Python scipy.copy函数代码示例

	def initialize(self,data,random=False):
		self.data = data
		self.n_dim = data.shape[1]
		if random:
			mins = sp.zeros(self.n_dim)
			maxes = sp.zeros(self.n_dim)
			sds = sp.zeros(self.n_dim)
			centers = sp.zeros((self.n_components,self.n_dim))
			for i in xrange(self.n_dim):
				mins[i] = min(self.data[:,i])
				maxes[i] = max(self.data[:,i])
				sds[i] = sp.std(self.data[:,i])
				centers[:,i] = sp.random.uniform(mins[i],maxes[i],self.n_components)
			self.comp = sp.ones(self.n_components)/float(self.n_components) + sp.random.uniform(-1./self.n_components,1./self.n_components,self.n_components)
			self.comp /= sp.sum(self.comp)
			covars = sp.array([sp.diag(sds**2) for i in xrange(self.n_components)])
			self.centers = centers
			self.covars = covars
		else:
			clust = cluster.KMeans(self.n_components)
			clust.fit(self.data)
			self.centers = sp.copy(clust.cluster_centers_)
			labels = sp.copy(clust.labels_)
			self.covars = sp.zeros((self.n_components,self.n_dim,self.n_dim))
			self.comp = sp.zeros(self.n_components)
			for i in xrange(self.n_components):
				inds = labels == i
				temp = self.data[inds,:]
				self.covars[i,:,:] = sp.dot(temp.T,temp)
				self.comp[i] = sum(inds)/float(self.data.shape[0])

def NumpyTensorInitializerForVacancy(gridShape, filename, vacancyfile=None):
    """
    Initialize a 10 component plasticity state by reading from a numpy "tofile" type file or two files.
    """
    dict = {('x','x') : (0,0), ('x','y') : (0,1), ('x','z') : (0,2),\
            ('y','x') : (1,0), ('y','y') : (1,1), ('y','z') : (1,2),\
            ('z','x') : (2,0), ('z','y') : (2,1), ('z','z') : (2,2)}
    data = fromfile(filename)
    if vacancyfile is None:
        data = data.reshape([10] + list(gridShape))
    else:
        data = data.reshape([3,3] + list(gridShape))
        dataV = fromfile(vacancyfile)
        dataV = dataV.reshape(list(gridShape))
    state = VacancyState.VacancyState(gridShape)
    field = state.GetOrderParameterField() 
    if vacancyfile is None:
        i = 0
        for component in field.components:
            field[component] = copy(data[i]) 
            i += 1
    else:
        for component in field.components:
            if component[0] not in [x,y,z]:
                field[component] = copy(dataV) 
            else:
                field[component] = copy(data[dict[component]]) 
    return state

 def __init__(self,fitness_func,npop = 20,w = 0.5,c1 = 2.01,c2 = 2.02,debug = False):
  seed()
  self.debug = debug
  self.c1 = c1
  self.c2 = c2
  self.w = w
  self.ns = int(npop) 
  self.fitness_func = fitness_func  
  # gera pop inicial
  if os.path.isfile("dump_pso.pkl"):
   dump_fd = open("dump_pso.pkl",'r')
   self.pop = cPickle.load(dump_fd)
   self.fit = cPickle.load(dump_fd)
   self.v = cPickle.load(dump_fd)
   self.bfg = cPickle.load(dump_fd)
   self.bfg_fitness = cPickle.load(dump_fd)
   self.bfp = cPickle.load(dump_fd)
   self.bfp_fitness  = cPickle.load(dump_fd)
  else:
   self.pop = scipy.array([self.gera_individuo() for i in scipy.arange(self.ns)])
   self.fit = scipy.zeros(self.ns)
   # avalia fitness de toda populacao
   for i in scipy.arange(self.ns):
    self.fit[i],self.pop[i] = self.avalia_aptidao(self.pop[i])  
   # inicializa velocidades iniciais
   self.v = scipy.zeros((self.ns,Dim))
   # guarda a melhor posicao de cada particula 
   self.bfp = scipy.copy(self.pop)
   self.bfp_fitness = scipy.copy(self.fit)
   # guarda a melhor posicao global
   self.bfg = self.pop[self.bfp_fitness.argmin()].copy()
   self.bfg_fitness = self.bfp_fitness.min().copy()

