def test_bad(self):
with self.assertRaises(ValueError):
xraylib.GetCompoundDataNISTByName("jwjfpfj")
with self.assertRaises(TypeError):
xraylib.GetCompoundDataNISTByName(0)
with self.assertRaises(ValueError):
xraylib.GetCompoundDataNISTByName(None)
with self.assertRaises(ValueError):
xraylib.GetCompoundDataNISTByIndex(-1)
with self.assertRaises(ValueError):
xraylib.GetCompoundDataNISTByIndex(180)
with self.assertRaises(TypeError):
xraylib.GetCompoundDataNISTByIndex(None)
with self.assertRaises(TypeError):
xraylib.GetCompoundDataNISTByIndex("jpwjfpfwj")
def find_nist_name(compound_name):
'''
Get physical properties of one of the compounds registered in nist database
'''
import xraylib
return xraylib.GetCompoundDataNISTByName(compound_name)
def GetDensity(material):
if material == 'H2C':
cpH2C = xrl.GetCompoundDataNISTByName('Polyethylene')
density = cpH2C['density']
else:
Z = xrl.SymbolToAtomicNumber(material)
density = xrl.ElementDensity(Z)
return density
def test_good(self):
list = xraylib.GetCompoundDataNISTList()
self.assertEqual(len(list), 180)
for i, v in enumerate(list):
cdn = xraylib.GetCompoundDataNISTByIndex(i)
self.assertEqual(cdn['name'], v)
cdn = xraylib.GetCompoundDataNISTByName(v)
self.assertEqual(cdn['name'], v)
cdn = xraylib.GetCompoundDataNISTByIndex(5)
self.assertEqual(cdn['nElements'], 4)
self.assertEqual(cdn['density'], 0.001205)
self.assertEqual(cdn['Elements'], [6, 7, 8, 18])
self.assertAlmostEqual(cdn['massFractions'],
[0.000124, 0.755267, 0.231781, 0.012827])
self.assertEqual(cdn['name'], 'Air, Dry (near sea level)')
cdn = xraylib.GetCompoundDataNISTByName('Air, Dry (near sea level)')
self.assertEqual(cdn['nElements'], 4)
self.assertEqual(cdn['density'], 0.001205)
self.assertEqual(cdn['Elements'], [6, 7, 8, 18])
self.assertAlmostEqual(cdn['massFractions'],
[0.000124, 0.755267, 0.231781, 0.012827])
self.assertEqual(cdn['name'], 'Air, Dry (near sea level)')
def __init__(self, nistname, name=None):
"""
Args:
nistname(str): NIST name
name(Optional[str]): compound name
"""
data = xraylib.GetCompoundDataNISTByName(nistname)
if name is None:
name = data["name"]
super(CompoundFromNist, self).__init__(
data["Elements"],
data["massFractions"],
types.fraction.mass,
data["density"],
name=name,
)
def phantom_assign_concentration(ph_or, data_type=np.float32):
"""Builds the phantom used in:
- N. Viganò and V. A. Solé, “Physically corrected forward operators for
induced emission tomography: a simulation study,” Meas. Sci. Technol., no.
Advanced X-Ray Tomography, pp. 1–26, Nov. 2017.
