From d49750341146252917a93a5996553d7e82cc4562 Mon Sep 17 00:00:00 2001 From: Martin Diehl Date: Tue, 26 Apr 2016 22:49:58 +0200 Subject: [PATCH 1/3] renamed options.coords/options.coordinates consistently to options.pos --- processing/post/addCompatibilityMismatch.py | 14 +++++++------- processing/post/addCurl.py | 8 ++++---- processing/post/addDisplacement.py | 16 ++++++++-------- processing/post/addDivergence.py | 8 ++++---- processing/post/addEuclideanDistance.py | 10 +++++----- processing/post/addGradient.py | 8 ++++---- processing/post/averageDown.py | 8 ++++---- processing/post/blowUp.py | 10 +++++----- processing/post/stddevDown.py | 10 +++++----- processing/pre/geom_fromTable.py | 8 ++++---- 10 files changed, 50 insertions(+), 50 deletions(-) diff --git a/processing/post/addCompatibilityMismatch.py b/processing/post/addCompatibilityMismatch.py index 884702b93..3a73859e1 100755 --- a/processing/post/addCompatibilityMismatch.py +++ b/processing/post/addCompatibilityMismatch.py @@ -21,7 +21,7 @@ Operates on periodic three-dimensional x,y,z-ordered data sets. parser.add_option('-c','--coordinates', - dest = 'coords', + dest = 'pos', type = 'string', metavar = 'string', help = 'column heading of coordinates [%default]') parser.add_option('-f','--defgrad', @@ -36,10 +36,10 @@ parser.add_option('--no-volume','-v', dest = 'volume', action = 'store_false', help = 'omit volume mismatch') -parser.set_defaults(coords = 'pos', - defgrad = 'f', - shape = True, - volume = True, +parser.set_defaults(pos = 'pos', + defgrad = 'f', + shape = True, + volume = True, ) (options,filenames) = parser.parse_args() @@ -64,8 +64,8 @@ for name in filenames: errors = [] remarks = [] - if table.label_dimension(options.coords) != 3: errors.append('coordinates {} are not a vector.'.format(options.coords)) - else: colCoord = table.label_index(options.coords) + if table.label_dimension(options.pos) != 3: errors.append('coordinates {} are not a vector.'.format(options.pos)) + else: colCoord = table.label_index(options.pos) if table.label_dimension(options.defgrad) != 9: errors.append('deformation gradient {} is not a tensor.'.format(options.defgrad)) else: colF = table.label_index(options.defgrad) diff --git a/processing/post/addCurl.py b/processing/post/addCurl.py index e368dc482..5c9a4b411 100755 --- a/processing/post/addCurl.py +++ b/processing/post/addCurl.py @@ -71,7 +71,7 @@ Deals with both vector- and tensor fields. """, version = scriptID) parser.add_option('-p','--pos','--periodiccellcenter', - dest = 'coords', + dest = 'pos', type = 'string', metavar = 'string', help = 'label of coordinates [%default]') parser.add_option('-v','--vector', @@ -83,7 +83,7 @@ parser.add_option('-t','--tensor', action = 'extend', metavar = '', help = 'label(s) of tensor field values') -parser.set_defaults(coords = 'pos', +parser.set_defaults(pos = 'pos', ) (options,filenames) = parser.parse_args() @@ -114,8 +114,8 @@ for name in filenames: remarks = [] column = {} - if table.label_dimension(options.coords) != 3: errors.append('coordinates {} are not a vector.'.format(options.coords)) - else: colCoord = table.label_index(options.coords) + if table.label_dimension(options.pos) != 3: errors.append('coordinates {} are not a vector.'.format(options.pos)) + else: colCoord = table.label_index(options.pos) for type, data in items.iteritems(): for what in (data['labels'] if data['labels'] is not None else []): diff --git a/processing/post/addDisplacement.py b/processing/post/addDisplacement.py index 0bafdb6cc..f52c8b19b 100755 --- a/processing/post/addDisplacement.py +++ b/processing/post/addDisplacement.py @@ -101,7 +101,7 @@ parser.add_option('-f', help = 'column label of deformation gradient [%default]') parser.add_option('-p', '--pos', '--position', - dest = 'coords', + dest = 'pos', metavar = 'string', help = 'label of coordinates [%default]') parser.add_option('--nodal', @@ -110,7 +110,7 @@ parser.add_option('--nodal', help = 'output nodal (instad of cell-centered) displacements') parser.set_defaults(defgrad = 'f', - coords = 'pos', + pos = 'pos', nodal = False, ) @@ -141,13 +141,13 @@ for name in filenames: if table.label_dimension(options.defgrad) != 9: errors.append('deformation gradient "{}" is not a 3x3 tensor.'