Merge branch 'PythonImprovements' into no-crystallite
This commit is contained in:
Martin Diehl
commit
b937ed594b
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|
@ -65,7 +65,7 @@ for filename in options.filenames:
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x = results.get_dataset_location(label)
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if len(x) == 0:
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continue
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array = results.read_dataset(x,0)
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array = results.read_dataset(x,0,plain=True)
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d = int(np.product(np.shape(array)[1:]))
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data = np.concatenate((data,np.reshape(array,[np.product(results.grid),d])),1)
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@ -80,7 +80,7 @@ for filename in options.filenames:
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x = results.get_dataset_location(label)
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if len(x) == 0:
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continue
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array = results.read_dataset(x,0)
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array = results.read_dataset(x,0,plain=True)
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d = int(np.product(np.shape(array)[1:]))
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data = np.concatenate((data,np.reshape(array,[np.product(results.grid),d])),1)
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@ -5,9 +5,6 @@ import sys
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from io import StringIO
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from optparse import OptionParser
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from scipy import ndimage
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import numpy as np
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import damask
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@ -15,11 +12,6 @@ scriptName = os.path.splitext(os.path.basename(__file__))[0]
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scriptID = ' '.join([scriptName,damask.version])
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def mostFrequent(arr):
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unique, inverse = np.unique(arr, return_inverse=True)
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return unique[np.argmax(np.bincount(inverse))]
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#--------------------------------------------------------------------------------------------------
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# MAIN
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#--------------------------------------------------------------------------------------------------
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@ -46,9 +38,8 @@ for name in filenames:
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geom = damask.Geom.from_file(StringIO(''.join(sys.stdin.read())) if name is None else name)
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damask.util.croak(geom.update(ndimage.filters.generic_filter(
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geom.microstructure,mostFrequent,
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size=(options.stencil,)*3).astype(geom.microstructure.dtype)))
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damask.util.croak(geom.clean(options.stencil))
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geom.add_comments(scriptID + ' ' + ' '.join(sys.argv[1:]))
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if name is None:
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|
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@ -5,8 +5,6 @@ import sys
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from io import StringIO
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from optparse import OptionParser
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import numpy as np
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import damask
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@ -38,16 +36,6 @@ parser.set_defaults(reflect = False)
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(options, filenames) = parser.parse_args()
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if options.directions is None:
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parser.error('no direction given.')
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if not set(options.directions).issubset(validDirections):
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invalidDirections = [str(e) for e in set(options.directions).difference(validDirections)]
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parser.error('invalid directions {}. '.format(*invalidDirections))
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limits = [None,None] if options.reflect else [-2,0]
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if filenames == []: filenames = [None]
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for name in filenames:
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@ -55,15 +43,7 @@ for name in filenames:
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geom = damask.Geom.from_file(StringIO(''.join(sys.stdin.read())) if name is None else name)
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microstructure = geom.get_microstructure()
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if 'z' in options.directions:
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microstructure = np.concatenate([microstructure,microstructure[:,:,limits[0]:limits[1]:-1]],2)
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if 'y' in options.directions:
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microstructure = np.concatenate([microstructure,microstructure[:,limits[0]:limits[1]:-1,:]],1)
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if 'x' in options.directions:
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microstructure = np.concatenate([microstructure,microstructure[limits[0]:limits[1]:-1,:,:]],0)
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damask.util.croak(geom.update(microstructure,rescale=True))
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damask.util.croak(geom.mirror(options.directions,options.reflect))
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geom.add_comments(scriptID + ' ' + ' '.join(sys.argv[1:]))
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if name is None:
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|
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@ -2,7 +2,7 @@ import os
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import sys
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import re
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import shlex
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from collections import Iterable
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from collections.abc import Iterable
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import numpy as np
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@ -15,7 +15,7 @@ except NameError:
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# ------------------------------------------------------------------
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class ASCIItable():
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"""Read and write to ASCII tables"""
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"""Read and write to ASCII tables."""
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tmpext = '_tmp' # filename extension for in-place access
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@ -27,6 +27,7 @@ class ASCIItable():
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labeled = True, # assume table has labels
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readonly = False, # no reading from file
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):
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"""Read and write to ASCII tables."""
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self.__IO__ = {'output': [],
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'buffered': buffered,
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'labeled': labeled, # header contains labels
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@ -72,7 +73,7 @@ class ASCIItable():
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# ------------------------------------------------------------------
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def _removeCRLF(self,
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string):
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"""Delete any carriage return and line feed from string"""
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"""Delete any carriage return and line feed from string."""
