streamlined geom-info reporting; added --float option to some scripts; hardened against NaN; "microstructures" now reports uniques not max

This commit is contained in:
Philip Eisenlohr 2019-05-23 13:03:24 -04:00
parent e6cec6ecbe
commit eb13fbc0ce
14 changed files with 85 additions and 137 deletions

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@ -35,7 +35,7 @@ parser.add_option('-f',
type = 'float', metavar = 'float', type = 'float', metavar = 'float',
help = '(background) canvas grain index. "0" selects maximum microstructure index + 1 [%default]') help = '(background) canvas grain index. "0" selects maximum microstructure index + 1 [%default]')
parser.add_option('--float', parser.add_option('--float',
dest = 'real', dest = 'float',
action = 'store_true', action = 'store_true',
help = 'use float input') help = 'use float input')
parser.add_option('--blank', parser.add_option('--blank',
@ -45,13 +45,13 @@ parser.add_option('--blank',
parser.set_defaults(grid = ['0','0','0'], parser.set_defaults(grid = ['0','0','0'],
offset = (0,0,0), offset = (0,0,0),
fill = 0, fill = 0.0,
real = False, float = False,
) )
(options, filenames) = parser.parse_args() (options, filenames) = parser.parse_args()
datatype = 'f' if options.real else 'i' datatype = 'f' if options.float else 'i'
options.grid = ['1','1','1'] if options.blank and options.grid == ['0','0','0'] else options.grid options.grid = ['1','1','1'] if options.blank and options.grid == ['0','0','0'] else options.grid
options.fill = 1 if options.blank and options.fill == 0 else options.fill options.fill = 1 if options.blank and options.fill == 0 else options.fill
@ -107,7 +107,7 @@ for name in filenames:
newInfo['grid'] = np.where(newInfo['grid'] > 0, newInfo['grid'],info['grid']) newInfo['grid'] = np.where(newInfo['grid'] > 0, newInfo['grid'],info['grid'])
microstructure_cropped = np.zeros(newInfo['grid'],datatype) microstructure_cropped = np.zeros(newInfo['grid'],datatype)
microstructure_cropped.fill(options.fill if options.real or options.fill > 0 else microstructure.max()+1) microstructure_cropped.fill(options.fill if options.float or options.fill > 0 else np.nanmax(microstructure)+1)
if not options.blank: if not options.blank:
xindex = np.arange(max(options.offset[0],0),min(options.offset[0]+newInfo['grid'][0],info['grid'][0])) xindex = np.arange(max(options.offset[0],0),min(options.offset[0]+newInfo['grid'][0],info['grid'][0]))
@ -130,7 +130,7 @@ for name in filenames:
newInfo['size'] = info['size']/info['grid']*newInfo['grid'] if np.all(info['grid'] > 0) else newInfo['grid'] newInfo['size'] = info['size']/info['grid']*newInfo['grid'] if np.all(info['grid'] > 0) else newInfo['grid']
newInfo['origin'] = info['origin']+(info['size']/info['grid'] if np.all(info['grid'] > 0) \ newInfo['origin'] = info['origin']+(info['size']/info['grid'] if np.all(info['grid'] > 0) \
else newInfo['size']/newInfo['grid'])*options.offset else newInfo['size']/newInfo['grid'])*options.offset
newInfo['microstructures'] = microstructure_cropped.max() newInfo['microstructures'] = len(np.unique(microstructure_cropped))
# --- report --------------------------------------------------------------------------------------- # --- report ---------------------------------------------------------------------------------------
@ -172,7 +172,7 @@ for name in filenames:
# --- write microstructure information ------------------------------------------------------------ # --- write microstructure information ------------------------------------------------------------
format = '%g' if options.real else '%{}i'.format(int(math.floor(math.log10(microstructure_cropped.max())+1))) format = '%g' if options.float else '%{}i'.format(int(math.floor(math.log10(np.nanmax(microstructure_cropped))+1)))
table.data = microstructure_cropped.reshape((newInfo['grid'][0],newInfo['grid'][1]*newInfo['grid'][2]),order='F').transpose() table.data = microstructure_cropped.reshape((newInfo['grid'][0],newInfo['grid'][1]*newInfo['grid'][2]),order='F').transpose()
table.data_writeArray(format,delimiter=' ') table.data_writeArray(format,delimiter=' ')

