Python numpy.hsplit函数代码示例

def otsuthresh(hist):
    #http://docs.opencv.org/master/d7/d4d/tutorial_py_thresholding.html
    # find normalized_histogram, and its cumulative distribution function
    hist_norm = old_div(hist.astype("float").ravel(),hist.max())
    Q = hist_norm.cumsum()

    bins = np.arange(len(hist_norm))

    fn_min = np.inf
    thresh = -1

    for i in range(1,len(hist_norm)):
        p1,p2 = np.hsplit(hist_norm,[i]) # probabilities
        q1,q2 = Q[i],Q[len(hist_norm)-1]-Q[i] # cum sum of classes
        b1,b2 = np.hsplit(bins,[i]) # weights

        # finding means and variances
        m1,m2 = old_div(np.sum(p1*b1),q1), old_div(np.sum(p2*b2),q2)
        v1,v2 = old_div(np.sum(((b1-m1)**2)*p1),q1),old_div(np.sum(((b2-m2)**2)*p2),q2)

        # calculates the minimization function
        fn = v1*q1 + v2*q2
        if fn < fn_min:
            fn_min = fn
            thresh = i

    return thresh

def zero_directions(zero_vec, tf, e=0.0001):
    """
    Parameters: zero_vec => a vector containing all the transmission zeros of a system
                tf       => the transfer function G(s) of the system
                e        => this avoids possible divide by zero errors in G(z)
    Returns:    zero_dir => zero directions in the form:
                            (zero, input direction, output direction)
    Notes: this method is going to give dubious answers if the function G has pole zero cancellation...
    """
    zero_dir = []
    for z in zero_vec:
        num, den = cn.tfdata(tf)
        rows, cols = np.shape(num)

        G = np.empty(shape=(rows, cols))

        for x in range(rows):
            for y in range(cols):
                top = np.polyval(num[x][y], z)
                bot = np.polyval(den[x][y], z)
                if bot == 0.0:
                    bot = e

                entry = float(top) / bot
                G[x][y] = entry

        U, S, V = np.linalg.svd(G)
        V = np.transpose(np.conjugate(V))
        u_rows, u_cols = np.shape(U)
        v_rows, v_cols = np.shape(V)
        yz = np.hsplit(U, u_cols)[-1]
        uz = np.hsplit(V, v_cols)[-1]
        zero_dir.append((z, uz, yz))
    return zero_dir

    def _projTGraph(self,g):

        sentry = TH1AddDirSentry()

        y      = numpy.ndarray( (g.GetN(),),dtype=numpy.double, buffer=g.GetY() )
        ysplit = numpy.hsplit(y,self._nfold)
        p_y    = numpy.sum(ysplit,axis=self._pax)

        eyh = numpy.ndarray( (g.GetN(),),dtype=numpy.double, buffer=g.GetEYhigh() )
        eyh2_split = numpy.hsplit( (eyh**2) ,self._nfold)
        p_eyh      = numpy.sqrt( numpy.sum(eyh2_split,axis=self._pax) )

        eyl = numpy.ndarray( (g.GetN(),),dtype=numpy.double, buffer=g.GetEYlow() )
        eyl2_split = numpy.hsplit( (eyl**2) ,self._nfold)
        p_eyl      = numpy.sqrt( numpy.sum(eyl2_split,axis=self._pax) )

        x = array.array('d',[0]*self._nbins)
        exh = array.array('d',[0]*self._nbins)
        exl = array.array('d',[0]*self._nbins)
        for i in xrange(self._nbins):
            x[i]            = (self._axdef[i+1]+self._axdef[i])/2.
            exh[i] = exl[i] = (self._axdef[i+1]-self._axdef[i])/2.

        p_g = ROOT.TGraphAsymmErrors(self._nbins, x, p_y, exl, exh, p_eyl, p_eyh)
        p_g.SetNameTitle('%s_proj_%s' % (g.GetName(),self._proj),'%s proj %s' % (g.GetTitle(),self._proj))

