Table class replaces ASCIItable class
This commit is contained in:
Martin Diehl
parent
0d975e7023
commit
dd318c8d1d
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@ -2,10 +2,10 @@
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import os
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import math
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import sys
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from optparse import OptionParser
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import numpy as np
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import scipy.ndimage
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import damask
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@ -13,26 +13,6 @@ import damask
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scriptName = os.path.splitext(os.path.basename(__file__))[0]
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scriptID = ' '.join([scriptName,damask.version])
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#--------------------------------------------------------------------------------------------------
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def cell2node(cellData,grid):
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nodeData = 0.0
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datalen = np.array(cellData.shape[3:]).prod()
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for i in range(datalen):
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node = scipy.ndimage.convolve(cellData.reshape(tuple(grid[::-1])+(datalen,))[...,i],
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np.ones((2,2,2))/8., # 2x2x2 neighborhood of cells
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mode = 'wrap',
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origin = -1, # offset to have cell origin as center
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) # now averaged at cell origins
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node = np.append(node,node[np.newaxis,0,:,:,...],axis=0) # wrap along z
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node = np.append(node,node[:,0,np.newaxis,:,...],axis=1) # wrap along y
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node = np.append(node,node[:,:,0,np.newaxis,...],axis=2) # wrap along x
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nodeData = node[...,np.newaxis] if i==0 else np.concatenate((nodeData,node[...,np.newaxis]),axis=-1)
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return nodeData
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#--------------------------------------------------------------------------------------------------
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def deformationAvgFFT(F,grid,size,nodal=False,transformed=False):
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"""Calculate average cell center (or nodal) deformation for deformation gradient field specified in each grid cell"""
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@ -82,7 +62,7 @@ def displacementFluctFFT(F,grid,size,nodal=False,transformed=False):
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displacement = np.fft.irfftn(displacement_fourier,grid[::-1],axes=(0,1,2))
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return cell2node(displacement,grid) if nodal else displacement
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return damask.grid_filters.cell_2_node(displacement) if nodal else displacement
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def volTetrahedron(coords):
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@ -241,92 +221,33 @@ parser.set_defaults(pos = 'pos',
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)
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(options,filenames) = parser.parse_args()
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# --- loop over input files -------------------------------------------------------------------------
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if filenames == []: filenames = [None]
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for name in filenames:
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try:
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table = damask.ASCIItable(name = name,
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buffered = False)
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except: continue
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damask.util.report(scriptName,name)
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# ------------------------------------------ read header ------------------------------------------
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table = damask.Table.from_ASCII(StringIO(''.join(sys.stdin.read())) if name is None else name)
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grid,size,origin = damask.grid_filters.cell_coord0_2_DNA(table.get(options.pos))
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table.head_read()
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# ------------------------------------------ sanity checks ----------------------------------------
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errors = []
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remarks = []
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if table.label_dimension(options.defgrad) != 9:
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errors.append('deformation gradient "{}" is not a 3x3 tensor.'.format(options.defgrad))
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coordDim = table.label_dimension(options.pos)
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if not 3 >= coordDim >= 1:
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errors.append('coordinates "{}" need to have one, two, or three dimensions.'.format(options.pos))
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elif coordDim < 3:
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remarks.append('appending {} dimension{} to coordinates "{}"...'.format(3-coordDim,
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's' if coordDim < 2 else '',
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options.pos))
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if remarks != []: damask.util.croak(remarks)
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if errors != []:
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damask.util.croak(errors)
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table.close(dismiss=True)
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continue
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# --------------- figure out size and grid ---------------------------------------------------------
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table.data_readArray([options.defgrad,options.pos])
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table.data_rewind()
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if table.data[:,9:].shape[1] < 3:
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table.data = np.hstack((table.data,
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np.zeros((table.data.shape[0],
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3-table.data[:,9:].shape[1]),dtype='f'))) # fill coords up to 3D with zeros
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grid,size = damask.util.coordGridAndSize(table.data[:,9:12])
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N = grid.prod()
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if N != len(table.data): errors.append('data count {} does not match grid {}x{}x{}.'.format(N,*grid))
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if errors != []:
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damask.util.croak(errors)
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table.close(dismiss = True)
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continue
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# -----------------------------process data and assemble header -------------------------------------
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F_fourier = np.fft.rfftn(table.data[:,:9].reshape(grid[2],grid[1],grid[0],3,3),axes=(0,1,2)) # perform transform only once...
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F_fourier = np.fft.rfftn(table.get(options.defgrad).reshape(grid[2],grid[1],grid[0],3,3),axes=(0,1,2)) # perform transform only once...
