From f6758ecc283a3d71e9144c967c13c32dbad119e9 Mon Sep 17 00:00:00 2001 From: Martin Diehl Date: Mon, 14 Sep 2020 07:04:01 +0200 Subject: [PATCH 01/11] table class operates out of place --- .gitlab-ci.yml | 7 - processing/post/DADF5_postResults.py | 4 +- processing/post/addCompatibilityMismatch.py | 12 +- processing/post/addCurl.py | 6 +- processing/post/addDerivative.py | 6 +- processing/post/addDisplacement.py | 20 +-- processing/post/addDivergence.py | 6 +- processing/post/addEuclideanDistance.py | 6 +- processing/post/addGaussian.py | 10 +- processing/post/addGradient.py | 6 +- processing/post/addIndexed.py | 64 --------- processing/post/addLinked.py | 118 ---------------- processing/post/addOrientations.py | 10 +- processing/post/addSchmidfactors.py | 2 +- processing/post/groupTable.py | 142 -------------------- processing/post/permuteData.py | 2 +- processing/pre/seeds_fromGeom.py | 5 +- processing/pre/seeds_fromRandom.py | 4 +- python/damask/_table.py | 77 +++++++---- python/tests/test_Orientation.py | 2 +- python/tests/test_Table.py | 47 +++---- 21 files changed, 121 insertions(+), 435 deletions(-) delete mode 100755 processing/post/addIndexed.py delete mode 100755 processing/post/addLinked.py delete mode 100755 processing/post/groupTable.py diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml index 4c33f83e7..9407ffc7c 100644 --- a/.gitlab-ci.yml +++ b/.gitlab-ci.yml @@ -141,13 +141,6 @@ Pre_General: - release ################################################################################################### -Post_ASCIItable: - stage: postprocessing - script: ASCIItable/test.py - except: - - master - - release - Post_General: stage: postprocessing script: PostProcessing/test.py diff --git a/processing/post/DADF5_postResults.py b/processing/post/DADF5_postResults.py index 08c8c7070..9c520ac33 100755 --- a/processing/post/DADF5_postResults.py +++ b/processing/post/DADF5_postResults.py @@ -39,7 +39,7 @@ for filename in options.filenames: N_digits = 5 # hack to keep test intact for inc in damask.util.show_progress(results.iterate('increments'),len(results.increments)): table = damask.Table(np.ones(np.product(results.grid),dtype=int)*int(inc[3:]),{'inc':(1,)}) - table.add('pos',coords.reshape(-1,3)) + table = table.add('pos',coords.reshape(-1,3)) results.pick('materialpoints',False) results.pick('constituents', True) @@ -53,7 +53,7 @@ for filename in options.filenames: for label in options.mat: x = results.get_dataset_location(label) if len(x) != 0: - table.add(label,results.read_dataset(x,0,plain=True).reshape(results.grid.prod(),-1)) + table = table.add(label,results.read_dataset(x,0,plain=True).reshape(results.grid.prod(),-1)) dirname = os.path.abspath(os.path.join(os.path.dirname(filename),options.dir)) if not os.path.isdir(dirname): diff --git a/processing/post/addCompatibilityMismatch.py b/processing/post/addCompatibilityMismatch.py index bd55ab66a..5009d44a0 100755 --- a/processing/post/addCompatibilityMismatch.py +++ b/processing/post/addCompatibilityMismatch.py @@ -181,14 +181,14 @@ for name in filenames: if options.shape: centers = damask.grid_filters.cell_coord(size,F) shapeMismatch = shapeMismatch(size,F,nodes,centers) - table.add('shapeMismatch(({}))'.format(options.defgrad), - shapeMismatch.reshape(-1,1,order='F'), - scriptID+' '+' '.join(sys.argv[1:])) + table = table.add('shapeMismatch(({}))'.format(options.defgrad), + shapeMismatch.reshape(-1,1,order='F'), + scriptID+' '+' '.join(sys.argv[1:])) if options.volume: volumeMismatch = volumeMismatch(size,F,nodes) - table.add('volMismatch(({}))'.format(options.defgrad), - volumeMismatch.reshape(-1,1,order='F'), - scriptID+' '+' '.join(sys.argv[1:])) + table = table.add('volMismatch(({}))'.format(options.defgrad), + volumeMismatch.reshape(-1,1,order='F'), + scriptID+' '+' '.join(sys.argv[1:])) table.to_file(sys.stdout if name is None else name) diff --git a/processing/post/addCurl.py b/processing/post/addCurl.py index a9ddc8ae8..1033e3303 100755 --- a/processing/post/addCurl.py +++ b/processing/post/addCurl.py @@ -51,8 +51,8 @@ for name in filenames: shape = (3,) if np.prod(field.shape)//np.prod(grid) == 3 else (3,3) # vector or tensor field = field.reshape(tuple(grid)+(-1,),order='F').reshape(tuple(grid)+shape) curl = damask.grid_filters.curl(size,field) - table.add('curlFFT({})'.format(label), - curl.reshape(tuple(grid)+(-1,)).reshape(-1,np.prod(shape),order='F'), - scriptID+' '+' '.join(sys.argv[1:])) + table = table.add('curlFFT({})'.format(label), + curl.reshape(tuple(grid)+(-1,)).reshape(-1,np.prod(shape),order='F'), + scriptID+' '+' '.join(sys.argv[1:])) table.to_file(sys.stdout if name is None else name) diff --git a/processing/post/addDerivative.py b/processing/post/addDerivative.py index 9030ae83b..b6b19c98a 100755 --- a/processing/post/addDerivative.py +++ b/processing/post/addDerivative.py @@ -67,8 +67,8 @@ for name in filenames: table = damask.Table.from_ASCII(StringIO(''.join(sys.stdin.read())) if name is None else name) for label in options.labels: - table.add('d({})/d({})'.format(label,options.coordinates), - derivative(table.get(options.coordinates),table.get(label)), - scriptID+' '+' '.join(sys.argv[1:])) + table = table.add('d({})/d({})'.format(label,options.coordinates), + derivative(table.get(options.coordinates),table.get(label)), + scriptID+' '+' '.join(sys.argv[1:])) table.to_file(sys.stdout if name is None else name) diff --git a/processing/post/addDisplacement.py b/processing/post/addDisplacement.py index 80725410d..f1ab565b0 100755 --- a/processing/post/addDisplacement.py +++ b/processing/post/addDisplacement.py @@ -53,19 +53,19 @@ for name in filenames: F = table.get(options.f).reshape(tuple(grid)+(-1,),order='F').reshape(tuple(grid)+(3,3)) if options.nodal: table = damask.Table(damask.grid_filters.node_coord0(grid,size).reshape(-1,3,order='F'), - {'pos':(3,)}) - table.add('avg({}).{}'.format(options.f,options.pos), - damask.grid_filters.node_displacement_avg(size,F).reshape(-1,3,order='F'), - scriptID+' '+' '.join(sys.argv[1:])) - table.add('fluct({}).{}'.format(options.f,options.pos), - damask.grid_filters.node_displacement_fluct(size,F).reshape(-1,3,order='F'), - scriptID+' '+' '.join(sys.argv[1:])) + {'pos':(3,)})\ + .add('avg({}).{}'.format(options.f,options.pos), + damask.grid_filters.node_displacement_avg(size,F).reshape(-1,3,order='F'), + scriptID+' '+' '.join(sys.argv[1:]))\ + .add('fluct({}).{}'.format(options.f,options.pos), + damask.grid_filters.node_displacement_fluct(size,F).reshape(-1,3,order='F'), + scriptID+' '+' '.join(sys.argv[1:])) table.to_file(sys.stdout if name is None else os.path.splitext(name)[0]+'_nodal.txt') else: - table.add('avg({}).{}'.format(options.f,options.pos), + table = table.add('avg({}).{}'.format(options.f,options.pos), damask.grid_filters.cell_displacement_avg(size,F).reshape(-1,3,order='F'), - scriptID+' '+' '.join(sys.argv[1:])) - table.add('fluct({}).{}'.format(options.f,options.pos), + scriptID+' '+' '.join(sys.argv[1:]))\ + .add('fluct({}).{}'.format(options.f,options.pos), damask.grid_filters.cell_displacement_fluct(size,F).reshape(-1,3,order='F'), scriptID+' '+' '.join(sys.argv[1:])) table.to_file(sys.stdout if name is None else name) diff --git a/processing/post/addDivergence.py b/processing/post/addDivergence.py index 9abe1e2c6..6495793cf 100755 --- a/processing/post/addDivergence.py +++ b/processing/post/addDivergence.py @@ -51,8 +51,8 @@ for name in filenames: shape = (3,) if np.prod(field.shape)//np.prod(grid) == 3 else (3,3) # vector or tensor field = field.reshape(tuple(grid)+(-1,),order='F').reshape(tuple(grid)+shape) div = damask.grid_filters.divergence(size,field) - table.add('divFFT({})'.format(label), - div.reshape(tuple(grid)+(-1,)).reshape(-1,np.prod(shape)//3,order='F'), - scriptID+' '+' '.join(sys.argv[1:])) + table = table.add('divFFT({})'.format(label), + div.reshape(tuple(grid)+(-1,)).reshape(-1,np.prod(shape)//3,order='F'), + scriptID+' '+' '.join(sys.argv[1:])) table.to_file(sys.stdout if name is None else name) diff --git a/processing/post/addEuclideanDistance.py b/processing/post/addEuclideanDistance.py index 921afc826..f5cf58ab3 100755 --- a/processing/post/addEuclideanDistance.py +++ b/processing/post/addEuclideanDistance.py @@ -180,8 +180,8 @@ for name in filenames: for i,feature in enumerate(feature_list): - table.add('ED_{}({})'.format(features[feature]['names'][0],options.id), - distance[i,:], - scriptID+' '+' '.join(sys.argv[1:])) + table = table.add('ED_{}({})'.format(features[feature]['names'][0],options.id), + distance[i,:], + scriptID+' '+' '.join(sys.argv[1:])) table.to_file(sys.stdout if name is None else name) diff --git a/processing/post/addGaussian.py b/processing/post/addGaussian.py index 93397e215..8e58da884 100755 --- a/processing/post/addGaussian.py +++ b/processing/post/addGaussian.py @@ -67,10 +67,10 @@ for name in filenames: damask.grid_filters.coord0_check(table.get(options.pos)) for label in options.labels: - table.add('Gauss{}({})'.format(options.sigma,label), - ndimage.filters.gaussian_filter(table.get(label).reshape(-1), - options.sigma,options.order, - mode = 'wrap' if options.periodic else 'nearest'), - scriptID+' '+' '.join(sys.argv[1:])) + table = table.add('Gauss{}({})'.format(options.sigma,label), + ndimage.filters.gaussian_filter(table.get(label).reshape(-1), + options.sigma,options.order, + mode = 'wrap' if options.periodic else 'nearest'), + scriptID+' '+' '.join(sys.argv[1:])) table.to_file(sys.stdout if name is None else name) diff --git a/processing/post/addGradient.py b/processing/post/addGradient.py index 3aee29374..718a972f3 100755 --- a/processing/post/addGradient.py +++ b/processing/post/addGradient.py @@ -51,8 +51,8 @@ for name in filenames: shape = (1,) if np.prod(field.shape)//np.prod(grid) == 1 else (3,) # scalar or vector field = field.reshape(tuple(grid)+(-1,),order='F') grad = damask.grid_filters.gradient(size,field) - table.add('gradFFT({})'.format(label), - grad.reshape(tuple(grid)+(-1,)).reshape(-1,np.prod(shape)*3,order='F'), - scriptID+' '+' '.join(sys.argv[1:])) + table = table.add('gradFFT({})'.format(label), + grad.reshape(tuple(grid)+(-1,)).reshape(-1,np.prod(shape)*3,order='F'), + scriptID+' '+' '.join(sys.argv[1:])) table.to_file(sys.stdout if name is None else name) diff --git a/processing/post/addIndexed.py b/processing/post/addIndexed.py deleted file mode 100755 index 50db36c20..000000000 --- a/processing/post/addIndexed.py +++ /dev/null @@ -1,64 +0,0 @@ -#!