spam-ddic working, ldmax needs implementing

scripts/spam-ldic

@@ -21,17 +21,18 @@ this program.  If not, see <http://www.gnu.org/licenses/>.
 import os
 os.environ['OPENBLAS_NUM_THREADS'] = '1'
 
+import spam.DIC
+import spam.deformation
+import spam.helpers
 import argparse
+
+import numpy
+import scipy.ndimage
 import tifffile
 import multiprocessing
 import progressbar
 
-import numpy
-import scipy.ndimage
 
-import spam.DIC
-import spam.deformation
-import spam.helpers
 
 
 
@@ -256,19 +257,16 @@ for im2number in range(1, len(args.inFiles)):
 
                     # Check if we've hit the same point in the two grids
                     if numpy.any(distance == 0):
-
                         # Copy F of that point to the F in the current grid point
                         PhiField[node] = fieldValues[indices][numpy.where(distance == 0)].copy()
 
                     # If not, consider the closest neighbours
                     else:
-
                         # Compute the "Inverse Distance Weighting" since the closest points should have the major influence
                         weightSumInv = sum(1/distance)
 
                         # Loop over each neighbour
                         for neighbour in range(nNeighbours):
-
                             # Calculate it's weight
                             weightInv = (1/distance[neighbour])/float(weightSumInv)
 

scripts/spam-pixelSearch

@@ -25,18 +25,19 @@ this program.  If not, see <http://www.gnu.org/licenses/>.
 import os
 os.environ['OPENBLAS_NUM_THREADS'] = '1'
 
-import argparse
+import spam.DIC
+import spam.deformation
+import spam.helpers
+#import spam.mesh
+import spam.label
+
+import numpy
 import multiprocessing
 import progressbar
+import argparse
 import tifffile
 
-import numpy
 
-import spam.helpers
-#import spam.mesh
-import spam.label
-import spam.DIC
-import spam.deformation
 
 
 
@@ -381,9 +382,9 @@ if args.TIFF:
 
 
 # Collect data into VTK output
-if args.VTK:
+if args.VTK and args.LAB1 is None:
     cellData = {}
-    cellData['displacements'] =  PhiField[:, :-1, 3].reshape((nodesDim[0], nodesDim[1], nodesDim[2], 3))
+    cellData['displacements'] = PhiField[:, :-1, 3].reshape((nodesDim[0], nodesDim[1], nodesDim[2], 3))
     cellData['pixelSearchCC'] = pixelSearchCC.reshape(nodesDim)
 
     # Overwrite nans and infs with 0, rubbish I know
@@ -396,3 +397,15 @@ if args.VTK:
     # If you insist on overlapping, then perhaps it's better to save each point as a cube glyph
     #   and actually *have* overlapping
     spam.helpers.writeStructuredVTK(origin=nodePositions[0]-args.HWS, aspectRatio=args.NS, cellData=cellData, fileName=args.OUT_DIR+"/"+args.PREFIX+".vtk")
+
+elif args.VTK and args.LAB1 is not None:
+    # Redundant output for VTK visualisation
+    magDisp = numpy.zeros(numberOfNodes)
+    for node in range(numberOfNodes):
+        magDisp[node] = numpy.linalg.norm(PhiField[node][0:3,-1])
+
+    VTKglyphDict = {'displacements': PhiField[:, 0:3, -1],
+                    'mag(displacements)': magDisp,
+                    'pixelSearchCC': pixelSearchCC}
+
+    spam.helpers.writeGlyphsVTK(nodePositions, VTKglyphDict, fileName=args.OUT_DIR + "/" + args.PREFIX + ".vtk")

tools/helpers/optionsParser.py

@@ -356,6 +356,13 @@ def ddicParser(parser):
                         type=argparse.FileType('r'),
                         help="Greyscale image of deformed state for correlation")
 
+    parser.add_argument('-np',
+                        '--number-of-processes',
+                        default=None,
+                        type=int,
+                        dest='PROCESSES',
+                        help="Number of parallel processes to use. Default = multiprocessing.cpu_count()")
+
     parser.add_argument('-ld',
                         '--label-dilate',
                         type=int,
@@ -532,9 +539,13 @@ def ddicParser(parser):
         args.LABEL_DILATE_MAX = args.LABEL_DILATE
 
     if args.LABEL_DILATE_MAX < args.LABEL_DILATE:
-        print("spam-ddic: Warining \"label dilate max\" is less than \"label dilate\" setting them equal")
+        print("spam-ddic: Warning \"label dilate max\" is less than \"label dilate\" setting them equal")
         args.LABEL_DILATE_MAX = args.LABEL_DILATE
 
+    if args.DEBUG:
+        print("spam-ddic: DEBUG mode activated, forcing number of processes to 1")
+        args.PROCESSES = 1
+
     return args