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DAMASK_EICMD
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changed default label of coordinates to "pos"

This commit is contained in:
Philip Eisenlohr 2016-04-15 18:27:23 -04:00
parent 7567aae7c0
commit 81f6530f52
6 changed files with 73 additions and 74 deletions
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10
processing/post/addCurl.py
View File

@ -71,18 +71,18 @@ Deals with both vector- and tensor-valued fields.
parser.add_option('-c','--coordinates',
dest = 'coords',
type = 'string', metavar='string',
help = 'column heading for coordinates [%default]')
type = 'string', metavar = 'string',
help = 'column label of coordinates [%default]')
parser.add_option('-v','--vector',
dest = 'vector',
action = 'extend', metavar = '<string LIST>',
help = 'heading of columns containing vector field values')
help = 'column label(s) of vector field values')
parser.add_option('-t','--tensor',
dest = 'tensor',
action = 'extend', metavar = '<string LIST>',
help = 'heading of columns containing tensor field values')
help = 'column label(s) of tensor field values')
parser.set_defaults(coords = 'ipinitialcoord',
parser.set_defaults(coords = 'pos',
)
(options,filenames) = parser.parse_args()

5
processing/post/addDisplacements.py
View File

@ -88,8 +88,9 @@ def displacementFluctFFT(F,grid,size,nodal=False,transformed=False):
# --------------------------------------------------------------------
parser = OptionParser(option_class=damask.extendableOption, usage='%prog options file[s]', description = """
Add deformed configuration of given initial coordinates.
Add displacments resulting from deformation gradient field.
Operates on periodic three-dimensional x,y,z-ordered data sets.
Outputs at cell centers or cell nodes (into separate file).
""", version = scriptID)
@ -107,7 +108,7 @@ parser.add_option('--nodal',
help = 'output nodal (not cell-centered) displacements')
parser.set_defaults(defgrad = 'f',
coords = 'ipinitialcoord',
coords = 'pos',
nodal = False,
)

8
processing/post/addDivergence.py
View File

@ -58,17 +58,17 @@ Deals with both vector- and tensor-valued fields.
parser.add_option('-c','--coordinates',
dest = 'coords',
type = 'string', metavar = 'string',
help = 'column heading for coordinates [%default]')
help = 'column label of coordinates [%default]')
parser.add_option('-v','--vector',
dest = 'vector',
action = 'extend', metavar = '<string LIST>',
help = 'heading of columns containing vector field values')
help = 'column label(s) of vector field values')
parser.add_option('-t','--tensor',
dest = 'tensor',
action = 'extend', metavar = '<string LIST>',
help = 'heading of columns containing tensor field values')
help = 'column label(s) of tensor field values')
parser.set_defaults(coords = 'ipinitialcoord',
parser.set_defaults(coords = 'pos',
)
(options,filenames) = parser.parse_args()

14
processing/post/addGradient.py
View File

@ -9,7 +9,9 @@ import damask
scriptName = os.path.splitext(os.path.basename(__file__))[0]
scriptID = ' '.join([scriptName,damask.version])
#--------------------------------------------------------------------------------------------------
def gradFFT(geomdim,field):
grid = np.array(np.shape(field)[2::-1])
N = grid.prod() # field size
n = np.array(np.shape(field)[3:]).prod() # data size
@ -17,7 +19,7 @@ def gradFFT(geomdim,field):
elif n == 1: dataType = 'scalar'
field_fourier = np.fft.fftpack.rfftn(field,axes=(0,1,2))
grad_fourier = np.zeros(field_fourier.shape+(3,),'c16')
grad_fourier = np.zeros(field_fourier.shape+(3,),'c16')
# differentiation in Fourier space
k_s = np.zeros([3],'i')
@ -61,17 +63,17 @@ Deals with both vector- and scalar fields.
parser.add_option('-c','--coordinates',
dest = 'coords',
type = 'string', metavar='string',
help = 'column heading for coordinates [%default]')
help = 'column label of coordinates [%default]')
parser.add_option('-v','--vector',
dest = 'vector',
action = 'extend', metavar = '<string LIST>',
help = 'heading of columns containing vector field values')
help = 'column label(s) of vector field values')
parser.add_option('-s','--scalar',
dest = 'scalar',
action = 'extend', metavar = '<string LIST>',
help = 'heading of columns containing scalar field values')
help = 'column label(s) of scalar field values')
parser.set_defaults(coords = 'ipinitialcoord',
parser.set_defaults(coords = 'pos',
)
(options,filenames) = parser.parse_args()
@ -96,7 +98,7 @@ for name in filenames:
items = {
'scalar': {'dim': 1, 'shape': [1], 'labels':options.scalar, 'active':[], 'column': []},
'vector': {'dim': 3, 'shape': [3], 'labels':options.vector, 'active':[], 'column': []},
'vector': {'dim': 3, 'shape': [3], 'labels':options.vector, 'active':[], 'column': []},
}
errors = []
remarks = []