        ROOT.TAttLine.Copy(g,p_g)
        ROOT.TAttFill.Copy(g,p_g)
        ROOT.TAttMarker.Copy(g,p_g)
        return p_g

    def compute_candidate_connections(self, paf, cand_a, cand_b, img_len, params):
        candidate_connections = []
        for joint_a in cand_a:
            for joint_b in cand_b:  # jointは(x, y)座標
                vector = joint_b[:2] - joint_a[:2]
                norm = np.linalg.norm(vector)
                if norm == 0:
                    continue

                ys = np.linspace(joint_a[1], joint_b[1], num=params['n_integ_points'])
                xs = np.linspace(joint_a[0], joint_b[0], num=params['n_integ_points'])
                integ_points = np.stack([ys, xs]).T.round().astype('i')  # joint_aとjoint_bの2点間を結ぶ線分上の座標点 [[x1, y1], [x2, y2]...]
                paf_in_edge = np.hstack([paf[0][np.hsplit(integ_points, 2)], paf[1][np.hsplit(integ_points, 2)]])
                unit_vector = vector / norm
                inner_products = np.dot(paf_in_edge, unit_vector)

                integ_value = inner_products.sum() / len(inner_products)
                # vectorの長さが基準値以上の時にペナルティを与える
                integ_value_with_dist_prior = integ_value + min(params['limb_length_ratio'] * img_len / norm - params['length_penalty_value'], 0)

                n_valid_points = sum(inner_products > params['inner_product_thresh'])
                if n_valid_points > params['n_integ_points_thresh'] and integ_value_with_dist_prior > 0:
                    candidate_connections.append([int(joint_a[3]), int(joint_b[3]), integ_value_with_dist_prior])
        candidate_connections = sorted(candidate_connections, key=lambda x: x[2], reverse=True)
        return candidate_connections

def ostu_algorithm(img, blursize=3):
    blur = cv2.GaussianBlur(img, (blursize, blursize), 0)
    hist = cv2.calcHist([blur], [0], None, [256], [0, 256])
    hist_norm = hist.ravel() / hist.max()
    Q = hist_norm.cumsum()
    bins = np.arange(256)
    fn_min = np.inf
    thresh = -1
    for i in xrange(1, 256):
        p1, p2 = np.hsplit(hist_norm, [i])  # probabilities
        q1, q2 = Q[i], Q[255] - Q[i]  # cum sum of classes
        b1, b2 = np.hsplit(bins, [i])  # weights

        if q1 == 0:
            continue
        if q2 == 0:
            continue
        m1, m2 = np.sum(p1 * b1) / q1, np.sum(p2 * b2) / q2
        v1, v2 = np.sum(((b1 - m1) ** 2) * p1) / q1, np.sum(((b2 - m2) ** 2) * p2) / q2
        fn = v1 * q1 + v2 * q2

        if fn < fn_min:
            fn_min = fn
            thresh = i
    _, otsu = cv2.threshold(blur, 0, 255, cv2.THRESH_BINARY + cv2.THRESH_OTSU)

    return otsu

def plotDensityPCA(args, pcaMatrix):
    outName = args.outputFileName
    outName = outName + '_PCAdensity_' + str(NBINS)
    pcaXCoord = numpy.hsplit(pcaMatrix, [1])[0]
    pcaXCoord = pcaXCoord.reshape(1, len(pcaXCoord))[0]
    pcaXCoord = pcaXCoord.real
    pcaYCoord = numpy.hsplit(pcaMatrix, [1])[1]
    pcaYCoord = pcaYCoord.reshape(1, len(pcaYCoord))[0]
    pcaYCoord = pcaYCoord.real
    #fig2.set_title('Density plot of main PCA components')
    H, edgeX, edgeY = numpy.histogram2d(pcaXCoord, pcaYCoord, bins = NBINS)
    H = numpy.rot90(H)
    H = numpy.flipud(H)
    # mask zeroes
    maskedH = numpy.ma.masked_where(H==0, H)
    #Plot the histogram
    fig2 = matplotlib.pyplot.figure()
    plt.pcolormesh(edgeX, edgeY, maskedH)
    plt.xlabel('Pricinpal Component 1')
    plt.ylabel('Principal Component 2') 
    cbar = plt.colorbar()
    cbar.ax.set_ylabel('Counts')
    fig2.savefig(outName, format='png')
    #show()
    return fig2

    def fit(self, features, classes):
        # TODO implement the above algorithm to build a random forest of decision trees
        self.trees = [] #list of root nodes
        esr = self.example_subsample_rate
        asr = self.attr_subsample_rate
        means = np.mean(features, axis=0)

        for i in xrange(self.num_trees):
            # a) Subsample the examples provided (with replacement) in accordance with a example subsampling rate.
            features_np = np.asarray(features)
            classes_np = np.asarray([classes]).transpose()
            merged = np.concatenate((features_np, classes_np), axis=1)
            merged_rand = np.random.permutation(merged)
            merged_rand_esr = merged_rand[0:int(esr*len(features_np))]
            split_rand = np.hsplit(merged_rand_esr, np.array([4, 6]))
            features_split = split_rand[0]
            classes_split = split_rand[1]

