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DAMASK_EICMD
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Merge remote branch 'origin/development' into pheno+

This commit is contained in:
zhangc43 2016-04-27 09:34:56 -04:00
parent 8ddb024df3 02021b9bb0
commit cf5a52be22
11 changed files with 51 additions and 51 deletions
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2
VERSION
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@ -1 +1 @@
v2.0.0-199-gaae41e0 v2.0.0-201-gd497503

8
processing/post/addCompatibilityMismatch.py
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@ -21,7 +21,7 @@ Operates on periodic three-dimensional x,y,z-ordered data sets.
parser.add_option('-c','--coordinates', parser.add_option('-c','--coordinates',
dest = 'coords', dest = 'pos',
type = 'string', metavar = 'string', type = 'string', metavar = 'string',
help = 'column heading of coordinates [%default]') help = 'column heading of coordinates [%default]')
parser.add_option('-f','--defgrad', parser.add_option('-f','--defgrad',
@ -36,7 +36,7 @@ parser.add_option('--no-volume','-v',
dest = 'volume', dest = 'volume',
action = 'store_false', action = 'store_false',
help = 'omit volume mismatch') help = 'omit volume mismatch')
parser.set_defaults(coords = 'pos', parser.set_defaults(pos = 'pos',
defgrad = 'f', defgrad = 'f',
shape = True, shape = True,
volume = True, volume = True,
@ -64,8 +64,8 @@ for name in filenames:
errors = [] errors = []
remarks = [] remarks = []
if table.label_dimension(options.coords) != 3: errors.append('coordinates {} are not a vector.'.format(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.coords) 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)) 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) else: colF = table.label_index(options.defgrad)

8
processing/post/addCurl.py
View File

@ -71,7 +71,7 @@ Deals with both vector- and tensor fields.
""", version = scriptID) """, version = scriptID)
parser.add_option('-p','--pos','--periodiccellcenter', parser.add_option('-p','--pos','--periodiccellcenter',
dest = 'coords', dest = 'pos',
type = 'string', metavar = 'string', type = 'string', metavar = 'string',
help = 'label of coordinates [%default]') help = 'label of coordinates [%default]')
parser.add_option('-v','--vector', parser.add_option('-v','--vector',
@ -83,7 +83,7 @@ parser.add_option('-t','--tensor',
action = 'extend', metavar = '<string LIST>', action = 'extend', metavar = '<string LIST>',
help = 'label(s) of tensor field values') help = 'label(s) of tensor field values')
parser.set_defaults(coords = 'pos', parser.set_defaults(pos = 'pos',
) )
(options,filenames) = parser.parse_args() (options,filenames) = parser.parse_args()
@ -114,8 +114,8 @@ for name in filenames:
remarks = [] remarks = []
column = {} column = {}
if table.label_dimension(options.coords) != 3: errors.append('coordinates {} are not a vector.'.format(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.coords) else: colCoord = table.label_index(options.pos)
for type, data in items.iteritems(): for type, data in items.iteritems():
for what in (data['labels'] if data['labels'] is not None else []): for what in (data['labels'] if data['labels'] is not None else []):

