Merge branch 'polishing-for-release' into 'development'

Polishing for release

See merge request damask/DAMASK!206
This commit is contained in:
Franz Roters 2020-08-27 17:01:43 +02:00
commit 9457435612
7 changed files with 5 additions and 293 deletions

@ -1 +1 @@
Subproject commit a16d1e45a2ed925e12244b0879b9d7e5a58d973b Subproject commit 1ca2223c68475bbcb9da633353dbe4a98c18db0d

2
README
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@ -8,6 +8,6 @@ Max-Planck-Str. 1
40237 Düsseldorf 40237 Düsseldorf
Germany Germany
Email: DAMASK@mpie.de damask@mpie.de
https://damask.mpie.de https://damask.mpie.de
https://magit1.mpie.de https://magit1.mpie.de

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@ -2,4 +2,3 @@
omit = tests/* omit = tests/*
damask/_asciitable.py damask/_asciitable.py
damask/_test.py damask/_test.py
damask/config/*

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@ -24,5 +24,4 @@ from . import solver # noqa
Environment = _ Environment = _
from ._asciitable import ASCIItable # noqa from ._asciitable import ASCIItable # noqa
from ._test import Test # noqa from ._test import Test # noqa
from .config import Material # noqa
from .util import extendableOption # noqa from .util import extendableOption # noqa

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@ -1,3 +0,0 @@
"""Aggregator for configuration file handling."""
from .material import Material # noqa

