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)
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)
iso_surface2.actor.property.color = (1.0, 1.0, 1.0)
iso_surface2.actor.property.opacity = 0.3
iso_surface2.contour.contours[0:1] = [0.01]
def plot(self):
'''
Plot a 3D visualisation of the Voronoi grid using mayavi.
This method requires mayavi to be installed and also needs the vertices
information to be available (see the class constructor).
Note that in order for this method to work in an interactive IPython session,
a series of environment variables and proper switches need to be used
depending on your system configuration. For instance, on a Linux machine
with PyQt4 and a recent IPython version, the following bash startup
command for IPython can be used:
``ETS_TOOLKIT=qt4 QT_API=pyqt ipython --gui=qt4``
This sets both the mayavi and the IPython GUI toolkit to qt4, and the ``QT_API``
variable is used to specify that we want the ``pyqt`` API (as opposed to the
``pyside`` alternative API - PySide is an alternative implementation of PyQt).
It should be possible to get this method working on different configurations,
but the details will be highly system-dependent.
'''
if not self._with_vertices:
raise ValueError(
'the class must be constructed with \'with_vertices=True\' in order to support plotting'
)
import numpy as np
try:
from tvtk.api import tvtk
from mayavi.api import Engine
from mayavi import mlab
from mayavi.sources.vtk_data_source import VTKDataSource
from mayavi.modules.surface import Surface
from mayavi.modules.scalar_cut_plane import ScalarCutPlane
except ImportError:
raise ImportError(
'the plot method requires Mayavi, please make sure it is correctly installed'
)
# Shortcut.
vertices = self._neighbours_table['vertices']
# This is a list of all the vertices composing all voronoi cells.
# points = [[x1,y1,z1],[x2,y2,z2],...]
points = []
# Array to describe each voronoi cell in terms of the points list above. E.g.,
# cells = [4,0,1,2,3,5,4,5,6,7,8]
# This describes two cells, the first with 4 vertices whose indices in the points array
# are 0,1,2,3, the second with 5 vertices whose indices are 4,5,6,7,8.
cells = []
cur_cell_idx = 0
# Indices in the cells array where each new cell starts. In the example above,
# offset = [0,5]
offset = []
cur_offset = 0
# Array of cell types. Cells will all be of the same type.
cell_types = []
# Build the above quantities.
for v in vertices:
# Drop the empty vertices coordinates, signalled by NaN.
arr = v[~np.isnan(v)]
assert (len(arr) % 3 == 0)
tmp = np.split(arr, len(arr) / 3)
# Append the vertices.
points = points + tmp
# Append the cell description.
cells = cells + \
[len(tmp)] + range(cur_cell_idx, cur_cell_idx + len(tmp))
cur_cell_idx += len(tmp)
# Append the offset info.
offset.append(cur_offset)
cur_offset += len(tmp) + 1
# Append the cell type.
cell_types.append(tvtk.ConvexPointSet().cell_type)
# Cache the sites' positions.
sites_arr = self._neighbours_table['coordinates']
# Setup the Mayavi engine and figure.
e = Engine()
e.start()
fig = mlab.figure(engine=e)
# Plot the sites.
mlab.points3d(sites_arr[:, 0],
sites_arr[:, 1],
sites_arr[:, 2],
figure=fig)
# Plot the cells with coloured surfaces.
# This is just an array of scalars to assign a "temperature" to each cell vertex, which will be
# used for coloring purposes.
temperature = np.arange(0, len(points) * 10, 10, 'd')
# Initialise the array of cells.
cell_array = tvtk.CellArray()
cell_array.set_cells(len(vertices), np.array(cells))
# Initialise the unstructured grid object.
ug = tvtk.UnstructuredGrid(points=np.array(points))
ug.set_cells(np.array(cell_types), np.array(offset), cell_array)
ug.point_data.scalars = temperature
ug.point_data.scalars.name = 'temperature'
# Create a data source from the unstructured grid object.
src = VTKDataSource(data=ug)
# Add the source to the engine.
e.add_source(src)
# Create a surface object with opacity 0.5
surf = Surface()
surf.actor.property.opacity = 0.5
# Add the surface object to the engine.
e.add_module(surf)
# Add a cut plane as well.
e.add_module(ScalarCutPlane())
