def plot_cam_location(camera_list, n, fig=None, ax=None):
FigSz = (8, 8)
L = np.array([list(c.location[n]) for c in camera_list])
x = L[:, 0]
y = L[:, 1]
z = L[:, 2]
if not fig:
fig = plt.figure(figsize=FigSz)
#view1 = np.array([-85., 60.])
if not ax:
ax = Axes3D(fig) #, azim=view1[0], elev=view1[1])
Axes3D.scatter(ax, x, y, zs=z, color='k')
zer = np.array
Axes3D.scatter(ax, zer([0]), zer([0]), zs=zer([5]), color='r')
ax.set_xlabel('X')
ax.set_ylabel('Y')
ax.set_zlabel('Z')
ax.set_ylim3d(-50, 50)
ax.set_xlim3d(-50, 50)
ax.set_zlim3d(0, 50)
#if Flag['ShowPositions']:
fig.show()
#else:
# fig.savefig(fName)
return ax, fig
def onpick(event):
# get event indices and x y z coord for click
ind = event.ind[0];
x_e, y_e, z_e = event.artist._offsets3d;
print x_e[ind], y_e[ind], z_e[ind];
seg_coord = [x_e[ind], y_e[ind], z_e[ind]];
seg_elecs.append(seg_coord);
# refresh plot with red dots picked and blue dots clean
#fig.clf();
seg_arr = np.array(seg_elecs);
x_f = seg_arr[:,0];
y_f = seg_arr[:,1];
z_f = seg_arr[:,2];
plt.cla();
Axes3D.scatter3D(ax,x_f,y_f,z_f,s=150,c='r', picker=5);
# get array of only clean elecs to re-plot as blue dots
clean_list = list(coords);
clean_list = [list(i) for i in clean_list];
for coordin in clean_list:
if list(coordin) in seg_elecs:
clean_list.pop(clean_list.index(coordin));
clean_coordis = np.array(clean_list);
x_c = clean_coordis[:,0];
y_c = clean_coordis[:,1];
z_c = clean_coordis[:,2];
Axes3D.scatter3D(ax,x_c, y_c, z_c, s=150,c='b', picker=5);
time.sleep(0.5);
plt.draw();
def plotFiguresTemp(xSolid, ySolid, zSolid, xFFDDeform, yFFDDeform, zFFDDeform):
fig = plt.figure()
ax = fig.add_subplot(111, projection='3d')
#fig = plt.figure()
#ax = fig.gca(projection='3d')
# Axes3D.plot_wireframe(ax, z, x, y)
ax.set_xlabel('Z axis')
ax.set_ylabel('X axis')
ax.set_zlabel('Y axis')
#ax.plot_trisurf(zSolid, xSolid, ySolid, cmap=cm.jet, linewidth=0.2)
ax.plot_wireframe(zSolid, xSolid, ySolid, rstride = 1, cstride = 1, color="y")
#Axes3D.scatter(ax, zSolid, xSolid, ySolid, s=10, c='b')
Axes3D.scatter(ax, zFFDDeform, xFFDDeform, yFFDDeform, s=30, c='r')
# Axes3D.set_ylim(ax, [-0.5,4.5])
# Axes3D.set_xlim(ax, [-0.5,4.5])
Axes3D.set_zlim(ax, [-0.7, 0.7])
plt.show(block=True)
def plotData(tuplesArray):
fig = plt.figure()
ax = fig.add_subplot(111, projection='3d')
x = []
y = []
z = []
for point in tuplesArray:
x.append(point[0])
y.append(point[1])
z.append(point[2])
if (FILEInQuestion == "newsbp.fuselageZ.dat"):
Axes3D.scatter(ax, x,y,z, s=30, c ='b')
Axes3D.set_zlim(ax, [0, 1000])
Axes3D.set_ylim(ax, [0, 3000])
Axes3D.set_xlim(ax, [0, 3000])
ax.set_xlabel('Z axis')
ax.set_ylabel('X axis')
ax.set_zlabel('Y axis')
else:
Axes3D.scatter(ax, z,x,y, s=30, c ='b')
ax.set_xlabel('Z axis')
ax.set_ylabel('X axis')
ax.set_zlabel('Y axis')
plt.show(block=True)
def plotData2files(tuplesArray1, tuplesArray2):
fig = plt.figure()
ax = fig.add_subplot(111, projection='3d')
x1 = []
y1 = []
z1 = []
for point in tuplesArray1:
x1.append(point[0])
y1.append(point[1])
z1.append(point[2])
x2 = []
y2 = []
z2 = []
for point in tuplesArray2:
x2.append(point[0])
y2.append(point[1])
z2.append(point[2])
Axes3D.scatter(ax, x1,y1,z1, s=30, c ='b')
Axes3D.scatter(ax, x2,y2,z2, s=30, c ='r')
Axes3D.set_xlim(ax, [0, 2000])
Axes3D.set_ylim(ax, [0, 3000])
Axes3D.set_zlim(ax, [0, 1000])
plt.show(block=True)
def updatePlot(self, X, Y, Z, population=None):
self.activePlot = (X,Y,Z)
x, y = np.meshgrid(X,Y)
if self.surface is not None:
self.surface.remove()
if self.scatter is not None:
self.scatter.remove()
# surface
self.surface = Axes3D.plot_surface(
self.axes,
x, y, Z,
rstride=1,
cstride=1,
cmap=cm.coolwarm,
linewidth=0,
antialiased=False,
shade=False,
alpha=0.5
)
# population
if population is not None:
self.activePopulation = population
x, y, z = self.preparePopulationData(population)
self.scatter = Axes3D.scatter(self.axes, x, y, z, c="r", marker="o")
self.scatter.set_alpha(1.0)
# Draw all
self.canvas.draw()
self.canvas.flush_events()
def volume_display(self, zstep = 3.00):
"""
This is a daring attempt for 3-D plots of all the blobs in the brain.
Prerequisites: self.blobs_archive are established.
The magnification of the microscope must be known.
"""
fig3 = plt.figure(figsize = (10,6))
ax_3d = fig3.add_subplot(111, projection = '3d')
for n_frame in self.valid_frames:
# below the coordinates of the cells are computed.
blobs_list = self.c_list[n_frame]
ys = blobs_list[:,0]*magni_lateral
xs = blobs_list[:,1]*magni_lateral
zs = np.ones(len(blobs_list))*n_frame*zstep
ss = (np.sqrt(2)*blobs_list[:,2]*magni_lateral)**2*np.pi
Axes3D.scatter(xs,ys, zs, zdir = 'z', s=ss, c='g')
ax_3d.set_xlabel('x (micron)', fontsize = 12)
ax_3d.set_xlabel('y (micron)', fontsize = 12)
return fig3
def clust(elect_coords, n_clusts, iters, init_clusts):
# Load resultant coordinates from Hough circles transform
#coords = scipy.io.loadmat(elect_coords);
#dat = coords.get('elect_coords');
dat = elect_coords;
# Configure Kmeans
cluster = sklearn.cluster.KMeans();
cluster.n_clusters= n_clusts;
cluster.init = 'k-means++';
cluster.max_iter = iters;
cluster.verbose = 0;
cluster.n_init = init_clusts;
cluster.fit(dat);
# Grab vector for plotting each dimension
x = list(cluster.cluster_centers_[:,0]);
y = list(cluster.cluster_centers_[:,1]);
z = list(cluster.cluster_centers_[:,2]);
c = list(cluster.labels_);
scipy.io.savemat('k_labels.mat', {'labels':cluster.labels_})
scipy.io.savemat('k_coords.mat', {'coords':cluster.cluster_centers_})
# plot the results of kmeans
cmap = colors.Colormap('hot');
norm = colors.Normalize(vmin=1, vmax=10);
s = 64;
fig = plt.figure();
ax = fig.add_subplot(111,projection='3d');
Axes3D.scatter3D(ax,x,y,z,s=s);
plt.show(fig);
return cluster.cluster_centers_,cluster.labels_;
def plotFigures(xSolid,ySolid,zSolid,xFFDDeform,yFFDDeform,zFFDDeform, xsolidInitial,
ysolidInitial, zsolidInitial, xFFDInitial, yFFDInitial, zFFDInitial):
fig = plt.figure()
ax = fig.add_subplot(111, projection='3d')
# Axes3D.plot_wireframe(ax, z, x, y)
ax.set_xlabel('Z axis')
ax.set_ylabel('X axis')
ax.set_zlabel('Y axis')
#Axes3D.scatter(ax, zSolid, xSolid, ySolid, s=10, c='b')
Axes3D.plot_wireframe(ax, zSolid, xSolid, ySolid, rstride = 1, cstride = 1, color="b")
Axes3D.scatter(ax, zFFDDeform, xFFDDeform, yFFDDeform, s=30, c='r')
#Axes3D.scatter(ax, zsolidInitial, xsolidInitial, ysolidInitial, s=10, c='y')
Axes3D.plot_wireframe(ax, zsolidInitial, xsolidInitial, ysolidInitial,rstride = 1, cstride = 1, color="y")
Axes3D.scatter(ax, zFFDInitial, xFFDInitial, yFFDInitial, s=30, c='g')
xZCross = []
yZCross = []
zZCross = []
#plot the points for the limits of each cross section
for zCrossSect in GLOBAL_zCrossSectionObjects:
zCrossSectionObject = GLOBAL_zCrossSectionObjects[zCrossSect]
#add to the arrays, for a fixed z, the following combinations
# (xmax, ymax) (xmax, ymin) (xmin, ymin) (xmin, ymax)
# (xmax, ymax)
xZCross.append(zCrossSectionObject.getXMax())
yZCross.append(zCrossSectionObject.getYMax())
zZCross.append(zCrossSect)
#(xmax, ymin)
xZCross.append(zCrossSectionObject.getXMax())
yZCross.append(zCrossSectionObject.getYMin())
zZCross.append(zCrossSect)
#(xmin, ymin)
xZCross.append(zCrossSectionObject.getXMin())
yZCross.append(zCrossSectionObject.getYMin())
zZCross.append(zCrossSect)
#(xmin, ymax)
xZCross.append(zCrossSectionObject.getXMin())
yZCross.append(zCrossSectionObject.getYMax())
zZCross.append(zCrossSect)
#Axes3D.plot_wireframe(ax, zZCross, xZCross, yZCross)
#Axes3D.set_ylim(ax, [-0.5,4.5])
#Axes3D.set_xlim(ax, [-0.5,4.5])
Axes3D.set_zlim(ax, [-0.7, 0.7])
plt.show(block=True)
def elecDetect(CT_dir, T1_dir, img, thresh, frac, num_gridStrips, n_elects):
# navigate to dir with CT img
os.chdir(T1_dir)
# Extract and apply CT brain mask
mask_CTBrain(CT_dir, T1_dir, frac)
masked_img = "masked_" + img
# run CT_electhresh
print "::: Thresholding CT at %f stdv :::" % (thresh)
electhresh(masked_img, thresh)
# run im_filt to gaussian smooth thresholded image
fname = "thresh_" + masked_img
print "::: Applying guassian smooth of 2.5mm to thresh-CT :::"
img_filt(fname)
# run hough transform to detect electrodes
new_fname = "smoothed_" + fname
print "::: Applying 2d Hough Transform to localize electrode clusts :::"
elect_coords = CT_hough(CT_dir, new_fname)
# set up x,y,z coords to view hough results
x = elect_coords[:, 0]
x = x.tolist()
y = elect_coords[:, 1]
y = y.tolist()
z = elect_coords[:, 2]
z = z.tolist()
# plot the hough results
s = 64
fig = plt.figure()
ax = fig.add_subplot(111, projection="3d")
Axes3D.scatter3D(ax, x, y, z, s=s)
plt.show(fig)
# run K means to find grid and strip clusters
n_clusts = num_gridStrips
# number of cluster to find = number of electrodes
iters = 1000
init_clusts = n_clusts
print "::: Performing K-means cluster to find %d grid-strip and noise clusters :::" % (n_clusts)
[clust_coords, clust_labels] = clust(elect_coords, n_clusts, iters, init_clusts)
# run K means to find electrode center coordinates
n_clusts = n_elects
# number of cluster to find = number of electrodes
iters = 1000
init_clusts = n_clusts
print "::: Performing K-means cluster to find %d electrode centers :::" % (n_clusts)
[center_coords, labels] = clust(elect_coords, n_clusts, iters, init_clusts)
print "::: Finished :::"
return elect_coords, clust_coords, clust_labels
def draw(self, axes: Axes3D):
R = (self.orientation * (self.orientation_origin.get_inverse())).to_rot_matrix()
xx = R[0, 0] * self.x + R[0, 1] * self.y + R[0, 2] * self.z
yy = R[1, 0] * self.x + R[1, 1] * self.y + R[1, 2] * self.z
zz = R[2, 0] * self.x + R[2, 1] * self.y + R[2, 2] * self.z
axes.plot_surface(xx, yy, zz, rstride=4, cstride=4, color='b')
return axes,
def water(self, *argv): # Dimension is unit type as V(olt) W(att), etc
# http://matplotlib.org/examples/mplot3d/polys3d_demo.html
Axes3D.plot_surface(self.signalx, self.signaly, self.signalz) # till better funcion
plt.xlabel('time [s]') # Or Sample number
plt.ylabel('Frequency [Hz]') # Or Freq Bins number
plt.zlabel('voltage [mV]') # auto add unit here
plt.title(' ') # set title
plt.grid(True)
plt.show()
def __init__(self,*args,**kwargs):
if (len(args) > 1) | kwargs.has_key('rect'):
_Axes3D.__init__(self,*args,**kwargs)
else:
rect = (0.1,0.1,0.8,0.8)
_Axes3D.__init__(self,*args,rect=rect,**kwargs)
self.cross_section_clim_set = False
self.pbaspect = np.array([1.0,1.0,1.0])
def addmpl(self, fig):
self.fig = fig
self.canvas = FigureCanvas(fig)
