import multiprocessing as mp import re import inspect import glob import os import datetime import xml.etree.ElementTree as ET import xml.dom.minidom from pathlib import Path from functools import partial import h5py import numpy as np from . import VTK from . import Table from . import Rotation from . import Orientation from . import Environment from . import grid_filters from . import mechanics from . import util from . import version class Result: """ Read and write to DADF5 files. DADF5 (DAMASK HDF5) files contain DAMASK results. """ def __init__(self,fname): """ Open an existing DADF5 file. Parameters ---------- fname : str name of the DADF5 file to be opened. """ with h5py.File(fname,'r') as f: try: self.version_major = f.attrs['DADF5_version_major'] self.version_minor = f.attrs['DADF5_version_minor'] except KeyError: self.version_major = f.attrs['DADF5-major'] self.version_minor = f.attrs['DADF5-minor'] if self.version_major != 0 or not 2 <= self.version_minor <= 6: raise TypeError(f'Unsupported DADF5 version {self.version_major}.{self.version_minor}') self.structured = 'grid' in f['geometry'].attrs.keys() if self.structured: self.grid = f['geometry'].attrs['grid'] self.size = f['geometry'].attrs['size'] self.origin = f['geometry'].attrs['origin'] if self.version_major == 0 and self.version_minor >= 5 else \ np.zeros(3) r=re.compile('inc[0-9]+') increments_unsorted = {int(i[3:]):i for i in f.keys() if r.match(i)} self.increments = [increments_unsorted[i] for i in sorted(increments_unsorted)] self.times = [round(f[i].attrs['time/s'],12) for i in self.increments] self.Nmaterialpoints, self.Nconstituents = np.shape(f['mapping/cellResults/constituent']) self.materialpoints = [m.decode() for m in np.unique(f['mapping/cellResults/materialpoint']['Name'])] self.constituents = [c.decode() for c in np.unique(f['mapping/cellResults/constituent'] ['Name'])] # faster, but does not work with (deprecated) DADF5_postResults #self.materialpoints = [m for m in f['inc0/materialpoint']] #self.constituents = [c for c in f['inc0/constituent']] self.con_physics = [] for c in self.constituents: self.con_physics += f['/'.join([self.increments[0],'constituent',c])].keys() self.con_physics = list(set(self.con_physics)) # make unique self.mat_physics = [] for m in self.materialpoints: self.mat_physics += f['/'.join([self.increments[0],'materialpoint',m])].keys() self.mat_physics = list(set(self.mat_physics)) # make unique self.selection = {'increments': self.increments, 'constituents': self.constituents,'materialpoints': self.materialpoints, 'con_physics': self.con_physics, 'mat_physics': self.mat_physics } self.fname = Path(fname).absolute() self._allow_modification = False def __repr__(self): """Show selected data.""" all_selected_increments = self.selection['increments'] self.pick('increments',all_selected_increments[0:1]) first = self.list_data() self.pick('increments',all_selected_increments[-1:]) last = '' if len(all_selected_increments) < 2 else self.list_data() self.pick('increments',all_selected_increments) in_between = '' if len(all_selected_increments) < 3 else \ ''.join([f'\n{inc}\n ...\n' for inc in all_selected_increments[1:-2]]) return util.srepr(first + in_between + last) def _manage_selection(self,action,what,datasets): """ Manages the visibility of the groups. Parameters ---------- action : str select from 'set', 'add', and 'del' what : str attribute to change (must be from self.selection) datasets : list of str or bool name of datasets as list, supports ? and * wildcards. True is equivalent to [*], False is equivalent to [] """ # allow True/False and string arguments if datasets is True: datasets = ['*'] elif datasets is False: datasets = [] choice = datasets if hasattr(datasets,'__iter__') and not isinstance(datasets,str) else \ [datasets] if what == 'increments': choice = [c if isinstance(c,str) and c.startswith('inc') else f'inc{c}' for c in choice] elif what == 'times': what = 'increments' if choice == ['*']: choice = self.increments else: iterator = map(float,choice) choice = [] for c in iterator: idx = np.searchsorted(self.times,c) if idx >= len(self.times): continue if np.isclose(c,self.times[idx]): choice.append(self.increments[idx]) elif np.isclose(c,self.times[idx+1]): choice.append(self.increments[idx+1]) valid = [e for e_ in [glob.fnmatch.filter(getattr(self,what),s) for s in choice] for e in e_] existing = set(self.selection[what]) if action == 'set': self.selection[what] = valid elif action == 'add': add = existing.union(valid) add_sorted = sorted(add, key=lambda x: int("".join([i for i in x if i.isdigit()]))) self.selection[what] = add_sorted elif action == 'del': diff = existing.difference(valid) diff_sorted = sorted(diff, key=lambda x: int("".join([i for i in x if i.isdigit()]))) self.selection[what] = diff_sorted def allow_modification(self): print(util.bcolors().WARNING+util.bcolors().BOLD+ 'Warning: Modification of existing datasets allowed!'+ util.bcolors().ENDC) self._allow_modification = True def disallow_modification(self): self._allow_modification = False def incs_in_range(self,start,end): selected = [] for i,inc in enumerate([int(i[3:]) for i in self.increments]): s,e = map(lambda x: int(x[3:] if isinstance(x,str) and x.startswith('inc') else x), (start,end)) if s <= inc <= e: selected.append(self.increments[i]) return selected def times_in_range(self,start,end): selected = [] for i,time in enumerate(self.times): if start <= time <= end: selected.append(self.times[i]) return selected def iterate(self,what): """ Iterate over selection items by setting each one selected. Parameters ---------- what : str attribute to change (must be from self.selection) """ datasets = self.selection[what] last_selection = datasets.copy() for dataset in datasets: if last_selection != self.selection[what]: self._manage_selection('set',what,datasets) raise Exception self._manage_selection('set',what,dataset) last_selection = self.selection[what] yield dataset self._manage_selection('set',what,datasets) def pick(self,what,datasets): """ Set selection. Parameters ---------- what : str attribute to change (must be from self.selection) datasets : list of str or bool name of datasets as list, supports ? and * wildcards. True is equivalent to [*], False is equivalent to [] """ self._manage_selection('set',what,datasets) def pick_more(self,what,datasets): """ Add to selection. Parameters ---------- what : str attribute to change (must be from self.selection) datasets : list of str or bool name of datasets as list, supports ? and * wildcards. True is equivalent to [*], False is equivalent to [] """ self._manage_selection('add',what,datasets) def pick_less(self,what,datasets): """ Delete from selection. Parameters ---------- what : str attribute to change (must be from self.selection) datasets : list of str or bool name of datasets as list, supports ? and * wildcards. True is equivalent to [*], False is equivalent to [] """ self._manage_selection('del',what,datasets) def rename(self,name_old,name_new): """ Rename datasets. Parameters ---------- name_old : str name of the datasets to be renamed name_new : str new name of the datasets """ if self._allow_modification: with h5py.File(self.fname,'a') as f: for path_old in self.get_dataset_location(name_old): path_new = os.path.join(os.path.dirname(path_old),name_new) f[path_new] = f[path_old] f[path_new].attrs['Renamed'] = 'Original name: {}'.encode() del f[path_old] else: raise PermissionError('Rename operation not permitted') # def datamerger(regular expression to filter groups into one copy) def place(self,datasets,component=0,tagged=False,split=True): """ Distribute datasets onto geometry and return Table or (split) dictionary of Tables. Must not mix nodal end cell data. Only data within - inc?????/constituent/*_*/* - inc?????/materialpoint/*_*/* - inc?????/geometry/* are considered. Parameters ---------- datasets : iterable or str component : int homogenization component to consider for constituent data tagged : bool tag Table.column name with '#component' defaults to False split : bool split Table by increment and return dictionary of Tables defaults to True """ sets = datasets if hasattr(datasets,'__iter__') and not isinstance(datasets,str) \ else [datasets] tag = f'#{component}' if tagged else '' tbl = {} if split else None inGeom = {} inData = {} with h5py.File(self.fname,'r') as f: for dataset in sets: for group in self.groups_with_datasets(dataset): path = os.path.join(group,dataset) inc,prop,name,cat,item = (path.split('/') + ['']*5)[:5] key = '/'.join([prop,name+tag]) if key not in inGeom: if prop == 'geometry': inGeom[key] = inData[key] = np.arange(self.Nmaterialpoints) elif prop == 'constituent': inGeom[key] = np.where(f['mapping/cellResults/constituent'][:,component]['Name'] == str.encode(name))[0] inData[key] = f['mapping/cellResults/constituent'][inGeom[key],component]['Position'] else: inGeom[key] = np.where(f['mapping/cellResults/materialpoint']['Name'] == str.encode(name))[0] inData[key] = f['mapping/cellResults/materialpoint'][inGeom[key].tolist()]['Position'] shape = np.shape(f[path]) data = np.full((self.Nmaterialpoints,) + (shape[1:] if len(shape)>1 else (1,)), np.nan, dtype=np.dtype(f[path])) data[inGeom[key]] = (f[path] if len(shape)>1 else np.expand_dims(f[path],1))[inData[key]] path = (os.path.join(*([prop,name]+([cat] if cat else [])+([item] if item else []))) if split else path)+tag if split: try: tbl[inc].add(path,data) except KeyError: tbl[inc] = Table(data.reshape(self.Nmaterialpoints,-1),{path:data.shape[1:]}) else: try: tbl.add(path,data) except AttributeError: tbl = Table(data.reshape(self.Nmaterialpoints,-1),{path:data.shape[1:]}) return tbl def groups_with_datasets(self,datasets): """ Return groups that contain all requested datasets. Only groups within - inc*/constituent/*/* - inc*/materialpoint/*/* - inc*/geometry/* are considered as they contain user-relevant data. Single strings will be treated as list with one entry. Wild card matching is allowed, but the number of arguments need to fit. Parameters ---------- datasets : iterable or str or bool Examples -------- datasets = False matches no group datasets = True matches all groups datasets = ['F','P'] matches a group with ['F','P','sigma'] datasets = ['*','P'] matches a group with ['F','P'] datasets = ['*'] does not match a group with ['F','P','sigma'] datasets = ['*','*'] does not match a group with ['F','P','sigma'] datasets = ['*','*','*'] matches a group with ['F','P','sigma'] """ if datasets is False: return [] sets = datasets if isinstance(datasets,bool) or (hasattr(datasets,'__iter__') and not isinstance(datasets,str)) else \ [datasets] groups = [] with h5py.File(self.fname,'r') as f: for i in self.iterate('increments'): for o,p in zip(['constituents','materialpoints'],['con_physics','mat_physics']): for oo in self.iterate(o): for pp in self.iterate(p): group = '/'.join([i,o[:-1],oo,pp]) # o[:-1]: plural/singular issue if sets is True: groups.append(group) else: match = [e for e_ in [glob.fnmatch.filter(f[group].keys(),s) for s in sets] for e in e_] if len(set(match)) == len(sets): groups.append(group) return groups def list_data(self): """Return information on all active datasets in the file.""" message = '' with h5py.File(self.fname,'r') as f: for i in self.iterate('increments'): message += f'\n{i} ({self.times[self.increments.index(i)]}s)\n' for o,p in zip(['constituents','materialpoints'],['con_physics','mat_physics']): message += f' {o[:-1]}\n' for oo in self.iterate(o): message += f' {oo}\n' for pp in self.iterate(p): message += f' {pp}\n' group = '/'.join([i,o[:-1],oo,pp]) # o[:-1]: plural/singular issue for d in f[group].keys(): try: dataset = f['/'.join([group,d])] unit = f" / {dataset.attrs['Unit'].decode()}" if 'Unit' in dataset.attrs else '' description = dataset.attrs['Description'].decode() message += f' {d}{unit}: {description}\n' except KeyError: pass return message def get_dataset_location(self,label): """Return the location of all active datasets with given label.""" path = [] with h5py.File(self.fname,'r') as f: for i in self.iterate('increments'): k = '/'.join([i,'geometry',label]) try: f[k] path.append(k) except KeyError: pass for o,p in zip(['constituents','materialpoints'],['con_physics','mat_physics']): for oo in self.iterate(o): for pp in self.iterate(p): k = '/'.join([i,o[:-1],oo,pp,label]) try: f[k] path.append(k) except KeyError: pass return path def get_constituent_ID(self,c=0): """Pointwise constituent ID.""" with h5py.File(self.fname,'r') as f: names = f['/mapping/cellResults/constituent']['Name'][:,c].astype('str') return np.array([int(n.split('_')[0]) for n in names.tolist()],dtype=np.int32) def get_crystal_structure(self): # ToDo: extension to multi constituents/phase """Info about the crystal structure.""" with h5py.File(self.fname,'r') as f: return