.format(options.defgrad)) - coordDim = table.label_dimension(options.coords) + coordDim = table.label_dimension(options.pos) if not 3 >= coordDim >= 1: - errors.append('coordinates "{}" need to have one, two, or three dimensions.'.format(options.coords)) + errors.append('coordinates "{}" need to have one, two, or three dimensions.'.format(options.pos)) elif coordDim < 3: remarks.append('appending {} dimension{} to coordinates "{}"...'.format(3-coordDim, 's' if coordDim < 2 else '', - options.coords)) + options.pos)) if remarks != []: damask.util.croak(remarks) if errors != []: @@ -157,7 +157,7 @@ for name in filenames: # --------------- figure out size and grid --------------------------------------------------------- - table.data_readArray([options.defgrad,options.coords]) + table.data_readArray([options.defgrad,options.pos]) table.data_rewind() if len(table.data.shape) < 2: table.data.shape += (1,) # expand to 2D shape @@ -196,8 +196,8 @@ for name in filenames: table.info_append(scriptID + '\t' + ' '.join(sys.argv[1:])) table.labels_append((['{}_pos' .format(i+1) for i in xrange(3)] if options.nodal else []) + - ['{}_avg({}).{}' .format(i+1,options.defgrad,options.coords) for i in xrange(3)] + - ['{}_fluct({}).{}'.format(i+1,options.defgrad,options.coords) for i in xrange(3)] ) + ['{}_avg({}).{}' .format(i+1,options.defgrad,options.pos) for i in xrange(3)] + + ['{}_fluct({}).{}'.format(i+1,options.defgrad,options.pos) for i in xrange(3)] ) table.head_write() # ------------------------------------------ output data ------------------------------------------- diff --git a/processing/post/addDivergence.py b/processing/post/addDivergence.py index d62c02fda..f13cb3a89 100755 --- a/processing/post/addDivergence.py +++ b/processing/post/addDivergence.py @@ -57,7 +57,7 @@ Deals with both vector- and tensor-valued fields. """, version = scriptID) parser.add_option('-p','--pos','--periodiccellcenter', - dest = 'coords', + dest = 'pos', type = 'string', metavar = 'string', help = 'label of coordinates [%default]') parser.add_option('-v','--vector', @@ -69,7 +69,7 @@ parser.add_option('-t','--tensor', action = 'extend', metavar = '', help = 'label(s) of tensor field values') -parser.set_defaults(coords = 'pos', +parser.set_defaults(pos = 'pos', ) (options,filenames) = parser.parse_args() @@ -100,8 +100,8 @@ for name in filenames: remarks = [] column = {} - if table.label_dimension(options.coords) != 3: errors.append('coordinates {} are not a vector.'.format(options.coords)) - else: colCoord = table.label_index(options.coords) + if table.label_dimension(options.pos) != 3: errors.append('coordinates {} are not a vector.'.format(options.pos)) + else: colCoord = table.label_index(options.pos) for type, data in items.iteritems(): for what in (data['labels'] if data['labels'] is not None else []): diff --git a/processing/post/addEuclideanDistance.py b/processing/post/addEuclideanDistance.py index 16c8e5234..9181e3785 100755 --- a/processing/post/addEuclideanDistance.py +++ b/processing/post/addEuclideanDistance.py @@ -90,7 +90,7 @@ Add column(s) containing Euclidean distance to grain structural features: bounda parser.add_option('-p', '--pos', '--position', - dest = 'coords', metavar = 'string', + dest = 'pos', metavar = 'string', help = 'label of coordinates [%default]') parser.add_option('-i', '--id', '--identifier', @@ -109,7 +109,7 @@ parser.add_option('-s', dest = 'scale', type = 'float', metavar = 'float', help = 'voxel size [%default]') -parser.set_defaults(coords = 'pos', +parser.set_defaults(pos = 'pos', id = 'texture', neighborhood = 'neumann', scale = 1.0, @@ -151,10 +151,10 @@ for name in filenames: remarks = [] column = {} - coordDim = table.label_dimension(options.coords) + coordDim = table.label_dimension(options.pos) if not 3 >= coordDim >= 1: - errors.append('coordinates "{}" need to have one, two, or three dimensions.'