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Merge branch 'keyword-view' into 'development' 

using keywords instead of strings to control view

Closes #133

See merge request damask/DAMASK!484
This commit is contained in:
Philip Eisenlohr 2021-12-24 23:07:10 +00:00
parent d8ef23fc91 25ab62402a
commit 2ea2930638
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.
"""
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:
f = open(fname)
except TypeError:
@ -629,7 +629,7 @@ class Grid:
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 \
+ ['grid a {} b {} c {}'.format(*self.cells),
'size x {} y {} z {}'.format(*self.size),

173
python/damask/_result.py
View File

@ -4,6 +4,7 @@ import fnmatch
import os
import copy
import datetime
import warnings
import xml.etree.ElementTree as ET
import xml.dom.minidom
from pathlib import Path
@ -27,6 +28,20 @@ h5py3 = h5py.__version__[0] == '3'
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):
"""Read a dataset and its metadata into a numpy.ndarray."""
@ -79,7 +94,7 @@ class Result:
>>> r.add_Cauchy()
>>> r.add_equivalent_Mises('sigma')
>>> r.export_VTK()
>>> r_last = r.view('increments',-1)
>>> r_last = r.view(increments=-1)
>>> sigma_vM_last = r_last.get('sigma_vM')
"""
@ -141,7 +156,7 @@ class Result:
self.fname = Path(fname).absolute()
self._allow_modification = False
self._protected = True
def __copy__(self):
@ -155,10 +170,10 @@ class Result:
"""Show summary of file content."""
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 \
self.view('increments',visible_increments[-1:]).list_data()
self.view(increments=visible_increments[-1:]).list_data()
in_between = '' if len(visible_increments) < 3 else \
''.join([f'\n{inc}\n ...\n' for inc in visible_increments[1:-1]])
@ -231,36 +246,6 @@ class Result:
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):
"""
Get all increments within a given range.
@ -285,7 +270,6 @@ class Result:
selected.append(self.increments[i])
return selected
def times_in_range(self,start,end):
"""
Get all increments within a given time range.
@ -310,17 +294,38 @@ class Result:
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.
Wildcard matching with '?' and '*' is supported.
True is equivalent to '*', False is equivalent to [].
Parameters
----------
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
Name of datasets; supports '?' and '*' wildcards.
Name of datasets; supports '?' and '*' wildcards. DEPRECATED.
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
-------
@ -333,29 +338,61 @@ class Result:
>>> import damask
>>> 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:
>>> import damask
>>> 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.
Wildcard matching with '?' and '*' is supported.
True is equivalent to '*', False is equivalent to [].
Parameters
----------
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
Name of datasets; supports '?' and '*' wildcards.
Name of datasets; supports '?' and '*' wildcards. DEPRECATED.
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
-------
@ -367,25 +404,44 @@ class Result:
Get a view that shows only results from first and last increment:
>>> import damask
>>> r_empty = damask.Result('my_file.hdf5').view('increments',False)
>>> r_first = r_empty.view_more('increments',0)
>>> r_first_and_last = r.first.view_more('increments',-1)
>>> r_empty = damask.Result('my_file.hdf5').view(increments=False)
>>> r_first = r_empty.view_more(increments=0)
>>> 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.
Wildcard matching with '?' and '*' is supported.
True is equivalent to '*', False is equivalent to [].
Parameters
----------
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
Name of datasets; supports '?' and '*' wildcards.
Name of datasets; supports '?' and '*' wildcards. DEPRECATED.
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
-------
@ -398,10 +454,11 @@ class Result:
>>> import damask
>>> 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):
@ -424,11 +481,11 @@ class Result:
>>> import damask
>>> r = damask.Result('my_file.hdf5')
>>> r_unprotected = r.modification_enable()
>>> r_unprotected = r.view(protected=False)
>>> r_unprotected.rename('F','def_grad')
"""
if not self._allow_modification:
if self._protected:
raise PermissionError('Renaming datasets not permitted')
with h5py.File(self.fname,'a') as f:
@ -463,11 +520,11 @@ class Result:
>>> import damask
>>> r = damask.Result('my_file.hdf5')
>>> r_unprotected = r.modification_enable()
>>> r_unprotected = r.view(protected=False)
>>> r_unprotected.remove('F')
"""
if not self._allow_modification:
if self._protected:
raise PermissionError('Removing datasets not permitted')
with h5py.File(self.fname,'a') as f:
@ -1358,7 +1415,7 @@ class Result:
lock.acquire()
with h5py.File(self.fname, 'a') as f:
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[...] = result['data']
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'
shutil.copy(ref_path/fname,tmp_path)
f = Result(tmp_path/fname)
return f.view('times',20.0)
return f.view(times=20.0)
@pytest.fixture
def single_phase(tmp_path,ref_path):
@ -58,14 +58,14 @@ class TestResult:
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',default.increments_in_range(0,np.iinfo(int).max)).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('times',True).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=True).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'))
@pytest.mark.parametrize('what',['increments','times','phases','fields']) # ToDo: discuss homogenizations
def test_view_none(self,default,what):
@ -314,7 +314,7 @@ class TestResult:
@pytest.mark.parametrize('overwrite',['off','on'])
def test_add_overwrite(self,default,overwrite):
last = default.view('increments',-1)
last = default.view(increments=-1)
last.add_stress_Cauchy()
@ -322,9 +322,9 @@ class TestResult:
created_first = datetime.strptime(created_first,'%Y-%m-%d %H:%M:%S%z')
if overwrite == 'on':
last = last.modification_enable()
last = last.view(protected=False)
else:
last = last.modification_disable()
last = last.view(protected=True)
time.sleep(2.)
try:
@ -344,10 +344,10 @@ class TestResult:
def test_rename(self,default,allowed):
if allowed == 'on':
F = default.place('F')
default = default.modification_enable()
default = default.view(protected=False)
default.rename('F','new_name')
assert np.all(F == default.place('new_name'))
default = default.modification_disable()
default = default.view(protected=True)
with pytest.raises(PermissionError):
default.rename('P','another_new_name')
@ -355,7 +355,7 @@ class TestResult:
@pytest.mark.parametrize('allowed',['off','on'])
def test_remove(self,default,allowed):
if allowed == 'on':
unsafe = default.modification_enable()
unsafe = default.view(protected=False)
unsafe.remove('F')
assert unsafe.get('F') is None
else:
@ -377,7 +377,7 @@ class TestResult:
@pytest.mark.parametrize('inc',[4,0],ids=range(2))
@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):
result = Result(ref_path/fname).view('increments',inc)
result = Result(ref_path/fname).view(increments=inc)
os.chdir(tmp_path)
result.export_VTK(output,parallel=False)
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)
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_p = result.coordinates0_point + result.get('u_p')
assert len(c_n) > len(c_p)
@ -440,7 +440,7 @@ class TestResult:
dim_xdmf = reader_xdmf.GetOutput().GetDimensions()
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'
reader_vti = vtk.vtkXMLImageDataReader()
reader_vti.SetFileName(fname)