reflectorch 1.4.0__py3-none-any.whl → 1.5.0__py3-none-any.whl
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- reflectorch/__init__.py +17 -17
- reflectorch/data_generation/__init__.py +128 -128
- reflectorch/data_generation/dataset.py +210 -210
- reflectorch/data_generation/likelihoods.py +80 -80
- reflectorch/data_generation/noise.py +470 -470
- reflectorch/data_generation/priors/__init__.py +60 -60
- reflectorch/data_generation/priors/base.py +55 -55
- reflectorch/data_generation/priors/exp_subprior_sampler.py +298 -298
- reflectorch/data_generation/priors/independent_priors.py +195 -195
- reflectorch/data_generation/priors/multilayer_models.py +311 -311
- reflectorch/data_generation/priors/multilayer_structures.py +104 -104
- reflectorch/data_generation/priors/no_constraints.py +206 -206
- reflectorch/data_generation/priors/parametric_models.py +841 -841
- reflectorch/data_generation/priors/parametric_subpriors.py +369 -369
- reflectorch/data_generation/priors/params.py +252 -252
- reflectorch/data_generation/priors/sampler_strategies.py +369 -369
- reflectorch/data_generation/priors/scaler_mixin.py +65 -65
- reflectorch/data_generation/priors/subprior_sampler.py +371 -371
- reflectorch/data_generation/priors/utils.py +118 -118
- reflectorch/data_generation/process_data.py +41 -41
- reflectorch/data_generation/q_generator.py +280 -280
- reflectorch/data_generation/reflectivity/__init__.py +102 -102
- reflectorch/data_generation/reflectivity/abeles.py +97 -97
- reflectorch/data_generation/reflectivity/kinematical.py +70 -70
- reflectorch/data_generation/reflectivity/memory_eff.py +105 -105
- reflectorch/data_generation/reflectivity/numpy_implementations.py +120 -120
- reflectorch/data_generation/reflectivity/smearing.py +138 -138
- reflectorch/data_generation/reflectivity/smearing_pointwise.py +109 -109
- reflectorch/data_generation/scale_curves.py +112 -112
- reflectorch/data_generation/smearing.py +98 -98
- reflectorch/data_generation/utils.py +223 -223
- reflectorch/extensions/jupyter/__init__.py +11 -6
- reflectorch/extensions/jupyter/api.py +85 -0
- reflectorch/extensions/jupyter/callbacks.py +34 -34
- reflectorch/extensions/jupyter/components.py +758 -0
- reflectorch/extensions/jupyter/custom_select.py +268 -0
- reflectorch/extensions/jupyter/log_widget.py +241 -0
- reflectorch/extensions/jupyter/model_selection.py +495 -0
- reflectorch/extensions/jupyter/plotly_plot_manager.py +329 -0
- reflectorch/extensions/jupyter/widget.py +625 -0
- reflectorch/extensions/matplotlib/__init__.py +5 -5
- reflectorch/extensions/matplotlib/losses.py +32 -32
- reflectorch/extensions/refnx/refnx_conversion.py +76 -76
- reflectorch/inference/__init__.py +28 -24
- reflectorch/inference/inference_model.py +847 -1374
- reflectorch/inference/input_interface.py +239 -0
- reflectorch/inference/loading_data.py +36 -36
- reflectorch/inference/multilayer_fitter.py +171 -171
- reflectorch/inference/multilayer_inference_model.py +193 -193
- reflectorch/inference/plotting.py +523 -516
- reflectorch/inference/preprocess_exp/__init__.py +6 -6
- reflectorch/inference/preprocess_exp/attenuation.py +36 -36
- reflectorch/inference/preprocess_exp/cut_with_q_ratio.py +31 -31
- reflectorch/inference/preprocess_exp/footprint.py +81 -81
- reflectorch/inference/preprocess_exp/interpolation.py +19 -19
- reflectorch/inference/preprocess_exp/normalize.py +21 -21
- reflectorch/inference/preprocess_exp/preprocess.py +121 -121
- reflectorch/inference/query_matcher.py +81 -81
- reflectorch/inference/record_time.py +43 -43
- reflectorch/inference/sampler_solution.py +56 -56
- reflectorch/inference/scipy_fitter.py +272 -262
- reflectorch/inference/torch_fitter.py +87 -87
- reflectorch/ml/__init__.py +32 -32
- reflectorch/ml/basic_trainer.py +292 -292
- reflectorch/ml/callbacks.py +80 -80
- reflectorch/ml/dataloaders.py +26 -26
- reflectorch/ml/loggers.py +55 -55
- reflectorch/ml/schedulers.py +355 -355
- reflectorch/ml/trainers.py +200 -200
- reflectorch/ml/utils.py +2 -2
- reflectorch/models/__init__.py +15 -15
- reflectorch/models/activations.py +50 -50
- reflectorch/models/encoders/__init__.py +19 -19
- reflectorch/models/encoders/conv_encoder.py +218 -218
- reflectorch/models/encoders/conv_res_net.py +115 -115
- reflectorch/models/encoders/fno.py +133 -133
- reflectorch/models/encoders/integral_kernel_embedding.py +389 -389
