def add_data_to_dataset(self, dataset, data):
"""Add point and cell data to the dataset."""
dm = DatasetManager(dataset=dataset)
for key, val in six.iteritems(data):
if val.mode == 'vertex':
aux = self._reshape(val.data, self.dim)
dm.add_array(aux, key, 'point')
elif val.mode == 'cell':
aux = self._reshape(val.data, self.dim)
dm.add_array(aux, key, 'cell')
def add_data_to_dataset(self, dataset, data):
"""Add point and cell data to the dataset."""
dm = DatasetManager(dataset=dataset)
for key, val in six.iteritems(data):
if val.mode == 'vertex':
aux = self._reshape(val.data, self.dim)
dm.add_array(aux, key, 'point')
elif val.mode == 'cell':
aux = self._reshape(val.data, self.dim)
dm.add_array(aux, key, 'cell')
def create_source(self):
"""
Create a VTK source from data in a SfePy-supported file.
Notes
-----
All data need to be set here, otherwise time stepping will not
work properly - data added by user later will be thrown away on
time step change.
"""
if self.io is None:
self.read_common(self.filename)
dataset = self.create_dataset()
try:
out = self.io.read_data(self.step)
except ValueError:
out = None
if out is not None:
self.add_data_to_dataset(dataset, out)
if self.mat_id_name is not None:
mat_id = self.mesh.cmesh.cell_groups
if self.single_color:
rm = mat_id.min(), mat_id.max()
mat_id[mat_id > rm[0]] = rm[1]
dm = DatasetManager(dataset=dataset)
dm.add_array(mat_id, self.mat_id_name, 'cell')
src = VTKDataSource(data=dataset)
# src.print_traits()
# debug()
return src
def create_source(self):
"""
Create a VTK source from data in a SfePy-supported file.
Notes
-----
All data need to be set here, otherwise time stepping will not
work properly - data added by user later will be thrown away on
time step change.
"""
if self.io is None:
self.read_common(self.filename)
dataset = self.create_dataset()
try:
out = self.io.read_data(self.step)
except ValueError:
out = None
if out is not None:
self.add_data_to_dataset(dataset, out)
if self.mat_id_name is not None:
mat_id = self.mesh.cmesh.cell_groups
if self.single_color:
rm = mat_id.min(), mat_id.max()
mat_id[mat_id > rm[0]] = rm[1]
dm = DatasetManager(dataset=dataset)
dm.add_array(mat_id, self.mat_id_name, 'cell')
src = VTKDataSource(data=dataset)
# src.print_traits()
# debug()
return src
def add_data_to_dataset(self, dataset, data):
"""Add point and cell data to the dataset."""
dim = self.dim
sym = (dim + 1) * dim // 2
dm = DatasetManager(dataset=dataset)
for key, val in six.iteritems(data):
vd = val.data
## print vd.shape
if val.mode == 'vertex':
if vd.shape[1] == 1:
aux = vd.reshape((vd.shape[0], ))
elif vd.shape[1] == 2:
zz = nm.zeros((vd.shape[0], 1), dtype=vd.dtype)
aux = nm.c_[vd, zz]
elif vd.shape[1] == 3:
aux = vd
else:
raise ValueError('unknown vertex data format! (%s)'\
% vd.shape)
dm.add_array(aux, key, 'point')
elif val.mode == 'cell':
ne, aux, nr, nc = vd.shape
if (nr == 1) and (nc == 1):
aux = vd.reshape((ne, ))
elif (nr == dim) and (nc == 1):
if dim == 3:
aux = vd.reshape((ne, dim))
else:
zz = nm.zeros((vd.shape[0], 1), dtype=vd.dtype)
aux = nm.c_[vd.squeeze(), zz]
elif (((nr == sym) or (nr == (dim * dim))) and (nc == 1)) \
or ((nr == dim) and (nc == dim)):
vd = vd.squeeze()
if dim == 3:
if nr == sym:
aux = vd[:, [0, 3, 4, 3, 1, 5, 4, 5, 2]]
elif nr == (dim * dim):
aux = vd[:, [0, 3, 4, 6, 1, 5, 7, 8, 2]]
else:
aux = vd.reshape((vd.shape[0], dim * dim))
else:
zz = nm.zeros((vd.shape[0], 1), dtype=vd.dtype)
if nr == sym:
aux = nm.c_[vd[:, [0, 2]], zz, vd[:, [2, 1]], zz,
zz, zz, zz]
elif nr == (dim * dim):
aux = nm.c_[vd[:, [0, 2]], zz, vd[:, [3, 1]], zz,
zz, zz, zz]
else:
aux = nm.c_[vd[:, 0, [0, 1]], zz, vd[:, 1, [0, 1]],
zz, zz, zz, zz]
dm.add_array(aux, key, 'cell')
def add_data_to_dataset(self, dataset, data):
"""Add point and cell data to the dataset."""
