Merge branch 'MoreImprovements' into PGI-support

processing/post/addAPS34IDEstrainCoords.py

@@ -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,
+    damask.util.report(scriptName,name)
-                                    buffered = False)
-  except: continue
-  damask.util.report(scriptName,name)
 
-# ------------------------------------------ read header ------------------------------------------
+    table = damask.Table.from_ASCII(StringIO(''.join(sys.stdin.read())) if name is None else name)
     
-  table.head_read()
+    coord      = - table.get(options.frame)
+    coord[:,2] += table.get(options.depth)[:,0]
 
-# ------------------------------------------ sanity checks -----------------------------------------
+    table.add('coord',
-  errors  = []
+              np.einsum('ijk,ik->ij',np.broadcast_to(RotMat2TSL,(coord.shape[0],3,3)),coord),
-  if table.label_dimension(options.frame) != 3:
+              scriptID+' '+' '.join(sys.argv[1:]))
-    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:]))
+    table.to_ASCII(sys.stdout if name is None else name)
-
-# ------------------------------------------ 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

processing/post/addCompatibilityMismatch.py

@@ -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)

processing/post/addCurl.py

@@ -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)

processing/post/addDisplacement.py

@@ -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:

processing/post/addDivergence.py

@@ -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)

processing/post/addEuclideanDistance.py

@@ -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')

processing/post/addGradient.py

@@ -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)

processing/post/averageDown.py

@@ -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')

processing/post/blowUp.py

@@ -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

processing/pre/geom_fromTable.py

@@ -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

python/damask/grid_filters.py

@@ -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.
 

python/tests/test_grid_filters.py

@@ -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):