def PlaneSphereActors():
ps = vtk.vtkPlaneSource()
ps.SetXResolution(10)
ps.SetYResolution(10)
ss = vtk.vtkSphereSource()
ss.SetRadius(0.3)
group = vtk.vtkMultiBlockDataGroupFilter()
group.AddInputConnection(ps.GetOutputPort())
group.AddInputConnection(ss.GetOutputPort())
ag = vtk.vtkRandomAttributeGenerator()
ag.SetInputConnection(group.GetOutputPort())
ag.GenerateCellScalarsOn()
ag.AttributesConstantPerBlockOn()
n = vtk.vtkPolyDataNormals()
n.SetInputConnection(ag.GetOutputPort())
n.Update()
actors = []
it = n.GetOutputDataObject(0).NewIterator()
it.InitTraversal()
while not it.IsDoneWithTraversal():
pm = vtk.vtkPolyDataMapper()
pm.SetInputData(it.GetCurrentDataObject())
a = vtk.vtkActor()
a.SetMapper(pm)
actors.append(a)
it.GoToNextItem()
return actors
def procrustes(sources, rigid=False, legend=None):
'''
Return an Assembly of aligned source actors with
the vtkProcrustesAlignmentFilter class. Assembly is normalized in space.
Takes N set of points and aligns them in a least-squares sense
to their mutual mean. The algorithm is iterated until convergence,
as the mean must be recomputed after each alignment.
'''
group = vtk.vtkMultiBlockDataGroupFilter()
for source in sources:
if sources[0].N() != source.N():
vc.printc('Procrustes error in align():' , c=1)
vc.printc(' sources have different nr of points', c=1)
exit(0)
group.AddInputData(source.polydata())
procrustes = vtk.vtkProcrustesAlignmentFilter()
procrustes.StartFromCentroidOn()
procrustes.SetInputConnection(group.GetOutputPort())
if rigid:
procrustes.GetLandmarkTransform().SetModeToRigidBody()
procrustes.Update()
acts = []
for i in range(len(sources)):
poly = procrustes.GetOutput().GetBlock(i)
actor = Actor(poly)
actor.SetProperty(sources[i].GetProperty())
acts.append(actor)
assem = Assembly(acts, legend=legend)
assem.info['transform'] = procrustes.GetLandmarkTransform()
return assem
def PlaneSphereActors():
ps = vtk.vtkPlaneSource()
ps.SetXResolution(10)
ps.SetYResolution(10)
ss = vtk.vtkSphereSource()
ss.SetRadius (0.3)
group = vtk.vtkMultiBlockDataGroupFilter()
group.AddInputConnection(ps.GetOutputPort())
group.AddInputConnection(ss.GetOutputPort())
ag = vtk.vtkRandomAttributeGenerator()
ag.SetInputConnection(group.GetOutputPort())
ag.GenerateCellScalarsOn()
ag.AttributesConstantPerBlockOn()
n = vtk.vtkPolyDataNormals()
n.SetInputConnection(ag.GetOutputPort())
n.Update ();
actors = []
it = n.GetOutputDataObject(0).NewIterator()
it.InitTraversal()
while not it.IsDoneWithTraversal():
pm = vtk.vtkPolyDataMapper()
pm.SetInputData(it.GetCurrentDataObject())
a = vtk.vtkActor()
a.SetMapper(pm)
actors.append (a)
it.GoToNextItem()
return actors
def ComputeMeanLandmarks(targetNameList, dirlandmarks, dirOutput, sourceName):
# loading landmarks into vtk polydata object
group = vtk.vtkMultiBlockDataGroupFilter()
for name in targetNameList:
filename = os.path.join(dirlandmarks, name + '.txt')
if not os.path.isfile(filename):
print('Can not read landmark file: %s' % filename)
continue
npLandmarks = np.loadtxt(filename, skiprows=2)
numberOfLandmarks = int(np.size(npLandmarks) / 3)
vtkLandmarks = vtk.vtkPoints()
for landmark in npLandmarks:
vtkLandmarks.InsertNextPoint(landmark)
vtkPolyDataLandmarks = vtk.vtkPolyData()
vtkPolyDataLandmarks.SetPoints(vtkLandmarks)
group.AddInputData(vtkPolyDataLandmarks)
group.Update()
Procrustes = vtk.vtkProcrustesAlignmentFilter()
Procrustes.SetInputConnection(group.GetOutputPort())
Procrustes.GetLandmarkTransform().SetModeToRigidBody()
#===========================================================================
# Procrustes.GetLandmarkTransform().SetModeToSimilarity()
#===========================================================================
Procrustes.Update()
MeanPoints = Procrustes.GetMeanPoints()
return MeanPoints
def ComputeMeanSuface(targetNameList,
dirSurface,
dirOutput,
sourceName,
StatsFile=None,
thRMS=100):
print("================ STATSFILE ======================")
print(StatsFile)
rmsMetric = np.loadtxt(StatsFile, dtype=str, delimiter=',')
RMS = rmsMetric[:, -1]
nameList = rmsMetric[:, 0]
count = 1
skibedSurface = 0
# loading surface into vtk group
group = vtk.vtkMultiBlockDataGroupFilter()
for targetName in targetNameList:
filename = os.path.join(dirSurface, targetName + '.vtk')
if not os.path.isfile(filename):
print('Can not read file: %s' % filename)
continue
nameIdx = -1
for name in nameList:
# if '%d' % int(name) == targetName:
if name == targetName:
break
nameIdx += 1
if np.float(RMS[nameIdx]) > thRMS:
print('To high RMS for surface: %s RMS = %0.2f' %
(targetName, np.float(RMS[nameIdx])))
count += 1
skibedSurface += 1
continue
reader = vtk.vtkPolyDataReader()
reader.SetFileName(filename)
reader.Update()
group.AddInputConnection(reader.GetOutputPort())
count += 1
Procrustes = vtk.vtkProcrustesAlignmentFilter()
Procrustes.SetInputConnection(group.GetOutputPort())
Procrustes.GetLandmarkTransform().SetModeToRigidBody()
#===========================================================================
# Procrustes.GetLandmarkTransform().SetModeToSimilarity()
#===========================================================================
Procrustes.Update()
polydata = reader.GetOutput()
polydata.SetPoints(Procrustes.GetMeanPoints())
polydata = computeNormals(polydata)
writer = vtk.vtkPolyDataWriter()
filename = os.path.join(dirOutput, sourceName + '.vtk')
writer.SetFileName(filename)
writer.SetInputData(polydata)
writer.Write()
def tovtk(fdrw, fvtk):
"""
Reads drw file ``fvtk`` and writes ``fvtk``.
"""
# All separate ugirds represetning each element are collected together with
# the data group filter
gf = vtk.vtkMultiBlockDataGroupFilter()
for e in read_drw(open(fdrw, 'r')):
ug = _2ugrid(e)
gf.AddInputData(ug)
# Save to file
w = vtk.vtkXMLMultiBlockDataWriter()
w.SetFileName(fvtk)
w.SetInputConnection(gf.GetOutputPort())
w.Update()
return
def procrustesAlignment(sources, rigid=False):
"""
Return an ``Assembly`` of aligned source meshes with
the `Procrustes` algorithm. The output ``Assembly`` is normalized in size.
`Procrustes` algorithm takes N set of points and aligns them in a least-squares sense
to their mutual mean. The algorithm is iterated until convergence,
as the mean must be recomputed after each alignment.
The set of average points generated by the algorithm can be accessed with
``algoutput.info['mean']`` as a numpy array.
:param bool rigid: if `True` scaling is disabled.
|align3| |align3.py|_
"""
from vedo.mesh import Mesh
group = vtk.vtkMultiBlockDataGroupFilter()
for source in sources:
if sources[0].N() != source.N():
colors.printc("Error in procrustesAlignment():", c='r')
colors.printc(" sources have different nr of points", c='r')
raise RuntimeError()
group.AddInputData(source.polydata())
procrustes = vtk.vtkProcrustesAlignmentFilter()
procrustes.StartFromCentroidOn()
procrustes.SetInputConnection(group.GetOutputPort())
if rigid:
procrustes.GetLandmarkTransform().SetModeToRigidBody()
procrustes.Update()
acts = []
for i, s in enumerate(sources):
poly = procrustes.GetOutput().GetBlock(i)
mesh = Mesh(poly)
mesh.SetProperty(s.GetProperty())
if hasattr(s, 'name'):
mesh.name = s.name
mesh.flagText = s.flagText
acts.append(mesh)
assem = Assembly(acts)
assem.transform = procrustes.GetLandmarkTransform()
assem.info['mean'] = vtk_to_numpy(procrustes.GetMeanPoints().GetData())
return assem
def surface_statistics(target_names,
dir_surface,
dir_output,
source_name,
stats_file=None,
rms_threshold=100):
print('Reading', stats_file)
rms_metric = np.loadtxt(stats_file, dtype=str, delimiter=',')
n_rms = len(rms_metric)
surface_group = vtk.vtkMultiBlockDataGroupFilter()
for idx in range(n_rms):
name = rms_metric[idx, 0]
rms = float(rms_metric[idx, -1])
print('Surface:', name, 'RMS:', rms)
if rms < rms_threshold:
filename = os.path.join(dir_surface, name + '.vtk')
reader = vtk.vtkPolyDataReader()
reader.SetFileName(filename)
reader.Update()
if reader.GetOutput().GetNumberOfPoints() < 3:
print('Could not read', filename)
else:
surface_group.AddInputConnection(reader.GetOutputPort())
else:
print('Surface', name, 'excluded due to high RMS:', rms)
procrustes = vtk.vtkProcrustesAlignmentFilter()
procrustes.SetInputConnection(surface_group.GetOutputPort())
procrustes.GetLandmarkTransform().SetModeToRigidBody()
# ===========================================================================
# Procrustes.GetLandmarkTransform().SetModeToSimilarity()
# ===========================================================================
procrustes.Update()
polydata = reader.GetOutput()
polydata.SetPoints(procrustes.GetMeanPoints())
polydata = computeNormals(polydata)
writer = vtk.vtkPolyDataWriter()
filename = os.path.join(dir_output, source_name + '_Procrustes_mean.vtk')
writer.SetFileName(filename)
writer.SetInputData(polydata)
writer.Write()
def write(objct, fileoutput, binary=True):
"""
Write 3D object to file. (same as `save()`).
Possile extensions are:
- vtk, vti, npy, ply, obj, stl, byu, vtp, vti, mhd, xyz, tif, png, bmp.
"""
obj = objct
if isinstance(obj, Actor): # picks transformation
obj = objct.polydata(True)
elif isinstance(obj, (vtk.vtkActor, vtk.vtkVolume)):
obj = objct.GetMapper().GetInput()
elif isinstance(obj, (vtk.vtkPolyData, vtk.vtkImageData)):
obj = objct
fr = fileoutput.lower()
if ".vtk" in fr:
writer = vtk.vtkPolyDataWriter()
elif ".ply" in fr:
writer = vtk.vtkPLYWriter()
pscal = obj.GetPointData().GetScalars()
if not pscal:
pscal = obj.GetCellData().GetScalars()
if pscal and pscal.GetName():
writer.SetArrayName(pscal.GetName())
#writer.SetColorMode(0)
lut = objct.GetMapper().GetLookupTable()
if lut:
writer.SetLookupTable(lut)
elif ".stl" in fr:
writer = vtk.vtkSTLWriter()
elif ".obj" in fr:
writer = vtk.vtkOBJWriter()
elif ".vtp" in fr:
writer = vtk.vtkXMLPolyDataWriter()
elif ".vtm" in fr:
g = vtk.vtkMultiBlockDataGroupFilter()
for ob in objct:
g.AddInputData(ob)
g.Update()
mb = g.GetOutputDataObject(0)
wri = vtk.vtkXMLMultiBlockDataWriter()
wri.SetInputData(mb)
wri.SetFileName(fileoutput)
wri.Write()
return mb
elif ".xyz" in fr:
writer = vtk.vtkSimplePointsWriter()
elif ".facet" in fr:
writer = vtk.vtkFacetWriter()
elif ".tif" in fr:
writer = vtk.vtkTIFFWriter()
writer.SetFileDimensionality(len(obj.GetDimensions()))
elif ".vti" in fr:
writer = vtk.vtkXMLImageDataWriter()
elif ".mhd" in fr:
writer = vtk.vtkMetaImageWriter()
elif ".nii" in fr:
writer = vtk.vtkNIFTIImageWriter()
elif ".png" in fr:
writer = vtk.vtkPNGWriter()
elif ".jpg" in fr:
writer = vtk.vtkJPEGWriter()
elif ".bmp" in fr:
writer = vtk.vtkBMPWriter()
elif ".npy" in fr:
if utils.isSequence(objct):
objslist = objct
else:
objslist = [objct]
dicts2save = []
for obj in objslist:
dicts2save.append( _np_dump(obj) )
np.save(fileoutput, dicts2save)
return dicts2save
elif ".xml" in fr: # write tetrahedral dolfin xml
vertices = objct.coordinates().astype(str)
faces = np.array(objct.faces()).astype(str)
ncoords = vertices.shape[0]
outF = open(fileoutput, "w")
outF.write('<?xml version="1.0" encoding="UTF-8"?>\n')
outF.write('<dolfin xmlns:dolfin="http://www.fenicsproject.org">\n')
if len(faces[0]) == 4:# write tetrahedral mesh
ntets = faces.shape[0]
outF.write(' <mesh celltype="tetrahedron" dim="3">\n')
outF.write(' <vertices size="' + str(ncoords) + '">\n')
for i in range(ncoords):
x, y, z = vertices[i]
outF.write(' <vertex index="'+str(i)+'" x="'+x+'" y="'+y+'" z="'+z+'"/>\n')
outF.write(' </vertices>\n')
outF.write(' <cells size="' + str(ntets) + '">\n')
for i in range(ntets):
v0, v1, v2, v3 = faces[i]
outF.write(' <tetrahedron index="'+str(i)
+ '" v0="'+v0+'" v1="'+v1+'" v2="'+v2+'" v3="'+v3+'"/>\n')
elif len(faces[0]) == 3:# write triangle mesh
ntri = faces.shape[0]
outF.write(' <mesh celltype="triangle" dim="2">\n')
outF.write(' <vertices size="' + str(ncoords) + '">\n')
for i in range(ncoords):
x, y, dummy_z = vertices[i]
outF.write(' <vertex index="'+str(i)+'" x="'+x+'" y="'+y+'"/>\n')
outF.write(' </vertices>\n')
outF.write(' <cells size="' + str(ntri) + '">\n')
for i in range(ntri):
v0, v1, v2 = faces[i]
outF.write(' <triangle index="'+str(i)+'" v0="'+v0+'" v1="'+v1+'" v2="'+v2+'"/>\n')
outF.write(' </cells>\n')
outF.write(" </mesh>\n")
outF.write("</dolfin>\n")
outF.close()
return objct
else:
colors.printc("~noentry Unknown format", fileoutput, "file not saved.", c="r")
return objct
try:
if hasattr(writer, 'SetFileTypeToBinary'):
if binary:
writer.SetFileTypeToBinary()
else:
writer.SetFileTypeToASCII()
writer.SetInputData(obj)
writer.SetFileName(fileoutput)
writer.Write()
colors.printc("~save Saved file: " + fileoutput, c="g")
except Exception as e:
colors.printc("~noentry Error saving: " + fileoutput, "\n", e, c="r")
return objct
df_apoe_f = df_apoe[df_apoe["vol_l"] >= 1500.0]
df_apoe_f = df_apoe_f[df_apoe_f["vol_r"] >= 1500.0]
df_apoe_f = df_apoe_f[~df_apoe_f["id_alomar"].isin(visual_outliers_list)]
df_apoe_f.drop(df_apoe_f.columns[[0]], axis=1, inplace=True)
df_apoe_f.to_csv(out_csv, index=False, index_label=False)
print(len(df_apoe_f))
# %% markdown
# For both left and right hippocampus, use similarity alignment to alineate the meshes, using vtk.vtkProcustesAlignmentFilter()
# %%
# Group left and right meshes into a MultiBlockData
# la patillada del if vol xd
# Prova random: calcular el mean a mà, punt a punt.
# Left mesh
i = 0
meshes_left = vtk.vtkMultiBlockDataGroupFilter()
points_left = []
for mesh in X_left:
# Add to group
vol_r = float(df_ids.iloc[i, :].vol_r)
vol_l = float(df_ids.iloc[i, :].vol_l)
idb = int(df_ids.iloc[i, :].id_alomar)
if vol_r >= 2000 and vol_l >= 1500 and idb not in visual_outliers_list:
meshes_left.AddInputData(mesh)
# Compute mean points
points = ExtractVTKPoints(mesh)
points_left.append(points)
i += 1
# Right mesh
i = 0
def write(objct, fileoutput, binary=True):
"""
Write 3D object to file. (same as `save()`).
Possile extensions are:
- vtk, vti, npy, ply, obj, stl, byu, vtp, vti, mhd, xyz, tif, png, bmp.
"""
obj = objct
if isinstance(obj, Mesh): # picks transformation
obj = objct.polydata(True)
elif isinstance(obj, (vtk.vtkActor, vtk.vtkVolume)):
obj = objct.GetMapper().GetInput()
elif isinstance(obj, (vtk.vtkPolyData, vtk.vtkImageData)):
obj = objct
fr = fileoutput.lower()
if fr.endswith(".vtk"):
writer = vtk.vtkPolyDataWriter()
elif fr.endswith(".ply"):
writer = vtk.vtkPLYWriter()
pscal = obj.GetPointData().GetScalars()
if not pscal:
pscal = obj.GetCellData().GetScalars()
if pscal and pscal.GetName():
writer.SetArrayName(pscal.GetName())
#writer.SetColorMode(0)
lut = objct.GetMapper().GetLookupTable()
if lut:
writer.SetLookupTable(lut)
elif fr.endswith(".stl"):
writer = vtk.vtkSTLWriter()
elif fr.endswith(".vtp"):
writer = vtk.vtkXMLPolyDataWriter()
elif fr.endswith(".vtm"):
g = vtk.vtkMultiBlockDataGroupFilter()
for ob in objct:
if isinstance(ob, Mesh): # picks transformation
ob = ob.polydata(True)
elif isinstance(ob, (vtk.vtkActor, vtk.vtkVolume)):
ob = ob.GetMapper().GetInput()
g.AddInputData(ob)
g.Update()
mb = g.GetOutputDataObject(0)
wri = vtk.vtkXMLMultiBlockDataWriter()
wri.SetInputData(mb)
wri.SetFileName(fileoutput)
wri.Write()
return mb
elif fr.endswith(".xyz"):
writer = vtk.vtkSimplePointsWriter()
elif fr.endswith(".facet"):
writer = vtk.vtkFacetWriter()
elif fr.endswith(".tif"):
writer = vtk.vtkTIFFWriter()
writer.SetFileDimensionality(len(obj.GetDimensions()))
elif fr.endswith(".vti"):
writer = vtk.vtkXMLImageDataWriter()
elif fr.endswith(".mhd"):
writer = vtk.vtkMetaImageWriter()
elif fr.endswith(".nii"):
writer = vtk.vtkNIFTIImageWriter()
elif fr.endswith(".png"):
writer = vtk.vtkPNGWriter()
elif fr.endswith(".jpg"):
writer = vtk.vtkJPEGWriter()
