migrating to new Table class ...
... and stripping old ASCIItable down
This commit is contained in:
Martin Diehl
parent
f7a6ac4a0e
commit
7d47418381
|
|
@ -15,7 +15,7 @@ scriptName = os.path.splitext(os.path.basename(__file__))[0]
|
|||
scriptID = ' '.join([scriptName,damask.version])
|
||||
|
||||
|
||||
def Laguerre_tessellation(grid, coords, weights, grains, periodic = True, cpus = 2):
|
||||
def Laguerre_tessellation(grid, seeds, weights, grains, periodic = True, cpus = 2):
|
||||
|
||||
def findClosestSeed(fargs):
|
||||
point, seeds, myWeights = fargs
|
||||
|
|
@ -58,9 +58,9 @@ def Laguerre_tessellation(grid, coords, weights, grains, periodic = True, cpus =
|
|||
]).astype(float)
|
||||
|
||||
repeatweights = np.tile(weights,len(copies)).flatten(order='F') # Laguerre weights (1,2,3,1,2,3,...,1,2,3)
|
||||
for i,vec in enumerate(copies): # periodic copies of seed points ...
|
||||
try: seeds = np.append(seeds, coords+vec, axis=0) # ... (1+a,2+a,3+a,...,1+z,2+z,3+z)
|
||||
except NameError: seeds = coords+vec
|
||||
for vec in copies: # periodic copies of seed points ...
|
||||
try: seeds = np.append(seeds, seeds+vec, axis=0) # ... (1+a,2+a,3+a,...,1+z,2+z,3+z)
|
||||
except NameError: seeds = seeds+vec
|
||||
|
||||
damask.util.croak('...using {} cpu{}'.format(options.cpus, 's' if options.cpus > 1 else ''))
|
||||
arguments = [[arg,seeds,repeatweights] for arg in list(grid)]
|
||||
|
|
@ -77,12 +77,12 @@ def Laguerre_tessellation(grid, coords, weights, grains, periodic = True, cpus =
|
|||
closestSeeds[i] = findClosestSeed(arg)
|
||||
|
||||
# closestSeed is modulo number of original seed points (i.e. excluding periodic copies)
|
||||
return grains[closestSeeds%coords.shape[0]]
|
||||
return grains[closestSeeds%seeds.shape[0]]
|
||||
|
||||
|
||||
def Voronoi_tessellation(grid, coords, grains, size, periodic = True):
|
||||
def Voronoi_tessellation(grid, seeds, grains, size, periodic = True):
|
||||
|
||||
KDTree = spatial.cKDTree(coords,boxsize=size) if periodic else spatial.cKDTree(coords)
|
||||
KDTree = spatial.cKDTree(seeds,boxsize=size) if periodic else spatial.cKDTree(seeds)
|
||||
devNull,closestSeeds = KDTree.query(grid)
|
||||
return grains[closestSeeds]
|
||||
|
||||
|
|
@ -202,100 +202,69 @@ parser.set_defaults(pos = 'pos',
|
|||
if filenames == []: filenames = [None]
|
||||
|
||||
for name in filenames:
|
||||
damask.util.report(scriptName,name)
|
||||
damask.util.report(scriptName,name)
|
||||
|
||||
table = damask.ASCIItable(name = name, readonly = True)
|
||||
table = damask.Table.from_ASCII(StringIO(''.join(sys.stdin.read())) if name is None else name)
|
||||
size = np.zeros(3)
|
||||
origin = np.zeros(3)
|
||||
for line in table.comments:
|
||||
items = line.lower().strip().split()
|
||||
key = items[0] if items else ''
|
||||
if key == 'grid':
|
||||
grid = np.array([ int(dict(zip(items[1::2],items[2::2]))[i]) for i in ['a','b','c']])
|
||||
elif key == 'size':
|
||||
size = np.array([float(dict(zip(items[1::2],items[2::2]))[i]) for i in ['x','y','z']])
|
||||
elif key == 'origin':
|
||||
origin = np.array([float(dict(zip(items[1::2],items[2::2]))[i]) for i in ['x','y','z']])
|
||||
|
||||
if options.grid: grid = np.array(options.grid)
|
||||
if options.size: size = np.array(options.size)
|
||||
if options.origin: origin = np.array(options.origin)
|
||||
|
||||
size = np.where(size <= 0.0,grid/grid.max(),size)
|
||||
|
||||
# --- read header ----------------------------------------------------------------------------
|
||||
seeds = table.get(options.pos) * size if options.normalized else table.get(options.pos) - origin
|
||||
|
||||
table.head_read()
|
||||
info,extra_header = table.head_getGeom()
|
||||
if options.eulers in table.labels:
|
||||
eulers = table.get(options.eulers)
|
||||
|
||||
grains = table.get(options.microstructure) if options.microstructure in table.labels else np.arange(len(seeds))+1
|
||||
|
||||
if options.grid is not None: info['grid'] = options.grid
|
||||
if options.size is not None: info['size'] = options.size
|
||||
if options.origin is not None: info['origin'] = options.origin
|
||||
grainIDs = np.unique(grains).astype('i')
|
||||
NgrainIDs = len(grainIDs)
|
||||
|
||||
# ------------------------------------------ sanity checks ---------------------------------------
|
||||
coords = damask.grid_filters.cell_coord0(grid,size).reshape(-1,3)
|
||||
|
||||
remarks = []
|
||||
errors = []
|
||||
labels = []
|
||||
damask.util.croak('tessellating...')