:param ph_or: DESCRIPTION
:type ph_or: TYPE
:param data_type: DESCRIPTION, defaults to np.float32
:type data_type: TYPE, optional
:return: DESCRIPTION
:rtype: TYPE
"""
# ph_air = ph_or < 0.1
ph_FeO = 0.5 < ph_or
ph_CaO = np.logical_and(0.25 < ph_or, ph_or < 0.5)
ph_CaC = np.logical_and(0.1 < ph_or, ph_or < 0.25)
conv_mm_to_cm = 1e-1
conv_um_to_mm = 1e-3
voxel_size_um = 0.5
voxel_size_cm = voxel_size_um * conv_um_to_mm * conv_mm_to_cm # cm to micron
print("Sample size: [%g %g] um" %
(ph_or.shape[0] * voxel_size_um, ph_or.shape[1] * voxel_size_um))
import xraylib
xraylib.XRayInit()
cp_fo = xraylib.GetCompoundDataNISTByName("Ferric Oxide")
cp_co = xraylib.GetCompoundDataNISTByName("Calcium Oxide")
cp_cc = xraylib.GetCompoundDataNISTByName("Calcium Carbonate")
ca_an = xraylib.SymbolToAtomicNumber("Ca")
ca_kal = xraylib.LineEnergy(ca_an, xraylib.KA_LINE)
in_energy_keV = 20
out_energy_keV = ca_kal
ph_lin_att_in = (
ph_FeO * xraylib.CS_Total_CP("Ferric Oxide", in_energy_keV) *
cp_fo["density"] +
ph_CaC * xraylib.CS_Total_CP("Calcium Carbonate", in_energy_keV) *
cp_cc["density"] + ph_CaO *
xraylib.CS_Total_CP("Calcium Oxide", in_energy_keV) * cp_co["density"])
ph_lin_att_out = (
ph_FeO * xraylib.CS_Total_CP("Ferric Oxide", out_energy_keV) *
cp_fo["density"] +
ph_CaC * xraylib.CS_Total_CP("Calcium Carbonate", out_energy_keV) *
cp_cc["density"] +
ph_CaO * xraylib.CS_Total_CP("Calcium Oxide", out_energy_keV) *
cp_co["density"])
vol_att_in = ph_lin_att_in * voxel_size_cm
vol_att_out = ph_lin_att_out * voxel_size_cm
ca_cs = xraylib.CS_FluorLine_Kissel(
ca_an, xraylib.KA_LINE, in_energy_keV) # fluo production for cm2/g
ph_CaC_mass_fract = cp_cc["massFractions"][np.where(
np.array(cp_cc["Elements"]) == ca_an)[0][0]]
ph_CaO_mass_fract = cp_co["massFractions"][np.where(
np.array(cp_co["Elements"]) == ca_an)[0][0]]
ph = ph_CaC * ph_CaC_mass_fract * cp_cc[
"density"] + ph_CaO * ph_CaO_mass_fract * cp_co["density"]
ph = ph * ca_cs * voxel_size_cm
return (ph, vol_att_in, vol_att_out)
FH = xraylib.Crystal_F_H_StructureFactor(cryst, energy, 3, 3, 1,
debye_temp_factor, rel_angle)
print(" FH(3,3,1) structure factor: ({}, {})".format(FH.real, FH.imag))
F0 = xraylib.Crystal_F_H_StructureFactor(cryst, energy, 0, 0, 0,
debye_temp_factor, rel_angle)
print(" F0=FH(0,0,0) structure factor: ({}, {})".format(F0.real, F0.imag))
crystals = xraylib.Crystal_GetCrystalsList()
print("List of available crystals:")
for i in range(len(crystals)):
print(" Crystal {}: {}".format(i, crystals[i]))
print("")
cdn = xraylib.GetCompoundDataNISTByName("Uranium Monocarbide")
print("Uranium Monocarbide")
print(" Name: {}".format(cdn['name']))
print(" Density: {}".format(cdn['density']))
for i in range(cdn['nElements']):
print(" Element {}: {} %%".format(cdn['Elements'][i],
cdn['massFractions'][i] * 100.0))
cdn = xraylib.GetCompoundDataNISTByIndex(xraylib.NIST_COMPOUND_BRAIN_ICRP)
print("NIST_COMPOUND_BRAIN_ICRP")
print(" Name: {}".format(cdn['name']))
print(" Density: {}".format(cdn['density']))
for i in range(cdn['nElements']):
print(" Element {}: {} %%".format(cdn['Elements'][i],
cdn['massFractions'][i] * 100.0))
0.95,
name="pe")
compounddb["pan"] = compoundfromformula.CompoundFromFormula("C3H3N",
1.184,
name="pan")
compounddb["pva"] = compoundfromformula.CompoundFromFormula("C3H3N",
1.19,
name="pva")
compounddb["pp"] = compoundfromformula.CompoundFromFormula("C3H6",
0.86,
name="pp")
compounddb["specx pp"] = compoundfromformula.CompoundFromFormula(
"C3H6", 1.1289633445, name="pp")
data = xraylib.GetCompoundDataNISTByName("Kapton Polyimide Film")
compounddb["kapton"] = compound.Compound(
data["Elements"],
data["massFractions"],
types.fraction.mass,
data["density"],
name="kapton",
)
compounddb["specx kapton"] = compound.Compound(
data["Elements"],
data["massFractions"],
types.fraction.mass,
1.35297609903,
name="kapton",
)
def find_name(compound_name):
return xraylib.GetCompoundDataNISTByName(compound_name)
