diff --git a/python/damask/geom.py b/python/damask/geom.py index 176d2bd12..5bf4f7750 100644 --- a/python/damask/geom.py +++ b/python/damask/geom.py @@ -10,380 +10,378 @@ from . import version class Geom(): - """Geometry definition for grid solvers.""" + """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. + def __init__(self,microstructure,size,origin=[0.0,0.0,0.0],homogenization=1,comments=[]): + """ + New geometry definition from array of microstructures and size. - Parameters - ---------- - microstructure : numpy.ndarray - microstructure array (3D) - size : list or numpy.ndarray - physical size of the microstructure in meter. - origin : list or numpy.ndarray, optional - physical origin of the microstructure in meter. - homogenization : integer, optional - homogenization index. - comments : list of str, optional - comments lines. + Parameters + ---------- + microstructure : numpy.ndarray + microstructure array (3D) + size : list or numpy.ndarray + physical size of the microstructure in meter. + origin : list or numpy.ndarray, optional + physical origin of the microstructure in meter. + homogenization : integer, optional + homogenization index. + comments : list of str, optional + comments lines. - """ - self.__transforms__ = \ - self.set_microstructure(microstructure) - self.set_size(size) - self.set_origin(origin) - self.set_homogenization(homogenization) - self.set_comments(comments) - - - def __repr__(self): - """Basic information on geometry definition.""" - return util.srepr([ - 'grid a b c: {}'.format(' x '.join(map(str,self.get_grid ()))), - 'size x y z: {}'.format(' x '.join(map(str,self.get_size ()))), - 'origin x y z: {}'.format(' '.join(map(str,self.get_origin()))), - 'homogenization: {}'.format(self.get_homogenization()), - '# microstructures: {}'.format(len(np.unique(self.microstructure))), - 'max microstructure: {}'.format(np.nanmax(self.microstructure)), - ]) - - def update(self,microstructure=None,size=None,origin=None,rescale=False): - """ - Updates microstructure and size. - - Parameters - ---------- - microstructure : numpy.ndarray, optional - microstructure array (3D). - size : list or numpy.ndarray, optional - physical size of the microstructure in meter. - origin : list or numpy.ndarray, optional - physical origin of the microstructure in meter. - rescale : bool, optional - ignore size parameter and rescale according to change of grid points. - - """ - 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_origin(origin) - - if size is not None: - self.set_size(size) - elif rescale: - self.set_size(self.get_grid()/grid_old*self.size) - - 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(util.emph('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(util.emph('size x y z: {}'.format(' x '.join(map(str,self.get_size()))))) - - message.append('origin x y z: {}'.format(' '.join(map(str,origin_old)))) - if np.any(origin_old != self.get_origin()): - message[-1] = util.delete(message[-1]) - message.append(util.emph('origin x y z: {}'.format(' '.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(util.emph('# 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(util.emph('max microstructure: {}'.format(np.nanmax(self.microstructure)))) - - return util.return_message(message) - - def set_comments(self,comments): - """ - Replaces all existing comments. - - Parameters - ---------- - comments : list of str - new comments. - - """ - self.comments = [] - self.add_comments(comments) - - def add_comments(self,comments): - """ - Appends comments to existing comments. - - Parameters - ---------- - comments : list of str - new comments. - - """ - self.comments += [str(c) for c in comments] if isinstance(comments,list) else [str(comments)] - - def set_microstructure(self,microstructure): - """ - Replaces the existing microstructure representation. - - Parameters - ---------- - microstructure : numpy.ndarray - microstructure array (3D). - - """ - if microstructure is not None: - if len(microstructure.shape) != 3: - raise ValueError('Invalid microstructure shape {}'.format(*microstructure.shape)) - elif microstructure.dtype not in np.sctypes['float'] + np.sctypes['int']: - raise TypeError('Invalid data type {} for microstructure'.format(microstructure.dtype)) - else: - self.microstructure = np.copy(microstructure) - - def set_size(self,size): - """ - Replaces the existing size information. - - Parameters - ---------- - size : list or numpy.ndarray - physical size of the microstructure in meter. - - """ - if size is None: - grid = np.asarray(self.microstructure.shape) - self.size = grid/np.max(grid) - else: - 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): - """ - Replaces the existing origin information. - - Parameters - ---------- - origin : list or numpy.ndarray - physical origin of the microstructure in meter - - """ - 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): - """ - Replaces the existing homogenization index. - - Parameters - ---------- - homogenization : integer - homogenization index - - """ - 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 the microstructure representation.""" - return np.copy(self.microstructure) - - def get_size(self): - """Return the physical size in meter.""" - return np.copy(self.size) - - def get_origin(self): - """Return the origin in meter.""" - return np.copy(self.origin) - - def get_grid(self): - """Return the grid discretization.""" - return np.array(self.microstructure.shape) - - def get_homogenization(self): - """Return the homogenization index.""" - return self.homogenization - - def get_comments(self): - """Return the comments.""" - return self.comments[:] - - def get_header(self): - """Return the full header (grid, size, origin, homogenization, comments).""" - 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 + """ + self.