Clarifying spam-moveGrains options

scripts/spam-moveGrains

@@ -69,7 +69,7 @@ def work_on_one_job(worker_number, q_jobs, q_results):
             getLabelReturn = ltk.getLabel(lab,
                                           label,
                                           labelDilate=0,
-                                          margin=args.DISPLACEMENT_MARGIN,
+                                          margin=args.LABEL_MARGIN,
                                           boundingBoxes=boundingBoxes,
                                           centresOfMass=centresOfMass)
 
@@ -77,7 +77,7 @@ def work_on_one_job(worker_number, q_jobs, q_results):
                 subVolSize = numpy.array(getLabelReturn['subvol'].shape)
 
                 Phi = DVC['PhiField'][label].copy()
-                Phi[0:3,-1] *= float(args.MULTIPLY_DISPLACEMENTS)
+                Phi[0:3,-1] *= float(args.PHIFILE_BIN_RATIO)
 
                 # Phi will be split into a local part and a part of floored displacements
                 disp = numpy.floor(Phi[0:3,-1])

tools/helpers/optionsParser.py

@@ -71,7 +71,7 @@ def ldicParser(parser):
                         type=int,
                         default=1,
                         dest='PHIFILE_BIN_RATIO',
-                        help="Ratio of binning level between loaded F file and current calculation. If the input F file has been obtained on a 500x500x500 image and now the calculation is on 1000x1000x1000, this should be 2. Default = 1")
+                        help="Ratio of binning level between loaded Phi file and current calculation. If the input Phi file has been obtained on a 500x500x500 image and now the calculation is on 1000x1000x1000, this should be 2. Default = 1")
 
     parser.add_argument('-glt',
                         '--grey-low-threshold',
@@ -312,7 +312,7 @@ def ldicParser(parser):
     # 2018-03-24 check for 2D without loading images
     # try:
     # except BaseException:
-    #     print("DICregularGrid: Input TIFF files need to be writeable in order to guess their dimensionality")
+    #     print("DICregularGrid: Input TIFPhi files need to be writeable in order to guess their dimensionality")
     #     exit()
     # 2019-03-21 EA: better check for dimensions, doesn't depend on writability of files
     import tifffile
@@ -532,7 +532,7 @@ def ddicParser(parser):
                         type=int,
                         default=1,
                         dest='PHIFILE_BIN_RATIO',
-                        help="Ratio of binning level between loaded F file and current calculation. If the input F file has been obtained on a 500x500x500 image and now the calculation is on 1000x1000x1000, this should be 2. Default = 1")
+                        help="Ratio of binning level between loaded Phi file and current calculation. If the input Phi file has been obtained on a 500x500x500 image and now the calculation is on 1000x1000x1000, this should be 2. Default = 1")
 
 
     parser.add_argument('-pfd',
@@ -824,7 +824,7 @@ def multiModalRegistrationParser(parser):
     # type=int,
     # default=1,
     # dest='PHIFILE_BIN_RATIO',
-    # help="Ratio of binning level between loaded F file and current calculation. If the input F file has been obtained on a 500x500x500 image and now the calculation is on 1000x1000x1000, this should be 2. Default = 1")
+    # help="Ratio of binning level between loaded Phi file and current calculation. If the input Phi file has been obtained on a 500x500x500 image and now the calculation is on 1000x1000x1000, this should be 2. Default = 1")
 
     # parser.add_argument('-tra',
     # '--translation',
@@ -931,7 +931,7 @@ def gdicParser(parser):
                         type=int,
                         default=1,
                         dest='PHIFILE_BIN_RATIO',
-                        help="Ratio of binning level between loaded F file and current calculation. If the input F file has been obtained on a 500x500x500 image and now the calculation is on 1000x1000x1000, this should be 2. Default = 1")
+                        help="Ratio of binning level between loaded Phi file and current calculation. If the input Phi file has been obtained on a 500x500x500 image and now the calculation is on 1000x1000x1000, this should be 2. Default = 1")
 
     # parser.add_argument('-glt',
     #                     '--grey-low-threshold',
@@ -1391,7 +1391,7 @@ def moveGrainsParser(parser):
                         type=str,
                         default=None,
                         dest='PREFIX',
-                        help='Prefix for output TIFF file (without extension). Default is basename of input file')
+                        help='Prefix for output TIFPhi file (without extension). Default is basename of input file')
 
     parser.add_argument('-com',
                         '--apply-phi-centre-of-mass',
@@ -1406,13 +1406,6 @@ def moveGrainsParser(parser):
                         dest='THRESH',
                         help='Greyscale threshold to keep interpolated voxels. Default = 0.5')
 
