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visio.py
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visio.py
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#!/usr/bin/env python
import os
os.environ['ETS_TOOLKIT'] = 'qt4'
import logging
logger = logging.getLogger(__name__)
from pyface.qt import QtGui, QtCore
from PyQt4 import uic
from traits.api import HasTraits, Instance, on_trait_change, \
Int, Dict
from traitsui.api import View, Item
from mayavi.core.ui.api import MayaviScene, MlabSceneModel, \
SceneEditor
import numpy as np
from mayavi import mlab
#mlab.options.backend = 'envisage'
from neuron import h
################################################################################
#The actual visualization
class Visualization(HasTraits):
scene = Instance(MlabSceneModel, ())
@on_trait_change('scene.activated')
def update_plot(self):
# This function is called when the view is opened. We don't
# populate the scene when the view is not yet open, as some
# VTK features require a GLContext.
# We can do normal mlab calls on the embedded scene.
# self.scene.mlab.test_points3d()
pass
# the layout of the dialog screated
view = View(Item('scene', editor=SceneEditor(scene_class=MayaviScene),
height=1000, width=1000,
show_label=False),
resizable=True, # We need this to resize with the parent widget
)
################################################################################
# The QWidget containing the visualization, this is pure PyQt4 code.
class MayaviQWidget(QtGui.QWidget):
def __init__(self, parent=None):
QtGui.QWidget.__init__(self, parent)
layout = QtGui.QVBoxLayout(self)
layout.setContentsMargins(0,0,0,0)
layout.setSpacing(0)
self.visualization = Visualization()
# If you want to debug, beware that you need to remove the Qt
# input hook.
#QtCore.pyqtRemoveInputHook()
#import pdb ; pdb.set_trace()
#QtCore.pyqtRestoreInputHook()
# The edit_traits call will generate the widget to embed.
self.ui = self.visualization.edit_traits(parent=self,
kind='subpanel').control
layout.addWidget(self.ui)
self.ui.setParent(self)
class Visio(object):
def __init__(self):
## Needed when user pick the cylinder from visio and
## we need to get the section
self.cyl2sec = {}
## Needed to update the value of a cyl bound to a section
self.sec2cyl = {}
self.seg2id = {}
self.sec2coords = {}
#self.connections = []
self.n3dpoints_per_sec = {}
self.selected_cyl = None # Used for storing the cyl when picked
#self.sec_info_label = sec_info_label # Info for the selected sec
#self.manager = manager
#self.manager = {'v'}
container = QtGui.QWidget()
container.setWindowTitle("Hell Yeah!")
self.mayavi = MayaviQWidget(container)
layout = QtGui.QVBoxLayout(container)
layout.addWidget(self.mayavi)
# Tell visual to use this as the viewer.
#visual.set_viewer(self.mayavi.visualization.scene)
# binding to hide event.
container.connect(container, QtCore.SIGNAL('closeEvent()'),
self.closeEvent)
container.show()
self.container = container
## Connecting the picker.
#figure = self.mayavi.visualization.scene.mlab.gcf()
#self.outline = None
#self.picker = figure.on_mouse_pick(self.picker_callback, type='cell')
#
## ScalarBar and time_point
#self.colorbar = None
#self.timelabel = None
def get_idx_section(self, allsec, section='soma[0]'):
idxvec = np.zeros(len(allsec))
secnamelist = []
i = 0
for sec in allsec:
if sec == section:
idxvec[i] += 1
i += 1
[idx] = np.where(idxvec)
return idx
def draw_stick_model(self, cell, color=(1,0,0)):
'''draw the model as set of line sources'''
# Disable the render. Faster drawing.
self.mayavi.visualization.scene.disable_render = True
x,y,z,d = [], [], [], []
voltage = []
connections = []
for sec in cell.allsecnames:
#section = sec.name()
idx = self.get_idx_section(cell.allsec, section=sec)
for i, xi in enumerate(idx):
x.append(cell.xstart[idx[i]])
y.append(cell.ystart[idx[i]])
z.append(cell.zstart[idx[i]])
d.append(cell.diam[idx[i]])
indx_geom_seg = len(x) - 1
if len(x) > 1 and i > 0:
connections.append([indx_geom_seg, indx_geom_seg-1])
x.append(cell.xend[idx[i]])
y.append(cell.yend[idx[i]])
z.append(cell.zend[idx[i]])
d.append(cell.diam[idx[i]])
indx_geom_seg = len(x) - 1
connections.append([indx_geom_seg, indx_geom_seg-1])
self.edges = connections
self.x = x
self.y = y
self.z = z
# Mayavi pipeline
d = np.array(d) # Transforming for easy division
self.draw_mayavi(x, y, z, d, self.edges, color)
def draw_model(self):
"""Draw the model.
Params:
controls - the main gui obj."""
# Draw the new one
h.define_shape()
num_sections = 0
# Disable the render. Faster drawing.
self.mayavi.visualization.scene.disable_render = True
x,y,z,d = [], [], [], []
voltage = []
connections = []
for sec in h.allsec():
x_sec, y_sec, z_sec, d_sec = self.retrieve_coordinate(sec)
self.sec2coords[sec.name()] = [x_sec, y_sec, z_sec]
# Store the section. later.
radius = sec.diam/2.
sec_coords_bound = ((x_sec.min(), x_sec.max()),
(y_sec.min() - radius,
y_sec.max() + radius),
(z_sec.min() - radius,
z_sec.max() + radius))
self.cyl2sec[sec_coords_bound] = sec
self.sec2cyl[sec] = sec_coords_bound
for i,xi in enumerate(x_sec):
x.append(x_sec[i])
y.append(y_sec[i])
z.append(z_sec[i])
d.append(d_sec[i])
indx_geom_seg = len(x) -1
if len(x) > 1 and i > 0:
connections.append([indx_geom_seg, indx_geom_seg-1])
self.edges = connections
self.x = x
self.y = y
self.z = z
# Mayavi pipeline
d = np.array(d) # Transforming for easy division
self.draw_mayavi(x, y, z, d, self.edges)
def draw_mayavi(self, x, y, z, d, edges, color=(1, 0, 0)):
"Draw the surface the first time"
# rendering disabled
self.mayavi.visualization.scene.disable_render = True
points = mlab.pipeline.scalar_scatter(x, y, z, d/2.0)
dataset = points.mlab_source.dataset
dataset.point_data.get_array(0).name = 'diameter'
dataset.lines = np.vstack(edges)
dataset.point_data.update()
self.dataset = dataset
# The tube
src = mlab.pipeline.set_active_attribute(points, point_scalars='diameter')
stripper = mlab.pipeline.stripper(src)
tube = mlab.pipeline.tube(stripper, tube_sides = 6, tube_radius = 1)
tube.filter.capping = True
# tube.filter.use_default_normal = False
tube.filter.vary_radius = 'vary_radius_by_absolute_scalar'
self.tube = tube
# Setting the voltage
# Making room for the voltage
v = []
for sec in h.allsec():
sec.push()
v.extend(np.repeat(0.0, h.n3d()))
h.pop_section()
v = np.array(v)
v = np.ones(len(x)) * np.random.rand()
self.draw_surface(v, 'v', color)
# ReEnable the rendering
self.mayavi.visualization.scene.disable_render = True
def draw_surface(self, scalar, scalar_name, color):
self.tube.children= [] # Removing the old ones
#scalar = self.get_var_data('v', 0)
scalar = np.array(scalar)
array_id = self.dataset.point_data.add_array(scalar)
self.dataset.point_data.get_array(array_id).name = scalar_name
self.dataset.point_data.update()
src2 = mlab.pipeline.set_active_attribute(self.tube,
point_scalars=scalar_name)
#self.surf = mlab.pipeline.surface(src2, colormap='blue-red')
self.surf = mlab.pipeline.surface(src2, color=color)
def closeEvent(self):
"""Just hide the window to not loose the mayavi hook"""
self.container.hide()
def retrieve_coordinate(self, sec):
"""Retrieve the coordinates of the section avoiding duplicates"""
sec.push()
x, y, z, d = [],[],[],[]
tot_points = 0
connect_next = False
for i in range(int(h.n3d())):
present = False
x_i = h.x3d(i)
y_i = h.y3d(i)
z_i = h.z3d(i)
d_i = h.diam3d(i)
# Avoiding duplicates in the sec
if x_i in x:
ind = len(x) - 1 - x[::-1].index(x_i) # Getting the index of last value
if y_i == y[ind]:
if z_i == z[ind]:
present = True
if not present:
k =(x_i, y_i, z_i)
x.append(x_i)
y.append(y_i)
z.append(z_i)
d.append(d_i)
h.pop_section()
#adding num 3d points per section
self.n3dpoints_per_sec[sec.name()] = len(d)
return (np.array(x),np.array(y),np.array(z),np.array(d))
def get_var_data(self, var, time_point=0):
"""Retrieve the value of the `var` for the `time_point`.