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@ -1,282 +0,0 @@
import re
import os
from damask import util
class Section():
def __init__(self,data = {'__order__':[]},part = ''):
"""New material.config section."""
classes = {
'homogenization':Homogenization,
'microstructure':Microstructure,
'crystallite':Crystallite,
'phase':Phase,
'texture':Texture,
}
self.parameters = {}
for key in data:
self.parameters[key] = data[key] if isinstance(data[key], list) else [data[key]]
if '__order__' not in self.parameters:
self.parameters['__order__'] = list(self.parameters.keys())
if part.lower() in classes:
self.__class__ = classes[part.lower()]
self.__init__(data)
def add_multiKey(self,key,data):
multiKey = '(%s)'%key
if multiKey not in self.parameters: self.parameters[multiKey] = []
if multiKey not in self.parameters['__order__']: self.parameters['__order__'] += [multiKey]
self.parameters[multiKey] += [[item] for item in data] if isinstance(data, list) else [[data]]
def data(self):
return self.parameters
class Homogenization(Section):
def __init__(self,data = {'__order__':[]}):
"""New material.config <homogenization> section."""
Section.__init__(self,data)
class Crystallite(Section):
def __init__(self,data = {'__order__':[]}):
"""New material.config <crystallite> section."""
Section.__init__(self,data)
class Phase(Section):
def __init__(self,data = {'__order__':[]}):
"""New material.config <Phase> section."""
Section.__init__(self,data)
class Microstructure(Section):
def __init__(self,data = {'__order__':[]}):
"""New material.config <microstructure> section."""
Section.__init__(self,data)
class Texture(Section):
def __init__(self,data = {'__order__':[]}):
"""New material.config <texture> section."""
Section.__init__(self,data)
def add_component(self,theType,properties):
scatter = properties['scatter'] if 'scatter' in list(map(str.lower,list(properties.keys()))) else 0.0
fraction = properties['fraction'] if 'fraction' in list(map(str.lower,list(properties.keys()))) else 1.0
try:
multiKey = theType.lower()
except AttributeError:
pass
if multiKey == 'gauss':
self.add_multiKey(multiKey,'phi1 %g\tPhi %g\tphi2 %g\tscatter %g\tfraction %g'%(
properties['eulers'][0],
properties['eulers'][1],
properties['eulers'][2],
scatter,
fraction,
)
)
class Material():
"""Read, manipulate, and write material.config files."""
def __init__(self,verbose=True):
"""Generates ordered list of parts."""
self.parts = [
'homogenization',
'crystallite',
'phase',
'texture',
'microstructure',
]
self.data = {
'homogenization': {'__order__': []},
'microstructure': {'__order__': []},
'crystallite': {'__order__': []},
'phase': {'__order__': []},
'texture': {'__order__': []},
}
self.verbose = verbose
def __repr__(self):
"""Returns current data structure in material.config format."""
me = []
for part in self.parts:
if self.verbose: print(f'processing <{part}>')
me += ['',
'#'*100,
f'<{part}>',
'#'*100,
]
for section in self.data[part]['__order__']:
me += [f'[{section}] {"#"+"-"*max(0,96-len(section))}']
for key in self.data[part][section]['__order__']:
if key.startswith('(') and key.endswith(')'): # multiple (key)
me += [f'{key}\t{" ".join(values)}' for values in self.data[part][section][key]]
else: # plain key
me += [f'{key}\t{util.srepr(self.data[part][section][key]," ")}']
return '\n'.join(me) + '\n'
def parse(self, part=None, sections=[], content=None):
re_part = re.compile(r'^<(.+)>$') # pattern for part
re_sec = re.compile(r'^\[(.+)\]$') # pattern for section
name_section = ''
active = False
for line in content:
line = line.split('#')[0].strip() # kill comments and extra whitespace
line = line.split('/echo/')[0].strip() # remove '/echo/' tags
line = line.lower() # be case insensitive
if line: # content survives...
match_part = re_part.match(line)
if match_part: # found <...> separator
active = (match_part.group(1) == part) # only active in <part>
continue
if active:
match_sec = re_sec.match(line)
if match_sec: # found [section]
name_section = match_sec.group(1) # remember name ...
if '__order__' not in self.data[part]: self.data[part]['__order__'] = []
self.data[part]['__order__'].append(name_section) # ... and position
self.data[part][name_section] = {'__order__':[]}
continue
if sections == [] or name_section in sections: # possibly restrict to subset
items = line.split()
if items[0] not in self.data[part][name_section]: # first encounter of key?
self.data[part][name_section][items[0]] = [] # create item
self.data[part][name_section]['__order__'].append(items[0])
if items[0].startswith('(') and items[0].endswith(')'): # multiple "(key)"
self.data[part][name_section][items[0]].append(items[1:])
else: # plain key
self.data[part][name_section][items[0]] = items[1:]
def read(self,filename=None):
"""Read material.config file."""
def recursiveRead(filename):
"""Takes care of include statements like '{}'."""
result = []
re_include = re.compile(r'^{(.+)}$')
with open(filename) as f: lines = f.readlines()
for line in lines:
match = re_include.match(line.split()[0]) if line.strip() else False
result += [line] if not match else \
recursiveRead(match.group(1) if match.group(1).startswith('/') else
os.path.normpath(os.path.join(os.path.dirname(filename),match.group(1))))
return result
c = recursiveRead(filename)
for p in self.parts:
self.parse(part=p, content=c)
def write(self,filename='material.config', overwrite=False):
"""Write to material.config."""
i = 0
outname = filename
while os.path.exists(outname) and not overwrite:
i += 1
outname = f'{filename}_{i}'
if self.verbose: print(f'Writing material data to {outname}')
with open(outname,'w') as f:
f.write(str(self))
return outname
def add_section(self, part=None, section=None, initialData=None, merge=False):
"""Add Update."""
part = part.lower()
section = section.lower()
if part not in self.parts: raise Exception(f'invalid part {part}')
if not isinstance(initialData, dict):
initialData = initialData.data()
if section not in self.data[part]: self.data[part]['__order__'] += [section]
if section in self.data[part] and merge:
for existing in self.data[part][section]['__order__']: # replace existing
if existing in initialData['__order__']:
if existing.startswith('(') and existing.endswith(')'): # multiple (key)
self.data[part][section][existing] += initialData[existing] # add new multiple entries to existing ones
else: # regular key
self.data[part][section][existing] = initialData[existing] # plain replice
for new in initialData['__order__']: # merge new content
if new not in self.data[part][section]['__order__']:
self.data[part][section][new] = initialData[new]
self.data[part][section]['__order__'] += [new]
else:
self.data[part][section] = initialData
def add_microstructure(self, section='',
components={}, # dict of phase,texture, and fraction lists
):
"""Experimental! Needs expansion to multi-constituent microstructures..."""
microstructure = Microstructure()
# make keys lower case (http://stackoverflow.com/questions/764235/dictionary-to-lowercase-in-python)
components=dict((k.lower(), v) for k,v in components.items())
for key in ['phase','texture','fraction','crystallite']:
if isinstance(components[key], list):
for i, x in enumerate(components[key]):
try:
components[key][i] = x.lower()
except AttributeError:
pass
else:
try:
components[key] = [components[key].lower()]
except AttributeError:
components[key] = [components[key]]
for (phase,texture,fraction,crystallite) in zip(components['phase'],components['texture'],
components['fraction'],components['crystallite']):
microstructure.add_multiKey('constituent','phase %i\ttexture %i\tfraction %g\ncrystallite %i'%(
self.data['phase']['__order__'].index(phase)+1,
self.data['texture']['__order__'].index(texture)+1,
fraction,
self.data['crystallite']['__order__'].index(crystallite)+1))
self.add_section('microstructure',section,microstructure)
def change_value(self, part=None,
section=None,
key=None,
value=None):
if not isinstance(value,list):
if not isinstance(value,str):
value = '%s'%value
value = [value]
newlen = len(value)
oldval = self.data[part.lower()][section.lower()][key.lower()]
oldlen = len(oldval)
print('changing %s:%s:%s from %s to %s '%(part.lower(),section.lower(),key.lower(),oldval,value))
self.data[part.lower()][section.lower()][key.lower()] = value
if newlen is not oldlen:
print('Length of value was changed from %i to %i!'%(oldlen,newlen))
def add_value(self, part=None,
section=None,
key=None,
value=None):
if not isinstance(value,list):
if not isinstance(value,str):
value = '%s'%value
value = [value]
print('adding %s:%s:%s with value %s '%(part.lower(),section.lower(),key.lower(),value))
self.data[part.lower()][section.lower()][key.lower()] = value
self.data[part.lower()][section.lower()]['__order__'] += [key.lower()]

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@ -16,12 +16,11 @@ setuptools.setup(
packages=setuptools.find_packages(), packages=setuptools.find_packages(),
include_package_data=True, include_package_data=True,
install_requires = [ install_requires = [
"pandas", "pandas", # requires numpy
"scipy", "scipy",
"h5py", "h5py", # requires numpy
"vtk", "vtk",
"matplotlib", "matplotlib", # requires numpy, pillow
"PIL",
], ],
classifiers = [ classifiers = [
"Intended Audience :: Science/Research", "Intended Audience :: Science/Research",