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DAMASK_EICMD
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Merge branch 'python-improvements' into 'development' 

Python improvements

See merge request damask/DAMASK!343
This commit is contained in:
Sharan Roongta 2021-02-22 12:22:02 +00:00
parent 36db53f260 5517be5078
commit 23a3354ac1
7 changed files with 28 additions and 32 deletions
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6
DAMASK_prerequisites.sh
View File

@ -84,7 +84,7 @@ for executable in python python3; do
done done
secondLevel "Details on $DEFAULT_PYTHON:" secondLevel "Details on $DEFAULT_PYTHON:"
echo $(ls -la $(which $DEFAULT_PYTHON)) echo $(ls -la $(which $DEFAULT_PYTHON))
for module in numpy scipy pandas;do for module in numpy scipy pandas matplotlib yaml h5py;do
thirdLevel $module thirdLevel $module
$DEFAULT_PYTHON -c "import $module; \ $DEFAULT_PYTHON -c "import $module; \
print('Version: {}'.format($module.__version__)); \ print('Version: {}'.format($module.__version__)); \
@ -94,10 +94,6 @@ thirdLevel vtk
$DEFAULT_PYTHON -c "import vtk; \ $DEFAULT_PYTHON -c "import vtk; \
print('Version: {}'.format(vtk.vtkVersion.GetVTKVersion())); \ print('Version: {}'.format(vtk.vtkVersion.GetVTKVersion())); \
print('Location: {}'.format(vtk.__file__))" print('Location: {}'.format(vtk.__file__))"
thirdLevel h5py
$DEFAULT_PYTHON -c "import h5py; \
print('Version: {}'.format(h5py.version.version)); \
print('Location: {}'.format(h5py.__file__))"
firstLevel "GNU Compiler Collection" firstLevel "GNU Compiler Collection"
for executable in gcc g++ gfortran ;do for executable in gcc g++ gfortran ;do

5
python/damask/_configmaterial.py
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@ -103,7 +103,6 @@ class ConfigMaterial(Config):
"""Check for completeness.""" """Check for completeness."""
ok = True ok = True
for top_level in ['homogenization','phase','material']: for top_level in ['homogenization','phase','material']:
# ToDo: With python 3.8 as prerequisite we can shorten with :=
ok &= top_level in self ok &= top_level in self
if top_level not in self: print(f'{top_level} entry missing') if top_level not in self: print(f'{top_level} entry missing')
@ -203,7 +202,7 @@ class ConfigMaterial(Config):
""" """
dup = self.copy() dup = self.copy()
for i,m in enumerate(dup['material']): for i,m in enumerate(dup['material']):
if ID and i not in ID: continue if ID is not None and i not in ID: continue
for c in m['constituents']: for c in m['constituents']:
if constituent is not None and c not in constituent: continue if constituent is not None and c not in constituent: continue
try: try:
@ -227,7 +226,7 @@ class ConfigMaterial(Config):
""" """
dup = self.copy() dup = self.copy()
for i,m in enumerate(dup['material']): for i,m in enumerate(dup['material']):
if ID and i not in ID: continue if ID is not None and i not in ID: continue
try: try:
m['homogenization'] = mapping[m['homogenization']] m['homogenization'] = mapping[m['homogenization']]
except KeyError: except KeyError:

6
python/damask/_grid.py
View File

@ -202,7 +202,7 @@ class Grid:
Geometry file to read. Geometry file to read.
""" """
warnings.warn('Support for ASCII-based geom format will be removed in DAMASK 3.1.0', DeprecationWarning) warnings.warn('Support for ASCII-based geom format will be removed in DAMASK 3.1.0', DeprecationWarning,2)
try: try:
f = open(fname) f = open(fname)
except TypeError: except TypeError:
@ -541,7 +541,7 @@ 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) warnings.warn('Support for ASCII-based geom format will be removed in DAMASK 3.1.0', 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),
@ -760,7 +760,7 @@ class Grid:
""" """
if fill is None: fill = np.nanmax(self.material) + 1 if fill is None: fill = np.nanmax(self.material) + 1
dtype = float if np.isnan(fill) or int(fill) != fill or self.material.dtype==np.float else int dtype = float if isinstance(fill,float) or self.material.dtype in np.sctypes['float'] else int
material = self.material material = self.material
# These rotations are always applied in the reference coordinate system, i.e. (z,x,z) not (z,x',z'') # These rotations are always applied in the reference coordinate system, i.e. (z,x,z) not (z,x',z'')

