From be0668dc272ffaadce5fff61dc03a8ebf72a665e Mon Sep 17 00:00:00 2001 From: Philip Eisenlohr Date: Thu, 3 Sep 2020 11:19:19 -0400 Subject: [PATCH] fixed all affected shell scripts --- processing/legacy/addAPS34IDEstrainCoords.py | 2 +- processing/legacy/addCumulative.py | 2 +- processing/post/DADF5_postResults.py | 2 +- processing/post/addCompatibilityMismatch.py | 2 +- processing/post/addCurl.py | 2 +- processing/post/addDerivative.py | 2 +- processing/post/addDisplacement.py | 4 ++-- processing/post/addDivergence.py | 2 +- processing/post/addEuclideanDistance.py | 2 +- processing/post/addGaussian.py | 2 +- processing/post/addGradient.py | 2 +- processing/post/addIndexed.py | 4 ++-- processing/post/addOrientations.py | 2 +- processing/post/addSchmidfactors.py | 2 +- processing/post/permuteData.py | 2 +- processing/pre/geom_fromDREAM3D.py | 2 +- processing/pre/geom_fromMinimalSurface.py | 2 +- processing/pre/geom_fromOsteonGeometry.py | 2 +- processing/pre/geom_fromTable.py | 3 ++- processing/pre/geom_fromVoronoiTessellation.py | 3 ++- processing/pre/geom_grainGrowth.py | 2 +- processing/pre/seeds_fromDistribution.py | 2 +- processing/pre/seeds_fromGeom.py | 4 ++-- processing/pre/seeds_fromPokes.py | 4 ++-- processing/pre/seeds_fromRandom.py | 2 +- 25 files changed, 31 insertions(+), 29 deletions(-) diff --git a/processing/legacy/addAPS34IDEstrainCoords.py b/processing/legacy/addAPS34IDEstrainCoords.py index d71116c6a..9ba51ada1 100755 --- a/processing/legacy/addAPS34IDEstrainCoords.py +++ b/processing/legacy/addAPS34IDEstrainCoords.py @@ -49,4 +49,4 @@ for name in filenames: table.add('coord',rot_to_TSL.broadcast_to(coord.shape[0]) @ coord,scriptID+' '+' '.join(sys.argv[1:])) - table.to_ASCII(sys.stdout if name is None else name) + table.to_file(sys.stdout if name is None else name) diff --git a/processing/legacy/addCumulative.py b/processing/legacy/addCumulative.py index 958c6a70a..f84828a89 100755 --- a/processing/legacy/addCumulative.py +++ b/processing/legacy/addCumulative.py @@ -45,4 +45,4 @@ for name in filenames: np.cumprod(table.get(label),0) if options.product else np.cumsum(table.get(label),0), scriptID+' '+' '.join(sys.argv[1:])) - table.to_ASCII(sys.stdout if name is None else name) + table.to_file(sys.stdout if name is None else name) diff --git a/processing/post/DADF5_postResults.py b/processing/post/DADF5_postResults.py index 2230ba563..08c8c7070 100755 --- a/processing/post/DADF5_postResults.py +++ b/processing/post/DADF5_postResults.py @@ -60,4 +60,4 @@ for filename in options.filenames: os.mkdir(dirname,0o755) file_out = '{}_inc{}.txt'.format(os.path.splitext(os.path.split(filename)[-1])[0], inc[3:].zfill(N_digits)) - table.to_ASCII(os.path.join(dirname,file_out)) + table.to_file(os.path.join(dirname,file_out)) diff --git a/processing/post/addCompatibilityMismatch.py b/processing/post/addCompatibilityMismatch.py index 59eafc077..bd55ab66a 100755 --- a/processing/post/addCompatibilityMismatch.py +++ b/processing/post/addCompatibilityMismatch.py @@ -191,4 +191,4 @@ for name in filenames: volumeMismatch.reshape(-1,1,order='F'), scriptID+' '+' '.join(sys.argv[1:])) - table.to_ASCII(sys.stdout if name is None else name) + table.to_file(sys.stdout if name is None else name) diff --git a/processing/post/addCurl.py b/processing/post/addCurl.py index 17459a2df..a9ddc8ae8 100755 --- a/processing/post/addCurl.py +++ b/processing/post/addCurl.py @@ -55,4 +55,4 @@ for name in filenames: curl.reshape(tuple(grid)+(-1,)).reshape(-1,np.prod(shape),order='F'), scriptID+' '+' '.join(sys.argv[1:])) - table.to_ASCII(sys.stdout if name is None else name) + table.to_file(sys.stdout if name is None else name) diff --git a/processing/post/addDerivative.py b/processing/post/addDerivative.py index 4e9410794..9030ae83b 100755 --- a/processing/post/addDerivative.py +++ b/processing/post/addDerivative.py @@ -71,4 +71,4 @@ for name in filenames: derivative(table.get(options.coordinates),table.get(label)), scriptID+' '+' '.join(sys.argv[1:])) - table.to_ASCII(sys.stdout if name is None else name) + table.to_file(sys.stdout if name is None else name) diff --git a/processing/post/addDisplacement.py b/processing/post/addDisplacement.py index 6f4a60192..80725410d 100755 --- a/processing/post/addDisplacement.py +++ b/processing/post/addDisplacement.py @@ -60,7 +60,7 @@ for name in filenames: 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:])) - table.to_ASCII(sys.stdout if name is None else os.path.splitext(name)[0]+'_nodal.txt') + 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), damask.grid_filters.cell_displacement_avg(size,F).reshape(-1,3,order='F'), @@ -68,4 +68,4 @@ for name in filenames: table.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_ASCII(sys.stdout if name is None else name) + table.to_file(sys.stdout if name is None else name) diff --git a/processing/post/addDivergence.py b/processing/post/addDivergence.py index 50048b44e..9abe1e2c6 100755 --- a/processing/post/addDivergence.py +++ b/processing/post/addDivergence.py @@ -55,4 +55,4 @@ for name in filenames: div.reshape(tuple(grid)+(-1,)).reshape(-1,np.prod(shape)//3,order='F'), scriptID+' '+' '.join(sys.argv[1:])) - table.to_ASCII(sys.stdout if name is None else name) + table.to_file(sys.stdout if name is None else name) diff --git a/processing/post/addEuclideanDistance.py b/processing/post/addEuclideanDistance.py index be820220a..921afc826 100755 --- a/processing/post/addEuclideanDistance.py +++ b/processing/post/addEuclideanDistance.py @@ -184,4 +184,4 @@ for name in filenames: distance[i,:], scriptID+' '+' '.join(sys.argv[1:])) - table.to_ASCII(sys.stdout if name is None else name) + table.to_file(sys.stdout if name is None else name) diff --git a/processing/post/addGaussian.py b/processing/post/addGaussian.py index 86552deca..93397e215 100755 --- a/processing/post/addGaussian.py +++ b/processing/post/addGaussian.py @@ -73,4 +73,4 @@ for name in filenames: mode = 'wrap' if options.periodic else 'nearest'), scriptID+' '+' '.join(sys.argv[1:])) - table.to_ASCII(sys.stdout if name is None else name) + table.to_file(sys.stdout if name is None else name) diff --git a/processing/post/addGradient.py b/processing/post/addGradient.py index f63f24789..3aee29374 100755 --- a/processing/post/addGradient.py +++ b/processing/post/addGradient.py @@ -55,4 +55,4 @@ for name in filenames: grad.reshape(tuple(grid)+(-1,)).reshape(-1,np.prod(shape)*3,order='F'), scriptID+' '+' '.join(sys.argv[1:])) - table.to_ASCII(sys.stdout if name is None else name) + table.to_file(sys.stdout if name is None else name) diff --git a/processing/post/addIndexed.py b/processing/post/addIndexed.py index 98fed597b..50db36c20 100755 --- a/processing/post/addIndexed.py +++ b/processing/post/addIndexed.py @@ -57,8 +57,8 @@ for name in filenames: 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_ASCII(sys.stdout if name is None else name) + table.to_file(sys.stdout if name is None else name) diff --git a/processing/post/addOrientations.py b/processing/post/addOrientations.py index 706a959ad..79da15fdd 100755 --- a/processing/post/addOrientations.py +++ b/processing/post/addOrientations.py @@ -147,4 +147,4 @@ for name in filenames: if 'axisangle' in options.output: table.add('om({})'.format(label),o.as_axisangle(options.degrees), scriptID+' '+' '.join(sys.argv[1:])) - table.to_ASCII(sys.stdout if name is None else name) + table.to_file(sys.stdout if name is None else name) diff --git a/processing/post/addSchmidfactors.py b/processing/post/addSchmidfactors.py index d1899e9a0..26a0c5c93 100755 --- a/processing/post/addSchmidfactors.py +++ b/processing/post/addSchmidfactors.py @@ -189,4 +189,4 @@ for name in filenames: for i,label in enumerate(labels): table.add(label,S[:,i],scriptID+' '+' '.join(sys.argv[1:])) - table.to_ASCII(sys.stdout if name is None else name) + table.to_file(sys.stdout if name is None else name) diff --git a/processing/post/permuteData.py b/processing/post/permuteData.py index 1f4b80532..766558216 100755 --- a/processing/post/permuteData.py +++ b/processing/post/permuteData.py @@ -58,4 +58,4 @@ for name in filenames: rng.shuffle(uniques) table.set(label,uniques[inverse], scriptID+' '+' '.join(sys.argv[1:])) - table.to_ASCII(sys.stdout if name is None else name) + table.to_file(sys.stdout if name is None else name) diff --git a/processing/pre/geom_fromDREAM3D.py b/processing/pre/geom_fromDREAM3D.py index c48698e53..6b7ccc21a 100755 --- a/processing/pre/geom_fromDREAM3D.py +++ b/processing/pre/geom_fromDREAM3D.py @@ -154,4 +154,4 @@ for name in filenames: homogenization=options.homogenization,comments=header) damask.util.croak(geom) - geom.to_file(os.path.splitext(name)[0]+'.geom',pack=False) + geom.to_file(os.path.splitext(name)[0]+'.geom',format='ASCII',pack=False) diff --git a/processing/pre/geom_fromMinimalSurface.py b/processing/pre/geom_fromMinimalSurface.py index bb6859b54..e6289ba0a 100755 --- a/processing/pre/geom_fromMinimalSurface.py +++ b/processing/pre/geom_fromMinimalSurface.py @@ -89,4 +89,4 @@ geom=damask.Geom(microstructure,options.size, comments=[scriptID + ' ' + ' '.join(sys.argv[1:])]) damask.util.croak(geom) -geom.to_file(sys.stdout if name is None else name,pack=False) +geom.to_file(sys.stdout if name is None else name,format='ASCII',pack=False) diff --git a/processing/pre/geom_fromOsteonGeometry.py b/processing/pre/geom_fromOsteonGeometry.py index 627d92728..6c6326163 100755 --- a/processing/pre/geom_fromOsteonGeometry.py +++ b/processing/pre/geom_fromOsteonGeometry.py @@ -142,4 +142,4 @@ geom = damask.Geom(microstructure.reshape(grid), homogenization=options.homogenization,comments=header) damask.util.croak(geom) -geom.to_file(sys.stdout if name is None else name,pack=False) +geom.to_file(sys.stdout if name is None else name,format='ASCII',pack=False) diff --git a/processing/pre/geom_fromTable.py b/processing/pre/geom_fromTable.py index be5b3a23c..dc968b82e 100755 --- a/processing/pre/geom_fromTable.py +++ b/processing/pre/geom_fromTable.py @@ -105,4 +105,5 @@ for name in filenames: homogenization=options.homogenization,comments=header) damask.util.croak(geom) - geom.to_file(sys.stdout if name is None else os.path.splitext(name)[0]+'.geom',pack=False) + geom.to_file(sys.stdout if name is None else os.path.splitext(name)[0]+'.geom', + format='ASCII',pack=False) diff --git a/processing/pre/geom_fromVoronoiTessellation.py b/processing/pre/geom_fromVoronoiTessellation.py index e6755c28e..67a0dfecc 100755 --- a/processing/pre/geom_fromVoronoiTessellation.py +++ b/processing/pre/geom_fromVoronoiTessellation.py @@ -228,4 +228,5 @@ for name in filenames: homogenization=options.homogenization,comments=header) damask.util.croak(geom) - geom.to_file(sys.stdout if name is None else os.path.splitext(name)[0]+'.geom',pack=False) + geom.to_file(sys.stdout if name is None else os.path.splitext(name)[0]+'.geom', + format='ASCII',pack=False) diff --git a/processing/pre/geom_grainGrowth.py b/processing/pre/geom_grainGrowth.py index 6d1985ee3..0652d0583 100755 --- a/processing/pre/geom_grainGrowth.py +++ b/processing/pre/geom_grainGrowth.py @@ -172,4 +172,4 @@ for name in filenames: geom=geom.duplicate(microstructure[0:grid_original[0],0:grid_original[1],0:grid_original[2]]) geom.add_comments(scriptID + ' ' + ' '.join(sys.argv[1:])) - geom.to_file(sys.stdout if name is None else name,pack=False) + geom.to_file(sys.stdout if name is None else name,format='ASCII',pack=False) diff --git a/processing/pre/seeds_fromDistribution.py b/processing/pre/seeds_fromDistribution.py index d00016865..1a4ec6971 100755 --- a/processing/pre/seeds_fromDistribution.py +++ b/processing/pre/seeds_fromDistribution.py @@ -90,7 +90,7 @@ class myThread (threading.Thread): direction[i]*=2. i+= 1 perturbedSeedsTable.set('pos',coords) - perturbedSeedsTable.to_ASCII(perturbedSeedsVFile) + perturbedSeedsTable.to_file(perturbedSeedsVFile) #--- do tesselation with perturbed seed file ------------------------------------------------------ perturbedGeomVFile.close() diff --git a/processing/pre/seeds_fromGeom.py b/processing/pre/seeds_fromGeom.py index 0b741a077..ab64c6b1e 100755 --- a/processing/pre/seeds_fromGeom.py +++ b/processing/pre/seeds_fromGeom.py @@ -65,5 +65,5 @@ for name in filenames: table = damask.Table(seeds[mask],{'pos':(3,)},comments) table.add('microstructure',microstructure[mask]) - table.to_ASCII(sys.stdout if name is None else \ - os.path.splitext(name)[0]+'.seeds') + table.to_file(sys.stdout if name is None else \ + os.path.splitext(name)[0]+'.seeds') diff --git a/processing/pre/seeds_fromPokes.py b/processing/pre/seeds_fromPokes.py index 49bbe3429..78172fc23 100755 --- a/processing/pre/seeds_fromPokes.py +++ b/processing/pre/seeds_fromPokes.py @@ -92,5 +92,5 @@ for name in filenames: table = damask.Table(seeds,{'pos':(3,),'microstructure':(1,)},comments) table.set('microstructure',table.get('microstructure').astype(np.int)) - table.to_ASCII(sys.stdout if name is None else \ - os.path.splitext(name)[0]+'_poked_{}.seeds'.format(options.N)) + table.to_file(sys.stdout if name is None else \ + os.path.splitext(name)[0]+f'_poked_{options.N}.seeds') diff --git a/processing/pre/seeds_fromRandom.py b/processing/pre/seeds_fromRandom.py index be690713c..b9e419391 100755 --- a/processing/pre/seeds_fromRandom.py +++ b/processing/pre/seeds_fromRandom.py @@ -162,4 +162,4 @@ for name in filenames: else np.random.normal(loc = options.mean, scale = options.sigma, size = options.N) table.add('weight',weights) - table.to_ASCII(sys.stdout if name is None else name) + table.to_file(sys.stdout if name is None else name)