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try:
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return string.replace('\n','').replace('\r','')
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except AttributeError:
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|
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@ -82,7 +83,7 @@ class ASCIItable():
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# ------------------------------------------------------------------
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def _quote(self,
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what):
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"""Quote empty or white space-containing output"""
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"""Quote empty or white space-containing output."""
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return '{quote}{content}{quote}'.format(
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quote = ('"' if str(what)=='' or re.search(r"\s",str(what)) else ''),
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content = what)
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@ -103,7 +104,7 @@ class ASCIItable():
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# ------------------------------------------------------------------
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def output_write(self,
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what):
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"""Aggregate a single row (string) or list of (possibly containing further lists of) rows into output"""
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"""Aggregate a single row (string) or list of (possibly containing further lists of) rows into output."""
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if isinstance(what, (str, unicode)):
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self.__IO__['output'] += [what]
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else:
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@ -143,7 +144,7 @@ class ASCIItable():
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# ------------------------------------------------------------------
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def head_read(self):
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"""
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Get column labels
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Get column labels.
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by either reading the first row or,
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if keyword "head[*]" is present, the last line of the header
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@ -154,7 +155,7 @@ class ASCIItable():
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pass
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firstline = self.__IO__['in'].readline().strip()
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m = re.search('(\d+)\s+head', firstline.lower()) # search for "head" keyword
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m = re.search(r'(\d+)\s+head', firstline.lower()) # search for "head" keyword
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if m: # proper ASCIItable format
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@ -194,7 +195,7 @@ class ASCIItable():
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# ------------------------------------------------------------------
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def head_write(self,
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header = True):
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"""Write current header information (info + labels)"""
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"""Write current header information (info + labels)."""
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head = ['{}\theader'.format(len(self.info)+self.__IO__['labeled'])] if header else []
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head.append(self.info)
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if self.__IO__['labeled']:
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|
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@ -205,7 +206,7 @@ class ASCIItable():
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# ------------------------------------------------------------------
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def head_getGeom(self):
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"""Interpret geom header"""
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"""Interpret geom header."""
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identifiers = {
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'grid': ['a','b','c'],
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'size': ['x','y','z'],
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|
|
@ -247,7 +248,7 @@ class ASCIItable():
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def labels_append(self,
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what,
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reset = False):
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"""Add item or list to existing set of labels (and switch on labeling)"""
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"""Add item or list to existing set of labels (and switch on labeling)."""
|
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if isinstance(what, (str, unicode)):
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self.tags += [self._removeCRLF(what)]
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else:
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@ -261,7 +262,7 @@ class ASCIItable():
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# ------------------------------------------------------------------
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def labels_clear(self):
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"""Delete existing labels and switch to no labeling"""
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"""Delete existing labels and switch to no labeling."""
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self.tags = []
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self.__IO__['labeled'] = False
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@ -392,7 +393,7 @@ class ASCIItable():
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# ------------------------------------------------------------------
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def info_append(self,
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what):
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"""Add item or list to existing set of infos"""
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"""Add item or list to existing set of infos."""
|
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if isinstance(what, (str, unicode)):
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self.info += [self._removeCRLF(what)]
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else:
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|
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@ -403,7 +404,7 @@ class ASCIItable():
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|
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# ------------------------------------------------------------------
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def info_clear(self):
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"""Delete any info block"""
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"""Delete any info block."""
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self.info = []
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# ------------------------------------------------------------------
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@ -416,7 +417,7 @@ class ASCIItable():
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# ------------------------------------------------------------------
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def data_skipLines(self,
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count):
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"""Wind forward by count number of lines"""
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"""Wind forward by count number of lines."""
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for i in range(count):
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alive = self.data_read()
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@ -426,7 +427,7 @@ class ASCIItable():
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def data_read(self,
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advance = True,
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respectLabels = True):
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"""Read next line (possibly buffered) and parse it into data array"""
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"""Read next line (possibly buffered) and parse it into data array."""
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self.line = self.__IO__['readBuffer'].pop(0) if len(self.__IO__['readBuffer']) > 0 \
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else self.__IO__['in'].readline().strip() # take buffered content or get next data row from file
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|
|
@ -446,9 +447,11 @@ class ASCIItable():
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# ------------------------------------------------------------------
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def data_readArray(self,
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labels = []):
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"""Read whole data of all (given) labels as numpy array"""
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try: self.data_rewind() # try to wind back to start of data
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except: pass # assume/hope we are at data start already...