4
python/damask/_vtk.py
View File

@ -246,8 +246,8 @@ class VTK:
raise ValueError('No label defined for numpy.ndarray') raise ValueError('No label defined for numpy.ndarray')
N_data = data.shape[0] N_data = data.shape[0]
d = np_to_vtk((data.astype(np.float32) if data.dtype in [np.float64, np.float128] d = np_to_vtk((data.astype(np.single) if data.dtype in [np.double, np.longdouble] else
else data).reshape(N_data,-1),deep=True) # avoid large files data).reshape(N_data,-1),deep=True) # avoid large files
d.SetName(label) d.SetName(label)
if N_data == N_points: if N_data == N_points:

2
python/damask/util.py
View File

@ -183,7 +183,7 @@ def scale_to_coprime(v):
# Python 3.9 provides math.lcm, see https://stackoverflow.com/questions/51716916. # Python 3.9 provides math.lcm, see https://stackoverflow.com/questions/51716916.
return a * b // np.gcd(a, b) return a * b // np.gcd(a, b)
m = (np.array(v) * reduce(lcm, map(lambda x: int(get_square_denominator(x)),v)) ** 0.5).astype(np.int) m = (np.array(v) * reduce(lcm, map(lambda x: int(get_square_denominator(x)),v)) ** 0.5).astype(int)
m = m//reduce(np.gcd,m) m = m//reduce(np.gcd,m)
with np.errstate(invalid='ignore'): with np.errstate(invalid='ignore'):

35
python/setup.py
View File

@ -6,28 +6,29 @@ with open(Path(__file__).parent/'damask/VERSION') as f:
version = re.sub(r'(-([^-]*)).*$',r'.\2',re.sub(r'^v(\d+\.\d+(\.\d+)?)',r'\1',f.readline().strip())) version = re.sub(r'(-([^-]*)).*$',r'.\2',re.sub(r'^v(\d+\.\d+(\.\d+)?)',r'\1',f.readline().strip()))
setuptools.setup( setuptools.setup(
name="damask", name='damask',
version=version, version=version,
author="The DAMASK team", author='The DAMASK team',
author_email="damask@mpie.de", author_email='damask@mpie.de',
description="DAMASK library", description='DAMASK library',
long_description="Python library for pre and post processing of DAMASK simulations", long_description='Python library for pre and post processing of DAMASK simulations',
url="https://damask.mpie.de", url='https://damask.mpie.de',
packages=setuptools.find_packages(), packages=setuptools.find_packages(),
include_package_data=True, include_package_data=True,
python_requires = '>=3.6',
install_requires = [ install_requires = [
"pandas", # requires numpy 'pandas>=0.24', # requires numpy
"scipy", 'scipy>=1.2',
"h5py", # requires numpy 'h5py>=2.9', # requires numpy
"vtk", 'vtk>=8.1',
"matplotlib", # requires numpy, pillow 'matplotlib>=3.0', # requires numpy, pillow
"pyaml" 'pyaml>=3.12'
], ],
classifiers = [ classifiers = [
"Intended Audience :: Science/Research", 'Intended Audience :: Science/Research',
"Topic :: Scientific/Engineering", 'Topic :: Scientific/Engineering',
"Programming Language :: Python :: 3", 'Programming Language :: Python :: 3',
"License :: OSI Approved :: GNU General Public License v3 or later (GPLv3+)", 'License :: OSI Approved :: GNU General Public License v3 or later (GPLv3+)',
"Operating System :: OS Independent", 'Operating System :: OS Independent',
], ],
) )

2
python/tests/test_Grid.py
View File

@ -347,7 +347,7 @@ class TestGrid:
@pytest.mark.parametrize('approach',['Laguerre','Voronoi']) @pytest.mark.parametrize('approach',['Laguerre','Voronoi'])
def test_tessellate_bicrystal(self,approach): def test_tessellate_bicrystal(self,approach):
cells = np.random.randint(5,10,3)*2 cells = np.random.randint(5,10,3)*2
size = cells.astype(np.float) size = cells.astype(float)
seeds = np.vstack((size*np.array([0.5,0.25,0.5]),size*np.array([0.5,0.75,0.5]))) seeds = np.vstack((size*np.array([0.5,0.25,0.5]),size*np.array([0.5,0.75,0.5])))
material = np.zeros(cells) material = np.zeros(cells)
material[:,cells[1]//2:,:] = 1 material[:,cells[1]//2:,:] = 1