149 lines
5.2 KiB
Python
149 lines
5.2 KiB
Python
|
#!/usr/bin/python
|
||
|
|
|
||
|
|
import os,re,sys,math,string,numpy
|
||
|
|
from optparse import OptionParser, Option
|
||
|
|
|
||
|
|
# -----------------------------
|
||
|
|
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)
|
||
|
|
|
||
|
|
|
||
|
|
|
||
|
|
def location(idx,res):
|
||
|
|
|
||
|
|
return numpy.array([ idx % res[0], \
|
||
|
|
(idx // res[0]) % res[1], \
|
||
|
|
(idx // res[0] // res[1]) % res[2] ])
|
||
|
|
|
||
|
|
def index(location,res):
|
||
|
|
|
||
|
|
return ( location[0] % res[0] + \
|
||
|
|
(location[1] % res[1]) * res[0] + \
|
||
|
|
(location[2] % res[2]) * res[0] * res[1] )
|
||
|
|
|
||
|
|
|
||
|
|
# --------------------------------------------------------------------
|
||
|
|
# MAIN
|
||
|
|
# --------------------------------------------------------------------
|
||
|
|
|
||
|
|
parser = OptionParser(option_class=extendableOption, usage='%prog [options] [file[s]]', description = """
|
||
|
|
Average each data block of size 'packing' into single values thus reducing the former resolution
|
||
|
|
to resolution/packing. (Requires numpy.)
|
||
|
|
|
||
|
|
""" + string.replace('$Id$','\n','\\n')
|
||
|
|
)
|
||
|
|
|
||
|
|
|
||
|
|
parser.add_option('-m','--memory', dest='memory', action='store_true', \
|
||
|
|
help='load complete file into memory [%default]')
|
||
|
|
parser.add_option('-r','--resolution', dest='res', type='int', nargs=3, \
|
||
|
|
help='resolution in fast, medium, and slow dimension [%default]')
|
||
|
|
parser.add_option('-p','--packing', dest='packing', type='int', nargs=3, \
|
||
|
|
help='number of data points to average down in each dimension [%default]')
|
||
|
|
|
||
|
|
parser.set_defaults(memory = False)
|
||
|
|
parser.set_defaults(resolution = [32,32,32])
|
||
|
|
parser.set_defaults(packing = [2,2,2])
|
||
|
|
|
||
|
|
(options,filenames) = parser.parse_args()
|
||
|
|
|
||
|
|
if len(options.resolution) < 3:
|
||
|
|
parser.error('resolution needs three parameters...')
|
||
|
|
if len(options.packing) < 3:
|
||
|
|
parser.error('packing needs three parameters...')
|
||
|
|
options.packing = numpy.array(options.packing)
|
||
|
|
|
||
|
|
# ------------------------------------------ setup file handles ---------------------------------------
|
||
|
|
|
||
|
|
files = []
|
||
|
|
if filenames == []:
|
||
|
|
files.append({'name':'STDIN', 'input':sys.stdin, 'output':sys.stdout})
|
||
|
|
else:
|
||
|
|
for name in filenames:
|
||
|
|
if os.path.exists(name):
|
||
|
|
(head,tail) = os.path.split(name)
|
||
|
|
files.append({'name':name, 'input':open(name), 'output':open(os.path.join(head,'avgDown_%s'%tail),'w')})
|
||
|
|
|
||
|
|
# ------------------------------------------ loop over input files ---------------------------------------
|
||
|
|
|
||
|
|
for file in files:
|
||
|
|
print file['name']
|
||
|
|
|
||
|
|
# get labels by either read the first row, or - if keyword header is present - the last line of the header
|
||
|
|
|
||
|
|
firstline = file['input'].readline()
|
||
|
|
m = re.search('(\d+)\s*head', firstline.lower())
|
||
|
|
if m:
|
||
|
|
headerlines = int(m.group(1))
|
||
|
|
passOn = [file['input'].readline() for i in range(1,headerlines)]
|
||
|
|
headers = file['input'].readline().split()
|
||
|
|
else:
|
||
|
|
headerlines = 1
|
||
|
|
passOn = []
|
||
|
|
headers = firstline.split()
|
||
|
|
|
||
|
|
if options.memory:
|
||
|
|
data = file['input'].readlines()
|
||
|
|
else:
|
||
|
|
data = []
|
||
|
|
|
||
|
|
# ------------------------------------------ assemble header ---------------------------------------
|
||
|
|
|
||
|
|
output = '%i\theader'%(headerlines+1) + '\n' + \
|
||
|
|
''.join(passOn) + \
|
||
|
|
string.replace('$Id$','\n','\\n')+ '\t' + \
|
||
|
|
' '.join(sys.argv[1:]) + '\n' + \
|
||
|
|
'\t'.join(headers) + '\n' # build extended header
|
||
|
|
|
||
|
|
if not options.memory:
|
||
|
|
file['output'].write(output)
|
||
|
|
output = ''
|
||
|
|
|
||
|
|
# ------------------------------------------ read file ---------------------------------------
|
||
|
|
|
||
|
|
averagedDown = numpy.zeros([options.res[2]/options.packing[2],
|
||
|
|
options.res[1]/options.packing[1],
|
||
|
|
options.res[0]/options.packing[0],
|
||
|
|
len(headers)])
|
||
|
|
|
||
|
|
idx = 0
|
||
|
|
for line in {True : data,
|
||
|
|
False : file['input']}[options.memory]:
|
||
|
|
items = numpy.array(map(float,line.split()[:len(headers)]))
|
||
|
|
if len(items) < len(headers):
|
||
|
|
continue
|
||
|
|
|
||
|
|
loc = location(idx,options.res)//options.packing
|
||
|
|
averagedDown[loc[2],loc[1],loc[0],:] += items
|
||
|
|
|
||
|
|
idx += 1
|
||
|
|
|
||
|
|
averagedDown /= options.packing[0]*options.packing[1]*options.packing[2]
|
||
|
|
for z in range(options.res[2]/options.packing[2]):
|
||
|
|
for y in range(options.res[1]/options.packing[1]):
|
||
|
|
for x in range(options.res[0]/options.packing[0]):
|
||
|
|
output += '\t'.join(map(str,averagedDown[z,y,x,:])) + '\n'
|
||
|
|
|
||
|
|
file['input'].close()
|
||
|
|
|
||
|
|
# ------------------------------------------ output result ---------------------------------------
|
||
|
|
|
||
|
|
file['output'].write(output)
|
||
|
|
|
||
|
|
if file['name'] != 'STDIN':
|
||
|
|
file['output'].close
|