def mcrtmv(frames, mvname, dt, Lx, Ly, Nx, Ny):
x = np.linspace(0, Lx, Nx)
y = np.linspace(0, Ly, Ny)
X, Y = np.meshgrid(x, y)
size = 500, 500
fig = ml.figure(size=size, bgcolor=(1., 1., 1.))
#fig.scene.anti_aliasing_frames=07
#extent = [0,Nx-1,0,Ny-1,-30,30]
ml.clf(figure=fig)
u = np.loadtxt('test.d%07d' % 1)
fname = '_tmp%07d.png' % 1
s = ml.surf(x, y, u, figure=fig, vmin=-0, vmax=1)
ml.axes(extent=[0, Lx, 0, Ly, -2, 2])
ml.colorbar()
ml.xlabel('x position')
ml.ylabel('y position')
ml.zlabel('wave amplitude')
"""
pl.ion()
arr = ml.screenshot()
img = pl.imshow(arr)
pl.axis('off')
"""
for i in range(2, frames):
#arr = ml.screenshot()
#img.set_array(arr)
u = np.loadtxt('test.d%07d' % i)
s.mlab_source.scalars = u
fname = '_tmp%07d.png' % i
def plot3D(name, X, Y, Z, zlabel):
"""
Plots a 3d surface plot of Z using the mayavi mlab.mesh function.
Parameters
----------
name: string
The name of the figure.
X: 2d ndarray
The x-axis data.
Y: 2d ndarray
The y-axis data.
Z: 2d nd array
The z-axis data.
zlabel: The title that appears on the z-axis.
"""
mlab.figure(name)
mlab.clf()
plotData = mlab.mesh(X/(np.max(X) - np.min(X)),
Y/(np.max(Y) - np.min(Y)),
Z/(np.max(Z) - np.min(Z)))
mlab.outline(plotData)
mlab.axes(plotData, ranges=[np.min(X), np.max(X),
np.min(Y), np.max(Y),
np.min(Z), np.max(Z)])
mlab.xlabel('Space ($x$)')
mlab.ylabel('Time ($t$)')
mlab.zlabel(zlabel)
def plot_3D( self ):
x = self.compute3D_plot[0]
y = self.compute3D_plot[1]
z = self.compute3D_plot[2]
# print x_axis, y_axis, z_axis
if self.autowarp_bool:
x = x / x[-1]
y = y / y[-1]
z = z / z[-1] * self.z_scale
mlab.surf( x, y , z, representation = 'wireframe' )
engine = Engine()
engine.start()
if len( engine.scenes ) == 75.5:
engine.new_scene()
surface = engine.scenes[0].children[0].children[0].children[0].children[0].children[0]
surface.actor.mapper.scalar_range = np.array( [ 6.97602671, 8.8533387 ] )
surface.actor.mapper.scalar_visibility = False
scene = engine.scenes[0]
scene.scene.background = ( 1.0, 1.0, 1.0 )
surface.actor.property.specular_color = ( 0.0, 0.0, 0.0 )
surface.actor.property.diffuse_color = ( 0.0, 0.0, 0.0 )
surface.actor.property.ambient_color = ( 0.0, 0.0, 0.0 )
surface.actor.property.color = ( 0.0, 0.0, 0.0 )
surface.actor.property.line_width = 1.
scene.scene.isometric_view()
mlab.xlabel( self.x_name3D )
mlab.ylabel( self.y_name3D )
mlab.outline()
mlab.show()
def labels(xlabel="x", ylabel="y", zlabel="z", obj=None):
if xlabel:
mlab.xlabel(xlabel, obj)
if ylabel:
mlab.ylabel(ylabel, obj)
if zlabel:
mlab.zlabel(zlabel, obj)
def plot_mayavi(self):
"""Use mayavi to plot a phenotype phase plane in 3D.
The resulting figure will be quick to interact with in real time,
but might be difficult to save as a vector figure.
returns: mlab figure object"""
from mayavi import mlab
figure = mlab.figure(bgcolor=(1, 1, 1), fgcolor=(0, 0, 0))
figure.name = "Phenotype Phase Plane"
max = 10.0
xmax = self.reaction1_fluxes.max()
ymax = self.reaction2_fluxes.max()
zmax = self.growth_rates.max()
xgrid, ygrid = meshgrid(self.reaction1_fluxes, self.reaction2_fluxes)
xgrid = xgrid.transpose()
ygrid = ygrid.transpose()
xscale = max / xmax
yscale = max / ymax
zscale = max / zmax
mlab.surf(xgrid * xscale, ygrid * yscale, self.growth_rates * zscale,
representation="wireframe", color=(0, 0, 0), figure=figure)
mlab.mesh(xgrid * xscale, ygrid * yscale, self.growth_rates * zscale,
scalars=self.shadow_prices1 + self.shadow_prices2,
resolution=1, representation="surface", opacity=0.75,
figure=figure)
# draw axes
mlab.outline(extent=(0, max, 0, max, 0, max))
mlab.axes(opacity=0, ranges=[0, xmax, 0, ymax, 0, zmax])
mlab.xlabel(self.reaction1_name)
mlab.ylabel(self.reaction2_name)
mlab.zlabel("Growth rates")
return figure
def main(argv):
if ( len(argv) != 1 ):
print ("Usage: python visualizeField.py <datafile.json>")
return
# Read input file
try:
infile = open( argv[0], 'r' )
except:
print ("Error when opening file %s"%(argv[0]))
return
data = json.load( infile )
infile.close()
y = np.array( data["points"]["y"] )
z = np.array( data["points"]["z"] )
x = np.zeros( len(y) )
Ex = np.array( data["field"]["x"] )
pts = mlab.points3d( y, z, x, Ex, scale_mode="scalar", scale_factor=0.0, mode="point")
mesh = mlab.pipeline.delaunay2d( pts )
surf = mlab.pipeline.surface( mesh )
fname = "Figures/fieldyzPlane.png"
mlab.view(0.0,0.0,1.0, (0.0,0.0,0.0))
mlab.scalarbar()
mlab.xlabel( "y" )
mlab.ylabel( "z" )
mlab.show()
def draw_min_cost_surface(graph):
graph = sim.graph
X = []
Y = []
Z = []
for day,sizes in graph.items():
for size,days_const in sizes.items():
days_const, node = sorted(days_const.items())[0]
X.append(day)
Y.append(size/10.)
Z.append(node.min_cost)
pts = mlab.points3d(X, Y, Z, Z)
mesh = mlab.pipeline.delaunay2d(pts)
# Remove the point representation from the plot
pts.remove()
# Draw a surface based on the triangulation
surf = mlab.pipeline.surface(mesh)
mlab.xlabel("time")
mlab.ylabel("size")
mlab.zlabel("cost")
mlab.show()
def draw_min_feed_surface(graph):
graph = sim.graph
X = []
Y = []
Z = []
for day,sizes in graph.items():
for size,days_const in sizes.items():
days_const, node = sorted(days_const.items())[-1]
X.append(day)
Y.append(size/10.)
Z.append(node.min_rate*10)
# for i in range(len(X)):
# print ("%d,%f,%f" % (X[i], Y[i], Z[i]))
pts = mlab.points3d(X, Y, Z, Z)
mesh = mlab.pipeline.delaunay2d(pts)
# Remove the point representation from the plot
pts.remove()
# Draw a surface based on the triangulation
surf = mlab.pipeline.surface(mesh)
mlab.xlabel("time")
mlab.ylabel("size")
mlab.zlabel("rate")
mlab.show()
def plot_mayavi(self):
"""Use mayavi to plot a phenotype phase plane in 3D.
The resulting figure will be quick to interact with in real time,
but might be difficult to save as a vector figure.
returns: mlab figure object"""
from mayavi import mlab
figure = mlab.figure(bgcolor=(1, 1, 1), fgcolor=(0, 0, 0))
figure.name = "Phenotype Phase Plane"
max = 10.0
xmax = self.reaction1_fluxes.max()
ymax = self.reaction2_fluxes.max()
zmax = self.growth_rates.max()
xgrid, ygrid = meshgrid(self.reaction1_fluxes, self.reaction2_fluxes)
xgrid = xgrid.transpose()
ygrid = ygrid.transpose()
xscale = max / xmax
yscale = max / ymax
zscale = max / zmax
mlab.surf(xgrid * xscale, ygrid * yscale, self.growth_rates * zscale,
representation="wireframe", color=(0, 0, 0), figure=figure)
mlab.mesh(xgrid * xscale, ygrid * yscale, self.growth_rates * zscale,
scalars=self.shadow_prices1 + self.shadow_prices2,
resolution=1, representation="surface", opacity=0.75,
figure=figure)
# draw axes
mlab.outline(extent=(0, max, 0, max, 0, max))
mlab.axes(opacity=0, ranges=[0, xmax, 0, ymax, 0, zmax])
mlab.xlabel(self.reaction1_name)
mlab.ylabel(self.reaction2_name)
mlab.zlabel("Growth rates")
return figure
def mcrtmv(frames,
dt,
mesh,
d_nodes,
map,
savemovie=False,
mvname='test',
vmin=-1,
vmax=1):
"""
Creates move from numpyfied results in 2d, using mencoder. Prolly does not work on mac!
"""
size = 500, 500
fig = ml.figure(size=size, bgcolor=(1., 1., 1.))
#fig.scene.anti_aliasing_frames=07
#extent = [0,Nx-1,0,Ny-1,-30,30]
xaxis = np.linspace(0, 1, d_nodes[0] + 1)
yaxis = np.linspace(0, 1, d_nodes[1] + 1)
ml.clf(figure=fig)
u = np.load('solution_%06d.npy' % 1)
u = numpyfy(u, mesh, d_nodes, map)
fname = '_tmp%07d.png' % 1
s = ml.imshow(xaxis, yaxis, u, figure=fig, vmin=vmin, vmax=vmax)
#scale = 1./np.max(np.abs(u))
u = u
ml.axes(extent=[0, 1, 0, 1, 0, 2])
ml.colorbar()
ml.xlabel('x position')
ml.ylabel('y position')
ml.zlabel('wave amplitude')
if savemovie == True:
pl.ion()
arr = ml.screenshot()
img = pl.imshow(arr)
pl.axis('off')
for i in range(2, frames):
u = np.load('solution_%06d.npy' % i)
u = numpyfy(u, mesh, d_nodes, map)
s.mlab_source.scalars = u
fname = '_tmp%07d.png' % i
if savemovie == True:
arr = ml.screenshot()
img.set_array(arr)
pl.savefig(filename=fname) #,figure=fig)
print 'Saving frame', fname
pl.draw()
fig.scene.disable_render = False
if savemovie:
os.system(
"mencoder 'mf://_tmp*.png' -mf type=png:fps=20 -ovc lavc -lavcopts vcodec=wmv2 -oac copy -o %s.mpg"
% mvname)
def setLabels(self, xlabel="", ylabel="", zlabel=""):
"""
sets the label
input:
- xlabel
- ylabel
- zlabel
"""
mlab.xlabel(xlabel)
mlab.ylabel(ylabel)
mlab.zlabel(zlabel)
def mcrtmv(frames, dt,mesh, d_nodes, map, savemovie=False, mvname='test', vmin=-1, vmax=1):
"""
Creates move from numpyfied results in 2d, using mencoder. Prolly does not work on mac!
"""
size = 500,500
fig = ml.figure(size= size, bgcolor=(1.,1.,1.));
#fig.scene.anti_aliasing_frames=07
#extent = [0,Nx-1,0,Ny-1,-30,30]
xaxis = np.linspace(0,1,d_nodes[0]+1)
yaxis = np.linspace(0,1,d_nodes[1]+1)
ml.clf(figure=fig)
u = np.load('solution_%06d.npy'%1);
u = numpyfy(u, mesh, d_nodes, map)
fname = '_tmp%07d.png' % 1
s = ml.imshow(xaxis, yaxis, u,figure=fig,vmin=vmin, vmax=vmax)
#scale = 1./np.max(np.abs(u))
u = u
ml.axes(extent=[0,1,0,1,0,2])
ml.colorbar()
ml.xlabel('x position')
ml.ylabel('y position')
ml.zlabel('wave amplitude')
if savemovie == True:
pl.ion()
arr = ml.screenshot()
img = pl.imshow(arr)
pl.axis('off')
for i in range(2,frames):
u = np.load('solution_%06d.npy'%i);
u = numpyfy(u, mesh, d_nodes, map)
s.mlab_source.scalars = u
fname = '_tmp%07d.png' % i
if savemovie == True:
arr = ml.screenshot()
img.set_array(arr)
pl.savefig(filename=fname)#,figure=fig)
print 'Saving frame', fname
pl.draw()
fig.scene.disable_render = False
if savemovie:
os.system("mencoder 'mf://_tmp*.png' -mf type=png:fps=20 -ovc lavc -lavcopts vcodec=wmv2 -oac copy -o %s.mpg" % mvname);
def plot_cartesian(traj, xaxis=None, yaxis=None, zaxis=None, color='b',label='_nolegend_',
linewidth=2, scatter_size=10, plot_velocity=False):
import matplotlib_util.util as mpu
import arm_trajectories as at
#if traj.__class__ == at.JointTrajectory:
if isinstance(traj,at.JointTrajectory):
traj = joint_to_cartesian(traj)
pts = np.matrix(traj.p_list).T
label_list = ['X coord (m)', 'Y coord (m)', 'Z coord (m)']
x = pts[xaxis,:].A1.tolist()
y = pts[yaxis,:].A1.tolist()
if plot_velocity:
vels = np.matrix(traj.v_list).T
xvel = vels[xaxis,:].A1.tolist()
yvel = vels[yaxis,:].A1.tolist()
if zaxis == None:
mpu.plot_yx(y, x, color, linewidth, '-', scatter_size, label,
axis = 'equal', xlabel = label_list[xaxis],
ylabel = label_list[yaxis],)
if plot_velocity:
mpu.plot_quiver_yxv(y, x, np.matrix([xvel,yvel]),
width = 0.001, scale = 1.)
mpu.legend()
else:
from numpy import array
from enthought.mayavi.api import Engine
engine = Engine()
engine.start()
if len(engine.scenes) == 0:
engine.new_scene()
z = pts[zaxis,:].A1.tolist()
time_list = [t-traj.time_list[0] for t in traj.time_list]
mlab.plot3d(x,y,z,time_list,tube_radius=None,line_width=4)
mlab.axes()
mlab.xlabel(label_list[xaxis])
mlab.ylabel(label_list[yaxis])
mlab.zlabel(label_list[zaxis])
mlab.colorbar(title='Time')
# -------------------------------------------
axes = engine.scenes[0].children[0].children[0].children[1]
axes.axes.position = array([ 0., 0.])
axes.axes.label_format = '%-#6.2g'
axes.title_text_property.font_size=4
def plot_cartesian(traj, xaxis=None, yaxis=None, zaxis=None, color='b',label='_nolegend_',
linewidth=2, scatter_size=10, plot_velocity=False):
import arm_trajectories as at
#if traj.__class__ == at.JointTrajectory:
if isinstance(traj,at.JointTrajectory):
traj = joint_to_cartesian(traj)
pts = np.matrix(traj.p_list).T
label_list = ['X coord (m)', 'Y coord (m)', 'Z coord (m)']
x = pts[xaxis,:].A1.tolist()
y = pts[yaxis,:].A1.tolist()
if plot_velocity:
vels = np.matrix(traj.v_list).T
xvel = vels[xaxis,:].A1.tolist()
yvel = vels[yaxis,:].A1.tolist()
if zaxis == None:
mpu.plot_yx(y, x, color, linewidth, '-', scatter_size, label,
axis = 'equal', xlabel = label_list[xaxis],
ylabel = label_list[yaxis],)
if plot_velocity:
mpu.plot_quiver_yxv(y, x, np.matrix([xvel,yvel]),
width = 0.001, scale = 1.)
mpu.legend()
else:
from numpy import array
from enthought.mayavi.api import Engine
engine = Engine()
engine.start()
if len(engine.scenes) == 0:
engine.new_scene()
z = pts[zaxis,:].A1.tolist()
time_list = [t-traj.time_list[0] for t in traj.time_list]
mlab.plot3d(x,y,z,time_list,tube_radius=None,line_width=4)
mlab.axes()
mlab.xlabel(label_list[xaxis])
mlab.ylabel(label_list[yaxis])
mlab.zlabel(label_list[zaxis])
mlab.colorbar(title='Time')
# -------------------------------------------
axes = engine.scenes[0].children[0].children[0].children[1]
axes.axes.position = array([ 0., 0.])
axes.axes.label_format = '%-#6.2g'
axes.title_text_property.font_size=4
def plot_2D( points, a=0, b=301 ):
'''
Perfom a 2D plot.
INPUTS:
- points: numpy array of points to plot in the order of (x, y, z).
- a : placeholder for now
- b : placeholder for now
OUTPUT:
- No return; generates a 2D plot.
'''
x, y = points # Store data into arrays
z = np.zeros_like(x) # We don't want th
scene = mlab.figure( size= (1000, 800), # Create scene
fgcolor=(0, 0, 0), # Set foreground color
bgcolor=(1, 1, 1) ) # Set background color
nodes = mlab.points3d( x, y, z, # ...
figure = scene, # Insert collected data to plot
scale_factor=5.0 ) # ...
xlab = mlab.xlabel( "x" ) # Set x-axis label
ylab = mlab.ylabel( "y" ) # Set y-axis label
mlab.axes( extent = [0, b-1, 0, b-1, 0, 0.5], # Set extent of axes
figure = scene, # The figure to populate
y_axis_visibility=False) # Remove the z-axis (designated y for some MayaVi reason)
scene.scene.z_plus_view() # Look at it from the top!
