def _makeColorBar(text, axes=None):
'''
Convenience function that finds the current colorbar in the axes
or creates a new one if one does not exist.
The reason is that colorbars can not be deleted without clearing
the whole figure, and several colorbars can exist simultaneously.
This should be avoided.
'''
if axes is None:
axes = vv.gca()
colBar = getColorbar(axes)
if colBar is None:
vv.colorbar(axes).SetLabel(text) #Creates a colorbar and sets the label.
else:
colBar.SetLabel(text)# A colorbar already exists, Change label.
#!/usr/bin/env python
import visvis as vv
app = vv.use()
# Get green channel of lena image
im = vv.imread('lena.png')[:,:,1]
# Make 4 subplots with different colormaps
cmaps = [vv.CM_GRAY, vv.CM_JET, vv.CM_SUMMER, vv.CM_HOT]
for i in range(4):
a = vv.subplot(2,2,i+1)
t = vv.imshow(im, clim=(0,255))
a.axis.visible = 0
t.colormap = cmaps[i]
vv.colorbar()
app.Run()
#!/usr/bin/env python
import visvis as vv
app = vv.use()
# Get green channel of lena image
im = vv.imread('astronaut.png')[:, :, 1]
# Make 4 subplots with different colormaps
cmaps = [vv.CM_GRAY, vv.CM_JET, vv.CM_SUMMER, vv.CM_HOT]
for i in range(4):
a = vv.subplot(2, 2, i + 1)
t = vv.imshow(im, clim=(0, 255))
a.axis.visible = 0
t.colormap = cmaps[i]
vv.colorbar()
app.Run()
def plot_3d_diameter_map(name,
data,
unit_scale=1.0,
measure_quantity='vox',
radius_structure_elem=1,
output_dir=None,
width=512,
height=512,
camera_azth=44.5,
camera_elev=35.8,
camera_roll=0.0,
camera_fov=35.0,
camera_zoom=0.0035,
camera_loc=(67.0, 81.6, 45.2),
xlabel='',
ylabel='',
zlabel='',
axis_color='w',
background_color='k',
cb_x_offset=10):
"""Renders orientation data in 3D with RGB angular color-coding.
Parameters
----------
name : str
Indicates the name of the output png file.
data : 3D array
Indicates the 3D array containing diameter at every point of the skeleton.
unit_scale : float
Indicates the scale factor of the data values.
measure_quantity : str
Indicates the name of measure of the values.
radius_structure_elem : integer
Indicates the size of the structure element of the dilation process to
thicken the skeleton.
output_dir : str
Indicates the path to the output folder where the image will be stored.
camera_azth : float
Indicates the azimuth angle of the camera.
width : int
Indicates the width of the visualization window.
height : int
Indicates the width of the visualization window.
camera_elev : float
Indicates the latitude / elevation angle of the camera.
camera_roll : float
Indicates the roll angle of the camera.
camera_fov : float
Indicates the field of view of the camera.
camera_zoom : float
Indicates the zoom level of the camera.
camera_loc : tuple
Indicates the camera location.
xlabel : str
Indicates the label along the x-axis.
ylabel : str
Indicates the label along the y-axis.
zlabel : str
Indicates the label along the z-axis.
axis_color : str
Indicates the color of axes.
background_color : str
Indicates the background color of the figure.
cb_x_offset : int
Indicates the offset of the colorbar from the right window side.
"""
if not visvis_available:
print(
'The visvis package is not found. The visualization cannot be done.'
)
return
rmin, rmax, cmin, cmax, zmin, zmax = _bbox_3D(data)
dmtr = data[rmin:rmax, cmin:cmax, zmin:zmax] * unit_scale
skel = np.zeros_like(dmtr, dtype=np.uint8)
skel[dmtr.nonzero()] = 1
dmtr = ndi.grey_dilation(dmtr,
structure=morphology.ball(radius_structure_elem))
skel = ndi.binary_dilation(
skel,
structure=morphology.ball(radius_structure_elem)).astype(np.float32)
skel[skel.nonzero()] = 1.
dmtr = dmtr * skel
app = vv.use()
fig = vv.figure()
fig._currentAxes = None
fig.relativeFontSize = 2.
fig.position.w = width
fig.position.h = height
t = vv.volshow(dmtr[:, :, :], renderStyle='iso')
t.isoThreshold = 0.5
t.colormap = vv.CM_JET
a = vv.gca()
a.camera.azimuth = camera_azth
a.camera.elevation = camera_elev
a.camera.roll = camera_roll
a.camera.fov = camera_fov
a.camera.zoom = camera_zoom
a.camera.loc = camera_loc
a.bgcolor = background_color
a.axis.axisColor = axis_color
a.axis.xLabel = xlabel
a.axis.yLabel = ylabel
a.axis.zLabel = zlabel
cb = vv.colorbar()
cb.SetLabel('Diameter, [{}]'.format(measure_quantity))
cb._label.position.x += cb_x_offset
if output_dir is not None:
if not os.path.exists(output_dir):
os.makedirs(output_dir)
vv.screenshot(os.path.join(output_dir,
'{}_3d_diameter.png'.format(name)),
sf=1,
bg='w')
app.Run()
def __init__(self,
ptcode,
ctcode,
basedir,
showVol='mip',
meshWithColors=False,
motion='amplitude',
clim2=(0, 2)):
"""
Script to show the stent model. [ nellix]
"""
import os
import pirt
import visvis as vv
from stentseg.utils.datahandling import select_dir, loadvol, loadmodel
from pirt.utils.deformvis import DeformableTexture3D, DeformableMesh
from stentseg.stentdirect.stentgraph import create_mesh
from stentseg.stentdirect import stentgraph
from stentseg.utils.visualization import show_ctvolume
from stentseg.motion.vis import create_mesh_with_abs_displacement
import copy
from stentseg.motion.dynamic import incorporate_motion_nodes, incorporate_motion_edges
from lspeas.utils.ecgslider import runEcgSlider
from stentseg.utils import _utils_GUI
import numpy as np
cropname = 'prox'
# params
nr = 1
# motion = 'amplitude' # amplitude or sum
dimension = 'xyz'
showVol = showVol # MIP or ISO or 2D or None
clim0 = (0, 2000)
# clim2 = (0,2)
motionPlay = 9, 1 # each x ms, a step of x %
s = loadvol(basedir, ptcode, ctcode, cropname, what='deforms')
m = loadmodel(basedir, ptcode, ctcode, cropname,
'centerline_total_modelavgreg_deforms')
v = loadmodel(basedir,
ptcode,
ctcode,
cropname,
modelname='centerline_total_modelvesselavgreg_deforms')
s2 = loadvol(basedir, ptcode, ctcode, cropname, what='avgreg')
vol_org = copy.deepcopy(s2.vol)
s2.vol.sampling = [
vol_org.sampling[1], vol_org.sampling[1], vol_org.sampling[2]
]
s2.sampling = s2.vol.sampling
vol = s2.vol
# merge models into one for dynamic visualization
model_total = stentgraph.StentGraph()
for key in dir(m):
if key.startswith('model'):
model_total.add_nodes_from(
m[key].nodes(data=True)) # also attributes
model_total.add_edges_from(m[key].edges(data=True))
for key in dir(v):
if key.startswith('model'):
model_total.add_nodes_from(
v[key].nodes(data=True)) # also attributes
model_total.add_edges_from(v[key].edges(data=True))
# Load deformations (forward for mesh)
deformkeys = []
for key in dir(s):
if key.startswith('deform'):
deformkeys.append(key)
deforms = [s[key] for key in deformkeys]
deforms = [[field[::2, ::2, ::2] for field in fields]
for fields in deforms]
# These deforms are forward mapping. Turn into DeformationFields.
# Also get the backwards mapping variants (i.e. the inverse deforms).
# The forward mapping deforms should be used to deform meshes (since
# the information is used to displace vertices). The backward mapping
# deforms should be used to deform textures (since they are used in
# interpolating the texture data).
deforms_f = [pirt.DeformationFieldForward(*f) for f in deforms]
deforms_b = [f.as_backward() for f in deforms_f]
# Create mesh
if meshWithColors:
try:
modelmesh = create_mesh_with_abs_displacement(model_total,
radius=0.7,
dim=dimension,
motion=motion)
except KeyError:
print('Centerline model has no pathdeforms so we create them')
# use unsampled deforms
deforms2 = [s[key] for key in deformkeys]
# deforms as backward for model
deformsB = [
pirt.DeformationFieldBackward(*fields)
for fields in deforms2
]
