reflectorch 1.2.0__py3-none-any.whl → 1.3.0__py3-none-any.whl
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- reflectorch/data_generation/__init__.py +2 -0
- reflectorch/data_generation/dataset.py +27 -7
- reflectorch/data_generation/noise.py +115 -9
- reflectorch/data_generation/priors/parametric_models.py +90 -15
- reflectorch/data_generation/priors/parametric_subpriors.py +28 -7
- reflectorch/data_generation/priors/sampler_strategies.py +67 -3
- reflectorch/data_generation/q_generator.py +31 -11
- reflectorch/data_generation/reflectivity/__init__.py +56 -14
- reflectorch/data_generation/reflectivity/abeles.py +31 -16
- reflectorch/data_generation/reflectivity/kinematical.py +5 -6
- reflectorch/data_generation/reflectivity/memory_eff.py +1 -1
- reflectorch/data_generation/reflectivity/smearing.py +25 -10
- reflectorch/data_generation/reflectivity/smearing_pointwise.py +110 -0
- reflectorch/data_generation/smearing.py +42 -11
- reflectorch/data_generation/utils.py +92 -18
- reflectorch/extensions/refnx/refnx_conversion.py +77 -0
- reflectorch/inference/inference_model.py +220 -105
- reflectorch/inference/plotting.py +98 -0
- reflectorch/inference/scipy_fitter.py +84 -7
- reflectorch/ml/__init__.py +2 -0
- reflectorch/ml/basic_trainer.py +18 -6
- reflectorch/ml/callbacks.py +5 -4
- reflectorch/ml/loggers.py +25 -0
- reflectorch/ml/schedulers.py +116 -0
- reflectorch/ml/trainers.py +122 -23
- reflectorch/models/__init__.py +1 -1
- reflectorch/models/encoders/__init__.py +0 -2
- reflectorch/models/encoders/conv_encoder.py +54 -40
- reflectorch/models/encoders/fno.py +23 -16
- reflectorch/models/networks/__init__.py +2 -0
- reflectorch/models/networks/mlp_networks.py +324 -152
- reflectorch/models/networks/residual_net.py +31 -5
- reflectorch/runs/train.py +0 -1
- reflectorch/runs/utils.py +43 -9
- {reflectorch-1.2.0.dist-info → reflectorch-1.3.0.dist-info}/METADATA +19 -17
- {reflectorch-1.2.0.dist-info → reflectorch-1.3.0.dist-info}/RECORD +39 -36
- {reflectorch-1.2.0.dist-info → reflectorch-1.3.0.dist-info}/WHEEL +1 -1
- {reflectorch-1.2.0.dist-info → reflectorch-1.3.0.dist-info/licenses}/LICENSE.txt +0 -0
- {reflectorch-1.2.0.dist-info → reflectorch-1.3.0.dist-info}/top_level.txt +0 -0
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@@ -50,6 +50,8 @@ class ConstantQ(QGenerator):
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q = q[1:]
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else:
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q = q[:-1]
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self.q_min = q.min().item()
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self.q_max = q.max().item()
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self.q = q
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def get_batch(self, batch_size: int, context: dict = None) -> Tensor:
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"""
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return self.q.clone()[None].expand(batch_size, self.q.shape[0])
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def scale_q(self, q):
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"""Scales the q values to the range [-1, 1].
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Args:
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q (Tensor): unscaled q values
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Returns:
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Tensor: scaled q values
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"""
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scaled_q_01 = (q - self.q_min) / (self.q_max - self.q_min)
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return 2.0 * (scaled_q_01 - 0.5)
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class VariableQ(QGenerator):
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"""Q generator for reflectivity curves with variable discretization
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Args:
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q_min_range (list, optional): the range for sampling the minimum q value of the curves,
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q_max_range (list, optional): the range for sampling the maximum q value of the curves,
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n_q_range (list, optional): the range for the number of points in the curves (equidistantly sampled between
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q_min_range (list, optional): the range for sampling the minimum q value of the curves, q_min. Defaults to [0.01, 0.03].
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q_max_range (list, optional): the range for sampling the maximum q value of the curves, q_max. Defaults to [0.1, 0.5].
