Merge remote-tracking branch 'origin/geom-attributes-as-checked-properties' into development
This commit is contained in:
Martin Diehl
commit
e90c20ccd6
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@ -20,7 +20,7 @@ class Geom:
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def __init__(self,material,size,origin=[0.0,0.0,0.0],comments=[]):
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"""
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New geometry definition from array of material, size, and origin.
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New geometry definition from array of materials, size, and origin.
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Parameters
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----------
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@ -34,28 +34,10 @@ class Geom:
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Comment lines.
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"""
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if len(material.shape) != 3:
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raise ValueError(f'Invalid material shape {material.shape}.')
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elif material.dtype not in np.sctypes['float'] + np.sctypes['int']:
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raise TypeError(f'Invalid material data type {material.dtype}.')
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else:
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self.material = np.copy(material)
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if self.material.dtype in np.sctypes['float'] and \
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np.all(self.material == self.material.astype(int).astype(float)):
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self.material = self.material.astype(int)
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if len(size) != 3 or any(np.array(size) <= 0):
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raise ValueError(f'Invalid size {size}.')
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else:
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self.size = np.array(size)
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if len(origin) != 3:
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raise ValueError(f'Invalid origin {origin}.')
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else:
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self.origin = np.array(origin)
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self.comments = [str(c) for c in comments] if isinstance(comments,list) else [str(comments)]
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self.material = material
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self.size = size
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self.origin = origin
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self.comments = comments
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def __repr__(self):
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@ -113,13 +95,68 @@ class Geom:
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return util.return_message(message)
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@property
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def material(self):
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"""Material indices."""
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return self._material
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@material.setter
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def material(self,material):
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if len(material.shape) != 3:
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raise ValueError(f'Invalid material shape {material.shape}.')
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elif material.dtype not in np.sctypes['float'] + np.sctypes['int']:
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raise TypeError(f'Invalid material data type {material.dtype}.')
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else:
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self._material = np.copy(material)
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if self.material.dtype in np.sctypes['float'] and \
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np.all(self.material == self.material.astype(int).astype(float)):
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self._material = self.material.astype(int)
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@property
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def size(self):
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"""Physical size of geometry in meter."""
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return self._size
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@size.setter
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def size(self,size):
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if len(size) != 3 or any(np.array(size) <= 0):
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raise ValueError(f'Invalid size {size}.')
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else:
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self._size = np.array(size)
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@property
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def origin(self):
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"""Coordinates of geometry origin in meter."""
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return self._origin
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@origin.setter
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def origin(self,origin):
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if len(origin) != 3:
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raise ValueError(f'Invalid origin {origin}.')
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else:
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self._origin = np.array(origin)
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@property
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def comments(self):
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"""Comments/history of geometry."""
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return self._comments
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@comments.setter
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def comments(self,comments):
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self._comments = [str(c) for c in comments] if isinstance(comments,list) else [str(comments)]
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@property
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def grid(self):
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"""Grid dimension of geometry."""
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return np.asarray(self.material.shape)
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@property
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def N_materials(self):
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"""Number of (unique) material indices within geometry."""
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return np.unique(self.material).size
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@ -132,7 +169,7 @@ class Geom:
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----------
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fname : str or or pathlib.Path
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Geometry file to read.
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Valid extension is .vtr, it will be appended if not given.
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Valid extension is .vtr, which will be appended if not given.
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"""
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v = VTK.load(fname if str(fname).endswith('.vtr') else str(fname)+'.vtr')
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@ -153,7 +190,7 @@ class Geom:
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Parameters
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----------
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fname : str or file handle
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fname : str, pathlib.Path, or file handle
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Geometry file to read.
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"""
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@ -221,26 +258,26 @@ class Geom:
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fname : str
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Filename of the DREAM.3D file
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base_group : str
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Name of the group (folder) below 'DataContainers'. For example
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'SyntheticVolumeDataContainer'.
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Name of the group (folder) below 'DataContainers',
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for example 'SyntheticVolumeDataContainer'.
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point_data : str, optional
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Name of the group (folder) containing the point wise material data,
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for example 'CellData'. Defaults to None, in which case points consecutively numbered.
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Name of the group (folder) containing the pointwise material data,
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for example 'CellData'. Defaults to None, in which case points are consecutively numbered.
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material : str, optional
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Name of the dataset containing the material ID. Defaults to
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'FeatureIds'.
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Name of the dataset containing the material ID.
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Defaults to 'FeatureIds'.
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"""
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root_dir ='DataContainers'
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f = h5py.File(fname, 'r')
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g = path.join(root_dir,base_group,'_SIMPL_GEOMETRY')
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size = f[path.join(g,'DIMENSIONS')][()] * f[path.join(g,'SPACING')][()]
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grid = f[path.join(g,'DIMENSIONS')][()]
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size = f[path.join(g,'SPACING')][()] * grid
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origin = f[path.join(g,'ORIGIN')][()]
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group_pointwise = path.join(root_dir,base_group,point_data)
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ma = np.arange(1,np.product(grid)+1,dtype=int) if point_data is None else \
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np.reshape(f[path.join(group_pointwise,material)],grid.prod())
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ma = np.arange(grid.prod(),dtype=int) \
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if point_data is None else \
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np.reshape(f[path.join(root_dir,base_group,point_data,material)],grid.prod())
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return Geom(ma.reshape(grid,order='F'),size,origin,util.execution_stamp('Geom','load_DREAM3D'))
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@ -248,18 +285,18 @@ class Geom:
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@staticmethod
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def from_table(table,coordinates,labels):
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"""
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Load an ASCII table.
