def srcdiff_plot(env, model, **kwargs):
obj_index = kwargs.pop('obj_index', 0)
src_index = kwargs.pop('src_index', 0)
with_colorbar = kwargs.pop('with_colorbar', False)
xlabel = kwargs.pop('xlabel', r'arcsec')
ylabel = kwargs.pop('ylabel', r'arcsec')
obj, data = model['obj,data'][obj_index]
S = obj.basis.subdivision
R = obj.basis.mapextent
g = obj.basis.srcdiff_grid(data)[src_index]
vmin = np.log10(np.amin(g[g>0]))
g = g.copy() + 1e-10
kw = default_kw(R, kwargs) #, vmin=vmin, vmax=vmin+2)
#loglev = logspace(1, log(amax(g)-amin(g)), 20, base=math.e) + amin(g)
pl.matshow(np.log10(g), **kw)
matplotlib.rcParams['contour.negative_linestyle'] = 'solid'
if with_colorbar: glspl.colorbar()
# pl.over(contour, g, 50, colors='w', linewidths=1,
# extent=[-R,R,-R,R], origin='upper', extend='both')
#pl.grid()
pl.xlabel(xlabel)
pl.ylabel(ylabel)
def showDistMatrix(distMatrix): pylab.matshow(distMatrix) ax = pylab.gca() bottom, top = ax.get_ylim() ax.set_ylim(top, bottom) pylab.colorbar() pylab.show()
def srcdiff_plot(env, model, **kwargs):
obj_index = kwargs.pop('obj_index', 0)
src_index = kwargs.pop('src_index', 0)
with_colorbar = kwargs.pop('with_colorbar', False)
xlabel = kwargs.pop('xlabel', r'arcsec')
ylabel = kwargs.pop('ylabel', r'arcsec')
obj, data = model['obj,data'][obj_index]
S = obj.basis.subdivision
R = obj.basis.mapextent
g = obj.basis.srcdiff_grid(data)[src_index]
vmin = np.log10(np.amin(g[g > 0]))
g = g.copy() + 1e-10
kw = default_kw(R, kwargs) #, vmin=vmin, vmax=vmin+2)
#loglev = logspace(1, log(amax(g)-amin(g)), 20, base=math.e) + amin(g)
pl.matshow(np.log10(g), **kw)
matplotlib.rcParams['contour.negative_linestyle'] = 'solid'
if with_colorbar: glspl.colorbar()
# pl.over(contour, g, 50, colors='w', linewidths=1,
# extent=[-R,R,-R,R], origin='upper', extend='both')
#pl.grid()
pl.xlabel(xlabel)
pl.ylabel(ylabel)
def transect(x,y,z,x0,y0,x1,y1,plots=0):
#convert coord to pixel coord
d0=sqrt( (x-x0)**2+ (y-y0)**2 );
i0=d0.argmin();
x0,y0=unravel_index(i0,x.shape); #overwrite x0,y0
d1=plt.np.sqrt( (x-x1)**2+ (y-y1)**2 );
i1=d1.argmin();
x1,y1=unravel_index(i1,x.shape); #overwrite x1,y1
#-- Extract the line...
# Make a line with "num" points...
length = int(plt.np.hypot(x1-x0, y1-y0))
xi, yi = plt.np.linspace(x0, x1, length), plt.np.linspace(y0, y1, length)
# Extract the values along the line
#y is the first dimension and x is the second, row,col
zi = z[xi.astype(plt.np.int), yi.astype(plt.np.int)]
mz=nonaninf(z.ravel()).mean()
sz=nonaninf(z.ravel()).std()
if plots==1:
plt.matshow(z);plt.clim([mz-2*sz,mz+2*sz]);plt.colorbar();plt.title('transect: (' + str(x0) + ',' + str(y0) + ') (' +str(x1) + ',' +str(y1) + ')' );
plt.scatter(yi,xi,5,c='r',edgecolors='none')
plt.figure();plt.scatter(sqrt( (xi-xi[0])**2 + (yi-yi[0])**2 ) , zi)
#plt.figure();plt.scatter(xi, zi)
#plt.figure();plt.scatter(yi, zi)
return (xi, yi, zi);
def potential_plot(env,
model,
obj_index,
src_index,
with_colorbar=True,
with_contours=False):
obj, data = model['obj,data'][obj_index]
R = obj.basis.mapextent
grid = obj.basis.potential_grid(data)
levs = obj.basis.potential_contour_levels(data)
# pl.matshow(grid, fignum=False, extent=[-R,R,-R,R], interpolation='nearest')
pl.matshow(grid,
fignum=False,
cmap=cm.bone,
extent=[-R, R, -R, R],
interpolation='nearest')
if with_colorbar: glspl.colorbar()
# pl.contour(grid, extent=[-R,R,-R,R], origin='upper')
#print levs
if with_contours:
for i, lev in enumerate(levs):
pl.over(contour,
grid,
lev,
colors=system_color(i),
extent=[-R, R, -R, R],