15
processing/post/averageDown.py
View File

@ -22,7 +22,7 @@ Average each data block of size 'packing' into single values thus reducing the f
parser.add_option('-c','--coordinates',
dest = 'coords',
type = 'string', metavar = 'string',
help = 'column heading for coordinates [%default]')
help = 'column label of coordinates [%default]')
parser.add_option('-p','--packing',
dest = 'packing',
type = 'int', nargs = 3, metavar = 'int int int',
@ -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 = 'ipinitialcoord',
parser.set_defaults(coords = 'pos',
packing = (2,2,2),
shift = (0,0,0),
grid = (0,0,0),
@ -59,11 +59,10 @@ if any(shift != 0): prefix += 'shift{:+}{:+}{:+}_'.format(*shift)
if filenames == []: filenames = [None]
for name in filenames:
try:
table = damask.ASCIItable(name = name,
outname = os.path.join(os.path.dirname(name),
prefix+os.path.basename(name)) if name else name,
buffered = False)
try: table = damask.ASCIItable(name = name,
outname = os.path.join(os.path.dirname(name),
prefix+os.path.basename(name)) if name else name,
buffered = False)
except: continue
damask.util.report(scriptName,name)
@ -75,7 +74,6 @@ for name in filenames:
errors = []
remarks = []
colCoord = None
if table.label_dimension(options.coords) != 3: errors.append('coordinates {} are not a vector.'.format(options.coords))
else: colCoord = table.label_index(options.coords)
@ -86,7 +84,6 @@ for name in filenames:
table.close(dismiss = True)
continue
# ------------------------------------------ assemble header ---------------------------------------
table.info_append(scriptID + '\t' + ' '.join(sys.argv[1:]))