elif fr.endswith(".bmp"):
writer = vtk.vtkBMPWriter()
elif fr.endswith(".npy"):
if utils.isSequence(objct):
objslist = objct
else:
objslist = [objct]
dicts2save = []
for obj in objslist:
dicts2save.append( _np_dump(obj) )
np.save(fileoutput, dicts2save)
return dicts2save
elif fr.endswith(".obj"):
outF = open(fileoutput, "w")
outF.write('# OBJ file format with ext .obj\n')
outF.write('# File Created by vtkplotter\n')
cobjct = objct.clone().clean()
for p in cobjct.points():
outF.write('v '+ str(p[0]) +" "+ str(p[1])+" "+ str(p[2])+'\n')
for vn in cobjct.normals(cells=False):
outF.write('vn '+str(vn[0])+" "+str(vn[1])+" "+str(vn[2])+'\n')
#pdata = cobjct.polydata().GetPointData().GetScalars()
#if pdata:
# ndata = vtk_to_numpy(pdata)
# for vd in ndata:
# outF.write('vp '+ str(vd) +'\n')
#ptxt = cobjct.polydata().GetPointData().GetTCoords() # not working
#if ptxt:
# ntxt = vtk_to_numpy(ptxt)
# print(len(cobjct.faces()), cobjct.points().shape, ntxt.shape)
# for vt in ntxt:
# outF.write('vt '+ str(vt[0]) +" "+ str(vt[1])+ ' 0\n')
for f in cobjct.faces():
fs = ''
for fi in f:
fs += " "+str(fi+1)
outF.write('f' + fs + '\n')
#ldata = cobjct.polydata().GetLines().GetData()
#print(cobjct.polydata().GetLines())
#if ldata:
# ndata = vtk_to_numpy(ldata)
# print(ndata)
# for l in ndata:
# ls = ''
# for li in l:
# ls += str(li+1)+" "
# outF.write('l '+ ls + '\n')
outF.close()
return objct
elif fr.endswith(".xml"): # write tetrahedral dolfin xml
vertices = objct.points().astype(str)
faces = np.array(objct.faces()).astype(str)
ncoords = vertices.shape[0]
outF = open(fileoutput, "w")
outF.write('<?xml version="1.0" encoding="UTF-8"?>\n')
outF.write('<dolfin xmlns:dolfin="http://www.fenicsproject.org">\n')
if len(faces[0]) == 4:# write tetrahedral mesh
ntets = faces.shape[0]
outF.write(' <mesh celltype="tetrahedron" dim="3">\n')
outF.write(' <vertices size="' + str(ncoords) + '">\n')
for i in range(ncoords):
x, y, z = vertices[i]
outF.write(' <vertex index="'+str(i)+'" x="'+x+'" y="'+y+'" z="'+z+'"/>\n')
outF.write(' </vertices>\n')
outF.write(' <cells size="' + str(ntets) + '">\n')
for i in range(ntets):
v0, v1, v2, v3 = faces[i]
outF.write(' <tetrahedron index="'+str(i)
+ '" v0="'+v0+'" v1="'+v1+'" v2="'+v2+'" v3="'+v3+'"/>\n')
elif len(faces[0]) == 3:# write triangle mesh
ntri = faces.shape[0]
outF.write(' <mesh celltype="triangle" dim="2">\n')
outF.write(' <vertices size="' + str(ncoords) + '">\n')
for i in range(ncoords):
x, y, dummy_z = vertices[i]
outF.write(' <vertex index="'+str(i)+'" x="'+x+'" y="'+y+'"/>\n')
outF.write(' </vertices>\n')
outF.write(' <cells size="' + str(ntri) + '">\n')
for i in range(ntri):
v0, v1, v2 = faces[i]
outF.write(' <triangle index="'+str(i)+'" v0="'+v0+'" v1="'+v1+'" v2="'+v2+'"/>\n')
outF.write(' </cells>\n')
outF.write(" </mesh>\n")
outF.write("</dolfin>\n")
outF.close()
return objct
else:
colors.printc("~noentry Unknown format", fileoutput, "file not saved.", c="r")
return objct
try:
if hasattr(writer, 'SetFileTypeToBinary'):
if binary:
writer.SetFileTypeToBinary()
else:
writer.SetFileTypeToASCII()
writer.SetInputData(obj)
writer.SetFileName(fileoutput)
writer.Write()
except Exception as e:
colors.printc("~noentry Error saving: " + fileoutput, "\n", e, c="r")
return objct
def write(objct, fileoutput, binary=True):
"""
Write 3D object to file. (same as `save()`).