- reflectorch/models/networks/__init__.py +14 -14
- reflectorch/models/networks/mlp_networks.py +434 -434
- reflectorch/models/networks/residual_net.py +156 -156
- reflectorch/paths.py +29 -27
- reflectorch/runs/__init__.py +31 -31
- reflectorch/runs/config.py +25 -25
- reflectorch/runs/slurm_utils.py +93 -93
- reflectorch/runs/train.py +78 -78
- reflectorch/runs/utils.py +404 -404
- reflectorch/test_config.py +4 -4
- reflectorch/train.py +4 -4
- reflectorch/train_on_cluster.py +4 -4
- reflectorch/utils.py +97 -97
- {reflectorch-1.4.0.dist-info → reflectorch-1.5.0.dist-info}/METADATA +129 -126
- reflectorch-1.5.0.dist-info/RECORD +96 -0
- {reflectorch-1.4.0.dist-info → reflectorch-1.5.0.dist-info}/licenses/LICENSE.txt +20 -20
- reflectorch-1.4.0.dist-info/RECORD +0 -88
- {reflectorch-1.4.0.dist-info → reflectorch-1.5.0.dist-info}/WHEEL +0 -0
- {reflectorch-1.4.0.dist-info → reflectorch-1.5.0.dist-info}/top_level.txt +0 -0
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from typing import Tuple
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import torch
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from torch import Tensor
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__all__ = [
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"MULTILAYER_MODELS",
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"MultilayerModel",
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]
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class MultilayerModel(object):
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NAME: str = ''
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PARAMETER_NAMES: Tuple[str, ...]
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def __init__(self, max_num_layers: int):
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self.max_num_layers = max_num_layers
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def to_standard_params(self, parametrized_model: Tensor) -> dict:
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raise NotImplementedError
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def from_standard_params(self, params: dict) -> Tensor:
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class BasicMultilayerModel1(MultilayerModel):
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NAME = 'repeating_multilayer_v1'
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PARAMETER_NAMES = (
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"d_full_rel",
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"rel_sigmas",
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"d_block",
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"s_block_rel",
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"r_block",
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"dr",
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"d3_rel",
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"s3_rel",
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"r3",
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"d_sio2",
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"s_sio2",
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"s_si",
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"r_sio2",
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"r_si",
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)
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def to_standard_params(self, parametrized_model: Tensor) -> dict:
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return multilayer_model1(parametrized_model, self.max_num_layers)
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class BasicMultilayerModel2(MultilayerModel):
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NAME = 'repeating_multilayer_v2'
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PARAMETER_NAMES = (
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"d_full_rel",
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"rel_sigmas",
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"dr_sigmoid_rel_pos",
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"dr_sigmoid_rel_width",
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"d_block",
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"s_block_rel",
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"dr",