f[self.get_dataset_location('orientation')[0]].attrs['Lattice'].astype('str') # np.bytes_ to string def read_dataset(self,path,c=0,plain=False): """ Dataset for all points/cells. If more than one path is given, the dataset is composed of the individual contributions. """ with h5py.File(self.fname,'r') as f: shape = (self.Nmaterialpoints,) + np.shape(f[path[0]])[1:] if len(shape) == 1: shape = shape +(1,) dataset = np.full(shape,np.nan,dtype=np.dtype(f[path[0]])) for pa in path: label = pa.split('/')[2] if pa.split('/')[1] == 'geometry': dataset = np.array(f[pa]) continue p = np.where(f['mapping/cellResults/constituent'][:,c]['Name'] == str.encode(label))[0] if len(p)>0: u = (f['mapping/cellResults/constituent']['Position'][p,c]) a = np.array(f[pa]) if len(a.shape) == 1: a=a.reshape([a.shape[0],1]) dataset[p,:] = a[u,:] p = np.where(f['mapping/cellResults/materialpoint']['Name'] == str.encode(label))[0] if len(p)>0: u = (f['mapping/cellResults/materialpoint']['Position'][p.tolist()]) a = np.array(f[pa]) if len(a.shape) == 1: a=a.reshape([a.shape[0],1]) dataset[p,:] = a[u,:] if plain and dataset.dtype.names is not None: return dataset.view(('float64',len(dataset.dtype.names))) else: return dataset def cell_coordinates(self): """Return initial coordinates of the cell centers.""" if self.structured: return grid_filters.cell_coord0(self.grid,self.size,self.origin).reshape(-1,3,order='F') else: with h5py.File(self.fname,'r') as f: return f['geometry/x_c'][()] def node_coordinates(self): """Return initial coordinates of the cell centers.""" if self.structured: return grid_filters.node_coord0(self.grid,self.size,self.origin).reshape(-1,3,order='F') else: with h5py.File(self.fname,'r') as f: return f['geometry/x_n'][()] @staticmethod def _add_absolute(x): return { 'data': np.abs(x['data']), 'label': f'|{x["label"]}|', 'meta': { 'Unit': x['meta']['Unit'], 'Description': f"Absolute value of {x['label']} ({x['meta']['Description']})", 'Creator': inspect.stack()[0][3][1:] } } def add_absolute(self,x): """ Add absolute value. Parameters ---------- x : str Label of scalar, vector, or tensor dataset to take absolute value of. """ self._add_generic_pointwise(self._add_absolute,{'x':x}) @staticmethod def _add_calculation(**kwargs): formula = kwargs['formula'] for d in re.findall(r'#(.*?)#',formula): formula = formula.replace(f'#{d}#',f"kwargs['{d}']['data']") return { 'data': eval(formula), 'label': kwargs['label'], 'meta': { 'Unit': kwargs['unit'], 'Description': f"{kwargs['description']} (formula: {kwargs['formula']})", 'Creator': inspect.stack()[0][3][1:] } } def add_calculation(self,label,formula,unit='n/a',description=None,vectorized=True): """ Add result of a general formula. Parameters ---------- label : str Label of resulting dataset. formula : str Formula to calculate resulting dataset. Existing datasets are referenced by ‘#TheirLabel#‘. unit : str, optional Physical unit of the result. description : str, optional Human-readable description of the result. vectorized : bool, optional Indicate whether the formula can be used in vectorized form. Defaults to ‘True’. """ if not vectorized: raise NotImplementedError dataset_mapping = {d:d for d in set(re.findall(r'#(.*?)#',formula))} # datasets used in the formula args = {'formula':formula,'label':label,'unit':unit,'description':description} self._add_generic_pointwise(self._add_calculation,dataset_mapping,args) @staticmethod def _add_Cauchy(P,F): return { 'data': mechanics.Cauchy(P['data'],F['data']), 'label': 'sigma', 'meta': { 'Unit': P['meta']['Unit'], 'Description': "Cauchy stress calculated " f"from {P['label']} ({P['meta']['Description']})" f" and {F['label']} ({F['meta']['Description']})", 'Creator': inspect.stack()[0][3][1:] } } def add_Cauchy(self,P='P',F='F'): """ Add Cauchy stress calculated from first Piola-Kirchhoff stress and deformation gradient. Parameters ---------- P : str, optional Label of the dataset containing the first Piola-Kirchhoff stress. Defaults to ‘P’. F : str, optional Label of the dataset containing the deformation gradient. Defaults to ‘F’. """ self._add_generic_pointwise(self._add_Cauchy,{'P':P,'F':F}) @staticmethod def _add_determinant(T): return { 'data': np.linalg.det(T['data']), 'label': f"det({T['label']})", 'meta': { 'Unit': T['meta']['Unit'], 'Description': f"Determinant of tensor {T['label']} ({T['meta']['Description']})", 'Creator': inspect.stack()[0][3][1:] } } def add_determinant(self,T): """ Add the determinant of a tensor. Parameters ---------- T : str Label of tensor dataset. """ self._add_generic_pointwise(self._add_determinant,{'T':T}) @staticmethod def _add_deviator(T): return { 'data': mechanics.deviatoric_part(T['data']), 'label': f"s_{T['label']}", 'meta': { 'Unit': T['meta']['Unit'], 'Description': f"Deviator of tensor {T['label']} ({T['meta']['Description']})", 'Creator': inspect.stack()[0][3][1:] } } def add_deviator(self,T): """ Add the deviatoric part of a tensor. Parameters ---------- T : str Label of tensor dataset. """ self._add_generic_pointwise(self._add_deviator,{'T':T}) @staticmethod def _add_eigenvalue(T_sym,eigenvalue): if eigenvalue == 'max': label,p = 'Maximum',2 elif eigenvalue == 'mid': label,p = 'Intermediate',1 elif eigenvalue == 'min': label,p = 'Minimum',0 return { 'data': mechanics.eigenvalues(T_sym['data'])[:,p], 'label': f"lambda_{eigenvalue}({T_sym['label']})", 'meta' : { 'Unit': T_sym['meta']['Unit'], 'Description': f"{label} eigenvalue of {T_sym['label']} ({T_sym['meta']['Description']})", 'Creator': inspect.stack()[0][3][1:] } } def add_eigenvalue(self,T_sym,eigenvalue='max'): """ Add eigenvalues of symmetric tensor. Parameters ---------- T_sym : str Label of symmetric tensor dataset. eigenvalue : str, optional Eigenvalue. Select from ‘max’, ‘mid’, ‘min’. Defaults to ‘max’. """ self._add_generic_pointwise(self._add_eigenvalue,{'T_sym':T_sym},{'eigenvalue':eigenvalue}) @staticmethod def _add_eigenvector(T_sym,eigenvalue): if eigenvalue == 'max': label,p = 'maximum',2 elif eigenvalue == 'mid': label,p = 'intermediate',1 elif eigenvalue == 'min': label,p = 'minimum',0 return { 'data': mechanics.eigenvectors(T_sym['data'])[:,p], 'label': f"v_{eigenvalue}({T_sym['label']})", 'meta' : { 'Unit': '1', 'Description': f"Eigenvector corresponding to {label} eigenvalue" f" of {T_sym['label']} ({T_sym['meta']['Description']})", 'Creator': inspect.stack()[0][3][1:] } } def add_eigenvector(self,T_sym,eigenvalue='max'): """ Add eigenvector of symmetric tensor. Parameters ---------- T_sym : str Label of symmetric tensor dataset. eigenvalue : str, optional Eigenvalue to which the eigenvector corresponds. Select from ‘max’, ‘mid’, ‘min’. Defaults to ‘max’. """ self._add_generic_pointwise(self._add_eigenvector,{'T_sym':T_sym},{'eigenvalue':eigenvalue}) @staticmethod def _add_IPFcolor(q,l): d = np.array(l) d_unit = d/np.linalg.norm(d) m = util.scale_to_coprime(d) colors = np.empty((len(q['data']),3),np.uint8) lattice = q['meta']['Lattice'] for i,qu in enumerate(q['data']): o = Orientation(np.array([qu['w'],qu['x'],qu['y'],qu['z']]),lattice).reduced() colors[i] = np.uint8(o.IPFcolor(d_unit)*255) return { 'data': colors, 'label': 'IPFcolor_[{} {} {}]'.format(*m), 'meta' : { 'Unit': 'RGB (8bit)', 'Lattice': lattice, 'Description': 'Inverse Pole Figure (IPF) colors along sample direction [{} {} {}]'.format(*m), 'Creator': inspect.stack()[0][3][1:] } } def add_IPFcolor(self,q,l): """ Add RGB color tuple of inverse pole figure (IPF) color. Parameters ---------- q : str Label of the dataset containing the crystallographic orientation as quaternions. l : numpy.array of shape (3) Lab frame direction for inverse pole figure. """ self._add_generic_pointwise(self._add_IPFcolor,{'q':q},{'l':l}) @staticmethod def _add_maximum_shear(T_sym): return { 'data': mechanics.maximum_shear(T_sym['data']), 'label': f"max_shear({T_sym['label']})", 'meta': { 'Unit': T_sym['meta']['Unit'], 'Description': f"Maximum shear component of {T_sym['label']} ({T_sym['meta']['Description']})", 'Creator': inspect.stack()[0][3][1:] } } def add_maximum_shear(self,T_sym): """ Add maximum shear components of symmetric tensor. Parameters ---------- T_sym : str Label of symmetric tensor dataset. """ self._add_generic_pointwise(self._add_maximum_shear,{'T_sym':T_sym}) @staticmethod def _add_Mises(T_sym): t = 'strain' if T_sym['meta']['Unit'] == '1' else \ 'stress' return { 'data': (mechanics.Mises_strain if t=='strain' else mechanics.Mises_stress)(T_sym['data']), 'label': f"{T_sym['label']}_vM", 'meta': { 'Unit': T_sym['meta']['Unit'], 'Description': f"Mises equivalent {t} of {T_sym['label']} ({T_sym['meta']['Description']})", 