Python numpy.asfortranarray函数代码示例

    def adjoint(self, inputs, outputs):
        """The adjoint operator.

        Reads from inputs and writes to outputs.
        """


        if self.implementation == Impl['halide'] :

            #Halide implementation
            if len(self.H.shape) == 2:
                tmpin = np.asfortranarray( inputs[0][..., np.newaxis].astype(np.float32) )
            else:
                tmpin = np.asfortranarray( inputs[0].astype(np.float32) )

            Halide('At_warp.cpp').At_warp( tmpin, self.Hf, self.tmpadj ) #Call
            np.copyto(outputs[0], self.tmpadj )

        else:

            #CV2 version
            inimg = inputs[0]
            if len(self.H.shape) == 2:
                # + cv2.WARP_INVERSE_MAP
                warpedInput = cv2.warpPerspective(np.asfortranarray(inimg), self.Hinv.T, inimg.shape[1::-1], flags=cv2.INTER_LINEAR,
                                    borderMode=cv2.BORDER_CONSTANT, borderValue=0.)
                np.copyto( outputs[0], warpedInput )

            else:
                outputs[0][:] = 0.0
                for j in range(self.H.shape[2]):
                    warpedInput = cv2.warpPerspective(np.asfortranarray(inimg[:,:,:,j]), self.Hinv[:,:,j].T, inimg.shape[1::-1], flags=cv2.INTER_LINEAR,
                                                    borderMode=cv2.BORDER_CONSTANT, borderValue=0.) #Necessary due to array layout in opencv
                    outputs[0] += warpedInput

def test_bind():
    mod = Representation(1, k_states=2)

    # Test invalid endogenous array (it must be ndarray)
    assert_raises(ValueError, lambda: mod.bind([1,2,3,4]))

    # Test valid (nobs x 1) endogenous array
    mod.bind(np.arange(10)*1.)
    assert_equal(mod.nobs, 10)

    # Test valid (k_endog x 0) endogenous array
    mod.bind(np.zeros(0,dtype=np.float64))

    # Test invalid (3-dim) endogenous array
    assert_raises(ValueError, lambda: mod.bind(np.arange(12).reshape(2,2,3)*1.))

    # Test valid F-contiguous
    mod.bind(np.asfortranarray(np.arange(10).reshape(1,10)))
    assert_equal(mod.nobs, 10)

    # Test valid C-contiguous
    mod.bind(np.arange(10).reshape(10,1))
    assert_equal(mod.nobs, 10)

    # Test invalid F-contiguous
    assert_raises(ValueError, lambda: mod.bind(np.asfortranarray(np.arange(10).reshape(10,1))))

    # Test invalid C-contiguous
    assert_raises(ValueError, lambda: mod.bind(np.arange(10).reshape(1,10)))

def test_mem_layout():
    # Test with different memory layouts of X and y
    X_ = np.asfortranarray(X)
    clf = GradientBoostingClassifier(n_estimators=100, random_state=1)
    clf.fit(X_, y)
    assert_array_equal(clf.predict(T), true_result)
    assert_equal(100, len(clf.estimators_))

    X_ = np.ascontiguousarray(X)
    clf = GradientBoostingClassifier(n_estimators=100, random_state=1)
    clf.fit(X_, y)
    assert_array_equal(clf.predict(T), true_result)
    assert_equal(100, len(clf.estimators_))

    y_ = np.asarray(y, dtype=np.int32)
    y_ = np.ascontiguousarray(y_)
    clf = GradientBoostingClassifier(n_estimators=100, random_state=1)
    clf.fit(X, y_)
    assert_array_equal(clf.predict(T), true_result)
    assert_equal(100, len(clf.estimators_))

    y_ = np.asarray(y, dtype=np.int32)
    y_ = np.asfortranarray(y_)
    clf = GradientBoostingClassifier(n_estimators=100, random_state=1)
    clf.fit(X, y_)
    assert_array_equal(clf.predict(T), true_result)
    assert_equal(100, len(clf.estimators_))

    def psiDerivativecomputations(self, dL_dpsi0, dL_dpsi1, dL_dpsi2, variance, lengthscale, Z, variational_posterior):
        ARD = (len(lengthscale)!=1)
        