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"d3_rel",
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"s3_rel",
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"r3",
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"d_sio2",
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"s_sio2",
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"s_si",
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"r_sio2",
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"r_si",
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def to_standard_params(self, parametrized_model: Tensor) -> dict:
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return multilayer_model2(parametrized_model, self.max_num_layers)
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class BasicMultilayerModel3(MultilayerModel):
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NAME = 'repeating_multilayer_v3'
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PARAMETER_NAMES = (
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"d_full_rel",
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"rel_sigmas",
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"dr_sigmoid_rel_pos",
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"dr_sigmoid_rel_width",
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"d_block1_rel",
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"d_block",
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"s_block_rel",
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"r_block",
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"dr",
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"d3_rel",
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"s3_rel",
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"r3",
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"d_sio2",
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"s_sio2",
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"s_si",
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def to_standard_params(self, parametrized_model: Tensor) -> dict:
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return multilayer_model3(parametrized_model, self.max_num_layers)
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MULTILAYER_MODELS = {
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'repeating_multilayer_v1': BasicMultilayerModel1,
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'repeating_multilayer_v2': BasicMultilayerModel2,
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'repeating_multilayer_v3': BasicMultilayerModel3,
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}
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def multilayer_model1(parametrized_model: Tensor, d_full_rel_max: int = 50) -> dict:
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(
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d_full_rel,
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d_block,
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s_block_rel,
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dr,
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r3,
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) = parametrized_model.T
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batch_size = parametrized_model.shape[0]
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r_positions = 2 * n - torch.arange(2 * n, dtype=dr.dtype, device=dr.device)[None].repeat(batch_size, 1)
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r_modulations = torch.sigmoid(-(r_positions - 2 * d_full_rel[..., None]) / rel_sigmas[..., None])
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r_block = r_block[:, None].repeat(1, n)
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dr = dr[:, None].repeat(1, n)
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sld_blocks = torch.stack([r_block, r_block + dr], -1).flatten(1)
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sld_blocks = r_modulations * sld_blocks
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thicknesses = torch.cat(
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s_block = s_block_rel * d_block
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roughnesses = torch.cat(
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params = dict(
