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Updates backgrounds and resolutions in line with the MATLAB #100

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Merged
alexhroom merged 15 commits into from
Jan 10, 2025
Merged

Updates backgrounds and resolutions in line with the MATLAB #100

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eb2fee9
refactored backgrounds and resolutions to use source parameter
alexhroom Dec 9, 2024
a5697b3
added model renaming for data and function backgrounds/resolutions
alexhroom Dec 9, 2024
65febe3
added validators for value warnings and unimplemented behaviour
alexhroom Dec 10, 2024
a432de5
added data and function background examples and example test
alexhroom Dec 11, 2024
8096230
updated check_indices to be nested
alexhroom Dec 11, 2024
7bc5cf0
data backgrounds add to contrast data
alexhroom Dec 11, 2024
e659a1f
added source/value wiping for type change
alexhroom Dec 11, 2024
9a7c304
created shared parent class for backgrounds and resolutions
alexhroom Dec 11, 2024
5fd7390
review fixes to docstrings and data backgrounds
alexhroom Dec 12, 2024
9194225
reordered check_indices list to match packParams
alexhroom Dec 12, 2024
c8a2cf4
added backgrounds to outputs
alexhroom Dec 13, 2024
9d08b45
updated tests
alexhroom Jan 7, 2025
0d3dd58
review fixes to docstrings
alexhroom Jan 8, 2025
6aff106
ruff format
alexhroom Jan 9, 2025
841cbd1
added warning for fields clearing
alexhroom Jan 10, 2025
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6 changes: 5 additions & 1 deletion RATapi/examples/__init__.py
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Original file line number Diff line number Diff line change
@@ -1,10 +1,12 @@
from RATapi.examples.absorption.absorption import absorption
from RATapi.examples.convert_rascal_project import convert_rascal
from RATapi.examples.convert_rascal_project.convert_rascal import convert_rascal
from RATapi.examples.domains.domains_custom_layers import domains_custom_layers
from RATapi.examples.domains.domains_custom_XY import domains_custom_XY
from RATapi.examples.domains.domains_standard_layers import domains_standard_layers
from RATapi.examples.non_polarised.DSPC_custom_layers import DSPC_custom_layers
from RATapi.examples.non_polarised.DSPC_custom_XY import DSPC_custom_XY
from RATapi.examples.non_polarised.DSPC_data_background import DSPC_data_background
from RATapi.examples.non_polarised.DSPC_function_background import DSPC_function_background
from RATapi.examples.non_polarised.DSPC_standard_layers import DSPC_standard_layers

__all__ = [
Expand All @@ -15,5 +17,7 @@
"DSPC_custom_layers",
"DSPC_custom_XY",
"DSPC_standard_layers",
"DSPC_data_background",
"DSPC_function_background",
"convert_rascal",
]
8 changes: 4 additions & 4 deletions RATapi/examples/absorption/absorption.ipynb
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Expand Up @@ -140,10 +140,10 @@
"problem.background_parameters.append(name=\"Background parameter 3\", min=1.0e-06, value=9.01e-06, max=9.0e-05, fit=True)\n",
"problem.background_parameters.append(name=\"Background parameter 4\", min=1.0e-06, value=5.61e-06, max=9.0e-05, fit=True)\n",
"\n",
"problem.backgrounds.append(name=\"Background 1\", type=\"constant\", value_1=\"Background parameter 1\")\n",
"problem.backgrounds.append(name=\"Background 2\", type=\"constant\", value_1=\"Background parameter 2\")\n",
"problem.backgrounds.append(name=\"Background 3\", type=\"constant\", value_1=\"Background parameter 3\")\n",
"problem.backgrounds.append(name=\"Background 4\", type=\"constant\", value_1=\"Background parameter 4\")\n",
"problem.backgrounds.append(name=\"Background 1\", type=\"constant\", source=\"Background parameter 1\")\n",
"problem.backgrounds.append(name=\"Background 2\", type=\"constant\", source=\"Background parameter 2\")\n",
"problem.backgrounds.append(name=\"Background 3\", type=\"constant\", source=\"Background parameter 3\")\n",
"problem.backgrounds.append(name=\"Background 4\", type=\"constant\", source=\"Background parameter 4\")\n",
"\n",
"# Make the resolution fittable\n",
"problem.resolution_parameters.set_fields(0, fit=True)\n"
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8 changes: 4 additions & 4 deletions RATapi/examples/absorption/absorption.py
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Expand Up @@ -68,10 +68,10 @@ def absorption():
name="Background parameter 4", min=1.0e-06, value=5.61e-06, max=9.0e-05, fit=True
)

