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

reflectorch/inference/scipy_fitter.py

@@ -1,248 +1,272 @@
-import warnings
-
-import numpy as np
-from scipy.optimize import minimize, curve_fit
-import torch
-
-from reflectorch.data_generation.priors.base import PriorSampler
-from reflectorch.data_generation.reflectivity import abeles_np
-
-__all__ = [
-    "standard_refl_fit",
-    "refl_fit",
-    "fit_refl_curve",
-    "restore_masked_params",
-    "get_fit_with_growth",
-]
-
-
-def standard_restore_params(fitted_params) -> dict:
-    num_layers = (fitted_params.size - 2) // 3
-
-    return dict(
-        thickness=fitted_params[:num_layers],
-        roughness=fitted_params[num_layers:2 * num_layers + 1],
-        sld=fitted_params[2 * num_layers + 1:],
-    )
-
-
-def mse_loss(curve1, curve2):
-    return np.sum((curve1 - curve2) ** 2)
-
-def standard_refl_fit(
-        q: np.ndarray, curve: np.ndarray,
-        init_params: np.ndarray,
-        bounds: np.ndarray = None,
-        refl_generator=abeles_np,
-        restore_params_func=standard_restore_params,
-        scale_curve_func=np.log10,
-        **kwargs
-):
-    if bounds is not None:
-        kwargs['bounds'] = bounds
-        init_params = np.clip(init_params, *bounds)
-
-    res = curve_fit(
-        standard_get_scaled_curve_func(
-            refl_generator=refl_generator,
-            restore_params_func=restore_params_func,
-            scale_curve_func=scale_curve_func,
-        ),
-        q, scale_curve_func(curve),
-        p0=init_params, **kwargs
-    )
-
-    curve = refl_generator(q, **restore_params_func(res[0]))
-    return res[0], curve
-
-def refl_fit(
-        q: np.ndarray, 
-        curve: np.ndarray,
-        init_params: np.ndarray,
-        prior_sampler: PriorSampler,
-        bounds: np.ndarray = None,
-        error_bars: np.ndarray = None,
-        scale_curve_func=np.log10,
-        reflectivity_kwargs: dict = None,
-        **kwargs
-):
-    if bounds is not None:
-        # introduce a small perturbation for fixed bounds
-        epsilon = 1e-6
-        adjusted_bounds = bounds.copy()
-
-        for i in range(bounds.shape[1]): 
-            if bounds[0, i] == bounds[1, i]:
-                adjusted_bounds[0, i] -= epsilon
-                adjusted_bounds[1, i] += epsilon
-
-        init_params = np.clip(init_params, *adjusted_bounds)
-        kwargs['bounds'] = adjusted_bounds
-
-    reflectivity_kwargs = reflectivity_kwargs or {}
-    for key, value in reflectivity_kwargs.items():
-        if isinstance(value, float):
-            reflectivity_kwargs[key] = torch.tensor([[value]], dtype=torch.float64)
-        elif isinstance(value, np.ndarray):
-            reflectivity_kwargs[key] = torch.tensor(value, dtype=torch.float32).unsqueeze(0)       
-
-    res = curve_fit(
-        f=get_scaled_curve_func(
-            scale_curve_func=scale_curve_func,
-            prior_sampler=prior_sampler,
-            reflectivity_kwargs=reflectivity_kwargs,
-        ),
-        xdata=q, 
-        ydata=scale_curve_func(curve),
-        p0=init_params,
-        sigma=error_bars if error_bars is not None else None,
-        absolute_sigma=True,
-        **kwargs
-    )
-
-    curve = prior_sampler.param_model.reflectivity(torch.tensor(q, dtype=torch.float64), 
-                                                   torch.tensor(res[0], dtype=torch.float64).unsqueeze(0), 
-                                                   **reflectivity_kwargs).squeeze().numpy()
-    return res[0], curve
-
-
-def get_fit_with_growth(
-        q: np.ndarray, 
-        curve: np.ndarray,
-        init_params: np.ndarray,
-        bounds: np.ndarray = None,
-        init_d_change: float = 0.,
-        max_d_change: float = 30.,
-        scale_curve_func=np.log10,
-        **kwargs
-):
-    init_params = np.array(list(init_params) + [init_d_change])
-    if bounds is not None:
-        bounds = np.concatenate([bounds, np.array([0, max_d_change])[..., None]], -1)
-
-    params, curve = standard_refl_fit(
-        q, 
-        curve, 
-        init_params, 
-        bounds, 
-        refl_generator=growth_reflectivity,
-        restore_params_func=get_restore_params_with_growth_func(q_size=q.size, d_idx=0),
-        scale_curve_func=scale_curve_func, 
-        **kwargs
-    )
-
-    params[0] += params[-1] / 2
-    return params, curve
-
-
-def fit_refl_curve(q: np.ndarray, curve: np.ndarray,
-                   init_params: np.ndarray,
-                   bounds: np.ndarray = None,
-                   refl_generator=abeles_np,
-                   restore_params_func=standard_restore_params,
-                   scale_curve_func=np.log10,
-                   **kwargs
-                   ) -> np.ndarray:
-    fitting_func = get_fitting_func(
-        q=q, curve=curve,
-        refl_generator=refl_generator,
-        restore_params_func=restore_params_func,
-        scale_curve_func=scale_curve_func,
-    )
-
-    res = minimize(fitting_func, init_params, bounds=bounds, **kwargs)
-
-    if not res.success:
-        warnings.warn(f"Minimization did not converge.")
