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updated transmission code
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@drhlxiao
drhlxiao committed Jun 17, 2022
1 parent e749291 commit 3d8b057
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222 changes: 112 additions & 110 deletions stixdcpy/transmission.py
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Original file line number Diff line number Diff line change
Expand Up @@ -15,10 +15,8 @@

MIL_SI = 0.0254 * u.mm

# TODO move to configuration files
NEW_COMPONENTS_MEAN= OrderedDict([
('front_window', [('solarblack', 0.005 * u.mm),
('be-s200fh', 2 * u.mm)]),
COMPONENTS = OrderedDict([
('front_window', [('solarblack', 0.005 * u.mm), ('be-s200fh', 2 * u.mm)]),
('rear_window', [('be-s200fh', 1 * u.mm)]),
('grid_covers', [('kapton', 4 * 2 * MIL_SI)]),
('dem', [('kapton', 2 * 3 * MIL_SI)]),
Expand All @@ -27,95 +25,95 @@
('al', 40 * 1000 * u.angstrom), ('mylar', 20 * 0.25 * MIL_SI),
('pet', 21 * 0.005 * u.mm), ('kapton', 3 * MIL_SI),
('al', 1000 * u.angstrom)]),

('calibration_foil', [('al', 4 * 1000 * u.angstrom),
('kapton', 4 * 2 * MIL_SI)]),
('dead_layer', [('te_o2', 392 * u.nm )]),
('single_grid',[('tungsten',0.4*u.mm )]),
('double_grid',[('tungsten',0.8*u.mm )]),
('caliste', [('cdte', 1*u.mm)]),
]) #old materials, not valid anymore

NEW_COMPONENTS_MAX= OrderedDict([
('front_window', [('solarblack', 0.005 * u.mm),
('be-s200fh', 2 * u.mm)]),
('rear_window', [('be-s200fh', 1 * u.mm)]),
('grid_covers', [('kapton', 4 * 2 * MIL_SI)]),
('dem', [('kapton', 2 * 3 * MIL_SI)]),
('attenuator', [('alum7075-max', 0.6 * u.mm)]),
('mli', [('al', 1000 * u.angstrom), ('kapton', 3 * MIL_SI),
('al', 40 * 1000 * u.angstrom), ('mylar', 20 * 0.25 * MIL_SI),
('pet', 21 * 0.005 * u.mm), ('kapton', 3 * MIL_SI),
('al', 1000 * u.angstrom)]),

('calibration_foil', [('al', 4 * 1000 * u.angstrom),
('kapton', 4 * 2 * MIL_SI)]),
('dead_layer', [('te_o2', 392 * u.nm )]),
('single_grid',[('tungsten',0.4*u.mm )]),
('double_grid',[('tungsten',0.8*u.mm )]),
('caliste', [('cdte', 1*u.mm)]),
]) #old materials, not valid anymore


OLD_COMPONENTS = OrderedDict([
('front_window', [('solarblack', 0.005 * u.mm),
('be', 2 * u.mm)]),
('caliste', [('cdte', 1*u.mm)]),
('rear_window', [('be', 1 * u.mm)]),
('grid_covers', [('kapton', 4 * 2 * MIL_SI)]),
('dem', [('kapton', 2 * 3 * MIL_SI)]),
('attenuator', [('al', 0.6 * u.mm)]),
('mli', [('al', 1000 * u.angstrom), ('kapton', 3 * MIL_SI),
('al', 40 * 1000 * u.angstrom), ('mylar', 20 * 0.25 * MIL_SI),
('pet', 21 * 0.005 * u.mm), ('kapton', 3 * MIL_SI),
('al', 1000 * u.angstrom)]),
('dead_layer', [('te_o2', 392 * u.nm)]),
('single_grid', [('tungsten', 0.4 * u.mm)]),
('double_grid', [('tungsten', 0.8 * u.mm)]),
('caliste', [('cdte', 1 * u.mm)]),
]) #old materials, not valid anymore

('calibration_foil', [('al', 4 * 1000 * u.angstrom),
('kapton', 4 * 2 * MIL_SI)]),
('dead_layer', [('te_o2', 392 * u.nm )]),
('single_grid',[('tungsten',0.4*u.mm )]),
('double_grid',[('tungsten',0.8*u.mm )]),
])
MATERIALS = OrderedDict([
('al', ({
'Al': 1.0
}, 2.7 * u.g / u.cm**3)),
('cdte', ({
'Te': 0.53164,
'Cd': 0.46836
}, 6.2* u.g / u.cm**3)),
('tungsten',({
'W':1.0
},19.28*u.g/u.cm**3)),
('alum7075',({
'Al': 0.876,
'Zn': 0.056,
'Cr': 0.023,
'Mg': 0.025,
'Cu': 0.016,
'Fe': 0.0025,
'Mn': 0.0015},
2.8*u.g/u.cm**3)),

('be-s200fh',({
'Be': 0.985,
'O': 0.00555,
'Al': 0.0005,
'C': 0.0075,
'Fe': 0.00075,
'Mg': 0.0004,
'Si': 0.0003}, 1.84*u.g/u.cm**3)
),

