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DAMASK_EICMD
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Merge commit 'v3.0.0-alpha5-324-gac7caa0a6'

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Test User 2021-12-25 08:39:14 +01:00
parent 68b34f6022 ac7caa0a64
commit 7acf3d8a02
3 changed files with 133 additions and 76 deletions
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4
python/damask/_grid.py
View File

@ -197,7 +197,7 @@ class Grid:
Grid-based geometry from file. Grid-based geometry from file.
""" """
warnings.warn('Support for ASCII-based geom format will be removed in DAMASK 3.1.0', DeprecationWarning,2) warnings.warn('Support for ASCII-based geom format will be removed in DAMASK 3.0.0', DeprecationWarning,2)
try: try:
f = open(fname) f = open(fname)
except TypeError: except TypeError:
@ -629,7 +629,7 @@ class Grid:
Compress geometry with 'x of y' and 'a to b'. Compress geometry with 'x of y' and 'a to b'.
""" """
warnings.warn('Support for ASCII-based geom format will be removed in DAMASK 3.1.0', DeprecationWarning,2) warnings.warn('Support for ASCII-based geom format will be removed in DAMASK 3.0.0', DeprecationWarning,2)
header = [f'{len(self.comments)+4} header'] + self.comments \ header = [f'{len(self.comments)+4} header'] + self.comments \
+ ['grid a {} b {} c {}'.format(*self.cells), + ['grid a {} b {} c {}'.format(*self.cells),
'size x {} y {} z {}'.format(*self.size), 'size x {} y {} z {}'.format(*self.size),

173
python/damask/_result.py
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@ -4,6 +4,7 @@ import fnmatch
import os import os
import copy import copy
import datetime import datetime
import warnings
import xml.etree.ElementTree as ET import xml.etree.ElementTree as ET
import xml.dom.minidom import xml.dom.minidom
from pathlib import Path from pathlib import Path
@ -27,6 +28,20 @@ h5py3 = h5py.__version__[0] == '3'
chunk_size = 1024**2//8 # for compression in HDF5 chunk_size = 1024**2//8 # for compression in HDF5
def _view_transition(what,datasets,increments,times,phases,homogenizations,fields):
if (datasets is not None and what is None) or (what is not None and datasets is None):
raise ValueError('"what" and "datasets" need to be used as a pair')
if datasets is not None or what is not None:
warnings.warn('Arguments "what" and "datasets" will be removed in DAMASK v3.0.0-alpha7', DeprecationWarning,2)
return what,datasets
if sum(1 for _ in filter(None.__ne__, [increments,times,phases,homogenizations,fields])) > 1:
raise ValueError('Only one out of "increments", "times", "phases", "homogenizations", and "fields" can be used')
else:
if increments is not None: return "increments", increments
if times is not None: return "times", times
if phases is not None: return "phases", phases
if homogenizations is not None: return "homogenizations", homogenizations
if fields is not None: return "fields", fields
def _read(dataset): def _read(dataset):
"""Read a dataset and its metadata into a numpy.ndarray.""" """Read a dataset and its metadata into a numpy.ndarray."""
@ -79,7 +94,7 @@ class Result:
>>> r.add_Cauchy() >>> r.add_Cauchy()
>>> r.add_equivalent_Mises('sigma') >>> r.add_equivalent_Mises('sigma')
>>> r.export_VTK() >>> r.export_VTK()
>>> r_last = r.view('increments',-1) >>> r_last = r.view(increments=-1)
>>> sigma_vM_last = r_last.get('sigma_vM') >>> sigma_vM_last = r_last.get('sigma_vM')
""" """
@ -141,7 +156,7 @@ class Result:
self.fname = Path(fname).absolute() self.fname = Path(fname).absolute()
self._allow_modification = False self._protected = True
def __copy__(self): def __copy__(self):
@ -155,10 +170,10 @@ class Result:
"""Show summary of file content.""" """Show summary of file content."""
visible_increments = self.visible['increments'] visible_increments = self.visible['increments']
first = self.view('increments',visible_increments[0:1]).list_data() first = self.view(increments=visible_increments[0:1]).list_data()
last = '' if len(visible_increments) < 2 else \ last = '' if len(visible_increments) < 2 else \
self.view('increments',visible_increments[-1:]).list_data() self.view(increments=visible_increments[-1:]).list_data()
in_between = '' if len(visible_increments) < 3 else \ in_between = '' if len(visible_increments) < 3 else \
''.join([f'\n{inc}\n ...\n' for inc in visible_increments[1:-1]]) ''.join([f'\n{inc}\n ...\n' for inc in visible_increments[1:-1]])
@ -231,36 +246,6 @@ class Result:
return dup return dup
def modification_enable(self):
"""
Allow modification of existing data.
