improvements to grid generation

- handling of origin
- inverse functions: calculate grid,size,origin from regular coordinates
(cell or node). should replace corresponding functionality in util
This commit is contained in:
Martin Diehl 2019-12-08 17:57:02 +01:00
parent 75e93d9f0c
commit 8d0c4310cf
1 changed files with 57 additions and 9 deletions

View File

@ -57,12 +57,13 @@ def gradient(size,field):
return np.fft.irfftn(gradient,axes=(0,1,2),s=field.shape[:3]) return np.fft.irfftn(gradient,axes=(0,1,2),s=field.shape[:3])
def cell_coord0(grid,size): def cell_coord0(grid,size,origin=np.zeros(3)):
"""Cell center positions (undeformed).""" """Cell center positions (undeformed)."""
delta = size/grid*0.5 start = origin + size/grid*.5
x, y, z = np.meshgrid(np.linspace(delta[2],size[2]-delta[2],grid[2]), end = origin - size/grid*.5 + size
np.linspace(delta[1],size[1]-delta[1],grid[1]), x, y, z = np.meshgrid(np.linspace(start[2],end[2],grid[2]),
np.linspace(delta[0],size[0]-delta[0],grid[0]), np.linspace(start[1],end[1],grid[1]),
np.linspace(start[0],end[0],grid[0]),
indexing = 'ij') indexing = 'ij')
return np.concatenate((z[:,:,:,None],y[:,:,:,None],x[:,:,:,None]),axis = 3) return np.concatenate((z[:,:,:,None],y[:,:,:,None],x[:,:,:,None]),axis = 3)
@ -88,12 +89,37 @@ def cell_displacement_avg(size,F):
F_avg = np.average(F,axis=(0,1,2)) F_avg = np.average(F,axis=(0,1,2))
return np.einsum('ml,ijkl->ijkm',F_avg-np.eye(3),cell_coord0(F.shape[:3],size)) return np.einsum('ml,ijkl->ijkm',F_avg-np.eye(3),cell_coord0(F.shape[:3],size))
def cell_coord0_2_DNA(coord0,ordered=False):
coords = [np.unique(coord0[:,i]) for i in range(3)]
mincorner = np.array(list(map(min,coords)))
maxcorner = np.array(list(map(max,coords)))
grid = np.array(list(map(len,coords)),'i')
size = grid/np.maximum(grid-1,1) * (maxcorner-mincorner)
delta = size/grid
origin = mincorner - delta*.5
def node_coord0(grid,size): if grid.prod() != len(coord0):
raise ValueError('Data count {} does not match grid {}.'.format(len(coord0),grid))
start = origin + delta*.5
end = origin + size -delta*.5
if not np.allclose(coords[0],np.linspace(start[0],end[0],grid[0])) and \
np.allclose(coords[1],np.linspace(start[1],end[1],grid[1])) and \
np.allclose(coords[2],np.linspace(start[2],end[2],grid[2])):
raise ValueError('Regular grid spacing violated.')
if ordered:
if not np.allclose(coord0.reshape(tuple(grid[::-1])+(3,)),cell_coord0(grid,size,origin)):
raise ValueError('Input data is not a regular grid.')
return (grid,size,origin)
def node_coord0(grid,size,origin=np.zeros(3)):
"""Nodal positions (undeformed).""" """Nodal positions (undeformed)."""
x, y, z = np.meshgrid(np.linspace(0,size[2],1+grid[2]), x, y, z = np.meshgrid(np.linspace(origin[2],size[2]+origin[2],1+grid[2]),
np.linspace(0,size[1],1+grid[1]), np.linspace(origin[1],size[1]+origin[1],1+grid[1]),
np.linspace(0,size[0],1+grid[0]), np.linspace(origin[0],size[0]+origin[0],1+grid[0]),
indexing = 'ij') indexing = 'ij')
return np.concatenate((z[:,:,:,None],y[:,:,:,None],x[:,:,:,None]),axis = 3) return np.concatenate((z[:,:,:,None],y[:,:,:,None],x[:,:,:,None]),axis = 3)
@ -124,6 +150,28 @@ def node_2_cell(node_data):
return c[:-1,:-1,:-1] return c[:-1,:-1,:-1]
def node_coord0_2_DNA(coord0,ordered=False):
coords = [np.unique(coord0[:,i]) for i in range(3)]
mincorner = np.array(list(map(min,coords)))
maxcorner = np.array(list(map(max,coords)))
grid = np.array(list(map(len,coords)),'i') - 1
size = maxcorner-mincorner
origin = mincorner
if (grid+1).prod() != len(coord0):
raise ValueError('Data count {} does not match grid {}.'.format(len(coord0),grid))
if not np.allclose(coords[0],np.linspace(mincorner[0],maxcorner[0],grid[0]+1)) and \
np.allclose(coords[1],np.linspace(mincorner[1],maxcorner[1],grid[1]+1)) and \
np.allclose(coords[2],np.linspace(mincorner[2],maxcorner[2],grid[2]+1)):
raise ValueError('Regular grid spacing violated.')
if ordered:
if not np.allclose(coord0.reshape(tuple((grid+1)[::-1])+(3,)),node_coord0(grid,size,origin)):
raise ValueError('Input data is not a regular grid.')
return (grid,size,origin)
def regrid(size,F,new_grid): def regrid(size,F,new_grid):
"""tbd.""" """tbd."""
c = cell_coord0(F.shape[:3][::-1],size) \ c = cell_coord0(F.shape[:3][::-1],size) \