Added test on lpls, updated centering in blm, added pls_qvals

pyblm/__init__.py

@@ -1,5 +1,5 @@
 from crossvalidation import lpls_val
-from statistics import lpls_qvals
+from statistics import lpls_qvals, pls_qvals
 from engines import pca, pcr, pls
 from engines import nipals_lpls as lpls
 #from tests import *

pyblm/crossvalidation.py

@@ -9,10 +9,11 @@ from numpy import dot,empty,zeros,sqrt,atleast_2d,argmax,asarray,median,\
      array_split,arange
 from numpy.random import shuffle
 
+from engines import pls
 from engines import nipals_lpls as lpls
 
 
-def lpls_val(X, Y, Z, a_max=2, nsets=None,alpha=.5, mean_ctr=[2,0,2], zorth=False, verbose=False):
+def lpls_val(X, Y, Z, a_max=2, nsets=None,alpha=.5, center_axis=[2,0,2], zorth=False, verbose=False):
     """Performs crossvalidation for generalisation error in lpls.
 
     The L-PLS crossvalidation is estimated just like an ordinary pls
@@ -35,7 +36,7 @@ def lpls_val(X, Y, Z, a_max=2, nsets=None,alpha=.5, mean_ctr=[2,0,2], zorth=Fals
         alpha : {float}, optional
             Parameter to control the amount of influence from Z-matrix.
             0 is none, which returns a pls-solution, 1 is max
-        mean_center : {array-like}, optional
+        center_axis : {array-like}, optional
             A three element array-like structure with elements in [-1,0,1,2],
             that decides the type of centering used.
             -1 : nothing
@@ -74,14 +75,14 @@ def lpls_val(X, Y, Z, a_max=2, nsets=None,alpha=.5, mean_ctr=[2,0,2], zorth=Fals
     for cal, val in cv(nsets, k):
         # do the training model
         dat = lpls(X[cal], Y[cal], Z, a_max=a_max, alpha=alpha,
-                   mean_ctr=mean_ctr, zorth=zorth, verbose=verbose)
+                   center_axis=center_axis, zorth=zorth, verbose=verbose)
 
         # center test data
-        if mean_ctr[0] != 1:
+        if center_axis[0] != 1:
             xi = X[val,:] - dat['mnx']
         else:
             xi = X[val] - X[cal].mean(1)[:,newaxis]
-        if mean_ctr[2] != 1:
+        if center_axis[2] != 1:
             ym = dat['mny']
         else:
             ym = Y[cal].mean(1)[:,newaxis]
@@ -94,7 +95,7 @@ def lpls_val(X, Y, Z, a_max=2, nsets=None,alpha=.5, mean_ctr=[2,0,2], zorth=Fals
         #        for n in range(10):
         #            shuffle(cal)
         #            dat = lpls(xcal, Y[cal], Z, a_max=a_max, alpha=alpha,
-        #                       mean_ctr=mean_ctr, verbose=verbose)
+        #                       center_axis=center_axis, verbose=verbose)
                     
             
     # todo: need a better support for classification error
@@ -110,7 +111,7 @@ def lpls_val(X, Y, Z, a_max=2, nsets=None,alpha=.5, mean_ctr=[2,0,2], zorth=Fals
     
     return rmsep, Yhat, aopt
 
-def pca_jk(a, aopt, n_blocks=None):
+def pca_jk(a, aopt, center_axis=[0], nsets=None):
     """Returns jack-knife segements from PCA.
     
     *Parameters*:
@@ -119,6 +120,8 @@ def pca_jk(a, aopt, n_blocks=None):
             data matrix (n x m)
         aopt : {integer}
             number of components in model.
+        center_axis:
+            Centering
         nsets : {integer}
             number of segments
 
@@ -141,13 +144,13 @@ def pca_jk(a, aopt, n_blocks=None):
         old_values = a.take(ind)
         new_values = mn_a.take(ind)
         a.put(ind, new_values)
-        dat = pca(a, aopt, mode='fast', scale='loads', center=center)
+        dat = pca(a, aopt, mode='fast', scale='loads', center_axis=center_axis)
-        PP[nn,:,:] = dat['P']
+        PP[i,:,:] = dat['P']
         a.put(ind, old_values)
         
     return PP
 
-def pls_jk(X, Y, a_opt, nsets=None, center=True, verbose=False):
+def pls_jk(X, Y, a_opt, nsets=None, center_axis=True, verbose=False):
     """ Returns jack-knife segements of W.
     