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n_q_range (list, optional): the range for the number of points in the curves (equidistantly sampled between q_min and q_max,
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the number of points varies between batches but is constant within a batch). Defaults to [64, 256].
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device (optional): the Pytorch device. Defaults to DEFAULT_DEVICE.
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dtype (optional): the Pytorch data type. Defaults to DEFAULT_DTYPE.
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@@ -80,12 +94,14 @@ class VariableQ(QGenerator):
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q_min_range: Tuple[float, float] = (0.01, 0.03),
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q_max_range: Tuple[float, float] = (0.1, 0.5),
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n_q_range: Tuple[int, int] = (64, 256),
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mode: str = 'equidistant',
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device=DEFAULT_DEVICE,
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dtype=DEFAULT_DTYPE,
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):
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self.q_min_range = q_min_range
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self.q_max_range = q_max_range
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self.n_q_range = n_q_range
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self.mode = mode
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self.device = device
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self.dtype = dtype
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Returns:
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Tensor: generated batch of q values
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"""
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q_min = torch.rand(batch_size, device=self.device, dtype=self.dtype) * (self.q_min_range[1] - self.q_min_range[0]) + self.q_min_range[0]
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q_max = torch.rand(batch_size, device=self.device, dtype=self.dtype) * (self.q_max_range[1] - self.q_max_range[0]) + self.q_max_range[0]
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n_q = torch.randint(self.n_q_range[0], self.n_q_range[1] + 1, (1,), device=self.device).item()
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if self.mode == 'equidistant':
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q = torch.linspace(0, 1, n_q, device=self.device, dtype=self.dtype)
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elif self.mode == 'random':
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q = torch.rand(n_q, device=self.device, dtype=self.dtype).sort().values
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q = q_min[:, None] + q * (q_max - q_min)[:, None]
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return q
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@@ -10,6 +10,7 @@ from reflectorch.data_generation.reflectivity.numpy_implementations import (
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abeles_np,
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)
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from reflectorch.data_generation.reflectivity.smearing import abeles_constant_smearing
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from reflectorch.data_generation.reflectivity.smearing_pointwise import abeles_pointwise_smearing
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from reflectorch.data_generation.reflectivity.kinematical import kinematical_approximation
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@@ -20,9 +21,15 @@ def reflectivity(
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sld: Tensor,
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dq: Tensor = None,
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gauss_num: int = 51,
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constant_dq: bool =
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constant_dq: bool = False,
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log: bool = False,
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q_shift: Tensor = 0.0,
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r_scale: Tensor = 1.0,
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background: Tensor = 0.0,
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solvent_vf = None,
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solvent_mode = 'fronting',
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abeles_func = None,
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**abeles_kwargs
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"""Function which computes the reflectivity curves from thin film parameters.
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By default it uses the fast implementation of the Abeles matrix formalism.
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q (Tensor): tensor of momentum transfer (q) values with shape [batch_size, n_points] or [n_points]
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thickness (Tensor): tensor containing the layer thicknesses (ordered from top to bottom) with shape [batch_size, n_layers]
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roughness (Tensor): tensor containing the interlayer roughnesses (ordered from top to bottom) with shape [batch_size, n_layers + 1]
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sld (Tensor):
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sld (Tensor): tensor containing the layer SLDs (real or complex; ordered from top to bottom) with shape
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[batch_size, n_layers + 1] (excluding ambient SLD which is assumed to be 0) or [batch_size, n_layers + 2] (including ambient SLD; only for the default ``abeles_func='abeles'``)
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dq (Tensor, optional): tensor of resolutions used for curve smearing with shape [batch_size, 1].
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Either dq if ``constant_dq`` is ``True`` or dq/q if ``constant_dq`` is ``False``. Defaults to None.
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gauss_num (int, optional): the number of gaussians for curve smearing. Defaults to 51.
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constant_dq (bool, optional): if ``True`` the smearing is constant (constant dq at each point in the curve)
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otherwise the smearing is linear (constant dq/q at each point in the curve). Defaults to
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otherwise the smearing is linear (constant dq/q at each point in the curve). Defaults to False.
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log (bool, optional): if True the base 10 logarithm of the reflectivity curves is returned. Defaults to False.
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q_shift (float or Tensor, optional): misalignment in q.
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r_scale (float or Tensor, optional): normalization factor (scales reflectivity).
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background (float or Tensor, optional): background intensity.
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abeles_func (Callable, optional): a function implementing the simulation of the reflectivity curves, if different than the default Abeles matrix implementation ('abeles'). Defaults to None.
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abeles_kwargs: Additional arguments specific to the chosen `abeles_func`.
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Returns:
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Tensor:
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Tensor: the computed reflectivity curves
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"""
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abeles_func = abeles_func or abeles
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q = torch.atleast_2d(q)
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q = torch.atleast_2d(q) + q_shift
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q = torch.clamp(q, min=0.0)
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if solvent_vf is not None:
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num_layers = thickness.shape[-1]
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if solvent_mode == 'fronting':
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assert sld.shape[-1] == num_layers + 2
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assert solvent_vf.shape[-1] == num_layers
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solvent_sld = sld[..., [0]]
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idx = slice(1, num_layers)
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sld[..., idx] = solvent_vf * solvent_sld + (1.0 - solvent_vf) * sld[..., idx]
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elif solvent_mode == 'backing':
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solvent_sld = sld[..., [-1]]
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idx = slice(1, num_layers) if sld.shape[-1] == num_layers + 2 else slice(0, num_layers)
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sld[..., idx] = solvent_vf * solvent_sld + (1.0 - solvent_vf) * sld[..., idx]
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else:
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raise NotImplementedError
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if dq is None:
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reflectivity_curves = abeles_func(q, thickness, roughness, sld)
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reflectivity_curves = abeles_func(q, thickness, roughness, sld, **abeles_kwargs)
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else:
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if dq.shape[-1] > 1:
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reflectivity_curves = abeles_pointwise_smearing(
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q=q, dq=dq, thickness=thickness, roughness=roughness, sld=sld,
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abeles_func=abeles_func, gauss_num=gauss_num,
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**abeles_kwargs,
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)
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else:
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reflectivity_curves = abeles_constant_smearing(
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q, thickness, roughness, sld,
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dq=dq, gauss_num=gauss_num, constant_dq=constant_dq, abeles_func=abeles_func,
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**abeles_kwargs,
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)
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if isinstance(r_scale, Tensor):
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r_scale = r_scale.view(-1, *[1] * (reflectivity_curves.dim() - 1))
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if isinstance(background, Tensor):
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background = background.view(-1, *[1] * (reflectivity_curves.dim() - 1))
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reflectivity_curves = reflectivity_curves * r_scale + background
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reflectivity_curves = torch.log10(reflectivity_curves)
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return reflectivity_curves
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thickness (Tensor): tensor containing the layer thicknesses (ordered from top to bottom) with shape [batch_size, n_layers]
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sld (Tensor): tensor containing the layer SLDs (real or complex; ordered from top to bottom). The tensor shape should be one of the following:
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- [batch_size, n_layers + 1]: in this case, the ambient SLD is not included but assumed to be 0
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sld = torch.cat([torch.zeros(batch_size, 1).to(sld), sld], -1)
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thickness = torch.cat([torch.zeros(batch_size, 1).to(thickness), thickness], -1)[
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sld = (sld - sld[..., :1]) * 1e-6 + 1e-36j
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rn = (k_n - k_np1) / (k_n + k_np1) * torch.exp(-
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thickness (Tensor): tensor containing the layer thicknesses (ordered from top to bottom) with shape [batch_size, n_layers]
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sld (Tensor): tensor containing the layer SLDs (real or complex; ordered from top to bottom) with shape [batch_size, n_layers + 1].
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It includes the substrate but excludes the ambient medium which is assumed to have an SLD of 0.
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apply_fresnel (bool, optional): whether to use the Fresnel coefficient in the computation. Defaults to ``True``.
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sld (Tensor):
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@@ -14,26 +14,41 @@ def abeles_constant_smearing(
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**abeles_kwargs
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):
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curves = abeles_func(q_lin, thickness, roughness, sld)
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)
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)
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q_lin = q_lin.repeat(repeat_factor, 1)
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@@ -55,7 +70,7 @@ def _get_t_gauss_kernels(resolutions: Tensor, gaussnum: int = 51):
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def _get_q_axes(q: Tensor, resolutions: Tensor, gaussnum: int = 51, constant_dq: bool =
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def _get_q_axes(q: Tensor, resolutions: Tensor, gaussnum: int = 51, constant_dq: bool = False):
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@@ -0,0 +1,110 @@
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import torch
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import scipy
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import numpy as np
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from functools import lru_cache
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from typing import Tuple
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from reflectorch.data_generation.reflectivity.abeles import abeles
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#Pytorch version based on the JAX implementation of pointwise smearing in the refnx package.
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+
@lru_cache(maxsize=128)
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def gauss_legendre(n: int) -> Tuple[torch.Tensor, torch.Tensor]:
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"""
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Calculate Gaussian quadrature abscissae and weights.
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Args:
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n (int): Gaussian quadrature order.
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Returns:
|
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Tuple[torch.Tensor, torch.Tensor]: The abscissae and weights for Gauss-Legendre integration.
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+
"""
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+
return scipy.special.p_roots(n)
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def gauss(x: torch.Tensor) -> torch.Tensor:
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"""
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Calculate the Gaussian function.
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Args:
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x (torch.Tensor): Input tensor.
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Returns:
|
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torch.Tensor: Output tensor after applying the Gaussian function.
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+
"""
|
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|
+
return torch.exp(-0.5 * x * x)
|
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+
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|
+
def abeles_pointwise_smearing(
|
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+
q: torch.Tensor,
|
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|
+
dq: torch.Tensor,
|
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|
+
thickness: torch.Tensor,
|
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|
+
roughness: torch.Tensor,
|
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|
+
sld: torch.Tensor,
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|
+
gauss_num: int = 17,
|
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|
+
abeles_func=None,
|
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+
**abeles_kwargs,
|
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45
|
+
) -> torch.Tensor:
|
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46
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+
"""
|
|
47
|
+
Compute reflectivity with variable smearing using Gaussian quadrature.
|
|
48
|
+
|
|
49
|
+
Args:
|
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50
|
+
q (torch.Tensor): The momentum transfer (q) values.
|
|
51
|
+
dq (torch.Tensor): The resolution for curve smearing.
|
|
52
|
+
thickness (torch.Tensor): The layer thicknesses.
|
|
53
|
+
roughness (torch.Tensor): The interlayer roughnesses.
|
|
54
|
+
sld (torch.Tensor): The SLDs of the layers.
|
|
55
|
+
sld_magnetic (torch.Tensor, optional): The magnetic SLDs of the layers.
|
|
56
|
+
magnetization_angle (torch.Tensor, optional): The magnetization angles.
|
|
57
|
+
polarizer_eff (torch.Tensor, optional): The polarizer efficiency.
|
|
58
|
+
analyzer_eff (torch.Tensor, optional): The analyzer efficiency.
|
|
59
|
+
abeles_func (Callable, optional): A function implementing the simulation of the reflectivity curves.
|
|
60
|
+
gauss_num (int, optional): Gaussian quadrature order. Defaults to 17.
|
|
61
|
+
|
|
62
|
+
Returns:
|
|
63
|
+
torch.Tensor: The computed reflectivity curves.
|
|
64
|
+
"""
|
|
65
|
+
abeles_func = abeles_func or abeles
|
|
66
|
+
|
|
67
|
+
if q.shape[0] == 1:
|
|
68
|
+
q = q.repeat(thickness.shape[0], 1)
|
|
69
|
+
|
|
70
|
+
_FWHM = 2 * np.sqrt(2 * np.log(2.0))
|
|
71
|
+
_INTLIMIT = 3.5
|
|
72
|
+
|
|
73
|
+
bs = q.shape[0]
|
|
74
|
+
nq = q.shape[-1]
|
|
75
|
+
device = q.device
|
|
76
|
+
|
|
77
|
+
quad_order = gauss_num
|
|
78
|
+
abscissa, weights = gauss_legendre(quad_order)
|
|
79
|
+
abscissa = torch.tensor(abscissa)[None, :, None].to(device)
|
|
80
|
+
weights = torch.tensor(weights)[None, :, None].to(device)
|
|
81
|
+
prefactor = 1.0 / np.sqrt(2 * np.pi)
|
|
82
|
+
|
|
83
|
+
gaussvals = prefactor * gauss(abscissa * _INTLIMIT)
|
|
84
|
+
|
|
85
|
+
va = q[:, None, :] - _INTLIMIT * dq[:, None, :] / _FWHM
|
|
86
|
+
vb = q[:, None, :] + _INTLIMIT * dq[:, None, :] / _FWHM
|
|
87
|
+
|
|
88
|
+
qvals_for_res_0 = (abscissa * (vb - va) + vb + va) / 2
|
|
89
|
+
qvals_for_res = qvals_for_res_0.reshape(bs, -1)
|
|
90
|
+
|
|
91
|
+
refl_curves = abeles_func(
|
|
92
|
+
q=qvals_for_res,
|
|
93
|
+
thickness=thickness,
|
|
94
|
+
roughness=roughness,
|
|
95
|
+
sld=sld,
|
|
96
|
+
**abeles_kwargs
|
|
97
|
+
)
|
|
98
|
+
|
|
99
|
+
# Handle multiple channels
|
|
100
|
+
if refl_curves.dim() == 3:
|
|
101
|
+
n_channels = refl_curves.shape[1]
|
|
102
|
+
refl_curves = refl_curves.reshape(bs, n_channels, quad_order, nq)
|
|
103
|
+
refl_curves = refl_curves * gaussvals.unsqueeze(1) * weights.unsqueeze(1)
|
|
104
|
+
refl_curves = torch.sum(refl_curves, dim=2) * _INTLIMIT
|
|
105
|
+
else:
|
|
106
|
+
refl_curves = refl_curves.reshape(bs, quad_order, nq)
|
|
107
|
+
refl_curves = refl_curves * gaussvals * weights
|
|
108
|
+
refl_curves = torch.sum(refl_curves, dim=1) * _INTLIMIT
|
|
109
|
+
|
|
110
|
+
return refl_curves
|
|
@@ -9,15 +9,15 @@ class Smearing(object):
|
|
|
9
9
|
The intensity at a q point will be the average of the intensities of neighbouring q points, weighted by a gaussian profile.
|
|
10
10
|
|
|
11
11
|
Args:
|
|
12
|
-
sigma_range (tuple, optional): the range for sampling the resolutions. Defaults to (
|
|
12
|
+
sigma_range (tuple, optional): the range for sampling the resolutions. Defaults to (0.01, 0.1).
|
|
13
13
|
constant_dq (bool, optional): if ``True`` the smearing is constant (the resolution is given by the constant dq at each point in the curve)
|
|
14
14
|
otherwise the smearing is linear (the resolution is given by the constant dq/q at each point in the curve). Defaults to True.
|
|
15
15
|
gauss_num (int, optional): the number of interpolating gaussian profiles. Defaults to 31.
|
|
16
16
|
share_smeared (float, optional): the share of curves in the batch for which the resolution smearing is applied. Defaults to 0.2.
|
|
17
17
|
"""
|
|
18
18
|
def __init__(self,
|
|
19
|
-
sigma_range: tuple = (
|
|
20
|
-
constant_dq: bool =
|
|
19
|
+
sigma_range: tuple = (0.01, 0.1),
|
|
20
|
+
constant_dq: bool = False,
|
|
21
21
|
gauss_num: int = 31,
|
|
22
22
|
share_smeared: float = 0.2,
|
|
23
23
|
):
|
|
@@ -38,31 +38,62 @@ class Smearing(object):
|
|
|
38
38
|
indices = torch.zeros(batch_size, device=device, dtype=torch.bool)
|
|
39
39
|
indices[torch.randperm(batch_size, device=device)[:num_smeared]] = True
|
|
40
40
|
return dq, indices
|
|
41
|
+
|
|
42
|
+
def scale_resolutions(self, resolutions: Tensor) -> Tensor:
|
|
43
|
+
"""Scales the q-resolution values to [-1,1] range using the internal sigma range"""
|
|
44
|
+
sigma_min = 0.0 if self.share_smeared != 1.0 else self.sigma_min
|
|
45
|
+
return 2 * (resolutions - sigma_min) / (self.sigma_max - sigma_min) - 1
|
|
46
|
+
|
|
47
|
+
def get_curves(self, q_values: Tensor, params: BasicParams, refl_kwargs:dict = None):
|
|
48
|
+
refl_kwargs = refl_kwargs or {}
|
|
41
49
|
|
|
42
|
-
def get_curves(self, q_values: Tensor, params: BasicParams):
|
|
43
50
|
dq, indices = self.generate_resolutions(params.batch_size, device=params.device, dtype=params.dtype)
|
|
51
|
+
q_resolutions = torch.zeros(q_values.shape[0], 1, dtype=q_values.dtype, device=q_values.device)
|
|
44
52
|
|
|
45
53
|
if dq is None:
|
|
46
|
-
return params.reflectivity(q_values,
|
|
47
|
-
|
|
48
|
-
|
|
54
|
+
return params.reflectivity(q_values, **refl_kwargs), q_resolutions
|
|
55
|
+
|
|
56
|
+
refl_kwargs_not_smeared = {}
|
|
57
|
+
refl_kwargs_smeared = {}
|
|
58
|
+
for key, value in refl_kwargs.items():
|
|
59
|
+
if isinstance(value, torch.Tensor) and value.shape[0] == params.batch_size:
|
|
60
|
+
refl_kwargs_not_smeared[key] = value[~indices]
|
|
61
|
+
refl_kwargs_smeared[key] = value[indices]
|
|
62
|
+
else:
|
|
63
|
+
refl_kwargs_not_smeared[key] = value
|
|
64
|
+
refl_kwargs_smeared[key] = value
|
|
49
65
|
|
|
66
|
+
# Compute unsmeared reflectivity
|
|
50
67
|
if (~indices).sum().item():
|
|
51
68
|
if q_values.dim() == 2 and q_values.shape[0] > 1:
|
|
52
69
|
q = q_values[~indices]
|
|
53
70
|
else:
|
|
54
71
|
q = q_values
|
|
55
72
|
|
|
56
|
-
|
|
73
|
+
reflectivity_not_smeared = params[~indices].reflectivity(q, **refl_kwargs_not_smeared)
|
|
74
|
+
else:
|
|
75
|
+
reflectivity_not_smeared = None
|
|
57
76
|
|
|
77
|
+
# Compute smeared reflectivity
|
|
58
78
|
if indices.sum().item():
|
|
59
79
|
if q_values.dim() == 2 and q_values.shape[0] > 1:
|
|
60
80
|
q = q_values[indices]
|
|
61
81
|
else:
|
|
62
82
|
q = q_values
|
|
63
83
|
|
|
64
|
-
|
|
65
|
-
q, dq=dq, constant_dq=self.constant_dq,
|
|
84
|
+
reflectivity_smeared = params[indices].reflectivity(
|
|
85
|
+
q, dq=dq, constant_dq=self.constant_dq, gauss_num=self.gauss_num, **refl_kwargs_smeared
|
|
66
86
|
)
|
|
87
|
+
else:
|
|
88
|
+
reflectivity_smeared = None
|
|
89
|
+
|
|
90
|
+
curves = torch.empty(params.batch_size, q_values.shape[-1], device=params.device, dtype=params.dtype)
|
|
91
|
+
|
|
92
|
+
if (~indices).sum().item():
|
|
93
|
+
curves[~indices] = reflectivity_not_smeared
|
|
94
|
+
|
|
95
|
+
curves[indices] = reflectivity_smeared
|
|
96
|
+
|
|
97
|
+
q_resolutions[indices] = dq
|
|
67
98
|
|
|
68
|
-
return curves
|
|
99
|
+
return curves, q_resolutions
|