improved file handling etc. to follow newest style
This commit is contained in:
parent
11a4b59c69
commit
2f0ecdf7e8
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@ -3,6 +3,7 @@
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import os,re,sys,math,string
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import numpy as np
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from collections import defaultdict
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from optparse import OptionParser
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import damask
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@ -18,10 +19,9 @@ Add column(s) containing curl of requested column(s).
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Operates on periodic ordered three-dimensional data sets.
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Deals with both vector- and tensor-valued fields.
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""", version=string.replace('$Id$','\n','\\n')
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""", version = string.replace(scriptID,'\n','\\n')
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)
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parser.add_option('-c','--coordinates', dest='coords', type='string', metavar='string', \
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help='column heading for coordinates [%default]')
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parser.add_option('-v','--vector', dest='vector', action='extend', type='string', metavar='<string LIST>', \
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@ -49,19 +49,15 @@ if options.tensor != None: datainfo['tensor']['label'] += options.tensor
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# ------------------------------------------ setup file handles ------------------------------------
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files = []
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if filenames == []:
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files.append({'name':'STDIN', 'input':sys.stdin, 'output':sys.stdout, 'croak':sys.stderr})
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else:
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for name in filenames:
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if os.path.exists(name):
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files.append({'name':name, 'input':open(name), 'output':open(name+'_tmp','w'), 'croak':sys.stderr})
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for name in filenames:
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if os.path.exists(name):
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files.append({'name':name, 'input':open(name), 'output':open(name+'_tmp','w'), 'croak':sys.stderr})
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#--- loop over input files ------------------------------------------------------------------------
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for file in files:
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if file['name'] != 'STDIN': file['croak'].write('\033[1m'+scriptName+'\033[0m: '+file['name']+'\n')
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else: file['croak'].write('\033[1m'+scriptName+'\033[0m\n')
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file['croak'].write('\033[1m'+scriptName+'\033[0m: '+file['name']+'\n')
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table = damask.ASCIItable(file['input'],file['output'],False) # make unbuffered ASCII_table
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table = damask.ASCIItable(file['input'],file['output'],True) # make unbuffered ASCII_table
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table.head_read() # read ASCII header info
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table.info_append(string.replace(scriptID,'\n','\\n') + '\t' + ' '.join(sys.argv[1:]))
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@ -73,29 +69,27 @@ for file in files:
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continue
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grid = [{},{},{}]
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while table.data_read(): # read next data line of ASCII table
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while table.data_read(): # read next data line of ASCII table
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for j in xrange(3):
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grid[j][str(table.data[locationCol+j])] = True # remember coordinate along x,y,z
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grid[j][str(table.data[locationCol+j])] = True # remember coordinate along x,y,z
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resolution = np.array([len(grid[0]),\
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len(grid[1]),\
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len(grid[2]),],'i') # resolution is number of distinct coordinates found
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len(grid[1]),\
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len(grid[2]),],'i') # resolution is number of distinct coordinates found
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dimension = resolution/np.maximum(np.ones(3,'d'),resolution-1.0)* \
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np.array([max(map(float,grid[0].keys()))-min(map(float,grid[0].keys())),\
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max(map(float,grid[1].keys()))-min(map(float,grid[1].keys())),\
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max(map(float,grid[2].keys()))-min(map(float,grid[2].keys())),\
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],'d') # dimension from bounding box, corrected for cell-centeredness
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max(map(float,grid[1].keys()))-min(map(float,grid[1].keys())),\
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max(map(float,grid[2].keys()))-min(map(float,grid[2].keys())),\
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],'d') # dimension from bounding box, corrected for cell-centeredness
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if resolution[2] == 1:
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dimension[2] = min(dimension[:2]/resolution[:2])
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N = resolution.prod()
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# --------------- figure out columns to process
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active = {}
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column = {}
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values = {}
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curl = {}
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head = []
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# --------------- figure out columns to process --------------------------------------------------
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active = defaultdict(list)
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column = defaultdict(dict)
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values = defaultdict(dict)
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curl = defaultdict(dict)
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missingColumns = False
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for datatype,info in datainfo.items():
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for label in info['label']:
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@ -104,28 +98,28 @@ for file in files:
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if key not in table.labels:
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sys.stderr.write('column %s not found...\n'%key)
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else:
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if datatype not in active: active[datatype] = []
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if datatype not in column: column[datatype] = {}
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if datatype not in values: values[datatype] = {}
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if datatype not in curl: curl[datatype] = {}
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active[datatype].append(label)
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column[datatype][label] = table.labels.index(key) # remember columns of requested data
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values[datatype][label] = np.array([0.0 for i in xrange(N*datainfo[datatype]['len'])]).\
