refnx
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API reference
refnx
Index
Index
_
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A
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B
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C
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D
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E
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F
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G
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H
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I
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L
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M
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N
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O
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P
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Q
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R
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S
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T
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U
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V
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W
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X
|
Y
_
__annotations__ (refnx.reflect.Exponential attribute)
(refnx.reflect.FresnelTransform attribute)
(refnx.reflect.FunctionalForm attribute)
(refnx.reflect.Interface attribute)
(refnx.reflect.Linear attribute)
(refnx.reflect.LipidLeaflet attribute)
(refnx.reflect.LipidLeafletGuest attribute)
(refnx.reflect.MagneticSlab attribute)
(refnx.reflect.MixedSlab attribute)
(refnx.reflect.ReflectModel attribute)
(refnx.reflect.ReflectModelTL attribute)
(refnx.reflect.Sinusoidal attribute)
(refnx.reflect.Slab attribute)
(refnx.reflect.SLD attribute)
(refnx.reflect.Spline attribute)
(refnx.reflect.Stack attribute)
(refnx.reflect.Step attribute)
(refnx.reflect.Structure attribute)
(refnx.reflect.Tanh attribute)
__call__() (refnx.reflect.Erf method)
(refnx.reflect.Exponential method)
(refnx.reflect.FresnelTransform method)
(refnx.reflect.Interface method)
(refnx.reflect.Linear method)
(refnx.reflect.MixedReflectModel method)
(refnx.reflect.Motofit method)
(refnx.reflect.ReflectModel method)
(refnx.reflect.Sinusoidal method)
(refnx.reflect.Spline method)
(refnx.reflect.Step method)
(refnx.reflect.Tanh method)
__complex__() (refnx.reflect.MaterialSLD method)
(refnx.reflect.SLD method)
__ior__() (refnx.reflect.Stack method)
(refnx.reflect.Structure method)
__mul__() (refnx.reflect.Component method)
__or__() (refnx.reflect.Component method)
(refnx.reflect.Structure method)
__setitem__() (refnx.reflect.Stack method)
(refnx.reflect.Structure method)
__str__() (refnx.reflect.Component method)
(refnx.reflect.MagneticSlab method)
(refnx.reflect.MixedSlab method)
(refnx.reflect.Slab method)
(refnx.reflect.Stack method)
(refnx.reflect.Structure method)
A
abeles() (in module refnx.reflect)
accumulate_HDF_files() (in module refnx.reduce)
acf() (refnx.analysis.CurveFitter method)
actual_footprint() (in module refnx.util)
add_data() (refnx.dataset.Data1D method)
angle() (in module refnx.util)
append() (refnx.reflect.Stack method)
(refnx.reflect.Structure method)
autocorrelation_chain() (in module refnx.analysis)
AutoReducer (class in refnx.reduce)
available_backends() (in module refnx.reflect)
B
basename_datafile() (in module refnx.reduce)
BaseObjective (class in refnx.analysis)
BatchReducer (class in refnx.reduce)
beamfrac() (in module refnx.util)
beamfrackernel() (in module refnx.util)
