def make_actor(self):
self.mapper = vtk.vtkOpenGLPolyDataMapper()
# normals
normals = vtk.vtkPolyDataNormals()
normals.SetInputData(self.vtk_obj)
normals.ComputePointNormalsOn()
normals.SplittingOff()
normals.AutoOrientNormalsOn()
normals.ConsistencyOn()
normals.Update()
self.mapper.SetInputData(normals.GetOutput())
self.actor = vtk.vtkOpenGLActor()
self.actor.SetMapper(self.mapper)
self.actor.GetProperty().SetColor(self.colour)
if self.vtk_args.wireframe:
self.actor.GetProperty().SetRepresentationToWireframe()
if self.alpha:
self.actor.GetProperty().SetOpacity(self.alpha)
if self.vtk_args.view_edges:
self.actor.GetProperty().EdgeVisibilityOn()
self.actor.GetProperty().SetEdgeColor(*self.edge_colour)
# lighting and shading
# self.actor.GetProperty().SetInterpolationToPhong()
# self.actor.GetProperty().SetDiffuse(0.7)
# self.actor.GetProperty().SetSpecular(0.5)
# self.actor.GetProperty().SetSpecularPower(40)
# self.actor.GetProperty().BackfaceCullingOn()
# self.actor.GetProperty().FrontfaceCullingOn()
return self.actor
def GridSurface(self):
#----------------------------------------------------------------------
# ELECTRODE CONTACT DELAUNAY TRIANGULATION ----------------------------
deln = vtk.vtkDelaunay3D()
deln.SetInput(self.electrodePolyData)
deln.SetTolerance(0.01)
tmapper = vtk.vtkTextureMapToSphere()
tmapper.SetInputConnection(deln.GetOutputPort())
#tmapper.PreventSeamOn()
mapper = vtk.vtkDataSetMapper()
mapper.SetInputConnection(tmapper.GetOutputPort())
# TEST TEXTURE PART
atext = vtk.vtkOpenGLTexture()
self.contactScalarData = vtk.vtkDoubleArray()
self.contactScalarData.SetNumberOfComponents(1)
for tupleID in range(self.electrodePolyData.GetNumberOfPoints()):
self.contactScalarData.InsertNextValue(random.uniform(0, 1))
self.UpdateGridSurface()
atext.SetInput(self.electrodePolyData)
self.triangulation = vtk.vtkOpenGLActor()
self.triangulation.SetMapper(mapper)
self.triangulation.SetTexture(atext)
self.triangulation.GetProperty().SetOpacity(1)
def extract(color, isovalue):
skinExtractor = vtk.vtkDiscreteMarchingCubes()
skinExtractor.SetInputConnection(dataImporter.GetOutputPort())
skinExtractor.SetValue(0, isovalue)
smooth = vtk.vtkSmoothPolyDataFilter()
smooth.SetInputConnection(skinExtractor.GetOutputPort())
smooth.SetNumberOfIterations(15)
smooth.SetRelaxationFactor(0.2)
smooth.FeatureEdgeSmoothingOff()
smooth.BoundarySmoothingOn()
smooth.Update()
skinStripper = vtk.vtkStripper()
skinStripper.SetInputConnection(smooth.GetOutputPort())
skinMapper = vtk.vtkOpenGLPolyDataMapper()
skinMapper.SetInputConnection(skinStripper.GetOutputPort())
skinMapper.ScalarVisibilityOff()
skin = vtk.vtkOpenGLActor()
skin.SetMapper(skinMapper)
skin.GetProperty().SetDiffuseColor(colors.GetColor3d(color))
skin.GetProperty().SetSpecular(.3)
skin.GetProperty().SetSpecularPower(20)
return skin
def GridSurface(self):
#----------------------------------------------------------------------
# ELECTRODE CONTACT DELAUNAY TRIANGULATION ----------------------------
deln = vtk.vtkDelaunay3D()
deln.SetInput(self.electrodePolyData)
deln.SetTolerance(0.01)
tmapper = vtk.vtkTextureMapToSphere()
tmapper.SetInputConnection(deln.GetOutputPort())
#tmapper.PreventSeamOn()
mapper = vtk.vtkDataSetMapper()
mapper.SetInputConnection(tmapper.GetOutputPort())
# TEST TEXTURE PART
atext = vtk.vtkOpenGLTexture()
self.contactScalarData = vtk.vtkDoubleArray()
self.contactScalarData.SetNumberOfComponents(1)
for tupleID in range(self.electrodePolyData.GetNumberOfPoints()):
self.contactScalarData.InsertNextValue(random.uniform(0, 1))
self.UpdateGridSurface()
atext.SetInput(self.electrodePolyData)
self.triangulation = vtk.vtkOpenGLActor()
self.triangulation.SetMapper(mapper)
self.triangulation.SetTexture(atext)
self.triangulation.GetProperty().SetOpacity(1)
def render(self, renderer):
assert isinstance(renderer, vtk.vtkRenderer)
if any([
self._vtk_args.all_contours, self._vtk_args.x_contours,
self._vtk_args.y_contours, self._vtk_args.z_contours
]):
_d = list()
if self._vtk_args.all_contours:
_d = ['x', 'y', 'z']
else:
if self._vtk_args.x_contours:
_d += ['x']
if self._vtk_args.y_contours:
_d += ['y']
if self._vtk_args.z_contours:
_d += ['z']
for d in _d:
self.mapper = vtk.vtkOpenGLPolyDataMapper()
self.mapper.SetInputData(getattr(self, '{}_vtkcontours'.format(d)))
self.actor = vtk.vtkOpenGLActor()
self.actor.SetMapper(self.mapper)