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nodes = displacementFluctFFT(F_fourier,grid,size,True,transformed=True)\
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+ deformationAvgFFT (F_fourier,grid,size,True,transformed=True)
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if options.shape:
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table.labels_append(['shapeMismatch({})'.format(options.defgrad)])
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centres = displacementFluctFFT(F_fourier,grid,size,False,transformed=True)\
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+ deformationAvgFFT (F_fourier,grid,size,False,transformed=True)
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shapeMismatch = shapeMismatch( size,table.get(options.defgrad).reshape(grid[2],grid[1],grid[0],3,3),nodes,centres)
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table.add('shapeMismatch(({}))'.format(options.defgrad),
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shapeMismatch.reshape((-1,1)),
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scriptID+' '+' '.join(sys.argv[1:]))
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if options.volume:
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table.labels_append(['volMismatch({})'.format(options.defgrad)])
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volumeMismatch = volumeMismatch(size,table.get(options.defgrad).reshape(grid[2],grid[1],grid[0],3,3),nodes)
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table.add('volMismatch(({}))'.format(options.defgrad),
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volumeMismatch.reshape((-1,1)),
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scriptID+' '+' '.join(sys.argv[1:]))
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table.head_write()
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if options.shape:
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shapeMismatch = shapeMismatch( size,table.data[:,:9].reshape(grid[2],grid[1],grid[0],3,3),nodes,centres)
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if options.volume:
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volumeMismatch = volumeMismatch(size,table.data[:,:9].reshape(grid[2],grid[1],grid[0],3,3),nodes)
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# ------------------------------------------ output data -------------------------------------------
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for i in range(grid[2]):
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for j in range(grid[1]):
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for k in range(grid[0]):
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table.data_read()
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if options.shape: table.data_append(shapeMismatch[i,j,k])
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if options.volume: table.data_append(volumeMismatch[i,j,k])
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table.data_write()
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# ------------------------------------------ output finalization -----------------------------------
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table.close() # close ASCII tables
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table.to_ASCII(sys.stdout if name is None else name)
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@ -43,54 +43,25 @@ parser.set_defaults(pole = (0.0,0.0,1.0),
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)
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(options, filenames) = parser.parse_args()
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if filenames == []: filenames = [None]
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# damask.Orientation requires Bravais lattice, but we are only interested in symmetry
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symmetry2lattice={'cubic':'bcc','hexagonal':'hex','tetragonal':'bct'}
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symmetry2lattice={'cubic':'fcc','hexagonal':'hex','tetragonal':'bct'}
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lattice = symmetry2lattice[options.symmetry]
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pole = np.array(options.pole)
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pole /= np.linalg.norm(pole)
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# --- loop over input files ------------------------------------------------------------------------
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if filenames == []: filenames = [None]
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for name in filenames:
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try:
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table = damask.ASCIItable(name = name,
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buffered = False)
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except: continue
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damask.util.report(scriptName,name)
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damask.util.report(scriptName,name)
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# ------------------------------------------ read header ------------------------------------------
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table = damask.Table.from_ASCII(StringIO(''.join(sys.stdin.read())) if name is None else name)
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orientation = table.get(options.quaternion)
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color = np.empty((orientation.shape[0],3))
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for i,o in enumerate(orientation):
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color[i] = damask.Orientation(o,lattice = lattice).IPFcolor(pole)
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table.head_read()
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# ------------------------------------------ sanity checks ----------------------------------------
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if not table.label_dimension(options.quaternion) == 4:
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damask.util.croak('input {} does not have dimension 4.'.format(options.quaternion))
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table.close(dismiss = True) # close ASCIItable and remove empty file
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continue
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column = table.label_index(options.quaternion)
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# ------------------------------------------ assemble header ---------------------------------------
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table.info_append(scriptID + '\t' + ' '.join(sys.argv[1:]))
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table.labels_append(['{}_IPF_{:g}{:g}{:g}_{sym}'.format(i+1,*options.pole,sym = options.symmetry.lower()) for i in range(3)])
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table.head_write()
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# ------------------------------------------ process data ------------------------------------------
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outputAlive = True
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while outputAlive and table.data_read(): # read next data line of ASCII table
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o = damask.Orientation(np.array(list(map(float,table.data[column:column+4]))),
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lattice = lattice).reduced()
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table.data_append(o.IPFcolor(pole))
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outputAlive = table.data_write() # output processed line
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# ------------------------------------------ output finalization -----------------------------------
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table.close() # close ASCII tables
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table.add('IPF_{:g}{:g}{:g}_{sym}'.format(*options.pole,sym = options.symmetry.lower()),
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color,
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scriptID+' '+' '.join(sys.argv[1:]))
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table.to_ASCII(sys.stdout if name is None else name)
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@ -42,7 +42,7 @@ parser.add_option('-n','--norm',
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type = 'choice', choices = normChoices, metavar='string',
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help = 'type of element-wise p-norm [frobenius] {%s}'%(','.join(map(str,normChoices))))
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parser.add_option('-l','--label',
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dest = 'label',
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dest = 'labels',
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action = 'extend', metavar = '<string LIST>',
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help = 'heading of column(s) to calculate norm of')
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@ -50,62 +50,25 @@ parser.set_defaults(norm = 'frobenius',
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)
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(options,filenames) = parser.parse_args()
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if options.norm.lower() not in normChoices:
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parser.error('invalid norm ({}) specified.'.format(options.norm))
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if options.label is None:
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parser.error('no data column specified.')
