Regparam grid bug fix

.github/workflows/ci_scheduled.yml

@@ -12,7 +12,7 @@ jobs:
       fail-fast: false
       matrix:
         os: [ubuntu-latest, macos-latest, windows-latest]
-        python-version: [3.8, 3.9, "3.10", "3.11", "3.12","3.12"]
+        python-version: [3.8, 3.9, "3.10", "3.11", "3.12"]
     steps:
       - uses: actions/checkout@v3
 

LICENSE

@@ -1,6 +1,6 @@
 MIT License
 
-Copyright (c) 2019-2023 Luis Fabregas, Stefan Stoll, Gunnar Jeschke, and other contributors
+Copyright (c) 2019-2024 Luis Fabregas, Stefan Stoll, Gunnar Jeschke, and other contributors
 
 Permission is hereby granted, free of charge, to any person obtaining a copy
 of this software and associated documentation files (the "Software"), to deal

deerlab/selregparam.py

@@ -8,8 +8,8 @@
 import math as m
 import deerlab as dl
 
-def selregparam(y, A, solver, method='aic', algorithm='brent', noiselvl=None,
-                searchrange=[1e-8,1e2],regop=None, weights=None, full_output=False, candidates=None):
+def selregparam(y, A, solver, method='aic', algorithm='auto', noiselvl=None,
+                searchrange=[1e-8,1e2],regop=None, weights=None, full_output=False):
     r"""
     Selection of optimal regularization parameter based on a selection criterion.
 
@@ -52,6 +52,8 @@ def selregparam(y, A, solver, method='aic', algorithm='brent', noiselvl=None,
         * ``'ncp'`` - Normalized Cumulative Periodogram (NCP)
         * ``'gml'`` - Generalized Maximum Likelihood (GML)
         * ``'mcl'`` - Mallows' C_L (MCL)
+
+        If  ``'lr'`` or ``'lc'`` is specified, the search algorithm is automatically set to ``'grid'``.
 
     weights : array_like, optional
         Array of weighting coefficients for the individual datasets in global fitting.
@@ -60,18 +62,16 @@ def selregparam(y, A, solver, method='aic', algorithm='brent', noiselvl=None,
     algorithm : string, optional
         Search algorithm: 
 
+        * ``'auto'`` - Automatically, selects algrothium based on the searchrange. If the searchrange has two elements its set to ``'brent'`` otherwise to ``'grid'``.
         * ``'grid'`` - Grid-search, slow.
         * ``'brent'`` - Brent-algorithm, fast.
 
-        The default is ``'brent'``.
-
-    searchrange : two-element list, optional 
-        Search range for the optimization of the regularization parameter with the ``'brent'`` algorithm.
-        If not specified the default search range defaults to ``[1e-8,1e2]``.
+        The default is ``'auto'``.
 
-    candidates : list, optional
-        List or array of candidate regularization parameter values to be evaluated with the ``'grid'`` algorithm. 
-        If not specified, these are automatically computed from a grid within ``searchrange``.
+    searchrange : list, optional 
+        Either the search range for the optimization of the regularization parameter with the ``'brent'`` algorithm.
+        Or if more than two values are specified, then it is interpreted as candidates for the ``'grid'`` algorithm.
+        If not specified the default search range defaults to ``[1e-8,1e2]`` and the ``'brent'`` algorithm.
 
     regop : 2D array_like, optional
         Regularization operator matrix, the default is the second-order differential operator.
@@ -108,6 +108,13 @@ def selregparam(y, A, solver, method='aic', algorithm='brent', noiselvl=None,
     # If multiple datasets are passed, concatenate the datasets and kernels
     y, A, weights,_,__, noiselvl = dl.utils.parse_multidatasets(y, A, weights, noiselvl)
 
+    if algorithm == 'auto' and len(searchrange) == 2:
+        algorithm = 'brent'
+    elif algorithm == 'auto' and len(searchrange) > 2:
+        algorithm = 'grid'
+    elif algorithm  == 'auto' and len(searchrange) < 2:
+        raise ValueError("`searchrange` must have at least two elements if `algorithm` is set to `'auto'")
+
     # The L-curve criteria require a grid-evaluation
     if method == 'lr' or method == 'lc':
         algorithm = 'grid'
@@ -121,9 +128,11 @@ def selregparam(y, A, solver, method='aic', algorithm='brent', noiselvl=None,
     evalalpha = lambda alpha: _evalalpha(alpha, y, A, L, solver, method, noiselvl, weights)
 