scene.scene.parallel_projection = True # 2D projection of 3D plane
mlab.show()
def drawSurfaceDelaunay(point_list):
x = [i[0] for i in point_list]
y = [i[1] for i in point_list]
z = [i[2] for i in point_list]
pts = mlab.points3d(x, y, z, z)
mesh = mlab.pipeline.delaunay2d(pts)
pts.remove()
surf = mlab.pipeline.surface(mesh)
mlab.xlabel('x')
mlab.ylabel('y')
mlab.zlabel('z')
mlab.show()
def plot_fiber_voltage(filename,fibertype):
data = pickle.load( open(filename, "rb" ) )
decimate_s = 1
decimate_t = 1
nproc = len(data)
data_plot = []
ddata2dx2 = []
ddata2dx2_plot = []
dx = 1
dt = 1
for proc in range(len(data)):
data_plot.append(data[proc][fibertype][::decimate_s, ::decimate_t])
ddata2dx2.append(np.gradient(data[proc][fibertype],dx))
ddata2dx2_plot.append(ddata2dx2[proc][0][::decimate_t, ::decimate_s])
nseg, nsamp = ddata2dx2_plot[0].shape
x = np.arange(nseg)
t_plot = []
t_plot.append(data[0]['tvec'][::decimate_t])
y = t_plot[0]
X,Y = np.meshgrid(x, y)
fig = plt.figure()
ax = fig.add_subplot(111, projection='3d')
mlab.figure(1, fgcolor=(0, 0, 0), bgcolor=(1, 1, 1))
s = mlab.surf(data_plot[0], warp_scale="auto", extent = [0,1,0,5,0,1])
#pdb.set_trace()
ax=mlab.axes(s, ranges = [0, 43.306, np.min(y), np.max(y), np.min(data_plot[0]), np.max(data_plot[0])])
#
ax.axes.label_format='%.2f'
ax.label_text_property.font_family = 'arial'
mlab.xlabel('Distance along axon (mm)')
mlab.ylabel('Time (msec)')
mlab.zlabel('Membrane voltage (mV)')
ax.axes.font_factor=0.9
mlab.savefig('3d_voltage.png', size=(1920, 1080))
#pdb.set_trace()
bla = input()
def mcrtmv(frames, dt, Lx, Ly, Nx, Ny, savemovie=False, mvname='test'):
x = np.linspace(0, Lx, Nx)
y = np.linspace(0, Lx, Nx)
X, Y = np.meshgrid(x, y)
size = 500, 500
fig = ml.figure(size=size, bgcolor=(1., 1., 1.))
#fig.scene.anti_aliasing_frames=07
#extent = [0,Nx-1,0,Ny-1,-30,30]
ml.clf(figure=fig)
u = np.loadtxt('solution_%06d.txt' % 1)
fname = '_tmp%07d.png' % 1
s = ml.surf(x, y, u, figure=fig, vmin=-1, vmax=1)
ml.axes(extent=[0, Lx, 0, Ly, -2, 2])
ml.colorbar()
ml.xlabel('x position')
ml.ylabel('y position')
ml.zlabel('wave amplitude')
if savemovie == True:
pl.ion()
arr = ml.screenshot()
img = pl.imshow(arr)
pl.axis('off')
for i in range(2, frames):
u = np.loadtxt('solution_%06d.txt' % i)
s.mlab_source.scalars = u
fname = '_tmp%07d.png' % i
if savemovie == True:
arr = ml.screenshot()
img.set_array(arr)
pl.savefig(filename=fname) #,figure=fig)
print 'Saving frame', fname
pl.draw()
fig.scene.disable_render = False
os.system(
"mencoder 'mf://_tmp*.png' -mf type=png:fps=20 -ovc lavc -lavcopts vcodec=wmv2 -oac copy -o %s.mpg"
% mvname)
def sigma_m( m ):
dataname = "sigmaOPT25_with_m{}.npy".format( m )
res = np.load( dataname )
print 'max', np.max( res ), 'min', np.min( res )
from mayavi.api import Engine
engine = Engine()
engine.start()
if len( engine.scenes ) == 0:
engine.new_scene()
mlab.surf( x_axis1 , y_axis1 , res , representation = 'wireframe' )
surface = engine.scenes[0].children[0].children[0].children[0].children[0].children[0]
surface.actor.mapper.scalar_range = np.array( [ 6.97602671, 8.8533387 ] )
surface.actor.mapper.scalar_visibility = False
scene = engine.scenes[0]
scene.scene.background = ( 1.0, 1.0, 1.0 )
surface.actor.property.specular_color = ( 0.0, 0.0, 0.0 )
surface.actor.property.diffuse_color = ( 0.0, 0.0, 0.0 )
surface.actor.property.ambient_color = ( 0.0, 0.0, 0.0 )
surface.actor.property.color = ( 0.0, 0.0, 0.0 )
surface.actor.property.line_width = 0.
warp_scalar = engine.scenes[0].children[0].children[0]
module_manager = engine.scenes[0].children[0].children[0].children[0].children[0]
warp_scalar.filter.normal = np.array( [ 0. , 0. , 0.8] )
module_manager.scalar_lut_manager.scalar_bar.global_warning_display = 1
module_manager.scalar_lut_manager.scalar_bar.position2 = np.array( [ 0.8 , 0.17] )
module_manager.scalar_lut_manager.scalar_bar.position = np.array( [ 0.1 , 0.01] )
module_manager.scalar_lut_manager.data_range = np.array( [ 6.97602671, 8.8533387 ] )
module_manager.scalar_lut_manager.default_data_range = np.array( [ 6.97602671, 8.8533387 ] )
module_manager.vector_lut_manager.scalar_bar.global_warning_display = 1
module_manager.vector_lut_manager.scalar_bar.position2 = np.array( [ 0.8 , 0.17] )
module_manager.vector_lut_manager.scalar_bar.position = np.array( [ 0.1 , 0.01] )
module_manager.vector_lut_manager.data_range = np.array( [ 0., 1.] )
module_manager.vector_lut_manager.default_data_range = np.array( [ 0., 1.] )
scene.scene.isometric_view()
# mlab.surf( x_axis2, y_axis2, res2 )
mlab.xlabel( "rand tau" )
mlab.ylabel( "rand r" )
mlab.zlabel( "z" )
mlab.show()
def mcrtmv(frames, dt,Lx,Ly,Nx,Ny,savemovie=False, mvname='test'):
x = np.linspace(0,Lx,Nx);
y = np.linspace(0,Lx,Nx);
X,Y = np.meshgrid(x,y);
size = 500,500
fig = ml.figure(size= size, bgcolor=(1.,1.,1.));
#fig.scene.anti_aliasing_frames=07
#extent = [0,Nx-1,0,Ny-1,-30,30]
ml.clf(figure=fig)
u = np.loadtxt('solution_%06d.txt'%1);
fname = '_tmp%07d.png' % 1
s = ml.surf(x,y,u,figure=fig,vmin=-1,vmax=1)
ml.axes(extent=[0,Lx,0,Ly,-2,2])
ml.colorbar()
ml.xlabel('x position')
ml.ylabel('y position')
ml.zlabel('wave amplitude')
if savemovie == True:
pl.ion()
arr = ml.screenshot()
img = pl.imshow(arr)
pl.axis('off')
for i in range(2,frames):
u = np.loadtxt('solution_%06d.txt'%i);
s.mlab_source.scalars = u
fname = '_tmp%07d.png' % i
if savemovie == True:
arr = ml.screenshot()
img.set_array(arr)
pl.savefig(filename=fname)#,figure=fig)
print 'Saving frame', fname
pl.draw()
fig.scene.disable_render = False
os.system("mencoder 'mf://_tmp*.png' -mf type=png:fps=20 -ovc lavc -lavcopts vcodec=wmv2 -oac copy -o %s.mpg" % mvname);
def mayavi_version(X,Y,Z):
from mayavi import mlab
# Define the points in 3D space
# including color code based on Z coordinate.
pts = mlab.points3d(X, Y, Z, Z)
# Triangulate based on X, Y with Delaunay 2D algorithm.
# Save resulting triangulation.
mesh = mlab.pipeline.delaunay2d(pts)
# Remove the point representation from the plot
pts.remove()
# Draw a surface based on the triangulation
surf = mlab.pipeline.surface(mesh)
# Simple plot.
mlab.xlabel("x")
mlab.ylabel("y")
mlab.zlabel("z")
mlab.show()
def mayavi_version(X, Y, Z):
from mayavi import mlab
# Define the points in 3D space
# including color code based on Z coordinate.
pts = mlab.points3d(X, Y, Z, Z)
# Triangulate based on X, Y with Delaunay 2D algorithm.
# Save resulting triangulation.
mesh = mlab.pipeline.delaunay2d(pts)
# Remove the point representation from the plot
pts.remove()
# Draw a surface based on the triangulation
surf = mlab.pipeline.surface(mesh)
# Simple plot.
mlab.xlabel("x")
mlab.ylabel("y")
mlab.zlabel("z")
mlab.show()
def show_net():
"""
Visualizes the current Q(s,a_1) and Q(s,a_2) values of neural net
Use BlueSky command SHOW_NET
"""
mlab.clf()
x = np.linspace(-180, 180, 100)
y = np.linspace(-180, 180, 100)
X, Y = np.meshgrid(x, y)
Z_Left = []
Z_Right = []
Z_Contour = []
for _x in x:
Z_Left.append([])
Z_Right.append([])
Z_Contour.append([])
for _y in y:
nn_input = tensor([_x, 7.0, _y])
nn_output = atc_net.forward(nn_input)
Z_Left[-1].append(float(nn_output[0]))
Z_Right[-1].append(float(nn_output[2]))
Z_Contour[-1].append(nn_output.max(0)[1])
Z_Left = np.array(Z_Left)
Z_Right = np.array(Z_Right)
Z_Contour = np.array(Z_Contour)
mlab.surf(x, y, Z_Left, colormap="Greens")
mlab.surf(x, y, Z_Right, colormap="Reds")
mlab.xlabel('qdr + self_hdg')
mlab.ylabel('rel_hdg')
mlab.title("Values for LEFT (g) and RIGHT (r)")
mlab.show()
def show_point_cloud(self,fig):
X,Y = np.meshgrid(self.X,self.Y)
mesh = mlab.mesh(X, Y, self.Z,figure = fig,color=(0.3, 0.3, 0.3))
mlab.xlabel('x')
mlab.ylabel('y')
# including color code based on Z coordinate.
pts = mlab.points3d(X, Y, Z, Z)
# Triangulate based on X, Y with Delaunay 2D algorithm.
# Save resulting triangulation.
mesh = mlab.pipeline.delaunay2d(pts)
# Remove the point representation from the plot
pts.remove()
# Draw a surface based on the triangulation
surf = mlab.pipeline.surface(mesh)
# Simple plot.
mlab.xlabel("x")
mlab.ylabel("y")
mlab.zlabel("z")
mlab.show()
print x
print y
print s
j=mlab.quiver3d(xs,ys,zs,jx,jy,jz, scale_factor=.002,color=(1,0,0),name='J')
m=mlab.quiver3d(xs,ys,zs,baryX,baryY,baryZ, scale_factor=.013,color=(0,0,1),name='Mb')
t=mlab.quiver3d(xs,ys,zs,tx,ty,tz, scale_factor=.1,color=(0,1,0),name='T/W')
pt=mlab.quiver3d(xs,ys,zs,us,vs,ws, scale_factor=.01,color=(1,1,1),name='projT/W')
mlab.text(.01,.2,'J ',color=(1,0,0),width=0.1)
mlab.text(.01,.4,'Mb ',color=(0,0,1),width=0.1)
mlab.text(.01,.5,'T/W ',color=(0,1,0),width=0.1)
mlab.text(.01,.6,'-projT/W',color=(1,1,1),width=0.1)
mlab.title("Gradients along track")
mlab.axes(color=(.7,.7,.7),xlabel='a')
mlab.xlabel('a')
mlab.ylabel('edMax')
mlab.zlabel('rpoe')
mlab.show()
exit()
###############################
# TEST plotting and stepDown function
def func(a,T):
return -2*(a*a + T*T/2. -a*T/2.) + (a*a*a*a*.7 + T*T*T*T*.34)
p0=(.10,.10,.15)
p1=(.30,.20,.10)
except TypeError:
a_result = np.NaN
delta = np.NaN
delta_dspace = np.append(delta_dspace, [delta])
print(i)
#Kw_zspace_sap = Kw_zspace_sap * 10**1
#Ka2_yspace_sap = Ka2_yspace_sap * 10**-2
#Ka1_xspace_sap = Ka1_xspace_sap * 10**-2
#use for wrong scaling correction
figure = mlab.figure('DensityPlot')
pts = mlab.points3d(Ka1_xspace_sap,
Ka2_yspace_sap,
Kw_zspace_sap,
delta_dspace,
scale_mode='none',
scale_factor=0.0005)
#scale_factor = 0.0000001 or 0.001
mlab.xlabel('Ka1,unit : 10^2')
mlab.ylabel('Ka2,unit : 10^2')
mlab.zlabel('Kw,unit : 10^-1')
mlab.axes(None, extent=[0, 0.1, 0, 0.1, 0, 0.1])
#use for wrong scaling correction too
#mlab.axes()
mlab.show()
u_y=numpy.zeros((N,N), dtype=float)
v_x=numpy.zeros((N,N), dtype=float)
omega=numpy.zeros((N,N), dtype=float)
# Initial conditions
for i in range(len(x)):
for j in range(len(y)):
u[i][j]=numpy.sin(2*math.pi*x[i])*numpy.cos(2*math.pi*y[j])
v[i][j]=-numpy.cos(2*math.pi*x[i])*numpy.sin(2*math.pi*y[j])
u_y[i][j]=-2*math.pi*numpy.sin(2*math.pi*x[i])*numpy.sin(2*math.pi*y[j])
v_x[i][j]=2*math.pi*numpy.sin(2*math.pi*x[i])*numpy.sin(2*math.pi*y[j])
omega[i][j]=v_x[i][j]-u_y[i][j]
src = mlab.imshow(xx,yy,omega,colormap='jet')
mlab.scalarbar(object=src)
mlab.xlabel('x',object=src)
mlab.ylabel('y',object=src)
# Wavenumber
k_x = 2*math.pi*numpy.array([complex(0,1)*n for n in range(0,N/2) \
+ [0] + range(-N/2+1,0)])
k_y=k_x
kx=numpy.zeros((N,N), dtype=complex)
ky=numpy.zeros((N,N), dtype=complex)
kxx=numpy.zeros((N,N), dtype=complex)
kyy=numpy.zeros((N,N), dtype=complex)
for i in xrange(N):
for j in xrange(N):
kx[i,j] = k_x[i]
def plotWithCondition(self, condition):
assert isinstance(condition,str), "must enter a condition!"
cursor=self.dbConnection.cursor()
xname = self.independentVars[0]
yname = self.independentVars[1]
xs=[]
for i in cursor.execute("SELECT DISTINCT " + xname + " FROM models ORDER BY "
+ xname):
val = i[0]
if xname == "edMax":
val = val#/1.0e15
xs.append(val)
ys=[]
for i in cursor.execute("SELECT DISTINCT " + yname + " FROM models ORDER BY "
+ yname):
val = i[0]
if yname == "edMax":
val = val#/1.0e15
ys.append(val)
#print xs
#print ys
#####
#
xs, ys = meshgrid(xs,ys)
# reverse order since mlab uses mgrid format which returns transpose of matrices in meshgrid style
xs = xs.transpose()
ys = ys.transpose()
#
#####
def lookup(x,y):
assert x >= 0., "Lookup only well defined for x >=0"
assert y >= 0., "Lookup only well defined for y >=0"
tolerance = 1.0001
additionalConditions=[]
if not x == 0:
additionalConditions.append( xname + ">" + str(x/tolerance) )
additionalConditions.append( xname + "<" + str(x*tolerance) )
else:
additionalConditions.append(xname + "=" + str(x))
if not y == 0:
additionalConditions.append(yname + ">" + str(y/tolerance))
additionalConditions.append( yname + "<" + str(y*tolerance))
else:
additionalConditions.append(yname + "=" + str(y))
additionalConditions.append(condition)
#print additionalConditions
value= queryDBGivenParams(self.dependentVar,
{},
cursor,"models", tuple( additionalConditions ))
#print x,y, value
if value:
if len(value[0]) > 1 :
print "WARNING MORE THAN ONE VALUE FOUND!!!"
return value[0][0]
else:
print "WARNING: no value"
return 0.0
zs = zeros(xs.shape)
for i in range(len(xs)):
row = xs[i]
#print row
for j in range(len(row)):
#print xs[i][j], ys[i][j]
zs[i][j] = lookup(xs[i][j], ys[i][j] )
if xname == "edMax":
xs = array(xs*1e-15)
else:
xs = array(xs)
if yname == "edMax":
ys=array(ys*1e-15)
else:
ys = array(ys)
zs = array(zs)
#print xs
#print ys
#print zs
#print size(xs)
#print size(ys)
#print size(zs)
fig=mlab.figure(bgcolor=(.5,.5,.5))
extents=[xs.min(),xs.max(),
ys.min(),ys.max(),
zs.min(),zs.max()]
mlab.surf(xs,ys,zs, colormap="bone",representation='wireframe',
extent=extents
)
mlab.axes(extent=extents,nb_labels=6)
mlab.outline(extent=extents)
mlab.xlabel(xname)
mlab.ylabel(yname)
mlab.zlabel(self.dependentVar)
forceY = []
forceZ = []
originX = []
originY = []
originZ = []
i = 0
with open("forceOnObject.txt", "r") as f:
for line in f:
vect = line.split('[')[1].split(']')[0].split(',') # Parse list
forceX.append(float(vect[0]))
forceY.append(float(vect[1]))
forceZ.append(float(vect[2]))
originX.append(0.0)
originY.append(time[i])
originZ.append(0.0)
i += 1
m.quiver3d(originX, originY, originZ, forceX, forceY, forceZ)
# m.title('Force applied on the house over time')
m.vectorbar(orientation='vertical')
m.ylabel('time (s)')
m.axes()
m.show()
thetag = np.linspace(0.,2.*pi,ntheta)
phi, theta = np.meshgrid(phig,thetag)
rho = np.zeros_like(phi)
sinphi = sin(phi); cosphi = cos(phi); sinth = sin(theta); costh = cos(theta)
m = 0
for k in range(K):
for j in range(J):
for i in range(I):
rho += (c[m]*np.power(sinphi,i+j) *
np.power(cosphi,k) *
np.power(sinth,j) *
np.power(costh,i))
m += 1
xs = rho * sin(phi) * cos(theta)
ys = rho * sin(phi) * sin(theta)
zs = rho * cos(phi)
import mayavi.mlab as mylab
fig=mylab.figure(1,bgcolor=(0,0,0))
mylab.clf()
ps = 1.*np.ones_like(x)
mylab.points3d(x,y,z,(ps), scale_factor=0.025,colormap='Spectral',opacity=1.)
mylab.mesh(xs, ys, zs, colormap="bone",opacity=0.5)
mylab.outline();
mylab.xlabel('X'); mylab.ylabel('Y'); mylab.zlabel('Z')
#!/usr/bin/env python
# -*- coding: iso-8859-1 -*-
import numpy as np
from mayavi import mlab
X = np.array([0, 1, 0, 1, 0.75])
Y = np.array([0, 0, 1, 1, 0.75])
Z = np.array([1, 1, 1, 1, 2])
# Define the points in 3D space
# including color code based on Z coordinate.
pts = mlab.points3d(X, Y, Z, Z)
# Triangulate based on X, Y with Delaunay 2D algorithm.
# Save resulting triangulation.
mesh = mlab.pipeline.delaunay2d(pts)
# Remove the point representation from the plot
pts.remove()
# Draw a surface based on the triangulation
surf = mlab.pipeline.surface(mesh)
# Simple plot.
mlab.xlabel("x")
mlab.ylabel("y")
mlab.zlabel("z")
mlab.show()
def plot3(history, *args, title=None, give=False, plot_style='default',
axis_label=None, make_square=True, figsize=None,backend='matplotlib',
**kwargs):
'''
Parameters:
> *args,**kwargs : are passed to matplotlib's pyplot.plot function
> FIG_TITLE: the title given to the figure. Only used is a figure is not given to plot on
> GIVE : this command makes the method return the figure after the path data is
plotted.
