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DAMASK_EICMD
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streamlining and bugfixing of geom-class

This commit is contained in:
Philip Eisenlohr 2019-05-27 19:14:09 -06:00
parent b69f0efbbc
commit 1f56ac6a4a
19 changed files with 495 additions and 309 deletions
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28
processing/pre/geom_addPrimitive.py
View File

@ -78,7 +78,7 @@ parser.set_defaults(center = (.0,.0,.0),
if options.dimension is None: if options.dimension is None:
parser.error('no dimension specified.') parser.error('no dimension specified.')
if [options.angleaxis,options.quaternion].count(None) == 2: if [options.angleaxis,options.quaternion].count(None) == 0:
parser.error('more than one rotation specified.') parser.error('more than one rotation specified.')
if options.angleaxis is not None: if options.angleaxis is not None:
@ -99,27 +99,18 @@ if filenames == []: filenames = [None]
for name in filenames: for name in filenames:
damask.util.report(scriptName,name) damask.util.report(scriptName,name)
if name is None: geom = damask.Geom.from_file(StringIO(''.join(sys.stdin.read())) if name is None else name)
virt_file = StringIO(''.join(sys.stdin.read())) grid = geom.get_grid()
geom = damask.Geom.from_file(virt_file) size = geom.get_size()
else: origin = geom.get_origin()
geom = damask.Geom.from_file(name)
microstructure = geom.get_microstructure() microstructure = geom.get_microstructure()
fill = options.fill if options.fill is not None else np.nanmax(microstructure)+1 # coordinates given in real space, not (default) voxel space
origin = np.zeros(3)
for i,line in enumerate(geom.comments):
if line.lower().strip().startswith('origin'):
origin= np.array([float(line.split()[j]) for j in [2,4,6]]) # assume correct order (x,y,z)
# coordinates given in real space (default) vs voxel space
if options.realspace: if options.realspace:
options.center -= origin options.center -= origin
options.center *= geom.get_grid() / geom.get_size() options.center *= grid / size
options.dimension *= geom.get_grid() / geom.get_size() options.dimension *= grid / size
grid = microstructure.shape
# change to coordinate space where the primitive is the unit sphere/cube/etc # change to coordinate space where the primitive is the unit sphere/cube/etc
if options.periodic: # use padding to achieve periodicity if options.periodic: # use padding to achieve periodicity
@ -158,6 +149,7 @@ for name in filenames:
Y /= options.dimension[1] * 0.5 Y /= options.dimension[1] * 0.5
Z /= options.dimension[2] * 0.5 Z /= options.dimension[2] * 0.5
fill = np.nanmax(microstructure)+1 if options.fill is None else options.fill
# High exponents can cause underflow & overflow - loss of precision is okay here, we just compare it to 1, so +infinity and 0 are fine # High exponents can cause underflow & overflow - loss of precision is okay here, we just compare it to 1, so +infinity and 0 are fine
old_settings = np.seterr() old_settings = np.seterr()
@ -191,7 +183,7 @@ for name in filenames:
microstructure if options.inside else fill) microstructure if options.inside else fill)
damask.util.croak(geom.update(microstructure)) damask.util.croak(geom.update(microstructure))
geom.add_comment(scriptID + ' ' + ' '.join(sys.argv[1:])) geom.add_comments(scriptID + ' ' + ' '.join(sys.argv[1:]))
if name is None: if name is None:
sys.stdout.write(str(geom.show())) sys.stdout.write(str(geom.show()))

105
processing/pre/geom_canvas.py
View File

@ -1,80 +1,111 @@
#!/usr/bin/env python3 #!/usr/bin/env python3
# -*- coding: UTF-8 no BOM -*-
import os import os
import sys import sys
import numpy as np
import damask
from io import StringIO from io import StringIO
from optparse import OptionParser from optparse import OptionParser
import numpy as np
import damask
scriptName = os.path.splitext(os.path.basename(__file__))[0] scriptName = os.path.splitext(os.path.basename(__file__))[0]
scriptID = ' '.join([scriptName,damask.version]) scriptID = ' '.join([scriptName,damask.version])
# -------------------------------------------------------------------- # --------------------------------------------------------------------
# MAIN # MAIN
# -------------------------------------------------------------------- # --------------------------------------------------------------------
parser = OptionParser(option_class=damask.extendableOption, usage='%prog options [geomfile(s)]', description = """ parser = OptionParser(option_class=damask.extendableOption, usage='%prog option(s) [geomfile(s)]', description = """
Increases or decreases the (three-dimensional) canvas. Changes the (three-dimensional) canvas of a spectral geometry description.
Grid can be given as absolute or relative values, e.g. 16 16 16 or 2x 0.5x 32. Grid can be given as absolute or relative values, e.g. 16 16 16 or 2x 0.5x 32.
""", version = scriptID) """, version = scriptID)
parser.add_option('-g','--grid', parser.add_option('-g',
'--grid',
dest = 'grid', dest = 'grid',
type = 'string', nargs = 3, metavar = ' '.join(['string']*3), type = 'string', nargs = 3, metavar = ' '.join(['string']*3),
help = 'a,b,c grid of hexahedral box') help = 'a,b,c grid of hexahedral box. [auto]')
parser.add_option('-o','--offset', parser.add_option('-o',
'--offset',
dest = 'offset', dest = 'offset',
type = 'int', nargs = 3, metavar = ' '.join(['int']*3), type = 'int', nargs = 3, metavar = ' '.join(['int']*3),
help = 'a,b,c offset from old to new origin of grid [%default]') help = 'a,b,c offset from old to new origin of grid [%default]')
parser.add_option('-f','--fill', parser.add_option('-f',
'--fill',
dest = 'fill', dest = 'fill',
type = 'float', metavar = 'int', type = 'float', metavar = 'float',
help = 'background microstructure index, defaults to max microstructure index + 1') help = '(background) canvas grain index. "0" selects maximum microstructure index + 1 [%default]')
parser.add_option('--blank',
dest = 'blank',
action = 'store_true',
help = 'blank out (optional) input canvas content')
parser.set_defaults(offset = (0,0,0)) parser.set_defaults(grid = ['0','0','0'],
offset = (0,0,0),
)
(options, filenames) = parser.parse_args() (options, filenames) = parser.parse_args()
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 is None else options.fill
# --- loop over input files -------------------------------------------------------------------------
if filenames == []: filenames = [None] if filenames == []: filenames = [None]
for name in filenames: for name in filenames:
damask.util.report(scriptName,name) damask.util.report(scriptName,name)
if name is None: if name is None and options.blank:
virt_file = StringIO(''.join(sys.stdin.read())) grid = np.array(list(map(int,options.grid)))
geom = damask.Geom.from_file(virt_file) geom = damask.Geom(size=grid,microstructure=options.fill*np.ones(grid))
else: else:
geom = damask.Geom.from_file(name) geom = damask.Geom.from_file(StringIO(''.join(sys.stdin.read())) if name is None else name)
microstructure = geom.get_microstructure()
grid = geom.get_grid() grid = geom.get_grid()
if options.grid is not None: size = geom.get_size()
for i,g in enumerate(options.grid): origin = geom.get_origin()
grid[i] = int(round(grid[i]*float(g.lower().replace('x','')))) if g.lower().endswith('x') \ microstructure = geom.get_microstructure()
else int(options.grid[i]) fill = np.nanmax(microstructure)+1 if options.fill is None else options.fill
dtype = float if np.isnan(fill) or int(fill) != fill or microstructure.dtype==np.float else int
new = np.full(grid,options.fill if options.fill is not None else np.nanmax(microstructure)+1, damask.util.croak(geom)
microstructure.dtype)
for x in range(microstructure.shape[0]): # --- do work ------------------------------------------------------------------------------------
X = x + options.offset[0]
if not 0 <= X < new.shape[0]: continue
for y in range(microstructure.shape[1]):
Y = y + options.offset[1]
if not 0 <= Y < new.shape[1]: continue
for z in range(microstructure.shape[2]):
Z = z + options.offset[2]
if not 0 <= Z < new.shape[2]: continue
new[X,Y,Z] = microstructure[x,y,z]
damask.util.croak(geom.update(new,rescale=True)) new_grid = np.array([int(o*float(n.lower().replace('x',''))) if n.lower().endswith('x') \
geom.add_comment(scriptID + ' ' + ' '.join(sys.argv[1:])) else int(n) for o,n in zip(grid,options.grid)],dtype=int)
new_grid = np.where(new_grid > 0, new_grid,grid)
microstructure_cropped = np.zeros(new_grid,dtype=dtype)
microstructure_cropped.fill(fill)
if not options.blank:
xindex = np.arange(max(options.offset[0],0),min(options.offset[0]+new_grid[0],grid[0]))
yindex = np.arange(max(options.offset[1],0),min(options.offset[1]+new_grid[1],grid[1]))
zindex = np.arange(max(options.offset[2],0),min(options.offset[2]+new_grid[2],grid[2]))
translate_x = [i - options.offset[0] for i in xindex]
translate_y = [i - options.offset[1] for i in yindex]
translate_z = [i - options.offset[2] for i in zindex]
if 0 in map(len,[xindex,yindex,zindex,translate_x,translate_y,translate_z]):
damask.util.croak('invaldid combination of grid and offset.')
continue
microstructure_cropped[min(translate_x):max(translate_x)+1,
min(translate_y):max(translate_y)+1,
min(translate_z):max(translate_z)+1] \
= microstructure[min(xindex):max(xindex)+1,
min(yindex):max(yindex)+1,
min(zindex):max(zindex)+1]
new_size = size/grid*new_grid if np.all(grid > 0) else new_grid
new_origin = origin + (size/grid if np.all(grid > 0) else new_size/new_grid) * options.offset
geom.set_microstructure(microstructure_cropped)
geom.set_size(new_size)
geom.set_origin(new_origin)
geom.add_comments(scriptID + ' ' + ' '.join(sys.argv[1:]))
if name is None: if name is None:
sys.stdout.write(str(geom.show())) sys.stdout.write(str(geom.show()))

8
processing/pre/geom_clean.py
View File

@ -44,18 +44,14 @@ if filenames == []: filenames = [None]
for name in filenames: for name in filenames:
damask.util.report(scriptName,name) damask.util.report(scriptName,name)
if name is None: geom = damask.Geom.from_file(StringIO(''.join(sys.stdin.read())) if name is None else name)
virt_file = StringIO(''.join(sys.stdin.read()))
geom = damask.Geom.from_file(virt_file)
else:
geom = damask.Geom.from_file(name)
microstructure = geom.get_microstructure() microstructure = geom.get_microstructure()
microstructure = ndimage.filters.generic_filter(microstructure,mostFrequent, microstructure = ndimage.filters.generic_filter(microstructure,mostFrequent,
size=(options.stencil,)*3).astype(microstructure.dtype) size=(options.stencil,)*3).astype(microstructure.dtype)
damask.util.croak(geom.update(microstructure)) damask.util.croak(geom.update(microstructure))
geom.add_comment(scriptID + ' ' + ' '.join(sys.argv[1:])) geom.add_comments(scriptID + ' ' + ' '.join(sys.argv[1:]))
if name is None: if name is None:
sys.stdout.write(str(geom.show())) sys.stdout.write(str(geom.show()))

7
processing/pre/geom_fromMinimalSurface.py
View File

@ -82,13 +82,14 @@ for name in filenames:
Y = options.periods*2.0*np.pi*(np.arange(options.grid[1])+0.5)/options.grid[1] Y = options.periods*2.0*np.pi*(np.arange(options.grid[1])+0.5)/options.grid[1]
Z = options.periods*2.0*np.pi*(np.arange(options.grid[2])+0.5)/options.grid[2] Z = options.periods*2.0*np.pi*(np.arange(options.grid[2])+0.5)/options.grid[2]
microstructure = np.empty(options.grid,dtype='int') microstructure = np.empty(options.grid,dtype=int)
for x in range(options.grid[0]): for x in range(options.grid[0]):
for y in range(options.grid[1]): for y in range(options.grid[1]):
for z in range(options.grid[2]): for z in range(options.grid[2]):
microstructure[x,y,z]=options.microstructure[options.threshold < surface[options.type](X[x],Y[y],Z[z])] microstructure[x,y,z]=options.microstructure[int(options.threshold < surface[options.type](X[x],Y[y],Z[z]))]
geom=damask.Geom(microstructure,options.size,options.homogenization, geom=damask.Geom(microstructure,options.size,
homogenization=options.homogenization,
comments=[scriptID + ' ' + ' '.join(sys.argv[1:])]) comments=[scriptID + ' ' + ' '.join(sys.argv[1:])])
damask.util.croak(geom) damask.util.croak(geom)

3
processing/pre/geom_fromTable.py
View File

@ -171,7 +171,8 @@ for name in filenames:
if options.axes is not None: config_header += ['axes\t{} {} {}'.format(*options.axes)] if options.axes is not None: config_header += ['axes\t{} {} {}'.format(*options.axes)]
header = [scriptID + ' ' + ' '.join(sys.argv[1:])] + config_header + ['origin x {} y {} z {}'.format(*origin)] header = [scriptID + ' ' + ' '.join(sys.argv[1:])] + config_header + ['origin x {} y {} z {}'.format(*origin)]
geom = damask.Geom(grain.reshape(grid,order='F'),size,options.homogenization,comments=header) geom = damask.Geom(grain.reshape(grid,order='F'),size,
homogenization=options.homogenization,comments=header)
damask.util.croak(geom) damask.util.croak(geom)
if name is None: if name is None:

3
processing/pre/geom_fromVoronoiTessellation.py
View File

@ -311,7 +311,8 @@ for name in filenames:
config_header += ['<!skip>'] config_header += ['<!skip>']
header = [scriptID + ' ' + ' '.join(sys.argv[1:])] + config_header + ['origin x {} y {} z {}'.format(*info['origin'])] header = [scriptID + ' ' + ' '.join(sys.argv[1:])] + config_header + ['origin x {} y {} z {}'.format(*info['origin'])]
geom = damask.Geom(indices.reshape(info['grid'],order='F'),info['size'],options.homogenization,comments=header) geom = damask.Geom(indices.reshape(info['grid'],order='F'),info['size'],
homogenization=options.homogenization,comments=header)
damask.util.croak(geom) damask.util.croak(geom)
if name is None: if name is None:

9
processing/pre/geom_grainGrowth.py
View File

@ -59,11 +59,8 @@ options.immutable = list(map(int,options.immutable))
for name in filenames: for name in filenames:
damask.util.report(scriptName,name) damask.util.report(scriptName,name)
if name is None: geom = damask.Geom.from_file(StringIO(''.join(sys.stdin.read())) if name is None else name)
virt_file = StringIO(''.join(sys.stdin.read())) microstructure = geom.get_microstructure()
geom = damask.Geom.from_file(virt_file)
else:
geom = damask.Geom.from_file(name)
damask.util.croak(geom) damask.util.croak(geom)
grid_original = geom.get_grid() grid_original = geom.get_grid()
@ -171,7 +168,7 @@ for name in filenames:
microstructure = np.where(immutable, microstructure_original,microstructure) microstructure = np.where(immutable, microstructure_original,microstructure)
damask.util.croak(geom.update(microstructure[0:grid_original[0],0:grid_original[1],0:grid_original[2]])) damask.util.croak(geom.update(microstructure[0:grid_original[0],0:grid_original[1],0:grid_original[2]]))
geom.add_comment(scriptID + ' ' + ' '.join(sys.argv[1:])) geom.add_comments(scriptID + ' ' + ' '.join(sys.argv[1:]))
if name is None: if name is None:
sys.stdout.write(str(geom.show())) sys.stdout.write(str(geom.show()))

10
processing/pre/geom_mirror.py
View File

@ -50,12 +50,8 @@ if filenames == []: filenames = [None]
for name in filenames: for name in filenames:
damask.util.report(scriptName,name) damask.util.report(scriptName,name)
if name is None: geom = damask.Geom.from_file(StringIO(''.join(sys.stdin.read())) if name is None else name)
virt_file = StringIO(''.join(sys.stdin.read())) microstructure = geom.get_microstructure()
geom = damask.Geom.from_file(virt_file)
else:
geom = damask.Geom.from_file(name)
microstructure = geom.microstructure
if 'z' in options.directions: if 'z' in options.directions:
microstructure = np.concatenate([microstructure,microstructure[:,:,limits[0]:limits[1]:-1]],2) microstructure = np.concatenate([microstructure,microstructure[:,:,limits[0]:limits[1]:-1]],2)
@ -65,7 +61,7 @@ for name in filenames:
microstructure = np.concatenate([microstructure,microstructure[limits[0]:limits[1]:-1,:,:]],0) microstructure = np.concatenate([microstructure,microstructure[limits[0]:limits[1]:-1,:,:]],0)
damask.util.croak(geom.update(microstructure,rescale=True)) damask.util.croak(geom.update(microstructure,rescale=True))
geom.add_comment(scriptID + ' ' + ' '.join(sys.argv[1:])) geom.add_comments(scriptID + ' ' + ' '.join(sys.argv[1:]))
if name is None: if name is None:
sys.stdout.write(str(geom.show())) sys.stdout.write(str(geom.show()))

40
processing/pre/geom_pack.py
View File

@ -29,14 +29,10 @@ if filenames == []: filenames = [None]
for name in filenames: for name in filenames:
damask.util.report(scriptName,name) damask.util.report(scriptName,name)
if name is None: geom = damask.Geom.from_file(StringIO(''.join(sys.stdin.read())) if name is None else name)
virt_file = StringIO(''.join(sys.stdin.read()))
geom = damask.Geom.from_file(virt_file)
else:
geom = damask.Geom.from_file(name)
damask.util.croak(geom)
microstructure = geom.get_microstructure().flatten('F') microstructure = geom.get_microstructure().flatten('F')
damask.util.croak(geom)
geom.add_comments(scriptID + ' ' + ' '.join(sys.argv[1:]))
compressType = None compressType = None
former = start = -1 former = start = -1
@ -51,13 +47,13 @@ for name in filenames:
reps += 1 reps += 1
else: else:
if compressType is None: if compressType is None:
out = [] out = geom.get_header()
elif compressType == '.': elif compressType == '.':
out.append('{}\n'.format(former)) out.append('{}'.format(former))
elif compressType == 'to': elif compressType == 'to':
out.append('{} to {}\n'.format(start,former)) out.append('{} to {}'.format(start,former))
elif compressType == 'of': elif compressType == 'of':
out.append('{} of {}\n'.format(reps,former)) out.append('{} of {}'.format(reps,former))
compressType = '.' compressType = '.'
start = current start = current
@ -66,18 +62,18 @@ for name in filenames:
former = current former = current
if compressType == '.': if compressType == '.':
out.append('{}\n'.format(former)) out.append('{}'.format(former))
elif compressType == 'to': elif compressType == 'to':
out.append('{} to {}\n'.format(start,former)) out.append('{} to {}'.format(start,former))
elif compressType == 'of': elif compressType == 'of':
out.append('{} of {}\n'.format(reps,former)) out.append('{} of {}'.format(reps,former))
geom.add_comment(scriptID + ' ' + ' '.join(sys.argv[1:]))
comments = geom.get_comments() if name is None:
sys.stdout.write('\n'.join(out)+'\n')
else:
with open(name,'w') as f: with open(name,'w') as f:
f.write('{} header\n'.format(3+len(comments))) f.write('\n'.join(out)+'\n')
f.writelines(["{}\n".format(comment) for comment in comments])
f.write('grid a {} b {} c {}\n'.format(*geom.get_grid()))
f.write('size x {} y {} z {}\n'.format(*geom.get_size()))
f.write('homogenization {}\n'.format(geom.get_homogenization()))
f.writelines(out)

8
processing/pre/geom_renumber.py
View File

@ -31,11 +31,7 @@ if filenames == []: filenames = [None]
for name in filenames: for name in filenames:
damask.util.report(scriptName,name) damask.util.report(scriptName,name)
if name is None: geom = damask.Geom.from_file(StringIO(''.join(sys.stdin.read())) if name is None else name)
virt_file = StringIO(''.join(sys.stdin.read()))
geom = damask.Geom.from_file(virt_file)
else:
geom = damask.Geom.from_file(name)
microstructure = geom.get_microstructure() microstructure = geom.get_microstructure()
renumbered = np.copy(microstructure) renumbered = np.copy(microstructure)
@ -43,7 +39,7 @@ for name in filenames:
renumbered = np.where(microstructure == oldID, i+1, renumbered) renumbered = np.where(microstructure == oldID, i+1, renumbered)
damask.util.croak(geom.update(renumbered)) damask.util.croak(geom.update(renumbered))
geom.add_comment(scriptID + ' ' + ' '.join(sys.argv[1:])) geom.add_comments(scriptID + ' ' + ' '.join(sys.argv[1:]))
if name is None: if name is None:
sys.stdout.write(str(geom.show())) sys.stdout.write(str(geom.show()))

38
processing/pre/geom_rescale.py
View File

@ -2,9 +2,10 @@
import os import os
import sys import sys
import numpy as np
from io import StringIO from io import StringIO
from optparse import OptionParser from optparse import OptionParser
from scipy import ndimage from scipy import ndimage
import damask import damask
@ -41,30 +42,25 @@ if filenames == []: filenames = [None]
for name in filenames: for name in filenames:
damask.util.report(scriptName,name) damask.util.report(scriptName,name)
if name is None: geom = damask.Geom.from_file(StringIO(''.join(sys.stdin.read())) if name is None else name)
virt_file = StringIO(''.join(sys.stdin.read()))
geom = damask.Geom.from_file(virt_file)
else:
geom = damask.Geom.from_file(name)
microstructure = geom.get_microstructure() microstructure = geom.get_microstructure()
grid = geom.get_grid()
scale = geom.get_grid().astype('float')
if options.grid is not None:
for i,g in enumerate(options.grid):
scale[i] = scale[i]*float(g.lower().replace('x','')) if g.lower().endswith('x') \
else float(options.grid[i])/scale[i]
size = geom.get_size() size = geom.get_size()
if options.size is not None:
for i,s in enumerate(options.size):
size[i] = size[i]*float(s.lower().replace('x','')) if s.lower().endswith('x') \
else options.size[i]
microstructure = ndimage.interpolation.zoom(microstructure, scale, output=microstructure.dtype, new_grid = grid if options.grid is None else \
order=0, mode='nearest', prefilter=False) np.array([int(o*float(n.lower().replace('x',''))) if n.lower().endswith('x') \
else int(n) for o,n in zip(grid,options.grid)],dtype=int)
damask.util.croak(geom.update(microstructure,size)) new_size = size if options.size is None else \
geom.add_comment(scriptID + ' ' + ' '.join(sys.argv[1:])) np.array([o*float(n.lower().replace('x','')) if n.lower().endswith('x') \
else float(n) for o,n in zip(size,options.size)],dtype=float)
if np.any(new_grid != grid):
microstructure = ndimage.interpolation.zoom(microstructure, new_grid/grid,output=microstructure.dtype,
order=0,mode='nearest', prefilter=False)
damask.util.croak(geom.update(microstructure,new_size))
geom.add_comments(scriptID + ' ' + ' '.join(sys.argv[1:]))
if name is None: if name is None:
sys.stdout.write(str(geom.show())) sys.stdout.write(str(geom.show()))

29
processing/pre/geom_rotate.py
View File

@ -27,7 +27,7 @@ Rotates original microstructure and embeddeds it into buffer material.
parser.add_option('-r', '--rotation', parser.add_option('-r', '--rotation',
dest='rotation', dest='rotation',
type = 'float', nargs = 4, metavar = ' '.join(['float']*4), type = 'float', nargs = 4, metavar = ' '.join(['float']*4),
help = 'rotation given as angle and axis') help = 'rotation given as axis and angle')
parser.add_option('-e', '--eulers', parser.add_option('-e', '--eulers',
dest = 'eulers', dest = 'eulers',
type = 'float', nargs = 3, metavar = ' '.join(['float']*3), type = 'float', nargs = 3, metavar = ' '.join(['float']*3),
@ -59,41 +59,38 @@ if [options.rotation,options.eulers,options.matrix,options.quaternion].count(Non
parser.error('no rotation specified.') parser.error('no rotation specified.')
if options.quaternion is not None: if options.quaternion is not None:
eulers = damask.Rotation.fromQuaternion(np.array(options.quaternion)).asEulers(degrees=True) rot = damask.Rotation.fromQuaternion(np.array(options.quaternion)) # we might need P=+1 here, too...
if options.rotation is not None: if options.rotation is not None:
eulers = damask.Rotation.fromAxisAngle(np.array(options.rotation,degrees=options.degrees)).asEulers(degrees=True) rot = damask.Rotation.fromAxisAngle(np.array(options.rotation),degrees=options.degrees,P=+1)
if options.matrix is not None: if options.matrix is not None:
eulers = damask.Rotation.fromMatrix(np.array(options.Matrix)).asEulers(degrees=True) rot = damask.Rotation.fromMatrix(np.array(options.Matrix))
if options.eulers is not None: if options.eulers is not None:
eulers = damask.Rotation.fromEulers(np.array(options.eulers),degrees=options.degrees).asEulers(degrees=True) rot = damask.Rotation.fromEulers(np.array(options.eulers),degrees=options.degrees)
eulers = rot.asEulers(degrees=True)
if filenames == []: filenames = [None] if filenames == []: filenames = [None]
for name in filenames: for name in filenames:
damask.util.report(scriptName,name) damask.util.report(scriptName,name)
if name is None: geom = damask.Geom.from_file(StringIO(''.join(sys.stdin.read())) if name is None else name)
virt_file = StringIO(''.join(sys.stdin.read()))
geom = damask.Geom.from_file(virt_file)
else:
geom = damask.Geom.from_file(name)
microstructure = geom.get_microstructure() microstructure = geom.get_microstructure()
fill = np.nanmax(microstructure)+1 if options.fill is None else options.fill
fill = options.fill if options.fill is not None else np.nanmax(microstructure)+1 dtype = float if np.isnan(fill) or int(fill) != fill or microstructure.dtype==np.float else int
# These rotations are always applied in the reference coordinate system, i.e. (z,x,z) not (z,x',z'') # These rotations are always applied in the reference coordinate system, i.e. (z,x,z) not (z,x',z'')
# this seems to be ok, see https://www.cs.utexas.edu/~theshark/courses/cs354/lectures/cs354-14.pdf # this seems to be ok, see https://www.cs.utexas.edu/~theshark/courses/cs354/lectures/cs354-14.pdf
microstructure = ndimage.rotate(microstructure,eulers[2],(0,1),order=0, microstructure = ndimage.rotate(microstructure,eulers[2],(0,1),order=0,
prefilter=False,output=microstructure.dtype,cval=fill) # rotation around z prefilter=False,output=dtype,cval=fill) # rotation around z
microstructure = ndimage.rotate(microstructure,eulers[1],(1,2),order=0, microstructure = ndimage.rotate(microstructure,eulers[1],(1,2),order=0,
prefilter=False,output=microstructure.dtype,cval=fill) # rotation around x prefilter=False,output=dtype,cval=fill) # rotation around x
microstructure = ndimage.rotate(microstructure,eulers[0],(0,1),order=0, microstructure = ndimage.rotate(microstructure,eulers[0],(0,1),order=0,
prefilter=False,output=microstructure.dtype,cval=fill) # rotation around z prefilter=False,output=dtype,cval=fill) # rotation around z
damask.util.croak(geom.update(microstructure,rescale=True)) damask.util.croak(geom.update(microstructure,rescale=True))
geom.add_comment(scriptID + ' ' + ' '.join(sys.argv[1:])) geom.add_comments(scriptID + ' ' + ' '.join(sys.argv[1:]))
if name is None: if name is None:
sys.stdout.write(str(geom.show())) sys.stdout.write(str(geom.show()))

13
processing/pre/geom_toTable.py
View File

@ -31,19 +31,12 @@ if filenames == []: filenames = [None]
for name in filenames: for name in filenames:
damask.util.report(scriptName,name) damask.util.report(scriptName,name)
if name is None: geom = damask.Geom.from_file(StringIO(''.join(sys.stdin.read())) if name is None else name)
virt_file = StringIO(''.join(sys.stdin.read()))
geom = damask.Geom.from_file(virt_file)
else:
geom = damask.Geom.from_file(name)
damask.util.croak(geom) damask.util.croak(geom)
microstructure = geom.get_microstructure().flatten('F') microstructure = geom.get_microstructure().flatten('F')
grid = geom.get_grid() grid = geom.get_grid()
size = geom.get_size() size = geom.get_size()
origin = geom.get_origin()
for i,line in enumerate(geom.get_comments()):
if line.lower().strip().startswith('origin'):
origin= np.array([float(line.split()[j]) for j in [2,4,6]]) # assume correct order (x,y,z)
#--- generate grid -------------------------------------------------------------------------------- #--- generate grid --------------------------------------------------------------------------------
@ -58,7 +51,7 @@ for name in filenames:
# ------------------------------------------ finalize output --------------------------------------- # ------------------------------------------ finalize output ---------------------------------------
table = damask.ASCIItable(outname = os.path.splitext(name)[0]+'.txt' if name else name) table = damask.ASCIItable(outname = os.path.splitext(name)[0]+'.txt' if name else name)
table.info_append([scriptID + '\t' + ' '.join(sys.argv[1:])] + geom.get_comments()) table.info_append(geom.get_comments() + [scriptID + '\t' + ' '.join(sys.argv[1:])])
table.labels_append(['{}_{}'.format(1+i,'pos') for i in range(3)]+['microstructure']) table.labels_append(['{}_{}'.format(1+i,'pos') for i in range(3)]+['microstructure'])
table.head_write() table.head_write()
table.output_flush() table.output_flush()

28
processing/pre/geom_translate.py
View File

@ -43,36 +43,22 @@ parser.set_defaults(origin = (0.0,0.0,0.0),
(options, filenames) = parser.parse_args() (options, filenames) = parser.parse_args()
sub = {} sub = list(map(int,options.substitute))
for i in range(len(options.substitute)//2): # split substitution list into "from" -> "to"
sub[int(options.substitute[i*2])] = int(options.substitute[i*2+1])
if filenames == []: filenames = [None] if filenames == []: filenames = [None]
for name in filenames: for name in filenames:
damask.util.report(scriptName,name) damask.util.report(scriptName,name)
if name is None: geom = damask.Geom.from_file(StringIO(''.join(sys.stdin.read())) if name is None else name)
virt_file = StringIO(''.join(sys.stdin.read()))
geom = damask.Geom.from_file(virt_file)
else:
geom = damask.Geom.from_file(name)
microstructure = geom.get_microstructure() microstructure = geom.get_microstructure()
new = np.copy(microstructure) substituted = np.copy(microstructure)
for k, v in sub.items(): new[microstructure==k] = v # substitute microstructure indices and shift for old,new in zip(sub[0::2],sub[1::2]): substituted[microstructure==old] = new # substitute microstructure indices
substituted += options.microstructure # constant shift
microstructure += options.microstructure # constant shift damask.util.croak(geom.update(substituted,origin=geom.get_origin()+options.origin))
geom.add_comments(scriptID + ' ' + ' '.join(sys.argv[1:]))
for i,line in enumerate(geom.get_comments()):
if line.lower().strip().startswith('origin'):
origin= np.array([float(line.split()[j]) for j in [2,4,6]]) # assume correct order (x,y,z)
origin += np.array(origin)
geom.comments[i] = 'origin x {} y {} z {}'.format(*origin)
damask.util.croak(geom.update(microstructure))
geom.add_comment(scriptID + ' ' + ' '.join(sys.argv[1:]))
if name is None: if name is None:
sys.stdout.write(str(geom.show())) sys.stdout.write(str(geom.show()))

8
processing/pre/geom_unpack.py
View File

@ -29,14 +29,10 @@ if filenames == []: filenames = [None]
for name in filenames: for name in filenames:
damask.util.report(scriptName,name) damask.util.report(scriptName,name)
if name is None: geom = damask.Geom.from_file(StringIO(''.join(sys.stdin.read())) if name is None else name)
virt_file = StringIO(''.join(sys.stdin.read()))
geom = damask.Geom.from_file(virt_file)
else:
geom = damask.Geom.from_file(name)
damask.util.croak(geom) damask.util.croak(geom)
geom.add_comment(scriptID + ' ' + ' '.join(sys.argv[1:])) geom.add_comments(scriptID + ' ' + ' '.join(sys.argv[1:]))
if name is None: if name is None:
sys.stdout.write(str(geom.show())) sys.stdout.write(str(geom.show()))

14
processing/pre/geom_vicinityOffset.py
View File

@ -41,10 +41,10 @@ parser.add_option('-v', '--vicinity',
dest = 'vicinity', dest = 'vicinity',
type = 'int', metavar = 'int', type = 'int', metavar = 'int',
help = 'voxel distance checked for presence of other microstructure [%default]') help = 'voxel distance checked for presence of other microstructure [%default]')
parser.add_option('-m', '--microstructureoffset', parser.add_option('-o', '--offset',
dest='offset', dest='offset',
type = 'int', metavar = 'int', type = 'int', metavar = 'int',
help='offset (positive or negative) to tag microstructure indices, defaults to max microstructure index + 1') help='offset (positive or negative) to tag microstructure indices, defaults to max microstructure index')
parser.add_option('-t', '--trigger', parser.add_option('-t', '--trigger',
dest = 'trigger', dest = 'trigger',
action = 'extend', metavar = '<int LIST>', action = 'extend', metavar = '<int LIST>',
@ -69,14 +69,10 @@ if filenames == []: filenames = [None]
for name in filenames: for name in filenames:
damask.util.report(scriptName,name) damask.util.report(scriptName,name)
if name is None: geom = damask.Geom.from_file(StringIO(''.join(sys.stdin.read())) if name is None else name)
virt_file = StringIO(''.join(sys.stdin.read()))
geom = damask.Geom.from_file(virt_file)
else:
geom = damask.Geom.from_file(name)
microstructure = geom.get_microstructure() microstructure = geom.get_microstructure()
offset = options.offset if options.offset is not None else np.nanmax(microstructure) offset = np.nanmax(microstructure) if options.offset is None else options.offset
microstructure = np.where(ndimage.filters.generic_filter(microstructure, microstructure = np.where(ndimage.filters.generic_filter(microstructure,
taintedNeighborhood, taintedNeighborhood,
@ -86,7 +82,7 @@ for name in filenames:
microstructure + offset,microstructure) microstructure + offset,microstructure)
damask.util.croak(geom.update(microstructure)) damask.util.croak(geom.update(microstructure))
geom.add_comment(scriptID + ' ' + ' '.join(sys.argv[1:])) geom.add_comments(scriptID + ' ' + ' '.join(sys.argv[1:]))
if name is None: if name is None:
sys.stdout.write(str(geom.show())) sys.stdout.write(str(geom.show()))