dim = self.dim
sym = (dim + 1) * dim / 2
dm = DatasetManager(dataset=dataset)
for key, val in data.iteritems():
vd = val.data
## print vd.shape
if val.mode == 'vertex':
if vd.shape[1] == 1:
aux = vd.reshape((vd.shape[0],))
elif vd.shape[1] == 2:
zz = nm.zeros((vd.shape[0], 1), dtype=vd.dtype)
aux = nm.c_[vd, zz]
elif vd.shape[1] == 3:
aux = vd
else:
raise ValueError('unknown vertex data format! (%s)'\
% vd.shape)
dm.add_array(aux, key, 'point')
elif val.mode == 'cell':
ne, aux, nr, nc = vd.shape
if (nr == 1) and (nc == 1):
aux = vd.reshape((ne,))
elif (nr == dim) and (nc == 1):
if dim == 3:
aux = vd.reshape((ne, dim))
else:
zz = nm.zeros((vd.shape[0], 1), dtype=vd.dtype);
aux = nm.c_[vd.squeeze(), zz]
elif (((nr == sym) or (nr == (dim * dim))) and (nc == 1)) \
or ((nr == dim) and (nc == dim)):
vd = vd.squeeze()
if dim == 3:
if nr == sym:
aux = vd[:,[0,3,4,3,1,5,4,5,2]]
elif nr == (dim * dim):
aux = vd[:,[0,3,4,6,1,5,7,8,2]]
else:
aux = vd.reshape((vd.shape[0], dim*dim))
else:
zz = nm.zeros((vd.shape[0], 1), dtype=vd.dtype);
if nr == sym:
aux = nm.c_[vd[:,[0,2]], zz, vd[:,[2,1]],
zz, zz, zz, zz]
elif nr == (dim * dim):
aux = nm.c_[vd[:,[0,2]], zz, vd[:,[3,1]],
zz, zz, zz, zz]
else:
aux = nm.c_[vd[:,0,[0,1]], zz, vd[:,1,[0,1]],
zz, zz, zz, zz]
dm.add_array(aux, key, 'cell')
class MeshDiagnostics(Filter):
"""
Identifies stiff elements of a solid mesh.
Also includes diagnostics from vtkMeshQuality:
<http://www.vtk.org/doc/release/5.0/html/a01739.html>
"""
# The version of this class. Used for persistence.
__version__ = 0
_dataset_manager = Instance(DatasetManager, allow_none=False)
_surface_grid = Instance(tvtk.PointSet, allow_none=False)
stiff_elements = Bool
_first_time_stiff_elements = Bool(True)
_mesh_quality_filter = Instance(tvtk.MeshQuality, args=(), allow_none=False)
tet_quality_measure = Enum('Edge ratio', 'Aspect ratio', 'Radius ratio', 'Min angle', 'Frobenius norm', 'Volume')
triangle_quality_measure = Enum('Edge ratio', 'Aspect ratio', 'Radius ratio', 'Min angle', 'Frobenius norm')
quad_quality_measure = Enum('Edge ratio', 'Aspect ratio', 'Radius ratio', 'Min angle', 'Med Frobenius norm', 'Max Frobenius norm')
hex_quality_measure = Enum('Edge ratio')
tet_stats = triangle_stats = quad_stats = hex_stats = Tuple(Float,Float,Float,Float,Float)