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Derive geometry from an ASCII table.
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Parameters
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----------
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table : damask.Table
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Table that contains material information.
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coordinates : str
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Label of the column containing the vector of spatial coordinates.
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Label of the vector column containing the spatial coordinates.
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Need to be ordered (1./x fast, 3./z slow).
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labels : str or list of str
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Label(s) of the columns containing the material definition.
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Each unique combintation of values results in a material.
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Each unique combintation of values results in one material ID.
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"""
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grid,size,origin = grid_filters.cell_coord0_gridSizeOrigin(table.get(coordinates))
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@ -293,8 +330,8 @@ class Geom:
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weights : numpy.ndarray of shape (seeds.shape[0])
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Weights of the seeds. Setting all weights to 1.0 gives a standard Voronoi tessellation.
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material : numpy.ndarray of shape (seeds.shape[0]), optional
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Material ID of the seeds. Defaults to None, in which case materials are
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consecutively numbered.
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Material ID of the seeds.
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Defaults to None, in which case materials are consecutively numbered.
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periodic : Boolean, optional
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Perform a periodic tessellation. Defaults to True.
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@ -342,8 +379,8 @@ class Geom:
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seeds : numpy.ndarray of shape (:,3)
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Position of the seed points in meter. All points need to lay within the box.
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material : numpy.ndarray of shape (seeds.shape[0]), optional
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Material ID of the seeds. Defaults to None, in which case materials are
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consecutively numbered.
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Material ID of the seeds.
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Defaults to None, in which case materials are consecutively numbered.
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periodic : Boolean, optional
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Perform a periodic tessellation. Defaults to True.
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@ -438,19 +475,19 @@ class Geom:
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References
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----------
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Surface curvature in triply-periodic minimal surface architectures as
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a distinct design parameter in preparing advanced tissue engineering scaffolds
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Sébastien B G Blanquer, Maike Werner, Markus Hannula, Shahriar Sharifi,
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Guillaume P R Lajoinie, David Eglin, Jari Hyttinen, André A Poot, and Dirk W Grijpma
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10.1088/1758-5090/aa6553
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Surface curvature in triply-periodic minimal surface architectures as
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a distinct design parameter in preparing advanced tissue engineering scaffolds
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https://doi.org/10.1088/1758-5090/aa6553
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Triply Periodic Bicontinuous Cubic Microdomain Morphologies by Symmetries
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Meinhard Wohlgemuth, Nataliya Yufa, James Hoffman, and Edwin L. Thomas
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10.1021/ma0019499
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Triply Periodic Bicontinuous Cubic Microdomain Morphologies by Symmetries
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https://doi.org/10.1021/ma0019499
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Minisurf – A minimal surface generator for finite element modeling and additive manufacturing
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Meng-Ting Hsieh, Lorenzo Valdevit
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10.1016/j.simpa.2020.100026
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Minisurf – A minimal surface generator for finite element modeling and additive manufacturing
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https://doi.org/10.1016/j.simpa.2020.100026
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"""
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x,y,z = np.meshgrid(periods*2.0*np.pi*(np.arange(grid[0])+0.5)/grid[0],
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@ -465,7 +502,7 @@ class Geom:
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def save(self,fname,compress=True):
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"""
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Store as vtk rectilinear grid.
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Store as VTK rectilinear grid.
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Parameters
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----------
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@ -521,15 +558,15 @@ class Geom:
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Parameters
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----------
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dimension : int or float numpy.ndarray of shape(3)
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dimension : int or float numpy.ndarray of shape (3)
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Dimension (diameter/side length) of the primitive. If given as
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integers, grid point locations (cell centers) are addressed.
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If given as floats, coordinates are addressed.
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center : int or float numpy.ndarray of shape(3)
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center : int or float numpy.ndarray of shape (3)
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Center of the primitive. If given as integers, grid point
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locations (cell centers) are addressed.
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If given as floats, coordinates are addressed.
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exponent : numpy.ndarray of shape(3) or float
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exponent : numpy.ndarray of shape (3) or float
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Exponents for the three axes.
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0 gives octahedron (ǀxǀ^(2^0) + ǀyǀ^(2^0) + ǀzǀ^(2^0) < 1)
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1 gives sphere (ǀxǀ^(2^1) + ǀyǀ^(2^1) + ǀzǀ^(2^1) < 1)
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@ -689,7 +726,7 @@ class Geom:
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def renumber(self):
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"""Renumber sorted material indices to 0,...,N-1."""
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"""Renumber sorted material indices as 0,...,N-1."""
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_,renumbered = np.unique(self.material,return_inverse=True)
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return Geom(material = renumbered.reshape(self.grid),
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@ -825,7 +862,7 @@ class Geom:
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Defaults to 1.
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offset : int, optional
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Offset (positive or negative) to tag material indices,
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defaults to material.max() + 1.
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defaults to material.max()+1.
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trigger : list of ints, optional
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List of material indices that trigger a change.
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Defaults to [], meaning that any different neighbor triggers a change.
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