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return params
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def multilayer_model2(parametrized_model: Tensor, d_full_rel_max: int = 50) -> dict:
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thickness_blocks = torch.stack([d1[:, None].repeat(1, n), d2[:, None].repeat(1, n)], -1).flatten(1)
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return params
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from typing import Tuple
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import torch
|
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from torch import Tensor
|
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+
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__all__ = [
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"MULTILAYER_MODELS",
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"MultilayerModel",
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9
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]
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+
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11
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+
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class MultilayerModel(object):
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NAME: str = ''
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PARAMETER_NAMES: Tuple[str, ...]
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15
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+
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def __init__(self, max_num_layers: int):
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self.max_num_layers = max_num_layers
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+
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+
def to_standard_params(self, parametrized_model: Tensor) -> dict:
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raise NotImplementedError
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+
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def from_standard_params(self, params: dict) -> Tensor:
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raise NotImplementedError
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+
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+
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class BasicMultilayerModel1(MultilayerModel):
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NAME = 'repeating_multilayer_v1'
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28
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+
|
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29
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+
PARAMETER_NAMES = (
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+
"d_full_rel",
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31
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+
"rel_sigmas",
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32
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+
"d_block",
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33
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+
"s_block_rel",
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34
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+
"r_block",
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35
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+
"dr",
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36
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+
"d3_rel",
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37
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+
"s3_rel",
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38
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+
"r3",
|
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39
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+
"d_sio2",
|
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40
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+
"s_sio2",
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41
|
+
"s_si",
|
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42
|
+
"r_sio2",
|
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43
|
+
"r_si",
|
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44
|
+
)
|