> BACKEND: either matplotlib or mayavi.
'''
if backend == 'matplotlib':
# setting style
style.use(plot_style)
# creating figure
if figsize:
fig = plt.figure(figsize=figsize)
else:
fig = plt.figure()
ax = fig.gca(projection='3d')
ax.set_aspect('equal')
# makes history a numpy array
history = array(history)
# getting motion history
X = history[:, 0]
Y = history[:, 1]
Z = history[:, 2]
# To Do add optional label to the first point
# Plots the 3 past printer positions on figure
ax.plot(X, Y, Z, *args, **kwargs)
# Keeps aspect ratio square but can be computationally expensive for large GCODE
if make_square:
# Keeps aspect ratio square
# http://stackoverflow.com/questions/13685386
# numpy array
max_range = array([X.max()-X.min(),
Y.max()-Y.min(),
Z.max()-Z.min()]).max() / 2.0
mean_x = X.mean()
mean_y = Y.mean()
mean_z = Z.mean()
ax.set_xlim(mean_x - max_range, mean_x + max_range)
ax.set_ylim(mean_y - max_range, mean_y + max_range)
ax.set_zlim(mean_z - max_range, mean_z + max_range)
# labeling figure axes
if axis_label:
ax.set_xlabel(axis_label[0])
ax.set_ylabel(axis_label[1])
ax.set_zlabel(axis_label[2])
# sets the figure title
if title:
ax.set_title(title)
# determines whether to show the figure or to return it
if give:
return ax
else:
# showing figure
plt.show()
elif backend == 'mayavi':
# getting the needing import to plot in mayavi
from mayavi import mlab
# makes history a numpy array
history = array(history)
# getting x,y,z coordinates
x = history[:,0]
y = history[:,1]
z = history[:,2]
# changin the figure size
if figsize:
mlab.figure(size=figsize)
else:
mlab.figure()
# plotting the line plot
fig = mlab.plot3d(x,y,z, *args, **kwargs)
# setting label corrdinates
# labeling figure axes
if axis_label:
mlab.xlabel(axis_label[0])
mlab.ylabel(axis_label[1])
mlab.zlabel(axis_label[2])
# sets the figure title
if title:
mlab.title(title)
# showing the figure
if give:
return fig, mlab
else:
mlab.show()
# end of view
return
import numpy as np
from mayavi import mlab
X = np.array([.49,.98,1.47,1.96,2.45,.49,.98,1.47,1.96,2.45,.49,.98,1.47,1.96,2.45,.49,.98,1.47,1.96,2.45,.49,.98,1.47,1.96,2.45])
Y = np.array([.49,.49,.49,.49,.49,.98,.98,.98,.98,.98,1.47,1.47,1.47,1.47,1.47,1.96,1.96,1.96,1.96,1.96,2.45,2.45,2.45,2.45,2.45])
Z = np.array([0,.0078,.0245,.0485,.0784,.0230,.0235,.0358,.0578,.0887,.0583,.0505,.0573,.0760,.1034,.1005,.0892,.0916,.1078,.1318,.1593,.1507,.1421,.1504,.1715])
#X = np.array([0,1,0,1,.75])
#Y = np.array([0,0,1,1,.75])
#Z = np.array([1,1,1,1,2])
pts = mlab.points3d(X,Y,Z,Z)
mesh = mlab.pipeline.delaunay2d(pts)
pts.remove()
surf = mlab.pipeline.surface(mesh)
mlab.xlabel("Fx (N)")
mlab.ylabel("Fy (N)")
mlab.zlabel("Delta Potential (J)")
mlab.show()
sinth = sin(theta)
costh = cos(theta)
m = 0
for k in range(K):
for j in range(J):
for i in range(I):
rho += (c[m] * np.power(sinphi, i + j) * np.power(cosphi, k) *
np.power(sinth, j) * np.power(costh, i))
m += 1
xs = rho * sin(phi) * cos(theta)
ys = rho * sin(phi) * sin(theta)
zs = rho * cos(phi)
import mayavi.mlab as mylab
fig = mylab.figure(1, bgcolor=(0, 0, 0))
mylab.clf()
ps = 1. * np.ones_like(x)
mylab.points3d(x,
y,
z, (ps),
scale_factor=0.025,
colormap='Spectral',
opacity=1.)
mylab.mesh(xs, ys, zs, colormap="bone", opacity=0.5)
mylab.outline()
mylab.xlabel('X')
mylab.ylabel('Y')
mylab.zlabel('Z')
una = numpy.zeros((Nx, Ny), dtype=complex)
unb = numpy.zeros((Nx, Ny), dtype=complex)
v = numpy.zeros((Nx, Ny), dtype=complex)
vna = numpy.zeros((Nx, Ny), dtype=complex)
vnb = numpy.zeros((Nx, Ny), dtype=complex)
mass = numpy.zeros((Nx, Ny), dtype=complex)
test = numpy.zeros((numplots - 1), dtype=float)
tdata = numpy.zeros((numplots - 1), dtype=float)
u = numpy.exp(-(xx**2 + yy**2))
v = numpy.fft.fftn(u)
usquared = abs(u)**2
src = mlab.surf(xx, yy, usquared, colormap='YlGnBu', warp_scale='auto')
mlab.scalarbar()
mlab.xlabel('x', object=src)
mlab.ylabel('y', object=src)
mlab.zlabel('abs(u)^2', object=src)
# initial mass
usquared = abs(u)**2
mass = numpy.fft.fftn(usquared)
ma = numpy.real(mass[0, 0])
print(ma)
maO = ma
t = 0.0
tdata[0] = t
plotnum = 0
#solve pde and plot results
for nt in xrange(numplots - 1):
for n in xrange(plotgap):
vna = v * numpy.exp(complex(0, 0.5) * dt * (k2xm + k2ym))
def plotWithCondition(self, condition):
assert isinstance(condition, str), "must enter a condition!"
cursor = self.dbConnection.cursor()
xname = self.independentVars[0]
yname = self.independentVars[1]
xs = []
for i in cursor.execute("SELECT DISTINCT " + xname +
" FROM models ORDER BY " + xname):
val = i[0]
if xname == "edMax":
val = val #/1.0e15
xs.append(val)
ys = []
for i in cursor.execute("SELECT DISTINCT " + yname +
" FROM models ORDER BY " + yname):
val = i[0]
if yname == "edMax":
val = val #/1.0e15
ys.append(val)
#print xs
#print ys
#####
#
xs, ys = meshgrid(xs, ys)
# reverse order since mlab uses mgrid format which returns transpose of matrices in meshgrid style
xs = xs.transpose()
ys = ys.transpose()
#
#####
def lookup(x, y):
assert x >= 0., "Lookup only well defined for x >=0"
assert y >= 0., "Lookup only well defined for y >=0"
tolerance = 1.0001
additionalConditions = []
if not x == 0:
additionalConditions.append(xname + ">" + str(x / tolerance))
additionalConditions.append(xname + "<" + str(x * tolerance))
else:
additionalConditions.append(xname + "=" + str(x))
if not y == 0:
additionalConditions.append(yname + ">" + str(y / tolerance))
additionalConditions.append(yname + "<" + str(y * tolerance))
else:
additionalConditions.append(yname + "=" + str(y))
additionalConditions.append(condition)
#print additionalConditions
value = queryDBGivenParams(self.dependentVar, {}, cursor, "models",
tuple(additionalConditions))
#print x,y, value
if value:
if len(value[0]) > 1:
print "WARNING MORE THAN ONE VALUE FOUND!!!"