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"""Read whole data of all (given) labels as numpy array."""
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try:
|
||||
self.data_rewind() # try to wind back to start of data
|
||||
except IOError:
|
||||
pass # assume/hope we are at data start already...
|
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|
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if labels is None or labels == []:
|
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use = None # use all columns (and keep labels intact)
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|
|
@ -480,7 +483,7 @@ class ASCIItable():
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|||
# ------------------------------------------------------------------
|
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def data_write(self,
|
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delimiter = '\t'):
|
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"""Write current data array and report alive output back"""
|
||||
"""Write current data array and report alive output back."""
|
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if len(self.data) == 0: return True
|
||||
|
||||
if isinstance(self.data[0],list):
|
||||
|
|
@ -492,16 +495,16 @@ class ASCIItable():
|
|||
def data_writeArray(self,
|
||||
fmt = None,
|
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delimiter = '\t'):
|
||||
"""Write whole numpy array data"""
|
||||
"""Write whole numpy array data."""
|
||||
for row in self.data:
|
||||
try:
|
||||
output = [fmt % value for value in row] if fmt else list(map(repr,row))
|
||||
except:
|
||||
except Exception:
|
||||
output = [fmt % row] if fmt else [repr(row)]
|
||||
|
||||
try:
|
||||
self.__IO__['out'].write(delimiter.join(output) + '\n')
|
||||
except:
|
||||
except Exception:
|
||||
pass
|
||||
|
||||
# ------------------------------------------------------------------
|
||||
|
|
@ -545,7 +548,7 @@ class ASCIItable():
|
|||
grid,
|
||||
type = 'i',
|
||||
strict = False):
|
||||
"""Read microstructure data (from .geom format)"""
|
||||
"""Read microstructure data (from .geom format)."""
|
||||
def datatype(item):
|
||||
return int(item) if type.lower() == 'i' else float(item)
|
||||
|
||||
|
|
|
|||
|
|
@ -369,7 +369,7 @@ class DADF5():
|
|||
return f[self.get_dataset_location('orientation')[0]].attrs['Lattice'].astype('str') # np.bytes_ to string
|
||||
|
||||
|
||||
def read_dataset(self,path,c):
|
||||
def read_dataset(self,path,c=0,plain=False):
|
||||
"""
|
||||
Dataset for all points/cells.
|
||||
|
||||
|
|
@ -402,7 +402,7 @@ class DADF5():
|
|||
a=a.reshape([a.shape[0],1])
|
||||
dataset[p,:] = a[u,:]
|
||||
|
||||
return dataset
|
||||
return dataset if not plain else dataset.view(('float64',len(dataset.dtype.names)))
|
||||
|
||||
|
||||
def cell_coordinates(self):
|
||||
|
|
@ -620,7 +620,7 @@ class DADF5():
|
|||
raise ValueError
|
||||
|
||||
return {
|
||||
'data': mechanics.deviator(x['data']),
|
||||
'data': mechanics.deviatoric_part(x['data']),
|
||||
'label': 's_{}'.format(x['label']),
|
||||
'meta': {
|
||||
'Unit': x['meta']['Unit'],
|
||||
|
|
|
|||
|
|
@ -2,6 +2,7 @@ import os
|
|||
from io import StringIO
|
||||
|
||||
import numpy as np
|
||||
from scipy import ndimage
|
||||
import vtk
|
||||
from vtk.util import numpy_support
|
||||
|
||||
|
|
@ -30,7 +31,6 @@ class Geom():
|
|||
comments lines.
|
||||
|
||||
"""
|
||||
self.__transforms__ = \
|
||||
self.set_microstructure(microstructure)
|
||||
self.set_size(size)
|
||||
self.set_origin(origin)
|
||||
|
|
@ -286,7 +286,6 @@ class Geom():
|
|||
abs(int(items[2])-int(items[0]))+1,dtype=float)
|
||||
else: items = list(map(float,items))
|
||||
else: items = list(map(float,items))
|
||||
|
||||
microstructure[i:i+len(items)] = items
|
||||
i += len(items)
|
||||
|
||||
|
|
@ -299,6 +298,7 @@ class Geom():
|
|||
|
||||
return cls(microstructure.reshape(grid),size,origin,homogenization,comments)
|
||||
|
||||
|
||||
def to_file(self,fname):
|
||||
"""
|
||||
Writes a geom file.