     *Parameters*:
@@ -161,7 +164,7 @@ def pls_jk(X, Y, a_opt, nsets=None, center=True, verbose=False):
         nsets : (integer), optional
             Number of jack-knife segments
         
-        center : {boolean}, optional
+        center_axis : {boolean}, optional
             - -1 : nothing
             - 0 : row center
             - 1 : column center
@@ -183,13 +186,13 @@ def pls_jk(X, Y, a_opt, nsets=None, center=True, verbose=False):
     Wcv = empty((nsets, X.shape[1], a_opt), dtype=X.dtype)
     for i, (cal, val) in enumerate(cv(k, nsets)):
         if verbose:
-            print "Segement number: %d" %i
+            print "Segment number: %d" %i
-        dat = pls(X[cal,:], Y[cal,:], a_opt, scale='loads', mode='fast')
+        dat = pls(X[cal,:], Y[cal,:], a_opt, scale='loads', mode='fast', center_axis=[0, 0])
-        Wcv[nn,:,:] = dat['W']
+        Wcv[i,:,:] = dat['W']
         
     return Wcv
 
-def lpls_jk(X, Y, Z, a_opt, nsets=None, xz_alpha=.5, mean_ctr=[2,0,2], verbose=False):
+def lpls_jk(X, Y, Z, a_opt, nsets=None, xz_alpha=.5, center_axis=[2,0,2], zorth=False, verbose=False):
     """Returns jack-knifed segments of lpls model.
 
     Jack-knifing is a method to perturb the model paramters, hopefully
@@ -215,7 +218,7 @@ def lpls_jk(X, Y, Z, a_opt, nsets=None, xz_alpha=.5, mean_ctr=[2,0,2], verbose=F
         xz_alpha : {float}, optional
             Parameter to control the amount of influence from Z-matrix.
             0 is none, which returns a pls-solution, 1 is max
-        mean_center : {array-like}, optional
+        center_axis : {array-like}, optional
             A three element array-like structure with elements in [-1,0,1,2],
             that decides the type of centering used.
             -1 : nothing
@@ -244,8 +247,8 @@ def lpls_jk(X, Y, Z, a_opt, nsets=None, xz_alpha=.5, mean_ctr=[2,0,2], verbose=F
     WWz = empty((nsets, o, a_opt), 'd')
     #WWy = empty((nsets, l, a_opt), 'd')
     for i, (cal, val) in enumerate(cv(k, nsets)):
-        dat = lpls(X[cal], Y[cal], Z, a_max=a_opt,alpha=xz_alpha, mean_ctr=mean_ctr,
+        dat = lpls(X[cal], Y[cal], Z, a_max=a_opt,alpha=xz_alpha, center_axis=center_axis,
-                   scale='loads', verbose=verbose)
+                   scale='loads', zorth=zorth, verbose=verbose)
         WWx[i,:,:] = dat['W']
         WWz[i,:,:] = dat['L']
         #WWy[i,:,:] = dat['Q']
@@ -328,8 +331,8 @@ def cv(N, K, randomise=True, sequential=False):
         otherwise interleaved ordering is used.
     