return value[0][0]
else:
print "WARNING: no value"
return 0.0
zs = zeros(xs.shape)
for i in range(len(xs)):
row = xs[i]
#print row
for j in range(len(row)):
#print xs[i][j], ys[i][j]
zs[i][j] = lookup(xs[i][j], ys[i][j])
if xname == "edMax":
xs = array(xs * 1e-15)
else:
xs = array(xs)
if yname == "edMax":
ys = array(ys * 1e-15)
else:
ys = array(ys)
zs = array(zs)
#print xs
#print ys
#print zs
#print size(xs)
#print size(ys)
#print size(zs)
fig = mlab.figure(bgcolor=(.5, .5, .5))
extents = [xs.min(), xs.max(), ys.min(), ys.max(), zs.min(), zs.max()]
mlab.surf(xs,
ys,
zs,
colormap="bone",
representation='wireframe',
extent=extents)
mlab.axes(extent=extents, nb_labels=6)
mlab.outline(extent=extents)
mlab.xlabel(xname)
mlab.ylabel(yname)
mlab.zlabel(self.dependentVar)
mlab.figure()
xmin = qx[0] * 1E0
xmax = qx[-1] * 1E0
ymin = qy[0] * 1E0
ymax = qy[-1] * 1E0
zmin = qz[0] * 1E0
zmax = qz[-1] * 1E0
obj = mlab.contour3d(plot_data,
contours=10,
opacity=0.5,
transparent=False,
extent=[qz[0], qz[-1], qy[0], qy[-1], qx[0],
qx[-1]]) # , vmin=0, vmax=0.8)
mlab.axes(ranges=[xmin, xmax, ymin, ymax, zmin, zmax])
mlab.xlabel('$Q_z$ [$\AA^{-1}$]')
mlab.ylabel('$Q_y$ [$\AA^{-1}$]')
mlab.zlabel('$Q_z$ [$\AA^{-1}$]')
#C:\Users\Sanna\Documents\Beamtime\NanoMAX062017\Analysis_ptypy\scan461_\bragg_peak_stacking\InP\
#mlab.savefig('pos_'+ str(pos) +'.jpg')
# Another way to maka an iso surface. Can also be combined with cut planes
position = 0
def iso_pipeline_plot():
src = mlab.pipeline.scalar_field(
plot_data) # this creates a regular space data
mlab.pipeline.iso_surface(src,
contours=[
diff_data[position].min() +
0.1 * diff_data[position].ptp(),
obj = mlab.pipeline.surface(normals, colormap='gist_ncar')
mlab.outline(extent=[
np.min(x1),
np.max(x1),
np.min(x2),
np.max(x2), v0, v1
])
#WARNING: the z-axis will include the warp factor and is highly misleading
#mlab.axes(src,z_axis_visibility=False,extent=ext,xlabel=plot_dict['xlabel'],ylabel=plot_dict['ylabel'],zlabel=plotter.name)
mlab.view(azimuth=90,
elevation=60,
distance=5 * np.max(sizes),
focalpoint=origin)
s = s0 * len(slices[1]) + s1
mlab.xlabel(plot_dict['xlabel'])
mlab.ylabel(plot_dict['ylabel'])
mlab.zlabel(plot_dict['blabel'])
mlab.savefig('tempfile{:03d}.png'.format(s))
# 3D PLOTS
if num_slice_axes == 1:
for s in slices[0]:
print('Rendering frame', s, '...')
data_slice, plot_dict = plotter.volume3d(slicing_spec, s, dyn_range)
data_slice = data_slice.astype(np.double)
ext = plot_dict['extent']
dims = plot_dict['dims']
x1 = np.einsum('i,j,k', plot_dict['xpts'], np.ones(dims[1]),
np.ones(dims[2])).astype(np.double)
x2 = np.einsum('i,j,k', np.ones(dims[0]), plot_dict['ypts'],
def Apply(db_tested, db_train, sysnames, alpha=0.05, N=50):
"""
Inputs: A data frame of objects to be tested, a training data set, and a list of ratios to use
Outputs: An array of booleans of indices in the test data frame which have passed the filter
"""
#Reconstruct element names from ratio names
el_list = []
for r in sysnames:
el_list.extend(DecomposeR(r))
#Get matrices for the tested and training datasets
print("ApplyLOF: Normalise & take logarithms")
dTest = LogRatioMatrix(db_tested, el_list, stripNaNs=False)
dTrain = LogRatioMatrix(db_train, el_list, stripNaNs=True)
#Compute extents of training data for each dimension, renormalise all data
dTrain, midpts, extents = Renormalise(dTrain)
dTest = Renormalise(dTest, midpts, extents)[0]
#Fill in missing data
print("ApplyLOF: Interpolate missing values")
dTest = FillNaNs(dTrain, dTest, N)
print("ApplyLOF: Compute testing set factors")
LOF_test = ComputeLOF(dTest, dTrain, N)
print("ApplyLOF: Compute training set factors")
LOF_ref = ComputeLOF2(dTrain, N)
#Prepare the rejections filter
Filter = np.full(dTest.shape[0], True, dtype=np.bool)
#Find cutoff LOF value for the training set
c = np.percentile(LOF_ref, 100 * (1 - alpha))
passing_samples = (LOF_test < c)
Filter = (Filter & passing_samples)
print("ApplyLOF: Evaluate with c=" + str(c))
# DEBUG: Plot results with mayavi
if _debugVisualise:
from mayavi import mlab
dTest[np.isinf(dTest)] = 1000
LOF_test[np.isinf(LOF_test)] = 1000
mlab.figure('RSV ')
mlab.points3d(dTrain.T[-3],
dTrain.T[-2],
dTrain.T[-1],
LOF_ref,
scale_mode='none',
scale_factor=0.01)
mlab.axes()
mlab.xlabel(sysnames[-3])
mlab.ylabel(sysnames[-2])
mlab.zlabel(sysnames[-1])
mlab.show()
mlab.figure('RSV ')
mlab.points3d(dTrain.T[-6],
dTrain.T[-5],
dTrain.T[-4],
LOF_ref,
scale_mode='none',
scale_factor=0.01)
mlab.axes()
mlab.xlabel(sysnames[-6])
mlab.ylabel(sysnames[-5])
mlab.zlabel(sysnames[-4])
mlab.show()
#Return boolean mask for test data frame
return Filter
# Loop over the values of the slice array, to produce an image of the vector
# field for each slice
for i in range(len(slice_arr)):
# Create a new figure
fig = mlab.figure(size = (800,700))
# Create an image of the vector field for this slice of the array
mlab.quiver3d(X[slice_arr[i],::8,::8], Y[slice_arr[i],::8,::8],\
Z[slice_arr[i],::8,::8], mag_x[slice_arr[i],::8,::8],\
mag_y[slice_arr[i],::8,::8],mag_z[slice_arr[i],::8,::8],scalars =\
B_mag[slice_arr[i],::8,::8], vmax=vmax,vmin=vmin)
# Make the co-ordinate axes appear on the plot
mlab.xlabel('x-axis')
mlab.ylabel('y-axis')
mlab.zlabel('z-axis')
# Rotate the camera so that it is face on
mlab.view(azimuth=0, elevation = 90)
# Add a colourbar to the figure
mlab.colorbar(orientation='vertical')
# Save the figure
mlab.savefig(data_loc + 'B_vectors_slice_{}.jpg'.format(slice_arr[i]))
# Close the figure
mlab.close()
# Print a line to the screen to show that the figure has been saved
# Loop over the values of the slice array, to produce an image of the vector
# field for each slice
for i in range(len(slice_arr)):
# Create a new figure
fig = mlab.figure(size=(800, 700))
# Create an image of the vector field for this slice of the array
mlab.quiver3d(X[slice_arr[i],::8,::8], Y[slice_arr[i],::8,::8],\
Z[slice_arr[i],::8,::8], mag_x[slice_arr[i],::8,::8],\
mag_y[slice_arr[i],::8,::8],mag_z[slice_arr[i],::8,::8],scalars =\
B_mag[slice_arr[i],::8,::8], vmax=vmax,vmin=vmin)
# Make the co-ordinate axes appear on the plot
mlab.xlabel('x-axis')
mlab.ylabel('y-axis')
mlab.zlabel('z-axis')
# Rotate the camera so that it is face on
mlab.view(azimuth=0, elevation=90)
# Add a colourbar to the figure
mlab.colorbar(orientation='vertical')
# Save the figure
mlab.savefig(data_loc + 'B_vectors_slice_{}.jpg'.format(slice_arr[i]))
# Close the figure
mlab.close()
# Print a line to the screen to show that the figure has been saved
from mayavi import mlab
import numpy as np
from numpy import pi, sin, cos
phi, theta = np.mgrid[0:pi:20j, 0:2 * pi:20j]
x = sin(phi) * cos(theta)
y = sin(phi) * sin(theta)
z = cos(phi)
mlab.clf()
mlab.mesh(x, y, z, scalars=z, representation='wireframe')
mlab.colorbar(orientation='vertical')
mlab.title('Sphere')
mlab.outline()
mlab.axes()
mlab.xlabel('X')
mlab.ylabel('Y')
mlab.savefig('sphere.png')
mlab.show()
mlab.view(azimuth=38, elevation=63, distance=distance)
else:
mlab.view(azimuth=38,
elevation=63,
distance=np.sqrt(qx.max()**2 + qz.max()**2 + qy.max()**2))
# azimut is the rotation around z axis of mayavi (x)
mlab.roll(0)
if crop_symmetric:
ax = mlab.axes(line_width=2.0, nb_labels=2 * half_labels + 1)
else:
ax = mlab.axes(line_width=2.0, nb_labels=4)
mlab.xlabel('Qx (1/nm)')
mlab.ylabel('Qz (1/nm)')
mlab.zlabel('-Qy (1/nm)')
mlab.savefig(savedir + 'S' + str(scan) + comment + '_labels.png', figure=myfig)
ax.label_text_property.opacity = 0.0
ax.title_text_property.opacity = 0.0
mlab.savefig(savedir + 'S' + str(scan) + comment + '_axes.png', figure=myfig)
ax.axes.x_axis_visibility = False
ax.axes.y_axis_visibility = False
ax.axes.z_axis_visibility = False
mlab.savefig(savedir + 'S' + str(scan) + comment + '.png', figure=myfig)
mlab.draw(myfig)
if make_movie:
if output_format == 'mp4':
animation = mpy.VideoClip(rotate_scene,
duration=duration).resize(width=fig_size[0],
import tables as tb
import mayavi.mlab as ml
f = tb.openFile('/Users/fpaolo/data/gps/amery_gps_all.h5')
t = f.root.time[:]
x = f.root.x[:]
y = f.root.y[:]
h = f.root.h[:]
f.close()
ml.figure(1, size=(700, 600), fgcolor=(1, 1, 1), bgcolor=(0.5, 0.5, 0.5))
ml.points3d(x, y, h, t.round(1), mode='point')
#ml.plot3d(x, y, h, t.round(1), tube_radius=.3)
ml.colorbar(title='campaigns', orientation='vertical',
nb_labels=5, label_fmt='%.0f', nb_colors=5)
ml.outline()
ml.axes(nb_labels=4).axes.label_format = '%.0f'
ml.title('Amery GPS', size=.7)
ml.xlabel('x (km)')
ml.ylabel('y (km)')
