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DAMASK_EICMD
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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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14
processing/pre/geom_canvas.py
View File

@ -35,7 +35,7 @@ parser.add_option('-f',
type = 'float', metavar = 'float',
help = '(background) canvas grain index. "0" selects maximum microstructure index + 1 [%default]')
parser.add_option('--float',
dest = 'real',
dest = 'float',
action = 'store_true',
help = 'use float input')
parser.add_option('--blank',
@ -45,13 +45,13 @@ parser.add_option('--blank',
parser.set_defaults(grid = ['0','0','0'],
offset = (0,0,0),
fill = 0,
real = False,
fill = 0.0,
float = False,
)
(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.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'])
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:
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['origin'] = info['origin']+(info['size']/info['grid'] if np.all(info['grid'] > 0) \
else newInfo['size']/newInfo['grid'])*options.offset
newInfo['microstructures'] = microstructure_cropped.max()
newInfo['microstructures'] = len(np.unique(microstructure_cropped))
# --- report ---------------------------------------------------------------------------------------
@ -172,7 +172,7 @@ for name in filenames:
# --- 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_writeArray(format,delimiter=' ')

14
processing/pre/geom_clean.py
View File

@ -50,13 +50,7 @@ for name in filenames:
table.head_read()
info,extra_header = table.head_getGeom()
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']),
])
damask.util.report_geom(info)
errors = []
if np.any(info['grid'] < 1): errors.append('invalid grid a b c.')
@ -73,7 +67,7 @@ for name in filenames:
# --- do work ------------------------------------------------------------------------------------
microstructure = ndimage.filters.generic_filter(microstructure,mostFrequent,size=(options.stencil,)*3).astype('int_')
newInfo = {'microstructures': microstructure.max()}
newInfo = {'microstructures': len(np.unique(microstructure))}
# --- report ---------------------------------------------------------------------------------------
if ( newInfo['microstructures'] != info['microstructures']):
@ -91,9 +85,9 @@ for name in filenames:
# --- 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_writeArray('%%%ii'%(formatwidth),delimiter = ' ')
table.data_writeArray('%{}i'.format(formatwidth),delimiter = ' ')
# --- output finalization --------------------------------------------------------------------------

7
processing/pre/geom_fromMinimalSurface.py
View File

@ -90,12 +90,7 @@ for name in filenames:
#--- report ---------------------------------------------------------------------------------------
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'],
])
damask.util.report_geom(info)
errors = []
if np.any(info['grid'] < 1): errors.append('invalid grid a b c.')

9
processing/pre/geom_fromTable.py
View File

@ -192,12 +192,7 @@ for name in filenames:
'homogenization': options.homogenization,
}
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']),
])
damask.util.report_geom(info)
# --- write header ---------------------------------------------------------------------------------
@ -230,7 +225,7 @@ for name in filenames:
# --- write microstructure information ------------------------------------------------------------
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 --------------------------------------------------------------------------

13
processing/pre/geom_grainGrowth.py
View File

@ -69,13 +69,7 @@ for name in filenames:
table.head_read()
info,extra_header = table.head_getGeom()
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']),
])
damask.util.report_geom(info)
errors = []
if np.any(info['grid'] < 1): errors.append('invalid grid a b c.')
@ -200,8 +194,7 @@ for name in filenames:
newID += 1
microstructure = np.where(microstructure == microstructureID, newID, microstructure)
newInfo = {'microstructures': 0,}
newInfo['microstructures'] = microstructure.max()
newInfo = {'microstructures': len(np.unique(microstructure)),}
# --- report --------------------------------------------------------------------------------------
@ -226,7 +219,7 @@ for name in filenames:
# --- 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,
::1 if info['grid'][1]>1 else 2,
::1 if info['grid'][2]>1 else 2,].\