origin='upper',
extend='both')
pl.xlabel('arcsec')
pl.ylabel('arcsec')
def showDistMatrix(distMatrix):
pylab.matshow(distMatrix)
ax = pylab.gca()
bottom, top = ax.get_ylim()
ax.set_ylim(top, bottom)
pylab.colorbar()
pylab.show()
def benchmark(clf_class, params, name):
print "parameters:", params
t0 = time()
clf = clf_class(**params).fit(X_train, y_train)
print "done in %fs" % (time() - t0)
if hasattr(clf, 'coef_'):
print "Percentage of non zeros coef: %f" % (
np.mean(clf.coef_ != 0) * 100)
print "Predicting the outcomes of the testing set"
t0 = time()
pred = clf.predict(X_test)
print "done in %fs" % (time() - t0)
print "Classification report on test set for classifier:"
print clf
print
print classification_report(y_test, pred,
target_names=news_test.target_names)
cm = confusion_matrix(y_test, pred)
print "Confusion matrix:"
print cm
# Show confusion matrix
pl.matshow(cm)
pl.title('Confusion matrix of the %s classifier' % name)
pl.colorbar()
def gradient_grid_plot(env, model, obj_index):
obj, data = model['obj,data'][obj_index]
b = obj.basis
kappa = data['kappa']
grid = np.zeros_like(kappa)
#wght = lambda x: 1.0 / len(x) if len(x) else 0
wght = lambda x: b.cell_size[x]**2 / np.sum(b.cell_size[x]**2)
for i, r in enumerate(b.ploc):
n, e, s, w = b.nbrs3[i][2]
dx = np.sum(kappa[w] * wght(w)) - np.sum(kappa[e] * wght(e))
dy = np.sum(kappa[s] * wght(s)) - np.sum(kappa[n] * wght(n))
dx *= -1
dy *= -1
#print dx, dy
dr = np.sqrt(dx**2 + dy**2)
grid[i] = dr
grid = grid
kw = default_kw(b.mapextent, vmin=np.amin(grid), vmax=np.amax(grid))
grid = b._to_grid(grid, b.subdivision)
pl.matshow(grid, **kw)
glscolorbar()
def benchmark(clf_class, params, name):
print("parameters:", params)
t0 = time()
clf = clf_class(**params).fit(X_train, y_train)
print("done in %fs" % (time() - t0))
if hasattr(clf, 'coef_'):
print("Percentage of non zeros coef: %f"
% (np.mean(clf.coef_ != 0) * 100))
print("Predicting the outcomes of the testing set")
t0 = time()
pred = clf.predict(X_test)
print("done in %fs" % (time() - t0))
print("Classification report on test set for classifier:")
print(clf)
print()
print(classification_report(y_test, pred,
target_names=news_test.target_names))
cm = confusion_matrix(y_test, pred)
print("Confusion matrix:")
print(cm)
# Show confusion matrix
pl.matshow(cm)
pl.title('Confusion matrix of the %s classifier' % name)
pl.colorbar()
def grad_kappa_plot(env, model, obj_index, which='x', with_contours=False, only_contours=False, clevels=30, with_colorbar=True):
obj, data = model['obj,data'][obj_index]
R = obj.basis.mapextent
grid = obj.basis.kappa_grid(data)
grid = grid.copy()
kw = default_kw(R)
kw['vmin'] = -1
kw['vmax'] = 2
if not only_contours:
print '!!!!!!', grid.shape
if which == 'x': grid = np.diff(grid, axis=1)
if which == 'y': grid = np.diff(grid, axis=0)
print '!!!!!!', grid.shape
pl.matshow(grid, **kw)
if with_colorbar:
glspl.colorbar()
if with_contours:
kw.pop('cmap')
pl.over(contour, grid, clevels, extend='both', colors='k', alpha=0.7, **kw)
pl.xlabel('arcsec')
pl.ylabel('arcsec')
def plotMatrix(cm):
pl.matshow(cm)
pl.title('Confusion matrix')
pl.colorbar()
pl.ylabel('True label')
pl.xlabel('Predicted label')
pl.show()
def transect(x, y, z, x0, y0, x1, y1, plots=0):
#convert coord to pixel coord
d0 = sqrt((x - x0)**2 + (y - y0)**2)
i0 = d0.argmin()
x0, y0 = unravel_index(i0, x.shape)
#overwrite x0,y0
d1 = plt.np.sqrt((x - x1)**2 + (y - y1)**2)
i1 = d1.argmin()
x1, y1 = unravel_index(i1, x.shape)
#overwrite x1,y1
#-- Extract the line...
