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alexhroom merged 2 commits into from
May 6, 2025
Merged

Adds JSON to projectClass utility script #397

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315f436
added json to project script and tests
alexhroom May 2, 2025
dc5dff5
fixed paths
alexhroom May 2, 2025
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1 change: 1 addition & 0 deletions tests/testJsonToProject/DSPC_custom_XY.json
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1 change: 1 addition & 0 deletions tests/testJsonToProject/DSPC_custom_layers.json
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1 change: 1 addition & 0 deletions tests/testJsonToProject/DSPC_standard_layers.json
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{"name": "original_dspc_bilayer", "calculation": "normal", "model": "standard layers", "geometry": "substrate/liquid", "absorption": false, "parameters": [{"name": "Substrate Roughness", "min": 1.0, "value": 3.0, "max": 10.0, "fit": true, "prior_type": "uniform", "mu": 0.0, "sigma": Infinity, "show_priors": false}, {"name": "Oxide Thickness", "min": 5.0, "value": 19.54, "max": 60.0, "fit": true, "prior_type": "uniform", "mu": 0.0, "sigma": Infinity, "show_priors": false}, {"name": "Oxide SLD", "min": 3.39e-06, "value": 3.39e-06, "max": 3.41e-06, "fit": false, "prior_type": "uniform", "mu": 0.0, "sigma": Infinity, "show_priors": false}, {"name": "SAM Tails Thickness", "min": 15.0, "value": 22.66, "max": 35.0, "fit": true, "prior_type": "uniform", "mu": 0.0, "sigma": Infinity, "show_priors": false}, {"name": "SAM Tails SLD", "min": -5e-07, "value": -4.01e-07, "max": -3e-07, "fit": false, "prior_type": "uniform", "mu": 0.0, "sigma": Infinity, "show_priors": false}, {"name": "SAM Tails Hydration", "min": 1.0, "value": 5.252, "max": 50.0, "fit": true, "prior_type": "uniform", "mu": 0.0, "sigma": Infinity, "show_priors": false}, {"name": "SAM Roughness", "min": 1.0, "value": 5.64, "max": 15.0, "fit": true, "prior_type": "uniform", "mu": 0.0, "sigma": Infinity, "show_priors": false}, {"name": "CW Thickness", "min": 10.0, "value": 17.12, "max": 28.0, "fit": true, "prior_type": "uniform", "mu": 0.0, "sigma": Infinity, "show_priors": false}, {"name": "CW SLD", "min": 0.0, "value": 0.0, "max": 1e-09, "fit": false, "prior_type": "uniform", "mu": 0.0, "sigma": Infinity, "show_priors": false}, {"name": "SAM Heads Thickness", "min": 5.0, "value": 8.56, "max": 17.0, "fit": true, "prior_type": "gaussian", "mu": 10.0, "sigma": 2.0, "show_priors": false}, {"name": "SAM Heads SLD", "min": 1e-07, "value": 1.75e-06, "max": 2e-06, "fit": false, "prior_type": "uniform", "mu": 0.0, "sigma": Infinity, "show_priors": false}, {"name": "SAM Heads Hydration", "min": 10.0, "value": 45.45, "max": 50.0, "fit": true, "prior_type": "gaussian", "mu": 30.0, "sigma": 3.0, "show_priors": false}, {"name": "Bilayer Heads