Possile extensions are:
- vtk, vti, ply, obj, stl, byu, vtp, vti, mhd, xyz, tif, png, bmp.
"""
obj = objct
if isinstance(obj, Actor): # picks transformation
obj = objct.polydata(True)
elif isinstance(obj, (vtk.vtkActor, vtk.vtkVolume)):
obj = objct.GetMapper().GetInput()
elif isinstance(obj, (vtk.vtkPolyData, vtk.vtkImageData)):
obj = objct
fr = fileoutput.lower()
if ".vtk" in fr:
w = vtk.vtkPolyDataWriter()
elif ".ply" in fr:
w = vtk.vtkPLYWriter()
elif ".stl" in fr:
w = vtk.vtkSTLWriter()
elif ".vtp" in fr:
w = vtk.vtkXMLPolyDataWriter()
elif ".vtm" in fr:
g = vtk.vtkMultiBlockDataGroupFilter()
for ob in objct:
g.AddInputData(ob)
g.Update()
mb = g.GetOutputDataObject(0)
wri = vtk.vtkXMLMultiBlockDataWriter()
wri.SetInputData(mb)
wri.SetFileName(fileoutput)
wri.Write()
return mb
elif ".xyz" in fr:
w = vtk.vtkSimplePointsWriter()
elif ".facet" in fr:
w = vtk.vtkFacetWriter()
elif ".tif" in fr:
w = vtk.vtkTIFFWriter()
w.SetFileDimensionality(len(obj.GetDimensions()))
elif ".vti" in fr:
w = vtk.vtkXMLImageDataWriter()
elif ".mhd" in fr:
w = vtk.vtkMetaImageWriter()
elif ".png" in fr:
w = vtk.vtkPNGWriter()
elif ".jpg" in fr:
w = vtk.vtkJPEGWriter()
elif ".bmp" in fr:
w = vtk.vtkBMPWriter()
elif ".xml" in fr: # write tetrahedral dolfin xml
vertices = obj.coordinates()
faces = obj.cells()
ncoords = vertices.shape[0]
ntets = faces.shape[0]
outF = open(fileoutput, "w")
outF.write('<?xml version="1.0" encoding="UTF-8"?>\n')
outF.write('<dolfin xmlns:dolfin="http://www.fenicsproject.org">\n')
outF.write(' <mesh celltype="tetrahedron" dim="3">\n')
outF.write(' <vertices size="' + str(ncoords) + '">\n')
for i in range(ncoords):
x, y, z = vertices[i]
outF.write(' <vertex index="' + str(i) + '" x="' + str(x) +
'" y="' + str(y) + '" z="' + str(z) + '"/>\n')
outF.write(' </vertices>\n')
outF.write(' <cells size="' + str(ntets) + '">\n')
for i in range(ntets):
v0, v1, v2, v3 = faces[i]
outF.write(' <tetrahedron index="' + str(i) + '" v0="' +
str(v0) + '" v1="' + str(v1) + '" v2="' + str(v2) +
'" v3="' + str(v3) + '"/>\n')
outF.write(' </cells>\n')
outF.write(" </mesh>\n")
outF.write("</dolfin>\n")
outF.close()
return objct
else:
colors.printc("~noentry Unknown format",
fileoutput,
"file not saved.",
c="r")
return objct
try:
if hasattr(w, 'SetFileTypeToBinary'):
if binary:
w.SetFileTypeToBinary()
else:
w.SetFileTypeToASCII()
w.SetInputData(obj)
w.SetFileName(fileoutput)
w.Write()
colors.printc("~save Saved file: " + fileoutput, c="g")
except Exception as e:
colors.printc("~noentry Error saving: " + fileoutput, "\n", e, c="r")
return objct
map1a.SetInputConnection(sphere.GetOutputPort()) Actor1a = vtk.vtkActor() Actor1a.SetMapper(map1a) Actor1a.GetProperty().SetDiffuseColor(1.0000,0.3882,0.2784) map1b = vtk.vtkPolyDataMapper() map1b.SetInputConnection(transformer1.GetOutputPort()) Actor1b = vtk.vtkActor() Actor1b.SetMapper(map1b) Actor1b.GetProperty().SetDiffuseColor(0.3882,1.0000,0.2784) map1c = vtk.vtkPolyDataMapper() map1c.SetInputConnection(transformer2.GetOutputPort()) Actor1c = vtk.vtkActor() Actor1c.SetMapper(map1c) Actor1c.GetProperty().SetDiffuseColor(0.3882,0.2784,1.0000) # -- align the shapes using Procrustes (using SetModeToRigidBody) -- group = vtk.vtkMultiBlockDataGroupFilter() group.AddInputConnection(sphere.GetOutputPort()) group.AddInputConnection(transformer1.GetOutputPort()) group.AddInputConnection(transformer2.GetOutputPort()) procrustes1 = vtk.vtkProcrustesAlignmentFilter() procrustes1.SetInputConnection(group.GetOutputPort()) procrustes1.GetLandmarkTransform().SetModeToRigidBody() procrustes1.Update() # map the aligned shapes into the second renderer map2a = vtk.vtkPolyDataMapper() map2a.SetInputData(procrustes1.GetOutput().GetBlock(0)) Actor2a = vtk.vtkActor() Actor2a.SetMapper(map2a) Actor2a.GetProperty().SetDiffuseColor(1.0000,0.3882,0.2784) map2b = vtk.vtkPolyDataMapper() map2b.SetInputData(procrustes1.GetOutput().GetBlock(1))