# Make a line with "num" points...
length = int(plt.np.hypot(x1 - x0, y1 - y0))
xi, yi = plt.np.linspace(x0, x1, length), plt.np.linspace(y0, y1, length)
# Extract the values along the line
#y is the first dimension and x is the second, row,col
zi = z[xi.astype(plt.np.int), yi.astype(plt.np.int)]
mz = nonaninf(z.ravel()).mean()
sz = nonaninf(z.ravel()).std()
if plots == 1:
plt.matshow(z)
plt.clim([mz - 2 * sz, mz + 2 * sz])
plt.colorbar()
plt.title('transect: (' + str(x0) + ',' + str(y0) + ') (' + str(x1) +
',' + str(y1) + ')')
plt.scatter(yi, xi, 5, c='r', edgecolors='none')
plt.figure()
plt.scatter(sqrt((xi - xi[0])**2 + (yi - yi[0])**2), zi)
#plt.figure();plt.scatter(xi, zi)
#plt.figure();plt.scatter(yi, zi)
return (xi, yi, zi)
def matrix_picture(matrix):
pl.matshow(matrix)
pl.title('Confusion matrix')
pl.colorbar()
pl.ylabel('True label')
pl.xlabel('Predicted label')
pl.show()
def plotMatrix(cm):
pl.matshow(cm)
pl.title('Confusion matrix')
pl.colorbar()
pl.ylabel('True label')
pl.xlabel('Predicted label')
pl.show()
def draw_astar_graph(obs_map, graph):
"""Debugging function which will show the current state of the m*
graph
"""
# Draw the obstacles
pylab.hold(False)
sizex = len(obs_map)
sizey = len(obs_map[0])
pylab.plot([-.5, sizex - .5, sizex - .5, -.5, -.5],
[-.5, -.5, sizey - .5, sizey - .5, -.5], 'k')
pylab.hold(True)
pylab.matshow((1 - numpy.array(obs_map)).T, fignum=0)
pylab.gray()
pylab.clim(-2, 1)
# Assemble the quiver
X, Y, U, V = [[] for i in xrange(4)]
for node in graph.graph.itervalues():
x, y = node.coord
u, v = map(lambda w, v: w - v, node.policy, node.coord)
X.append(x)
Y.append(y)
U.append(u)
V.append(v)
pylab.quiver(X, Y, U, V)
pylab.xlim([-.5, sizex - .5])
pylab.ylim([-.5, sizey - .5])
pylab.xticks([])
pylab.yticks([])
pylab.hold(False)
pylab.show()
def show_chains(rbm, state, dataset, num_particles=20, num_samples=20, show_every=10, display=True,
figname='Gibbs chains', figtitle='Gibbs chains'):
samples = gnp.zeros((num_particles, num_samples, state.v.shape[1]))
state = state[:num_particles, :, :]
for i in range(num_samples):
samples[:, i, :] = rbm.vis_expectations(state.h)
for j in range(show_every):
state = rbm.step(state)
npix = dataset.num_rows * dataset.num_cols
rows = [vm.hjoin([samples[i, j, :npix].reshape((dataset.num_rows, dataset.num_cols)).as_numpy_array()
for j in range(num_samples)],
normalize=False)
for i in range(num_particles)]
grid = vm.vjoin(rows, normalize=False)
if display:
pylab.figure(figname)
pylab.matshow(grid, cmap='gray', fignum=False)
pylab.title(figtitle)
pylab.gcf().canvas.draw()
return grid
def plot_mandelbot(xmin=-2.25,
xmax=0.75,
xres=3000,
ymin=-1.25,
ymax=1.25,
yres=2500,
maxiter=200,
horizon=2.0**40):
z, n = mandelbrot_set(xmin, xmax, ymin, ymax, xres, yres, maxiter, horizon)