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# --- loop over input files -------------------------------------------------------------------------
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if filenames == []: filenames = [None]
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if options.norm.lower() not in normChoices:
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parser.error('invalid norm ({}) specified.'.format(options.norm))
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if options.labels is None:
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parser.error('no data column specified.')
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for name in filenames:
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try:
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table = damask.ASCIItable(name = name,
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buffered = False)
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except: continue
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damask.util.report(scriptName,name)
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damask.util.report(scriptName,name)
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# ------------------------------------------ read header ------------------------------------------
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table = damask.Table.from_ASCII(StringIO(''.join(sys.stdin.read())) if name is None else name)
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for label in options.labels:
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data = table.get(label)
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data_norm = np.empty((data.shape[0],1))
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for i,d in enumerate(data):
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data_norm[i] = norm(options.norm.capitalize(),d)
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table.head_read()
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table.add('norm{}({})'.format(options.norm.capitalize(),label),
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data_norm,
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scriptID+' '+' '.join(sys.argv[1:]))
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# ------------------------------------------ sanity checks ----------------------------------------
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errors = []
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remarks = []
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columns = []
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dims = []
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for what in options.label:
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dim = table.label_dimension(what)
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if dim < 0: remarks.append('column {} not found...'.format(what))
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else:
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dims.append(dim)
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columns.append(table.label_index(what))
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table.labels_append('norm{}({})'.format(options.norm.capitalize(),what)) # extend ASCII header with new labels
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if remarks != []: damask.util.croak(remarks)
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if errors != []:
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damask.util.croak(errors)
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table.close(dismiss = True)
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continue
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# ------------------------------------------ assemble header --------------------------------------
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table.info_append(scriptID + '\t' + ' '.join(sys.argv[1:]))
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table.head_write()
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# ------------------------------------------ process data ------------------------------------------
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outputAlive = True
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while outputAlive and table.data_read(): # read next data line of ASCII table
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for column,dim in zip(columns,dims):
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table.data_append(norm(options.norm.capitalize(),
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map(float,table.data[column:column+dim])))
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outputAlive = table.data_write() # output processed line
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# ------------------------------------------ output finalization -----------------------------------
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table.close() # close input ASCII table (works for stdin)
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table.to_ASCII(sys.stdout if name is None else name)
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@ -42,52 +42,23 @@ parser.set_defaults(pole = (1.0,0.0,0.0),
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)
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(options, filenames) = parser.parse_args()
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if filenames == []: filenames = [None]
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pole = np.array(options.pole)
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pole /= np.linalg.norm(pole)
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# --- loop over input files -------------------------------------------------------------------------
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if filenames == []: filenames = [None]
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for name in filenames:
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try:
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table = damask.ASCIItable(name = name,
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buffered = False)
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except: continue
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damask.util.report(scriptName,name)
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damask.util.report(scriptName,name)
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# ------------------------------------------ read header ------------------------------------------
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table = damask.Table.from_ASCII(StringIO(''.join(sys.stdin.read())) if name is None else name)
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orientation = table.get(options.quaternion)
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poles = np.empty((orientation.shape[0],2))
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for i,o in enumerate(orientation):
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rotatedPole = damask.Rotation(o)*pole # rotate pole according to crystal orientation
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(x,y) = rotatedPole[0:2]/(1.+abs(pole[2])) # stereographic projection
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poles[i] = [np.sqrt(x*x+y*y),np.arctan2(y,x)] if options.polar else [x,y] # cartesian coordinates
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table.head_read()
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# ------------------------------------------ sanity checks ----------------------------------------
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if not table.label_dimension(options.quaternion) == 4:
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damask.util.croak('input {} does not have dimension 4.'.format(options.quaternion))
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table.close(dismiss = True) # close ASCIItable and remove empty file
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continue
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column = table.label_index(options.quaternion)
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# ------------------------------------------ assemble header ---------------------------------------
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table.info_append(scriptID + '\t' + ' '.join(sys.argv[1:]))
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table.labels_append(['{}_pole_{}{}{}'.format(i+1,*options.pole) for i in range(2)])
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table.head_write()
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# ------------------------------------------ process data ------------------------------------------
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outputAlive = True
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while outputAlive and table.data_read(): # read next data line of ASCII table
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o = damask.Rotation(np.array(list(map(float,table.data[column:column+4]))))
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rotatedPole = o*pole # rotate pole according to crystal orientation
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(x,y) = rotatedPole[0:2]/(1.+abs(pole[2])) # stereographic projection
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table.data_append([np.sqrt(x*x+y*y),np.arctan2(y,x)] if options.polar else [x,y]) # cartesian coordinates
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outputAlive = table.data_write() # output processed line
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# ------------------------------------------ output finalization -----------------------------------
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table.close() # close ASCII tables
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table.add('pole_{}{}{}'.format(*options.pole),
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poles,
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scriptID+' '+' '.join(sys.argv[1:]))
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table.to_ASCII(sys.stdout if name is None else name)
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