self.mplvl.addWidget(self.canvas)
self.canvas.draw()
self.toolbar = NavigationToolbar(self.canvas,
self.mplwindow, coordinates=True)
self.mplvl.addWidget(self.toolbar)
ax = fig.get_axes()[0]
Axes3D.mouse_init(ax)
def addcurve( ax, path, endpoints, color ) : px = path[ :,0 ] py = path[ :,1 ] pz = path[ :,2 ] n = len(px) - 1 q = Axes3D.plot(ax, px, py, zs=pz, c=color, linewidth=2 ) px = endpoints[ :,0 ] py = endpoints[ :,1 ] pz = endpoints[ :,2 ] print px, py, pz q = Axes3D.scatter(ax, px,py, zs=pz, c=color, marker='o', s=60)
def main():
# initialize ros node
rospy.init_node('compute_calibration')
# get path to folder containing recorded data
filesPath = rospy.get_param('~files_path')
# load trajectories
kinectTraj = np.loadtxt('%skinect_trajectory' % (filesPath), delimiter=',')
baxterTraj = np.loadtxt('%sbaxter_trajectory' % (filesPath), delimiter=',')
# compute absolute orientation
kinectOut, rot, trans = absOrientation(kinectTraj,baxterTraj)
# plot both point sets together
fig = plt.figure()
ax = fig.add_subplot(111, projection='3d')
# plot the data
Axes3D.scatter(ax, kinectOut[:,0], kinectOut[:,1], kinectOut[:,2], s=20, c='r')
Axes3D.scatter(ax, baxterTraj[:,0],baxterTraj[:,1], baxterTraj[:,2], s=20, c='b')
# add labels and title
ax.set_xticks([])
ax.set_yticks([])
ax.set_zticks([])
ax.set_xlabel('X-axis')
ax.set_ylabel('Y-axis')
ax.set_zlabel('Z-axis')
plt.title('Kinect-Baxter Calibration')
plt.legend(['Kinect','Baxter'])
plt.show()
# get rotation matrix as quaternion and euler angles
euler = tf.transformations.euler_from_matrix(rot)
quat = tf.transformations.quaternion_from_euler(*euler)
# save results to yaml file
f = open('%skinect_calibration.yaml' % (filesPath), 'w')
lines = ['trans: [', 'rot: [', 'rot_euler: [']
for elem in trans: lines[0] += str(elem) + ', '
lines[0] += ']\n'
for elem in quat: lines[1] += str(elem) + ', '
lines[1] += ']\n'
for elem in euler: lines[2] += str(elem) + ', '
lines[2] += ']\n'
lines.append('parent: /base\n')
lines.append('child: /kinect2_link\n')
f.writelines(lines)
f.close()
def Spect(self): #, dimension): # Dimension is unit type as V(olt) W(att), etc
Axes3D.plot_surface(self.signalx, self.signaly, self.signalz)
if self.signalx.shape == self.signaly.shape == self.signalz.shape:
pass
elif self.signalx.shape == (len(self.signalx), ) or self.signaly.shape == (len(self.signaly), ):
# Check for 1D array both
if self.signalx.shape == (len(self.signalx), ) and self.signaly.shape == (len(self.signaly), ):
self.signalx, self.signaly = np.meshgrid(self.signalx, self.signaly)
nx, mx = np.shape(self.signalx)
nz, mz = np.shape(self.signalz)
if nx == nz and mx == mz:
pass
elif nx == mz and mx == nz:
self.signalz = np.rot90(self.signalz, 1)
# find out if it has to be 1 or 3
elif self.signalx.shape == (len(self.signalx), ):
pass
elif self.signaly.shape == (len(self.signaly), ):
pass
if self.signalx.shape == self.signaly.shape != self.signalz.shape:
nx, mx = np.shape(self.signalx)
nz, mz = np.shape(self.signalz)
if nx == nz and mx == mz:
pass
elif nx == mz and mx == nz:
self.signalz = np.rot90(self.signalz, 1)
# find out if it has to be 1 or 3
elif self.signalx.shape == self.signalz.shape != self.signaly.shape:
nx, mx = np.shape(self.signalx)
ny, my = np.shape(self.signalz)
if nx == ny and mx == my:
pass
elif nx == my and mx == ny:
self.signaly = np.rot90(self.signaly, 1)
# find out if it has to be 1 or 3
elif self.signaly.shape == self.signalz.shape != self.signalx.shape:
ny, my = np.shape(self.signaly)
nx, mx = np.shape(self.signalx)
if ny == nx and my == mx:
pass
elif ny == mx and my == nx:
self.signalz = np.rot90(self.signalz, 1)
# find out if it has to be 1 or 3
else:
raise MeasError.DataError("No Valid data found in at least one of the axis")
plt.xlabel('time [s]') # Or Sample number
plt.ylabel('Frequency [Hz]') # Or Freq Bins number
plt.zlabel('voltage [mV]') # auto add unit here
plt.title(' ') # set title
plt.grid(True)
plt.show()
def plotPCA(proj3D, X_r, PCs, ligs, colors, csvPath, save_flag):
"""
Plot the PCA data on 2D plot
"""
# Main figure
fig = plt.figure(figsize=(13, 12), dpi=100)
if proj3D:
ax = fig.add_subplot(111, projection="3d")
for label, col, x, y, z in zip(ligs, colors,
X_r[:, 0], X_r[:, 1], X_r[:, 2]):
newCol = makeColor(col)
Axes3D.scatter(ax, x, y, z, label=label, color=newCol,
marker="o", lw=1, s=800)
ax.set_xlabel("PC1 (" + '{0:g}'.format(PCs[0]) + " %)", fontsize=30)
ax.set_ylabel("PC2 (" + '{0:g}'.format(PCs[1]) + " %)", fontsize=30)
ax.set_zlabel("PC3 (" + '{0:g}'.format(PCs[2]) + " %)", fontsize=30)
ax.tick_params(axis="both", which="major", labelsize=20)
pngPath = csvPath.replace(".csv", "_3D.png")
else:
ax = fig.add_subplot(111)
for label, col, x, y in zip(ligs, colors, X_r[:, 0], X_r[:, 1]):
newCol = makeColor(col)
ax.scatter(x, y, label=label, color=newCol, marker="o", lw=1, s=800)
# ax.annotate(label, xy=(x, y - 0.05), fontsize=10,
# ha='center', va='top')
ax.set_xlabel("PC1 (" + '{0:g}'.format(PCs[0]) + " %)", fontsize=30)
ax.set_ylabel("PC2 (" + '{0:g}'.format(PCs[1]) + " %)", fontsize=30)
ax.tick_params(axis="both", which="major", labelsize=30)
pngPath = csvPath.replace(".csv", "_2D.png")
# figTitle = "PCA on " + csvPath + " (PC1=" + pcVals[0] + ", PC2=" +
# pcVals[1] + ")"
# ax.text(0.5, 1.04, figTitle, horizontalalignment="center", fontsize=30,
# transform=ax.transAxes)
# Legend figure
fig_legend = plt.figure(figsize=(13, 12), dpi=100)
plt.figlegend(*ax.get_legend_handles_labels(), scatterpoints=1,
loc="center", fancybox=True,
shadow=True, prop={"size": 30})
# Save figures if save flag was used
if save_flag:
print("\nSAVING figures\n")
fig.savefig(pngPath, bbox_inches="tight")
fig_legend.savefig(pngPath.replace(".png", "_legend.png"))
# Otherwise show the plots
else:
print("\nSHOWING figures\n")
plt.show()
def makeequator( ax ) :
npts = 256
x = numpy.zeros( npts )
y = numpy.zeros( npts )
z = numpy.zeros( npts )
n = 0
for phi in numpy.arange( 0., 2*math.pi, 2*math.pi/npts ) :
x[n] = math.cos(phi)
y[n] = math.sin(phi)
n = n+1
q = Axes3D.plot(ax, x, y, zs=z, c='gray' )
q = Axes3D.plot(ax, x, z, zs=y, c='gray' )
q = Axes3D.plot(ax, z, y, zs=x, c='gray' )
def __init__(self, parent):
self.figure = Figure(tight_layout=True)
self.canvas = FigureCanvas(self.figure)
self.canvas.setContentsMargins(0,0,0,0)
self.axes = self.figure.add_subplot(111, projection='3d')
Axes3D.set_autoscale_on(self.axes, True)
Axes3D.autoscale_view(self.axes)
self.canvas.setParent(parent)
self.activePlot = None
self.activePopulation = None
self.surface = None
self.scatter = None
def custom_plot(self, additional):
for k in additional:
if(k == Simulation.DISCRETIZE):
for i in range(self.examples.noutputs):
for j in range(self.nbr_epoch):
if(self.plots['discretize_div'][i][j] != 0):
self.plots['discretize'][i][j] /= (self.plots['discretize_div'][i][j] * (self.nbDiscre ** self.nbDiscre))
colors = [(0.2, 0.8, 0.88), 'b', 'g', 'r', 'c', 'm', 'y', 'k', (0.8, 0.1, 0.8), (0., 0.2, 0.5)]
fig = plt.figure()
ax = fig.add_subplot(111, projection='3d')
for j in range(self.examples.noutputs):
ax.scatter([self.plots['discretize'][j][k] for k in self.plots['discretize_valid'][j]], [j] *
len(self.plots['discretize_valid'][j]), self.plots['discretize_valid'][j], color=colors[j], marker='x')
ax.set_xlabel('DISCRETIZED VALUE')
ax.set_ylabel('SHAPE')
ax.set_zlabel('EPOCH')
path = "/tmp/pyplot.%s.%s.png" % (sys.argv[0], time.strftime("%m-%d-%H-%M-%S", time.localtime()))
plt.savefig(path)
plt.show()
plt.title('Discretize hidden layer')
plt.ylabel('DISCRETIZED VALUE')
plt.xlabel("EPOCHS")
for j in range(self.examples.noutputs):
plt.plot(self.plots['discretize_valid'][j], [self.plots['discretize'][j][k]
for k in self.plots['discretize_valid'][j]], '.', color=colors[j])
path = "/tmp/pyplot.%s.%s.png" % (sys.argv[0], time.strftime("%m-%d-%H-%M-%S", time.localtime()))
try:
plt.savefig(path)
except ValueError:
print('Cannot save discretize_cloud')
try:
plt.show()
except ValueError:
print('Cannot display discretize_cloud')
elif(k == Simulation.PROTOTYPE):
lplot = [[0. for _ in range(self.examples.ninputs)] for _ in range(self.examples.noutputs)]
for network in self.networks:
for i in range(len(self.examples.inputs)):
network['FoN'].calc_output(self.examples.inputs[i])
network['SoN'].calc_output(network['FoN'].stateHiddenNeurons)
im = index_max(self.examples.outputs[i])
for j in range(self.examples.ninputs):
lplot[im][j] += network['SoN'].stateOutputNeurons[j]
fig = plt.figure()
plt.clf()
for i in range(self.examples.noutputs):
rpr.show_repr(lplot[i], self.width, fig, 250 + i, i)
path = "/tmp/pyplot.%s.%s.png" % (sys.argv[0], time.strftime("%m-%d-%H-%M-%S", time.localtime()))
plt.savefig(path)
plt.show()
def main():
global rR
global v
#v = polynomial_surface2(rR)
fig = plt.figure()
ax = fig.add_subplot(111, projection='3d')
v=[ 345.01147843, -731.53883648, 701.43498064, -333.41157482, 61.69405675, 434.95848754, -734.92037163, 468.45066799, -108.66899203, 197.05683428, -229.38490931, 73.72852732, 38.62490216, -23.11704968, 2.79760705, 1112.02959271, -1850.90352232, 1243.44148281, -301.1366546, 1096.50133704, -1278.21349214, 419.17838208, 338.80540403, -201.95899053, 33.68403733, 1333.97626976, -1566.15905716, 552.3302448, 922.09578713, -558.92492054, 145.7445413, 705.90344671, -442.88105472, 259.89354682, 138.22604583]
#ax=implicit.plot_implicit(fn4,bbox=(-1.5,0,-3.5,-1.5,-2,1),rc=200,ns=30,colors='b', ax=ax)
v=[ 2.18930311, 0.24260729, 57.46589779, 3.38543536, -9.56889825, 34.36258001, -36.2221404, 4.86597348, 12.89329227, 21.10709896, -4.36372996, -5.89323474, 3.98227029, 0.9848254, 0.23593784, -36.46890674, -25.34400559, 81.86028261, 14.43120124, 44.89510312, -52.04801532, -9.90597384, 16.49023335, 2.29875215, 0.40597427, -55.46318028, -39.9563639, 26.95078929, 35.15384941, -18.2399162, 5.13417155, -31.78519693, -14.89522473, 10.38829065, -6.66988281]
#ax=implicit.plot_implicit(fn4,bbox=(-1.5,0,-3.5,-1.5,-2,1),rc=200,ns=30,colors='r', ax=ax)
#rR = tree_time.tree_time(rR,0.05)
rR=array(rR)
Axes3D.scatter(ax,rR[:,0],rR[:,1],rR[:,2])
Axes3D.scatter(ax,-0.87676517,-2.5211104,-0.76908632,color='green')
plt.show()
def visualize( Z, solution=[]):
Y = np.arange(0,YSIZE,1)
X = np.arange(0,XSIZE,1)
fig = plt.figure()
ax = fig.gca(projection='3d')
X, Y = np.meshgrid(X, Y)
surf = ax.plot_surface(X, Y, Z, rstride=1, cstride=1, cmap=cm.coolwarm, linewidth=0, antialiased=False)
if 0 < len( solution) :
# TODO plot line not implemented - which function again?
Axes3D.plot(X, Y, solution)
ax.set_zlim(0.0, 1.01)
ax.zaxis.set_major_locator(LinearLocator(10))
ax.zaxis.set_major_formatter(FormatStrFormatter('%.02f'))
fig.colorbar(surf, shrink=0.5, aspect=5)
plt.show()
def plot_3d(self, z_data, x_coverage, y_coverage, title=None, x_axis_label="X", y_axis_label="Y", z_axis_label="Z"):
# 3D plotting is sort of a pain in the neck, and heavily dependent on data formatting. This routine assumes that you are
# providing the z height data as a two dimensional array array, and that the overall X and Y spans are
# given, so the routine can automatically compute arrays comprising the X and Y positions. If your data files contain the X and Y
# positions explicitly, this routine AND the data file reader will require heavy modification to ensure that the data gets
# passed and plotted correctly.
# takes Z data as an X by Y array of z values, and computes the X and Y arrays based on the "coverage" provided and the size
# of the Z array
# \todo design a better way of handling x and y coordinates
# these might be passed as strings by the config parser, so ensure that they are recast as integers
# \todo use configobj validators to handle this casting
x_coverage = int(x_coverage)
y_coverage = int(y_coverage)
z_data = npy.array(z_data)
self.clear_figure()
# set up some borders
# these borders never go away, and screw up the other plots - leave them out until a better way is found to elegently fix them
# self.fig.subplots_adjust(left=0.05)
# self.fig.subplots_adjust(right=0.95)
# self.fig.subplots_adjust(top=0.97)
# self.fig.subplots_adjust(bottom = 0.03)
axes = self.fig.add_subplot(111, projection="3d")
# allow us to use the mouse to spin the 3d plot around
Axes3D.mouse_init(axes)
(x_data, y_data) = compute_3d_coordinates(z_data, x_coverage, y_coverage)
axes.plot_wireframe(x_data, y_data, z_data)
if title:
axes.set_title(title)
axes.set_xlabel(x_axis_label)
axes.set_ylabel(y_axis_label)
axes.set_zlabel(z_axis_label)
axes.view_init(self.elev_3d, self.azim_3d)
self.canvas.draw()
self.current_plot_type = "3D"
def drawcylinder( ax ) :
npts = 2048
xa = numpy.array( [-1, 1] )
ya = numpy.array( [0.,0.] )
za = numpy.array( [40.,40.] )
q = Axes3D.plot(ax, xa, za, zs=ya, c='gray' )
q = Axes3D.plot(ax, ya, za, zs=xa, c='gray' )
za = numpy.array( [-40.,-40.] )
q = Axes3D.plot(ax, xa, za, zs=ya, c='gray' )
q = Axes3D.plot(ax, ya, za, zs=xa, c='gray' )
xa = numpy.array( [0.,0.] )
za = numpy.array( [0.,0.] )
ya = numpy.array( [-40.,40.] )
q = Axes3D.plot(ax, xa, ya, zs=za, c='gray', linestyle='--' )
x = numpy.zeros( npts )
y = -30.*numpy.ones( npts )
z = numpy.zeros( npts )
xx = numpy.zeros( npts )
yy = numpy.zeros( npts )
zz = numpy.zeros( npts )
n = 0
for phi in numpy.arange( 0., 2*math.pi, 2*math.pi/npts ) :
x[n] = math.cos(phi)
z[n] = math.sin(phi)
n = n+1
#q = Axes3D.plot(ax, x, y, zs=z, c='gray' )
y = 30.* numpy.ones( npts )
#q = Axes3D.plot(ax, x, y, zs=z, c='gray' )
n = 0
for phi in numpy.arange( -30., 30.0, (60./npts) ) :
yy[n] = phi
amp = math.cos(phi)
zz[n] = amp * math.cos( .007 * (30.-phi) )
xx[n] = -1.* amp * math.sin( .007 * (30.-phi) )
#zz[n] = math.cos(phi)
n = n+1
q = Axes3D.plot(ax, xx, yy, zs=zz, c='black' )
xxx = numpy.zeros( 2 )
yyy = 40.*numpy.ones( 2 )
zzz = numpy.zeros( 2 )
zzz[0] = -1.
zzz[1] = 1.
q = Axes3D.plot(ax, xxx, yyy, zs=zzz, c='black' )
xxxx = numpy.zeros( 2 )
yyyy = -40.*numpy.ones( 2 )
zzzz = numpy.zeros( 2 )
xxxx[0] = -1.* math.sin( .007 * (60.) )
zzzz[0] = math.cos( .007 * (60.) )
xxxx[1] = 1.* math.sin( .007 * (60.) )
zzzz[1] = -1.* math.cos( .007 * (60.) )
q = Axes3D.plot(ax, xxxx, yyyy, zs=zzzz, c='black' )
def vectorplot(Points_From,Points_To):
import matplotlib.pyplot as plt
from mpl_toolkits.mplot3d import Axes3D
from matplotlib.patches import FancyArrowPatch
from mpl_toolkits.mplot3d import proj3d
fig = plt.figure()
ax = fig.add_subplot(111, projection='3d')
for i in range(len(Points_From)):
# ax.plot([Points_From[i][0], Points_To[i][0]], [Points_From[i][1], Points_To[i][1]],zs=[Points_From[i][2], Points_To[i][2]])
a=Arrow3D([Points_From[i][0], Points_To[i][0]], [Points_From[i][1], Points_To[i][1]],[Points_From[i][2], Points_To[i][2]],mutation_scale=2000, lw=3, arrowstyle="-|>", color="r")
ax.add_artist(a)
plt.show()
Axes3D.plot()
def updatePopulation(self, population):
self.activePopulation = population
x, y, z = self.preparePopulationData(population)
if self.scatter is not None:
self.scatter.remove()
self.scatter = Axes3D.scatter(self.axes, x, y, z, c="r", marker="o")
# self.surface.set_zorder(2)
# self.scatter.set_zorder(100)
self.scatter.set_alpha(1.0)
self.canvas.draw()
self.canvas.flush_events()
def plotElements(PhysicalElementMatrix):
fig = plt.figure()
ax = fig.add_subplot(111, projection='3d')
# Axes3D.plot_wireframe(ax, z, x, y)
ax.set_xlabel('X axis')
ax.set_ylabel('Y axis')
ax.set_zlabel('Z axis')
xVector = []
yVector = []
zVector = []
for i in range(CONST_DIMENSION_X):
for j in range(CONST_DIMENSION_Y):
for k in range(CONST_DIMENSION_Z):
elementObject = PhysicalElementMatrix[i][j][k]
for gridPointObject in elementObject.gridPointList:
xVector.append(gridPointObject.getX())
yVector.append(gridPointObject.getY())
zVector.append(gridPointObject.getZ())
Axes3D.scatter(ax, xVector, yVector, zVector, s=30, c='r')
#Axes3D.plot_wireframe(ax, zSolid, xSolid, ySolid, rstride = 1, cstride = 1, color="b")
# create the lines around all the elements
for i in range(CONST_DIMENSION_X):
for j in range(CONST_DIMENSION_Y):
for k in range(CONST_DIMENSION_Z):
elementObject = PhysicalElementMatrix[i][j][k]
ListXVectors,ListYVectors,ListZVectors = elementObject.getOuterLineVectors()
for l in range(len(ListXVectors)):
plt.plot(ListXVectors[l],ListYVectors[l], ListZVectors[l], c = 'b')
Axes3D.set_ylim(ax, [-10,10])
Axes3D.set_xlim(ax, [-10,10])
Axes3D.set_zlim(ax, [-10, 10])
plt.show(block=True)
def plotElements(fig, ax, ElementsSbpData, ElementsFFDData, NumElements,c1,c2,\
c3,c4):
for i in range(NumElements):
xSolid = []
ySolid = []
zSolid = []
xFFD = []
yFFD = []
zFFD = []
#fill the Solid body points
for SBPTuple in ElementsSbpData[i]:
xSolid.append(SBPTuple[0][0])
ySolid.append(SBPTuple[0][1])
zSolid.append(SBPTuple[0][2])
for FFDTuple in ElementsFFDData[i]:
xFFD.append(FFDTuple[1][0])
yFFD.append(FFDTuple[1][1])
zFFD.append(FFDTuple[1][2])
# element 1 is the fuselage whose x and z values were switched
# to make z cross sections. So switch these back when plotting
if(i == 0):
#ax.plot_trisurf(zSolid, xSolid, ySolid, cmap=cm.jet, linewidth=0.2)
Axes3D.scatter(ax, zSolid,xSolid, ySolid, s=20, c=c1)
Axes3D.scatter(ax, zFFD, xFFD, yFFD, s=30, c= c2)
#Axes3D.plot_wireframe(ax, zFFD, xFFD, yFFD)
if(i == 1):
#ax.plot_trisurf(xSolid, zSolid, ySolid, cmap=cm.jet, linewidth=0.2)
Axes3D.scatter(ax, zSolid,xSolid, ySolid, s=20, c=c3)
Axes3D.scatter(ax, zFFD, xFFD, yFFD, s=30, c= c4)
def plotFiguresTemp(xSolid, ySolid, zSolid, xFFDDeform, yFFDDeform, zFFDDeform):
fig = plt.figure()
ax = fig.add_subplot(111, projection='3d')
# Axes3D.plot_wireframe(ax, z, x, y)
ax.set_xlabel('Z axis')
ax.set_ylabel('X axis')
ax.set_zlabel('Y axis')
Axes3D.scatter(ax, zSolid, xSolid, ySolid, s=10, c='b')
Axes3D.scatter(ax, zFFDDeform, xFFDDeform, yFFDDeform, s=30, c='r')
# Axes3D.set_ylim(ax, [-0.5,4.5])
# Axes3D.set_xlim(ax, [-0.5,4.5])
Axes3D.set_zlim(ax, [-0.7, 0.7])
plt.show(block=True)
def train(net, x_train, x_test, y_train, y_test, lr, epoches):
train_losses = []
test_losses = []
plt.ion()
print_interval = int(epoches*0.2)
for i in range(epoches):
print('i=', i)
# 为了得到更好的效果，适当改变学习率
if i%print_interval==0 and i!=0:
lr=lr*0.8
print('-----------learning rate=',lr,'------------')
for j in range(len(x_train)):
net.back_propagation(x_train[j], y_train[j], lr)
if i%print_interval==0:
# 均方差
train_loss = np.mean(np.square(y_train - net.forward_propagation(x_train)))
test_loss = np.mean(np.square(y_test - net.forward_propagation(x_test)))
train_losses.append(train_loss)
test_losses.append(test_loss)
print('Epoch=', i, ', train_loss=', train_loss, ', test_loss=', test_loss)
# 回想泛化实况
plt.figure(1)
plt.cla()
xx = np.linspace(1, len(test_losses), len(test_losses))
plt.title("generalization")
plt.xlabel('epoches')
plt.ylabel('test_loss')
plt.plot(xx, test_losses)
# plt.show()
plt.figure(2)
plt.cla()
xx = np.linspace(1, len(train_losses), len(train_losses))
plt.title("recall")
plt.xlabel('epoches')
plt.ylabel('train_loss')
plt.plot(xx, train_losses)
# 二维空间函数拟合
if len(x_train[0])==1:
plt.figure(3)
plt.cla()
plt.scatter(x_train, y_train, s=5)
plt.scatter(x_train,net.forward_propagation(x_train),s=4 , color='red')
plt.text(1.5,0.2,'train loss=%.6lf'%train_loss,fontdict={'size':15,'color':'red','style':'italic'})
plt.figure(4)
plt.cla()
plt.scatter(x_test, y_test, s=5)
plt.scatter(x_test, net.forward_propagation(x_test), s=4, color='black')
plt.text(plt.axis()[0]+0.1,plt.axis()[2]+0.1,'test loss=%.6lf'%test_loss,fontdict={'size':15,'color':'blue','style':'italic'})
plt.pause(0.01)
# 三维空间函数拟合
elif len(x_train[0])==2:
x1_train = x_train[:, 0]
x2_train = x_train[:, 1]
x1_train, x2_train = np.meshgrid(x1_train, x2_train)
trainY = np.add(x1_train, x2_train)
x1_test = x_test[:, 0]
x2_test = x_test[:, 1]
x1_test, x2_test = np.meshgrid(x1_test, x2_test)
testY = np.add(x1_test, x2_test)
a = []
b = []
for k in x1_train:
for p in x2_train:
m = np.vstack((k, p)).T
a.append(m)
a = np.array(a)
a.resize((x1_train.shape[0]*x2_train.shape[0], 2))
for k in x1_test:
for p in x2_test:
m = np.vstack((k, p)).T
b.append(m)
b = np.array(b)
b.resize((x1_test.shape[0]*x2_test.shape[0], 2))
trainy = net.forward_propagation(a).reshape((x1_train.shape[0], x2_train.shape[0]))
testy = net.forward_propagation(b).reshape((x1_test.shape[0], x2_test.shape[0]))
# print(trainy.shape, testy.shape) #(280, 280), (120, 120)
fig1 = plt.figure(3, figsize=(6, 4))
plt.cla()
ax1=Axes3D(fig1)
ax1.scatter(x1_train, x2_train, trainY, ) # 预期输出
ax1.scatter(x1_train, x2_train, trainy, ) # 实际输出
ax1.text(plt.axis()[1]-0.1, plt.axis()[2]+0.1, 0, 'train loss=%.6lf'%train_loss, fontdict={'size':15,'color':'blue','style':'italic'})
ax1.set_xlabel('x1')
ax1.set_ylabel('x2')
ax1.set_zlabel('y')
fig2 = plt.figure(4, figsize=(6, 4))
plt.cla()
ax2=Axes3D(fig2)
ax2.scatter(x1_test, x2_test, testY, )
ax2.scatter(x1_test, x2_test, testy, )
ax2.text(plt.axis()[1]-0.1, plt.axis()[2]+0.1, 0, 'test loss=%.6lf'%test_loss, fontdict={'size':15,'color':'blue','style':'italic'})
ax2.set_xlabel('x1')
ax2.set_ylabel('x2')
ax2.set_zlabel('y')
plt.pause(0.01)
plt.show()
plt.ioff()
return train_losses, test_losses
def plot_surf(surf_mesh,
surf_map=None,
bg_map=None,
hemi='left',
view='lateral',
cmap=None,
colorbar=False,
avg_method='mean',
threshold=None,
alpha='auto',
bg_on_data=False,
darkness=1,
vmin=None,
vmax=None,
cbar_vmin=None,
cbar_vmax=None,
title=None,
output_file=None,
axes=None,
figure=None,
**kwargs):
""" Plotting of surfaces with optional background and data
.. versionadded:: 0.3
Parameters
----------
surf_mesh: str or list of two numpy.ndarray
Surface mesh geometry, can be a file (valid formats are
.gii or Freesurfer specific files such as .orig, .pial,
.sphere, .white, .inflated) or
a list of two Numpy arrays, the first containing the x-y-z coordinates
of the mesh vertices, the second containing the indices
(into coords) of the mesh faces.
surf_map: str or numpy.ndarray, optional.
Data to be displayed on the surface mesh. Can be a file (valid formats
are .gii, .mgz, .nii, .nii.gz, or Freesurfer specific files such as
.thickness, .curv, .sulc, .annot, .label) or
a Numpy array with a value for each vertex of the surf_mesh.
bg_map: Surface data object (to be defined), optional,
Background image to be plotted on the mesh underneath the
surf_data in greyscale, most likely a sulcal depth map for
realistic shading.
hemi : {'left', 'right'}, default is 'left'
Hemisphere to display.
view: {'lateral', 'medial', 'dorsal', 'ventral', 'anterior', 'posterior'},
default is 'lateral'
View of the surface that is rendered.
cmap: matplotlib colormap, str or colormap object, default is None
To use for plotting of the stat_map. Either a string
which is a name of a matplotlib colormap, or a matplotlib
colormap object. If None, matplotlib default will be chosen
colorbar : bool, optional, default is False
If True, a colorbar of surf_map is displayed.
avg_method: {'mean', 'median'}, default is 'mean'
How to average vertex values to derive the face value, mean results
in smooth, median in sharp boundaries.
threshold : a number or None, default is None.
If None is given, the image is not thresholded.
If a number is given, it is used to threshold the image, values
below the threshold (in absolute value) are plotted as transparent.
alpha: float, alpha level of the mesh (not surf_data), default 'auto'
If 'auto' is chosen, alpha will default to .5 when no bg_map
is passed and to 1 if a bg_map is passed.
bg_on_data: bool, default is False
If True, and a bg_map is specified, the surf_data data is multiplied
by the background image, so that e.g. sulcal depth is visible beneath
the surf_data.
NOTE: that this non-uniformly changes the surf_data values according
to e.g the sulcal depth.
darkness: float, between 0 and 1, default is 1
Specifying the darkness of the background image.
1 indicates that the original values of the background are used.
.5 indicates the background values are reduced by half before being
applied.
vmin, vmax: lower / upper bound to plot surf_data values
If None , the values will be set to min/max of the data
title : str, optional
Figure title.
output_file: str, or None, optional
The name of an image file to export plot to. Valid extensions
are .png, .pdf, .svg. If output_file is not None, the plot
is saved to a file, and the display is closed.
axes: instance of matplotlib axes, None, optional
The axes instance to plot to. The projection must be '3d' (e.g.,
`figure, axes = plt.subplots(subplot_kw={'projection': '3d'})`,
where axes should be passed.).
If None, a new axes is created.
figure: instance of matplotlib figure, None, optional
The figure instance to plot to. If None, a new figure is created.
See Also
--------
nilearn.datasets.fetch_surf_fsaverage : For surface data object to be
used as background map for this plotting function.
nilearn.plotting.plot_surf_roi : For plotting statistical maps on brain
surfaces.
nilearn.plotting.plot_surf_stat_map : for plotting statistical maps on
brain surfaces.
"""
# load mesh and derive axes limits
mesh = load_surf_mesh(surf_mesh)
coords, faces = mesh[0], mesh[1]
limits = [coords.min(), coords.max()]
# set view
if hemi == 'right':
if view == 'lateral':
elev, azim = 0, 0
elif view == 'medial':
elev, azim = 0, 180
elif view == 'dorsal':
elev, azim = 90, 0
elif view == 'ventral':
elev, azim = 270, 0
elif view == 'anterior':
elev, azim = 0, 90
elif view == 'posterior':
elev, azim = 0, 270
else:
raise ValueError('view must be one of lateral, medial, '
'dorsal, ventral, anterior, or posterior')
elif hemi == 'left':
if view == 'medial':
elev, azim = 0, 0
elif view == 'lateral':
elev, azim = 0, 180
elif view == 'dorsal':
elev, azim = 90, 0
elif view == 'ventral':
elev, azim = 270, 0
elif view == 'anterior':
elev, azim = 0, 90
elif view == 'posterior':
elev, azim = 0, 270
else:
raise ValueError('view must be one of lateral, medial, '
'dorsal, ventral, anterior, or posterior')
else:
raise ValueError('hemi must be one of right or left')
# set alpha if in auto mode
if alpha == 'auto':
if bg_map is None:
alpha = .5
else:
alpha = 1
# if no cmap is given, set to matplotlib default
if cmap is None:
cmap = plt.cm.get_cmap(plt.rcParamsDefault['image.cmap'])
else:
# if cmap is given as string, translate to matplotlib cmap
if isinstance(cmap, str):
cmap = plt.cm.get_cmap(cmap)
# initiate figure and 3d axes
if axes is None:
if figure is None:
figure = plt.figure()
axes = Axes3D(figure, rect=[0, 0, 1, 1], xlim=limits, ylim=limits)
else:
if figure is None:
figure = axes.get_figure()
axes.set_xlim(*limits)
axes.set_ylim(*limits)
axes.view_init(elev=elev, azim=azim)
axes.set_axis_off()
# plot mesh without data
p3dcollec = axes.plot_trisurf(coords[:, 0],
coords[:, 1],
coords[:, 2],
triangles=faces,
linewidth=0.,
antialiased=False,
color='white')
# reduce viewing distance to remove space around mesh
axes.dist = 8
# set_facecolors function of Poly3DCollection is used as passing the
# facecolors argument to plot_trisurf does not seem to work
face_colors = np.ones((faces.shape[0], 4))
if bg_map is None:
bg_data = np.ones(coords.shape[0]) * 0.5
else:
bg_data = load_surf_data(bg_map)
if bg_data.shape[0] != coords.shape[0]:
raise ValueError('The bg_map does not have the same number '
'of vertices as the mesh.')
bg_faces = np.mean(bg_data[faces], axis=1)
if bg_faces.min() != bg_faces.max():
bg_faces = bg_faces - bg_faces.min()
bg_faces = bg_faces / bg_faces.max()
# control background darkness
bg_faces *= darkness
face_colors = plt.cm.gray_r(bg_faces)
# modify alpha values of background
face_colors[:, 3] = alpha * face_colors[:, 3]
# should it be possible to modify alpha of surf data as well?
if surf_map is not None:
surf_map_data = load_surf_data(surf_map)
if surf_map_data.ndim != 1:
raise ValueError('surf_map can only have one dimension but has'
'%i dimensions' % surf_map_data.ndim)
if surf_map_data.shape[0] != coords.shape[0]:
raise ValueError('The surf_map does not have the same number '
'of vertices as the mesh.')
# create face values from vertex values by selected avg methods
if avg_method == 'mean':
surf_map_faces = np.mean(surf_map_data[faces], axis=1)
elif avg_method == 'median':
surf_map_faces = np.median(surf_map_data[faces], axis=1)
# if no vmin/vmax are passed figure them out from data
if vmin is None:
vmin = np.nanmin(surf_map_faces)
if vmax is None:
vmax = np.nanmax(surf_map_faces)
# treshold if inidcated
if threshold is None:
kept_indices = np.arange(surf_map_faces.shape[0])
else:
kept_indices = np.where(np.abs(surf_map_faces) >= threshold)[0]
surf_map_faces = surf_map_faces - vmin
surf_map_faces = surf_map_faces / (vmax - vmin)
# multiply data with background if indicated
if bg_on_data:
face_colors[kept_indices] = cmap(surf_map_faces[kept_indices])\
* face_colors[kept_indices]
else:
face_colors[kept_indices] = cmap(surf_map_faces[kept_indices])
if colorbar:
our_cmap = get_cmap(cmap)
norm = Normalize(vmin=vmin, vmax=vmax)
nb_ticks = 5
ticks = np.linspace(vmin, vmax, nb_ticks)
bounds = np.linspace(vmin, vmax, our_cmap.N)
if threshold is not None:
cmaplist = [our_cmap(i) for i in range(our_cmap.N)]
# set colors to grey for absolute values < threshold
istart = int(norm(-threshold, clip=True) * (our_cmap.N - 1))
istop = int(norm(threshold, clip=True) * (our_cmap.N - 1))
for i in range(istart, istop):
cmaplist[i] = (0.5, 0.5, 0.5, 1.)
our_cmap = LinearSegmentedColormap.from_list(
'Custom cmap', cmaplist, our_cmap.N)
# we need to create a proxy mappable
proxy_mappable = ScalarMappable(cmap=our_cmap, norm=norm)
proxy_mappable.set_array(surf_map_faces)
cax, kw = make_axes(axes,
location='right',
fraction=.1,
shrink=.6,
pad=.0)
cbar = figure.colorbar(proxy_mappable,
cax=cax,
ticks=ticks,
boundaries=bounds,
spacing='proportional',
format='%.2g',
orientation='vertical')
_crop_colorbar(cbar, cbar_vmin, cbar_vmax)
p3dcollec.set_facecolors(face_colors)
if title is not None:
axes.set_title(title, position=(.5, .95))
# save figure if output file is given
if output_file is not None:
figure.savefig(output_file)
plt.close(figure)
else:
return figure
def hist3d(y_label, x_label, z_value, \
y_label_name = "y", x_label_name = "x", z_label_name = "z", output_filepath = "..\\result\\lsfs_featue_namuda.png"):
"""
y -> row -> data.shape[0]
x -> column -> data->shape[1]
"""
column_names = x_label.copy()
row_names = y_label.copy()
data = z_value.copy()
fig = plt.figure(figsize=(8, 5))
ax = Axes3D(fig)
lx= len(data[0]) # Work out matrix dimensions
ly= len(data[:,0])
xpos = np.arange(0,lx,1) # Set up a mesh of positions
ypos = np.arange(0,ly,1)
xpos, ypos = np.meshgrid(xpos+0.25, ypos+0.25)
xpos = xpos.flatten() # Convert positions to 1D array
ypos = ypos.flatten()
zpos = np.zeros(lx*ly)
dx = 0.5 * np.ones_like(zpos)
dy = dx.copy()
dz = data.flatten()
bar_colors = ['red', 'green', 'blue', 'aqua',
'burlywood', 'cadetblue', 'chocolate', 'cornflowerblue',
'crimson', 'darkcyan', 'darkgoldenrod', 'darkgreen',
'purple', 'darkred', 'darkslateblue', 'darkviolet']
colors = []
for i in range(len(y_label)):
for j in range(len(x_label)):
colors.append(bar_colors[i])
ax.bar3d(xpos,ypos,zpos, dx, dy, dz, color=colors, alpha = 0.6)
#sh()
ax.w_xaxis.set_ticklabels(x_label)
ax.w_yaxis.set_ticklabels(y_label)
ax.set_xlabel(x_label_name)
ax.set_ylabel(y_label_name)
ax.set_zlabel(z_label_name)
#ax.w_xaxis.set_ticklabels(column_names)
#ax.w_yaxis.set_ticklabels(row_names)
# start, stop, step
ticksx = np.arange(0.5, lx, 1)
plt.xticks(ticksx, x_label)
ticksy = np.arange(0.6, ly, 1)
plt.yticks(ticksy, y_label)
plt.savefig(output_filepath)
print("save to ", output_filepath)
plt.close()
import os
import pylab as pl
from mpl_toolkits.mplot3d import Axes3D
import matplotlib.pyplot as plt
from matplotlib import cm
from matplotlib.ticker import LinearLocator, FormatStrFormatter
import numpy as np
os.system("clear")
fig = pl.figure()
axx = Axes3D(fig)
raiz=np.sqrt
ln=np.log
X = np.arange(-2, 12, 0.1)
Y = np.arange(-2, 12, 0.1)
X[25]=0.49
X[65]=4.49
X[105]=8.49
Y[25]=0.49
Y[65]=4.49
Y[105]=8.49
X, Y = np.meshgrid(X, Y)
ax, ay = 0, 0
bx, by = 4, 0
vind = [[node1[i], node2[i], node3[i]]
for i in range(ntria)]
# vind = np.matrix([[node1[i], node2[i], node3[i]]
# for i in range(ntria)])
print(vind)
x = xpts
y = ypts
z = zpts
r = [[x[i], y[i], z[i]]
for i in range(nverts)]
# r = np.matrix([[x[i], y[i], z[i]]
# for i in range(nverts)])
print(r)
# inicio plot
fig1 = plt.figure()
ax = Axes3D(fig1)
# print(x[int(vind[0][0])])
# print(vind[0][0])
# int(vind[0][0])
# print(isinstance(int(vind[0][0]), float))
print(x)
for i in range(ntria):
# print(int(vind[i][0]))
# Xa = [x[int(vind[0][0])]]# , x[int(vind[i][1])], x[int(vind[i][2])], x[int(vind[i][0])]]
Xa = [int(r[int(vind[i][0])-1][0]), int(r[int(vind[i][1])-1][0]), int(r[int(vind[i][2])-1][0]), int(r[int(vind[i][0])-1][0])]
print(Xa)
Ya = [int(r[int(vind[i][0])-1][1]), int(r[int(vind[i][1])-1][1]), int(r[int(vind[i][2])-1][1]), int(r[int(vind[i][0])-1][1])]
# print(Ya)
Za = [int(r[int(vind[i][0])-1][2]), int(r[int(vind[i][1])-1][2]), int(r[int(vind[i][2])-1][2]), int(r[int(vind[i][0])-1][2])]
# print(Za)
# ax.plot3D(Xa, Ya, Za)
import matplotlib.pyplot as plt from mpl_toolkits.mplot3d import Axes3D X = [1, 1, 2, 2] Y = [3, 4, 4, 3] Z = [1, 100, 1, 1] figure = plt.figure() ax = Axes3D(figure) ax.plot_trisurf(X, Y, Z) plt.show()
import math
def fonction(X, Y):
return X * np.exp(-X**2 - Y**2) + (X**2 + Y**2) / 20
def gradient_fonction(X, Y):
g_x = np.exp(-X**2 - Y**2) + X * -2 * X * np.exp(-X**2 - Y**2) + X / 10
g_y = -2 * Y * X * np.exp(-X**2 - Y**2) + Y / 10
return g_x, g_y
fig = plt.figure()
fig.set_size_inches(9, 7, forward=True)
ax = Axes3D(fig, azim=-29, elev=49)
X = np.arange(-3, 3, 0.2)
Y = np.arange(-3, 3, 0.2)
X, Y = np.meshgrid(X, Y)
Z = fonction(X, Y)
ax.plot_wireframe(X, Y, Z, rstride=1, cstride=1)
#ax.contour(X, Y, Z, 70, rstride=1, cstride=1, cmap='plasma')
plt.xlabel("Paramètre 1 (x)")
plt.ylabel("Paramètre 2 (y)")
x = np.random.random_integers(-2, 2) + np.random.rand(1)[0]
y = np.random.random_integers(-2, 2) + np.random.rand(1)[0]
lr = 0.2
lr2 = 0.9
def sphereplot(theta, phi, values, fig=None, ax=None, save=False):
"""Plots a matrix of values on a sphere
Parameters
----------
theta : float
Angle with respect to z-axis
phi : float
Angle in x-y plane
values : array
Data set to be plotted
fig : a matplotlib Figure instance
The Figure canvas in which the plot will be drawn.