Thickness", "min": 7.0, "value": 10.7, "max": 17.0, "fit": true, "prior_type": "gaussian", "mu": 10.0, "sigma": 2.0, "show_priors": false}, {"name": "Bilayer Heads SLD", "min": 5e-07, "value": 1.47e-06, "max": 1.5e-06, "fit": false, "prior_type": "uniform", "mu": 0.0, "sigma": Infinity, "show_priors": false}, {"name": "Bilayer Roughness", "min": 2.0, "value": 6.014, "max": 15.0, "fit": true, "prior_type": "uniform", "mu": 0.0, "sigma": Infinity, "show_priors": false}, {"name": "Bilayer Tails Thickness", "min": 14.0, "value": 17.82, "max": 22.0, "fit": true, "prior_type": "uniform", "mu": 0.0, "sigma": Infinity, "show_priors": false}, {"name": "Bilayer Tails SLD", "min": -5e-07, "value": -4.61e-07, "max": 0.0, "fit": false, "prior_type": "uniform", "mu": 0.0, "sigma": Infinity, "show_priors": false}, {"name": "Bilayer Tails Hydration", "min": 10.0, "value": 17.64, "max": 50.0, "fit": true, "prior_type": "uniform", "mu": 0.0, "sigma": Infinity, "show_priors": false}, {"name": "Bilayer Heads Hydration", "min": 10.0, "value": 36.15, "max": 50.0, "fit": true, "prior_type": "uniform", "mu": 0.0, "sigma": Infinity, "show_priors": false}, {"name": "CW Hydration", "min": 99.9, "value": 100.0, "max": 100.0, "fit": false, "prior_type": "uniform", "mu": 0.0, "sigma": Infinity, "show_priors": false}, {"name": "Oxide Hydration", "min": 0.0, "value": 23.61, "max": 60.0, "fit": true, "prior_type": "uniform", "mu": 0.0, "sigma": Infinity, "show_priors": false}], "bulk_in": [{"name": "Silicon", "min": 2e-06, "value": 2.073e-06, "max": 2.1e-06, "fit": false, "prior_type": "uniform", "mu": 0.0, "sigma": Infinity, "show_priors": false}], "bulk_out": [{"name": "D2O", "min": 5.5e-06, "value": 5.98e-06, "max": 6.4e-06, "fit": true, "prior_type": "uniform", "mu": 0.0, "sigma": Infinity, "show_priors": false}, {"name": "SMW", "min": 1e-06, "value": 2.21e-06, "max": 4.99e-06, "fit": true, "prior_type": "uniform", "mu": 0.0, "sigma": Infinity, "show_priors": false}], "scalefactors": [{"name": "Scalefactor 1", "min": 0.05, "value": 0.1, "max": 0.2, "fit": false, "prior_type": "uniform", "mu": 0.0, "sigma": Infinity, "show_priors": false}, {"name": "Scalefactor 2", "min": 0.05, "value": 0.15, "max": 0.2, "fit": false, "prior_type": "uniform", "mu": 0.0, "sigma": Infinity, "show_priors": false}], "domain_ratios": [], "background_parameters": [{"name": "Background parameter D2O", "min": 5e-10, "value": 2.23e-06, "max": 7e-06, "fit": true, "prior_type": "uniform", "mu": 0.0, "sigma": Infinity, "show_priors": false}, {"name": "Background parameter SMW", "min": 1e-10, "value": 3.38e-06, "max": 4.99e-06, "fit": true, "prior_type": "uniform", "mu": 0.0, "sigma": Infinity, "show_priors": false}], "backgrounds": [{"name": "D2O Background", "type": "constant", "source": "Background parameter D2O", "value_1": "", "value_2": "", "value_3": "", "value_4": "", "value_5": ""}, {"name": "SMW