reflectorch 1.2.0__py3-none-any.whl → 1.2.1__py3-none-any.whl

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/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/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/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/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.dist-info → reflectorch-1.2.1.dist-info}/METADATA

@@ -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.dist-info → reflectorch-1.2.1.dist-info}/RECORD

@@ -27,10 +27,10 @@ reflectorch/data_generation/priors/sampler_strategies.py,sha256=U-v5dXpFLJq939aQ
 reflectorch/data_generation/priors/scaler_mixin.py,sha256=gI64v2KOZugSJWaLKASR34fn6qVFl-aoeVA1BR5yXNg,2648
 reflectorch/data_generation/priors/subprior_sampler.py,sha256=TE8DOQhxVr69VmWSjwHyElpgVjOhZKBIPChFWNVYzRc,14769
 reflectorch/data_generation/priors/utils.py,sha256=bmIZYHq95gG68kETfNH6ygR39oitUEJ0eCO_Fb8maH0,3836
-reflectorch/data_generation/reflectivity/__init__.py,sha256=x8XivTg1ygz1Ky_N1eVvDfz2KS-9j9U2px0kQM3Bgf4,3145
-reflectorch/data_generation/reflectivity/abeles.py,sha256=3NXGXaBiOyAiFfy3Za7WATNLhTpKrNzieYdCsmljvQ8,2625
-reflectorch/data_generation/reflectivity/kinematical.py,sha256=QLX3erfSmEwP2n_x8gQlfaGr3pNAxcJ95Efx4Uu2CKk,2626
-reflectorch/data_generation/reflectivity/memory_eff.py,sha256=iIufbdEJGv9nc-Sr51gFQHEYVdgmbrAD-F3ydNE30nU,4024
+reflectorch/data_generation/reflectivity/__init__.py,sha256=MxVtNqO52iORdual2TtmSRN41TC9VmVSFH5ov-wuAJc,3202
+reflectorch/data_generation/reflectivity/abeles.py,sha256=Pcov-m0HImw1DOR57t0OsBOLZs3MA6fk7RePf_VCEZU,3097
+reflectorch/data_generation/reflectivity/kinematical.py,sha256=78E128l3DQif_vz2Ae6hjRg-69kRz7cbN0Ak5dOc5PM,2625
+reflectorch/data_generation/reflectivity/memory_eff.py,sha256=pbsXkcGwDorey6qVx2SlBK6IlzNJY1FeeF84cEJB_hY,4023
 reflectorch/data_generation/reflectivity/numpy_implementations.py,sha256=QBzn4yVnOdlkHeeR-ZFPS115GnLdO9lMTGO2d3YhG9I,3177
 reflectorch/data_generation/reflectivity/smearing.py,sha256=pc95Lig9NIWtHDCKnKbLp7G_kmL7_3YB6ZpDphgC2D8,4001
 reflectorch/extensions/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
@@ -39,7 +39,7 @@ reflectorch/extensions/jupyter/callbacks.py,sha256=K4Z8Mlm_Pa80YDsNOdMZLIJZyVrg0
 reflectorch/extensions/matplotlib/__init__.py,sha256=ARmc228xbZUj4fWNq5fVxZ8PN444fjDNxNP4ytVCyfo,104
 reflectorch/extensions/matplotlib/losses.py,sha256=H2vrjNqzmQ0BP4377uN4uhlH88aS5OAfA7pwRM2WHqA,686
 reflectorch/inference/__init__.py,sha256=i0KNn83XN33mLrV7bpHdLd0SXxuGCKfbQcIoa247Uts,834
-reflectorch/inference/inference_model.py,sha256=aVAZkTfVe2cweitcVVyVuqDsb6FkLbh4Wun4_K_MkTM,36599
+reflectorch/inference/inference_model.py,sha256=uxzdL2S01CN6lN737B4x5L_NIFnaCkHrNUQKwh4xNW0,36739
 reflectorch/inference/multilayer_fitter.py,sha256=0CxDpLOEp1terR4N39yFlxhvA8qAbHf_01NbmvYadck,5510
 reflectorch/inference/multilayer_inference_model.py,sha256=hH_-dJGdMOox8GHXdM_nODXDlNgh_v449xW5FmklRdo,7575
 reflectorch/inference/query_matcher.py,sha256=Dk49dW0XreeCjufzYBTKchfTdVbG6759ryV6I-wQL60,3387
@@ -76,8 +76,8 @@ reflectorch/runs/config.py,sha256=8YtUOXr_DvNvgpu59CNAr3KrQijx1AGDE95gYrsuwsM,80
 reflectorch/runs/slurm_utils.py,sha256=Zyj4_K5YpiWNJhgpFLWYHsSaaI-mgVEWsN15Gd_BhI0,2600
 reflectorch/runs/train.py,sha256=e-Jj0fwYlUB2NLDxCzy0cLsSrJbNqd5pN5T1L7-Eiig,2560
 reflectorch/runs/utils.py,sha256=bp3Nwd6pfX5yFlTVX28zDtSTo2gg2JZh9HCpZpvnJWk,12637
-reflectorch-1.2.0.dist-info/LICENSE.txt,sha256=2kX9kLKiIRiQRqUXwk3J-Ba3fqmztNu8ORskLBlAuKM,1098
-reflectorch-1.2.0.dist-info/METADATA,sha256=dulVsQJvbWfaEPJ71tgp_CVS1AwUnba2Y-Wph3c1pRk,7805
-reflectorch-1.2.0.dist-info/WHEEL,sha256=R0nc6qTxuoLk7ShA2_Y-UWkN8ZdfDBG2B6Eqpz2WXbs,91
-reflectorch-1.2.0.dist-info/top_level.txt,sha256=2EyIWrt4SeZ3hNadLXvEVpPFhyoZ4An7YflP4y_E3Fc,12
-reflectorch-1.2.0.dist-info/RECORD,,
+reflectorch-1.2.1.dist-info/LICENSE.txt,sha256=2kX9kLKiIRiQRqUXwk3J-Ba3fqmztNu8ORskLBlAuKM,1098
+reflectorch-1.2.1.dist-info/METADATA,sha256=ANjKriMGr9vTl5pvhgqpsCL40aZxh1ryKrfy66Eh_wU,7805
+reflectorch-1.2.1.dist-info/WHEEL,sha256=R0nc6qTxuoLk7ShA2_Y-UWkN8ZdfDBG2B6Eqpz2WXbs,91
+reflectorch-1.2.1.dist-info/top_level.txt,sha256=2EyIWrt4SeZ3hNadLXvEVpPFhyoZ4An7YflP4y_E3Fc,12
+reflectorch-1.2.1.dist-info/RECORD,,