ptcode = 'LSPEAS_002'
# ctcode, nr = 'discharge', 1
ctcode, nr = 'pre', 2
cropname = 'stent'
meshfile = 'LSPEAS_002_Smoothed5x0.8_Wrapped5mm_plus r renalis2 9_001.stl'
# Load ssdf
s = loadvol(basedir, ptcode, ctcode, cropname, 'avgreg')
volavg = s.vol
origin = volavg.origin # z y x
# Load deformations (apply forward for mesh)
s = loadvol(basedir, ptcode, ctcode, cropname, 'deforms')
deforms = [s['deform%i' % (i * 10)] for i in range(10)]
deforms = [[field[::2, ::2, ::2] for field in fields] for fields in deforms]
deforms_f = [pirt.DeformationFieldForward(*f) for f in deforms]
# Load mesh
basedir2 = select_dir(r'C:\MedData\LSPEAS_Mimics', r'F:\LSPEAS_Mimics_backup',
r'E:\LSPEAS_Mimics_backup')
mesh = vv.meshRead(os.path.join(basedir2, ptcode + '_' + ctcode, meshfile))
# z is negative, must be flipped to match dicom orientation
for vertice in mesh._vertices:
vertice[-1] = vertice[-1] * -1
#mesh = vv.meshRead(r'D:\Profiles\koenradesma\Desktop\001_preavgreg 20150522 test itk.stl')
# x and y values of vertices are negative (as in original dicom), flip to match local coordinates
#mesh._vertices = mesh._vertices*-1 # when stl from itksnap
## Start vis
f = vv.figure(1)
vv.clf()
sigma = 20
amplitude = 25
deform = []
for d in range(2):
a = np.zeros_like(im)
if d == 1:
amplitude_ = amplitude * 1
else:
amplitude_ = amplitude * 0.0
k = pirt.gaussfun.gaussiankernel2(sigma, 0, 0, N=-6 * sigma)
k *= amplitude_ * (1.0 / k.max())
# k[k>amplitude_*0.5] = amplitude_
# k[k<amplitude_] = 0.0
patch_image(a, k, (51, 51))
deform.append(a)
deform_forward = pirt.DeformationFieldForward(deform)
# Create a deformations in backward mode
deform = []
for d in range(2):
a = np.zeros_like(im)
if d == 1:
amplitude_ = amplitude * 1
else:
amplitude_ = amplitude * 0.0
k = pirt.gaussfun.gaussiankernel2(sigma, 0, 0, N=-6 * sigma)
k *= amplitude_ * (1.0 / k.max())
# k[k>amplitude_*0.5] = amplitude_
# k[k<amplitude_] = 0.0
patch_image(a, -k, (51, 51 + amplitude_))
deform.append(a)
foo = recordMovie(frameRate=7)
## Show 3D movie, by showing one volume that is moved by motion fields
# Load volume
s = loadvol(basedir, ptcode, ctcode, cropname, 'avgreg')
vol = s.vol
# Load deformations (use backward mapping to deform texture 3D volume)
s = loadvol(basedir, ptcode, ctcode, cropname, 'deforms')
deforms_forward = [s['deform%i' % (i * 10)] for i in range(10)]
deforms_forward = [[field[::2, ::2, ::2] for field in fields]
for fields in deforms_forward]
deforms_forward = [
pirt.DeformationFieldForward(*fields) for fields in deforms_forward
] # wrap fields
deforms_backward = [deform.as_backward()
for deform in deforms_forward] # get backward mapping
# Start vis
f = vv.figure(nr)
vv.clf()
if nr == 1:
f.position = 8.00, 30.00, 667.00, 690.00
else:
f.position = 691.00, 30.00, 667.00, 690.00
a = vv.gca()
a.axis.axisColor = 1, 1, 1
a.axis.visible = False
a.bgcolor = 0, 0, 0
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)