ax : a matplotlib axes instance
The axes context in which the plot will be drawn.
save : bool {False , True}
Whether to save the figure or not
Returns
-------
fig, ax : tuple
A tuple of the matplotlib figure and axes instances used to produce
the figure.
"""
if fig is None or ax is None:
fig = plt.figure()
ax = Axes3D(fig)
thetam, phim = np.meshgrid(theta, phi)
xx = sin(thetam) * cos(phim)
yy = sin(thetam) * sin(phim)
zz = cos(thetam)
r = array(abs(values))
ph = angle(values)
# normalize color range based on phase angles in list ph
nrm = mpl.colors.Normalize(ph.min(), ph.max())
# plot with facecolors set to cm.jet colormap normalized to nrm
surf = ax.plot_surface(r * xx,
r * yy,
r * zz,
rstride=1,
cstride=1,
facecolors=cm.jet(nrm(ph)),
linewidth=0)
# create new axes on plot for colorbar and shrink it a bit.
# pad shifts location of bar with repsect to the main plot
cax, kw = mpl.colorbar.make_axes(ax, shrink=.66, pad=.02)
# create new colorbar in axes cax with cm jet and normalized to nrm like
# our facecolors
cb1 = mpl.colorbar.ColorbarBase(cax, cmap=cm.jet, norm=nrm)
# add our colorbar label
cb1.set_label('Angle')
if save:
plt.savefig("sphereplot.png")
return fig, ax
def plot_spin_distribution_3d(P,
THETA,
PHI,
fig=None,
ax=None,
figsize=(8, 6)):
"""Plots a matrix of values on a sphere
Parameters
----------
P : matrix
Distribution values as a meshgrid matrix.
THETA : matrix
Meshgrid matrix for the theta coordinate.
PHI : matrix
Meshgrid matrix for the phi coordinate.
fig : a matplotlib figure instance
The figure canvas on which the plot will be drawn.
ax : a matplotlib axis instance
The axis context in which the plot will be drawn.
figsize : (width, height)
The size of the matplotlib figure (in inches) if it is to be created
(that is, if no 'fig' and 'ax' arguments are passed).
Returns
-------
fig, ax : tuple
A tuple of the matplotlib figure and axes instances used to produce
the figure.
"""
if fig is None or ax is None:
fig = plt.figure(figsize=figsize)
ax = Axes3D(fig, azim=-35, elev=35)
xx = sin(THETA) * cos(PHI)
yy = sin(THETA) * sin(PHI)
zz = cos(THETA)
if P.min() < -1e12:
cmap = cm.RdBu
norm = mpl.colors.Normalize(-P.max(), P.max())
else:
cmap = cm.RdYlBu
norm = mpl.colors.Normalize(P.min(), P.max())
surf = ax.plot_surface(xx,
yy,
zz,
rstride=1,
cstride=1,
facecolors=cmap(norm(P)),
linewidth=0)
cax, kw = mpl.colorbar.make_axes(ax, shrink=.66, pad=.02)
cb1 = mpl.colorbar.ColorbarBase(cax, cmap=cmap, norm=norm)
cb1.set_label('magnitude')
return fig, ax
def matrix_histogram(M,
xlabels=None,
ylabels=None,
title=None,
limits=None,
colorbar=True,
fig=None,
ax=None):
"""
Draw a histogram for the matrix M, with the given x and y labels and title.
Parameters
----------
M : Matrix of Qobj
The matrix to visualize
xlabels : list of strings
list of x labels
ylabels : list of strings
list of y labels
title : string
title of the plot (optional)
limits : list/array with two float numbers
The z-axis limits [min, max] (optional)
ax : a matplotlib axes instance
The axes context in which the plot will be drawn.
Returns
-------
fig, ax : tuple
A tuple of the matplotlib figure and axes instances used to produce
the figure.
Raises
------
ValueError
Input argument is not valid.
"""
if isinstance(M, Qobj):
# extract matrix data from Qobj
M = M.full()
n = np.size(M)
xpos, ypos = np.meshgrid(range(M.shape[0]), range(M.shape[1]))
xpos = xpos.T.flatten() - 0.5
ypos = ypos.T.flatten() - 0.5
zpos = np.zeros(n)
dx = dy = 0.8 * np.ones(n)
dz = np.real(M.flatten())
if limits and type(limits) is list and len(limits) == 2:
z_min = limits[0]
z_max = limits[1]
else:
z_min = min(dz)
z_max = max(dz)
if z_min == z_max:
z_min -= 0.1
z_max += 0.1
norm = mpl.colors.Normalize(z_min, z_max)
cmap = cm.get_cmap('jet') # Spectral
colors = cmap(norm(dz))
if ax is None:
fig = plt.figure()
ax = Axes3D(fig, azim=-35, elev=35)
ax.bar3d(xpos, ypos, zpos, dx, dy, dz, color=colors)
if title and fig:
ax.set_title(title)
# x axis
ax.axes.w_xaxis.set_major_locator(plt.IndexLocator(1, -0.5))
if xlabels:
ax.set_xticklabels(xlabels)
ax.tick_params(axis='x', labelsize=14)
# y axis
ax.axes.w_yaxis.set_major_locator(plt.IndexLocator(1, -0.5))
if ylabels:
ax.set_yticklabels(ylabels)
ax.tick_params(axis='y', labelsize=14)
# z axis
ax.axes.w_zaxis.set_major_locator(plt.IndexLocator(1, 0.5))
ax.set_zlim3d([min(z_min, 0), z_max])
# color axis
if colorbar:
cax, kw = mpl.colorbar.make_axes(ax, shrink=.75, pad=.0)
cb1 = mpl.colorbar.ColorbarBase(cax, cmap=cmap, norm=norm)
return fig, ax
np.random.seed(5)
iris = datasets.load_iris()
X = iris.data
y = iris.target
estimators = [('k_means_iris_8', KMeans(n_clusters=8)),
('k_means_iris_3', KMeans(n_clusters=3)),
('k_means_iris_bad_init',
KMeans(n_clusters=3, n_init=1, init='random'))]
fignum = 1
titles = ['8 clusters', '3 clusters', '3 clusters, bad initialization']
for name, est in estimators:
fig = plt.figure(fignum, figsize=(4, 3))
ax = Axes3D(fig, rect=[0, 0, .95, 1], elev=48, azim=134)
est.fit(X)
labels = est.labels_
ax.scatter(X[:, 3],
X[:, 0],
X[:, 2],
c=labels.astype(np.float),
edgecolor='k')
ax.w_xaxis.set_ticklabels([])
ax.w_yaxis.set_ticklabels([])
ax.w_zaxis.set_ticklabels([])
ax.set_xlabel('Petal width')
ax.set_ylabel('Sepal length')
ax.set_zlabel('Petal length')
def contour_plot(self,
data=None,
labels=None,
interval=0.2,
title="adaboost",
name=None,
make_gif=False,
mode="3d"):
if data is None:
data = self.X
labels = self.y
if labels is None:
labels = np.ones([len(data)])
x_min, x_max = data[:, 0].min() - .5, data[:, 0].max() + .5
y_min, y_max = data[:, 1].min() - .5, data[:, 1].max() + .5
#xx, yy, Z_grid are used for plotting surface
xx, yy = np.meshgrid(np.arange(x_min, x_max, interval),
np.arange(y_min, y_max, interval))
X_grid = np.concatenate([
np.expand_dims(np.ravel(xx), axis=-1),
np.expand_dims(np.ravel(yy), axis=-1)
],
axis=-1)
Z_grid = self.predict(data=X_grid, reduction="mean")
Z_grid = Z_grid.reshape(xx.shape)
if mode == "3d":
fig = plt.figure()
ax = Axes3D(fig)
ax.set_zlim(Z_grid.min() * 1.1, Z_grid.max() * 1.1)
ax.view_init(azim=120)
plt.title(title)
ax.plot_surface(xx, yy, Z_grid, cmap=plt.cm.summer, alpha=0.6)
ax.scatter(xs=data[labels == 1][:, 0],
ys=data[labels == 1][:, 1],
zs=self.predict(data=data,
reduction="mean")[labels == 1],
c='#00CED1')
ax.scatter(xs=data[labels == -1][:, 0],
ys=data[labels == -1][:, 1],
zs=self.predict(data=data,
reduction="mean")[labels == -1],
c='#DC143C')
if not os.path.exists('temp'):
os.mkdir('temp')
if name is None:
plt.savefig(title + '.png')
plt.close()
else:
plt.savefig('temp/' + name + '.png')
plt.close()
if mode == "2d":
plt.contourf(xx, yy, Z_grid, cmap=plt.cm.RdBu, alpha=.8)
plt.scatter(data[:, 0],
data[:, 1],
c=labels,
cmap=ListedColormap(['#FF0000', '#0000FF']),
edgecolors='k')
plt.title(title)
if name is None:
plt.savefig(title + '.png')
plt.close()
else:
plt.savefig('temp/' + name + '.png')
plt.close()
if make_gif == True:
imgs = []
for i in range(len(os.listdir('temp'))):
imgs.append(imageio.imread('temp/' + str(i + 1) + '.png'))
imageio.mimsave('AdaBoost.gif', imgs, 'GIF', duration=0.1)
def matrix_histogram_complex(M,
xlabels=None,
ylabels=None,
title=None,
limits=None,
phase_limits=None,
colorbar=True,
fig=None,
ax=None,
threshold=None):
"""
Draw a histogram for the amplitudes of matrix M, using the argument
of each element for coloring the bars, with the given x and y labels
and title.
Parameters
----------
M : Matrix of Qobj
The matrix to visualize
xlabels : list of strings
list of x labels
ylabels : list of strings
list of y labels
title : string
title of the plot (optional)
limits : list/array with two float numbers
The z-axis limits [min, max] (optional)
phase_limits : list/array with two float numbers
The phase-axis (colorbar) limits [min, max] (optional)
ax : a matplotlib axes instance
The axes context in which the plot will be drawn.
threshold: float (None)
Threshold for when bars of smaller height should be transparent. If
not set, all bars are colored according to the color map.
Returns
-------
fig, ax : tuple
A tuple of the matplotlib figure and axes instances used to produce
the figure.
Raises
------
ValueError
Input argument is not valid.