     """
-    if N > K:
+    if K > N:
-        raise ValueError, "You cannot divide a list of %d samples into more than %d segments. Yout tried: %s" %(K, K, N)
+        raise ValueError, "You cannot divide a list of %d samples into more than %d segments. Yout tried: %s" %(N, N, K)
     index = xrange(N)
     if randomise:
         from random import shuffle
@@ -375,19 +378,44 @@ def diag_cv(shape, nsets=9):
         yield training, validation
         
 
-def class_error(Yhat, Y, method='vanilla'):
+def class_error(y_hat, y, method='vanilla'):
     """ Not used.
     """
-    a_opt, k, l = Yhat.shape
+    a_opt, k, l = y_hat.shape
-    Yhat_c = zeros((k, l), dtype='d')
+    y_hat_c = zeros((k, l), dtype='d')
+    if method == vanilla:
+        pass
     for a in range(a_opt):
         for i in range(k):
-            Yhat_c[a, val, argmax(Yhat[a,val,:])] = 1.0
+            y_hat_c[a, val, argmax(y_hat[a,val,:])] = 1.0
-    err = 100*((Yhat_c + Y) == 2).sum(1)/Y.sum(0).astype('d')
+    err = 100*((y_hat_c + y) == 2).sum(1)/y.sum(0).astype('d')
 
-    return Yhat_c, err
+    return y_hat_c, err
 
-def _class_errorII(T, Y, method='lda'):
+def prediction_error(y_hat, y, method='squared'):
-    """ Not used ...
+    """Loss function on multiclass Y.
+
+    Assumes y is a binary dummy class matrix (samples, classes)
     """
-    pass
+    k, l = y.shape
+    
+    if method == 'hinge':
+        pass
+    elif method == 'smooth_hinge':
+        z = 90
+    elif method == 'abs':
+        err = abs(y - y_hat)
+    elif method == 'squared':
+        err = (y - y_hat)**2
+    elif method == '0/1':
+        pred = zeros_like(y_hat)
+        for i, row in enumerate(y_hat):
+            largest = row.argsort()[-1]
+            pred[i, largest] = 1.
+        err = abs(y - pred)
+    elif method == '1/2':
+        y_hat[y_hat>.5] = 1
+        y_hat[y_hat<.5] = 0
+        err = abs(y - y_hat)
+        
+    return err

pyblm/engines.py

@@ -13,7 +13,7 @@ from numpy.linalg import inv,svd
 from scipy.sandbox import arpack
 
 
-def pca(X, aopt, scale='scores', mode='normal', center_axis=0):
+def pca(X, aopt, scale='scores', mode='normal', center_axis=[0]):
     """ Principal Component Analysis.
 
     PCA is a low rank bilinear aprroximation to a data matrix that sequentially
@@ -80,8 +80,8 @@ def pca(X, aopt, scale='scores', mode='normal', center_axis=0):
     
     m, n = X.shape
     min_aopt = min(m, n)
-    if center_axis >= 0:
+    if center_axis != None:
-        X = X - expand_dims(X.mean(center_axis), center_axis)
+        X, mnx = center(X, center_axis[0])
         min_aopt = min_aopt - 1
     assert(aopt <= min_aopt)
     if m > (n+100) or n > (m+100):
@@ -107,10 +107,10 @@ def pca(X, aopt, scale='scores', mode='normal', center_axis=0):
         T = T/s
         P = P*s
 
-    if mode == 'fast':
+    if mode in ['fast', 'f', 'F']:
         return {'T':T, 'P':P, 'aopt':aopt}
     
-    if mode=='detailed':
+    if mode in ['detailed', 'd', 'D']:
         E = empty((aopt, m, n))
         ssq = []
         lev = []
@@ -137,7 +137,7 @@ def pca(X, aopt, scale='scores', mode='normal', center_axis=0):
     return {'T': T, 'P': P, 'E': E, 'evx': expvarx, 'leverage': lev, 'ssqx': ssq,
             'aopt': aopt, 'eigvals': e}
 
-def pcr(a, b, aopt, scale='scores',mode='normal',center_axis=0):
+def pcr(a, b, aopt, scale='scores',mode='normal',center_axis=[0, 0]):
     """ Principal Component Regression.
 
     Performs PCR on given matrix and returns results in a dictionary.
@@ -197,8 +197,7 @@ def pcr(a, b, aopt, scale='scores',mode='normal',center_axis=0):
     except:
         b = atleast_2d(b).T
         k, l = b.shape
-    if center_axis >= 0:
+        b, mny = center(b, center_axis[1])
-        b = b - expand_dims(b.mean(center_axis), center_axis)
     dat = pca(a, aopt=aopt, scale=scale, mode=mode, center_axis=center_axis)
     T = dat['T']
     weights = apply_along_axis(vnorm, 0, T)**2
@@ -207,11 +206,11 @@ def pcr(a, b, aopt, scale='scores',mode='normal',center_axis=0):
     else:
         Q = dot(b.T, T/weights)
 
-    if mode == 'fast':
+    if mode in ['fast', 'f', 'F']:
         dat.update({'Q':Q})
         return dat
 
-    if mode == 'detailed':
+    if mode in ['detailed', 'd', 'D']:
         F = empty((aopt, k, l))
         ssqy = []
         for i in range(aopt):
@@ -224,10 +223,10 @@ def pcr(a, b, aopt, scale='scores',mode='normal',center_axis=0):
     
     expvary = r_[0,  100*((T**2).sum(0)*(Q**2).sum(0)/(b**2).sum()).cumsum()[:aopt]]
     
-    dat.update({'Q': Q, 'F': F, 'evy': expvary, 'ssqy': ssqy})
+    dat.update({'Q': Q, 'F': F, 'evy': expvary, 'ssqy': ssqy, 'mny': mny})
     return dat
 
-def pls(X, Y, aopt=2, scale='scores', mode='normal', center_axis=-1):
+def pls(X, Y, aopt=2, scale='scores', mode='normal', center_axis=[0, 0]):
     """Partial Least Squares Regression.
 
     Performs PLS on given matrix and returns results in a dictionary.
@@ -316,12 +315,10 @@ def pls(X, Y, aopt=2, scale='scores', mode='normal', center_axis=-1):
     assert(m == k)
     mnx, mny = 0, 0
     min_aopt = min(m, n)
-    if center_axis >= 0:
+    if center_axis != None:
-        mnx = expand_dims(X.mean(center_axis), center_axis)
+        X, mnx = center(X, center_axis[0])
-        X = X - mnx
+        Y, mny = center(Y, center_axis[1])
         min_aopt = min_aopt - 1
-        mny = expand_dims(Y.mean(center_axis), center_axis)
-        Y = Y - mny 
     assert(aopt > 0 and aopt < min_aopt)
     
     W = empty((n, aopt))
@@ -361,7 +358,7 @@ def pls(X, Y, aopt=2, scale='scores', mode='normal', center_axis=-1):
         T[:,i] = t.ravel()
         W[:,i] = w.ravel()
 
-        if mode == 'fast' and i == (aopt - 1):
+        if mode in ['fast', 'f', 'F'] and i == (aopt - 1):
             if scale == 'loads':
                 tnorm = sqrt(tt)
                 T = T/tnorm
@@ -376,7 +373,7 @@ def pls(X, Y, aopt=2, scale='scores', mode='normal', center_axis=-1):
     qnorm = apply_along_axis(vnorm, 0, Q)
     tnorm = sqrt(tt)
     pp = (P**2).sum(0)
-    if mode == 'detailed':
+    if mode in ['detailed', 'd', 'D']:
         E = empty((aopt, m, n))
         F = empty((aopt, k, l))
         ssqx, ssqy = [], []
@@ -416,7 +413,7 @@ def pls(X, Y, aopt=2, scale='scores', mode='normal', center_axis=-1):
             'evx': expvarx, 'evy': expvary, 'ssqx': ssqx, 'ssqy': ssqy,
             'leverage': leverage, 'mnx': mnx, 'mny': mny}
 
-def nipals_lpls(X, Y, Z, a_max, alpha=.7, mean_ctr=[2, 0, 2], scale='scores', zorth = False, verbose=False):
+def nipals_lpls(X, Y, Z, a_max, alpha=.7, center_axis=[2, 0, 2], scale='scores', zorth = False, verbose=False):
     """ L-shaped Partial Least Sqaures Regression by the nipals algorithm.
 
