reflectorch 1.3.0__py3-none-any.whl → 1.5.0__py3-none-any.whl

reflectorch/inference/multilayer_inference_model.py

@@ -1,193 +1,193 @@
-from typing import Tuple
-
-import torch
-from torch import Tensor
-import numpy as np
-
-from reflectorch.inference.inference_model import (
-    InferenceModel,
-)
-from reflectorch.data_generation.reflectivity import kinematical_approximation_np, abeles_np
-
-from reflectorch.data_generation.priors import (
-    MultilayerStructureParams,
-    SimpleMultilayerSampler,
-)
-from reflectorch.inference.record_time import print_time
-from reflectorch.inference.scipy_fitter import standard_refl_fit
-from reflectorch.inference.multilayer_fitter import MultilayerFit
-
-
-class MultilayerInferenceModel(InferenceModel):
-    def predict(self,
-                intensity: np.ndarray,
-                scattering_angle: np.ndarray,
-                attenuation: np.ndarray,
-                priors: np.ndarray = None,
-                preprocessing_parameters: dict = None,
-                polish: bool = True,
-                use_raw_q: bool = False,
-                **kwargs
-                ) -> dict:
-
-        with print_time("everything"):
-            with print_time("preprocess"):
-                preprocessed_dict = self.preprocess(
-                    intensity, scattering_angle, attenuation, **(preprocessing_parameters or {})
-                )
-
-            preprocessed_curve = preprocessed_dict["curve_interp"]
-
-            raw_curve, raw_q = preprocessed_dict["curve"], preprocessed_dict["q_values"]
-
-            with print_time("predict_from_preprocessed_curve"):
-                preprocessed_dict.update(self.predict_from_preprocessed_curve(
-                    preprocessed_curve, priors,
-                    raw_curve=(raw_curve if use_raw_q else None),
-                    raw_q=raw_q,
-                    polish=polish,
-                    use_raw_q=use_raw_q,
-                    **kwargs
-                ))
-
-            return preprocessed_dict
-
-    def predict_from_preprocessed_curve(self,
-                                        curve: np.ndarray,
-                                        priors: np.ndarray = None, *,  # ignore the priors so far
-                                        polish: bool = True,
-                                        raw_curve: np.ndarray = None,
-                                        raw_q: np.ndarray = None,
-                                        clip_prediction: bool = True,
-                                        use_raw_q: bool = False,
-                                        use_sampler: bool = False,
-                                        fitted_time_limit: float = 3.,
-                                        sampler_rel_bounds: float = 0.3,
-                                        polish_with_abeles: bool = False,
-                                        **kwargs
-                                        ) -> dict:
-
-        scaled_curve = self._scale_curve(curve)
-
-        predicted_params, parametrized = self._simple_prediction(scaled_curve)
-
-        if use_sampler:
-            parametrized: Tensor = self._sampler_solution(
-                curve, parametrized,
-                time_limit=fitted_time_limit,
-                rel_bounds=sampler_rel_bounds,
-            )
-
-        init_raw_q = raw_q
-
-        if raw_curve is None:
-            raw_curve = curve
-            raw_q = self.q.squeeze().cpu().numpy()
-            raw_q_t = self.q
-        else:
-            raw_q_t = torch.from_numpy(raw_q).to(self.q)
-
-        # if q_ratio != 1.:
-        #     predicted_params.scale_with_q(q_ratio)
-        #     raw_q = raw_q * q_ratio
-        #     raw_q_t = raw_q_t * q_ratio
-
-        prediction_dict = {
-            "params": parametrized.squeeze().cpu().numpy(),
-            "param_names": list(self._prior_sampler.multilayer_model.PARAMETER_NAMES),
-            "curve_predicted": predicted_params.reflectivity(raw_q_t).squeeze().cpu().numpy()
-        }
-
-        # sld_x_axis, sld_profile, _ = get_density_profiles(
-        #     predicted_params.thicknesses, predicted_params.roughnesses, predicted_params.slds, num=1024,
-        # )
-        #
-        # prediction_dict['sld_profile'] = sld_profile.squeeze().cpu().numpy()
-        # prediction_dict['sld_x_axis'] = sld_x_axis.squeeze().cpu().numpy()
-
-        if polish:
-            prediction_dict.update(self._polish_prediction(
-                raw_q, raw_curve, parametrized, q_values=init_raw_q, use_kinematical=True
-            ))
-        if polish_with_abeles:
-            prediction_dict.update(self._polish_prediction(
-                raw_q, raw_curve, parametrized, q_values=init_raw_q, use_kinematical=False
-            ))
-
-        return prediction_dict
-
-    def _simple_prediction(self, scaled_curve) -> Tuple[MultilayerStructureParams, Tensor]:
-        with torch.no_grad():
-            self.trainer.model.eval()
-            scaled_params = self.trainer.model(scaled_curve)
-
-        predicted_params, parametrized = self._restore_predicted_params(scaled_params)