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45
|
+
|
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46
|
+
def to_standard_params(self, parametrized_model: Tensor) -> dict:
|
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47
|
+
return multilayer_model1(parametrized_model, self.max_num_layers)
|
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48
|
+
|
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49
|
+
|
|
50
|
+
class BasicMultilayerModel2(MultilayerModel):
|
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51
|
+
NAME = 'repeating_multilayer_v2'
|
|
52
|
+
|
|
53
|
+
PARAMETER_NAMES = (
|
|
54
|
+
"d_full_rel",
|
|
55
|
+
"rel_sigmas",
|
|
56
|
+
"dr_sigmoid_rel_pos",
|
|
57
|
+
"dr_sigmoid_rel_width",
|
|
58
|
+
"d_block",
|
|
59
|
+
"s_block_rel",
|
|
60
|
+
"r_block",
|
|
61
|
+
"dr",
|
|
62
|
+
"d3_rel",
|
|
63
|
+
"s3_rel",
|
|
64
|
+
"r3",
|
|
65
|
+
"d_sio2",
|
|
66
|
+
"s_sio2",
|
|
67
|
+
"s_si",
|
|
68
|
+
"r_sio2",
|
|
69
|
+
"r_si",
|
|
70
|
+
)
|
|
71
|
+
|
|
72
|
+
def to_standard_params(self, parametrized_model: Tensor) -> dict:
|
|
73
|
+
return multilayer_model2(parametrized_model, self.max_num_layers)
|
|
74
|
+
|
|
75
|
+
|
|
76
|
+
class BasicMultilayerModel3(MultilayerModel):
|
|
77
|
+
NAME = 'repeating_multilayer_v3'
|
|
78
|
+
|
|
79
|
+
PARAMETER_NAMES = (
|
|
80
|
+
"d_full_rel",
|
|
81
|
+
"rel_sigmas",
|
|
82
|
+
"dr_sigmoid_rel_pos",
|
|
83
|
+
"dr_sigmoid_rel_width",
|
|
84
|
+
"d_block1_rel",
|
|
85
|
+
"d_block",
|
|
86
|
+
"s_block_rel",
|
|
87
|
+
"r_block",
|
|
88
|
+
"dr",
|
|
89
|
+
"d3_rel",
|
|
90
|
+
"s3_rel",
|
|
91
|
+
"r3",
|
|
92
|
+
"d_sio2",
|
|
93
|
+
"s_sio2",
|
|
94
|
+
"s_si",
|
|
95
|
+
"r_sio2",
|
|
96
|
+
"r_si",
|
|
97
|
+
)
|
|
98
|
+
|
|
99
|
+
def to_standard_params(self, parametrized_model: Tensor) -> dict:
|
|
100
|
+
return multilayer_model3(parametrized_model, self.max_num_layers)
|
|
101
|
+
|
|
102
|
+
|
|
103
|
+
MULTILAYER_MODELS = {
|
|
104
|
+
'repeating_multilayer_v1': BasicMultilayerModel1,
|
|
105
|
+
'repeating_multilayer_v2': BasicMultilayerModel2,
|
|
106
|
+
'repeating_multilayer_v3': BasicMultilayerModel3,
|
|
107
|
+
}
|
|
108
|
+
|
|
109
|
+
|
|
110
|
+
def multilayer_model1(parametrized_model: Tensor, d_full_rel_max: int = 50) -> dict:
|
|
111
|
+
n = d_full_rel_max
|
|
112
|
+
|
|
113
|
+
(
|
|
114
|
+
d_full_rel,
|
|
115
|
+
rel_sigmas,
|
|
116
|
+
d_block,
|
|
117
|
+
s_block_rel,
|
|
118
|
+
r_block,
|
|
119
|
+
dr,
|
|
120
|
+
d3_rel,
|
|
121
|
+
s3_rel,
|
|
122
|
+
r3,
|
|
123
|
+
d_sio2,
|
|
124
|
+
s_sio2,
|
|
125
|
+
s_si,
|
|
126
|
+
r_sio2,
|
|
127
|
+
r_si,
|
|
128
|
+
) = parametrized_model.T
|
|
129
|
+
|
|
130
|
+
batch_size = parametrized_model.shape[0]
|
|
131
|
+
|
|
132
|
+
r_positions = 2 * n - torch.arange(2 * n, dtype=dr.dtype, device=dr.device)[None].repeat(batch_size, 1)
|
|
133
|
+
|
|
134
|
+
r_modulations = torch.sigmoid(-(r_positions - 2 * d_full_rel[..., None]) / rel_sigmas[..., None])
|
|
135
|
+
|
|
136
|
+
r_block = r_block[:, None].repeat(1, n)
|
|
137
|
+
dr = dr[:, None].repeat(1, n)
|
|
138
|
+
|
|
139
|
+
sld_blocks = torch.stack([r_block, r_block + dr], -1).flatten(1)
|
|
140
|
+
|
|
141
|
+
sld_blocks = r_modulations * sld_blocks
|
|
142
|
+
|
|
143
|
+
d3 = d3_rel * d_block
|
|
144
|
+
|
|
145
|
+
thicknesses = torch.cat(
|
|
146
|
+
[(d_block / 2)[:, None].repeat(1, n * 2), d3[:, None], d_sio2[:, None]], -1
|
|
147
|
+
)
|
|
148
|
+
|
|
149
|
+
s_block = s_block_rel * d_block
|
|
150
|
+
|
|
151
|
+
roughnesses = torch.cat(
|
|
152
|
+
[s_block[:, None].repeat(1, n * 2), (s3_rel * d3)[:, None], s_sio2[:, None], s_si[:, None]], -1
|
|
153
|
+
)
|
|
154
|
+
|
|
155
|
+
slds = torch.cat(
|
|
156
|
+
[sld_blocks, r3[:, None], r_sio2[:, None], r_si[:, None]], -1
|
|
157
|
+
)
|
|
158
|
+
|
|
159
|
+
params = dict(
|
|
160
|
+
thicknesses=thicknesses,
|
|
161
|
+
roughnesses=roughnesses,
|
|
162
|
+
slds=slds
|
|
163
|
+
)
|
|
164
|
+
return params
|
|
165
|
+
|
|
166
|
+
|
|
167
|
+
def multilayer_model2(parametrized_model: Tensor, d_full_rel_max: int = 50) -> dict:
|
|
168
|
+
n = d_full_rel_max
|
|
169
|
+
|
|
170
|
+
(
|
|
171
|
+
d_full_rel,
|
|
172
|
+
rel_sigmas,
|
|
173
|
+
dr_sigmoid_rel_pos,
|
|
174
|
+
dr_sigmoid_rel_width,
|
|
175
|
+
d_block,
|
|
176
|
+
s_block_rel,
|
|
177
|
+
r_block,
|
|
178
|
+
dr,
|
|
179
|
+