bkg (refnx.reflect.MixedReflectModel property)
(refnx.reflect.ReflectModel property)
Bounds (class in refnx.analysis)
bounds (refnx.analysis.Parameter property)
C
Catalogue (class in refnx.reduce)
catalogue() (in module refnx.reduce)
chain (refnx.analysis.CurveFitter property)
(refnx.analysis.MCMCResult attribute)
channels (refnx.reduce.SpinSet attribute)
chisqr() (refnx.analysis.Objective method)
chod() (refnx.reduce.PlatypusNexus method)
(refnx.reduce.SpatzNexus method)
choose_dq_type() (in module refnx.reflect)
code (refnx.reflect.Motofit property)
complex() (refnx.reflect.MaterialSLD method)
Component (class in refnx.reflect)
components (refnx.reflect.Stack property)
(refnx.reflect.Structure property)
constrained_parameters() (refnx.analysis.Parameters method)
constraint (refnx.analysis.Parameter property)
contract (refnx.reflect.Structure attribute)
corner() (refnx.analysis.Objective method)
(refnx.analysis.Parameter method)
correct_for_gravity() (refnx.reduce.PlatypusNexus method)
covar() (refnx.analysis.BaseObjective method)
(refnx.analysis.Objective method)
create_detector_norm() (refnx.reduce.PlatypusNexus method)
(refnx.reduce.SpatzNexus method)
create_occupancy() (in module refnx.reflect)
create_reflect_nexus() (in module refnx.reduce)
CurveFitter (class in refnx.analysis)
curvefitter (refnx.reflect.Motofit property)
custom_efficiencies() (refnx.reduce.PolarisationEfficiency method)
D
data (refnx.dataset.Data1D property)
Data1D (class in refnx.dataset)
datafile_number (refnx.reduce.Catalogue property)
datafile_number() (in module refnx.reduce)
dataset (refnx.reflect.Motofit attribute)
dd (refnx.reduce.SpinSet attribute)
(refnx.reduce.SpinSet property)
detector_average_unwanted_direction() (refnx.reduce.PlatypusNexus method)
(refnx.reduce.SpatzNexus method)
div() (in module refnx.util)
do_fit() (refnx.reflect.Motofit method)
double_chopper_frequency() (in module refnx.util)
DOWN_DOWN (refnx.reduce.SpinChannel attribute)
(refnx.reflect.SpinChannel attribute)
DOWN_UP (refnx.reduce.SpinChannel attribute)
(refnx.reflect.SpinChannel attribute)
dq (refnx.reflect.MixedReflectModel property)
(refnx.reflect.ReflectModel property)
du (refnx.reduce.SpinSet attribute)
(refnx.reduce.SpinSet property)
E
energy_wavelength() (in module refnx.util)
EPadd() (in module refnx.util)
EPcos() (in module refnx.util)
EPdiv() (in module refnx.util)
EPexp() (in module refnx.util)
EPlog() (in module refnx.util)
EPlog10() (in module refnx.util)
EPmul() (in module refnx.util)
EPmulk() (in module refnx.util)
EPpow() (in module refnx.util)
EPpowk() (in module refnx.util)
EPsin() (in module refnx.util)
EPsub() (in module refnx.util)
EPtan() (in module refnx.util)
Erf (class in refnx.reflect)
estimated_beam_width_at_detector() (refnx.reduce.PlatypusNexus method)
(refnx.reduce.SpatzNexus method)
Exponential (class in refnx.reflect)
F
fig (refnx.reflect.Motofit attribute)
filename (refnx.dataset.Data1D attribute)
finite_data (refnx.dataset.Data1D property)
fit() (refnx.analysis.CurveFitter method)
fitfunc (refnx.analysis.Model property)
fitfunc() (in module refnx.analysis)
flattened() (refnx.analysis.Parameters method)
formula (refnx.reflect.MaterialSLD property)
FresnelTransform (class in refnx.reflect)
from_orso() (refnx.reflect.Structure class method)
from_slabs() (refnx.reflect.Structure class method)
FunctionalForm (class in refnx.reflect)
G
generative() (refnx.analysis.GlobalObjective method)
(refnx.analysis.Objective method)
get_scaling_in_overlap() (in module refnx.util)
GlobalObjective (class in refnx.analysis)
gui() (in module refnx.reduce)
(in module refnx.reflect)