|
||||
|
|
@ -311,14 +311,12 @@ class Geom():
|
|||
"""
|
||||
header = self.get_header()
|
||||
grid = self.get_grid()
|
||||
format_string = '%{}i'.format(1+int(np.floor(np.log10(np.nanmax(self.microstructure))))) if self.microstructure.dtype == int \
|
||||
else '%g'
|
||||
format_string = '%g' if self.microstructure in np.sctypes['float'] else \
|
||||
'%{}i'.format(1+int(np.floor(np.log10(np.nanmax(self.microstructure)))))
|
||||
np.savetxt(fname,
|
||||
self.microstructure.reshape([grid[0],np.prod(grid[1:])],order='F').T,
|
||||
header='\n'.join(header), fmt=format_string, comments='')
|
||||
|
||||
|
||||
|
||||
def to_vtk(self,fname=None):
|
||||
"""
|
||||
Generates vtk file.
|
||||
|
|
@ -387,3 +385,55 @@ class Geom():
|
|||
self.to_file(f)
|
||||
f.seek(0)
|
||||
return ''.join(f.readlines())
|
||||
|
||||
|
||||
def mirror(self,directions,reflect=False):
|
||||
"""
|
||||
Mirror microstructure along given directions.
|
||||
|
||||
Parameters
|
||||
----------
|
||||
directions : iterable containing str
|
||||
direction(s) along which the microstructure is mirrored. Valid entries are 'x', 'y', 'z'.
|
||||
reflect : bool, optional
|
||||
reflect (include) outermost layers.
|
||||
|
||||
"""
|
||||
valid = {'x','y','z'}
|
||||
if not all(isinstance(d, str) for d in directions):
|
||||
raise TypeError('Directions are not of type str.')
|
||||
elif not set(directions).issubset(valid):
|
||||
raise ValueError('Invalid direction specified {}'.format(*set(directions).difference(valid)))
|
||||
|
||||
limits = [None,None] if reflect else [-2,0]
|
||||
ms = self.get_microstructure()
|
||||
|
||||
if 'z' in directions:
|
||||
ms = np.concatenate([ms,ms[:,:,limits[0]:limits[1]:-1]],2)
|
||||
if 'y' in directions:
|
||||
ms = np.concatenate([ms,ms[:,limits[0]:limits[1]:-1,:]],1)
|
||||
if 'x' in directions:
|
||||
ms = np.concatenate([ms,ms[limits[0]:limits[1]:-1,:,:]],0)
|
||||
|
||||
return self.update(ms,rescale=True)
|
||||
#self.add_comments('tbd')
|
||||
|
||||
|
||||
def clean(self,stencil=3):
|
||||
"""
|
||||
Smooth microstructure by selecting most frequent index within given stencil at each location.
|
||||
|
||||
Parameters
|
||||
----------
|
||||
stencil : int, optional
|
||||
size of smoothing stencil.
|
||||
|
||||
"""
|
||||
def mostFrequent(arr):
|
||||
unique, inverse = np.unique(arr, return_inverse=True)
|
||||
return unique[np.argmax(np.bincount(inverse))]
|
||||
|
||||
return self.update(ndimage.filters.generic_filter(self.microstructure,
|
||||
mostFrequent,
|
||||
size=(stencil,)*3).astype(self.microstructure.dtype))
|
||||
#self.add_comments('tbd')
|
||||
|
|
|
|||
|
|
@ -48,10 +48,10 @@ def strain_tensor(F,t,m):
|
|||
|
||||
if m > 0.0:
|
||||
eps = 1.0/(2.0*abs(m)) * (+ np.matmul(n,np.einsum('ij,ikj->ijk',w**m,n))
|
||||
- np.broadcast_to(np.ones(3),[F_.shape[0],3]))
|
||||
- np.broadcast_to(np.eye(3),[F_.shape[0],3,3]))
|
||||
elif m < 0.0:
|
||||
eps = 1.0/(2.0*abs(m)) * (- np.matmul(n,np.einsum('ij,ikj->ijk',w**m,n))
|
||||
+ np.broadcast_to(np.ones(3),[F_.shape[0],3]))
|
||||
+ np.broadcast_to(np.eye(3),[F_.shape[0],3,3]))
|
||||
else:
|
||||
eps = np.matmul(n,np.einsum('ij,ikj->ijk',0.5*np.log(w),n))
|
||||
|
||||
|
|
@ -190,7 +190,7 @@ def rotational_part(x):
|
|||
Tensor of which the rotational part is computed.
