Merge branch 'development' of magit1.mpie.de:damask/DAMASK into development
This commit is contained in:
Martin Diehl
commit
a5620359e5
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@ -540,5 +540,4 @@ class ASCIItable():
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microstructure[i:i+s] = items[:s]
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i += len(items)
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return (microstructure, i == N and not self.data_read() if strict # check for proper point count and end of file
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else microstructure)
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return (microstructure, i == N and not self.data_read()) if strict else microstructure # check for proper point count and end of file
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@ -22,11 +22,11 @@ class Test():
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logger = logging.getLogger()
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logger.setLevel(0)
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fh = logging.FileHandler('test.log') # create file handler which logs even debug messages
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fh = logging.FileHandler('test.log') # create file handler which logs even debug messages
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fh.setLevel(logging.DEBUG)
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full = logging.Formatter('%(asctime)s - %(levelname)s: \n%(message)s')
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fh.setFormatter(full)
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ch = logging.StreamHandler(stream=sys.stdout) # create console handler with a higher log level
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ch = logging.StreamHandler(stream=sys.stdout) # create console handler with a higher log level
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ch.setLevel(logging.INFO)
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# create formatter and add it to the handlers
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plain = logging.Formatter('%(message)s')
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@ -60,10 +60,10 @@ class Test():
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try:
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self.postprocess(variant)
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if not self.compare(variant):
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return variant+1 # return culprit
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return variant+1 # return culprit
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except Exception as e :
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logging.critical('\nWARNING:\n %s\n'%e)
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return variant+1 # return culprit
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logging.critical('\nWARNING:\n {}\n'.format(e))
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return variant+1 # return culprit
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return 0
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else:
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if not self.testPossible(): return -1
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@ -74,13 +74,13 @@ class Test():
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self.prepare(variant)
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self.run(variant)
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self.postprocess(variant)
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if self.updateRequested: # update requested
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if self.updateRequested: # update requested
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self.update(variant)
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elif not (self.options.accept or self.compare(variant)): # no update, do comparison
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return variant+1 # return culprit
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elif not (self.options.accept or self.compare(variant)): # no update, do comparison
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return variant+1 # return culprit
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except Exception as e :
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logging.critical('\nWARNING:\n %s\n'%e)
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return variant+1 # return culprit
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logging.critical('\nWARNING:\n {}\n'.format(e))
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return variant+1 # return culprit
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return 0
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def testPossible(self):
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@ -94,13 +94,13 @@ class Test():
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try:
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shutil.rmtree(self.dirCurrent())
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except:
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logging.warning('removal of directory "%s" not possible...'%(self.dirCurrent()))
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logging.warning('removal of directory "{}" not possible...'.format(self.dirCurrent()))
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status = status and False
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try:
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os.mkdir(self.dirCurrent())
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except:
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logging.critical('creation of directory "%s" failed...'%(self.dirCurrent()))
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logging.critical('creation of directory "{}" failed...'.format(self.dirCurrent()))
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status = status and False
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return status
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@ -193,19 +193,19 @@ class Test():
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try:
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shutil.copy2(self.fileInReference(file),self.fileInCurrent(targetfiles[i]))
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except:
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logging.critical('Reference2Current: Unable to copy file %s'%file)
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logging.critical('Reference2Current: Unable to copy file "{}"'.format(file))
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def copy_Base2Current(self,sourceDir,sourcefiles=[],targetfiles=[]):
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source=os.path.normpath(os.path.join(self.dirBase,'../../../'+sourceDir))
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source=os.path.normpath(os.path.join(self.dirBase,'../../..',sourceDir))
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if len(targetfiles) == 0: targetfiles = sourcefiles
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for i,file in enumerate(sourcefiles):
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try:
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shutil.copy2(os.path.join(source,file),self.fileInCurrent(targetfiles[i]))
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except:
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logging.error(os.path.join(source,file))
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logging.critical('Base2Current: Unable to copy file %s'%file)
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logging.critical('Base2Current: Unable to copy file "{}"'.format(file))
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def copy_Current2Reference(self,sourcefiles=[],targetfiles=[]):
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@ -215,7 +215,7 @@ class Test():
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try:
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shutil.copy2(self.fileInCurrent(file),self.fileInReference(targetfiles[i]))
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except:
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logging.critical('Current2Reference: Unable to copy file %s'%file)
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logging.critical('Current2Reference: Unable to copy file "{}"'.format(file))