# Create another representation of the grid, this time using only white wireframe
# to highlight to shape of the cells.
# Rebuild the ug.
ug = tvtk.UnstructuredGrid(points=np.array(points))
ug.set_cells(np.array(cell_types), np.array(offset), cell_array)
src = VTKDataSource(data=ug)
e.add_source(src)
surf = Surface()
surf.actor.property.representation = 'wireframe'
e.add_module(surf)
cp = ScalarCutPlane()
e.add_module(cp)
image_plane_widget.ipw.point1 = array([ 1. , 128.5, 0.5]) image_plane_widget.ipw.point2 = array([ 1. , 0.5, 128.5]) image_plane_widget.ipw.origin = array([ 1. , 0.5, 0.5]) image_plane_widget.ipw.point1 = array([ 1. , 128.5, 0.5]) image_plane_widget.ipw.point2 = array([ 1. , 0.5, 128.5]) scene.scene.show_axes = True scene.scene.camera.position = [486.97762996578587, 32.807552030816318, 127.31721271939678] scene.scene.camera.focal_point = [64.5, 64.5, 64.5] scene.scene.camera.view_angle = 30.0 scene.scene.camera.view_up = [-0.16242997732460931, -0.57282261680926339, 0.80342439105252128] scene.scene.camera.clipping_range = [270.27987283787792, 628.23960958969758] scene.scene.camera.compute_view_plane_normal() scene.scene.render() from mayavi.core.module_manager import ModuleManager module_manager3 = ModuleManager() engine.add_module(module_manager3, obj=None) module_manager3.scalar_lut_manager.reverse_lut = True module_manager3.scalar_lut_manager.reverse_lut = False module_manager3.scalar_lut_manager.reverse_lut = True module_manager3.scalar_lut_manager.reverse_lut = False array_source2 = engine.scenes[0].children[2] array_source2.children[1:2] = [] module_manager4 = ModuleManager() engine.add_module(module_manager4, obj=None) array_source = engine.scenes[0].children[0] array_source.children[1:2] = [] from mayavi.modules.axes import Axes axes = Axes() module_manager = engine.scenes[0].children[0].children[0] engine.add_filter(axes, module_manager)
import numpy as np
from mayavi.mlab import *
from mayavi.modules.contour_grid_plane import ContourGridPlane
def mytest_contour3d(trans):
x, y, z = np.ogrid[-5:5:64j, -5:5:64j, -5:5:64j]
scalars = x * x * 0.5 + y * y + z * z * 2.0
obj = contour3d(scalars, contours=4, transparent=trans, opacity=1)
return obj
from mayavi.api import Engine
engine = Engine()
engine.start()
if len(engine.scenes) == 0:
engine.new_scene()
# --------------------------
engine.new_scene()
a = mytest_contour3d(False)
cgp = ContourGridPlane()
engine.add_module(cgp)
cgp.grid_plane.axis = 'y'
show()
def plot(self):
'''
Plot a 3D visualisation of the Voronoi grid using mayavi.
This method requires mayavi to be installed and also needs the vertices
information to be available (see the class constructor).
Note that in order for this method to work in an interactive IPython session,
a series of environment variables and proper switches need to be used
depending on your system configuration. For instance, on a Linux machine
with PyQt4 and a recent IPython version, the following bash startup
command for IPython can be used:
``ETS_TOOLKIT=qt4 QT_API=pyqt ipython --gui=qt4``
This sets both the mayavi and the IPython GUI toolkit to qt4, and the ``QT_API``
variable is used to specify that we want the ``pyqt`` API (as opposed to the
``pyside`` alternative API - PySide is an alternative implementation of PyQt).
It should be possible to get this method working on different configurations,
but the details will be highly system-dependent.
