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added some more post processing tests 

DAMASK env now reports in MiB (GiB is too big for small machines)
This commit is contained in:
Martin Diehl 2014-08-07 16:51:26 +00:00
parent df50707445
commit 15a6015bc2
5 changed files with 180 additions and 305 deletions
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4
DAMASK_env.sh
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@ -60,8 +60,8 @@ if [ ! -z "$PS1" ]; then
echo "FFTW $FFTW_ROOT" echo "FFTW $FFTW_ROOT"
echo "HDF5 $HDF5_ROOT (for future use)" echo "HDF5 $HDF5_ROOT (for future use)"
echo echo
echo -n "heap size/GiB "; echo "`ulimit -d`/1024/1024" | bc echo -n "heap size/MiB "; echo "`ulimit -d`/1024" | bc
echo -n "stack size/GiB "; echo "`ulimit -s`/1024/1024" | bc echo -n "stack size/MiB "; echo "`ulimit -s`/1024" | bc
fi fi
export DAMASK_NUM_THREADS export DAMASK_NUM_THREADS

112
processing/post/permuteData.py
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@ -1,48 +1,30 @@
#!/usr/bin/env python #!/usr/bin/env python
# -*- coding: UTF-8 no BOM -*- # -*- coding: UTF-8 no BOM -*-
import os,re,sys,math,numpy,string import os,sys,string
import numpy as np
from optparse import OptionParser
import damask import damask
from collections import defaultdict
from optparse import OptionParser, Option
scriptID = '$Id$'
scriptName = scriptID.split()[1]
# -----------------------------
class extendableOption(Option):
# -----------------------------
# used for definition of new option parser action 'extend', which enables to take multiple option arguments
# taken from online tutorial http://docs.python.org/library/optparse.html
ACTIONS = Option.ACTIONS + ("extend",)
STORE_ACTIONS = Option.STORE_ACTIONS + ("extend",)
TYPED_ACTIONS = Option.TYPED_ACTIONS + ("extend",)
ALWAYS_TYPED_ACTIONS = Option.ALWAYS_TYPED_ACTIONS + ("extend",)
def take_action(self, action, dest, opt, value, values, parser):
if action == "extend":
lvalue = value.split(",")
values.ensure_value(dest, []).extend(lvalue)
else:
Option.take_action(self, action, dest, opt, value, values, parser)
scriptID = string.replace('$Id$','\n','\\n')
scriptName = scriptID.split()[1][:-3]
# -------------------------------------------------------------------- # --------------------------------------------------------------------
# MAIN # MAIN
# -------------------------------------------------------------------- # --------------------------------------------------------------------
parser = OptionParser(option_class=extendableOption, usage='%prog options [file[s]]', description = """ parser = OptionParser(option_class=damask.extendableOption, usage='%prog options [file[s]]', description = """
Permute all values in given column(s). Permute all values in given column(s).
""" + string.replace(scriptID,'\n','\\n') """, version = scriptID)
)
parser.add_option('-l','--label', dest='label', action='extend', type='string', parser.add_option('-l','--label', dest='label', action='extend', metavar='<strig LIST>',
help='heading(s) of column to permute', help='heading(s) of column to permute')
metavar='<label>') parser.add_option('-r', '--rnd', dest='randomSeed', type='int', metavar='int',
help='seed of random number generator [%default]')
parser.set_defaults(label = []) parser.set_defaults(label = [])
parser.set_defaults(randomSeed = None)
(options,filenames) = parser.parse_args() (options,filenames) = parser.parse_args()
@ -55,71 +37,59 @@ datainfo = { # lis
} }
if options.label != None: datainfo['scalar']['label'] += options.label if options.label != None: datainfo['scalar']['label'] += options.label
np.random.seed(options.randomSeed)
# ------------------------------------------ setup file handles --------------------------------------- # ------------------------------------------ setup file handles ------------------------------------
files = [] files = []
if filenames == []: for name in filenames:
files.append({'name':'STDIN', 'input':sys.stdin, 'output':sys.stdout, 'croak':sys.stderr})
else:
for name in filenames:
if os.path.exists(name): if os.path.exists(name):
files.append({'name':name, 'input':open(name), 'output':open(name+'_tmp','w'), 'croak':sys.stderr}) files.append({'name':name, 'input':open(name), 'output':open(name+'_tmp','w'), 'croak':sys.stderr})
#--- loop over input files ------------------------------------------------------------------------ #--- loop over input files -------------------------------------------------------------------------
for file in files: for file in files:
if file['name'] != 'STDIN': file['croak'].write('\033[1m'+scriptName+'\033[0m: '+file['name']+'\n') file['croak'].write('\033[1m'+scriptName+'\033[0m: '+file['name']+'\n')
else: file['croak'].write('\033[1m'+scriptName+'\033[0m\n')
table = damask.ASCIItable(file['input'],file['output'],False) # make unbuffered ASCII_table table = damask.ASCIItable(file['input'],file['output'],True) # make unbuffered ASCII_table
table.head_read() # read ASCII header info table.head_read() # read ASCII header info
table.info_append(string.replace(scriptName,'\n','\\n') + \ table.info_append(scriptID + '\t' + ' '.join(sys.argv[1:]))
'\t' + ' '.join(sys.argv[1:]))
