new script: Add data in column(s) of second ASCIItable selected from row that is given by the value in a mapping column
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Philip Eisenlohr
parent
63c1a0a212
commit
59e8cd1d7e
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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,damask
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from optparse import OptionParser, Option
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scriptID = '$Id: addNorm.py 3167 2014-06-06 09:43:28Z p.eisenlohr $'
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scriptName = scriptID.split()[1]
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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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# --------------------------------------------------------------------
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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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Add data in column(s) of second ASCIItable selected from row that is given by the value in a mapping column.
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""" + string.replace(scriptID,'\n','\\n')
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)
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parser.add_option('-a','--asciitable', dest='asciitable', type='string', metavar='FILE',
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help='heading of column containing row mapping')
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parser.add_option('-c','--map', dest='map', type='string', metavar='LABEL',
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help='heading of column containing row mapping')
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parser.add_option('-o','--offset', dest='offset', type='int', metavar='n',
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help='offset between mapped column value and row')
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parser.add_option('-v','--vector', dest='vector', action='extend', type='string', metavar='LABEL',
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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', metavar='LABEL',
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help='heading of columns containing tensor field values')
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parser.add_option('-s','--special', dest='special', action='extend', type='string', metavar='LABEL',
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help='heading of columns containing field values of special dimension')
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parser.add_option('-d','--dimension', dest='N', action='store', type='int', \
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help='dimension of special field values [%default]')
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parser.set_defaults(vector = [])
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parser.set_defaults(tensor = [])
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parser.set_defaults(special = [])
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parser.set_defaults(offset = 0)
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parser.set_defaults(N = 1)
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(options,filenames) = parser.parse_args()
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if len(options.vector) + len(options.tensor) + len(options.special) == 0:
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parser.error('no data column specified...')
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datainfo = { # list of requested labels per datatype
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'vector': {'len':3,
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'label':[]},
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'tensor': {'len':9,
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'label':[]},
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'special': {'len':options.N,
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'label':[]},
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}
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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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if options.special != None: datainfo['special']['label'] += options.special
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if options.asciitable != None and os.path.isfile(options.asciitable):
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mappedTable = damask.ASCIItable(open(options.asciitable),open(options.asciitable),False)
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mappedTable.head_read() # read ASCII header info of mapped table
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labels = []
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indices = []
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for datatype,info in datainfo.items():
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for label in info['label']:
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foundIt = False
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for key in ['1_'+label,label]:
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if key in mappedTable.labels:
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foundIt = True
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labels.append(label) # extend labels
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indices += range(mappedTable.labels.index(key),
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mappedTable.labels.index(key)+datainfo[datatype]['len'])
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if not foundIt:
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file['croak'].write('column %s not found...\n'%label)
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break
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mappedTable.data_readArray(indices)
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mappedTable.input_close() # close mapped input ASCII table
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mappedTable.output_close() # close mapped output (same as input) ASCII table
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sys.stderr.write('%s\n'%(mappedTable.data))
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else:
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parser.error("Missing mapped ASCIItable")
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if options.map == None:
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parser.error("Missing mapping column")
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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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#--- 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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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(scriptID,'\n','\\n') + '\t' + ' '.join(sys.argv[1:]))
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# --------------- figure out columns to process
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if options.map not in table.labels:
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continue
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mappedColumn = table.labels.index(options.map)
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for label in labels:
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table.labels_append(label) # extend ASCII header of current table with new labels
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# ------------------------------------------ assemble header ---------------------------------------
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table.head_write()
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# ------------------------------------------ process data ---------------------------------------
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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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# file['croak'].write('%i\n'%(int(table.data[mappedColumn])+options.offset-1))
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table.data_append(mappedTable.data[int(table.data[mappedColumn])+options.offset-1]) # add all mapped data types
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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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table.input_close() # close input ASCII table
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if file['name'] != 'STDIN':
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table.output_close() # close output ASCII table
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os.rename(file['name']+'_tmp',file['name']) # overwrite old one with tmp new
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