self.actor.GetProperty().SetColor(1, 1, 0)
self.actor.GetProperty().SetOpacity(1)
renderer.AddActor(self.actor)
return renderer
def MakeActor(polydata):
mapper = vtk.vtkOpenGLPolyDataMapper()
mapper.SetInputData(polydata)
#Disable VBO shfit and scale
mapper.SetVBOShiftScaleMethod(0)
actor = vtk.vtkOpenGLActor()
actor.SetMapper(mapper)
return actor
def load_maps(mol,rendmod,gfx,atomcol): mol.reader = vtk.vtkStructuredPointsReader() mol.reader.SetFileName(mol.mod.dfn) mol.reader.Update() #by calling Update() we read the file mol.iso = vtk.vtkMarchingContourFilter() mol.iso.UseScalarTreeOn() mol.iso.ComputeNormalsOn() mol.iso.SetInputConnection(mol.reader.GetOutputPort()) mol.iso.SetValue(0,mol.mod.isov*mol.mod.sigavg[0]+mol.mod.sigavg[1]) clean = vtk.vtkCleanPolyData() clean.SetInputConnection(mol.iso.GetOutputPort()) clean.ConvertStripsToPolysOn() smooth = vtk.vtkWindowedSincPolyDataFilter() smooth.SetInputConnection(clean.GetOutputPort()) smooth.BoundarySmoothingOn() smooth.GenerateErrorVectorsOn() smooth.GenerateErrorScalarsOn() smooth.NormalizeCoordinatesOn() smooth.NonManifoldSmoothingOn() smooth.FeatureEdgeSmoothingOn() smooth.SetEdgeAngle(90) smooth.SetFeatureAngle(90) smooth.Update() mol.mapper = vtk.vtkOpenGLPolyDataMapper() mol.mapper.SetInputConnection(smooth.GetOutputPort()) ### <- connection here mol.mapper.ScalarVisibilityOff() mol.mapper.Update() mol.acteur= vtk.vtkOpenGLActor() mol.acteur.SetMapper(mol.mapper) mol.acteur.GetProperty().SetColor(mol.col) if rendmod==5: mol.acteur.GetProperty().SetRepresentationToSurface() elif rendmod==6: mol.acteur.GetProperty().SetRepresentationToWireframe() elif rendmod==7: mol.acteur.GetProperty().SetRepresentationToPoints() else : mol.acteur.GetProperty().SetRepresentationToSurface() mol.acteur.GetProperty().SetInterpolationToGouraud() mol.acteur.GetProperty().SetSpecular(.4) mol.acteur.GetProperty().SetSpecularPower(10) gfx.renderer.AddActor(mol.acteur) gfx.renwin.Render()
def __init__(self, data, app=None):
self.patient_data = data
self.app = app
self.centroid = None
self.principal_dir = None
self.vtavoxels = None
self.polygonActor = None
self.clabel = -1
self.linethickness = 1.0
self.falloff = 10.0
self.gl_mapper = vtk.vtkOpenGLPolyDataMapper()
self.actor = vtk.vtkOpenGLActor()
self.polydata = vtk.vtkPolyData()
self.findVTAVoxels()
self.computeDataCentroid()
self.computePrincipalDirection()
self.generateVolumetricLine()
def load_spectra(self, gfx, mod, nbstep):
self.renderer.RemoveAllViewProps()
gfx.itf.status.set('Loading all conformers, please wait ...')
spectra = []
cpt = 0
self.nbstep = nbstep
self.display_progression()
for outnb in range(-nbstep, nbstep + 1):
fn = gfx.tmpdir + '/%s/' % mod.un + 'out%s' % (outnb)
if path.exists(fn):
cpt += 1
pdb = open(fn, 'r')
nat = 0
vx = []
vy = []
vz = []
for l in pdb:
if l[0:4] == 'ATOM':
nat += 1
x = float(l[30:38])
y = float(l[38:46])
z = float(l[46:54])
vx += [x]
vy += [y]
vz += [z]
pdb.close()
camax = 50
reader = vtk.vtkAppendPolyData()
for i in range(nat - 1):
#if ( (vx[i]-vx[i+1])**2+(vy[i]-vy[i+1])**2+(vz[i]-vz[i+1])**2 ) < camax :#avoid long lines
s = vtk.vtkLineSource()
s.SetPoint1([vx[i], vy[i], vz[i]])
s.SetPoint2([vx[i + 1], vy[i + 1], vz[i + 1]])
reader.AddInput(s.GetOutput())
mapper = vtk.vtkPolyDataMapper()
mapper.SetInputConnection(reader.GetOutputPort())
mapper.UseLookupTableScalarRangeOff()
mapper.SetScalarVisibility(1)
mapper.SetScalarModeToDefault()
acteur = vtk.vtkOpenGLActor()
acteur.SetMapper(mapper)
acteur.GetProperty().SetColor(0, 1, 0)
acteur.GetProperty().SetLineWidth(3)
acteur.SetMapper(mapper)
spectra += [acteur]
self.renderer.AddActor(acteur)
acteur.VisibilityOff()
self.tm.SetInput("%3.1f" % ((100. * cpt) / (nbstep * 2. + 1)) +
' %')
self.renwin.Render()
self.tm.SetInput("")
self.renderer.ResetCameraClippingRange()
self.renwin.Render()
mod.nmcl = spectra[:]
self.currentmod = mod
self.currentmod.nmcl[
self.nbstep].VisibilityOn() #on allume la structure non déformée
self.oldon = None
self.renwin.Render()
self.renderer.ResetCameraClippingRange()
gfx.itf.confscroll.configure(from_=-self.nbstep, to=self.nbstep)
gfx.itf.varconformer.set(0)
gfx.itf.status.clear()
def display_in_situ(self, gfx, mol, nbstep):
gfx.itf.status.set(
'Loading all conformers, progression : 0.0 percents ')
spectra = []
cpt = 0
self.nbstep = nbstep
for outnb in range(-nbstep, nbstep + 1):