problem.backgrounds.append(name="Background 1", type="constant", value_1="Background parameter 1")
problem.backgrounds.append(name="Background 2", type="constant", value_1="Background parameter 2")
problem.backgrounds.append(name="Background 3", type="constant", value_1="Background parameter 3")
problem.backgrounds.append(name="Background 4", type="constant", value_1="Background parameter 4")
problem.backgrounds.append(name="Background 1", type="constant", source="Background parameter 1")
problem.backgrounds.append(name="Background 2", type="constant", source="Background parameter 2")
problem.backgrounds.append(name="Background 3", type="constant", source="Background parameter 3")
problem.backgrounds.append(name="Background 4", type="constant", source="Background parameter 4")

# Make the resolution fittable
problem.resolution_parameters.set_fields(0, fit=True)
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82 changes: 82 additions & 0 deletions RATapi/examples/data/d2o_background_data.dat
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@@ -0,0 +1,82 @@
0.011403 1.90034798968076e-06 -9.65035874608547e-07
0.011973 1.81361996101478e-06 -4.67852140773275e-09
0.012572 1.5763144199176e-06 -1.36151693657437e-06
0.013201 2.66861902156408e-06 5.28737972088124e-07
0.013861 1.19184137102607e-06 6.5429177234931e-07
0.014554 1.75409120253422e-06 -4.50039804064594e-07
0.015281 1.51534921649628e-06 3.54060605152339e-07
0.016045 1.76294603973655e-06 2.30273872099416e-07
0.016848 1.66691808740296e-06 1.02729272466451e-06
0.01769 2.2391873415575e-06 2.02710446930881e-07
0.018575 1.47947093349392e-06 9.31566506641381e-07
0.019503 1.58967045467121e-06 6.58308695637623e-09
0.020479 2.05056480300655e-06 -4.18637528083399e-07
0.021502 2.54199126843229e-06 6.96150360898885e-08
0.022578 1.07273638130851e-06 -5.94598550176916e-08
0.023706 2.89987639289405e-06 8.05335897612554e-07
0.024892 1.56081284721073e-06 5.50847432744533e-08
0.026136 2.32386636321661e-06 -5.72991095509919e-07
0.027443 2.52478251612625e-06 -2.38750704688337e-08
0.028815 2.66154668842285e-06 1.05087573637142e-06
0.030256 1.74132051718101e-06 -2.3192582338868e-07
0.031769 2.01215747485553e-06 -4.26893410009117e-07
0.033357 1.91881656322323e-06 8.87192534478923e-07
0.035025 1.69716945696631e-06 1.80981995646851e-07
0.036777 2.13585488200451e-06 -1.90164659296111e-07
0.038615 2.17932170608953e-06 -4.91062265460096e-07
0.040546 1.82384243860966e-06 -1.08387392818395e-06
0.042573 2.06617996409986e-06 2.22697399577916e-07
0.044702 3.33679088859971e-06 -1.53613977488785e-07
0.046937 1.99621696227773e-06 3.55134601922439e-07
0.049284 2.3551514683307e-06 -1.06523727035749e-06
0.051748 1.76873031859355e-06 1.15746760150783e-06
0.054336 1.73606104969994e-06 4.89763150040874e-07
0.057052 1.82710646654775e-06 -1.15330099931726e-06
0.059905 2.28227888686718e-06 9.45647703159621e-07
0.0629 1.59923042799896e-06 -3.70062237263438e-07
0.066045 1.07352660741589e-06 3.41777294345909e-07
0.069348 2.02660800872659e-06 2.75569910736786e-07
0.072815 1.78179239147256e-06 -6.0256088120987e-07
0.076456 2.14000373613308e-06 -2.18911980741668e-06
0.080279 2.04230294359047e-06 5.284442372682e-07
0.084292 2.36455952978407e-06 -1.73629847921614e-07
0.088507 2.45037654782291e-06 -3.78287083788833e-07
0.092932 1.33718085273407e-06 4.35130166728242e-07
0.097579 1.23771058575749e-06 -4.51744576618967e-07
0.10246 2.25121666653143e-06 6.36952833032752e-07
0.10758 2.15319571282475e-06 2.20717968415214e-07
0.11296 1.53041976734067e-06 -6.93055107868105e-07
0.11861 2.61870106321507e-06 7.69463958198665e-07
0.12454 2.01650595727752e-06 4.79607176188218e-07
0.13077 2.06178415911062e-06 1.10173268381594e-06
0.1373 2.13696968977538e-06 -6.14098124528528e-07
0.14417 2.3770829041412e-06 -6.16219383494697e-07
0.15138 2.7622487528669e-06 3.50660742020884e-07
0.15895 1.86901211887215e-06 6.33626529015099e-07
0.16689 1.13465824611353e-06 7.62493241842828e-07
0.17524 2.50673214999504e-06 1.05207422581854e-07
0.184 1.53613195077685e-06 -8.87137577093779e-08
0.1932 2.62184014311179e-06 6.22256875962273e-07
0.20286 1.70525565120706e-06 1.67162600924891e-06
0.213 2.74574086739327e-06 8.07667338780613e-07
0.22365 1.59701095264287e-06 1.67629565660922e-07
0.23484 1.4437004736234e-06 -3.59611249006791e-07
0.24658 2.47846978404969e-06 4.99800504594724e-07
0.25891 1.31847420553136e-06 -2.87283586089481e-07
0.27185 2.34029248136207e-06 2.90756508518823e-07
0.28544 2.21891181128286e-06 7.22598553179947e-07
0.29972 1.92836622666398e-06 8.39418345516717e-07
0.3147 1.82923374769972e-06 5.70510331434857e-07
0.33044 3.02890531703209e-06 1.20234742176368e-06
0.34696 1.8127324822871e-06 1.58096394623758e-06
0.36431 1.90489840127358e-06 -1.41813181395574e-06
0.38252 1.53063379469415e-06 -1.32294734328625e-06
0.40165 1.59326881780842e-06 -6.38112989285387e-07
0.42173 1.7081906242357e-06 -1.49834166690205e-06
0.44282 2.85476268526193e-06 -1.85680046178151e-07
0.46496 1.80479009111448e-06 -1.69120607911057e-07
0.48821 1.6549673183601e-06 3.00340803829798e-07
0.51262 1.77588964903545e-06 3.28929520936145e-07
0.53825 2.35718817504981e-06 -4.48934854489947e-07
0.56516 1.34213437585845e-06 -5.50651590195596e-07
0.59342 2.31356104763158e-06 7.347220470815e-07
6 changes: 3 additions & 3 deletions RATapi/examples/languages/setup_problem.py
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Expand Up @@ -82,11 +82,11 @@ def make_example_problem():
)