# Plot the results... dig the fancy pylab skills!
xaxis_res = int(xres / 20)
yaxis_res = int(yres / 20)
x_axis = np.linspace(xmin, xmax, num=xres)
y_axis = np.linspace(ymin, ymax, num=yres)
x_labels = []
y_labels = []
for i in range(0, len(x_axis), xaxis_res):
x_labels.append(str(round(x_axis[i], 2)))
for i in range(0, len(y_axis), yaxis_res):
y_labels.append(str(round(y_axis[i], 2)))
pylab.matshow(n, cmap=plt.cm.hot, interpolation='nearest')
pylab.xticks(np.arange(0, xres, xaxis_res), x_labels)
pylab.yticks(np.arange(0, yres, yaxis_res), y_labels)
pylab.xticks(rotation=90)
pylab.xlim(0, xres)
pylab.ylim(yres, 0)
pylab.xlabel('x')
pylab.ylabel('y')
ax = pylab.colorbar()
ax.set_label('Iterations till divergence')
pylab.draw()
def calcola(X, y):
for train_index, test_index in kf.split(X, y):
#separa le variabili per l'addestramento da quelle per il test
X_train, X_test = X[train_index], X[test_index]
y_train, y_test = y[train_index], y[test_index]
clf.fit(X_train, y_train)
pred = clf.predict(X_test)
score = accuracy_score(y_test, pred)
MCC = matthews_corrcoef(y_test, pred)
print("\n\nEtichette Corrette")
print("TRAIN:", y_train, "\nTEST:", y_test)
print("\nEtichette Predette")
print("TEST:",
pred) #0 Setosa, 1 Versicolor, 2 Virginica Etichette Predette
cm = confusion_matrix(y_test, pred)
pl.matshow(cm)
pl.title('Matrice di confusione\n')
pl.colorbar()
pl.show()
print(classification_report(y_test, pred))
print("Accuracy:", score)
print("Matthew Coefficient:", MCC)
def gradient_grid_plot(env, model, obj_index):
obj,data = model['obj,data'][obj_index]
b = obj.basis
kappa = data['kappa']
grid = np.zeros_like(kappa)
#wght = lambda x: 1.0 / len(x) if len(x) else 0
wght = lambda x: b.cell_size[x]**2 / np.sum(b.cell_size[x]**2)
for i,r in enumerate(b.ploc):
n,e,s,w = b.nbrs3[i][2]
dx = np.sum(kappa[w] * wght(w)) - np.sum(kappa[e] * wght(e))
dy = np.sum(kappa[s] * wght(s)) - np.sum(kappa[n] * wght(n))
dx*=-1
dy*=-1
#print dx, dy
dr = np.sqrt(dx**2 + dy**2)
grid[i] = dr
grid = grid
kw = default_kw(b.mapextent, vmin=np.amin(grid), vmax=np.amax(grid))
grid = b._to_grid(grid, b.subdivision)
pl.matshow(grid, **kw)
glscolorbar()
def HarmonicResponseViewer(bw,harmonicResponse,title="",mode="COS_SIN"):
#
# okay I should make the matrix full of zeros and then set the values
# as I go through the harmonicResponse
#First we do regular bar charts plot
#pprint(harmonicResponse)
data=[[a,b,c,d] for (a,b),(c,d) in harmonicResponse]
for mval in range(bw+1):
HarmonicBarChart(mval,data,mchoiceMinusOne=False)
HarmonicBarChart(mval,data,showPrime=True,mchoiceMinusOne=False)
#Then the matrix plots
mat_cos=zeros((bw,bw))
mat_sin=mat_cos
for (x,y),(c,s) in harmonicResponse:
mat_cos[y][x]=c
mat_sin[y][x]=s
pylab.matshow(mat_cos)
pylab.title(title+" cos")
pylab.xlabel("n")
pylab.ylabel("m")
pylab.show()
pylab.matshow(mat_sin)
pylab.title(title+" sin")
pylab.xlabel("n")
pylab.ylabel("m")
pylab.show()
def networkPerformance(RX,test_inputs,labels_test):
from sklearn.metrics import classification_report
from sklearn.metrics import confusion_matrix
import pylab as pl
expected = labels_test
t1 = time.clock()
predicted = RX.compute_predictions(test_inputs)
t2 = time.clock()
print 'Ca nous a pris ', t2-t1, ' secondes pour calculer les predictions sur ', test_inputs.shape[0],' points de test'
err = 1.0 - np.mean(labels_test==predicted)
print "L'erreur de test est de ", 100.0 * err,"%"
np.save('erreurTest_cae_full',100.0 * err)
print "Classification report for classifier %s:\n%s\n" % (
RX, classification_report(expected, predicted))
cm=confusion_matrix(expected, predicted)
print "Confusion matrix:\n%s" % cm
# Show confusion matrix in a separate window
pl.matshow(cm)
pl.title('Confusion matrix')
pl.colorbar()
pl.ylabel('True label')
pl.xlabel('Predicted label')
pl.show()
return
def kappa_residual_grid_plot(env, model, base_model, obj_index, with_contours=False, only_contours=False, with_colorbar=True):
obj0,data0 = base_model['obj,data'][obj_index]
obj1,data1 = model['obj,data'][obj_index]
