Merge branch 'addGradient' into 'development'

Add gradient

FFT-based gradient calculation similar to addCurl and addDivergence. Polished other two while on it anyway.

See merge request !2
This commit is contained in:
Philip Eisenlohr 2016-03-16 20:28:04 +01:00
commit 2b7524ed1d
3 changed files with 199 additions and 52 deletions

View File

@ -10,40 +10,35 @@ scriptName = os.path.splitext(os.path.basename(__file__))[0]
scriptID = ' '.join([scriptName,damask.version]) scriptID = ' '.join([scriptName,damask.version])
def curlFFT(geomdim,field): def curlFFT(geomdim,field):
N = grid.prod() # field size grid = np.array(np.shape(field)[2::-1])
n = np.array(np.shape(field)[3:]).prod() # data size N = grid.prod() # field size
n = np.array(np.shape(field)[3:]).prod() # data size
if n == 3: if n == 3: dataType = 'vector'
dataType = 'vector' elif n == 9: dataType = 'tensor'
elif n == 9:
dataType = 'tensor'
field_fourier = np.fft.fftpack.rfftn(field,axes=(0,1,2)) field_fourier = np.fft.fftpack.rfftn(field,axes=(0,1,2))
curl_fourier = np.zeros(field_fourier.shape,'c16') curl_fourier = np.zeros(field_fourier.shape,'c16')
# differentiation in Fourier space # differentiation in Fourier space
k_s = np.zeros([3],'i') k_s = np.zeros([3],'i')
TWOPIIMG = (0.0+2.0j*math.pi) TWOPIIMG = 2.0j*math.pi
for i in xrange(grid[2]): for i in xrange(grid[2]):
k_s[0] = i k_s[0] = i
if(grid[2]%2==0 and i == grid[2]//2): # for even grid, set Nyquist freq to 0 (Johnson, MIT, 2011) if grid[2]%2 == 0 and i == grid[2]//2: k_s[0] = 0 # for even grid, set Nyquist freq to 0 (Johnson, MIT, 2011)
k_s[0]=0 elif i > grid[2]//2: k_s[0] -= grid[2]
elif (i > grid[2]//2):
k_s[0] = k_s[0] - grid[2]
for j in xrange(grid[1]): for j in xrange(grid[1]):
k_s[1] = j k_s[1] = j
if(grid[1]%2==0 and j == grid[1]//2): # for even grid, set Nyquist freq to 0 (Johnson, MIT, 2011) if grid[1]%2 == 0 and j == grid[1]//2: k_s[1] = 0 # for even grid, set Nyquist freq to 0 (Johnson, MIT, 2011)
k_s[1]=0 elif j > grid[1]//2: k_s[1] -= grid[1]
elif (j > grid[1]//2):
k_s[1] = k_s[1] - grid[1]
for k in xrange(grid[0]//2+1): for k in xrange(grid[0]//2+1):
k_s[2] = k k_s[2] = k
if(grid[0]%2==0 and k == grid[0]//2): # for even grid, set Nyquist freq to 0 (Johnson, MIT, 2011) if grid[0]%2 == 0 and k == grid[0]//2: k_s[2] = 0 # for even grid, set Nyquist freq to 0 (Johnson, MIT, 2011)
k_s[2]=0
xi = (k_s/geomdim)[2::-1].astype('c16') # reversing the field input order
xi = np.array([k_s[2]/geomdim[2]+0.0j,k_s[1]/geomdim[1]+0.j,k_s[0]/geomdim[0]+0.j],'c16')
if dataType == 'tensor': if dataType == 'tensor':
for l in xrange(3): for l in xrange(3):
curl_fourier[i,j,k,0,l] = ( field_fourier[i,j,k,l,2]*xi[1]\ curl_fourier[i,j,k,0,l] = ( field_fourier[i,j,k,l,2]*xi[1]\
@ -100,10 +95,8 @@ if options.vector is None and options.tensor is None:
if filenames == []: filenames = [None] if filenames == []: filenames = [None]
for name in filenames: for name in filenames:
try: try: table = damask.ASCIItable(name = name,buffered = False)
table = damask.ASCIItable(name = name,buffered = False) except: continue
except:
continue
damask.util.report(scriptName,name) damask.util.report(scriptName,name)
# ------------------------------------------ read header ------------------------------------------ # ------------------------------------------ read header ------------------------------------------
@ -161,9 +154,10 @@ for name in filenames:
stack = [table.data] stack = [table.data]
for type, data in items.iteritems(): for type, data in items.iteritems():
for i,label in enumerate(data['active']): for i,label in enumerate(data['active']):
stack.append(curlFFT(size[::-1], # we need to reverse order here, because x # we need to reverse order here, because x is fastest,ie rightmost, but leftmost in our x,y,z notation
table.data[:,data['column'][i]:data['column'][i]+data['dim']]. # is fastest,ie rightmost, but leftmost in stack.append(curlFFT(size[::-1],
reshape([grid[2],grid[1],grid[0]]+data['shape']))) # our x,y,z notation table.data[:,data['column'][i]:data['column'][i]+data['dim']].
reshape([grid[2],grid[1],grid[0]]+data['shape'])))
# ------------------------------------------ output result ----------------------------------------- # ------------------------------------------ output result -----------------------------------------

View File

@ -10,39 +10,35 @@ scriptName = os.path.splitext(os.path.basename(__file__))[0]
scriptID = ' '.join([scriptName,damask.version]) scriptID = ' '.join([scriptName,damask.version])
def divFFT(geomdim,field): def divFFT(geomdim,field):
N = grid.prod() # field size grid = np.array(np.shape(field)[2::-1])
n = np.array(np.shape(field)[3:]).prod() # data size N = grid.prod() # field size
n = np.array(np.shape(field)[3:]).prod() # data size
field_fourier = np.fft.fftpack.rfftn(field,axes=(0,1,2)) field_fourier = np.fft.fftpack.rfftn(field,axes=(0,1,2))
div_fourier = np.zeros(field_fourier.shape[0:len(np.shape(field))-1],'c16') # size depents on whether tensor or vector div_fourier = np.zeros(field_fourier.shape[0:len(np.shape(field))-1],'c16') # size depents on whether tensor or vector
# differentiation in Fourier space # differentiation in Fourier space
k_s=np.zeros([3],'i') k_s=np.zeros([3],'i')
TWOPIIMG = (0.0+2.0j*math.pi) TWOPIIMG = 2.0j*math.pi
for i in xrange(grid[2]): for i in xrange(grid[2]):
k_s[0] = i k_s[0] = i
if(grid[2]%2==0 and i == grid[2]//2): # for even grid, set Nyquist freq to 0 (Johnson, MIT, 2011) if grid[2]%2 == 0 and i == grid[2]//2: k_s[0] = 0 # for even grid, set Nyquist freq to 0 (Johnson, MIT, 2011)
k_s[0]=0 elif i > grid[2]//2: k_s[0] -= grid[2]
elif (i > grid[2]//2):
k_s[0] = k_s[0] - grid[2]
for j in xrange(grid[1]): for j in xrange(grid[1]):
k_s[1] = j k_s[1] = j
if(grid[1]%2==0 and j == grid[1]//2): # for even grid, set Nyquist freq to 0 (Johnson, MIT, 2011) if grid[1]%2 == 0 and j == grid[1]//2: k_s[1] = 0 # for even grid, set Nyquist freq to 0 (Johnson, MIT, 2011)
k_s[1]=0 elif j > grid[1]//2: k_s[1] -= grid[1]
elif (j > grid[1]//2):
k_s[1] = k_s[1] - grid[1]
for k in xrange(grid[0]//2+1): for k in xrange(grid[0]//2+1):
k_s[2] = k k_s[2] = k
if(grid[0]%2==0 and k == grid[0]//2): # for even grid, set Nyquist freq to 0 (Johnson, MIT, 2011) if grid[0]%2 == 0 and k == grid[0]//2: k_s[2] = 0 # for even grid, set Nyquist freq to 0 (Johnson, MIT, 2011)
k_s[2]=0
xi=np.array([k_s[2]/geomdim[2]+0.0j,k_s[1]/geomdim[1]+0.j,k_s[0]/geomdim[0]+0.j],'c16') xi = (k_s/geomdim)[2::-1].astype('c16') # reversing the field input order
if n == 9: # tensor, 3x3 -> 3 if n == 9: # tensor, 3x3 -> 3
for l in xrange(3): for l in xrange(3):
div_fourier[i,j,k,l] = sum(field_fourier[i,j,k,l,0:3]*xi) *TWOPIIMG div_fourier[i,j,k,l] = sum(field_fourier[i,j,k,l,0:3]*xi) *TWOPIIMG
elif n == 3: # vector, 3 -> 1 elif n == 3: # vector, 3 -> 1
div_fourier[i,j,k] = sum(field_fourier[i,j,k,0:3]*xi) *TWOPIIMG div_fourier[i,j,k] = sum(field_fourier[i,j,k,0:3]*xi) *TWOPIIMG
return np.fft.fftpack.irfftn(div_fourier,axes=(0,1,2)).reshape([N,n/3]) return np.fft.fftpack.irfftn(div_fourier,axes=(0,1,2)).reshape([N,n/3])