# --------------- figure out columns to process # --------------- figure out columns to process ---------------------------------------------------
active = defaultdict(list) active = []
column = defaultdict(dict) column = {}
for datatype,info in datainfo.items(): for label in datainfo['scalar']['label']:
for label in info['label']: if label in table.labels:
foundIt = False active.append(label)
for key in ['1_'+label,label]: column[label] = table.labels.index(label) # remember columns of requested data
if key in table.labels: else:
foundIt = True
active[datatype].append(label)
column[datatype][label] = table.labels.index(key) # remember columns of requested data
if not foundIt:
file['croak'].write('column %s not found...\n'%label) file['croak'].write('column %s not found...\n'%label)
# ------------------------------------------ assemble header --------------------------------------- # ------------------------------------------ assemble header ---------------------------------------
table.head_write() table.head_write()
# ------------------------------------------ process data --------------------------------------- # ------------------------------------------ process data ------------------------------------------
permutation = {} permutation = {}
table.data_readArray([column['scalar'][label] for label in active['scalar']]) table.data_readArray([column[label] for label in active])
for i,label in enumerate(active['scalar']): for i,label in enumerate(active):
mySeed = np.random.randint(9999999)
np.random.seed(mySeed)
unique = list(set(table.data[:,i])) unique = list(set(table.data[:,i]))
permutated = numpy.random.permutation(unique) permutated = np.random.permutation(unique)
permutation[label] = dict(zip(unique,permutated)) permutation[label] = dict(zip(unique,permutated))
table.data_rewind() table.data_rewind()
while table.data_read(): # read next data line of ASCII table outputAlive = True
while outputAlive and table.data_read(): # read next data line of ASCII table
for datatype,labels in active.items(): # loop over vector,tensor for label in active: # loop over all requested stiffnesses
for label in labels: # loop over all requested stiffnesses for c in xrange(column[label],
for c in xrange(column[datatype][label], column[label]+datainfo['scalar']['len']):
column[datatype][label]+datainfo[datatype]['len']):
table.data[c] = permutation[label][float(table.data[c])] # apply permutation table.data[c] = permutation[label][float(table.data[c])] # apply permutation
table.data_write() # output processed line outputAlive = table.data_write() # output processed line
# ------------------------------------------ output result --------------------------------------- # ------------------------------------------ output result -----------------------------------------
outputAlive and table.output_flush() # just in case of buffered ASCII table
table.output_flush() # just in case of buffered ASCII table
if file['name'] != 'STDIN':
file['input'].close() # close input ASCII table file['input'].close() # close input ASCII table
file['output'].close() # close output ASCII table file['output'].close() # close output ASCII table
os.rename(file['name']+'_tmp',file['name']) # overwrite old one with tmp new os.rename(file['name']+'_tmp',file['name']) # overwrite old one with tmp new

96
processing/post/rotateData.py
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@ -1,57 +1,36 @@
#!/usr/bin/env python #!/usr/bin/env python
# -*- coding: UTF-8 no BOM -*- # -*- coding: UTF-8 no BOM -*-
import os,re,sys,math,numpy,string import os,sys,string
import damask import numpy as np
from collections import defaultdict from collections import defaultdict
from optparse import OptionParser, Option from optparse import OptionParser
import damask
scriptID = '$Id$'
scriptName = scriptID.split()[1]
# -----------------------------
class extendableOption(Option):
# -----------------------------
# used for definition of new option parser action 'extend', which enables to take multiple option arguments
# taken from online tutorial http://docs.python.org/library/optparse.html
ACTIONS = Option.ACTIONS + ("extend",)
STORE_ACTIONS = Option.STORE_ACTIONS + ("extend",)
TYPED_ACTIONS = Option.TYPED_ACTIONS + ("extend",)
ALWAYS_TYPED_ACTIONS = Option.ALWAYS_TYPED_ACTIONS + ("extend",)
def take_action(self, action, dest, opt, value, values, parser):
if action == "extend":
lvalue = value.split(",")
values.ensure_value(dest, []).extend(lvalue)
else:
Option.take_action(self, action, dest, opt, value, values, parser)
scriptID = string.replace('$Id$','\n','\\n')
scriptName = scriptID.split()[1][:-3]
# -------------------------------------------------------------------- # --------------------------------------------------------------------
# MAIN # MAIN
# -------------------------------------------------------------------- # --------------------------------------------------------------------
parser = OptionParser(option_class=extendableOption, usage='%prog options [file[s]]', description = """ parser = OptionParser(option_class=damask.extendableOption, usage='%prog options [file[s]]', description = """
Uniformly scale values of scalar, vector, or tensor columns by given factor. Uniformly scale values of scalar, vector, or tensor columns by given factor.