H
height_of_beam_after_dx() (in module refnx.util)
I
index_max_prob (refnx.analysis.CurveFitter property)
initialise() (refnx.analysis.CurveFitter method)
initialise_with_chain() (refnx.analysis.CurveFitter method)
integrated_time() (in module refnx.analysis)
Interface (class in refnx.reflect)
interfaces (refnx.reflect.Component property)
(refnx.reflect.Stack property)
(refnx.reflect.Structure property)
Interval (class in refnx.analysis)
invcdf() (refnx.analysis.Bounds method)
(refnx.analysis.Interval method)
(refnx.analysis.PDF method)
is_magnetic (refnx.reflect.Component property)
(refnx.reflect.MagneticSlab property)
(refnx.reflect.Stack property)
(refnx.reflect.Structure property)
is_parameter() (in module refnx.analysis)
is_parameters() (in module refnx.analysis)
L
lb (refnx.analysis.Interval property)
Linear (class in refnx.reflect)
LipidLeaflet (class in refnx.reflect)
LipidLeafletGuest (class in refnx.reflect)
load() (refnx.dataset.Data1D method)
(refnx.dataset.OrsoDataset method)
(refnx.dataset.ReflectDataset method)
load_chain() (in module refnx.analysis)
load_data() (in module refnx.dataset)
(refnx.reflect.Motofit method)
load_model() (refnx.reflect.Motofit method)
load_runs() (refnx.reduce.BatchReducer method)
logl() (refnx.analysis.BaseObjective method)
(refnx.analysis.GlobalObjective method)
(refnx.analysis.Objective method)
logp() (refnx.analysis.BaseObjective method)
(refnx.analysis.Bounds method)
(refnx.analysis.GlobalObjective method)
(refnx.analysis.Interval method)
(refnx.analysis.Model method)
(refnx.analysis.Objective method)
(refnx.analysis.Parameter method)
(refnx.analysis.Parameters method)
(refnx.analysis.PDF method)
(refnx.reflect.Component method)
(refnx.reflect.LipidLeaflet method)
(refnx.reflect.LipidLeafletGuest method)
(refnx.reflect.MixedReflectModel method)
(refnx.reflect.ReflectModel method)
(refnx.reflect.Spline method)
(refnx.reflect.Structure method)
logpost (refnx.analysis.CurveFitter property)
logpost() (refnx.analysis.BaseObjective method)
(refnx.analysis.Objective method)
M
MagneticSlab (class in refnx.reflect)
main() (in module refnx.reduce)
(in module refnx.reflect)
make_constraint() (refnx.reflect.LipidLeaflet method)
make_sampler() (refnx.analysis.CurveFitter method)
mask (refnx.dataset.Data1D property)
match_datasets() (refnx.reduce.AutoReducer method)
match_direct_beam() (refnx.reduce.AutoReducer method)
MaterialSLD (class in refnx.reflect)
MCMCResult (class in refnx.analysis)
median (refnx.analysis.MCMCResult attribute)
metadata (refnx.dataset.Data1D attribute)
MixedReflectModel (class in refnx.reflect)
MixedSlab (class in refnx.reflect)
Model (class in refnx.analysis)
model (refnx.reflect.Motofit attribute)
model() (refnx.analysis.Model method)
(refnx.reflect.MixedReflectModel method)
(refnx.reflect.PolarisedReflectModel method)
(refnx.reflect.ReflectModel method)
(refnx.reflect.ReflectModelTL method)
module
refnx.analysis
refnx.dataset
refnx.reduce
refnx.reflect
refnx.util
Motofit (class in refnx.reflect)
N
name (refnx.analysis.MCMCResult attribute)
(refnx.reflect.Structure property)
names() (refnx.analysis.Parameters method)
neutron_transmission() (in module refnx.util)
nll() (refnx.analysis.BaseObjective method)
(refnx.analysis.Objective method)
nlpost() (refnx.analysis.BaseObjective method)
nparam (refnx.analysis.Parameters property)
npoints (refnx.analysis.GlobalObjective property)
(refnx.analysis.Objective property)
number_datafile() (in module refnx.reduce)
nvary (refnx.analysis.CurveFitter property)
nvary() (refnx.analysis.Parameters method)
O
Objective (class in refnx.analysis)
