DAMASK_EICMD/processing/post/addMapped.py

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#!/usr/bin/env python
# -*- coding: UTF-8 no BOM -*-
import os,sys,string
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from optparse import OptionParser
import damask
scriptID = string.replace('$Id$','\n','\\n')
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scriptName = os.path.splitext(scriptID.split()[1])[0]
# --------------------------------------------------------------------
# MAIN
# --------------------------------------------------------------------
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parser = OptionParser(option_class=damask.extendableOption, usage='%prog options [file[s]]', description = """
Add data in column(s) of second ASCIItable selected from row that is given by the value in a mapping column.
""", version = scriptID)
parser.add_option('-c','--map',
dest = 'map',
type = 'string', metavar = 'string',
help = 'heading of column containing row mapping')
parser.add_option('-o','--offset',
dest = 'offset',
type = 'int', metavar = 'int',
help = 'offset between mapping column value and actual row in mapped table [%default]')
parser.add_option('-l','--label',
dest = 'label',
action = 'extend', metavar = '<string LIST>',
help='heading of column(s) to be mapped')
parser.add_option('-a','--asciitable',
dest = 'asciitable',
type = 'string', metavar = 'string',
help = 'mapped ASCIItable')
parser.set_defaults(offset = 0,
)
(options,filenames) = parser.parse_args()
if options.label == None:
parser.error('no data columns specified.')
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if options.map == None:
parser.error('no mapping column given.')
# ------------------------------------------ process mapping ASCIItable ---------------------------
if options.asciitable != None and os.path.isfile(options.asciitable):
mappedTable = damask.ASCIItable(name = options.asciitable,buffered = False, readonly = True)
mappedTable.head_read() # read ASCII header info of mapped table
missing_labels = mappedTable.data_readArray(options.label)
if len(missing_labels) > 0:
mappedTable.croak('column{} {} not found...'.format('s' if len(missing_labels) > 1 else '',', '.join(missing_labels)))
else:
parser.error('no mapped ASCIItable given.')
# --- loop over input files -------------------------------------------------------------------------
if filenames == []: filenames = ['STDIN']
for name in filenames:
if not (name == 'STDIN' or os.path.exists(name)): continue
table = damask.ASCIItable(name = name, outname = name+'_tmp',
buffered = False)
table.croak('\033[1m'+scriptName+'\033[0m'+(': '+name if name != 'STDIN' else ''))
# ------------------------------------------ read header ------------------------------------------
table.head_read()
# ------------------------------------------ sanity checks ----------------------------------------
errors = []
mappedColumn = table.label_index(options.map)
if mappedColumn < 0: errors.append('mapping column {} not found.'.format(options.map))
if errors != []:
table.croak(errors)
table.close(dismiss = True)
continue
# ------------------------------------------ assemble header --------------------------------------
table.info_append(scriptID + '\t' + ' '.join(sys.argv[1:]))
table.labels_append(mappedTable.labels) # extend ASCII header with new labels
table.head_write()
# ------------------------------------------ process data ------------------------------------------
outputAlive = True
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while outputAlive and table.data_read(): # read next data line of ASCII table
table.data_append(mappedTable.data[int(table.data[mappedColumn])+options.offset-1]) # add all mapped data types
outputAlive = table.data_write() # output processed line
# ------------------------------------------ output finalization -----------------------------------
table.close() # close ASCII tables
if name != 'STDIN': os.rename(name+'_tmp',name) # overwrite old one with tmp new
mappedTable.close() # close mapped input ASCII table