ml.zlabel('h (m)')
ml.show()
rho[i + 1] = rho[i] + h * f(rho[i], u[i], v[i], w)
u[i + 1] = u[i] + h * g1(rho[i], u[i], v[i])
v[i + 1] = v[i] + h * g2(rho[i], u[i], v[i])
time[i + 1] = time[i] + h
ux, vx, rhox = np.mgrid[-2:2:50j, -2:2:50j, -1.5:1.5:50j]
values = -(rhox**3 - rhox) * (3.0 * rhox**2 -
1) - ux * (rhox + 1) - vx * rhox - w * (rhox - 1)
mlab.contour3d(ux, vx, rhox, values, contours=[0], opacity=0.5)
# values_u = a*(1.0 - ux) - eta(rhox+1, c1)
# mlab.contour3d(ux, vx, rhox, values_u, color = (0.7, 0.4, 0.4), contours=[0], opacity = 0.5)
# values_v = b*(1.0 - vx) - eta(rhox, c1)
# mlab.contour3d(ux, vx, rhox, values_v, color = (0.7, 0.4, 0.4), contours=[0], opacity = 0.5)
mlab.axes()
mlab.xlabel('u')
mlab.ylabel('v')
mlab.zlabel('rho')
mlab.plot3d(u, v, rho, tube_radius=0.02, line_width=2.0)
print('Mean u: ', np.mean(u))
print('Mean v: ', np.mean(v))
fig, ax = plt.subplots(1, 2)
ax[0].plot(time, u, label='u')
ax[0].plot(time, v, label='v')
ax[0].legend()
ax[0].set_xlabel('time')
ax[1].plot(time, rho)
ax[1].set_ylabel('rho')
ax[1].set_xlabel('time')
def main_function(file):
# Process the data to arrays
# file = "HP_1a1.csv"
data = pd.read_csv(file)
data = np.array(data)
# x: Retention time
# y: m/z ratio
# z: Intensity
x = data[:, 0]
y = data[:, 1]
z = data[:, 2]
# Retrieve scaling scalars from scale function
x_scale, y_scale, z_scale = scale_function(data)
# Retrieve rate to downsample data
rate = rate_downsampling(file)
# Begin full downsampling of data
# These lists store the final data of each axis
xnew = []
ynew = []
znew = []
# These lists are temporary placeholders for each section/bucket of each axis
data_BucketX = []
data_BucketY = []
data_BucketZ = []
index = 0
for item in x:
# Ignore the first line
if index == 0:
index += 1
continue
# Retention values are the same, grouped into same bucket
if item == x[index - 1]:
data_BucketX.append(item)
data_BucketY.append(y[index])
data_BucketZ.append(z[index])
# Different bucket
else:
# Ignore buckets with fewer than 100 data points
if len(data_BucketX) < 100:
index += 1
continue
xn = []
yn = []
zn = []
# Downsample length of each bucket
# TODO: Fix the rate error
# An error like the one below may occur with regards to rate:
# ERROR: In C:\VPP\standalone-build\VTK-source\Filters\Core\vtkDelaunay2D.cxx, line 819
# vtkDelaunay2D (0000027AE2A2ACF0): ERROR: Edge [118461 118462] is non-manifold!!!
sample = int(len(data_BucketX) / rate)
xn.extend(signal.resample(data_BucketX, sample))
yn.extend(signal.resample(data_BucketY, sample))
zn.extend(signal.resample(data_BucketZ, sample))
i = 0
for foo in zn:
# Rescaled each axis
xnew.append(xn[i] * x_scale)
ynew.append(yn[i] / y_scale)
znew.append(zn[i] / z_scale)
i += 1
data_BucketX.clear()
data_BucketY.clear()
data_BucketZ.clear()
index += 1
# From here, continue to remove data, specifically intensity values, that are too small and irrelevant
# Temporary list to store indices
foo = []
# Set a max z-axis threshold
z_threshold = max(znew) * 0.01
# Loop through intensity list
for i in range(len(znew)):
# Append to the temporary list the indices of intensity values that are less than the threshold
if znew[i] < z_threshold:
foo.append(i)
# Removes all corresponding elements from each array
# Must remove from all three lists to preserve uniformity
xnew = np.delete(xnew, foo)
ynew = np.delete(ynew, foo)
znew = np.delete(znew, foo)
# From here, we are ready to get our plots set up
# Dummy object to get accurate and original intensity values for colorbar label
original = mlab.points3d(x, y, z, z, mode='point')
original.remove()
# Visualize the points
pts = mlab.points3d(xnew, ynew, znew, znew, mode='point')
# Create and visualize the mesh
mesh = mlab.pipeline.delaunay2d(pts)
surf = mlab.pipeline.surface(mesh)
pts.remove()
# Simple plot axis info rendering
mlab.xlabel("Retention")
mlab.ylabel("m/z")
mlab.zlabel("Intensity")
# Add text to plot indicating how each axis was rescaled
mlab.text(0.5, 0.80, 'Retention scaled up by %.2f' % x_scale, width=0.8)
mlab.text(0.5, 0.85, 'm/z scaled down by %.2f' % y_scale, width=0.8)
mlab.text(0.5, 0.90, 'Intensity scaled down by %.2f' % z_scale, width=1.0)
# Colorbar with original intensity values
colorbar = mlab.colorbar(object=original,
title='Intensity',
orientation='vertical')
colorbar.scalar_bar_representation.position = [0.85, 0.18]
# Show the final plot scene
mlab.show()
def drawGraph(self, colormap='jet', mapping=None, surfaceOnly=False):
"""
"""
self.figure = mlab.figure(1, fgcolor=(0, 0, 0), bgcolor=(1, 1, 1), size=(1200, 900))
self.gcf = mlab.gcf()
# mlab.clf()
self.figure.scene.disable_render = True
self.crds = {}
print("root information:",self.root_wcrd, self.root)
# create drawables for bifurcations and endpoints
self.narray = np.zeros((len(self.nodes), 3), dtype=np.float32)
nodeSize = np.zeros((len(self.nodes),))
labels = []
for i in range(self.narray.shape[0]):
n = self.nodes[i]
self.narray[i, :] = n[1]['wcrd']
dg = self.og.degree(n[0])
if(dg == 1):
tmp = (self.narray[i, 0], self.narray[i, 1], self.narray[i, 2])
nodeSize[i] = 1 if tuple(map(int, tmp)) != self.root_wcrd else 1.5
labels.append((n[0], tmp))
else:
nodeSize[i] = 0.5
# # create random mapping
if mapping is None:
mapping = {}
for e in self.edges:
clr = random.randint(0, 1)
mapping[(e[0], e[1])] = clr
# now draw
self.lines = {}
surface = None
self.surfaces = None
x = np.array([0, 0])
y = np.array([0, 0])
z = np.array([0, 0])
s = np.array([0, 4])
for e in self.edges:
try:
mp = e[2]["mappedPoints"]
x = np.concatenate((x, mp[::4, 0]))
y = np.concatenate((y, mp[::4, 1]))
z = np.concatenate((z, mp[::4, 2]))
clr = mapping[(e[0], e[1])]
# clr_t = clr, clr, clr
s = np.concatenate((s, np.linspace(clr, clr, len(mp[::4, 0]))))
#print "%s->%s mapping=%s"%(e[0],e[1],clr)
if surface is None:
surface = e[2]['mappedPoints']
else:
try:
surface = np.concatenate((surface, mp), axis=0)
except ValueError:
pass
sp = e[2]['d0']
if(sp):
if not surfaceOnly:
self.lines[(e[0], e[1])] = mlab.plot3d(sp[0],
sp[1],
sp[2],
color=(0, 0, 0),
# color=clrt,
tube_radius=.3)
except KeyError as error:
print("KeyError", error)
except IndexError as error:
print("IndexError", error)
self.surfaces = mlab.points3d(x, y, z, s,
# colormap="Greys",
colormap="jet",
scale_mode='none',
scale_factor=.4,
opacity=0.5)
if not surfaceOnly:
self.npts = mlab.points3d(self.narray[:, 0],
self.narray[:, 1],
self.narray[:, 2],
nodeSize,
colormap="jet",
scale_factor=4.0)
x = surface[::1, 0]
y = surface[::1, 1]
z = surface[::1, 2]
minx = min(x)
maxx = max(x)
miny = min(y)
maxy = max(y)
minz = min(z)
maxz = max(z)
X, Y, Z = np.mgrid[minx:maxx:100j, miny:maxy:100j, minz:maxz:100j]
# Visualize the points3d
clr = (1, 0, 0)
# Labels and legends
if(self.showAxes):
mlab.xlabel("x")
mlab.ylabel("y")
mlab.xlabel("z")
mlab.title(self.title, size=.5, height=.90)
for label in labels:
l = label[1]
fl = tuple(map(int, l))
if fl == self.root_wcrd:
mlab.text(l[0], l[1], repr(label[0]) + " (root)", z=l[2], width=.2, color=(0, 0, 0))
else:
mlab.text(l[0], l[1], repr(label[0]), z=l[2], width=.15, color=(0, 0, 0))
#adjust lut transparency
lut = self.surfaces.module_manager.scalar_lut_manager.lut.table.to_array()
lut[:, -1] = np.linspace(110, 110, 256)
self.surfaces.module_manager.scalar_lut_manager.lut.table = lut
# add scale bar
if self.surfaces is not None:
mlab.scalarbar(title="scale", orientation='vertical', nb_labels=5)
self.figure.scene.disable_render = False
mlab.view(0, 180, 400, roll=180)
#saveFileName = os.path.join(os.path.expanduser("~"), "desktop", self.title + ".png")
#mlab.savefig(saveFileName)
#mlab.close()
mlab.show()
foo = []
# set a max z-axis threshold
z_threshold = max(znew) * 0.01
for i in range(len(znew)):
# append to a list the indices of z-axis values that are less than the threshold
if znew[i] < z_threshold:
foo.append(i)
# removes all corresponding elements from each array
xnew = np.delete(xnew, foo)
ynew = np.delete(ynew, foo)
znew = np.delete(znew, foo)
# Visualize the points
# pts = mlab.points3d(x_3d, y_3d, z_3d, z_3d, mode='point')
pts = mlab.points3d(xnew, ynew, znew, znew, mode='point')
# pts = mlab.points3d(xnew, ynew, znew, znew, mode='point', scale_factor=3.0)
# Create and visualize the mesh
mesh = mlab.pipeline.delaunay2d(pts)
surf = mlab.pipeline.surface(mesh)
pts.remove()
# Simple plot axis info rendering
mlab.xlabel("Retention")
mlab.ylabel("m/z")
mlab.zlabel("Intensity")
mlab.show()
def plotter(profiles, smsh):
"""
Mesh and profiles plotter.