26
processing/pre/geom_mirror.py
View File

@ -23,6 +23,13 @@ parser.add_option('-d','--direction',
dest = 'directions',
action = 'extend', metavar = '<string LIST>',
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()
@ -32,6 +39,8 @@ if not set(options.directions).issubset(validDirections):
invalidDirections = [str(e) for e in set(options.directions).difference(validDirections)]
parser.error('invalid directions {}. '.format(*invalidDirections))
datatype = 'f' if options.float else 'i'
# --- loop over input files -------------------------------------------------------------------------
if filenames == []: filenames = [None]
@ -39,7 +48,8 @@ if filenames == []: filenames = [None]
for name in filenames:
try:
table = damask.ASCIItable(name = name,
buffered = False, labeled = False)
buffered = False,
labeled = False)
except: continue
damask.util.report(scriptName,name)
@ -47,13 +57,7 @@ for name in filenames:
table.head_read()
info,extra_header = table.head_getGeom()
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'],
])
damask.util.report_geom(info)
errors = []
if np.any(info['grid'] < 1): errors.append('invalid grid a b c.')
@ -65,7 +69,7 @@ for name in filenames:
# --- 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:
microstructure = np.concatenate([microstructure,microstructure[:,:,::-1]],2)
@ -107,9 +111,9 @@ for name in filenames:
# --- 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_writeArray('%%%ii'%(formatwidth),delimiter = ' ')
table.data_writeArray('%{}i'.format(formatwidth),delimiter = ' ')
# --- output finalization --------------------------------------------------------------------------

8
processing/pre/geom_pack.py
View File

@ -35,13 +35,7 @@ for name in filenames:
table.head_read()
info,extra_header = table.head_getGeom()
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']),
])
damask.util.report_geom(info)
errors = []
if np.any(info['grid'] < 1): errors.append('invalid grid a b c.')

10
processing/pre/geom_renumber.py
View File

@ -35,13 +35,7 @@ for name in filenames:
table.head_read()
info,extra_header = table.head_getGeom()
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'],
])
damask.util.report_geom(info)
errors = []
if np.any(info['grid'] < 1): errors.append('invalid grid a b c.')
@ -93,7 +87,7 @@ for name in filenames:
# --- 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_writeArray(format,delimiter = ' ')

26
processing/pre/geom_rescale.py
View File

@ -31,14 +31,21 @@ parser.add_option('-r', '--renumber',
dest = 'renumber',
action = 'store_true',
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,
grid = ['0','0','0'],
size = ['0.0','0.0','0.0'],
float = False,
)
(options, filenames) = parser.parse_args()
datatype = 'f' if options.float else 'i'
# --- loop over input files -------------------------------------------------------------------------
if filenames == []: filenames = [None]
@ -46,7 +53,8 @@ if filenames == []: filenames = [None]
for name in filenames:
try:
table = damask.ASCIItable(name = name,
buffered = False, labeled = False)
buffered = False,
labeled = False)
except: continue
damask.util.report(scriptName,name)
@ -54,13 +62,7 @@ for name in filenames:
table.head_read()
info,extra_header = table.head_getGeom()
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'],
])
damask.util.report_geom(info)
errors = []
if np.any(info['grid'] < 1): errors.append('invalid grid a b c.')
@ -72,7 +74,7 @@ for name in filenames:
# --- read data ------------------------------------------------------------------------------------
microstructure = table.microstructure_read(info['grid']) # read microstructure
microstructure = table.microstructure_read(info['grid'],datatype) # read microstructure
# --- do work ------------------------------------------------------------------------------------
@ -113,7 +115,7 @@ for name in filenames:
newID += 1
microstructure = np.where(microstructure == microstructureID, newID,microstructure).reshape(microstructure.shape)
newInfo['microstructures'] = microstructure.max()
newInfo['microstructures'] = len(np.unique(microstructure))
# --- report ---------------------------------------------------------------------------------------
@ -152,9 +154,9 @@ for name in filenames:
# --- 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_writeArray('%%%ii'%(formatwidth),delimiter = ' ')
table.data_writeArray(format,delimiter=' ')
# --- output finalization --------------------------------------------------------------------------