     An L-shaped low rank model aproximates three matrices in a hyploid
@@ -437,7 +434,7 @@ def nipals_lpls(X, Y, Z, a_max, alpha=.7, mean_ctr=[2, 0, 2], scale='scores', zo
         alpha : {float}, optional
             Parameter to control the amount of influence from Z-matrix.
             0 is none, which returns a pls-solution, 1 is max
-        mean_center : {array-like}, optional
+        center_axis : {array-like}, optional
             A three element array-like structure with elements in [-1,0,1,2],
             that decides the type of centering used.
             -1 : nothing
@@ -500,16 +497,19 @@ def nipals_lpls(X, Y, Z, a_max, alpha=.7, mean_ctr=[2, 0, 2], scale='scores', zo
     m, n = X.shape
     k, l = Y.shape
     u, o = Z.shape
-    max_rank = min(m, n) + 1
+    max_rank = min(m, n)
-    assert (a_max > 0 and a_max < max_rank), "Number of comp error:\
-    tried: %d, max_rank: %d" %(a_max, max_rank)
     
-    if mean_ctr != None:
+    
-        xctr, yctr, zctr = mean_ctr
+    if center_axis != None:
+        xctr, yctr, zctr = center_axis
         X, mnX = center(X, xctr)
         Y, mnY = center(Y, yctr)
         Z, mnZ = center(Z, zctr)
+        max_rank = max_rank -1
+    assert (a_max > 0 and a_max < max_rank), "Number of comp error:\
+    tried: %d, max_rank: %d" %(a_max, max_rank)    
 
+    # initial variance
     varX = (X**2).sum()
     varY = (Y**2).sum()
     varZ = (Z**2).sum()
@@ -670,7 +670,13 @@ def center(a, axis):
             Centered data matrix
         mn : {array}
             Location vector/matrix
+
     """
+
+    ### TODO ###
+    # Perhaps not(!) use broadcasting and return full centering
+    # matrix instead ?
+
     
     # check if we have a vector
     is_vec = len(a.shape) == 1
@@ -678,13 +684,13 @@ def center(a, axis):
         is_vec = a.shape[0] == 1 or a.shape[1] == 1
     if is_vec:
         if axis == 2:
-            warnings.warn("Double centering of vecor ignored, using ordinary centering")
+            warnings.warn("Double centering of vector ignored, using ordinary centering")
         if axis == -1:
             mn = 0
         else:
             mn = a.mean()
         return a - mn, mn
-    # !!!fixme: use broadcasting
+    
     if axis == -1:
         mn = zeros((1,a.shape[1],))
         #mn = tile(mn, (a.shape[0], 1))
@@ -695,6 +701,7 @@ def center(a, axis):
         mn = a.mean(1)[:,newaxis]
         #mn = tile(mn, (1, a.shape[1]))
     elif axis == 2:
+        #fixme: double centering returns column mean as loc-vector, ok?
         mn = a.mean(0)[newaxis] + a.mean(1)[:,newaxis] - a.mean()
         return a - mn , a.mean(0)[newaxis]
     else:

pyblm/statistics.py

@@ -1,6 +1,6 @@
 """ A collection of some statistical utitlites used.
 """
-__all__ = ['hotelling', 'lpls_qvals']
+__all__ = ['hotelling', 'lpls_qvals', 'pls_qvals']
 __docformat__ = 'restructuredtext en'
 
 from math import sqrt as msqrt
@@ -9,7 +9,8 @@ from numpy import dot,empty,zeros,eye,median,sign,arange,argsort
 from numpy.linalg import svd,inv,det
 from numpy.random import shuffle
 
-from crossvalidation import lpls_jk
+from crossvalidation import lpls_jk, pls_jk
+from engines import pls
 from engines import nipals_lpls as lpls
 
 
@@ -174,8 +175,9 @@ def _ensure_strict(C, only_flips=True):
     return Cm*S
 
 def lpls_qvals(X, Y, Z, aopt=None, alpha=.3, zx_alpha=.5, n_iter=20,
-               sim_method='shuffle',p_center='med', cov_center=median,
+               sim_method='shuffle', p_center='med', cov_center=median,
-               crot=True,strict=False,mean_ctr=[2,0,2], nsets=None):
+               crot=True, strict=False, center_axis=[2,0,2], nsets=None,
+               zorth=False):
 
     """Returns qvals for l-pls model by permutation analysis.
 