######################################################################
# The view.
######################################################################
stats_editor = TupleEditor(labels=['Minimum','Average','Maximum','Variance','Number of cells'])
traits_view = \
View(
Item(name='stiff_elements'),
Group(
Group(
Item(name='tet_quality_measure'),
Item(name='tet_stats', style='custom', editor=stats_editor),
label='Tetrahedron quality measure',
show_labels=False,
show_border=True,
),
Group(
Item(name='triangle_quality_measure'),
Item(name='triangle_stats', style='custom', editor=stats_editor),
label='Triangle quality measure',
show_labels=False,
show_border=True,
),
Group(
Item(name='quad_quality_measure'),
Item(name='quad_stats', style='custom', editor=stats_editor),
label='Quadrilateral quality measure',
show_labels=False,
show_border=True,
),
Group(
Item(name='hex_quality_measure'),
Item(name='hex_stats', style='custom', editor=stats_editor),
label='Hexahedron quality measure',
show_labels=False,
show_border=True,
),
enabled_when='stiff_elements==False',
show_border=False
),
width=300
)
"""
Hexahedron quality measure - EdgeRatio
Quadrilateral quality measure - EdgeRatio
- AspectRatio
- RadiusRatio
- MinAngle
- MedFrobeniusNorm
- MaxFrobeniusNorm
Tetrahedron quality measure - EdgeRatio
- AspectRatio
- RadiusRatio
- MinAngle
- FrobeniusNorm
- Volume (compatibility mode on/off)
Triangle quality measure - EdgeRatio
- AspectRatio
- RadiusRatio
- MinAngle
- FrobeniusNorm
"""
######################################################################
# `Filter` interface.
######################################################################
def update_pipeline(self):
if len(self.inputs) == 0 or len(self.inputs[0].outputs) == 0:
return
self._mesh_quality_filter.set_input(self.inputs[0].outputs[0])
for type in ['tet','triangle','quad','hex']:
self._change_quality_measure(type, 'Edge ratio')
self._mesh_quality_filter.update()
self._set_outputs([self._mesh_quality_filter.output])
def update_data(self):
self.data_changed = True
######################################################################
# Non-public interface.
######################################################################
def _stiff_elements_changed(self, value):
if (value):
self._find_stiff_elements()
self._set_outputs([self._surface_grid])
else:
self._set_outputs([self._mesh_quality_filter.output])
def _tet_quality_measure_changed(self, value):
self._change_quality_measure('tet', value)
def _change_quality_measure(self, cell_type, quality_measure):
if (quality_measure == 'Volume'):
self._mesh_quality_filter.compatibility_mode = True
self._mesh_quality_filter.volume = True
else:
self._mesh_quality_filter.compatibility_mode = False
self._mesh_quality_filter.volume = False
quality_measure_names = {'Edge ratio':'edge_ratio', 'Aspect ratio':'aspect_ratio', 'Radius ratio':'radius_ratio',
'Min angle':'min_angle', 'Frobenius norm':'frobenius_norm', 'Max Frobenius norm':'max_frobenius_norm',
'Med Frobenius norm':'med_frobenius_norm'}
setattr(self._mesh_quality_filter, '%s_quality_measure' %cell_type, quality_measure_names.get(quality_measure))
self._mesh_quality_filter.update()
self._set_outputs([self._mesh_quality_filter.output])
cell_type_fullnames = {'tet':'Tetrahedron', 'triangle':'Triangle', 'quad':'Quadrilateral', 'hex':'Hexahedron'}
stats = self._mesh_quality_filter.output.field_data.get_array('Mesh %s Quality' %cell_type_fullnames.get(cell_type))[0]
setattr(self, '%s_stats' %cell_type, stats)
def _find_stiff_elements(self):
if (self._first_time_stiff_elements):
self._first_time_stiff_elements = False
self._surface_grid = type(self.inputs[0].outputs[0])()