# And add the two new constant backgrounds
problem.backgrounds.append(name="Background SMW", type="constant", value_1="Background parameter SMW")
problem.backgrounds.append(name="Background H2O", type="constant", value_1="Background parameter H2O")
problem.backgrounds.append(name="Background SMW", type="constant", source="Background parameter SMW")
problem.backgrounds.append(name="Background H2O", type="constant", source="Background parameter H2O")

# And edit the other one
problem.backgrounds.set_fields(0, name="Background D2O", value_1="Background parameter D2O")
problem.backgrounds.set_fields(0, name="Background D2O", source="Background parameter D2O")

# Finally modify some of the other parameters to be more suitable values for a solid / liquid experiment
problem.scalefactors.set_fields(0, value=1.0, min=0.5, max=2.0, fit=True)
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6 changes: 3 additions & 3 deletions RATapi/examples/non_polarised/DSPC_custom_XY.py
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Expand Up @@ -90,11 +90,11 @@ def DSPC_custom_XY():
problem.background_parameters.append(name="Background parameter H2O", min=0.0, value=1.0e-7, max=1.0e-5, fit=True)

# And add the two new constant backgrounds
problem.backgrounds.append(name="Background SMW", type="constant", value_1="Background parameter SMW")
problem.backgrounds.append(name="Background H2O", type="constant", value_1="Background parameter H2O")
problem.backgrounds.append(name="Background SMW", type="constant", source="Background parameter SMW")
problem.backgrounds.append(name="Background H2O", type="constant", source="Background parameter H2O")