fn = gfx.tmpdir + '/%s/' % mol.mod.un + 'out%s' % (outnb)
if path.exists(fn):
cpt += 1
pdb = open(fn, 'r')
nat = 0
vx = []
vy = []
vz = []
for l in pdb:
if l[0:4] == 'ATOM':
nat += 1
x = float(l[30:38])
y = float(l[38:46])
z = float(l[46:54])
vx += [x]
vy += [y]
vz += [z]
pdb.close()
camax = 50
reader = vtk.vtkAppendPolyData()
for i in range(nat - 1):
#if ( (vx[i]-vx[i+1])**2+(vy[i]-vy[i+1])**2+(vz[i]-vz[i+1])**2 ) < camax :#avoid long lines
s = vtk.vtkLineSource()
s.SetPoint1([vx[i], vy[i], vz[i]])
s.SetPoint2([vx[i + 1], vy[i + 1], vz[i + 1]])
reader.AddInput(s.GetOutput())
mapper = vtk.vtkPolyDataMapper()
mapper.SetInputConnection(reader.GetOutputPort())
mapper.UseLookupTableScalarRangeOff()
mapper.SetScalarVisibility(1)
mapper.SetScalarModeToDefault()
acteur = vtk.vtkOpenGLActor()
acteur.SetMapper(mapper)
if mol.acteur.GetClassName() == 'vtkAssembly':
acteur.GetProperty().SetColor(
mol.acteur.GetParts().GetItemAsObject(
0).GetProperty().GetColor())
acteur.GetProperty().SetLineWidth(
mol.acteur.GetParts().GetItemAsObject(
0).GetProperty().GetLineWidth())
else:
acteur.GetProperty().SetColor(
mol.acteur.GetProperty().GetColor())
acteur.GetProperty().SetLineWidth(
mol.acteur.GetProperty().GetLineWidth())
assigne_rotra(mol, acteur)
spectra += [acteur]
gfx.renderer.AddActor(acteur)
acteur.VisibilityOff()
gfx.itf.status.set(
'Loading all conformers, progression : %3.1f percents' %
((100. * cpt) / (nbstep * 2. + 1)))
gfx.renwin.Render()
gfx.renderer.ResetCameraClippingRange()
gfx.renwin.Render()
mol.nmcl = spectra[:]
self.currentmol = mol
self.oldon = None
self.currentmol.nmcl[0].VisibilityOn()
self.currentmol.acteur.VisibilityOff()
if self.currentmol.lsm != []:
self.currentmol.lsm[0].VisibilityOff()
gfx.renwin.Render()
gfx.renderer.ResetCameraClippingRange()
self.loop = Callbackinsitu(gfx)
self.loopobs = gfx.iren.AddObserver('TimerEvent', self.loop.loop)
gfx.iren.CreateRepeatingTimer(100)
gfx.iren.TimerEventResetsTimerOn()
gfx.iren.Start()
gfx.itf.status.clear()
def load_map(gfx, mapfile, root, status, scale, rendtype, isov, opct,
cropentry, nfv, vardeci, varsmooth, color, caller):
if caller != 'fit':
root.configure(cursor='watch')
status.set('Map loading ... please wait')
if mapfile == '' or mapfile == None or mapfile == ():
MB.showwarning('Info', 'Select map file')
status.clear()
root.configure(cursor='arrow')
return
try:
gfx.renderer.RemoveActor(gfx.map[0].acteur)
gfx.renderer.RemoveActor(gfx.map[0].box)
except:
pass
if mapfile == 0:
mapfile = gfx.map[0].fn
if gfx.map == []:
gfx.map = [Map()]
gfx.map[0].id = 0
if 'map' in caller:
clean_map(gfx) #supression des fichiers sort.s xudi et iudi
if '.vtk' in mapfile:
chdir(gfx.tmpdir)
v2v_out = 'info_map'
if caller != 'crop':
gfx.map[0].sigma, gfx.map[0].avg = map_sigma_avg(v2v_out)
if scale != gfx.map[0].scale:
spc = None
o = None
f = open(mapfile, 'r')
for l in f:
if l.startswith('SPACING'):
spc = l.split()[1:4]
if l.startswith('ORIGIN'):
o = l.split()[1:4]
if spc != None and o != None:
break
f.close()
gfx.map[0].ratio = scale / gfx.map[0].scale
if spc != None and o != None:
system("sed -i -e /^SPACING/s/.*/'SPACING %f %f %f'/ %s" %
(float(spc[0]) * gfx.map[0].ratio,
float(spc[1]) * gfx.map[0].ratio,
float(spc[2]) * gfx.map[0].ratio, mapfile))
system("sed -i -e /^ORIGIN/s/.*/'ORIGIN %f %f %f'/ %s" %
(float(o[0]) * gfx.map[0].ratio,
float(o[1]) * gfx.map[0].ratio,
float(o[2]) * gfx.map[0].ratio, mapfile))
chdir(gfx.workdir)
if '.ezd' in mapfile:
chdir(gfx.tmpdir)
mapfileout = extract_file_from_path(mapfile)[:-4] + '.vtk'
e2v_out = 'info_map'
system(gfx.vedabin +
'/e2v.exe >> %s <<ENDOF\n%s \n%f \n%s \nENDOF' %
(e2v_out, mapfile, scale, mapfileout))
mapfile = gfx.tmpdir + '/' + mapfileout
gfx.map[0].sigma, gfx.map[0].avg = map_sigma_avg(e2v_out)
chdir(gfx.workdir)
gfx.map[0].fn = mapfile
gfx.map[0].id = set_map_id(gfx)
gfx.map[0].color = color
gfx.map[0].oldscale = gfx.map[0].scale
gfx.map[0].scale = scale
if nfv != None:
nfv.set(extract_file_from_path(gfx.map[0].fn))
reader = vtk.vtkStructuredPointsReader()
reader.SetFileName(mapfile)
reader.Update() #by calling Update() we read the file
gfx.map[0].reader = reader
iso = vtk.vtkMarchingContourFilter()
iso.UseScalarTreeOn()
iso.ComputeNormalsOn()
iso.SetInputConnection(reader.GetOutputPort())
iso.SetValue(0, isov * gfx.map[0].sigma + gfx.map[0].avg)
gfx.map[0].iso = iso
gfx.map[0].isov = isov
if varsmooth == '1':