/usr/bin/env python3 - -import os -import sys -from io import StringIO -from optparse import OptionParser - -import numpy as np - -import damask - - -scriptName = os.path.splitext(os.path.basename(__file__))[0] -scriptID = ' '.join([scriptName,damask.version]) - -# -------------------------------------------------------------------- -# MAIN -# -------------------------------------------------------------------- - -parser = OptionParser(option_class=damask.extendableOption, usage='%prog options [ASCIItable(s)]', description = """ -Add data in column(s) of mapped ASCIItable selected from the row indexed by the value in a mapping column. -Row numbers start at 1. - -""", version = scriptID) - -parser.add_option('--index', - dest = 'index', - type = 'string', metavar = 'string', - help = 'column label containing row index') -parser.add_option('-o','--offset', - dest = 'offset', - type = 'int', metavar = 'int', - help = 'constant offset for index column value [%default]') -parser.add_option('-l','--label', - dest = 'label', - action = 'extend', metavar = '', - help = 'column label(s) to be appended') -parser.add_option('-a','--asciitable', - dest = 'asciitable', - type = 'string', metavar = 'string', - help = 'indexed ASCIItable') - -parser.set_defaults(offset = 0, - ) - -(options,filenames) = parser.parse_args() -if filenames == []: filenames = [None] - -if options.label is None: - parser.error('no data columns specified.') -if options.index is None: - parser.error('no index column given.') - -for name in filenames: - damask.util.report(scriptName,name) - - table = damask.Table.from_ASCII(StringIO(''.join(sys.stdin.read())) if name is None else name) - indexedTable = damask.Table.from_ASCII(options.asciitable) - idx = np.reshape(table.get(options.index).astype(int) + options.offset,(-1))-1 - - for data in options.label: - table.add(data+'_addIndexed',indexedTable.get(data)[idx],scriptID+' '+' '.join(sys.argv[1:])) - - table.to_file(sys.stdout if name is None else name) diff --git a/processing/post/addLinked.py b/processing/post/addLinked.py deleted file mode 100755 index 9b09cb7c7..000000000 --- a/processing/post/addLinked.py +++ /dev/null @@ -1,118 +0,0 @@ -#!/usr/bin/env python3 - -import os -import sys -from optparse import OptionParser - -import numpy as np - -import damask - - -scriptName = os.path.splitext(os.path.basename(__file__))[0] -scriptID = ' '.join([scriptName,damask.version]) - -# -------------------------------------------------------------------- -# MAIN -# -------------------------------------------------------------------- - -parser = OptionParser(option_class=damask.extendableOption, usage='%prog options [ASCIItable(s)]', description = """ -Add data of selected column(s) from (first) row of linked 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 of table and linked table containing linking values') -parser.add_option('-l','--label', - dest = 'label', - action = 'extend', metavar = '', - help = 'column label(s) to add from linked ASCIItable') -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, readonly = True) - linkedTable.head_read() # read ASCII header info of linked table - linkDim = linkedTable.label_dimension(options.link[1]) # dimension of linking column - - missing_labels = linkedTable.data_readArray([options.link[1]]+options.label) # try reading linked ASCII table - 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))) - if len(missing_labels) >= len(options.label): - damask.util.croak('aborting...') - sys.exit() - - index = linkedTable.data[:,:linkDim] - data = linkedTable.data[:,linkDim:] -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) - except IOError: - continue - damask.util.report(scriptName,"{} {} <== {} {}".format(name,damask.util.deemph('@ '+options.link[0]), - options.asciitable,damask.util.deemph('@ '+options.link[1]))) - -# ------------------------------------------ read header ------------------------------------------ - - table.head_read() - -# ------------------------------------------ sanity checks ---------------------------------------- - - errors = [] - - myLink = table.label_index (options.link[0]) - myLinkDim = table.label_dimension(options.link[0]) - if myLink < 0: errors.append('linking column {} not found.'