223031012
/
DAMASK_EICMD
mirror of https://github.com/achalhp/DAMASK_EICMD.git
1
0
Fork 0
Code Issues Projects Releases Wiki Activity

Merge branch 'development' of magit1.mpie.de:damask/DAMASK into development

This commit is contained in:
Martin Diehl 2016-03-22 09:04:16 +01:00
parent be42311eeb 1b22b6e4ee
commit a5620359e5
3 changed files with 95 additions and 91 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

3
lib/damask/asciitable.py
View File

@ -540,5 +540,4 @@ class ASCIItable():
microstructure[i:i+s] = items[:s] microstructure[i:i+s] = items[:s]
i += len(items) i += len(items)
return (microstructure, i == N and not self.data_read() if strict # check for proper point count and end of file return (microstructure, i == N and not self.data_read()) if strict else microstructure # check for proper point count and end of file
else microstructure)

145
lib/damask/test/test.py
View File

@ -22,11 +22,11 @@ class Test():
logger = logging.getLogger() logger = logging.getLogger()
logger.setLevel(0) logger.setLevel(0)
fh = logging.FileHandler('test.log') # create file handler which logs even debug messages fh = logging.FileHandler('test.log') # create file handler which logs even debug messages
fh.setLevel(logging.DEBUG) fh.setLevel(logging.DEBUG)
full = logging.Formatter('%(asctime)s - %(levelname)s: \n%(message)s') full = logging.Formatter('%(asctime)s - %(levelname)s: \n%(message)s')
fh.setFormatter(full) fh.setFormatter(full)
ch = logging.StreamHandler(stream=sys.stdout) # create console handler with a higher log level ch = logging.StreamHandler(stream=sys.stdout) # create console handler with a higher log level
ch.setLevel(logging.INFO) ch.setLevel(logging.INFO)
# create formatter and add it to the handlers # create formatter and add it to the handlers
plain = logging.Formatter('%(message)s') plain = logging.Formatter('%(message)s')
@ -60,10 +60,10 @@ class Test():
try: try:
self.postprocess(variant) self.postprocess(variant)
if not self.compare(variant): if not self.compare(variant):
return variant+1 # return culprit return variant+1 # return culprit
except Exception as e : except Exception as e :
logging.critical('\nWARNING:\n %s\n'%e) logging.critical('\nWARNING:\n {}\n'.format(e))
return variant+1 # return culprit return variant+1 # return culprit
return 0 return 0
else: else:
if not self.testPossible(): return -1 if not self.testPossible(): return -1
@ -74,13 +74,13 @@ class Test():
self.prepare(variant) self.prepare(variant)
self.run(variant) self.run(variant)
self.postprocess(variant) self.postprocess(variant)
if self.updateRequested: # update requested if self.updateRequested: # update requested
self.update(variant) self.update(variant)
elif not (self.options.accept or self.compare(variant)): # no update, do comparison elif not (self.options.accept or self.compare(variant)): # no update, do comparison
return variant+1 # return culprit return variant+1 # return culprit
except Exception as e : except Exception as e :
logging.critical('\nWARNING:\n %s\n'%e) logging.critical('\nWARNING:\n {}\n'.format(e))
return variant+1 # return culprit return variant+1 # return culprit
return 0 return 0
def testPossible(self): def testPossible(self):
@ -94,13 +94,13 @@ class Test():
try: try:
shutil.rmtree(self.dirCurrent()) shutil.rmtree(self.dirCurrent())
except: except:
logging.warning('removal of directory "%s" not possible...'%(self.dirCurrent())) logging.warning('removal of directory "{}" not possible...'.format(self.dirCurrent()))
status = status and False status = status and False
try: try:
os.mkdir(self.dirCurrent()) os.mkdir(self.dirCurrent())
except: except:
logging.critical('creation of directory "%s" failed...'%(self.dirCurrent())) logging.critical('creation of directory "{}" failed...'.format(self.dirCurrent()))
status = status and False status = status and False
return status return status
@ -193,19 +193,19 @@ class Test():
try: try:
shutil.copy2(self.fileInReference(file),self.fileInCurrent(targetfiles[i])) shutil.copy2(self.fileInReference(file),self.fileInCurrent(targetfiles[i]))
except: except:
logging.critical('Reference2Current: Unable to copy file %s'%file) logging.critical('Reference2Current: Unable to copy file "{}"'.format(file))
def copy_Base2Current(self,sourceDir,sourcefiles=[],targetfiles=[]): def copy_Base2Current(self,sourceDir,sourcefiles=[],targetfiles=[]):
source=os.path.normpath(os.path.join(self.dirBase,'../../../'+sourceDir)) source=os.path.normpath(os.path.join(self.dirBase,'../../..',sourceDir))
if len(targetfiles) == 0: targetfiles = sourcefiles if len(targetfiles) == 0: targetfiles = sourcefiles
for i,file in enumerate(sourcefiles): for i,file in enumerate(sourcefiles):
try: try:
shutil.copy2(os.path.join(source,file),self.fileInCurrent(targetfiles[i])) shutil.copy2(os.path.join(source,file),self.fileInCurrent(targetfiles[i]))
except: except:
logging.error(os.path.join(source,file)) logging.error(os.path.join(source,file))
logging.critical('Base2Current: Unable to copy file %s'%file) logging.critical('Base2Current: Unable to copy file "{}"'.format(file))
def copy_Current2Reference(self,sourcefiles=[],targetfiles=[]): def copy_Current2Reference(self,sourcefiles=[],targetfiles=[]):
@ -215,7 +215,7 @@ class Test():
try: try:
shutil.copy2(self.fileInCurrent(file),self.fileInReference(targetfiles[i])) shutil.copy2(self.fileInCurrent(file),self.fileInReference(targetfiles[i]))
except: except:
logging.critical('Current2Reference: Unable to copy file %s'%file) logging.critical('Current2Reference: Unable to copy file "{}"'.format(file))
def copy_Proof2Current(self,sourcefiles=[],targetfiles=[]): def copy_Proof2Current(self,sourcefiles=[],targetfiles=[]):
@ -225,7 +225,7 @@ class Test():
try: try:
shutil.copy2(self.fileInProof(file),self.fileInCurrent(targetfiles[i])) shutil.copy2(self.fileInProof(file),self.fileInCurrent(targetfiles[i]))
except: except:
logging.critical('Proof2Current: Unable to copy file %s'%file) logging.critical('Proof2Current: Unable to copy file "{}"'.format(file))
def copy_Current2Current(self,sourcefiles=[],targetfiles=[]): def copy_Current2Current(self,sourcefiles=[],targetfiles=[]):
@ -234,7 +234,7 @@ class Test():
try: try:
shutil.copy2(self.fileInReference(file),self.fileInCurrent(targetfiles[i])) shutil.copy2(self.fileInReference(file),self.fileInCurrent(targetfiles[i]))
except: except:
logging.critical('Current2Current: Unable to copy file %s'%file) logging.critical('Current2Current: Unable to copy file "{}"'.format(file))
def execute_inCurrentDir(self,cmd,streamIn=None): def execute_inCurrentDir(self,cmd,streamIn=None):
@ -252,7 +252,7 @@ class Test():
def compare_Array(self,File1,File2): def compare_Array(self,File1,File2):
import numpy as np import numpy as np
logging.info('comparing\n '+File1+'\n '+File2) logging.info('\n '.join(['comparing',File1,File2]))
table1 = damask.ASCIItable(name=File1,readonly=True) table1 = damask.ASCIItable(name=File1,readonly=True)
table1.head_read() table1.head_read()
len1=len(table1.info)+2 len1=len(table1.info)+2
@ -270,8 +270,9 @@ class Test():
max_loc=np.argmax(abs(refArrayNonZero[curArray.nonzero()]/curArray[curArray.nonzero()]-1.)) max_loc=np.argmax(abs(refArrayNonZero[curArray.nonzero()]/curArray[curArray.nonzero()]-1.))
