Merge branch 'speedup' into 'main'

Speed up prediction and outlier detection.

See merge request !9

pes_to_spec/__init__.py

@@ -2,4 +2,4 @@
 Estimate high-resolution photon spectrometer data from low-resolution non-invasive measurements.
 """
 
-VERSION = "0.2.0"
+VERSION = "0.2.1"

pes_to_spec/model.py

@@ -14,10 +14,11 @@ from sklearn.pipeline import Pipeline
 from sklearn.kernel_approximation import Nystroem
 #from sklearn.linear_model import ARDRegression
 from sklearn.linear_model import BayesianRidge
-from sklearn.covariance import EllipticEnvelope
+#from sklearn.covariance import EllipticEnvelope
 from scipy.stats import gaussian_kde
 from functools import reduce
 from itertools import product
+from time import time_ns
 
 from sklearn.base import clone, MetaEstimatorMixin
 from joblib import Parallel, delayed
@@ -637,7 +638,7 @@ class MultiOutputWithStd(MetaEstimatorMixin, BaseEstimator):
         """
         if n_jobs is None:
             n_jobs = self.n_jobs
-        y = Parallel(n_jobs=n_jobs)(
+        y = Parallel(n_jobs=n_jobs, backend="threading")(
             delayed(e.predict)(X, return_std) for e in self.estimators_
             #delayed(e.predict)(X) for e in self.estimators_
         )
@@ -650,31 +651,40 @@ class MultiOutputWithStd(MetaEstimatorMixin, BaseEstimator):
 
 class UncorrelatedDeviation(OutlierMixin, BaseEstimator):
     """
-    Detect outliers from uncorrelated whitened mean-centered inputs.
+    Detect outliers from uncorrelated inputs.
+    It uses a chi^2 sum over the features to flatten the features.
+    The standard deviation is estimated using quantiles.
+
+    Args:
+      sigma: Number of standard deviations of the chi^2 distribution.
+
     """
-    def __init__(self, contamination: float=0.0000005):
+    def __init__(self, sigma: float=5.0):
         super().__init__()
-        self.contamination = contamination
+        self.sigma = sigma
 
     def fit(self, X, y=None) -> OutlierMixin:
         """
         Does nothing.
 
         Args:
-          X: Irrelevant.
+          X: Data where outliers are.
           y: Irrelevant.
 
         Returns: Itself.
         """
-        self.dist_ = self.score_samples(X)
-        self.offset_ = -np.percentile(-self.dist_, 100.0 * self.contamination)
+        bounds_ = np.quantile(X, (0.003/2.0, 0.5, 1.0 - 0.003/2.0), axis=0)
+        self.ndof_ = float(X.shape[1] - 1.0)
+        self.med_ = bounds_[1, np.newaxis, ...]
+        self.sigma_ = (bounds_[2, np.newaxis, ...] - bounds_[0, np.newaxis, ...])/3.0
         return self
 
     def decision_function(self, X: np.ndarray) -> np.ndarray:
         """
         Return the decision function.
+        This is chi^2/ndof - 1 - sigma*sqrt(var_chi2)
         """
-        return self.offset_ - self.score_samples(X)
+        return (self.score_samples(X) - 1.0 - self.sigma*np.sqrt(2.0/self.ndof_))
 
     def score_samples(self, X: np.ndarray) -> np.ndarray:
         """
@@ -683,9 +693,9 @@ class UncorrelatedDeviation(OutlierMixin, BaseEstimator):
         Args:
           X: The new input data.
 
-        Returns: The Mahalanobis distance.
+        Returns: The chi^2 test statistic.
         """
-        return np.sqrt(np.sum(X**2, axis=1))
+        return np.sum(((X - self.med_)/self.sigma_)**2, axis=1)/float(self.ndof_)
 
     def predict(self, X):
         """
@@ -700,9 +710,8 @@ class UncorrelatedDeviation(OutlierMixin, BaseEstimator):
             Returns -1 for anomalies/outliers and +1 for inliers.
         """
         values = self.decision_function(X)
-        is_inlier = np.full(values.shape[0], -1, dtype=int)
-        is_inlier[values >= 0] = 1
-
+        is_inlier = np.full(values.shape[0], 1, dtype=int)
+        is_inlier[values > 0] = -1
         return is_inlier
 