Background", "type": "constant", "source": "Background parameter SMW", "value_1": "", "value_2": "", "value_3": "", "value_4": "", "value_5": ""}], "resolution_parameters": [{"name": "Resolution Param 1", "min": 0.01, "value": 0.03, "max": 0.05, "fit": false, "prior_type": "uniform", "mu": 0.0, "sigma": Infinity, "show_priors": false}], "resolutions": [{"name": "Resolution 1", "type": "constant", "source": "Resolution Param 1", "value_1": "", "value_2": "", "value_3": "", "value_4": "", "value_5": ""}], "custom_files": [], "data": [{"name": "Simulation", "data": [], "data_range": [], "simulation_range": [0.005, 0.7]}, {"name": "dspc_bil_D2O", "data": [[0.011403, 0.10063, 0.0019003], [0.011973, 0.11082, 0.001883], [0.012572, 0.10766, 0.0016413], [0.013201, 0.10652, 0.0014669], [0.013861, 0.090118, 0.0011774], [0.014554, 0.034255, 0.00048888], [0.015281, 0.017209, 0.00026267], [0.016045, 0.010465, 0.00017551], [0.016848, 0.0070455, 0.00013083], [0.01769, 0.0045958, 9.7193e-05], [0.018575, 0.0034925, 8.0937e-05], [0.019503, 0.002451, 6.4505e-05], [0.020479, 0.0017544, 5.1254e-05], [0.021502, 0.0013384, 4.2675e-05], [0.022578, 0.0010447, 3.5865e-05], [0.023706, 0.00076523, 2.9299e-05], [0.024892, 0.00064257, 2.6236e-05], [0.026136, 0.00050024, 1.3657e-05], [0.027443, 0.00039982, 1.1639e-05], [0.028815, 0.00034301, 1.0137e-05], [0.030256, 0.00027746, 8.5758e-06], [0.031769, 0.00026396, 8.2806e-06], [0.033357, 0.00023596, 7.8864e-06], [0.035025, 0.0002028, 1.0041e-05], [0.036777, 0.00018591, 4.9391e-06], [0.038615, 0.00015427, 4.3142e-06], [0.040546, 0.00014273, 3.958e-06], [0.042573, 0.00012868, 3.6645e-06], [0.044702, 0.00011002, 3.2644e-06], [0.046937, 9.1148e-05, 2.8227e-06], [0.049284, 9.1217e-05, 2.7234e-06], [0.051748, 7.6323e-05, 2.3706e-06], [0.054336, 6.6691e-05, 2.1365e-06], [0.057052, 6.4594e-05, 2.4647e-06], [0.059905, 6.0971e-05, 1.3241e-06], [0.0629, 6.3097e-05, 1.2946e-06], [0.066045, 6.0729e-05, 1.1791e-06], [0.069348, 5.9985e-05, 1.1102e-06], [0.072815, 6.1021e-05, 1.1013e-06], [0.076456, 5.6755e-05, 1.035e-06], [0.080279, 5.8755e-05, 1.5569e-06], [0.084292, 5.4071e-05, 9.5338e-07], [0.088507, 4.6964e-05, 8.4392e-07], [0.092932, 4.2634e-05, 7.7134e-07], [0.097579, 3.27e-05, 6.528e-07], [0.10246, 2.54e-05, 5.4648e-07], [0.10758, 1.7075e-05, 4.2154e-07], [0.11296, 1.2197e-05, 3.4055e-07], [0.11861, 7.8205e-06, 2.5881e-07], [0.12454, 5.091e-06, 2.0153e-07], [0.13077, 4.1579e-06, 1.762e-07], [0.1373, 3.6345e-06, 1.6248e-07], [0.14417, 3.3455e-06, 1.5143e-07], [0.15138, 2.7295e-06, 1.3191e-07], [0.15895, 1.8245e-06, 1.0679e-07], [0.16689, 1.2171e-06, 8.7591e-08], [0.17524, 4.9313e-07, 5.6663e-08], [0.184, 2.4038e-07, 4.1253e-08], [0.1932, 3.3832e-07, 5.3216e-08], [0.20286, 3.2022e-07, 5.5047e-08], [0.213, 4.1948e-07, 6.8549e-08], [0.22365, 3.1493e-07, 6.3396e-08], [0.23484, 2.3214e-07, 5.5974e-08], [0.24658, 3.3414e-07, 6.8415e-08], [0.25891, 