def linesBody(mb, bodyName, successorJointsName):
"""
Return a mesh represented by lines and the appropriate static transform.
"""
apd = tvtk.AppendPolyData()
sources = []
# create a line from the body base to the next joint
for s in map(mb.jointIndexByName, successorJointsName[bodyName]):
X_s = mb.transform(s)
sources.append(tvtk.LineSource(point1=(0., 0., 0.),
point2=tuple(X_s.translation())))
# add an empty source to avoid a warning if AppendPolyData have 0 source
if len(sources) == 0:
sources.append(tvtk.PointSource(radius=0.))
map(lambda s: apd.add_input(s.output), sources)
apd.update()
pdm = tvtk.PolyDataMapper()
pdm.input_connection = apd.output_port
actor = tvtk.Actor(mapper=pdm)
actor.property.color = (0., 0., 0.)
actor.user_transform = tvtk.Transform()
return actor, sva.PTransformd.Identity()
def endEffectorBody(X_s, size, color):
"""
Return a end effector reprsented by a plane
and the appropriate static transform.
"""
apd = tvtk.AppendPolyData()
ls = tvtk.LineSource(point1=(0., 0., 0.), point2=tuple(X_s.translation()))
p1 = (sva.PTransformd(e.Vector3d.UnitX() * size) * X_s).translation()
p2 = (sva.PTransformd(e.Vector3d.UnitY() * size) * X_s).translation()
ps = tvtk.PlaneSource(origin=tuple(X_s.translation()),
point1=tuple(p1),
point2=tuple(p2),
center=tuple(X_s.translation()))
apd.add_input(ls.output)
apd.add_input(ps.output)
pdm = tvtk.PolyDataMapper(input=apd.output)
actor = tvtk.Actor(mapper=pdm)
actor.property.color = color
actor.user_transform = tvtk.Transform()
return actor, sva.PTransformd.Identity()
def test_property_change_notification(self):
"""Test if changes to properties generate notification events."""
# Create a dummy class to test with.
class Junk:
def f(self, obj, name, old, new):
self.data = obj, name, old, new
z = Junk()
cs = tvtk.ConeSource()
m = tvtk.PolyDataMapper()
if vtk_major_version < 6:
m.on_trait_change(z.f, 'input')
m.input = cs.output
self.assertEqual(z.data, (m, 'input', None, cs.output))
m.input = None
self.assertEqual(z.data, (m, 'input', cs.output, None))
m.on_trait_change(z.f, 'input', remove=True)
m.input = cs.output
else:
m.on_trait_change(z.f, 'input_connection')
m.input_connection = cs.output_port
self.assertEqual(z.data,
(m, 'input_connection', None, cs.output_port))
m.input_connection = None
self.assertEqual(z.data,
(m, 'input_connection', cs.output_port, None))
m.on_trait_change(z.f, 'input_connection', remove=True)
m.input_connection = cs.output_port
a = tvtk.Actor()
a.on_trait_change(z.f, 'mapper')
a.on_trait_change(z.f, 'property')
a.mapper = m
self.assertEqual(z.data, (a, 'mapper', None, m))
old = a.property
new = tvtk.Property()
a.property = new
self.assertEqual(z.data, (a, 'property', old, new))
# Check if property notification occurs on add_input/remove_input
a = tvtk.AppendPolyData()
pd = tvtk.PolyData()
if vtk_major_version < 6:
a.on_trait_change(z.f, 'input')
a.add_input(pd)
old, new = None, pd
self.assertEqual(z.data, (a, 'input', old, new))
a.remove_input(pd)
old, new = pd, None
self.assertEqual(z.data, (a, 'input', old, new))
a.remove_all_inputs()
old, new = None, None
self.assertEqual(z.data, (a, 'input', old, new))
else:
a.add_input_data(pd)
self.assertEqual(a.input, pd)
a.remove_input_data(pd)
self.assertEqual(a.input, None)
a.remove_all_inputs()
self.assertEqual(a.input, None)
def _pipeline_default(self):
sqrt2 = numpy.sqrt(2)
x = -sqrt2 * numpy.cos(numpy.pi * 2. / 3)
y = sqrt2 * numpy.sin(numpy.pi * 2. / 3)
p1 = tvtk.PlaneSource(origin=(0,0,0), \
point1=(-sqrt2,0,1), point2=(x,y,1))
p2 = tvtk.PlaneSource(origin=(0,0,0), \
point1=(x,y,1), point2=(x,-y,1))
p3 = tvtk.PlaneSource(origin=(0,0,0), \
point1=(x,-y,1), point2=(-sqrt2,0,1))
for p in (p1, p2, p3):
p.set_resolution(32, 32)
append = tvtk.AppendPolyData()
append.add_input_connection(p1.output_port)
append.add_input_connection(p2.output_port)
append.add_input_connection(p3.output_port)
scale_f = tvtk.TransformFilter(input_connection=append.output_port,
transform=self.scale)
trans = tvtk.Transform()
trans.rotate_x(90.0)
self.imp_cyl.transform = trans
clip = tvtk.ClipPolyData(input_connection=scale_f.output_port,
clip_function=self.imp_cyl,
inside_out=True)
transF2 = tvtk.TransformFilter(input_connection=clip.output_port,
transform=self.transform)
self.config_pipeline()
return transF2
def _pipeline_default(self):
cyl = self.vtk_disk
norms = tvtk.PolyDataNormals(input_connection=cyl.output_port)
tube = tvtk.TubeFilter(input_connection=self.line.output_port)
append = tvtk.AppendPolyData()
append.add_input_connection(norms.output_port)
append.add_input_connection(tube.output_port)
transF1 = tvtk.TransformFilter(input_connection=append.output_port,
transform=self.cyl_trans)
transF2 = tvtk.TransformFilter(input_connection=transF1.output_port,
transform=self.transform)
self.config_pipeline()
return transF2
def _pipeline_default(self):
grid = self.vtk_grid
#grid.set_execute_method(self.create_grid)
grid.modified()
trans = tvtk.Transform()
trans.rotate_x(90.)