 def __init__(self, field, system_dir, nprocs=4, **kwargs):
     #
     super().__init__()
     #
     # field attributes that are copied over
     field.create_point_data()
     self.nx = field.nx
     self.nz = field.nz
     self.data_vector = field.data_vector
     self.data_map = field.data_map
     self.point_data = field.point_data
     self._field = field.clone()
     self._mask = sp.ones(self.data_map.shape, dtype=bool)
     #
     self.offset_map = sp.zeros(self.data_map.shape)
     self.offset_points = sp.zeros(self.point_data.shape)
     if kwargs.get('offset_field', None):
         kwargs['offset_field'].create_point_data()
         self.offset_map = sp.copy(kwargs['offset_field'].data_map)
         self.offset_points = sp.copy(kwargs['offset_field'].point_data)
     #
     self.system_dir = system_dir
     self.nprocs = nprocs
     self.avg_fact = kwargs.get('avg_fact', 1.0)
     self.mesh_params = kwargs.get('mesh_params', {})
     self.merge_groups = []

 def _read_sky_logfile(self):
     #TODO : expand to read errors, msgs etc
     # read in the whole sky log file, shouldn't be big
     f = open(self.skylogfile)
     lines = f.readlines()
     f.close()
     dust = [line.split()[1:] for line in lines if line.startswith('dtau_dust')]
     line = [line.split()[1:] for line in lines if line.startswith('dtau_line')]
     dust = _sp.array(dust, dtype='float')
     line = _sp.array(line, dtype='float')
     transitions = _sp.unique(dust[:,0])
     shells = _sp.unique(dust[:,1])
     dtau_dust = dict()
     dtau_line = dict()
     dtau_tot = dict()
     for t in transitions:
         d = []
         l = []
         for s in shells:
             d.append( _sp.mean([i[2] for i in dust if ((i[0]==t) * (i[1]==s))]) )
             l.append( _sp.mean([i[2] for i in line if ((i[0]==t) * (i[1]==s))]) )
         dtau_dust[t] = _sp.copy(d)
         dtau_line[t] = _sp.copy(l)
         dtau_tot[t] = _sp.array(d) + _sp.array(l)
     # create object to store in main class
     class Tau(object):pass
     Tau.dtau_dust = dtau_dust
     Tau.dtau_line = dtau_line
     Tau.dtau_tot = dtau_tot
     Tau.transitions = transitions
     Tau.shells = shells
     self.Tau = Tau

	def __init__(self,n_components,comp=None,centers=None,covars=None):
		self.n_components = n_components
		self.comp = sp.copy(comp)
		self.centers = sp.copy(centers)
		self.covars = sp.copy(covars)
		if centers != None:
			self.n_dim = centers.shape[1]

 def copy_data(self, obj):
     r"""
     Copies data properites of the field onto another object created
     """
     obj.nx = self.nx
     obj.nz = self.nz
     obj.data_map = sp.copy(self.data_map)
     obj.data_vector = sp.copy(self.data_vector)
     obj.point_data = sp.copy(self.point_data)

def wigner(psi,xvec,yvec,g=sqrt(2)):
    """Wigner function for a state vector or density matrix 
    at points xvec+i*yvec.
    
    Parameters
    ----------
    state : qobj 
        A state vector or density matrix.
    
    xvec : array_like
        x-coordinates at which to calculate the Wigner function.
    
    yvec : array_like
        y-coordinates at which to calculate the Wigner function.
        
    g : float
        Scaling factor for a = 0.5*g*(x+iy), default g=sqrt(2).
    
    Returns
    --------
    W : array
        Values representing the Wigner function calculated over the specified range [xvec,yvec].
    
    
    """
    if psi.type=='ket' or psi.type=='oper':
        M=prod(psi.shape[0])
    elif psi.type=='bra':
        M=prod(psi.shape[1])
    else:
        raise TypeError('Input state is not a valid operator.')
    X,Y = meshgrid(xvec, yvec)
    amat = 0.5*g*(X + 1.0j*Y)
    wmat=zeros(shape(amat))
    Wlist=array([zeros(shape(amat),dtype=complex) for k in range(M)])
    Wlist[0]=exp(-2.0*abs(amat)**2)/pi
    if psi.type=='ket' or psi.type=='bra':
        psi=ket2dm(psi)
    wmat=real(psi[0,0])*real(Wlist[0])
    for n in range(1,M):
        Wlist[n]=(2.0*amat*Wlist[n-1])/sqrt(n)
        wmat+= 2.0*real(psi[0,n]*Wlist[n])
    for m in range(M-1):
        temp=copy(Wlist[m+1])
        Wlist[m+1]=(2.0*conj(amat)*temp-sqrt(m+1)*Wlist[m])/sqrt(m+1)
        for n in range(m+1,M-1):
            temp2=(2.0*amat*Wlist[n]-sqrt(m+1)*temp)/sqrt(n+1)
            temp=copy(Wlist[n+1])
            Wlist[n+1]=temp2
        wmat+=real(psi[m+1,m+1]*Wlist[m+1])
        for k in range(m+2,M):
            wmat+=2.0*real(psi[m+1,k]*Wlist[k])
    return 0.5*wmat*g**2

 def clone(self):
     r"""
     Creates a fully qualified DataField object from the existing one.
     """
     # instantiating class and adding attributes
     clone = DataField(None)
     #
     self.copy_data(clone)
     clone._raw_data = sp.copy(self._raw_data)
     clone._cell_interfaces = sp.copy(self._cell_interfaces)
     #
     return clone

def run():
    data = sp.copy(housing_data)
    x = data[:, [0, 1]]
    y = data[:, [2]]
    m = sp.shape(y)[0]
    
    # Normalize the x values
    (x, mu, sigma) = graddesc.featureNormalize(x)
    
    # Add intercept term to x
    x = sp.concatenate((sp.ones((m, 1)), x), axis=1)
    
    # Init Theta and run Gradient Descent
    num_iters = 400
    
    # Choose some alpha value
    alphas = [0.01, 0.03, 0.1, 0.3, 1.0]
    
    for alpha in alphas:
        theta = sp.zeros((3, 1))
        (theta, J_history) = graddesc.gradientDescent(x, y, theta, alpha, num_iters)
        # Plot the value of J by number of iterations
        plt.plot(range(1, J_history.size+1), J_history, '-b')
        plt.title('Alpha = %f' % (alpha))
        plt.xlabel('Number of iterations')
        plt.ylabel('J')
        plt.xlim([0, 50])
        plt.show(block=True)
    
        # Estimate the price of a 1650 sq-ft, 3 br house
        price = 0
        house = sp.array([[1.0, 1650.0, 3.0]])
        # Normalize the features
        house[0, 1:] = (house[0, 1:] - mu) / sigma
        price = house.dot(theta)
        print('The estimated price with alpha', alpha, 'is', price[0, 0])
    
    # Reload the data
    data = sp.copy(housing_data)
    
    x = data[:, [0, 1]]
    y = data[:, [2]]
    
    # Add intercept term to x
    x = sp.concatenate((sp.ones((m, 1)), x), axis=1)
    
    # Calculate the normal equation
    theta = graddesc.normalEqn(x, y)
    print('Theta computed from the normal equations:')
    print(theta)

def run():
    theta = sp.zeros((3, 1))
    data = sp.copy(admission_data)
    X = data[:, [0, 1]]
    y = data[:, [2]]
    m = sp.shape(y)[0]

    # Add intercept term to x
    X = sp.concatenate((sp.ones((m, 1)), X), axis=1)

    """
    Part 1: Plotting
    """

    print('Plotting data with + indicating (y = 1) examples and o indicating (y = 0) examples.')
    logres.plotData(data)
    plt.xlabel('Exam 1 score')
    plt.ylabel('Exam 2 score')
    plt.legend('Admitted', 'Not admitted')
    plt.show()

    print('Program paused. Press enter to continue.')
    raw_input()

    """
    Part 2: Compute Cost and Gradient
    """

    (m, n) = X.shape

    initial_theta = sp.zeros((n, 1))

    (cost, grad) = logres.costFunction(initial_theta, X, y)

    print('Cost at initial theta (zeros): ', cost)
    print('Gradient at initial theta (zeros): ', grad)

    print('Program paused. Press enter to continue.')
    raw_input()

    """
    Part 3: Optimizing using fminunc
    """

    (theta, cost) = logres.find_minimum_theta(theta, X, y)

    print('Cost at theta found by fmin: ', cost)
    print('Theta: ', theta)

    logres.plotDecisionBoundary(data, X, theta)

    plt.show()

    """
    Part 4: Predict and Accuracies
    """

    prob = logres.sigmoid(sp.asmatrix([1, 45, 85]).dot(theta))
    print('For a student with scores 45 and 85, we predict an admission probability of ', prob[0, 0])
    print('Program paused. Press enter to continue.')

    def getX(self,standardized=True,maf=None):
        """
        return SNPs, if neccessary standardize them
        """
        X = SP.copy(self.X)

        # test for missing values
        isnan = SP.isnan(X)
        for i in isnan.sum(0).nonzero()[0]:
            # set to mean 
            X[isnan[:,i],i] = X[~isnan[:,i],i].mean()
                
        if maf!=None:
            LG.debug('filter SNPs')
            LG.debug('... number of SNPs(before filtering): %d'%X.shape[1])
            idx_snps = SP.logical_and(X[self.idx_samples].mean(0)>0.1,X[self.idx_samples].mean(0)<0.9)
            LG.debug('... number of SNPs(after filtering) : %d'%idx_snps.sum())
        else:
            idx_snps = SP.ones(self.n_f,dtype=bool)
        
        if standardized:
            LG.debug('standardize SNPs')
            X = X[self.idx_samples][:,idx_snps]
            X-= X.mean(0)
            X /= X.std(0,dtype=NP.float32)
            X /= SP.sqrt(X.shape[1])
            return X
      
        return X[self.idx_samples][:,idx_snps]

def GP_train(x, y, cov_par, cov_func = None, cov_typ ='SE', \
             cov_fixed = None, prior = None, \
             MF = None, MF_par = None, MF_args = None, \
             MF_fixed = None):
    '''    
    Max likelihood optimization of GP hyper-parameters. Calls
    GP_negloglik. Takes care of merging / splitting the fixed /
    variable and cov / MF parameters
    '''
    if MF != None:
        merged_par = scipy.append(cov_par, MF_par)
        n_MF_par = len(MF_par)
        fixed = scipy.append(scipy.zeros(len(cov_par), 'bool'), \
                             scipy.zeros(n_MF_par, 'bool'))
        if (cov_fixed != None): fixed[0:-n_MF_par] = cov_fixed
        if (MF_fixed != None): fixed[-n_MF_par:] = MF_fixed
        if MF_args == None: MF_args = x[:]
    else:
        merged_par = cov_par[:]
        n_MF_par = 0
        fixed = scipy.zeros(len(cov_par), 'bool')
        if cov_fixed != None: fixed[:] = cov_fixed
    var_par_in = merged_par[fixed == False]
    fixed_par = merged_par[fixed == True]
    args = (x, y, cov_func, cov_typ, MF, n_MF_par, MF_args, fixed, \
            fixed_par, prior)
    var_par_out = \
        sop.fmin(GP_negloglik, var_par_in, args, disp = 0)
    par_out = scipy.copy(merged_par)
    par_out[fixed == False] = var_par_out
    par_out[fixed == True] = fixed_par
    if MF != None:
        return par_out[:-n_MF_par], par_out[-n_MF_par:]
    else:
        return par_out

