merged functionality of fillTable (change existing column values) into addCalculation. If labels already exist, they are altered. Otherwise, new columns are appended.
This commit is contained in:
Aritra Chakraborty
parent
1c36380a8a
commit
8e01247597
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@ -1,4 +1,4 @@
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#!/usr/bin/env python2
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#!/usr/bin/env python
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# -*- coding: UTF-8 no BOM -*-
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# -*- coding: UTF-8 no BOM -*-
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import os,re,sys
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import os,re,sys
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@ -10,16 +10,12 @@ import damask
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scriptName = os.path.splitext(os.path.basename(__file__))[0]
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scriptName = os.path.splitext(os.path.basename(__file__))[0]
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scriptID = ' '.join([scriptName,damask.version])
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scriptID = ' '.join([scriptName,damask.version])
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def unravel(item):
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if hasattr(item,'__contains__'): return ' '.join(map(unravel,item))
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else: return str(item)
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# --------------------------------------------------------------------
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# --------------------------------------------------------------------
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# MAIN
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# MAIN
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# --------------------------------------------------------------------
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# --------------------------------------------------------------------
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parser = OptionParser(option_class=damask.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) with derived values according to user-defined arithmetic operation between column(s).
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Add or alter column(s) with derived values according to user-defined arithmetic operation between column(s).
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Column labels are tagged by '#label#' in formulas. Use ';' for ',' in functions.
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Column labels are tagged by '#label#' in formulas. Use ';' for ',' in functions.
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Numpy is available as np.
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Numpy is available as np.
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@ -37,6 +33,13 @@ parser.add_option('-f','--formula',
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action = 'extend', metavar = '<string LIST>',
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action = 'extend', metavar = '<string LIST>',
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help = '(list of) formulas corresponding to labels')
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help = '(list of) formulas corresponding to labels')
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parser.add_option('-c','--condition',
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dest = 'condition', metavar='string',
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help = 'condition to filter rows')
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parser.set_defaults(condition = None,
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)
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(options,filenames) = parser.parse_args()
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(options,filenames) = parser.parse_args()
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if options.labels is None or options.formulas is None:
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if options.labels is None or options.formulas is None:
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@ -53,7 +56,10 @@ if filenames == []: filenames = [None]
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for name in filenames:
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for name in filenames:
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try:
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try:
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table = damask.ASCIItable(name = name, buffered = False)
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table = damask.ASCIItable(name = name,
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buffered = False)
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output = damask.ASCIItable(name = name,
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buffered = False)
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except:
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except:
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continue
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continue
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damask.util.report(scriptName,name)
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damask.util.report(scriptName,name)
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@ -62,14 +68,41 @@ for name in filenames:
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table.head_read()
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table.head_read()
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# ------------------------------------------ build formulae ----------------------------------------
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# -----------------------------------------------------------------------------------------------------
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specials = { \
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specials = { \
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'_row_': 0,
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'_row_': 0,
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}
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}
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# ------------------------------------------ Evaluate condition ---------------------------------------
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if options.condition:
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interpolator = []
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condition = options.condition # copy per file, since might be altered inline
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breaker = False
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for position,operand in enumerate(set(re.findall(r'#(([s]#)?(.+?))#',condition))): # find three groups
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condition = condition.replace('#'+operand[0]+'#',
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{ '': '{%i}'%position,
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's#':'"{%i}"'%position}[operand[1]])
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if operand[2] in specials: # special label
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interpolator += ['specials["%s"]'%operand[2]]
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else:
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try:
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interpolator += ['%s(table.data[%i])'%({ '':'float',
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's#':'str'}[operand[1]],
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table.label_index(operand[2]))] # ccould be generalized to indexrange as array lookup
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except:
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damask.util.croak('column "{}" not found.'.format(operand[2]))
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breaker = True
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if breaker: continue # found mistake in condition evaluation --> next file
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evaluator_condition = "'" + condition + "'.format(" + ','.join(interpolator) + ")"
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else: condition = ''
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# ------------------------------------------ build formulae ----------------------------------------
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evaluator = {}
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evaluator = {}
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brokenFormula = {}
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for label,formula in zip(options.labels,options.formulas):
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for label,formula in zip(options.labels,options.formulas):
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for column in re.findall(r'#(.+?)#',formula): # loop over column labels in formula
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for column in re.findall(r'#(.+?)#',formula): # loop over column labels in formula
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@ -82,15 +115,15 @@ for name in filenames:
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elif dim > 1: # multidimensional input (vector, tensor, etc.)
