diff --git a/processing/post/blowUp.py b/processing/post/blowUp.py new file mode 100755 index 000000000..49b12ed08 --- /dev/null +++ b/processing/post/blowUp.py @@ -0,0 +1,169 @@ +#!/usr/bin/env python + +import os,re,sys,math,string,numpy,damask,time +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: averageDown.py 1857 2012-10-31 10:06:11Z MPIE\m.diehl $','\n','\\n') +) + +parser.add_option('-c','--coordinates', dest='coords', type='string',\ + help='column heading for coordinates [%default]') +parser.add_option('-p','--packing', dest='packing', type='int', nargs=3, \ + help='dimension of packed group %default') +parser.add_option('-r','--resolution', dest='resolution', type='int', nargs=3, \ + help='resolution in x,y,z [autodetect]') +parser.add_option('-d','--dimension', dest='dimension', type='float', nargs=3, \ + help='dimension in x,y,z [autodetect]') +parser.set_defaults(coords = 'ip') +parser.set_defaults(packing = [2,2,2]) +parser.set_defaults(resolution = [0,0,0]) +parser.set_defaults(dimension = [0.0,0.0,0.0]) + +(options,filenames) = parser.parse_args() + +if len(options.packing) < 3: + parser.error('packing needs three parameters...') + +options.packing = numpy.array(options.packing) + +prefix = 'blowUp%ix%ix%i_'%(options.packing[0],options.packing[1],options.packing[2]) + +# ------------------------------------------ setup file handles --------------------------------------- + +files = [] +if filenames == []: + files.append({'name':'STDIN', 'input':sys.stdin, 'output':sys.stdout}) +else: + for name in filenames: + name = os.path.relpath(name) + if os.path.exists(name): + files.append({'name':name, 'input':open(name), + 'output':open(os.path.join(os.path.dirname(name),prefix+os.path.basename(name)),'w')}) + + +# ------------------------------------------ loop over input files --------------------------------------- + +for file in files: + if file['name'] != 'STDIN': print file['name'], + + table = damask.ASCIItable(file['input'],file['output'],False) # make unbuffered ASCII_table + table.head_read() # read ASCII header info + table.info_append(string.replace('$Id: averageDown.py 1857 2012-10-31 10:06:11Z MPIE\m.diehl $','\n','\\n') + \ + '\t' + ' '.join(sys.argv[1:])) + + + try: + locationCol = table.labels.index('%s.x'%options.coords) # columns containing location data + elemCol = table.labels.index('elem') # columns containing location data + except ValueError: + print 'no coordinate data or element data found...' + continue + + if (any(options.resolution)==0 or any(options.dimension)==0.0): + 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 + else: + resolution = numpy.array(options.resolution,'i') + dimension = numpy.array(options.dimension,'d') + + if resolution[2] == 1: + options.packing[2] = 1 + dimension[2] = min(dimension[:2]/resolution[:2]) # z spacing equal to smaller of x or y spacing + + packing = numpy.array(options.packing,'i') + outSize = resolution*packing + + print '\t%s @ %s --> %s'%(dimension,resolution,outSize) + +# ------------------------------------------ assemble header --------------------------------------- + + table.head_write() + +# ------------------------------------------ process data --------------------------------------- + table.data_rewind() + data = numpy.zeros(outSize.tolist()+[len(table.labels)]) + p = numpy.zeros(3,'i') + + for p[2] in xrange(resolution[2]): + for p[1] in xrange(resolution[1]): + for p[0] in xrange(resolution[0]): + d = p*packing + table.data_read() + data[d[0]:d[0]+packing[0], + d[1]:d[1]+packing[1], + d[2]:d[2]+packing[2], + : ] = numpy.tile(numpy.array(table.data_asFloat(),'d'),packing.tolist()+[1]) # tile to match blowUp voxel size + + elementSize = dimension/resolution/packing + elem = 1 + for c in xrange(outSize[2]): + for b in xrange(outSize[1]): + for a in xrange(outSize[0]): + data[a,b,c,locationCol:locationCol+3] = [a+0.5,b+0.5,c+0.5]*elementSize + data[a,b,c,elemCol] = elem + table.data = data[a,b,c,:].tolist() + table.data_write() # output processed line + elem += 1 + + +# ------------------------------------------ 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 diff --git a/processing/post/stddevDown.py b/processing/post/stddevDown.py new file mode 100755 index 000000000..8fc5f8d83 --- /dev/null +++ b/processing/post/stddevDown.py @@ -0,0 +1,192 @@ +#!