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DAMASK_EICMD
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small adjustments for autodoc

This commit is contained in:
Martin Diehl 2019-02-16 14:53:56 +01:00
parent 4ce151c967
commit fa003e8077
17 changed files with 43 additions and 53 deletions
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17
processing/post/addCalculation.py
View File

@ -41,10 +41,7 @@ parser.add_option('-f','--formula',
parser.add_option('-c','--condition',
dest = 'condition', metavar='string',
help = 'condition to alter existing column data')
parser.set_defaults(condition = None,
)
help = 'condition to alter existing column data (optional)')
(options,filenames) = parser.parse_args()
@ -80,7 +77,7 @@ for name in filenames:
condition = options.condition # copy per file, since might be altered inline
breaker = False
for position,(all,marker,column) in enumerate(set(re.findall(r'#(([s]#)?(.+?))#',condition))): # find three groups
for position,(all,marker,column) in enumerate(set(re.findall(r'#(([s]#)?(.+?))#',condition))): # find three groups
idx = table.label_index(column)
dim = table.label_dimension(column)
if idx < 0 and column not in specials:
@ -89,15 +86,15 @@ for name in filenames:
else:
if column in specials:
replacement = 'specials["{}"]'.format(column)
elif dim == 1: # scalar input
elif dim == 1: # scalar input
replacement = '{}(table.data[{}])'.format({ '':'float',
's#':'str'}[marker],idx) # take float or string value of data column
elif dim > 1: # multidimensional input (vector, tensor, etc.)
replacement = 'np.array(table.data[{}:{}],dtype=float)'.format(idx,idx+dim) # use (flat) array representation
's#':'str'}[marker],idx) # take float or string value of data column
elif dim > 1: # multidimensional input (vector, tensor, etc.)
replacement = 'np.array(table.data[{}:{}],dtype=float)'.format(idx,idx+dim) # use (flat) array representation
condition = condition.replace('#'+all+'#',replacement)
if breaker: continue # found mistake in condition evaluation --> next file
if breaker: continue # found mistake in condition evaluation --> next file
# ------------------------------------------ build formulas ----------------------------------------

5
processing/post/addCumulative.py
View File

@ -22,12 +22,9 @@ parser.add_option('-l','--label',
action = 'extend', metavar = '<string LIST>',
help = 'columns to cumulate')
parser.set_defaults(label = [],
)
(options,filenames) = parser.parse_args()
if len(options.label) == 0:
if options.label is None:
parser.error('no data column(s) specified.')
# --- loop over input files -------------------------------------------------------------------------

1
processing/post/addDisplacement.py
View File

@ -111,7 +111,6 @@ parser.add_option('--nodal',
parser.set_defaults(defgrad = 'f',
pos = 'pos',
nodal = False,
)
(options,filenames) = parser.parse_args()

5
processing/post/addGaussian.py
View File

@ -34,12 +34,12 @@ parser.add_option('-o','--order',
dest = 'order',
type = int,
metavar = 'int',
help = 'order of the filter')
help = 'order of the filter [%default]')
parser.add_option('--sigma',
dest = 'sigma',
type = float,
metavar = 'float',
help = 'standard deviation')
help = 'standard deviation [%default]')
parser.add_option('--periodic',
dest = 'periodic',
action = 'store_true',
@ -50,7 +50,6 @@ parser.add_option('--periodic',
parser.set_defaults(pos = 'pos',
order = 0,
sigma = 1,
periodic = False,
)
(options,filenames) = parser.parse_args()

6
processing/post/addGrainID.py
View File

@ -28,9 +28,9 @@ parser.add_option('-d',
help = 'disorientation threshold in degrees [%default]')
parser.add_option('-s',
'--symmetry',
dest = 'symmetry',
dest = 'symmetry', type = 'choice', choices = damask.Symmetry.lattices[1:],
metavar = 'string',
help = 'crystal symmetry [%default]')
help = 'crystal symmetry [%default] {{{}}} '.format(', '.join(damask.Symmetry.lattices[1:])))
parser.add_option('-o',
'--orientation',
dest = 'quaternion',
@ -49,7 +49,7 @@ parser.add_option('--quiet',
parser.set_defaults(disorientation = 5,
verbose = True,
quaternion = 'orientation',
symmetry = 'cubic',
symmetry = damask.Symmetry.lattices[-1],
pos = 'pos',
)