sphere2.SetThetaResolution(15)
sphere2.SetPhiResolution(15)
sphere2.Update()
cylinder = vtk.vtkCylinderSource()
cylinder.SetRadius(attrs[0])
cylinder.SetHeight(attrs[1])
cylinder.SetResolution(15)
cylinder.Update()
data = vtk.vtkMultiBlockDataSet()
data.SetNumberOfBlocks(3)
data.SetBlock(0, sphere1.GetOutput())
data.SetBlock(1, sphere2.GetOutput())
data.SetBlock(2, cylinder.GetOutput())
source = vtk.vtkMultiBlockDataGroupFilter()
add_compatiblity_methods(source)
source.AddInputData(data)
readers[shape_name] = source
mapper = vtk.vtkCompositePolyDataMapper()
mapper.SetInputConnection(source.GetOutputPort())
mappers[shape_name] = (x for x in [mapper])
fixed_mappers = dict()
for shape_name in io.shapes():
if shape_name not in fixed_mappers:
fixed_mappers[shape_name] = mappers[shape_name].next()
for instance_name in io.instances():
def compute_mean_surface_and_lm(targetNameList,
dirSurface,
dirLM,
dirOutput,
sourceName,
StatsFile=None,
thRMS=100):
rmsMetric = np.loadtxt(StatsFile, dtype=str, delimiter=',')
RMS = rmsMetric[:, -1]
nameList = rmsMetric[:, 0]
count = 1
skibedSurface = 0
# loading surface into vtk group
group = vtk.vtkMultiBlockDataGroupFilter()
lm_group = vtk.vtkMultiBlockDataGroupFilter()
for targetName in targetNameList:
filename = os.path.join(dirSurface, targetName + '.vtk')
if not os.path.isfile(filename):
print('Can not read file: %s' % filename)
continue
nameIdx = 0
for name in nameList:
# if '%d' % int(name) == targetName:
if name == targetName:
break
nameIdx += 1
if nameIdx >= len(nameList):
print('Can not read RMS stat for file: %s' % filename)
continue
if np.float(RMS[nameIdx]) > thRMS:
print('To high RMS for surface: %s RMS = %0.2f' %
(targetName, np.float(RMS[nameIdx])))
count += 1
skibedSurface += 1
continue
reader = vtk.vtkPolyDataReader()
reader.SetFileName(filename)
reader.Update()
group.AddInputConnection(reader.GetOutputPort())
group.Update()
lmfilename = os.path.join(dirLM, targetName + '.txt')
npLandmarks = np.loadtxt(lmfilename, skiprows=2)
vtkLandmarks = vtk.vtkPoints()
for landmark in npLandmarks:
vtkLandmarks.InsertNextPoint(landmark)
vtkPolyDataLandmarks = vtk.vtkPolyData()
vtkPolyDataLandmarks.SetPoints(vtkLandmarks)
lm_group.AddInputData(vtkPolyDataLandmarks)
lm_group.Update()
count += 1
Procrustes = vtk.vtkProcrustesAlignmentFilter()
Procrustes.SetInputConnection(group.GetOutputPort())
Procrustes.GetLandmarkTransform().SetModeToRigidBody()
Procrustes.Update()
polydata = reader.GetOutput()
polydata.SetPoints(Procrustes.GetMeanPoints())
polydata = computeNormals(polydata)
writer = vtk.vtkPolyDataWriter()
filename = os.path.join(dirOutput, sourceName + '.vtk')
writer.SetFileName(filename)
writer.SetInputData(polydata)
writer.Write()
lm_procrustes = vtk.vtkProcrustesAlignmentFilter()
lm_procrustes.SetInputConnection(lm_group.GetOutputPort())
lm_procrustes.StartFromCentroidOff()
lm_procrustes.GetLandmarkTransform().SetModeToRigidBody()
lm_procrustes.Update()
mean_points = lm_procrustes.GetMeanPoints()
filename = os.path.join(dirOutput, sourceName + '.txt')
WriteLandmarkFile(mean_points, filename)
for j in range(nPt):