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reshape(list(resolution)+[datainfo[datatype]['len']//3,3])
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curl[datatype][label] = np.array([0.0 for i in xrange(N*datainfo[datatype]['len'])]).\
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reshape(list(resolution)+[datainfo[datatype]['len']//3,3])
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table.labels_append(['%i_curlFFT(%s)'%(i+1,label)
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for i in xrange(datainfo[datatype]['len'])]) # extend ASCII header with new labels
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if missingColumns:
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continue
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# ------------------------------------------ assemble header ---------------------------------------
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for datatype,info in datainfo.items():
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for label in info['label']:
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table.labels_append(['%i_curlFFT(%s)'%(i+1,label)
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for i in xrange(datainfo[datatype]['len'])]) # extend ASCII header with new labels
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table.head_write()
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# ------------------------------------------ read value field --------------------------------------
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table.data_rewind()
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idx = 0
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while table.data_read(): # read next data line of ASCII table
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(x,y,z) = damask.gridLocation(idx,resolution) # figure out (x,y,z) position from line count
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(x,y,z) = damask.util.gridLocation(idx,resolution) # figure out (x,y,z) position from line count
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idx += 1
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for datatype,labels in active.items(): # loop over vector,tensor
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for label in labels: # loop over all requested curls
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@ -141,10 +135,10 @@ for file in files:
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# ------------------------------------------ process data ---------------------------------------
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table.data_rewind()
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outputAlive = True
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idx = 0
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outputAlive = True
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while outputAlive and table.data_read(): # read next data line of ASCII table
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(x,y,z) = damask.gridLocation(idx,resolution) # figure out (x,y,z) position from line count
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(x,y,z) = damask.util.gridLocation(idx,resolution) # figure out (x,y,z) position from line count
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idx += 1
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for datatype,labels in active.items(): # loop over vector,tensor
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for label in labels: # loop over all requested norms
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@ -152,11 +146,9 @@ for file in files:
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outputAlive = table.data_write() # output processed line
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# ------------------------------------------ output result ---------------------------------------
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outputAlive and table.output_flush() # just in case of buffered ASCII table
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file['input'].close() # close input ASCII table (works for stdin)
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file['output'].close() # close output ASCII table (works for stdout)
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if file['name'] != 'STDIN':
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os.rename(file['name']+'_tmp',file['name']) # overwrite old one with tmp new
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os.rename(file['name']+'_tmp',file['name']) # overwrite old one with tmp new
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@ -1,64 +1,38 @@
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#!/usr/bin/env python
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# -*- coding: UTF-8 no BOM -*-
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import os,re,sys,math,string,numpy,damask
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from optparse import OptionParser, Option
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# -----------------------------
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class extendableOption(Option):
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# -----------------------------
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# used for definition of new option parser action 'extend', which enables to take multiple option arguments
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# taken from online tutorial http://docs.python.org/library/optparse.html
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ACTIONS = Option.ACTIONS + ("extend",)
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STORE_ACTIONS = Option.STORE_ACTIONS + ("extend",)
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TYPED_ACTIONS = Option.TYPED_ACTIONS + ("extend",)
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ALWAYS_TYPED_ACTIONS = Option.ALWAYS_TYPED_ACTIONS + ("extend",)
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def take_action(self, action, dest, opt, value, values, parser):
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if action == "extend":
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lvalue = value.split(",")
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values.ensure_value(dest, []).extend(lvalue)
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else:
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Option.take_action(self, action, dest, opt, value, values, parser)
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def location(idx,res):
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return ( idx % res[0], \
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( idx // res[0]) % res[1], \
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( idx // res[0] // res[1]) % res[2] )
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def index(location,res):
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return ( location[0] % res[0] + \
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( location[1] % res[1]) * res[0] + \
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( location[2] % res[2]) * res[1] * res[0] )
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import os,re,sys,math,string
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import numpy as np
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from collections import defaultdict
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from optparse import OptionParser
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import damask
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scriptID = '$Id$'
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scriptName = scriptID.split()[1]
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accuracyChoices = ['2','4','6','8']
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# --------------------------------------------------------------------
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# MAIN
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# --------------------------------------------------------------------
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parser = OptionParser(option_class=extendableOption, usage='%prog options [file[s]]', description = """
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parser = OptionParser(option_class=damask.extendableOption, usage='%prog options [file[s]]', description = """
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Add column(s) containing divergence of requested column(s).