self._surface_grid.copy_structure(self.inputs[0].outputs[0])
if (self._surface_grid.points.data_type == 'double'):
# tvtk.DataSetSurfaceFilter produces surface points as float
# so we need to convert input points from doubles to floats
# if necessary
float_points = array(self._surface_grid.points, 'float32')
self._surface_grid.points = float_points
self._dataset_manager = DatasetManager(dataset=self._surface_grid)
surface_points = self._get_surface_points()
self._add_stiff_elements(surface_points)
def _get_surface_points(self):
surface_filter = tvtk.DataSetSurfaceFilter()
surface_filter.set_input(self._surface_grid)
surface_filter.update()
return surface_filter.output.points
def _add_stiff_elements(self, surface_points):
stiff_elements = []
surface_points = Set(surface_points)
for i in range(self._surface_grid.number_of_cells):
cell = self._surface_grid.get_cell(i)
points = Set(cell.points)
val = int(points.issubset(surface_points))
stiff_elements.append(val)
array_name = 'Stiff Elements'
self._dataset_manager.add_array(array(stiff_elements), array_name, 'cell')
self._dataset_manager.activate(array_name, 'cell')
class MeshDiagnostics(Filter):
"""
Identifies stiff elements of a solid mesh.
Also includes diagnostics from vtkMeshQuality:
<http://www.vtk.org/doc/release/5.0/html/a01739.html>
"""
# The version of this class. Used for persistence.
__version__ = 0
_dataset_manager = Instance(DatasetManager, allow_none=False)
_surface_grid = Instance(tvtk.PointSet, allow_none=False)
stiff_elements = Bool
_first_time_stiff_elements = Bool(True)
_mesh_quality_filter = Instance(tvtk.MeshQuality,
args=(),
allow_none=False)
tet_quality_measure = Enum('Edge ratio', 'Aspect ratio', 'Radius ratio',
'Min angle', 'Frobenius norm', 'Volume')
triangle_quality_measure = Enum('Edge ratio', 'Aspect ratio',
'Radius ratio', 'Min angle',
'Frobenius norm')
quad_quality_measure = Enum('Edge ratio', 'Aspect ratio', 'Radius ratio',
'Min angle', 'Med Frobenius norm',
'Max Frobenius norm')
hex_quality_measure = Enum('Edge ratio')
tet_stats = triangle_stats = quad_stats = hex_stats = Tuple(
Float, Float, Float, Float, Float)
######################################################################
# The view.
######################################################################
stats_editor = TupleEditor(labels=[
'Minimum', 'Average', 'Maximum', 'Variance', 'Number of cells'
])
traits_view = \
View(
Item(name='stiff_elements'),
Group(
Group(
Item(name='tet_quality_measure'),
Item(name='tet_stats', style='custom', editor=stats_editor),
label='Tetrahedron quality measure',
show_labels=False,
show_border=True,
),
Group(
Item(name='triangle_quality_measure'),
Item(name='triangle_stats', style='custom', editor=stats_editor),
label='Triangle quality measure',
show_labels=False,
show_border=True,
),
Group(
Item(name='quad_quality_measure'),
Item(name='quad_stats', style='custom', editor=stats_editor),
label='Quadrilateral quality measure',
show_labels=False,
show_border=True,
),
Group(
Item(name='hex_quality_measure'),
Item(name='hex_stats', style='custom', editor=stats_editor),
label='Hexahedron quality measure',
show_labels=False,
show_border=True,
),
enabled_when='stiff_elements==False',
show_border=False
),
width=300
)
"""
Hexahedron quality measure - EdgeRatio
Quadrilateral quality measure - EdgeRatio
- AspectRatio
- RadiusRatio
- MinAngle
- MedFrobeniusNorm
- MaxFrobeniusNorm
Tetrahedron quality measure - EdgeRatio
- AspectRatio
- RadiusRatio
- MinAngle
- FrobeniusNorm
- Volume (compatibility mode on/off)
Triangle quality measure - EdgeRatio
- AspectRatio
- RadiusRatio
- MinAngle
- FrobeniusNorm
"""