|
||||
|
||||
"""
|
||||
return __polar_decomposition(x,'R')
|
||||
return __polar_decomposition(x,'R')[0]
|
||||
|
||||
|
||||
def left_stretch(x):
|
||||
|
|
@ -203,7 +203,7 @@ def left_stretch(x):
|
|||
Tensor of which the left stretch is computed.
|
||||
|
||||
"""
|
||||
return __polar_decomposition(x,'V')
|
||||
return __polar_decomposition(x,'V')[0]
|
||||
|
||||
|
||||
def right_stretch(x):
|
||||
|
|
@ -216,7 +216,7 @@ def right_stretch(x):
|
|||
Tensor of which the right stretch is computed.
|
||||
|
||||
"""
|
||||
return __polar_decomposition(x,'U')
|
||||
return __polar_decomposition(x,'U')[0]
|
||||
|
||||
|
||||
def __polar_decomposition(x,requested):
|
||||
|
|
@ -227,7 +227,7 @@ def __polar_decomposition(x,requested):
|
|||
----------
|
||||
x : numpy.array of shape (:,3,3) or (3,3)
|
||||
Tensor of which the singular values are computed.
|
||||
requested : list of str
|
||||
requested : iterable of str
|
||||
Requested outputs: ‘R’ for the rotation tensor,
|
||||
‘V’ for left stretch tensor and ‘U’ for right stretch tensor.
|
||||
|
||||
|
|
|
|||
|
|
@ -79,9 +79,9 @@ class Marc(Solver):
|
|||
exitnumber = -1
|
||||
fid_out = open(outFile,'r')
|
||||
for line in fid_out:
|
||||
if (string.find(line,'tress iteration') is not -1):
|
||||
if (string.find(line,'tress iteration') != -1):
|
||||
print(line)
|
||||
elif (string.find(line,'Exit number') is not -1):
|
||||
elif (string.find(line,'Exit number') != -1):
|
||||
substr = line[string.find(line,'Exit number'):len(line)]
|
||||
exitnumber = int(substr[12:16])
|
||||
|
||||
|
|
|
|||
|
|
@ -1,10 +1,8 @@
|
|||
# -*- coding: UTF-8 no BOM -*-
|
||||
|
||||
import os,sys,shutil
|
||||
import logging,logging.config
|
||||
import damask
|
||||
import numpy as np
|
||||
from collections import Iterable
|
||||
from collections.abc import Iterable
|
||||
from optparse import OptionParser
|
||||
|
||||
class Test():
|
||||
|
|
@ -17,7 +15,7 @@ class Test():
|
|||
variants = []
|
||||
|
||||
def __init__(self, **kwargs):
|
||||
|
||||
"""New test."""
|
||||
defaults = {'description': '',
|
||||
'keep': False,
|
||||
'accept': False,
|
||||
|
|
@ -120,22 +118,22 @@ class Test():
|
|||
"""Delete directory tree containing current results."""
|
||||
try:
|
||||
shutil.rmtree(self.dirCurrent())
|
||||
except:
|
||||
except FileNotFoundError:
|
||||
logging.warning('removal of directory "{}" not possible...'.format(self.dirCurrent()))
|
||||
|
||||
try:
|
||||
os.mkdir(self.dirCurrent())
|
||||
return True
|
||||
except:
|
||||
except FileExistsError:
|
||||
logging.critical('creation of directory "{}" failed.'.format(self.dirCurrent()))
|
||||
return False
|
||||
|
||||
def prepareAll(self):
|
||||
"""Do all necessary preparations for the whole test"""
|
||||
"""Do all necessary preparations for the whole test."""
|
||||
return True
|
||||
|
||||
def prepare(self,variant):
|
||||
"""Do all necessary preparations for the run of each test variant"""
|
||||
"""Do all necessary preparations for the run of each test variant."""