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def copy_Proof2Current(self,sourcefiles=[],targetfiles=[]):
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@ -225,7 +225,7 @@ class Test():
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try:
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shutil.copy2(self.fileInProof(file),self.fileInCurrent(targetfiles[i]))
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except:
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logging.critical('Proof2Current: Unable to copy file %s'%file)
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logging.critical('Proof2Current: Unable to copy file "{}"'.format(file))
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def copy_Current2Current(self,sourcefiles=[],targetfiles=[]):
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@ -234,7 +234,7 @@ class Test():
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try:
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shutil.copy2(self.fileInReference(file),self.fileInCurrent(targetfiles[i]))
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except:
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logging.critical('Current2Current: Unable to copy file %s'%file)
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logging.critical('Current2Current: Unable to copy file "{}"'.format(file))
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def execute_inCurrentDir(self,cmd,streamIn=None):
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@ -252,7 +252,7 @@ class Test():
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def compare_Array(self,File1,File2):
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import numpy as np
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logging.info('comparing\n '+File1+'\n '+File2)
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logging.info('\n '.join(['comparing',File1,File2]))
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table1 = damask.ASCIItable(name=File1,readonly=True)
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table1.head_read()
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len1=len(table1.info)+2
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@ -270,8 +270,9 @@ class Test():
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max_loc=np.argmax(abs(refArrayNonZero[curArray.nonzero()]/curArray[curArray.nonzero()]-1.))
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refArrayNonZero = refArrayNonZero[curArray.nonzero()]
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curArray = curArray[curArray.nonzero()]
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print(' ********\n * maximum relative error %e for %e and %e\n ********'
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%(max_err, refArrayNonZero[max_loc],curArray[max_loc]))
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print(' ********\n * maximum relative error {} between {} and {}\n ********'.format(max_err,
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refArrayNonZero[max_loc],
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curArray[max_loc]))
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return max_err
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else:
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raise Exception('mismatch in array size to compare')
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@ -295,7 +296,7 @@ class Test():
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absoluteTolerance=False,perLine=False,skipLines=[]):
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import numpy as np
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logging.info('comparing ASCII Tables\n %s \n %s'%(file0,file1))
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logging.info('\n '.join(['comparing ASCII Tables',file0,file1]))
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if normHeadings == '': normHeadings = headings0
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# check if comparison is possible and determine lenght of columns
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@ -315,7 +316,7 @@ class Test():
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for i in xrange(dataLength):
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if headings0[i]['shape'] != headings1[i]['shape']:
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raise Exception('shape mismatch when comparing %s with %s '%(headings0[i]['label'],headings1[i]['label']))
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raise Exception('shape mismatch between {} and {} '.format(headings0[i]['label'],headings1[i]['label']))
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shape[i] = headings0[i]['shape']
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for j in xrange(np.shape(shape[i])[0]):
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length[i] *= shape[i][j]
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@ -323,7 +324,9 @@ class Test():
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for j in xrange(np.shape(normShape[i])[0]):
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normLength[i] *= normShape[i][j]
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else:
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raise Exception('trying to compare %i with %i normed by %i data sets'%(len(headings0),len(headings1),len(normHeadings)))
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raise Exception('trying to compare {} with {} normed by {} data sets'.format(len(headings0),
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len(headings1),
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len(normHeadings)))
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table0 = damask.ASCIItable(name=file0,readonly=True)
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table0.head_read()
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@ -331,37 +334,34 @@ class Test():
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table1.head_read()
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for i in xrange(dataLength):
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key0 = {True :'1_%s',
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False:'%s' }[length[i]>1]%headings0[i]['label']
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key1 = {True :'1_%s',
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False:'%s' }[length[i]>1]%headings1[i]['label']
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normKey = {True :'1_%s',
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False:'%s' }[normLength[i]>1]%normHeadings[i]['label']
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key0 = ('1_' if length[i]>1 else '') + headings0[i]['label']
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key1 = ('1_' if length[i]>1 else '') + headings1[i]['label']
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normKey = ('1_' if normLength[i]>1 else '') + normHeadings[i]['label']
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if key0 not in table0.labels:
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raise Exception('column %s not found in 1. table...\n'%key0)
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raise Exception('column {} not found in 1. table...\n'.format(key0))
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elif key1 not in table1.labels:
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raise Exception('column %s not found in 2. table...\n'%key1)
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raise Exception('column {} not found in 2. table...\n'.format(key1))
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elif normKey not in table0.labels:
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raise Exception('column %s not found in 1. table...\n'%normKey)
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raise Exception('column {} not found in 1. table...\n'.format(normKey))
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else:
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column[0][i] = table0.labels.index(key0) # remember columns of requested data
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column[1][i] = table1.labels.index(key1) # remember columns of requested data in second column
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normColumn[i] = table0.labels.index(normKey) # remember columns of requested data in second column
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column[0][i] = table0.labels.index(key0)