pts_str = pts_data[j][i]
pts_str_parsed = ''.join(
(ch if ch in '0123456789.-e' else ' ') for ch in pts_str)
pt_j = [float(pt_j_str) for pt_j_str in pts_str_parsed.split()]
pts_list_i.append(pt_j)
pts_list.append(pts_list_i)
# Procrustes Filter
procrustes_filter = vtk.vtkProcrustesAlignmentFilter()
group = vtk.vtkMultiBlockDataGroupFilter()
pts_polyData_list = []
scale_obs_list = []
# Check
# nObs = 3
for i in range(nObs):
pt_polyData = vtk.vtkPolyData()
pt_Points = vtk.vtkPoints()
pt_lines = vtk.vtkCellArray()
# Set Points
for j in range(nPt):
import vtk.numpy_interface.dataset_adapter as dsa import vtk.numpy_interface.algorithms as algs w = vtk.vtkRTAnalyticSource() bp = vtk.vtkBrownianPoints() bp.SetInputConnection(w.GetOutputPort()) bp.Update() elev = vtk.vtkElevationFilter() elev.SetInputConnection(bp.GetOutputPort()) elev.SetLowPoint(-10, 0, 0) elev.SetHighPoint(10, 0, 0) elev.SetScalarRange(0, 20) g = vtk.vtkMultiBlockDataGroupFilter() g.AddInputConnection(elev.GetOutputPort()) g.AddInputConnection(elev.GetOutputPort()) g.Update() elev2 = vtk.vtkElevationFilter() elev2.SetInputConnection(bp.GetOutputPort()) elev2.SetLowPoint(0, -10, 0) elev2.SetHighPoint(0, 10, 0) elev2.SetScalarRange(0, 20) g2 = vtk.vtkMultiBlockDataGroupFilter() g2.AddInputConnection(elev2.GetOutputPort()) g2.AddInputConnection(elev2.GetOutputPort())
sphere2.SetThetaResolution(15)
sphere2.SetPhiResolution(15)
sphere2.Update()
cylinder = vtk.vtkCylinderSource()
cylinder.SetRadius(attrs[0])
cylinder.SetHeight(attrs[1])
cylinder.SetResolution(15)
cylinder.Update()
data = vtk.vtkMultiBlockDataSet()
data.SetNumberOfBlocks(3)
data.SetBlock(0, sphere1.GetOutput())
data.SetBlock(1, sphere2.GetOutput())
data.SetBlock(2, cylinder.GetOutput())
source = vtk.vtkMultiBlockDataGroupFilter()
source.AddInput(data)
readers.append(source)
for instance in instances:
mapper = vtk.vtkCompositePolyDataMapper()
mapper.SetInputConnection(readers[shape[int(instance)]].GetOutputPort())
mappers.append(mapper)
actor = vtk.vtkActor()
if int(instance) >= 0:
actor.GetProperty().SetOpacity(0.7)
actor.GetProperty().SetColor(random_color())
actor.SetMapper(mapper)
actors.append(actor)
renderer.AddActor(actor)
import vtk.numpy_interface.dataset_adapter as dsa import vtk.numpy_interface.algorithms as algs w = vtk.vtkRTAnalyticSource() bp = vtk.vtkBrownianPoints() bp.SetInputConnection(w.GetOutputPort()) bp.Update() elev = vtk.vtkElevationFilter() elev.SetInputConnection(bp.GetOutputPort()) elev.SetLowPoint(-10, 0, 0) elev.SetHighPoint(10, 0, 0) elev.SetScalarRange(0, 20) g = vtk.vtkMultiBlockDataGroupFilter() g.AddInputConnection(elev.GetOutputPort()) g.AddInputConnection(elev.GetOutputPort()) g.Update() elev2 = vtk.vtkElevationFilter() elev2.SetInputConnection(bp.GetOutputPort()) elev2.SetLowPoint(0, -10, 0) elev2.SetHighPoint(0, 10, 0) elev2.SetScalarRange(0, 20) g2 = vtk.vtkMultiBlockDataGroupFilter() g2.AddInputConnection(elev2.GetOutputPort()) g2.AddInputConnection(elev2.GetOutputPort())
if len(args) > 0:
io_filename = args[0]
else:
usage()
exit(1)
transforms = dict()
transformers = dict()
data_connectors_v = dict()
data_connectors_t = dict()
data_connectors_d = dict()
big_data_source = vtk.vtkMultiBlockDataGroupFilter()
add_compatiblity_methods(big_data_source)
big_data_writer = vtk.vtkXMLMultiBlockDataWriter()
add_compatiblity_methods(big_data_writer)
contactors = dict()
offsets = dict()
vtkmath = vtk.vtkMath()
class Quaternion():
def __init__(self, *args):
self._data = vtk.vtkQuaternion[float](*args)
