more detailed documentation
This commit is contained in:
Martin Diehl
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@ -10,10 +10,27 @@ from . import version
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class Geom():
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"""Geometry definition for grid solvers"""
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"""Geometry definition for grid solvers."""
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def __init__(self,microstructure,size,origin=[0.0,0.0,0.0],homogenization=1,comments=[]):
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"""New geometry definition from array of microstructures and size"""
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"""
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New geometry definition from array of microstructures and size.
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Parameters
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----------
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microstructure : numpy.ndarray
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microstructure array (3D)
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size : list or numpy.ndarray
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physical size of the microstructure in meter.
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origin : list or numpy.ndarray, optional
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physical origin of the microstructure in meter.
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homogenization : integer, optional
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homogenization index.
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comments : list of str, optional
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comments lines.
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"""
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self.__transforms__ = \
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self.set_microstructure(microstructure)
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self.set_size(size)
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self.set_origin(origin)
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@ -22,7 +39,7 @@ class Geom():
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def __repr__(self):
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"""Basic information on geometry definition"""
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"""Basic information on geometry definition."""
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return util.srepr([
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'grid a b c: {}'.format(' x '.join(map(str,self.get_grid ()))),
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'size x y z: {}'.format(' x '.join(map(str,self.get_size ()))),
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@ -33,7 +50,21 @@ class Geom():
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])
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def update(self,microstructure=None,size=None,origin=None,rescale=False):
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"""Updates microstructure and size"""
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"""
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Updates microstructure and size.
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Parameters
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----------
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microstructure : numpy.ndarray, optional
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microstructure array (3D).
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size : list or numpy.ndarray, optional
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physical size of the microstructure in meter.
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origin : list or numpy.ndarray, optional
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physical origin of the microstructure in meter.
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rescale : bool, optional
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ignore size parameter and rescale according to change of grid points.
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"""
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grid_old = self.get_grid()
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size_old = self.get_size()
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origin_old = self.get_origin()
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@ -77,13 +108,40 @@ class Geom():
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return util.return_message(message)
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def set_comments(self,comments):
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"""
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Replaces all existing comments.
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Parameters
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----------
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comments : list of str
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new comments.
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"""
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self.comments = []
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self.add_comments(comments)
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def add_comments(self,comments):
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"""
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Appends comments to existing comments.
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Parameters
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----------
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comments : list of str
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new comments.
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"""
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self.comments += [str(c) for c in comments] if isinstance(comments,list) else [str(comments)]
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def set_microstructure(self,microstructure):
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"""
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Replaces the existing microstructure representation.
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Parameters
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----------
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microstructure : numpy.ndarray
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microstructure array (3D).
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"""
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if microstructure is not None:
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if len(microstructure.shape) != 3:
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raise ValueError('Invalid microstructure shape {}'.format(*microstructure.shape))
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@ -93,6 +151,15 @@ class Geom():
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self.microstructure = np.copy(microstructure)
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def set_size(self,size):
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"""
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Replaces the existing size information.
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Parameters
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----------
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size : list or numpy.ndarray
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physical size of the microstructure in meter.
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"""
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if size is None:
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grid = np.asarray(self.microstructure.shape)
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self.size = grid/np.max(grid)
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@ -103,6 +170,15 @@ class Geom():
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self.size = np.array(size)
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def set_origin(self,origin):
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"""
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Replaces the existing origin information.
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Parameters
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----------
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origin : list or numpy.ndarray
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physical origin of the microstructure in meter
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"""
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if origin is not None:
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if len(origin) != 3:
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raise ValueError('Invalid origin {}'.format(*origin))
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@ -110,6 +186,15 @@ class Geom():
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self.origin = np.array(origin)
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def set_homogenization(self,homogenization):
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"""
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Replaces the existing homogenization index.
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Parameters
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----------
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homogenization : integer
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homogenization index
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"""
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if homogenization is not None:
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if not isinstance(homogenization,int) or homogenization < 1:
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raise TypeError('Invalid homogenization {}'.format(homogenization))
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@ -118,24 +203,31 @@ class Geom():
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def get_microstructure(self):
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"""Return the microstructure representation."""
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return np.copy(self.microstructure)
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def get_size(self):
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"""Return the physical size in meter."""
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return np.copy(self.size)
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def get_origin(self):
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"""Return the origin in meter."""
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return np.copy(self.origin)
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def get_grid(self):
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"""Return the grid discretization."""
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return np.array(self.microstructure.shape)
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def get_homogenization(self):
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"""Return the homogenization index."""
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return self.homogenization
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def get_comments(self):
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"""Return the comments."""
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return self.comments[:]
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def get_header(self):
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"""Return the full header (grid, size, origin, homogenization, comments)."""
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header = ['{} header'.format(len(self.comments)+4)] + self.comments
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header.append('grid a {} b {} c {}'.format(*self.get_grid()))
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header.append('size x {} y {} z {}'.format(*self.get_size()))
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@ -145,7 +237,15 @@ class Geom():
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@classmethod
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def from_file(cls,fname):
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"""Reads a geom file"""
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"""
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Reads a geom file.
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Parameters
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----------
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fname : str or file handle
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geometry file to read.
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"""
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with (open(fname) if isinstance(fname,str) else fname) as f:
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f.seek(0)
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header_length,keyword = f.readline().split()[:2]
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@ -196,7 +296,15 @@ class Geom():
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return cls(microstructure.reshape(grid),size,origin,homogenization,comments)
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def to_file(self,fname):
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"""Writes to file"""
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"""
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Writes a geom file.
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Parameters
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----------
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fname : str or file handle
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geometry file to write.
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"""
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header = self.get_header()
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grid = self.get_grid()
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format_string = '%{}i'.format(1+int(np.floor(np.log10(np.nanmax(self.microstructure))))) if self.microstructure.dtype == int \
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@ -208,7 +316,15 @@ class Geom():
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def to_vtk(self,fname=None):
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"""Generates vtk file. If file name is given, stored in file otherwise returned as string"""
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"""
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Generates vtk file.
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Parameters
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----------
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fname : str, optional
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vtk file to write. If no file is given, a string is returned.
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"""
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grid = self.get_grid() + np.ones(3,dtype=int)
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size = self.get_size()
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origin = self.get_origin()
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@ -262,7 +378,7 @@ class Geom():
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def show(self):
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"""Show raw content (as in file)"""
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"""Show raw content (as in file)."""
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f=StringIO()
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self.to_file(f)
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f.seek(0)
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