refArrayNonZero = refArrayNonZero[curArray.nonzero()] refArrayNonZero = refArrayNonZero[curArray.nonzero()]
curArray = curArray[curArray.nonzero()] curArray = curArray[curArray.nonzero()]
print(' ********\n * maximum relative error %e for %e and %e\n ********' print(' ********\n * maximum relative error {} between {} and {}\n ********'.format(max_err,
%(max_err, refArrayNonZero[max_loc],curArray[max_loc])) refArrayNonZero[max_loc],
curArray[max_loc]))
return max_err return max_err
else: else:
raise Exception('mismatch in array size to compare') raise Exception('mismatch in array size to compare')
@ -295,7 +296,7 @@ class Test():
absoluteTolerance=False,perLine=False,skipLines=[]): absoluteTolerance=False,perLine=False,skipLines=[]):
import numpy as np import numpy as np
logging.info('comparing ASCII Tables\n %s \n %s'%(file0,file1)) logging.info('\n '.join(['comparing ASCII Tables',file0,file1]))
if normHeadings == '': normHeadings = headings0 if normHeadings == '': normHeadings = headings0
# check if comparison is possible and determine lenght of columns # check if comparison is possible and determine lenght of columns
@ -315,7 +316,7 @@ class Test():
for i in xrange(dataLength): for i in xrange(dataLength):
if headings0[i]['shape'] != headings1[i]['shape']: if headings0[i]['shape'] != headings1[i]['shape']:
raise Exception('shape mismatch when comparing %s with %s '%(headings0[i]['label'],headings1[i]['label'])) raise Exception('shape mismatch between {} and {} '.format(headings0[i]['label'],headings1[i]['label']))
shape[i] = headings0[i]['shape'] shape[i] = headings0[i]['shape']
for j in xrange(np.shape(shape[i])[0]): for j in xrange(np.shape(shape[i])[0]):
length[i] *= shape[i][j] length[i] *= shape[i][j]
@ -323,7 +324,9 @@ class Test():
for j in xrange(np.shape(normShape[i])[0]): for j in xrange(np.shape(normShape[i])[0]):
normLength[i] *= normShape[i][j] normLength[i] *= normShape[i][j]
else: else:
raise Exception('trying to compare %i with %i normed by %i data sets'%(len(headings0),len(headings1),len(normHeadings))) 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 = damask.ASCIItable(name=file0,readonly=True)
table0.head_read() table0.head_read()
@ -331,37 +334,34 @@ class Test():
table1.head_read() table1.head_read()
for i in xrange(dataLength): for i in xrange(dataLength):
key0 = {True :'1_%s', key0 = ('1_' if length[i]>1 else '') + headings0[i]['label']
False:'%s' }[length[i]>1]%headings0[i]['label'] key1 = ('1_' if length[i]>1 else '') + headings1[i]['label']
key1 = {True :'1_%s', normKey = ('1_' if normLength[i]>1 else '') + normHeadings[i]['label']
False:'%s' }[length[i]>1]%headings1[i]['label']
normKey = {True :'1_%s',
False:'%s' }[normLength[i]>1]%normHeadings[i]['label']
if key0 not in table0.labels: if key0 not in table0.labels:
raise Exception('column %s not found in 1. table...\n'%key0) raise Exception('column {} not found in 1. table...\n'.format(key0))
elif key1 not in table1.labels: elif key1 not in table1.labels:
raise Exception('column %s not found in 2. table...\n'%key1) raise Exception('column {} not found in 2. table...\n'.format(key1))
elif normKey not in table0.labels: elif normKey not in table0.labels:
raise Exception('column %s not found in 1. table...\n'%normKey) raise Exception('column {} not found in 1. table...\n'.format(normKey))
else: else:
column[0][i] = table0.labels.index(key0) # remember columns of requested data column[0][i] = table0.labels.index(key0)
column[1][i] = table1.labels.index(key1) # remember columns of requested data in second column column[1][i] = table1.labels.index(key1)
normColumn[i] = table0.labels.index(normKey) # remember columns of requested data in second column normColumn[i] = table0.labels.index(normKey)