@@ -195,7 +197,7 @@ def lpls_qvals(X, Y, Z, aopt=None, alpha=.3, zx_alpha=.5, n_iter=20,
         alpha : {float}, optional
             Parameter to control the amount of influence from Z-matrix.
             0 is none, which returns a pls-solution, 1 is max
-        mean_center : {array-like}, optional
+        center_axis : {array-like}, optional
             A three element array-like structure with elements in [-1,0,1,2],
             that decides the type of centering used.
             -1 : nothing
@@ -242,8 +244,8 @@ def lpls_qvals(X, Y, Z, aopt=None, alpha=.3, zx_alpha=.5, n_iter=20,
     pert_tsq_z = zeros((k, n_iter), dtype='d') # (nzvars x n_subsets)
 
     # Full model
-    dat = lpls(X, Y, Z, aopt, scale='loads', mean_ctr=mean_ctr)
+    dat = lpls(X, Y, Z, aopt, scale='loads', center_axis=center_axis, zorth=zorth)
-    Wc, Lc = lpls_jk(X, Y, Z ,aopt)
+    Wc, Lc = lpls_jk(X, Y, Z ,aopt, zorth=zorth)
     cal_tsq_x = hotelling(Wc, dat['W'], alpha=alpha)
     cal_tsq_z = hotelling(Lc, dat['L'], alpha=alpha)
     
@@ -252,13 +254,92 @@ def lpls_qvals(X, Y, Z, aopt=None, alpha=.3, zx_alpha=.5, n_iter=20,
     for i in range(n_iter):
         indi = index.copy()
         shuffle(indi)
-        dat = lpls(X, Y[indi,:], Z, aopt, scale='loads', mean_ctr=mean_ctr)
+        dat = lpls(X, Y[indi,:], Z, aopt, scale='loads', center_axis=center_axis, zorth=zorth)
         Wi, Li = lpls_jk(X, Y[indi,:], Z, aopt, nsets=nsets)
         pert_tsq_x[:,i] = hotelling(Wi, dat['W'], alpha=alpha)
         pert_tsq_z[:,i] = hotelling(Li, dat['L'], alpha=alpha)
    
     return _fdr(cal_tsq_z, pert_tsq_z, median), _fdr(cal_tsq_x, pert_tsq_x, median)
 
+
+def pls_qvals(X, Y, aopt, alpha=.3, zx_alpha=.5, n_iter=20,
+              sim_method='shuffle',p_center='med', cov_center=median,
+              crot=True,strict=False, center_axis=[0,0], nsets=None, zorth=False):
+
+    """Returns qvals for pls model by permutation analysis.
+
+    The response (Y) is randomly permuted, and the number of false positives
+    is registered by comparing hotellings T2 statistics of the calibration model.
+    
+    *Parameters*:
+    
+        X : {array}
+            Main data matrix (m, n)
+        Y : {array}
+            External row data (m, l)
+        aopt : {integer}
+            Optimal number of components
+        center_axis : {array-like}, optional
+            A two element array-like structure with elements in [-1,0,1,2],
+            that decides the type of centering used.
+            -1 : nothing
+            0 : row center
+            1 : column center
+            2 : double center
+        n_iter : {integer}, optional
+            Number of permutations
+        sim_method : ['shuffle'], optional
+            Permutation method
+        p_center : {'median', 'mean', 'cal_model'}, optional
+            Location method for sub-segments
+        cov_center : {py_func}, optional
+            Location function
+        alpha : {float}, optional
+            Regularisation towards pooled covariance estimate.
+        crot : {boolean}, optional
+            Rotate sub-segmentss toward calibration model.
+        strict : {boolean}, optional
+            Only rotate 90 degree
+        nsets : {integer}
+            Number of crossvalidation segements
+    
+    *Reference*:
+
+        Gidskehaug et al., A framework for significance analysis of
+        gene expression data using dimension reduction methods, BMC
+        bioinformatics, 2007
+    """
+    
+    m, n = X.shape
+    try:
+        my, l = Y.shape
+    except:
+        # make Y a column vector
+        Y = atleast_2d(Y).T
+        my, l = Y.shape
+    assert(m==my)
+
+    # Full model
+    dat = pls(X, Y, aopt, scale='loads')
+    # Submodels
+    Wc = pls_jk(X, Y , aopt)
+
+    cal_tsq_x = hotelling(Wc, dat['W'], alpha=alpha)
+    
+    # Perturbations
+    pert_tsq_x = zeros((n, n_iter), dtype='d') # (nxvars x n_subsets)
+    index = arange(m)
+    for i in range(n_iter):
+        indi = index.copy()
+        shuffle(indi)
+        dat = pls(X, Y[indi,:], aopt, scale='loads', center_axis=center_axis)
+        Wi = pls_jk(X, Y[indi,:], aopt, nsets=nsets, center_axis=center_axis)
+        pert_tsq_x[:,i] = hotelling(Wi, dat['W'], alpha=alpha)
+   
+    return _fdr(cal_tsq_x, pert_tsq_x, median)
+
+
+
 def _fdr(tsq, tsqp, loc_method=median):
     """Returns false discovery rate.
 
