Fix custom file issue and other bugs (#210)

Author: StephenNneji

examples/DSPC_custom_XY/project.json

@@ -1 +1 @@
-{"name": "", "calculation": "domains", "model": "custom xy", "geometry": "substrate/liquid", "absorption": false, "parameters": [{"name": "Substrate Roughness", "min": 1.0, "value": 3.0, "max": 5.0, "fit": true, "prior_type": "uniform", "mu": 0.0, "sigma": Infinity, "show_priors": false}, {"name": "Oxide Thickness", "min": 10.0, "value": 20.0, "max": 50.0, "fit": true, "prior_type": "uniform", "mu": 0.0, "sigma": Infinity, "show_priors": false}, {"name": "Layer Thickness", "min": 1.0, "value": 30.0, "max": 500.0, "fit": true, "prior_type": "uniform", "mu": 0.0, "sigma": Infinity, "show_priors": false}, {"name": "Layer SLD", "min": -5e-07, "value": -5e-07, "max": 0.0, "fit": true, "prior_type": "uniform", "mu": 0.0, "sigma": Infinity, "show_priors": false}, {"name": "Layer Roughness", "min": 2.0, "value": 5.0, "max": 7.0, "fit": true, "prior_type": "uniform", "mu": 0.0, "sigma": Infinity, "show_priors": false}, {"name": "Domain SLD", "min": 1e-06, "value": 1e-06, "max": 5e-06, "fit": true, "prior_type": "uniform", "mu": 0.0, "sigma": Infinity, "show_priors": false}], "bulk_in": [{"name": "Silicon", "min": 0.0, "value": 2.073e-06, "max": 1.0, "fit": false, "prior_type": "uniform", "mu": 0.0, "sigma": Infinity, "show_priors": false}], "bulk_out": [{"name": "SLD D2O", "min": 6.2e-06, "value": 6.35e-06, "max": 6.35e-06, "fit": false, "prior_type": "uniform", "mu": 0.0, "sigma": Infinity, "show_priors": false}, {"name": "SLD SMW", "min": 2e-06, "value": 2.073e-06, "max": 2.1e-06, "fit": false, "prior_type": "uniform", "mu": 0.0, "sigma": Infinity, "show_priors": false}, {"name": "SLD H2O", "min": -6e-07, "value": -5.6e-07, "max": -5e-07, "fit": false, "prior_type": "uniform", "mu": 0.0, "sigma": Infinity, "show_priors": false}], "scalefactors": [{"name": "Scalefactor 1", "min": 0.8, "value": 1.0, "max": 1.1, "fit": true, "prior_type": "uniform", "mu": 0.0, "sigma": Infinity, "show_priors": false}], "domain_ratios": [{"name": "Domain Ratio 1", "min": 0.4, "value": 0.5, "max": 0.6, "fit": false, "prior_type": "uniform", "mu": 0.0, "sigma": Infinity, "show_priors": false}], "background_parameters": [{"name": "Background Param 1", "min": 1e-07, "value": 1e-06, "max": 1e-05, "fit": false, "prior_type": "uniform", "mu": 0.0, "sigma": Infinity, "show_priors": false}], "backgrounds": [{"name": "Background 1", "type": "constant", "source": "Background Param 1", "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": [{"name": "Domain Layer", "filename": "domains_XY_model.py", "language": "python", "path": ".", "function_name": "domains_XY_model"}], "data": [{"name": "Simulation", "data": [], "data_range": [], "simulation_range": [0.005, 0.7]}], "layers": [], "domain_contrasts": [], "contrasts": [{"name": "D2O", "data": "Simulation", "background": "Background 1", "background_action": "add", "bulk_in": "Silicon", "bulk_out": "SLD D2O", "scalefactor": "Scalefactor 1", "resolution": "Resolution 1", "resample": true, "repeat_layers": 1, "domain_ratio": "Domain Ratio 1", "model": ["Domain Layer"]}, {"name": "SMW", "data": "Simulation", "background": "Background 1", "background_action": "add", "bulk_in": "Silicon", "bulk_out": "SLD SMW", "scalefactor": "Scalefactor 1", "resolution": "Resolution 1", "resample": true, "repeat_layers": 1, "domain_ratio": "Domain Ratio 1", "model": ["Domain Layer"]}, {"name": "H2O", "data": "Simulation", "background": "Background 1", "background_action": "add", "bulk_in": "Silicon", "bulk_out": "SLD H2O", "scalefactor": "Scalefactor 1", "resolution": "Resolution 1", "resample": true, "repeat_layers": 1, "domain_ratio": "Domain Ratio 1", "model": ["Domain Layer"]}]}