-    return res.x
-
-def standard_get_scaled_curve_func(
-        refl_generator=abeles_np,
-        restore_params_func=standard_restore_params,
-        scale_curve_func=np.log10,
-):
-    def scaled_curve_func(q, *fitted_params):
-        fitted_params = restore_params_func(np.asarray(fitted_params))
-        fitted_curve = refl_generator(q, **fitted_params)
-        scaled_curve = scale_curve_func(fitted_curve)
-        return scaled_curve
-
-    return scaled_curve_func
-
-def get_scaled_curve_func(
-        scale_curve_func=np.log10,
-        prior_sampler: PriorSampler = None,
-        reflectivity_kwargs: dict = None,
-):  
-    reflectivity_kwargs = reflectivity_kwargs or {}
-    
-    def scaled_curve_func(q, *fitted_params):
-        q_tensor = torch.from_numpy(q).to(torch.float64)
-        fitted_params_tensor = torch.tensor(fitted_params, dtype=torch.float64).unsqueeze(0)
-        
-        fitted_curve_tensor = prior_sampler.param_model.reflectivity(q_tensor, fitted_params_tensor, **reflectivity_kwargs)
-        fitted_curve = fitted_curve_tensor.squeeze().numpy()
-        
-        scaled_curve = scale_curve_func(fitted_curve)
-        return scaled_curve
-
-    return scaled_curve_func
-
-
-def get_fitting_func(
-        q: np.ndarray,
-        curve: np.ndarray,
-        refl_generator=abeles_np,
-        restore_params_func=standard_restore_params,
-        scale_curve_func=np.log10,
-        loss_func=mse_loss,
-):
-    scaled_curve = scale_curve_func(curve)
-
-    def fitting_func(fitted_params):
-        fitted_params = restore_params_func(fitted_params)
-        fitted_curve = refl_generator(q, **fitted_params)
-        loss = loss_func(scale_curve_func(fitted_curve), scaled_curve)
-        return loss
-
-    return fitting_func
-
-
-def restore_masked_params(fixed_params, fixed_mask):
-    def restore_params(fitted_params) -> dict:
-        params = np.empty_like(fixed_mask).astype(fitted_params.dtype)
-        params[fixed_mask] = fixed_params
-        params[~fixed_mask] = fitted_params
-        return standard_restore_params(params)
-
-    return restore_params
-
-
-def base_params2growth(base_params: dict, d_shift: np.ndarray, d_idx: int = 0) -> dict:
-    d_init = base_params['thickness'][None]
-    q_size = d_shift.size
-    d = d_init.repeat(q_size, 0)
-    d[:, d_idx] = d[:, d_idx] + d_shift
-
-    roughness = np.broadcast_to(base_params['roughness'][None], (q_size, base_params['roughness'].size))
-    sld = np.broadcast_to(base_params['sld'][None], (q_size, base_params['sld'].size))
-
-    return {
-        'thickness': d,
-        'roughness': roughness,
-        'sld': sld,
-    }
-
-
-def get_restore_params_with_growth_func(q_size: int, d_idx: int = 0):
-    def restore_params_with_growth(fitted_params) -> dict:
-        fitted_params, delta_d = fitted_params[:-1], fitted_params[-1]
-        base_params = standard_restore_params(fitted_params)
-        d_shift = np.linspace(0, delta_d, q_size)
-        return base_params2growth(base_params, d_shift, d_idx)
-
-    return restore_params_with_growth
-
-
-def growth_reflectivity(q: np.ndarray, **kwargs):
-    return abeles_np(q[..., None], **kwargs).flatten()
+import warnings
+
+import numpy as np
+from scipy.optimize import minimize, curve_fit
+import torch
+
+from reflectorch.data_generation.priors.base import PriorSampler
+from reflectorch.data_generation.reflectivity import abeles_np
+
+__all__ = [
+    "standard_refl_fit",
+    "refl_fit",
+    "fit_refl_curve",
+    "restore_masked_params",
+    "get_fit_with_growth",
+]
+
+
+def standard_restore_params(fitted_params) -> dict:
+    num_layers = (fitted_params.size - 2) // 3
+
+    return dict(
+        thickness=fitted_params[:num_layers],
+        roughness=fitted_params[num_layers:2 * num_layers + 1],
+        sld=fitted_params[2 * num_layers + 1:],
+    )
+
+
+def mse_loss(curve1, curve2):
+    return np.sum((curve1 - curve2) ** 2)
+
+def standard_refl_fit(
+        q: np.ndarray, curve: np.ndarray,
+        init_params: np.ndarray,
+        bounds: np.ndarray = None,
+        refl_generator=abeles_np,
+        restore_params_func=standard_restore_params,
+        scale_curve_func=np.log10,
+        **kwargs
+):
+    if bounds is not None:
+        kwargs['bounds'] = bounds
+        init_params = np.clip(init_params, *bounds)
+
+    res = curve_fit(
+        standard_get_scaled_curve_func(
+            refl_generator=refl_generator,
+            restore_params_func=restore_params_func,
+            scale_curve_func=scale_curve_func,
