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DAMASK_EICMD
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Merge branch 'MoreImprovements' into PGI-support

This commit is contained in:
Martin Diehl 2020-01-13 08:01:03 +01:00
parent a025edd09f ff60cf0b67
commit 93d7d080ec
12 changed files with 30 additions and 57 deletions
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59
processing/post/addAPS34IDEstrainCoords.py
View File

@ -2,6 +2,7 @@
import os
import sys
from io import StringIO
from optparse import OptionParser
import numpy as np
@ -24,61 +25,33 @@ Transform X,Y,Z,F APS BeamLine 34 coordinates to x,y,z APS strain coordinates.
parser.add_option('-f','--frame',dest='frame', metavar='string',
help='label of APS X,Y,Z coords')
parser.add_option('--depth', dest='depth', metavar='string',
parser.add_option('--depth', dest='depth', metavar='string',
help='depth')
(options,filenames) = parser.parse_args()
if filenames == []: filenames = [None]
if options.frame is None:
parser.error('frame not specified')
if options.depth is None:
parser.error('depth not specified')
# --- loop over input files ------------------------------------------------------------------------
if filenames == []: filenames = [None]
theta=-0.75*np.pi
RotMat2TSL=np.array([[1., 0., 0.],
[0., np.cos(theta), np.sin(theta)], # Orientation to account for -135 deg
[0., -np.sin(theta), np.cos(theta)]]) # rotation for TSL convention
for name in filenames:
try: table = damask.ASCIItable(name = name,
buffered = False)
except: continue
damask.util.report(scriptName,name)
damask.util.report(scriptName,name)
# ------------------------------------------ read header ------------------------------------------
table = damask.Table.from_ASCII(StringIO(''.join(sys.stdin.read())) if name is None else name)
coord = - table.get(options.frame)
coord[:,2] += table.get(options.depth)[:,0]
table.head_read()
table.add('coord',
np.einsum('ijk,ik->ij',np.broadcast_to(RotMat2TSL,(coord.shape[0],3,3)),coord),
scriptID+' '+' '.join(sys.argv[1:]))
# ------------------------------------------ sanity checks -----------------------------------------
errors = []
if table.label_dimension(options.frame) != 3:
errors.append('input {} does not have dimension 3.'.format(options.frame))
if table.label_dimension(options.depth) != 1:
errors.append('input {} does not have dimension 1.'.format(options.depth))
if errors != []:
damask.util.croak(errors)
table.close(dismiss = True)
continue
table.info_append(scriptID + '\t' + ' '.join(sys.argv[1:]))
# ------------------------------------------ assemble header ---------------------------------------
table.labels_append(['%i_coord'%(i+1) for i in range(3)]) # extend ASCII header with new labels
table.head_write()
# ------------------------------------------ process data ------------------------------------------
theta=-0.75*np.pi
RotMat2TSL=np.array([[1., 0., 0.],
[0., np.cos(theta), np.sin(theta)], # Orientation to account for -135 deg
[0., -np.sin(theta), np.cos(theta)]]) # rotation for TSL convention
outputAlive = True
while outputAlive and table.data_read(): # read next data line of ASCII table
coord = list(map(float,table.data[table.label_index(options.frame):table.label_index(options.frame)+3]))
depth = float(table.data[table.label_index(options.depth)])
table.data_append(np.dot(RotMat2TSL,np.array([-coord[0],-coord[1],-coord[2]+depth])))
outputAlive = table.data_write() # output processed line
# ------------------------------------------ output finalization -----------------------------------
table.close() # close ASCII tables
table.to_ASCII(sys.stdout if name is None else name)

2
processing/post/addCompatibilityMismatch.py
View File

@ -176,7 +176,7 @@ for name in filenames:
damask.util.report(scriptName,name)
table = damask.Table.from_ASCII(StringIO(''.join(sys.stdin.read())) if name is None else name)
grid,size,origin = damask.grid_filters.cell_coord0_2_DNA(table.get(options.pos))
grid,size,origin = damask.grid_filters.cell_coord0_gridSizeOrigin(table.get(options.pos))
F = table.get(options.defgrad).reshape(grid[2],grid[1],grid[0],3,3)
nodes = damask.grid_filters.node_coord(size,F)

2
processing/post/addCurl.py
View File

@ -44,7 +44,7 @@ for name in filenames:
damask.util.report(scriptName,name)
table = damask.Table.from_ASCII(StringIO(''.join(sys.stdin.read())) if name is None else name)
grid,size,origin = damask.grid_filters.cell_coord0_2_DNA(table.get(options.pos))
grid,size,origin = damask.grid_filters.cell_coord0_gridSizeOrigin(table.get(options.pos))
for label in options.labels:
field = table.get(label)

2
processing/post/addDisplacement.py
View File

@ -50,7 +50,7 @@ for name in filenames:
damask.util.report(scriptName,name)
table = damask.Table.from_ASCII(StringIO(''.join(sys.stdin.read())) if name is None else name)
grid,size,origin = damask.grid_filters.cell_coord0_2_DNA(table.get(options.pos))
grid,size,origin = damask.grid_filters.cell_coord0_gridSizeOrigin(table.get(options.pos))
F = table.get(options.f).reshape(np.append(grid[::-1],(3,3)))
if options.nodal:

2
processing/post/addDivergence.py
View File

@ -44,7 +44,7 @@ for name in filenames:
damask.util.report(scriptName,name)
table = damask.Table.from_ASCII(StringIO(''.join(sys.stdin.read())) if name is None else name)
grid,size,origin = damask.grid_filters.cell_coord0_2_DNA(table.get(options.pos))
grid,size,origin = damask.grid_filters.cell_coord0_gridSizeOrigin(table.get(options.pos))
for label in options.labels:
field = table.get(label)

2
processing/post/addEuclideanDistance.py
View File

@ -143,7 +143,7 @@ for name in filenames:
damask.util.report(scriptName,name)
table = damask.Table.from_ASCII(StringIO(''.join(sys.stdin.read())) if name is None else name)
grid,size,origin = damask.grid_filters.cell_coord0_2_DNA(table.get(options.pos))
grid,size,origin = damask.grid_filters.cell_coord0_gridSizeOrigin(table.get(options.pos))
neighborhood = neighborhoods[options.neighborhood]
diffToNeighbor = np.empty(list(grid+2)+[len(neighborhood)],'i')

2
processing/post/addGradient.py
View File

@ -44,7 +44,7 @@ for name in filenames:
damask.util.report(scriptName,name)
table = damask.Table.from_ASCII(StringIO(''.join(sys.stdin.read())) if name is None else name)
grid,size,origin = damask.grid_filters.cell_coord0_2_DNA(table.get(options.pos))
grid,size,origin = damask.grid_filters.cell_coord0_gridSizeOrigin(table.get(options.pos))
for label in options.labels:
field = table.get(label)

2
processing/post/averageDown.py
View File

@ -65,7 +65,7 @@ for name in filenames:
table = damask.Table.from_ASCII(StringIO(''.join(sys.stdin.read())) if name is None else name)
if (options.grid is None or options.size is None):
grid,size,origin = damask.grid_filters.cell_coord0_2_DNA(table.get(options.pos))
grid,size,origin = damask.grid_filters.cell_coord0_gridSizeOrigin(table.get(options.pos))
else:
grid = np.array(options.grid,'i')
size = np.array(options.size,'d')

2
processing/post/blowUp.py
View File

@ -54,7 +54,7 @@ for name in filenames:
damask.util.report(scriptName,name)
table = damask.Table.from_ASCII(StringIO(''.join(sys.stdin.read())) if name is None else name)
grid,size,origin = damask.grid_filters.cell_coord0_2_DNA(table.get(options.pos))
grid,size,origin = damask.grid_filters.cell_coord0_gridSizeOrigin(table.get(options.pos))
packing = np.array(options.packing,'i')
outSize = grid*packing

2
processing/pre/geom_fromTable.py
View File

@ -86,7 +86,7 @@ for name in filenames:
if options.phase is None:
table.data = np.column_stack((table.data,np.ones(len(table.data)))) # add single phase if no phase column given
grid,size,origin = damask.grid_filters.cell_coord0_2_DNA(table.data[:,0:3])
grid,size,origin = damask.grid_filters.cell_coord0_gridSizeOrigin(table.data[:,0:3])
indices = np.lexsort((table.data[:,0],table.data[:,1],table.data[:,2])) # indices of position when sorting x fast, z slow
microstructure = np.empty(grid,dtype = int) # initialize empty microstructure

6
python/damask/grid_filters.py
View File

@ -181,7 +181,7 @@ def cell_coord(size,F,origin=np.zeros(3)):
"""
return cell_coord0(F.shape[:3][::-1],size,origin) + cell_displacement(size,F)
def cell_coord0_2_DNA(coord0,ordered=True):
def cell_coord0_gridSizeOrigin(coord0,ordered=True):
"""
Return grid 'DNA', i.e. grid, size, and origin from array of cell positions.
@ -231,7 +231,7 @@ def coord0_check(coord0):
array of undeformed cell coordinates.
"""
cell_coord0_2_DNA(coord0,ordered=True)
cell_coord0_gridSizeOrigin(coord0,ordered=True)
@ -331,7 +331,7 @@ def node_2_cell(node_data):
return c[:-1,:-1,:-1]
def node_coord0_2_DNA(coord0,ordered=False):
def node_coord0_gridSizeOrigin(coord0,ordered=False):
"""
Return grid 'DNA', i.e. grid, size, and origin from array of nodal positions.

4
python/tests/test_grid_filters.py
View File

@ -26,12 +26,12 @@ class TestGridFilters:
@pytest.mark.parametrize('mode',[('cell'),('node')])
def test_grid_DNA(self,mode):
"""Ensure that xx_coord0_2_DNA is the inverse of xx_coord0."""
"""Ensure that xx_coord0_gridSizeOrigin is the inverse of xx_coord0."""
grid = np.random.randint(8,32,(3))
size = np.random.random(3)
origin = np.random.random(3)
coord0 = eval('grid_filters.{}_coord0(grid,size,origin)'.format(mode)) # noqa
_grid,_size,_origin = eval('grid_filters.{}_coord0_2_DNA(coord0.reshape((-1,3)))'.format(mode))
_grid,_size,_origin = eval('grid_filters.{}_coord0_gridSizeOrigin(coord0.reshape((-1,3)))'.format(mode))
assert np.allclose(grid,_grid) and np.allclose(size,_size) and np.allclose(origin,_origin)
def test_displacement_fluct_equivalence(self):