+{"name": "Domain Custom XY", "calculation": "domains", "model": "custom xy", "geometry": "substrate/liquid", "absorption": false, "parameters": [{"name": "Substrate Roughness", "min": 1.0, "value": 3.0, "max": 5.0, "fit": true, "prior_type": "uniform", "mu": 0.0, "sigma": Infinity, "show_priors": false}, {"name": "Oxide Thickness", "min": 10.0, "value": 20.0, "max": 50.0, "fit": true, "prior_type": "uniform", "mu": 0.0, "sigma": Infinity, "show_priors": false}, {"name": "Layer Thickness", "min": 1.0, "value": 30.0, "max": 500.0, "fit": true, "prior_type": "uniform", "mu": 0.0, "sigma": Infinity, "show_priors": false}, {"name": "Layer SLD", "min": -5e-07, "value": -5e-07, "max": 0.0, "fit": true, "prior_type": "uniform", "mu": 0.0, "sigma": Infinity, "show_priors": false}, {"name": "Layer Roughness", "min": 2.0, "value": 5.0, "max": 7.0, "fit": true, "prior_type": "uniform", "mu": 0.0, "sigma": Infinity, "show_priors": false}, {"name": "Domain SLD", "min": 1e-06, "value": 1e-06, "max": 5e-06, "fit": true, "prior_type": "uniform", "mu": 0.0, "sigma": Infinity, "show_priors": false}], "bulk_in": [{"name": "Silicon", "min": 0.0, "value": 2.073e-06, "max": 1.0, "fit": false, "prior_type": "uniform", "mu": 0.0, "sigma": Infinity, "show_priors": false}], "bulk_out": [{"name": "SLD D2O", "min": 6.2e-06, "value": 6.35e-06, "max": 6.35e-06, "fit": false, "prior_type": "uniform", "mu": 0.0, "sigma": Infinity, "show_priors": false}, {"name": "SLD SMW", "min": 2e-06, "value": 2.073e-06, "max": 2.1e-06, "fit": false, "prior_type": "uniform", "mu": 0.0, "sigma": Infinity, "show_priors": false}, {"name": "SLD H2O", "min": -6e-07, "value": -5.6e-07, "max": -5e-07, "fit": false, "prior_type": "uniform", "mu": 0.0, "sigma": Infinity, "show_priors": false}], "scalefactors": [{"name": "Scalefactor 1", "min": 0.8, "value": 1.0, "max": 1.1, "fit": true, "prior_type": "uniform", "mu": 0.0, "sigma": Infinity, "show_priors": false}], "domain_ratios": [{"name": "Domain Ratio 1", "min": 0.4, "value": 0.5, "max": 0.6, "fit": false, "prior_type": "uniform", "mu": 0.0, "sigma": Infinity, "show_priors": false}], "background_parameters": [{"name": "Background Param 1", "min": 1e-07, "value": 1e-06, "max": 1e-05, "fit": false, "prior_type": "uniform", "mu": 0.0, "sigma": Infinity, "show_priors": false}], "backgrounds": [{"name": "Background 1", "type": "constant", "source": "Background Param 1", "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": [{"name": "Domain Layer", "filename": "domains_XY_model.py", "language": "python", "path": ".", "function_name": "domains_XY_model"}], "data": [{"name": "Simulation", "data": [], "data_range": [], "simulation_range": [0.005, 0.7]}], "layers": [], "domain_contrasts": [], "contrasts": [{"name": "D2O", "data": "Simulation", "background": "Background 1", "background_action": "add", "bulk_in": "Silicon", "bulk_out": "SLD D2O", "scalefactor": "Scalefactor 1", "resolution": "Resolution 1", "resample": true, "repeat_layers": 1, "domain_ratio": "Domain Ratio 1", "model": ["Domain