######################################################################
# `Filter` interface.
######################################################################
def update_pipeline(self):
if len(self.inputs) == 0 or len(self.inputs[0].outputs) == 0:
return
self._mesh_quality_filter.set_input(self.inputs[0].outputs[0])
for type in ['tet', 'triangle', 'quad', 'hex']:
self._change_quality_measure(type, 'Edge ratio')
self._mesh_quality_filter.update()
self._set_outputs([self._mesh_quality_filter.output])
def update_data(self):
self.data_changed = True
######################################################################
# Non-public interface.
######################################################################
def _stiff_elements_changed(self, value):
if (value):
self._find_stiff_elements()
self._set_outputs([self._surface_grid])
else:
self._set_outputs([self._mesh_quality_filter.output])
def _tet_quality_measure_changed(self, value):
self._change_quality_measure('tet', value)
def _change_quality_measure(self, cell_type, quality_measure):
if (quality_measure == 'Volume'):
self._mesh_quality_filter.compatibility_mode = True
self._mesh_quality_filter.volume = True
else:
self._mesh_quality_filter.compatibility_mode = False
self._mesh_quality_filter.volume = False
quality_measure_names = {
'Edge ratio': 'edge_ratio',
'Aspect ratio': 'aspect_ratio',
'Radius ratio': 'radius_ratio',
'Min angle': 'min_angle',
'Frobenius norm': 'frobenius_norm',
'Max Frobenius norm': 'max_frobenius_norm',
'Med Frobenius norm': 'med_frobenius_norm'
}
setattr(self._mesh_quality_filter,
'%s_quality_measure' % cell_type,
quality_measure_names.get(quality_measure))
self._mesh_quality_filter.update()
self._set_outputs([self._mesh_quality_filter.output])
cell_type_fullnames = {
'tet': 'Tetrahedron',
'triangle': 'Triangle',
'quad': 'Quadrilateral',
'hex': 'Hexahedron'
}
stats = self._mesh_quality_filter.output.field_data.get_array(
'Mesh %s Quality' % cell_type_fullnames.get(cell_type))[0]
setattr(self, '%s_stats' % cell_type, stats)
def _find_stiff_elements(self):
if (self._first_time_stiff_elements):
self._first_time_stiff_elements = False
self._surface_grid = type(self.inputs[0].outputs[0])()
self._surface_grid.copy_structure(self.inputs[0].outputs[0])
if (self._surface_grid.points.data_type == 'double'):
# tvtk.DataSetSurfaceFilter produces surface points as float
# so we need to convert input points from doubles to floats
# if necessary
float_points = array(self._surface_grid.points, 'float32')
self._surface_grid.points = float_points
self._dataset_manager = DatasetManager(dataset=self._surface_grid)
surface_points = self._get_surface_points()
self._add_stiff_elements(surface_points)
def _get_surface_points(self):
surface_filter = tvtk.DataSetSurfaceFilter()
surface_filter.set_input(self._surface_grid)
surface_filter.update()
return surface_filter.output.points
def _add_stiff_elements(self, surface_points):
stiff_elements = []
surface_points = Set(surface_points)
for i in range(self._surface_grid.number_of_cells):
cell = self._surface_grid.get_cell(i)
points = Set(cell.points)
val = int(points.issubset(surface_points))
stiff_elements.append(val)
array_name = 'Stiff Elements'
self._dataset_manager.add_array(array(stiff_elements), array_name,
'cell')
self._dataset_manager.activate(array_name, 'cell')