/usr/bin/env python + +import os,re,sys,math,string,numpy,damask,time +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: averageDown.py 1857 2012-10-31 10:06:11Z MPIE\m.diehl $','\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.add_option('-r','--resolution', dest='resolution', type='int', nargs=3, \ + help='resolution in x,y,z [autodetect]') +parser.add_option('-d','--dimension', dest='dimension', type='float', nargs=3, \ + help='dimension in x,y,z [autodetect]') +parser.set_defaults(coords = 'ip') +parser.set_defaults(packing = [2,2,2]) +parser.set_defaults(shift = [0,0,0]) +parser.set_defaults(resolution = [0,0,0]) +parser.set_defaults(dimension = [0.0,0.0,0.0]) + +(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 = 'stddevDown%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: + name = os.path.relpath(name) + if os.path.exists(name): + files.append({'name':name, 'input':open(name), + 'output':open(os.path.join(os.path.dirname(name),prefix+os.path.basename(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: averageDown.py 1857 2012-10-31 10:06:11Z MPIE\m.diehl $','\n','\\n') + \ + '\t' + ' '.join(sys.argv[1:])) + + + try: + locationCol = table.labels.index('%s.x'%options.coords) # columns containing location data + elemCol = table.labels.index('elem') # columns containing location data + except ValueError: + print 'no coordinate data or element data found...' + continue + + if (any(options.resolution)==0 or any(options.dimension)==0.0): + 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 + else: + resolution = numpy.array(options.resolution,'i') + dimension = numpy.array(options.dimension,'d') + + if resolution[2] == 1: + options.packing[2] = 1 + options.shift[2] = 0 + dimension[2] = min(dimension[:2]/resolution[:2]) # z spacing equal to smaller of x or y spacing + + packing = numpy.array(options.packing,'i') + shift = numpy.array(options.shift,'i') + downSized = numpy.maximum(numpy.ones(3,'i'),resolution//packing) + outSize = numpy.ceil(numpy.array(resolution,'d')/numpy.array(packing,'d')) + + print '\t%s @ %s --> %s'%(dimension,resolution,downSized) + +# ------------------------------------------ assemble header --------------------------------------- + + table.head_write() + +# ------------------------------------------ process data --------------------------------------- + + dataavg = numpy.zeros(outSize.tolist()+[len(table.labels)]) + datavar = numpy.zeros(outSize.tolist()+[len(table.labels)]) + p = numpy.zeros(3,'i') + + table.data_rewind() + for p[2] in xrange(resolution[2]): + for p[1] in xrange(resolution[1]): + for p[0] in xrange(resolution[0]): + d = ((p-shift)%resolution)//packing + table.data_read() + dataavg[d[0],d[1],d[2],:] += numpy.array(table.data_asFloat(),'d') # convert to numpy array + + dataavg /= packing.prod() + + table.data_rewind() + for p[2] in xrange(resolution[2]): + for p[1] in xrange(resolution[1]): + for p[0] in xrange(resolution[0]): + d = ((p-shift)%resolution)//packing + table.data_read() + datavar[d[0],d[1],d[2],:] += (numpy.array(table.data_asFloat(),'d') - dataavg[d[0],d[1],d[2],:])**2 + + datavar = numpy.sqrt(datavar/packing.prod()) + + posOffset = (shift+[0.5,0.5,0.5])*dimension/resolution + elementSize = dimension/resolution*packing + elem = 1 + for c in xrange(downSized[2]): + for b in xrange(downSized[1]): + for a in xrange(downSized[0]): + datavar[a,b,c,locationCol:locationCol+3] = posOffset + [a,b,c]*elementSize + datavar[a,b,c,elemCol] = elem + table.data = datavar[a,b,c,:].tolist() + table.data_write() # output processed line + elem += 1 + + +# ------------------------------------------ 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