""" + string.replace(scriptID,'\n','\\n') """, version = scriptID)
)
parser.add_option('-v','--vector', dest = 'vector', action = 'extend', type = 'string', parser.add_option('-v','--vector', dest = 'vector', action = 'extend', metavar='string',
help = 'column heading of vector to scale', help = 'column heading of vector to scale')
metavar = '<label(s)>') parser.add_option('-t','--tensor', dest = 'tensor', action = 'extend', metavar='string',
parser.add_option('-t','--tensor', dest = 'tensor', action = 'extend', type = 'string', help = 'column heading of tensor to scale')
help = 'column heading of tensor to scale', parser.add_option('-r', '--rotation',dest = 'rotation', type = 'float', nargs = 4, metavar='int int int int',
metavar = '<label(s)>') help = 'angle and axis to rotate data %default')
parser.add_option('-r', '--rotation', dest = 'rotation', type = 'float', nargs = 4,
help = 'angle and axis to rotate data')
parser.add_option('-d', '--degrees', dest = 'degrees', action = 'store_true', parser.add_option('-d', '--degrees', dest = 'degrees', action = 'store_true',
help = 'angles are given in degrees [%default]') help = 'angles are given in degrees [%default]')
parser.set_defaults(vector = []) parser.set_defaults(vector = [])
parser.set_defaults(tensor = []) parser.set_defaults(tensor = [])
parser.set_defaults(rotation = [0.,1.,1.,1.]) # no rotation about 1,1,1 parser.set_defaults(rotation = (0.,1.,1.,1.)) # no rotation about 1,1,1
parser.set_defaults(degrees = False) parser.set_defaults(degrees = False)
(options,filenames) = parser.parse_args() (options,filenames) = parser.parse_args()
@ -63,7 +42,6 @@ datainfo = { # lis
'label':[]}, 'label':[]},
} }
if options.vector != []: datainfo['vector']['label'] += options.vector if options.vector != []: datainfo['vector']['label'] += options.vector
if options.tensor != []: datainfo['tensor']['label'] += options.tensor if options.tensor != []: datainfo['tensor']['label'] += options.tensor
@ -71,8 +49,7 @@ toRadians = math.pi/180.0 if options.degrees else 1.0
r = damask.Quaternion().fromAngleAxis(toRadians*options.rotation[0],options.rotation[1:]) r = damask.Quaternion().fromAngleAxis(toRadians*options.rotation[0],options.rotation[1:])
R = r.asMatrix() R = r.asMatrix()
# ------------------------------------------ setup file handles --------------------------------------- # ------------------------------------------ setup file handles ------------------------------------
files = [] files = []
if filenames == []: if filenames == []:
files.append({'name':'STDIN', 'input':sys.stdin, 'output':sys.stdout, 'croak':sys.stderr}) files.append({'name':'STDIN', 'input':sys.stdin, 'output':sys.stdout, 'croak':sys.stderr})
@ -81,62 +58,55 @@ else:
if os.path.exists(name): if os.path.exists(name):
files.append({'name':name, 'input':open(name), 'output':open(name+'_tmp','w'), 'croak':sys.stderr}) files.append({'name':name, 'input':open(name), 'output':open(name+'_tmp','w'), 'croak':sys.stderr})
#--- loop over input files ------------------------------------------------------------------------ # ------------------------------------------ loop over input files ---------------------------------
for file in files: for file in files:
if file['name'] != 'STDIN': file['croak'].write('\033[1m'+scriptName+'\033[0m: '+file['name']+'\n') if file['name'] != 'STDIN': file['croak'].write('\033[1m'+scriptName+'\033[0m: '+file['name']+'\n')
else: file['croak'].write('\033[1m'+scriptName+'\033[0m\n') else: file['croak'].write('\033[1m'+scriptName+'\033[0m\n')
table = damask.ASCIItable(file['input'],file['output'],False) # make unbuffered ASCII_table table = damask.ASCIItable(file['input'],file['output'],False) # make unbuffered ASCII_table
table.head_read() # read ASCII header info table.head_read() # read ASCII header info
table.info_append(string.replace(scriptName,'\n','\\n') + \ table.info_append(scriptID + '\t' + ' '.join(sys.argv[1:]))
'\t' + ' '.join(sys.argv[1:]))
# --------------- figure out columns to process --------------------------------------- # --------------- figure out columns to process ---------------------------------------------------
active = defaultdict(list) active = defaultdict(list)