"""
if isinstance(M, Qobj):
# extract matrix data from Qobj
M = M.full()
n = np.size(M)
xpos, ypos = np.meshgrid(range(M.shape[0]), range(M.shape[1]))
xpos = xpos.T.flatten() - 0.5
ypos = ypos.T.flatten() - 0.5
zpos = np.zeros(n)
dx = dy = 0.8 * np.ones(n)
Mvec = M.flatten()
dz = abs(Mvec)
# make small numbers real, to avoid random colors
idx, = np.where(abs(Mvec) < 0.001)
Mvec[idx] = abs(Mvec[idx])
if phase_limits: # check that limits is a list type
phase_min = phase_limits[0]
phase_max = phase_limits[1]
else:
phase_min = -pi
phase_max = pi
norm = mpl.colors.Normalize(phase_min, phase_max)
cmap = complex_phase_cmap()
colors = cmap(norm(angle(Mvec)))
if threshold is not None:
colors[:, 3] = 1 * (dz > threshold)
if ax is None:
fig = plt.figure()
ax = Axes3D(fig, azim=-35, elev=35)
ax.bar3d(xpos, ypos, zpos, dx, dy, dz, color=colors)
if title and fig:
ax.set_title(title)
# x axis
ax.axes.w_xaxis.set_major_locator(plt.IndexLocator(1, -0.5))
if xlabels:
ax.set_xticklabels(xlabels)
ax.tick_params(axis='x', labelsize=12)
# y axis
ax.axes.w_yaxis.set_major_locator(plt.IndexLocator(1, -0.5))
if ylabels:
ax.set_yticklabels(ylabels)
ax.tick_params(axis='y', labelsize=12)
# z axis
if limits and isinstance(limits, list):
ax.set_zlim3d(limits)
else:
ax.set_zlim3d([0, 1]) # use min/max
# ax.set_zlabel('abs')
# color axis
if colorbar:
cax, kw = mpl.colorbar.make_axes(ax, shrink=.75, pad=.0)
cb = mpl.colorbar.ColorbarBase(cax, cmap=cmap, norm=norm)
cb.set_ticks([-pi, -pi / 2, 0, pi / 2, pi])
cb.set_ticklabels(
(r'$-\pi$', r'$-\pi/2$', r'$0$', r'$\pi/2$', r'$\pi$'))
cb.set_label('arg')
return fig, ax
def plot_3D(data): fig = plt.figure() ax = fig.add_subplot(111, projection='3d') Axes3D.scatter(ax,data[:,0],data[:,1],data[:,2]) ax.view_init(azim=160) plt.show()
self.b_2 += -0.5*b2
# --- Dane ---
X = []
X.append(rand(100)*6 - 3)
X.append(rand(100)*4 - 1)
X = np.matrix(X)
Y = np.sin(2 * X[0] + X[1])
# --- Uczenie sieci na 100000 iteracji ---
N= Neuron()
blad= []
for i in range(10000):
blad.append(np.sum(((N.impuls(X)-Y)@(N.impuls(X)-Y).T)))
N.aktualizacja_wag(X,Y)
plt.plot(blad)
x1 = np.linspace(-3 ,3, 50)
y1 = np.linspace(-1 ,3, 50)
x1, y1 = np.meshgrid(x1,y1)
z = np.sin(2*x1 + y1)to
H = Axes3D(plt.figure(1))
H.plot_surface(x1 , y1, z , cmap = 'Greens' ,alpha=0.8)
H.scatter(X[0],X[1],N.impuls(X),c='red',marker='^')
plt.show()
gamma2 = 0.2 # qubit dephasing rate
# initial state
a = 1.0
psi0 = (a * basis(2, 0) + (1 - a) * basis(2, 1)) / (sqrt(a**2 + (1 - a)**2))
tlist = linspace(0, 4, 250)
sx, sy, sz = qubit_integrate(w, theta, gamma1, gamma2, psi0, tlist)
## animate the dynamics on the Bloch sphere
from pylab import *
import matplotlib.animation as animation
from mpl_toolkits.mplot3d import Axes3D
fig = figure()
ax = Axes3D(fig, azim=-40, elev=30)
sphere = Bloch(axes=ax)
def animate(i):
sphere.clear()
sphere.add_vectors([sin(theta), 0, cos(theta)])
sphere.add_points([sx[:i + 1], sy[:i + 1], sz[:i + 1]])
sphere.make_sphere()
return ax
def init():
sphere.vector_color = ['r']
return ax
def plot_attractor(steps=15000,
dt=0.001,
attractor='lorenz',
random=True,
color='b'):
"""
Plots a the chosen attractor
:param steps: timesteps to integrate
:param dt: delta t
:param attractor: type of attractor
:return:
"""
# Need one more for the initial values
xo_vals = np.empty(steps)
yo_vals = np.empty(steps)
zo_vals = np.empty(steps)
xo_dot = 0
yo_dot = 0
zo_dot = 0
if random:
if attractor == 'lorenz':
xo_vals[0], yo_vals[0], zo_vals[0] = init_random(x_variance=20.0,
y_variance=20.0,
z_variance=20.0)
elif attractor == 'rossler':
xo_vals[0], yo_vals[0], zo_vals[0] = init_random(x_variance=10.0,
y_variance=10.0,
z_variance=10.0)
elif attractor == 'chua':
xo_vals[0], yo_vals[0], zo_vals[0] = init_random(x_variance=2.0,
y_variance=0.5,
z_variance=2.0)
else:
log.out.error("Attractor: " + attractor + " not defined.")
sys.exit(-1)
else:
if attractor == 'lorenz':
xo_vals[0] = 1.0
yo_vals[0] = 1.0
zo_vals[0] = 1.0
elif attractor == 'rossler':
xo_vals[0] = 1.0
yo_vals[0] = 1.0
zo_vals[0] = 1.0
elif attractor == 'chua':
xo_vals[0] = 0.777
yo_vals[0] = -0.222
zo_vals[0] = -1.222
else:
log.out.error("Attractor: " + attractor + " not defined.")
sys.exit(-1)
# Stepping through time
for i in range(0, steps - 1):
# Calculate the derivatives of the X, Y, Z state
if attractor == 'lorenz':
xo_dot, yo_dot, zo_dot = lorenz(xo_vals[i], yo_vals[i], zo_vals[i])
elif attractor == 'rossler':
xo_dot, yo_dot, zo_dot = rossler(xo_vals[i], yo_vals[i],
zo_vals[i])
elif attractor == 'chua':
xo_dot, yo_dot, zo_dot = chua(xo_vals[i], yo_vals[i], zo_vals[i])
# Propagate the system
xo_vals[i + 1] = xo_vals[i] + (xo_dot * dt)
yo_vals[i + 1] = yo_vals[i] + (yo_dot * dt)
zo_vals[i + 1] = zo_vals[i] + (zo_dot * dt)
fig3d = plt.figure()
fig3d.canvas.set_window_title('3D View (model)')
ax3d = Axes3D(fig3d)
ax3d.plot(xo_vals, yo_vals, zo_vals, color=color, linewidth=0.5)
ax3d.set_xlabel("X Axis")
ax3d.set_ylabel("Y Axis")
ax3d.set_zlabel("Z Axis")
if attractor == 'lorenz':
ax3d.set_title("Lorenz Attractor")
elif attractor == 'rossler':
ax3d.set_title("Rössler Attractor")
elif attractor == 'chua':
ax3d.set_title("Chua's Circuit Attractor")
plt.show()
return k*cm.exp(1j*b*t*t)
def signal_u2(t):
return k*cm.exp(-1j*b*t*t)
def signal_u(t):
if -T<t<T:
return signal_u1(t)+signal_u2(t)
else:
return 0
def X11(t,f):
k1 = 0.5*(1-abs(t)/T)*il.m.sin(il.m.pi*(f-b*t/il.m.pi)*(T - abs(t)))
k2 = cm.exp(1j*(il.m.pi*f*(T+t)-b*t*T))
if (il.m.pi*(f-b*t/il.m.pi)*(T - abs(t)))==0:
return 1
else:
return k1*k2/(il.m.pi*(f-b*t/il.m.pi)*(T - abs(t)))
def X22(t,f):
return X11(t,-f)*cm.exp(1j*2*il.m.pi*f*t)
def Lchm_V(t,f):
return X11(t,f) + X22(t,f)
if __name__ == "__main__":
time = [t for t in il.np.arange(-6,6,100*T)]
freq = [f for f in il.np.arange(-2e3,2e3,1/T)]
xgrid, ygrid = il.np.meshgrid(time, freq)
Z = [[abs(Lchm_V(t,f)) for t in time ] for f in freq]
import pylab
from mpl_toolkits.mplot3d import Axes3D
fig = pylab.figure()
axes = Axes3D(fig)
axes.plot_surface(xgrid, ygrid,Z, rstride=1, cstride=1)
pylab.show()
model.score(X, y) # is the R2 score for full model
## Creating testing and training data
from sklearn.model_selection import train_test_split
X_train, X_test, y_train, y_test = train_test_split(X, y, random_state = 42, stratify = y) # The stratify means that the testing data and training
#data will contain the same ratio. For instance, if the training data is 60% female, the testing data will also be 60% female.
## Multiple Linear Regression
from sklearn.datasets import make_regression
X, y = make_regression(n_samples=30, n_features=3, n_informative=3, random_state=42, noise = 0.5, bias = 100)
# To visualize on a 3 D plot
from mpl_toolkits.mplot3d import Axes3D
fig = plt.figure(1, figsize=(5,5))
axes = Axes3D(fig, elev=20, azim=45)
axes.scatter(X[:,0], X[:,1], X[:,2], c=y, cmap=plt.cm.get_cmap("Spectra"))
plt.show
# Can still fit model as normal (The Linear Regression model in sklearn uses the Ordinary Least Squares method)
model = LinearRegression()
model.fit(X, y) # to fit against the 3D dataset.
##To plot residuals
predictions = model.predict(X)
plt.scatter(predictions, predictions - y)
plt.hlines(y=0, xmin=predictions.min(), xmax=predictions.max())
plt.show()
## Data where the residuals looks random is good. Data where the residuals follow a patter, such as a curve, suggest we're missing something in our training
##Example code (from class) on charting the residuals for training and testing data on the same plot.
plt.scatter(model.predict(X_train), model.predict(X_train - y_train), c="blue")
def plot_mag_3d(measured, calibrated, p):
# set up points for sphere and ellipsoid wireframes
u = r_[0:2 * pi:20j]
v = r_[0:pi:20j]
wx = outer(cos(u), sin(v))
wy = outer(sin(u), sin(v))
wz = outer(ones(size(u)), cos(v))
ex = p[0] * ones(size(u)) + outer(cos(u), sin(v)) / p[3]
ey = p[1] * ones(size(u)) + outer(sin(u), sin(v)) / p[4]
ez = p[2] * ones(size(u)) + outer(ones(size(u)), cos(v)) / p[5]
# measurements
mx = measured[:, 0]
my = measured[:, 1]
mz = measured[:, 2]
m_max = amax(abs(measured))
# calibrated values
cx = calibrated[:, 0]
cy = calibrated[:, 1]
cz = calibrated[:, 2]
# axes size
left = 0.02
bottom = 0.05
width = 0.46
height = 0.9
rect_l = [left, bottom, width, height]
rect_r = [left / 2 + 0.5, bottom, width, height]
fig = figure(figsize=figaspect(0.5))
if matplotlib.__version__.startswith('0'):
ax = Axes3D(fig, rect=rect_l)
else:
ax = fig.add_subplot(1, 2, 1, position=rect_l, projection='3d')
# plot measurements
ax.scatter(mx, my, mz)
hold(True)
# plot line from center to ellipsoid center
ax.plot([0.0, p[0]], [0.0, p[1]], [0.0, p[2]], color='black', marker='+')
# plot ellipsoid
ax.plot_wireframe(ex, ey, ez, color='grey', alpha=0.5)
ax.set_title('MAG raw with fitted ellipsoid and center offset')
ax.set_xlabel('x')
ax.set_ylabel('y')
ax.set_zlabel('z')
ax.set_xlim3d(-m_max, m_max)
ax.set_ylim3d(-m_max, m_max)
ax.set_zlim3d(-m_max, m_max)
if matplotlib.__version__.startswith('0'):
ax = Axes3D(fig, rect=rect_r)
else:
ax = fig.add_subplot(1, 2, 2, position=rect_r, projection='3d')
ax.plot_wireframe(wx, wy, wz, color='grey', alpha=0.5)
hold(True)
ax.scatter(cx, cy, cz)
ax.set_title('MAG calibrated on unit sphere')
ax.set_xlabel('x')
ax.set_ylabel('y')
ax.set_zlabel('z')
ax.set_xlim3d(-1, 1)
ax.set_ylim3d(-1, 1)
ax.set_zlim3d(-1, 1)
show()
def __init__(self):
super(MainWindow, self).__init__()
self.expression_index = 0
self.point_index = 0
self.size = 0
self.current_full_filename = ''
self.current_filename = ''
self.limits = 96
self.x_ = []
self.y_ = []
self.z_ = []
self.head_data = ()
self.head_data_copy = ()
self.setFixedSize(800, 600)
self.setWindowTitle('HeadEditor')
self.center()
main_layout = QtGui.QHBoxLayout()
layout_left = QtGui.QVBoxLayout()
self.figure = matplotlib.figure.Figure() # Plot
self.canvas = FigureCanvas(self.figure)
self.axes = Axes3D(self.figure)
group_box = QGroupBox("Editing:")
self.cb = QComboBox()
self.cb.currentIndexChanged.connect(self.select_change)
slider_lim = 128
slider_interval = 32
self.x_slider = QSlider(Qt.Horizontal)
self.x_slider.valueChanged.connect(self.x_slider_change)
self.x_slider.setMinimum(-slider_lim)
self.x_slider.setMaximum(slider_lim)
self.x_slider.setTickPosition(QSlider.TicksBelow)
self.x_slider.setTickInterval(slider_interval)
self.x_slider.setEnabled(False)