objective (refnx.reflect.Motofit attribute)
OrsoDataset (class in refnx.dataset)
overall_sld() (refnx.reflect.Structure method)
P
param (refnx.analysis.MCMCResult attribute)
Parameter (class in refnx.analysis)
Parameters (class in refnx.analysis)
parameters (refnx.analysis.GlobalObjective property)
(refnx.analysis.Model property)
(refnx.analysis.Objective property)
(refnx.analysis.Parameters property)
(refnx.reflect.Component property)
(refnx.reflect.FunctionalForm property)
(refnx.reflect.LipidLeaflet property)
(refnx.reflect.LipidLeafletGuest property)
(refnx.reflect.MagneticSlab property)
(refnx.reflect.MaterialSLD property)
(refnx.reflect.MixedReflectModel property)
(refnx.reflect.MixedSlab property)
(refnx.reflect.ReflectModel property)
(refnx.reflect.Slab property)
(refnx.reflect.SLD property)
(refnx.reflect.Spline property)
(refnx.reflect.Stack property)
(refnx.reflect.Structure property)
PDF (class in refnx.analysis)
penetration_depth() (in module refnx.util)
pgen() (refnx.analysis.Objective method)
(refnx.analysis.Parameters method)
phase_angle() (refnx.reduce.PlatypusNexus method)
(refnx.reduce.SpatzNexus method)
PlatypusNexus (class in refnx.reduce)
PlatypusReduce (class in refnx.reduce)
plot() (refnx.analysis.GlobalObjective method)
(refnx.analysis.Objective method)
(refnx.dataset.Data1D method)
(refnx.reflect.Structure method)
plot_spectra() (refnx.reduce.SpinSet method)
PolarisationEfficiency (class in refnx.reduce)
PolarisedReduce (class in refnx.reduce)
PolarisedReflectModel (class in refnx.reflect)
possibly_create_parameter() (in module refnx.analysis)
possibly_create_scatterer() (in module refnx.reflect)
prior_transform() (refnx.analysis.Objective method)
process() (refnx.reduce.SpinSet method)
process_chain() (in module refnx.analysis)
pvals (refnx.analysis.Parameters property)
pymc_model() (in module refnx.analysis)
Q
q() (in module refnx.util)
q2() (in module refnx.util)
q_offset (refnx.reflect.MixedReflectModel property)
(refnx.reflect.ReflectModel property)
(refnx.reflect.ReflectModelTL property)
qcrit() (in module refnx.util)
R
range() (refnx.analysis.Parameter method)
redraw() (refnx.reflect.Motofit method)
reduce() (refnx.reduce.BatchReducer method)
(refnx.reduce.PolarisedReduce method)
reduce_stitch() (in module refnx.reduce)
reduce_xrdml() (in module refnx.reduce)
reducers (refnx.reduce.PolarisedReduce attribute)
ReductionOptions (class in refnx.reduce)
ReflectDataset (class in refnx.dataset)
reflectivity() (in module refnx.reflect)
(refnx.reflect.Structure method)
ReflectModel (class in refnx.reflect)
ReflectModelTL (class in refnx.reflect)
refnx.analysis
module
refnx.dataset
module
refnx.reduce
module
refnx.reflect
module
refnx.util
module
refplot() (in module refnx.util)
refresh() (refnx.dataset.Data1D method)
(refnx.dataset.OrsoDataset method)
reset() (refnx.analysis.CurveFitter method)
residuals() (refnx.analysis.GlobalObjective method)
(refnx.analysis.Objective method)
resolution_double_chopper() (in module refnx.util)
resolution_single_chopper() (in module refnx.util)
reverse_structure (refnx.reflect.Structure property)
rv (refnx.analysis.Interval property)
rvs() (refnx.analysis.Bounds method)
(refnx.analysis.Interval method)
(refnx.analysis.PDF method)
S
sample() (refnx.analysis.CurveFitter method)
save() (refnx.dataset.Data1D method)
save_model() (refnx.reflect.Motofit method)
save_xml() (refnx.dataset.ReflectDataset method)
sc_opts (refnx.reduce.SpinSet attribute)
scale (refnx.reflect.ReflectModel property)
scale() (refnx.dataset.Data1D method)
scales (refnx.reflect.MixedReflectModel property)
