diff --git a/PRIVATE b/PRIVATE index 62df7f24f..bb989504b 160000 --- a/PRIVATE +++ b/PRIVATE @@ -1 +1 @@ -Subproject commit 62df7f24f2a95fda255f7d20b130afcfeecb1b4a +Subproject commit bb989504bea36fe2dbb881bc9232b0ea3193631a diff --git a/python/.coveragerc b/python/.coveragerc index e15d64f56..d1d5590a6 100644 --- a/python/.coveragerc +++ b/python/.coveragerc @@ -1,2 +1,4 @@ [run] source = damask +[report] +show_missing = true diff --git a/python/damask/_result.py b/python/damask/_result.py index 5b6ac71d5..8b4b70e35 100644 --- a/python/damask/_result.py +++ b/python/damask/_result.py @@ -2,7 +2,6 @@ import re import fnmatch import os import copy -import datetime import xml.etree.ElementTree as ET # noqa import xml.dom.minidom import functools @@ -117,30 +116,30 @@ class Result: self.origin = f['geometry'].attrs['origin'] r = re.compile(rf'{prefix_inc}([0-9]+)') - self.increments = sorted([i for i in f.keys() if r.match(i)],key=util.natural_sort) - self.times = np.around([f[i].attrs['t/s'] for i in self.increments],12) - if len(self.increments) == 0: + self._increments = sorted([i for i in f.keys() if r.match(i)],key=util.natural_sort) + self._times = {int(i.split('_')[1]):np.around(f[i].attrs['t/s'],12) for i in self._increments} + if len(self._increments) == 0: raise ValueError('incomplete DADF5 file') self.N_materialpoints, self.N_constituents = np.shape(f['cell_to/phase']) - self.homogenization = f['cell_to/homogenization']['label'].astype('str') - self.homogenizations = sorted(np.unique(self.homogenization),key=util.natural_sort) - self.phase = f['cell_to/phase']['label'].astype('str') - self.phases = sorted(np.unique(self.phase),key=util.natural_sort) + self.homogenization = f['cell_to/homogenization']['label'].astype('str') + self._homogenizations = sorted(np.unique(self.homogenization),key=util.natural_sort) + self.phase = f['cell_to/phase']['label'].astype('str') + self._phases = sorted(np.unique(self.phase),key=util.natural_sort) - self.fields: List[str] = [] - for c in self.phases: - self.fields += f['/'.join([self.increments[0],'phase',c])].keys() - for m in self.homogenizations: - self.fields += f['/'.join([self.increments[0],'homogenization',m])].keys() - self.fields = sorted(set(self.fields),key=util.natural_sort) # make unique + fields: List[str] = [] + for c in self._phases: + fields += f['/'.join([self._increments[0],'phase',c])].keys() + for m in self._homogenizations: + fields += f['/'.join([self._increments[0],'homogenization',m])].keys() + self._fields = sorted(set(fields),key=util.natural_sort) # make unique - self.visible = {'increments': self.increments, - 'phases': self.phases, - 'homogenizations': self.homogenizations, - 'fields': self.fields, - } + self._visible = {'increments': self._increments, + 'phases': self._phases, + 'homogenizations': self._homogenizations, + 'fields': self._fields, + } self.fname = Path(fname).expanduser().absolute() @@ -170,7 +169,7 @@ class Result: header = [f'Created by {f.attrs["creator"]}', f' on {f.attrs["created"]}', f' executing "{f.attrs["call"]}"'] - visible_increments = self.visible['increments'] + visible_increments = self._visible['increments'] first = self.view(increments=visible_increments[0:1]).list_data() @@ -221,32 +220,33 @@ class Result: if what == 'increments': choice = [c if isinstance(c,str) and c.startswith(prefix_inc) else - self.increments[c] if isinstance(c,int) and c<0 else + self._increments[c] if isinstance(c,int) and c<0 else f'{prefix_inc}{c}' for c in choice] elif what == 'times': - atol = 1e-2 * np.min(np.diff(self.times)) + times = list(self._times.values()) + atol = 1e-2 * np.min(np.diff(times)) what = 'increments' if choice == ['*']: - choice = self.increments + choice = self._increments else: iterator = np.array(choice).astype(float) choice = [] for c in iterator: - idx = np.searchsorted(self.times,c,side='left') - if idx0 and np.isclose(c,self.times[idx-1],rtol=0,atol=atol): - choice.append(self.increments[idx-1]) + idx = np.searchsorted(times,c,side='left') + if idx0 and np.isclose(c,times[idx-1],rtol=0,atol=atol): + choice.append(self._increments[idx-1]) - valid = _match(choice,getattr(self,what)) - existing = set(self.visible[what]) + valid = _match(choice,getattr(self,'_'+what)) + existing = set(self._visible[what]) if action == 'set': - dup.visible[what] = sorted(set(valid), key=util.natural_sort) + dup._visible[what] = sorted(set(valid), key=util.natural_sort) elif action == 'add': - dup.visible[what] = sorted(existing.union(valid), key=util.natural_sort) + dup._visible[what] = sorted(existing.union(valid), key=util.natural_sort) elif action == 'del': - dup.visible[what] = sorted(existing.difference(valid), key=util.natural_sort) + dup._visible[what] = sorted(existing.difference(valid), key=util.natural_sort) return dup @@ -271,9 +271,9 @@ class Result: """ s,e = map(lambda x: int(x.split(prefix_inc)[-1] if isinstance(x,str) and x.startswith(prefix_inc) else x), - (self.incs[ 0] if start is None else start, - self.incs[-1] if end is None else end)) - return [i for i in self.incs if s <= i <= e] + (self._incs[ 0] if start is None else start, + self._incs[-1] if end is None else end)) + return [i for i in self._incs if s <= i <= e] def times_in_range(self, start: Optional[float] = None, @@ -295,7 +295,7 @@ class Result: """ s,e = (self.times[ 0] if start is None else start, - self.times[-1] if end is None else end) + self.times[-1] if end is None else end) return [t for t in self.times if s <= t <= e] @@ -441,6 +441,19 @@ class Result: return self._manage_view('del',increments,times,phases,homogenizations,fields) + def view_all(self): + """ + Make all attributes visible. + + Returns + ------- + modified_view : damask.Result + View with all attributes visible. + + """ + return self.view(increments='*',phases='*',homogenizations='*',fields='*') + + def rename(self, name_src: str, name_dst: str): @@ -471,10 +484,10 @@ class Result: raise PermissionError('rename datasets') with h5py.File(self.fname,'a') as f: - for inc in self.visible['increments']: + for inc in self._visible['increments']: for ty in ['phase','homogenization']: - for label in self.visible[ty+'s']: - for field in _match(self.visible['fields'],f['/'.join([inc,ty,label])].keys()): + for label in self._visible[ty+'s']: + for field in _match(self._visible['fields'],f['/'.join([inc,ty,label])].keys()): path_src = '/'.join([inc,ty,label,field,name_src]) path_dst = '/'.join([inc,ty,label,field,name_dst]) if path_src in f.keys(): @@ -510,10 +523,10 @@ class Result: raise PermissionError('delete datasets') with h5py.File(self.fname,'a') as f: - for inc in self.visible['increments']: + for inc in self._visible['increments']: for ty in ['phase','homogenization']: - for label in self.visible[ty+'s']: - for field in _match(self.visible['fields'],f['/'.join([inc,ty,label])].keys()): + for label in self._visible[ty+'s']: + for field in _match(self._visible['fields'],f['/'.join([inc,ty,label])].keys()): path = '/'.join([inc,ty,label,field,name]) if path in f.keys(): del f[path] @@ -530,13 +543,13 @@ class Result: """ msg = [] with h5py.File(self.fname,'r') as f: - for inc in self.visible['increments']: - msg += [f'\n{inc} ({self.times[self.increments.index(inc)]} s)'] + for inc in self._visible['increments']: + msg += [f'\n{inc} ({self._times[int(inc.split("_")[1])]} s)'] for ty in ['phase','homogenization']: msg += [f' {ty}'] - for label in self.visible[ty+'s']: + for label in self._visible[ty+'s']: msg += [f' {label}'] - for field in _match(self.visible['fields'],f['/'.join([inc,ty,label])].keys()): + for field in _match(self._visible['fields'],f['/'.join([inc,ty,label])].keys()): msg += [f' {field}'] for d in f['/'.join([inc,ty,label,field])].keys(): dataset = f['/'.join([inc,ty,label,field,d])] @@ -564,8 +577,28 @@ class Result: return files @property - def incs(self): - return [int(i.split(prefix_inc)[-1]) for i in self.increments] + def _incs(self): + return [int(i.split(prefix_inc)[-1]) for i in self._increments] + + @property + def increments(self): + return [int(i.split(prefix_inc)[-1]) for i in self._visible['increments']] + + @property + def times(self): + return [self._times[i] for i in self.increments] + + @property + def phases(self): + return self._visible['phases'] + + @property + def homogenizations(self): + return self._visible['homogenizations'] + + @property + def fields(self): + return self._visible['fields'] @property @@ -1426,7 +1459,7 @@ class Result: 'meta':d.data.dtype.metadata}} r = func(**dataset,**args) result = r['data'].reshape((-1,)+r['data'].shape[3:]) - for x in self.visible[ty[0]+'s']: + for x in self._visible[ty[0]+'s']: if ty[0] == 'phase': result1 = result[at_cell_ph[0][x]] if ty[0] == 'homogenization': @@ -1435,9 +1468,8 @@ class Result: path = '/'.join(['/',increment[0],ty[0],x,field[0]]) h5_dataset = f[path].create_dataset(r['label'],data=result1) - now = datetime.datetime.now().astimezone() - h5_dataset.attrs['created'] = now.strftime('%Y-%m-%d %H:%M:%S%z') if h5py3 else \ - now.strftime('%Y-%m-%d %H:%M:%S%z').encode() + h5_dataset.attrs['created'] = util.time_stamp() if h5py3 else \ + util.time_stamp().encode() for l,v in r['meta'].items(): h5_dataset.attrs[l.lower()]=v.encode() if not h5py3 and type(v) is str else v @@ -1489,10 +1521,10 @@ class Result: groups = [] with h5py.File(self.fname,'r') as f: - for inc in self.visible['increments']: + for inc in self._visible['increments']: for ty in ['phase','homogenization']: - for label in self.visible[ty+'s']: - for field in _match(self.visible['fields'],f['/'.join([inc,ty,label])].keys()): + for label in self._visible[ty+'s']: + for field in _match(self._visible['fields'],f['/'.join([inc,ty,label])].keys()): group = '/'.join([inc,ty,label,field]) if set(datasets.values()).issubset(f[group].keys()): groups.append(group) @@ -1522,9 +1554,8 @@ class Result: compression_opts = 6 if compress else None, shuffle=True,fletcher32=True) - now = datetime.datetime.now().astimezone() - dataset.attrs['created'] = now.strftime('%Y-%m-%d %H:%M:%S%z') if h5py3 else \ - now.strftime('%Y-%m-%d %H:%M:%S%z').encode() + dataset.attrs['created'] = util.time_stamp() if h5py3 else \ + util.time_stamp().encode() for l,v in result['meta'].items(): dataset.attrs[l.lower()]=v.encode() if not h5py3 and type(v) is str else v @@ -1545,14 +1576,14 @@ class Result: in_data_ph = [] for c in range(self.N_constituents): at_cell_ph.append({label: np.where(self.phase[:,c] == label)[0] \ - for label in self.visible['phases']}) + for label in self._visible['phases']}) in_data_ph.append({label: f['/'.join(['cell_to','phase'])]['entry'][at_cell_ph[c][label]][:,c] \ - for label in self.visible['phases']}) + for label in self._visible['phases']}) at_cell_ho = {label: np.where(self.homogenization[:] == label)[0] \ - for label in self.visible['homogenizations']} + for label in self._visible['homogenizations']} in_data_ho = {label: f['/'.join(['cell_to','homogenization'])]['entry'][at_cell_ho[label]] \ - for label in self.visible['homogenizations']} + for label in self._visible['homogenizations']} return at_cell_ph,in_data_ph,at_cell_ho,in_data_ho @@ -1585,16 +1616,16 @@ class Result: r: Dict[str,Any] = {} with h5py.File(self.fname,'r') as f: - for inc in util.show_progress(self.visible['increments']): + for inc in