'''
if not self._with_vertices:
raise ValueError(
'the class must be constructed with \'with_vertices=True\' in order to support plotting')
import numpy as np
try:
from tvtk.api import tvtk
from mayavi.api import Engine
from mayavi import mlab
from mayavi.sources.vtk_data_source import VTKDataSource
from mayavi.modules.surface import Surface
from mayavi.modules.scalar_cut_plane import ScalarCutPlane
except ImportError:
raise ImportError(
'the plot method requires Mayavi, please make sure it is correctly installed')
# Shortcut.
vertices = self._neighbours_table['vertices']
# This is a list of all the vertices composing all voronoi cells.
# points = [[x1,y1,z1],[x2,y2,z2],...]
points = []
# Array to describe each voronoi cell in terms of the points list above. E.g.,
# cells = [4,0,1,2,3,5,4,5,6,7,8]
# This describes two cells, the first with 4 vertices whose indices in the points array
# are 0,1,2,3, the second with 5 vertices whose indices are 4,5,6,7,8.
cells = []
cur_cell_idx = 0
# Indices in the cells array where each new cell starts. In the example above,
# offset = [0,5]
offset = []
cur_offset = 0
# Array of cell types. Cells will all be of the same type.
cell_types = []
# Build the above quantities.
for v in vertices:
# Drop the empty vertices coordinates, signalled by NaN.
arr = v[~np.isnan(v)]
assert(len(arr) % 3 == 0)
tmp = np.split(arr, len(arr) / 3)
# Append the vertices.
points = points + tmp
# Append the cell description.
cells = cells + \
[len(tmp)] + range(cur_cell_idx, cur_cell_idx + len(tmp))
cur_cell_idx += len(tmp)
# Append the offset info.
offset.append(cur_offset)
cur_offset += len(tmp) + 1
# Append the cell type.
cell_types.append(tvtk.ConvexPointSet().cell_type)
# Cache the sites' positions.
sites_arr = self._neighbours_table['coordinates']
# Setup the Mayavi engine and figure.
e = Engine()
e.start()
fig = mlab.figure(engine=e)
# Plot the sites.
mlab.points3d(
sites_arr[:, 0], sites_arr[:, 1], sites_arr[:, 2], figure=fig)
# Plot the cells with coloured surfaces.
# This is just an array of scalars to assign a "temperature" to each cell vertex, which will be
# used for coloring purposes.
temperature = np.arange(0, len(points) * 10, 10, 'd')
# Initialise the array of cells.
cell_array = tvtk.CellArray()
cell_array.set_cells(len(vertices), np.array(cells))
# Initialise the unstructured grid object.
ug = tvtk.UnstructuredGrid(points=np.array(points))
ug.set_cells(np.array(cell_types), np.array(offset), cell_array)
ug.point_data.scalars = temperature
ug.point_data.scalars.name = 'temperature'
# Create a data source from the unstructured grid object.
src = VTKDataSource(data=ug)
# Add the source to the engine.
e.add_source(src)
# Create a surface object with opacity 0.5
surf = Surface()
surf.actor.property.opacity = 0.5
# Add the surface object to the engine.
e.add_module(surf)
# Add a cut plane as well.
e.add_module(ScalarCutPlane())