kappa = data1['kappa'] - data0['kappa']
grid = obj1.basis._to_grid(kappa, obj1.basis.subdivision)
R = obj1.basis.mapextent
kw = {'extent': [-R,R,-R,R],
'interpolation': 'nearest',
'aspect': 'equal',
'origin': 'upper',
'cmap': cm.gist_stern,
'fignum': False}
#'vmin': -1,
#'vmax': 1}
if not only_contours:
pl.matshow(grid, **kw)
if only_contours or with_contours:
kw.update({'colors':'k', 'linewidths':1, 'cmap':None})
pl.contour(grid, **kw)
kw.update({'colors':'k', 'linewidths':2, 'cmap':None})
pl.contour(grid, [0], **kw)
if with_colorbar:
glscolorbar()
return
def main():
import pylab
# Create the gaussian data
Xin, Yin = pylab.mgrid[0:201, 0:201]
data = gaussian(3, 100, 100, 20, 40)(Xin, Yin) + np.random.random(Xin.shape)
pylab.matshow(data, cmap='gist_rainbow')
params = fitgaussian(data)
fit = gaussian(*params)
pylab.contour(fit(*pylab.indices(data.shape)), cmap='copper')
ax = pylab.gca()
(height, x, y, width_x, width_y) = params
pylab.text(0.95, 0.05, """
x : %.1f
y : %.1f
width_x : %.1f
width_y : %.1f""" %(x, y, width_x, width_y),
fontsize=16, horizontalalignment='right',
verticalalignment='bottom', transform=ax.transAxes)
pylab.show()
def train_model(trainset):
word_vector = TfidfVectorizer(analyzer="word", ngram_range=(2,2), binary = False, max_features= 2000,min_df=1,decode_error="ignore")
# print word_vector
print "works fine"
char_vector = TfidfVectorizer(ngram_range=(2,3), analyzer="char", binary = False, min_df = 1, max_features = 2000,decode_error= "ignore")
vectorizer =FeatureUnion([ ("chars", char_vector),("words", word_vector) ])
corpus = []
classes = []
for item in trainset:
corpus.append(item['text'])
classes.append(item['label'])
print "Training instances : ", 0.8*len(classes)
print "Testing instances : ", 0.2*len(classes)
matrix = vectorizer.fit_transform(corpus)
print "feature count : ", len(vectorizer.get_feature_names())
print "training model"
X = matrix.toarray()
y = numpy.asarray(classes)
model =LinearSVC()
X_train, X_test, y_train, y_test= train_test_split(X,y,train_size=0.8,test_size=.2,random_state=0)
y_pred = OneVsRestClassifier(model).fit(X_train, y_train).predict(X_test)
#y_prob = OneVsRestClassifier(model).fit(X_train, y_train).decision_function(X_test)
#print y_prob
#con_matrix = []
#for row in range(len(y_prob)):
# temp = [y_pred[row]]
# for prob in y_prob[row]:
# temp.append(prob)
# con_matrix.append(temp)
#for row in con_matrix:
# output.write(str(row)+"\n")
#print y_pred
#print y_test
res1=[i for i, j in enumerate(y_pred) if j == 'anonEdited']
res2=[i for i, j in enumerate(y_test) if j == 'anonEdited']
reset=[]
for r in res1:
if y_test[r] != "anonEdited":
reset.append(y_test[r])
for r in res2:
if y_pred[r] != "anonEdited":
reset.append(y_pred[r])
output=open(sys.argv[2],"w")
for suspect in reset:
output.write(str(suspect)+"\n")
cm = confusion_matrix(y_test, y_pred)
print(cm)
pl.matshow(cm)
pl.title('Confusion matrix')
pl.colorbar()
pl.ylabel('True label')
pl.xlabel('Predicted label')
pl.show()
print accuracy_score(y_pred,y_test)
def visualize(self):
import pylab
'''Generates visualizationss of the A and E matrices.'''
# Construct a matrix that is upper-triangle flux and lower-triangle error
fluxAndError = self.A.copy()
for i in range(len(self.A)):
fluxAndError[i, 0:i] = self.E[i, 0:i]
# pylab.clf()
pylab.matshow(fluxAndError, cmap=pylab.cm.gray)
l = len(self.A)
pylab.plot([0, l], [0, l])
pylab.xlim(0, l)
pylab.ylim(0, 1)
pylab.gray()
pylab.xlabel("Flux matrix: A(i,j)")
# pylab.ylabel("Error matrix: E(i,j)")
# I'm abusing the 'title' attribute here just to get the x2label where I want it
pylab.title("Error matrix: E(i,j)")
print(self.dates)
datelabels = self.mjd2date(self.dates)
datelabels.reverse()
pylab.yticks(arange(len(self.A), 0, -1), (datelabels))
# pylab.xticks(arange(len(self.A))+0.5,(datelabels), rotation='vertical')
# pylab.yticks(arange(len(self.A)),(self.gooddates))
# pylab.xticks(arange(len(self.A)),(self.gooddates))
pylab.show()
def test_plot_dist_matrix(self):
"""
Can we create and possibly plot a dist_matrix?