'Creator': inspect.stack()[0][3][1:] } } def add_Mises(self,T_sym): """ Add the equivalent Mises stress or strain of a symmetric tensor. Parameters ---------- T_sym : str Label of symmetric tensorial stress or strain dataset. """ self._add_generic_pointwise(self._add_Mises,{'T_sym':T_sym}) @staticmethod def _add_norm(x,ord): o = ord if len(x['data'].shape) == 2: axis = 1 t = 'vector' if o is None: o = 2 elif len(x['data'].shape) == 3: axis = (1,2) t = 'tensor' if o is None: o = 'fro' else: raise ValueError return { 'data': np.linalg.norm(x['data'],ord=o,axis=axis,keepdims=True), 'label': f"|{x['label']}|_{o}", 'meta': { 'Unit': x['meta']['Unit'], 'Description': f"{o}-norm of {t} {x['label']} ({x['meta']['Description']})", 'Creator': inspect.stack()[0][3][1:] } } def add_norm(self,x,ord=None): """ Add the norm of vector or tensor. Parameters ---------- x : str Label of vector or tensor dataset. ord : {non-zero int, inf, -inf, ‘fro’, ‘nuc’}, optional Order of the norm. inf means NumPy’s inf object. For details refer to numpy.linalg.norm. """ self._add_generic_pointwise(self._add_norm,{'x':x},{'ord':ord}) @staticmethod def _add_PK2(P,F): return { 'data': mechanics.PK2(P['data'],F['data']), 'label': 'S', 'meta': { 'Unit': P['meta']['Unit'], 'Description': "2. Piola-Kirchhoff stress calculated " f"from {P['label']} ({P['meta']['Description']})" f" and {F['label']} ({F['meta']['Description']})", 'Creator': inspect.stack()[0][3][1:] } } def add_PK2(self,P='P',F='F'): """ Add second Piola-Kirchhoff stress calculated from first Piola-Kirchhoff stress and deformation gradient. Parameters ---------- P : str, optional Label of first Piola-Kirchhoff stress dataset. Defaults to ‘P’. F : str, optional Label of deformation gradient dataset. Defaults to ‘F’. """ self._add_generic_pointwise(self._add_PK2,{'P':P,'F':F}) @staticmethod def _add_pole(q,p,polar): pole = np.array(p) unit_pole = pole/np.linalg.norm(pole) m = util.scale_to_coprime(pole) rot = Rotation(q['data'].view(np.double).reshape(-1,4)) rotatedPole = rot @ np.broadcast_to(unit_pole,rot.shape+(3,)) # rotate pole according to crystal orientation xy = rotatedPole[:,0:2]/(1.+abs(unit_pole[2])) # stereographic projection coords = xy if not polar else \ np.block([np.sqrt(xy[:,0:1]*xy[:,0:1]+xy[:,1:2]*xy[:,1:2]),np.arctan2(xy[:,1:2],xy[:,0:1])]) return { 'data': coords, 'label': 'p^{}_[{} {} {})'.format(u'rφ' if polar else 'xy',*m), 'meta' : { 'Unit': '1', 'Description': '{} coordinates of stereographic projection of pole (direction/plane) in crystal frame'\ .format('Polar' if polar else 'Cartesian'), 'Creator': inspect.stack()[0][3][1:] } } def add_pole(self,q,p,polar=False): """ Add coordinates of stereographic projection of given pole in crystal frame. Parameters ---------- q : str Label of the dataset containing the crystallographic orientation as quaternions. p : numpy.array of shape (3) Crystallographic direction or plane. polar : bool, optional Give pole in polar coordinates. Defaults to False. """ self._add_generic_pointwise(self._add_pole,{'q':q},{'p':p,'polar':polar}) @staticmethod def _add_rotational_part(F): return { 'data': mechanics.rotational_part(F['data']), 'label': f"R({F['label']})", 'meta': { 'Unit': F['meta']['Unit'], 'Description': f"Rotational part of {F['label']} ({F['meta']['Description']})", 'Creator': inspect.stack()[0][3][1:] } } def add_rotational_part(self,F): """ Add rotational part of a deformation gradient. Parameters ---------- F : str, optional Label of deformation gradient dataset. """ self._add_generic_pointwise(self._add_rotational_part,{'F':F}) @staticmethod def _add_spherical(T): return { 'data': mechanics.spherical_part(T['data']), 'label': f"p_{T['label']}", 'meta': { 'Unit': T['meta']['Unit'], 'Description': f"Spherical component of tensor {T['label']} ({T['meta']['Description']})", 'Creator': inspect.stack()[0][3][1:] } } def add_spherical(self,T): """ Add the spherical (hydrostatic) part of a tensor. Parameters ---------- T : str Label of tensor dataset. """ self._add_generic_pointwise(self._add_spherical,{'T':T}) @staticmethod def _add_strain_tensor(F,t,m): return { 'data': mechanics.strain_tensor(F['data'],t,m), 'label': f"epsilon_{t}^{m}({F['label']})", 'meta': { 'Unit': F['meta']['Unit'], 'Description': f"Strain tensor of {F['label']} ({F['meta']['Description']})", 'Creator': inspect.stack()[0][3][1:] } } def add_strain_tensor(self,F='F',t='V',m=0.0): """ Add strain tensor of a deformation gradient. For details refer to damask.mechanics.strain_tensor Parameters ---------- F : str, optional Label of deformation gradient dataset. Defaults to ‘F’. t : {‘V’, ‘U’}, optional Type of the polar decomposition, ‘V’ for left stretch tensor and ‘U’ for right stretch tensor. Defaults to ‘V’. m : float, optional Order of the strain calculation. Defaults to ‘0.0’. """ self._add_generic_pointwise(self._add_strain_tensor,{'F':F},{'t':t,'m':m}) @staticmethod def _add_stretch_tensor(F,t): return { 'data': (mechanics.left_stretch if t.upper() == 'V' else mechanics.right_stretch)(F['data']), 'label': f"{t}({F['label']})", 'meta': { 'Unit': F['meta']['Unit'], 'Description': '{} stretch tensor of {} ({})'.format('Left' if t.upper() == 'V' else 'Right', F['label'],F['meta']['Description']), 'Creator': inspect.stack()[0][3][1:] } } def add_stretch_tensor(self,F='F',t='V'): """ Add stretch tensor of a deformation gradient. Parameters ---------- F : str, optional Label of deformation gradient dataset. Defaults to ‘F’. t : {‘V’, ‘U’}, optional Type of the polar decomposition, ‘V’ for left stretch tensor and ‘U’ for right stretch tensor. Defaults to ‘V’. """ self._add_generic_pointwise(self._add_stretch_tensor,{'F':F},{'t':t}) def _job(self,group,func,datasets,args,lock): """Execute job for _add_generic_pointwise.""" try: datasets_in = {} lock.acquire() with h5py.File(self.fname,'r') as f: for arg,label in datasets.items(): loc = f[group+'/'+label] datasets_in[arg]={'data' :loc[()], 'label':label, 'meta': {k:v.decode() for k,v in loc.attrs.items()}} lock.release() r = func(**datasets_in,**args) return [group,r] except Exception as err: print(f'Error during calculation: {err}.') return None def _add_generic_pointwise(self,func,datasets,args={}): """ General function to add pointwise data. Parameters ---------- func : function Callback function that calculates a new dataset from one or more datasets per HDF5 group. datasets : dictionary Details of the datasets to be used: label (in HDF5 file) and arg (argument to which the data is parsed in func). args : dictionary, optional Arguments parsed to func. """ num_threads = Environment().options['DAMASK_NUM_THREADS'] pool = mp.Pool(int(num_threads) if num_threads is not None else None) lock = mp.Manager().Lock() groups = self.groups_with_datasets(datasets.values()) default_arg = partial(self._job,func=func,datasets=datasets,args=args,lock=lock) for result in util.show_progress(pool.imap_unordered(default_arg,groups),len(groups)): if not result: continue lock.acquire() with h5py.File(self.fname, 'a') as f: try: if self._allow_modification and result[0]+'/'+result[1]['label'] in f: dataset = f[result[0]+'/'+result[1]['label']] dataset[...] = result[1]['data'] dataset.attrs['Overwritten'] = 'Yes'.encode() else: dataset = f[result[0]].create_dataset(result[1]['label'],data=result[1]['data']) now = datetime.datetime.now().astimezone() dataset.attrs['Created'] = now.strftime('%Y-%m-%d %H:%M:%S%z').encode() for l,v in result[1]['meta'].items(): dataset.attrs[l]=v.encode() creator = f"damask.Result.{dataset.attrs['Creator'].decode()} v{version}" dataset.attrs['Creator'] = creator.encode() except (OSError,RuntimeError) as err: print(f'Could not add dataset: {err}.') lock.release() pool.close() pool.join() def write_XDMF(self): """ Write XDMF file to directly visualize data in DADF5 file. This works only for scalar, 3-vector and 3x3-tensor data. Selection is not taken into account. """ if len(self.constituents) != 1 or not self.structured: raise NotImplementedError('XDMF only available for grid results with 1 constituent.') xdmf=ET.Element('Xdmf') xdmf.attrib={'Version': '2.0', 'xmlns:xi': 'http://www.w3.org/2001/XInclude'} domain=ET.SubElement(xdmf, 'Domain') collection = ET.SubElement(domain, 'Grid') collection.attrib={'GridType': 'Collection', 'CollectionType': 'Temporal'} time = ET.SubElement(collection, 'Time') time.attrib={'TimeType': 'List'} time_data = ET.SubElement(time, 'DataItem') time_data.attrib={'Format': 'XML', 'NumberType': 'Float', 'Dimensions': f'{len(self.times)}'} time_data.text = ' '.join(map(str,self.times)) attributes = [] data_items = [] for inc in self.increments: grid=ET.SubElement(collection,'Grid') grid.attrib = {'GridType': 'Uniform', 'Name': inc} topology=ET.SubElement(grid, 'Topology') topology.attrib={'TopologyType': '3DCoRectMesh', 'Dimensions': '{} {} {}'.format(*self.grid+1)} geometry=ET.SubElement(grid, 'Geometry') geometry.attrib={'GeometryType':'Origin_DxDyDz'} origin=ET.SubElement(geometry, 'DataItem') origin.attrib={'Format': 'XML', 'NumberType': 'Float', 'Dimensions': '3'} origin.text="{} {} {}".format(*self.origin) delta=ET.SubElement(geometry, 'DataItem') delta.attrib={'Format': 'XML', 'NumberType': 'Float', 'Dimensions': '3'} delta.text="{} {} {}".format(*(self.size/self.grid)) with h5py.File(self.fname,'r') as f: attributes.append(ET.SubElement(grid, 'Attribute')) attributes[-1].attrib={'Name': 'u', 'Center': 'Node', 'AttributeType': 'Vector'} data_items.append(ET.SubElement(attributes[-1], 'DataItem')) data_items[-1].attrib={'Format': 'HDF', 'Precision': '8', 'Dimensions': '{} {} {} 3'.format(*(self.grid+1))} data_items[-1].text=f'{os.path.split(self.fname)[1]}:/{inc}/geometry/u_n' for o,p in zip(['constituents','materialpoints'],['con_physics','mat_physics']): for oo in getattr(self,o): for pp in getattr(self,p): g = '/'.join([inc,o[:-1],oo,pp]) for l in f[g]: name = '/'.join([g,l]) shape = f[name].shape[1:] dtype = f[name].dtype prec = f[name].dtype.itemsize if (shape not in [(1,), (3,), (3,3)]) or dtype != np.float64: continue attributes.append(ET.SubElement(grid, 'Attribute')) attributes[-1].attrib={'Name': name.split('/',2)[2], 'Center': 'Cell', 'AttributeType': 'Tensor'} data_items.append(ET.SubElement(attributes[-1], 'DataItem')) data_items[-1].attrib={'Format': 'HDF', 'NumberType': 'Float', 'Precision': f'{prec}', 'Dimensions': '{} {} {} {}'.format(*self.grid,np.prod(shape))} data_items[-1].text=f'{os.path.split(self.fname)[1]}:{name}' with open(self.fname.with_suffix('.xdmf').name,'w') as f: f.write(xml.dom.minidom.parseString(ET.tostring(xdmf).decode()).toprettyxml()) def to_vtk(self,labels=[],mode='cell'): """ Export to vtk cell/point data. Parameters ---------- labels : str or list of, optional Labels of the datasets to be exported. mode : str, either 'cell' or 'point' Export in cell format or point format. Defaults to 'cell'. """ if mode.lower()=='cell': if self.structured: v = VTK.from_rectilinearGrid(self.grid,self.size,self.origin) else: with h5py.File(self.fname,'r') as f: v = VTK.from_unstructuredGrid(f['/geometry/x_n'][()], f['/geometry/T_c'][()]-1, f['/geometry/T_c'].attrs['VTK_TYPE'].decode()) elif mode.lower()=='point': v = VTK.from_polyData(self.cell_coordinates()) N_digits = int(np.floor(np.log10(int(self.increments[-1][3:]))))+1 for inc in util.show_progress(self.iterate('increments'),len(self.selection['increments'])): materialpoints_backup = self.selection['materialpoints'].copy() self.pick('materialpoints',False) for label in (labels if isinstance(labels,list) else [labels]): for p in self.iterate('con_physics'): if p != 'generic': for c in self.iterate('constituents'): x = self.get_dataset_location(label) if len(x) == 0: continue array = self.read_dataset(x,0) v.add(array,'1_'+x[0].split('/',1)[1]) #ToDo: hard coded 1! else: x = self.get_dataset_location(label) if len(x) == 0: continue array = self.read_dataset(x,0) ph_name = re.compile(r'(?<=(constituent\/))(.*?)(?=(generic))') # identify phase name dset_name = '1_' + re.sub(ph_name,r'',x[0].split('/',1)[1]) # removing phase name v.add(array,dset_name) self.pick('materialpoints',materialpoints_backup) constituents_backup = self.selection['constituents'].copy() self.pick('constituents',False) for label in (labels if isinstance(labels,list) else [labels]): for p in self.iterate('mat_physics'): if p != 'generic': for m in self.iterate('materialpoints'): x = self.get_dataset_location(label) if len(x) == 0: continue array = self.read_dataset(x,0) v.add(array,'1_'+x[0].split('/',1)[1]) #ToDo: why 1_? else: x = self.get_dataset_location(label) if len(x) == 0: continue array = self.read_dataset(x,0) v.add(array,'1_'+x[0].split('/',1)[1]) self.pick('constituents',constituents_backup) u = self.read_dataset(self.get_dataset_location('u_n' if mode.lower() == 'cell' else 'u_p')) v.add(u,'u') v.write(f'{self.fname.stem}_inc{inc[3:].zfill(N_digits)}')