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@ -50,13 +50,7 @@ for name in filenames:
table.head_read() table.head_read()
info,extra_header = table.head_getGeom() info,extra_header = table.head_getGeom()
damask.util.report_geom(info)
damask.util.croak(['grid a b c: {}'.format(' x '.join(map(str,info['grid']))),
'size x y z: {}'.format(' x '.join(map(str,info['size']))),
'origin x y z: {}'.format(' : '.join(map(str,info['origin']))),
'homogenization: {}'.format(info['homogenization']),
'microstructures: {}'.format(info['microstructures']),
])
errors = [] errors = []
if np.any(info['grid'] < 1): errors.append('invalid grid a b c.') if np.any(info['grid'] < 1): errors.append('invalid grid a b c.')
@ -73,7 +67,7 @@ for name in filenames:
# --- do work ------------------------------------------------------------------------------------ # --- do work ------------------------------------------------------------------------------------
microstructure = ndimage.filters.generic_filter(microstructure,mostFrequent,size=(options.stencil,)*3).astype('int_') microstructure = ndimage.filters.generic_filter(microstructure,mostFrequent,size=(options.stencil,)*3).astype('int_')
newInfo = {'microstructures': microstructure.max()} newInfo = {'microstructures': len(np.unique(microstructure))}
# --- report --------------------------------------------------------------------------------------- # --- report ---------------------------------------------------------------------------------------
if ( newInfo['microstructures'] != info['microstructures']): if ( newInfo['microstructures'] != info['microstructures']):
@ -91,9 +85,9 @@ for name in filenames:
# --- write microstructure information ------------------------------------------------------------ # --- write microstructure information ------------------------------------------------------------
formatwidth = int(math.floor(math.log10(microstructure.max())+1)) formatwidth = int(math.floor(math.log10(np.nanmax(microstructure))+1))
table.data = microstructure.reshape((info['grid'][0],np.prod(info['grid'][1:])),order='F').transpose() table.data = microstructure.reshape((info['grid'][0],np.prod(info['grid'][1:])),order='F').transpose()
table.data_writeArray('%%%ii'%(formatwidth),delimiter = ' ') table.data_writeArray('%{}i'.format(formatwidth),delimiter = ' ')
# --- output finalization -------------------------------------------------------------------------- # --- output finalization --------------------------------------------------------------------------

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@ -90,12 +90,7 @@ for name in filenames:
#--- report --------------------------------------------------------------------------------------- #--- report ---------------------------------------------------------------------------------------
damask.util.croak(['grid a b c: %s'%(' x '.join(map(str,info['grid']))), damask.util.report_geom(info)
'size x y z: %s'%(' x '.join(map(str,info['size']))),
'origin x y z: %s'%(' : '.join(map(str,info['origin']))),
'homogenization: %i'%info['homogenization'],
'microstructures: %i'%info['microstructures'],
])
errors = [] errors = []
if np.any(info['grid'] < 1): errors.append('invalid grid a b c.') if np.any(info['grid'] < 1): errors.append('invalid grid a b c.')

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@ -192,12 +192,7 @@ for name in filenames:
'homogenization': options.homogenization, 'homogenization': options.homogenization,
} }
damask.util.croak(['grid a b c: {}'.format(' x '.join(map(str,info['grid']))), damask.util.report_geom(info)
'size x y z: {}'.format(' x '.join(map(str,info['size']))),
'origin x y z: {}'.format(' : '.join(map(str,info['origin']))),
'homogenization: {}'.format(info['homogenization']),
'microstructures: {}'.format(info['microstructures']),
])
# --- write header --------------------------------------------------------------------------------- # --- write header ---------------------------------------------------------------------------------
@ -230,7 +225,7 @@ for name in filenames:
# --- write microstructure information ------------------------------------------------------------ # --- write microstructure information ------------------------------------------------------------
table.data = grain.reshape(info['grid'][1]*info['grid'][2],info['grid'][0]) table.data = grain.reshape(info['grid'][1]*info['grid'][2],info['grid'][0])
table.data_writeArray('%%%ii'%(formatwidth),delimiter=' ') table.data_writeArray('%{}i'.format(formatwidth),delimiter=' ')
#--- output finalization -------------------------------------------------------------------------- #--- output finalization --------------------------------------------------------------------------