            # b) From the sample in a), choose attributes at random to learn on, in accordance with an attribute subsampling rate.
            num_attrs = int(asr * features.shape[1])
            rand_attrs = np.random.randint(features.shape[1], num_attrs)
            for i in xrange(len(rand_attrs)):
                attr_features_split = np.hsplit(features_split, np.array([rand_attrs[i], 6]))[0]    #need to rewrite

            # c) Fit a decision tree to the subsample of data we've chosen (to a certain depth)
            

            leaf0 = DecisionNode(None, None, None, class_label=0)
            leaf1 = DecisionNode(None, None, None, class_label=1)
            nodeA1 = DecisionNode(leaf1, leaf0, lambda x: 1 if x[0]<means[0] else 0)
            root_node = nodeA1

            self.trees.append(root_node)

def calculate(db):
    rep = "1"
    i = 0
    while (rep == "y" or rep == "Y" or rep == "1"):
        search = str(raw_input("Substance: "))
        k = i
    
        with open(db,'r') as dbfile:
            for line in dbfile:
                if (search == line.split()[0]):
                    mass = float(input("Mass (g): "))
                    prop = mass/100*numpy.array([line.split()[1:]], dtype=float)
                    i = i + 1
                    if (rep == "1"):
                        propall = prop
                    else:
                        propall = numpy.vstack([propall, prop])
        
        if (i == k):
            print ("Substance "+search+" not found!")
        rep = str(raw_input("Repeat [y/n]: "))
    
    if (i != 0):
        prot = sum(numpy.hsplit(propall,  (0, 1))[1])
        lip = sum(numpy.hsplit(propall,  (1, 2))[1])
        carb = sum(numpy.hsplit(propall,  (2, 3))[1])
        ccal = sum(numpy.hsplit(propall,  (3, 4))[1])
        glyc = sum(numpy.hsplit(propall,  (4, 4))[2])
    
    print ("\nProteins: "+str(round(prot, 2))+"\nLipids: "+str(round(lip, 2))+"\nCarbohydrates: "+str(round(carb, 2))+"\nccal: "+str(round(ccal, 2))+"\nGlycemic index: "+str(round(glyc, 2)))

def run(name, source, quick=False):
    print time.asctime(time.localtime()), "Filling BDT Branches"  

    branch_names = joblib.load("pickle/variables.pkl")
    
    if quick == True:
        signal = joblib.load('pickle/all_signalq.pkl')   
        clf = joblib.load("pickle/" + name + "quick.pkl")     
    else:
        signal = joblib.load('pickle/all_signal.pkl')
        clf = joblib.load("pickle/" + name + ".pkl")

    # predict and write probability of each MC event being signal
    bdt_MC_predicted = clf.predict_proba(signal)
    bdt_MC_predicted.dtype = [('GradBoost_prob', np.float64)]
    array2root((np.hsplit(bdt_MC_predicted,2)[1]), "/net/storage03/data/users/dlafferty/NTuples/SignalMC/2012/combined/Bs2phiphi_MC_2012_combined_corrected_TupleA_BDT.root", "DecayTree")

    # predict and write probability of every data event being signal
    all_data = root2array("/net/storage03/data/users/dlafferty/NTuples/data/2012/combined/Bs2phiphi_data_2012_corrected_TupleA_BDT.root", "DecayTree", branch_names)
    all_data = rec2array(all_data)

    bdt_data_predicted = clf.predict_proba(all_data)
    bdt_data_predicted.dtype = [('GradBoost_prob', np.float64)]
    array2root((np.hsplit(bdt_data_predicted,2)[1]), "/net/storage03/data/users/dlafferty/NTuples/data/2012/combined/Bs2phiphi_data_2012_corrected_TupleA_BDT.root", "DecayTree")
        
    print time.asctime(time.localtime()), "Branches Filled!"