self.y_slider = QSlider(Qt.Horizontal)
self.y_slider.valueChanged.connect(self.y_slider_change)
self.y_slider.setMinimum(-slider_lim)
self.y_slider.setMaximum(slider_lim)
self.y_slider.setTickPosition(QSlider.TicksBelow)
self.y_slider.setTickInterval(slider_interval)
self.y_slider.setEnabled(False)
self.z_slider = QSlider(Qt.Horizontal)
self.z_slider.valueChanged.connect(self.z_slider_change)
self.z_slider.setMinimum(-slider_lim)
self.z_slider.setMaximum(slider_lim)
self.z_slider.setTickPosition(QSlider.TicksBelow)
self.z_slider.setTickInterval(slider_interval)
self.z_slider.setEnabled(False)
self.expression_slider = QSlider(Qt.Horizontal)
self.expression_slider.valueChanged.connect(
self.expression_slider_change)
self.expression_slider.setMinimum(0)
self.expression_slider.setMaximum(4)
self.expression_slider.setValue(0)
self.expression_slider.setTickPosition(QSlider.TicksBelow)
self.expression_slider.setTickInterval(1)
self.expression_slider.setEnabled(False)
self.load_button = QtGui.QPushButton('Load', self)
self.load_button.clicked.connect(self.load_data)
self.save_button = QtGui.QPushButton('Save', self)
self.save_button.clicked.connect(self.save_data)
self.x_slider_label = QLabel("x : 0")
self.y_slider_label = QLabel("y : 0")
self.z_slider_label = QLabel("z : 0")
self.exp_slider_label = QLabel("Expression : 1")
hbox = QVBoxLayout()
hbox.addWidget(self.x_slider_label)
hbox.addWidget(self.x_slider)
hbox.addWidget(self.y_slider_label)
hbox.addWidget(self.y_slider)
hbox.addWidget(self.z_slider_label)
hbox.addWidget(self.z_slider)
hbox.addWidget(self.exp_slider_label)
hbox.addWidget(self.expression_slider)
hbox.addWidget(self.load_button)
hbox.addWidget(self.save_button)
hbox.addStretch(1)
allitems = QVBoxLayout()
allitems.addWidget(self.cb)
allitems.addLayout(hbox)
group_box.setLayout(allitems)
layout_left.addWidget(self.canvas)
main_layout.addLayout(layout_left)
main_layout.addWidget(group_box)
self.setLayout(main_layout)
self.axes.view_init(20, 60)
self.plot_3d()
%matplotlib notebook
from sklearn import linear_model
import numpy as np
import matplotlib.pyplot as plt
from mpl_toolkits.mplot3d import Axes3D
X = np.array([[0, 0], [1,2], [2,4], [3,0], [4,1]])
y = np.array([0, 0.3, 0.75, 1, 2])
lin_regr = linear_model.LinearRegression()
lin_regr.fit(X, y)
fig = plt.figure(figsize=(6, 5))
ax = Axes3D(fig, elev=45, azim=-120)
ax.scatter(X[:, 0], X[:, 1], y, c='r', marker='o', label='training set')
ax.plot_surface(np.array([[-1, -1], [5, 5]]), np.array([[-1, 5], [-1, 5]]), lin_regr.predict(np.array([[-1, -1, 5, 5], [-1, 5, -1, 5]]).T).reshape((2, 2)), alpha=.5, label='linear regression predictor')
ax.set_xlabel('input X_1')
ax.set_ylabel('input X_2')
ax.set_zlabel('output Y')
plt.title("Simplistic test of linear regression on 2d input")
plt.show()
y_train = np.loadtxt(y_train_file_file)
y_final_test = np.loadtxt(y_final_test_file)
activity_labels = np.loadtxt(activity_labels_file, dtype=str)
X_train_file.close()
X_final_test_file.close()
y_train_file_file.close()
y_final_test_file.close()
activity_labels_file.close()
k_means = cluster.KMeans(n_clusters=6)
km = k_means.fit(X_train)
labels = km.predict(X_final_test)
fig1 = plt.figure(1, figsize=(10, 8))
ax = Axes3D(fig1, rect=[0, 0, .95, 1], elev=48, azim=134)
ax.scatter(X_final_test[:, 0],
X_final_test[:, 40],
X_final_test[:, 80],
c=labels.astype(np.float),
edgecolor='k')
ax.w_xaxis.set_ticklabels([])
ax.w_yaxis.set_ticklabels([])
ax.w_zaxis.set_ticklabels([])
ax.set_xlabel('tBodyAcc-XYZ')
ax.set_ylabel('tGravityAcc-XYZ')
ax.set_zlabel('tBodyAccJerk-XYZ')
ax.set_title("6 Clusters")
ax.dist = 10
def graph():
# 连接数据库
conn = mdb.connect(host='127.0.0.1',
port=3306,
user='******',
passwd='root',
db='alibaba_trace',
charset='utf8')
# 如果使用事务引擎，可以设置自动提交事务，或者在每次操作完成后手动提交事务conn.commit()
conn.autocommit(1) # conn.autocommit(True)
# 使用cursor()方法获取操作游标
cursor = conn.cursor()
# 因该模块底层其实是调用CAPI的，所以，需要先得到当前指向数据库的指针。
try:
# 查询数据条目
job_duration = cursor.execute(
"SELECT max(end_timestamp) - min(start_timestamp) FROM batch_instance WHERE status = 'Terminated' and real_mem_avg != 0 group by job_id ASC "
)
job_duration = cursor.fetchall()
list_job_duration = list(job_duration)
arr_job_duration = [x[0] for x in list_job_duration]
print(arr_job_duration)
arr_job_duration_norm = MaxMinNormalization(arr_job_duration,
max(arr_job_duration),
min(arr_job_duration))
cursor.execute(
"select t.job_id, avg(t.avg_cpu), avg(t.avg_mem) from (select job_id, task_id, avg(real_cpu_avg) as avg_cpu, avg(real_mem_avg) as avg_mem from batch_instance where status='Terminated' and real_mem_avg != 0 group by task_id )t group by job_id ASC"
)
# cursor.execute("select t.job_id, avg(t.avg_cpu), avg(t.avg_mem) from (select job_id, task_id, avg(cpu) as avg_cpu, avg(mem) as avg_mem from test group by task_id )t group by job_id ")
records = cursor.fetchall()
list_records = list(records)
res = []
res[:] = map(list, list_records)
job_arr = [x[0] for x in res]
cpu_arr = [x[1] for x in res]
print(cpu_arr)
cpu_arr_norm = MaxMinNormalization(cpu_arr, max(cpu_arr), min(cpu_arr))
mem_arr = [x[2] for x in res]
print(mem_arr)
mem_arr_norm = MaxMinNormalization(mem_arr, max(mem_arr), min(cpu_arr))
# 如果没有设置自动提交事务，则这里需要手动提交一次
conn.commit()
# k-means聚类
# 设置类别为3
clf = KMeans(n_clusters=3)
# 将数据带入到聚类模型中
loan = []
loan.append(arr_job_duration_norm)
loan.append(cpu_arr_norm)
loan.append(mem_arr_norm)
loan = np.asarray(loan)
loan = loan.transpose()
clf = clf.fit(loan)
loan = np.insert(loan, 3, values=clf.labels_, axis=1)
fig = plt.figure()
ax = Axes3D(fig)
loan_df = pd.DataFrame(loan)
class_1 = loan_df[loan_df.iloc[:, 3] == 0]
print('class_1:')
print(class_1)
x1 = class_1.iloc[:, 0].values
y1 = class_1.iloc[:, 1].values
z1 = class_1.iloc[:, 2].values
class_2 = loan_df[loan_df.iloc[:, 3] == 1]
x2 = class_2.iloc[:, 0].values
y2 = class_2.iloc[:, 1].values
z2 = class_2.iloc[:, 2].values
print("class_2:")
print(class_2)
class_3 = loan_df[loan_df.iloc[:, 3] == 2]
x3 = class_3.iloc[:, 0].values
y3 = class_3.iloc[:, 1].values
z3 = class_3.iloc[:, 2].values
print("class_3")
print(class_3)
ax.scatter(x1, y1, z1, color='red', s=1)
ax.scatter(x2, y2, z2, color='blue', s=1)
ax.scatter(x3, y3, z3, color='yellow', s=1)
ax.set_xlabel('job duration')
ax.set_ylabel('average cpu(per job)')
ax.set_zlabel('average memory(per job)')
ax.set_xlim(0, 1)
ax.view_init(elev=20., azim=-35)
ax.grid(False)
plt.savefig('../imgs_mysql/knn_job.png')
plt.show()
except:
import traceback
traceback.print_exc()
# 发生错误时回滚
conn.rollback()
finally:
# 关闭游标连接
cursor.close()
# 关闭数据库连接
conn.close()
#call the animator. blit=True means only re-draw the parts that have changed.
anim = animation.FuncAnimation(fig,
animate,
frames=time,
interval=10,
blit=False)
anim.save('dynamic_images3.gif', fps=60)
plt.show()
T_list = np.array(T_list)
from mpl_toolkits.mplot3d import Axes3D
fig2 = plt.figure(figsize=(10, 10))
ax2 = Axes3D(fig2)
ax2.set_title('Heat Simulation 0.0s', fontsize=30)
ax2.plot_surface(X,
Y,
T_list[0],
rstride=1,
cstride=1,
vmin=min(U),
vmax=max(U),
cmap='hot')
ax2.contourf(X,
Y,
T_list[0],
zdir='z',
offset=min(U),
ols_trainX1 = trainX1.copy()
ols_trainX1 = sm.add_constant(ols_trainX1)
est = sm.OLS(trainY, ols_trainX1).fit()
est.summary()
# %% 3D Plot
x0 = ols_trainX1.T[0]
x1 = ols_trainX1.T[1]
Z = est.params[0] + est.params[1] * x0 + est.params[2] * x1
fig = plt.figure(figsize=(12, 8))
ax = Axes3D(fig, azim=-115, elev=15)
#ax = fig.add_subplot(111, projection='3d')
x0 = ols_trainX1.T[0]
x1 = ols_trainX1.T[1]
xx0, xx1 = np.meshgrid(np.linspace(x0.min(), x0.max(), len(x0)),
np.linspace(x1.min(), x1.max(), len(x1)))
Z0 = est.params[0] + est.params[1] * xx0 + est.params[2] * xx1
Z1 = est.params[0] + est.params[1] * x0 + est.params[2] * x1
surf = ax.plot_surface(xx0, xx1, Z1, cmap=plt.cm.RdBu_r, alpha=.1, linewidth=0)
resid = trainY.T[0] - est.predict(ols_trainX1)
ax.scatter(x0[resid >= 0],
x1[resid >= 0],
trainY[resid >= 0],
def run():
# Configure parameters
N = 10 # number of cavity fock states
wc = 2 * pi * 1.0 # cavity frequency
wa = 2 * pi * 1.0 # atom frequency
g = 2 * pi * 0.1 # coupling strength
kappa = 0.05 # cavity dissipation rate
gamma = 0.15 # atom dissipation rate
use_rwa = True
# a coherent initial state the in cavity
psi0 = tensor(coherent(N, 1.5), basis(2, 0))
# Hamiltonian
a = tensor(destroy(N), qeye(2))
sm = tensor(qeye(N), destroy(2))
if use_rwa:
# use the rotating wave approxiation
H = wc * a.dag() * a + wa * sm.dag() * sm + g * (a.dag() * sm +
a * sm.dag())
else:
H = wc * a.dag() * a + wa * sm.dag() * sm + g * (a.dag() +
a) * (sm + sm.dag())
# collapse operators
c_op_list = []
n_th_a = 0.0 # zero temperature
rate = kappa * (1 + n_th_a)
if rate > 0.0:
c_op_list.append(sqrt(rate) * a)
rate = kappa * n_th_a
if rate > 0.0:
c_op_list.append(sqrt(rate) * a.dag())
rate = gamma
if rate > 0.0:
c_op_list.append(sqrt(rate) * sm)
# evolve the system
tlist = linspace(0, 10, 100)
output = mesolve(H, psi0, tlist, c_op_list, [])
# calculate the wigner function
xvec = linspace(-5., 5., 100)
X, Y = meshgrid(xvec, xvec)
#for idx, rho in enumerate(output.states): # suggestion: try to loop over all rho
for idx, rho in enumerate([output.states[44]
]): # for a selected time t=4.4
rho_cavity = ptrace(rho, 0)
W = wigner(rho_cavity, xvec, xvec)
# plot the wigner function
fig = figure(figsize=(9, 6))
ax = Axes3D(fig, azim=-107, elev=49)
ax.set_xlim3d(-5, 5)
ax.set_ylim3d(-5, 5)
ax.set_zlim3d(-0.30, 0.30)
surf = ax.plot_surface(X,
Y,
W,
rstride=1,
cstride=1,
cmap=cm.jet,
alpha=1.0,
linewidth=0.05,
vmax=0.4,
vmin=-0.4)
fig.colorbar(surf, shrink=0.65, aspect=20)
#savefig("jc_model_wigner_"+str(idx)+".png")
show()
def dbscan():
data = a
sse = []
ch = []
sc = []
purity = []
nmi = []
ari = []
xs = []
ys = []
zs = []
labels_true = [1, 1, 1, 0, 0, 0, 1, 1] # 实际分类
epsmax = 13
minspmax = 4
for ms in range(1, minspmax):
for e in range(2, epsmax):
xs.append(ms) #建立x数列
ys.append(e) #建立y数列
#开始分类
db = DBSCAN(eps=e, min_samples=ms,
metric='euclidean') #esp聚类半径，min半径内最少点数，metric距离
predict = db.fit_predict(data)
print(predict) #打印分类结果
labels = db.labels_
print('labels=', labels)
#可视化结果
purity.append(ACC(labels_true, predict))
# 设计算NMI
nmi.append(
metrics.normalized_mutual_info_score(labels_true, predict))
# 计算ARI
ari.append(metrics.adjusted_rand_score(labels_true, predict))
# 计算CH系数 轮廓系数
ch.append(metrics.calinski_harabasz_score(data, labels))