select_runs() (refnx.reduce.BatchReducer method)
sequence_to_parameters() (in module refnx.analysis)
set_constraint() (refnx.analysis.Parameter method)
set_model() (refnx.reflect.Motofit method)
setp() (refnx.analysis.BaseObjective method)
(refnx.analysis.Objective method)
(refnx.analysis.Parameter method)
Sinusoidal (class in refnx.reflect)
Slab (class in refnx.reflect)
slabs() (refnx.reflect.Component method)
(refnx.reflect.FunctionalForm method)
(refnx.reflect.LipidLeaflet method)
(refnx.reflect.LipidLeafletGuest method)
(refnx.reflect.MagneticSlab method)
(refnx.reflect.MixedSlab method)
(refnx.reflect.Slab method)
(refnx.reflect.Spline method)
(refnx.reflect.Stack method)
(refnx.reflect.Structure method)
SLD (class in refnx.reflect)
sld_profile() (in module refnx.reflect)
(refnx.reflect.Structure method)
slit_optimiser() (in module refnx.util)
solvent (refnx.reflect.Structure property)
sort() (refnx.dataset.Data1D method)
SpatzNexus (class in refnx.reduce)
SpatzReduce (class in refnx.reduce)
spin_channels (refnx.reduce.SpinSet property)
spin_set_direct (refnx.reduce.PolarisedReduce attribute)
spin_set_reflect (refnx.reduce.PolarisedReduce attribute)
SpinChannel (class in refnx.reduce)
(class in refnx.reflect)
SpinSet (class in refnx.reduce)
splice_datasets() (refnx.reduce.AutoReducer method)
Spline (class in refnx.reflect)
Stack (class in refnx.reflect)
standard_efficiencies() (refnx.reduce.PolarisationEfficiency method)
stderr (refnx.analysis.MCMCResult attribute)
Step (class in refnx.reflect)
Structure (class in refnx.reflect)
structure (refnx.reflect.ReflectModel property)
(refnx.reflect.ReflectModelTL property)
structures (refnx.reflect.MixedReflectModel property)
synthesise() (refnx.dataset.Data1D method)
T
t_offset (refnx.reflect.ReflectModelTL property)
Tanh (class in refnx.reflect)
tauC() (in module refnx.util)
time_offset() (refnx.reduce.PlatypusNexus method)
(refnx.reduce.SpatzNexus method)
to_orso() (refnx.reflect.Structure method)
Transform (class in refnx.analysis)
transmission_double_chopper() (in module refnx.util)
transmission_single_chopper() (in module refnx.util)
U
ub (refnx.analysis.Interval property)
ud (refnx.reduce.SpinSet attribute)
(refnx.reduce.SpinSet property)
unmasked_data (refnx.dataset.Data1D property)
UP_DOWN (refnx.reduce.SpinChannel attribute)
(refnx.reflect.SpinChannel attribute)
UP_UP (refnx.reduce.SpinChannel attribute)
(refnx.reflect.SpinChannel attribute)
update_model() (refnx.reflect.Motofit method)
use_reflect_backend() (in module refnx.reflect)
uu (refnx.reduce.SpinSet attribute)
(refnx.reduce.SpinSet property)
V
valid() (refnx.analysis.Bounds method)
(refnx.analysis.Interval method)
(refnx.analysis.Parameter method)
(refnx.analysis.PDF method)
value (refnx.analysis.Parameter property)
vary (refnx.analysis.Parameter property)
varying_parameters() (refnx.analysis.BaseObjective method)
(refnx.analysis.Objective method)
(refnx.analysis.Parameters method)
velocity_wavelength() (in module refnx.util)
volfrac_guest (refnx.reflect.LipidLeafletGuest property)
volfrac_h (refnx.reflect.LipidLeaflet property)
volfrac_t (refnx.reflect.LipidLeaflet property)
W
wavelength() (in module refnx.util)
wavelength_energy() (in module refnx.util)
wavelength_velocity() (in module refnx.util)
weighted (refnx.analysis.GlobalObjective property)
(refnx.analysis.Objective property)
(refnx.dataset.Data1D attribute)
X
x (refnx.dataset.Data1D property)
x_err (refnx.dataset.Data1D property)
xray_energy() (in module refnx.util)
xray_wavelength() (in module refnx.util)
Y
y (refnx.dataset.Data1D property)
y_err (refnx.dataset.Data1D property)