.format(options.link[0])) - if myLinkDim != linkDim: errors.append('dimension mismatch for column {}.'.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)[linkDim:]) # extend with new labels (except for linked column) - - table.head_write() - -# ------------------------------------------ process data ------------------------------------------ - - outputAlive = True - while outputAlive and table.data_read(): # read next data line of ASCII table - try: - table.data_append(data[np.argwhere(np.all((list(map(float,table.data[myLink:myLink+myLinkDim])) - index)==0, - axis=1))[0]]) # add data of first matching line - except IndexError: - table.data_append(np.nan*np.ones_like(data[0])) # or add NaNs - outputAlive = table.data_write() # output processed line - -# ------------------------------------------ output finalization ----------------------------------- - - table.close() # close ASCII tables diff --git a/processing/post/addOrientations.py b/processing/post/addOrientations.py index 51d668eb9..dddc14193 100755 --- a/processing/post/addOrientations.py +++ b/processing/post/addOrientations.py @@ -137,14 +137,14 @@ for name in filenames: if 'rodrigues' in options.output: - table.add('ro({})'.format(label),o.as_Rodrigues(), scriptID+' '+' '.join(sys.argv[1:])) + table = table.add('ro({})'.format(label),o.as_Rodrigues(), scriptID+' '+' '.join(sys.argv[1:])) if 'eulers' in options.output: - table.add('eu({})'.format(label),o.as_Eulers(options.degrees), scriptID+' '+' '.join(sys.argv[1:])) + table = table.add('eu({})'.format(label),o.as_Eulers(options.degrees), scriptID+' '+' '.join(sys.argv[1:])) if 'quaternion' in options.output: - table.add('qu({})'.format(label),o.as_quaternion(), scriptID+' '+' '.join(sys.argv[1:])) + table = table.add('qu({})'.format(label),o.as_quaternion(), scriptID+' '+' '.join(sys.argv[1:])) if 'matrix' in options.output: - table.add('om({})'.format(label),o.as_matrix(), scriptID+' '+' '.join(sys.argv[1:])) + table = table.add('om({})'.format(label),o.as_matrix(), scriptID+' '+' '.join(sys.argv[1:])) if 'axisangle' in options.output: - table.add('om({})'.format(label),o.as_axisangle(options.degrees), scriptID+' '+' '.join(sys.argv[1:])) + table = table.add('om({})'.format(label),o.as_axisangle(options.degrees), scriptID+' '+' '.join(sys.argv[1:])) table.to_file(sys.stdout if name is None else name) diff --git a/processing/post/addSchmidfactors.py b/processing/post/addSchmidfactors.py index 26a0c5c93..dc4117d78 100755 --- a/processing/post/addSchmidfactors.py +++ b/processing/post/addSchmidfactors.py @@ -187,6 +187,6 @@ for name in filenames: np.einsum('ijk,ik->ij',slip_normal, (o@normal))) for i,label in enumerate(labels): - table.add(label,S[:,i],scriptID+' '+' '.join(sys.argv[1:])) + table = table.add(label,S[:,i],scriptID+' '+' '.join(sys.argv[1:])) table.to_file(sys.stdout if name is None else name) diff --git a/processing/post/groupTable.py b/processing/post/groupTable.py deleted file mode 100755 index a73e7d505..000000000 --- a/processing/post/groupTable.py +++ /dev/null @@ -1,142 +0,0 @@ -#!/usr/bin/env python3 - -import os -import sys -from optparse import OptionParser, OptionGroup -import math # noqa - -import numpy as np - -import damask - - -def periodicAverage(coords, limits): - """Centroid in periodic domain, see https://en.wikipedia.org/wiki/Center_of_mass#Systems_with_periodic_boundary_conditions.""" - theta = 2.0*np.pi * (coords - limits[0])/(limits[1] - limits[0]) - theta_avg = np.pi + np.arctan2(-np.sin(theta).mean(axis=0), -np.cos(theta).mean(axis=0)) - return limits[0] + theta_avg * (limits[1] - limits[0])/2.0/np.pi - - -scriptName = os.path.splitext(os.path.basename(__file__))[0] -scriptID = ' '.join([scriptName,damask.version]) - -# -------------------------------------------------------------------- -# MAIN -# -------------------------------------------------------------------- - -parser = OptionParser(option_class=damask.extendableOption, usage='%prog options [ASCIItable(s)]', description = """ -Apply a user-specified function to condense into a single row all those rows for which columns 'label' have identical values. -Output table will contain as many rows as there are different (unique) values in the grouping column(s). -Periodic domain averaging of coordinate values is supported. - -Examples: -For grain averaged values, replace all rows of particular 'texture' with a single row containing their average. -{name} --label texture --function np.average data.txt -""".format(name = scriptName), version = scriptID) - -parser.add_option('-l','--label', - dest = 'label', - action = 'extend', metavar = '', - help = 'column label(s) for grouping rows') -parser.add_option('-f','--function', - dest = 'function', - type = 'string', metavar = 'string', - help = 'mapping function [%default]') -parser.add_option('-a','--all', - dest = 'all', - action = 'store_true', - help = 'apply mapping function also to grouping column(s)') - -group = OptionGroup(parser, "periodic averaging", "") - -group.add_option ('-p','--periodic', - dest = 'periodic', - action = 'extend', metavar = '', - help = 'coordinate label(s) to average across periodic domain') -group.add_option ('--limits', - dest = 'boundary', - type = 'float', metavar = 'float float', nargs = 2, - help = 'min and max of periodic domain %default') - -parser.add_option_group(group) - -parser.set_defaults(function = 'np.average', - all = False, - label = [], - boundary = [0.0, 1.0]) - -(options,filenames) = parser.parse_args() - -funcModule,funcName = options.function.split('.') - -try: - mapFunction = getattr(locals().get(funcModule) or - globals().get(funcModule) or - __import__(funcModule), - funcName) -except Exception: - mapFunction = None - -if options.label is []: - parser.error('no grouping column specified.') -if not hasattr(mapFunction,'__call__'): - parser.error('function "{}" is not callable.'.format(options.function)) - - -# --- loop over input files ------------------------------------------------------------------------- - -if filenames == []: filenames = [None] - -for name in filenames: - try: - table = damask.ASCIItable(name = name) - except IOError: - continue - damask.util.report(scriptName,name) - -# ------------------------------------------ sanity checks --------------------------------------- - - remarks = [] - errors = [] - - table.head_read() - grpColumns = table.label_index(options.label)[::-1] - grpColumns = grpColumns[np.where(grpColumns>=0)] - - if len(grpColumns) == 0: errors.append('no valid grouping column present.') - - if remarks != []: damask.util.croak(remarks) - if errors != []: - damask.util.croak(errors) - table.close(dismiss=True) - continue - -# ------------------------------------------ assemble info --------------------------------------- - - table.info_append(scriptID + '\t' + ' '.join(sys.argv[1:])) - table.head_write() - -# ------------------------------------------ process data -------------------------------- - - table.data_readArray() - indexrange = table.label_indexrange(options.periodic) if options.periodic is not None else [] - rows,cols = table.data.shape - - table.data = table.data[np.lexsort(table.data[:,grpColumns].T)] # sort data by grpColumn(s) - values,index = np.unique(table.data[:,grpColumns], axis=0, return_index=True) # unique grpColumn values and their positions - index = sorted(np.append(index,rows)) # add termination position - grpTable = np.empty((len(values), cols)) # initialize output - - for i in range(len(values)): # iterate over groups (unique values in grpColumn) - grpTable[i] = np.apply_along_axis(mapFunction,0,table.data[index[i]:index[i+1]]) # apply (general) mapping function - grpTable[i,indexrange] = \ - periodicAverage(table.data[index[i]:index[i+1],indexrange],options.boundary) # apply periodicAverage mapping function - - if not options.all: grpTable[i,grpColumns] = table.data[index[i],grpColumns] # restore grouping column value - - table.data = grpTable - -# ------------------------------------------ output result ------------------------------- - - table.data_writeArray() - table.close() # close ASCII table diff --git a/processing/post/permuteData.py b/processing/post/permuteData.py index 766558216..316fdd3da 100755 --- a/processing/post/permuteData.py +++ b/processing/post/permuteData.py @@ -56,6 +56,6 @@ for name in filenames: data = table.get(label) uniques,inverse = np.unique(data,return_inverse=True,axis=0) if options.unique else (data,np.arange(len(data))) rng.shuffle(uniques) - table.set(label,uniques[inverse], scriptID+' '+' '.join(sys.argv[1:])) + table = table.set(label,uniques[inverse], scriptID+' '+' '.join(sys.argv[1:])) table.to_file(sys.stdout if name is None else name) diff --git a/processing/pre/seeds_fromGeom.py b/processing/pre/seeds_fromGeom.py index ab64c6b1e..97550ce13 100755 --- a/processing/pre/seeds_fromGeom.py +++ b/processing/pre/seeds_fromGeom.py @@ -64,6 +64,5 @@ for name in filenames: 'homogenization\t{}'.format(geom.homogenization)] table = damask.Table(seeds[mask],{'pos':(3,)},comments) - table.add('microstructure',microstructure[mask]) - table.to_file(sys.stdout if name is None else \ - os.path.splitext(name)[0]+'.seeds') + table = table.add('microstructure',microstructure[mask]) + table.to_file(sys.stdout if name is None else os.path.splitext(name)[0]+'.seeds') diff --git a/processing/pre/seeds_fromRandom.py b/processing/pre/seeds_fromRandom.py index b9e419391..a544528cf 100755 --- a/processing/pre/seeds_fromRandom.py +++ b/processing/pre/seeds_fromRandom.py @@ -155,11 +155,11 @@ for name in filenames: ] table = damask.Table(np.hstack((seeds,eulers)),{'pos':(3,),'euler':(3,)},comments) - table.add('microstructure',np.arange(options.microstructure,options.microstructure + options.N,dtype=int)) + table = table.add('microstructure',np.arange(options.microstructure,options.microstructure + options.N,dtype=int)) if options.weights: weights = np.random.uniform(low = 0, high = options.max, size = options.N) if options.max > 0.0 \ else np.random.normal(loc = options.mean, scale = options.sigma, size = options.N) - table.add('weight',weights) + table = table.add('weight',weights) table.to_file(sys.stdout if name is None else name) diff --git a/python/damask/_table.py b/python/damask/_table.py index 180c51f6f..b4fd2975a 100644 --- a/python/damask/_table.py +++ b/python/damask/_table.py @@ -1,4 +1,5 @@ import re +import copy import pandas as pd import numpy as np @@ -29,6 +30,15 @@ class Table: self._label_condensed() + def __copy__(self): + """Copy Table.""" + return copy.deepcopy(self) + + def copy(self): + """Copy Table.""" + return self.__copy__() + + def _label_flat(self): """Label data individually, e.g. v v v ==> 1_v 2_v 3_v.""" labels = [] @@ -191,15 +201,16 @@ class Table: Human-readable information about the new data. """ - self._add_comment(label,data.shape[1:],info) + dup = self.copy() + dup._add_comment(label,data.shape[1:],info) if re.match(r'[0-9]*?_',label): idx,key = label.split('_',1) - iloc = self.data.columns.get_loc(key).tolist().index(True) + int(idx) -1 - self.data.iloc[:,iloc] = data + iloc = dup.data.columns.get_loc(key).tolist().index(True) + int(idx) -1 + dup.data.iloc[:,iloc] = data else: - self.data[label] = data.reshape(self.data[label].shape) - + dup.data[label] = data.reshape(dup.data[label].shape) + return dup def add(self,label,data,info=None): """ @@ -215,15 +226,17 @@ class Table: Human-readable information about the modified data. """ - self._add_comment(label,data.shape[1:],info) + dup = self.copy() + dup._add_comment(label,data.shape[1:],info) - self.shapes[label] = data.shape[1:] if len(data.shape) > 1 else (1,) + dup.shapes[label] = data.shape[1:] if len(data.shape) > 1 else (1,) size = np.prod(data.shape[1:],dtype=int) new = pd.DataFrame(data=data.reshape(-1,size), columns=[label]*size, ) - new.index = self.data.index - self.data = pd.concat([self.data,new],axis=1) + new.index = dup.data.index + dup.data = pd.concat([dup.data,new],axis=1) + return dup def delete(self,label): @@ -236,25 +249,31 @@ class Table: Column label. """ - self.data.drop(columns=label,inplace=True) - del self.shapes[label] + dup = self.copy() + dup.data.drop(columns=label,inplace=True) + del dup.shapes[label] + return dup - def rename(self,label_old,label_new,info=None): + def rename(self,old,new,info=None): """ Rename column data. Parameters ---------- - label_old : str - Old column label. - label_new : str - New column label. + label_old : str or iterable of str + Old column label(s). + label_new : str or iterable of str + New column label(s). """ - self.data.rename(columns={label_old:label_new},inplace=True) - self.comments.append(f'{label_old} => {label_new}'+('' if info is None else f': {info}')) - self.shapes = {(label if label != label_old else label_new):self.shapes[label] for label in self.shapes} + dup = self.copy() + columns = dict(zip([old] if isinstance(old,str) else old, + [new] if isinstance(new,str) else new)) + dup.data.rename(columns=columns,inplace=True) + dup.comments.append(f'{old} => {new}'+('' if info is None else f': {info}')) + dup.shapes = {(label if label not in columns else columns[label]):dup.shapes[label] for label in dup.shapes} + return dup def sort_by(self,labels,ascending=True): @@ -269,10 +288,12 @@ class Table: Set sort order. """ - self._label_flat() - self.data.sort_values(labels,axis=0,inplace=True,ascending=ascending) - self._label_condensed() - self.comments.append(f'sorted by [{", ".join(labels)}]') + dup = self.copy() + dup._label_flat() + dup.data.sort_values(labels,axis=0,inplace=True,ascending=ascending) + dup._label_condensed() + dup.comments.append(f'sorted {"ascending" if ascending else "descending"} by {labels}') + return dup def append(self,other): @@ -290,7 +311,9 @@ class Table: if self.shapes != other.shapes or not self.data.columns.equals(other.data.columns): raise KeyError('Labels or shapes or order do not match') else: - self.data = self.data.append(other.data,ignore_index=True) + dup = self.copy() + dup.data = dup.data.append(other.data,ignore_index=True) + return dup def join(self,other): @@ -308,9 +331,11 @@ class Table: if set(self.shapes) & set(other.shapes) or self.data.shape[0] != other.data.shape[0]: raise KeyError('Dublicated keys or row count mismatch') else: - self.data = self.data.join(other.data) + dup = self.copy() + dup.data = dup.data.join(other.data) for key in other.shapes: - self.shapes[key] = other.shapes[key] + dup.shapes[key] = other.shapes[key] + return dup def to_file(self,fname,format='ASCII',new_style=False): diff --git a/python/tests/test_Orientation.py b/python/tests/test_Orientation.py index 636eeb0c4..9a23dc0ed 100644 --- a/python/tests/test_Orientation.py +++ b/python/tests/test_Orientation.py @@ -105,7 +105,7 @@ class TestOrientation: if update: coords = np.array([(1,i+1) for i,x in enumerate(eu)]) table = Table(eu,{'Eulers':(3,)}) - table.add('pos',coords) + table = table.add('pos',coords) table.to_ASCII(reference) assert np.allclose(eu,Table.from_ASCII(reference).get('Eulers')) diff --git a/python/tests/test_Table.py b/python/tests/test_Table.py index 6f9eca2d5..1763e27ef 100644 --- a/python/tests/test_Table.py +++ b/python/tests/test_Table.py @@ -81,13 +81,11 @@ class TestTable: Table.from_ASCII(f) def test_set(self,default): - default.set('F',np.zeros((5,3,3)),'set to zero') - d=default.get('F') + d = default.set('F',np.zeros((5,3,3)),'set to zero').get('F') assert np.allclose(d,0.0) and d.shape[1:] == (3,3) def test_set_component(self,default): - default.set('1_F',np.zeros((5)),'set to zero') - d=default.get('F') + d = default.set('1_F',np.zeros((5)),'set to zero').get('F') assert np.allclose(d[...,0,0],0.0) and d.shape[1:] == (3,3) def test_labels(self,default): @@ -95,36 +93,34 @@ class TestTable: def test_add(self,default): d = np.random.random((5,9)) - default.add('nine',d,'random data') - assert np.allclose(d,default.get('nine')) + assert np.allclose(d,default.add('nine',d,'random data').get('nine')) def test_rename_equivalent(self): x = np.random.random((5,13)) t = Table(x,{'F':(3,3),'v':(3,),'s':(1,)},['random test data']) s = t.get('s') - t.rename('s','u') - u = t.get('u') + u = t.rename('s','u').get('u') assert np.all(s == u) def test_rename_gone(self,default): - default.rename('v','V') - assert 'v' not in default.shapes and 'v' not in default.data.columns + gone = default.rename('v','V') + assert 'v' not in gone.shapes and 'v' not in gone.data.columns with pytest.raises(KeyError): - default.get('v') + gone.get('v') def test_delete(self,default): - default.delete('v') - assert 'v' not in default.shapes and 'v' not in default.data.columns + delete = default.delete('v') + assert 'v' not in delete.shapes and 'v' not in delete.data.columns with pytest.raises(KeyError): - default.get('v') + delete.get('v') def test_join(self): x = np.random.random((5,13)) a = Table(x,{'F':(3,3),'v':(3,),'s':(1,)},['random test data']) y = np.random.random((5,3)) b = Table(y,{'u':(3,)},['random test data']) - a.join(b) - assert np.array_equal(a.get('u'), b.get('u')) + c = a.join(b) + assert np.array_equal(c.get('u'), b.get('u')) def test_join_invalid(self): x = np.random.random((5,13)) @@ -135,8 +131,8 @@ class TestTable: def test_append(self): x = np.random.random((5,13)) a = Table(x,{'F':(3,3),'v':(3,),'s':(1,)},['random test data']) - a.append(a) - assert np.array_equal(a.data[:5].to_numpy(),a.data[5:].to_numpy()) + b = a.append(a) + assert np.array_equal(b.data[:5].to_numpy(),b.data[5:].to_numpy()) def test_append_invalid(self): x = np.random.random((5,13)) @@ -163,29 +159,26 @@ class TestTable: x = np.random.random((5,13)) t = Table(x,{'F':(3,3),'v':(3,),'s':(1,)},['random test data']) unsort = t.get('s') - t.sort_by('s') - sort = t.get('s') + sort = t.sort_by('s').get('s') assert np.all(np.sort(unsort,0)==sort) def test_sort_component(self): x = np.random.random((5,12)) t = Table(x,{'F':(3,3),'v':(3,)},['random test data']) unsort = t.get('4_F') - t.sort_by('4_F') - sort = t.get('4_F') + sort = t.sort_by('4_F').get('4_F') assert np.all(np.sort(unsort,0)==sort) def test_sort_revert(self): x = np.random.random((5,12)) t = Table(x,{'F':(3,3),'v':(3,)},['random test data']) - t.sort_by('4_F',ascending=False) - sort = t.get('4_F') + sort = t.sort_by('4_F',ascending=False).get('4_F') assert np.all(np.sort(sort,0)==sort[::-1,:]) def test_sort(self): t = Table(np.array([[0,1,],[2,1,]]), {'v':(2,)}, - ['test data']) - t.add('s',np.array(['b','a'])) - t.sort_by('s') + ['test data'])\ + .add('s',np.array(['b','a']))\ + .sort_by('s') assert np.all(t.get('1_v') == np.array([2,0]).reshape(2,1)) From e0375ef5ddcfaba9043c2dcbde94af18da5aa8ac Mon Sep 17 00:00:00 2001 From: Martin Diehl Date: Mon, 14 Sep 2020 08:09:49 +0200 Subject: [PATCH 02/11] testset without tests for old shell scripts --- PRIVATE | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/PRIVATE b/PRIVATE index 92ca3e83b..1e398d1e3 160000 --- a/PRIVATE +++ b/PRIVATE @@ -1 +1 @@ -Subproject commit 92ca3e83b6093c1af277cfc06a504e4bb09fe8bc +Subproject commit 1e398d1e3a4cd627d1902285159c7711a4a4e9d4 From 1da0c64fd41e0f746a7497aef9d8ae70d31435a6 Mon Sep 17 00:00:00 2001 From: Martin Diehl Date: Mon, 14 Sep 2020 10:52:59 +0200 Subject: [PATCH 03/11] fixed tests --- PRIVATE | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/PRIVATE b/PRIVATE index 1e398d1e3..dc3aa7b20 160000 --- a/PRIVATE +++ b/PRIVATE @@ -1 +1 @@ -Subproject commit 1e398d1e3a4cd627d1902285159c7711a4a4e9d4 +Subproject commit dc3aa7b20590f9f72afc6a3d2c4cbee0424208a6 From 7d6a1dc58373672b8ae08e0934c488e606cac732 Mon Sep 17 00:00:00 2001 From: Martin Diehl Date: Mon, 14 Sep 2020 11:52:54 +0200 Subject: [PATCH 04/11] 'fixed' broken test actually, old pandas version was broken. Now (after an update) it should work --- PRIVATE | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/PRIVATE b/PRIVATE index dc3aa7b20..8e3ca0385 160000 --- a/PRIVATE +++ b/PRIVATE @@ -1 +1 @@ -Subproject commit dc3aa7b20590f9f72afc6a3d2c4cbee0424208a6 +Subproject commit 8e3ca03857b569ffa73baf78ac0cffd288e4eec2 From 8a32a1529929399a1c26f9ef3ca3fa01a02b43ca Mon Sep 17 00:00:00 2001 From: Martin Diehl Date: Mon, 14 Sep 2020 12:17:43 +0200 Subject: [PATCH 05/11] changed to out-of-place mode --- PRIVATE | 2 +- processing/post/DADF5_postResults.py | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/PRIVATE b/PRIVATE index 8e3ca0385..3a43b550b 160000 --- a/PRIVATE +++ b/PRIVATE @@ -1 +1 @@ -Subproject commit 8e3ca03857b569ffa73baf78ac0cffd288e4eec2 +Subproject commit 3a43b550b5a0054c708e7cc5b70af9dd6a41d141 diff --git a/processing/post/DADF5_postResults.py b/processing/post/DADF5_postResults.py index 9c520ac33..e81330581 100755 --- a/processing/post/DADF5_postResults.py +++ b/processing/post/DADF5_postResults.py @@ -46,7 +46,7 @@ for filename in options.filenames: for label in options.con: x = results.get_dataset_location(label) if len(x) != 0: - table.add(label,results.read_dataset(x,0,plain=True).reshape(results.grid.prod(),-1)) + table = table.add(label,results.read_dataset(x,0,plain=True).reshape(results.grid.prod(),-1)) results.pick('constituents', False) results.pick('materialpoints',True) From 4738ab6a5997263aaf0ca5d3fb4f54098135584b Mon Sep 17 00:00:00 2001 From: Martin Diehl Date: Mon, 14 Sep 2020 14:15:55 +0200 Subject: [PATCH 06/11] out-of place example test --- PRIVATE | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/PRIVATE b/PRIVATE index 3a43b550b..6abc9c275 160000 --- a/PRIVATE +++ b/PRIVATE @@ -1 +1 @@ -Subproject commit 3a43b550b5a0054c708e7cc5b70af9dd6a41d141 +Subproject commit 6abc9c2757794b345bcf81d7c966de312b8fb93d From df548e95fc70894b7b11a4ea0eee0e859d826a81 Mon Sep 17 00:00:00 2001 From: Philip Eisenlohr Date: Mon, 14 Sep 2020 15:11:48 +0200 Subject: [PATCH 07/11] [skip ci] added reference to explain Fp_0 = O_0 --- src/crystallite.f90 | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/crystallite.f90 b/src/crystallite.f90 index 9d2d534d7..018293f63 100644 --- a/src/crystallite.f90 +++ b/src/crystallite.f90 @@ -255,7 +255,7 @@ subroutine crystallite_init do e = FEsolving_execElem(1),FEsolving_execElem(2) myNcomponents = homogenization_Ngrains(material_homogenizationAt(e)) do i = FEsolving_execIP(1), FEsolving_execIP(2); do c = 1, myNcomponents - crystallite_Fp0(1:3,1:3,c,i,e) = material_orientation0(c,i,e)%asMatrix() ! plastic def gradient reflects init orientation + crystallite_Fp0(1:3,1:3,c,i,e) = material_orientation0(c,i,e)%asMatrix() ! Fp reflects initial orientation (see 10.1016/j.actamat.2006.01.005) crystallite_Fp0(1:3,1:3,c,i,e) = crystallite_Fp0(1:3,1:3,c,i,e) & / math_det33(crystallite_Fp0(1:3,1:3,c,i,e))**(1.0_pReal/3.0_pReal) crystallite_Fi0(1:3,1:3,c,i,e) = constitutive_initialFi(c,i,e) From 89875c900d84203ea264f6ee592868088e9ef6df Mon Sep 17 00:00:00 2001 From: Philip Eisenlohr Date: Mon, 14 Sep 2020 13:19:49 -0400 Subject: [PATCH 08/11] adopted fixed runtime/memory plotting in tests --- PRIVATE | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/PRIVATE b/PRIVATE index 6abc9c275..8d5e08a8a 160000 --- a/PRIVATE +++ b/PRIVATE @@ -1 +1 @@ -Subproject commit 6abc9c2757794b345bcf81d7c966de312b8fb93d +Subproject commit 8d5e08a8a4dab7ed61f50ee37efb3fd115483437 From 2cb9b86353071a13b2ff5c162d131c5cbf7c3740 Mon Sep 17 00:00:00 2001 From: Philip Eisenlohr Date: Mon, 14 Sep 2020 15:59:49 -0400 Subject: [PATCH 09/11] use corrected testing --- PRIVATE | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/PRIVATE b/PRIVATE index 8d5e08a8a..313467be7 160000 --- a/PRIVATE +++ b/PRIVATE @@ -1 +1 @@ -Subproject commit 8d5e08a8a4dab7ed61f50ee37efb3fd115483437 +Subproject commit 313467be79a420a03985e0a04ecd72283380725f From 117f85ecd9be067c360447f45b76b93d73dd44ce Mon Sep 17 00:00:00 2001 From: Martin Diehl Date: Tue, 15 Sep 2020 01:02:04 +0200 Subject: [PATCH 10/11] missing from merge of 'table-out-of-place-only' server side problems with plotting are hopefully fixed now --- PRIVATE | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/PRIVATE b/PRIVATE index 313467be7..65ec74c07 160000 --- a/PRIVATE +++ b/PRIVATE @@ -1 +1 @@ -Subproject commit 313467be79a420a03985e0a04ecd72283380725f +Subproject commit 65ec74c07052e77f35a4b5e80bf110aff1f5ae61 From 77026e5d53dbcffc2a9935844e049ced4ff36a4c Mon Sep 17 00:00:00 2001 From: Test User Date: Tue, 15 Sep 2020 03:43:40 +0200 Subject: [PATCH 11/11] [skip ci] updated version information after successful test of v3.0.0-alpha-160-g117f85ec --- VERSION | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/VERSION b/VERSION index 2d2d2952b..6f2aeecd0 100644 --- a/VERSION +++ b/VERSION @@ -1 +1 @@ -v3.0.0-alpha-147-gf0806a9e +v3.0.0-alpha-160-g117f85ec