        N,M,Q = self.get_dimensions(Z, variational_posterior)
        psi1_gpu = self.gpuCache['psi1_gpu']
        psi2n_gpu = self.gpuCache['psi2n_gpu']
        l_gpu = self.gpuCache['l_gpu']
        Z_gpu = self.gpuCache['Z_gpu']
        mu_gpu = self.gpuCache['mu_gpu']
        S_gpu = self.gpuCache['S_gpu']
        gamma_gpu = self.gpuCache['gamma_gpu']
        dvar_gpu = self.gpuCache['dvar_gpu']
        dl_gpu = self.gpuCache['dl_gpu']
        dZ_gpu = self.gpuCache['dZ_gpu']
        dmu_gpu = self.gpuCache['dmu_gpu']
        dS_gpu = self.gpuCache['dS_gpu']
        dgamma_gpu = self.gpuCache['dgamma_gpu']
        grad_l_gpu = self.gpuCache['grad_l_gpu']
        grad_mu_gpu = self.gpuCache['grad_mu_gpu']
        grad_S_gpu = self.gpuCache['grad_S_gpu']
        grad_gamma_gpu = self.gpuCache['grad_gamma_gpu']
        log_denom1_gpu = self.gpuCache['log_denom1_gpu']
        log_denom2_gpu = self.gpuCache['log_denom2_gpu']
        log_gamma_gpu = self.gpuCache['log_gamma_gpu']
        log_gamma1_gpu = self.gpuCache['log_gamma1_gpu']
        
        if self.GPU_direct:
            dL_dpsi1_gpu = dL_dpsi1
            dL_dpsi2_gpu = dL_dpsi2
            dL_dpsi0_sum = gpuarray.sum(dL_dpsi0).get()
        else:
            dL_dpsi1_gpu = self.gpuCache['dL_dpsi1_gpu']
            dL_dpsi2_gpu = self.gpuCache['dL_dpsi2_gpu']
            dL_dpsi1_gpu.set(np.asfortranarray(dL_dpsi1))
            dL_dpsi2_gpu.set(np.asfortranarray(dL_dpsi2))
            dL_dpsi0_sum = dL_dpsi0.sum()

        self.reset_derivative()
        # t=self.g_psi1compDer(dvar_gpu,dl_gpu,dZ_gpu,dmu_gpu,dS_gpu,dL_dpsi1_gpu,psi1_gpu, np.float64(variance),l_gpu,Z_gpu,mu_gpu,S_gpu, np.int32(N), np.int32(M), np.int32(Q), block=(self.threadnum,1,1), grid=(self.blocknum,1),time_kernel=True)
        # print 'g_psi1compDer '+str(t)
        # t=self.g_psi2compDer(dvar_gpu,dl_gpu,dZ_gpu,dmu_gpu,dS_gpu,dL_dpsi2_gpu,psi2n_gpu, np.float64(variance),l_gpu,Z_gpu,mu_gpu,S_gpu, np.int32(N), np.int32(M), np.int32(Q), block=(self.threadnum,1,1), grid=(self.blocknum,1),time_kernel=True)
        # print 'g_psi2compDer '+str(t)
        self.g_psi1compDer.prepared_call((self.blocknum,1),(self.threadnum,1,1),dvar_gpu.gpudata,dl_gpu.gpudata,dZ_gpu.gpudata,dmu_gpu.gpudata,dS_gpu.gpudata,dgamma_gpu.gpudata,dL_dpsi1_gpu.gpudata,psi1_gpu.gpudata, log_denom1_gpu.gpudata, log_gamma_gpu.gpudata, log_gamma1_gpu.gpudata, np.float64(variance),l_gpu.gpudata,Z_gpu.gpudata,mu_gpu.gpudata,S_gpu.gpudata,gamma_gpu.gpudata,np.int32(N), np.int32(M), np.int32(Q))
        self.g_psi2compDer.prepared_call((self.blocknum,1),(self.threadnum,1,1),dvar_gpu.gpudata,dl_gpu.gpudata,dZ_gpu.gpudata,dmu_gpu.gpudata,dS_gpu.gpudata,dgamma_gpu.gpudata,dL_dpsi2_gpu.gpudata,psi2n_gpu.gpudata, log_denom2_gpu.gpudata, log_gamma_gpu.gpudata, log_gamma1_gpu.gpudata, np.float64(variance),l_gpu.gpudata,Z_gpu.gpudata,mu_gpu.gpudata,S_gpu.gpudata,gamma_gpu.gpudata,np.int32(N), np.int32(M), np.int32(Q))

        dL_dvar = dL_dpsi0_sum + gpuarray.sum(dvar_gpu).get()
        sum_axis(grad_mu_gpu,dmu_gpu,N*Q,self.blocknum)
        dL_dmu = grad_mu_gpu.get()
        sum_axis(grad_S_gpu,dS_gpu,N*Q,self.blocknum)
        dL_dS = grad_S_gpu.get()
        sum_axis(grad_gamma_gpu,dgamma_gpu,N*Q,self.blocknum)
        dL_dgamma = grad_gamma_gpu.get()
        dL_dZ = dZ_gpu.get()
        if ARD:
            sum_axis(grad_l_gpu,dl_gpu,Q,self.blocknum)
            dL_dlengscale = grad_l_gpu.get()
        else:
            dL_dlengscale = gpuarray.sum(dl_gpu).get()
            