"""
try:
comm = create_comm_of_size(12)
except InvalidCommSizeError:
pass
else:
try:
da = densedistarray.DistArray((10, 10),
dist=('c', 'c'),
comm=comm)
except NullCommError:
pass
else:
if False:
if comm.Get_rank() == 0:
import pylab
pylab.ion()
pylab.matshow(a)
pylab.colorbar()
pylab.draw()
pylab.show()
comm.Free()
def main():
#from pylab import *
import pylab
# Create the gaussian data
Xin, Yin = pylab.mgrid[0:201, 0:201]
data = gaussian(3, 100, 100, 20, 40)(Xin, Yin) + np.random.random(
Xin.shape)
pylab.matshow(data, cmap='gist_rainbow')
params = fitgaussian(data)
fit = gaussian(*params)
pylab.contour(fit(*pylab.indices(data.shape)), cmap='copper')
ax = pylab.gca()
(height, x, y, width_x, width_y) = params
pylab.text(0.95,
0.05,
"""
x : %.1f
y : %.1f
width_x : %.1f
width_y : %.1f""" % (x, y, width_x, width_y),
fontsize=16,
horizontalalignment='right',
verticalalignment='bottom',
transform=ax.transAxes)
pylab.show()
def showConn(self,N,conns):
matrix = np.zeros((N,N))
for n in conns:
matrix[int(n/N),np.remainder(n,N)]=1.0
plt.matshow(matrix)
plt.show()
def visualize_row(g, nvis=196, nhid=20, title=''):
ncols = np.sqrt(nvis).astype(int)
title = 'vishid'
vishid = g[nvis+nhid:].reshape((nvis, nhid))
imgs = [vishid[:, j].reshape((ncols, ncols)) for j in range(nhid)]
pylab.matshow(vm.pack(imgs), cmap='gray')
pylab.title(title)
def plot_mh_ckk(prefix):
k49max=10;k51max=10
ckk = np.load('MMIXDISTR/'+prefix+'_cgrid.npy')
plt.matshow(ckk)
plt.colorbar()
plt.xlabel(r'$k_{51}$')
plt.ylabel(r'$k_{49}$')
plt.savefig("PLOTS/"+prefix+'_ckk.png')
def showNetCDF(filename):
"""
matshows the netcdf in filename
"""
img=readNetCDF(filename,'intensity')
pyl.matshow(img)
def plot_dist_matrix(name, mec):
mec.execute('_dm = %s.get_dist_matrix()' % name, 0)
_dm = mec.zip_pull('_dm', 0)
import pylab
pylab.ion()
pylab.matshow(_dm)
pylab.colorbar()
pylab.show()
def show_gfx(world):
if VISUAL:
top=world.max()
if top>50.0: cscheme=hot
elif top>0.0: cscheme=temp
else: cscheme=cold
pylab.matshow(world, fignum=1, cmap=cscheme)
pylab.draw()
def plot_dist_matrix(name, mec):
mec.execute('_dm = %s.get_dist_matrix()' % name, 0)
_dm = mec.zip_pull('_dm', 0)
import pylab
pylab.ion()
pylab.matshow(_dm)
pylab.colorbar()
pylab.show()
def displayResult(keypoints, currentImage): pl.ion() pl.gray() pl.matshow(currentImage) for feature in keypoints: print feature pl.plot(feature[0], feature[1], 'bo') pl.show()
def plot_mat(mat, title_, xticks_, yticks_, label_x, label_y, xlabel_, ylabel_, min=None, max=None, type_plot="matshow", format_string="%.3f"):
def reformat_labels(lab):
print "label",lab
print "len(lab)",len(lab)
# if len(lab)>8:
if len(lab)>10:
# q = len(lab)/8 + 1
# q = int(mdp.numx.ceil(len(lab)/8.))
# q = int(mdp.numx.floor(len(lab)/8.))
# q = int(mdp.numx.ceil(len(lab)/10.))
q = int(mdp.numx.floor(len(lab)/10.))