|
||||
return True
|
||||
|
||||
|
||||
|
|
@ -207,9 +205,9 @@ class Test():
|
|||
for source,target in zip(list(map(mapA,A)),list(map(mapB,B))):
|
||||
try:
|
||||
shutil.copy2(source,target)
|
||||
except:
|
||||
except FileNotFoundError:
|
||||
logging.critical('error copying {} to {}'.format(source,target))
|
||||
raise
|
||||
raise FileNotFoundError
|
||||
|
||||
|
||||
def copy_Reference2Current(self,sourcefiles=[],targetfiles=[]):
|
||||
|
|
@ -218,9 +216,9 @@ class Test():
|
|||
for i,f in enumerate(sourcefiles):
|
||||
try:
|
||||
shutil.copy2(self.fileInReference(f),self.fileInCurrent(targetfiles[i]))
|
||||
except:
|
||||
except FileNotFoundError:
|
||||
logging.critical('Reference2Current: Unable to copy file "{}"'.format(f))
|
||||
raise
|
||||
raise FileNotFoundError
|
||||
|
||||
|
||||
def copy_Base2Current(self,sourceDir,sourcefiles=[],targetfiles=[]):
|
||||
|
|
@ -230,10 +228,10 @@ class Test():
|
|||
for i,f in enumerate(sourcefiles):
|
||||
try:
|
||||
shutil.copy2(os.path.join(source,f),self.fileInCurrent(targetfiles[i]))
|
||||
except:
|
||||
except FileNotFoundError:
|
||||
logging.error(os.path.join(source,f))
|
||||
logging.critical('Base2Current: Unable to copy file "{}"'.format(f))
|
||||
raise
|
||||
raise FileNotFoundError
|
||||
|
||||
|
||||
def copy_Current2Reference(self,sourcefiles=[],targetfiles=[]):
|
||||
|
|
@ -242,9 +240,9 @@ class Test():
|
|||
for i,f in enumerate(sourcefiles):
|
||||
try:
|
||||
shutil.copy2(self.fileInCurrent(f),self.fileInReference(targetfiles[i]))
|
||||
except:
|
||||
except FileNotFoundError:
|
||||
logging.critical('Current2Reference: Unable to copy file "{}"'.format(f))
|
||||
raise
|
||||
raise FileNotFoundError
|
||||
|
||||
|
||||
def copy_Proof2Current(self,sourcefiles=[],targetfiles=[]):
|
||||
|
|
@ -253,9 +251,9 @@ class Test():
|
|||
for i,f in enumerate(sourcefiles):
|
||||
try:
|
||||
shutil.copy2(self.fileInProof(f),self.fileInCurrent(targetfiles[i]))
|
||||
except:
|
||||
except FileNotFoundError:
|
||||
logging.critical('Proof2Current: Unable to copy file "{}"'.format(f))
|
||||
raise
|
||||
raise FileNotFoundError
|
||||
|
||||
|
||||
def copy_Current2Current(self,sourcefiles=[],targetfiles=[]):
|
||||
|
|
@ -263,9 +261,10 @@ class Test():
|
|||
for i,f in enumerate(sourcefiles):
|
||||
try:
|
||||
shutil.copy2(self.fileInReference(f),self.fileInCurrent(targetfiles[i]))
|
||||
except:
|
||||
except FileNotFoundError:
|
||||
logging.critical('Current2Current: Unable to copy file "{}"'.format(f))
|
||||
raise
|
||||
raise FileNotFoundError
|
||||
|
||||
|
||||
def execute_inCurrentDir(self,cmd,streamIn=None,env=None):
|
||||
|
||||
|
|
@ -439,7 +438,7 @@ class Test():
|
|||
stdTol = 1.0e-6,
|
||||
preFilter = 1.0e-9):
|
||||
"""
|
||||
Calculate statistics of tables
|
||||
Calculate statistics of tables.
|
||||
|
||||
threshold can be used to ignore small values (a negative number disables this feature)
|
||||
"""
|
||||
|
|
@ -492,7 +491,7 @@ class Test():
|
|||
rtol = 1e-5,
|
||||
atol = 1e-8,
|
||||
debug = False):
|
||||
"""Compare multiple tables with np.allclose"""
|
||||
"""Compare multiple tables with np.allclose."""
|
||||
if not (isinstance(files, Iterable) and not isinstance(files, str)): # check whether list of files is requested
|
||||
files = [str(files)]
|
||||
|
||||
|
|
@ -1,3 +0,0 @@
|
|||
"""Test functionality."""
|
||||
|
||||
from .test import Test # noqa
|
||||
Loading…
Reference in New Issue