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column[1][i] = table1.labels.index(key1)
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normColumn[i] = table0.labels.index(normKey)
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line0 = 0
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while table0.data_read(): # read next data line of ASCII table
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while table0.data_read(): # read next data line of ASCII table
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if line0 not in skipLines:
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for i in xrange(dataLength):
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myData = np.array(map(float,table0.data[column[0][i]:\
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column[0][i]+length[i]]),'d')
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column[0][i]+length[i]]),'d')
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normData = np.array(map(float,table0.data[normColumn[i]:\
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normColumn[i]+normLength[i]]),'d')
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normColumn[i]+normLength[i]]),'d')
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data[i] = np.append(data[i],np.reshape(myData,shape[i]))
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if normType == 'pInf':
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norm[i] = np.append(norm[i],np.max(np.abs(normData)))
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else:
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norm[i] = np.append(norm[i],np.linalg.norm(np.reshape(normData,normShape[i]),normType))
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line0 +=1
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line0 += 1
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for i in xrange(dataLength):
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if not perLine: norm[i] = [np.max(norm[i]) for j in xrange(line0-len(skipLines))]
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@ -370,12 +370,12 @@ class Test():
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norm[i] = [1.0 for j in xrange(line0-len(skipLines))]
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absTol[i] = True
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if perLine:
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logging.warning('At least one norm of %s in 1. table is 0.0, using absolute tolerance'%headings0[i]['label'])
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logging.warning('At least one norm of {} in 1. table is 0.0, using absolute tolerance'.format(headings0[i]['label']))
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else:
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logging.warning('Maximum norm of %s in 1. table is 0.0, using absolute tolerance'%headings0[i]['label'])
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logging.warning('Maximum norm of {} in 1. table is 0.0, using absolute tolerance'.format(headings0[i]['label']))
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line1 = 0
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while table1.data_read(): # read next data line of ASCII table
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while table1.data_read(): # read next data line of ASCII table
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if line1 not in skipLines:
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for i in xrange(dataLength):
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myData = np.array(map(float,table1.data[column[1][i]:\
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@ -384,21 +384,25 @@ class Test():
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norm[i][line1-len(skipLines)])
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line1 +=1
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if (line0 != line1): raise Exception('found %s lines in 1. table and %s in 2. table'%(line0,line1))
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if (line0 != line1): raise Exception('found {} lines in 1. table but {} in 2. table'.format(line0,line1))
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logging.info(' ********')
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for i in xrange(dataLength):
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if absTol[i]:
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logging.info(' * maximum absolute error %e for %s and %s'%(maxError[i],headings0[i]['label'],headings1[i]['label']))
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logging.info(' * maximum absolute error {} between {} and {}'.format(maxError[i],
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headings0[i]['label'],
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headings1[i]['label']))
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else:
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logging.info(' * maximum relative error %e for %s and %s'%(maxError[i],headings0[i]['label'],headings1[i]['label']))
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logging.info(' * maximum relative error {} between {} and {}'.format(maxError[i],
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headings0[i]['label'],
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headings1[i]['label']))
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logging.info(' ********')
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return maxError
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def compare_TablesStatistically(self,
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files = [None,None], # list of file names
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columns = [None], # list of list of column labels (per file)
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files = [None,None], # list of file names
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columns = [None], # list of list of column labels (per file)
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meanTol = 1.0e-4,
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stdTol = 1.0e-6,
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preFilter = 1.0e-9):
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@ -407,18 +411,18 @@ class Test():
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threshold can be used to ignore small values (a negative number disables this feature)
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"""
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if not (isinstance(files, Iterable) and not isinstance(files, str)): # check whether list of files is requested
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if not (isinstance(files, Iterable) and not isinstance(files, str)): # check whether list of files is requested
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files = [str(files)]
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tables = [damask.ASCIItable(name = filename,readonly = True) for filename in files]
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for table in tables:
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table.head_read()
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columns += [columns[0]]*(len(files)-len(columns)) # extend to same length as files
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columns = columns[:len(files)] # truncate to same length as files
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columns += [columns[0]]*(len(files)-len(columns)) # extend to same length as files
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columns = columns[:len(files)] # truncate to same length as files
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for i,column in enumerate(columns):
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if column is None: columns[i] = tables[i].labels # if no column is given, read all
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if column is None: columns[i] = tables[i].labels # if no column is given, read all
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logging.info('comparing ASCIItables statistically')
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for i in xrange(len(columns)):
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@ -428,7 +432,7 @@ class Test():
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)
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logging.info(files[i]+':'+','.join(columns[i]))
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if len(files) < 2: return True # single table is always close to itself...