5
processing/post/addInfo.py
View File

@ -23,11 +23,12 @@ parser.add_option('-i',
dest = 'info', action = 'extend', metavar = '<string LIST>',
help = 'items to add')
parser.set_defaults(info = [],
)
(options,filenames) = parser.parse_args()
if options.info is None:
parser.error('no info specified.')
# --- loop over input files ------------------------------------------------------------------------
if filenames == []: filenames = [None]

6
processing/post/addMises.py
View File

@ -38,13 +38,9 @@ parser.add_option('-s','--stress',
action = 'extend', metavar = '<string LIST>',
help = 'heading(s) of columns containing stress tensors')
parser.set_defaults(strain = [],
stress = [],
)
(options,filenames) = parser.parse_args()
if len(options.stress+options.strain) == 0:
if options.stress is None and options.strain is None:
parser.error('no data column specified...')
# --- loop over input files -------------------------------------------------------------------------

7
processing/post/addNorm.py
View File

@ -9,6 +9,7 @@ scriptName = os.path.splitext(os.path.basename(__file__))[0]
scriptID = ' '.join([scriptName,damask.version])
# definition of element-wise p-norms for matrices
# ToDo: better use numpy.linalg.norm
def norm(which,object):
@ -18,6 +19,8 @@ def norm(which,object):
return math.sqrt(sum([x*x for x in object]))
elif which == 'Max': # p = inf
return max(map(abs, object))
else:
return -1
# --------------------------------------------------------------------
# MAIN
@ -43,6 +46,8 @@ parser.set_defaults(norm = 'frobenius',
(options,filenames) = parser.parse_args()
if options.norm.lower() not in normChoices:
parser.error('invalid norm ({}) specified.'.format(options.norm))
if options.label is None:
parser.error('no data column specified.')
@ -74,7 +79,7 @@ for name in filenames:
else:
dims.append(dim)
columns.append(table.label_index(what))
table.labels_append('norm{}({})'.format(options.norm.capitalize(),what)) # extend ASCII header with new labels
table.labels_append('norm{}({})'.format(options.norm.capitalize(),what)) # extend ASCII header with new labels
if remarks != []: damask.util.croak(remarks)
if errors != []:

5
processing/post/addOrientations.py
View File

@ -68,12 +68,12 @@ parser.add_option('-R',
'--labrotation',
dest='labrotation',
type = 'float', nargs = 4, metavar = ' '.join(['float']*4),
help = 'angle and axis of additional lab frame rotation')
help = 'angle and axis of additional lab frame rotation [%default]')
parser.add_option('-r',
'--crystalrotation',
dest='crystalrotation',
type = 'float', nargs = 4, metavar = ' '.join(['float']*4),
help = 'angle and axis of additional crystal frame rotation')
help = 'angle and axis of additional crystal frame rotation [%default]')
parser.add_option('--eulers',
dest = 'eulers',
metavar = 'string',
@ -106,7 +106,6 @@ parser.add_option('-z',
parser.set_defaults(output = [],
labrotation = (0.,1.,1.,1.), # no rotation about 1,1,1
crystalrotation = (0.,1.,1.,1.), # no rotation about 1,1,1
degrees = False,
)
(options, filenames) = parser.parse_args()

1
processing/post/addPole.py
View File

@ -35,7 +35,6 @@ parser.add_option('-o',
parser.set_defaults(pole = (1.0,0.0,0.0),
quaternion = 'orientation',
polar = False,
)
(options, filenames) = parser.parse_args()

2
processing/post/addSchmidfactors.py
View File

@ -115,7 +115,7 @@ parser.add_option('-l',
help = 'type of lattice structure [%default] {}'.format(latticeChoices))
parser.add_option('--covera',
dest = 'CoverA', type = 'float', metavar = 'float',
help = 'C over A ratio for hexagonal systems')
help = 'C over A ratio for hexagonal systems [%default]')
parser.add_option('-f',
'--force',
dest = 'force',