3.9863e-07, 8.2061e-08], [0.27185, 2.5113e-07, 6.271e-08], [0.28544, 2.2469e-07, 6.3286e-08], [0.29972, 2.0862e-07, 6.0631e-08], [0.3147, 2.0861e-07, 6.1379e-08], [0.33044, 3.3381e-07, 7.7193e-08], [0.34696, 1.8378e-07, 6.049e-08], [0.36431, 2.3515e-07, 6.6222e-08], [0.38252, 2.1154e-07, 6.3084e-08], [0.40165, 2.4662e-07, 6.6637e-08], [0.42173, 2.017e-07, 6.2432e-08], [0.44282, 2.4563e-07, 6.9088e-08], [0.46496, 1.9906e-07, 6.0793e-08], [0.48821, 2.8635e-07, 7.3878e-08], [0.51262, 1.9471e-07, 6.1764e-08], [0.53825, 2.8836e-07, 7.5438e-08], [0.56516, 2.3816e-07, 7.061e-08], [0.59342, 2.1782e-07, 6.6918e-08]], "data_range": [0.011403, 0.59342], "simulation_range": [0.011403, 0.59342]}, {"name": "dspc_bil_smw", "data": [[0.011403, 0.0018074, 0.00010983], [0.011973, 0.0014774, 9.0584e-05], [0.012572, 0.001325, 7.7039e-05], [0.013201, 0.0012216, 6.6408e-05], [0.013861, 0.0010077, 5.5778e-05], [0.014554, 0.0010266, 5.1388e-05], [0.015281, 0.00091489, 4.521e-05], [0.016045, 0.00080921, 3.995e-05], [0.016848, 0.00061576, 3.3466e-05], [0.01769, 0.00060308, 3.1557e-05], [0.018575, 0.00046074, 2.6813e-05], [0.019503, 0.00040453, 2.4355e-05], [0.020479, 0.00036496, 2.2031e-05], [0.021502, 0.00032468, 2.0023e-05], [0.022578, 0.0002479, 1.6581e-05], [0.023706, 0.00027709, 1.7017e-05], [0.024892, 0.00021141, 1.4388e-05], [0.026136, 0.00017034, 7.5065e-06], [0.027443, 0.00015127, 6.7139e-06], [0.028815, 0.00013632, 5.9548e-06], [0.030256, 0.00011151, 5.2534e-06], [0.031769, 9.5843e-05, 4.7729e-06], [0.033357, 7.5905e-05, 4.2186e-06], [0.035025, 6.919e-05, 6.2034e-06], [0.036777, 5.272e-05, 2.3936e-06], [0.038615, 3.9182e-05, 1.9828e-06], [0.040546, 2.938e-05, 1.6381e-06], [0.042573, 2.2329e-05, 1.3936e-06], [0.044702, 1.471e-05, 1.0942e-06], [0.046937, 8.1966e-06, 7.7674e-07], [0.049284, 6.4866e-06, 6.6572e-07], [0.051748, 3.0853e-06, 4.3607e-07], [0.054336, 2.6025e-06, 3.888e-07], [0.057052, 2.7294e-06, 4.9982e-07], [0.059905, 4.3615e-06, 3.1992e-07], [0.0629, 5.4926e-06, 3.4522e-07], [0.066045, 7.2943e-06, 3.6968e-07], [0.069348, 8.9112e-06, 3.8947e-07], [0.072815, 1.0612e-05, 4.1912e-07], [0.076456, 1.2411e-05, 4.4241e-07], [0.080279, 1.4576e-05, 7.0225e-07], [0.084292, 1.4768e-05, 4.5606e-07], [0.088507, 1.3957e-05, 4.2438e-07], [0.092932, 1.1624e-05, 3.7299e-07], [0.097579, 1.0598e-05, 3.4827e-07], [0.10246, 7.7689e-06, 2.8497e-07], [0.10758, 6.4311e-06, 2.4647e-07], [0.11296, 4.952e-06, 2.0748e-07], [0.11861, 2.8957e-06, 1.5122e-07], [0.12454, 1.9786e-06, 1.2104e-07], [0.13077, 1.1837e-06, 9.0553e-08], [0.1373, 9.5591e-07, 8.0264e-08], [0.14417, 9.9179e-07, 7.9466e-08], [0.15138, 8.1026e-07, 6.9286e-08], [0.15895, 7.8161e-07, 6.7637e-08], [0.16689, 6.039e-07, 5.9878e-08], [0.17524, 4.8559e-07, 5.489e-08], [0.184, 4.1425e-07, 5.2852e-08], [0.1932, 4.375e-07, 5.9223e-08], [0.20286, 3.0001e-07, 5.1646e-08], [0.213, 4.9488e-07, 7.1141e-08], [0.22365, 