#generate vectors
clean = vtk.vtkCleanPolyData()
clean.SetInputConnection(iso.GetOutputPort())
clean.ConvertStripsToPolysOn()
smooth = vtk.vtkWindowedSincPolyDataFilter()
smooth.SetInputConnection(clean.GetOutputPort())
smooth.BoundarySmoothingOn()
smooth.GenerateErrorVectorsOn()
smooth.GenerateErrorScalarsOn()
smooth.NormalizeCoordinatesOn()
smooth.NonManifoldSmoothingOn()
smooth.FeatureEdgeSmoothingOn()
smooth.SetEdgeAngle(90)
smooth.SetFeatureAngle(90)
smooth.Update()
if vardeci == '1':
deci = vtk.vtkDecimatePro()
if varsmooth == '0':
deci.SetInput(iso.GetOutput())
else:
deci.SetInput(smooth.GetOutput())
deci.PreserveTopologyOn()
deci.BoundaryVertexDeletionOn()
deci.SplittingOn()
deci.PreSplitMeshOn()
deci.SetTargetReduction(0.97)
gfx.map[0].isdeci = '1'
mapper = vtk.vtkOpenGLPolyDataMapper()
mapper.SetInputConnection(deci.GetOutputPort())
else:
mapper = vtk.vtkOpenGLPolyDataMapper()
if varsmooth == '1':
mapper.SetInputConnection(
smooth.GetOutputPort()) ### <- connection here
else:
mapper.SetInputConnection(iso.GetOutputPort())
#mapper.SetInput(newpd) ### <- newpd connect there
gfx.map[0].isdeci = '0'
mapper.ScalarVisibilityOff()
mapper.Update()
gfx.map[0].mapper = mapper
actor = vtk.vtkOpenGLActor()
actor.SetMapper(mapper)
gfx.map[0].acteur = actor
#actor.SetScale(scale,scale,scale) gerer differament
actor.GetProperty().SetColor(gfx.map[0].color)
actor.PickableOff()
#definition de la box
outline = vtk.vtkOutlineFilter()
outline.SetInput(reader.GetOutput())
outlineMapper = vtk.vtkPolyDataMapper()
outlineMapper.SetInput(outline.GetOutput())
box = vtk.vtkActor()
box.SetMapper(outlineMapper)
box.GetProperty().SetColor((invcolor(gfx.map[0].color)))
box.PickableOff()
#box.SetScale(scale,scale,scale)
gfx.map[0].box = box
#get boxwidget bounds and set axes lenth
(xmin, xmax, ymin, ymax, zmin, zmax) = box.GetBounds()
x = abs(xmin - xmax) / 2.0
y = abs(ymin - ymax) / 2.0
z = abs(zmin - zmax) / 2.0
gfx.axes.SetTotalLength(x, y, z) #defini la longeurs des axe
init_cam_slab(
gfx, (xmin, xmax, ymin, ymax, zmin, zmax)) #defini le slab correct
gfx.map[0].rendtype = rendtype
if rendtype == 'Wireframe':
actor.GetProperty().SetRepresentationToWireframe()
elif rendtype == 'Surface':
actor.GetProperty().SetRepresentationToSurface()
elif rendtype == 'Points':
actor.GetProperty().SetRepresentationToPoints()
actor.GetProperty().SetPointSize(5)
else:
actor.GetProperty().SetRepresentationToWireframe()
gfx.map[0].opct = opct
actor.GetProperty().SetOpacity(opct)
actor.GetProperty().SetInterpolationToGouraud()
actor.GetProperty().SetSpecular(.4)
actor.GetProperty().SetSpecularPower(10)
if cropentry != None:
if gfx.crop == None:
gfx.crop = Crop(gfx, iso, cropentry, None) #here entryval = None
rendermap(gfx)
#ajustement pour la symetry helicoidale
if gfx.map[0].scale != gfx.map[0].oldscale: #changement de scale
gfx.itf.propagate_scale(gfx, scale, caller)
if gfx.ps != None:
if gfx.ps.solidtype == 'Helicoidal':
gfx.ps.display_tube(gfx, caller)
elif gfx.ps.solidtype == 'Icosahedral' or gfx.ps.solidtype == 'Octahedral' or gfx.ps.solidtype == 'Tetrahedral':
gfx.ps.display_platonic(gfx, gfx.ps.ori)
elif gfx.ps.solidtype == 'Cn' or gfx.ps.solidtype == 'Dn':
gfx.ps.display_Xn(gfx)
if caller == 'crop': #crop uniquement helicoidal
if gfx.ps != None:
if gfx.ps.solidtype == 'Helicoidal':
gfx.ps.display_tube(gfx, caller)
if caller != 'fit':
status.clear()
root.configure(cursor='arrow')
def __init__(self, electrode_data):
def __pca(A):
"""
Principal Component Analaysis
"""
# Get Dimensions
num_data, dim = A.shape
# Center data
mean_A = A.mean(axis=0)
for i in range(num_data):
A[i] -= mean_A
u, s, v = np.linalg.svd(A)
normPos = s.argmin()
return v[:, normPos]
"""
Setup Surface Rendering
"""
# Apply a discrete marching cubes algorithm to extract segmented
# surface contours with incremental values
self.electrodeExtractor = vtk.vtkDiscreteMarchingCubes()
self.electrodeExtractor.SetInput(electrode_data.GetOutput())
self.electrodeExtractor.GenerateValues(1,\
np.min(electrode_data.GetArray()),\
np.max(electrode_data.GetArray()))
self.electrodeMapper = vtk.vtkPolyDataMapper()
self.electrodeMapper.SetInputConnection(\
self.electrodeExtractor.GetOutputPort())
self.electrodeMapper.ScalarVisibilityOff()
self.electrodeProperty = vtk.vtkProperty()
self.electrodeProperty.SetColor(1.0, 0.5, 0.0)
self.SetMapper(self.electrodeMapper)