cyl = self.vtk_cylinder
cyl.transform = trans
clip1 = tvtk.ClipVolume(input_connection=grid.output_port,
clip_function=self.vtk_cylinder,
inside_out=1)
self.clip2.set(input_connection=clip1.output_port,
clip_function=self.vtk_sphere1,
inside_out=1)
self.clip3.set(input_connection=self.clip2.output_port,
clip_function=self.vtk_sphere3,
inside_out=1)
clip4 = tvtk.ClipDataSet(input_connection=self.clip3.output_port,
clip_function=self.vtk_sphere2,
inside_out=1)
clip5 = tvtk.ClipDataSet(input_connection=self.clip3.output_port,
clip_function=self.vtk_sphere2,
inside_out=0)
topoly = tvtk.GeometryFilter(input_connection=clip4.output_port)
topoly2 = tvtk.GeometryFilter(input_connection=clip5.output_port)
append = tvtk.AppendPolyData()
append.add_input_connection(topoly.output_port)
append.add_input_connection(topoly2.output_port)
norms = tvtk.PolyDataNormals(input_connection=append.output_port)
transF = tvtk.TransformFilter(input_connection=norms.output_port,
transform=self.transform)
self.on_geometry_changed()
self.config_pipeline()
grid.modified()
return transF
def endEffectorBody(X_s, size, color):
"""
Return a end effector reprsented by a plane
and the appropriate static transform.
"""
apd = tvtk.AppendPolyData()
ls = tvtk.LineSource(point1=(0., 0., 0.),
point2=tuple(X_s.translation()))
p1 = (sva.PTransformd(e.Vector3d.UnitX()*size)*X_s).translation()
p2 = (sva.PTransformd(e.Vector3d.UnitY()*size)*X_s).translation()
ps = tvtk.PlaneSource(origin=tuple(X_s.translation()),
point1=tuple(p1),
point2=tuple(p2),
center=tuple(X_s.translation()))
# apd.add_input(ls.output)
# apd.add_input(ps.output)
# https://github.com/enthought/mayavi/blob/ac5c8e316335078c25461a0bce4a724ae86f1836/tvtk/tests/test_tvtk.py#L586
apd.add_input_data(ls.output)
apd.add_input_data(ps.output)
# pdm = tvtk.PolyDataMapper(input=apd.output)
# arcPdm = tvtk.PolyDataMapper(input=arcSource.output)
pdm = tvtk.PolyDataMapper()
# https://stackoverflow.com/questions/35089379/how-to-fix-traiterror-the-input-trait-of-a-instance-is-read-only
# configure_input_data(textPdm, textSource)# https://github.com/enthought/mayavi/issues/521
pdm.input_connection = apd.output_port
prop = tvtk.Property(color=color)
# https://github.com/enthought/mayavi/issues/521
# arcPdm.input_connection = arcSource.output_port
actor = tvtk.Actor(mapper=pdm, property=prop)
actor.property.color = color
actor.user_transform = tvtk.Transform()
return actor, sva.PTransformd.Identity()
def test_append_poly_data_input(self):
"""Test if AppendPolyData has its get_input wrapped right."""