.format(options.coords)) - else: coordCol = table.label_index(options.coords) + errors.append('coordinates "{}" need to have one, two, or three dimensions.'.format(options.pos)) + else: coordCol = table.label_index(options.pos) if table.label_dimension(options.id) != 1: errors.append('grain identifier {} not found.'.format(options.id)) else: idCol = table.label_index(options.id) diff --git a/processing/post/addGradient.py b/processing/post/addGradient.py index b2d004bd2..12ecf218d 100755 --- a/processing/post/addGradient.py +++ b/processing/post/addGradient.py @@ -61,7 +61,7 @@ Deals with both vector- and scalar fields. """, version = scriptID) parser.add_option('-p','--pos','--periodiccellcenter', - dest = 'coords', + dest = 'pos', type = 'string', metavar = 'string', help = 'label of coordinates [%default]') parser.add_option('-v','--vector', @@ -73,7 +73,7 @@ parser.add_option('-s','--scalar', action = 'extend', metavar = '', help = 'label(s) of scalar field values') -parser.set_defaults(coords = 'pos', +parser.set_defaults(pos = 'pos', ) (options,filenames) = parser.parse_args() @@ -104,8 +104,8 @@ for name in filenames: remarks = [] column = {} - if table.label_dimension(options.coords) != 3: errors.append('coordinates {} are not a vector.'.format(options.coords)) - else: colCoord = table.label_index(options.coords) + if table.label_dimension(options.pos) != 3: errors.append('coordinates {} are not a vector.'.format(options.pos)) + else: colCoord = table.label_index(options.pos) for type, data in items.iteritems(): for what in (data['labels'] if data['labels'] is not None else []): diff --git a/processing/post/averageDown.py b/processing/post/averageDown.py index 0af56e176..808ed28bb 100755 --- a/processing/post/averageDown.py +++ b/processing/post/averageDown.py @@ -20,7 +20,7 @@ Average each data block of size 'packing' into single values thus reducing the f """, version = scriptID) parser.add_option('-c','--coordinates', - dest = 'coords', + dest = 'pos', type = 'string', metavar = 'string', help = 'column label of coordinates [%default]') parser.add_option('-p','--packing', @@ -39,7 +39,7 @@ parser.add_option('-s', '--size', dest = 'size', type = 'float', nargs = 3, metavar = 'float float float', help = 'size in x,y,z [autodetect]') -parser.set_defaults(coords = 'pos', +parser.set_defaults(pos = 'pos', packing = (2,2,2), shift = (0,0,0), grid = (0,0,0), @@ -75,8 +75,8 @@ for name in filenames: errors = [] remarks = [] - if table.label_dimension(options.coords) != 3: errors.append('coordinates {} are not a vector.'.format(options.coords)) - else: colCoord = table.label_index(options.coords) + if table.label_dimension(options.pos) != 3: errors.append('coordinates {} are not a vector.'.format(options.pos)) + else: colCoord = table.label_index(options.pos) if remarks != []: damask.util.croak(remarks) if errors != []: diff --git a/processing/post/blowUp.py b/processing/post/blowUp.py index 7e6266837..6a73fe15a 100755 --- a/processing/post/blowUp.py +++ b/processing/post/blowUp.py @@ -20,7 +20,7 @@ to resolution*packing. """, version = scriptID) parser.add_option('-c','--coordinates', - dest = 'coords', metavar = 'string', + dest = 'pos', metavar = 'string', help = 'column label of coordinates [%default]') parser.add_option('-p','--packing', dest = 'packing', type = 'int', nargs = 3, metavar = 'int int int', @@ -31,7 +31,7 @@ parser.add_option('-g','--grid', parser.add_option('-s','--size', dest = 'dimension', type = 'float', nargs = 3, metavar = 'int int int', help = 'dimension in x,y,z [autodetect]') -parser.set_defaults(coords = 'pos', +parser.set_defaults(pos = 'pos', packing = (2,2,2), grid = (0,0,0), size = (0.0,0.0,0.0), @@ -63,8 +63,8 @@ for name in filenames: errors = [] remarks = [] - if table.label_dimension(options.coords) != 3: errors.append('coordinates {} are not a vector.'