|
||||
if options.laguerre:
|
||||
indices = Laguerre_tessellation(coords,seeds,table.get(options.weight),grains,options.periodic,options.cpus)
|
||||
else:
|
||||
indices = Voronoi_tessellation(coords,seeds,grains,size,options.periodic)
|
||||
|
||||
hasGrains = table.label_dimension(options.microstructure) == 1
|
||||
hasEulers = table.label_dimension(options.eulers) == 3
|
||||
if options.laguerre and table.label_dimension(options.weight) != 1:
|
||||
errors.append('missing seed weights...')
|
||||
config_header = []
|
||||
if options.config:
|
||||
|
||||
for i in range(3):
|
||||
if info['size'][i] <= 0.0: # any invalid size?
|
||||
info['size'][i] = float(info['grid'][i])/max(info['grid']) # normalize to grid
|
||||
remarks.append('rescaling size {} to {}...'.format(['x','y','z'][i],info['size'][i]))
|
||||
if options.eulers in table.labels:
|
||||
config_header += ['<texture>']
|
||||
for ID in grainIDs:
|
||||
eulerID = np.nonzero(grains == ID)[0][0] # find first occurrence of this grain id
|
||||
config_header += ['[Grain{}]'.format(ID),
|
||||
'(gauss)\tphi1 {:.2f}\tPhi {:.2f}\tphi2 {:.2f}'.format(*eulers[eulerID])
|
||||
]
|
||||
if options.axes: config_header += ['axes\t{} {} {}'.format(*options.axes)]
|
||||
|
||||
if table.label_dimension(options.pos) != 3:
|
||||
errors.append('seed positions "{}" have dimension {}.'.format(options.pos,
|
||||
table.label_dimension(options.pos)))
|
||||
else:
|
||||
labels += [options.pos]
|
||||
config_header += ['<microstructure>']
|
||||
for ID in grainIDs:
|
||||
config_header += ['[Grain{}]'.format(ID),
|
||||
'(constituent)\tphase {}\ttexture {}\tfraction 1.0'.format(options.phase,ID)
|
||||
]
|
||||
|
||||
if not options.normalized: remarks.append('using real-space seed coordinates...')
|
||||
if not hasEulers: remarks.append('missing seed orientations...')
|
||||
else: labels += [options.eulers]
|
||||
if not hasGrains: remarks.append('missing seed microstructure indices...')
|
||||
else: labels += [options.microstructure]
|
||||
config_header += ['<!skip>']
|
||||
|
||||
if remarks != []: damask.util.croak(remarks)
|
||||
if errors != []:
|
||||
damask.util.croak(errors)
|
||||
table.close(dismiss=True)
|
||||
continue
|
||||
header = [scriptID + ' ' + ' '.join(sys.argv[1:])]\
|
||||
+ config_header
|
||||
geom = damask.Geom(indices.reshape(grid,order='F'),size,origin,
|
||||
homogenization=options.homogenization,comments=header)
|
||||
damask.util.croak(geom)
|
||||
|
||||
# ------------------------------------------ read seeds ---------------------------------------
|
||||
|
||||
table.data_readArray(labels)
|
||||
coords = table.data[:,table.label_indexrange(options.pos)] * info['size'] if options.normalized \
|
||||
else table.data[:,table.label_indexrange(options.pos)] - info['origin']
|
||||
if hasEulers:
|
||||
eulers = table.data[:,table.label_indexrange(options.eulers)]
|
||||
grains = table.data[:,table.label_indexrange(options.microstructure)].astype(int) if hasGrains \
|
||||
else np.arange(len(coords))+1
|
||||
|
||||
grainIDs = np.unique(grains).astype('i')
|
||||
NgrainIDs = len(grainIDs)
|
||||
|
||||
# --- tessellate microstructure ------------------------------------------------------------
|
||||
grid = damask.grid_filters.cell_coord0(info['grid'],info['size']).reshape(-1,3)
|
||||
damask.util.croak('tessellating...')