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@ -69,13 +69,7 @@ for name in filenames:
table.head_read() table.head_read()
info,extra_header = table.head_getGeom() info,extra_header = table.head_getGeom()
damask.util.report_geom(info)
damask.util.croak(['grid a b c: {}'.format(' x '.join(list(map(str,info['grid'])))),
'size x y z: {}'.format(' x '.join(list(map(str,info['size'])))),
'origin x y z: {}'.format(' : '.join(list(map(str,info['origin'])))),
'homogenization: {}'.format(info['homogenization']),
'microstructures: {}'.format(info['microstructures']),
])
errors = [] errors = []
if np.any(info['grid'] < 1): errors.append('invalid grid a b c.') if np.any(info['grid'] < 1): errors.append('invalid grid a b c.')
@ -200,8 +194,7 @@ for name in filenames:
newID += 1 newID += 1
microstructure = np.where(microstructure == microstructureID, newID, microstructure) microstructure = np.where(microstructure == microstructureID, newID, microstructure)
newInfo = {'microstructures': 0,} newInfo = {'microstructures': len(np.unique(microstructure)),}
newInfo['microstructures'] = microstructure.max()
# --- report -------------------------------------------------------------------------------------- # --- report --------------------------------------------------------------------------------------
@ -226,7 +219,7 @@ for name in filenames:
# --- write microstructure information ------------------------------------------------------------ # --- write microstructure information ------------------------------------------------------------
formatwidth = int(math.floor(math.log10(microstructure.max())+1)) formatwidth = int(math.floor(math.log10(np.nanmax(microstructure))+1))
table.data = microstructure[::1 if info['grid'][0]>1 else 2, table.data = microstructure[::1 if info['grid'][0]>1 else 2,
::1 if info['grid'][1]>1 else 2, ::1 if info['grid'][1]>1 else 2,
::1 if info['grid'][2]>1 else 2,].\ ::1 if info['grid'][2]>1 else 2,].\

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@ -23,6 +23,13 @@ parser.add_option('-d','--direction',
dest = 'directions', dest = 'directions',
action = 'extend', metavar = '<string LIST>', action = 'extend', metavar = '<string LIST>',
help = "directions in which to mirror {'x','y','z'}") help = "directions in which to mirror {'x','y','z'}")
parser.add_option('--float',
dest = 'float',
action = 'store_true',
help = 'use float input')
parser.set_defaults(float = False,
)
(options, filenames) = parser.parse_args() (options, filenames) = parser.parse_args()
@ -32,6 +39,8 @@ if not set(options.directions).issubset(validDirections):
invalidDirections = [str(e) for e in set(options.directions).difference(validDirections)] invalidDirections = [str(e) for e in set(options.directions).difference(validDirections)]
parser.error('invalid directions {}. '.format(*invalidDirections)) parser.error('invalid directions {}. '.format(*invalidDirections))
datatype = 'f' if options.float else 'i'
# --- loop over input files ------------------------------------------------------------------------- # --- loop over input files -------------------------------------------------------------------------
if filenames == []: filenames = [None] if filenames == []: filenames = [None]
@ -39,7 +48,8 @@ if filenames == []: filenames = [None]
for name in filenames: for name in filenames:
try: try:
table = damask.ASCIItable(name = name, table = damask.ASCIItable(name = name,
buffered = False, labeled = False) buffered = False,
labeled = False)
except: continue except: continue
damask.util.report(scriptName,name) damask.util.report(scriptName,name)
@ -47,13 +57,7 @@ for name in filenames:
table.head_read() table.head_read()
info,extra_header = table.head_getGeom() info,extra_header = table.head_getGeom()
damask.util.report_geom(info)
damask.util.croak(['grid a b c: %s'%(' x '.join(map(str,info['grid']))),
'size x y z: %s'%(' x '.join(map(str,info['size']))),
'origin x y z: %s'%(' : '.join(map(str,info['origin']))),
'homogenization: %i'%info['homogenization'],
'microstructures: %i'%info['microstructures'],
])
errors = [] errors = []
if np.any(info['grid'] < 1): errors.append('invalid grid a b c.') if np.any(info['grid'] < 1): errors.append('invalid grid a b c.')
@ -65,7 +69,7 @@ for name in filenames:
# --- read data ------------------------------------------------------------------------------------ # --- read data ------------------------------------------------------------------------------------
microstructure = table.microstructure_read(info['grid']).reshape(info['grid'],order='F') # read microstructure microstructure = table.microstructure_read(info['grid'],datatype).reshape(info['grid'],order='F') # read microstructure
if 'z' in options.directions: if 'z' in options.directions:
microstructure = np.concatenate([microstructure,microstructure[:,:,::-1]],2) microstructure = np.concatenate([microstructure,microstructure[:,:,::-1]],2)
@ -107,9 +111,9 @@ for name in filenames:
# --- write microstructure information ------------------------------------------------------------ # --- write microstructure information ------------------------------------------------------------
formatwidth = int(math.floor(math.log10(microstructure.max())+1)) formatwidth = int(math.floor(math.log10(np.nanmax(microstructure))+1))
table.data = microstructure.reshape((newInfo['grid'][0],np.prod(newInfo['grid'][1:])),order='F').transpose() table.data = microstructure.reshape((newInfo['grid'][0],np.prod(newInfo['grid'][1:])),order='F').transpose()
table.data_writeArray('%%%ii'%(formatwidth),delimiter = ' ') table.data_writeArray('%{}i'.format(formatwidth),delimiter = ' ')
# --- output finalization -------------------------------------------------------------------------- # --- output finalization --------------------------------------------------------------------------

