9, 0.1, 0.6, -0.8, 50000.0, 700.0]
region.regionDimensions = RegionDimensions.RegionDimensionsCylinder(parameters)
specimen.regions.append(region)
region = Region.Region()
region.numberElements = 1
element = Element.Element(56)
region.elements.append(element)
region.regionType = RegionType.REGION_TYPE_SPHERE
parameters = [0.5, 0.6, 102.0, 101.0]
region.regionDimensions = RegionDimensions.RegionDimensionsSphere(parameters)
specimen.regions.append(region)
elif title == "AlMgBulk5keV_version_1_2_1":
specimen.numberRegions = 3
specimen.version = Version.Version(1, 2, 1)
region = Region.Region()
region.numberElements = 2
element = Element.Element(14, 0.4)
region.elements.append(element)
element = Element.Element(15, 0.6)
region.elements.append(element)
region.regionMassDensity_g_cm3 = 23.0
region.regionType = RegionType.REGION_TYPE_BOX
parameters = [-2000000000.0, 6000000000.0, -4000000000.0, 5000000000.0, 0.8, 70000.0]
region.regionDimensions = RegionDimensions.RegionDimensionsBox(parameters)
specimen.regions.append(region)
region = Region.Region()
region.numberElements = 1
element = Element.Element(7)
region.elements.append(element)
region.regionType = RegionType.REGION_TYPE_CYLINDER
parameters = [0.4, -8000.0, 0.9, 0.1, 0.6, -0.8, 50000.0, 700.0]
region.regionDimensions = RegionDimensions.RegionDimensionsCylinder(parameters)
specimen.regions.append(region)
region = Region.Region()
region.numberElements = 1
element = Element.Element(56)
region.elements.append(element)
region.regionType = RegionType.REGION_TYPE_SPHERE
parameters = [0.5, 0.6, 102.0, 101.0]
region.regionDimensions = RegionDimensions.RegionDimensionsSphere(parameters)
specimen.regions.append(region)
elif title == "AlMgBulk5keV_version_1_4_1":
specimen.numberRegions = 3
specimen.version = Version.Version(1, 4, 1)
region = Region.Region()
region.numberElements = 2
element = Element.Element(14, 0.4)
region.elements.append(element)
element = Element.Element(15, 0.6)
region.elements.append(element)
region.regionMassDensity_g_cm3 = 23.0
region.regionType = RegionType.REGION_TYPE_BOX
parameters = [-2000000000.0, 6000000000.0, -4000000000.0, 5000000000.0, 0.8, 70000.0]
region.regionDimensions = RegionDimensions.RegionDimensionsBox(parameters)
specimen.regions.append(region)
region = Region.Region()
region.numberElements = 1
element = Element.Element(7)
region.elements.append(element)
region.regionType = RegionType.REGION_TYPE_CYLINDER
parameters = [0.4, -8000.0, 0.9, 0.1, 0.6, -0.8, 50000.0, 700.0]
region.regionDimensions = RegionDimensions.RegionDimensionsCylinder(parameters)
specimen.regions.append(region)
region = Region.Region()
region.numberElements = 1
element = Element.Element(56)
region.elements.append(element)
region.regionType = RegionType.REGION_TYPE_SPHERE
parameters = [0.5, 0.6, 102.0, 101.0]
region.regionDimensions = RegionDimensions.RegionDimensionsSphere(parameters)
specimen.regions.append(region)
return specimen
def test_read_1_4_1(self):
"""
Tests for method `read`.
"""
specimen = Specimen.Specimen()
title = "AlMgBulk5keV_version_1_4_1"
filepath = os.path.abspath(os.path.join(self.testDataPath, "inputs", "%s.sam" % (title)))
specimen.read(filepath)
self.assertEquals(Version.VERSION_1_4_1.major, specimen.version.major)
self.assertEquals(Version.VERSION_1_4_1.minor, specimen.version.minor)
self.assertEquals(Version.VERSION_1_4_1.revision, specimen.version.revision)
self.assertEquals(Version.VERSION_1_4_1, specimen.version)
specimenRef = self.getSpecimenReference(title)
self.assertEquals(specimenRef.version.major, specimen.version.major)
self.assertEquals(specimenRef.version.minor, specimen.version.minor)
self.assertEquals(specimenRef.version.revision, specimen.version.revision)
self.assertEquals(specimenRef.version, specimen.version)
self.assertEquals(specimenRef.numberRegions, specimen.numberRegions)
indexRegion = 0
region = specimen.regions[indexRegion]
regionRef = specimenRef.regions[indexRegion]
self.assertEquals(regionRef.numberElements, region.numberElements)
self.assertEquals(regionRef.regionMassDensity_g_cm3, region.regionMassDensity_g_cm3)
self.assertEquals(regionRef.regionType, region.regionType)
self.assertEquals(regionRef.regionDimensions, region.regionDimensions)
indexElement = 0
element = region.elements[indexElement]
elementRef = regionRef.elements[indexElement]
self.assertEquals(elementRef.atomicNumber, element.atomicNumber)
self.assertEquals(elementRef.massFraction, element.massFraction)
indexElement = 1
element = region.elements[indexElement]
elementRef = regionRef.elements[indexElement]
self.assertEquals(elementRef.atomicNumber, element.atomicNumber)
self.assertEquals(elementRef.massFraction, element.massFraction)
indexRegion = 1
region = specimen.regions[indexRegion]
regionRef = specimenRef.regions[indexRegion]
self.assertEquals(regionRef.numberElements, region.numberElements)
self.assertEquals(regionRef.regionMassDensity_g_cm3, region.regionMassDensity_g_cm3)
