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DAMASK_EICMD
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redefined attributes material,size,origin,comments as properties; enhanced help/descriptions

This commit is contained in:
Philip Eisenlohr 2020-11-08 12:11:30 -05:00
parent b8503e84b7
commit f105631015
1 changed files with 93 additions and 56 deletions
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149
python/damask/_geom.py
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@ -20,7 +20,7 @@ class Geom:
def __init__(self,material,size,origin=[0.0,0.0,0.0],comments=[]):
"""
New geometry definition from array of material, size, and origin.
New geometry definition from array of materials, size, and origin.
Parameters
----------
@ -34,28 +34,10 @@ class Geom:
Comment lines.
"""
if len(material.shape) != 3:
raise ValueError(f'Invalid material shape {material.shape}.')
elif material.dtype not in np.sctypes['float'] + np.sctypes['int']:
raise TypeError(f'Invalid material data type {material.dtype}.')
else:
self.material = np.copy(material)
if self.material.dtype in np.sctypes['float'] and \
np.all(self.material == self.material.astype(int).astype(float)):
self.material = self.material.astype(int)
if len(size) != 3 or any(np.array(size) <= 0):
raise ValueError(f'Invalid size {size}.')
else:
self.size = np.array(size)
if len(origin) != 3:
raise ValueError(f'Invalid origin {origin}.')
else:
self.origin = np.array(origin)
self.comments = [str(c) for c in comments] if isinstance(comments,list) else [str(comments)]
self.material = material
self.size = size
self.origin = origin
self.comments = comments
def __repr__(self):
@ -113,13 +95,68 @@ class Geom:
return util.return_message(message)
@property
def material(self):
"""Material indices."""
return self._material
@material.setter
def material(self,material):
if len(material.shape) != 3:
raise ValueError(f'Invalid material shape {material.shape}.')
elif material.dtype not in np.sctypes['float'] + np.sctypes['int']:
raise TypeError(f'Invalid material data type {material.dtype}.')
else:
self._material = np.copy(material)
if self.material.dtype in np.sctypes['float'] and \
np.all(self.material == self.material.astype(int).astype(float)):
self._material = self.material.astype(int)
@property
def size(self):
"""Physical size of geometry in meter."""
return self._size
@size.setter
def size(self,size):
if len(size) != 3 or any(np.array(size) <= 0):
raise ValueError(f'Invalid size {size}.')
else:
self._size = np.array(size)
@property
def origin(self):
"""Coordinates of geometry origin in meter."""
return self._origin
@origin.setter
def origin(self,origin):
if len(origin) != 3:
raise ValueError(f'Invalid origin {origin}.')
else:
self._origin = np.array(origin)
@property
def comments(self):
"""Comments/history of geometry."""
return self._comments
@comments.setter
def comments(self,comments):
self._comments = [str(c) for c in comments] if isinstance(comments,list) else [str(comments)]
@property
def grid(self):
"""Grid dimension of geometry."""
return np.asarray(self.material.shape)
@property
def N_materials(self):
"""Number of (unique) material indices within geometry."""
return np.unique(self.material).size
@ -130,9 +167,9 @@ class Geom:
Parameters
----------
fname : str or or pathlib.Path
©˝fname : str or pathlib.Path
Geometry file to read.
Valid extension is .vtr, it will be appended if not given.
Valid extension is .vtr, which will be appended if not given.
"""
v = VTK.load(fname if str(fname).endswith('.vtr') else str(fname)+'.vtr')
@ -153,7 +190,7 @@ class Geom:
Parameters
----------
fname : str or file handle
fname : str, pathlib.Path, or file handle
Geometry file to read.
"""
@ -221,26 +258,26 @@ class Geom:
fname : str
Filename of the DREAM.3D file
base_group : str
Name of the group (folder) below 'DataContainers'. For example
'SyntheticVolumeDataContainer'.
Name of the group (folder) below 'DataContainers',
for example 'SyntheticVolumeDataContainer'.
point_data : str, optional
Name of the group (folder) containing the point wise material data,
for example 'CellData'. Defaults to None, in which case points consecutively numbered.
Name of the group (folder) containing the pointwise material data,
for example 'CellData'. Defaults to None, in which case points are consecutively numbered.
material : str, optional
Name of the dataset containing the material ID. Defaults to
'FeatureIds'.
Name of the dataset containing the material ID.
Defaults to 'FeatureIds'.
"""
root_dir ='DataContainers'
f = h5py.File(fname, 'r')
g = path.join(root_dir,base_group,'_SIMPL_GEOMETRY')
size = f[path.join(g,'DIMENSIONS')][()] * f[path.join(g,'SPACING')][()]
grid = f[path.join(g,'DIMENSIONS')][()]
size = f[path.join(g,'SPACING')][()] * grid
origin = f[path.join(g,'ORIGIN')][()]
group_pointwise = path.join(root_dir,base_group,point_data)
ma = np.arange(1,np.product(grid)+1,dtype=int) if point_data is None else \
np.reshape(f[path.join(group_pointwise,material)],grid.prod())
ma = np.arange(grid.prod(),dtype=int) \
if point_data is None else \
np.reshape(f[path.join(root_dir,base_group,point_data,material)],grid.prod())
return Geom(ma.reshape(grid,order='F'),size,origin,util.execution_stamp('Geom','load_DREAM3D'))
@ -248,18 +285,18 @@ class Geom:
@staticmethod
def from_table(table,coordinates,labels):
"""
Load an ASCII table.