Prameters:
var - variable to retrieve
time_point - point in the simulation"""
var_scalar = []
for sec in h.allsec():
var_value = 0
#if self.manager.refs.has_key('VecRef'):
# for vecRef in self.manager.refs['VecRef']:
# if vecRef.sec.name() == sec.name():
# if vecRef.vecs.has_key(var):
# vec = vecRef.vecs[var]
# try:
# var_value = vec[time_point]
# except IndexError:
# pass # vector exist, but not initialized.
sec_scalar = self.build_sec_scalar(sec, var_value)
var_scalar.extend(sec_scalar)
if len(var_scalar) == 0:
logger.debug( "Var scalar 0 length. Var: %s point_time: %s" %(var,
time_point))
return np.array(var_scalar)
def build_sec_scalar(self, sec, var_value):
sec.push()
npoints = self.n3dpoints_per_sec[sec.name()]
sec_scalar = np.repeat(var_value, npoints)
h.pop_section()
return sec_scalar
class VisioAnim(Visio):
'''subclassing Visio, as animatings are broken and will not break old usage'''
def __init__(self):
Visio.__init__(self)
def draw_stick_model(self, cell, values='vmem'):
'''draw the model as set of line sources'''
# Disable the render. Faster drawing.
self.mayavi.visualization.scene.disable_render = True
x,y,z,d = [], [], [], []
v = []
connections = []
for sec in cell.allsecnames:
#section = sec.name()
idx = self.get_idx_section(cell.allsec, section=sec)
for i, xi in enumerate(idx):
x.append(cell.xstart[idx[i]])
y.append(cell.ystart[idx[i]])
z.append(cell.zstart[idx[i]])
d.append(cell.diam[idx[i]])
v.append(values[idx[i], :])
indx_geom_seg = len(x) - 1
if len(x) > 1 and i > 0:
connections.append([indx_geom_seg, indx_geom_seg-1])
x.append(cell.xend[idx[i]])
y.append(cell.yend[idx[i]])
z.append(cell.zend[idx[i]])
d.append(cell.diam[idx[i]])
v.append(values[idx[i], :])
indx_geom_seg = len(x) - 1
connections.append([indx_geom_seg, indx_geom_seg-1])
# Mayavi pipeline
d = np.array(d) # Transforming for easy division
#self.draw_mayavi(x, y, z, d, v, self.edges)
self.draw_mayavi(x, y, z, d, v, connections)
# ReEnable the rendering
self.mayavi.visualization.scene.disable_render = True
def draw_mayavi(self, x, y, z, d, v, edges):
"Draw the surface the first time"
# rendering disabled
self.mayavi.visualization.scene.disable_render = True
points = mlab.pipeline.scalar_scatter(x, y, z, d)
dataset = points.mlab_source.dataset
dataset.point_data.get_array(0).name = 'diameter'
dataset.lines = np.vstack(edges)
dataset.point_data.update()
if not hasattr(self, 'datasets'):
self.datasets = []
self.datasets.append(dataset)
# The tube
src = mlab.pipeline.set_active_attribute(points,
point_scalars='diameter')
stripper = mlab.pipeline.stripper(src)
tube = mlab.pipeline.tube(stripper, tube_sides = 6, tube_radius = 1)
tube.filter.capping = True
# tube.filter.use_default_normal = False
tube.filter.vary_radius = 'vary_radius_by_absolute_scalar'
if not hasattr(self, 'tubes'):
self.tubes = []
self.tubes.append(tube)
# Setting the voltage
# Making room for the voltage
if not hasattr(self, 'voltages'):
self.voltages = []
self.voltages.append(np.array(v))
##draw the surface
#self.draw_surface(self.v[:, 0], 'v')
#
## ReEnable the rendering
#self.mayavi.visualization.scene.disable_render = False
def draw_surface(self, i, scalar, scalar_name, colormap='spectral', vmin=-80., vmax=20.):
tube = self.tubes[i]
tube.children= [] # Removing the old ones
#scalar = self.get_var_data('v', 0)
scalar = np.array(scalar)
#for dataset in self.datasets:
dataset = self.datasets[i]
array_id = dataset.point_data.add_array(scalar)
dataset.point_data.get_array(array_id).name = scalar_name
dataset.point_data.update()
src2 = mlab.pipeline.set_active_attribute(tube,
point_scalars=scalar_name)
self.surf = mlab.pipeline.surface(src2, opacity=1.,
colormap=colormap,
vmin=vmin, vmax=vmax)