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Operates on periodic ordered three-dimensional data sets.
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Deals with both vector- and tensor-valued fields.
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""" + string.replace('$Id$','\n','\\n')
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""", version = string.replace(scriptID,'\n','\\n')
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)
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accuracyChoices = ['2','4','6','8']
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parser.add_option('--fdm', dest='accuracy', action='extend', type='string', \
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parser.add_option('--fdm', dest='accuracy', action='extend', type='string', metavar='<int LIST>', \
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help='degree of central difference accuracy (%s)'%(','.join(accuracyChoices)))
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parser.add_option('--fft', dest='fft', action='store_true', \
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help='calculate divergence in Fourier space')
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parser.add_option('-c','--coordinates', dest='coords', type='string',\
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parser.add_option('-c','--coordinates', dest='coords', type='string', metavar = 'string', \
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help='column heading for coordinates [%default]')
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parser.add_option('-v','--vector', dest='vector', action='extend', type='string', \
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parser.add_option('-v','--vector', dest='vector', action='extend', type='string', metavar='<string LIST>', \
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help='heading of columns containing vector field values')
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parser.add_option('-t','--tensor', dest='tensor', action='extend', type='string', \
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parser.add_option('-t','--tensor', dest='tensor', action='extend', type='string', metavar='<string LIST>', \
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help='heading of columns containing tensor field values')
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parser.set_defaults(coords = 'ip')
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parser.set_defaults(accuracy = [])
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parser.set_defaults(fft = False)
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@ -87,60 +61,49 @@ datainfo = { # lis
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if options.vector != None: datainfo['vector']['label'] += options.vector
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if options.tensor != None: datainfo['tensor']['label'] += options.tensor
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# ------------------------------------------ setup file handles ---------------------------------------
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# ------------------------------------------ setup file handles ------------------------------------
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files = []
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if filenames == []:
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files.append({'name':'STDIN', 'input':sys.stdin, 'output':sys.stdout})
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else:
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for name in filenames:
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if os.path.exists(name):
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files.append({'name':name, 'input':open(name), 'output':open(name+'_tmp','w')})
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# ------------------------------------------ loop over input files ---------------------------------------
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for name in filenames:
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if os.path.exists(name):
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files.append({'name':name, 'input':open(name), 'output':open(name+'_tmp','w'), 'croak':sys.stderr})
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#--- loop over input files ------------------------------------------------------------------------
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for file in files:
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if file['name'] != 'STDIN': print file['name'],
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file['croak'].write('\033[1m'+scriptName+'\033[0m: '+file['name']+'\n')
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table = damask.ASCIItable(file['input'],file['output'],False) # make unbuffered ASCII_table
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table.head_read() # read ASCII header info
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table.info_append(string.replace('$Id$','\n','\\n') + \
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'\t' + ' '.join(sys.argv[1:]))
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table = damask.ASCIItable(file['input'],file['output'],True) # make unbuffered ASCII_table
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table.head_read() # read ASCII header info
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table.info_append(string.replace(scriptID,'\n','\\n') + '\t' + ' '.join(sys.argv[1:]))
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# --------------- figure out dimension and resolution
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# --------------- figure out dimension and resolution ----------------------------------------------
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try:
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locationCol = table.labels.index('%s.x'%options.coords) # columns containing location data
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locationCol = table.labels.index('%s.x'%options.coords) # columns containing location data
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except ValueError:
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print 'no coordinate data found...'