column = defaultdict(dict) column = defaultdict(dict)
for datatype,info in datainfo.items(): for datatype,info in datainfo.items():
for label in info['label']: for label in info['label']:
foundIt = False key = '1_'+label
for key in ['1_'+label,label]:
if key in table.labels: if key in table.labels:
foundIt = True
active[datatype].append(label) active[datatype].append(label)
column[datatype][label] = table.labels.index(key) # remember columns of requested data column[datatype][label] = table.labels.index(key) # remember columns of requested data
if not foundIt: else:
file['croak'].write('column %s not found...\n'%label) file['croak'].write('column %s not found...\n'%label)
# ------------------------------------------ assemble header --------------------------------------- # ------------------------------------------ assemble header ---------------------------------------
table.head_write() table.head_write()
# ------------------------------------------ process data --------------------------------------- # ------------------------------------------ process data ------------------------------------------
outputAlive = True outputAlive = True
while outputAlive and table.data_read(): # read next data line of ASCII table while outputAlive and table.data_read(): # read next data line of ASCII table
datatype = 'vector' datatype = 'vector'
for label in active[datatype] if datatype in active else []: # loop over all requested labels for label in active[datatype] if datatype in active else []: # loop over all requested labels
table.data[column[datatype][label]:column[datatype][label]+datainfo[datatype]['len']] = \ table.data[column[datatype][label]:column[datatype][label]+datainfo[datatype]['len']] = \
r * numpy.array(map(float, r * np.array(map(float,
table.data[column[datatype][label]:\ table.data[column[datatype][label]:\
column[datatype][label]+datainfo[datatype]['len']])) column[datatype][label]+datainfo[datatype]['len']]))
datatype = 'tensor' datatype = 'tensor'
for label in active[datatype] if datatype in active else []: # loop over all requested labels
table.data[column[datatype][label]:column[datatype][label]+column[datatype]['len']] = \
(numpy.array(map(float,
table.data[column[datatype][label]:\
column[datatype][label]+column[datatype]['len']])).reshape(numpy.sqrt(datainfo[datatype]['len']),\
numpy.sqrt(datainfo[datatype]['len'])) * R).reshape(datainfo[datatype]['len'])
for label in active[datatype] if datatype in active else []: # loop over all requested labels
table.data[column[datatype][label]:column[datatype][label]+datainfo[datatype]['len']] = \
(np.array(map(float,table.data[column[datatype][label]:\
column[datatype][label]+datainfo[datatype]['len']])).\
reshape(np.sqrt(datainfo[datatype]['len']),\
np.sqrt(datainfo[datatype]['len'])) * R).reshape(datainfo[datatype]['len'])
outputAlive = table.data_write() # output processed line outputAlive = table.data_write() # output processed line
# ------------------------------------------ output result --------------------------------------- # ------------------------------------------ output result -----------------------------------------
outputAlive and table.output_flush()
outputAlive and table.output_flush() # just in case of buffered ASCII table
file['input'].close() # close input ASCII table (works for stdin)
file['output'].close() # close output ASCII table (works for stdout)
if file['name'] != 'STDIN': if file['name'] != 'STDIN':
file['input'].close() # close input ASCII table
file['output'].close() # close output ASCII table
os.rename(file['name']+'_tmp',file['name']) # overwrite old one with tmp new os.rename(file['name']+'_tmp',file['name']) # overwrite old one with tmp new

87
processing/post/scaleData.py
View File

@ -1,55 +1,32 @@
#!/usr/bin/env python #!/usr/bin/env python
# -*- coding: UTF-8 no BOM -*- # -*- coding: UTF-8 no BOM -*-
import os,re,sys,math,numpy,string import os,sys,string
import damask import numpy as np
from collections import defaultdict from collections import defaultdict