+        ),
+        q, scale_curve_func(curve),
+        p0=init_params, **kwargs
+    )
+
+    curve = refl_generator(q, **restore_params_func(res[0]))
+    return res[0], curve
+
+def refl_fit(
+        q: np.ndarray, 
+        curve: np.ndarray,
+        init_params: np.ndarray,
+        prior_sampler: PriorSampler,
+        bounds: np.ndarray = None,
+        error_bars: np.ndarray = None,
+        scale_curve_func=np.log10,
+        method: str = 'trf', #'lm', 'trf'
+        polishing_max_steps: int = None,
+        reflectivity_kwargs: dict = None,
+        **kwargs
+):
+    if bounds is not None:
+        # introduce a small perturbation for fixed bounds
+        epsilon = 1e-6
+        adjusted_bounds = bounds.copy()
+
+        for i in range(bounds.shape[1]): 
+            if bounds[0, i] == bounds[1, i]:
+                adjusted_bounds[0, i] -= epsilon
+                adjusted_bounds[1, i] += epsilon
+
+        init_params = np.clip(init_params, *adjusted_bounds)
+        if method != 'lm':
+            kwargs['bounds'] = adjusted_bounds
+
+    reflectivity_kwargs = reflectivity_kwargs or {}
+    for key, value in reflectivity_kwargs.items():
+        if isinstance(value, float):
+            reflectivity_kwargs[key] = torch.tensor([[value]], dtype=torch.float64)
+        elif isinstance(value, np.ndarray):
+            reflectivity_kwargs[key] = torch.tensor(value, dtype=torch.float32).unsqueeze(0)     
+
+    curve = np.clip(curve, a_min=1e-12, a_max=None)
+
+    if error_bars is not None and scale_curve_func == np.log10:
+        error_bars = np.clip(error_bars, a_min=1e-20, a_max=None)
+        scaled_error_bars = error_bars / (curve * np.log(10))
+    else:
+        scaled_error_bars = None  
+
+    if polishing_max_steps is not None:
+        if method == 'lm':
+            kwargs['maxfev'] = polishing_max_steps
+        else:
+            kwargs['max_nfev'] = polishing_max_steps
+
+    res = curve_fit(
+        f=get_scaled_curve_func(
+            scale_curve_func=scale_curve_func,
+            prior_sampler=prior_sampler,
+            reflectivity_kwargs=reflectivity_kwargs,
+        ),
+        xdata=q, 
+        ydata=scale_curve_func(curve).reshape(-1),
+        p0=init_params,
+        sigma=scaled_error_bars,
+        absolute_sigma=True,
+        method=method,
+        **kwargs
+    )
+
+    curve = prior_sampler.param_model.reflectivity(torch.tensor(q, dtype=torch.float64), 
+                                                   torch.tensor(res[0], dtype=torch.float64).unsqueeze(0), 
+                                                   **reflectivity_kwargs).squeeze().numpy()
+    # cov matrix --> variance of the parameter estimate
+    if res[1] is not None and np.ndim(res[1]) == 2 and np.all(np.isfinite(res[1])):
+        pol_param_errs = np.sqrt(np.diag(res[1]))
+    else: 
+        pol_param_errs = np.full_like(res[1], np.nan)
+    return res[0], pol_param_errs, curve
+
+
+def get_fit_with_growth(
+        q: np.ndarray, 
+        curve: np.ndarray,
+        init_params: np.ndarray,
+        bounds: np.ndarray = None,
+        init_d_change: float = 0.,
+        max_d_change: float = 30.,
+        scale_curve_func=np.log10,
+        **kwargs
+):
+    init_params = np.array(list(init_params) + [init_d_change])
+    if bounds is not None:
+        bounds = np.concatenate([bounds, np.array([0, max_d_change])[..., None]], -1)
+
+    params, curve = standard_refl_fit(
+        q, 
+        curve, 
+        init_params, 
+        bounds, 
+        refl_generator=growth_reflectivity,
+        restore_params_func=get_restore_params_with_growth_func(q_size=q.size, d_idx=0),
+        scale_curve_func=scale_curve_func, 
+        **kwargs
+    )
+    
+    params[0] += params[-1] / 2
+    return params, curve
+
+
+def fit_refl_curve(q: np.ndarray, curve: np.ndarray,
+                   init_params: np.ndarray,
+                   bounds: np.ndarray = None,
+                   refl_generator=abeles_np,
+                   restore_params_func=standard_restore_params,
+                   scale_curve_func=np.log10,
+                   **kwargs
+                   ) -> np.ndarray:
+    fitting_func = get_fitting_func(
+        q=q, curve=curve,
+        refl_generator=refl_generator,
+        restore_params_func=restore_params_func,
+        scale_curve_func=scale_curve_func,
+    )
+
+    res = minimize(fitting_func, init_params, bounds=bounds, **kwargs)
+
+    if not res.success:
+        warnings.warn(f"Minimization did not converge.")