        return dL_dvar, dL_dlengscale, dL_dZ, dL_dmu, dL_dS, dL_dgamma

def test_nmf():
    img_file = 'boat.png'
    try:
        img = Image.open(img_file)
    except:
        print("Cannot load image %s : skipping test" %img_file)
        return None
    I = np.array(img) / 255.
    if I.ndim == 3:
        A = np.asfortranarray(I.reshape((I.shape[0],I.shape[1] * I.shape[2])),dtype = myfloat)
        rgb = True
    else:
        A = np.asfortranarray(I,dtype = myfloat)
        rgb = False

    m = 16;n = 16;
    X = spams.im2col_sliding(A,m,n,rgb)
    X = X[:,::10]
    X = np.asfortranarray(X / np.tile(np.sqrt((X * X).sum(axis=0)),(X.shape[0],1)),dtype = myfloat)
    ########## FIRST EXPERIMENT ###########
    tic = time.time()
    (U,V) = spams.nmf(X,return_lasso= True,K = 49,numThreads=4,iter = -5)
    tac = time.time()
    t = tac - tic
    print('time of computation for Dictionary Learning: %f' %t)

    print('Evaluating cost function...')
    Y = X - U * V
    R = np.mean(0.5 * (Y * Y).sum(axis=0))
    print('objective function: %f' %R)
    return None

def test_mul():
    ## Test multiply method of a distributed matrix
    ms, ns = 5, 14

    gA = np.random.standard_normal((ms, ns)).astype(np.float64)
    gA = np.asfortranarray(gA)
    dA = core.DistributedMatrix.from_global_array(gA, rank=0)

    gB = np.random.standard_normal((ms, ns)).astype(np.float64)
    gB = np.asfortranarray(gB)
    dB = core.DistributedMatrix.from_global_array(gB, rank=0)

    dC = dA * dB
    gC = dC.to_global_array(rank=0)

    a = np.random.standard_normal(ns).astype(np.float64)
    comm.Bcast(a, root=0) # ensure all process have the same data
    dD = dA * a
    gD = dD.to_global_array(rank=0)

    alpha = 2.345
    dE = dA * alpha
    gE = dE.to_global_array(rank=0)

    if rank == 0:
        assert allclose(gA * gB, gC)
        assert allclose(gA * a, gD)
        assert allclose(gA * alpha, gE)

def subset_selection_xtx(X, Y):
    """ Subsets selection using EvalSubsetsUsingXtx in the Earth package.
    """
    X = numpy.asfortranarray(X, dtype=ctypes.c_double)
    Y = numpy.asfortranarray(Y, dtype=ctypes.c_double)
    if Y.ndim == 1:
        Y = Y.reshape((-1, 1), order="F")

    if X.shape[0] != Y.shape[0]:
        raise ValueError("First dimensions of bx and y must be the same")

    var_count = X.shape[1]
    resp_count = Y.shape[1]
    cases = X.shape[0]
    subsets = numpy.zeros((var_count, var_count), dtype=ctypes.c_bool,
                              order="F")
    rss_vec = numpy.zeros((var_count,), dtype=ctypes.c_double, order="F")
    weights = numpy.ones((cases,), dtype=ctypes.c_double, order="F")

    rval = _c_eval_subsets_xtx(subsets, rss_vec, cases, resp_count, var_count,
                        X, Y, weights)
    if rval == 1:
        raise numpy.linalg.LinAlgError("Lin. dep. terms in X")
    elif rval == 2:
        raise Exception("Trying to prune the intercept.")
    elif rval != 0:
        raise Exception("Error %i" % rval)

    subsets_ind = numpy.zeros((var_count, var_count), dtype=int)
    for i, used in enumerate(subsets.T):
        subsets_ind[i, :i + 1] = numpy.where(used)[0]

    return subsets_ind, rss_vec

    def test_mask_halide(self):
        """Test mask lin op in halide.
        """
        if halide_installed():
            # Load image
            testimg_filename = os.path.join(os.path.dirname(os.path.realpath(__file__)),
                                            'data', 'angela.jpg')
            # opens the file using Pillow - it's not an array yet
            img = Image.open(testimg_filename)
            np_img = np.asfortranarray(im2nparray(img))

            # Test problem
            output = np.zeros_like(np_img)
            mask = np.asfortranarray(np.random.randn(*list(np_img.shape)).astype(np.float32))
            mask = np.maximum(mask, 0.)