util.show_progress(self._visible['increments']): r[inc] = {'phase':{},'homogenization':{},'geometry':{}} for out in _match(output,f['/'.join([inc,'geometry'])].keys()): r[inc]['geometry'][out] = _read(f['/'.join([inc,'geometry',out])]) for ty in ['phase','homogenization']: - for label in self.visible[ty+'s']: + for label in self._visible[ty+'s']: r[inc][ty][label] = {} - for field in _match(self.visible['fields'],f['/'.join([inc,ty,label])].keys()): + for field in _match(self._visible['fields'],f['/'.join([inc,ty,label])].keys()): r[inc][ty][label][field] = {} for out in _match(output,f['/'.join([inc,ty,label,field])].keys()): r[inc][ty][label][field][out] = _read(f['/'.join([inc,ty,label,field,out])]) @@ -1660,15 +1691,15 @@ class Result: with h5py.File(self.fname,'r') as f: - for inc in util.show_progress(self.visible['increments']): + for inc in util.show_progress(self._visible['increments']): r[inc] = {'phase':{},'homogenization':{},'geometry':{}} for out in _match(output,f['/'.join([inc,'geometry'])].keys()): r[inc]['geometry'][out] = ma.array(_read(f['/'.join([inc,'geometry',out])]),fill_value = fill_float) for ty in ['phase','homogenization']: - for label in self.visible[ty+'s']: - for field in _match(self.visible['fields'],f['/'.join([inc,ty,label])].keys()): + for label in self._visible[ty+'s']: + for field in _match(self._visible['fields'],f['/'.join([inc,ty,label])].keys()): if field not in r[inc][ty].keys(): r[inc][ty][field] = {} @@ -1752,11 +1783,10 @@ class Result: time.attrib = {'TimeType': 'List'} time_data = ET.SubElement(time, 'DataItem') - times = [self.times[self.increments.index(i)] for i in self.visible['increments']] time_data.attrib = {'Format': 'XML', 'NumberType': 'Float', - 'Dimensions': f'{len(times)}'} - time_data.text = ' '.join(map(str,times)) + 'Dimensions': f'{len(self.times)}'} + time_data.text = ' '.join(map(str,self.times)) attributes = [] data_items = [] @@ -1767,7 +1797,7 @@ class Result: hdf5_link = (hdf5_dir if absolute_path else Path(os.path.relpath(hdf5_dir,out_dir.resolve())))/hdf5_name with h5py.File(self.fname,'r') as f: - for inc in self.visible['increments']: + for inc in self._visible['increments']: grid = ET.SubElement(collection,'Grid') grid.attrib = {'GridType': 'Uniform', @@ -1802,8 +1832,8 @@ class Result: 'Dimensions': '{} {} {} 3'.format(*(self.cells[::-1]+1))} data_items[-1].text = f'{hdf5_link}:/{inc}/geometry/u_n' for ty in ['phase','homogenization']: - for label in self.visible[ty+'s']: - for field in _match(self.visible['fields'],f['/'.join([inc,ty,label])].keys()): + for label in self._visible[ty+'s']: + for field in _match(self._visible['fields'],f['/'.join([inc,ty,label])].keys()): for out in _match(output,f['/'.join([inc,ty,label,field])].keys()): name = '/'.join([inc,ty,label,field,out]) shape = f[name].shape[1:] @@ -1879,7 +1909,7 @@ class Result: v.comments = [util.execution_stamp('Result','export_VTK')] - N_digits = int(np.floor(np.log10(max(1,self.incs[-1]))))+1 + N_digits = int(np.floor(np.log10(max(1,self._incs[-1]))))+1 constituents_ = constituents if isinstance(constituents,Iterable) else \ (range(self.N_constituents) if constituents is None else [constituents]) # type: ignore @@ -1893,20 +1923,20 @@ class Result: out_dir.mkdir(parents=True,exist_ok=True) with h5py.File(self.fname,'r') as f: - if self.version_minor >= 13: + if self.version_major == 1 or self.version_minor >= 13: creator = f.attrs['creator'] if h5py3 else f.attrs['creator'].decode() created = f.attrs['created'] if h5py3 else f.attrs['created'].decode() v.comments += [f'{creator} ({created})'] - for inc in util.show_progress(self.visible['increments']): + for inc in util.show_progress(self._visible['increments']): u = _read(f['/'.join([inc,'geometry','u_n' if mode.lower() == 'cell' else 'u_p'])]) v = v.set('u',u) for ty in ['phase','homogenization']: - for field in self.visible['fields']: + for field in self._visible['fields']: outs: Dict[str, np.ma.core.MaskedArray] = {} - for label in self.visible[ty+'s']: + for label in self._visible[ty+'s']: if field not in f['/'.join([inc,ty,label])].keys(): continue for out in _match(output,f['/'.join([inc,ty,label,field])].keys()): @@ -1974,7 +2004,7 @@ class Result: if self.N_constituents != 1 or not self.structured: raise NotImplementedError('not a structured grid with one constituent') - N_digits = int(np.floor(np.log10(max(1,self.incs[-1]))))+1 + N_digits = int(np.floor(np.log10(max(1,self._incs[-1]))))+1 at_cell_ph,in_data_ph,_,_ = self._mappings() @@ -1982,14 +2012,14 @@ class Result: out_dir.mkdir(parents=True,exist_ok=True) with h5py.File(self.fname,'r') as f: - for inc in util.show_progress(self.visible['increments']): + for inc in util.show_progress(self._visible['increments']): for c in range(self.N_constituents): crystal_structure = [999] phase_name = ['Unknown Phase Type'] cell_orientation = np.zeros((np.prod(self.cells),3),np.float32) phase_ID = np.zeros((np.prod(self.cells)),dtype=np.int32) count = 1 - for label in self.visible['phases']: + for label in self._visible['phases']: try: data = _read(f['/'.join([inc,'phase',label,'mechanical',q])]) lattice = data.dtype.metadata['lattice'] @@ -2043,12 +2073,12 @@ class Result: cell_ensemble.create_dataset(name='PhaseName',data = phase_name, dtype=h5py.Datatype(tid)) cell_ensemble.attrs['AttributeMatrixType'] = np.array([11],np.uint32) - cell_ensemble.attrs['TupleDimensions'] = np.array([len(self.phases) + 1], np.uint64) + cell_ensemble.attrs['TupleDimensions'] = np.array([len(self._phases) + 1], np.uint64) for group in ['CrystalStructures','PhaseTypes','PhaseName']: add_attribute(cell_ensemble[group], 'ComponentDimensions', np.array([1],np.uint64)) - add_attribute(cell_ensemble[group], 'Tuple Axis Dimensions', f'x={len(self.phases)+1}') + add_attribute(cell_ensemble[group], 'Tuple Axis Dimensions', f'x={len(self._phases)+1}') add_attribute(cell_ensemble[group], 'DataArrayVersion', np.array([2],np.int32)) - add_attribute(cell_ensemble[group], 'TupleDimensions', np.array([len(self.phases) + 1],np.uint64)) + add_attribute(cell_ensemble[group], 'TupleDimensions', np.array([len(self._phases) + 1],np.uint64)) for group in ['CrystalStructures','PhaseTypes']: add_attribute(cell_ensemble[group], 'ObjectType', 'DataArray') add_attribute(cell_ensemble['PhaseName'], 'ObjectType', 'StringDataArray') @@ -2124,7 +2154,7 @@ class Result: f_out['cell_to'].create_dataset('homogenization',data=mapping_homog.flatten()) - for inc in util.show_progress(self.visible['increments']): + for inc in util.show_progress(self._visible['increments']): f_in.copy(inc,f_out,shallow=True) if mapping is None: for label in ['u_p','u_n']: @@ -2136,14 +2166,14 @@ class Result: f_out[inc]['geometry'].create_dataset('u_n',data=u_n) - for label in self.homogenizations: + for label in self._homogenizations: f_in[inc]['homogenization'].copy(label,f_out[inc]['homogenization'],shallow=True) - for label in self.phases: + for label in self._phases: f_in[inc]['phase'].copy(label,f_out[inc]['phase'],shallow=True) for ty in ['phase','homogenization']: - for label in self.visible[ty+'s']: - for field in _match(self.visible['fields'],f_in['/'.join([inc,ty,label])].keys()): + for label in self._visible[ty+'s']: + for field in _match(self._visible['fields'],f_in['/'.join([inc,ty,label])].keys()): p = '/'.join([inc,ty,label,field]) for out in _match(output,f_in[p].keys()): cp(f_in[p],f_out[p],out,None if mapping is None else mappings[ty][label.encode()]) diff --git a/python/damask/util.py b/python/damask/util.py index 9b606de7a..b4ee64283 100644 --- a/python/damask/util.py +++ b/python/damask/util.py @@ -223,13 +223,15 @@ def open_text(fname: _FileHandle, else: yield fname +def time_stamp() -> str: + """Provide current time as formatted string.""" + return _datetime.datetime.now().astimezone().strftime('%Y-%m-%d %H:%M:%S%z') def execution_stamp(class_name: str, function_name: _Optional[str] = None) -> str: """Timestamp the execution of a (function within a) class.""" - now = _datetime.datetime.now().astimezone().strftime('%Y-%m-%d %H:%M:%S%z') _function_name = '' if function_name is None else f'.