+    return res.x
+
+def standard_get_scaled_curve_func(
+        refl_generator=abeles_np,
+        restore_params_func=standard_restore_params,
+        scale_curve_func=np.log10,
+):
+    def scaled_curve_func(q, *fitted_params):
+        fitted_params = restore_params_func(np.asarray(fitted_params))
+        fitted_curve = refl_generator(q, **fitted_params)
+        scaled_curve = scale_curve_func(fitted_curve)
+        return scaled_curve
+
+    return scaled_curve_func
+
+def get_scaled_curve_func(
+        scale_curve_func=np.log10,
+        prior_sampler: PriorSampler = None,
+        reflectivity_kwargs: dict = None,
+):  
+    reflectivity_kwargs = reflectivity_kwargs or {}
+    
+    def scaled_curve_func(q, *fitted_params):
+        q_tensor = torch.from_numpy(q).to(torch.float64)
+        fitted_params_tensor = torch.tensor(fitted_params, dtype=torch.float64).unsqueeze(0)
+        
+        fitted_curve_tensor = prior_sampler.param_model.reflectivity(q_tensor, fitted_params_tensor, **reflectivity_kwargs)
+        fitted_curve = fitted_curve_tensor.squeeze().numpy()
+        
+        scaled_curve = scale_curve_func(fitted_curve)
+
+        return scaled_curve.reshape(-1)
+
+    return scaled_curve_func
+
+
+def get_fitting_func(
+        q: np.ndarray,
+        curve: np.ndarray,
+        refl_generator=abeles_np,
+        restore_params_func=standard_restore_params,
+        scale_curve_func=np.log10,
+        loss_func=mse_loss,
+):
+    scaled_curve = scale_curve_func(curve)
+
+    def fitting_func(fitted_params):
+        fitted_params = restore_params_func(fitted_params)
+        fitted_curve = refl_generator(q, **fitted_params)
+        loss = loss_func(scale_curve_func(fitted_curve), scaled_curve)
+        return loss
+
+    return fitting_func
+
+
+def restore_masked_params(fixed_params, fixed_mask):
+    def restore_params(fitted_params) -> dict:
+        params = np.empty_like(fixed_mask).astype(fitted_params.dtype)
+        params[fixed_mask] = fixed_params
+        params[~fixed_mask] = fitted_params
+        return standard_restore_params(params)
+
+    return restore_params
+
+
+def base_params2growth(base_params: dict, d_shift: np.ndarray, d_idx: int = 0) -> dict:
+    d_init = base_params['thickness'][None]
+    q_size = d_shift.size
+    d = d_init.repeat(q_size, 0)
+    d[:, d_idx] = d[:, d_idx] + d_shift
+
+    roughness = np.broadcast_to(base_params['roughness'][None], (q_size, base_params['roughness'].size))
+    sld = np.broadcast_to(base_params['sld'][None], (q_size, base_params['sld'].size))
+
+    return {
+        'thickness': d,
+        'roughness': roughness,
+        'sld': sld,
+    }
+
+
+def get_restore_params_with_growth_func(q_size: int, d_idx: int = 0):
+    def restore_params_with_growth(fitted_params) -> dict:
+        fitted_params, delta_d = fitted_params[:-1], fitted_params[-1]
+        base_params = standard_restore_params(fitted_params)
+        d_shift = np.linspace(0, delta_d, q_size)
+        return base_params2growth(base_params, d_shift, d_idx)
+
+    return restore_params_with_growth
+
+
+def growth_reflectivity(q: np.ndarray, **kwargs):
+    return abeles_np(q[..., None], **kwargs).flatten()