249
python/damask/geom.py
View File

@ -9,102 +9,105 @@ from . import util
class Geom(): class Geom():
"""Geometry definition for grid solvers""" """Geometry definition for grid solvers"""
def __init__(self,microstructure,size,homogenization=1,comments=[]): def __init__(self,microstructure,size,origin=[0.0,0.0,0.0],homogenization=1,comments=[]):
"""New geometry definition from array of microstructures and size""" """New geometry definition from array of microstructures and size"""
self.set_size(size)
self.set_origin(origin)
self.set_microstructure(microstructure)
self.set_homogenization(homogenization)
self.set_comments(comments)
def __repr__(self):
"""Basic information on geometry definition"""
return 'grid a b c: {}\n'.format(' x '.join(map(str,self.get_grid ()))) + \
'size x y z: {}\n'.format(' x '.join(map(str,self.get_size ()))) + \
'origin x y z: {}\n'.format(' x '.join(map(str,self.get_origin()))) + \
'homogenization: {}\n'.format(self.get_homogenization()) + \
'# microstructures: {}\n'.format(len(np.unique(self.microstructure))) + \
'max microstructures: {}\n'.format(np.nanmax(self.microstructure))
def update(self,microstructure=None,size=None,origin=None,rescale=False):
"""Updates microstructure and size"""
grid_old = self.get_grid()
size_old = self.get_size()
origin_old = self.get_origin()
unique_old = len(np.unique(self.microstructure))
max_old = np.nanmax(self.microstructure)
if size is not None and rescale:
raise ValueError('Either set size explicitly or rescale automatically')
self.set_microstructure(microstructure)
self.set_size(self.get_grid()/grid_old if rescale else size)
self.set_origin(origin)
message = ['grid a b c: {}'.format(' x '.join(map(str,grid_old)))]
if np.any(grid_old != self.get_grid()):
message[-1] = util.delete(message[-1])
message.append('grid a b c: {}'.format(' x '.join(map(str,self.get_grid()))))
message.append('size x y z: {}'.format(' x '.join(map(str,size_old))))
if np.any(size_old != self.get_size()):
message[-1] = util.delete(message[-1])
message.append('size x y z: {}'.format(' x '.join(map(str,self.get_size()))))
message.append('origin x y z: {}'.format(' x '.join(map(str,origin_old))))
if np.any(origin_old != self.get_origin()):
message[-1] = util.delete(message[-1])
message.append('origin x y z: {}'.format(' x '.join(map(str,self.get_origin()))))
message.append('homogenization: {}'.format(self.get_homogenization()))
message.append('# microstructures: {}'.format(unique_old))
if unique_old != len(np.unique(self.microstructure)):
message[-1] = util.delete(message[-1])
message.append('# microstructures: {}'.format(len(np.unique(self.microstructure))))
message.append('max microstructure: {}'.format(max_old))
if max_old != np.nanmax(self.microstructure):
message[-1] = util.delete(message[-1])
message.append('max microstructure: {}'.format(np.nanmax(self.microstructure)))
return util.srepr(message)
def set_comments(self,comments):
self.comments = []
self.add_comments(comments)
def add_comments(self,comments):
self.comments += [str(c) for c in comments] if isinstance(comments,list) else [str(comments)]
def set_microstructure(self,microstructure):
if microstructure is not None:
if len(microstructure.shape) != 3: if len(microstructure.shape) != 3:
raise ValueError('Invalid microstructure shape {}'.format(*microstructure.shape)) raise ValueError('Invalid microstructure shape {}'.format(*microstructure.shape))
elif microstructure.dtype not in [int,float]: elif microstructure.dtype not in [int,float]:
raise TypeError('Invalid data type {} for microstructure'.format(microstructure.dtype)) raise TypeError('Invalid data type {} for microstructure'.format(microstructure.dtype))
else: else:
self.microstructure = microstructure self.microstructure = np.copy(microstructure)
if len(size) != 3 or any(np.array(size)<=0):
raise ValueError('Invalid size {}'.format(*size))
else:
self.size = np.array(size)
if not isinstance(homogenization,int) or homogenization < 1:
raise TypeError('Invalid homogenization {}'.format(homogenization))
else:
self.homogenization = homogenization
if not isinstance(comments,list):
self.comments = [str(comments)]
else:
self.comments = [str(comment) for comment in comments]
def __repr__(self):
"""Basic information on geometry definition"""
return 'grid a b c: {}\n'.format(' x '.join(map(str,self.get_grid()))) + \
'size x y z: {}\n'.format(' x '.join(map(str,self.size))) + \
'homogenization: {}\n'.format(self.homogenization) + \
'# microstructures: {}\n'.format(len(np.unique(self.microstructure))) + \
'max microstructures: {}\n'.format(np.max(self.microstructure))
def update(self,microstructure=None,size=None,rescale=False):
"""Updates microstructure and size"""
grid_old = self.get_grid()
size_old = self.get_size()
unique_old = len(np.unique(self.microstructure))
max_old = np.max(self.microstructure)
if size is not None and rescale:
raise ValueError('Either set size explicitly or rescale automatically')
if microstructure is not None:
if len(microstructure.shape) != 3:
raise ValueError('Invalid microstructure shape {}'.format(*microstructure.shape))
elif microstructure.dtype not in ['int','float']:
raise TypeError('Invalid data type {} for microstructure'.format(microstructure.dtype))
else:
self.microstructure = microstructure
def set_size(self,size):
if size is not None: if size is not None:
if len(size) != 3 or any(np.array(size)<=0): if len(size) != 3 or any(np.array(size)<=0):
raise ValueError('Invalid size {}'.format(*size)) raise ValueError('Invalid size {}'.format(*size))
else: else:
self.size = np.array(size) self.size = np.array(size)
if rescale: def set_origin(self,origin):
self.size = self.size * self.get_grid()/grid_old if origin is not None:
if len(origin) != 3:
message = ['grid a b c: {}'.format(' x '.join(map(str,grid_old)))] raise ValueError('Invalid origin {}'.format(*origin))
if np.any(grid_old != self.get_grid()):
message[-1] = util.bcolors.CROSSOUT+message[-1]+util.bcolors.ENDC
message.append('grid a b c: {}'.format(' x '.join(map(str,self.get_grid()))))
message.append('size x y z: {}'.format(' x '.join(map(str,size_old))))
if np.any(size_old != self.size):
message[-1] = util.bcolors.CROSSOUT+message[-1]+util.bcolors.ENDC