('alum7075-max',({
'Al': 0.858,
'Zn': 0.061,
'Cr': 0.028,
'Mg': 0.029,
'Cu': 0.02,
'Fe': 0.0025,
'Mn': 0.0015},
2.8*u.g/u.cm**3)),
}, 5.85 * u.g / u.cm**3)),
('tungsten', ({
'W': 1.0
}, 19.28 * u.g / u.cm**3)),
(
'alum7075-max',
(
{
'Si':
0.004, #the mass fractions of other elements are the maximum
'Fe': 0.005,
'Cu': 0.02,
'Mn': 0.003,
'Mg': 0.029,
'Cr': 0.0028,
'Ni': 0.0005,
'Zn': 0.061,
'Ti': 0.002,
'Al': 0.8727
},
2.8 * u.g / u.cm**3)),
(
'alum7075-mean',
(
{
'Si':
0.002, #take the mean of the min and max the mass fractions of other elements
'Fe': 0.0025,
'Cu': 0.016,
'Mn': 0.0015,
'Mg': 0.025,
'Cr': 0.0023,
'Ni': 0.00025,
'Zn': 0.056,
'Ti': 0.001,
'Al': 0.89345
},
2.8 * u.g / u.cm**3)),
(
'alum7075-min',
(
{
'Si':
0.0, #the mass fractions of other elements are the minimum
'Fe': 0.0,
'Cu': 0.012,
'Mn': 0.0,
'Mg': 0.021,
'Cr': 0.0018,
'Ni': 0.0,
'Zn': 0.051,
'Ti': 0.0,
'Al': 0.9142
},
2.8 * u.g / u.cm**3)),
('be-s200fh-max', ({
'Al': 0.001,
'Be': 0.98676,
'O': 0.00954,
'Fe': 0.0013,
'Mg': 0.0008,
'Si': 0.0006
}, 1.84 * u.g / u.cm**3)),
('be-s200fh-min', ({
'Be': 1
}, 1.85 * u.g / u.cm**3)),
('be-s200fh-mean', ({
'Al': 0.0005,
'Be': 0.99338,
'O': 0.00477,
'Fe': 0.00065,
'Mg': 0.0004,
'Si': 0.0003
}, 1.84 * u.g / u.cm**3)),
('be', ({
'Be': 1.0
}, 1.85 * u.g / u.cm**3)),
Expand Down Expand Up @@ -240,7 +238,8 @@ class Transmission:
"""
Calculate the energy dependant transmission of X-ray through the instrument
"""
def __init__(self, solarblack='solarblack_carbon', material_version=1):

def __init__(self, solarblack='solarblack_carbon', matlist='mean'):
"""
Create a new instance of the transmission with the given solar black composition.
Expand All @@ -249,38 +248,44 @@ def __init__(self, solarblack='solarblack_carbon', material_version=1):
solarblack : `str` optional
The SolarBlack composition to use.
matlist: str optional
'old': use the old material info
'min': take the minimum mass fractions for other elements in the alloys
'max': take the maximum mass fractions for other elements in the alloys
'mean': take the mean mass fractions for other elements in the alloys
"""
if solarblack not in ['solarblack_oxygen', 'solarblack_carbon']:
raise ValueError(
"solarblack must be either 'solarblack_oxygen' or "
"'solarblack_carbon'.")

if matlist not in ['old', 'min', 'max','mean']:
raise ValueError("'matlist' must be 'old', 'min','max' or 'mean'!")
self.solarblack = solarblack
self.materials = MATERIALS
self.load_components(material_version)
self.matlist = matlist
self.load_components(matlist)

def load_components(self, version=1):
def load_components(self, matlist):
self.components = {}
if version==0:
comps= OLD_COMPONENTS
elif version==1:
comps=NEW_COMPONENTS_MEAN
elif version==2:
comps=NEW_COMPONENTS_MAX


for name, layers in comps.items():
for name, layers in COMPONENTS.items():
parts = []
for material, thickness in layers:
if material == 'solarblack':
material = self.solarblack
elif material == 'be-s200fh':
material = 'be' if matlist == 'old' else material + '-' + matlist
elif material == 'alum7075':
material = 'al' if matlist == 'old' else material + '-' + matlist

#print('material:', material)
mass_frac, den = MATERIALS[material]
#if material == 'al':
# thickness = thickness * 0.8
part=self.create_material(name=material,
fractional_masses=mass_frac,
thickness=thickness,
density=den)
part = self.create_material(name=material,
fractional_masses=mass_frac,
thickness=thickness,
density=den)
parts.append(part)
self.components[name] = Compound(parts)

Expand Down Expand Up @@ -348,7 +353,7 @@ def get_detector_transmission(self,
Returns
--------
transmission for the energy bins
'''
base_comps = [
self.components[name] for name in [
Expand All @@ -374,19 +379,18 @@ def get_detector_transmission(self,
mean_trans = np.mean(det_trans.reshape((-1, 2)), axis=1)
#calculate mean energy transmission factors for energy bins
return mean_trans
def get_transmission_of_component(self, component_name:str, energies_keV:np.array):

def get_transmission_of_component(self, component_name: str,
energies_keV: np.array):
"""
get the transmission of a list of components
"""
base_comp=[self.components[component_name]]
base_comp = [self.components[component_name]]
comp = Compound(base_comp)
print(comp)
energies_keV=energies_keV*u.keV
energies_keV = energies_keV * u.keV
return comp.transmission(energies_keV)




def get_transmission_by_component(self):
"""
Get the contributions to the total transmission by broken down by component.
Expand Down Expand Up @@ -463,8 +467,6 @@ def create_material(cls,
# probably don't need this
material.density = density

# TODO remove in favour of upstream fix when completed
# see https://github.com/ehsteve/roentgen/issues/26
def func(composition, e):
return sum([
MassAttenuationCoefficient(element).func(e) * frac_mass
Expand Down
232 changes: 116 additions & 116 deletions tests/.ipynb_checkpoints/STIX_transmission_calculator-checkpoint.ipynb
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232 changes: 116 additions & 116 deletions tests/STIX_transmission_calculator.ipynb
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