DAMASK_EICMD/processing/post/averageDown.py

162 lines
7.0 KiB
Python
Executable File

#!/usr/bin/env python
import os,re,sys,math,string,numpy,damask
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('-c','--coordinates', dest='coords', type='string',\
help='column heading for coordinates [%default]')
parser.add_option('-p','--packing', dest='packing', type='int', nargs=3, \
help='dimension of packed group %default')
parser.add_option('-s','--shift', dest='shift', type='int', nargs=3, \
help='shift vector of packing stencil %default')
parser.set_defaults(coords = 'ip')
parser.set_defaults(packing = [2,2,2])
parser.set_defaults(shift = [0,0,0])
(options,filenames) = parser.parse_args()
if len(options.packing) < 3:
parser.error('packing needs three parameters...')
if len(options.shift) < 3:
parser.error('shift needs three parameters...')
options.packing = numpy.array(options.packing)
options.shift = numpy.array(options.shift)
prefix = 'averagedDown%ix%ix%i'%(options.packing[0],options.packing[1],options.packing[2])
if numpy.any(options.shift != 0):
prefix += '_shift%+i%+i%+i'%(options.shift[0],options.shift[1],options.shift[2])
# ------------------------------------------ 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):
files.append({'name':name, 'input':open(name), 'output':open(prefix+'_'+name,'w')})
# ------------------------------------------ loop over input files ---------------------------------------
for file in files:
if file['name'] != 'STDIN': print file['name'],
table = damask.ASCIItable(file['input'],file['output'],False) # make unbuffered ASCII_table
table.head_read() # read ASCII header info
table.info_append(string.replace('$Id$','\n','\\n') + \
'\t' + ' '.join(sys.argv[1:]))
try:
locationCol = table.labels.index('%s.x'%options.coords) # columns containing location data
except ValueError:
print 'no coordinate data found...'
continue
grid = [{},{},{}]
while table.data_read(): # read next data line of ASCII table
for j in xrange(3):
grid[j][str(table.data[locationCol+j])] = True # remember coordinate along x,y,z
resolution = numpy.array([len(grid[0]),\
len(grid[1]),\
len(grid[2]),],'i') # resolution is number of distinct coordinates found
dimension = resolution/numpy.maximum(numpy.ones(3,'d'),resolution-1.0)* \
numpy.array([max(map(float,grid[0].keys()))-min(map(float,grid[0].keys())),\
max(map(float,grid[1].keys()))-min(map(float,grid[1].keys())),\
max(map(float,grid[2].keys()))-min(map(float,grid[2].keys())),\
],'d') # dimension from bounding box, corrected for cell-centeredness
if resolution[2] == 1:
options.packing[2] = 1
options.shift[2] = 0
dimension[2] = min(dimension[:2]/resolution[:2])
downSized = numpy.maximum(numpy.ones(3,'i'),resolution//options.packing)
print '\t%s @ %s --> %s'%(dimension,resolution,downSized)
# ------------------------------------------ assemble header ---------------------------------------
table.head_write()
# ------------------------------------------ process data ---------------------------------------
table.data_rewind()
averagedDown = numpy.zeros(downSized.tolist()+[len(table.labels)])
for z in xrange(-options.shift[2],-options.shift[2]+resolution[2]):
for y in xrange(-options.shift[1],-options.shift[1]+resolution[1]):
for x in xrange(-options.shift[0],-options.shift[0]+resolution[0]):
table.data_read()
data = numpy.array(table.data_asFloat(),'d') # convert to numpy array
me = numpy.array((x,y,z),'i') # my location as array
data[locationCol:locationCol+3] -= dimension*(me//resolution) # shift coordinates if periodic image
(a,b,c) = (me%resolution)//options.packing # bin to condense my location into
averagedDown[a,b,c,:] += data # store the (coord-updated) data there
averagedDown /= options.packing.prod() # normalize data by element count
for c in xrange(downSized[2]):
for b in xrange(downSized[1]):
for a in xrange(downSized[0]):
table.data = averagedDown[a,b,c,:].tolist()
table.data_write() # output processed line
# ------------------------------------------ output result ---------------------------------------
table.output_flush() # just in case of buffered ASCII table
# ------------------------------------------ close file handles ---------------------------------------
for file in files:
file['input'].close() # close input ASCII table
if file['name'] != 'STDIN':
file['output'].close # close output ASCII table