sc.append(
metrics.silhouette_score(
data, labels, metric='euclidean')) # 此处算法一定要与上面ag中的算法一致
print('min_samples:', xs)
print('eps:', ys)
print('SC:', sc)
print('CH:', ch)
print('purity:', purity)
print('NMI:', nmi)
print('ARI:', ari)
#开始绘图
#绘制min_samples-esp-SC图
fig = plt.figure() # 创建一个画布figure，然后在这个画布上加各种元素。
ax = Axes3D(fig) # 将画布作用于 Axes3D 对象上。
# 基于ax变量绘制三维图
# xs表示x方向的变量
# ys表示y方向的变量
# zs表示z方向的变量，这三个方向上的变量都可以用list的形式表示
# m表示点的形式，o是圆形的点，^是三角形（marker)
# c表示颜色（color for short）
ax.plot(xs, ys, sc, c='r', marker='X', label='Silhouette Score') # 点为红色三角形
# 显示图例
ax.legend()
# 设置坐标轴
plt.rcParams['font.sans-serif'] = ['SimHei'] # 用来正常显示中文标签
ax.set_xlabel('min samples')
ax.set_ylabel('eps')
ax.set_zlabel('Silhouette Score')
ax.set_title('min_samples-eps-SC for JDD')
for x, y, z in zip(xs, ys, sc):
ax.text(x,
y,
z,
str(np.around(z, 2)),
ha='center',
va='bottom',
fontsize=8.5)
# 显示图形
plt.show()
# 绘制min_samples-esp-ch图
fig = plt.figure() # 创建一个画布figure，然后在这个画布上加各种元素。
ax = Axes3D(fig) # 将画布作用于 Axes3D 对象上。
ax.plot(xs, ys, ch, c='r', marker='o', label='Calinski-Harabasz')
# 显示图例
ax.legend()
# 设置坐标轴
plt.rcParams['font.sans-serif'] = ['SimHei'] # 用来正常显示中文标签
ax.set_xlabel('min samples')
ax.set_ylabel('eps')
ax.set_zlabel('Calinski-Harabasz')
ax.set_title('min_samples-eps-ch for JDD')
for x, y, z in zip(xs, ys, ch):
ax.text(x,
y,
z,
str(np.around(z, 2)),
ha='center',
va='bottom',
fontsize=8.5)
# 显示图形
plt.show()
# 绘制min_samples-eps-purity图
fig = plt.figure() # 创建一个画布figure，然后在这个画布上加各种元素。
ax = Axes3D(fig) # 将画布作用于 Axes3D 对象上。
ax.plot(xs, ys, purity, c='r', marker='o', label='purity') # 点为红色圆形
# 显示图例
ax.legend()
# 设置坐标轴
plt.rcParams['font.sans-serif'] = ['SimHei'] # 用来正常显示中文标签
ax.set_xlabel('min samples')
ax.set_ylabel('eps')
ax.set_zlabel('purity')
ax.set_title('min_samples-eps-purity for JDD')
for x, y, z in zip(xs, ys, purity):
ax.text(x,
y,
z,
str(np.around(z, 2)),
ha='center',
va='bottom',
fontsize=8.5)
# 显示图形
plt.show()
# 绘制min_samples-eps-NMI图
fig = plt.figure() # 创建一个画布figure，然后在这个画布上加各种元素。
ax = Axes3D(fig) # 将画布作用于 Axes3D 对象上。
ax.plot(xs, ys, nmi, c='r', marker='*', label='NMI') # 点为红色*形
# 显示图例
ax.legend()
# 设置坐标轴
plt.rcParams['font.sans-serif'] = ['SimHei'] # 用来正常显示中文标签
ax.set_xlabel('min samples')
ax.set_ylabel('eps')
ax.set_zlabel('NMI')
ax.set_title('min_samples-eps-NMI for JDD')
for x, y, z in zip(xs, ys, nmi):
ax.text(x,
y,
z,
str(np.around(z, 2)),
ha='center',
va='bottom',
fontsize=8.5)
# 显示图形
plt.show()
# 绘制min_samples-eps-ARI图
fig = plt.figure() # 创建一个画布figure，然后在这个画布上加各种元素。
ax = Axes3D(fig) # 将画布作用于 Axes3D 对象上。
ax.plot(xs, ys, ari, c='r', marker='X', label='ARI') # 点为红色X形
# 显示图例
ax.legend()
# 设置坐标轴
plt.rcParams['font.sans-serif'] = ['SimHei'] # 用来正常显示中文标签
ax.set_xlabel('min samples')
ax.set_ylabel('eps')
ax.set_zlabel('ARI')
ax.set_title('min_samples-eps-ARI for JDD')
for x, y, z in zip(xs, ys, ari):
ax.text(x,
y,
z,
str(np.around(z, 2)),
ha='center',
va='bottom',
fontsize=8.5)
# 显示图形
plt.show()
from mpl_toolkits.mplot3d import Axes3D
from sklearn.decomposition import FastICA
from sklearn.random_projection import GaussianRandomProjection
from sklearn.feature_selection import VarianceThreshold
fn = "phishing_dataset.csv"
writeFn = fn[:-4] + "_vtresh_kmeans_output.csv"
print(writeFn)
norms = [True, False]
#whitens = [False,False]
#algs = ['parallel','deflation']
treshs = [0,.035,.04,.045]
fig = plot.figure(1)
ax = Axes3D(fig)
def runEverything():
data,x,y,normx,normy = preProcessData(fn)
results = []
for tresh in treshs:
for norm in norms:
err = classify(x,y,normx,normy,tresh,norm)
print(tresh,norm,":",err)
results.append([tresh,norm,err])
file = open(writeFn,"w",newline="")
csvW = csv.writer(file)
csvW.writerow(["tresh","norm","error"])
csvW.writerows(results)
print("Open your file")
def get_TPI(params, bvec1, graphs):
start_time = time.clock()
(S, T, beta, sigma, chi_n_vec, b_ellip, mu, l_tilde, A, alpha, delta, b_ss,
n_ss, K_ss, C_ss, L_ss, maxiter_TPI, mindist_TPI, xi, TPI_tol,
EulDiff) = params
K1, K1_cnstr = fun3.get_K(bvec1)
# Create time paths for K and L
Kpath_init = np.zeros(T + S - 2)
Kpath_init[:T] = get_path(K1, K_ss, T, "linear")
Kpath_init[T:] = K_ss
Lpath_init = L_ss * np.ones(T + S - 2)
iter_TPI = int(0)
dist_TPI = 10.
Kpath_new = Kpath_init.copy()
Lpath_new = Lpath_init.copy()
r_params = (A, alpha, delta)
w_params = (A, alpha)
cbne_params = (S, T, beta, sigma, chi_n_vec, b_ellip, mu, l_tilde, bvec1,
b_ss, n_ss, TPI_tol, EulDiff)
while (iter_TPI < maxiter_TPI) and (dist_TPI >= mindist_TPI):
iter_TPI += 1
Kpath_init = xi * Kpath_new + (1 - xi) * Kpath_init
Lpath_init = xi * Lpath_new + (1 - xi) * Lpath_init
rpath = fun3.get_r(r_params, Kpath_init, Lpath_init)
wpath = fun3.get_w(w_params, Kpath_init, Lpath_init)
cpath, bpath, npath, EulErrPath_inter, EulErrPath_intra = get_cbnepath(
cbne_params, rpath, wpath)
Kpath_new = np.zeros(T + S - 2)
Kpath_new[:T], Kpath_cnstr = fun3.get_K(bpath[:, :T])
Kpath_new[T:] = K_ss * np.ones(S - 2)
Lpath_new[:T - 1] = fun3.get_L(npath[:, :T - 1])
Lpath_new[T - 1:] = L_ss * np.ones(S - 1)
Kpath_cnstr = np.append(Kpath_cnstr, np.zeros(S - 2, dtype=bool))
Kpath_new[Kpath_cnstr] = 0.1
dist_TPI = ((Kpath_new[1:T] - Kpath_init[1:T]) ** 2).sum() + \
((Lpath_new[:T] - Lpath_init[:T]) ** 2).sum()
if iter_TPI == maxiter_TPI and dist_TPI > mindist_TPI:
print('TPI reached maximum interation but did not converge.')
Kpath = Kpath_new
Lpath = Lpath_new
Y_params = (A, alpha)
Ypath = fun3.get_Y(Y_params, Kpath, Lpath)
Cpath = np.zeros(T + S - 2)
Cpath[:T - 1] = fun3.get_C(cpath[:, :T - 1])
Cpath[T - 1:] = C_ss * np.ones(S - 1)
RCerrPath = (Ypath[:-1] - Cpath[:-1] - Kpath[1:] +
(1 - delta) * Kpath[:-1])
tpi_time = time.clock() - start_time
tpi_output = {
'bpath': bpath,
'cpath': cpath,
'npath': npath,
'wpath': wpath,
'rpath': rpath,
'Kpath': Kpath,
'Lpath': Lpath,
'Ypath': Ypath,
'Cpath': Cpath,
'EulErrPath IntraTemporal': EulErrPath_intra,
'EulErrPath InterTemporal': EulErrPath_inter,
'RCerrPath': RCerrPath,
'tpi_time': tpi_time
}
# Print TPI computation time
fun3.print_time(tpi_time, 'TPI')
if graphs:
# Create directory if images directory does not already exist
cur_path = os.path.split(os.path.abspath(__file__))[0]
output_fldr = "images"
output_dir = os.path.join(cur_path, output_fldr)
if not os.access(output_dir, os.F_OK):
os.makedirs(output_dir)
# Plot time path of aggregate capital stock
tvec = np.linspace(1, T + S - 2, T + S - 2)
minorLocator = MultipleLocator(1)
fig, ax = plt.subplots()
plt.plot(tvec, Kpath, marker='D')
# for the minor ticks, use no labels; default NullFormatter
ax.xaxis.set_minor_locator(minorLocator)
plt.grid(b=True, which='major', color='0.65', linestyle='-')
plt.title('Time path for aggregate capital stock K')
plt.xlabel(r'Period $t$')
plt.ylabel(r'Aggregate capital $K_{t}$')
output_path = os.path.join(output_dir, "Kpath")
plt.savefig(output_path)
plt.show()
plt.plot(tvec, Lpath, marker='D')
# for the minor ticks, use no labels; default NullFormatter
ax.xaxis.set_minor_locator(minorLocator)
plt.grid(b=True, which='major', color='0.65', linestyle='-')
plt.title('Time path for aggregate labor supply L')
plt.xlabel(r'Period $t$')
plt.ylabel(r'Aggregate labor supply $L_{t}$')
output_path = os.path.join(output_dir, "Lpath")
plt.savefig(output_path)
plt.show()
# Plot time path of aggregate output (GDP)
fig, ax = plt.subplots()
plt.plot(tvec, Ypath, marker='D')
# for the minor ticks, use no labels; default NullFormatter
ax.xaxis.set_minor_locator(minorLocator)
plt.grid(b=True, which='major', color='0.65', linestyle='-')
plt.title('Time path for aggregate output (GDP) Y')
plt.xlabel(r'Period $t$')
plt.ylabel(r'Aggregate output $Y_{t}$')
output_path = os.path.join(output_dir, "Ypath")
plt.savefig(output_path)
# plt.show()
# Plot time path of aggregate consumption
fig, ax = plt.subplots()
plt.plot(tvec, Cpath, marker='D')
# for the minor ticks, use no labels; default NullFormatter
ax.xaxis.set_minor_locator(minorLocator)
plt.grid(b=True, which='major', color='0.65', linestyle='-')
plt.title('Time path for aggregate consumption C')
plt.xlabel(r'Period $t$')
plt.ylabel(r'Aggregate consumption $C_{t}$')
output_path = os.path.join(output_dir, "C_aggr_path")
plt.savefig(output_path)
# plt.show()
# Plot time path of real wage
fig, ax = plt.subplots()
plt.plot(tvec, wpath, marker='D')
# for the minor ticks, use no labels; default NullFormatter
ax.xaxis.set_minor_locator(minorLocator)
plt.grid(b=True, which='major', color='0.65', linestyle='-')
plt.title('Time path for real wage w')
plt.xlabel(r'Period $t$')
plt.ylabel(r'Real wage $w_{t}$')
output_path = os.path.join(output_dir, "wpath")
plt.savefig(output_path)
# plt.show()
# Plot time path of real interest rate
fig, ax = plt.subplots()
plt.plot(tvec, rpath, marker='D')
# for the minor ticks, use no labels; default NullFormatter
ax.xaxis.set_minor_locator(minorLocator)
plt.grid(b=True, which='major', color='0.65', linestyle='-')
plt.title('Time path for real interest rate r')
plt.xlabel(r'Period $t$')
plt.ylabel(r'Real interest rate $r_{t}$')
output_path = os.path.join(output_dir, "rpath")
plt.savefig(output_path)
# plt.show()
# Plot time path of individual savings distribution
tgridT = np.linspace(1, T, T)
sgrid2 = np.linspace(2, S, S - 1)
tmatb, smatb = np.meshgrid(tgridT, sgrid2)
cmap_bp = matplotlib.cm.get_cmap('summer')
fig = plt.figure()
ax = Axes3D(fig)
# ax = fig.gca(projection='3d')
ax.set_xlabel(r'period-$t$')
ax.set_ylabel(r'age-$s$')
ax.set_zlabel(r'individual savings $b_{s,t}$')
strideval = max(int(1), int(round(S / 10)))
ax.plot_surface(tmatb,
smatb,
bpath[:, :T],
rstride=strideval,
cstride=strideval,
cmap=cmap_bp)
output_path = os.path.join(output_dir, "bpath")
plt.savefig(output_path)
# plt.show()
# Plot time path of individual consumption distribution
tgridTm1 = np.linspace(1, T - 1, T - 1)
sgrid = np.linspace(1, S, S)
tmatc, smatc = np.meshgrid(tgridTm1, sgrid)
cmap_cp = matplotlib.cm.get_cmap('summer')
fig = plt.figure()
ax = Axes3D(fig)
# ax = fig.gca(projection='3d')
ax.set_xlabel(r'period-$t$')
ax.set_ylabel(r'age-$s$')
ax.set_zlabel(r'individual consumption $c_{s,t}$')
strideval = max(int(1), int(round(S / 10)))
ax.plot_surface(tmatc,
smatc,
cpath[:, :T - 1],
rstride=strideval,
cstride=strideval,
cmap=cmap_cp)
output_path = os.path.join(output_dir, "cpath")
plt.savefig(output_path)
# plt.show()
return tpi_output