def __init__(self, atoms):
assert isinstance(atoms, Atoms)
self.pbc = atoms.get_pbc()
cell = atoms.get_cell()
"""
if not isinstance(cell, np.ndarray):
cell = np.array(cell)
if cell.shape == (3,):
cell = np.diag(cell)
assert cell.dtype == float and cell.shape == (3, 3)
"""
self.vtk_outline = vtkOutlineSource()
if (cell - np.diag(cell.diagonal())).any():
corners = np.empty((8, 3), dtype=float)
# edges = [map(int,[(i-1)%2==0,i%4>=2,i>=4]) for i in range(8)]
for c,a in enumerate([(0, 0, 0), (1, 0, 0), (0, 1, 0), (1, 1, 0), \
(0, 0, 1), (1, 0, 1), (0, 1, 1), (1, 1, 1)]):
corners[c] = np.dot(a, cell)
self.bbox = np.array(zip(np.min(corners, axis=0), \
np.max(corners, axis=0))).ravel()
self.vtk_outline.SetCorners(corners.ravel())
self.vtk_outline.SetBoxTypeToOriented()
else:
self.bbox = np.array(zip(np.zeros(3), cell.diagonal())).ravel()
self.vtk_outline.SetBounds(self.bbox)
vtkPolyDataModule.__init__(self, self.vtk_outline)
def __init__(self, atoms):
assert isinstance(atoms, Atoms)
cell = atoms.get_cell()
"""
if not isinstance(cell, np.ndarray):
cell = np.array(cell)
if cell.shape == (3,):
cell = np.diag(cell)
assert cell.dtype == float and cell.shape == (3, 3)
"""
#TODO bounding box with general unit cell
diagcell = np.diag(cell.diagonal())
assert (cell == diagcell).all(), 'Unit cell must be orthogonal'
self.bbox = np.array(zip(np.zeros(3),cell.diagonal())).ravel()
self.pbc = atoms.get_pbc()
self.vtk_outline = vtkOutlineSource()
self.vtk_outline.SetBounds(self.bbox)
vtkPolyDataModule.__init__(self, self.vtk_outline)
def __init__(self, atoms):
assert isinstance(atoms, Atoms)
self.pbc = atoms.get_pbc()
cell = atoms.get_cell()
"""
if not isinstance(cell, np.ndarray):
cell = np.array(cell)
if cell.shape == (3,):
cell = np.diag(cell)
assert cell.dtype == float and cell.shape == (3, 3)
"""
self.vtk_outline = vtkOutlineSource()
if (cell - np.diag(cell.diagonal())).any():
corners = np.empty((8,3), dtype=float)
# edges = [map(int,[(i-1)%2==0,i%4>=2,i>=4]) for i in range(8)]
for c,a in enumerate([(0, 0, 0), (1, 0, 0), (0, 1, 0), (1, 1, 0), \
(0, 0, 1), (1, 0, 1), (0, 1, 1), (1, 1, 1)]):
corners[c] = np.dot(a, cell)
self.bbox = np.array(list(zip(np.min(corners, axis=0), \
np.max(corners, axis=0)))).ravel()
self.vtk_outline.SetCorners(corners.ravel())
self.vtk_outline.SetBoxTypeToOriented()
else:
self.bbox = np.array(list(zip(np.zeros(3),cell.diagonal()))).ravel()
self.vtk_outline.SetBounds(self.bbox)
vtkPolyDataModule.__init__(self, self.vtk_outline)
def __init__(self, data, cell, vtk_renderer, contours=1, depthsort=True):
#TODO don't require vtk_renderer... implement vtkScene
#TODO contour values from list or autocontours if int
# Make sure data argument is a valid array
if not isinstance(data, np.ndarray):
data = np.array(data)
vtkVolumeGrid.__init__(self, data.shape, cell)
self.vtk_iso = vtkContourFilter() #vtkMarchingContourFilter?
self.vtk_iso.SetInput(self.get_structured_points()) #TODO non-orthogonal
self.vtk_iso.SetValue(0, 0.25)
self.vtk_iso.SetValue(1, -0.25)
self.smoothpipe = vtkSurfaceSmootherPipeline(self, vtk_iso)
#TODO use vtkDepthSortPipeline - but vtkPolyDataModule isn't a pipeline
self.depthsort = depthsort
if self.depthsort:
# The depht sort object is set up to generate scalars representing
# the sort depth. A camera is assigned for the sorting. The camera
# defines the sort vector (position and focal point).
self.vtk_ds = vtkDepthSortPolyData()
self.vtk_ds.SetCamera(vtk_renderer.GetActiveCamera())
self.vtk_ds.SetInputConnection(self.vtk_iso.GetOutputPort())
self.vtk_ds.SetDirectionToBackToFront()
#vtk_ds.SetVector(1, 1, 1)
#vtk_ds.SortScalarsOn()
#vtk_ds.Update()
vtk_renderer.ResetCamera()
vtkPolyDataModule.__init__(self, self.vtk_ds)
else:
vtkPolyDataModule.__init__(self, self.vtk_iso)
#TODO add color function
"""