     # Evaluate functional over search range, using specified search method
-    if algorithm == 'brent':
-                    
+    if algorithm == 'brent':    
+
         # Search boundaries
+        if len(searchrange) != 2:
+            raise ValueError("Search range must have two elements for the 'brent' algorithm.")
         lga_min = m.log10(searchrange[0])
         lga_max = m.log10(searchrange[1])
 
@@ -148,10 +157,10 @@ def register_ouputs(optout):
     elif algorithm=='grid':
 
         # Get range of potential alpha values candidates
-        if candidates is None:
+        if len(searchrange) == 2:
             alphaCandidates = 10**np.linspace(np.log10(searchrange[0]),np.log10(searchrange[1]),60)
         else: 
-            alphaCandidates = np.atleast_1d(candidates)
+            alphaCandidates = np.atleast_1d(searchrange)
 
         # Evaluate the full grid of alpha-candidates 
         functional,residuals,penalties,alphas_evaled = tuple(zip(*[evalalpha(alpha) for alpha in alphaCandidates]))
@@ -176,6 +185,10 @@ def register_ouputs(optout):
 
         # Find minimum of the selection functional              
         alphaOpt = alphaCandidates[np.argmin(functional)]
+        functional = np.array(functional)
+        residuals = np.array(residuals)
+        penalties = np.array(penalties)
+        alphas_evaled = np.array(alphas_evaled)
     else: 
         raise KeyError("Search method not found. Must be either 'brent' or 'grid'.")
 

deerlab/solvers.py

@@ -602,8 +602,8 @@ def linear_problem(y,A,optimize_alpha,alpha):
         if optimize_alpha:
             linsolver_result = lambda AtA, Aty: parseResult(linSolver(AtA, Aty))
             output = dl.selregparam((y-yfrozen)[mask], Ared[mask,:], linsolver_result, regparam, 
-                                        weights=weights[mask], regop=L, candidates=regparamrange, 
-                                        noiselvl=noiselvl,searchrange=regparamrange,full_output=True)
+                                        weights=weights[mask], regop=L, noiselvl=noiselvl,
+                                        searchrange=regparamrange,full_output=True)
             alpha = output[0]
             alpha_stats['alphas_evaled'] = output[1]
             alpha_stats['functional'] = output[2]

docsrc/source/changelog.rst

@@ -24,12 +24,13 @@ Release Notes
 - |fix| : Something which was not working as expected or leading to errors has been fixed.
 - |api| : This will require changes in your scripts or code.
 
-Release ``v1.1.3`` - Ongoing
+Release ``v1.1.3`` - July 2024
 ------------------------------------------
 - |fix| : Removes unnecessary files from the docs
 - |efficiency| : Improves the performance of the ``dipolarkernel`` function by 10-30% (:pr:`473`), by caching the interpolation of he effective dipolar evolution time vector.
-- |fix| : Add support for Python 3.12
+- |api| : Removes the `candidates` input from `selregparam` and integrates its function into `regparamrange`.
 - |fix| : Adds support for Numpy 2.0
+- |fix| : Add support for Python 3.12
 
 
 Release ``v1.1.2`` - November 2023

examples/intermediate/ex_selregparam.py

@@ -33,7 +33,7 @@
 t = t + tmin   
 
 # Distance vector
-r = np.linspace(1.5,7,50) # nm
+r = np.linspace(1.5,7,100) # nm
 
 # Construct the model
 Vmodel = dl.dipolarmodel(t,r, experiment=dl.ex_4pdeer(tau1,tau2, pathways=[1]))
@@ -101,7 +101,7 @@
 
 # %%
 # Over and Under selection of the regularisation parameter
-# --------------------------------------------------------
+# ++++++++++++++++++++++++++++++++++++++++++++++++++++++++
 # Here we will demonstrate the effect of selecting a regularisation parameter
 # that is either too small or too large. 
 