-        return predicted_params, parametrized
-
-    def _restore_predicted_params(self, scaled_params: Tensor) -> Tuple[MultilayerStructureParams, Tensor]:
-        parametrized = self._prior_sampler.restore_params2parametrized(scaled_params)
-        predicted_params: MultilayerStructureParams = self._prior_sampler.restore_params(scaled_params)
-        return predicted_params, parametrized
-
-    @print_time
-    def _sampler_solution(
-            self,
-            curve: Tensor or np.ndarray,
-            predicted_params: Tensor,
-            batch_size: int = 2 ** 13,
-            time_limit: float = 3.,
-            rel_bounds: float = 0.3,
-    ) -> Tensor:
-
-        fit_obj = MultilayerFit.from_prediction(
-            predicted_params, self._prior_sampler, self.q, torch.as_tensor(curve).to(self.q),
-            batch_size=batch_size, rel_bounds=rel_bounds,
-        )
-
-        fit_obj.run_fixed_time(time_limit)
-
-        best_params = fit_obj.get_best_solution()
-
-        return best_params
-
-    @property
-    def _prior_sampler(self) -> SimpleMultilayerSampler:
-        return self.trainer.loader.prior_sampler
-
-    @print_time
-    def _polish_prediction(self,
-                           q: np.ndarray,
-                           curve: np.ndarray,
-                           predicted_params: Tensor,
-                           q_values: np.ndarray,
-                           use_kinematical: bool = True,
-                           ) -> dict:
-
-        params = predicted_params.squeeze().cpu().numpy()
-        polished_params_dict = {}
-
-        if use_kinematical:
-            refl_generator = kinematical_approximation_np
-        else:
-            refl_generator = abeles_np
-
-        try:
-            polished_params_arr, curve_polished = standard_refl_fit(
-                q, curve, params, restore_params_func=self._prior_sampler.restore_np_params,
-                refl_generator=refl_generator,
-                bounds=self._prior_sampler.get_np_bounds(),
-            )
-            params = self._prior_sampler.restore_np_params(polished_params_arr)
-            if q_values is None:
-                q_values = q
-            curve_polished = abeles_np(q_values, **params)
-
-        except Exception as err:
-            self.log.exception(err)
-            polished_params_arr = params
-            curve_polished = np.zeros_like(q)
-
-        polished_params_dict['params_polished'] = polished_params_arr
-        polished_params_dict['curve_polished'] = curve_polished
-
-        return polished_params_dict
+from typing import Tuple
+
+import torch
+from torch import Tensor
+import numpy as np
+
+from reflectorch.inference.inference_model import (
+    InferenceModel,
+)
+from reflectorch.data_generation.reflectivity import kinematical_approximation_np, abeles_np
+
+from reflectorch.data_generation.priors import (
+    MultilayerStructureParams,
+    SimpleMultilayerSampler,
+)
+from reflectorch.inference.record_time import print_time
+from reflectorch.inference.scipy_fitter import standard_refl_fit
+from reflectorch.inference.multilayer_fitter import MultilayerFit
+
+
+class MultilayerInferenceModel(InferenceModel):
+    def predict(self,
+                intensity: np.ndarray,
+                scattering_angle: np.ndarray,
+                attenuation: np.ndarray,
+                priors: np.ndarray = None,
+                preprocessing_parameters: dict = None,
+                polish: bool = True,
+                use_raw_q: bool = False,
+                **kwargs
+                ) -> dict:
+
+        with print_time("everything"):
+            with print_time("preprocess"):
+                preprocessed_dict = self.preprocess(
+                    intensity, scattering_angle, attenuation, **(preprocessing_parameters or {})
+                )
+
+            preprocessed_curve = preprocessed_dict["curve_interp"]
+
+            raw_curve, raw_q = preprocessed_dict["curve"], preprocessed_dict["q_values"]
+
+            with print_time("predict_from_preprocessed_curve"):
+                preprocessed_dict.update(self.predict_from_preprocessed_curve(
+                    preprocessed_curve, priors,
+                    raw_curve=(raw_curve if use_raw_q else None),
+                    raw_q=raw_q,
+                    polish=polish,
+                    use_raw_q=use_raw_q,
+                    **kwargs
+                ))
+
+            return preprocessed_dict
+
+    def predict_from_preprocessed_curve(self,
+                                        curve: np.ndarray,
+                                        priors: np.ndarray = None, *,  # ignore the priors so far
+                                        polish: bool = True,
+                                        raw_curve: np.ndarray = None,
+                                        raw_q: np.ndarray = None,
+                                        clip_prediction: bool = True,
+                                        use_raw_q: bool = False,
+                                        use_sampler: bool = False,