.format(options.coords)) - else: colCoord = table.label_index(options.coords) + if table.label_dimension(options.pos) != 3: errors.append('coordinates {} are not a vector.'.format(options.pos)) + else: colCoord = table.label_index(options.pos) colElem = table.label_index('elem') @@ -76,7 +76,7 @@ for name in filenames: # --------------- figure out size and grid --------------------------------------------------------- - table.data_readArray(options.coords) + table.data_readArray(options.pos) table.data_rewind() coords = [np.unique(table.data[:,i]) for i in xrange(3)] diff --git a/processing/post/stddevDown.py b/processing/post/stddevDown.py index e14ee0058..f4fdf5a90 100755 --- a/processing/post/stddevDown.py +++ b/processing/post/stddevDown.py @@ -19,7 +19,7 @@ to resolution/packing. """, version = scriptID) -parser.add_option('-c','--coordinates', dest='coords', type='string',\ +parser.add_option('-c','--coordinates', dest='pos', type='string',\ help='column heading for coordinates [%default]') parser.add_option('-p','--packing', dest='packing', type='int', nargs=3, \ help='dimension of packed group %default') @@ -29,7 +29,7 @@ parser.add_option('-r','--resolution', dest='resolution', type='int', nargs=3, help='resolution in x,y,z [autodetect]') parser.add_option('-d','--dimension', dest='dimension', type='float', nargs=3, \ help='dimension in x,y,z [autodetect]') -parser.set_defaults(coords = 'ipinitialcoord') +parser.set_defaults(coords = 'pos') parser.set_defaults(packing = [2,2,2]) parser.set_defaults(shift = [0,0,0]) parser.set_defaults(resolution = [0,0,0]) @@ -75,12 +75,12 @@ for file in files: # --------------- figure out size and grid --------------------------------------------------------- try: - locationCol = table.labels.index('1_%s'%options.coords) # columns containing location data + locationCol = table.labels.index('1_%s'%options.pos) # columns containing location data except ValueError: try: - locationCol = table.labels.index('%s.x'%options.coords) # columns containing location data (legacy naming scheme) + locationCol = table.labels.index('%s.x'%options.pos) # columns containing location data (legacy naming scheme) except ValueError: - file['croak'].write('no coordinate data (1_%s/%s.x) found...\n'%(options.coords,options.coords)) + file['croak'].write('no coordinate data (1_%s/%s.x) found...\n'%(options.pos,options.pos)) continue if (any(options.resolution)==0 or any(options.dimension)==0.0): diff --git a/processing/pre/geom_fromTable.py b/processing/pre/geom_fromTable.py index 53281c5df..5466236e8 100755 --- a/processing/pre/geom_fromTable.py +++ b/processing/pre/geom_fromTable.py @@ -21,7 +21,7 @@ Generate geometry description and material configuration from position, phase, a """, version = scriptID) parser.add_option('--coordinates', - dest = 'coordinates', + dest = 'pos', type = 'string', metavar = 'string', help = 'coordinates label') parser.add_option('--phase', @@ -135,11 +135,11 @@ for name in filenames: # ------------------------------------------ sanity checks --------------------------------------- - coordDim = table.label_dimension(options.coordinates) + coordDim = table.label_dimension(options.pos) errors = [] if not 3 >= coordDim >= 2: - errors.append('coordinates "{}" need to have two or three dimensions.'.format(options.coordinates)) + errors.append('coordinates "{}" need to have two or three dimensions.'.format(options.pos)) if not np.all(table.label_dimension(label) == dim): errors.append('input "{}" needs to have dimension {}.'