__transforms__ = \ + self.set_microstructure(microstructure) + self.set_size(size) + self.set_origin(origin) + self.set_homogenization(homogenization) + self.set_comments(comments) - @classmethod - def from_file(cls,fname): - """ - Reads a geom file. - Parameters - ---------- - fname : str or file handle - geometry file to read. + def __repr__(self): + """Basic information on geometry definition.""" + return util.srepr([ + 'grid a b c: {}'.format(' x '.join(map(str,self.get_grid ()))), + 'size x y z: {}'.format(' x '.join(map(str,self.get_size ()))), + 'origin x y z: {}'.format(' '.join(map(str,self.get_origin()))), + 'homogenization: {}'.format(self.get_homogenization()), + '# microstructures: {}'.format(len(np.unique(self.microstructure))), + 'max microstructure: {}'.format(np.nanmax(self.microstructure)), + ]) - """ - 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() + def update(self,microstructure=None,size=None,origin=None,rescale=False): + """ + Updates microstructure and size. - if not keyword.startswith('head') or header_length < 3: - raise TypeError('Header length information missing or invalid') + Parameters + ---------- + microstructure : numpy.ndarray, optional + microstructure array (3D). + size : list or numpy.ndarray, optional + physical size of the microstructure in meter. + origin : list or numpy.ndarray, optional + physical origin of the microstructure in meter. + rescale : bool, optional + ignore size parameter and rescale according to change of grid points. - 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()) + """ + 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') - 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)) + self.set_microstructure(microstructure) + self.set_origin(origin) + + if size is not None: + self.set_size(size) + elif rescale: + self.set_size(self.get_grid()/grid_old*self.size) + + 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(util.emph('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(util.emph('size x y z: {}'.format(' x '.join(map(str,self.get_size()))))) + + message.append('origin x y z: {}'.format(' '.join(map(str,origin_old)))) + if np.any(origin_old != self.get_origin()): + message[-1] = util.delete(message[-1]) + message.append(util.emph('origin x y z: {}'.format(' '.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(util.emph('# 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(util.emph('max microstructure: {}'.format(np.nanmax(self.microstructure)))) + + return util.return_message(message) + + def set_comments(self,comments): + """ + Replaces all existing comments. + + Parameters + ---------- + comments : list of str + new comments. + + """ + self.comments = [] + self.add_comments(comments) - microstructure[i:i+len(items)] = items - i += len(items) + def add_comments(self,comments): + """ + Appends comments to existing comments. + + Parameters + ---------- + comments : list of str + new comments. + + """ + self.comments += [str(c) for c in comments] if isinstance(comments,list) else [str(comments)] + + def set_microstructure(self,microstructure): + """ + Replaces the existing microstructure representation. + + Parameters + ---------- + microstructure : numpy.ndarray + microstructure array (3D). + + """ + if microstructure is not None: + if len(microstructure.shape) != 3: + raise ValueError('Invalid microstructure shape {}'.format(*microstructure.shape)) + elif microstructure.dtype not in np.sctypes['float'] + np.sctypes['int']: + raise TypeError('Invalid data type {} for microstructure'.format(microstructure.dtype)) + else: + self.microstructure = np.copy(microstructure) + + def set_size(self,size): + """ + Replaces the existing size information. + + Parameters + ---------- + size : list or numpy.ndarray + physical size of the microstructure in meter. + + """ + if size is None: + grid = np.asarray(self.microstructure.shape) + self.size = grid/np.max(grid) + else: + 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): + """ + Replaces the existing origin information. + + Parameters + ---------- + origin : list or numpy.ndarray + physical origin of the microstructure in meter + + """ + 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): + """ + Replaces the existing homogenization index. + + Parameters + ---------- + homogenization : integer + homogenization index + + """ + 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 the