fixed Geom.canvas bug, added Geom.from_vtk, added mode,selection options to Geom.clean

This commit is contained in:
Philip Eisenlohr 2020-08-22 21:33:38 -04:00
parent 70d1b0b987
commit 2b09a7d31d
1 changed files with 52 additions and 12 deletions

View File

@ -175,7 +175,7 @@ class Geom:
if len(self.microstructure.shape) != 3: if len(self.microstructure.shape) != 3:
raise ValueError(f'Invalid microstructure shape {microstructure.shape}') raise ValueError(f'Invalid microstructure shape {microstructure.shape}')
elif self.microstructure.dtype not in np.sctypes['float'] + np.sctypes['int']: elif self.microstructure.dtype not in np.sctypes['float'] + np.sctypes['int']:
raise TypeError(f'Invalid microstructue data type {microstructure.dtype}') raise TypeError(f'Invalid microstructure data type {microstructure.dtype}')
def set_size(self,size): def set_size(self,size):
@ -345,6 +345,34 @@ class Geom:
return Geom(microstructure.reshape(grid,order='F'),size,origin,homogenization,comments) return Geom(microstructure.reshape(grid,order='F'),size,origin,homogenization,comments)
@staticmethod
def from_vtk(fname):
"""
Read a geom from a VTK file.
Parameters
----------
fname : str or file handle
Geometry file to read.
"""
g = VTK.from_file(fname).geom
N_cells = g.GetNumberOfCells()
microstructure = np.zeros(N_cells)
grid = np.array(g.GetDimensions())-1
bbox = np.array(g.GetBounds()).reshape(3,2).T
size = bbox[1] - bbox[0]
celldata = g.GetCellData()
for a in range(celldata.GetNumberOfArrays()):
if celldata.GetArrayName(a) == 'microstructure':
array = celldata.GetArray(a)
for c in range(N_cells):
microstructure[c] = array.GetValue(c)
return Geom(microstructure.reshape(grid,order='F'),size,bbox[0])
@staticmethod @staticmethod
def _find_closest_seed(seeds, weights, point): def _find_closest_seed(seeds, weights, point):
return np.argmin(np.sum((np.broadcast_to(point,(len(seeds),3))-seeds)**2,axis=1) - weights) return np.argmin(np.sum((np.broadcast_to(point,(len(seeds),3))-seeds)**2,axis=1) - weights)
@ -621,7 +649,7 @@ class Geom:
) )
def clean(self,stencil=3): def clean(self,stencil=3,mode='nearest',selection=None):
""" """
Smooth microstructure by selecting most frequent index within given stencil at each location. Smooth microstructure by selecting most frequent index within given stencil at each location.
@ -629,17 +657,28 @@ class Geom:
---------- ----------
stencil : int, optional stencil : int, optional
Size of smoothing stencil. Size of smoothing stencil.
mode : string, optional
The mode parameter determines how the input array is extended beyond its boundaries.
Default is 'nearest'. See scipy.ndimage.generic_filter for all options.
selection : list, optional
Field values that can be altered. Defaults to all.
""" """
def mostFrequent(arr): def mostFrequent(arr,selection=None):
me = arr[arr.size//2]
if selection is None or me in selection:
unique, inverse = np.unique(arr, return_inverse=True) unique, inverse = np.unique(arr, return_inverse=True)
return unique[np.argmax(np.bincount(inverse))] return unique[np.argmax(np.bincount(inverse))]
else:
return me
#ToDo: self.add_comments('geom.py:clean v{}'.format(version) #ToDo: self.add_comments('geom.py:clean v{}'.format(version)
return self.update(ndimage.filters.generic_filter( return self.update(ndimage.filters.generic_filter(
self.microstructure, self.microstructure,
mostFrequent, mostFrequent,
size=(stencil,)*3 size=(stencil if selection is None else stencil//2*2+1,)*3,
mode=mode,
extra_keywords=dict(selection=selection),
).astype(self.microstructure.dtype) ).astype(self.microstructure.dtype)
) )
@ -708,14 +747,15 @@ class Geom:
dtype = float if int(fill) != fill or self.microstructure.dtype==np.float else int dtype = float if int(fill) != fill or self.microstructure.dtype==np.float else int
canvas = np.full(self.grid if grid is None else grid, canvas = np.full(self.grid if grid is None else grid,
fill if fill is not None else np.nanmax(self.microstructure)+1,dtype) np.nanmax(self.microstructure)+1 if fill is None else fill,
dtype)
l = np.clip( offset, 0,np.minimum(self.grid +offset,grid)) # noqa LL = np.clip( offset, 0,np.minimum(self.grid, grid+offset)) # noqa
r = np.clip( offset+self.grid,0,np.minimum(self.grid*2+offset,grid)) UR = np.clip( offset+grid, 0,np.minimum(self.grid, grid+offset))
L = np.clip(-offset, 0,np.minimum(grid -offset,self.grid)) ll = np.clip(-offset, 0,np.minimum( grid,self.grid-offset))
R = np.clip(-offset+grid, 0,np.minimum(grid*2 -offset,self.grid)) ur = np.clip(-offset+self.grid,0,np.minimum( grid,self.grid-offset))
canvas[l[0]:r[0],l[1]:r[1],l[2]:r[2]] = self.microstructure[L[0]:R[0],L[1]:R[1],L[2]:R[2]] canvas[ll[0]:ur[0],ll[1]:ur[1],ll[2]:ur[2]] = self.microstructure[LL[0]:UR[0],LL[1]:UR[1],LL[2]:UR[2]]
#ToDo: self.add_comments('geom.py:canvas v{}'.format(version) #ToDo: self.add_comments('geom.py:canvas v{}'.format(version)
return self.update(canvas,origin=self.origin+offset*self.size/self.grid,rescale=True) return self.update(canvas,origin=self.origin+offset*self.size/self.grid,rescale=True)