Layer"]}, {"name": "SMW", "data": "Simulation", "background": "Background 1", "background_action": "add", "bulk_in": "Silicon", "bulk_out": "SLD SMW", "scalefactor": "Scalefactor 1", "resolution": "Resolution 1", "resample": true, "repeat_layers": 1, "domain_ratio": "Domain Ratio 1", "model": ["Domain Layer"]}, {"name": "H2O", "data": "Simulation", "background": "Background 1", "background_action": "add", "bulk_in": "Silicon", "bulk_out": "SLD H2O", "scalefactor": "Scalefactor 1", "resolution": "Resolution 1", "resample": true, "repeat_layers": 1, "domain_ratio": "Domain Ratio 1", "model": ["Domain Layer"]}]}

examples/DSPC_custom_layers/project.json

@@ -1 +1 @@
-{"name": "", "calculation": "domains", "model": "custom layers", "geometry": "substrate/liquid", "absorption": false, "parameters": [{"name": "Substrate Roughness", "min": 1.0, "value": 3.0, "max": 5.0, "fit": true, "prior_type": "uniform", "mu": 0.0, "sigma": Infinity, "show_priors": false}, {"name": "Alloy Thickness", "min": 100.0, "value": 150.0, "max": 200.0, "fit": true, "prior_type": "uniform", "mu": 0.0, "sigma": Infinity, "show_priors": false}, {"name": "Alloy SLD up", "min": 9e-06, "value": 1.1e-05, "max": 1.3e-05, "fit": true, "prior_type": "uniform", "mu": 0.0, "sigma": Infinity, "show_priors": false}, {"name": "Alloy SLD down", "min": 5e-06, "value": 7e-06, "max": 1e-05, "fit": true, "prior_type": "uniform", "mu": 0.0, "sigma": Infinity, "show_priors": false}, {"name": "Alloy Roughness", "min": 5.0, "value": 7.0, "max": 11.0, "fit": true, "prior_type": "uniform", "mu": 0.0, "sigma": Infinity, "show_priors": false}, {"name": "Gold Thickness", "min": 100.0, "value": 150.0, "max": 200.0, "fit": true, "prior_type": "uniform", "mu": 0.0, "sigma": Infinity, "show_priors": false}, {"name": "Gold SLD", "min": 4e-06, "value": 4.5e-06, "max": 5e-06, "fit": true, "prior_type": "uniform", "mu": 0.0, "sigma": Infinity, "show_priors": false}, {"name": "Gold Roughness", "min": 5.0, "value": 7.0, "max": 11.0, "fit": true, "prior_type": "uniform", "mu": 0.0, "sigma": Infinity, "show_priors": false}], "bulk_in": [{"name": "Silicon", "min": 0.0, "value": 2.073e-06, "max": 1.0, "fit": false, "prior_type": "uniform", "mu": 0.0, "sigma": Infinity, "show_priors": false}], "bulk_out": [{"name": "SLD D2O", "min": 6.2e-06, "value": 6.35e-06, "max": 6.35e-06, "fit": false, "prior_type": "uniform", "mu": 0.0, "sigma": Infinity, "show_priors": false}], "scalefactors": [{"name": "Scalefactor 1", "min": 0.02, "value": 0.23, "max": 0.25, "fit": false, "prior_type": "uniform", "mu": 0.0, "sigma": Infinity, "show_priors": false}], "domain_ratios": [{"name": "Domain Ratio 1", "min": 0.4, "value": 0.5, "max": 0.6, "fit": false, "prior_type": "uniform", "mu": 0.0, "sigma": Infinity, "show_priors": false}], "background_parameters": [{"name": "Background Param 1", "min": 1e-07, "value": 1e-06, "max": 1e-05, "fit": false, "prior_type": "uniform", "mu": 0.0, "sigma": Infinity, "show_priors": false}], "backgrounds": [{"name": "Background 1", "type": "constant", "source": "Background Param 1", "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": [{"name": "Alloy domains", "filename": "alloy_domains.py", "language": "python", "path": ".", "function_name": "alloy_domains"}], "data": [{"name": "Simulation", "data": [], "data_range": [], "simulation_range": [0.005, 0.7]}], "layers": [], "domain_contrasts": [], "contrasts": [{"name": "D2O Contrast", "data": "Simulation", "background": "Background 1", "background_action": "add", "bulk_in": "Silicon", "bulk_out": "SLD D2O", "scalefactor": "Scalefactor 1", "resolution": "Resolution 1", "resample": false, "repeat_layers": 1, "domain_ratio": "Domain Ratio 1", "model": ["Alloy domains"]}]}