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@ -35,13 +35,7 @@ for name in filenames:
table.head_read() table.head_read()
info,extra_header = table.head_getGeom() info,extra_header = table.head_getGeom()
damask.util.report_geom(info)
damask.util.croak(['grid a b c: {}'.format(' x '.join(map(str,info['grid']))),
'size x y z: {}'.format(' x '.join(map(str,info['size']))),
'origin x y z: {}'.format(' : '.join(map(str,info['origin']))),
'homogenization: {}'.format(info['homogenization']),
'microstructures: {}'.format(info['microstructures']),
])
errors = [] errors = []
if np.any(info['grid'] < 1): errors.append('invalid grid a b c.') if np.any(info['grid'] < 1): errors.append('invalid grid a b c.')

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@ -35,13 +35,7 @@ for name in filenames:
table.head_read() table.head_read()
info,extra_header = table.head_getGeom() info,extra_header = table.head_getGeom()
damask.util.report_geom(info)
damask.util.croak(['grid a b c: %s'%(' x '.join(map(str,info['grid']))),
'size x y z: %s'%(' x '.join(map(str,info['size']))),
'origin x y z: %s'%(' : '.join(map(str,info['origin']))),
'homogenization: %i'%info['homogenization'],
'microstructures: %i'%info['microstructures'],
])
errors = [] errors = []
if np.any(info['grid'] < 1): errors.append('invalid grid a b c.') if np.any(info['grid'] < 1): errors.append('invalid grid a b c.')
@ -93,7 +87,7 @@ for name in filenames:
# --- write microstructure information ----------------------------------------------------------- # --- write microstructure information -----------------------------------------------------------
format = '%{}i'.format(int(math.floor(math.log10(newInfo['microstructures'])+1))) format = '%{}i'.format(int(math.floor(math.log10(np.nanmax(renumbered))+1)))
table.data = renumbered.reshape((info['grid'][0],info['grid'][1]*info['grid'][2]),order='F').transpose() table.data = renumbered.reshape((info['grid'][0],info['grid'][1]*info['grid'][2]),order='F').transpose()
table.data_writeArray(format,delimiter = ' ') table.data_writeArray(format,delimiter = ' ')