     def score(self, X, y, sample_weight=None):
@@ -781,10 +790,10 @@ class Model(TransformerMixin, BaseEstimator):
                                 ])
         #self.ood = {ch: IsolationForest(n_jobs=-1)
         #            for ch in channels+['full']}
-        #self.ood = {ch: UncorrelatedDeviation(contamination=0.003)
-        #            for ch in channels+['full']}
-        self.ood = {ch: EllipticEnvelope(contamination=0.003)
+        self.ood = {ch: UncorrelatedDeviation(sigma=5)
                     for ch in channels+['full']}
+        #self.ood = {ch: EllipticEnvelope(contamination=0.003)
+        #            for ch in channels+['full']}
         #self.fit_model = MultiOutputWithStd(ARDRegression(n_iter=300, tol=1e-8, verbose=True), n_jobs=8)
         self.fit_model = MultiOutputWithStd(BayesianRidge(n_iter=300, tol=1e-8, verbose=True), n_jobs=8)
         #self.fit_model = FitModel()
@@ -928,13 +937,13 @@ class Model(TransformerMixin, BaseEstimator):
         E = np.fft.fftfreq(len(e), de)
         e_axis = np.linspace(-0.5*(e[-1] - e[0]), 0.5*(e[-1] - e[0]), len(e))
         # generate a gaussian
-        gaussian = np.exp(-0.5*(e_axis)**2/self.high_res_sigma**2)
-        gaussian /= np.sum(gaussian, axis=0, keepdims=True)
-        gaussian = np.clip(gaussian, a_min=1e-6, a_max=None)
-        gaussian_ft = np.fft.fft(gaussian)
+        #gaussian = np.exp(-0.5*(e_axis)**2/self.high_res_sigma**2)
+        #gaussian /= np.sum(gaussian, axis=0, keepdims=True)
+        #gaussian = np.clip(gaussian, a_min=1e-6, a_max=None)
+        #gaussian_ft = np.fft.fft(gaussian)
 
         H = np.mean(Z/D, axis=0)
-        N = np.absolute(gaussian_ft*V)**2
+        N = np.absolute(V)**2
         S = np.mean(np.absolute(D)**2, axis=0)
         H2 = np.absolute(H)**2
         nonzero = np.absolute(H) > 0.2
@@ -1080,23 +1089,45 @@ class Model(TransformerMixin, BaseEstimator):
                  the expected prediction in key "expected", the stat. uncertainty in key "unc" and
                  a (1, energy channel) array for the PCA syst. uncertainty in key "pca".
         """
+        #t = list()
+        #n = list()
+        #t += [time_ns()*1e-9]
+        #n += ["Initial"]
+
         low_res_pre = self.x_select.transform(low_res_data)
+        #t += [time_ns()*1e-9]
+        #n += ["Select"]
+
         low_pca = self.x_model.transform(low_res_pre)
-        high_pca, high_pca_unc = self.fit_model.predict(low_pca, return_std=True, n_jobs=-1)
-        #high_pca = self.fit_model.predict(low_pca)
-        #high_pca_unc = 0
+        #t += [time_ns()*1e-9]
+        #n += ["PCA x"]
+
+        high_pca, high_pca_unc = self.fit_model.predict(low_pca, return_std=True)
+        #t += [time_ns()*1e-9]
+        #n += ["Fit model"]
+
         n_trains = high_pca.shape[0]
         # Note: The whiten=True setting in the PCA model leads to an affine transformation
         pca_y = np.concatenate((high_pca,
                                 high_pca + high_pca_unc,
                                ),
                                axis=0)
+        #t += [time_ns()*1e-9]
+        #n += ["Concat"]
+
         high_res_predicted = self.y_model["pca"].inverse_transform(pca_y)
         expected = high_res_predicted[:n_trains, :]
         e_plus = high_res_predicted[n_trains:(2*n_trains), :]
         unc = np.fabs(e_plus - expected)
         pca_unc = self.y_model['unc'].uncertainty()
         total_unc = np.sqrt(pca_unc**2 + unc**2)
+        #t += [time_ns()*1e-9]
+        #n += ["Unc"]
+
+        #t = np.diff(np.array(t))
+        #n = n[1:]
+        #print("Times")
+        #print(dict(zip(n, t)))
 
         return dict(expected=expected,
                     unc=unc,