2.7977e-07, 5.7809e-08], [0.23484, 2.3853e-07, 5.4901e-08], [0.24658, 2.1767e-07, 5.3744e-08], [0.25891, 2.5677e-07, 6.3708e-08], [0.27185, 5.7975e-07, 9.3465e-08], [0.28544, 3.2659e-07, 7.4563e-08], [0.29972, 3.0527e-07, 7.1553e-08], [0.3147, 3.3603e-07, 7.6342e-08], [0.33044, 3.8583e-07, 8.1122e-08], [0.34696, 2.9402e-07, 7.285e-08], [0.36431, 3.0297e-07, 7.2958e-08], [0.38252, 4.0996e-07, 8.5727e-08], [0.40165, 4.0612e-07, 8.3403e-08], [0.42173, 5.3059e-07, 9.7535e-08], [0.44282, 4.9546e-07, 9.5624e-08], [0.46496, 3.5423e-07, 7.8721e-08], [0.48821, 3.5614e-07, 7.9969e-08], [0.51262, 3.7628e-07, 8.3392e-08], [0.53825, 5.8915e-07, 1.0457e-07], [0.56516, 3.2619e-07, 7.9702e-08], [0.59342, 3.068e-07, 7.7062e-08]], "data_range": [0.011403, 0.59342], "simulation_range": [0.011403, 0.59342]}], "layers": [{"name": "Oxide", "thickness": "Oxide Thickness", "SLD": "Oxide SLD", "roughness": "Substrate Roughness", "hydration": "Oxide Hydration", "hydrate_with": "bulk out"}, {"name": "SAM Tails", "thickness": "SAM Tails Thickness", "SLD": "SAM Tails SLD", "roughness": "SAM Roughness", "hydration": "SAM Tails Hydration", "hydrate_with": "bulk out"}, {"name": "SAM Heads", "thickness": "SAM Heads Thickness", "SLD": "SAM Heads SLD", "roughness": "SAM Roughness", "hydration": "SAM Heads Hydration", "hydrate_with": "bulk out"}, {"name": "Central Water", "thickness": "CW Thickness", "SLD": "CW SLD", "roughness": "Bilayer Roughness", "hydration": "CW Hydration", "hydrate_with": "bulk out"}, {"name": "Bilayer Heads", "thickness": "Bilayer Heads Thickness", "SLD": "Bilayer Heads SLD", "roughness": "Bilayer Roughness", "hydration": "Bilayer Heads Hydration", "hydrate_with": "bulk out"}, {"name": "Bilayer Tails", "thickness": "Bilayer Tails Thickness", "SLD": "Bilayer Tails SLD", "roughness": "Bilayer Roughness", "hydration": "Bilayer Tails Hydration", "hydrate_with": "bulk out"}], "domain_contrasts": [], "contrasts": [{"name": "D2O", "data": "dspc_bil_D2O", "background": "D2O Background", "background_action": "add", "bulk_in": "Silicon", "bulk_out": "D2O", "scalefactor": "Scalefactor 1", "resolution": "Resolution 1", "resample": false, "model": ["Oxide", "SAM Tails", "SAM Heads", "Central Water", "Bilayer Heads", "Bilayer Tails", "Bilayer Tails", "Bilayer Heads"]}, {"name": "SMW", "data": "dspc_bil_smw", "background": "SMW Background", "background_action": "add", "bulk_in": "Silicon", "bulk_out": "SMW", "scalefactor": "Scalefactor 2", "resolution": "Resolution 1", "resample": false, "model": ["Oxide", "SAM Tails", "SAM Heads", "Central Water", "Bilayer Heads", "Bilayer Tails", "Bilayer Tails", "Bilayer Heads"]}]}
1 change: 1 addition & 0 deletions tests/testJsonToProject/absorption.json
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1 change: 1 addition & 0 deletions tests/testJsonToProject/domains_custom_XY.json
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