+{"name": "Domain Custom Layers", "calculation": "domains", "model": "custom layers", "geometry": "substrate/liquid", "absorption": false, "parameters": [{"name": "Substrate Roughness", "min": 1.0, "value": 3.0, "max": 5.0, "fit": true, "prior_type": "uniform", "mu": 0.0, "sigma": Infinity, "show_priors": false}, {"name": "Alloy Thickness", "min": 100.0, "value": 150.0, "max": 200.0, "fit": true, "prior_type": "uniform", "mu": 0.0, "sigma": Infinity, "show_priors": false}, {"name": "Alloy SLD up", "min": 9e-06, "value": 1.1e-05, "max": 1.3e-05, "fit": true, "prior_type": "uniform", "mu": 0.0, "sigma": Infinity, "show_priors": false}, {"name": "Alloy SLD down", "min": 5e-06, "value": 7e-06, "max": 1e-05, "fit": true, "prior_type": "uniform", "mu": 0.0, "sigma": Infinity, "show_priors": false}, {"name": "Alloy Roughness", "min": 5.0, "value": 7.0, "max": 11.0, "fit": true, "prior_type": "uniform", "mu": 0.0, "sigma": Infinity, "show_priors": false}, {"name": "Gold Thickness", "min": 100.0, "value": 150.0, "max": 200.0, "fit": true, "prior_type": "uniform", "mu": 0.0, "sigma": Infinity, "show_priors": false}, {"name": "Gold SLD", "min": 4e-06, "value": 4.5e-06, "max": 5e-06, "fit": true, "prior_type": "uniform", "mu": 0.0, "sigma": Infinity, "show_priors": false}, {"name": "Gold Roughness", "min": 5.0, "value": 7.0, "max": 11.0, "fit": true, "prior_type": "uniform", "mu": 0.0, "sigma": Infinity, "show_priors": false}], "bulk_in": [{"name": "Silicon", "min": 0.0, "value": 2.073e-06, "max": 1.0, "fit": false, "prior_type": "uniform", "mu": 0.0, "sigma": Infinity, "show_priors": false}], "bulk_out": [{"name": "SLD D2O", "min": 6.2e-06, "value": 6.35e-06, "max": 6.35e-06, "fit": false, "prior_type": "uniform", "mu": 0.0, "sigma": Infinity, "show_priors": false}], "scalefactors": [{"name": "Scalefactor 1", "min": 0.02, "value": 0.23, "max": 0.25, "fit": false, "prior_type": "uniform", "mu": 0.0, "sigma": Infinity, "show_priors": false}], "domain_ratios": [{"name": "Domain Ratio 1", "min": 0.4, "value": 0.5, "max": 0.6, "fit": false, "prior_type": "uniform", "mu": 0.0, "sigma": Infinity, "show_priors": false}], "background_parameters": [{"name": "Background Param 1", "min": 1e-07, "value": 1e-06, "max": 1e-05, "fit": false, "prior_type": "uniform", "mu": 0.0, "sigma": Infinity, "show_priors": false}], "backgrounds": [{"name": "Background 1", "type": "constant", "source": "Background Param 1", "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": [{"name": "Alloy domains", "filename": "alloy_domains.py", "language": "python", "path": ".", "function_name": "alloy_domains"}], "data": [{"name": "Simulation", "data": [], "data_range": [], "simulation_range": [0.005, 0.7]}], "layers": [], "domain_contrasts": [], "contrasts": [{"name": "D2O Contrast", "data": "Simulation", "background": "Background 1", "background_action": "add", "bulk_in": "Silicon", "bulk_out": "SLD D2O", "scalefactor": "Scalefactor 1", "resolution": "Resolution 1", "resample": false, "repeat_layers": 1, "domain_ratio": "Domain Ratio 1", "model": ["Alloy domains"]}]}