DAMASK_EICMD/lib/damask/test/test.py

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# -*- coding: UTF-8 no BOM -*-
import os,sys,shutil
import logging,logging.config
import damask
import numpy as np
from collections import Iterable
from optparse import OptionParser
class Test():
"""
General class for testing.
Is sub-classed by the individual tests.
"""
variants = []
def __init__(self,test_description):
logger = logging.getLogger()
logger.setLevel(0)
fh = logging.FileHandler('test.log') # create file handler which logs even debug messages
fh.setLevel(logging.DEBUG)
full = logging.Formatter('%(asctime)s - %(levelname)s: \n%(message)s')
fh.setFormatter(full)
ch = logging.StreamHandler(stream=sys.stdout) # create console handler with a higher log level
ch.setLevel(logging.INFO)
# create formatter and add it to the handlers
plain = logging.Formatter('%(message)s')
ch.setFormatter(plain)
# add the handlers to the logger
logger.addHandler(fh)
logger.addHandler(ch)
logging.info('!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!\n\n' \
+'----------------------------------------------------------------\n' \
+'| '+test_description+'\n' \
+'----------------------------------------------------------------')
self.dirBase = os.path.dirname(os.path.realpath(sys.modules[self.__class__.__module__].__file__))
self.parser = OptionParser(
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description = test_description+' (using class: {})'.format(damask.version),
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usage='./test.py [options]')
self.updateRequested = False
self.parser.add_option("-d", "--debug", action="store_true",\
dest="debug",\
help="debug run, don't calculate but use existing results")
self.parser.add_option("-p", "--pass", action="store_true",\
dest="accept",\
help="calculate results but always consider test as successfull")
self.parser.set_defaults(debug=False,
accept=False)
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def execute(self):
"""Run all variants and report first failure."""
if self.options.debug:
for variant in xrange(len(self.variants)):
try:
self.postprocess(variant)
if not self.compare(variant):
return variant+1 # return culprit
except Exception as e :
logging.critical('\nWARNING:\n {}\n'.format(e))
return variant+1 # return culprit
return 0
else:
if not self.testPossible(): return -1
self.clean()
self.prepareAll()
for variant in xrange(len(self.variants)):
try:
self.prepare(variant)
self.run(variant)
self.postprocess(variant)
if self.updateRequested: # update requested
self.update(variant)
elif not (self.options.accept or self.compare(variant)): # no update, do comparison
return variant+1 # return culprit
except Exception as e :
logging.critical('\nWARNING:\n {}\n'.format(e))
return variant+1 # return culprit
return 0
def testPossible(self):
"""Check if test is possible or not (e.g. no license available)."""
return True
def clean(self):
"""Delete directory tree containing current results."""
status = True
try:
shutil.rmtree(self.dirCurrent())
except:
logging.warning('removal of directory "{}" not possible...'.format(self.dirCurrent()))
status = status and False
try:
os.mkdir(self.dirCurrent())
except:
logging.critical('creation of directory "{}" failed...'.format(self.dirCurrent()))
status = status and False
return status
def prepareAll(self):
"""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"""
return True
def run(self,variant):
"""Execute the requested test variant."""
return True
def postprocess(self,variant):
"""Perform post-processing of generated results for this test variant."""
return True
def compare(self,variant):
"""Compare reference to current results."""
return True
def update(self,variant):
"""Update reference with current results."""
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logging.debug('Update not necessary')
return True
def dirReference(self):
"""Directory containing reference results of the test."""
return os.path.normpath(os.path.join(self.dirBase,'reference/'))
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def dirCurrent(self):
"""Directory containing current results of the test."""
return os.path.normpath(os.path.join(self.dirBase,'current/'))
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def dirProof(self):
"""Directory containing human readable proof of correctness for the test."""
return os.path.normpath(os.path.join(self.dirBase,'proof/'))
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def fileInRoot(self,dir,file):
"""Path to a file in the root directory of DAMASK."""
return os.path.join(damask.Environment().rootDir(),dir,file)
def fileInReference(self,file):
"""Path to a file in the refrence directory for the test."""
return os.path.join(self.dirReference(),file)
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def fileInCurrent(self,file):
"""Path to a file in the current results directory for the test."""
return os.path.join(self.dirCurrent(),file)
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def fileInProof(self,file):
"""Path to a file in the proof directory for the test."""
return os.path.join(self.dirProof(),file)
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def copy(self, mapA, mapB,
A = [], B = []):
"""
copy list of files from (mapped) source to target.
mapA/B is one of self.fileInX.
"""
if not B or len(B) == 0: B = A
for source,target in zip(map(mapA,A),map(mapB,B)):
try:
shutil.copy2(source,target)
except:
logging.critical('error copying {} to {}'.format(source,target))
def copy_Reference2Current(self,sourcefiles=[],targetfiles=[]):
if len(targetfiles) == 0: targetfiles = sourcefiles
for i,file in enumerate(sourcefiles):
try:
shutil.copy2(self.fileInReference(file),self.fileInCurrent(targetfiles[i]))
except:
logging.critical('Reference2Current: Unable to copy file "{}"'.format(file))
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def copy_Base2Current(self,sourceDir,sourcefiles=[],targetfiles=[]):
source=os.path.normpath(os.path.join(self.dirBase,'../../..',sourceDir))
if len(targetfiles) == 0: targetfiles = sourcefiles
for i,file in enumerate(sourcefiles):
try:
shutil.copy2(os.path.join(source,file),self.fileInCurrent(targetfiles[i]))
except:
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logging.error(os.path.join(source,file))
logging.critical('Base2Current: Unable to copy file "{}"'.format(file))
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def copy_Current2Reference(self,sourcefiles=[],targetfiles=[]):
if len(targetfiles) == 0: targetfiles = sourcefiles
for i,file in enumerate(sourcefiles):
try:
shutil.copy2(self.fileInCurrent(file),self.fileInReference(targetfiles[i]))
except:
logging.critical('Current2Reference: Unable to copy file "{}"'.format(file))
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def copy_Proof2Current(self,sourcefiles=[],targetfiles=[]):
if len(targetfiles) == 0: targetfiles = sourcefiles
for i,file in enumerate(sourcefiles):
try:
shutil.copy2(self.fileInProof(file),self.fileInCurrent(targetfiles[i]))
except:
logging.critical('Proof2Current: Unable to copy file "{}"'.format(file))
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def copy_Current2Current(self,sourcefiles=[],targetfiles=[]):
for i,file in enumerate(sourcefiles):
try:
shutil.copy2(self.fileInReference(file),self.fileInCurrent(targetfiles[i]))
except:
logging.critical('Current2Current: Unable to copy file "{}"'.format(file))
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def execute_inCurrentDir(self,cmd,streamIn=None):
logging.info(cmd)
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out,error = damask.util.execute(cmd,streamIn,self.dirCurrent())
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logging.info(error)
logging.debug(out)
return out,error
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def compare_Array(self,File1,File2):
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import numpy as np
logging.info('\n '.join(['comparing',File1,File2]))
table1 = damask.ASCIItable(name=File1,readonly=True)
table1.head_read()
len1=len(table1.info)+2
table2 = damask.ASCIItable(name=File2,readonly=True)
table2.head_read()
len2=len(table2.info)+2
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refArray = np.nan_to_num(np.genfromtxt(File1,missing_values='n/a',skip_header = len1,autostrip=True))
curArray = np.nan_to_num(np.genfromtxt(File2,missing_values='n/a',skip_header = len2,autostrip=True))
if len(curArray) == len(refArray):
refArrayNonZero = refArray[refArray.nonzero()]
curArray = curArray[refArray.nonzero()]
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max_err=np.max(abs(refArrayNonZero[curArray.nonzero()]/curArray[curArray.nonzero()]-1.))
max_loc=np.argmax(abs(refArrayNonZero[curArray.nonzero()]/curArray[curArray.nonzero()]-1.))
refArrayNonZero = refArrayNonZero[curArray.nonzero()]
curArray = curArray[curArray.nonzero()]
print(' ********\n * maximum relative error {} between {} and {}\n ********'.format(max_err,
refArrayNonZero[max_loc],
curArray[max_loc]))
return max_err
else:
raise Exception('mismatch in array size to compare')
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def compare_ArrayRefCur(self,ref,cur=''):
if cur =='': cur = ref
refName = self.fileInReference(ref)
curName = self.fileInCurrent(cur)
return self.compare_Array(refName,curName)
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def compare_ArrayCurCur(self,cur0,cur1):
cur0Name = self.fileInCurrent(cur0)
cur1Name = self.fileInCurrent(cur1)
return self.compare_Array(cur0Name,cur1Name)
def compare_Table(self,headings0,file0,headings1,file1,normHeadings='',normType=None,
absoluteTolerance=False,perLine=False,skipLines=[]):
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import numpy as np
logging.info('\n '.join(['comparing ASCII Tables',file0,file1]))
if normHeadings == '': normHeadings = headings0
# check if comparison is possible and determine lenght of columns
if len(headings0) == len(headings1) == len(normHeadings):
dataLength = len(headings0)
length = [1 for i in xrange(dataLength)]
shape = [[] for i in xrange(dataLength)]
data = [[] for i in xrange(dataLength)]
maxError = [0.0 for i in xrange(dataLength)]
absTol = [absoluteTolerance for i in xrange(dataLength)]
column = [[1 for i in xrange(dataLength)] for j in xrange(2)]
norm = [[] for i in xrange(dataLength)]
normLength = [1 for i in xrange(dataLength)]
normShape = [[] for i in xrange(dataLength)]
normColumn = [1 for i in xrange(dataLength)]
for i in xrange(dataLength):
if headings0[i]['shape'] != headings1[i]['shape']:
raise Exception('shape mismatch between {} and {} '.format(headings0[i]['label'],headings1[i]['label']))
shape[i] = headings0[i]['shape']
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for j in xrange(np.shape(shape[i])[0]):
length[i] *= shape[i][j]
normShape[i] = normHeadings[i]['shape']
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for j in xrange(np.shape(normShape[i])[0]):
normLength[i] *= normShape[i][j]
else:
raise Exception('trying to compare {} with {} normed by {} data sets'.format(len(headings0),
len(headings1),
len(normHeadings)))
table0 = damask.ASCIItable(name=file0,readonly=True)
table0.head_read()
table1 = damask.ASCIItable(name=file1,readonly=True)
table1.head_read()
for i in xrange(dataLength):
key0 = ('1_' if length[i]>1 else '') + headings0[i]['label']
key1 = ('1_' if length[i]>1 else '') + headings1[i]['label']
normKey = ('1_' if normLength[i]>1 else '') + normHeadings[i]['label']
if key0 not in table0.labels:
raise Exception('column {} not found in 1. table...\n'.format(key0))
elif key1 not in table1.labels:
raise Exception('column {} not found in 2. table...\n'.format(key1))
elif normKey not in table0.labels:
raise Exception('column {} not found in 1. table...\n'.format(normKey))
else:
column[0][i] = table0.labels.index(key0)
column[1][i] = table1.labels.index(key1)
normColumn[i] = table0.labels.index(normKey)
line0 = 0
while table0.data_read(): # read next data line of ASCII table
if line0 not in skipLines:
for i in xrange(dataLength):
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myData = np.array(map(float,table0.data[column[0][i]:\
column[0][i]+length[i]]),'d')
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normData = np.array(map(float,table0.data[normColumn[i]:\
normColumn[i]+normLength[i]]),'d')
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data[i] = np.append(data[i],np.reshape(myData,shape[i]))
if normType == 'pInf':
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norm[i] = np.append(norm[i],np.max(np.abs(normData)))
else:
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norm[i] = np.append(norm[i],np.linalg.norm(np.reshape(normData,normShape[i]),normType))
line0 += 1
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))]
data[i] = np.reshape(data[i],[line0-len(skipLines),length[i]])
if any(norm[i]) == 0.0 or absTol[i]:
norm[i] = [1.0 for j in xrange(line0-len(skipLines))]
absTol[i] = True
if perLine:
logging.warning('At least one norm of {} in 1. table is 0.0, using absolute tolerance'.format(headings0[i]['label']))
else:
logging.warning('Maximum norm of {} in 1. table is 0.0, using absolute tolerance'.format(headings0[i]['label']))
line1 = 0
while table1.data_read(): # read next data line of ASCII table
if line1 not in skipLines:
for i in xrange(dataLength):
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myData = np.array(map(float,table1.data[column[1][i]:\
column[1][i]+length[i]]),'d')
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maxError[i] = max(maxError[i],np.linalg.norm(np.reshape(myData-data[i][line1-len(skipLines),:],shape[i]))/
norm[i][line1-len(skipLines)])
line1 +=1
if (line0 != line1): raise Exception('found {} lines in 1. table but {} in 2. table'.format(line0,line1))
logging.info(' ********')
for i in xrange(dataLength):
if absTol[i]:
logging.info(' * maximum absolute error {} between {} and {}'.format(maxError[i],
headings0[i]['label'],
headings1[i]['label']))
else:
logging.info(' * maximum relative error {} between {} and {}'.format(maxError[i],
headings0[i]['label'],
headings1[i]['label']))
logging.info(' ********')
return maxError
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def compare_TablesStatistically(self,
files = [None,None], # list of file names
columns = [None], # list of list of column labels (per file)
meanTol = 1.0e-4,
stdTol = 1.0e-6,
preFilter = 1.0e-9):
"""
calculate statistics of tables
threshold can be used to ignore small values (a negative number disables this feature)
"""
if not (isinstance(files, Iterable) and not isinstance(files, str)): # check whether list of files is requested
files = [str(files)]
tables = [damask.ASCIItable(name = filename,readonly = True) for filename in files]
for table in tables:
table.head_read()
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):
if column is None: columns[i] = tables[i].labels # if no column is given, read all
logging.info('comparing ASCIItables statistically')
for i in xrange(len(columns)):
columns[i] = columns[0] if not columns[i] else \
([columns[i]] if not (isinstance(columns[i], Iterable) and not isinstance(columns[i], str)) else \
columns[i]
)
logging.info(files[i]+':'+','.join(columns[i]))
if len(files) < 2: return True # single table is always close to itself...
data = []
for table,labels in zip(tables,columns):
table.data_readArray(labels)
data.append(table.data)
table.close()
for i in xrange(1,len(data)):
delta = data[i]-data[i-1]
normBy = (np.abs(data[i]) + np.abs(data[i-1]))*0.5
normedDelta = np.where(normBy>preFilter,delta/normBy,0.0)
mean = np.amax(np.abs(np.mean(normedDelta,0)))
std = np.amax(np.std(normedDelta,0))
logging.info('mean: {:f}'.format(mean))
logging.info('std: {:f}'.format(std))
return (mean<meanTol) & (std < stdTol)
def compare_Tables(self,
files = [None,None], # list of file names
columns = [None], # list of list of column labels (per file)
rtol = 1e-5,
atol = 1e-8,
preFilter = -1.0,
postFilter = -1.0,
debug = False):
"""
compare tables with np.allclose
threshold can be used to ignore small values (a negative number disables this feature)
"""
if not (isinstance(files, Iterable) and not isinstance(files, str)): # check whether list of files is requested
files = [str(files)]
tables = [damask.ASCIItable(name = filename,readonly = True) for filename in files]
for table in tables:
table.head_read()
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):
if column is None: columns[i] = tables[i].labels # if no column is given, read all
logging.info('comparing ASCIItables')
for i in xrange(len(columns)):
columns[i] = columns[0] if not columns[i] else \
([columns[i]] if not (isinstance(columns[i], Iterable) and not isinstance(columns[i], str)) else \
columns[i]
)
logging.info(files[i]+':'+','.join(columns[i]))
if len(files) < 2: return True # single table is always close to itself...
maximum = np.zeros(len(columns[0]),dtype='f')
data = []
for table,labels in zip(tables,columns):
table.data_readArray(labels)
data.append(np.where(np.abs(table.data)<preFilter,np.zeros_like(table.data),table.data))
maximum += np.abs(table.data).max(axis=0)
table.close()
maximum /= len(tables)
maximum = np.where(maximum >0.0, maximum, 1) # avoid div by zero for empty columns
for i in xrange(len(data)):
data[i] /= maximum
mask = np.zeros_like(table.data,dtype='bool')
for table in data:
mask |= np.where(np.abs(table)<postFilter,True,False) # mask out (all) tiny values
allclose = True # start optimistic
for i in xrange(1,len(data)):
if debug:
t0 = np.where(mask,0.0,data[i-1])
t1 = np.where(mask,0.0,data[i ])
j = np.argmin(np.abs(t1)*rtol+atol-np.abs(t0-t1))
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"
return allclose
def compare_TableRefCur(self,headingsRef,ref,headingsCur='',cur='',normHeadings='',normType=None,\
absoluteTolerance=False,perLine=False,skipLines=[]):
if cur == '': cur = ref
if headingsCur == '': headingsCur = headingsRef
refName = self.fileInReference(ref)
curName = self.fileInCurrent(cur)
return self.compare_Table(headingsRef,refName,headingsCur,curName,normHeadings,normType,
absoluteTolerance,perLine,skipLines)
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def compare_TableCurCur(self,headingsCur0,Cur0,Cur1,headingsCur1='',normHeadings='',normType=None,\
absoluteTolerance=False,perLine=False,skipLines=[]):
if headingsCur1 == '': headingsCur1 = headingsCur0
cur0Name = self.fileInCurrent(Cur0)
cur1Name = self.fileInCurrent(Cur1)
return self.compare_Table(headingsCur0,cur0Name,headingsCur1,cur1Name,normHeadings,normType,
absoluteTolerance,perLine,skipLines)
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def report_Success(self,culprit):
if culprit == 0:
logging.critical(('The test' if len(self.variants) == 1 else 'All {} tests'.format(len(self.variants))) + ' passed')
logging.critical('\n!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!\n')
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return 0
if culprit == -1:
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logging.warning('Warning: Could not start test')
return 0
else:
logging.critical(' ********\n * Test {} failed...\n ********'.format(culprit))
logging.critical('\n!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!\n')
return culprit