def main():
   global args
   args = parse()
   # Run through desc stats for file 1
   prefix = args.files[0].split(".")[0] 
   fn = prefix+".txt"
   outfile = prefix+"_results.txt"
   data = np.genfromtxt(fn)
#   ligindex = [4,5,6,7,8,27,28,29,30,31,32,33,34] # Can be used to analyse a subset of ligands
#   data = data[ligindex]
#   print data
   data = np.hsplit(data,[1]) # Split expt values apart
   expt = data[0]
   comput = data[1]
   anova = np.copy(comput) # Beginning of array for anova
   origdata = np.hstack((expt,np.reshape(np.mean(comput,axis=1),(47,1)))) # Reshape then stack, now each ligand has an entry of length 2
   write_data(outfile,origdata)
   # Now do stats and t test for others
   for argfile in args.files[1:]:
      prefix = argfile.split(".")[0] 
      fn = prefix+".txt"
      outfile = prefix+"_results_vs_file1.txt"
      data = np.genfromtxt(fn)
#      data = data[ligindex]
      data = np.hsplit(data,[1]) # Split expt values apart
      expt = data[0]
      comput = data[1]
      anova = np.hstack((anova,comput)) # Add data to Anova array
      currdata = np.hstack((expt,np.reshape(np.mean(comput,axis=1),(47,1)))) # Reshape then stack, now each ligand has an entry of length 2
      write_data(outfile,currdata)
      t_test_diffs(origdata,currdata,outfile)
   # Now do Anova      
   calc_anova(anova,"Anovas.txt")

 def logistic_test(self, X, Y, train_results, predict_with_intercept=True,
                   predict_with_fixed_effects=True, use_prior_beta_split=True):
     
     training_betas = train_results.params
     print training_betas
     
     # please add fixed effects BEFORE intercept, for now! 
     if self.fixed_effects_set:
         if not predict_with_fixed_effects:
             if use_prior_beta_split:
                 print np.shape(X), self.prior_beta_split, len(training_betas)
                 X = np.hsplit(X, [len(self.subject_indices.keys())])[1]
                 training_betas = training_betas[self.prior_beta_split:]
                 print np.shape(X), len(training_betas)
             else:
                 X = np.hsplit(X, [len(self.subject_indices.keys())])[1]
                 training_betas = training_betas[len(self.subject_indices.keys()):]
     
     
     if self.intercept_set:
         if not predict_with_intercept:
             X = np.hsplit(X, 1)[1]
             training_betas = training_betas[1:]
             
     
     test_eta = np.dot(X, training_betas)
     test_p = np.exp(test_eta) / (1. + np.exp(test_eta))
     test_predict = (test_p > 0.5)
     return (Y == test_predict).sum()*1. / Y.shape[0]

    def ChangeSize(self,n_nodes):
        self.masses.resize((1,n_nodes),refcheck=False)
        #self.masses=np.resize(self.masses,(1,n_nodes))
        #self.masses[0][-1] #bug in resize??
        self.initDisp.resize((1,n_nodes),refcheck=False)
        self.initVel.resize((1,n_nodes),refcheck=False)
        #self.initDisp=np.resize(self.initDisp,(1,n_nodes))
        #self.initVel=np.resize(self.initVel,(1,n_nodes))
        

        if n_nodes>self.n_nodes:
            #Take care of 2D array manipulation
            delta=n_nodes-self.n_nodes
            hor=np.zeros((self.n_nodes,delta))
            ver=np.zeros((delta,n_nodes))
            self.springs=np.vstack((np.hstack((self.springs,hor)),ver))
            self.dampers=np.vstack((np.hstack((self.dampers,hor)),ver))
            # Take care of displacement and forces list
            print self.n_nodes,n_nodes
            for i in range(0,n_nodes-self.n_nodes):
                #print i
                self.displacements.append(-1)
                self.forces.append(-1)
            #addArray=[0 for x in range(self.syst.n_nodes,n_nodes)]
        elif n_nodes<self.n_nodes:
            self.springs=np.hsplit(np.vsplit(self.springs,(n_nodes,n_nodes))[0],(n_nodes,n_nodes))[0]
            self.dampers=np.hsplit(np.vsplit(self.dampers,(n_nodes,n_nodes))[0],(n_nodes,n_nodes))[0]
            self.displacements=self.displacements[0:n_nodes]
            self.forces=self.forces[0:n_nodes]
        self.n_nodes=n_nodes

def scale_up(a, x=2, y=2, num_z=None):
    """Scale the input array repeating the array values up by the
    x and y factors.

