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Merge branch 'user_defined_add_calculation' into 'development' 

User defined add calculation

See merge request damask/DAMASK!195
This commit is contained in:
Karo 2020-08-06 00:53:16 +02:00
parent ce00371f52 3f2e63977d
commit 7824a61f2e
6 changed files with 62 additions and 32 deletions
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15
python/damask/_result.py
View File

@ -466,6 +466,11 @@ class Result:
return f[self.get_dataset_location('orientation')[0]].attrs['Lattice'].astype('str') # np.bytes_ to string
def enable_user_function(self,func):
globals()[func.__name__]=func
print(f'Function {func.__name__} enabled in add_calculation.')
def read_dataset(self,path,c=0,plain=False):
"""
Dataset for all points/cells.
@ -504,7 +509,7 @@ class Result:
else:
return dataset
@property
def cell_coordinates(self):
"""Return initial coordinates of the cell centers."""
if self.structured:
@ -513,6 +518,7 @@ class Result:
with h5py.File(self.fname,'r') as f:
return f['geometry/x_c'][()]
@property
def node_coordinates(self):
"""Return initial coordinates of the cell centers."""
if self.structured:
@ -561,7 +567,7 @@ class Result:
'Creator': inspect.stack()[0][3][1:]
}
}
def add_calculation(self,label,formula,unit='n/a',description=None,vectorized=True):
def add_calculation(self,label,formula,unit='n/a',description=None):
"""
Add result of a general formula.
@ -575,13 +581,8 @@ class Result:
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)

11
python/tests/test_Geom.py
View File

@ -1,5 +1,4 @@
import copy
import os
import pytest
import numpy as np
@ -26,7 +25,7 @@ def default():
@pytest.fixture
def reference_dir(reference_dir_base):
"""Directory containing reference results."""
return os.path.join(reference_dir_base,'Geom')
return reference_dir_base/'Geom'
class TestGeom:
@ -87,7 +86,7 @@ class TestGeom:
modified = copy.deepcopy(default)
modified.mirror(directions,reflect)
tag = f'directions={"-".join(directions)}_reflect={reflect}'
reference = os.path.join(reference_dir,f'mirror_{tag}.geom')
reference = reference_dir/f'mirror_{tag}.geom'
if update: modified.to_file(reference)
assert geom_equal(modified,Geom.from_file(reference))
@ -96,7 +95,7 @@ class TestGeom:
modified = copy.deepcopy(default)
modified.clean(stencil)
tag = f'stencil={stencil}'
reference = os.path.join(reference_dir,f'clean_{tag}.geom')
reference = reference_dir/f'clean_{tag}.geom'
if update: modified.to_file(reference)
assert geom_equal(modified,Geom.from_file(reference))
@ -113,7 +112,7 @@ class TestGeom:
modified = copy.deepcopy(default)
modified.scale(grid)
tag = f'grid={util.srepr(grid,"-")}'
reference = os.path.join(reference_dir,f'scale_{tag}.geom')
reference = reference_dir/f'scale_{tag}.geom'
if update: modified.to_file(reference)
assert geom_equal(modified,Geom.from_file(reference))
@ -152,7 +151,7 @@ class TestGeom:
modified = copy.deepcopy(default)
modified.rotate(Rotation.from_Eulers(Eulers,degrees=True))
tag = f'Eulers={util.srepr(Eulers,"-")}'
reference = os.path.join(reference_dir,f'rotate_{tag}.geom')
reference = reference_dir/f'rotate_{tag}.geom'
if update: modified.to_file(reference)
assert geom_equal(modified,Geom.from_file(reference))

2
python/tests/test_Orientation.py
View File

@ -33,7 +33,7 @@ def inverse_pole(orientation,axis,proper=False,SST=True):
@pytest.fixture
def reference_dir(reference_dir_base):
"""Directory containing reference results."""
return os.path.join(reference_dir_base,'Rotation')
return reference_dir_base/'Rotation'
class TestOrientation:

35
python/tests/test_Result.py
View File

@ -1,6 +1,7 @@
import time
import shutil
import os
import sys
from datetime import datetime
import pytest
@ -10,13 +11,14 @@ import h5py
import damask
from damask import Result
from damask import mechanics
from damask import grid_filters
@pytest.fixture
def default(tmp_path,reference_dir):
"""Small Result file in temp location for modification."""
fname = '12grains6x7x8_tensionY.hdf5'
shutil.copy(os.path.join(reference_dir,fname),tmp_path)
f = Result(os.path.join(tmp_path,fname))
shutil.copy(reference_dir/fname,tmp_path)
f = Result(tmp_path/fname)
f.pick('times',20.0)
return f
@ -24,13 +26,13 @@ def default(tmp_path,reference_dir):
def single_phase(tmp_path,reference_dir):
"""Single phase Result file in temp location for modification."""
fname = '6grains6x7x8_single_phase_tensionY.hdf5'
shutil.copy(os.path.join(reference_dir,fname),tmp_path)
return Result(os.path.join(tmp_path,fname))
shutil.copy(reference_dir/fname,tmp_path)
return Result(tmp_path/fname)
@pytest.fixture
def reference_dir(reference_dir_base):
"""Directory containing reference results."""
return os.path.join(reference_dir_base,'Result')
return reference_dir_base/'Result'
class TestResult:
@ -98,8 +100,19 @@ class TestResult:
in_file = default.read_dataset(loc['|Fe|'],0)
assert np.allclose(in_memory,in_file)
def test_add_calculation(self,default):
@pytest.mark.parametrize('mode',['direct','function'])
def test_add_calculation(self,default,tmp_path,mode):
if mode == 'direct':
default.add_calculation('x','2.0*np.abs(#F#)-1.0','-','my notes')
else:
with open(tmp_path/'f.py','w') as f:
f.write("import numpy as np\ndef my_func(field):\n return 2.0*np.abs(field)-1.0\n")
sys.path.insert(0,str(tmp_path))
import f
default.enable_user_function(f.my_func)
default.add_calculation('x','my_func(#F#)','-','my notes')
loc = {'F': default.get_dataset_location('F'),
'x': default.get_dataset_location('x')}
in_memory = 2.0*np.abs(default.read_dataset(loc['F'],0))-1.0
@ -312,6 +325,16 @@ class TestResult:
with pytest.raises(PermissionError):
default.rename('P','another_new_name')
@pytest.mark.parametrize('mode',['cell','node'])
def test_coordinates(self,default,mode):
if mode == 'cell':
a = grid_filters.cell_coord0(default.grid,default.size,default.origin)
b = default.cell_coordinates.reshape(tuple(default.grid)+(3,),order='F')
elif mode == 'node':
a = grid_filters.node_coord0(default.grid,default.size,default.origin)
b = default.node_coordinates.reshape(tuple(default.grid+1)+(3,),order='F')
assert np.allclose(a,b)
@pytest.mark.parametrize('output',['F',[],['F','P']])
def test_vtk(self,tmp_path,default,output):
os.chdir(tmp_path)

2
python/tests/test_Rotation.py
View File

@ -6,7 +6,7 @@ import numpy as np
from damask import Rotation
from damask import _rotation
n = 1100
n = 1000
atol=1.e-4
@pytest.fixture

27
python/tests/test_Table.py
View File

@ -1,5 +1,3 @@
import os
import pytest
import numpy as np
@ -15,7 +13,7 @@ def default():
@pytest.fixture
def reference_dir(reference_dir_base):
"""Directory containing reference results."""
return os.path.join(reference_dir_base,'Table')
return reference_dir_base/'Table'
class TestTable:
@ -35,9 +33,13 @@ class TestTable:
d = default.get('5_F')
assert np.allclose(d,1.0) and d.shape[1:] == (1,)
def test_write_read_str(self,default,tmpdir):
default.to_ASCII(str(tmpdir.join('default.txt')))
new = Table.from_ASCII(str(tmpdir.join('default.txt')))
@pytest.mark.parametrize('mode',['str','path'])
def test_write_read(self,default,tmpdir,mode):
default.to_ASCII(tmpdir/'default.txt')
if mode == 'path':
new = Table.from_ASCII(tmpdir/'default.txt')
elif mode == 'str':
new = Table.from_ASCII(str(tmpdir/'default.txt'))
assert all(default.data==new.data) and default.shapes == new.shapes
def test_write_read_file(self,default,tmpdir):
@ -54,20 +56,25 @@ class TestTable:
new = Table.from_ASCII(f)
assert all(default.data==new.data) and default.shapes == new.shapes
def test_read_ang_str(self,reference_dir):
new = Table.from_ang(os.path.join(reference_dir,'simple.ang'))
@pytest.mark.parametrize('mode',['str','path'])
def test_read_ang(self,reference_dir,mode):
if mode == 'path':
new = Table.from_ang(reference_dir/'simple.ang')
elif mode == 'str':
new = Table.from_ang(str(reference_dir/'simple.ang'))
assert new.data.shape == (4,10) and \
new.labels == ['eu', 'pos', 'IQ', 'CI', 'ID', 'intensity', 'fit']
def test_read_ang_file(self,reference_dir):
f = open(os.path.join(reference_dir,'simple.ang'))
f = open(reference_dir/'simple.ang')
new = Table.from_ang(f)
assert new.data.shape == (4,10) and \
new.labels == ['eu', 'pos', 'IQ', 'CI', 'ID', 'intensity', 'fit']
@pytest.mark.parametrize('fname',['datatype-mix.txt','whitespace-mix.txt'])
def test_read_strange(self,reference_dir,fname):
with open(os.path.join(reference_dir,fname)) as f:
with open(reference_dir/fname) as f:
Table.from_ASCII(f)
def test_set(self,default):