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if len(files) < 2: return True # single table is always close to itself...
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data = []
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for table,labels in zip(tables,columns):
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@ -443,16 +447,16 @@ class Test():
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normedDelta = np.where(normBy>preFilter,delta/normBy,0.0)
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mean = np.amax(np.abs(np.mean(normedDelta,0)))
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std = np.amax(np.std(normedDelta,0))
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logging.info('mean: %f'%mean)
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logging.info('std: %f'%std)
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logging.info('mean: {:f}'.format(mean))
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logging.info('std: {:f}'.format(std))
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return (mean<meanTol) & (std < stdTol)
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|
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def compare_Tables(self,
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files = [None,None], # list of file names
|
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columns = [None], # list of list of column labels (per file)
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files = [None,None], # list of file names
|
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columns = [None], # list of list of column labels (per file)
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rtol = 1e-5,
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atol = 1e-8,
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preFilter = -1.0,
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|
@ -463,18 +467,18 @@ class Test():
|
|||
|
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threshold can be used to ignore small values (a negative number disables this feature)
|
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"""
|
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if not (isinstance(files, Iterable) and not isinstance(files, str)): # check whether list of files is requested
|
||||
if not (isinstance(files, Iterable) and not isinstance(files, str)): # check whether list of files is requested
|
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files = [str(files)]
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|
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tables = [damask.ASCIItable(name = filename,readonly = True) for filename in files]
|
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for table in tables:
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table.head_read()
|
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|
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columns += [columns[0]]*(len(files)-len(columns)) # extend to same length as files
|
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columns = columns[:len(files)] # truncate to same length as files
|
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columns += [columns[0]]*(len(files)-len(columns)) # extend to same length as files
|
||||
columns = columns[:len(files)] # truncate to same length as files
|
||||
|
||||
for i,column in enumerate(columns):
|
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if column is None: columns[i] = tables[i].labels # if no column is given, read all
|
||||
if column is None: columns[i] = tables[i].labels # if no column is given, read all
|
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|
||||
logging.info('comparing ASCIItables')
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for i in xrange(len(columns)):
|
||||
|
|
@ -484,7 +488,7 @@ class Test():
|
|||
)
|
||||
logging.info(files[i]+':'+','.join(columns[i]))
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|
||||
if len(files) < 2: return True # single table is always close to itself...
|
||||
if len(files) < 2: return True # single table is always close to itself...
|
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|
||||
maximum = np.zeros(len(columns[0]),dtype='f')
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data = []
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@ -495,26 +499,26 @@ class Test():
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|||
table.close()
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maximum /= len(tables)
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maximum = np.where(maximum >0.0, maximum, 1) # do not devide by zero for empty columns
|
||||
maximum = np.where(maximum >0.0, maximum, 1) # avoid div by zero for empty columns
|
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for i in xrange(len(data)):
|
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data[i] /= maximum
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||||
mask = np.zeros_like(table.data,dtype='bool')
|
||||
|
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for table in data:
|
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mask |= np.where(np.abs(table)<postFilter,True,False) # mask out (all) tiny values
|
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mask |= np.where(np.abs(table)<postFilter,True,False) # mask out (all) tiny values
|
||||
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||||
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||||
allclose = True # start optimistic
|
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allclose = True # start optimistic
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||||
for i in xrange(1,len(data)):
|
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if debug:
|
||||
t0 = np.where(mask,0.0,data[i-1])
|
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t1 = np.where(mask,0.0,data[i ])
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j = np.argmin(np.abs(t1)*rtol+atol-np.abs(t0-t1))
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logging.info('%f'%np.amax(np.abs(t0-t1)/(np.abs(t1)*rtol+atol)))
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||||
logging.info('%f %f'%((t0*maximum).flatten()[j],(t1*maximum).flatten()[j]))
|
||||
logging.info('{:f}'.format(np.amax(np.abs(t0-t1)/(np.abs(t1)*rtol+atol))))
|
||||
logging.info('{:f} {:f}'.format((t0*maximum).flatten()[j],(t1*maximum).flatten()[j]))
|
||||
allclose &= np.allclose(np.where(mask,0.0,data[i-1]),
|
||||
np.where(mask,0.0,data[i ]),rtol,atol) # accumulate "pessimism"
|
||||
np.where(mask,0.0,data[i ]),rtol,atol) # accumulate "pessimism"
|
||||
|
||||
return allclose
|
||||
|
||||
|
|
@ -543,14 +547,13 @@ class Test():
|
|||
def report_Success(self,culprit):
|
||||
|
||||
if culprit == 0:
|
||||
logging.critical('%s passed.'%({False: 'The test',
|
||||
True: 'All %i tests'%(len(self.variants))}[len(self.variants) > 1]))
|
||||
logging.critical(('The test' if len(self.variants) == 1 else 'All {} tests'.format(len(self.variants))) + ' passed')
|
||||
logging.critical('\n!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!\n')
|
||||
return 0
|
||||
if culprit == -1:
|
||||
logging.warning('Warning: Could not start test')
|
||||
return 0
|
||||
else:
|
||||
logging.critical(' ********\n * Test %i failed...\n ********'%(culprit))
|
||||
logging.critical(' ********\n * Test {} failed...\n ********'.format(culprit))
|
||||
logging.critical('\n!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!\n')
|
||||
return culprit
|
||||
|
|
|
|||
|
|
@ -58,6 +58,24 @@ def emph(what):
|
|||
"""emphasizes string on screen"""
|
||||
return bcolors.BOLD+srepr(what)+bcolors.ENDC
|
||||
|
||||
# -----------------------------
|
||||
def execute(cmd,
|
||||
streamIn = None,
|
||||
wd = './'):
|
||||
"""executes a command in given directory and returns stdout and stderr for optional stdin"""
|
||||
initialPath = os.getcwd()
|
||||
os.chdir(wd)
|
||||
process = subprocess.Popen(shlex.split(cmd),
|
||||
stdout = subprocess.PIPE,
|
||||
stderr = subprocess.PIPE,
|
||||
stdin = subprocess.PIPE)
|
||||
out,error = [i.replace("\x08","") for i in (process.communicate() if streamIn is None
|
||||
else process.communicate(streamIn.read()))]
|
||||
os.chdir(initialPath)
|
||||
if process.returncode != 0: raise RuntimeError('{} failed with returncode {}'.format(cmd,process.returncode))
|
||||
return out,error
|
||||
|
||||
|
||||
# -----------------------------
|
||||
# Matlab like trigonometric functions that take and return angles in degrees.
|
||||
# -----------------------------
|
||||
|
|
@ -75,7 +93,7 @@ def gridLocation(idx,res):
|
|||
|
||||
# -----------------------------
|
||||
def gridIndex(location,res):
|
||||
return ( location[0] % res[0] + \
|
||||
return ( location[0] % res[0] + \
|
||||
( location[1] % res[1]) * res[0] + \
|
||||
( location[2] % res[2]) * res[1] * res[0] )
|
||||
|
||||
|
|
@ -432,20 +450,4 @@ def curve_fit_bound(f, xdata, ydata, p0=None, sigma=None, bounds=None, **kw):
|
|||
else:
|
||||
pcov = np.inf
|
||||
|
||||
return popt, pcov, infodict, errmsg, ier if return_full else popt, pcov
|
||||
|
||||
|
||||
def execute(cmd,streamIn = None,wd = './'):
|
||||
"""executes a command in given directory and returns stdout and stderr for optional stdin"""
|
||||
initialPath = os.getcwd()
|
||||
os.chdir(wd)
|
||||
process = subprocess.Popen(shlex.split(cmd),
|
||||
stdout = subprocess.PIPE,
|
||||
stderr = subprocess.PIPE,
|
||||
stdin = subprocess.PIPE)
|
||||
out,error = [i.replace("\x08","") for i in (process.communicate if streamIn is None
|
||||
else process.communicate(streamIn.read()))]
|
||||
os.chdir(initialPath)
|
||||
if process.returncode != 0: raise RuntimeError('{} failed with returncode {}'.format(cmd,process.returncode))
|
||||
return out,error
|
||||
|
||||
return (popt, pcov, infodict, errmsg, ier) if return_full else (popt, pcov)
|
||||
|
|
|
|||
Loading…
Reference in New Issue