@@ -306,3 +387,4 @@ def _fdr(tsq, tsqp, loc_method=median):
     fd_rate = fp/n_signif
     fd_rate[fd_rate>1] = 1
     return fd_rate
+

tests/test_lplsengine.py

@@ -10,8 +10,8 @@ from numpy.random import rand, randn
 from numpy.linalg import svd,norm
 restore_path()
 
-def blm_array(shape=(5,10), comp=3, noise=0,seed=1,dtype='d'):
+def blm_array(shape=(5, 10), comp=3, noise=0, seed=1, dtype='d'):
-    assert(min(*shape)>=comp)
+    assert(min(*shape) >= comp)
     random.seed(seed)
     t = rand(shape[0], comp)
     p = rand(shape[1], comp)
@@ -44,6 +44,7 @@ class LplsTestCase(NumpyTestCase):
         pass
         #raise NotImplementedError
 
+
 class testAlphaZero(LplsTestCase):
     def do(self):
         #dat = lpls(self.a, self.b, self.c, self.nc, alpha=0.0)
@@ -51,9 +52,11 @@ class testAlphaZero(LplsTestCase):
         #assert_almost_equal(t1, t2)
         pass
     
+
 class testAlphaOne(LplsTestCase):
     pass
 
+
 class testZidentity(LplsTestCase):
     def do(self):
         I = eye(self.a.shape[1])
@@ -61,6 +64,7 @@ class testZidentity(LplsTestCase):
         dat2 = lpls(self.a, self.b, self.c, self.nc, alpha=0.0)
         assert_almost_equal(dat['T'], dat2['T'])
 
+
 class testYidentity(LplsTestCase):
     def do(self):
         I = eye(self.b.shape[0], dtype=self.a.dtype)
@@ -69,33 +73,43 @@ class testYidentity(LplsTestCase):
         T = u*s
         assert_almost_equal(abs(T0), abs(T[:,:self.nc]),5)
 
+
 class testWideX(LplsTestCase):
     pass
 
+
 class testTallX(LplsTestCase):
     pass
 
+
 class testWideY(LplsTestCase):
     pass
 
+
 class testTallY(LplsTestCase):
     pass
 
+
 class testWideZ(LplsTestCase):
     pass
 
+
 class testTallZ(LplsTestCase):
     pass
 
+
 class testRankDeficientX(LplsTestCase):
     pass
 
+
 class testRankDeficientY(LplsTestCase):
     pass
 
+
 class testRankDeficientZ(LplsTestCase):
     pass
 
+
 class testCenterX(LplsTestCase):
     def do(self):
         T = lpls(self.a, self.b, self.c, self.nc, mean_ctr=[0,-1,-1])['T']