{function_name}' - return f'damask.{class_name}{_function_name} v{_version} ({now})' + return f'damask.{class_name}{_function_name} v{_version} ({time_stamp()})' def natural_sort(key: str) -> _List[_Union[int, str]]: diff --git a/python/tests/test_Result.py b/python/tests/test_Result.py index c7e4187ab..b03b0249a 100644 --- a/python/tests/test_Result.py +++ b/python/tests/test_Result.py @@ -78,7 +78,8 @@ class TestResult: def test_view_all(self,default): - a = default.view(increments=True).get('F') + default = Result(default.fname) + a = default.view_all().get('F') assert dict_equal(a,default.view(increments='*').get('F')) assert dict_equal(a,default.view(increments=default.increments_in_range(0,np.iinfo(int).max)).get('F')) @@ -95,7 +96,7 @@ class TestResult: label = 'increments' if what == 'times' else what assert n0.get('F') is n1.get('F') is None and \ - len(n0.visible[label]) == len(n1.visible[label]) == 0 + len(n0._visible[label]) == len(n1._visible[label]) == 0 @pytest.mark.parametrize('what',['increments','times','phases','fields']) # ToDo: discuss homogenizations def test_view_more(self,default,what): @@ -116,7 +117,7 @@ class TestResult: label = 'increments' if what == 'times' else what assert n0.get('F') is n1.get('F') is None and \ - len(n0.visible[label]) == len(n1.visible[label]) == 0 + len(n0._visible[label]) == len(n1._visible[label]) == 0 def test_view_invalid_incstimes(self,default): with pytest.raises(ValueError): @@ -126,7 +127,23 @@ class TestResult: @pytest.mark.parametrize('sign',[+1,-1]) def test_view_approxtimes(self,default,inc,sign): eps = sign*1e-3 - assert [default.increments[inc]] == default.view(times=default.times[inc]+eps).visible['increments'] + times = list(default._times.values()) + assert [default._increments[inc]] == default.view(times=times[inc]+eps)._visible['increments'] + + def test_getters(self,default): + file_layout = default.get('non-existing',prune=False,flatten=False) + for i in default.increments: + increment = file_layout[f'increment_{i}'] + fields = [] + for p in default.phases: + phase = increment['phase'][p] + for f in default.fields: + fields.append(phase[f]) + for h in default.homogenizations: + homogenization = increment['homogenization'][h] + for f in default.fields: + fields.append(homogenization[f]) + assert len(fields) > 0 def test_add_invalid(self,default): default.add_absolute('xxxx') @@ -470,7 +487,7 @@ class TestResult: assert np.array_equal(dset,cur[path]) else: c = [_.decode() for _ in cur[path]] - r = ['Unknown Phase Type'] + result.phases + r = ['Unknown Phase Type'] + result._phases assert c == r grp = str(path).rpartition('/')[0] for attr in ref[grp].attrs: @@ -654,8 +671,8 @@ class TestResult: 'check_compile_job1.hdf5',]) def test_export_DADF5(self,res_path,tmp_path,fname): r = Result(res_path/fname) - r = r.view(phases = random.sample(r.phases,1)) - r = r.view(increments = random.sample(r.increments,np.random.randint(1,len(r.increments)))) + r = r.view(phases = random.sample(r._phases,1)) + r = r.view(increments = random.sample(r._increments,np.random.randint(1,len(r._increments)))) r.export_DADF5(tmp_path/fname) r_exp = Result(tmp_path/fname) assert str(r.get()) == str(r_exp.get())