@@ -145,8 +145,58 @@
 # As we can see when the regularisation parameter is too small we still get a high
 # quality fit in the time domain, however, our distance domain data is now way too
 # spikey and non-physical. 
+
 # In contrast when the regularisation parameter is too large we struggle to get
 # a good fit, however, we get a much smoother distance distribution.
 # This could have been seen from the selection functional above. The effect of
 # lower regularisation parameter had a smaller effect on the functional than the 
 # effect of going to a larger one. 
+
+# Plotting the full L-Curve
+# ++++++++++++++++++++++++++
+# Normally the selection of the regularisation parameter is done through a Brent optimisation
+# algorithm. This results in the L-Curve being sparsely sampled. However, the full L-Curve can be
+# generated by evaluating the functional at specified regularisation paramters.
+
+# This has the disadvantage of being computationally expensive, however, it can be useful.
+
+regparamrange = 10**np.linspace(np.log10(1e-6),np.log10(1e1),60) # Builds the range of regularisation parameters
+results_grid= dl.fit(Vmodel,Vexp,regparam='bic',regparamrange=regparamrange)
+print(results_grid)
+
+fig, axs =plt.subplots(1,3, figsize=(9,4),width_ratios=(1,1,0.1))
+alphas = results_grid.regparam_stats['alphas_evaled'][:]
+funcs = results_grid.regparam_stats['functional'][:]
+
+
+idx = np.argsort(alphas)
+
+axs[0].semilogx(alphas[idx], funcs[idx],marker='.',ls='-')
+axs[0].set_title(r"$\alpha$ selection functional");
+axs[0].set_xlabel("Regularisation Parameter")
+axs[0].set_ylabel("Functional Value ")
+
+# Just the final L-Curve
+x = results_grid.regparam_stats['residuals']
+y = results_grid.regparam_stats['penalties']
+idx = np.argsort(x)
+
+
+axs[1].loglog(x[idx],y[idx])
+
+n_points = results_grid.regparam_stats['alphas_evaled'].shape[-1]
+lams = results_grid.regparam_stats['alphas_evaled']
+norm = mpl.colors.LogNorm(vmin=lams[:].min(), vmax=lams.max())
+for i in range(n_points):
+    axs[1].plot(x[i], y[i],marker = '.', ms=8, color=cmap(norm(lams[i])))
+
+i_optimal = np.argmin(np.abs(lams - results_grid.regparam))
+axs[1].annotate(fr"$\alpha =$ {results_grid.regparam:.2g}", xy = (x[i_optimal],y[i_optimal]),arrowprops=dict(facecolor='black', shrink=0.05, width=5), xytext=(20, 20),textcoords='offset pixels')
+fig.colorbar(mpl.cm.ScalarMappable(norm=norm, cmap=cmap),cax=axs[2])
+axs[1].set_ylabel("Penalties")
+axs[2].set_ylabel("Regularisation Parameter")
+axs[1].set_xlabel("Residuals")
+axs[1].set_title("L-Curve");
+fig.tight_layout()
+
+# %%

test/test_selregparam.py

@@ -102,10 +102,11 @@ def test_unconstrained(dataset,design_matrix,regularization_matrix):
 #=======================================================================
 def test_manual_candidates(dataset,design_matrix,regularization_matrix):
     "Check that the alpha-search range can be manually passed"
-    alphas = np.linspace(-8,2,60)
-    alpha_manual = np.log10(selregparam(dataset,design_matrix,cvxnnls,method='aic',candidates=alphas,regop=regularization_matrix))
-    alpha_auto = np.log10(selregparam(dataset,design_matrix,cvxnnls,method='aic',regop=regularization_matrix))
-    assert abs(alpha_manual-alpha_auto)<1e-4
+    alphas = np.logspace(-8,3,60,base=10)
+    alpha_manual = np.log10(selregparam(dataset,design_matrix,cvxnnls,method='aic',searchrange=alphas,regop=regularization_matrix))
+    alpha_auto = np.log10(selregparam(dataset,design_matrix,cvxnnls,method='aic',searchrange=(1e-8,1e-3), regop=regularization_matrix))
+
+    assert abs(alpha_manual-alpha_auto)<1
 #=======================================================================
 
 #=======================================================================