35
processing/pre/geom_rotate.py
View File

@ -43,9 +43,15 @@ parser.add_option('-f', '--fill',
dest = 'fill',
type = 'int', metavar = 'int',
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,
fill = 0)
fill = 0,
float = False,
)
(options, filenames) = parser.parse_args()
@ -61,6 +67,8 @@ if options.matrix is not None:
if options.eulers is not None:
eulers = damask.Rotation.fromEulers(np.array(options.eulers),degrees=True).asEulers(degrees=True)
datatype = 'f' if options.float else 'i'
# --- loop over input files -------------------------------------------------------------------------
if filenames == []: filenames = [None]
@ -77,13 +85,7 @@ for name in filenames:
table.head_read()
info,extra_header = table.head_getGeom()
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']),
])
damask.util.report_geom(info)
errors = []
if np.any(info['grid'] < 1): errors.append('invalid grid a b c.')
@ -95,9 +97,9 @@ for name in filenames:
# --- 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[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
@ -107,19 +109,18 @@ for name in filenames:
newInfo = {
'size': microstructure.shape*info['size']/info['grid'],
'grid': microstructure.shape,
'microstructures': microstructure.max(),
'microstructures': len(np.unique(microstructure)),
}
# --- report ---------------------------------------------------------------------------------------
remarks = []
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'])):
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']):
remarks.append('--> microstructures: %i'%newInfo['microstructures'])
remarks.append('--> microstructures: {}'.format(newInfo['microstructures']))
if remarks != []: damask.util.croak(remarks)
# --- write header ---------------------------------------------------------------------------------
@ -138,9 +139,9 @@ for name in filenames:
# --- 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_writeArray('%%%ii'%(formatwidth),delimiter = ' ')
table.data_writeArray(format,delimiter=' ')
# --- output finalization --------------------------------------------------------------------------

14
processing/pre/geom_toTable.py
View File

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

20
processing/pre/geom_translate.py
View File

@ -31,19 +31,19 @@ parser.add_option('-s', '--substitute',
action = 'extend', metavar = '<string LIST>',
help = 'substitutions of microstructure indices from,to,from,to,...')
parser.add_option('--float',
dest = 'real',
dest = 'float',
action = 'store_true',
help = 'use float input')
parser.set_defaults(origin = (0.0,0.0,0.0),
microstructure = 0,
substitute = [],
real = False,
float = False,
)
(options, filenames) = parser.parse_args()
datatype = 'f' if options.real else 'i'
datatype = 'f' if options.float else 'i'
sub = {}
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()
info,extra_header = table.head_getGeom()
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'],
])
damask.util.report_geom(info)
errors = []
if np.any(info['grid'] < 1): errors.append('invalid grid a b c.')
@ -103,9 +97,9 @@ for name in filenames:
remarks = []
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']):
remarks.append('--> microstructures: %i'%newInfo['microstructures'])
remarks.append('--> microstructures: {}'.format(newInfo['microstructures']))
if remarks != []: damask.util.croak(remarks)
# --- write header -------------------------------------------------------------------------------
@ -124,7 +118,7 @@ for name in filenames:
# --- 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_writeArray(format,delimiter = ' ')

8
processing/pre/geom_unpack.py
View File

@ -43,13 +43,7 @@ for name in filenames:
table.head_read()
info,extra_header = table.head_getGeom()
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'],
])
damask.util.report_geom(info)
errors = []
if np.any(info['grid'] < 1): errors.append('invalid grid a b c.')

14
processing/pre/geom_vicinityOffset.py
View File

@ -73,13 +73,7 @@ for name in filenames:
table.head_read()
info,extra_header = table.head_getGeom()
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'],
])
damask.util.report_geom(info)
errors = []
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}),
microstructure + options.offset,microstructure)
newInfo['microstructures'] = microstructure.max()
newInfo['microstructures'] = len(np.unique(microstructure))
# --- report ---------------------------------------------------------------------------------------
@ -131,9 +125,9 @@ for name in filenames:
# --- 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_writeArray('%%%ii'%(formatwidth),delimiter = ' ')
table.data_writeArray('%{}i'.format(formatwidth),delimiter = ' ')
# --- output finalization --------------------------------------------------------------------------