line0 = 0 line0 = 0
while table0.data_read(): # read next data line of ASCII table while table0.data_read(): # read next data line of ASCII table
if line0 not in skipLines: if line0 not in skipLines:
for i in xrange(dataLength): for i in xrange(dataLength):
myData = np.array(map(float,table0.data[column[0][i]:\ myData = np.array(map(float,table0.data[column[0][i]:\
column[0][i]+length[i]]),'d') column[0][i]+length[i]]),'d')
normData = np.array(map(float,table0.data[normColumn[i]:\ normData = np.array(map(float,table0.data[normColumn[i]:\
normColumn[i]+normLength[i]]),'d') normColumn[i]+normLength[i]]),'d')
data[i] = np.append(data[i],np.reshape(myData,shape[i])) data[i] = np.append(data[i],np.reshape(myData,shape[i]))
if normType == 'pInf': if normType == 'pInf':
norm[i] = np.append(norm[i],np.max(np.abs(normData))) norm[i] = np.append(norm[i],np.max(np.abs(normData)))
else: else:
norm[i] = np.append(norm[i],np.linalg.norm(np.reshape(normData,normShape[i]),normType)) norm[i] = np.append(norm[i],np.linalg.norm(np.reshape(normData,normShape[i]),normType))
line0 +=1 line0 += 1
for i in xrange(dataLength): for i in xrange(dataLength):
if not perLine: norm[i] = [np.max(norm[i]) for j in xrange(line0-len(skipLines))] if not perLine: norm[i] = [np.max(norm[i]) for j in xrange(line0-len(skipLines))]
@ -370,12 +370,12 @@ class Test():
norm[i] = [1.0 for j in xrange(line0-len(skipLines))] norm[i] = [1.0 for j in xrange(line0-len(skipLines))]
absTol[i] = True absTol[i] = True
if perLine: if perLine:
logging.warning('At least one norm of %s in 1. table is 0.0, using absolute tolerance'%headings0[i]['label']) logging.warning('At least one norm of {} in 1. table is 0.0, using absolute tolerance'.format(headings0[i]['label']))
else: else:
logging.warning('Maximum norm of %s in 1. table is 0.0, using absolute tolerance'%headings0[i]['label']) logging.warning('Maximum norm of {} in 1. table is 0.0, using absolute tolerance'.format(headings0[i]['label']))
line1 = 0 line1 = 0
while table1.data_read(): # read next data line of ASCII table while table1.data_read(): # read next data line of ASCII table
if line1 not in skipLines: if line1 not in skipLines:
for i in xrange(dataLength): for i in xrange(dataLength):
myData = np.array(map(float,table1.data[column[1][i]:\ myData = np.array(map(float,table1.data[column[1][i]:\
@ -384,21 +384,25 @@ class Test():
norm[i][line1-len(skipLines)]) norm[i][line1-len(skipLines)])
line1 +=1 line1 +=1
if (line0 != line1): raise Exception('found %s lines in 1. table and %s in 2. table'%(line0,line1)) if (line0 != line1): raise Exception('found {} lines in 1. table but {} in 2. table'.format(line0,line1))
logging.info(' ********') logging.info(' ********')
for i in xrange(dataLength): for i in xrange(dataLength):
if absTol[i]: if absTol[i]:
logging.info(' * maximum absolute error %e for %s and %s'%(maxError[i],headings0[i]['label'],headings1[i]['label'])) logging.info(' * maximum absolute error {} between {} and {}'.format(maxError[i],
headings0[i]['label'],
headings1[i]['label']))
else: else:
logging.info(' * maximum relative error %e for %s and %s'%(maxError[i],headings0[i]['label'],headings1[i]['label'])) logging.info(' * maximum relative error {} between {} and {}'.format(maxError[i],
headings0[i]['label'],
headings1[i]['label']))
logging.info(' ********') logging.info(' ********')
return maxError return maxError
def compare_TablesStatistically(self, def compare_TablesStatistically(self,
files = [None,None], # list of file names files = [None,None], # list of file names
columns = [None], # list of list of column labels (per file) columns = [None], # list of list of column labels (per file)
meanTol = 1.0e-4, meanTol = 1.0e-4,
stdTol = 1.0e-6, stdTol = 1.0e-6,
preFilter = 1.0e-9): preFilter = 1.0e-9):
@ -407,18 +411,18 @@ class Test():
threshold can be used to ignore small values (a negative number disables this feature) 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 if not (isinstance(files, Iterable) and not isinstance(files, str)): # check whether list of files is requested
files = [str(files)] files = [str(files)]
tables = [damask.ASCIItable(name = filename,readonly = True) for filename in files] tables = [damask.ASCIItable(name = filename,readonly = True) for filename in files]
for table in tables: for table in tables:
table.head_read() table.head_read()
columns += [columns[0]]*(len(files)-len(columns)) # extend to same length as files columns += [columns[0]]*(len(files)-len(columns)) # extend to same length as files
columns = columns[:len(files)] # truncate to same length as files columns = columns[:len(files)] # truncate to same length as files
for i,column in enumerate(columns): for i,column in enumerate(columns):
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
logging.info('comparing ASCIItables statistically') logging.info('comparing ASCIItables statistically')
for i in xrange(len(columns)): for i in xrange(len(columns)):
@ -428,7 +432,7 @@ class Test():
) )
logging.info(files[i]+':'+','.join(columns[i])) logging.info(files[i]+':'+','.join(columns[i]))
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...
data = [] data = []
for table,labels in zip(tables,columns): for table,labels in zip(tables,columns):
@ -443,16 +447,16 @@ class Test():
normedDelta = np.where(normBy>preFilter,delta/normBy,0.0) normedDelta = np.where(normBy>preFilter,delta/normBy,0.0)
mean = np.amax(np.abs(np.mean(normedDelta,0))) mean = np.amax(np.abs(np.mean(normedDelta,0)))
std = np.amax(np.std(normedDelta,0)) std = np.amax(np.std(normedDelta,0))
logging.info('mean: %f'%mean) logging.info('mean: {:f}'.format(mean))
logging.info('std: %f'%std) logging.info('std: {:f}'.format(std))
return (mean<meanTol) & (std < stdTol) return (mean<meanTol) & (std < stdTol)
def compare_Tables(self, def compare_Tables(self,
files = [None,None], # list of file names files = [None,None], # list of file names
columns = [None], # list of list of column labels (per file) columns = [None], # list of list of column labels (per file)
rtol = 1e-5, rtol = 1e-5,
atol = 1e-8, atol = 1e-8,
preFilter = -1.0, preFilter = -1.0,
@ -463,18 +467,18 @@ class Test():
threshold can be used to ignore small values (a negative number disables this feature) 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 if not (isinstance(files, Iterable) and not isinstance(files, str)): # check whether list of files is requested
files = [str(files)] files = [str(files)]
tables = [damask.ASCIItable(name = filename,readonly = True) for filename in files] tables = [damask.ASCIItable(name = filename,readonly = True) for filename in files]
for table in tables: for table in tables:
table.head_read() table.head_read()
columns += [columns[0]]*(len(files)-len(columns)) # extend to same length as files columns += [columns[0]]*(len(files)-len(columns)) # extend to same length as files
columns = columns[:len(files)] # truncate to same length as files columns = columns[:len(files)] # truncate to same length as files
for i,column in enumerate(columns): for i,column in enumerate(columns):
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
logging.info('comparing ASCIItables') logging.info('comparing ASCIItables')
for i in xrange(len(columns)): for i in xrange(len(columns)):
@ -484,7 +488,7 @@ class Test():
) )
logging.info(files[i]+':'+','.join(columns[i])) logging.info(files[i]+':'+','.join(columns[i]))
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...
maximum = np.zeros(len(columns[0]),dtype='f') maximum = np.zeros(len(columns[0]),dtype='f')
data = [] data = []
@ -495,26 +499,26 @@ class Test():
table.close() table.close()
maximum /= len(tables) maximum /= len(tables)
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
for i in xrange(len(data)): for i in xrange(len(data)):
data[i] /= maximum data[i] /= maximum
mask = np.zeros_like(table.data,dtype='bool') mask = np.zeros_like(table.data,dtype='bool')
for table in data: for table in data:
mask |= np.where(np.abs(table)<postFilter,True,False) # mask out (all) tiny values mask |= np.where(np.abs(table)<postFilter,True,False) # mask out (all) tiny values
allclose = True # start optimistic allclose = True # start optimistic
for i in xrange(1,len(data)): for i in xrange(1,len(data)):
if debug: if debug:
t0 = np.where(mask,0.0,data[i-1]) t0 = np.where(mask,0.0,data[i-1])
t1 = np.where(mask,0.0,data[i ]) t1 = np.where(mask,0.0,data[i ])
j = np.argmin(np.abs(t1)*rtol+atol-np.abs(t0-t1)) j = np.argmin(np.abs(t1)*rtol+atol-np.abs(t0-t1))
logging.info('%f'%np.amax(np.abs(t0-t1)/(np.abs(t1)*rtol+atol))) logging.info('{:f}'.format(np.amax(np.abs(t0-t1)/(np.abs(t1)*rtol+atol))))
logging.info('%f %f'%((t0*maximum).flatten()[j],(t1*maximum).flatten()[j])) logging.info('{:f} {:f}'.format((t0*maximum).flatten()[j],(t1*maximum).flatten()[j]))
allclose &= np.allclose(np.where(mask,0.0,data[i-1]), 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 return allclose
@ -543,14 +547,13 @@ class Test():
def report_Success(self,culprit): def report_Success(self,culprit):
if culprit == 0: if culprit == 0:
logging.critical('%s passed.'%({False: 'The test', logging.critical(('The test' if len(self.variants) == 1 else 'All {} tests'.format(len(self.variants))) + ' passed')
True: 'All %i tests'%(len(self.variants))}[len(self.variants) > 1]))
logging.critical('\n!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!\n') logging.critical('\n!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!\n')
return 0 return 0
if culprit == -1: if culprit == -1:
logging.warning('Warning: Could not start test') logging.warning('Warning: Could not start test')
return 0 return 0
else: else:
logging.critical(' ********\n * Test %i failed...\n ********'%(culprit)) logging.critical(' ********\n * Test {} failed...\n ********'.format(culprit))
logging.critical('\n!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!\n') logging.critical('\n!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!\n')
return culprit return culprit

38
lib/damask/util.py
View File

@ -58,6 +58,24 @@ def emph(what):
"""emphasizes string on screen""" """emphasizes string on screen"""
return bcolors.BOLD+srepr(what)+bcolors.ENDC 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. # Matlab like trigonometric functions that take and return angles in degrees.
# ----------------------------- # -----------------------------
@ -75,7 +93,7 @@ def gridLocation(idx,res):
# ----------------------------- # -----------------------------
def gridIndex(location,res): def gridIndex(location,res):
return ( location[0] % res[0] + \ return ( location[0] % res[0] + \
( location[1] % res[1]) * res[0] + \ ( location[1] % res[1]) * res[0] + \
( location[2] % res[2]) * 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: else:
pcov = np.inf pcov = np.inf
return popt, pcov, infodict, errmsg, ier if return_full else popt, pcov 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