# And edit the other one
problem.backgrounds.set_fields(0, name="Background D2O", value_1="Background parameter D2O")
problem.backgrounds.set_fields(0, name="Background D2O", source="Background parameter D2O")

# Finally modify some of the other parameters to be more suitable values for a solid / liquid experiment
problem.scalefactors.set_fields(0, value=1.0, min=0.5, max=2.0, fit=True)
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6 changes: 3 additions & 3 deletions RATapi/examples/non_polarised/DSPC_custom_layers.ipynb
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Expand Up @@ -534,11 +534,11 @@
"problem.background_parameters.append(name=\"Background parameter H2O\", min=1.0e-10, value=1.0e-7, max=1.0e-5, fit=True)\n",
"\n",
"# And add the two new constant backgrounds\n",
"problem.backgrounds.append(name=\"Background SMW\", type=\"constant\", value_1=\"Background parameter SMW\")\n",
"problem.backgrounds.append(name=\"Background H2O\", type=\"constant\", value_1=\"Background parameter H2O\")\n",
"problem.backgrounds.append(name=\"Background SMW\", type=\"constant\", source=\"Background parameter SMW\")\n",
"problem.backgrounds.append(name=\"Background H2O\", type=\"constant\", source=\"Background parameter H2O\")\n",
"\n",
"# And edit the other one\n",
"problem.backgrounds.set_fields(0, name=\"Background D2O\", value_1=\"Background parameter D2O\")\n",
"problem.backgrounds.set_fields(0, name=\"Background D2O\", source=\"Background parameter D2O\")\n",
"\n",
"# Finally modify some of the other parameters to be more suitable values for a solid / liquid experiment\n",
"problem.scalefactors.set_fields(0, value=1.0, min=0.5, max=2.0, fit=True)"
Expand Down
6 changes: 3 additions & 3 deletions RATapi/examples/non_polarised/DSPC_custom_layers.py
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Expand Up @@ -74,11 +74,11 @@ def DSPC_custom_layers():
)

# And add the two new constant backgrounds
problem.backgrounds.append(name="Background SMW", type="constant", value_1="Background parameter SMW")
problem.backgrounds.append(name="Background H2O", type="constant", value_1="Background parameter H2O")
problem.backgrounds.append(name="Background SMW", type="constant", source="Background parameter SMW")
problem.backgrounds.append(name="Background H2O", type="constant", source="Background parameter H2O")

# And edit the other one
problem.backgrounds.set_fields(0, name="Background D2O", value_1="Background parameter D2O")
problem.backgrounds.set_fields(0, name="Background D2O", source="Background parameter D2O")

# Finally modify some of the other parameters to be more suitable values for a solid / liquid experiment
problem.scalefactors.set_fields(0, value=1.0, min=0.5, max=2.0, fit=True)
Expand Down
6 changes: 3 additions & 3 deletions RATapi/examples/non_polarised/DSPC_custom_xy.ipynb
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Expand Up @@ -175,11 +175,11 @@
"problem.background_parameters.append(name=\"Background parameter H2O\", min=0.0, value=1.0e-7, max=1.0e-5, fit=True)\n",
"\n",
"# And add the two new constant backgrounds\n",
"problem.backgrounds.append(name=\"Background SMW\", type=\"constant\", value_1=\"Background parameter SMW\")\n",
"problem.backgrounds.append(name=\"Background H2O\", type=\"constant\", value_1=\"Background parameter H2O\")\n",
"problem.backgrounds.append(name=\"Background SMW\", type=\"constant\", source=\"Background parameter SMW\")\n",
"problem.backgrounds.append(name=\"Background H2O\", type=\"constant\", source=\"Background parameter H2O\")\n",
"\n",
"# And edit the other one\n",
"problem.backgrounds.set_fields(0, name=\"Background D2O\", value_1=\"Background parameter D2O\")\n",
"problem.backgrounds.set_fields(0, name=\"Background D2O\", source=\"Background parameter D2O\")\n",
"\n",
"# Finally modify some of the other parameters to be more suitable values for a solid / liquid experiment\n",
"problem.scalefactors.set_fields(0, value=1.0, min=0.5, max=2.0, fit=True)\n",
Expand Down
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