DAMASK_EICMD/processing/post/addLinked.py

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#!/usr/bin/env python2.7
# -*- coding: UTF-8 no BOM -*-
import os,sys
import numpy as np
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from optparse import OptionParser
import damask
scriptName = os.path.splitext(os.path.basename(__file__))[0]
scriptID = ' '.join([scriptName,damask.version])
# --------------------------------------------------------------------
# MAIN
# --------------------------------------------------------------------
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parser = OptionParser(option_class=damask.extendableOption, usage='%prog options [file[s]]', description = """
Add data of selected column(s) from (first) row of second ASCIItable that shares the linking column value.
""", version = scriptID)
parser.add_option('--link',
dest = 'link', nargs = 2,
type = 'string', metavar = 'string string',
help = 'column labels containing linked values')
parser.add_option('-l','--label',
dest = 'label',
action = 'extend', metavar = '<string LIST>',
help = 'column label(s) to be appended')
parser.add_option('-a','--asciitable',
dest = 'asciitable',
type = 'string', metavar = 'string',
help = 'linked ASCIItable')
parser.set_defaults()
(options,filenames) = parser.parse_args()
if options.label is None:
parser.error('no data columns specified.')
if options.link is None:
parser.error('no linking columns given.')
# -------------------------------------- process linked ASCIItable --------------------------------
if options.asciitable is not None and os.path.isfile(options.asciitable):
linkedTable = damask.ASCIItable(name = options.asciitable,
buffered = False,
readonly = True)
linkedTable.head_read() # read ASCII header info of linked table
if linkedTable.label_dimension(options.link[1]) != 1:
parser.error('linking column {} needs to be scalar valued.'.format(options.link[1]))
missing_labels = linkedTable.data_readArray([options.link[1]]+options.label)
linkedTable.close() # close linked ASCII table
if len(missing_labels) > 0:
damask.util.croak('column{} {} not found...'.format('s' if len(missing_labels) > 1 else '',', '.join(missing_labels)))
index = linkedTable.data[:,0]
data = linkedTable.data[:,1:]
else:
parser.error('no linked ASCIItable given.')
# --- loop over input files -----------------------------------------------------------------------
if filenames == []: filenames = [None]
for name in filenames:
try: table = damask.ASCIItable(name = name,
buffered = False)
except: continue
damask.util.report(scriptName,name)
# ------------------------------------------ read header ------------------------------------------
table.head_read()
# ------------------------------------------ sanity checks ----------------------------------------
errors = []
linkColumn = table.label_index(options.link[0])
if linkColumn < 0: errors.append('linking column {} not found.'.format(options.link[0]))
if errors != []:
damask.util.croak(errors)
table.close(dismiss = True)
continue
# ------------------------------------------ assemble header --------------------------------------
table.info_append(scriptID + '\t' + ' '.join(sys.argv[1:]))
table.labels_append(linkedTable.labels(raw = True)[1:]) # extend with new labels (except for linked column)
table.head_write()
# ------------------------------------------ process data ------------------------------------------
outputAlive = True
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while outputAlive and table.data_read(): # read next data line of ASCII table
try:
table.data_append(data[np.argwhere(index == float(table.data[linkColumn]))[0]]) # add data from first matching line
except IndexError:
table.data_append(np.nan*np.ones_like(data[0])) # or add NaNs
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outputAlive = table.data_write() # output processed line
# ------------------------------------------ output finalization -----------------------------------
table.close() # close ASCII tables