def _pickFull(self, context):
"""Perform picking in this item at given widget position.
:param PickContext context: Current picking context
:return: Object holding the results or None
:rtype: Union[None,PickingResult]
"""
rayObject = context.getPickingSegment(frame=self._getScenePrimitive())
if rayObject is None:
return None
rayObject = rayObject[:, :3]
data = self.getData(copy=False)
bins = utils.segmentVolumeIntersect(rayObject,
numpy.array(data.shape) - 1)
if bins is None:
return None
# gather bin data
offsets = [(i, j, k) for i in (0, 1) for j in (0, 1) for k in (0, 1)]
indices = bins[:, numpy.newaxis, :] + offsets
binsData = data[indices[:, :, 0], indices[:, :, 1], indices[:, :, 2]]
# binsData.shape = nbins, 8
# TODO up-to this point everything can be done once for all isosurfaces
# check bin candidates
level = self.getLevel()
mask = numpy.logical_and(
numpy.nanmin(binsData, axis=1) <= level,
level <= numpy.nanmax(binsData, axis=1))
bins = bins[mask]
binsData = binsData[mask]
if len(bins) == 0:
return None # No bin candidate
# do picking on candidates
intersections = []
depths = []
for currentBin, data in zip(bins, binsData):
mc = MarchingCubes(data.reshape(2, 2, 2), isolevel=level)
points = mc.get_vertices() + currentBin
triangles = points[mc.get_indices()]
t = glu.segmentTrianglesIntersection(rayObject, triangles)[1]
t = numpy.unique(t) # Duplicates happen on triangle edges
if len(t) != 0:
# Compute intersection points and get closest data point
points = t.reshape(
-1, 1) * (rayObject[1] - rayObject[0]) + rayObject[0]
# Get closest data points by rounding to int
intersections.extend(points)
depths.extend(t)
if len(intersections) == 0:
return None # No intersected triangles
intersections = numpy.array(intersections)[numpy.argsort(depths)]
indices = numpy.transpose(numpy.round(intersections).astype(numpy.int))
return PickingResult(self, positions=intersections, indices=indices)
def _pickFull(self, context):
"""Perform picking in this item at given widget position.
:param PickContext context: Current picking context
:return: Object holding the results or None
:rtype: Union[None,PickingResult]
"""
rayObject = context.getPickingSegment(frame=self._getScenePrimitive())
if rayObject is None:
return None
rayObject = rayObject[:, :3]
data = self.getData(copy=False)
bins = utils.segmentVolumeIntersect(
rayObject, numpy.array(data.shape) - 1)
if bins is None:
return None
# gather bin data
offsets = [(i, j, k) for i in (0, 1) for j in (0, 1) for k in (0, 1)]
indices = bins[:, numpy.newaxis, :] + offsets
binsData = data[indices[:, :, 0], indices[:, :, 1], indices[:, :, 2]]
# binsData.shape = nbins, 8
# TODO up-to this point everything can be done once for all isosurfaces
# check bin candidates
level = self.getLevel()
mask = numpy.logical_and(numpy.nanmin(binsData, axis=1) <= level,
level <= numpy.nanmax(binsData, axis=1))
bins = bins[mask]
binsData = binsData[mask]
if len(bins) == 0:
return None # No bin candidate
# do picking on candidates
intersections = []
depths = []
for currentBin, data in zip(bins, binsData):
mc = MarchingCubes(data.reshape(2, 2, 2), isolevel=level)
points = mc.get_vertices() + currentBin
triangles = points[mc.get_indices()]
t = utils.segmentTrianglesIntersection(rayObject, triangles)[1]
t = numpy.unique(t) # Duplicates happen on triangle edges
if len(t) != 0:
# Compute intersection points and get closest data point
points = t.reshape(-1, 1) * (rayObject[1] - rayObject[0]) + rayObject[0]
# Get closest data points by rounding to int
intersections.extend(points)
depths.extend(t)
if len(intersections) == 0:
return None # No intersected triangles
intersections = numpy.array(intersections)[numpy.argsort(depths)]
indices = numpy.transpose(numpy.round(intersections).astype(numpy.int))
return PickingResult(self, positions=intersections, indices=indices)
def _updateScenePrimitive(self):
"""Update underlying mesh"""
self._getScenePrimitive().children = []
data = self.getData(copy=False)
if data is None:
if self.isAutoLevel():
self._level = float('nan')
else:
if self.isAutoLevel():
st = time.time()
try:
level = float(self.getAutoLevelFunction()(data))
except Exception:
module_ = self.getAutoLevelFunction().__module__
name = self.getAutoLevelFunction().__name__
_logger.error(
"Error while executing iso level function %s.%s",
module_,
name,
exc_info=True)
level = float('nan')
else:
_logger.info(
'Computed iso-level in %f s.', time.time() - st)
if level != self._level:
self._level = level
self._updated(Item3DChangedType.ISO_LEVEL)
if not numpy.isfinite(self._level):
return
st = time.time()
vertices, normals, indices = MarchingCubes(
data,
isolevel=self._level)
_logger.info('Computed iso-surface in %f s.', time.time() - st)
if len(vertices) == 0:
return
else:
mesh = primitives.Mesh3D(vertices,
colors=self._color,
normals=normals,
mode='triangles',
indices=indices)
self._getScenePrimitive().children = [mesh]
def _update(self):
"""Update underlying mesh"""
self._group.children = []
if self._data is None:
if self.isAutoLevel():
self._level = float('nan')
else:
if self.isAutoLevel():
st = time.time()
try:
level = float(self.getAutoLevelFunction()(self._data))
except Exception:
module = self.getAutoLevelFunction().__module__
name = self.getAutoLevelFunction().__name__
_logger.error(
"Error while executing iso level function %s.%s",
module,
name,
exc_info=True)
level = float('nan')
else:
_logger.info('Computed iso-level in %f s.',
time.time() - st)
if level != self._level:
self._level = level
self.sigLevelChanged.emit(level)
if numpy.isnan(self._level):
return
st = time.time()
vertices, normals, indices = MarchingCubes(self._data,
isolevel=self._level)
_logger.info('Computed iso-surface in %f s.', time.time() - st)
if len(vertices) == 0:
return
else:
mesh = primitives.Mesh3D(vertices,
colors=self._color,
normals=normals,
mode='triangles',
indices=indices)
self._group.children = [mesh]
def _computeIsosurface(self):
"""Compute isosurface for current state.
:return: (vertices, normals, indices) arrays
:rtype: List[Union[None,numpy.ndarray]]
"""
data = self.getData(copy=False)
if data is None:
if self.isAutoLevel():
self._level = float('nan')
else:
if self.isAutoLevel():
st = time.time()
try:
level = float(self.getAutoLevelFunction()(data))
except Exception:
module_ = self.getAutoLevelFunction().__module__
name = self.getAutoLevelFunction().__name__
_logger.error(
"Error while executing iso level function %s.%s",
module_,
name,
exc_info=True)
level = float('nan')
else:
_logger.info(
'Computed iso-level in %f s.', time.time() - st)
if level != self._level:
self._level = level
self._updated(Item3DChangedType.ISO_LEVEL)
if numpy.isfinite(self._level):
st = time.time()
vertices, normals, indices = MarchingCubes(
data,
isolevel=self._level)
_logger.info('Computed iso-surface in %f s.', time.time() - st)
if len(vertices) != 0:
return vertices, normals, indices
return None, None, None