from optparse import OptionParser, Option from optparse import OptionParser
import damask
scriptID = '$Id$' scriptID = '$Id$'
scriptName = scriptID.split()[1] scriptName = scriptID.split()[1][:-3]
# -----------------------------
class extendableOption(Option):
# -----------------------------
# used for definition of new option parser action 'extend', which enables to take multiple option arguments
# taken from online tutorial http://docs.python.org/library/optparse.html
ACTIONS = Option.ACTIONS + ("extend",)
STORE_ACTIONS = Option.STORE_ACTIONS + ("extend",)
TYPED_ACTIONS = Option.TYPED_ACTIONS + ("extend",)
ALWAYS_TYPED_ACTIONS = Option.ALWAYS_TYPED_ACTIONS + ("extend",)
def take_action(self, action, dest, opt, value, values, parser):
if action == "extend":
lvalue = value.split(",")
values.ensure_value(dest, []).extend(lvalue)
else:
Option.take_action(self, action, dest, opt, value, values, parser)
# -------------------------------------------------------------------- # --------------------------------------------------------------------
# MAIN # MAIN
# -------------------------------------------------------------------- # --------------------------------------------------------------------
parser = OptionParser(option_class=extendableOption, usage='%prog options [file[s]]', description = """ parser = OptionParser(option_class=damask.extendableOption, usage='%prog options [file[s]]', description = """
Uniformly scale values of scalar, vector, or tensor columns by given factor. Uniformly scale values of scalar, vector, or tensor columns by given factor.
""" + string.replace(scriptID,'\n','\\n') """, version = scriptID)
)
parser.add_option('-s','--scalar', dest='scalar', action='extend', type='string', parser.add_option('-s','--scalar', dest='scalar', action='extend', metavar='<string LIST>',
help='column heading of scalar to scale', help='column heading of scalar to scale')
metavar='<label(s)>') parser.add_option('-v','--vector', dest='vector', action='extend', metavar='<string LIST>',
parser.add_option('-v','--vector', dest='vector', action='extend', type='string', help='column heading of vector to scale')
help='column heading of vector to scale', parser.add_option('-t','--tensor', dest='tensor', action='extend', metavar='<string LIST>',
metavar='<label(s)>') help='column heading of tensor to scale')
parser.add_option('-t','--tensor', dest='tensor', action='extend', type='string', parser.add_option('-f','--factor', dest='factor', action='extend', metavar='<float LIST>',
help='column heading of tensor to scale', help='list of scalar, vector, and tensor scaling factors (in this order!)')
metavar='<label(s)>')
parser.add_option('-f','--factor', dest='factor', action='extend', type='string',
help='list of scalar, vector, and tensor scaling factors (in this order!)',
metavar='<float(s)>')
parser.set_defaults(scalar = []) parser.set_defaults(scalar = [])
parser.set_defaults(vector = []) parser.set_defaults(vector = [])
@ -58,7 +35,7 @@ parser.set_defaults(factor = [])
(options,filenames) = parser.parse_args() (options,filenames) = parser.parse_args()
options.factor = numpy.array(map(float,options.factor)) options.factor = np.array(options.factor,'d')
datainfo = { # list of requested labels per datatype datainfo = { # list of requested labels per datatype
'scalar': {'len':1, 'scalar': {'len':1,
'label':[]}, 'label':[]},
@ -73,10 +50,9 @@ if options.scalar != []: datainfo['scalar']['label'] += options.scalar; length +
if options.vector != []: datainfo['vector']['label'] += options.vector; length += len(options.vector) if options.vector != []: datainfo['vector']['label'] += options.vector; length += len(options.vector)
if options.tensor != []: datainfo['tensor']['label'] += options.tensor; length += len(options.tensor) if options.tensor != []: datainfo['tensor']['label'] += options.tensor; length += len(options.tensor)
if len(options.factor) != length: if len(options.factor) != length:
parser.error('Length of scaling vector does not match column count.') parser.error('length of scaling vector does not match column count...')