+                                        fitted_time_limit: float = 3.,
+                                        sampler_rel_bounds: float = 0.3,
+                                        polish_with_abeles: bool = False,
+                                        **kwargs
+                                        ) -> dict:
+
+        scaled_curve = self._scale_curve(curve)
+
+        predicted_params, parametrized = self._simple_prediction(scaled_curve)
+
+        if use_sampler:
+            parametrized: Tensor = self._sampler_solution(
+                curve, parametrized,
+                time_limit=fitted_time_limit,
+                rel_bounds=sampler_rel_bounds,
+            )
+
+        init_raw_q = raw_q
+
+        if raw_curve is None:
+            raw_curve = curve
+            raw_q = self.q.squeeze().cpu().numpy()
+            raw_q_t = self.q
+        else:
+            raw_q_t = torch.from_numpy(raw_q).to(self.q)
+
+        # if q_ratio != 1.:
+        #     predicted_params.scale_with_q(q_ratio)
+        #     raw_q = raw_q * q_ratio
+        #     raw_q_t = raw_q_t * q_ratio
+
+        prediction_dict = {
+            "params": parametrized.squeeze().cpu().numpy(),
+            "param_names": list(self._prior_sampler.multilayer_model.PARAMETER_NAMES),
+            "curve_predicted": predicted_params.reflectivity(raw_q_t).squeeze().cpu().numpy()
+        }
+
+        # sld_x_axis, sld_profile, _ = get_density_profiles(
+        #     predicted_params.thicknesses, predicted_params.roughnesses, predicted_params.slds, num=1024,
+        # )
+        #
+        # prediction_dict['sld_profile'] = sld_profile.squeeze().cpu().numpy()
+        # prediction_dict['sld_x_axis'] = sld_x_axis.squeeze().cpu().numpy()
+
+        if polish:
+            prediction_dict.update(self._polish_prediction(
+                raw_q, raw_curve, parametrized, q_values=init_raw_q, use_kinematical=True
+            ))
+        if polish_with_abeles:
+            prediction_dict.update(self._polish_prediction(
+                raw_q, raw_curve, parametrized, q_values=init_raw_q, use_kinematical=False
+            ))
+
+        return prediction_dict
+
+    def _simple_prediction(self, scaled_curve) -> Tuple[MultilayerStructureParams, Tensor]:
+        with torch.no_grad():
+            self.trainer.model.eval()
+            scaled_params = self.trainer.model(scaled_curve)
+
+        predicted_params, parametrized = self._restore_predicted_params(scaled_params)
+        return predicted_params, parametrized
+
+    def _restore_predicted_params(self, scaled_params: Tensor) -> Tuple[MultilayerStructureParams, Tensor]:
+        parametrized = self._prior_sampler.restore_params2parametrized(scaled_params)
+        predicted_params: MultilayerStructureParams = self._prior_sampler.restore_params(scaled_params)
+        return predicted_params, parametrized
+
+    @print_time
+    def _sampler_solution(
+            self,
+            curve: Tensor or np.ndarray,
+            predicted_params: Tensor,
+            batch_size: int = 2 ** 13,
+            time_limit: float = 3.,
+            rel_bounds: float = 0.3,
+    ) -> Tensor:
+
+        fit_obj = MultilayerFit.from_prediction(
+            predicted_params, self._prior_sampler, self.q, torch.as_tensor(curve).to(self.q),
+            batch_size=batch_size, rel_bounds=rel_bounds,
+        )
+
+        fit_obj.run_fixed_time(time_limit)
+
+        best_params = fit_obj.get_best_solution()
+
+        return best_params
+
+    @property
+    def _prior_sampler(self) -> SimpleMultilayerSampler:
+        return self.trainer.loader.prior_sampler
+
+    @print_time
+    def _polish_prediction(self,
+                           q: np.ndarray,
+                           curve: np.ndarray,
+                           predicted_params: Tensor,
+                           q_values: np.ndarray,
+                           use_kinematical: bool = True,
+                           ) -> dict:
+
+        params = predicted_params.squeeze().cpu().numpy()
+        polished_params_dict = {}
+
+        if use_kinematical:
+            refl_generator = kinematical_approximation_np
+        else:
+            refl_generator = abeles_np
+
+        try:
+            polished_params_arr, curve_polished = standard_refl_fit(
+                q, curve, params, restore_params_func=self._prior_sampler.restore_np_params,
+                refl_generator=refl_generator,
+                bounds=self._prior_sampler.get_np_bounds(),
+            )
+            params = self._prior_sampler.restore_np_params(polished_params_arr)
+            if q_values is None:
+                q_values = q
+            curve_polished = abeles_np(q_values, **params)
+
+        except Exception as err:
+            self.log.exception(err)
+            polished_params_arr = params
+            curve_polished = np.zeros_like(q)
+
+        polished_params_dict['params_polished'] = polished_params_arr
+        polished_params_dict['curve_polished'] = curve_polished
+
+        return polished_params_dict