# q = int(mdp.numx.ceil(len(lab)/6.))
print "q:",q
print "returned:", str([lab[i] for i in range(len(lab)) if i%q==0])
return ([lab[i] for i in range(len(lab)) if i%q==0],q)
else:
return (lab, 1)
if type_plot=="imshow":
pl.figure()
pl.imshow(mat, interpolation='nearest', vmin=min, vmax=max)
else:
pl.matshow(mat, vmin=min, vmax=max)
pl.title(title_+'\n')
pl.xlabel(xlabel_)
pl.ylabel(ylabel_)
if xticks_ is not None:
pl.xticks = xticks_
if yticks_ is not None:
pl.yticks = yticks_
a = matplotlib.pyplot.gca()
locs, labels = pl.xticks()
print "locs, labels",locs, labels
## format values on x and y, so that they can be plotted entirely
# if label_x[0] is float:
if is_float(label_x[0]):
label_x = [format_string % x for x in label_x]
if is_float(label_y[0]):
label_y = [format_string % x for x in label_y]
(label_x_r, qx) = reformat_labels(label_x)
(label_y_r, qy) = reformat_labels(label_y)
if type_plot=="matshow":
# l_tmp = [-99999]
# l_tmp.extend(label_x)
# l_tmp = label_x
# print "l_tmp", l_tmp
# a.set_xticklabels(l_tmp, fontdict=None, minor=False) # set values on x ticks
pl.xticks( mdp.numx.arange(0.,len(label_x),float(qx)), label_x_r )
# l_tmp = [-99999]
# l_tmp.extend(label_y_r)
# print "l_tmp", l_tmp
# a.set_yticklabels(l_tmp, fontdict=None, minor=False) # set values on y ticks
pl.yticks( mdp.numx.arange(0.,len(label_y),float(qy)), label_y_r )
else:
a.set_xticklabels(label_x, fontdict=None, minor=False) # set values on x ticks
a.set_yticklabels(label_y, fontdict=None, minor=False) # set values on y ticks
# a.xaxis.set_tick()
# a.xaxis.set_ticklabels()
pl.colorbar()
def VisualizeConfusionMatrix(CM):
import pylab as pl
print(CM)
pl.matshow(CM)
pl.title('Confusion Matrix')
pl.colorbar()
pl.ylabel('True Label')
pl.xlabel('Predicted Label')
pl.show()
def VisualizeConfusionMatrix(CM):
import pylab as pl
print(CM)
pl.matshow(CM)
pl.title('Confusion Matrix')
pl.colorbar()
pl.ylabel('True Label')
pl.xlabel('Predicted Label')
pl.show()
def rseed345_basis(info):
basis = np.loadtxt("results/basis-RGBODGCN-r%s.txt" % info.rseed)
pl.figure(4)
pl.matshow(basis.dot(basis.T))
pl.colorbar()
pl.title("Similarity matrix.")
pl.savefig("results/matshow-RGBODGCN-r%s.pdf" % info.rseed)
#exit(1)
return basis
def draw_confusion_matrix(self, function, data_set):
y_true, y_predict = self.calculate_entire_ds(function, data_set)
cm = confusion_matrix(y_true, y_predict)
pl.matshow(cm)
pl.title('Confusion matrix')
pl.colorbar()
pl.ylabel('True label')
pl.xlabel('Predicted label')
pl.show()
def decompPCA(data=None,comp=None):
img = data[:,2:].T
size = np.sqrt(img.shape[0])
pca = PCA(n_components=20)
imgNew = pca.fit_transform(img)
pl.matshow(imgNew[:,comp-1].reshape(size,size))
pl.title('The '+str(comp)+' PC')
pl.colorbar()
return pca.explained_variance_ratio_
def plot_cor(mat, vmax=None, title=None):
"Plot correlation matrix"
if vmax is None:
vmax = np.max(np.abs(diff))
pl.matshow(mat, vmin=-vmax, vmax=vmax, cmap=pl.cm.RdBu_r)
pl.xticks(range(len(columns)), columns)
pl.yticks(range(len(columns)), columns)
if title:
pl.title(title)
def show_OneDigit(digits, index=0): if index>=digits.images.shape[0]: print 'index of out of %d' % (images.shape[0]) return import pylab as pl print 'label =', digits.target[index] pl.gray() pl.matshow(digits.images[index]) pl.show()
def showRP(RP):
pylab.matshow(- RP)
ax = pylab.gca()
bottom, top = ax.get_ylim()
ax.set_ylim(top, bottom)
pylab.axis('tight')
pylab.gray()
pylab.show()
def showRP(RP):
pylab.matshow(-RP)
ax = pylab.gca()
bottom, top = ax.get_ylim()
ax.set_ylim(top, bottom)
pylab.axis('tight')
pylab.gray()
pylab.show()
def confusion_matrik(y_rocni, y_program):
cm = confusion_matrix(y_rocni, y_program)
print cm
pl.matshow(cm)
pl.title('Confusion matrix')
pl.colorbar()
pl.ylabel('True label')
pl.xlabel('Predicted label')
pl.show()
def forwardTest():