message.append('size x y z: {}'.format(' x '.join(map(str,self.size))))
message.append('homogenization: {}'.format(self.homogenization))
message.append('# microstructures: {}'.format(unique_old))
if unique_old != len(np.unique(self.microstructure)):
message[-1] = util.bcolors.CROSSOUT+message[-1]+util.bcolors.ENDC
message.append('# microstructures: {}'.format(len(np.unique(self.microstructure))))
message.append('max microstructures: {}'.format(max_old))
if max_old != np.max(self.microstructure):
message[-1] = util.bcolors.CROSSOUT+message[-1]+util.bcolors.ENDC
message.append('max microstructures: {}'.format(np.max(self.microstructure)))
return '\n'.join(message)
def add_comment(self,comment):
if not isinstance(comment,list):
self.comments = [str(comment)] + self.comments
else: else:
self.comments = [str(c) for c in comment] + self.comments self.origin = np.array(origin)
def set_microstructure(self,microstructure): def set_homogenization(self,homogenization):
self.microstructure = np.copy(microstructure) if homogenization is not None:
if not isinstance(homogenization,int) or homogenization < 1:
def set_size(self,size): raise TypeError('Invalid homogenization {}'.format(homogenization))
self.size = np.array(size) else:
self.homogenization = homogenization
def get_microstructure(self): def get_microstructure(self):
@ -113,6 +116,9 @@ class Geom():
def get_size(self): def get_size(self):
return np.copy(self.size) return np.copy(self.size)
def get_origin(self):
return np.copy(self.origin)
def get_grid(self): def get_grid(self):
return np.array(self.microstructure.shape) return np.array(self.microstructure.shape)
@ -122,42 +128,44 @@ class Geom():
def get_comments(self): def get_comments(self):
return self.comments[:] return self.comments[:]
def get_header(self):
header = ['{} header'.format(len(self.comments)+4)] + self.comments
header.append('grid a {} b {} c {}'.format(*self.get_grid()))
header.append('size x {} y {} z {}'.format(*self.get_size()))
header.append('origin x {} y {} z {}'.format(*self.get_origin()))
header.append('homogenization {}'.format(self.get_homogenization()))
return header
@classmethod @classmethod
def from_file(cls,fname): def from_file(cls,fname):
"""Reads from *.geom file""" """Reads a geom file"""
if isinstance(fname,str): with (open(fname) if isinstance(fname,str) else fname) as f:
f = open(fname) f.seek(0)
header_length,keyword = f.readline().split() header_length,keyword = f.readline().split()[:2]
if not keyword.startswith('head') or int(header_length) < 3: header_length = int(header_length)
content = f.readlines()
if not keyword.startswith('head') or header_length < 3:
raise TypeError('Header length information missing or invalid') raise TypeError('Header length information missing or invalid')
comments_old = [f.readline() for i in range(int(header_length))]
else:
fname.seek(0)
header_length,keyword = fname.readline().split()
if not keyword.startswith('head') or int(header_length) < 3:
raise TypeError('Header length information missing or invalid')
comments_old = [fname.readline() for i in range(int(header_length))]
comments = [] comments = []
for i,line in enumerate(comments_old): for i,line in enumerate(content[:header_length]):
if line.lower().strip().startswith('grid'): items = line.lower().strip().split()
grid = np.array([int(line.split()[j]) for j in [2,4,6]]) # assume correct order (a,b,c) key = items[0] if len(items) > 0 else ''
elif line.lower().strip().startswith('size'): if key == 'grid':
size = np.array([float(line.split()[j]) for j in [2,4,6]]) # assume correct order (x,y,z) grid = np.array([ int(dict(zip(items[1::2],items[2::2]))[i]) for i in ['a','b','c']])
elif line.lower().strip().startswith('homogenization'): elif key == 'size':
homogenization = int(line.split()[1]) 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']])
elif key == 'homogenization':
homogenization = int(items[1])
else: else:
comments.append(line.rstrip().strip()) comments.append(line.strip())
if isinstance(fname,str):
raw = f.readlines()
f.close()
else:
raw = fname.readlines()
microstructure = np.empty(grid.prod()) # initialize as flat array microstructure = np.empty(grid.prod()) # initialize as flat array
i = 0 i = 0
for line in raw: for line in content[header_length:]:
items = line.split() items = line.split()
if len(items) == 3: if len(items) == 3:
if items[1].lower() == 'of': if items[1].lower() == 'of':
@ -175,28 +183,19 @@ class Geom():
raise TypeError('Invalid file: expected {} entries,found {}'.format(grid.prod(),i)) raise TypeError('Invalid file: expected {} entries,found {}'.format(grid.prod(),i))
microstructure = microstructure.reshape(grid,order='F') microstructure = microstructure.reshape(grid,order='F')
if not np.any(np.mod(microstructure.flatten(),1) != 0.0): # no float present
if '.' in raw[0]: # contains float values
pass
else: # assume int values
microstructure = microstructure.astype('int') microstructure = microstructure.astype('int')
return cls(microstructure.reshape(grid),size,homogenization,comments) return cls(microstructure.reshape(grid),size,origin,homogenization,comments)
def to_file(self,fname): def to_file(self,fname):
"""Saves to file""" """Writes to file"""
header = self.get_header()
grid = self.get_grid() grid = self.get_grid()
header = ['{} header'.format(len(self.comments)+3)] format_string = '%{}i'.format(int(math.floor(math.log10(self.microstructure.max())+1))) if self.microstructure.dtype == int \
header += self.comments else '%g'
header.append('grid a {} b {} c {}'.format(*grid)) np.savetxt(fname,
header.append('size x {} y {} z {}'.format(*self.size)) self.microstructure.reshape([grid[0],np.prod(grid[1:])],order='F').T,
header.append('homogenization {}'.format(self.get_homogenization()))
if self.microstructure.dtype == 'int':
format_string='%{}i'.format(int(math.floor(math.log10(self.microstructure.max())+1)))
else:
format_string='%.18e'
np.savetxt(fname, self.microstructure.reshape([grid[0],np.prod(grid[1:])],order='F').T,
header='\n'.join(header), fmt=format_string, comments='') header='\n'.join(header), fmt=format_string, comments='')
def show(self): def show(self):