d3_rel,
|
|
180
|
+
s3_rel,
|
|
181
|
+
r3,
|
|
182
|
+
d_sio2,
|
|
183
|
+
s_sio2,
|
|
184
|
+
s_si,
|
|
185
|
+
r_sio2,
|
|
186
|
+
r_si,
|
|
187
|
+
) = parametrized_model.T
|
|
188
|
+
|
|
189
|
+
batch_size = parametrized_model.shape[0]
|
|
190
|
+
|
|
191
|
+
r_positions = 2 * n - torch.arange(2 * n, dtype=dr.dtype, device=dr.device)[None].repeat(batch_size, 1)
|
|
192
|
+
|
|
193
|
+
r_modulations = torch.sigmoid(-(r_positions - 2 * d_full_rel[..., None]) / rel_sigmas[..., None])
|
|
194
|
+
|
|
195
|
+
r_block = r_block[:, None].repeat(1, n)
|
|
196
|
+
dr = dr[:, None].repeat(1, n)
|
|
197
|
+
|
|
198
|
+
dr_positions = r_positions[:, ::2]
|
|
199
|
+
|
|
200
|
+
dr_modulations = torch.sigmoid(
|
|
201
|
+
-(dr_positions - (2 * d_full_rel * dr_sigmoid_rel_pos)[..., None]) / dr_sigmoid_rel_width[..., None]
|
|
202
|
+
)
|
|
203
|
+
|
|
204
|
+
dr = dr * dr_modulations
|
|
205
|
+
|
|
206
|
+
sld_blocks = torch.stack([r_block, r_block + dr], -1).flatten(1)
|
|
207
|
+
|
|
208
|
+
sld_blocks = r_modulations * sld_blocks
|
|
209
|
+
|
|
210
|
+
d3 = d3_rel * d_block
|
|
211
|
+
|
|
212
|
+
thicknesses = torch.cat(
|
|
213
|
+
[(d_block / 2)[:, None].repeat(1, n * 2), d3[:, None], d_sio2[:, None]], -1
|
|
214
|
+
)
|
|
215
|
+
|
|
216
|
+
s_block = s_block_rel * d_block
|
|
217
|
+
|
|
218
|
+
roughnesses = torch.cat(
|
|
219
|
+
[s_block[:, None].repeat(1, n * 2), (s3_rel * d3)[:, None], s_sio2[:, None], s_si[:, None]], -1
|
|
220
|
+
)
|
|
221
|
+
|
|
222
|
+
slds = torch.cat(
|
|
223
|
+
[sld_blocks, r3[:, None], r_sio2[:, None], r_si[:, None]], -1
|
|
224
|
+
)
|
|
225
|
+
|
|
226
|
+
params = dict(
|
|
227
|
+
thicknesses=thicknesses,
|
|
228
|
+
roughnesses=roughnesses,
|
|
229
|
+
slds=slds
|
|
230
|
+
)
|
|
231
|
+
return params
|
|
232
|
+
|
|
233
|
+
|
|
234
|
+
def multilayer_model3(parametrized_model: Tensor, d_full_rel_max: int = 30):
|
|
235
|
+
n = d_full_rel_max
|
|
236
|
+
|
|
237
|
+
(
|
|
238
|
+
d_full_rel,
|
|
239
|
+
rel_sigmas,
|
|
240
|
+
dr_sigmoid_rel_pos,
|
|
241
|
+
dr_sigmoid_rel_width,
|
|
242
|
+
d_block1_rel,
|
|
243
|
+
d_block,
|
|
244
|
+
s_block_rel,
|
|
245
|
+
r_block,
|
|
246
|
+
dr,
|
|
247
|
+
d3_rel,
|
|
248
|
+
s3_rel,
|
|
249
|
+
r3,
|
|
250
|
+
d_sio2,
|
|
251
|
+
s_sio2,
|
|
252
|
+
s_si,
|
|
253
|
+
r_sio2,
|
|
254
|
+
r_si,
|
|
255
|
+
) = parametrized_model.T
|
|
256
|
+
|
|
257
|
+
batch_size = parametrized_model.shape[0]
|
|
258
|
+
|
|
259
|
+
r_positions = 2 * n - torch.arange(2 * n, dtype=dr.dtype, device=dr.device)[None].repeat(batch_size, 1)
|
|
260
|
+
|
|
261
|
+
r_modulations = torch.sigmoid(
|
|
262
|
+
-(
|
|
263
|
+
r_positions - 2 * d_full_rel[..., None]
|
|
264
|
+
) / rel_sigmas[..., None]
|
|
265
|
+
)
|
|
266
|
+
|
|
267
|
+
dr_positions = r_positions[:, ::2]
|
|
268
|
+
|
|
269
|
+
dr_modulations = dr[..., None] * (1 - torch.sigmoid(
|
|
270
|
+
-(
|
|
271
|
+
dr_positions - 2 * d_full_rel[..., None] + 2 * dr_sigmoid_rel_pos[..., None]
|
|
272
|
+
) / dr_sigmoid_rel_width[..., None]
|
|
273
|
+
))
|
|
274
|
+
|
|
275
|
+
r_block = r_block[..., None].repeat(1, n)
|
|
276
|
+
dr = dr[..., None].repeat(1, n)
|
|
277
|
+
|
|
278
|
+
sld_blocks = torch.stack(
|
|
279
|
+
[
|
|
280
|
+
r_block + dr_modulations * (1 - d_block1_rel[..., None]),
|
|
281
|
+
r_block + dr - dr_modulations * d_block1_rel[..., None]
|
|
282
|
+
], -1).flatten(1)
|
|
283
|
+
|
|
284
|
+
sld_blocks = r_modulations * sld_blocks
|
|
285
|
+
|
|
286
|
+
d3 = d3_rel * d_block
|
|
287
|
+
|
|
288
|
+
d1, d2 = d_block * d_block1_rel, d_block * (1 - d_block1_rel)
|
|
289
|
+
|
|
290
|
+
thickness_blocks = torch.stack([d1[:, None].repeat(1, n), d2[:, None].repeat(1, n)], -1).flatten(1)
|
|
291
|
+
|
|
292
|
+
thicknesses = torch.cat(
|
|
293
|
+
[thickness_blocks, d3[:, None], d_sio2[:, None]], -1
|
|
294
|
+
)
|
|
295
|
+
|
|
296
|
+
s_block = s_block_rel * d_block
|
|
297
|
+
|
|
298
|
+
roughnesses = torch.cat(
|
|
299
|
+
[s_block[:, None].repeat(1, n * 2), (s3_rel * d3)[:, None], s_sio2[:, None], s_si[:, None]], -1
|
|
300
|
+
)
|
|
301
|
+
|
|
302
|
+
slds = torch.cat(
|
|
303
|
+
[sld_blocks, r3[:, None], r_sio2[:, None], r_si[:, None]], -1
|
|
304
|
+
)
|
|
305
|
+
|
|
306
|
+
params = dict(
|
|
307
|
+
thicknesses=thicknesses,
|
|
308
|
+
roughnesses=roughnesses,
|
|
309
|
+
slds=slds
|
|
310
|
+
)
|
|
311
|
+
return params
|