9
processing/post/addStrainTensors.py
View File

@ -56,16 +56,15 @@ parser.add_option('-f','--defgrad',
metavar = '<string LIST>',
help = 'heading(s) of columns containing deformation tensor values [%default]')
parser.set_defaults(right = False,
left = False,
logarithmic = False,
biot = False,
green = False,
parser.set_defaults(
defgrad = ['f'],
)
(options,filenames) = parser.parse_args()
if len(options.defgrad) > 1:
options.defgrad = options.defgrad[1:]
stretches = []
strains = []

4
processing/post/addTable.py
View File

@ -24,6 +24,10 @@ parser.add_option('-a', '--add','--table',
(options,filenames) = parser.parse_args()
if options.table is None:
parser.error('no table specified.')
# --- loop over input files -------------------------------------------------------------------------
if filenames == []: filenames = [None]

8
processing/post/averageDown.py
View File

@ -34,16 +34,14 @@ parser.add_option('--shift',
parser.add_option('-g', '--grid',
dest = 'grid',
type = 'int', nargs = 3, metavar = 'int int int',
help = 'grid in x,y,z [autodetect]')
help = 'grid in x,y,z (optional)')
parser.add_option('-s', '--size',
dest = 'size',
type = 'float', nargs = 3, metavar = 'float float float',
help = 'size in x,y,z [autodetect]')
help = 'size in x,y,z (optional)')
parser.set_defaults(pos = 'pos',
packing = (2,2,2),
shift = (0,0,0),
grid = (0,0,0),
size = (0.0,0.0,0.0),
)
(options,filenames) = parser.parse_args()
@ -92,7 +90,7 @@ for name in filenames:
table.data_readArray()
if (any(options.grid) == 0 or any(options.size) == 0.0):
if (options.grid is None or options.size is None):
grid,size = damask.util.coordGridAndSize(table.data[:,table.label_indexrange(options.pos)])
else:
grid = np.array(options.grid,'i')

9
processing/post/binXY.py
View File

@ -37,15 +37,15 @@ parser.add_option('-t','--type',
parser.add_option('-x','--xrange',
dest = 'xrange',
type = 'float', nargs = 2, metavar = 'float float',
help = 'min max value in x direction [autodetect]')
help = 'min max limits in x direction (optional)')
parser.add_option('-y','--yrange',
dest = 'yrange',
type = 'float', nargs = 2, metavar = 'float float',
help = 'min max value in y direction [autodetect]')
help = 'min max limits in y direction (optional)')
parser.add_option('-z','--zrange',
dest = 'zrange',
type = 'float', nargs = 2, metavar = 'float float',
help = 'min max value in z direction [autodetect]')
help = 'min max limits in z direction (optional)')
parser.add_option('-i','--invert',
dest = 'invert',
action = 'store_true',
@ -64,9 +64,6 @@ parser.set_defaults(bins = (10,10),
xrange = (0.0,0.0),
yrange = (0.0,0.0),
zrange = (0.0,0.0),
invert = False,
normRow = False,
normCol = False,
)
(options,filenames) = parser.parse_args()

4
processing/post/blowUp.py
View File

@ -27,10 +27,10 @@ parser.add_option('-p','--packing',
help = 'dimension of packed group [%default]')
parser.add_option('-g','--grid',
dest = 'resolution', type = 'int', nargs = 3, metavar = 'int int int',
help = 'resolution in x,y,z [autodetect]')
help = 'grid in x,y,z (optional)')
parser.add_option('-s','--size',
dest = 'dimension', type = 'float', nargs = 3, metavar = 'int int int',
help = 'dimension in x,y,z [autodetect]')
help = 'size in x,y,z (optional)')
parser.set_defaults(pos = 'pos',
packing = (2,2,2),
grid = (0,0,0),

2
processing/post/rotateData.py
View File

@ -29,7 +29,7 @@ parser.add_option('-r', '--rotation',
parser.add_option('--degrees',
dest = 'degrees',
action = 'store_true',
help = 'angles are given in degrees [%default]')
help = 'angles are given in degrees')
parser.set_defaults(rotation = (0.,1.,1.,1.), # no rotation about 1,1,1
degrees = False,