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Fix custom file issue and other bugs #210

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Merged
StephenNneji merged 9 commits into from
Mar 11, 2026
+430 −117
Merged

Fix custom file issue and other bugs #210

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6ff6f54
another test
StephenNneji Jan 26, 2026
44c17c4
hhh
StephenNneji Jan 27, 2026
3ddd35b
copy
StephenNneji Feb 11, 2026
b92ab73
refactors
StephenNneji Feb 13, 2026
8c9bc09
Custom file table button rework, refactors global settings, and adds …
StephenNneji Mar 5, 2026
7005951
prevent saving to file when editing project
StephenNneji Mar 5, 2026
7c1dde4
Handle unicode error
StephenNneji Mar 6, 2026
c7c456e
Addresses review comments
StephenNneji Mar 10, 2026
173b617
update ratapi to dev13
StephenNneji Mar 11, 2026
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2 changes: 1 addition & 1 deletion examples/DSPC_custom_XY/project.json
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2 changes: 1 addition & 1 deletion examples/DSPC_custom_layers/project.json
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2 changes: 1 addition & 1 deletion examples/DSPC_standard_layers/project.json
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2 changes: 1 addition & 1 deletion examples/absorption/project.json
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2 changes: 1 addition & 1 deletion examples/domains_custom_XY/project.json
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{"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"]}]}
2 changes: 1 addition & 1 deletion examples/domains_custom_layers/project.json
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{"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"]}]}
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