def sqrtm3(X):
    M = sp.copy(X)
    m, fb, fe = block_structure(M)
    n = M.shape[0]
    for i in range(0,m):
        M[fb[i]:fe[i],fb[i]:fe[i]] = twobytworoot(M[fb[i]:fe[i],fb[i]:fe[i]])
        #print M

    for j in range(1,m):
        for i in range(0,m-j):
            #print M[fb[i]:fe[i],fb[JJ]:fe[JJ]]
            JJ = i+j
            Tnoto = M[fb[i]:fe[i],fb[JJ]:fe[JJ]] #dopo togliere il copy
            #print "Tnot: "
            #print Tnoto
            for k in range(i+1,JJ):
                Tnoto -= (M[fb[i]:fe[i],fb[k]:fe[k]]).dot(M[fb[k]:fe[k],fb[JJ]:fe[JJ]])
                #print M[fb[i]:fe[i],fb[k]:fe[k]]
                #print M[fb[k]:fe[k],fb[JJ]:fe[JJ]]

            if((M[fb[i]:fe[i],fb[JJ]:fe[JJ]]).shape==(1,1)):
                #print "forma 1"
                #print M[fb[i]:fe[i],fb[JJ]:fe[JJ]]           #  Uij
                #print M[fb[i]:fe[i],fb[i]:fe[i]]               #  Uii
                #print M[fb[JJ]:fe[JJ],fb[JJ]:fe[JJ]]       #  Ujj
                M[fb[i]:fe[i],fb[JJ]:fe[JJ]] = Tnoto/(M[fb[i]:fe[i],fb[i]:fe[i]] + M[fb[JJ]:fe[JJ],fb[JJ]:fe[JJ]])

            else:
                Uii = M[fb[i]:fe[i],fb[i]:fe[i]]
                Ujj = M[fb[JJ]:fe[JJ],fb[JJ]:fe[JJ]]
                shapeUii = Uii.shape[0]
                shapeUjj = Ujj.shape[0]
                """
                print "------------"
                print Tnoto
                print Tnoto.shape
                print sp.kron(sp.eye(shapeUjj),Uii)
                print sp.kron(Ujj.T,sp.eye(shapeUii))
                print Tnoto
                """
                #M[fb[i]:fe[i],fb[JJ]:fe[JJ]] = sp.linalg.solve_sylvester(Uii, Ujj, Tnoto)

                """
                x, scale, info = dtrsyl(Uii, Ujj, Tnoto

                if (scale==1.0):
                     = x

                else:
                    M[fb[i]:fe[i],fb[JJ]:fe[JJ]] = x*scale
                    print "scale!=0"
                """
                Tnoto = Tnoto.reshape((shapeUii*shapeUjj),1,order="F")
                M[fb[i]:fe[i],fb[JJ]:fe[JJ]] = \
                linalg.solve(sp.kron(sp.eye(shapeUjj),Uii) +
                sp.kron(Ujj.T,sp.eye(shapeUii)),
                Tnoto).reshape(shapeUii,shapeUjj,order="F")


    return M

def update_rule(Asp,states0,parameters,scale=0.0):
	thresh,personal,a,b,c,scale0=parameters #ignore scale ( = 0 )
	states=sp.copy(states0)
	#states is a list of states for all N individuals
	
	nei_sum=Asp*states
	degrees=Asp*sp.ones(len(states))
	
	##get average of all neighbours, i.e. s
	nei_av=[]
	for i in range(0,len(nei_sum)):
		if degrees[i]>0: nei_av.append(nei_sum[i]/degrees[i])
		else: nei_av.append(0.0)
	
	totav=sum(states)/len(states) #this is m
	
	for n in range(0,len(states)): #len means length, i.e. number of individuals
		
		utility=a[n]*personal[n]+b[n]*nei_av[n]+c[n]*totav
		if states[n] < 1.0: #if state == 0
			if utility <= thresh[n]: 
				states[n]=0.0#scale*utility ##i.e. zero if scale=0
			else:
				states[n]=1.0	
	return states