self.SetProperty(self.electrodeProperty)
self.electrodeExtractor.Update()
self.grid = vtk.vtkAssembly()
self.electrodePolyData = vtk.vtkPolyData()
electrodePoints = vtk.vtkPoints()
ePointMat = np.mat(np.zeros(shape=(36, 3)))
chanIdx = 0
for segLabel in np.unique(electrode_data.GetArray()):
# This is hacked for MAYO34 in order to show just the 6x6 grid
sphere = vtk.vtkSphereSource()
sphere.SetRadius(2)
sphereMap = vtk.vtkPolyDataMapper()
sphereMap.SetInput(sphere.GetOutput())
if (segLabel > 0 and segLabel < 37):
x, y, z = np.nonzero(electrode_data.GetArray() == segLabel)
nx = 0.9375 * np.mean(z)
ny = 0.9375 * np.mean(y)
nz = 1.5 * np.mean(x)
ePointMat[chanIdx] = [nx, ny, nz]
chanIdx = chanIdx + 1
normalVector = __pca(ePointMat.copy())
for chan in range(chanIdx):
xx = ePointMat[chan, 0]
yy = ePointMat[chan, 1]
zz = ePointMat[chan, 2]
sphereActor = vtk.vtkOpenGLActor()
sphereActor.SetMapper(sphereMap)
sphereActor.GetProperty().SetColor(1.0, 0.0, 1.0)
sphereActor.SetPosition(xx - 0 * normalVector[0],\
yy - 0 * normalVector[1],\
zz - 0 * normalVector[2])
electrodePoints.InsertNextPoint(xx - 0 * normalVector[0],\
yy - 0 * normalVector[1],\
zz - 0 * normalVector[2])
self.grid.AddPart(sphereActor)
self.electrodePolyData.SetPoints(electrodePoints)
self.GridSurface()
for min_max, color, opacity in settings:
# contour
data_contour = vtk.vtkMarchingCubes()
data_contour.SetInput(data)
data_contour.ComputeNormalsOn()
data_contour.GenerateValues(5, min_max[0], min_max[1])
data_contour.Update()
# geometry
data_geometry = vtk.vtkPolyDataMapper()
data_geometry.SetInputConnection(data_contour.GetOutputPort())
data_geometry.ScalarVisibilityOff()
# actor
data_actor = vtk.vtkOpenGLActor()
data_actor.SetMapper(data_geometry)
data_actor.GetProperty().SetColor(*color)
data_actor.GetProperty().SetOpacity(opacity)
actors.append(data_actor)
# to plot the outline
outline = vtk.vtkOutlineFilter()
outline.SetInput(data)
outline_mapper = vtk.vtkPolyDataMapper()
outline_mapper.SetInputConnection(outline.GetOutputPort())
outline_actor = vtk.vtkOpenGLActor()
outline_actor.SetMapper(outline_mapper)
outline_actor.GetProperty().SetColor(1, 1, 1)
# Wrap with sphere
# Delaynay
deln = vtk.vtkDelaunay3D()
deln.SetInputConnection(meshReader.GetOutputPort())
deln.SetTolerance(0.01)
tmapper = vtk.vtkTextureMapToSphere()
#tmapper.SetInputConnection(deln.GetOutputPort())
tmapper.SetInputConnection(meshReader.GetOutputPort())
#tmapper.PreventSeamOn()
mapper = vtk.vtkDataSetMapper()
mapper.SetInputConnection(tmapper.GetOutputPort())
triangulation = vtk.vtkOpenGLActor()
triangulation.SetMapper(mapper)
triangulation.SetTexture(texture)
triangulation.GetProperty().SetOpacity(1)
renderer = vtk.vtkRenderer()
renderer.AddActor(triangulation)
renderer.SetBackground(colors.GetColor3d("Black"))
renderWindow = vtk.vtkRenderWindow()
renderWindow.AddRenderer(renderer)
renderWindow.SetWindowName("TexturedSphere")
renWinInteractor = vtk.vtkRenderWindowInteractor()
renWinInteractor.SetRenderWindow(renderWindow)
def display(volumes, args):
"""Display the volumes provided in the iterable
This function relies on VTK to do the visualisation.
:param list volumes: a list of either MAP, STA or TransformedSTA object
:param args: command-line arguments
:type args: argparse.Namespace
"""
# display data
# create an actor for each datum
actors = list()
for volume in volumes:
# source
vol = vtk.vtkImageData()
z_size, y_size, x_size = volume.data.shape
x_origin, y_origin, z_origin = volume.origin
# this is a weirdly complex calculation
# suppose I have a distance of size D (distance)
# the index of the first position is S (start)
# the index of the last position is E (end)
# the relationship between these three values is
# E - S + 1 = D
# therefore, E = D + S - 1
vol.SetExtent(
x_origin, x_size + x_origin - 1,
y_origin, y_size + y_origin - 1,
z_origin, z_size + z_origin - 1,
)
vol.SetOrigin(x_origin, y_origin, z_origin)
sp_x = volume.x_voxel_size
sp_y = volume.y_voxel_size
sp_z = volume.z_voxel_size
vol.SetSpacing(sp_x, sp_y, sp_z)
vol.AllocateScalars(vtk.VTK_FLOAT, 1)
# voxel data
print(f"Inserting voxel data...", end="")
# numpy to vtk; https://pyscience.wordpress.com/2014/09/06/numpy-to-vtk-converting-your-numpy-arrays-to-vtk-arrays-and-files/
voxels = vtk.util.numpy_support.numpy_to_vtk(volume.data.ravel(), deep=1, array_type=vtk.VTK_FLOAT)
print(f"done!")