# ------------------------------------------ setup file handles ---------------------------------------
# ------------------------------------------ setup file handles ------------------------------------
files = [] files = []
if filenames == []: if filenames == []:
files.append({'name':'STDIN', 'input':sys.stdin, 'output':sys.stdout, 'croak':sys.stderr}) files.append({'name':'STDIN', 'input':sys.stdin, 'output':sys.stdout, 'croak':sys.stderr})
@ -85,54 +61,47 @@ else:
if os.path.exists(name): if os.path.exists(name):
files.append({'name':name, 'input':open(name), 'output':open(name+'_tmp','w'), 'croak':sys.stderr}) files.append({'name':name, 'input':open(name), 'output':open(name+'_tmp','w'), 'croak':sys.stderr})
#--- loop over input files ------------------------------------------------------------------------ # ------------------------------------------ loop over input files ---------------------------------
for file in files: for file in files:
if file['name'] != 'STDIN': file['croak'].write('\033[1m'+scriptName+'\033[0m: '+file['name']+'\n') if file['name'] != 'STDIN': file['croak'].write('\033[1m'+scriptName+'\033[0m: '+file['name']+'\n')
else: file['croak'].write('\033[1m'+scriptName+'\033[0m\n') else: file['croak'].write('\033[1m'+scriptName+'\033[0m\n')
table = damask.ASCIItable(file['input'],file['output'],False) # make unbuffered ASCII_table table = damask.ASCIItable(file['input'],file['output'],False) # make unbuffered ASCII_table
table.head_read() # read ASCII header info table.head_read() # read ASCII header info
table.info_append(string.replace(scriptName,'\n','\\n') + \ table.info_append(scriptID + '\t' + ' '.join(sys.argv[1:]))
'\t' + ' '.join(sys.argv[1:]))
# --------------- figure out columns to process --------------------------------------- # --------------- figure out columns to process ---------------------------------------------------
active = defaultdict(list) active = defaultdict(list)
column = defaultdict(dict) column = defaultdict(dict)
for datatype,info in datainfo.items(): for datatype,info in datainfo.items():
for label in info['label']: for label in info['label']:
foundIt = False key = {True :'1_%s',
for key in ['1_'+label,label]: False:'%s' }[info['len']>1]%label
if key in table.labels: if key in table.labels:
foundIt = True
active[datatype].append(label) active[datatype].append(label)
column[datatype][label] = table.labels.index(key) # remember columns of requested data column[datatype][label] = table.labels.index(key) # remember columns of requested data
if not foundIt: else:
file['croak'].write('column %s not found...\n'%label) file['croak'].write('column %s not found...\n'%label)
# ------------------------------------------ assemble header --------------------------------------- # ------------------------------------------ assemble header ---------------------------------------
table.head_write() table.head_write()
# ------------------------------------------ process data --------------------------------------- # ------------------------------------------ process data ------------------------------------------
outputAlive = True outputAlive = True
while outputAlive and table.data_read(): # read next data line of ASCII table while outputAlive and table.data_read(): # read next data line of ASCII table
i = 0 i = 0
for datatype,labels in sorted(active.items(),key=lambda x:datainfo[x[0]]['len']): # loop over scalar,vector,tensor for datatype,labels in sorted(active.items(),key=lambda x:datainfo[x[0]]['len']): # loop over scalar,vector,tensor
for label in labels: # loop over all requested labels for label in labels: # loop over all requested labels
for j in xrange(datainfo[datatype]['len']): # loop over entity elements for j in xrange(datainfo[datatype]['len']): # loop over entity elements
table.data[column[datatype][label]+j] = float(table.data[column[datatype][label]+j]) * options.factor[i] table.data[column[datatype][label]+j] = float(table.data[column[datatype][label]+j]) * options.factor[i]
i += 1 i += 1
outputAlive = table.data_write() # output processed line outputAlive = table.data_write() # output processed line
# ------------------------------------------ output result --------------------------------------- # ------------------------------------------ output result -----------------------------------------
outputAlive and table.output_flush() # just in case of buffered ASCII table outputAlive and table.output_flush() # just in case of buffered ASCII table
file['input'].close() # close input ASCII table (works for stdin)
file['output'].close() # close output ASCII table (works for stdout)
if file['name'] != 'STDIN': if file['name'] != 'STDIN':
file['input'].close() # close input ASCII table