-    parser.add_argument('-ld',
-                        '--label-dilate',
-                        type=int,
-                        default=0,
-                        dest='LABEL_DILATE',
-                        help="Number of times to dilate labels. Default = 0")
-
     parser.add_argument('-rst',
                         '--return-status-threshold',
                         type=int,
@@ -1427,33 +1420,34 @@ def moveGrainsParser(parser):
                         dest='GREY_FILE',
                         help='Input greylevel tiff file corresponding to the input labelled file. This option requires a threshold to be set with -thr')
 
-    #parser.add_argument('-gt',
-                        #'--grey-threshold',
-                        #type=float,
-                        #default=None,
-                        #dest='GREY_THRESHOLD',
-                        #help='Threshold for input greylevel file')
-
     parser.add_argument('-om',
                         '--overall-margin',
                         type=int,
                         default=10,
                         dest='OVERALL_MARGIN',
-                        help="Overall image margin for particle movement, this is how much the labelled image is increased before calculating. Default = 10")
+                        help="Overall image padding for label movement near edges, this is how much the labelled image is increased before starting to place label. Default = 10")
 
-    parser.add_argument('-dm',
-                        '--displacement-margin',
+    parser.add_argument('-lm',
+                        '--label-margin',
                         type=int,
                         default=3,
-                        dest='DISPLACEMENT_MARGIN',
-                        help="Displacement margin for particle movement, this the padding around the extraction of each objet and show allow for rotation. Default = 3")
+                        dest='LABEL_MARGIN',
+                        help="Bounding box margin for each label to allow for rotation/strain of the label. Default = 3")
+
+    parser.add_argument('-ld',
+                        '--label-dilate',
+                        type=int,
+                        default=0,
+                        dest='LABEL_DILATE',
+                        help="Number of times to dilate labels. Default = 0")
 
-    parser.add_argument('-md',
-                        '--multipy-displacements',
+    parser.add_argument('-pfb',
+                        '--phiFile-bin-ratio',
                         type=float,
-                        default=1.0,
-                        dest='MULTIPLY_DISPLACEMENTS',
-                        help="Displacement margin for particle movement, this must be AT LEAST equal to the mazimum displacement. Default = 1.0")
+                        default=1,
+                        dest='PHIFILE_BIN_RATIO',
+                        help="Ratio of binning level between loaded Phi file and labelled image. If the input Phi file has been obtained on a 500x500x500 image and the labelled image is 1000x1000x1000, this should be 2. Default = 1")
+
 
     parser.add_argument('-np',
                         '--number-parallel-process',
@@ -1497,7 +1491,7 @@ def ITKwatershedParser(parser):
     parser.add_argument('inFile',
                         metavar='inFile',
                         type=argparse.FileType('r'),
-                        help='Path to binary TIFF file to be watershedded')
+                        help='Path to binary TIFPhi file to be watershedded')
 
     parser.add_argument('-ld',
                         '--label-dilate',
@@ -1511,7 +1505,7 @@ def ITKwatershedParser(parser):
                         type=str,
                         default=None,
                         dest='MARKER_FILE',
-                        help='Path to labelled TIFF file to use as markers')
+                        help='Path to labelled TIFPhi file to use as markers')
 
     parser.add_argument('-pre',
                         '--prefix',
@@ -1708,7 +1702,7 @@ def deformImageFromFieldParser(parser):
     parser.add_argument('inFile',
                         metavar='inFile',
                         type=argparse.FileType('r'),
-                        help='Path to TIFF file containing the image to deform')
+                        help='Path to TIFPhi file containing the image to deform')
 
     parser.add_argument('-a',
                         '-triangulation-alpha-value',
@@ -1736,7 +1730,7 @@ def deformImageFromFieldParser(parser):
                         type=int,
                         default=1,
                         dest='PHIFILE_BIN_RATIO',
-                        help="Ratio of binning level between loaded F file and current calculation. If the input F file has been obtained on a 500x500x500 image and now the calculation is on 1000x1000x1000, this should be 2. Default = 1")
+                        help="Ratio of binning level between loaded Phi file and current calculation. If the input Phi file has been obtained on a 500x500x500 image and now the calculation is on 1000x1000x1000, this should be 2. Default = 1")
 
     parser.add_argument('-od',
                         '--out-dir',