[skip-ci] grid pixel search fully tested, starting on label mode, some trouble...

[skip-ci] grid pixel search fully tested, starting on label mode, some trouble re-reading previous result even without registration and zero search range...

scripts/spam-pixelSearch

@@ -82,6 +82,7 @@ if args.LAB1 is not None:
     nodePositions = spam.label.centresOfMass(lab1, boundingBoxes=boundingBoxes)
     numberOfNodes = nodePositions.shape[0]
     im1mask = None
+    im2mask = None
 
 ### Otherwise we are in node spacing and half-window size mode
 else:
@@ -101,6 +102,13 @@ else:
     else:
         im1mask = None
 
+    if args.MASK2:
+        im2mask = tifffile.imread(args.MASK2.name) != 0
+        if len(im2mask.shape) == 2:
+            im2mask = im2mask[numpy.newaxis, ...]
+    else:
+        im2mask = None
+
 ###############################################################
 
 # Now that we know how many points we want to correlate, initalise PhiField
@@ -144,6 +152,7 @@ if args.PHIFILE is not None:
     else:
         # Read the coordinates and values of the input F field
         fieldCoords = PhiFromFile["fieldCoords"]
+        fieldValues = PhiFromFile["PhiField"]
 
         # Create the k-d tree of the coordinates of the input F field
         from scipy.spatial import KDTree
@@ -220,6 +229,7 @@ def pixelSearchOneNode(nodeNumber):
 
             imagetteReturns['imagette1']     = imagette1def
             imagetteReturns['imagette1mask'] = gottenLabel['subvol']
+            imagetteReturns['imagette2mask'] = None
 
             # 2020-09-25 OS and EA: Prepare startStop array for imagette 2 to be extracted with new slicePadded
             startStopIm2 = [int(gottenLabel['boundingBox'][0] - max(args.LABEL_DILATE, 0) + initialDisplacement[0] + searchRange[0]    ),
@@ -237,13 +247,14 @@ def pixelSearchOneNode(nodeNumber):
             imagetteReturns['returnStatus']        = 0
 
     else:
-        imagetteReturns = spam.DIC.getImagettes(nodePositions[nodeNumber], PhiField[nodeNumber].copy(), searchRange.copy(), boundingBoxes[nodeNumber], im1, im2, im1mask, args.MASK_COVERAGE, greyThreshold, twoD)
+        imagetteReturns = spam.DIC.getImagettes(nodePositions[nodeNumber], PhiField[nodeNumber].copy(), searchRange.copy(), boundingBoxes[nodeNumber], im1, im2, im1mask, im2mask, args.MASK_COVERAGE, greyThreshold, twoD)
 
     # If getImagettes was successful (size check and mask coverage check)
     if imagetteReturns['returnStatus'] == 1:
         PSreturns = spam.DIC.correlate.pixelSearch(imagetteReturns['imagette1'],
                                                    imagetteReturns['imagette2'],
                                                    imagette1mask = imagetteReturns['imagette1mask'],
+                                                   imagette2mask = imagetteReturns['imagette2mask'],
                                                    returnError = True)
         pixelSearchOffset = imagetteReturns['pixelSearchOffset']
         writeReturns = True
@@ -266,7 +277,7 @@ returnStatus  = numpy.ones((numberOfNodes), dtype=int)
 deltaPhiNorm  = numpy.ones((numberOfNodes), dtype=int)
 iterations    = numpy.ones((numberOfNodes), dtype=int)
 
-if args.LAB1 is not None: firstNode = 1; finishedNodes = 1
+if args.LAB1 is not None: firstNode = 1; finishedNodes = 1; returnStatus[0] = 0
 else:                     firstNode = 0; finishedNodes = 0
 
 

tools/DIC/grid.py

@@ -144,12 +144,11 @@ Returns
 """
 
 # WARNING ------------------------- VVVVVVVVVVV--- gets easily overwritten, pass a .copy()!
-def getImagettes(nodePosition, Phi, searchRange, boundingBox, im1, im2, im1mask, minMaskCoverage, greyThreshold, twoD=False):
+def getImagettes(nodePosition, Phi, searchRange, boundingBox, im1, im2, im1mask, im2mask, minMaskCoverage, greyThreshold, twoD=False):
     returnStatus = 1
     imagette1mask = None
+    imagette2mask = None
     initialDisplacement = numpy.round(Phi[0:3, 3]).astype(int)
-    if twoD: m = 0
-    else: m = 0
 
     # Catch bad bounding boxes:
     if numpy.all((boundingBox[1::2] - boundingBox[0::2]) > 0) or ( numpy.all(boundingBox[3::2] - boundingBox[2::2] > 0) and twoD):
@@ -221,6 +220,8 @@ def getImagettes(nodePosition, Phi, searchRange, boundingBox, im1, im2, im1mask,
                                     int(boundingBox[5] + initialDisplacement[2] + searchRange[5] + 1)]
                     imagette2 = spam.helpers.slicePadded(im2, startStopIm2)
 
+                    if im2mask is not None: imagette2mask = spam.helpers.slicePadded(im2mask, startStopIm2)
+                        
                 # Failed minMaskVolume condition
                 else:
                     returnStatus = -5
@@ -248,6 +249,7 @@ def getImagettes(nodePosition, Phi, searchRange, boundingBox, im1, im2, im1mask,
     return {'imagette1':            imagette1def,
             'imagette1mask':        imagette1mask,
             'imagette2':            imagette2,
+            'imagette2mask':        imagette2mask,
             'returnStatus':         returnStatus,
             'pixelSearchOffset':    searchRange[0::2]
             }

tools/helpers/optionsParser.py

@@ -1888,6 +1888,8 @@ def register(parser):
     # Output file name prefix
     if args.PREFIX is None:
         args.PREFIX = os.path.splitext(os.path.basename(args.im1.name))[0] + "-" + os.path.splitext(os.path.basename(args.im2.name))[0] + "-registration"
+    else:
+        args.PREFIX += "-registration"
 
 
     return args
@@ -1932,6 +1934,13 @@ def pixelSearch(parser):
                         type=argparse.FileType('r'),
                         help="Path to tiff file containing the mask of image 1 -- masks zones not to correlate, which should be == 0")
 
+    parser.add_argument('-mf2',
+                        '--maskFile2',
+                        dest='MASK2',
+                        default=None,
+                        type=argparse.FileType('r'),
+                        help="Path to tiff file containing the mask of image 2 -- masks zones not to correlate, which should be == 0")
+
     parser.add_argument('-mc',
                         '--mask-coverage',
                         type=float,
@@ -2137,6 +2146,7 @@ def pixelSearch(parser):
     # Output file name prefix
     if args.PREFIX is None:
         args.PREFIX = os.path.splitext(os.path.basename(args.im1.name))[0] + "-" + os.path.splitext(os.path.basename(args.im2.name))[0] + "-pixelSearch"
-
+    else:
+        args.PREFIX += "-pixelSearch"
 
     return args