reflectorch 1.2.0__tar.gz → 1.2.1__tar.gz

{reflectorch-1.2.0 → reflectorch-1.2.1}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: reflectorch
-Version: 1.2.0
+Version: 1.2.1
 Summary: A Pytorch-based package for the analysis of reflectometry data
 Author-email: Vladimir Starostin <vladimir.starostin@uni-tuebingen.de>, Valentin Munteanu <valentin.munteanu@uni-tuebingen.de>
 Maintainer-email: Valentin Munteanu <valentin.munteanu@uni-tuebingen.de>, Vladimir Starostin <vladimir.starostin@uni-tuebingen.de>, Alexander Hinderhofer <alexander.hinderhofer@uni-tuebingen.de>

{reflectorch-1.2.0 → reflectorch-1.2.1}/pyproject.toml

@@ -4,7 +4,7 @@ build-backend = "setuptools.build_meta"
 
 [project]
 name = "reflectorch"
-version = "1.2.0"
+version = "1.2.1"
 authors = [
     {name = "Vladimir Starostin", email="vladimir.starostin@uni-tuebingen.de"},
     {name = "Valentin Munteanu", email="valentin.munteanu@uni-tuebingen.de"}

{reflectorch-1.2.0 → reflectorch-1.2.1}/reflectorch/data_generation/reflectivity/__init__.py

@@ -31,15 +31,15 @@ def reflectivity(
         q (Tensor): tensor of momentum transfer (q) values with shape [batch_size, n_points] or [n_points]
         thickness (Tensor): tensor containing the layer thicknesses (ordered from top to bottom) with shape [batch_size, n_layers]
         roughness (Tensor): tensor containing the interlayer roughnesses (ordered from top to bottom) with shape [batch_size, n_layers + 1]
-        sld (Tensor): tensors containing the layer SLDs (real or complex; ordered from top to bottom) with shape [batch_size, n_layers + 1]. 
-                    It includes the substrate but excludes the ambient medium which is assumed to have an SLD of 0.
+        sld (Tensor): tensor containing the layer SLDs (real or complex; ordered from top to bottom) with shape 
+            [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'``) 
         dq (Tensor, optional): tensor of resolutions used for curve smearing with shape [batch_size, 1].
                             Either dq if ``constant_dq`` is ``True`` or dq/q if ``constant_dq`` is ``False``. Defaults to None.
         gauss_num (int, optional): the number of gaussians for curve smearing. Defaults to 51.
         constant_dq (bool, optional): if ``True`` the smearing is constant (constant dq at each point in the curve) 
                                     otherwise the smearing is linear (constant dq/q at each point in the curve). Defaults to True.
         log (bool, optional): if True the base 10 logarithm of the reflectivity curves is returned. Defaults to False.
-        abeles_func (Callable, optional): a function implementing the simulation of the reflectivity curves, if different than the default Abeles matrix implementation. Defaults to None.
+        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.
 
     Returns:
         Tensor: tensor containing the simulated reflectivity curves with shape [batch_size, n_points]

{reflectorch-1.2.0 → reflectorch-1.2.1}/reflectorch/data_generation/reflectivity/abeles.py

@@ -1,5 +1,6 @@
 # -*- coding: utf-8 -*-
 import math
+from functools import reduce
 
 import torch
 from torch import Tensor
@@ -17,8 +18,9 @@ def abeles(
         q (Tensor): tensor of momentum transfer (q) values with shape [batch_size, n_points] or [n_points]
         thickness (Tensor): tensor containing the layer thicknesses (ordered from top to bottom) with shape [batch_size, n_layers]
         roughness (Tensor): tensor containing the interlayer roughnesses (ordered from top to bottom) with shape [batch_size, n_layers + 1]
-        sld (Tensor): tensors containing the layer SLDs (real or complex; ordered from top to bottom) with shape [batch_size, n_layers + 1]. 
-                    It includes the substrate but excludes the ambient medium which is assumed to have an SLD of 0.
+        sld (Tensor): tensor containing the layer SLDs (real or complex; ordered from top to bottom). The tensor shape should be one of the following:
+            - [batch_size, n_layers + 1]: in this case, the ambient SLD is not included but assumed to be 0
+            - [batch_size, n_layers + 2]: this shape includes the ambient SLD as the first element in the tensor
 
     Returns:
         Tensor: tensor containing the simulated reflectivity curves with shape [batch_size, n_points]
@@ -27,11 +29,24 @@ def abeles(
 
     batch_size, num_layers = thickness.shape
 
-    sld = torch.cat([torch.zeros(batch_size, 1).to(sld), sld], -1)[:, None]
-    thickness = torch.cat([torch.zeros(batch_size, 1).to(thickness), thickness], -1)[:, None]
+    if sld.shape[-1] == num_layers + 1:
+        # add zero ambient sld
+        sld = torch.cat([torch.zeros(batch_size, 1).to(sld), sld], -1)
+    if sld.shape[-1] != num_layers + 2:
+        raise ValueError(
+            "Number of SLD values does not equal to num_layers + 2 (substrate + ambient)."
+        )
+
+    sld = sld[:, None]
+
+    # add zero thickness for ambient layer:
+    thickness = torch.cat([torch.zeros(batch_size, 1).to(thickness), thickness], -1)[
+        :, None
+    ]
+
     roughness = roughness[:, None] ** 2
 
-    sld = sld * 1e-6 + 1e-30j
+    sld = (sld - sld[..., :1]) * 1e-6 + 1e-36j
 
     k_z0 = (q / 2).to(c_dtype)
 
@@ -41,7 +56,7 @@ def abeles(
     if k_z0.dim() == 2:
         k_z0.unsqueeze_(-1)
 
-    k_n = torch.sqrt(k_z0 ** 2 - 4 * math.pi * sld)
+    k_n = torch.sqrt(k_z0**2 - 4 * math.pi * sld)
 
     # k_n.shape - (batch, q, layers)
 
@@ -52,22 +67,22 @@ def abeles(
     exp_beta = torch.exp(beta)
     exp_m_beta = torch.exp(-beta)
 
-    rn = (k_n - k_np1) / (k_n + k_np1) * torch.exp(- 2 * k_n * k_np1 * roughness)
+    rn = (k_n - k_np1) / (k_n + k_np1) * torch.exp(-2 * k_n * k_np1 * roughness)
 
-    c_matrices = torch.stack([
-        torch.stack([exp_beta, rn * exp_m_beta], -1),
-        torch.stack([rn * exp_beta, exp_m_beta], -1),
-    ], -1)
+    c_matrices = torch.stack(
+        [
+            torch.stack([exp_beta, rn * exp_m_beta], -1),
+            torch.stack([rn * exp_beta, exp_m_beta], -1),
+        ],
+        -1,
+    )
 
     c_matrices = [c.squeeze(-3) for c in c_matrices.split(1, -3)]
 
-    m, c_matrices = c_matrices[0], c_matrices[1:]
-
-    for c in c_matrices:
-        m = m @ c
+    m = reduce(torch.matmul, c_matrices)
 
     r = (m[..., 1, 0] / m[..., 0, 0]).abs() ** 2
-    r = torch.clamp_max_(r, 1.)
+    r = torch.clamp_max_(r, 1.0)
 
     return r
 

{reflectorch-1.2.0 → reflectorch-1.2.1}/reflectorch/data_generation/reflectivity/kinematical.py

@@ -19,7 +19,7 @@ def kinematical_approximation(
         q (Tensor): tensor of momentum transfer (q) values with shape [batch_size, n_points] or [n_points]
         thickness (Tensor): tensor containing the layer thicknesses (ordered from top to bottom) with shape [batch_size, n_layers]
         roughness (Tensor): tensor containing the interlayer roughnesses (ordered from top to bottom) with shape [batch_size, n_layers + 1]
-        sld (Tensor): tensors containing the layer SLDs (real or complex; ordered from top to bottom) with shape [batch_size, n_layers + 1]. 
+        sld (Tensor): tensor containing the layer SLDs (real or complex; ordered from top to bottom) with shape [batch_size, n_layers + 1]. 
                     It includes the substrate but excludes the ambient medium which is assumed to have an SLD of 0.
         apply_fresnel (bool, optional): whether to use the Fresnel coefficient in the computation. Defaults to ``True``.
         log (bool, optional): if True the base 10 logarithm of the reflectivity curves is returned. Defaults to ``False``.

{reflectorch-1.2.0 → reflectorch-1.2.1}/reflectorch/data_generation/reflectivity/memory_eff.py

@@ -19,7 +19,7 @@ def abeles_memory_eff(
         q (Tensor): tensor of momentum transfer (q) values with shape [batch_size, n_points] or [n_points]
         thickness (Tensor): tensor containing the layer thicknesses (ordered from top to bottom) with shape [batch_size, n_layers]
         roughness (Tensor): tensor containing the interlayer roughnesses (ordered from top to bottom) with shape [batch_size, n_layers + 1]
-        sld (Tensor): tensors containing the layer SLDs (real or complex; ordered from top to bottom) with shape [batch_size, n_layers + 1]. 
+        sld (Tensor): tensor containing the layer SLDs (real or complex; ordered from top to bottom) with shape [batch_size, n_layers + 1]. 
                     It includes the substrate but excludes the ambient medium which is assumed to have an SLD of 0.
 
     Returns:

{reflectorch-1.2.0 → reflectorch-1.2.1}/reflectorch/inference/inference_model.py

@@ -354,7 +354,8 @@ class EasyInferenceModel(object):
                     torch.from_numpy(polished_params_arr[:-1][None]),
                     torch.from_numpy(priors.T[0][None]),
                     torch.from_numpy(priors.T[1][None]),
-                    #self.trainer.loader.prior_sampler.param_model
+                    self.trainer.loader.prior_sampler.max_num_layers,
+                    self.trainer.loader.prior_sampler.param_model
                     )
             else:
                 polished_params_arr, curve_polished = standard_refl_fit(
@@ -366,7 +367,8 @@ class EasyInferenceModel(object):
                     torch.from_numpy(polished_params_arr[None]),
                     torch.from_numpy(priors.T[0][None]),
                     torch.from_numpy(priors.T[1][None]),
-                    #self.trainer.loader.prior_sampler.param_model
+                    self.trainer.loader.prior_sampler.max_num_layers,
+                    self.trainer.loader.prior_sampler.param_model
                     )
         except Exception as err:
             polished_params = predicted_params

{reflectorch-1.2.0 → reflectorch-1.2.1}/reflectorch.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: reflectorch
-Version: 1.2.0
+Version: 1.2.1
 Summary: A Pytorch-based package for the analysis of reflectometry data
 Author-email: Vladimir Starostin <vladimir.starostin@uni-tuebingen.de>, Valentin Munteanu <valentin.munteanu@uni-tuebingen.de>
 Maintainer-email: Valentin Munteanu <valentin.munteanu@uni-tuebingen.de>, Vladimir Starostin <vladimir.starostin@uni-tuebingen.de>, Alexander Hinderhofer <alexander.hinderhofer@uni-tuebingen.de>