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Merge pull request #113 from PolarizedLightFieldMicroscopy/mbl_2024
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| { | ||
| "num_iterations": 100, | ||
| "regularization_weight": 0.1, | ||
| "lr": 1e-3, | ||
| "lr_birefringence": 1e-3, | ||
| "lr_optic_axis": 1e-1, | ||
| "optimizer": "Nadam", | ||
| "datafidelity": "euler", | ||
| "regularization_fcns": [ | ||
| ["birefringence active L2", 0], | ||
| ["birefringence active negative penalty", 0], | ||
| ["birefringence mask", 1000] | ||
| ], | ||
| "nerf_mode": false, | ||
| "from_simulation": true, | ||
| "mla_rays_at_once": true, | ||
| "two_optic_axis_components": true, | ||
| "free_memory_by_del_large_arrays": false, | ||
| "save_freq": 50, | ||
| "output_posfix": "", | ||
| "notes": "" | ||
| "general": { | ||
| "num_iterations": 1000, | ||
| "save_freq": 100, | ||
| "output_directory_postfix": "", | ||
| "notes": "" | ||
| }, | ||
| "learning_rates": { | ||
| "birefringence": 1e-4, | ||
| "optic_axis": 1e-1 | ||
| }, | ||
| "regularization": { | ||
| "weight": 1.0, | ||
| "functions": [ | ||
| ["birefringence active L2", 100], | ||
| ["birefringence active negative penalty", 0] | ||
| ] | ||
| }, | ||
| "file_paths": { | ||
| "initial_volume": null, | ||
| "saved_rays": null, | ||
| "vox_indices_by_mla_idx": null, | ||
| "ret_image": null, | ||
| "azim_image": null, | ||
| "radiometry": null | ||
| }, | ||
| "schedulers": { | ||
| "birefringence": { | ||
| "type": "ReduceLROnPlateau", | ||
| "params": { | ||
| "mode": "min", | ||
| "factor": 0.8, | ||
| "patience": 5, | ||
| "threshold": 1e-6, | ||
| "min_lr": 1e-8 | ||
| } | ||
| }, | ||
| "optic_axis": { | ||
| "type": "CosineAnnealingWarmRestarts", | ||
| "params": { | ||
| "T_0": 20, | ||
| "T_mult": 2, | ||
| "eta_min": 1e-4 | ||
| } | ||
| } | ||
| }, | ||
| "visualization": { | ||
| "plot_live": true, | ||
| "fig_size": [10, 11] | ||
| }, | ||
| "learnables": { | ||
| "all_prop_elements": false, | ||
| "two_optic_axis_components": true | ||
| }, | ||
| "misc": { | ||
| "from_simulation": true, | ||
| "save_ray_geometry": true, | ||
| "optimizer": "Nadam", | ||
| "datafidelity": "euler", | ||
| "warmup_iterations": 10, | ||
| "mla_rays_at_once": true, | ||
| "free_memory_by_del_large_arrays": false | ||
| } | ||
| } |
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7 changes: 4 additions & 3 deletions
7
config/optical_config_default.json → config/optical_config.json
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,117 @@ | ||
| # Reconstruction Configuration Key Descriptions | ||
|
|
||
| This document describes the various keys and their potential values in the JSON reconstruction configuration file. | ||
|
|
||
| --- | ||
|
|
||
| ## General Settings | ||
|
|
||
| | Key | Description | Possible Values | Default | | ||
| |-----------------------------|-----------------------------------------------------------------------------|---------------------------|----------------| | ||
| | `general.num_iterations` | Number of iterations for the training or reconstruction process. | Integer (e.g., 200) | 200 | | ||
| | `general.save_freq` | Frequency for saving intermediate results (in iterations). | Integer (e.g., 100) | 100 | | ||
| | `general.output_directory_postfix` | A string appended to the output directory for easier identification. | String | `""` (empty) | | ||
| | `general.notes` | Additional notes for the configuration run. | String | `""` (empty) | | ||
|
|
||
| --- | ||
|
|
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| ## Learning Rates | ||
|
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| | Key | Description | Possible Values | Default | | ||
| |-----------------------------|-----------------------------------------------------------------------------|---------------------------|----------------| | ||
| | `learning_rates.birefringence` | Learning rate for birefringence optimization. | Float (e.g., 1e-4) | 1e-4 | | ||
| | `learning_rates.optic_axis` | Learning rate for optic axis optimization. | Float (e.g., 1e-1) | 1e-1 | | ||
|
|
||
| --- | ||
|
|
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| ## Regularization | ||
|
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| | Key | Description | Possible Values | Default | | ||
| |-----------------------------|-----------------------------------------------------------------------------|---------------------------|----------------| | ||
| | `regularization.weight` | Weight of the regularization term in the loss function. | Float (e.g., 0.5) | 0.5 | | ||
| | `regularization.functions` | List of regularization functions and their associated weights. | List (e.g., `["function_name", weight]`) | N/A | | ||
|
|
||
| --- | ||
|
|
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| ## File Paths | ||
|
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| | Key | Description | Possible Values | Default | | ||
| |-----------------------------|-----------------------------------------------------------------------------|---------------------------|----------------| | ||
| | `file_paths.initial_volume` | Filepath for the initial volume, if any. | Filepath (string) | `null` | | ||
| | `file_paths.saved_rays` | Filepath for saved rays, if any. | Filepath (string) | `null` | | ||
| | `file_paths.vox_indices_by_mla_idx` | Filepath for voxel indices mapped by MLA index. | Filepath (string) | `null` | | ||
| | `file_paths.ret_image` | Filepath for the measured retardance image. | Filepath (string) | `null` | | ||
| | `file_paths.azim_image` | Filepath for the measured azimuth image. | Filepath (string) | `null` | | ||
| | `file_paths.radiometry` | Filepath for the radiometry data. | Filepath (string) | `null` | | ||
|
|
||
| --- | ||
|
|
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| ## Schedulers | ||
|
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| | Key | Description | Possible Values | Default | | ||
| |-----------------------------|-----------------------------------------------------------------------------|---------------------------|----------------| | ||
| | `schedulers.birefringence.type` | Scheduler type for birefringence learning rate. | String (e.g., "ReduceLROnPlateau") | "ReduceLROnPlateau" | | ||
| | `schedulers.birefringence.params.mode` | Mode for scheduler, controls if the scheduler is reducing learning rates based on min/max of the loss. | `"min"`, `"max"` | `"min"` | | ||
| | `schedulers.birefringence.params.factor` | Factor by which the learning rate is reduced. | Float (e.g., 0.8) | 0.8 | | ||
| | `schedulers.birefringence.params.patience` | Number of epochs with no improvement before reducing learning rate. | Integer (e.g., 5) | 5 | | ||
| | `schedulers.birefringence.params.threshold` | Threshold for measuring new optimal value. | Float (e.g., 1e-6) | 1e-6 | | ||
| | `schedulers.birefringence.params.min_lr` | Minimum learning rate after reductions. | Float (e.g., 1e-8) | 1e-8 | | ||
| | `schedulers.optic_axis.type` | Scheduler type for optic axis learning rate. | String (e.g., "CosineAnnealingWarmRestarts") | "ReduceLROnPlateau" | | ||
| | `schedulers.optic_axis.params.T_0` | Number of iterations for the first restart cycle. | Integer (e.g., 20) | N/A | | ||
| | `schedulers.optic_axis.params.T_mult` | Multiplication factor to increase the length of each cycle. | Integer (e.g., 2) | N/A | | ||
| | `schedulers.optic_axis.params.eta_min` | Minimum learning rate during annealing. | Float (e.g., 1e-4) | N/A | | ||
|
|
||
| --- | ||
|
|
||
| ## NeRF Settings | ||
|
|
||
| | Key | Description | Possible Values | Default | | ||
| |-----------------------------|-----------------------------------------------------------------------------|---------------------------|----------------| | ||
| | `nerf.enabled` | Boolean flag to enable or disable NeRF mode. | `true`, `false` | `false` | | ||
| | `nerf.learning_rates.fc1` | Learning rate for the first NeRF fully-connected layer (fc1). | Float (e.g., 1e-2) | 1e-2 | | ||
