more descriptive name
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@ -176,7 +176,7 @@ for name in filenames:
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damask.util.report(scriptName,name)
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damask.util.report(scriptName,name)
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table = damask.Table.from_ASCII(StringIO(''.join(sys.stdin.read())) if name is None else name)
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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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grid,size,origin = damask.grid_filters.cell_coord0_gridSizeOrigin(table.get(options.pos))
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F = table.get(options.defgrad).reshape(grid[2],grid[1],grid[0],3,3)
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F = table.get(options.defgrad).reshape(grid[2],grid[1],grid[0],3,3)
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nodes = damask.grid_filters.node_coord(size,F)
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nodes = damask.grid_filters.node_coord(size,F)
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@ -44,7 +44,7 @@ for name in filenames:
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damask.util.report(scriptName,name)
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damask.util.report(scriptName,name)
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table = damask.Table.from_ASCII(StringIO(''.join(sys.stdin.read())) if name is None else name)
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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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grid,size,origin = damask.grid_filters.cell_coord0_gridSizeOrigin(table.get(options.pos))
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for label in options.labels:
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for label in options.labels:
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field = table.get(label)
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field = table.get(label)
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@ -50,7 +50,7 @@ for name in filenames:
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damask.util.report(scriptName,name)
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damask.util.report(scriptName,name)
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table = damask.Table.from_ASCII(StringIO(''.join(sys.stdin.read())) if name is None else name)
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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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grid,size,origin = damask.grid_filters.cell_coord0_gridSizeOrigin(table.get(options.pos))
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F = table.get(options.f).reshape(np.append(grid[::-1],(3,3)))
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F = table.get(options.f).reshape(np.append(grid[::-1],(3,3)))
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if options.nodal:
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if options.nodal:
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@ -44,7 +44,7 @@ for name in filenames:
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damask.util.report(scriptName,name)
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damask.util.report(scriptName,name)
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table = damask.Table.from_ASCII(StringIO(''.join(sys.stdin.read())) if name is None else name)
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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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grid,size,origin = damask.grid_filters.cell_coord0_gridSizeOrigin(table.get(options.pos))
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for label in options.labels:
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for label in options.labels:
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field = table.get(label)
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field = table.get(label)
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@ -143,7 +143,7 @@ for name in filenames:
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damask.util.report(scriptName,name)
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damask.util.report(scriptName,name)
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table = damask.Table.from_ASCII(StringIO(''.join(sys.stdin.read())) if name is None else name)
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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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grid,size,origin = damask.grid_filters.cell_coord0_gridSizeOrigin(table.get(options.pos))
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neighborhood = neighborhoods[options.neighborhood]
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neighborhood = neighborhoods[options.neighborhood]
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diffToNeighbor = np.empty(list(grid+2)+[len(neighborhood)],'i')
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diffToNeighbor = np.empty(list(grid+2)+[len(neighborhood)],'i')
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@ -44,7 +44,7 @@ for name in filenames:
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damask.util.report(scriptName,name)
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damask.util.report(scriptName,name)
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table = damask.Table.from_ASCII(StringIO(''.join(sys.stdin.read())) if name is None else name)
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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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grid,size,origin = damask.grid_filters.cell_coord0_gridSizeOrigin(table.get(options.pos))
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for label in options.labels:
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for label in options.labels:
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field = table.get(label)
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field = table.get(label)
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@ -65,7 +65,7 @@ for name in filenames:
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table = damask.Table.from_ASCII(StringIO(''.join(sys.stdin.read())) if name is None else name)
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table = damask.Table.from_ASCII(StringIO(''.join(sys.stdin.read())) if name is None else name)
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if (options.grid is None or options.size is None):
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if (options.grid is None or options.size is None):
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grid,size,origin = damask.grid_filters.cell_coord0_2_DNA(table.get(options.pos))
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grid,size,origin = damask.grid_filters.cell_coord0_gridSizeOrigin(table.get(options.pos))
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else:
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else:
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grid = np.array(options.grid,'i')
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grid = np.array(options.grid,'i')
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size = np.array(options.size,'d')
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size = np.array(options.size,'d')
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@ -54,7 +54,7 @@ for name in filenames:
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damask.util.report(scriptName,name)
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damask.util.report(scriptName,name)
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table = damask.Table.from_ASCII(StringIO(''.join(sys.stdin.read())) if name is None else name)
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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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grid,size,origin = damask.grid_filters.cell_coord0_gridSizeOrigin(table.get(options.pos))
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packing = np.array(options.packing,'i')
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packing = np.array(options.packing,'i')
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outSize = grid*packing
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outSize = grid*packing
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@ -86,7 +86,7 @@ for name in filenames:
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if options.phase is None:
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if options.phase is None:
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table.data = np.column_stack((table.data,np.ones(len(table.data)))) # add single phase if no phase column given
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table.data = np.column_stack((table.data,np.ones(len(table.data)))) # add single phase if no phase column given
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grid,size,origin = damask.grid_filters.cell_coord0_2_DNA(table.data[:,0:3])
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grid,size,origin = damask.grid_filters.cell_coord0_gridSizeOrigin(table.data[:,0:3])
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indices = np.lexsort((table.data[:,0],table.data[:,1],table.data[:,2])) # indices of position when sorting x fast, z slow
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indices = np.lexsort((table.data[:,0],table.data[:,1],table.data[:,2])) # indices of position when sorting x fast, z slow
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microstructure = np.empty(grid,dtype = int) # initialize empty microstructure
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microstructure = np.empty(grid,dtype = int) # initialize empty microstructure
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@ -181,7 +181,7 @@ def cell_coord(size,F,origin=np.zeros(3)):
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"""
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"""
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return cell_coord0(F.shape[:3][::-1],size,origin) + cell_displacement(size,F)
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return cell_coord0(F.shape[:3][::-1],size,origin) + cell_displacement(size,F)
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def cell_coord0_2_DNA(coord0,ordered=True):
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def cell_coord0_gridSizeOrigin(coord0,ordered=True):
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"""
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"""
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Return grid 'DNA', i.e. grid, size, and origin from array of cell positions.
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Return grid 'DNA', i.e. grid, size, and origin from array of cell positions.
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@ -231,7 +231,7 @@ def coord0_check(coord0):
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array of undeformed cell coordinates.
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array of undeformed cell coordinates.
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"""
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"""
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cell_coord0_2_DNA(coord0,ordered=True)
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cell_coord0_gridSizeOrigin(coord0,ordered=True)
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@ -331,7 +331,7 @@ def node_2_cell(node_data):
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return c[:-1,:-1,:-1]
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return c[:-1,:-1,:-1]
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def node_coord0_2_DNA(coord0,ordered=False):
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def node_coord0_gridSizeOrigin(coord0,ordered=False):
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"""
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"""
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Return grid 'DNA', i.e. grid, size, and origin from array of nodal positions.
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Return grid 'DNA', i.e. grid, size, and origin from array of nodal positions.
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@ -26,12 +26,12 @@ class TestGridFilters:
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@pytest.mark.parametrize('mode',[('cell'),('node')])
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@pytest.mark.parametrize('mode',[('cell'),('node')])
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def test_grid_DNA(self,mode):
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def test_grid_DNA(self,mode):
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"""Ensure that xx_coord0_2_DNA is the inverse of xx_coord0."""
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"""Ensure that xx_coord0_gridSizeOrigin is the inverse of xx_coord0."""
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grid = np.random.randint(8,32,(3))
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grid = np.random.randint(8,32,(3))
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size = np.random.random(3)
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size = np.random.random(3)
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origin = np.random.random(3)
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origin = np.random.random(3)
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coord0 = eval('grid_filters.{}_coord0(grid,size,origin)'.format(mode)) # noqa
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coord0 = eval('grid_filters.{}_coord0(grid,size,origin)'.format(mode)) # noqa
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_grid,_size,_origin = eval('grid_filters.{}_coord0_2_DNA(coord0.reshape((-1,3)))'.format(mode))
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_grid,_size,_origin = eval('grid_filters.{}_coord0_gridSizeOrigin(coord0.reshape((-1,3)))'.format(mode))
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assert np.allclose(grid,_grid) and np.allclose(size,_size) and np.allclose(origin,_origin)
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assert np.allclose(grid,_grid) and np.allclose(size,_size) and np.allclose(origin,_origin)
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def test_displacement_fluct_equivalence(self):
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def test_displacement_fluct_equivalence(self):
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