# Create another representation of the grid, this time using only white wireframe
# to highlight to shape of the cells.
# Rebuild the ug.
ug = tvtk.UnstructuredGrid(points=np.array(points))
ug.set_cells(np.array(cell_types), np.array(offset), cell_array)
src = VTKDataSource(data=ug)
e.add_source(src)
surf = Surface()
surf.actor.property.representation = 'wireframe'
e.add_module(surf)
cp = ScalarCutPlane()
e.add_module(cp)
image_plane_widget.ipw.point2 = array([1., 0.5, 128.5])
scene.scene.show_axes = True
scene.scene.camera.position = [
486.97762996578587, 32.807552030816318, 127.31721271939678
]
scene.scene.camera.focal_point = [64.5, 64.5, 64.5]
scene.scene.camera.view_angle = 30.0
scene.scene.camera.view_up = [
-0.16242997732460931, -0.57282261680926339, 0.80342439105252128
]
scene.scene.camera.clipping_range = [270.27987283787792, 628.23960958969758]
scene.scene.camera.compute_view_plane_normal()
scene.scene.render()
from mayavi.core.module_manager import ModuleManager
module_manager3 = ModuleManager()
engine.add_module(module_manager3, obj=None)
module_manager3.scalar_lut_manager.reverse_lut = True
module_manager3.scalar_lut_manager.reverse_lut = False
module_manager3.scalar_lut_manager.reverse_lut = True
module_manager3.scalar_lut_manager.reverse_lut = False
array_source2 = engine.scenes[0].children[2]
array_source2.children[1:2] = []
module_manager4 = ModuleManager()
engine.add_module(module_manager4, obj=None)
array_source = engine.scenes[0].children[0]
array_source.children[1:2] = []
from mayavi.modules.axes import Axes
axes = Axes()
module_manager = engine.scenes[0].children[0].children[0]
engine.add_filter(axes, module_manager)
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)
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_6311gss_duals/z_15.vtk')
##vtk_file_reader2 = engine.open(u'/home/matcha/Desktop/RESEARCH/spammsand_may_10_2015/spammsand/350_6311gss/z_12.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)
iso_surface2.actor.property.color = (1.0, 1.0, 1.0)
iso_surface2.actor.property.opacity = 0.3
iso_surface2.contour.contours[0:1] = [0.01]
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 plotIsosurfaces3D(x3D,
y3D,
z3D,
surface3Dlist,
contourList,
slice3Dlist=(None, ),
boundSurface=(None, ),
customColors=(None, ),
figDir='./',
name='UntitledIsosurface',
sliceOriantations=(None, ),
sliceOffsets=(None, ),
boundSlice=(None, ),
sliceValRange=(None, )):
from mayavi import mlab
from mayavi.modules.contour_grid_plane import ContourGridPlane
from mayavi.modules.outline import Outline
from mayavi.api import Engine
import numpy as np
from warnings import warn
x3D, y3D, z3D = np.array(x3D), np.array(y3D), np.array(z3D)
engine = Engine()
engine.start()
# if len(engine.scenes) == 0:
# engine.new_scene()
if customColors[0] is not None:
customColors = iter(customColors)
else:
customColors = iter(
('inferno', 'viridis', 'coolwarm', 'Reds', 'Blues') * 2)
contourList = iter(contourList)
if sliceOriantations[0] is not None:
sliceOriantations = iter(sliceOriantations)
else:
sliceOriantations = iter(('z_axes', ) * len(slice3Dlist))
if boundSurface[0] is None:
boundSurface = (x3D.min(), x3D.max(), y3D.min(), y3D.max(), z3D.min(),
z3D.max())
if boundSlice[0] is None:
boundSlice = (x3D.min(), x3D.max(), y3D.min(), y3D.max(), z3D.min(),
z3D.max())
if sliceOffsets[0] is None:
sliceOffsets = iter((0, ) * len(slice3Dlist))
else:
sliceOffsets = iter(sliceOffsets)
if sliceValRange[0] is None:
sliceValRange = iter((None, None) * len(slice3Dlist))
else:
sliceValRange = iter(sliceValRange)
mlab.figure(name,
engine=engine,
size=(1200, 900),
bgcolor=(1, 1, 1),
fgcolor=(0.5, 0.5, 0.5))
for surface3D in surface3Dlist:
color = next(customColors)
# If a colormap given
if isinstance(color, str):
mlab.contour3d(x3D,
y3D,
z3D,
surface3D,
contours=next(contourList),
colormap=color,
extent=boundSurface)
# If only one color of (0-1, 0-1, 0-1) given
else:
mlab.contour3d(x3D,
y3D,
z3D,
surface3D,
contours=next(contourList),
color=color,
extent=boundSurface)