|
||||
if options.laguerre:
|
||||
weights = table.data[:,table.label_indexrange(options.weight)]
|
||||
indices = Laguerre_tessellation(grid, coords, weights, grains, options.periodic, options.cpus)
|
||||
else:
|
||||
indices = Voronoi_tessellation(grid, coords, grains, info['size'], options.periodic)
|
||||
|
||||
config_header = []
|
||||
if options.config:
|
||||
|
||||
if hasEulers:
|
||||
config_header += ['<texture>']
|
||||
for ID in grainIDs:
|
||||
eulerID = np.nonzero(grains == ID)[0][0] # find first occurrence of this grain id
|
||||
config_header += ['[Grain{}]'.format(ID),
|
||||
'(gauss)\tphi1 {:.2f}\tPhi {:.2f}\tphi2 {:.2f}'.format(*eulers[eulerID])
|
||||
]
|
||||
if options.axes is not None: config_header += ['axes\t{} {} {}'.format(*options.axes)]
|
||||
|
||||
config_header += ['<microstructure>']
|
||||
for ID in grainIDs:
|
||||
config_header += ['[Grain{}]'.format(ID),
|
||||
'(constituent)\tphase {}\ttexture {}\tfraction 1.0'.format(options.phase,ID)
|
||||
]
|
||||
|
||||
config_header += ['<!skip>']
|
||||
|
||||
header = [scriptID + ' ' + ' '.join(sys.argv[1:])]\
|
||||
+ config_header
|
||||
geom = damask.Geom(indices.reshape(info['grid'],order='F'),info['size'],info['origin'],
|
||||
homogenization=options.homogenization,comments=header)
|
||||
damask.util.croak(geom)
|
||||
|
||||
geom.to_file(sys.stdout if name is None else os.path.splitext(name)[0]+'.geom',pack=False)
|
||||
geom.to_file(sys.stdout if name is None else os.path.splitext(name)[0]+'.geom',pack=False)
|
||||
|
|
|
|||
|
|
@ -165,42 +165,6 @@ class ASCIItable():
|
|||
|
||||
return self.output_write(head)
|
||||
|
||||
# ------------------------------------------------------------------
|
||||
def head_getGeom(self):
|
||||
"""Interpret geom header."""
|
||||
identifiers = {
|
||||
'grid': ['a','b','c'],
|
||||
'size': ['x','y','z'],
|
||||
'origin': ['x','y','z'],
|
||||
}
|
||||
mappings = {
|
||||
'grid': lambda x: int(x),
|
||||
'size': lambda x: float(x),
|
||||
'origin': lambda x: float(x),
|
||||
}
|
||||
info = {
|
||||
'grid': np.zeros(3,'i'),
|
||||
'size': np.zeros(3,'d'),
|
||||
'origin': np.zeros(3,'d'),
|
||||
}
|
||||
extra_header = []
|
||||
|
||||
for header in self.info:
|
||||
headitems = list(map(str.lower,header.split()))
|
||||
if len(headitems) == 0: continue # skip blank lines
|
||||
if headitems[0] in list(mappings.keys()):
|
||||
if headitems[0] in list(identifiers.keys()):
|
||||
for i in range(len(identifiers[headitems[0]])):
|
||||
info[headitems[0]][i] = \
|
||||
mappings[headitems[0]](headitems[headitems.index(identifiers[headitems[0]][i])+1])
|
||||
else:
|
||||
info[headitems[0]] = mappings[headitems[0]](headitems[1])
|
||||
else:
|
||||
extra_header.append(header)
|
||||
|
||||
return info,extra_header
|
||||
|
||||
|
||||
# ------------------------------------------------------------------
|
||||
def labels_append(self,
|
||||
what,
|
||||
|
|
|
|||
Loading…
Reference in New Issue