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file['croak'].write('no coordinate data found...\n'%key)
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continue
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grid = [{},{},{}]
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while table.data_read(): # read next data line of ASCII table
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while table.data_read(): # read next data line of ASCII table
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for j in xrange(3):
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grid[j][str(table.data[locationCol+j])] = True # remember coordinate along x,y,z
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resolution = numpy.array([len(grid[0]),\
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len(grid[1]),\
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len(grid[2]),],'i') # resolution is number of distinct coordinates found
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dimension = resolution/numpy.maximum(numpy.ones(3,'d'),resolution-1.0)* \
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numpy.array([max(map(float,grid[0].keys()))-min(map(float,grid[0].keys())),\
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max(map(float,grid[1].keys()))-min(map(float,grid[1].keys())),\
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max(map(float,grid[2].keys()))-min(map(float,grid[2].keys())),\
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],'d') # dimension from bounding box, corrected for cell-centeredness
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grid[j][str(table.data[locationCol+j])] = True # remember coordinate along x,y,z
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resolution = np.array([len(grid[0]),\
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len(grid[1]),\
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len(grid[2]),],'i') # resolution is number of distinct coordinates found
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dimension = resolution/np.maximum(np.ones(3,'d'),resolution-1.0)* \
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np.array([max(map(float,grid[0].keys()))-min(map(float,grid[0].keys())),\
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max(map(float,grid[1].keys()))-min(map(float,grid[1].keys())),\
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max(map(float,grid[2].keys()))-min(map(float,grid[2].keys())),\
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],'d') # dimension from bounding box, corrected for cell-centeredness
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if resolution[2] == 1:
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dimension[2] = min(dimension[:2]/resolution[:2])
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N = resolution.prod()
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print '\t%s @ %s'%(dimension,resolution)
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# --------------- figure out columns to process
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active = {}
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column = {}
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values = {}
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divergence = {}
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head = []
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# --------------- figure out columns to process --------------------------------------------------
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active = defaultdict(list)
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column = defaultdict(dict)
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values = defaultdict(dict)
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divergence = defaultdict(dict)
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missingColumns = False
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for datatype,info in datainfo.items():
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for label in info['label']:
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@ -149,71 +112,67 @@ for file in files:
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if key not in table.labels:
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sys.stderr.write('column %s not found...\n'%key)
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else:
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if datatype not in active: active[datatype] = []
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if datatype not in column: column[datatype] = {}
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if datatype not in values: values[datatype] = {}
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if datatype not in divergence: divergence[datatype] = {}
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if label not in divergence[datatype]: divergence[datatype][label] = {}
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active[datatype].append(label)
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column[datatype][label] = table.labels.index(key) # remember columns of requested data
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values[datatype][label] = numpy.array([0.0 for i in xrange(N*datainfo[datatype]['len'])]).\
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column[datatype][label] = table.labels.index(key) # remember columns of requested data
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values[datatype][label] = np.array([0.0 for i in xrange(N*datainfo[datatype]['len'])]).\
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reshape(list(resolution)+[datainfo[datatype]['len']//3,3])
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if label not in divergence[datatype]: divergence[datatype][label] = {}
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for accuracy in options.accuracy:
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divergence[datatype][label][accuracy] = numpy.array([0.0 for i in xrange(N*datainfo[datatype]['len']//3)]).\
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divergence[datatype][label][accuracy] = np.array([0.0 for i in xrange(N*datainfo[datatype]['len']//3)]).\
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reshape(list(resolution)+[datainfo[datatype]['len']//3])
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if datatype == 'vector': # extend ASCII header with new labels
