[skip-ci] spam-pixelSearch with initial guess

scripts/spam-pixelSearch

@@ -56,7 +56,7 @@ halfWindowSize  = numpy.array(args.HWS)
 
 greyThreshold   = [args.GREY_LOW_THRESH, args.GREY_HIGH_THRESH]
 
-# Fill in search range as a dictionary
+# Fill in search range
 searchRange = numpy.array([args.SEARCH_RANGE[0], args.SEARCH_RANGE[1], args.SEARCH_RANGE[2], args.SEARCH_RANGE[3], args.SEARCH_RANGE[4], args.SEARCH_RANGE[5]])
 
 # Load reference image
@@ -130,14 +130,14 @@ if args.PHIFILE is not None:
         #   1. by copying the registration's little F to the Fs of all points
         #   2. by calling the decomposePhi function to compute the translation of each point
         for node in range(nodePositions.shape[0]):
-            PhiField[node] = regPhi.copy()
-            PhiField[node][0:3, -1] = spam.deformation.decomposePhi(regPhi.copy(), PhiCentre=regCentre, PhiPoint=nodePositions[node])["t"]
+            PhiField[node] = PhiInit.copy()
+            PhiField[node][0:3, -1] = spam.deformation.decomposePhi(PhiInit.copy(), PhiCentre=PhiFromFile["fieldCoords"][0], PhiPoint=nodePositions[node])["t"]
 
         ## Now recompute F to be only rigid, and calculate rigid-body translations for each point
         #if args.REGSUB:
-            #regPhiRigid = spam.deformation.computeRigidPhi(regPhi.copy())
+            #PhiInitRigid = spam.deformation.computeRigidPhi(PhiInit.copy())
             #for node in range(nodePositions.shape[0]):
-                #rigidDisp[node] = spam.deformation.decomposePhi(regPhiRigid.copy(),
+                #rigidDisp[node] = spam.deformation.decomposePhi(PhiInitRigid.copy(),
                                                                 #PhiCentre=regCentre,
                                                                 #PhiPoint=nodePositions[node])["t"]
 
@@ -239,6 +239,7 @@ Returns
             For each node, the NCC score obtained
 """
 
+# WARNING ------------------------- VVVVVVVVVVV--- gets easily overwritten, pass a .copy()!
 def getImagettes(nodePosition, Phi, searchRange, boundingBox, im1, im2, im1mask, minMaskCoverage, greyThreshold):
     returnStatus = 2
 
@@ -379,7 +380,7 @@ while finishedNodes != numberOfNodes:
         # Get the next node off the queue
         nodeNumber = q.get()
 
-        imagetteReturns = getImagettes(nodePositions[nodeNumber], PhiField[nodeNumber], searchRange, boundingBoxes[nodeNumber], im1, im2, im1mask, args.MASK_COVERAGE, greyThreshold)
+        imagetteReturns = getImagettes(nodePositions[nodeNumber], PhiField[nodeNumber], searchRange.copy(), boundingBoxes[nodeNumber], im1, im2, im1mask, args.MASK_COVERAGE, greyThreshold)
 
         if imagetteReturns['returnStatus'] == 2:
             if mpi: