diff --git a/processing/pre/geom_addPrimitive.py b/processing/pre/geom_addPrimitive.py index 3e147e24d..f33ba27b1 100755 --- a/processing/pre/geom_addPrimitive.py +++ b/processing/pre/geom_addPrimitive.py @@ -132,7 +132,4 @@ for name in filenames: damask.util.croak(geom.update(np.where(mask,geom.microstructure,fill))) geom.add_comments(scriptID + ' ' + ' '.join(sys.argv[1:])) - if name is None: - sys.stdout.write(str(geom.show())) - else: - geom.to_file(name) + geom.to_file(sys.stdout if name is None else name,pack=False) diff --git a/processing/pre/geom_canvas.py b/processing/pre/geom_canvas.py index e1093d33b..edd5fe622 100755 --- a/processing/pre/geom_canvas.py +++ b/processing/pre/geom_canvas.py @@ -61,7 +61,7 @@ for name in filenames: canvas = np.full(new,options.fill if options.fill is not None else np.nanmax(geom.microstructure)+1,geom.microstructure.dtype) - l = np.clip( offset, 0,np.minimum(old +offset,new)) + l = np.clip( offset, 0,np.minimum(old +offset,new)) # noqa r = np.clip( offset+old,0,np.minimum(old*2+offset,new)) L = np.clip(-offset, 0,np.minimum(new -offset,old)) R = np.clip(-offset+new,0,np.minimum(new*2-offset,old)) @@ -71,4 +71,4 @@ for name in filenames: damask.util.croak(geom.update(canvas,origin=origin+offset*size/old,rescale=True)) geom.add_comments(scriptID + ' ' + ' '.join(sys.argv[1:])) - geom.to_file(sys.stdout if name is None else name) + geom.to_file(sys.stdout if name is None else name,pack=False) diff --git a/processing/pre/geom_clean.py b/processing/pre/geom_clean.py index 153d1eebd..8883c1b2a 100755 --- a/processing/pre/geom_clean.py +++ b/processing/pre/geom_clean.py @@ -39,4 +39,4 @@ for name in filenames: geom = damask.Geom.from_file(StringIO(''.join(sys.stdin.read())) if name is None else name) damask.util.croak(geom.clean(options.stencil)) geom.add_comments(scriptID + ' ' + ' '.join(sys.argv[1:])) - geom.to_file(sys.stdout if name is None else name) + geom.to_file(sys.stdout if name is None else name,pack=False) diff --git a/processing/pre/geom_fromDREAM3D.py b/processing/pre/geom_fromDREAM3D.py index 5d41e05b9..b20749b45 100755 --- a/processing/pre/geom_fromDREAM3D.py +++ b/processing/pre/geom_fromDREAM3D.py @@ -155,4 +155,4 @@ for name in filenames: homogenization=options.homogenization,comments=header) damask.util.croak(geom) - geom.to_file(os.path.splitext(name)[0]+'.geom') + geom.to_file(os.path.splitext(name)[0]+'.geom',pack=False) diff --git a/processing/pre/geom_fromMinimalSurface.py b/processing/pre/geom_fromMinimalSurface.py index ab42ce5af..bb6859b54 100755 --- a/processing/pre/geom_fromMinimalSurface.py +++ b/processing/pre/geom_fromMinimalSurface.py @@ -89,7 +89,4 @@ geom=damask.Geom(microstructure,options.size, comments=[scriptID + ' ' + ' '.join(sys.argv[1:])]) damask.util.croak(geom) -if name is None: - sys.stdout.write(str(geom.show())) -else: - geom.to_file(name) +geom.to_file(sys.stdout if name is None else name,pack=False) diff --git a/processing/pre/geom_fromOsteonGeometry.py b/processing/pre/geom_fromOsteonGeometry.py index 146bf216c..499a8867f 100755 --- a/processing/pre/geom_fromOsteonGeometry.py +++ b/processing/pre/geom_fromOsteonGeometry.py @@ -145,7 +145,4 @@ geom = damask.Geom(microstructure.reshape(grid), homogenization=options.homogenization,comments=header) damask.util.croak(geom) -if name is None: - sys.stdout.write(str(geom.show())) -else: - geom.to_file(name) +geom.to_file(sys.stdout if name is None else name,pack=False) diff --git a/processing/pre/geom_fromScratch.py b/processing/pre/geom_fromScratch.py index bfb294080..89fd27be5 100755 --- a/processing/pre/geom_fromScratch.py +++ b/processing/pre/geom_fromScratch.py @@ -63,7 +63,4 @@ geom = damask.Geom(microstructure=np.full(options.grid,options.fill,dtype=dtype) comments=scriptID + ' ' + ' '.join(sys.argv[1:])) damask.util.croak(geom) -if name is None: - sys.stdout.write(str(geom.show())) -else: - geom.to_file(name) +geom.to_file(sys.stdout if name is None else name,pack=False) diff --git a/processing/pre/geom_fromTable.py b/processing/pre/geom_fromTable.py index aa37451c7..f513c4834 100755 --- a/processing/pre/geom_fromTable.py +++ b/processing/pre/geom_fromTable.py @@ -152,7 +152,4 @@ for name in filenames: homogenization=options.homogenization,comments=header) damask.util.croak(geom) - if name is None: - sys.stdout.write(str(geom.show())) - else: - geom.to_file(os.path.splitext(name)[0]+'.geom') + geom.to_file(sys.stdout if name is None else os.path.splitext(name)[0]+'.geom',pack=False) diff --git a/processing/pre/geom_fromVoronoiTessellation.py b/processing/pre/geom_fromVoronoiTessellation.py index 9d4573c2c..28e215f85 100755 --- a/processing/pre/geom_fromVoronoiTessellation.py +++ b/processing/pre/geom_fromVoronoiTessellation.py @@ -302,7 +302,4 @@ for name in filenames: homogenization=options.homogenization,comments=header) damask.util.croak(geom) - if name is None: - sys.stdout.write(str(geom.show())) - else: - geom.to_file(os.path.splitext(name)[0]+'.geom') + geom.to_file(sys.stdout if name is None else os.path.splitext(name)[0]+'.geom',pack=False) diff --git a/processing/pre/geom_grainGrowth.py b/processing/pre/geom_grainGrowth.py index b31fc13f2..bdf8d8efe 100755 --- a/processing/pre/geom_grainGrowth.py +++ b/processing/pre/geom_grainGrowth.py @@ -172,7 +172,4 @@ for name in filenames: damask.util.croak(geom.update(microstructure[0:grid_original[0],0:grid_original[1],0:grid_original[2]])) geom.add_comments(scriptID + ' ' + ' '.join(sys.argv[1:])) - if name is None: - sys.stdout.write(str(geom.show())) - else: - geom.to_file(name) + geom.to_file(sys.stdout if name is None else name,pack=False) diff --git a/processing/pre/geom_mirror.py b/processing/pre/geom_mirror.py index ff47cb88b..cca0a4e10 100755 --- a/processing/pre/geom_mirror.py +++ b/processing/pre/geom_mirror.py @@ -44,4 +44,4 @@ for name in filenames: geom = damask.Geom.from_file(StringIO(''.join(sys.stdin.read())) if name is None else name) damask.util.croak(geom.mirror(options.directions,options.reflect)) geom.add_comments(scriptID + ' ' + ' '.join(sys.argv[1:])) - geom.to_file(sys.stdout if name is None else name) + geom.to_file(sys.stdout if name is None else name,pack=False) diff --git a/processing/pre/geom_renumber.py b/processing/pre/geom_renumber.py index df817b1fc..1e28ca921 100755 --- a/processing/pre/geom_renumber.py +++ b/processing/pre/geom_renumber.py @@ -34,4 +34,4 @@ for name in filenames: geom = damask.Geom.from_file(StringIO(''.join(sys.stdin.read())) if name is None else name) damask.util.croak(self.renumber) geom.add_comments(scriptID + ' ' + ' '.join(sys.argv[1:])) - geom.to_file(sys.stdout if name is None else name) + geom.to_file(sys.stdout if name is None else name,pack=False) diff --git a/processing/pre/geom_rescale.py b/processing/pre/geom_rescale.py index 8f5276b9d..55c2e57a2 100755 --- a/processing/pre/geom_rescale.py +++ b/processing/pre/geom_rescale.py @@ -58,4 +58,4 @@ for name in filenames: geom.scale(new_grid) damask.util.croak(geom.update(microstructure = None,size = new_size)) geom.add_comments(scriptID + ' ' + ' '.join(sys.argv[1:])) - geom.to_file(sys.stdout if name is None else name) + geom.to_file(sys.stdout if name is None else name,pack=False) diff --git a/processing/pre/geom_rotate.py b/processing/pre/geom_rotate.py index 6cca99caf..977e00b65 100755 --- a/processing/pre/geom_rotate.py +++ b/processing/pre/geom_rotate.py @@ -95,4 +95,4 @@ for name in filenames: damask.util.croak(geom.update(microstructure,origin=origin-(np.asarray(microstructure.shape)-grid)/2*size/grid,rescale=True)) geom.add_comments(scriptID + ' ' + ' '.join(sys.argv[1:])) - geom.to_file(sys.stdout if name is None else name) + geom.to_file(sys.stdout if name is None else name,pack=False) diff --git a/processing/pre/geom_translate.py b/processing/pre/geom_translate.py index 4b91920ae..2d4279821 100755 --- a/processing/pre/geom_translate.py +++ b/processing/pre/geom_translate.py @@ -58,7 +58,4 @@ for name in filenames: damask.util.croak(geom.update(substituted,origin=geom.get_origin()+options.origin)) geom.add_comments(scriptID + ' ' + ' '.join(sys.argv[1:])) - if name is None: - sys.stdout.write(str(geom.show())) - else: - geom.to_file(name) + geom.to_file(sys.stdout if name is None else name,pack=False) diff --git a/processing/pre/geom_vicinityOffset.py b/processing/pre/geom_vicinityOffset.py index 0b86adfb9..e30779d31 100755 --- a/processing/pre/geom_vicinityOffset.py +++ b/processing/pre/geom_vicinityOffset.py @@ -82,4 +82,4 @@ for name in filenames: geom.microstructure + offset,geom.microstructure))) geom.add_comments(scriptID + ' ' + ' '.join(sys.argv[1:])) - geom.to_file(sys.stdout if name is None else name) + geom.to_file(sys.stdout if name is None else name,pack=False) diff --git a/python/damask/geom.py b/python/damask/geom.py index e544765a4..e2dcd9bcb 100644 --- a/python/damask/geom.py +++ b/python/damask/geom.py @@ -519,5 +519,5 @@ class Geom(): for i, oldID in enumerate(np.unique(self.microstructure)): renumbered = np.where(self.microstructure == oldID, i+1, renumbered) - return self.update(renumbered)) + return self.update(renumbered) #self.add_comments('tbd')