vol.GetPointData().SetScalars(voxels)
# contour
contours = vtk.vtkContourFilter()
contours.SetInputData(vol)
contours.SetValue(0, args.contour_level)
contours.Update()
contoursOutput = contours.GetOutput()
# data
obj = vtk.vtkPolyData()
obj.SetPoints(contoursOutput.GetPoints())
obj.SetPolys(contoursOutput.GetPolys())
# mapper
mapper = vtk.vtkOpenGLPolyDataMapper()
mapper.SetInputData(obj)
# actor & transform
actor = vtk.vtkOpenGLActor()
actor.SetMapper(mapper)
actor.GetProperty().SetColor(volume.colour)
actor.GetProperty().SetOpacity(volume.opacity)
if isinstance(volume, TransformedSTA):
transform = vtk.vtkTransform()
matrix = vtk.vtkMatrix4x4()
for i in range(4):
for j in range(4):
matrix.SetElement(i, j, volume.transform[i, j])
transform.SetMatrix(matrix)
print(transform)
actor.SetUserTransform(transform)
actors += [actor]
# renderer
renderer = vtk.vtkOpenGLRenderer()
[renderer.AddActor(actor) for actor in actors]
# cube axes
cubeAxesActor = vtk.vtkCubeAxesActor()
cubeAxesActor.SetBounds(renderer.ComputeVisiblePropBounds())
cubeAxesActor.SetCamera(renderer.GetActiveCamera())
cubeAxesActor.SetFlyMode(4)
cubeAxesActor.SetFlyModeToStaticEdges() # how the cube axes will appear
cubeAxesActor.GetTitleTextProperty(0).SetColor(1.0, 1.0, 1.0)
cubeAxesActor.GetTitleTextProperty(1).SetColor(1.0, 1.0, 1.0)
cubeAxesActor.GetTitleTextProperty(2).SetColor(1.0, 1.0, 1.0)
cubeAxesActor.XAxisMinorTickVisibilityOff()
cubeAxesActor.YAxisMinorTickVisibilityOff()
cubeAxesActor.ZAxisMinorTickVisibilityOff()
renderer.AddActor(cubeAxesActor)
# rendererwindow
render_window = vtk.vtkRenderWindow()
render_window.AddRenderer(renderer)
# render window interactor
render_window_interactor = vtk.vtkRenderWindowInteractor()
render_window_interactor.SetRenderWindow(render_window)
render_window_interactor.SetInteractorStyle(vtk.vtkInteractorStyleTrackballCamera())
axes_actor = vtk.vtkAxesActor()
axes_widget = vtk.vtkOrientationMarkerWidget()
axes_widget.SetOrientationMarker(axes_actor)
axes_widget.SetViewport(0, 0, 0.2, 0.2)
axes_widget.SetInteractor(render_window_interactor)
axes_widget.SetEnabled(1)
renderer.ResetCamera()
# display
render_window_interactor.Initialize()
render_window_interactor.Start()
return os.EX_OK
if __name__ == '__main__':
mixer = read_data()
mixer_contour = vtk.vtkMarchingCubes()
mixer_contour.SetInputConnection(mixer.GetOutputPort())
mixer_contour.ComputeNormalsOn()
mixer_contour.SetValue(0, 1)
stream_actors = make_stream_actors((0, 15, 30), (0, 1, 0))
stream_actors += make_stream_actors((0, 45, 30), (0, 0, 1))
mixer_geometry = vtk.vtkPolyDataMapper()
mixer_geometry.SetInputConnection(mixer_contour.GetOutputPort())
mixer_geometry.ScalarVisibilityOff()
mixer_actor = vtk.vtkOpenGLActor()
mixer_actor.SetMapper(mixer_geometry)
mixer_actor.GetProperty().SetColor(.5, .5, .5)
mixer_actor.GetProperty().SetOpacity(1.)
# Standard vtk environment stuff
renderer = vtk.vtkOpenGLRenderer()
render_window = vtk.vtkRenderWindow()
render_window.AddRenderer(renderer)
render_interactor = vtk.vtkRenderWindowInteractor()
renderer.AddActor(mixer_actor)
for actor in stream_actors:
renderer.AddActor(actor)
renderer.SetBackground(0.1, 0.1, 0.1)
render_window.SetSize(500, 500)
def display_mod(self,mod): self.renderer.RemoveAllViewProps() if mod.type == 'mol': if mod.dspmodtype == 'CA': reader = vtk.vtkPDBReader() reader.SetFileName(mod.dfn) reader.SetHBScale(0) reader.SetBScale(4.0) mapper = vtk.vtkPolyDataMapper() mapper.SetInputConnection(reader.GetOutputPort()) mapper.SetScalarModeToDefault() acteur = vtk.vtkActor() acteur.SetMapper(mapper) else: #all atoms or backbone case reader = vtk.vtkPDBReader() reader.SetFileName(mod.dfn) mapper = vtk.vtkPolyDataMapper() mapper.SetInputConnection(reader.GetOutputPort()) mapper.SetScalarModeToDefault() acteur = vtk.vtkActor() acteur.SetMapper(mapper) self.camera.SetFocalPoint(0, 0, 0) self.camera.SetPosition(0, 0, 250) elif mod.type=='map': reader = vtk.vtkStructuredPointsReader() reader.SetFileName(mod.dfn) reader.Update() #by calling Update() we read the file iso = vtk.vtkMarchingContourFilter() iso.UseScalarTreeOn() iso.ComputeNormalsOn() iso.SetInputConnection(reader.GetOutputPort()) iso.SetValue(0,mod.isov*mod.sigavg[0]+mod.sigavg[1]) mapper = vtk.vtkOpenGLPolyDataMapper() mapper.SetInputConnection(iso.GetOutputPort()) ### <- connection here mapper.ScalarVisibilityOff() mapper.Update() acteur= vtk.vtkOpenGLActor() acteur.SetMapper(mapper) acteur.GetProperty().SetColor(0,0.35,1) if mod.rep=='Wireframe': acteur.GetProperty().SetRepresentationToWireframe() elif mod.rep=='Surface': acteur.GetProperty().SetRepresentationToSurface() else : acteur.GetProperty().SetRepresentationToWireframe() acteur.GetProperty().SetInterpolationToGouraud() acteur.GetProperty().SetSpecular(.4) acteur.GetProperty().SetSpecularPower(10) (xmin,xmax,ymin,ymax,zmin,zmax)=acteur.GetBounds() maxi=max(xmax-xmin,ymax-ymin,zmax-zmin) mini=min(xmax-xmin,ymax-ymin,zmax-zmin) fp=((xmax+xmin)/2.,(ymax+ymin)/2.,(zmax+zmin)/2.) self.camera.SetFocalPoint(fp[0],fp[1],fp[2]) self.camera.SetPosition(fp[0],fp[1],fp[2]+(zmax-zmin)*4.) else : print 'strange Error in mod.type' (xl, xu, yl, yu, zl, zu)=acteur.GetBounds() mod.coldist = min(xu-xl,yu-yl,zu-zl)/2. mod.sphdist = max(xu-xl,yu-yl,zu-zl)/2. self.renderer.AddActor(acteur) self.renderer.ResetCameraClippingRange() self.renwin.Render()