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table.labels_append(['div%s(%s)'%(accuracy,label)])
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if datatype == 'tensor':
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table.labels_append(['%i_div%s(%s)'%(i+1,accuracy,label) for i in xrange(3)])
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if missingColumns:
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continue
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# ------------------------------------------ assemble header ---------------------------------------
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for datatype,info in datainfo.items():
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for label in info['label']:
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for accuracy in options.accuracy:
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if datatype == 'vector': # extend ASCII header with new labels
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table.labels_append(['div%s(%s)'%(accuracy,label)])
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if datatype == 'tensor':
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table.labels_append(['%i_div%s(%s)'%(i+1,accuracy,label) for i in xrange(3)])
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table.head_write()
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# ------------------------------------------ read value field ---------------------------------------
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# ------------------------------------------ read value field --------------------------------------
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table.data_rewind()
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idx = 0
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while table.data_read(): # read next data line of ASCII table
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(x,y,z) = location(idx,resolution) # figure out (x,y,z) position from line count
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while table.data_read(): # read next data line of ASCII table
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(x,y,z) = damask.util.gridLocation(idx,resolution) # figure out (x,y,z) position from line count
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idx += 1
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for datatype,labels in active.items(): # loop over vector,tensor
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for label in labels: # loop over all requested curls
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values[datatype][label][x,y,z] = numpy.array(
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map(float,table.data[column[datatype][label]:
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column[datatype][label]+datainfo[datatype]['len']]),'d').reshape(datainfo[datatype]['len']//3,3)
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# ------------------------------------------ process value field ---------------------------------------
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for datatype,labels in active.items(): # loop over vector,tensor
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for label in labels: # loop over all requested curls
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values[datatype][label][x,y,z] = np.array(
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map(float,table.data[column[datatype][label]:
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column[datatype][label]+datainfo[datatype]['len']]),'d') \
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.reshape(datainfo[datatype]['len']//3,3)
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for datatype,labels in active.items(): # loop over vector,tensor
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for label in labels: # loop over all requested divergencies
|
||||
# ------------------------------------------ process value field -----------------------------------
|
||||
for datatype,labels in active.items(): # loop over vector,tensor
|
||||
for label in labels: # loop over all requested divergencies
|
||||
for accuracy in options.accuracy:
|
||||
if accuracy == 'FFT':
|
||||
divergence[datatype][label][accuracy] = damask.core.math.divergenceFFT(dimension,values[datatype][label])
|
||||
else:
|
||||
divergence[datatype][label][accuracy] = damask.core.math.divergenceFDM(dimension,eval(accuracy)//2-1,values[datatype][label])
|
||||
# ------------------------------------------ process data ---------------------------------------
|
||||
|
||||
# ------------------------------------------ process data ---------------------------------------
|
||||
table.data_rewind()
|
||||
idx = 0
|
||||
while table.data_read(): # read next data line of ASCII table
|
||||
(x,y,z) = location(idx,resolution) # figure out (x,y,z) position from line count
|
||||
outputAlive = True
|
||||
while outputAlive and table.data_read(): # read next data line of ASCII table
|
||||
(x,y,z) = damask.util.gridLocation(idx,resolution) # figure out (x,y,z) position from line count
|
||||
idx += 1
|
||||
|
||||
for datatype,labels in active.items(): # loop over vector,tensor
|
||||
for label in labels: # loop over all requested
|
||||
for datatype,labels in active.items(): # loop over vector,tensor
|
||||
for label in labels: # loop over all requested
|
||||
for accuracy in options.accuracy:
|
||||
table.data_append(list(divergence[datatype][label][accuracy][x,y,z].reshape(datainfo[datatype]['len']//3)))
|
||||
|
||||
table.data_write() # output processed line
|
||||
|
||||
outputAlive = table.data_write() # output processed line
|
||||
|
||||
# ------------------------------------------ output result ---------------------------------------
|
||||
outputAlive and table.output_flush() # just in case of buffered ASCII table
|
||||
|
||||
table.output_flush() # just in case of buffered ASCII table
|
||||
|
||||
file['input'].close() # close input ASCII table
|
||||
if file['name'] != 'STDIN':
|
||||
file['output'].close # close output ASCII table
|
||||
os.rename(file['name']+'_tmp',file['name']) # overwrite old one with tmp new
|
||||
file['input'].close() # close input ASCII table (works for stdin)
|
||||
file['output'].close() # close output ASCII table (works for stdout)
|
||||
os.rename(file['name']+'_tmp',file['name']) # overwrite old one with tmp new
|
||||
|
|
Loading…
Reference in New Issue