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@ -31,14 +31,21 @@ parser.add_option('-r', '--renumber',
dest = 'renumber', dest = 'renumber',
action = 'store_true', action = 'store_true',
help = 'renumber microstructure indices from 1..N [%default]') help = 'renumber microstructure indices from 1..N [%default]')
parser.add_option('--float',
dest = 'float',
action = 'store_true',
help = 'use float input')
parser.set_defaults(renumber = False, parser.set_defaults(renumber = False,
grid = ['0','0','0'], grid = ['0','0','0'],
size = ['0.0','0.0','0.0'], size = ['0.0','0.0','0.0'],
float = False,
) )
(options, filenames) = parser.parse_args() (options, filenames) = parser.parse_args()
datatype = 'f' if options.float else 'i'
# --- loop over input files ------------------------------------------------------------------------- # --- loop over input files -------------------------------------------------------------------------
if filenames == []: filenames = [None] if filenames == []: filenames = [None]
@ -46,7 +53,8 @@ if filenames == []: filenames = [None]
for name in filenames: for name in filenames:
try: try:
table = damask.ASCIItable(name = name, table = damask.ASCIItable(name = name,
buffered = False, labeled = False) buffered = False,
labeled = False)
except: continue except: continue
damask.util.report(scriptName,name) damask.util.report(scriptName,name)
@ -54,13 +62,7 @@ for name in filenames:
table.head_read() table.head_read()
info,extra_header = table.head_getGeom() info,extra_header = table.head_getGeom()
damask.util.report_geom(info)
damask.util.croak(['grid a b c: %s'%(' x '.join(map(str,info['grid']))),
'size x y z: %s'%(' x '.join(map(str,info['size']))),
'origin x y z: %s'%(' : '.join(map(str,info['origin']))),
'homogenization: %i'%info['homogenization'],
'microstructures: %i'%info['microstructures'],
])
errors = [] errors = []
if np.any(info['grid'] < 1): errors.append('invalid grid a b c.') if np.any(info['grid'] < 1): errors.append('invalid grid a b c.')
@ -72,7 +74,7 @@ for name in filenames:
# --- read data ------------------------------------------------------------------------------------ # --- read data ------------------------------------------------------------------------------------
microstructure = table.microstructure_read(info['grid']) # read microstructure microstructure = table.microstructure_read(info['grid'],datatype) # read microstructure
# --- do work ------------------------------------------------------------------------------------ # --- do work ------------------------------------------------------------------------------------
@ -113,7 +115,7 @@ for name in filenames:
newID += 1 newID += 1
microstructure = np.where(microstructure == microstructureID, newID,microstructure).reshape(microstructure.shape) microstructure = np.where(microstructure == microstructureID, newID,microstructure).reshape(microstructure.shape)
newInfo['microstructures'] = microstructure.max() newInfo['microstructures'] = len(np.unique(microstructure))
# --- report --------------------------------------------------------------------------------------- # --- report ---------------------------------------------------------------------------------------
@ -152,9 +154,9 @@ for name in filenames:
# --- write microstructure information ------------------------------------------------------------ # --- write microstructure information ------------------------------------------------------------
formatwidth = int(math.floor(math.log10(microstructure.max())+1)) format = '%g' if options.float else '%{}i'.format(int(math.floor(math.log10(np.nanmax(microstructure))+1)))
table.data = microstructure.reshape((newInfo['grid'][0],newInfo['grid'][1]*newInfo['grid'][2]),order='F').transpose() table.data = microstructure.reshape((newInfo['grid'][0],newInfo['grid'][1]*newInfo['grid'][2]),order='F').transpose()
table.data_writeArray('%%%ii'%(formatwidth),delimiter = ' ') table.data_writeArray(format,delimiter=' ')
# --- output finalization -------------------------------------------------------------------------- # --- output finalization --------------------------------------------------------------------------