.format(label,dim)) if options.phase and table.label_dimension(options.phase) != 1: @@ -150,7 +150,7 @@ for name in filenames: table.close(dismiss = True) continue - table.data_readArray([options.coordinates] \ + table.data_readArray([options.pos] \ + ([label] if isinstance(label, types.StringTypes) else label) \ + ([options.phase] if options.phase else [])) From 02021b9bb0f1d7e7d270750c38706aa08511cddb Mon Sep 17 00:00:00 2001 From: Test User Date: Wed, 27 Apr 2016 04:13:14 +0200 Subject: [PATCH 2/3] updated version information after successful test of v2.0.0-201-gd497503 --- VERSION | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/VERSION b/VERSION index d0ea2c5ae..aeeddb7fb 100644 --- a/VERSION +++ b/VERSION @@ -1 +1 @@ -v2.0.0-199-gaae41e0 +v2.0.0-201-gd497503 From b3e987705805e9cb9d30cfde97c9cb510fc329f1 Mon Sep 17 00:00:00 2001 From: Philip Eisenlohr Date: Wed, 27 Apr 2016 09:28:43 -0400 Subject: [PATCH 3/3] changed from "coords" to "pos" remind user about (creating a new) nodal output file --- processing/post/addDisplacement.py | 25 +++++++++++++------------ 1 file changed, 13 insertions(+), 12 deletions(-) diff --git a/processing/post/addDisplacement.py b/processing/post/addDisplacement.py index 0bafdb6cc..782a7c24b 100755 --- a/processing/post/addDisplacement.py +++ b/processing/post/addDisplacement.py @@ -101,7 +101,7 @@ parser.add_option('-f', help = 'column label of deformation gradient [%default]') parser.add_option('-p', '--pos', '--position', - dest = 'coords', + dest = 'pos', metavar = 'string', help = 'label of coordinates [%default]') parser.add_option('--nodal', @@ -110,7 +110,7 @@ parser.add_option('--nodal', help = 'output nodal (instad of cell-centered) displacements') parser.set_defaults(defgrad = 'f', - coords = 'pos', + pos = 'pos', nodal = False, ) @@ -121,13 +121,14 @@ parser.set_defaults(defgrad = 'f', if filenames == []: filenames = [None] for name in filenames: + outname = (os.path.splitext(name)[0] + + '_nodal' + + os.path.splitext(name)[1]) if (options.nodal and name) else None try: table = damask.ASCIItable(name = name, - outname = (os.path.splitext(name)[0] + - '_nodal' + - os.path.splitext(name)[1]) if (options.nodal and name) else None, + outname = outname, buffered = False) except: continue - damask.util.report(scriptName,name) + damask.util.report(scriptName,'{}{}'.format(name,' --> {}'.format(outname) if outname else '')) # ------------------------------------------ read header ------------------------------------------ @@ -141,13 +142,13 @@ for name in filenames: if table.label_dimension(options.defgrad) != 9: errors.append('deformation gradient "{}" is not a 3x3 tensor.'.format(options.defgrad)) - coordDim = table.label_dimension(options.coords) + coordDim = table.label_dimension(options.pos) if not 3 >= coordDim >= 1: - errors.append('coordinates "{}" need to have one, two, or three dimensions.'.format(options.coords)) + errors.append('coordinates "{}" need to have one, two, or three dimensions.'.format(options.pos)) elif coordDim < 3: remarks.append('appending {} dimension{} to coordinates "{}"...'.format(3-coordDim, 's' if coordDim < 2 else '', - options.coords)) + options.pos)) if remarks != []: damask.util.croak(remarks) if errors != []: @@ -157,7 +158,7 @@ for name in filenames: # --------------- figure out size and grid --------------------------------------------------------- - table.data_readArray([options.defgrad,options.coords]) + table.data_readArray([options.defgrad,options.pos]) table.data_rewind() if len(table.data.shape) < 2: table.data.shape += (1,) # expand to 2D shape @@ -196,8 +197,8 @@ for name in filenames: table.info_append(scriptID + '\t' + ' '.join(sys.argv[1:])) table.labels_append((['{}_pos' .format(i+1) for i in xrange(3)] if options.nodal else []) + - ['{}_avg({}).{}' .format(i+1,options.defgrad,options.coords) for i in xrange(3)] + - ['{}_fluct({}).{}'.format(i+1,options.defgrad,options.coords) for i in xrange(3)] ) + ['{}_avg({}).{}' .format(i+1,options.defgrad,options.pos) for i in xrange(3)] + + ['{}_fluct({}).{}'.format(i+1,options.defgrad,options.pos) for i in xrange(3)] ) table.head_write() # ------------------------------------------ output data -------------------------------------------