@ -80,15 +76,13 @@ parser.set_defaults(coords = 'ipinitialcoord',
if options.vector is None and options.tensor is None: if options.vector is None and options.tensor is None:
parser.error('no data column specified.') parser.error('no data column specified.')
# --- loop over input files ------------------------------------------------------------------------- # --- loop over input files ------------------------------------------------------------------------
if filenames == []: filenames = [None] if filenames == []: filenames = [None]
for name in filenames: for name in filenames:
try: try: table = damask.ASCIItable(name = name,buffered = False)
table = damask.ASCIItable(name = name,buffered = False) except: continue
except:
continue
damask.util.report(scriptName,name) damask.util.report(scriptName,name)
# ------------------------------------------ read header ------------------------------------------ # ------------------------------------------ read header ------------------------------------------
@ -140,16 +134,17 @@ for name in filenames:
maxcorner = np.array(map(max,coords)) maxcorner = np.array(map(max,coords))
grid = np.array(map(len,coords),'i') grid = np.array(map(len,coords),'i')
size = grid/np.maximum(np.ones(3,'d'), grid-1.0) * (maxcorner-mincorner) # size from edge to edge = dim * n/(n-1) size = grid/np.maximum(np.ones(3,'d'), grid-1.0) * (maxcorner-mincorner) # size from edge to edge = dim * n/(n-1)
size = np.where(grid > 1, size, min(size[grid > 1]/grid[grid > 1])) # spacing for grid==1 set to smallest among other spacings size = np.where(grid > 1, size, min(size[grid > 1]/grid[grid > 1])) # spacing for grid==1 equal to smallest among other ones
# ------------------------------------------ process value field ----------------------------------- # ------------------------------------------ process value field -----------------------------------
stack = [table.data] stack = [table.data]
for type, data in items.iteritems(): for type, data in items.iteritems():
for i,label in enumerate(data['active']): for i,label in enumerate(data['active']):
stack.append(divFFT(size[::-1], # we need to reverse order here, because x # we need to reverse order here, because x is fastest,ie rightmost, but leftmost in our x,y,z notation
table.data[:,data['column'][i]:data['column'][i]+data['dim']]. # is fastest,ie rightmost, but leftmost in stack.append(divFFT(size[::-1],
reshape([grid[2],grid[1],grid[0]]+data['shape']))) # our x,y,z notation table.data[:,data['column'][i]:data['column'][i]+data['dim']].
reshape([grid[2],grid[1],grid[0]]+data['shape'])))
# ------------------------------------------ output result ----------------------------------------- # ------------------------------------------ output result -----------------------------------------