self.assertEquals(regionRef.regionType, region.regionType)
self.assertEquals(regionRef.regionDimensions, region.regionDimensions)
indexElement = 0
element = region.elements[indexElement]
elementRef = regionRef.elements[indexElement]
self.assertEquals(elementRef.atomicNumber, element.atomicNumber)
self.assertEquals(elementRef.massFraction, element.massFraction)
indexRegion = 2
region = specimen.regions[indexRegion]
regionRef = specimenRef.regions[indexRegion]
self.assertEquals(regionRef.numberElements, region.numberElements)
self.assertEquals(regionRef.regionMassDensity_g_cm3, region.regionMassDensity_g_cm3)
self.assertEquals(regionRef.regionType, region.regionType)
self.assertEquals(regionRef.regionDimensions, region.regionDimensions)
indexElement = 0
element = region.elements[indexElement]
elementRef = regionRef.elements[indexElement]
self.assertEquals(elementRef.atomicNumber, element.atomicNumber)
self.assertEquals(elementRef.massFraction, element.massFraction)
def createSpecimen(self, parameters):
specimen = Specimen.Specimen()
specimen.name = "Maps01"
specimen.numberRegions = 10
# Region 0
region = Region.Region()
region.numberElements = 0
region.regionType = RegionType.REGION_TYPE_BOX
parameters = [
-10000000000.0, 10000000000.0, -10000000000.0, 10000000000.0, 0.0,
20000000000.0
]
region.regionDimensions = RegionDimensions.RegionDimensionsBox(
parameters)
specimen.regions.append(region)
# Region 1
region = Region.Region()
region.numberElements = 2
region.elements = [
Element.Element(27, massFraction=0.01),
Element.Element(26, massFraction=0.99)
]
region.regionType = RegionType.REGION_TYPE_BOX
parameters = [-7.5e4, -2.5e4, -7.5e4, -2.5e4, 0.0, 0.2e4]
region.regionDimensions = RegionDimensions.RegionDimensionsBox(
parameters)
specimen.regions.append(region)
# Region 2
region = Region.Region()
region.numberElements = 2
region.elements = [
Element.Element(27, massFraction=0.02),
Element.Element(26, massFraction=0.98)
]
region.regionType = RegionType.REGION_TYPE_BOX
parameters = [-2.5e4, 2.5e4, -7.5e4, -2.5e4, 0.0, 0.2e4]
region.regionDimensions = RegionDimensions.RegionDimensionsBox(
parameters)
specimen.regions.append(region)
# Region 3
region = Region.Region()
region.numberElements = 2
region.elements = [
Element.Element(27, massFraction=0.05),
Element.Element(26, massFraction=0.95)
]
region.regionType = RegionType.REGION_TYPE_BOX
parameters = [2.5e4, 7.5e4, -7.5e4, -2.5e4, 0.0, 0.2e4]
region.regionDimensions = RegionDimensions.RegionDimensionsBox(
parameters)
specimen.regions.append(region)
# Region 4
region = Region.Region()
region.numberElements = 2
region.elements = [
Element.Element(28, massFraction=0.01),
Element.Element(27, massFraction=0.99)
]
region.regionType = RegionType.REGION_TYPE_BOX
parameters = [-7.5e4, -2.5e4, -2.5e4, 2.5e4, 0.0, 0.2e4]
region.regionDimensions = RegionDimensions.RegionDimensionsBox(
parameters)
specimen.regions.append(region)
# Region 5
region = Region.Region()
region.numberElements = 2
region.elements = [
Element.Element(28, massFraction=0.02),
Element.Element(27, massFraction=0.98)
]
region.regionType = RegionType.REGION_TYPE_BOX
parameters = [-2.5e4, 2.5e4, -2.5e4, 2.5e4, 0.0, 0.2e4]
region.regionDimensions = RegionDimensions.RegionDimensionsBox(
parameters)
specimen.regions.append(region)
# Region 6
region = Region.Region()
region.numberElements = 2
region.elements = [
Element.Element(28, massFraction=0.05),
Element.Element(27, massFraction=0.95)
]
region.regionType = RegionType.REGION_TYPE_BOX
parameters = [2.5e4, 7.5e4, -2.5e4, 2.5e4, 0.0, 0.2e4]
region.regionDimensions = RegionDimensions.RegionDimensionsBox(
parameters)
specimen.regions.append(region)
# Region 7
region = Region.Region()
region.numberElements = 3
region.elements = [
Element.Element(27, massFraction=0.01),
Element.Element(26, massFraction=0.495),
Element.Element(28, massFraction=0.495)
]
region.regionType = RegionType.REGION_TYPE_BOX
parameters = [-7.5e4, -2.5e4, 2.5e4, 7.5e4, 0.0, 0.2e4]
region.regionDimensions = RegionDimensions.RegionDimensionsBox(
parameters)
specimen.regions.append(region)
# Region 8
region = Region.Region()
region.numberElements = 3
region.elements = [
Element.Element(27, massFraction=0.02),
Element.Element(26, massFraction=0.49),
Element.Element(28, massFraction=0.49)
]
region.regionType = RegionType.REGION_TYPE_BOX
parameters = [-2.5e4, 2.5e4, 2.5e4, 7.5e4, 0.0, 0.2e4]
region.regionDimensions = RegionDimensions.RegionDimensionsBox(
parameters)
specimen.regions.append(region)
# Region 9
region = Region.Region()
region.numberElements = 3
region.elements = [
Element.Element(27, massFraction=0.05),
Element.Element(26, massFraction=0.475),
Element.Element(28, massFraction=0.475)
]
region.regionType = RegionType.REGION_TYPE_BOX
parameters = [2.5e4, 7.5e4, 2.5e4, 7.5e4, 0.0, 0.2e4]
region.regionDimensions = RegionDimensions.RegionDimensionsBox(
parameters)
specimen.regions.append(region)
return specimen