95
processing/post/blowUp.py
View File

@ -19,83 +19,82 @@ to resolution*packing.
""", version = scriptID)
parser.add_option('-c','--coordinates', dest='coords', metavar='string',
help='column heading for coordinates [%default]')
parser.add_option('-p','--packing', dest='packing', type='int', nargs=3, metavar='int int int',
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]')
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 = 'ipinitialcoord')
parser.set_defaults(packing = (2,2,2))
parser.set_defaults(grid = (0,0,0))
parser.set_defaults(size = (0.0,0.0,0.0))
parser.add_option('-c','--coordinates',
dest = 'coords', metavar = 'string',
help = 'column label of coordinates [%default]')
parser.add_option('-p','--packing',
dest = 'packing', type = 'int', nargs = 3, metavar = 'int int int',
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]')
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',
packing = (2,2,2),
grid = (0,0,0),
size = (0.0,0.0,0.0),
)
(options,filenames) = parser.parse_args()
options.packing = np.array(options.packing)
prefix = 'blowUp%ix%ix%i_'%(options.packing[0],options.packing[1],options.packing[2])
prefix = 'blowUp{}x{}x{}_'.format(*options.packing)
# --- loop over input files -------------------------------------------------------------------------
if filenames == []: filenames = [None]
for name in filenames:
try:
table = damask.ASCIItable(name = name,
outname = os.path.join(os.path.dirname(name),
prefix+ \
os.path.basename(name)) if name else name,
buffered = False)
try: table = damask.ASCIItable(name = name,
outname = os.path.join(os.path.dirname(name),
prefix+os.path.basename(name)) if name else name,
buffered = False)
except: continue
damask.util.report(scriptName,name)
# ------------------------------------------ read header ------------------------------------------
table.head_read()
errors = []
# ------------------------------------------ sanity checks ----------------------------------------
if table.label_dimension(options.coords) != 3:
damask.util.croak('coordinates {} are not a vector.'.format(options.coords))
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)
colElem = table.label_index('elem')
if remarks != []: damask.util.croak(remarks)
if errors != []:
damask.util.croak(errors)
table.close(dismiss = True)
continue
else:
coordCol = table.label_index(options.coords)
# ------------------------------------------ assemble header --------------------------------------
table.info_append(scriptID + '\t' + ' '.join(sys.argv[1:]))
# --------------- figure out size and grid ---------------------------------------------------------
table.data_readArray()
coords = [{},{},{}]
for i in xrange(len(table.data)):
for j in xrange(3):
coords[j][str(table.data[i,coordCol+j])] = True
grid = np.array(map(len,coords),'i')
size = grid/np.maximum(np.ones(3,'d'),grid-1.0)* \
np.array([max(map(float,coords[0].keys()))-min(map(float,coords[0].keys())),\
max(map(float,coords[1].keys()))-min(map(float,coords[1].keys())),\
max(map(float,coords[2].keys()))-min(map(float,coords[2].keys())),\
],'d') # size from bounding box, corrected for cell-centeredness
size = np.where(grid > 1, size, min(size[grid > 1]/grid[grid > 1])) # spacing for grid==1 set to smallest among other spacings
table.data_readArray(options.coords)
coords = [np.unique(table.data[:,i]) for i in xrange(3)]
mincorner = np.array(map(min,coords))
maxcorner = np.array(map(max,coords))
grid = np.array(map(len,coords),'i')
size = grid/np.maximum(np.ones(3,'d'), grid-1.0) * (maxcorner-mincorner) # size from edge to edge = dim * n/(n-1)
size = np.where(grid > 1, size, min(size[grid > 1]/grid[grid > 1])) # spacing for grid==1 set to smallest among other spacings
packing = np.array(options.packing,'i')
outSize = grid*packing
# ------------------------------------------ assemble header ---------------------------------------
# ------------------------------------------ assemble header --------------------------------------
table.info_append(scriptID + '\t' + ' '.join(sys.argv[1:]))
table.head_write()
# ------------------------------------------ process data -------------------------------------------
table.data_rewind()
data = np.zeros(outSize.tolist()+[len(table.labels)])
p = np.zeros(3,'i')
@ -107,15 +106,15 @@ for name in filenames:
table.data_read()
data[d[0]:d[0]+packing[0],
d[1]:d[1]+packing[1],
d[2]:d[2]+packing[2],
d[2]:d[2]+packing[2],
: ] = np.tile(np.array(table.data_asFloat(),'d'),packing.tolist()+[1]) # tile to match blowUp voxel size
elementSize = size/grid/packing
elem = 1
for c in xrange(outSize[2]):
for b in xrange(outSize[1]):
for a in xrange(outSize[0]):
data[a,b,c,coordCol:coordCol+3] = [a+0.5,b+0.5,c+0.5]*elementSize
data[a,b,c,table.label_index('elem')] = elem
data[a,b,c,colCoord:colCoord+3] = [a+0.5,b+0.5,c+0.5]*elementSize
if colElem != -1: data[a,b,c,colElem] = elem
table.data = data[a,b,c,:].tolist()
outputAlive = table.data_write() # output processed line
elem += 1