Returns
-------
modified_view : damask.Result
View without write-protection of existing data.
"""
print(util.warn('Warning: Modification of existing datasets allowed!'))
dup = self.copy()
dup._allow_modification = True
return dup
def modification_disable(self):
"""
Prevent modification of existing data (default case).
Returns
-------
modified_view : damask.Result
View with write-protection of existing data.
"""
dup = self.copy()
dup._allow_modification = False
return dup
def increments_in_range(self,start,end): def increments_in_range(self,start,end):
""" """
Get all increments within a given range. Get all increments within a given range.
@ -285,7 +270,6 @@ class Result:
selected.append(self.increments[i]) selected.append(self.increments[i])
return selected return selected
def times_in_range(self,start,end): def times_in_range(self,start,end):
""" """
Get all increments within a given time range. Get all increments within a given time range.
@ -310,17 +294,38 @@ class Result:
return selected return selected
def view(self,what,datasets): def view(self,what=None,datasets=None,*,
increments=None,
times=None,
phases=None,
homogenizations=None,
fields=None,
protected=None):
""" """
Set view. Set view.
Wildcard matching with '?' and '*' is supported.
True is equivalent to '*', False is equivalent to [].
Parameters Parameters
---------- ----------
what : {'increments', 'times', 'phases', 'homogenizations', 'fields'} what : {'increments', 'times', 'phases', 'homogenizations', 'fields'}
Attribute to change. Attribute to change. DEPRECATED.
datasets : (list of) int (for increments), (list of) float (for times), (list of) str, or bool datasets : (list of) int (for increments), (list of) float (for times), (list of) str, or bool
Name of datasets; supports '?' and '*' wildcards. Name of datasets; supports '?' and '*' wildcards. DEPRECATED.
True is equivalent to '*', False is equivalent to []. True is equivalent to '*', False is equivalent to [].
increments: (list of) int, (list of) str, or bool, optional.
Number(s) of increments to select.
times: (list of) float, (list of) str, or bool, optional.
Simulation time(s) of increments to select.
phases: (list of) str, or bool, optional.
Name(s) of phases to select.
homogenizations: (list of) str, or bool, optional.
Name(s) of homogenizations to select.
fields: (list of) str, or bool, optional.
Name(s) of fields to select.
protected: bool, optional.
Protection status of existing data.
Returns Returns
------- -------
@ -333,29 +338,61 @@ class Result:
>>> import damask >>> import damask
>>> r = damask.Result('my_file.hdf5') >>> r = damask.Result('my_file.hdf5')
>>> r_first = r.view('increment',0) >>> r_first = r.view(increment=0)
Get a view that shows all results between simulation times of 10 to 40: Get a view that shows all results between simulation times of 10 to 40:
>>> import damask >>> import damask
>>> r = damask.Result('my_file.hdf5') >>> r = damask.Result('my_file.hdf5')
>>> r_t10to40 = r.view('times',r.times_in_range(10.0,40.0)) >>> r_t10to40 = r.view(times=r.times_in_range(10.0,40.0))
""" """
return self._manage_view('set',what,datasets) v = _view_transition(what,datasets,increments,times,phases,homogenizations,fields)
if protected is not None:
if v is None:
dup = self.copy()
else:
what_,datasets_ = v
dup = self._manage_view('set',what_,datasets_)
if not protected:
print(util.warn('Warning: Modification of existing datasets allowed!'))
dup._protected = protected
else:
what_,datasets_ = v
dup = self._manage_view('set',what_,datasets_)
return dup
def view_more(self,what,datasets): def view_more(self,what=None,datasets=None,*,
increments=None,
times=None,
phases=None,
homogenizations=None,
fields=None):
""" """
Add to view. Add to view.