# cgp = ContourGridPlane()
# engine.add_module(cgp)
# cgp.grid_plane.axis = 'y'
# cgp.grid_plane.position = x3D.shape[1] - 1
# cgp.contour.number_of_contours = 20
# # contour_grid_plane2.actor.mapper.scalar_range = array([298., 302.])
# # contour_grid_plane2.actor.mapper.progress = 1.0
# # contour_grid_plane2.actor.mapper.scalar_mode = 'use_cell_data'
# cgp.contour.filled_contours = True
# cgp.actor.property.lighting = False
for slice3D in slice3Dlist:
sliceOriantation = next(sliceOriantations)
sliceOffset = next(sliceOffsets)
if sliceOriantation == 'z_axes':
origin = np.array([boundSlice[0], boundSlice[2], sliceOffset])
point1 = np.array([boundSlice[1], boundSlice[2], sliceOffset])
point2 = np.array([boundSlice[0], boundSlice[3], sliceOffset])
elif sliceOriantation == 'x_axes':
origin = np.array([sliceOffset, boundSlice[2], boundSlice[4]])
point1 = np.array([sliceOffset, boundSlice[3], boundSlice[4]])
point2 = np.array([sliceOffset, boundSlice[2], boundSlice[5]])
else:
origin = np.array([boundSlice[0], sliceOffset, boundSlice[4]])
point1 = np.array([boundSlice[1], sliceOffset, boundSlice[4]])
point2 = np.array([boundSlice[0], sliceOffset, boundSlice[5]])
image_plane_widget = mlab.volume_slice(
x3D,
y3D,
z3D,
slice3D,
plane_orientation=sliceOriantation,
colormap=next(customColors),
vmin=next(sliceValRange),
vmax=next(sliceValRange))
image_plane_widget.ipw.reslice_interpolate = 'cubic'
image_plane_widget.ipw.origin = origin
image_plane_widget.ipw.point1 = point1
image_plane_widget.ipw.point2 = point2
# image_plane_widget.ipw.slice_index = 2
image_plane_widget.ipw.slice_position = sliceOffset
# Contour grid plane at last y if the last slice is in xy plane
if sliceOriantation == 'z_axes':
cgp2 = ContourGridPlane()
engine.add_module(cgp2)
cgp2.grid_plane.axis = 'y'
cgp2.grid_plane.position = x3D.shape[1] - 1
cgp2.contour.number_of_contours = 20
cgp2.contour.filled_contours = True
cgp2.actor.property.lighting = False
outline = Outline()
engine.add_module(outline)
outline.actor.property.color = (0.2, 0.2, 0.2)
outline.bounds = np.array(boundSurface)
outline.manual_bounds = True
mlab.view(azimuth=270, elevation=45)
mlab.move(-500, 0, 0)
mlab.savefig(figDir + '/' + name + '.png', magnification=3)
print('\nFigure ' + name + ' saved at ' + figDir)
mlab.show()
# In[5]:
r.initialize('heart.vtk')
e.add_source(r)
# In[6]:
from mayavi.modules import api
# In[7]:
o = api.Outline()
# In[8]:
e.add_module(o)
# In[9]:
cgp = api.ContourGridPlane()
e.add_module(cgp)
# In[10]:
cgp.grid_plane.axis = 'x'
# In[11]:
# get_ipython().set_next_input(u'iso = api.IsoSurface');get_ipython().magic(u'pinfo api.IsoSurface')
# In[12]:
#
#src = mlab.pipeline.scalar_field(s)
#mlab.pipeline.iso_surface(src, contours=[s.min()+0.1*s.ptp(), ], opacity=0.3)
#mlab.pipeline.iso_surface(src, contours=[s.max()-0.1*s.ptp(), ],)
def minc_reader(fname):
#Reader for .mnc files.
#Parameters:
#fname -- Filename to be read.
from tvtk.api import tvtk
from mayavi.sources.vtk_data_source import VTKDataSource
r = tvtk.MINCImageReader(file_name=fname)
r.update()
src = VTKDataSource(data=r.output)
print src.data
return src
from mayavi.api import Engine
e = Engine()
e.start()
s = e.new_scene()
source = minc_reader('/home/sulantha/Downloads/new_temp.mnc')
e.add_source(source)
from mayavi.modules.api import Surface
surf = Surface()
e.add_module(surf, obj=source)
mlab.show()