import math from io import StringIO import numpy as np from . import util class Geom(): """Geometry definition for grid solvers""" def __init__(self,microstructure,size,origin=[0.0,0.0,0.0],homogenization=1,comments=[]): """New geometry definition from array of microstructures and size""" self.set_size(size) self.set_origin(origin) self.set_microstructure(microstructure) self.set_homogenization(homogenization) self.set_comments(comments) def __repr__(self): """Basic information on geometry definition""" return 'grid a b c: {}\n'.format(' x '.join(map(str,self.get_grid ()))) + \ 'size x y z: {}\n'.format(' x '.join(map(str,self.get_size ()))) + \ 'origin x y z: {}\n'.format(' x '.join(map(str,self.get_origin()))) + \ 'homogenization: {}\n'.format(self.get_homogenization()) + \ '# microstructures: {}\n'.format(len(np.unique(self.microstructure))) + \ 'max microstructures: {}\n'.format(np.nanmax(self.microstructure)) def update(self,microstructure=None,size=None,origin=None,rescale=False): """Updates microstructure and size""" grid_old = self.get_grid() size_old = self.get_size() origin_old = self.get_origin() unique_old = len(np.unique(self.microstructure)) max_old = np.nanmax(self.microstructure) if size is not None and rescale: raise ValueError('Either set size explicitly or rescale automatically') self.set_microstructure(microstructure) self.set_size(self.get_grid()/grid_old if rescale else size) self.set_origin(origin) message = ['grid a b c: {}'.format(' x '.join(map(str,grid_old)))] if np.any(grid_old != self.get_grid()): message[-1] = util.delete(message[-1]) message.append('grid a b c: {}'.format(' x '.join(map(str,self.get_grid())))) message.append('size x y z: {}'.format(' x '.join(map(str,size_old)))) if np.any(size_old != self.get_size()): message[-1] = util.delete(message[-1]) message.append('size x y z: {}'.format(' x '.join(map(str,self.get_size())))) message.append('origin x y z: {}'.format(' x '.join(map(str,origin_old)))) if np.any(origin_old != self.get_origin()): message[-1] = util.delete(message[-1]) message.append('origin x y z: {}'.format(' x '.join(map(str,self.get_origin())))) message.append('homogenization: {}'.format(self.get_homogenization())) message.append('# microstructures: {}'.format(unique_old)) if unique_old != len(np.unique(self.microstructure)): message[-1] = util.delete(message[-1]) message.append('# microstructures: {}'.format(len(np.unique(self.microstructure)))) message.append('max microstructure: {}'.format(max_old)) if max_old != np.nanmax(self.microstructure): message[-1] = util.delete(message[-1]) message.append('max microstructure: {}'.format(np.nanmax(self.microstructure))) return util.return_message(message) def set_comments(self,comments): self.comments = [] self.add_comments(comments) def add_comments(self,comments): self.comments += [str(c) for c in comments] if isinstance(comments,list) else [str(comments)] def set_microstructure(self,microstructure): if microstructure is not None: if len(microstructure.shape) != 3: raise ValueError('Invalid microstructure shape {}'.format(*microstructure.shape)) elif microstructure.dtype not in [int,float]: raise TypeError('Invalid data type {} for microstructure'.format(microstructure.dtype)) else: self.microstructure = np.copy(microstructure) def set_size(self,size): if size is not None: if len(size) != 3 or any(np.array(size)<=0): raise ValueError('Invalid size {}'.format(*size)) else: self.size = np.array(size) def set_origin(self,origin): if origin is not None: if len(origin) != 3: raise ValueError('Invalid origin {}'.format(*origin)) else: self.origin = np.array(origin) def set_homogenization(self,homogenization): if homogenization is not None: if not isinstance(homogenization,int) or homogenization < 1: raise TypeError('Invalid homogenization {}'.format(homogenization)) else: self.homogenization = homogenization def get_microstructure(self): return np.copy(self.microstructure) def get_size(self): return np.copy(self.size) def get_origin(self): return np.copy(self.origin) def get_grid(self): return np.array(self.microstructure.shape) def get_homogenization(self): return self.homogenization def get_comments(self): return self.comments[:] def get_header(self): header = ['{} header'.format(len(self.comments)+4)] + self.comments header.append('grid a {} b {} c {}'.format(*self.get_grid())) header.append('size x {} y {} z {}'.format(*self.get_size())) header.append('origin x {} y {} z {}'.format(*self.get_origin())) header.append('homogenization {}'.format(self.get_homogenization())) return header @classmethod def from_file(cls,fname): """Reads a geom file""" with (open(fname) if isinstance(fname,str) else fname) as f: f.seek(0) header_length,keyword = f.readline().split()[:2] header_length = int(header_length) content = f.readlines() if not keyword.startswith('head') or header_length < 3: raise TypeError('Header length information missing or invalid') comments = [] for i,line in enumerate(content[:header_length]): items = line.lower().strip().split() key = items[0] if len(items) > 0 else '' if key == 'grid': grid = np.array([ int(dict(zip(items[1::2],items[2::2]))[i]) for i in ['a','b','c']]) elif key == 'size': size = np.array([float(dict(zip(items[1::2],items[2::2]))[i]) for i in ['x','y','z']]) elif key == 'origin': origin = np.array([float(dict(zip(items[1::2],items[2::2]))[i]) for i in ['x','y','z']]) elif key == 'homogenization': homogenization = int(items[1]) else: comments.append(line.strip()) microstructure = np.empty(grid.prod()) # initialize as flat array i = 0 for line in content[header_length:]: items = line.split() if len(items) == 3: if items[1].lower() == 'of': items = np.ones(int(items[0]))*float(items[2]) elif items[1].lower() == 'to': items = np.linspace(int(items[0]),int(items[2]), abs(int(items[2])-int(items[0]))+1,dtype=float) else: items = list(map(float,items)) else: items = list(map(float,items)) microstructure[i:i+len(items)] = items i += len(items) if i != grid.prod(): raise TypeError('Invalid file: expected {} entries,found {}'.format(grid.prod(),i)) microstructure = microstructure.reshape(grid,order='F') if not np.any(np.mod(microstructure.flatten(),1) != 0.0): # no float present microstructure = microstructure.astype('int') return cls(microstructure.reshape(grid),size,origin,homogenization,comments) def to_file(self,fname): """Writes to file""" header = self.get_header() grid = self.get_grid() format_string = '%{}i'.format(int(math.floor(math.log10(self.microstructure.max())+1))) if self.microstructure.dtype == int \ else '%g' np.savetxt(fname, self.microstructure.reshape([grid[0],np.prod(grid[1:])],order='F').T, header='\n'.join(header), fmt=format_string, comments='') def show(self): """Show raw content (as in file)""" f=StringIO() self.to_file(f) f.seek(0) return ''.join(f.readlines())