Wildcard matching with '?' and '*' is supported.
True is equivalent to '*', False is equivalent to [].
Parameters Parameters
---------- ----------
what : {'increments', 'times', 'phases', 'homogenizations', 'fields'} what : {'increments', 'times', 'phases', 'homogenizations', 'fields'}
Attribute to change. Attribute to change. DEPRECATED.
datasets : (list of) int (for increments), (list of) float (for times), (list of) str, or bool datasets : (list of) int (for increments), (list of) float (for times), (list of) str, or bool
Name of datasets; supports '?' and '*' wildcards. Name of datasets; supports '?' and '*' wildcards. DEPRECATED.
True is equivalent to '*', False is equivalent to []. True is equivalent to '*', False is equivalent to [].
increments: (list of) int, (list of) str, or bool, optional.
Number(s) of increments to select.
times: (list of) float, (list of) str, or bool, optional.
Simulation time(s) of increments to select.
phases: (list of) str, or bool, optional.
Name(s) of phases to select.
homogenizations: (list of) str, or bool, optional.
Name(s) of homogenizations to select.
fields: (list of) str, or bool, optional.
Name(s) of fields to select.
Returns Returns
------- -------
@ -367,25 +404,44 @@ class Result:
Get a view that shows only results from first and last increment: Get a view that shows only results from first and last increment:
>>> import damask >>> import damask
>>> r_empty = damask.Result('my_file.hdf5').view('increments',False) >>> r_empty = damask.Result('my_file.hdf5').view(increments=False)
>>> r_first = r_empty.view_more('increments',0) >>> r_first = r_empty.view_more(increments=0)
>>> r_first_and_last = r.first.view_more('increments',-1) >>> r_first_and_last = r.first.view_more(increments=-1)
""" """
return self._manage_view('add',what,datasets) what_, datasets_ = _view_transition(what,datasets,increments,times,phases,homogenizations,fields)
return self._manage_view('add',what_,datasets_)
def view_less(self,what,datasets): def view_less(self,what=None,datasets=None,*,
increments=None,
times=None,
phases=None,
homogenizations=None,
fields=None):
""" """
Remove from view. Remove from view.
Wildcard matching with '?' and '*' is supported.
True is equivalent to '*', False is equivalent to [].
Parameters Parameters
---------- ----------
what : {'increments', 'times', 'phases', 'homogenizations', 'fields'} what : {'increments', 'times', 'phases', 'homogenizations', 'fields'}
Attribute to change. Attribute to change. DEPRECATED.
datasets : (list of) int (for increments), (list of) float (for times), (list of) str, or bool datasets : (list of) int (for increments), (list of) float (for times), (list of) str, or bool
Name of datasets; supports '?' and '*' wildcards. Name of datasets; supports '?' and '*' wildcards. DEPRECATED.
True is equivalent to '*', False is equivalent to []. True is equivalent to '*', False is equivalent to [].
increments: (list of) int, (list of) str, or bool, optional.
Number(s) of increments to select.
times: (list of) float, (list of) str, or bool, optional.
Simulation time(s) of increments to select.
phases: (list of) str, or bool, optional.
Name(s) of phases to select.
homogenizations: (list of) str, or bool, optional.
Name(s) of homogenizations to select.
fields: (list of) str, or bool, optional.
Name(s) of fields to select.