Derive geometry from an ASCII table.
Parameters
----------
table : damask.Table
Table that contains material information.
coordinates : str
Label of the column containing the vector of spatial coordinates.
Label of the vector column containing the spatial coordinates.
Need to be ordered (1./x fast, 3./z slow).
labels : str or list of str
Label(s) of the columns containing the material definition.
Each unique combintation of values results in a material.
Each unique combintation of values results in one material ID.
"""
grid,size,origin = grid_filters.cell_coord0_gridSizeOrigin(table.get(coordinates))
@ -293,8 +330,8 @@ class Geom:
weights : numpy.ndarray of shape (seeds.shape[0])
Weights of the seeds. Setting all weights to 1.0 gives a standard Voronoi tessellation.
material : numpy.ndarray of shape (seeds.shape[0]), optional
Material ID of the seeds. Defaults to None, in which case materials are
consecutively numbered.
Material ID of the seeds.
Defaults to None, in which case materials are consecutively numbered.
periodic : Boolean, optional
Perform a periodic tessellation. Defaults to True.
@ -342,8 +379,8 @@ class Geom:
seeds : numpy.ndarray of shape (:,3)
Position of the seed points in meter. All points need to lay within the box.
material : numpy.ndarray of shape (seeds.shape[0]), optional
Material ID of the seeds. Defaults to None, in which case materials are
consecutively numbered.
Material ID of the seeds.
Defaults to None, in which case materials are consecutively numbered.
periodic : Boolean, optional
Perform a periodic tessellation. Defaults to True.
@ -438,19 +475,19 @@ class Geom:
References
----------
Surface curvature in triply-periodic minimal surface architectures as
a distinct design parameter in preparing advanced tissue engineering scaffolds
Sébastien B G Blanquer, Maike Werner, Markus Hannula, Shahriar Sharifi,
Guillaume P R Lajoinie, David Eglin, Jari Hyttinen, André A Poot, and Dirk W Grijpma
10.1088/1758-5090/aa6553
Surface curvature in triply-periodic minimal surface architectures as
a distinct design parameter in preparing advanced tissue engineering scaffolds
https://doi.org/10.1088/1758-5090/aa6553
Triply Periodic Bicontinuous Cubic Microdomain Morphologies by Symmetries
Meinhard Wohlgemuth, Nataliya Yufa, James Hoffman, and Edwin L. Thomas
10.1021/ma0019499
Triply Periodic Bicontinuous Cubic Microdomain Morphologies by Symmetries
https://doi.org/10.1021/ma0019499
Minisurf – A minimal surface generator for finite element modeling and additive manufacturing
Meng-Ting Hsieh, Lorenzo Valdevit
10.1016/j.simpa.2020.100026
Minisurf – A minimal surface generator for finite element modeling and additive manufacturing
https://doi.org/10.1016/j.simpa.2020.100026
"""
x,y,z = np.meshgrid(periods*2.0*np.pi*(np.arange(grid[0])+0.5)/grid[0],
@ -465,7 +502,7 @@ class Geom:
def save(self,fname,compress=True):
"""
Store as vtk rectilinear grid.
Store as VTK rectilinear grid.
Parameters
----------
@ -521,15 +558,15 @@ class Geom:
Parameters
----------
dimension : int or float numpy.ndarray of shape(3)
dimension : int or float numpy.ndarray of shape (3)
Dimension (diameter/side length) of the primitive. If given as
integers, grid point locations (cell centers) are addressed.
If given as floats, coordinates are addressed.
center : int or float numpy.ndarray of shape(3)
center : int or float numpy.ndarray of shape (3)
Center of the primitive. If given as integers, grid point
locations (cell centers) are addressed.
If given as floats, coordinates are addressed.
exponent : numpy.ndarray of shape(3) or float
exponent : numpy.ndarray of shape (3) or float
Exponents for the three axes.
0 gives octahedron (ǀxǀ^(2^0) + ǀyǀ^(2^0) + ǀzǀ^(2^0) < 1)
1 gives sphere (ǀxǀ^(2^1) + ǀyǀ^(2^1) + ǀzǀ^(2^1) < 1)
@ -689,7 +726,7 @@ class Geom:
def renumber(self):
"""Renumber sorted material indices to 0,...,N-1."""
"""Renumber sorted material indices as 0,...,N-1."""
_,renumbered = np.unique(self.material,return_inverse=True)
return Geom(material = renumbered.reshape(self.grid),
@ -825,7 +862,7 @@ class Geom:
Defaults to 1.
offset : int, optional
Offset (positive or negative) to tag material indices,
defaults to material.max() + 1.
defaults to material.max()+1.
trigger : list of ints, optional
List of material indices that trigger a change.
Defaults to [], meaning that any different neighbor triggers a change.