            Halide('A_mask.cpp').A_mask(np_img, mask, output)  # Call
            output_ref = mask * np_img

            # Transpose
            output_trans = np.zeros_like(np_img)
            Halide('At_mask.cpp').At_mask(np_img, mask, output_trans)  # Call

            self.assertItemsAlmostEqual(output, output_ref)
            self.assertItemsAlmostEqual(output_trans, output_ref)

 def test_matrix_multiply_ff(self):
     """matrix multiply two FORTRAN layout matrices"""
     a = np.asfortranarray(np.random.randn(M,N))
     b = np.asfortranarray(np.random.randn(N,K))
     res = gulinalg.matrix_multiply(a,b)
     ref = np.dot(a,b)
     assert_allclose(res, ref)

    def runRandomWalking(self, w, nAlgs, nWalks = 1, nIters=-1, nErrorsLimit=-1, allowSimilar=False, pTransition=0.8,
                         randomSeed=0):
        RunRandomWalkingResult = collections.namedtuple('RunRandomWalkingResult', 'W isSource')
        nFeatures = w.shape[0]
        w0 = np.tile(w, (nWalks, 1))
        sessionStats = self.getStats()

        if sessionStats.nFeatures != nFeatures:
            raise Exception('sessionStats.nFeatures != w0.shape[1]')

        W = np.asfortranarray(np.zeros((nAlgs, nFeatures)).astype(np.float32))
        isSource = np.asfortranarray(np.zeros((nAlgs, 1)).astype(np.uint8))

        w0_p = w0.ctypes.data_as(self.lsPlugin.c_float_p)
        W_p = W.ctypes.data_as(self.lsPlugin.c_float_p)
        isSource_p = isSource.ctypes.data_as(self.lsPlugin.c_uint8_p)

        pTransition_p = (ctypes.c_float * 1)()
        pTransition_p[0] = pTransition;
        #pTransition.ctypes.data_as(self.c_float_p)
        nAlgs = self.lsPlugin.dll.runRandomWalking(self.sessionId, w0_p, nWalks, nAlgs, nIters, nErrorsLimit,
                                                   allowSimilar, pTransition_p, randomSeed, W_p, isSource_p)
        self.lsPlugin.verifyCall(nAlgs)

        return RunRandomWalkingResult(W, isSource)

    def setup(self):
        self.p = numpy.array([[27, 51],
                              [66, 85],
                              [77, 45]])

        self.p3 = numpy.array([[27, 51, 37],
                               [66, 85, 25],
                               [77, 45, 73]])

        self.space = numpy.array((100, 100))
        self.space3 = numpy.array((100, 100, 100))
        self.radii = numpy.array((5, 6, 7))

        self.g = nanshe.syn.data.generate_hypersphere_masks(
            self.space, self.p, self.radii
        )

        self.g = self.g.reshape((self.g.shape[0], -1))
        self.g = self.g.transpose()
        self.g = numpy.asmatrix(self.g)
        self.g = numpy.asfortranarray(self.g)

        self.g3 = nanshe.syn.data.generate_hypersphere_masks(
            self.space3, self.p3, self.radii
        )

        self.g3 = self.g3.reshape((self.g3.shape[0], -1))
        self.g3 = self.g3.transpose()
        self.g3 = numpy.asmatrix(self.g3)
        self.g3 = numpy.asfortranarray(self.g3)

    def endog(self, value):
        self._endog = np.array(value, order='A')

        # (T x M)
        if (self.nobs, self.k_endog) == self._endog.shape:
            self._endog = self._endog.T
        # (M x T)
        elif (self.k_endog, self.nobs) == self._endog.shape:
            pass
        else:
            raise ValueError('Invalid endogenous array shape. Required'
                             '(%d, %d) or (%d, %d). Got %s'
                             % (self.nobs, self.k_endog, self.k_endog,
                                self.nobs, str(self._endog.shape)))

        if not self._endog.flags['F_CONTIGUOUS']:
                self._endog = np.asfortranarray(self._endog)

        # Create a new lag matrix, shaped (k_ar, nobs) = (k_ar, T)
        self._lagged = np.asfortranarray(np.hstack([
            self.endog[:, self.order-i:-i].T
            for i in range(1, self.order+1)
        ]).T)