158
processing/post/addGradient.py Executable file
View File

@ -0,0 +1,158 @@
#!/usr/bin/env python
# -*- coding: UTF-8 no BOM -*-
import os,sys,math
import numpy as np
from optparse import OptionParser
import damask
scriptName = os.path.splitext(os.path.basename(__file__))[0]
scriptID = ' '.join([scriptName,damask.version])
def gradFFT(geomdim,field):
grid = np.array(np.shape(field)[2::-1])
N = grid.prod() # field size
n = np.array(np.shape(field)[3:]).prod() # data size
if n == 3: dataType = 'vector'
elif n == 1: dataType = 'scalar'
field_fourier = np.fft.fftpack.rfftn(field,axes=(0,1,2))
grad_fourier = np.zeros(field_fourier.shape+(3,),'c16')
# differentiation in Fourier space
k_s = np.zeros([3],'i')
TWOPIIMG = 2.0j*math.pi
for i in xrange(grid[2]):
k_s[0] = i
if grid[2]%2 == 0 and i == grid[2]//2: k_s[0] = 0 # for even grid, set Nyquist freq to 0 (Johnson, MIT, 2011)
elif i > grid[2]//2: k_s[0] -= grid[2]
for j in xrange(grid[1]):
k_s[1] = j
if grid[1]%2 == 0 and j == grid[1]//2: k_s[1] = 0 # for even grid, set Nyquist freq to 0 (Johnson, MIT, 2011)
elif j > grid[1]//2: k_s[1] -= grid[1]
for k in xrange(grid[0]//2+1):
k_s[2] = k
if grid[0]%2 == 0 and k == grid[0]//2: k_s[2] = 0 # for even grid, set Nyquist freq to 0 (Johnson, MIT, 2011)
xi = (k_s/geomdim)[2::-1].astype('c16') # reversing the field order
grad_fourier[i,j,k,0,:] = field_fourier[i,j,k,0]*xi *TWOPIIMG # vector field from scalar data
if dataType == 'vector':
grad_fourier[i,j,k,1,:] = field_fourier[i,j,k,1]*xi *TWOPIIMG # tensor field from vector data
grad_fourier[i,j,k,2,:] = field_fourier[i,j,k,2]*xi *TWOPIIMG
return np.fft.fftpack.irfftn(grad_fourier,axes=(0,1,2)).reshape([N,3*n])
# --------------------------------------------------------------------
# MAIN
# --------------------------------------------------------------------
parser = OptionParser(option_class=damask.extendableOption, usage='%prog options [file[s]]', description = """
Add column(s) containing gradient of requested column(s).
Operates on periodic ordered three-dimensional data sets.
Deals with both vector- and scalar fields.
""", version = scriptID)
parser.add_option('-c','--coordinates',
dest = 'coords',
type = 'string', metavar='string',
help = 'column heading for coordinates [%default]')
parser.add_option('-v','--vector',
dest = 'vector',
action = 'extend', metavar = '<string LIST>',
help = 'heading of columns containing vector field values')
parser.add_option('-s','--scalar',
dest = 'scalar',
action = 'extend', metavar = '<string LIST>',
help = 'heading of columns containing scalar field values')
parser.set_defaults(coords = 'ipinitialcoord',
)
(options,filenames) = parser.parse_args()
if options.vector is None and options.scalar is None:
parser.error('no data column specified.')
# --- loop over input files ------------------------------------------------------------------------
if filenames == []: filenames = [None]
for name in filenames:
try: table = damask.ASCIItable(name = name,buffered = False)
except: continue
damask.util.report(scriptName,name)
# ------------------------------------------ read header ------------------------------------------
table.head_read()
# ------------------------------------------ sanity checks ----------------------------------------
items = {
'scalar': {'dim': 1, 'shape': [1], 'labels':options.scalar, 'active':[], 'column': []},
'vector': {'dim': 3, 'shape': [3], 'labels':options.vector, 'active':[], 'column': []},
}
errors = []
remarks = []
column = {}
if table.label_dimension(options.coords) != 3: errors.append('coordinates {} are not a vector.'.format(options.coords))
else: colCoord = table.label_index(options.coords)
for type, data in items.iteritems():
for what in (data['labels'] if data['labels'] is not None else []):
dim = table.label_dimension(what)
if dim != data['dim']: remarks.append('column {} is not a {}.'.format(what,type))
else:
items[type]['active'].append(what)
items[type]['column'].append(table.label_index(what))
if remarks != []: damask.util.croak(remarks)
if errors != []:
damask.util.croak(errors)
table.close(dismiss = True)
continue
# ------------------------------------------ assemble header --------------------------------------
table.info_append(scriptID + '\t' + ' '.join(sys.argv[1:]))
for type, data in items.iteritems():
for label in data['active']:
table.labels_append(['{}_gradFFT({})'.format(i+1,label) for i in xrange(3 * data['dim'])]) # extend ASCII header with new labels
table.head_write()
# --------------- figure out size and grid ---------------------------------------------------------
table.data_readArray()
coords = [np.unique(table.data[:,colCoord+i]) for i in xrange(3)]
mincorner = np.array(map(min,coords))
maxcorner = np.array(map(max,coords))
grid = np.array(map(len,coords),'i')
size = grid/np.maximum(np.ones(3,'d'), grid-1.0) * (maxcorner-mincorner) # size from edge to edge = dim * n/(n-1)
size = np.where(grid > 1, size, min(size[grid > 1]/grid[grid > 1]))
# ------------------------------------------ process value field -----------------------------------
stack = [table.data]
for type, data in items.iteritems():
for i,label in enumerate(data['active']):
# we need to reverse order here, because x is fastest,ie rightmost, but leftmost in our x,y,z notation
stack.append(gradFFT(size[::-1],
table.data[:,data['column'][i]:data['column'][i]+data['dim']].
reshape([grid[2],grid[1],grid[0]]+data['shape'])))
# ------------------------------------------ output result -----------------------------------------
if len(stack) > 1: table.data = np.hstack(tuple(stack))
table.data_writeArray('%.12g')
# ------------------------------------------ output finalization -----------------------------------
table.close() # close input ASCII table (works for stdin)