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elif dim > 1: # multidimensional input (vector, tensor, etc.)
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replacement = 'np.array(table.data[{}:{}],dtype=float)'.format(idx,idx+dim) # use (flat) array representation
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replacement = 'np.array(table.data[{}:{}],dtype=float)'.format(idx,idx+dim) # use (flat) array representation
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else:
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else:
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damask.util.croak('column {} not found...'.format(column))
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damask.util.croak('column {} not found, skipping {}...'.format(column,label))
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brokenFormula[label] = True
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options.labels.remove(label)
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break
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break
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formula = formula.replace('#'+column+'#',replacement)
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formula = formula.replace('#'+column+'#',replacement)
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if label not in brokenFormula:
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evaluator[label] = formula
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evaluator[label] = formula
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# ------------------------------------------ process data ------------------------------------------
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# ------------------------------------------ process data ------------------------------------------
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firstLine = True
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firstLine = True
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@ -98,32 +131,53 @@ for name in filenames:
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while outputAlive and table.data_read(): # read next data line of ASCII table
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while outputAlive and table.data_read(): # read next data line of ASCII table
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specials['_row_'] += 1 # count row
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specials['_row_'] += 1 # count row
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output.data_clear()
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# ------------------------------------------ calculate one result to get length of labels ---------
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# ------------------------------------------ calculate one result to get length of labels ---------
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if firstLine:
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if firstLine:
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firstLine = False
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firstLine = False
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labelDim = {}
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labelDim = {}
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for label in [x for x in options.labels if x not in set(brokenFormula)]:
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for label in [x for x in options.labels]:
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labelDim[label] = np.size(eval(evaluator[label]))
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labelDim[label] = np.size(eval(evaluator[label]))
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if labelDim[label] == 0: brokenFormula[label] = True
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if labelDim[label] == 0: options.labels.remove(label)
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# ------------------------------------------ assemble header ---------------------------------------
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# ------------------------------------------ assemble header ---------------------------------------
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if label not in brokenFormula:
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output.labels_clear()
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table.labels_append(['{}_{}'.format(i+1,label) for i in xrange(labelDim[label])] if labelDim[label] > 1
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tabLabels = table.labels()
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for label in tabLabels:
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dim = labelDim[label] if label in options.labels \
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else table.label_dimension(label)
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output.labels_append(['{}_{}'.format(i+1,label) for i in xrange(dim)] if dim > 1 else label)
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for label in options.labels:
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if label in tabLabels: continue
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output.labels_append(['{}_{}'.format(i+1,label) for i in xrange(labelDim[label])]
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if labelDim[label] > 1
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else label)
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else label)
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table.info_append(scriptID + '\t' + ' '.join(sys.argv[1:]))
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output.info = table.info
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table.head_write()
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output.info_append(scriptID + '\t' + ' '.join(sys.argv[1:]))
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output.head_write()
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# ------------------------------------------ process data ------------------------------------------
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# ------------------------------------------ process data ------------------------------------------
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for label in [x for x in options.labels if x not in set(brokenFormula)]:
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for label in output.labels():
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table.data_append(unravel(eval(evaluator[label])))
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oldIndices = table.label_indexrange(label)
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Nold = max(1,len(oldIndices)) # Nold could be zero for new columns
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Nnew = len(output.label_indexrange(label))
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output.data_append(eval(evaluator[label]) if label in options.labels
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and (condition == '' or eval(eval(evaluator_condition)))
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else np.tile([table.data[i] for i in oldIndices]
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if label in tabLabels
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else np.nan,
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np.ceil(float(Nnew)/Nold))[:Nnew]) # spread formula result into given number of columns
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outputAlive = table.data_write() # output processed line
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outputAlive = output.data_write() # output processed line
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# ------------------------------------------ output finalization -----------------------------------
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# ------------------------------------------ output finalization -----------------------------------
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table.close() # close ASCII tables
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table.input_close() # close ASCII tables
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output.close() # close ASCII tables
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@ -1,143 +0,0 @@
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#!/usr/bin/env python2
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# -*- coding: UTF-8 no BOM -*-
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import os,re,sys
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import math # noqa
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import numpy as np
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from optparse import OptionParser
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import damask
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scriptName = os.path.splitext(os.path.basename(__file__))[0]
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scriptID = ' '.join([scriptName,damask.version])
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def unravel(item):
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if hasattr(item,'__contains__'): return ' '.join(map(unravel,item))
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else: return str(item)
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# --------------------------------------------------------------------
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# MAIN
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# --------------------------------------------------------------------
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parser = OptionParser(option_class=damask.extendableOption, usage='%prog options [file[s]]', description = """
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Update existing value(s) to expression(s) respecting condition.
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Examples:
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Replace the 2nd value of column x by value "z - y" --> fillTable -l x -c "#_row_#==2" -f "#z#-#y#"
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""", version = scriptID)
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parser.add_option('-l','--label',
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dest = 'labels',
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action = 'extend', metavar = '<string LIST>',
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help = '(list) of columns to be filled with formula(e)')
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parser.add_option('-f','--formula',
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dest = 'formulae',
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action = 'extend', metavar = '<string LIST>',
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help = '(list of) formulae corresponding to labels')
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parser.add_option('-c','--condition',
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dest = 'condition', metavar='string',
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help = 'condition to filter rows')
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parser.set_defaults(condition = '',
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)
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(options,filenames) = parser.parse_args()
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if options.labels is None or options.formulae is None:
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parser.error('no formulae specified.')
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if len(options.labels) != len(options.formulae):
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parser.error('number of labels ({}) and formulae ({}) do not match.'.format(len(options.labels),len(options.formulae)))
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for i in xrange(len(options.formulae)):
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options.formulae[i] = options.formulae[i].replace(';',',')
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# --- loop over input files -------------------------------------------------------------------------
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if filenames == []: filenames = [None]
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for name in filenames:
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try:
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table = damask.ASCIItable(name = name,
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buffered = False)
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except: continue
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damask.util.report(scriptName,name)
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# ------------------------------------------ assemble info -----------------------------------------
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table.head_read()
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# ------------------------------------------ Evaluate condition ---------------------------------------
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specials = { \
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'_row_': 0,
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}
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interpolator = []
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condition = options.condition # copy per file, since might be altered inline
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breaker = False
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for position,operand in enumerate(set(re.findall(r'#(([s]#)?(.+?))#',condition))): # find three groups
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condition = condition.replace('#'+operand[0]+'#',
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{ '': '{%i}'%position,
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's#':'"{%i}"'%position}[operand[1]])
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if operand[2] in specials: # special label
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interpolator += ['specials["%s"]'%operand[2]]
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else:
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try:
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interpolator += ['%s(table.data[%i])'%({ '':'float',
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's#':'str'}[operand[1]],
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table.labels.index(operand[2]))] # ccould be generalized to indexrange as array lookup
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except:
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damask.util.croak('column %s not found.'%operand[2])
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breaker = True
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if breaker: continue # found mistake in condition evaluation --> next file
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evaluator_condition = "'" + condition + "'.format(" + ','.join(interpolator) + ")"
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#----------------------------------- Formula -------------------------------------------------------
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evaluator = {}
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brokenFormula = {}
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for label,formula in zip(options.labels,options.formulae):
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for column in re.findall(r'#(.+?)#',formula): # loop over column labels in formula
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idx = table.label_index(column)
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dim = table.label_dimension(column)
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if column in specials:
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replacement = 'specials["{}"]'.format(column)
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elif dim == 1: # scalar input
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replacement = 'float(table.data[{}])'.format(idx) # take float value of data column
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elif dim > 1: # multidimensional input (vector, tensor, etc.)
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replacement = 'np.array(table.data[{}:{}],dtype=float)'.format(idx,idx+dim) # use (flat) array representation
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else:
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damask.util.croak('column {} not found...'.format(column))
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brokenFormula[label] = True
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break
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formula = formula.replace('#'+column+'#',replacement)
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if label not in brokenFormula:
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evaluator[label] = formula
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# ------------------------------------------ assemble header ---------------------------------------
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table.info_append(scriptID + '\t' + ' '.join(sys.argv[1:])) # read ASCII header info
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table.labels # update with label set
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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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specials['_row_'] += 1
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if condition == '' or eval(eval(evaluator_condition)): # test row for condition
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for label in [x for x in options.labels if x not in set(brokenFormula)]:
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indices = table.label_indexrange(label) # affected columns
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probe = np.array(eval(evaluator[label])) # get formula result (scalar, array, etc.)
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container = np.tile(probe,np.ceil(float(len(indices))/probe.size))[:len(indices)] # spread formula result into given number of columns
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for i,ind in enumerate(indices): # copy one by one as table.data is NOT a numpy array
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table.data[ind] = container[i]
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outputAlive = table.data_write() # output processed line
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# ------------------------------------------ output finalization -----------------------------------
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table.close() # close ASCII tables
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