16
processing/post/addDisplacement.py
View File

@ -101,7 +101,7 @@ parser.add_option('-f',
help = 'column label of deformation gradient [%default]') help = 'column label of deformation gradient [%default]')
parser.add_option('-p', parser.add_option('-p',
'--pos', '--position', '--pos', '--position',
dest = 'coords', dest = 'pos',
metavar = 'string', metavar = 'string',
help = 'label of coordinates [%default]') help = 'label of coordinates [%default]')
parser.add_option('--nodal', parser.add_option('--nodal',
@ -110,7 +110,7 @@ parser.add_option('--nodal',
help = 'output nodal (instad of cell-centered) displacements') help = 'output nodal (instad of cell-centered) displacements')
parser.set_defaults(defgrad = 'f', parser.set_defaults(defgrad = 'f',
coords = 'pos', pos = 'pos',
nodal = False, nodal = False,
) )
@ -141,13 +141,13 @@ for name in filenames:
if table.label_dimension(options.defgrad) != 9: if table.label_dimension(options.defgrad) != 9:
errors.append('deformation gradient "{}" is not a 3x3 tensor.'.format(options.defgrad)) 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: 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: elif coordDim < 3:
remarks.append('appending {} dimension{} to coordinates "{}"...'.format(3-coordDim, remarks.append('appending {} dimension{} to coordinates "{}"...'.format(3-coordDim,
's' if coordDim < 2 else '', 's' if coordDim < 2 else '',
options.coords)) options.pos))
if remarks != []: damask.util.croak(remarks) if remarks != []: damask.util.croak(remarks)
if errors != []: if errors != []:
@ -157,7 +157,7 @@ for name in filenames:
# --------------- figure out size and grid --------------------------------------------------------- # --------------- figure out size and grid ---------------------------------------------------------
table.data_readArray([options.defgrad,options.coords]) table.data_readArray([options.defgrad,options.pos])
table.data_rewind() table.data_rewind()
if len(table.data.shape) < 2: table.data.shape += (1,) # expand to 2D shape 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.info_append(scriptID + '\t' + ' '.join(sys.argv[1:]))
table.labels_append((['{}_pos' .format(i+1) for i in xrange(3)] if options.nodal else []) + 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)] + ['{}_avg({}).{}' .format(i+1,options.defgrad,options.pos) for i in xrange(3)] +
['{}_fluct({}).{}'.format(i+1,options.defgrad,options.coords) for i in xrange(3)] ) ['{}_fluct({}).{}'.format(i+1,options.defgrad,options.pos) for i in xrange(3)] )
table.head_write() table.head_write()
# ------------------------------------------ output data ------------------------------------------- # ------------------------------------------ output data -------------------------------------------

8
processing/post/addDivergence.py
View File

@ -57,7 +57,7 @@ Deals with both vector- and tensor-valued fields.
""", version = scriptID) """, version = scriptID)
parser.add_option('-p','--pos','--periodiccellcenter', parser.add_option('-p','--pos','--periodiccellcenter',
dest = 'coords', dest = 'pos',
type = 'string', metavar = 'string', type = 'string', metavar = 'string',
help = 'label of coordinates [%default]') help = 'label of coordinates [%default]')
parser.add_option('-v','--vector', parser.add_option('-v','--vector',
@ -69,7 +69,7 @@ parser.add_option('-t','--tensor',
action = 'extend', metavar = '<string LIST>', action = 'extend', metavar = '<string LIST>',
help = 'label(s) of tensor field values') help = 'label(s) of tensor field values')
parser.set_defaults(coords = 'pos', parser.set_defaults(pos = 'pos',
) )
(options,filenames) = parser.parse_args() (options,filenames) = parser.parse_args()
@ -100,8 +100,8 @@ for name in filenames:
remarks = [] remarks = []
column = {} column = {}
if table.label_dimension(options.coords) != 3: errors.append('coordinates {} are not a vector.'.format(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.coords) else: colCoord = table.label_index(options.pos)
for type, data in items.iteritems(): for type, data in items.iteritems():
for what in (data['labels'] if data['labels'] is not None else []): for what in (data['labels'] if data['labels'] is not None else []):

10
processing/post/addEuclideanDistance.py
View File

@ -90,7 +90,7 @@ Add column(s) containing Euclidean distance to grain structural features: bounda
parser.add_option('-p', parser.add_option('-p',
'--pos', '--position', '--pos', '--position',
dest = 'coords', metavar = 'string', dest = 'pos', metavar = 'string',
help = 'label of coordinates [%default]') help = 'label of coordinates [%default]')
parser.add_option('-i', parser.add_option('-i',
'--id', '--identifier', '--id', '--identifier',
@ -109,7 +109,7 @@ parser.add_option('-s',
dest = 'scale', type = 'float', metavar = 'float', dest = 'scale', type = 'float', metavar = 'float',
help = 'voxel size [%default]') help = 'voxel size [%default]')
parser.set_defaults(coords = 'pos', parser.set_defaults(pos = 'pos',
id = 'texture', id = 'texture',
neighborhood = 'neumann', neighborhood = 'neumann',
scale = 1.0, scale = 1.0,
@ -151,10 +151,10 @@ for name in filenames:
remarks = [] remarks = []
column = {} column = {}
coordDim = table.label_dimension(options.coords) coordDim = table.label_dimension(options.pos)
if not 3 >= coordDim >= 1: 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))
else: coordCol = table.label_index(options.coords) else: coordCol = table.label_index(options.pos)
if table.label_dimension(options.id) != 1: errors.append('grain identifier {} not found.'.format(options.id)) if table.label_dimension(options.id) != 1: errors.append('grain identifier {} not found.'.format(options.id))
else: idCol = table.label_index(options.id) else: idCol = table.label_index(options.id)