spikeTimes = spt = [26, 50, 84, 128, 199, 247, 355]
P = setupSimData(spt = spikeTimes )
S = smc.forward(P.V, P)
pylab.figure()
pylab.plot(P.V.F)
pylab.title('Simulated Fluorescence')
cbar = numpy.zeros(P.V.T)
nbar = numpy.zeros(P.V.T)
for t in xrange(P.V.T):
for i in xrange(P.V.Nparticles):
weight = S.w_f[i,t]
cbar[t] += weight * S.C[i,t]
nbar[t] += weight * S.n[i,t]
#cbar /= P.V.Nparticles
#nbar /= P.V.Nparticles
pylab.figure()
pylab.hold(True)
pylab.title('expected Ca vs arbitrary particles')
pylab.plot(S.C[3,:], label='particle 3')
pylab.plot(S.C[10,:], label='particle 10')
pylab.plot(S.C[20,:], label='particle 20')
pylab.plot(cbar, label='E[C]')
pylab.plot(spikeTimes, 6+numpy.ones(len(spikeTimes)), 'k.', label='simulated spike times')
pylab.legend()
#print(nbar.shape)
pylab.figure()
pylab.hold(True)
pylab.plot(nbar, label='expected spikes')
pylab.plot(spikeTimes, 0.5*numpy.ones(len(spikeTimes)), 'k.', label='simulated spike times')
pylab.legend()
pylab.title('spike detection')
#pylab.figure()
pylab.matshow(S.w_f)
pylab.title('min s.w_f %f , max s.w_f: %f'%(numpy.min(S.w_f), numpy.max(S.w_f)))
pylab.figure()
pylab.hold(True)
pylab.plot(S.w_f[3,:], label='particle 3')
pylab.plot(S.w_f[10,:], label='particle 10')
pylab.plot(S.w_f[20,:], label='particle 20')
pylab.legend()
pylab.title('individual particle weights')
pylab.show()
def curve_densities(_data, bins=40):
bins_mult = bins / _data.max()
density_matrix = S.zeros((bins + 1, _data.shape[1]))
for row in _data:
for j in range(len(row)):
density_matrix[S.floor(row[j] * bins_mult), j] += 1.0
density_matrix[density_matrix == 0.0] = float("-inf")
density_figure = pylab.figure()
pylab.matshow(density_matrix[::-1])
def heatmap(self, N=None, standardize=True, log=False):
if standardize:
data_df = self.standardize_df(self.data_df, log=log)
else:
data_df = self.data_df
if N is not None:
plt.matshow(data_df[0:N])
else:
plt.matshow(data_df)
plt.colorbar()
def test_plot_dist_matrix(self):
"""Can we create and possibly plot a dist_matrix?"""
la = da.LocalArray((10,10), dist=('c','c'), comm=self.comm)
if self.comm.Get_rank() == 0:
import pylab
pylab.ion()
pylab.matshow(la)
pylab.colorbar()
pylab.draw()
pylab.show()
def get_crop_config_show(vid,fignum=1):
'''given a video, display crop keyframe and return empty cropdict'''
fr = vidtools.extract_keyframe(vid)
pylab.close(fignum)
pylab.matshow(fr,fignum=fignum)
these_inds = re.split('[-_](\d)[-_]',os.path.basename(os.path.dirname(vid)))
print >> sys.stderr, '\nZoom on antfarms and store crops, e.g.'
for af,ind in zip(these_inds[1::2],these_inds[2::2]):
print >> sys.stderr, "antfarm %s: cropsdict['%s'] = viz_vidtools.current_view_crop(%s,fr.shape)" % (af,ind,fignum)
return {},fr
def visualize_components(self, title=None):
"""Visualize the learned components. Each of the images shows the Bernoulli parameters
(probability of the pixel being 1) for one of the mixture components."""
pylab.figure('Mixture components')
pylab.matshow(util.arrange(self.params.theta.reshape((-1, IMAGE_DIM, IMAGE_DIM))),
fignum=False, cmap='gray')
if title is None:
title = 'Mixture components'
pylab.title(title)
pylab.draw()
def plotsolution(post):
import pylab
X = np.unique(post[0])
Y = np.unique(post[1])
Z = np.zeros((len(X), len(Y)))
sparseZ = dict(zip(map(tuple, post[:2].T), post[2]))
for x in range(len(X)):
for y in range(len(Y)):
if (X[x], Y[y]) in sparseZ.keys():
Z[x, y] = sparseZ[(X[x], Y[y])]
pylab.matshow(Z)
def test_results(y, y_res, lbl, algo = ''):
cm = confusion_matrix(y, y_res, labels=lbl)
cm = cm / cm.astype(np.float).sum(axis=1)
print classification_report(y, y_res, labels=lbl)
# Show confusion matrix in a separate window
pl.matshow(cm)
pl.title('Confusion matrix')
pl.colorbar()
pl.ylabel('True label')
pl.xlabel('Predicted label')
pl.savefig('/home/rolf/Desktop/Assignment 6/plots/matching/%s.pdf' % algo)