        # Set calculation flags
        self._recalculate = True

    def _set_params(self, p):
        new_kern_params = p[:self.kern.num_params_transformed()]
        new_likelihood_params = p[self.kern.num_params_transformed():]
        old_likelihood_params = self.likelihood._get_params()

        self.kern._set_params_transformed(new_kern_params)
        self.likelihood._set_params_transformed(new_likelihood_params)

        self.K = self.kern.K(self.X)

        #Re fit likelihood approximation (if it is an approx), as parameters have changed
        if isinstance(self.likelihood, Laplace):
            self.likelihood.fit_full(self.K)

        self.K += self.likelihood.covariance_matrix

        self.Ki, self.L, self.Li, self.K_logdet = pdinv(self.K)

        # the gradient of the likelihood wrt the covariance matrix
        if self.likelihood.YYT is None:
            # alpha = np.dot(self.Ki, self.likelihood.Y)
            alpha, _ = dpotrs(self.L, self.likelihood.Y, lower=1)

            self.dL_dK = 0.5 * (tdot(alpha) - self.output_dim * self.Ki)
        else:
            # tmp = mdot(self.Ki, self.likelihood.YYT, self.Ki)
            tmp, _ = dpotrs(self.L, np.asfortranarray(self.likelihood.YYT), lower=1)
            tmp, _ = dpotrs(self.L, np.asfortranarray(tmp.T), lower=1)
            self.dL_dK = 0.5 * (tmp - self.output_dim * self.Ki)

        #Adding dZ_dK (0 for a non-approximate likelihood, compensates for
        #additional gradients of K when log-likelihood has non-zero Z term)
        self.dL_dK += self.likelihood.dZ_dK

def test_conjGrad():
    A = np.asfortranarray(np.random.normal(size = (5000,500)))
#*    np.random.seed(0)
#*    A = np.asfortranarray(np.random.normal(size = (10,5)))
    A = np.asfortranarray(np.dot(A.T,A),dtype=myfloat)
    b = np.ones((A.shape[1],),dtype=myfloat,order="FORTRAN")
    x0 = b
    tol = 1e-4
    itermax = int(0.5 * len(b))

    tic = time.time()
    for i in xrange(0,20):
        y1 = np.linalg.solve(A,b)
    tac = time.time()
    print "  Time (numpy): ", tac - tic
    x1 = np.abs(b - np.dot(A,y1))
    print "Mean error on b : %f" %(x1.sum() / b.shape[0])

    tic = time.time()
    for i in xrange(0,20):
        y2 = spams.conjGrad(A,b,x0,tol,itermax)
#*        y2 = spams.conjGrad(A,b)
    tac = time.time()
    print "  Time (spams): ", tac - tic
    x1 = np.dot(A,y2)
    x2 = np.abs(b - x1)
    print "Mean error on b : %f" %(x2.sum() / b.shape[0])

    err = abs(y1 - y2)
    return err.max()

def test_cd():
    np.random.seed(0)
    X = np.asfortranarray(np.random.normal(size = (64,100)))
    X = np.asfortranarray(X / np.tile(np.sqrt((X*X).sum(axis=0)),(X.shape[0],1)),dtype=myfloat)
    D = np.asfortranarray(np.random.normal(size = (64,100)))
    D = np.asfortranarray(D / np.tile(np.sqrt((D*D).sum(axis=0)),(D.shape[0],1)),dtype=myfloat)
    # parameter of the optimization procedure are chosen
    lambda1 = 0.015
    mode = spams.PENALTY
    tic = time.time()
    alpha = spams.lasso(X,D,lambda1 = lambda1,mode = mode,numThreads = 4)
    tac = time.time()
    t = tac - tic
    xd = X - D * alpha
    E = np.mean(0.5 * (xd * xd).sum(axis=0) + lambda1 * np.abs(alpha).sum(axis=0))
    print("%f signals processed per second for LARS" %(X.shape[1] / t))
    print('Objective function for LARS: %g' %E)
    tol = 0.001
    itermax = 1000
    tic = time.time()
#    A0 = ssp.csc_matrix(np.empty((alpha.shape[0],alpha.shape[1])))
    A0 = ssp.csc_matrix((alpha.shape[0],alpha.shape[1]),dtype=myfloat)
    alpha2 = spams.cd(X,D,A0,lambda1 = lambda1,mode = mode,tol = tol, itermax = itermax,numThreads = 4)
    tac = time.time()
    t = tac - tic
    print("%f signals processed per second for CD" %(X.shape[1] / t))
    xd = X - D * alpha2
    E = np.mean(0.5 * (xd * xd).sum(axis=0) + lambda1 * np.abs(alpha).sum(axis=0))
    print('Objective function for CD: %g' %E)
    print('With Random Design, CD can be much faster than LARS')

    return None