    Requires:
    --------
    a : array
        An ndarray, 1D arrays will be upcast to 2D
    x, y : numbers
        Factors to scale the array in x (col) and y (row).  Scale factors
        must be greater than 2
    num_z : number
        For 3D, produces the 3rd dimension, ie. if num_z = 3 with the
        defaults, you will get an array with shape=(3, 6, 6).  If
        num_z != None or 0, then the options are 'repeat', 'random'.
        With 'repeat' the extras are kept the same and you can add random
        values to particular slices of the 3rd dimension, or multiply them.

    Returns:
    -------
    >>> a = np.array([[0, 1, 2], [3, 4, 5]]
    >>> b = scale(a, x=2, y=2)
    array([[0, 0, 1, 1, 2, 2],
           [0, 0, 1, 1, 2, 2],
           [3, 3, 4, 4, 5, 5],
           [3, 3, 4, 4, 5, 5]])

    Notes:
    -----
    >>> a = np.arange(2*2).reshape(2,2)
    array([[0, 1],
           [2, 3]])
    >>> f_(scale(a, x=2, y=2, num_z=2))
    Array... shape (3, 4, 4), ndim 3, not masked
    0, 0, 1, 1    0, 0, 1, 1    0, 0, 1, 1
    0, 0, 1, 1    0, 0, 1, 1    0, 0, 1, 1
    2, 2, 3, 3    2, 2, 3, 3    2, 2, 3, 3
    2, 2, 3, 3    2, 2, 3, 3    2, 2, 3, 3
    sub (0)       sub (1)       sub (2)

    """
    if (x < 1) or (y < 1):
        print("x or y scale < 1... \n{}".format(scale_up.__doc__))
        return None
    a = np.atleast_2d(a)
    z0 = np.tile(a.repeat(x), y)  # repeat for x, then tile
    z1 = np.hsplit(z0, y)         # split into y parts horizontally
    z2 = np.vstack(z1)            # stack them vertically
    if a.shape[0] > 1:            # if there are more, repeat
        z3 = np.hsplit(z2, a.shape[0])
        z3 = np.vstack(z3)
    else:
        z3 = np.vstack(z2)
    if num_z not in (0, None):
        d = [z3]
        for i in range(num_z):
            d.append(z3)
        z3 = np.dstack(d)
        z3 = np.rollaxis(z3, 2, 0)
    return z3

def phiSub(Q, k1, k2):
    """
    Calculate initial vector for any subset.

    Parameters
    ----------
    mec : dcpyps.Mechanism
        The mechanism to be analysed.

    Returns
    -------
    phi : ndarray, shape (kA)
    """

    u = np.ones((k2 - k1 + 1, 1))
    p = pinf(Q)
    p1, p2, p3 = np.hsplit(p,(k1, k2+1))
    p1c = np.hstack((p1, p3))

    #Q = Q.copy()
    Q1, Q2, Q3 = np.hsplit(Q,(k1, k2+1))
    Q21, Q22, Q23 = np.hsplit(Q2.transpose(),(k1, k2+1))
    Q22c = Q22.copy()
    Q12 = np.vstack((Q21.transpose(), Q23.transpose()))

    nom = np.dot(p1c, Q12)
    denom = np.dot(nom,u)
    phi = nom / denom
    return phi, Q22c

	def __init__(self,data=list(),Lambda=.1, gamma =.5, theta=None ):
	# SVM Class
	#
	# @param data		[Nxd] array of observations where N is the number of observations and d is the dimensionality of the abstract space
	# @param Lambda		Regularizer to control Smoothness / Accuracy.  Preliminary experimental results show the range 0-1 controls this parameter.
	# @param gamma		List of gamma values which define the kernel smoothness
	
		try:
			self.N,self.d = data.shape
		except ValueError:
			self.N,self.d = (len(data),1)
			self.X = data.reshape([ self.N, self.d ])
		else:
			self.X = data

		self.Lambda = Lambda
		self.gamma = gamma
		
		self.t = np.hsplit(self.X,[1])[0]
		self.offset = np.tile( np.hsplit(self.X,[1])[0], len(theta) )
		self.theta = np.repeat( np.array(theta), self.N )
		
		self.D = self._K( self.X.reshape([self.N,1,self.d]) - self.X.T.reshape([1,self.N,self.d]) )
		self.S = np.array( [ [ subset(self.X,self.D, t, theta ) for t in self.t ] for theta in self.theta ] ).flatten()
		
		self.SV = None			# X value array of SV
		self.NSV = None			# cardinality of SV
		self.alpha = None			# the full weight array for all observations
		self.beta = None			# weight array for SV
		self.K = None				# precomputed kernel matrix
		
		self._compute()