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@ -43,9 +43,15 @@ parser.add_option('-f', '--fill',
dest = 'fill', dest = 'fill',
type = 'int', metavar = 'int', type = 'int', metavar = 'int',
help = 'background grain index. "0" selects maximum microstructure index + 1 [%default]') help = 'background grain index. "0" selects maximum microstructure index + 1 [%default]')
parser.add_option('--float',
dest = 'float',
action = 'store_true',
help = 'use float input')
parser.set_defaults(degrees = False, parser.set_defaults(degrees = False,
fill = 0) fill = 0,
float = False,
)
(options, filenames) = parser.parse_args() (options, filenames) = parser.parse_args()
@ -61,6 +67,8 @@ if options.matrix is not None:
if options.eulers is not None: if options.eulers is not None:
eulers = damask.Rotation.fromEulers(np.array(options.eulers),degrees=True).asEulers(degrees=True) eulers = damask.Rotation.fromEulers(np.array(options.eulers),degrees=True).asEulers(degrees=True)
datatype = 'f' if options.float else 'i'
# --- loop over input files ------------------------------------------------------------------------- # --- loop over input files -------------------------------------------------------------------------
if filenames == []: filenames = [None] if filenames == []: filenames = [None]
@ -77,13 +85,7 @@ for name in filenames:
table.head_read() table.head_read()
info,extra_header = table.head_getGeom() info,extra_header = table.head_getGeom()
damask.util.report_geom(info)
damask.util.croak(['grid a b c: {}'.format(' x '.join(map(str,info['grid']))),
'size x y z: {}'.format(' x '.join(map(str,info['size']))),
'origin x y z: {}'.format(' : '.join(map(str,info['origin']))),
'homogenization: {}'.format(info['homogenization']),
'microstructures: {}'.format(info['microstructures']),
])
errors = [] errors = []
if np.any(info['grid'] < 1): errors.append('invalid grid a b c.') if np.any(info['grid'] < 1): errors.append('invalid grid a b c.')
@ -95,9 +97,9 @@ for name in filenames:
# --- read data ------------------------------------------------------------------------------------ # --- read data ------------------------------------------------------------------------------------
microstructure = table.microstructure_read(info['grid']).reshape(info['grid'],order='F') # read microstructure microstructure = table.microstructure_read(info['grid'],datatype).reshape(info['grid'],order='F') # read microstructure
newGrainID = options.fill if options.fill != 0 else microstructure.max()+1 newGrainID = options.fill if options.fill != 0 else np.nanmax(microstructure)+1
microstructure = ndimage.rotate(microstructure,eulers[2],(0,1),order=0,prefilter=False,output=int,cval=newGrainID) # rotation around Z microstructure = ndimage.rotate(microstructure,eulers[2],(0,1),order=0,prefilter=False,output=int,cval=newGrainID) # rotation around Z
microstructure = ndimage.rotate(microstructure,eulers[1],(1,2),order=0,prefilter=False,output=int,cval=newGrainID) # rotation around X microstructure = ndimage.rotate(microstructure,eulers[1],(1,2),order=0,prefilter=False,output=int,cval=newGrainID) # rotation around X
microstructure = ndimage.rotate(microstructure,eulers[0],(0,1),order=0,prefilter=False,output=int,cval=newGrainID) # rotation around Z microstructure = ndimage.rotate(microstructure,eulers[0],(0,1),order=0,prefilter=False,output=int,cval=newGrainID) # rotation around Z
@ -107,19 +109,18 @@ for name in filenames:
newInfo = { newInfo = {
'size': microstructure.shape*info['size']/info['grid'], 'size': microstructure.shape*info['size']/info['grid'],
'grid': microstructure.shape, 'grid': microstructure.shape,
'microstructures': microstructure.max(), 'microstructures': len(np.unique(microstructure)),
} }
# --- report --------------------------------------------------------------------------------------- # --- report ---------------------------------------------------------------------------------------
remarks = [] remarks = []
if (any(newInfo['grid'] != info['grid'])): if (any(newInfo['grid'] != info['grid'])):
remarks.append('--> grid a b c: %s'%(' x '.join(map(str,newInfo['grid'])))) remarks.append('--> grid a b c: {}'.format(' x '.join(map(str,newInfo['grid']))))
if (any(newInfo['size'] != info['size'])): if (any(newInfo['size'] != info['size'])):
remarks.append('--> size x y z: %s'%(' x '.join(map(str,newInfo['size'])))) remarks.append('--> size x y z: {}'.format(' x '.join(map(str,newInfo['size']))))
if ( newInfo['microstructures'] != info['microstructures']): if ( newInfo['microstructures'] != info['microstructures']):
remarks.append('--> microstructures: %i'%newInfo['microstructures']) remarks.append('--> microstructures: {}'.format(newInfo['microstructures']))
if remarks != []: damask.util.croak(remarks) if remarks != []: damask.util.croak(remarks)
# --- write header --------------------------------------------------------------------------------- # --- write header ---------------------------------------------------------------------------------
@ -138,9 +139,9 @@ for name in filenames:
# --- write microstructure information ------------------------------------------------------------ # --- write microstructure information ------------------------------------------------------------
formatwidth = int(math.floor(math.log10(microstructure.max())+1)) format = '%g' if options.float else '%{}i'.format(int(math.floor(math.log10(np.nanmax(microstructure))+1)))
table.data = microstructure.reshape((newInfo['grid'][0],np.prod(newInfo['grid'][1:])),order='F').transpose() table.data = microstructure.reshape((newInfo['grid'][0],np.prod(newInfo['grid'][1:])),order='F').transpose()
table.data_writeArray('%%%ii'%(formatwidth),delimiter = ' ') table.data_writeArray(format,delimiter=' ')
# --- output finalization -------------------------------------------------------------------------- # --- output finalization --------------------------------------------------------------------------