a = tvtk.AppendPolyData()
self.assertEqual(hasattr(a, 'get_input'), True)
self.assertEqual(a.input, None)
def img2polydata_simple(image, dictionnaire=None, verbose=True):
"""
Convert a |SpatialImage| to a PolyData object with cells surface
: Parameters :
dictionnaire : cell->scalar dictionary
"""
labels_provi = list(np.unique(image))
#ici on filtre déjà les listes
#~ labels= [i for i in labels_provi if i not in list_remove]
labels = labels_provi
try:
labels.remove(0)
except:
pass
try:
labels.remove(1)
except:
pass
#print image.shape
xyz = {}
if verbose: print "on récupère les bounding box"
bbox = nd.find_objects(image)
#print labels
for label in xrange(2, max(labels) + 1):
if not label in labels: continue
if verbose:
print "% until cells are built", label / float(max(labels)) * 100
slices = bbox[label - 1]
label_image = (image[slices] == label)
#here we could add a laplacian function to only have the external shape
mask = nd.laplace(label_image)
label_image[mask != 0] = 0
mask = nd.laplace(label_image)
label_image[mask == 0] = 0
# compute the indices of voxel with adequate label
a = np.array(label_image.nonzero()).T
a += [slices[0].start, slices[1].start, slices[2].start]
#print a.shape
if a.shape[1] == 4:
#print a
pass
else:
xyz[label] = a
vx, vy, vz = image.resolution
polydata = tvtk.AppendPolyData()
polys = {}
filtre = [i for i in xyz.keys() if i in dictionnaire.keys()]
k = 0.0
for c in filtre:
if verbose:
print "% until first polydata is built", k / float(
len(filtre)) * 100
k += 1.
p = xyz[c]
p = p.astype(np.float)
pd = tvtk.PolyData(points=xyz[c].astype(np.float))
pd.point_data.scalars = [
float(dictionnaire[c]) for i in xrange(len(xyz[c]))
]
f = tvtk.VertexGlyphFilter(input=pd)
f2 = tvtk.PointDataToCellData(input=f.output)
polys[c] = f2.output
polydata.add_input(polys[c])
polydata.set_input_array_to_process(0, 0, 0, 0, 0)
return polydata
def img2polydata_complexe(image, list_remove=[], sc=None, verbose=False):
"""
Convert a |SpatialImage| to a PolyData object with cells surface
: Parameters :
list_remove : a list of cells to be removed from the tissue before putting it on screen
sc : if you give a parameter here, it will use it as scalar. you need to give a
cell->scalar dictionary
"""
labels_provi = list(np.unique(image))
#ici on filtre déjà les listes
#~ labels= [i for i in labels_provi if i not in list_remove]
labels = labels_provi
try:
labels.remove(0)
except:
pass
try:
labels.remove(1)
except:
pass
#print image.shape
xyz = {}
if verbose: print "on récupère les bounding box"
bbox = nd.find_objects(image)
#print labels
for label in xrange(2, max(labels) + 1):
if not label in labels: continue
if verbose:
print "% until cells are built", label / float(max(labels)) * 100
slices = bbox[label - 1]
label_image = (image[slices] == label)
#here we could add a laplacian function to only have the external shape
mask = nd.laplace(label_image)
label_image[mask != 0] = 0
mask = nd.laplace(label_image)
label_image[mask == 0] = 0
# compute the indices of voxel with adequate label
a = np.array(label_image.nonzero()).T
a += [slices[0].start, slices[1].start, slices[2].start]
#print a.shape
if a.shape[1] == 4:
#print a
pass
else:
xyz[label] = a
vx, vy, vz = image.resolution
polydata = tvtk.AppendPolyData()
polys = {}
filtre = [i for i in xyz.keys() if i not in list_remove]
k = 0.0
for c in filtre:
if verbose:
print "% until first polydata is built", k / float(
len(filtre)) * 100
k += 1.
p = xyz[c]
p = p.astype(np.float)
pd = tvtk.PolyData(points=xyz[c].astype(np.float))
if sc:
try:
pd.point_data.scalars = [
float(sc[c]) for i in xrange(len(xyz[c]))
]
except:
pd.point_data.scalars = [float(0) for i in xrange(len(xyz[c]))]
else:
pd.point_data.scalars = [float(c) for i in xrange(len(xyz[c]))]
f = tvtk.VertexGlyphFilter(input=pd)
f2 = tvtk.PointDataToCellData(input=f.output)
polys[c] = f2.output
polydata.add_input(polys[c])
polydata.set_input_array_to_process(0, 0, 0, 0, 0)
try:
labels_not_in_sc = list(set(list(np.unique(image))) - set(sc))
except TypeError:
labels_not_in_sc = []
if 0 in labels_not_in_sc: labels_not_in_sc.remove(0)
if 1 in labels_not_in_sc: labels_not_in_sc.remove(1)
filtre = [
i for i in xyz.keys() if i in list_remove or i in labels_not_in_sc
]
if filtre != []:
polydata2 = tvtk.AppendPolyData()
polys2 = {}
k = 0.0
for c in filtre:
if verbose:
print "% until second polydata is built", k / float(
len(filtre)) * 100
k += 1.
p = xyz[c]
p = p.astype(np.float)
pd = tvtk.PolyData(points=xyz[c].astype(np.float))
pd.point_data.scalars = [0. for i in xrange(len(xyz[c]))]
f = tvtk.VertexGlyphFilter(input=pd)
f2 = tvtk.PointDataToCellData(input=f.output)
polys2[c] = f2.output
polydata2.add_input(polys2[c])
else:
polydata2 = tvtk.AppendPolyData()
polydata2.set_input_array_to_process(0, 0, 0, 0, 0)
polys2 = {}
pd = tvtk.PolyData()
polydata2.add_input(pd)
return polydata, polydata2