file['output'].close() # close output ASCII table
os.rename(file['name']+'_tmp',file['name']) # overwrite old one with tmp new os.rename(file['name']+'_tmp',file['name']) # overwrite old one with tmp new

92
processing/post/shiftData.py
View File

@ -1,55 +1,32 @@
#!/usr/bin/env python #!/usr/bin/env python
# -*- coding: UTF-8 no BOM -*- # -*- coding: UTF-8 no BOM -*-
import os,re,sys,math,numpy,string import os,sys,string
import damask import numpy as np
from collections import defaultdict from collections import defaultdict
from optparse import OptionParser, Option from optparse import OptionParser
import damask
scriptID = '$Id$'
scriptName = scriptID.split()[1]
# -----------------------------
class extendableOption(Option):
# -----------------------------
# used for definition of new option parser action 'extend', which enables to take multiple option arguments
# taken from online tutorial http://docs.python.org/library/optparse.html
ACTIONS = Option.ACTIONS + ("extend",)
STORE_ACTIONS = Option.STORE_ACTIONS + ("extend",)
TYPED_ACTIONS = Option.TYPED_ACTIONS + ("extend",)
ALWAYS_TYPED_ACTIONS = Option.ALWAYS_TYPED_ACTIONS + ("extend",)
def take_action(self, action, dest, opt, value, values, parser):
if action == "extend":
lvalue = value.split(",")
values.ensure_value(dest, []).extend(lvalue)
else:
Option.take_action(self, action, dest, opt, value, values, parser)
scriptID = string.replace('$Id$','\n','\\n')
scriptName = scriptID.split()[1][:-3]
# -------------------------------------------------------------------- # --------------------------------------------------------------------
# MAIN # MAIN
# -------------------------------------------------------------------- # --------------------------------------------------------------------
parser = OptionParser(option_class=extendableOption, usage='%prog options [file[s]]', description = """ parser = OptionParser(option_class=damask.extendableOption, usage='%prog options [file[s]]', description = """
Shift values of scalar, vector, or tensor columns by given offset. Shift values of scalar, vector, or tensor columns by given offset.
""" + string.replace(scriptID,'\n','\\n') """, version = scriptID)
)
parser.add_option('-s','--scalar', dest='scalar', action='extend', type='string', parser.add_option('-s','--scalar', dest='scalar', action='extend', metavar='<string LIST>',
help='column heading to shift by scalar', help='column heading to shift by scalar')
metavar='<label(s)>') parser.add_option('-v','--vector', dest='vector', action='extend', metavar='<string LIST>',
parser.add_option('-v','--vector', dest='vector', action='extend', type='string', help='column heading to shift by vector')
help='column heading to shift by vector', parser.add_option('-t','--tensor', dest='tensor', action='extend', metavar='<string LIST>',
metavar='<label(s)>') help='column heading to shift by tensor')
parser.add_option('-t','--tensor', dest='tensor', action='extend', type='string', parser.add_option('-d','--delta', dest='delta', action='extend', metavar='<float LIST>',
help='column heading to shift by tensor', help='list of scalar, vector, and tensor shifts (in this order!)')
metavar='<label(s)>')
parser.add_option('-d','--delta', dest='delta', action='extend', type='string',
help='list of scalar, vector, and tensor shifts (in this order!)',
metavar='<float(s)>')
parser.set_defaults(scalar = []) parser.set_defaults(scalar = [])
parser.set_defaults(vector = []) parser.set_defaults(vector = [])
@ -58,7 +35,7 @@ parser.set_defaults(delta = [])
(options,filenames) = parser.parse_args() (options,filenames) = parser.parse_args()
options.delta = numpy.array(map(float,options.delta)) options.delta = np.array(options.delta,'d')
datainfo = { # list of requested labels per datatype datainfo = { # list of requested labels per datatype
'scalar': {'len':1, 'scalar': {'len':1,
'label':[]}, 'label':[]},
@ -73,10 +50,9 @@ if options.scalar != []: datainfo['scalar']['label'] += options.scalar; length +
if options.vector != []: datainfo['vector']['label'] += options.vector; length += len(options.vector)*datainfo['vector']['len'] if options.vector != []: datainfo['vector']['label'] += options.vector; length += len(options.vector)*datainfo['vector']['len']
if options.tensor != []: datainfo['tensor']['label'] += options.tensor; length += len(options.tensor)*datainfo['tensor']['len'] if options.tensor != []: datainfo['tensor']['label'] += options.tensor; length += len(options.tensor)*datainfo['tensor']['len']
if len(options.delta) != length: if len(options.delta) != length:
parser.error('Length of offset vector does not match column types.') parser.error('length of offset vector does not match column types...')
