Table class instead of ASCIItable
This commit is contained in:
Martin Diehl
parent
a7d60dc52a
commit
343da2e54d
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@ -2,6 +2,7 @@
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import os
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import sys
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from io import StringIO
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from optparse import OptionParser
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import numpy as np
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@ -22,79 +23,26 @@ Add cumulative (sum of first to current row) values for given label(s).
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""", version = scriptID)
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parser.add_option('-l','--label',
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dest='label',
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dest='labels',
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action = 'extend', metavar = '<string LIST>',
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help = 'columns to cumulate')
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parser.add_option('-p','--product',
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dest='product', action = 'store_true',
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help = 'product of values instead of sum')
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(options,filenames) = parser.parse_args()
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if options.label is None:
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parser.error('no data column(s) specified.')
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# --- loop over input files -------------------------------------------------------------------------
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if filenames == []: filenames = [None]
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if options.labels is None:
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parser.error('no data column(s) specified.')
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for name in filenames:
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try:
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table = damask.ASCIItable(name = name, buffered = False)
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except IOError:
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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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# ------------------------------------------ read header ------------------------------------------
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table = damask.Table.from_ASCII(StringIO(''.join(sys.stdin.read())) if name is None else name)
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for label in options.labels:
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table.add('cum_{}({})'.format('prod' if options.product else 'sum',label),
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np.cumprod(table.get(label),0) if options.product else np.cumsum(table.get(label),0),
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scriptID+' '+' '.join(sys.argv[1:]))
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table.head_read()
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# ------------------------------------------ sanity checks ----------------------------------------
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errors = []
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remarks = []
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columns = []
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dims = []
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how = 'prod' if options.product else 'sum'
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for what in options.label:
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dim = table.label_dimension(what)
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if dim < 0: remarks.append('column {} not found...'.format(what))
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else:
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dims.append(dim)
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columns.append(table.label_index(what))
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table.labels_append('cum_{}({})'.format(how,what) if dim == 1 else
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['{}_cum_{}({})'.format(i+1,how,what) for i in range(dim)] ) # extend ASCII header with new labels
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if remarks != []: damask.util.croak(remarks)
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if errors != []:
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damask.util.croak(errors)
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table.close(dismiss = True)
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continue
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# ------------------------------------------ assemble header ---------------------------------------
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table.info_append(scriptID + '\t' + ' '.join(sys.argv[1:]))
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table.head_write()
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# ------------------------------------------ process data ------------------------------------------
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mask = []
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for col,dim in zip(columns,dims): mask += range(col,col+dim) # isolate data columns to cumulate
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cumulated = np.ones(len(mask)) if options.product else np.zeros(len(mask)) # prepare output field
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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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if options.product:
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for i,col in enumerate(mask):
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cumulated[i] *= float(table.data[col]) # cumulate values (multiplication)
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else:
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for i,col in enumerate(mask):
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cumulated[i] += float(table.data[col]) # cumulate values (addition)
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table.data_append(cumulated)
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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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table.to_ASCII(sys.stdout if name is None else name)
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@ -2,6 +2,7 @@
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import os
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import sys
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from io import StringIO
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from optparse import OptionParser
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import numpy as np
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@ -30,7 +31,7 @@ def derivative(coordinates,what):
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(coordinates[0] - coordinates[1])
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result[-1,:] = (what[-1,:] - what[-2,:]) / \
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(coordinates[-1] - coordinates[-2])
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return result
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@ -48,78 +49,26 @@ parser.add_option('-c','--coordinates',
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type = 'string', metavar='string',
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help = 'heading of coordinate column')
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parser.add_option('-l','--label',
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dest = 'label',
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dest = 'labels',
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action = 'extend', metavar = '<string LIST>',
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help = 'heading of column(s) to differentiate')
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(options,filenames) = parser.parse_args()
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if options.coordinates is None:
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parser.error('no coordinate column specified.')
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if options.label is None:
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parser.error('no data column specified.')
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# --- loop over input files -------------------------------------------------------------------------
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if filenames == []: filenames = [None]
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if options.coordinates is None:
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parser.error('no coordinate column specified.')
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if options.labels is None:
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parser.error('no data column specified.')
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for name in filenames:
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try: 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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damask.util.report(scriptName,name)
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# ------------------------------------------ read header ------------------------------------------
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table = damask.Table.from_ASCII(StringIO(''.join(sys.stdin.read())) if name is None else name)
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for label in options.labels:
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table.add('d({})/d({})'.format(label,options.coordinates),
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derivative(table.get(options.coordinates),table.get(label)),
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scriptID+' '+' '.join(sys.argv[1:]))
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table.head_read()
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# ------------------------------------------ sanity checks ----------------------------------------
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errors = []
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remarks = []
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columns = []
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dims = []
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if table.label_dimension(options.coordinates) != 1:
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errors.append('coordinate column {} is not scalar.'.format(options.coordinates))
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for what in options.label:
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dim = table.label_dimension(what)
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if dim < 0: remarks.append('column {} not found...'.format(what))
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else:
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dims.append(dim)
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columns.append(table.label_index(what))
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table.labels_append('d({})/d({})'.format(what,options.coordinates) if dim == 1 else
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['{}_d({})/d({})'.format(i+1,what,options.coordinates) for i in range(dim)] ) # extend ASCII header with new labels
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if remarks != []: damask.util.croak(remarks)
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if errors != []:
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damask.util.croak(errors)
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table.close(dismiss = True)
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continue
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# ------------------------------------------ assemble header --------------------------------------
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table.info_append(scriptID + '\t' + ' '.join(sys.argv[1:]))
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table.head_write()
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# ------------------------------------------ process data ------------------------------------------
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table.data_readArray()
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mask = []
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for col,dim in zip(columns,dims): mask += range(col,col+dim) # isolate data columns to differentiate
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differentiated = derivative(table.data[:,table.label_index(options.coordinates)].reshape((len(table.data),1)),
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table.data[:,mask]) # calculate numerical derivative
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table.data = np.hstack((table.data,differentiated))
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# ------------------------------------------ output result -----------------------------------------
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table.data_writeArray()
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# ------------------------------------------ output finalization -----------------------------------
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table.close() # close ASCII tables
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table.to_ASCII(sys.stdout if name is None else name)
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@ -33,49 +33,20 @@ parser.set_defaults(pos = 'pos',
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)
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(options, filenames) = parser.parse_args()
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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: table = damask.ASCIItable(name = name,
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buffered = False,
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readonly = True)
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except: continue
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damask.util.report(scriptName,name)
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# --- interpret header ----------------------------------------------------------------------------
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table.head_read()
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errors = []
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remarks = []
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coordDim = table.label_dimension(options.pos)
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if not 3 >= coordDim >= 1: errors.append('coordinates "{}" need to have one, two, or three dimensions.'.format(options.pos))
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elif coordDim < 3: remarks.append('appending {} dimension{} to coordinates "{}"...'.format(3-coordDim,
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's' if coordDim < 2 else '',
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options.pos))
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if remarks != []: damask.util.croak(remarks)
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if errors != []:
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damask.util.croak(errors)
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table.close(dismiss=True)
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continue
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table = damask.Table.from_ASCII(StringIO(''.join(sys.stdin.read())) if name is None else name)
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# ------------------------------------------ process data ---------------------------------------
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table.data_readArray(options.pos)
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if table.data.shape[1] < 3:
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table.data = np.hstack((table.data,
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np.zeros((table.data.shape[0],
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3-table.data.shape[1]),dtype='f'))) # fill coords up to 3D with zeros
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Polydata = vtk.vtkPolyData()
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Points = vtk.vtkPoints()
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Vertices = vtk.vtkCellArray()
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for p in table.data:
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for p in table.get(options.pos):
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pointID = Points.InsertNextPoint(p)
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Vertices.InsertNextCell(1)
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Vertices.InsertCellPoint(pointID)
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@ -104,5 +75,3 @@ for name in filenames:
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writer.Write()
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if name is None: sys.stdout.write(writer.GetOutputString())
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table.close()
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@ -40,48 +40,14 @@ parser.set_defaults(mode = 'cell',
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)
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(options, filenames) = parser.parse_args()
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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: table = damask.ASCIItable(name = name,
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buffered = False,
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labeled = True,
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readonly = True,
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)
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except: continue
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damask.util.report(scriptName,name)
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# --- interpret header ----------------------------------------------------------------------------
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table.head_read()
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remarks = []
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errors = []
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coordDim = table.label_dimension(options.pos)
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if not 3 >= coordDim >= 1: errors.append('coordinates "{}" need to have one, two, or three dimensions.'.format(options.pos))
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elif coordDim < 3: remarks.append('appending {} dimension{} to coordinates "{}"...'.format(3-coordDim,
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's' if coordDim < 2 else '',
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options.pos))
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if remarks != []: damask.util.croak(remarks)
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if errors != []:
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damask.util.croak(errors)
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table.close(dismiss=True)
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continue
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# --------------- figure out size and grid ---------------------------------------------------------
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table.data_readArray(options.pos)
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if table.data.shape[1] < 3:
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table.data = np.hstack((table.data,
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np.zeros((table.data.shape[0],
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3-table.data.shape[1]),dtype='f'))) # fill coords up to 3D with zeros
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coords = [np.unique(table.data[:,i]) for i in range(3)]
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table = damask.Table.from_ASCII(StringIO(''.join(sys.stdin.read())) if name is None else name)
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coords = [np.unique(table.get(options.pos)[:,i]) for i in range(3)]
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if options.mode == 'cell':
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coords = [0.5 * np.array([3.0 * coords[i][0] - coords[i][0 + int(len(coords[i]) > 1)]] + \
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[coords[i][j-1] + coords[i][j] for j in range(1,len(coords[i]))] + \
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@ -90,13 +56,6 @@ for name in filenames:
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grid = np.array(list(map(len,coords)),'i')
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N = grid.prod() if options.mode == 'point' else (grid-1).prod()
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if N != len(table.data):
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errors.append('data count {} does not match grid {}x{}x{}.'.format(N,*(grid - (options.mode == 'cell')) ))
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if errors != []:
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damask.util.croak(errors)
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table.close(dismiss = True)
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continue
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# ------------------------------------------ process data ---------------------------------------
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rGrid = vtk.vtkRectilinearGrid()
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@ -135,5 +94,3 @@ for name in filenames:
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writer.Write()
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if name is None: sys.stdout.write(writer.GetOutputString())
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table.close()
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