[skip-ci] work on spam-passPhiField

scripts/spam-discreteStrain

@@ -79,7 +79,7 @@ triangulationAvailable = False
 
 print("\nspam-discreteStrain: Loading kinematics...")
 if args.inFile.name[-3::] == "tsv":
-    if args.RETURN_STAT_THRESHOLD is not None:
+    if args.RETURN_STATUS_THRESHOLD is not None:
         TSV = spam.helpers.readCorrelationTSV(args.inFile.name, readOnlyDisplacements=True, readConvergence=True)
         returnStat    = TSV['returnStatus'][start:]
     else:
@@ -95,7 +95,7 @@ if args.inFile.name[-3::] == "tsv":
         radii = None
     del TSV
 elif args.inFile.name[-3::] == "vtk":
-    if args.RETURN_STAT_THRESHOLD is not None:
+    if args.RETURN_STATUS_THRESHOLD is not None:
         returnStat    = VTK['returnStatus']
     VTK = spam.helpers.readUnstructuredVTK(args.inFile.name)
     #dims = VTK[0].shape[0]
@@ -114,8 +114,8 @@ else:
 
 ### 2019-10-14 EA: Attempt to catch undesirable return statuses.
 # HACK: Set the failing particles positions to NaN
-if args.RETURN_STAT_THRESHOLD is not None:
-    points[returnStat < args.RETURN_STAT_THRESHOLD] = numpy.nan
+if args.RETURN_STATUS_THRESHOLD is not None:
+    points[returnStat < args.RETURN_STATUS_THRESHOLD] = numpy.nan
 
 ### 2020-03-23 EA and OS, nan mask for safety
 #mask = numpy.sum(numpy.isnan(points), axis=1) > 0

scripts/spam-ereg-discrete

@@ -85,7 +85,7 @@ class MainWindow(QWidget):
 
         # Issue #192 will be fixed here, by making sure the loew return stat list also has real boundin boxes
         #   (i.e., grains are really defined)
-        nonConvergedGrains = DDIC['returnStatus'][0:REFlabBB.shape[0]] < args.RETURN_STAT_THRESHOLD
+        nonConvergedGrains = DDIC['returnStatus'][0:REFlabBB.shape[0]] < args.RETURN_STATUS_THRESHOLD
         presentGrains      = REFlabBB[:,1]>REFlabBB[:,0]
         # In the very unlucky case that there is a nax numbered nonConverged grain that is not present at all:
         if REFlabBB.shape[0] < len(nonConvergedGrains):

tests/test_scripts.py

@@ -688,7 +688,7 @@ class testAll(unittest.TestCase):
 
         self.assertEqual(numpy.mean(imDefScript[10:-10, 10:-10, 10:-10]) > numpy.mean(imDefScriptCGS[10:-10, 10:-10, 10:-10]), True)
 
-    def _test_discreteDICtools(self):
+    def test_discreteDICtools(self):
         #######################################################
         ### 1. Generate Data
         #######################################################

tools/helpers/optionsParser.py

@@ -1206,7 +1206,7 @@ def discreteStrainsCalcParser(parser):
                         '--return-status-threshold',
                         type=int,
                         default=None,
-                        dest='RETURN_STAT_THRESHOLD',
+                        dest='RETURN_STATUS_THRESHOLD',
                         help='Lowest return status value to preserve in the triangulation. Default = 2')
 
     parser.add_argument('-pre',
@@ -1298,7 +1298,7 @@ def eregDiscreteParser(parser):
                         '--return-status-threshold',
                         type=int,
                         default=2,
-                        dest='RETURN_STAT_THRESHOLD',
+                        dest='RETURN_STATUS_THRESHOLD',
                         help='Skip labels already correlated with at least this return status (requires -pf obviously). Default = 2')
 
     parser.add_argument('-ld',
@@ -2542,11 +2542,25 @@ def passPhiField(parser):
                         help="Size of im1 in pixels Z Y X")
 
     parser.add_argument('-nr',
-                        '--neighbourhood-radius',
+                        '--neighbourhood-radius-px',
                         type=float,
                         default=None,
-                        dest='RADIUS',
-                        help="Radius (in pixels) inside which to select neighbours. Default = mean(hws)+mean(sr)")
+                        dest='NEIGHBOUR_RADIUS',
+                        help="Radius (in pixels) inside which to select neighbours for field interpolation. Excludes -nn option")
+
+    parser.add_argument('-nn',
+                        '--number-of-neighbours',
+                        type=int,
+                        default=None,
+                        dest='NUMBER_OF_NEIGHBOURS',
+                        help="Number of neighbours for field interpolation. Default = None (radius mode is default)")
+
+    parser.add_argument('-rst',
+                        '--return-status-threshold',
+                        type=int,
+                        default=-5,
+                        dest='RETURN_STATUS_THRESHOLD',
+                        help='Lowest return status value to preserve in input PhiField. Default = -5')
 
     parser.add_argument('-od',
                         '--out-dir',
@@ -2576,6 +2590,7 @@ def passPhiField(parser):
                         dest='TIFF',
                         help='Activate TIFFoutput format. Default = False')
 
+
     args = parser.parse_args()
 
     if args.PHIFILE is None: