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 show_gaussians(self, scale=1.0, r=1.0, show=True):
"""Show clusters as ellipsoids.
:param float scale: Number of standard deviations to show
:param float r: Thickness of the tubes used to represent
the unit cell
:param bool show: If True mlab.show() is executed
"""
from mayavi.api import Engine
from mayavi import mlab
engine = Engine()
engine.start()
scene = engine.new_scene()
scene.scene.disable_render = True # for speed
surfs = []
self._draw_cell(r=r)
for gauss in self.gaussians:
surf = self._show_one_gaussian(gauss, engine, scale=scale)
surfs.append(surf)
scene.scene.disable_render = False
for i, surf in enumerate(surfs):
vtk_srcs = mlab.pipeline.get_vtk_src(surf)
vtk_src = vtk_srcs[0]
npoints = len(vtk_src.point_data.scalars)
vtk_src.point_data.scalars = np.tile(i, npoints)
if show:
mlab.show()
def mayavi_init():
try:
engine = mayavi.engine
except NameError:
from mayavi.api import Engine
engine = Engine()
engine.start()
if len(engine.scenes) == 0:
engine.new_scene(size=(600, 800))
scene = engine.scenes[0]
fig = mlab.gcf(engine)
mlab.figure(figure=fig,
bgcolor=(1.0, 1.0, 1.0),
fgcolor=(0.0, 0.0, 0.0),
engine=engine)
return engine
def sigma_m( m ):
dataname = "sigmaOPT20_with_m{}.npy".format( m )
res = np.load( dataname )
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 = 1.
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. , 0.2] )
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()
scene.scene.camera.position = [1.2836424071875543, 1.4371492101974028, 4.0390558511994534]
scene.scene.camera.focal_point = [0.17361105930834225, 0.21417386120592863, 3.4874067491767562]
scene.scene.camera.view_angle = 30.0
scene.scene.camera.view_up = [-0.21371002618964222, -0.23386371429877953, 0.94849132196367569]
scene.scene.camera.clipping_range = [0.79163912587841923, 2.7365159886347699]
scene.scene.camera.compute_view_plane_normal()
#mlab.surf( x_axis2, y_axis2, res2 )
#mlab.xlabel( "rand tau" )
#mlab.ylabel( "rand r" )
#mlab.zlabel( "z" )
mlab.show()
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 view3d(sgrid):
from mayavi.sources.vtk_data_source import VTKDataSource
from mayavi.modules.api import Outline, GridPlane
from mayavi.api import Engine
from mayavi.core.ui.engine_view import EngineView
e=Engine()
e.start()
s = e.new_scene()
# Do this if you need to see the MayaVi tree view UI.
ev = EngineView(engine=e)
ui = ev.edit_traits()
# mayavi.new_scene()
src = VTKDataSource(data=sgrid)
e.add_source(src)
e.add_module(Outline())
g = GridPlane()
g.grid_plane.axis = 'x'
e.add_module(g)
def tresdeizar(X, Y, anchox, anchoy, angulo):
engine = Engine()
engine.start()
scene = engine.new_scene()
scene.scene.disable_render = True # for speed
visual.set_viewer(scene)
surfaces = []
for k in range(0, len(X)):
source = ParametricSurface()
source.function = 'ellipsoid'
engine.add_source(source)
surface = Surface()
source.add_module(surface)
actor = surface.actor # mayavi actor, actor.actor is tvtk actor
actor.property.opacity = 0.7
actor.property.color = (0, 0, 1) # tuple(np.random.rand(3))
actor.mapper.scalar_visibility = False # don't colour ellipses by their scalar indices into colour map
actor.actor.orientation = np.array([90, angulo[k], 0
]) #* 90 #(angulo[k]) # in degrees
actor.actor.position = np.array([X[k], Y[k], 0])
actor.actor.scale = np.array(
[anchox[k] / 2, anchox[k] / 2, anchoy[k] / 2])
surfaces.append(surface)
source.scene.background = (1.0, 1.0, 1.0)
CellScann.set_img_3deizada(mlab)
return mlab.show()
Co3O4_lat5 = rsp.lattice.lattice_from_cif('/home/finn/Documents/eclipse_workspace/2017_MA3074/preparation/structure_simulation/Co3O4.cif', HKL_normal = [1,0,0], HKL_para_x=[0,0,1])
PbBrF_lat = rsp.lattice.lattice_from_cif('/home/finn/Documents/eclipse_workspace/2017_MA3074/preparation/structure_simulation/PbBrF.cif', HKL_normal = [0,0,1], HKL_para_x=[0,1,0], energy_keV=25)
from mayavi import mlab
try:
engine = mayavi.engine
except NameError:
from mayavi.api import Engine
engine = Engine()
engine.start()
if len(engine.scenes) == 0:
engine.new_scene(size=(600, 800))
scene = engine.scenes[0]
fig = mlab.gcf(engine)
mlab.figure(figure=fig, bgcolor=(1.0, 1.0, 1.0), fgcolor=(0.0, 0.0, 0.0), engine=engine)
Au_lat = rsp.lattice(
a = 4.0782,
b = 4.0782,
c = 4.0782,
alpha = 90,
beta = 90,
gamma = 90,
basis = [['Au', 0,0,0],['Au', 0.5,0.5,0],['Au', 0,0.5,0.5],['Au', 0.5,0,0.5]],
HKL_normal = [0,0,1],
HKL_para_x = [0,1,0]
def view(prefix, name):
"""
construct a generic visualization of base mesh, refined mesh,
and potential/field/pseudopotential data in mayavi2
requires running within mayavi2 or ipython with threads or
something like::
from pyface.api import GUI
GUI().start_event_loop()
in your script to interact with it.
this is from a simplified macro recorded in mayavi2
"""
"""
wwc 11/23/2018
In both python 2.7 and 3.5, this 3D visualization with mayavi
works in Linux, but it's not compatible with X11 remote forwarding.
Install mayavi through conda channel "menpo" in python 3.5 or just
see environment setup of "ele35" in README. However, I haven't
found a mayavi version for python 3.6.
"""
import mayavi
try:
from mayavi.api import Engine
engine = Engine()
engine.start()
except AttributeError: # NameError:
engine = mayavi.engine
if len(engine.scenes) == 0:
engine.new_scene()
scene = engine.scenes[0]
base_mesh_name = "%s_mesh.vtk" % prefix
if os.access(base_mesh_name, os.R_OK):
base_mesh = engine.open(base_mesh_name)
surface = Surface()
engine.add_filter(surface, base_mesh)
surface.actor.property.representation = 'wireframe'
surface.actor.property.line_width = 1
mesh_name = "%s_%s_mesh.vtk" % (prefix, name)
if os.access(mesh_name, os.R_OK):
mesh = engine.open(mesh_name)
mesh.cell_scalars_name = 'charge'
surface = Surface()
engine.add_filter(surface, mesh)
module_manager = mesh.children[0]
module_manager.scalar_lut_manager.lut_mode = 'RdBu'
module_manager.scalar_lut_manager.use_default_range = False
r = np.fabs(module_manager.scalar_lut_manager.data_range).max()
module_manager.scalar_lut_manager.data_range = [-r, r]
surface.actor.property.backface_culling = True
data_name = "%s_%s.vtk" % (prefix, name)
if os.access(data_name, os.R_OK):
data = engine.open(data_name)
if "pseudo_potential" in data._point_scalars_list:
data.point_scalars_name = "pseudo_potential"
else:
data.point_scalars_name = "potential"
iso_surface = IsoSurface()
engine.add_filter(iso_surface, data)
module_manager = data.children[0]
module_manager.scalar_lut_manager.lut_mode = 'Greys'
iso_surface.contour.auto_contours = True
iso_surface.contour.number_of_contours = 5
try:
iso_surface.contour.maximum_contour = 1e-2
except:
pass
scene.scene.isometric_view()
scene.scene.render()
# coding: utf-8
# In[1]:
import numpy as np
from mayavi.api import Engine
from mayavi.sources.vtk_file_reader import VTKFileReader
# In[2]:
e = Engine()
e.start()
# In[3]:
s = e.new_scene()
# In[4]:
r = VTKFileReader()
# In[5]:
r.initialize('heart.vtk')
e.add_source(r)
# In[6]:
from mayavi.modules import api
# In[7]:
# Recorded script from Mayavi2
from numpy import array
try:
engine = mayavi.engine
except NameError:
from mayavi.api import Engine
engine = Engine()
engine.start()
if len(engine.scenes) == 0:
engine.new_scene()
# -------------------------------------------
from mayavi.filters.threshold import Threshold
threshold = Threshold()
mayavi.add_filter(threshold, ug_waterlevel)
surface_waterlevel = Surface()
mayavi.add_filter(surface2, threshold)
threshold.auto_reset_lower = False
threshold.auto_reset_upper = False
module_manager2 = threshold.children[0]
module_manager2.vector_lut_manager.data_range = array([ 0., 1.])
def __init__(self,
a,
b,
c,
alpha=90,
beta=90,
gamma=90,
basis=[0, 0, 0],
HKL_normal=[0, 0, 1],
HKL_para_x=[1, 0, 0],
offset_angle=0,
energy_keV=22.5):
self.a = a
self.b = b
self.c = c
self.alpha = np.deg2rad(alpha)
self.beta = np.deg2rad(beta)
self.gamma = np.deg2rad(gamma)
self.energy_keV = energy_keV
self.k0 = id03.get_K_0(energy_keV)
self.basis = basis # list of [Atomic_form_factor, x, y, z]
for i in xrange(len(self.basis)):
if (isinstance(self.basis[i][0], basestring)):
f1, f2 = elements.symbol(
self.basis[i][0]).xray.scattering_factors(
energy=energy_keV)
self.basis[i][0] = f1 + 1.j * f2
self.HKL_normal = HKL_normal
self.HKL_para_x = HKL_para_x
# calculate real space unit cell vectors
self.A1 = np.array([self.a, 0, 0])
self.A2 = np.array(
[self.b * np.cos(self.gamma), b * np.sin(self.gamma), 0])
A31 = self.c * np.cos(self.alpha)
A32 = self.c / np.sin(self.gamma) * (
np.cos(self.beta) - np.cos(self.gamma) * np.cos(self.alpha))
A33 = np.sqrt(self.c**2 - A31**2 - A32**2)
self.A3 = np.array([A31, A32, A33])
self.RealTM = np.array([[self.A1[0], self.A2[0], self.A3[0]],
[self.A1[1], self.A2[1], self.A3[1]],
[self.A1[2], self.A2[2], self.A3[2]]])
#TODO: remove
if (0):
from mayavi import mlab
try:
engine = mayavi.engine
except NameError:
from mayavi.api import Engine
engine = Engine()
engine.start()
if len(engine.scenes) == 0:
engine.new_scene(size=(600, 800))
scene = engine.scenes[0]
fig = mlab.gcf(engine)
mlab.figure(figure=fig,
bgcolor=(1.0, 1.0, 1.0),
fgcolor=(0.0, 0.0, 0.0),
engine=engine)
hkls = [[0, 0, 0], [1, 0, 0], [0, 1, 0], [1, 1, 0], [0, 0, 1],
[1, 0, 1], [0, 1, 1], [1, 1, 1]]
lines = [[0, 1], [0, 2], [0, 4], [5, 1], [5, 4], [5, 7], [3, 1],
[3, 2], [3, 7], [6, 4], [6, 2], [6, 7]]
for line in lines:
xyz1 = self.RealTM.dot(hkls[line[0]])
xyz2 = self.RealTM.dot(hkls[line[1]])
mlab.plot3d([xyz1[0], xyz2[0]], [xyz1[1], xyz2[1]],
[xyz1[2], xyz2[2]])
mlab.show()
# calculate reciprocal space unit cell vectors
self._V_real = self.A1.dot(np.cross(self.A2, self.A3))
self.B1 = 2 * np.pi * np.cross(self.A2, self.A3) / self._V_real
self.B2 = 2 * np.pi * np.cross(self.A3, self.A1) / self._V_real
self.B3 = 2 * np.pi * np.cross(self.A1, self.A2) / self._V_real
self.RecTM = np.array([[self.B1[0], self.B2[0], self.B3[0]],
[self.B1[1], self.B2[1], self.B3[1]],
[self.B1[2], self.B2[2], self.B3[2]]])
self._V_rec = self.B1.dot(np.cross(self.B2, self.B3))
# align surface normal to z axis
q_normal = self.q(HKL_normal)
q_normal /= np.sqrt(q_normal.dot(q_normal))
z = np.array([0, 0, 1])
v = np.cross(q_normal, z)
I = np.zeros((3, 3))
I[0, 0] = 1
I[1, 1] = 1
I[2, 2] = 1
R = np.zeros((3, 3))
if (v[0] == 0 and v[1] == 0 and v[2] == 0):
R = I # unit matrix
elif (q_normal[0] == 0 and q_normal[1] == 0 and q_normal[2] == -1):
R = np.array([[1, 0, 0], [0, -1, 0],
[0, 0, -1]]) # rotation by 180deg around x
else:
vx = np.array([[0, -v[2], v[1]], [v[2], 0, -v[0]],
[-v[1], v[0], 0]])
R = I + vx + vx.dot(vx) / (1. + q_normal.dot(z))
self.RecTM = R.dot(self.RecTM)
# align projection of HKL_para_x to x axis
q = self.q(HKL_para_x)
rot = -np.arctan2(q[1], q[0]) + np.deg2rad(offset_angle)
R = np.array([[np.cos(rot), -np.sin(rot), 0],
[np.sin(rot), np.cos(rot), 0], [0, 0, 1]])
self.RecTM = R.dot(self.RecTM)
self.RecTMInv = inv(self.RecTM)
def w_m(m):
dataname = "wOPT20_with_m{}.npy".format(m)
res = np.load(dataname)
#res2 = np.load( "sigmaAN_with_m7.0.npy" )
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 = 1.
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., 15])
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()
scene.scene.camera.position = [
1.2836424071875543, 1.4371492101974028, 4.0390558511994534
]
scene.scene.camera.focal_point = [
0.17361105930834225, 0.21417386120592863, 3.4874067491767562
]
scene.scene.camera.view_angle = 30.0
scene.scene.camera.view_up = [
-0.21371002618964222, -0.23386371429877953, 0.94849132196367569
]
scene.scene.camera.clipping_range = [
0.79163912587841923, 2.7365159886347699
]
scene.scene.camera.compute_view_plane_normal()
mlab.show()
""" displayVmrl.py Display a VMR file of a cube Created JRM 2015-11-24 Do "%gui qt" first @author: John Minter """ import os from mayavi.sources.vrml_importer import VRMLImporter from mayavi.api import Engine gitDir = os.environ["GIT_HOME"] relImg = "/OSImageAnalysis/images/vrml/" fName = "Lines" filePath = gitDir + relImg + fName + ".wrl" print(filePath) e = Engine() e.start() s = e.new_scene() src = VRMLImporter() src.initialize(filePath) e.add_source(src)
def draw(vtk_files,
coords_file,
conn_list=None,
brain_rgba=(0.5, 0.5, 0.5, 0.2),
node_rgba=(0.30, 0.69, 1.0, 1.0),
node_rad=2.5,
conn_thr=[0.75, 1.0],
conn_cmap='YlOrRd'):
### Setup the engine and scene
my_engine = Engine()
my_engine.start()
# Create a new scene
my_scene = my_engine.new_scene()
# Set background
my_scene.scene.background = (1.0, 1.0, 1.0)
# Initialize the rendering
my_scene.scene.disable_render = True
# Import VTK file to pipeline
for vtk_file in vtk_files:
vtk_source = my_engine.open(vtk_file)
# Render surface
vtk_surface = Surface()
my_engine.add_module(vtk_surface, obj=vtk_source)
vtk_surface.actor.property.specular_color = brain_rgba[:3]
vtk_surface.actor.property.diffuse_color = brain_rgba[:3]
vtk_surface.actor.property.ambient_color = brain_rgba[:3]
vtk_surface.actor.property.color = brain_rgba[:3]
vtk_surface.actor.property.opacity = brain_rgba[3]
# Reset camera
my_scene.scene.disable_render = False
my_scene.scene.reset_zoom()
### Sensor-Locations
# Load Coordinates in MRI-space
node_coords = np.loadtxt(coords_file, delimiter=',')
n_node = node_coords.shape[0]
n_conn = np.int(n_node * (n_node - 1) * 0.5)
# Import coordinates into pipeline
crd_source = mlab.pipeline.scalar_scatter(node_coords[:, 0],
node_coords[:, 1],
node_coords[:, 2])
# Render Glyphs for node points
crd_surface = mlab.pipeline.glyph(crd_source,
scale_mode='none',
scale_factor=node_rad,
mode='sphere',
colormap='cool',
color=node_rgba[:3],
opacity=node_rgba[3])
### Connection-Locations
if conn_list is None:
return
assert len(conn_list) == n_conn
# Generate all vectors
e_start = np.zeros((n_conn, 3))
e_vec = np.zeros((n_conn, 3))
triu_ix, triu_iy = np.triu_indices(n_node, k=1)
for ii, (ix, iy) in enumerate(zip(triu_ix, triu_iy)):
e_start[ii, :] = node_coords[ix, :]
e_vec[ii, :] = 1e-3 * (node_coords[iy, :] - node_coords[ix, :])
# Import vectors (connections) into pipeline
edg_source = mlab.pipeline.vector_scatter(e_start[:, 0], e_start[:, 1],
e_start[:, 2], e_vec[:, 0],
e_vec[:, 1], e_vec[:, 2])
edg_source.mlab_source.dataset.point_data.scalars = conn_list
edg_thresh = mlab.pipeline.threshold(
edg_source,
low=np.percentile(conn_list, 100 * conn_thr[0]),
up=np.percentile(conn_list, 100 * conn_thr[1]))
edg_thresh.auto_reset_lower = False
edg_thresh.auto_reset_upper = False
edg_surface = mlab.pipeline.vectors(edg_thresh,
colormap=conn_cmap,
line_width=3.0,
scale_factor=1000,
scale_mode='vector')
edg_surface.glyph.glyph.clamping = False
edg_surface.actor.property.opacity = 0.75
edg_surface.module_manager.vector_lut_manager.reverse_lut = True
edg_surface.glyph.glyph_source.glyph_source = (
edg_surface.glyph.glyph_source.glyph_dict['glyph_source2d'])
edg_surface.glyph.glyph_source.glyph_source.glyph_type = 'dash'
def view(prefix, name):
"""
construct a generic visualization of base mesh, refined mesh,
and potential/field/pseudopotential data in mayavi2
requires running within mayavi2 or ipython with threads or
something like::
from pyface.api import GUI
GUI().start_event_loop()
in your script to interact with it.
this is from a simplified macro recorded in mayavi2
"""
try:
engine = mayavi.engine
except NameError:
from mayavi.api import Engine
engine = Engine()
engine.start()
if len(engine.scenes) == 0:
engine.new_scene()
scene = engine.scenes[0]
base_mesh_name = "%s_mesh.vtk" % prefix
if os.access(base_mesh_name, os.R_OK):
base_mesh = engine.open(base_mesh_name)
surface = Surface()
engine.add_filter(surface, base_mesh)
surface.actor.property.representation = 'wireframe'
surface.actor.property.line_width = 1
mesh_name = "%s_%s_mesh.vtk" % (prefix, name)
if os.access(mesh_name, os.R_OK):
mesh = engine.open(mesh_name)
mesh.cell_scalars_name = 'charge'
surface = Surface()
engine.add_filter(surface, mesh)
module_manager = mesh.children[0]
module_manager.scalar_lut_manager.lut_mode = 'RdBu'
module_manager.scalar_lut_manager.use_default_range = False
r = np.fabs(module_manager.scalar_lut_manager.data_range).max()
module_manager.scalar_lut_manager.data_range = [-r, r]
surface.actor.property.backface_culling = True
data_name = "%s_%s.vtk" % (prefix, name)
if os.access(data_name, os.R_OK):
data = engine.open(data_name)
if "pseudo_potential" in data._point_scalars_list:
data.point_scalars_name = "pseudo_potential"
else:
data.point_scalars_name = "potential"
iso_surface = IsoSurface()
engine.add_filter(iso_surface, data)
module_manager = data.children[0]
module_manager.scalar_lut_manager.lut_mode = 'Greys'
iso_surface.contour.auto_contours = True
iso_surface.contour.number_of_contours = 5
try:
iso_surface.contour.maximum_contour = 1e-2
except:
pass
scene.scene.isometric_view()
scene.scene.render()
# Recorded script from Mayavi2
from numpy import array
try:
engine = mayavi.engine
except NameError:
from mayavi.api import Engine
engine = Engine()
engine.start()
if len(engine.scenes) == 0:
engine.new_scene()
# -------------------------------------------
from mayavi.modules.iso_surface import IsoSurface
#vtk_file_reader2 = engine.open(u'/home/m/spammsand/spammsand/water_to_duals/z_15.vtk')
vtk_file_reader2 = engine.open(
u'/home/matcha/Desktop/RESEARCH/spammsand_may_21_2015/spammsand/water_to_duals/z_14.vtk'
)
iso_surface2 = IsoSurface()
engine.add_module(iso_surface2, obj=None)
iso_surface2.actor.mapper.scalar_mode = 'use_field_data'
#iso_surface2.actor.property.specular_color = (0.5019607843137255, 0.5019607843137255, 0.5019607843137255)
#iso_surface2.actor.property.diffuse_color = (0.5019607843137255, 0.5019607843137255, 0.5019607843137255)
#iso_surface2.actor.property.ambient_color = (0.5019607843137255, 0.5019607843137255, 0.5019607843137255)
#iso_surface2.actor.property.color = (0.5019607843137255, 0.5019607843137255, 0.5019607843137255)
iso_surface2.actor.property.specular_color = (1.0, 1.0, 1.0)
iso_surface2.actor.property.diffuse_color = (1.0, 1.0, 1.0)
iso_surface2.actor.property.ambient_color = (1.0, 1.0, 1.0)
class Visualisation(object):
''' Class to visualize vascularNetworks in 3D
using vtk and mayavi to visualize the vascular network and
the area over time. The simulation results data as pressure and Flow
are mapped on the surface of the vessels'''
def __init__(self, vascularNetwork = None):
'''
Constructor of the Visualisation
'''
#dictionarys to save the src and actors
self.vizActors = {}
self.vizSources = {}
self.vizVTKGrids = {}
self.velArrowGrid = {}
self.velArrowSrc = {}
self.glyph = {}
self.vesselLengths = {}
self.vesselN = {}
# Solution data
# is numpyarray within numpyarrays
# control as
# AreaSolution[ vesselID ] [ point in time ]
# scalarSolution[ vesselID ] [ point in time ]
self.areaSolution = None
self.scalarSolution = None
self.scalarNames = None
self.scalarPosition = 0
self.solutionName = None
self.solutionPosition = 0
# set min max for look uptable
self.SourceMin = 0
self.SourceMax = 0
#dimensions | 2 radius (inner outer) | 24 points on circle
# | third dimension N = gridpoints in z axis: not fixed, vessel property
self.dims = [1, 24]
# vascularNetwork
self.vascularNetwork = vascularNetwork
# engine and scene for visualisation
self.engine = Engine()
self.scene = None
# to increase the radius change
# radius(t) = radius0 + deltaRadius * factor
self.factor = 50
# Movie
self.movieBool = False
self.movNumber = 0
self.movPath = None
# update control
self.moveWall = True
self.moveWallOff = False
self.pauseBool = True
self.calls = 0
self.currentTime = 0
self.endTime = None
self.updateTimeStep = 1
# bool for velocity profile
self.vecBool = False
self.powerLawCoefficient = 2.0
self.static = False
# 2 d plot figures
self.figspace = None
self.figtime = None
self.plotSpace = False
self.picked = None
#### init this stuff prob move to another function
self.initialize()
def __del__(self):
'''
Class Destructor
'''
del(self.vascularNetwork)
print " visualisation removed"
#-------------------## public methods##-------------------#
def initialize(self):
'''
Initialize and create a 3D representation of the network
'''
if self.vascularNetwork != None:
gc.enable()
for key,vessel in self.vascularNetwork.vessels.iteritems():
self.vesselLengths[key] = vessel.length
self.vesselN[key] = vessel.N
self.scene = self.engine.new_scene(name = self.vascularNetwork.name)
self.engine.scenes[0].name = str(self.vascularNetwork.name+' - '+'paused')
self.scene.scene.background = (0.0,0.0,0.0)
# start the engine
self.engine.start()
# set cameraposition
self.scene.scene.camera.azimuth(90)
self.scene.scene.camera.roll(90)
# create the initial network
self.createVizData()
# add the initial network
self.scene.scene.disable_render = True
for Id in self.vizSources.iterkeys():
self.engine.add_source(self.vizSources[Id],self.scene)
self.engine.add_module(self.vizActors[Id], obj=self.vizSources[Id])
self.engine.add_source(self.velArrowSrc[Id], self.scene)
self.glyph[Id].actor.actor.visibility = self.vecBool # set bool for visualize the arrows
self.engine.add_module(self.glyph[Id], obj=self.velArrowSrc[Id])
# refit the camera position
self.scene.scene.reset_zoom()
self.scene.scene.disable_render = False
if self.static == False:
# add interactor
self.scene.scene.interactor.add_observer("KeyPressEvent",self.key_press_N)
self.scene.scene.interactor.add_observer("KeyPressEvent",self.key_press_M)
self.scene.scene.interactor.add_observer("KeyPressEvent",self.key_press_B)
self.scene.scene.interactor.add_observer("KeyPressEvent",self.key_press_V)
self.scene.scene.interactor.add_observer("KeyPressEvent",self.key_press_C)
self.scene.scene.interactor.add_observer("KeyPressEvent",self.key_press_X)
self.scene.scene.interactor.add_observer("KeyPressEvent",self.key_press_Y)
self.scene.scene.interactor.add_observer("KeyPressEvent",self.key_press_J)
self.scene.scene.interactor.add_observer("KeyPressEvent",self.key_press_H)
self.scene.scene.interactor.add_observer("KeyPressEvent",self.key_press_U)
self.scene.scene.interactor.add_observer("KeyPressEvent",self.key_press_G)
self.scene.scene.interactor.add_observer("KeyPressEvent",self.key_press_komma)
self.scene.scene.interactor.add_observer("KeyPressEvent",self.key_press_punkt)
#self.scene.mayavi_scene.on_mouse_pick(self.picker_callback)
self.engine.scenes[0].on_mouse_pick(self.picker_callback)
print " ..3d visualisation initialized!"
def setVascularNetwork(self,vascularNetwork):
'''
Set the vascular Network if not set in constructor
and initialize the network
'''
self.vascularNetwork = vascularNetwork
self.initialize()
def setSolutionData(self,solutionData):
'''
Process the solutionData, calculates the velocity and set all needed varibles.
solutionData is a list with dictionarys containing the solution one or several simulation solutions.
solutionData = [ {'Pressure': pressureData, 'Flow': flowData, 'Area': areaData, 'Name': 'solution1' }, ...]
'''
#initialize
self.areaSolution = []
self.scalarSolution = []
self.scalarNames = []
self.solutionName = []
for solution in solutionData:
# save the solution name
currentSolutionName = solution.pop('Name')
#save the scalars of the solution
currentScalars = []
currentScalarNames = []
# transfer pressure to mmHg
Psol = {}
for vesselId,Ptemp in solution['Pressure'].iteritems():
Psol[vesselId] = Ptemp/133.32
currentScalars.append(Psol)
currentScalarNames.append('Pressure')
currentScalars.append(solution.pop('Flow'))
currentScalarNames.append('Flow')
currentScalars.append(solution.pop('Area'))
currentScalarNames.append('Area')
# calculate velocities
velocity = []
for i in range (0,len(currentScalars[1]),1):
vel_t = array([currentScalars[1][i][0]/currentScalars[2][i][0]])
for t in range(1,len(currentScalars[1][i]),1):
v = currentScalars[1][i][t]/currentScalars[2][i][t]
vel_t = append(vel_t,[v],axis = 0)
velocity.append(vel_t)
# set the velocity
currentScalars.append(velocity)
currentScalarNames.append('Velocity')
# check if additional solution data was passed:
for key,value in solution.iteritems():
currentScalars.append(value)
currentScalarNames.append(key)
# save the data in class variables
self.areaSolution.append(currentScalars[2])
self.scalarSolution.append(currentScalars)
self.scalarNames.append(currentScalarNames)
self.solutionName.append(currentSolutionName)
del(currentScalars)
del(currentScalarNames)
del(currentSolutionName)
self.endTime = len(self.areaSolution[self.solutionPosition][0])
self.engine.scenes[0].name = str(self.vascularNetwork.name +' - '+'paused'+' - '+self.solutionName[self.solutionPosition])
print ' .. solution data initialized!'
def visualize(self):
'''
Start the visualisation of the simulation result.
Set up Upgrade method and starts the main loop.
Use only if the simulation result was set!
'''
# update the lookuptables and set them
minL = []
maxL = []
for array in self.scalarSolution[self.solutionPosition][self.scalarPosition].itervalues():
minL.append(array.min())
maxL.append(array.max())
self.SourceMin = min(minL)
self.SourceMax = max(maxL)
for actor in self.vizActors.itervalues():
actor.module_manager.scalar_lut_manager.data_range = [self.SourceMin, self.SourceMax]
#self.vizActors[0].module_manager.scalar_lut_manager.data_name = self.scalarNames[self.solutionPosition][self.scalarPosition]
#self.vizActors[0].module_manager.scalar_lut_manager.show_scalar_bar = True
timer = Timer(0.03, self.update)
gui = GUI()
gui.busy = True
gui.start_event_loop()
def visualizeStatic(self):
gui = GUI()
self.engine.scenes[0].name = str(self.vascularNetwork.name +' - '+'static')
gui.start_event_loop()
def picker_callback(self, picker):
'''
Mouse pick callback, opens a 2D time plot if a vessel is picked; If the plotSpace is activated key "g"
the animated space plot of the vessel is loaded aswell
'''
printOut = ' .. world - picked'
if len(picker.actors) > 0:
picked = picker.actors[0]
for key,value in self.vizActors.iteritems():
if value.actor.actor._vtk_obj == picked._vtk_obj:
self.picked = self.vascularNetwork.vessels[key].name
printOut = str(' .. '+self.vascularNetwork.name +' - '+ self.picked + ' - picked')
string = ' '.join(['python',cur+'/class2dVisualisationSimple.py','-f',self.vascularNetwork.name, '-n 1','-i',str(key)])
subprocess.call(string, shell=True)
# if self.static == False:
#
# if self.figspace is not None and type(self.figspace) is not int:
# self.figspace.clf()
# if self.figtime is not None:
# self.figtime.clf()
#
# networkPlot = NetworkPlot([self.scalarSolution[self.solutionPosition][0][key]],
# [self.scalarSolution[self.solutionPosition][1][key]],
# [self.scalarSolution[self.solutionPosition][2][key]])
#
# #self.figspace,self.figtime = thread.start_new_thread(networkPlot, ({name: self.vascularNetwork.getSimulationDictionary()[name]},
# # 0,1,False,True,True,self.vascularNetwork.simulationContext['totalTime'],True))
# self.figspace,self.figtime = networkPlot(VesselNetwork = {self.picked: self.vascularNetwork.getSimulationDictionary()[key]},
# cutTime=0,CUT=1,plotVelocity=False,plotSpace=self.plotSpace,plotTime=True,
# totaltime = self.vascularNetwork.simulationContext['totalTime'], scaleplot=True)
print printOut
def key_press_G(self,obj,event):
'''
Key event G: enable / disable 2D space plot if vessel is picked
'''
key = obj.GetKeyCode()
if key=='G':
if self.plotSpace == False:
self.plotSpace = True
print " .. 2D space plot enabled"
else:
self.plotSpace = False
print " .. 2D space plot disabled"
elif key=='g':
if self.figtime is not None:
print " .. time plot for ",self.picked," saved"
path = str(cur+'/../network_files/'+self.vascularNetwork.name+'/2dTimePlots/')
if not os.path.exists(path):
os.makedirs(path)
self.figtime.savefig(str(path+self.vascularNetwork.name+'-'+self.solutionName[self.solutionPosition]+'-'+self.picked+'.png'))
def key_press_N(self,obj,event):
'''
Key event n: next lookup table - change the lookup and scalar mapping
'''
key = obj.GetKeyCode()
if key=='n' or key=='N':
self.scalarPosition = self.scalarPosition + 1
if self.scalarPosition == len(self.scalarNames[self.solutionPosition]):
self.scalarPosition = 0
minL = []
maxL = []
for array in self.scalarSolution[self.solutionPosition][self.scalarPosition].itervalues():
minL.append(array.min())
maxL.append(array.max())
self.SourceMin = min(minL)
self.SourceMax = max(maxL)
def key_press_J(self,obj,event):
'''
Key event j: last lookup table - change the lookup and scalar mapping
'''
key = obj.GetKeyCode()
if key=='j' or key=='J':
self.scalarPosition = self.scalarPosition - 1
if self.scalarPosition < 0:
self.scalarPosition = len(self.scalarNames[self.solutionPosition]) - 1
# recalculate the range of the lookuptable ## Note: change this in further version to save memory -> (list)
minL = []
maxL = []
for array in self.scalarSolution[self.solutionPosition][self.scalarPosition].itervalues():
minL.append(array.min())
maxL.append(array.max())
self.SourceMin = min(minL)
self.SourceMax = max(maxL)
def key_press_H(self,obj,event):
'''
Key event h: next solution data - show next soultion data set
'''
key = obj.GetKeyCode()
if key=='h' or key=='H':
self.solutionPosition = self.solutionPosition + 1
if self.solutionPosition == len(self.solutionName):
self.solutionPosition = 0
# recalculate the range of the lookuptable ##
self.scalarPosition = 0
minL = []
maxL = []
for array in self.scalarSolution[self.solutionPosition][self.scalarPosition].itervalues():
minL.append(array.min())
maxL.append(array.max())
self.SourceMin = min(minL)
self.SourceMax = max(maxL)
self.endTime = len(self.areaSolution[self.solutionPosition][0])
#set name of the solution
if self.pauseBool == False: self.engine.scenes[0].name = str(self.vascularNetwork.name +' - '+'paused'+' - '+self.solutionName[self.solutionPosition])
else: self.engine.scenes[0].name = str(self.vascularNetwork.name +' - '+'running'+' - '+'t = 0.000' +' - '+self.solutionName[self.solutionPosition])
#restart simulation
self.currentTime = 0
def key_press_U(self,obj,event):
'''
Key event u: last solution data - show last soultion data set
'''
key = obj.GetKeyCode()
if key=='u' or key=='U':
self.solutionPosition = self.solutionPosition - 1
if self.solutionPosition < 0:
self.solutionPosition = len(self.solutionName) - 1
# recalculate the range of the lookuptable ##
self.scalarPosition = 0
minL = []
maxL = []
for array in self.scalarSolution[self.solutionPosition][self.scalarPosition].itervalues():
minL.append(array.min())
maxL.append(array.max())
self.SourceMin = min(minL)
self.SourceMax = max(maxL)
#set time
self.endTime = len(self.areaSolution[self.solutionPosition][0])
#set name of the solution
if self.pauseBool == False: self.engine.scenes[0].name = str(self.vascularNetwork.name +' - '+'paused'+' - '+self.solutionName[self.solutionPosition])
else: self.engine.scenes[0].name = str(self.vascularNetwork.name +' - '+'running'+' - '+'t = 0.000' +' - '+self.solutionName[self.solutionPosition])
#restart simulation
self.currentTime = 0
def key_press_M(self,obj,event):
'''
Key event m: start saving png for movie
'''
key = obj.GetKeyCode()
if key=='m' or key=='M':
# create movie directory
if self.movPath == None:
self.movPath = str(cur+'/../NetworkFiles/'+self.vascularNetwork.name+'/movieTemplateData/')
if not os.path.exists(str(self.movPath)):
os.makedirs(str(self.movPath))
if self.movieBool == False:
self.movieBool = True
print " .. start creating movie files"
else:
self.movieBool = False
self.movNumber = 0
print " .. stop creating movie files"
def key_press_B(self,obj,event):
'''
Key event B: pause/break the simulation
'''
key = obj.GetKeyCode()
if key=='b' or key=='B':
if self.pauseBool == False:
self.pauseBool = True
self.engine.scenes[0].name = str(self.vascularNetwork.name +' - '+'paused'+' - '+self.solutionName[self.solutionPosition])
else:
self.pauseBool = False
self.engine.scenes[0].name = str(self.vascularNetwork.name +' - '+'running'+' - '+'t = 0.000' +' - '+self.solutionName[self.solutionPosition])
def key_press_V(self,obj,event):
'''
Key event V: open vessels and show vectorfields
'''
key = obj.GetKeyCode()
if key=='v' or key=='V':
if self.vecBool == False:
self.vecBool = True
for glyph in self.glyph.itervalues(): glyph.actor.actor.visibility = self.vecBool
self.scalarPosition = 3
minL = []
maxL = []
for array in self.scalarSolution[self.solutionPosition][self.scalarPosition].itervalues():
minL.append(array.min())
maxL.append(array.max())
self.SourceMin = min(minL)
self.SourceMax = max(maxL)
self.vizActors[0].module_manager.scalar_lut_manager.show_scalar_bar = False
self.glyph[0].module_manager.scalar_lut_manager.data_range = [0, self.SourceMax]
self.glyph[0].module_manager.scalar_lut_manager.show_scalar_bar = True
self.glyph[0].module_manager.scalar_lut_manager.data_name = self.scalarNames[self.solutionPosition][self.scalarPosition]
print " .. velocity profile enabled"
else:
self.vecBool = False
for glyph in self.glyph.itervalues(): glyph.actor.actor.visibility = self.vecBool
print " .. velocity profile disabled"
self.scalarPosition = 3
minL = []
maxL = []
for array in self.scalarSolution[self.solutionPosition][self.scalarPosition].itervalues():
minL.append(array.min())
maxL.append(array.max())
self.SourceMin = min(minL)
self.SourceMax = max(maxL)
self.vizActors[0].module_manager.scalar_lut_manager.data_name = self.scalarNames[self.solutionPosition][3]
self.vizActors[0].module_manager.scalar_lut_manager.show_scalar_bar = True
def key_press_C(self,obj,event):
'''
Key event C: stop/start simulation of the wall movement
'''
key = obj.GetKeyCode()
print key
if key=='c' or key=='C':
if self.moveWall == False:
self.moveWall = True
print " .. wall movement enabled"
else:
self.moveWallOff = True
print " .. wall movement disabled"
def key_press_X(self,obj,event):
'''
Key event X: increase the radius factor
'''
key = obj.GetKeyCode()
if key=='x' or key=='X':
self.factor = self.factor + 1
print " .. radius factor increased to: ",self.factor
def key_press_Y(self,obj,event):
'''
Key event Y: decrease the radius factor
'''
key = obj.GetKeyCode()
if key=='y' or key=='Y' or key=='z' or key=='Z':
if self.factor > 0:
self.factor = self.factor - 1
print " .. radius factor decreased to: ",self.factor
def key_press_komma(self,obj,event):
'''
Key event ,: increase the timestep
'''
key = obj.GetKeyCode()
if key==',' or key==',':
self.updateTimeStep = self.updateTimeStep + 1
print " .. update timestep increased to: ",self.updateTimeStep
def key_press_punkt(self,obj,event):
'''
Key event ,: decrease the timestep
'''
key = obj.GetKeyCode()
if key=='.' or key=='.':
if self.updateTimeStep > 1:
self.updateTimeStep = self.updateTimeStep - 1
print " .. update timestep decreased to: ",self.updateTimeStep
#-------------------## private methods##-------------------#
def update(self):
'''
update function: updates the scene,actors every time it is called
'''
if self.endTime == None:
self.endTime = len(self.areaSolution[self.solutionPosition][0])
if self.pauseBool == False:
Lstart = time.clock()
###start the update
# stop the rendering while updating grids and the piplines
# without mayavi is rendering during the update
# --> updateTime is 10x higher
# --> all vessels are updated at the same time
self.scene.scene.disable_render = True
# to accelerate fist calculat data then apply
TempColor = {}
TempPoints = {}
TempVelPoints = {}
TempVelColor = {}
#create new data
LstartD = time.clock()
for Id in self.vesselLengths.iterkeys():
if self.moveWall == True:
radiusAr = sqrt(self.areaSolution[self.solutionPosition][Id][0]/pi)+(sqrt(self.areaSolution[self.solutionPosition][Id][self.currentTime]/pi)-sqrt(self.areaSolution[self.solutionPosition][Id][0]/pi))*self.factor # calculate the radius from the area
if self.moveWallOff == True:
radiusAr = sqrt(self.areaSolution[self.solutionPosition][Id][0]/pi)
# create points for the vessels
TempPoints[Id] = self.generate_vertices(r_array = radiusAr, length = self.vesselLengths[Id], N = self.vesselN[Id])
# create points for the velocity arrows
TempVelPoints[Id] = self.generate_velocity_points(length = self.vesselLengths[Id], N = self.vesselN[Id], r_array= radiusAr)
# set size and color of the velocity arrows
if self.vecBool == True:
## here the 3 must refer to the velocity!! in scalarSolution
self.scalarPosition = 3
TempVelColor[Id] = self.generate_velocity_colorScalars(velArray = self.scalarSolution[self.solutionPosition][self.scalarPosition][Id][self.currentTime], N = self.vesselN[Id])
if Id == 1:
print self.scalarSolution[self.solutionPosition][self.scalarPosition][Id][self.currentTime][1]
#set the scalar color array to velocity
colorAr = self.scalarSolution[self.solutionPosition][self.scalarPosition][Id][0]
else:
# set the scalar color array to the current choosen
colorAr = self.scalarSolution[self.solutionPosition][self.scalarPosition][Id][self.currentTime]
# create scalar color map
TempColor[Id]= ravel(self.generate_colorScalars(colorAr, N = self.vesselN[Id]))
LendD = time.clock()
#print ' time:', LendD - LstartD
for Id,grid in self.vizVTKGrids.iteritems():
# modify grid of the vizVTKGrid
# create scalar color map
grid.point_data.scalars = TempColor[Id]
grid.point_data.scalars.name = 'scalars'
# create update data if wall movement is enabled
if self.moveWall == True:
grid.points = TempPoints[Id]
# set lut range (necessary)
self.vizActors[Id].module_manager.scalar_lut_manager.data_range = [self.SourceMin, self.SourceMax]
# set lut (for 1 actor is enough
# update velocity vectors
if self.vecBool == True:
for Id,grid in self.velArrowGrid.iteritems():
grid.point_data.scalars = TempVelColor[Id][1]
grid.point_data.scalars.name = 'scalars'
grid.point_data.vectors = TempVelColor[Id][0]
grid.point_data.vectors.name = 'vectors'
self.glyph[Id].glyph.scale_mode = 'scale_by_scalar'
self.glyph[Id].glyph.glyph.range = [0, self.SourceMax]
self.glyph[Id].glyph.color_mode = 'color_by_scalar'
self.glyph[Id].module_manager.scalar_lut_manager.data_range = [0, self.SourceMax]
self.glyph[Id].module_manager.scalar_lut_manager.use_default_range = False
self.glyph[0].module_manager.scalar_lut_manager.show_scalar_bar = True
self.glyph[0].module_manager.scalar_lut_manager.data_name = self.scalarNames[self.solutionPosition][self.scalarPosition]
# update position if they change (wallmovement)
if self.moveWall == True:
grid.points = TempVelPoints[Id]
#else:
#self.vizActors[0].module_manager.scalar_lut_manager.data_name = self.scalarNames[self.solutionPosition][self.scalarPosition]
#self.vizActors[0].module_manager.scalar_lut_manager.show_scalar_bar = True
if self.moveWallOff == True:
self.moveWall = False
self.moveWallOff = False
dt = (self.vascularNetwork.simulationContext['totalTime']/self.endTime)*self.currentTime
self.engine.scenes[0].name = str(self.vascularNetwork.name +' - '+'running'+' - '+'t = %0.4f' %dt+' - '+self.solutionName[self.solutionPosition])
# control the current timeStep
self.currentTime = self.currentTime+self.updateTimeStep
# restart simulation if end reached
if self.currentTime >= self.endTime:
self.currentTime = 0
# if no movie:
if self.movieBool == False:
#start the rendering again
self.scene.scene.disable_render = False
#save pictures for the movies
else:
#thread.start_new_thread(self.scene.scene.save_png,(('../data/temp/'+'movieTemplateData'+str(self.movNumber).zfill(4)+'.png'), ))
Lstart = time.clock()
self.scene.scene.save_png(self.movPath+'movieTemplateData'+str(self.movNumber).zfill(4)+'.png')
Lend = time.clock()
print" needed %1.6f sec to save the picture" %((Lend-Lstart))
self.movNumber = self.movNumber + 1
Lend = time.clock()
#print" update time %1.6f -- framerate: %1.2f -- increase in framerate: %1.2f " %((Lend-Lstart), 1.0/(Lend-Lstart), (1.0/(Lend-Lstart-LendD+LstartD))-(1.0/(Lend-Lstart)))
def generate_vertices(self,length,N,r_array = None,r_init = None):
'''
Calculates vertices of an vessel
either based on radius array with lenght N
or radius init = [radius start, radius end]
'''
N = int(N)
if r_array == None:
r_initA = r_init[0]
r_initB = r_init[1]
r_array = linspace(r_initA, r_initB, N)
# inner wall (not necesarry!)
#ri_array = r_array*array([0.9])
#r = vstack((ri_array,r_array)).transpose()
r = r_array.transpose()
if self.vecBool == False :
thetaFactor = 2
else:
thetaFactor = 1
theta = linspace(pi/2.0, pi/2.0+thetaFactor*pi, self.dims[1])
z = linspace(0, length, N)
## create Points
aLength = self.dims[0]*self.dims[1]
points = empty([aLength*N,3])
start = 0
for z_plane in range(0,len(z),1):
end = start+aLength
plane_points = points[start:end]
plane_points[:,0] = (cos(theta)*r[z_plane]).ravel() # for inner wall add r[z_plane,:][:,None]
plane_points[:,1] = (sin(theta)*r[z_plane]).ravel()
plane_points[:,2] = z[z_plane]
start = end
return points
def generate_colorScalars(self,colorArray, N):
'''
map the values of the colorArray to the points of the grid
'''
# for loop
#colors = array([])
#for z_plane in range(0,int(N),1):
# s_z = linspace(colorArray[z_plane] ,colorArray[z_plane], (self.dims[0]*self.dims[1]))
# colors = hstack((colors,s_z))
# matrix calculation
colors = column_stack(ones(((self.dims[0]*self.dims[1]),int(N)))*colorArray).ravel()
return colors
def generate_velocity_points(self, length, N , r_array = None,r_init = None, numberOfVec = 11):
'''
calculates the points for the velocity arrows of the velocity profil
'''
#numberOfVec should be odd
if r_array == None:
r_initA = r_init[0]
r_initB = r_init[1]
r_array = linspace(r_initA, r_initB, N)
dz = length/N
z = linspace(dz, length-dz, (N-2))
## create Points
aLength = numberOfVec
points = empty([aLength*(N-2),3])
start = 0
for z_plane in range(0,len(z),1):
end = start+aLength
y_plane = linspace(- r_array[z_plane]*0.9, r_array[z_plane]*0.9, numberOfVec)
plane_points = points[start:end]
plane_points[:,0] = 0
plane_points[:,1] = y_plane
plane_points[:,2] = z[z_plane]
start = end
return points
def generate_velocity_colorScalars(self, N, velArray = None, numberOfVec=11):
'''
Map the values of the velocity calculated of the mean velocity to the points of the grid
'''
if velArray == None:
velC = linspace(0.001,0.005,int((N-2)))
else:
velC = delete(velArray,[0,int(N-1)])
profileA = linspace(0.9,0.0,6)
profileB = linspace(0,0.9,6)
prof = append(profileA,profileB)
profile = delete(prof, 6)
#cast N
colorVectors = empty([numberOfVec*(N-2),3])
colorScalars = array([])
count = 0
for z in range(0,int(N-2),1):
for i in range (0,numberOfVec,1):
#velocity profile using powerlaw with n = self.powerLawCoefficient
vel = velC[z]*((self.powerLawCoefficient+2.0)/self.powerLawCoefficient)*(1.0-profile[i]**self.powerLawCoefficient)
# vectors are for direction of the arrows
t = 1.0
if vel != 0:
t = vel/abs(vel)
# scalares determine size and color
vec_i = array([0,0,t*abs(vel)])
colorVectors[count] = vec_i
colorScalars = hstack((colorScalars,[abs(vel)]))
count = count + 1
return [colorVectors,colorScalars]
def createVizData(self):
'''
Creates the actors and sources of the vascular network
parsing through the network as binary tree
using connection of mother and daughter vessels
'''
### INIT
viz = []
vessels = self.vascularNetwork.vessels
root = self.vascularNetwork.root[0]
### root vessel
## find data
#find initial rotation
rootRot = 0.0
if vessels[root].angleToMother != None:
rootRot = vessels[root].angleToMother
#find inital RadiusA
dRadiusA = 0.05
if vessels[root].radiusA != None:
dRadiusA = vessels[root].radiusA
#find inital RadiusB
dRadiusB = dRadiusA
if vessels[root].radiusB != None:
dRadiusB = vessels[root].radiusB
#find length of root
rLength = 1.0
if vessels[root].length != None:
rLength = vessels[root].length
## create visualisation Data
# create the data points
points = self.generate_vertices(r_init=[dRadiusA,dRadiusB],length = rLength, N = self.vesselN[root])
# create scalar color map
col = linspace(0.0, 0.0, self.vesselN[root])
color = self.generate_colorScalars(col, N = self.vesselN[root])
# generate structured grid, data source
self.vizVTKGrids[root] = tvtk.StructuredGrid(dimensions=(self.dims[1], self.dims[0], self.vesselN[root]))
#set data points
self.vizVTKGrids[root].points = points
#set scalar color map
self.vizVTKGrids[root].point_data.scalars = ravel(color)
self.vizVTKGrids[root].point_data.scalars.name = 'scalars' #self.scalarNames[self.scalarPosition]
# create datasource for mayavi
self.vizSources[root] = VTKDataSource(data = self.vizVTKGrids[root])
# create surface actor for the datas ource
self.vizActors[root] = Surface()
self.vizActors[root].actor.actor.position=0,0,0
self.vizActors[root].actor.actor.rotate_x(rootRot)
### create the velocity vector field
# creat gird for the velocity arrows
self.velArrowGrid[root] = tvtk.StructuredGrid(dimensions=(11, 1, self.vesselN[root]))
#set data points
self.velArrowGrid[root].points = self.generate_velocity_points(self.vesselLengths[root], self.vesselN[root], r_init=[dRadiusA,dRadiusB])
#set scalar color map
color = self.generate_velocity_colorScalars(self.vesselN[root])
self.velArrowGrid[root].point_data.vectors = color[0].copy()
self.velArrowGrid[root].point_data.vectors.name = 'vectors'
self.velArrowGrid[root].point_data.scalars = color[1].copy()
self.velArrowGrid[root].point_data.scalars.name = 'scalars'
# create source
self.velArrowSrc[root] = VTKDataSource(data = self.velArrowGrid[root])
# create vectors data
self.glyph[root] = Glyph()
self.glyph[root].glyph.scale_mode = 'scale_by_scalar'
self.glyph[root].glyph.color_mode = 'color_by_scalar'
self.glyph[root].glyph.glyph_source.glyph_source = self.glyph[root].glyph.glyph_source.glyph_dict['arrow_source']
self.glyph[root].glyph.glyph_source.glyph_position = 'tail'
self.glyph[root].glyph.glyph.scale_factor = self.vesselLengths[root] / self.vesselN[root] * 4 / 7
# set position
self.glyph[root].actor.actor.position = 0,0,0
self.glyph[root].actor.actor.rotate_x(rootRot)
viz.append(root)
## set rest of the network
while len(viz) != 0:
# Current left Daughter
currentVessel = viz.pop(0)
#find values of the current mother
moPos = self.vizActors[currentVessel].actor.actor.position
moRot = self.vizActors[currentVessel].actor.actor.orientation[0]
moRotY = self.vizActors[currentVessel].actor.actor.orientation[1]
moLength = 1.0
if vessels[currentVessel].length != None:
moLength = vessels[currentVessel].length
if vessels[currentVessel].radiusB != None:
moRadiusB = vessels[currentVessel].radiusB
elif vessels[currentVessel].radiusA != None:
moRadiusB = vessels[currentVessel].radiusA
else:
moRadiusB = 0.05
#find Daughters
rightDaughter = None
rightDaughter = vessels[currentVessel].rightDaughter
leftDaughter = None
leftDaughter = vessels[currentVessel].leftDaughter
# create left Daughter vessel visualisation
if leftDaughter is not None:
#find length of Daughter
dLength = 1.0
if vessels[leftDaughter].length != None:
dLength = vessels[leftDaughter].length
#find inital RadiusA
dRadiusA = moRadiusB
if vessels[leftDaughter].radiusA != None:
dRadiusA = vessels[leftDaughter].radiusA
#find inital RadiusB
dRadiusB = dRadiusA
if vessels[leftDaughter].radiusB != None:
dRadiusB = vessels[leftDaughter].radiusB
#set rotation
if rightDaughter is not None:
if vessels[leftDaughter].angleToMother is not None:
drot = -moRotY+(1+2/180.0*moRotY)*((1+2/180.0*moRotY)*-vessels[leftDaughter].angleToMother + moRot)
else:
drot = -moRotY+(1+2/180.0*moRotY)*((1+2/180.0*moRotY)*-30.0 + moRot)
else:
drot = moRot
#set z_position
pos_z = moLength*cos(moRot*pi/180)*(1+2/180.0*moRotY)
#set y_position
if moRot != 0.0:
pos_y = -moLength*sin(moRot*pi/180)
else:
pos_y = 0.0
# apply position changes
dpos = moPos[0],moPos[1]+pos_y,moPos[2]+pos_z
## create visualisation Data
# create the data points
points = self.generate_vertices(r_init=[dRadiusA,dRadiusB],length = dLength,N = self.vesselN[leftDaughter])
# create scalar color map
col = linspace(0.0, 0.0, self.vesselN[leftDaughter])
color = self.generate_colorScalars(col, N = self.vesselN[leftDaughter])
# generate structured grid, data source
self.vizVTKGrids[leftDaughter] = tvtk.StructuredGrid(dimensions=(self.dims[1], self.dims[0], self.vesselN[leftDaughter]))
#set data points
self.vizVTKGrids[leftDaughter].points = points
#set scalar color map
self.vizVTKGrids[leftDaughter].point_data.scalars = ravel(color.copy())
self.vizVTKGrids[leftDaughter].point_data.scalars.name = 'scalars' #self.scalarNames[self.scalarPosition]
# create datasource for mayavi
self.vizSources[leftDaughter] = VTKDataSource(data = self.vizVTKGrids[leftDaughter])
# create surface actor for the datas ource
self.vizActors[leftDaughter] = Surface()
self.vizActors[leftDaughter].actor.actor.position = dpos
self.vizActors[leftDaughter].actor.actor.rotate_x(drot)
## set arrows
self.velArrowGrid[leftDaughter] = tvtk.StructuredGrid(dimensions=(11, 1, self.vesselN[leftDaughter]))
#set data points
self.velArrowGrid[leftDaughter].points = self.generate_velocity_points(self.vesselLengths[leftDaughter], self.vesselN[leftDaughter], r_init=[dRadiusA,dRadiusB])
#set scalar color map
color = self.generate_velocity_colorScalars(self.vesselN[leftDaughter])
self.velArrowGrid[leftDaughter].point_data.vectors = color[0].copy()
self.velArrowGrid[leftDaughter].point_data.vectors.name = 'vectors'
self.velArrowGrid[leftDaughter].point_data.scalars = color[1].copy()
self.velArrowGrid[leftDaughter].point_data.scalars.name = 'scalars'
# create source
self.velArrowSrc[leftDaughter] = VTKDataSource(data = self.velArrowGrid[leftDaughter])
# create vectors data
self.glyph[leftDaughter] = Glyph()
self.glyph[leftDaughter].glyph.scale_mode = 'scale_by_scalar'
self.glyph[leftDaughter].glyph.color_mode = 'color_by_scalar'
self.glyph[leftDaughter].glyph.glyph_source.glyph_source = self.glyph[leftDaughter].glyph.glyph_source.glyph_dict['arrow_source']
self.glyph[leftDaughter].glyph.glyph_source.glyph_position = 'tail'
self.glyph[leftDaughter].glyph.glyph.scale_factor = self.vesselLengths[leftDaughter] / self.vesselN[leftDaughter] * 4 / 7
# set position
self.glyph[leftDaughter].actor.actor.position = dpos
self.glyph[leftDaughter].actor.actor.rotate_x(drot)
#check for children
if vessels[leftDaughter].leftDaughter is not None:
viz.append(leftDaughter)
# right Daughter (only if left Daughter)
if rightDaughter is not None:
#find length of Daughter
dLength = 1.0
if vessels[rightDaughter].length != None:
dLength = vessels[rightDaughter].length
#find inital RadiusA
dRadiusA = moRadiusB
if vessels[rightDaughter].radiusA != None:
dRadiusA = vessels[rightDaughter].radiusA
#find inital RadiusB
dRadiusB = dRadiusA
if vessels[rightDaughter].radiusB != None:
dRadiusB = vessels[rightDaughter].radiusB
# set values
if vessels[rightDaughter].angleToMother is not None:
drot = -moRotY+(1+2/180.0*moRotY)*( (1+2/180.0*moRotY)*vessels[rightDaughter].angleToMother + moRot)
else:
drot = -moRotY+(1+2/180.0*moRotY)*((1+2/180.0*moRotY)*30.0 + moRot)
# set z position
pos_z = moLength*cos(moRot*pi/180)*(1+2/180.0*moRotY) # truns with 180 degree
#set rotation
if moRot != 0:
pos_y = -moLength*sin(moRot*pi/180)
else:
pos_y = 0.0
dpos = moPos[0],moPos[1]+pos_y,moPos[2]+pos_z
## create visualisation Data
# create the data points
points = self.generate_vertices(r_init=[dRadiusA,dRadiusB],length = dLength,N = self.vesselN[rightDaughter])
# create scalar color map
col = linspace(0.0, 0.0, self.vesselN[rightDaughter])
color = self.generate_colorScalars(col, N = self.vesselN[rightDaughter])
# generate structured grid, data source
self.vizVTKGrids[rightDaughter] = tvtk.StructuredGrid(dimensions=(self.dims[1], self.dims[0], self.vesselN[rightDaughter]))
#set data points
self.vizVTKGrids[rightDaughter].points = points
#set scalar color map
self.vizVTKGrids[rightDaughter].point_data.scalars = ravel(color.copy())
self.vizVTKGrids[rightDaughter].point_data.scalars.name = 'scalars' #self.scalarNames[self.scalarPosition]
# create datasource for mayavi
self.vizSources[rightDaughter] = VTKDataSource(data = self.vizVTKGrids[rightDaughter])
# create surface actor for the datas ource
self.vizActors[rightDaughter] = Surface()
self.vizActors[rightDaughter].actor.actor.position = dpos
self.vizActors[rightDaughter].actor.actor.rotate_x(drot)
self.velArrowGrid[rightDaughter] = tvtk.StructuredGrid(dimensions=(11, 1, self.vesselN[rightDaughter]))
#set data points
self.velArrowGrid[rightDaughter].points = self.generate_velocity_points(self.vesselLengths[rightDaughter], self.vesselN[rightDaughter], r_init=[dRadiusA,dRadiusB])
#set scalar color map
color = self.generate_velocity_colorScalars(self.vesselN[rightDaughter])