def load_map(gfx,mapfile,root,status,scale,rendtype,isov,opct,cropentry,nfv,vardeci,varsmooth,color,caller):
if caller != 'fit':
root.configure(cursor='watch')
status.set('Map loading ... please wait')
if mapfile =='' or mapfile == None or mapfile ==() :
MB.showwarning('Info','Select map file')
status.clear()
root.configure(cursor='arrow')
return
try:
gfx.renderer.RemoveActor(gfx.map[0].acteur)
gfx.renderer.RemoveActor(gfx.map[0].box)
except:
pass
if mapfile == 0:
mapfile = gfx.map[0].fn
if gfx.map == []:
gfx.map = [Map()]
gfx.map[0].id=0
if 'map' in caller :
clean_map(gfx) #supression des fichiers sort.s xudi et iudi
if '.vtk' in mapfile:
chdir(gfx.tmpdir)
v2v_out='info_map'
if caller != 'crop':
gfx.map[0].sigma,gfx.map[0].avg = map_sigma_avg(v2v_out)
if scale != gfx.map[0].scale:
spc = None
o = None
f = open(mapfile,'r')
for l in f:
if l.startswith('SPACING'):
spc = l.split()[1:4]
if l.startswith('ORIGIN'):
o = l.split()[1:4]
if spc != None and o != None:
break
f.close()
gfx.map[0].ratio = scale/gfx.map[0].scale
if spc != None and o != None:
system("sed -i -e /^SPACING/s/.*/'SPACING %f %f %f'/ %s"%(float(spc[0])*gfx.map[0].ratio,float(spc[1])*gfx.map[0].ratio,float(spc[2])*gfx.map[0].ratio,mapfile))
system("sed -i -e /^ORIGIN/s/.*/'ORIGIN %f %f %f'/ %s"%(float(o[0])*gfx.map[0].ratio,float(o[1])*gfx.map[0].ratio,float(o[2])*gfx.map[0].ratio,mapfile))
chdir(gfx.workdir)
if '.ezd' in mapfile:
chdir(gfx.tmpdir)
mapfileout = extract_file_from_path(mapfile)[:-4]+'.vtk'
e2v_out='info_map'
system(gfx.vedabin+'/e2v.exe >> %s <<ENDOF\n%s \n%f \n%s \nENDOF'%(e2v_out,mapfile,scale,mapfileout))
mapfile = gfx.tmpdir + '/' + mapfileout
gfx.map[0].sigma,gfx.map[0].avg = map_sigma_avg(e2v_out)
chdir(gfx.workdir)
gfx.map[0].fn = mapfile
gfx.map[0].id = set_map_id(gfx)
gfx.map[0].color = color
gfx.map[0].oldscale = gfx.map[0].scale
gfx.map[0].scale = scale
if nfv !=None:
nfv.set(extract_file_from_path(gfx.map[0].fn))
reader = vtk.vtkStructuredPointsReader()
reader.SetFileName(mapfile)
reader.Update() #by calling Update() we read the file
gfx.map[0].reader=reader
iso = vtk.vtkMarchingContourFilter()
iso.UseScalarTreeOn()
iso.ComputeNormalsOn()
iso.SetInputConnection(reader.GetOutputPort())
iso.SetValue(0,isov*gfx.map[0].sigma+gfx.map[0].avg)
gfx.map[0].iso=iso
gfx.map[0].isov=isov
if varsmooth == '1':
#generate vectors
clean = vtk.vtkCleanPolyData()
clean.SetInputConnection(iso.GetOutputPort())
clean.ConvertStripsToPolysOn()
smooth = vtk.vtkWindowedSincPolyDataFilter()
smooth.SetInputConnection(clean.GetOutputPort())
smooth.BoundarySmoothingOn()
smooth.GenerateErrorVectorsOn()
smooth.GenerateErrorScalarsOn()
smooth.NormalizeCoordinatesOn()
smooth.NonManifoldSmoothingOn()
smooth.FeatureEdgeSmoothingOn()
smooth.SetEdgeAngle(90)
smooth.SetFeatureAngle(90)
smooth.Update()
if vardeci=='1':
deci = vtk.vtkDecimatePro()
if varsmooth == '0':
deci.SetInput(iso.GetOutput())
else :
deci.SetInput(smooth.GetOutput())
deci.PreserveTopologyOn()
deci.BoundaryVertexDeletionOn()
deci.SplittingOn()
deci.PreSplitMeshOn()
deci.SetTargetReduction(0.97)
gfx.map[0].isdeci='1'
mapper = vtk.vtkOpenGLPolyDataMapper()
mapper.SetInputConnection(deci.GetOutputPort())
else :
mapper = vtk.vtkOpenGLPolyDataMapper()
if varsmooth == '1':
mapper.SetInputConnection(smooth.GetOutputPort()) ### <- connection here
else :
mapper.SetInputConnection(iso.GetOutputPort())
#mapper.SetInput(newpd) ### <- newpd connect there
gfx.map[0].isdeci='0'
mapper.ScalarVisibilityOff()
mapper.Update()
gfx.map[0].mapper=mapper
actor = vtk.vtkOpenGLActor()
actor.SetMapper(mapper)
gfx.map[0].acteur=actor
#actor.SetScale(scale,scale,scale) gerer differament
actor.GetProperty().SetColor(gfx.map[0].color)
actor.PickableOff()
#definition de la box
outline = vtk.vtkOutlineFilter()
outline.SetInput(reader.GetOutput())
outlineMapper = vtk.vtkPolyDataMapper()
outlineMapper.SetInput(outline.GetOutput())
box=vtk.vtkActor()
box.SetMapper( outlineMapper )
box.GetProperty().SetColor((invcolor(gfx.map[0].color)))
box.PickableOff()
#box.SetScale(scale,scale,scale)
gfx.map[0].box = box
#get boxwidget bounds and set axes lenth