Returns Returns
------- -------
@ -398,10 +454,11 @@ class Result:
>>> import damask >>> import damask
>>> r_all = damask.Result('my_file.hdf5') >>> r_all = damask.Result('my_file.hdf5')
>>> r_deformed = r_all.view_less('increments',0) >>> r_deformed = r_all.view_less(increments=0)
""" """
return self._manage_view('del',what,datasets) what_, datasets_ = _view_transition(what,datasets,increments,times,phases,homogenizations,fields)
return self._manage_view('del',what_,datasets_)
def rename(self,name_src,name_dst): def rename(self,name_src,name_dst):
@ -424,11 +481,11 @@ class Result:
>>> import damask >>> import damask
>>> r = damask.Result('my_file.hdf5') >>> r = damask.Result('my_file.hdf5')
>>> r_unprotected = r.modification_enable() >>> r_unprotected = r.view(protected=False)
>>> r_unprotected.rename('F','def_grad') >>> r_unprotected.rename('F','def_grad')
""" """
if not self._allow_modification: if self._protected:
raise PermissionError('Renaming datasets not permitted') raise PermissionError('Renaming datasets not permitted')
with h5py.File(self.fname,'a') as f: with h5py.File(self.fname,'a') as f:
@ -463,11 +520,11 @@ class Result:
>>> import damask >>> import damask
>>> r = damask.Result('my_file.hdf5') >>> r = damask.Result('my_file.hdf5')
>>> r_unprotected = r.modification_enable() >>> r_unprotected = r.view(protected=False)
>>> r_unprotected.remove('F') >>> r_unprotected.remove('F')
""" """
if not self._allow_modification: if self._protected:
raise PermissionError('Removing datasets not permitted') raise PermissionError('Removing datasets not permitted')
with h5py.File(self.fname,'a') as f: with h5py.File(self.fname,'a') as f:
@ -1358,7 +1415,7 @@ class Result:
lock.acquire() lock.acquire()
with h5py.File(self.fname, 'a') as f: with h5py.File(self.fname, 'a') as f:
try: try:
if self._allow_modification and '/'.join([group,result['label']]) in f: if not self._protected and '/'.join([group,result['label']]) in f:
dataset = f['/'.join([group,result['label']])] dataset = f['/'.join([group,result['label']])]
dataset[...] = result['data'] dataset[...] = result['data']
dataset.attrs['overwritten'] = True dataset.attrs['overwritten'] = True

32
python/tests/test_Result.py
View File

@ -25,7 +25,7 @@ def default(tmp_path,ref_path):
fname = '12grains6x7x8_tensionY.hdf5' fname = '12grains6x7x8_tensionY.hdf5'
shutil.copy(ref_path/fname,tmp_path) shutil.copy(ref_path/fname,tmp_path)
f = Result(tmp_path/fname) f = Result(tmp_path/fname)
return f.view('times',20.0) return f.view(times=20.0)
@pytest.fixture @pytest.fixture
def single_phase(tmp_path,ref_path): def single_phase(tmp_path,ref_path):
@ -58,14 +58,14 @@ class TestResult:
def test_view_all(self,default): def test_view_all(self,default):
a = default.view('increments',True).get('F') a = default.view(increments=True).get('F')
assert dict_equal(a,default.view('increments','*').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')) assert dict_equal(a,default.view(increments=default.increments_in_range(0,np.iinfo(int).max)).get('F'))
assert dict_equal(a,default.view('times',True).get('F')) assert dict_equal(a,default.view(times=True).get('F'))
assert dict_equal(a,default.view('times','*').get('F')) assert dict_equal(a,default.view(times='*').get('F'))
assert dict_equal(a,default.view('times',default.times_in_range(0.0,np.inf)).get('F')) assert dict_equal(a,default.view(times=default.times_in_range(0.0,np.inf)).get('F'))
@pytest.mark.parametrize('what',['increments','times','phases','fields']) # ToDo: discuss homogenizations @pytest.mark.parametrize('what',['increments','times','phases','fields']) # ToDo: discuss homogenizations
def test_view_none(self,default,what): def test_view_none(self,default,what):
@ -314,7 +314,7 @@ class TestResult:
@pytest.mark.parametrize('overwrite',['off','on']) @pytest.mark.parametrize('overwrite',['off','on'])
def test_add_overwrite(self,default,overwrite): def test_add_overwrite(self,default,overwrite):
last = default.view('increments',-1) last = default.view(increments=-1)
last.add_stress_Cauchy() last.add_stress_Cauchy()
@ -322,9 +322,9 @@ class TestResult:
created_first = datetime.strptime(created_first,'%Y-%m-%d %H:%M:%S%z') created_first = datetime.strptime(created_first,'%Y-%m-%d %H:%M:%S%z')
if overwrite == 'on': if overwrite == 'on':
last = last.modification_enable() last = last.view(protected=False)
else: else:
last = last.modification_disable() last = last.view(protected=True)
time.sleep(2.) time.sleep(2.)