# set sampling to original
# for i in range(len(deformsB)):
# deformsB[i]._field_sampling = tuple(s.sampling)
# not needed because we use unsampled deforms
# Combine ...
incorporate_motion_nodes(model_total, deformsB, s2.origin)
convert_paths_to_PointSet(model_total)
incorporate_motion_edges(model_total, deformsB, s2.origin)
convert_paths_to_ndarray(model_total)
modelmesh = create_mesh_with_abs_displacement(model_total,
radius=0.7,
dim=dimension,
motion=motion)
else:
modelmesh = create_mesh(model_total, 0.7, fullPaths=True)
## Start vis
f = vv.figure(nr)
vv.clf()
if nr == 1:
f.position = 8.00, 30.00, 944.00, 1002.00
else:
f.position = 968.00, 30.00, 944.00, 1002.00
a = vv.gca()
a.axis.axisColor = 1, 1, 1
a.axis.visible = False
a.bgcolor = 0, 0, 0
a.daspect = 1, 1, -1
t = vv.volshow(vol, clim=clim0, renderStyle=showVol, axes=a)
vv.xlabel('x (mm)')
vv.ylabel('y (mm)')
vv.zlabel('z (mm)')
if meshWithColors:
if dimension == 'xyz':
dim = '3D'
vv.title(
'Model for chEVAS %s (color-coded %s of movement in %s in mm)'
% (ptcode[8:], motion, dim))
else:
vv.title('Model for chEVAS %s' % (ptcode[8:]))
colorbar = True
# Create deformable mesh
dm = DeformableMesh(a, modelmesh) # in x,y,z
dm.SetDeforms(*[list(reversed(deform))
for deform in deforms_f]) # from z,y,x to x,y,z
if meshWithColors:
dm.clim = clim2
dm.colormap = vv.CM_JET #todo: use colormap Viridis or Magma as JET is not linear (https://bids.github.io/colormap/)
if colorbar:
vv.colorbar()
colorbar = False
else:
dm.faceColor = 'g'
# Run mesh
a.SetLimits()
# a.SetView(viewringcrop)
dm.MotionPlay(motionPlay[0],
motionPlay[1]) # (10, 0.2) = each 10 ms do a step of 20%
dm.motionSplineType = 'B-spline'
dm.motionAmplitude = 0.5
## run ecgslider
ecg = runEcgSlider(dm, f, a, motionPlay)
def showModelsStatic(ptcode,codes, vols, ss, mm, vs, showVol, clim, isoTh, clim2,
clim2D, drawMesh=True, meshDisplacement=True, drawModelLines=True,
showvol2D=False, showAxis=False, drawVessel=False, vesselType=1,
meshColor=None, **kwargs):
""" show one to four models in multipanel figure.
Input: arrays of codes, vols, ssdfs; params from show_models_static
Output: axes, colorbars
"""
# init fig
f = vv.figure(1); vv.clf()
# f.position = 0.00, 22.00, 1920.00, 1018.00
mw = 5
if drawMesh == True:
lc = 'w'
meshColor = meshColor
else:
lc = 'g'
# create subplots
if isinstance(codes, str): # if 1 ctcode, otherwise tuple of strings
a1 = vv.subplot(111)
axes = [a1]
elif codes == (codes[0],codes[1]):
a1 = vv.subplot(121)
a2 = vv.subplot(122)
axes = [a1,a2]
elif codes == (codes[0],codes[1], codes[2]):
a1 = vv.subplot(131)
a2 = vv.subplot(132)
a3 = vv.subplot(133)
axes = [a1,a2,a3]
elif codes == (codes[0],codes[1], codes[2], codes[3]):
a1 = vv.subplot(141)
a2 = vv.subplot(142)
a3 = vv.subplot(143)
a4 = vv.subplot(144)
axes = [a1,a2,a3,a4]
elif codes == (codes[0],codes[1], codes[2], codes[3], codes[4]):
a1 = vv.subplot(151)
a2 = vv.subplot(152)
a3 = vv.subplot(153)
a4 = vv.subplot(154)
a5 = vv.subplot(155)
axes = [a1,a2,a3,a4,a5]
else:
a1 = vv.subplot(111)
axes = [a1]
for i, ax in enumerate(axes):
ax.MakeCurrent()
vv.xlabel('x (mm)');vv.ylabel('y (mm)');vv.zlabel('z (mm)')
vv.title('Model for LSPEAS %s - %s' % (ptcode[7:], codes[i]))
t = show_ctvolume(vols[i], ss[i].model, axis=ax, showVol=showVol, clim=clim, isoTh=isoTh, **kwargs)
label = pick3d(ax, vols[i])
if drawModelLines == True:
ss[i].model.Draw(mc='b', mw = mw, lc=lc)
if showvol2D:
for i, ax in enumerate(axes):
t2 = vv.volshow2(vols[i], clim=clim2D, axes=ax)
cbars = [] # colorbars
if drawMesh:
for i, ax in enumerate(axes):
m = vv.mesh(mm[i], axes=ax)
if meshDisplacement:
m.clim = clim2
m.colormap = vv.CM_JET #todo: use colormap Viridis or Magma as JET is not linear (https://bids.github.io/colormap/)
cb = vv.colorbar(ax)
cbars.append(cb)
elif meshColor is not None:
if len(meshColor) == 1:
m.faceColor = meshColor[0] # (0,1,0,1)
else:
m.faceColor = meshColor[i]
else:
m.faceColor = 'g'
if drawVessel:
for i, ax in enumerate(axes):
v = showVesselMesh(vs[i], ax, type=vesselType)
for ax in axes:
ax.axis.axisColor = 1,1,1
ax.bgcolor = 25/255,25/255,112/255 # midnightblue
# http://cloford.com/resources/colours/500col.htm
ax.daspect = 1, 1, -1 # z-axis flipped
ax.axis.visible = showAxis
# set colorbar position
for cbar in cbars:
p1 = cbar.position
cbar.position = (p1[0], 20, p1[2], 0.98) # x,y,w,h
# bind rotate view and view presets [1,2,3,4,5]
f = vv.gcf()
f.eventKeyDown.Bind(lambda event: _utils_GUI.RotateView(event,axes,axishandling=False) )
f.eventKeyDown.Bind(lambda event: _utils_GUI.ViewPresets(event,axes) )
return axes, cbars