| | `nerf.learning_rates.fc2` | Learning rate for the second NeRF fully-connected layer (fc2). | Float (e.g., 1e-4) | 1e-4 | | ||
| | `nerf.learning_rates.fc3` | Learning rate for the third NeRF fully-connected layer (fc3). | Float (e.g., 1e-4) | 1e-4 | | ||
| | `nerf.learning_rates.output` | Learning rate for the NeRF output layer. | Float (e.g., 1e-4) | 1e-4 | | ||
| | `nerf.optimizer.type` | Type of optimizer used in NeRF mode. | String (e.g., "NAdam") | `"NAdam"` | | ||
| | `nerf.optimizer.betas` | Betas for momentum terms in the NeRF optimizer. | List (e.g., `[0.9, 0.999]`) | `[0.9, 0.999]`| | ||
| | `nerf.optimizer.eps` | Epsilon value for numerical stability in NeRF optimizer. | Float (e.g., 1e-7) | 1e-7 | | ||
| | `nerf.optimizer.weight_decay` | Weight decay (L2 regularization) for the NeRF optimizer. | Float (e.g., 1e-4) | 1e-4 | | ||
| | `nerf.scheduler.type` | Scheduler type for NeRF learning rates. | String (e.g., "CosineAnnealingLR") | N/A | | ||
| | `nerf.scheduler.params` | Parameters for the NeRF scheduler. | Dictionary | N/A | | ||
| | `nerf.MLP.hidden_layers` | Hidden layers for the NeRF MLP. | List (e.g., `[256, 256, 256]`) | `[256, 256, 256]` | | ||
| | `nerf.MLP.num_frequencies` | Number of frequencies for the NeRF MLP. | Integer (e.g., 10) | 10 | | ||
| | `nerf.MLP.final_layer_bias_birefringence` | Bias for the final layer of the NeRF MLP for birefringence. | Float (e.g., -0.05) | -0.05 | | ||
| | `nerf.MLP.final_layer_weight_range` | Weight range for the final layer of the NeRF MLP for birefringence. | List (e.g., `[-0.01, 0.01]`) | `[-0.01, 0.01]` | | ||
|
|
||
| --- | ||
|
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| ## Visualization | ||
|
|
||
| | Key | Description | Possible Values | Default | | ||
| |-----------------------------|-----------------------------------------------------------------------------|---------------------------|----------------| | ||
| | `visualization.plot_live` | Boolean flag to determine whether to plot the reconstruction live. | `true`, `false` | `true` | | ||
|
|
||
| --- | ||
|
|
||
| ## Learnables | ||
|
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||
| | Key | Description | Possible Values | Default | | ||
| |-----------------------------|-----------------------------------------------------------------------------|---------------------------|----------------| | ||
| | `learnables.all_prop_elements` | Boolean flag to indicate if all properties are learned. | `true`, `false` | `false` | | ||
| | `learnables.two_optic_axis_components` | Boolean flag to indicate if two components are used for optic axis. | `true`, `false` | `true` | | ||
|
|
||
| --- | ||
|
|
||
| ## Miscellaneous Settings | ||
|
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||
| | Key | Description | Possible Values | Default | | ||
| |-----------------------------|-----------------------------------------------------------------------------|---------------------------|----------------| | ||
| | `misc.from_simulation` | Boolean flag to indicate if data comes from simulation or real-world measurements. | `true`, `false` | `false` | | ||
| | `misc.save_ray_geometry` | Boolean flag to determine whether to save the ray geometry. | `true`, `false` | `false` | | ||
| | `misc.optimizer` | Type of optimizer used for training or reconstruction. | String (e.g., "Nadam") | `"Nadam"` | | ||
| | `misc.datafidelity` | Term used in the loss function for data fidelity. | String (e.g., "euler") | `"euler"` | | ||
| | `misc.mla_rays_at_once` | Boolean flag to process MLA rays in batches. | `true`, `false` | `true` | | ||
| | `misc.free_memory_by_del_large_arrays` | Boolean flag to free memory by deleting large arrays when possible. | `true`, `false` | `false` | | ||
| | `misc.save_to_logfile` | Boolean flag to determine whether to save the output to a logfile. | `true`, `false` | `true` | | ||
|
|
||
| --- |
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