(xmin,xmax,ymin,ymax,zmin,zmax)=box.GetBounds()
x=abs(xmin-xmax)/2.0
y=abs(ymin-ymax)/2.0
z=abs(zmin-zmax)/2.0
gfx.axes.SetTotalLength( x, y , z ) #defini la longeurs des axe
init_cam_slab(gfx,(xmin,xmax,ymin,ymax,zmin,zmax)) #defini le slab correct
gfx.map[0].rendtype=rendtype
if rendtype=='Wireframe':
actor.GetProperty().SetRepresentationToWireframe()
elif rendtype=='Surface':
actor.GetProperty().SetRepresentationToSurface()
elif rendtype=='Points':
actor.GetProperty().SetRepresentationToPoints()
actor.GetProperty().SetPointSize(5)
else :
actor.GetProperty().SetRepresentationToWireframe()
gfx.map[0].opct=opct
actor.GetProperty().SetOpacity(opct)
actor.GetProperty().SetInterpolationToGouraud()
actor.GetProperty().SetSpecular(.4)
actor.GetProperty().SetSpecularPower(10)
if cropentry!=None:
if gfx.crop==None:
gfx.crop=Crop(gfx,iso,cropentry,None) #here entryval = None
rendermap(gfx)
#ajustement pour la symetry helicoidale
if gfx.map[0].scale != gfx.map[0].oldscale:#changement de scale
gfx.itf.propagate_scale(gfx,scale,caller)
if gfx.ps != None:
if gfx.ps.solidtype == 'Helicoidal':
gfx.ps.display_tube(gfx,caller)
elif gfx.ps.solidtype == 'Icosahedral' or gfx.ps.solidtype =='Octahedral' or gfx.ps.solidtype == 'Tetrahedral':
gfx.ps.display_platonic(gfx,gfx.ps.ori)
elif gfx.ps.solidtype =='Cn' or gfx.ps.solidtype == 'Dn':
gfx.ps.display_Xn(gfx)
if caller == 'crop':#crop uniquement helicoidal
if gfx.ps != None:
if gfx.ps.solidtype == 'Helicoidal':
gfx.ps.display_tube(gfx,caller)
if caller != 'fit':
status.clear()
root.configure(cursor='arrow')
if __name__ == "__main__":
np_data = getData()
vtk_data = numpy_to_vtk(np_data)
contour = vtk.vtkMarchingCubes()
contour.SetInputConnection(vtk_data.GetOutputPort())
contour.ComputeNormalsOn()
contour.SetValue(0, 7)
geometry = vtk.vtkPolyDataMapper()
geometry.SetInputConnection(contour.GetOutputPort())
geometry.ScalarVisibilityOff()
#actor = vtk.vtkLODActor()
actor = vtk.vtkOpenGLActor()
#actor.SetNumberOfCloudPoints(1000000)
actor.SetMapper(geometry)
actor.GetProperty().SetColor(0.333, 0.333, 0)#colors.green_to_white(0, 255))
actor.GetProperty().SetOpacity(0.3)#colors.default_opacity(0, 255, 0.5))
renderer = vtk.vtkOpenGLRenderer()
render_window = vtk.vtkRenderWindow()
renderer.AddActor(actor)
renderer.SetBackground(0.32157, 0.34118, 0.43137)
render_window.SetSize(500, 500)
render_window.AddRenderer(renderer)
render_interactor = vtk.vtkRenderWindowInteractor()
render_interactor.SetRenderWindow(render_window)
def __init__(self, electrode_data):
def __pca(A):
"""
Principal Component Analaysis
"""
# Get Dimensions
num_data, dim = A.shape
# Center data
mean_A = A.mean(axis=0)
for i in range(num_data):
A[i] -= mean_A
u,s,v = np.linalg.svd(A)
normPos = s.argmin()
return v[:, normPos]
"""
Setup Surface Rendering
"""
# Apply a discrete marching cubes algorithm to extract segmented
# surface contours with incremental values
self.electrodeExtractor = vtk.vtkDiscreteMarchingCubes()
self.electrodeExtractor.SetInput(electrode_data.GetOutput())
self.electrodeExtractor.GenerateValues(1,\
np.min(electrode_data.GetArray()),\
np.max(electrode_data.GetArray()))
self.electrodeMapper = vtk.vtkPolyDataMapper()
self.electrodeMapper.SetInputConnection(\
self.electrodeExtractor.GetOutputPort())
self.electrodeMapper.ScalarVisibilityOff()
self.electrodeProperty = vtk.vtkProperty()
self.electrodeProperty.SetColor(1.0, 0.5, 0.0)
self.SetMapper(self.electrodeMapper)
self.SetProperty(self.electrodeProperty)
self.electrodeExtractor.Update()
self.grid = vtk.vtkAssembly()
self.electrodePolyData = vtk.vtkPolyData()
electrodePoints = vtk.vtkPoints()
ePointMat = np.mat(np.zeros(shape = (36, 3)))
chanIdx = 0
for segLabel in np.unique(electrode_data.GetArray()):
# This is hacked for MAYO34 in order to show just the 6x6 grid
sphere = vtk.vtkSphereSource()
sphere.SetRadius(2)
sphereMap = vtk.vtkPolyDataMapper()
sphereMap.SetInput(sphere.GetOutput())
if (segLabel > 0 and segLabel < 37):
x,y,z = np.nonzero(electrode_data.GetArray() == segLabel)
nx = 0.9375*np.mean(z)
ny = 0.9375*np.mean(y)
nz = 1.5*np.mean(x)
ePointMat[chanIdx] = [nx, ny, nz]
chanIdx = chanIdx + 1
normalVector = __pca(ePointMat.copy())
for chan in range(chanIdx):
xx = ePointMat[chan, 0]
yy = ePointMat[chan, 1]
zz = ePointMat[chan, 2]
sphereActor = vtk.vtkOpenGLActor()
sphereActor.SetMapper(sphereMap)
sphereActor.GetProperty().SetColor(1.0, 0.0, 1.0)
sphereActor.SetPosition(xx - 0 * normalVector[0],\
yy - 0 * normalVector[1],\
zz - 0 * normalVector[2])
electrodePoints.InsertNextPoint(xx - 0 * normalVector[0],\
yy - 0 * normalVector[1],\
zz - 0 * normalVector[2])
self.grid.AddPart(sphereActor)
self.electrodePolyData.SetPoints(electrodePoints)
self.GridSurface()