try: try:
@ -344,10 +344,10 @@ class TestResult:
def test_rename(self,default,allowed): def test_rename(self,default,allowed):
if allowed == 'on': if allowed == 'on':
F = default.place('F') F = default.place('F')
default = default.modification_enable() default = default.view(protected=False)
default.rename('F','new_name') default.rename('F','new_name')
assert np.all(F == default.place('new_name')) assert np.all(F == default.place('new_name'))
default = default.modification_disable() default = default.view(protected=True)
with pytest.raises(PermissionError): with pytest.raises(PermissionError):
default.rename('P','another_new_name') default.rename('P','another_new_name')
@ -355,7 +355,7 @@ class TestResult:
@pytest.mark.parametrize('allowed',['off','on']) @pytest.mark.parametrize('allowed',['off','on'])
def test_remove(self,default,allowed): def test_remove(self,default,allowed):
if allowed == 'on': if allowed == 'on':
unsafe = default.modification_enable() unsafe = default.view(protected=False)
unsafe.remove('F') unsafe.remove('F')
assert unsafe.get('F') is None assert unsafe.get('F') is None
else: else:
@ -377,7 +377,7 @@ class TestResult:
@pytest.mark.parametrize('inc',[4,0],ids=range(2)) @pytest.mark.parametrize('inc',[4,0],ids=range(2))
@pytest.mark.xfail(int(vtk.vtkVersion.GetVTKVersion().split('.')[0])<9, reason='missing "Direction" attribute') @pytest.mark.xfail(int(vtk.vtkVersion.GetVTKVersion().split('.')[0])<9, reason='missing "Direction" attribute')
def test_vtk(self,request,tmp_path,ref_path,update,patch_execution_stamp,patch_datetime_now,output,fname,inc): def test_vtk(self,request,tmp_path,ref_path,update,patch_execution_stamp,patch_datetime_now,output,fname,inc):
result = Result(ref_path/fname).view('increments',inc) result = Result(ref_path/fname).view(increments=inc)
os.chdir(tmp_path) os.chdir(tmp_path)
result.export_VTK(output,parallel=False) result.export_VTK(output,parallel=False)
fname = fname.split('.')[0]+f'_inc{(inc if type(inc) == int else inc[0]):0>2}.vti' fname = fname.split('.')[0]+f'_inc{(inc if type(inc) == int else inc[0]):0>2}.vti'
@ -400,7 +400,7 @@ class TestResult:
result.export_VTK(output,mode) result.export_VTK(output,mode)
def test_marc_coordinates(self,ref_path): def test_marc_coordinates(self,ref_path):
result = Result(ref_path/'check_compile_job1.hdf5').view('increments',-1) result = Result(ref_path/'check_compile_job1.hdf5').view(increments=-1)
c_n = result.coordinates0_node + result.get('u_n') c_n = result.coordinates0_node + result.get('u_n')
c_p = result.coordinates0_point + result.get('u_p') c_p = result.coordinates0_point + result.get('u_p')
assert len(c_n) > len(c_p) assert len(c_n) > len(c_p)
@ -440,7 +440,7 @@ class TestResult:
dim_xdmf = reader_xdmf.GetOutput().GetDimensions() dim_xdmf = reader_xdmf.GetOutput().GetDimensions()
bounds_xdmf = reader_xdmf.GetOutput().GetBounds() bounds_xdmf = reader_xdmf.GetOutput().GetBounds()
single_phase.view('increments',0).export_VTK(parallel=False) single_phase.view(increments=0).export_VTK(parallel=False)
fname = os.path.splitext(os.path.basename(single_phase.fname))[0]+'_inc00.vti' fname = os.path.splitext(os.path.basename(single_phase.fname))[0]+'_inc00.vti'
reader_vti = vtk.vtkXMLImageDataReader() reader_vti = vtk.vtkXMLImageDataReader()
reader_vti.SetFileName(fname) reader_vti.SetFileName(fname)