5
python/damask/util.py
View File

@ -85,6 +85,11 @@ def delete(what):
"""Dims string""" """Dims string"""
return bcolors.DIM+srepr(what)+bcolors.ENDC return bcolors.DIM+srepr(what)+bcolors.ENDC
# -----------------------------
def strikeout(what):
"""Dims string"""
return bcolors.CROSSOUT+srepr(what)+bcolors.ENDC
# ----------------------------- # -----------------------------
def execute(cmd, def execute(cmd,
streamIn = None, streamIn = None,

211
test.log Normal file
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2019-05-27 22:44:00,700 - INFO:
++++++++++++++++++++++++++++++++++++++++
----------------------------------------
| Check geom-modifying scripts
----------------------------------------
2019-05-27 22:44:00,707 - INFO:
geom_addPrimitive -c 0.3 0.5 0.2 -a 1.0 0.8 0.9 0.4 -d 0.10 0.13 0.08 geom_addPrimitive.geom
2019-05-27 22:44:00,899 - INFO:
geom_addPrimitive: geom_addPrimitive.geom
grid a b c: 32 x 35 x 12
size x y z: 0.914285714286 x 1.0 x 0.342857142857
origin x y z: 0.0 x 1.0 x 2.0
homogenization: 1
# microstructures: 20
max microstructure: 26
2019-05-27 22:44:00,899 - DEBUG:
2019-05-27 22:44:00,899 - INFO:
comparing
/Users/philip/Documents/DAMASK/PRIVATE/testing/PreProcessing_GeomModification/reference/geom_addPrimitive_reference.geom
/Users/philip/Documents/DAMASK/PRIVATE/testing/PreProcessing_GeomModification/current/geom_addPrimitive.geom
2019-05-27 22:44:00,920 - INFO:
geom_canvas -g 40 35 20 -f 90 geom_canvas.geom
2019-05-27 22:44:01,103 - INFO:
geom_canvas: geom_canvas.geom
grid a b c: 32 x 35 x 12
size x y z: 0.914285714286 x 1.0 x 0.342857142857
origin x y z: 0.0 x 0.0 x 0.0
homogenization: 1
# microstructures: 20
max microstructures: 20
2019-05-27 22:44:01,103 - DEBUG:
2019-05-27 22:44:01,104 - INFO:
comparing
/Users/philip/Documents/DAMASK/PRIVATE/testing/PreProcessing_GeomModification/reference/geom_canvas_reference.geom
/Users/philip/Documents/DAMASK/PRIVATE/testing/PreProcessing_GeomModification/current/geom_canvas.geom
2019-05-27 22:44:01,135 - INFO:
geom_clean -s 2 geom_clean.geom
2019-05-27 22:44:03,219 - INFO:
geom_clean: geom_clean.geom
grid a b c: 53 x 52 x 52
size x y z: 1.0 x 0.981132075472 x 0.981132075472
origin x y z: 0.0 x 0.0 x 0.0
homogenization: 1
# microstructures: 23
max microstructure: 23
2019-05-27 22:44:03,219 - DEBUG:
2019-05-27 22:44:03,219 - INFO:
comparing
/Users/philip/Documents/DAMASK/PRIVATE/testing/PreProcessing_GeomModification/reference/geom_clean_reference.geom
/Users/philip/Documents/DAMASK/PRIVATE/testing/PreProcessing_GeomModification/current/geom_clean.geom
2019-05-27 22:44:03,378 - INFO:
geom_grainGrowth -N2 -i 4 -d 2 geom_grainGrowth.geom
2019-05-27 22:44:04,065 - INFO:
geom_grainGrowth: geom_grainGrowth.geom
grid a b c: 40 x 40 x 40
size x y z: 1.0 x 1.0 x 1.0
origin x y z: 0.0 x 0.0 x 0.0
homogenization: 1
# microstructures: 15
max microstructures: 15
grid a b c: 40 x 40 x 40
size x y z: 1.0 x 1.0 x 1.0
origin x y z: 0.0 x 0.0 x 0.0
homogenization: 1
# microstructures: 15
max microstructure: 15
2019-05-27 22:44:04,065 - DEBUG:
2019-05-27 22:44:04,065 - INFO:
comparing
/Users/philip/Documents/DAMASK/PRIVATE/testing/PreProcessing_GeomModification/reference/geom_grainGrowth_reference.geom
/Users/philip/Documents/DAMASK/PRIVATE/testing/PreProcessing_GeomModification/current/geom_grainGrowth.geom
2019-05-27 22:44:04,131 - INFO:
geom_mirror -d x,y,z --double geom_mirror.geom
2019-05-27 22:44:04,330 - INFO:
geom_mirror: geom_mirror.geom
grid a b c: 32 x 35 x 12
grid a b c: 64 x 70 x 24
size x y z: 0.914285714286 x 1.0 x 0.342857142857
size x y z: 2.0 x 2.0 x 2.0
origin x y z: 0.0 x 0.0 x 0.0
homogenization: 1
# microstructures: 20
max microstructure: 20
2019-05-27 22:44:04,331 - DEBUG:
2019-05-27 22:44:04,331 - INFO:
comparing
/Users/philip/Documents/DAMASK/PRIVATE/testing/PreProcessing_GeomModification/reference/geom_mirror_reference.geom
/Users/philip/Documents/DAMASK/PRIVATE/testing/PreProcessing_GeomModification/current/geom_mirror.geom
2019-05-27 22:44:04,447 - INFO:
geom_renumber geom_renumber.geom
2019-05-27 22:44:04,688 - INFO:
geom_renumber: geom_renumber.geom
grid a b c: 53 x 52 x 52
size x y z: 1.0 x 0.981132075472 x 0.981132075472
origin x y z: 0.0 x 0.0 x 0.0
homogenization: 1
# microstructures: 23
max microstructure: 42
max microstructure: 23
2019-05-27 22:44:04,688 - DEBUG:
2019-05-27 22:44:04,688 - INFO:
comparing
/Users/philip/Documents/DAMASK/PRIVATE/testing/PreProcessing_GeomModification/reference/geom_renumber_reference.geom
/Users/philip/Documents/DAMASK/PRIVATE/testing/PreProcessing_GeomModification/current/geom_renumber.geom
2019-05-27 22:44:04,864 - INFO:
geom_rescale -g 20 22 20 -s 0.1 0.2 0.3 geom_rescale.geom
2019-05-27 22:44:05,109 - INFO:
geom_rescale: geom_rescale.geom
grid a b c: 32 x 35 x 12
grid a b c: 20 x 22 x 20
size x y z: 0.914285714286 x 1.0 x 0.342857142857
size x y z: 0.1 x 0.2 x 0.3
origin x y z: 0.0 x 0.0 x 0.0
homogenization: 1
# microstructures: 20
max microstructure: 20
2019-05-27 22:44:05,109 - DEBUG:
2019-05-27 22:44:05,109 - INFO:
comparing
/Users/philip/Documents/DAMASK/PRIVATE/testing/PreProcessing_GeomModification/reference/geom_rescale_reference.geom
/Users/philip/Documents/DAMASK/PRIVATE/testing/PreProcessing_GeomModification/current/geom_rescale.geom
2019-05-27 22:44:05,122 - INFO:
geom_rotate -d -e 45 45 0 geom_rotate.geom
2019-05-27 22:44:05,529 - INFO:
geom_rotate: geom_rotate.geom
grid a b c: 53 x 52 x 52
grid a b c: 90 x 90 x 74
size x y z: 1.0 x 0.981132075472 x 0.981132075472
size x y z: 1.6981132075471699 x 1.7307692307692308 x 1.4230769230769231
origin x y z: 0.0 x 0.0 x 0.0
homogenization: 1
# microstructures: 23
# microstructures: 24
max microstructure: 23
max microstructure: 24
2019-05-27 22:44:05,530 - DEBUG:
2019-05-27 22:44:05,530 - INFO:
comparing
/Users/philip/Documents/DAMASK/PRIVATE/testing/PreProcessing_GeomModification/reference/geom_rotate_reference.geom
/Users/philip/Documents/DAMASK/PRIVATE/testing/PreProcessing_GeomModification/current/geom_rotate.geom
2019-05-27 22:44:06,282 - INFO:
geom_translate -o 0 1 2 -m 6 geom_translate.geom
2019-05-27 22:44:06,469 - INFO:
geom_translate: geom_translate.geom
grid a b c: 32 x 35 x 12
size x y z: 0.914285714286 x 1.0 x 0.342857142857
origin x y z: 0.0 x 0.0 x 0.0
origin x y z: 0.0 x 1.0 x 2.0
homogenization: 1
# microstructures: 20
max microstructure: 20
max microstructure: 26
2019-05-27 22:44:06,469 - DEBUG:
2019-05-27 22:44:06,469 - INFO:
comparing
/Users/philip/Documents/DAMASK/PRIVATE/testing/PreProcessing_GeomModification/reference/geom_translate_reference.geom
/Users/philip/Documents/DAMASK/PRIVATE/testing/PreProcessing_GeomModification/current/geom_translate.geom
2019-05-27 22:44:06,486 - INFO:
geom_vicinityOffset -v 2 geom_vicinityOffset.geom
2019-05-27 22:44:07,005 - INFO:
geom_vicinityOffset: geom_vicinityOffset.geom
grid a b c: 40 x 40 x 40
size x y z: 1.0 x 1.0 x 1.0
origin x y z: 0.0 x 0.0 x 0.0
homogenization: 1
# microstructures: 5
# microstructures: 10
max microstructure: 5
max microstructure: 10
2019-05-27 22:44:07,005 - DEBUG:
2019-05-27 22:44:07,005 - INFO:
comparing
/Users/philip/Documents/DAMASK/PRIVATE/testing/PreProcessing_GeomModification/reference/geom_vicinityOffset_reference.geom
/Users/philip/Documents/DAMASK/PRIVATE/testing/PreProcessing_GeomModification/current/geom_vicinityOffset.geom
2019-05-27 22:44:07,076 - CRITICAL:
****************************************
All 10 tests passed.
****************************************