:param profiles:
A list of :class:`openquake.hazardlib.geo.line.Line` instances
:param smsh:
A :class:`numpy.ndarray` instance
"""
#
if MAYAVI:
_ = mlab.figure(size=(600, 400))
#
scl = -0.01
delta = 0.1
wdt = 0.001
# initialize extremes
xmi = +1e10
ymi = +1e10
zmi = +1e10
xma = -1e10
yma = -1e10
zma = -1e10
# plotting profiles
for l in profiles:
coo = [[p.longitude, p.latitude, p.depth * scl] for p in l]
coo = np.array(coo)
mlab.plot3d(coo[:, 0],
coo[:, 1],
coo[:, 2],
color=(0, 1, 0),
line_width=wdt,
opacity=0.2)
mlab.points3d(coo[0, 0],
coo[0, 1],
coo[0, 2],
color=(1., 0.5, 0.),
line_width=wdt,
scale_factor=0.1)
xmi = min(xmi, np.amin(coo[:, 0]) - delta)
xma = max(xma, np.amax(coo[:, 0]) + delta)
ymi = min(ymi, np.amin(coo[:, 1]) - delta)
yma = max(yma, np.amax(coo[:, 1]) + delta)
zmi = min(zmi, np.amin(coo[:, 2]) - delta)
zma = max(zma, np.amax(coo[:, 2]) + delta)
# plotting mesh
smsh[:, :, 2] *= scl
for i in range(smsh.shape[0]):
k = np.isfinite(smsh[i, :, 0])
if np.any(k):
_ = mlab.plot3d(smsh[i, k, 0],
smsh[i, k, 1],
smsh[i, k, 2],
color=(1, 0, 0),
line_width=wdt,
tube_radius=0.01)
for i in range(smsh.shape[1]):
k = np.isfinite(smsh[:, i, 0])
if sum(k):
_ = mlab.plot3d(smsh[k, i, 0],
smsh[k, i, 1],
smsh[k, i, 2],
color=(1, 0, 0),
line_width=wdt,
tube_radius=0.01)
# decoration
axes = mlab.axes(extent=[xmi, xma, ymi, yma, zmi, zma])
axes.label_text_property.font_size = 6
axes.axes.font_factor = 1.0
mlab.xlabel('Longitude\n')
mlab.ylabel('Latitude\n')
mlab.zlabel('Depth\n [km*0.01]')
mlab.show()
def drawGraph(self, colormap='jet', mapping=None, surfaceOnly=False):
"""
"""
self.figure = mlab.figure(1,
fgcolor=(0, 0, 0),
bgcolor=(1, 1, 1),
size=(1200, 900))
self.gcf = mlab.gcf()
# mlab.clf()
self.figure.scene.disable_render = True
self.crds = {}
print("root information:", self.root_wcrd, self.root)
# create drawables for bifurcations and endpoints
self.narray = np.zeros((len(self.nodes), 3), dtype=np.float32)
nodeSize = np.zeros((len(self.nodes), ))
labels = []
for i in range(self.narray.shape[0]):
n = self.nodes[i]
self.narray[i, :] = n[1]['wcrd']
dg = self.og.degree(n[0])
if (dg == 1):
tmp = (self.narray[i, 0], self.narray[i, 1], self.narray[i, 2])
nodeSize[i] = 1 if tuple(map(int,
tmp)) != self.root_wcrd else 1.5
labels.append((n[0], tmp))
else:
nodeSize[i] = 0.5
# # create random mapping
if mapping is None:
mapping = {}
for e in self.edges:
clr = random.randint(0, 1)
mapping[(e[0], e[1])] = clr
# now draw
self.lines = {}
surface = None
self.surfaces = None
x = np.array([0, 0])
y = np.array([0, 0])
z = np.array([0, 0])
s = np.array([0, 4])
for e in self.edges:
try:
mp = e[2]["mappedPoints"]
x = np.concatenate((x, mp[::4, 0]))
y = np.concatenate((y, mp[::4, 1]))
z = np.concatenate((z, mp[::4, 2]))
clr = mapping[(e[0], e[1])]
# clr_t = clr, clr, clr
s = np.concatenate((s, np.linspace(clr, clr, len(mp[::4, 0]))))
#print "%s->%s mapping=%s"%(e[0],e[1],clr)
if surface is None:
surface = e[2]['mappedPoints']
else:
try:
surface = np.concatenate((surface, mp), axis=0)
except ValueError:
pass
sp = e[2]['d0']
if (sp):
if not surfaceOnly:
self.lines[(e[0], e[1])] = mlab.plot3d(
sp[0],
sp[1],
sp[2],
color=(0, 0, 0),
# color=clrt,
tube_radius=.3)
except KeyError as error:
print("KeyError", error)
except IndexError as error:
print("IndexError", error)
self.surfaces = mlab.points3d(
x,
y,
z,
s,
# colormap="Greys",
colormap="jet",
scale_mode='none',
scale_factor=.4,
opacity=0.5)
if not surfaceOnly:
self.npts = mlab.points3d(self.narray[:, 0],
self.narray[:, 1],
self.narray[:, 2],
nodeSize,
colormap="jet",
scale_factor=4.0)
x = surface[::1, 0]
y = surface[::1, 1]
z = surface[::1, 2]
minx = min(x)
maxx = max(x)
miny = min(y)
maxy = max(y)
minz = min(z)
maxz = max(z)
X, Y, Z = np.mgrid[minx:maxx:100j, miny:maxy:100j, minz:maxz:100j]
# Visualize the points3d
clr = (1, 0, 0)
# Labels and legends
if (self.showAxes):
mlab.xlabel("x")
mlab.ylabel("y")
mlab.xlabel("z")
mlab.title(self.title, size=.5, height=.90)
for label in labels:
l = label[1]
fl = tuple(map(int, l))
if fl == self.root_wcrd:
mlab.text(l[0],
l[1],
repr(label[0]) + " (root)",
z=l[2],
width=.2,
color=(0, 0, 0))
else:
mlab.text(l[0],
l[1],
repr(label[0]),
z=l[2],
width=.15,
color=(0, 0, 0))
#adjust lut transparency
lut = self.surfaces.module_manager.scalar_lut_manager.lut.table.to_array(
)
lut[:, -1] = np.linspace(110, 110, 256)
self.surfaces.module_manager.scalar_lut_manager.lut.table = lut
# add scale bar
if self.surfaces is not None:
mlab.scalarbar(title="scale", orientation='vertical', nb_labels=5)
self.figure.scene.disable_render = False
mlab.view(0, 180, 400, roll=180)
#saveFileName = os.path.join(os.path.expanduser("~"), "desktop", self.title + ".png")
#mlab.savefig(saveFileName)
#mlab.close()
mlab.show()