View File

@ -20,15 +20,15 @@ Translate geom description into ASCIItable containing position and microstructur
""", version = scriptID) """, version = scriptID)
parser.add_option('--float', parser.add_option('--float',
dest = 'real', dest = 'float',
action = 'store_true', action = 'store_true',
help = 'use float input') help = 'use float input')
parser.set_defaults(real = False, parser.set_defaults(float = False,
) )
(options, filenames) = parser.parse_args() (options, filenames) = parser.parse_args()
datatype = 'f' if options.real else 'i' datatype = 'f' if options.float else 'i'
# --- loop over input files ------------------------------------------------------------------------- # --- loop over input files -------------------------------------------------------------------------
@ -47,13 +47,7 @@ for name in filenames:
table.head_read() table.head_read()
info,extra_header = table.head_getGeom() info,extra_header = table.head_getGeom()
damask.util.report_geom(info)
damask.util.croak(['grid a b c: {}'.format(' x '.join(list(map(str,info['grid'])))),
'size x y z: {}'.format(' x '.join(list(map(str,info['size'])))),
'origin x y z: {}'.format(' : '.join(list(map(str,info['origin'])))),
'homogenization: {}'.format(info['homogenization']),
'microstructures: {}'.format(info['microstructures']),
])
errors = [] errors = []
if np.any(info['grid'] < 1): errors.append('invalid grid a b c.') if np.any(info['grid'] < 1): errors.append('invalid grid a b c.')

View File

@ -31,19 +31,19 @@ parser.add_option('-s', '--substitute',
action = 'extend', metavar = '<string LIST>', action = 'extend', metavar = '<string LIST>',
help = 'substitutions of microstructure indices from,to,from,to,...') help = 'substitutions of microstructure indices from,to,from,to,...')
parser.add_option('--float', parser.add_option('--float',
dest = 'real', dest = 'float',
action = 'store_true', action = 'store_true',
help = 'use float input') help = 'use float input')
parser.set_defaults(origin = (0.0,0.0,0.0), parser.set_defaults(origin = (0.0,0.0,0.0),
microstructure = 0, microstructure = 0,
substitute = [], substitute = [],
real = False, float = False,
) )
(options, filenames) = parser.parse_args() (options, filenames) = parser.parse_args()
datatype = 'f' if options.real else 'i' datatype = 'f' if options.float else 'i'
sub = {} sub = {}
for i in range(len(options.substitute)//2): # split substitution list into "from" -> "to" for i in range(len(options.substitute)//2): # split substitution list into "from" -> "to"
@ -64,13 +64,7 @@ for name in filenames:
table.head_read() table.head_read()
info,extra_header = table.head_getGeom() info,extra_header = table.head_getGeom()
damask.util.report_geom(info)
damask.util.croak(['grid a b c: %s'%(' x '.join(map(str,info['grid']))),
'size x y z: %s'%(' x '.join(map(str,info['size']))),
'origin x y z: %s'%(' : '.join(map(str,info['origin']))),
'homogenization: %i'%info['homogenization'],
'microstructures: %i'%info['microstructures'],
])
errors = [] errors = []
if np.any(info['grid'] < 1): errors.append('invalid grid a b c.') if np.any(info['grid'] < 1): errors.append('invalid grid a b c.')
@ -92,7 +86,7 @@ for name in filenames:
} }
substituted = np.copy(microstructure) substituted = np.copy(microstructure)
for k, v in sub.items(): substituted[microstructure==k] = v # substitute microstructure indices for k, v in sub.items(): substituted[microstructure==k] = v # substitute microstructure indices
substituted += options.microstructure # shift microstructure indices substituted += options.microstructure # shift microstructure indices
@ -103,9 +97,9 @@ for name in filenames:
remarks = [] remarks = []
if (any(newInfo['origin'] != info['origin'])): if (any(newInfo['origin'] != info['origin'])):
remarks.append('--> origin x y z: %s'%(' : '.join(map(str,newInfo['origin'])))) remarks.append('--> origin x y z: {}'.format(' : '.join(map(str,newInfo['origin']))))
if ( newInfo['microstructures'] != info['microstructures']): if ( newInfo['microstructures'] != info['microstructures']):
remarks.append('--> microstructures: %i'%newInfo['microstructures']) remarks.append('--> microstructures: {}'.format(newInfo['microstructures']))
if remarks != []: damask.util.croak(remarks) if remarks != []: damask.util.croak(remarks)
# --- write header ------------------------------------------------------------------------------- # --- write header -------------------------------------------------------------------------------
@ -124,7 +118,7 @@ for name in filenames:
# --- write microstructure information ----------------------------------------------------------- # --- write microstructure information -----------------------------------------------------------
format = '%g' if options.real else '%{}i'.format(int(math.floor(math.log10(microstructure.max())+1))) format = '%g' if options.float else '%{}i'.format(int(math.floor(math.log10(np.nanmax(substituted))+1)))
table.data = substituted.reshape((info['grid'][0],info['grid'][1]*info['grid'][2]),order='F').transpose() table.data = substituted.reshape((info['grid'][0],info['grid'][1]*info['grid'][2]),order='F').transpose()
table.data_writeArray(format,delimiter = ' ') table.data_writeArray(format,delimiter = ' ')