microstructure representation.""" + return np.copy(self.microstructure) + + def get_size(self): + """Return the physical size in meter.""" + return np.copy(self.size) + + def get_origin(self): + """Return the origin in meter.""" + return np.copy(self.origin) + + def get_grid(self): + """Return the grid discretization.""" + return np.array(self.microstructure.shape) + + def get_homogenization(self): + """Return the homogenization index.""" + return self.homogenization + + def get_comments(self): + """Return the comments.""" + return self.comments[:] + + def get_header(self): + """Return the full header (grid, size, origin, homogenization, comments).""" + 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. + + Parameters + ---------- + fname : str or file handle + geometry file to read. + + """ + 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 a geom file. + + Parameters + ---------- + fname : str or file handle + geometry file to write. + + """ + header = self.get_header() + grid = self.get_grid() + format_string = '%{}i'.format(1+int(np.floor(np.log10(np.nanmax(self.microstructure))))) 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 to_vtk(self,fname=None): + """ + Generates vtk file. + + Parameters + ---------- + fname : str, optional + vtk file to write. If no file is given, a string is returned. + + """ + grid = self.get_grid() + np.ones(3,dtype=int) + size = self.get_size() + origin = self.get_origin() + + coords = [ + np.linspace(0,size[0],grid[0]) + origin[0], + np.linspace(0,size[1],grid[1]) + origin[1], + np.linspace(0,size[2],grid[2]) + origin[2] + ] + + rGrid = vtk.vtkRectilinearGrid() + coordArray = [vtk.vtkDoubleArray(),vtk.vtkDoubleArray(),vtk.vtkDoubleArray()] + + rGrid.SetDimensions(*grid) + for d,coord in enumerate(coords): + for c in coord: + coordArray[d].InsertNextValue(c) + + rGrid.SetXCoordinates(coordArray[0]) + rGrid.SetYCoordinates(coordArray[1]) + rGrid.SetZCoordinates(coordArray[2]) + + ms = numpy_support.numpy_to_vtk(num_array=self.microstructure.flatten(order='F'), + array_type=vtk.VTK_INT if self.microstructure.dtype == int else vtk.VTK_FLOAT) + ms.SetName('microstructure') + rGrid.GetCellData().AddArray(ms) + + + if fname is None: + writer = vtk.vtkDataSetWriter() + writer.SetHeader('damask.Geom '+version) + writer.WriteToOutputStringOn() + else: + writer = vtk.vtkXMLRectilinearGridWriter() + writer.SetCompressorTypeToZLib() + writer.SetDataModeToBinary() + + ext = os.path.splitext(fname)[1] + if ext == '': + name = fname + '.' + writer.GetDefaultFileExtension() + elif ext == writer.GetDefaultFileExtension(): + name = fname + else: + raise ValueError("unknown extension {}".format(ext)) + writer.SetFileName(name) - 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) + writer.SetInputData(rGrid) + writer.Write() - def to_file(self,fname): - """ - Writes a geom file. + if fname is None: return writer.GetOutputString() - Parameters - ---------- - fname : str or file handle - geometry file to write. - - """ - header = self.get_header() - grid = self.get_grid() - format_string = '%{}i'.format(1+int(np.floor(np.log10(np.nanmax(self.microstructure))))) 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 to_vtk(self,fname=None): - """ - Generates vtk file. - - Parameters - ---------- - fname : str, optional - vtk file to write. If no file is given, a string is returned. - - """ - grid = self.get_grid() + np.ones(3,dtype=int) - size = self.get_size() - origin = self.get_origin() - - coords = [ - np.linspace(0,size[0],grid[0]) + origin[0], - np.linspace(0,size[1],grid[1]) + origin[1], - np.linspace(0,size[2],grid[2]) + origin[2] - ] - - rGrid = vtk.vtkRectilinearGrid() - coordArray = [vtk.vtkDoubleArray(),vtk.vtkDoubleArray(),vtk.vtkDoubleArray()] - - rGrid.SetDimensions(*grid) - for d,coord in enumerate(coords): - for c in coord: - coordArray[d].InsertNextValue(c) - - rGrid.SetXCoordinates(coordArray[0]) - rGrid.SetYCoordinates(coordArray[1]) - rGrid.SetZCoordinates(coordArray[2]) - - ms = numpy_support.numpy_to_vtk(num_array=self.microstructure.flatten(order='F'), - array_type=vtk.VTK_INT if self.microstructure.dtype == int else vtk.VTK_FLOAT) - ms.SetName('microstructure') - rGrid.GetCellData().AddArray(ms) - - - if fname is None: - writer = vtk.vtkDataSetWriter() - writer.SetHeader('damask.Geom '+version) - writer.WriteToOutputStringOn() - else: - writer = vtk.vtkXMLRectilinearGridWriter() - writer.SetCompressorTypeToZLib() - writer.SetDataModeToBinary() - - ext = os.path.splitext(fname)[1] - if ext == '': - name = fname + '.' + writer.GetDefaultFileExtension() - elif ext == writer.GetDefaultFileExtension(): - name = fname - else: - raise ValueError("unknown extension {}".format(ext)) - writer.SetFileName(name) - - writer.SetInputData(rGrid) - writer.Write() - - if fname is None: return writer.GetOutputString() - - - def show(self): - """Show raw content (as in file).""" - f=StringIO() - self.to_file(f) - f.seek(0) - return ''.join(f.readlines()) + + def show(self): + """Show raw content (as in file).""" + f=StringIO() + self.to_file(f) + f.seek(0) + return ''.join(f.readlines())