# ------------------------------------------ setup file handles ---------------------------------------
# ------------------------------------------ setup file handles ------------------------------------
files = [] files = []
if filenames == []: if filenames == []:
files.append({'name':'STDIN', 'input':sys.stdin, 'output':sys.stdout, 'croak':sys.stderr}) files.append({'name':'STDIN', 'input':sys.stdin, 'output':sys.stdout, 'croak':sys.stderr})
@ -85,57 +61,47 @@ else:
if os.path.exists(name): if os.path.exists(name):
files.append({'name':name, 'input':open(name), 'output':open(name+'_tmp','w'), 'croak':sys.stderr}) files.append({'name':name, 'input':open(name), 'output':open(name+'_tmp','w'), 'croak':sys.stderr})
#--- loop over input files ------------------------------------------------------------------------ # ------------------------------------------ loop over input files ---------------------------------
for file in files: for file in files:
if file['name'] != 'STDIN': file['croak'].write('\033[1m'+scriptName+'\033[0m: '+file['name']+'\n') if file['name'] != 'STDIN': file['croak'].write('\033[1m'+scriptName+'\033[0m: '+file['name']+'\n')
else: file['croak'].write('\033[1m'+scriptName+'\033[0m\n') else: file['croak'].write('\033[1m'+scriptName+'\033[0m\n')
table = damask.ASCIItable(file['input'],file['output'],False) # make unbuffered ASCII_table table = damask.ASCIItable(file['input'],file['output'],False) # make unbuffered ASCII_table
table.head_read() # read ASCII header info table.head_read() # read ASCII header info
table.info_append(string.replace(scriptName,'\n','\\n') + \ table.info_append(scriptID + '\t' + ' '.join(sys.argv[1:]))
'\t' + ' '.join(sys.argv[1:]))
# --------------- figure out columns to process --------------------------------------- # --------------- figure out columns to process ---------------------------------------------------
active = defaultdict(list) active = defaultdict(list)
column = defaultdict(dict) column = defaultdict(dict)
for datatype,info in datainfo.items(): for datatype,info in datainfo.items():
for label in info['label']: for label in info['label']:
foundIt = False key = {True :'1_%s',
for key in ['1_'+label,label]: False:'%s' }[info['len']>1]%label
if key in table.labels: if key in table.labels:
foundIt = True
active[datatype].append(label) active[datatype].append(label)
column[datatype][label] = table.labels.index(key) # remember columns of requested data column[datatype][label] = table.labels.index(key) # remember columns of requested data
if not foundIt: else:
file['croak'].write('column %s not found...\n'%label) file['croak'].write('column %s not found...\n'%label)
# ------------------------------------------ assemble header --------------------------------------- # ------------------------------------------ assemble header ---------------------------------------
table.head_write() table.head_write()
# ------------------------------------------ process data --------------------------------------- # ------------------------------------------ process data ------------------------------------------
outputAlive = True outputAlive = True
while outputAlive and table.data_read(): # read next data line of ASCII table while outputAlive and table.data_read(): # read next data line of ASCII table
i = 0 i = 0
for datatype,labels in sorted(active.items(),key=lambda x:datainfo[x[0]]['len']): # loop over scalar,vector,tensor for datatype,labels in sorted(active.items(),key=lambda x:datainfo[x[0]]['len']): # loop over scalar,vector,tensor
# file['croak'].write('%s\n'%datatype)
for label in labels: # loop over all requested labels for label in labels: # loop over all requested labels
# file['croak'].write('%s\n'%label)
for j in xrange(datainfo[datatype]['len']): # loop over entity elements for j in xrange(datainfo[datatype]['len']): # loop over entity elements
# file['croak'].write('%s\n'%table.data[column[datatype][label]+j])
table.data[column[datatype][label]+j] = float(table.data[column[datatype][label]+j]) + options.delta[i] table.data[column[datatype][label]+j] = float(table.data[column[datatype][label]+j]) + options.delta[i]
i += 1 i += 1
outputAlive = table.data_write() # output processed line outputAlive = table.data_write() # output processed line
# ------------------------------------------ output result --------------------------------------- # ------------------------------------------ output result -----------------------------------------
outputAlive and table.output_flush() # just in case of buffered ASCII table outputAlive and table.output_flush() # just in case of buffered ASCII table
file['input'].close() # close input ASCII table (works for stdin)
file['output'].close() # close output ASCII table (works for stdout)
if file['name'] != 'STDIN': if file['name'] != 'STDIN':
file['input'].close() # close input ASCII table
file['output'].close() # close output ASCII table
os.rename(file['name']+'_tmp',file['name']) # overwrite old one with tmp new os.rename(file['name']+'_tmp',file['name']) # overwrite old one with tmp new