View File

@ -43,13 +43,7 @@ for name in filenames:
table.head_read() table.head_read()
info,extra_header = table.head_getGeom() info,extra_header = table.head_getGeom()
damask.util.report_geom(info)
damask.util.croak(['grid a b c: %s'%(' x '.join(map(str,info['grid']))),
'size x y z: %s'%(' x '.join(map(str,info['size']))),
'origin x y z: %s'%(' : '.join(map(str,info['origin']))),
'homogenization: %i'%info['homogenization'],
'microstructures: %i'%info['microstructures'],
])
errors = [] errors = []
if np.any(info['grid'] < 1): errors.append('invalid grid a b c.') if np.any(info['grid'] < 1): errors.append('invalid grid a b c.')

View File

@ -73,13 +73,7 @@ for name in filenames:
table.head_read() table.head_read()
info,extra_header = table.head_getGeom() info,extra_header = table.head_getGeom()
damask.util.report_geom(info)
damask.util.croak(['grid a b c: %s'%(' x '.join(map(str,info['grid']))),
'size x y z: %s'%(' x '.join(map(str,info['size']))),
'origin x y z: %s'%(' : '.join(map(str,info['origin']))),
'homogenization: %i'%info['homogenization'],
'microstructures: %i'%info['microstructures'],
])
errors = [] errors = []
if np.any(info['grid'] < 1): errors.append('invalid grid a b c.') if np.any(info['grid'] < 1): errors.append('invalid grid a b c.')
@ -108,7 +102,7 @@ for name in filenames:
extra_keywords={"trigger":options.trigger,"size":1+2*options.vicinity}), extra_keywords={"trigger":options.trigger,"size":1+2*options.vicinity}),
microstructure + options.offset,microstructure) microstructure + options.offset,microstructure)
newInfo['microstructures'] = microstructure.max() newInfo['microstructures'] = len(np.unique(microstructure))
# --- report --------------------------------------------------------------------------------------- # --- report ---------------------------------------------------------------------------------------
@ -131,9 +125,9 @@ for name in filenames:
# --- write microstructure information ------------------------------------------------------------ # --- write microstructure information ------------------------------------------------------------
formatwidth = int(math.floor(math.log10(microstructure.max())+1)) formatwidth = int(math.floor(math.log10(np.nanmax(microstructure))+1))
table.data = microstructure.reshape((info['grid'][0],info['grid'][1]*info['grid'][2]),order='F').transpose() table.data = microstructure.reshape((info['grid'][0],info['grid'][1]*info['grid'][2]),order='F').transpose()
table.data_writeArray('%%%ii'%(formatwidth),delimiter = ' ') table.data_writeArray('%{}i'.format(formatwidth),delimiter = ' ')
# --- output finalization -------------------------------------------------------------------------- # --- output finalization --------------------------------------------------------------------------