8
processing/post/addGradient.py
View File

@ -61,7 +61,7 @@ Deals with both vector- and scalar fields.
""", version = scriptID) """, version = scriptID)
parser.add_option('-p','--pos','--periodiccellcenter', parser.add_option('-p','--pos','--periodiccellcenter',
dest = 'coords', dest = 'pos',
type = 'string', metavar = 'string', type = 'string', metavar = 'string',
help = 'label of coordinates [%default]') help = 'label of coordinates [%default]')
parser.add_option('-v','--vector', parser.add_option('-v','--vector',
@ -73,7 +73,7 @@ parser.add_option('-s','--scalar',
action = 'extend', metavar = '<string LIST>', action = 'extend', metavar = '<string LIST>',
help = 'label(s) of scalar field values') help = 'label(s) of scalar field values')
parser.set_defaults(coords = 'pos', parser.set_defaults(pos = 'pos',
) )
(options,filenames) = parser.parse_args() (options,filenames) = parser.parse_args()
@ -104,8 +104,8 @@ for name in filenames:
remarks = [] remarks = []
column = {} column = {}
if table.label_dimension(options.coords) != 3: errors.append('coordinates {} are not a vector.'.format(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.coords) else: colCoord = table.label_index(options.pos)
for type, data in items.iteritems(): for type, data in items.iteritems():
for what in (data['labels'] if data['labels'] is not None else []): for what in (data['labels'] if data['labels'] is not None else []):

8
processing/post/averageDown.py
View File

@ -20,7 +20,7 @@ Average each data block of size 'packing' into single values thus reducing the f
""", version = scriptID) """, version = scriptID)
parser.add_option('-c','--coordinates', parser.add_option('-c','--coordinates',
dest = 'coords', dest = 'pos',
type = 'string', metavar = 'string', type = 'string', metavar = 'string',
help = 'column label of coordinates [%default]') help = 'column label of coordinates [%default]')
parser.add_option('-p','--packing', parser.add_option('-p','--packing',
@ -39,7 +39,7 @@ parser.add_option('-s', '--size',
dest = 'size', dest = 'size',
type = 'float', nargs = 3, metavar = 'float float float', type = 'float', nargs = 3, metavar = 'float float float',
help = 'size in x,y,z [autodetect]') help = 'size in x,y,z [autodetect]')
parser.set_defaults(coords = 'pos', parser.set_defaults(pos = 'pos',
packing = (2,2,2), packing = (2,2,2),
shift = (0,0,0), shift = (0,0,0),
grid = (0,0,0), grid = (0,0,0),
@ -75,8 +75,8 @@ for name in filenames:
errors = [] errors = []
remarks = [] remarks = []
if table.label_dimension(options.coords) != 3: errors.append('coordinates {} are not a vector.'.format(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.coords) else: colCoord = table.label_index(options.pos)
if remarks != []: damask.util.croak(remarks) if remarks != []: damask.util.croak(remarks)
if errors != []: if errors != []:

10
processing/post/blowUp.py
View File

@ -20,7 +20,7 @@ to resolution*packing.
""", version = scriptID) """, version = scriptID)
parser.add_option('-c','--coordinates', parser.add_option('-c','--coordinates',
dest = 'coords', metavar = 'string', dest = 'pos', metavar = 'string',
help = 'column label of coordinates [%default]') help = 'column label of coordinates [%default]')
parser.add_option('-p','--packing', parser.add_option('-p','--packing',
dest = 'packing', type = 'int', nargs = 3, metavar = 'int int int', dest = 'packing', type = 'int', nargs = 3, metavar = 'int int int',
@ -31,7 +31,7 @@ parser.add_option('-g','--grid',
parser.add_option('-s','--size', parser.add_option('-s','--size',
dest = 'dimension', type = 'float', nargs = 3, metavar = 'int int int', dest = 'dimension', type = 'float', nargs = 3, metavar = 'int int int',
help = 'dimension in x,y,z [autodetect]') help = 'dimension in x,y,z [autodetect]')
parser.set_defaults(coords = 'pos', parser.set_defaults(pos = 'pos',
packing = (2,2,2), packing = (2,2,2),
grid = (0,0,0), grid = (0,0,0),
size = (0.0,0.0,0.0), size = (0.0,0.0,0.0),
@ -63,8 +63,8 @@ for name in filenames:
errors = [] errors = []
remarks = [] remarks = []
if table.label_dimension(options.coords) != 3: errors.append('coordinates {} are not a vector.'.format(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.coords) else: colCoord = table.label_index(options.pos)
colElem = table.label_index('elem') colElem = table.label_index('elem')
@ -76,7 +76,7 @@ for name in filenames:
# --------------- figure out size and grid --------------------------------------------------------- # --------------- figure out size and grid ---------------------------------------------------------
table.data_readArray(options.coords) table.data_readArray(options.pos)
table.data_rewind() table.data_rewind()
coords = [np.unique(table.data[:,i]) for i in xrange(3)] coords = [np.unique(table.data[:,i]) for i in xrange(3)]

10
processing/post/stddevDown.py
View File

@ -19,7 +19,7 @@ to resolution/packing.
""", version = scriptID) """, 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]') help='column heading for coordinates [%default]')
parser.add_option('-p','--packing', dest='packing', type='int', nargs=3, \ parser.add_option('-p','--packing', dest='packing', type='int', nargs=3, \
help='dimension of packed group %default') 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]') help='resolution in x,y,z [autodetect]')
parser.add_option('-d','--dimension', dest='dimension', type='float', nargs=3, \ parser.add_option('-d','--dimension', dest='dimension', type='float', nargs=3, \
help='dimension in x,y,z [autodetect]') 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(packing = [2,2,2])
parser.set_defaults(shift = [0,0,0]) parser.set_defaults(shift = [0,0,0])
parser.set_defaults(resolution = [0,0,0]) parser.set_defaults(resolution = [0,0,0])
@ -75,12 +75,12 @@ for file in files:
# --------------- figure out size and grid --------------------------------------------------------- # --------------- figure out size and grid ---------------------------------------------------------
try: 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: except ValueError:
try: 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: 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 continue
if (any(options.resolution)==0 or any(options.dimension)==0.0): if (any(options.resolution)==0 or any(options.dimension)==0.0):

8
processing/pre/geom_fromTable.py
View File

@ -21,7 +21,7 @@ Generate geometry description and material configuration from position, phase, a
""", version = scriptID) """, version = scriptID)
parser.add_option('--coordinates', parser.add_option('--coordinates',
dest = 'coordinates', dest = 'pos',
type = 'string', metavar = 'string', type = 'string', metavar = 'string',
help = 'coordinates label') help = 'coordinates label')
parser.add_option('--phase', parser.add_option('--phase',
@ -135,11 +135,11 @@ for name in filenames:
# ------------------------------------------ sanity checks --------------------------------------- # ------------------------------------------ sanity checks ---------------------------------------
coordDim = table.label_dimension(options.coordinates) coordDim = table.label_dimension(options.pos)
errors = [] errors = []
if not 3 >= coordDim >= 2: 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): if not np.all(table.label_dimension(label) == dim):
errors.append('input "{}" needs to have dimension {}.'.format(label,dim)) errors.append('input "{}" needs to have dimension {}.'.format(label,dim))
if options.phase and table.label_dimension(options.phase) != 1: if options.phase and table.label_dimension(options.phase) != 1:
@ -150,7 +150,7 @@ for name in filenames:
table.close(dismiss = True) table.close(dismiss = True)
continue continue
table.data_readArray([options.coordinates] \ table.data_readArray([options.pos] \
+ ([label] if isinstance(label, types.StringTypes) else label) \ + ([label] if isinstance(label, types.StringTypes) else label) \
+ ([options.phase] if options.phase else [])) + ([options.phase] if options.phase else []))