self.velArrowGrid[rightDaughter].point_data.vectors = color[0].copy()
self.velArrowGrid[rightDaughter].point_data.vectors.name = 'vectors'
self.velArrowGrid[rightDaughter].point_data.scalars = color[1].copy()
self.velArrowGrid[rightDaughter].point_data.scalars.name = 'scalars'
# create source
self.velArrowSrc[rightDaughter] = VTKDataSource(data = self.velArrowGrid[rightDaughter])
# create vectors data
self.glyph[rightDaughter] = Glyph()
self.glyph[rightDaughter].glyph.scale_mode = 'scale_by_scalar'
self.glyph[rightDaughter].glyph.color_mode = 'color_by_scalar'
self.glyph[rightDaughter].glyph.glyph_source.glyph_source = self.glyph[rightDaughter].glyph.glyph_source.glyph_dict['arrow_source']
self.glyph[rightDaughter].glyph.glyph_source.glyph_position = 'tail'
self.glyph[rightDaughter].glyph.glyph.scale_factor = self.vesselLengths[rightDaughter] / self.vesselN[rightDaughter] * 4 / 7
# set position
self.glyph[rightDaughter].actor.actor.position = dpos
self.glyph[rightDaughter].actor.actor.rotate_x(drot)
# check for children
if vessels[rightDaughter].leftDaughter is not None:
viz.append(rightDaughter)
def getFrames(pathThresh, pathSkel, totalTime, fps=24, totalRotation=360):
"""
Return 3 vertex clique removed graph
Parameters
----------
pathThresh : str
path of the .npy thresholded 3D Volume
pathSKel : str
path of the .npy skeleton 3D Volume
totalTime : integer
in seconds, duration of the video
fps : integer
frames per second, number of input frames per second
totalRotation : integer
angle in degrees frames should be captured in, integer between 0 and 360
Returns
-------
frames of png images in the same directory as pathThresh
mayavi scenes are saved as png images at different
angle of rotations as anim%i.png i is the ith frame
Notes
-----
threshold and skeletonized volume are overlapped,
they need not be of the same size, but assuming they are
for the same volume it asserted that they are of same size
thresholded volume's isosurface is transparent and
in grey and the skeletonized volume can be seen through
it and is in red
totalRotation can be any angle but it will be adjusted between 0 and
360 using the % (modulus) operator
"""
# modulus of totalRotation
totalRotation = totalRotation % 360
# total frames
totalFrameCount = fps * totalTime
# degree of rotation after each frame
degreePerFrame = totalRotation / totalFrameCount
# load the threshold and skeleton paths
threshold = np.load(pathThresh)
skeleton = np.load(pathSkel)
assertionStr = "threshold and skeleton must be of same shape"
assert threshold.shape == skeleton.shape, (assertionStr, threshold.shape, skeleton.shape)
mayaviEngine = Engine()
mayaviEngine.start()
# Create a new mayavi scene.
mayaviScene = mayaviEngine.new_scene()
mayaviScene.scene.background = WHITEBACKGROUND
# thresholded image in transparent grey
thresholdScene = mlab.contour3d(np.uint8(threshold), colormap='gray', contours=THRESHOLDCONTOURLIST)
thresholdScene.actor.property.opacity = THRESHOLDSCENEOPACITY
# skeleton in red
f = mlab.contour3d(np.uint8(skeleton), contours=SKELETONCONTOURLIST)
f.actor.property.representation = 'points'
f.actor.property.point_size = POINTSSIZE
mlab.options.offscreen = True
mlab.outline(f).actor.property.color = BOUNDINGBOXCOLOR
# extract rootDir of pathThresh
rootDir = os.path.split(pathThresh)[0] + os.sep
# Make an animation:
for i in range(totalFrameCount):
# Rotate the camera by 10 degrees.
mayaviScene.scene.camera.azimuth(degreePerFrame)
mayaviScene.scene.camera.elevation(ELEVATIONANGLE)
# Resets the camera clipping plane so everything fits and then
# renders.
mayaviScene.scene.reset_zoom()
# Save the scene. magnification=4 gives saves as an image when seen in fullscreen
mayaviScene.scene.magnification = 4
mayaviScene.scene.save(rootDir + "anim%d.png" % i)
class TubePlot:
"""
Class to generate pretty 3d pictures of polymers, based on inputted polymer coordinates.
"""
def __init__(self, polymer_coordinates, color_scheme='dark'):
self.engine = Engine()
self.engine.start()
self.engine.new_scene()
self.scene = self.engine.current_scene
assert color_scheme in ('dark', 'light') # we right now only have two color schemes
self.color_scheme = color_scheme
self.polymer_coordinates = polymer_coordinates
self.L = self.get_polymer_length()
self.set_colors()
self.make_new_fig()
def __enter__(self):
return self
def __exit__(self, exc_type, exc_val, exc_tb):
mlab.clf()
mlab.close()
@staticmethod
def _hex_to_rgb_(val):
return tuple(int(val.lstrip('#')[i:i + 2], 16) / 256 for i in (0, 2, 4))
def set_colors(self):
"""
Based on the private variable self.color_scheme this method sets various other private variables such as the polymer color etc.
"""
if self.color_scheme == 'dark':
self.color_polymer = (.8, .8, .8)
else:
self.color_polymer = (.5, .5, .5)
def make_new_fig(self):
"""
Constructs a figure object with the correct background color based on the color scheme.
"""
mlab.figure(figure=self.scene).scene.background = (.1, .1, .1) if self.color_scheme == 'dark' else (1., 1., 1.)
def get_polymer_length(self):
"""
:return: Length of the polymer, of type integer. Based on the raw_attributes.
"""
return len(self.polymer_coordinates)
@staticmethod
def make_coordinates_circular(coordinates):
"""
Add a coordinate at the end that is equal to the first coordinate.
:param coordinates: Nx3 numpy array of coordinates in space
"""
return np.concatenate([coordinates, [coordinates[0, :]]]) # add the first coordinate for constructing a circular interpolation
@staticmethod
def translate_coordinates_by_center_of_mass(coordinates):
"""
Returns coordinates displaced by their center of mass
:param coordinates: Nx3 numpy array of integer coordinates
:returns: Nx3 numpy array of displaced coordinates
"""
return coordinates - np.mean(coordinates, axis=0, dtype=int)
@staticmethod
def compute_interpolation(coordinates, interpolation_factor=20):
"""
Returns an interpolated version of the :param coordinates.
:param coordinates: Nx3 numpy array of coordinates in space
:param interpolation_factor: Number of coordinates to return per input coordinate (sets degree of smoothness for the interpolation)
:returns: N*interpolation x 3 numpy array of coordinates, where now the last coordinate is equal to the first
"""
# circular_coordinates = self.make_coordinates_circular(coordinates)
n = len(coordinates)
N = interpolation_factor * n
t_old = np.arange(n)
f = interpolate.interp1d(t_old, coordinates, axis=0, kind='cubic')
t_new = np.linspace(0, n - 1, num=N, endpoint=True)
return f(t_new)
def draw_tube(self, coordinates, color=None, opacity=1., tube_radius=0.5):
"""
Draws a Mayavi tubeplot on the canvas. Coordinates are retrieved using a different method in this same class.
"""
mlab.plot3d(coordinates[:, 0], coordinates[:, 1], coordinates[:, 2], np.abs(2*np.arange(-len(coordinates)/2,+len(coordinates)/2))/len(coordinates), tube_radius=tube_radius, tube_sides=40, opacity=opacity, colormap='Spectral', figure=self.scene)
def draw_all(self):
"""
Draw polymer, proteins, origin, terminus etc.
"""
coordinates = self.polymer_coordinates
coordinates_circular = self.make_coordinates_circular(coordinates)
coordinates_interpolated = self.compute_interpolation(coordinates_circular)
self.draw_tube(coordinates_interpolated)
def add_text(self, string):
"""
Adds some interesting text to the current mayavi-canvas.
:param string: String to put in the image
"""
c = (1.,1.,1.) if self.color_scheme == 'dark' else (0.,0.,0.)
mlab.text(0.025,0.025, string, color=c, width=0.3)