[skip-ci] sketchy progress on pixelSearch

scripts/spam-ddic

@@ -392,8 +392,6 @@ if mpiRank == boss or not mpi:
 
                         imagette2 = spam.helpers.slicePadded(im2, startStopIm2)
 
-                        # Catch 
-
                         # point in im2 that we are searching around
                         searchCentre = (numpy.array(imagette2.shape, dtype='<f4') - 1) / 2.0 + labelDisplacementInt - middleOfSearchRange
                         #searchCentre = (numpy.array(imagette2.shape, dtype='<f4') - 1) / 2.0

scripts/spam-pixelSearch

@@ -372,8 +372,12 @@ returnStatus  = numpy.ones((numberOfNodes), dtype=int)
 
 # Add nodes to a queue -- mostly useful for MPI
 q = queue.Queue()
-#for node in range(3):
-for node in range(numberOfNodes):
+
+
+if args.LAB1 is not None: firstNode = 1
+else:                     firstNode = 0
+
+for node in range(firstNode, numberOfNodes):
     q.put(node)
 finishedNodes = 0
 
@@ -391,7 +395,36 @@ while finishedNodes != numberOfNodes:
         # Get the next node off the queue
         nodeNumber = q.get()
 
-        imagetteReturns = getImagettes(nodePositions[nodeNumber], PhiField[nodeNumber].copy(), searchRange.copy(), boundingBoxes[nodeNumber], im1, im2, im1mask, args.MASK_COVERAGE, greyThreshold)
+        if args.LAB1 is not None:
+            imagetteReturns = {}
+            gottenLabel = spam.label.getLabel(lab1, nodeNumber, boundingBoxes=boundingBoxes, centresOfMass=nodePositions, maskOtherLabels=True, labelDilate=args.LABEL_DILATE, margin=1+args.LABEL_DILATE)
+            if gottenLabel is not None:
+                imagetteReturns['imagette1']     = im1[gottenLabel['slice']]
+                imagetteReturns['imagette1mask'] = gottenLabel['subvol']
+
+                # 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) + searchRange[0]    ),
+                                int(gottenLabel['boundingBox'][1] + max(args.LABEL_DILATE, 0) + searchRange[1] + 1),
+                                int(gottenLabel['boundingBox'][2] - max(args.LABEL_DILATE, 0) + searchRange[2]    ),
+                                int(gottenLabel['boundingBox'][3] + max(args.LABEL_DILATE, 0) + searchRange[3] + 1),
+                                int(gottenLabel['boundingBox'][4] - max(args.LABEL_DILATE, 0) + searchRange[4]    ),
+                                int(gottenLabel['boundingBox'][5] + max(args.LABEL_DILATE, 0) + searchRange[5] + 1)]
+                
+                imagetteReturns['imagette2']           = spam.helpers.slicePadded(im2, startStopIm2)
+                imagetteReturns['searchRange']         = searchRange.copy()
+                imagetteReturns['searchCentre']        = nodePositions[nodeNumber] - boundingBoxes[nodeNumber, 0::2] - searchRange[0::2] - numpy.array([max(args.LABEL_DILATE, 0)]*3)
+                imagetteReturns['initialDisplacement'] = PhiField[nodeNumber, 0:3, 3].astype(int)
+                imagetteReturns['returnStatus']        = 1
+                print(imagetteReturns['imagette1'].shape)
+                print(imagetteReturns['imagette1mask'].shape)
+                print(imagetteReturns['imagette2'].shape)
+                print(gottenLabel['boundingBox'])
+                print(startStopIm2)
+            else:
+                imagetteReturns['returnStatus']        = 0
+                
+        else:
+            imagetteReturns = getImagettes(nodePositions[nodeNumber], PhiField[nodeNumber].copy(), searchRange.copy(), boundingBoxes[nodeNumber], im1, im2, im1mask, args.MASK_COVERAGE, greyThreshold)
 
         if imagetteReturns['returnStatus'] == 1:
             if mpi:
@@ -420,6 +453,7 @@ while finishedNodes != numberOfNodes:
                                                          searchRange   = imagetteReturns['searchRange'],
                                                          searchCentre  = imagetteReturns['searchCentre'])
                 initialDisplacement = imagetteReturns['initialDisplacement']
+                print(returns)
                 writeReturns = True
 
         else:  # Regardless of MPI or single proc

tools/DIC/correlate.py

@@ -830,6 +830,8 @@ def pixelSearch(imagette1, imagette2, imagette1mask=None, searchCentre=None, sea
     topDiff =                                searchCentre.astype(int) - imagette1halfWindowSize + searchRange[0::2]
     botDiff = numpy.array(imagette2.shape) - searchCentre.astype(int) - imagette1halfWindowSize - searchRange[1::2]
 
+    print("searchRange in:", searchRange)
+
     # Check that the search range doesn't go outside imagette2, if it does, redact it
     if topDiff[0] < 0: searchRange[0] -= topDiff[0]
     if topDiff[1] < 0: searchRange[2] -= topDiff[1]
@@ -838,6 +840,8 @@ def pixelSearch(imagette1, imagette2, imagette1mask=None, searchCentre=None, sea
     if botDiff[1] < 0: searchRange[3] += botDiff[1]
     if botDiff[2] < 0: searchRange[5] += botDiff[2]
 
+    print("searchRange out:", searchRange)
+
     # Run the actual pixel search
     # print imagette1.shape, imagette2.shape, searchCentre, searchRange
     returns = numpy.zeros(4, dtype='<f4')

tools/DIC/src/pixelSearchGC.cpp

@@ -109,13 +109,13 @@ void pixelSearch(py::array_t<float> im1Numpy,
 
 //                 printf("zTop %i yTop %i xTop %i\n", zTop, yTop, xTop);
 // //                 printf("zDisp %i yDisp %i xDisp %i\n", zDisp, yDisp, xDisp);
-//                 std::cout << "Tops: "<< zTop << " " << yTop << " " << xTop << "\n" << std::endl;
-//                 std::cout << "Bots: "<< zBot << " " << yBot << " " << xBot << "\n" << std::endl;
+                std::cout << "Tops: "<< zTop << " " << yTop << " " << xTop << "\n" << std::endl;
+                std::cout << "Bots: "<< zBot << " " << yBot << " " << xBot << "\n" << std::endl;
                 /* Check we're not outside the boundaries... */
                 if ( zTop >=   0       && yTop >=   0       && xTop >=   0 &&
                      zBot <= (int)im2z && yBot <= (int)im2y && xBot <= (int)im2x )
                 {
-
+                    std::cout << "yo" << std::endl;
                     /* reset calculations */
                     /* three components to our NCC calculation (see documentation/C-remi.odt) */
                     float a,b,c;

tools/helpers/optionsParser.py

@@ -2095,6 +2095,13 @@ def pixelSearch(parser):
                         type=argparse.FileType('r'),
                         help="Path to tiff file containing a labelled image 1 that defines zones to correlate. Disactivates -hws and -ns options")
 
+    parser.add_argument('-ld',
+                        '--label-dilate',
+                        type=int,
+                        default=1,
+                        dest='LABEL_DILATE',
+                        help="Only if -lab1 is defined: Number of times to dilate labels. Default = 1")
+
     parser.add_argument('-mf1',
                         '--maskFile1',
                         dest='MASK1',