fix 2D images for spam-ldic (flatten +1 in z in grid.py). Auto margin now base...

fix 2D images for spam-ldic (flatten +1 in z in grid.py). Auto margin now base on min dimension and not max

tools/DIC/correlate.py

@@ -46,7 +46,7 @@ def register(im1, im2, im1mask=None, PhiInit=None, PhiRigid=False, PhiInitBinRat
     "Discrete correlation" can be performed by masking im1.
 
     im1 and im2 do not necessarily have to be the same size (`i.e.`, im2 can be bigger) -- this is good since there
-    is a zone to accommodate movement. In the case of a bigger im2, im1 and im2 are centred with respect to each other.
+    is a zone to accommodate movement. In the case of a bigger im2, im1 and im2 are assumed to be centred with respect to each other.
 
     Parameters
     ----------
@@ -139,9 +139,6 @@ def register(im1, im2, im1mask=None, PhiInit=None, PhiRigid=False, PhiInitBinRat
     ----
         This correlation was written in the style of S. Roux (especially "An extension of Digital Image Correlation for intermodality image registration")
         especially equations 12 and 13.
-
-        Since we're using classical DIC (without multimodal registration) there is no need to update the gradient image,
-        so this is calculated once at the beginning.
     """
     # Explicitly set input images to floats
     im1 = im1.astype('<f4')
@@ -183,8 +180,11 @@ def register(im1, im2, im1mask=None, PhiInit=None, PhiRigid=False, PhiInitBinRat
     # Automatically calculate margin if none is passed
     # Detect default case and calculate maring necessary for a 45deg rotation with no displacement
     if margin is None:
-        # sqrt
-        margin = [1+int(0.1 * max(im1.shape))] * 3
+        if twoD:
+            # z-margin will be overwritten below
+            margin = [1+int(0.1 * min(im1.shape[1:]))] * 3
+        else:
+            margin = [1+int(0.1 * min(im1.shape))] * 3
     elif type(margin) == list:
         pass
     else:

tools/DIC/grid.py

@@ -443,7 +443,11 @@ def registerOnGrid(im1, im2, nodePositions, halfWindowSize, PhiField=None, margi
 
     numberOfNodes = nodePositions.shape[0]
 
-    def getImagettes(nodeNumber, im1, im2, PhiField, nodePositions, margin, halfWindowSize, greyThreshold, im1mask, minMaskVolume):
+    def getImagettes(nodeNumber, im1, im2, PhiField, nodePositions, margin, halfWindowSize, greyThreshold, im1mask, minMaskVolume, twoD=False):
+        # We don't have many single letter variable names, but this is one to keep things aligned
+        # This variable is =0 in 2D and =1 in 3D
+        if twoD: m = 0
+        else:    m = 1
         # Initialise defaults
         imagette1mask = None
         PhiInit = None
@@ -459,7 +463,7 @@ def registerOnGrid(im1, im2, nodePositions, halfWindowSize, PhiField=None, margi
                             #slice(int(nodePositions[nodeNumber, 1] - halfWindowSize[1] - 1), int(nodePositions[nodeNumber, 1] + halfWindowSize[1] + 1 + 1)),
                             #slice(int(nodePositions[nodeNumber, 2] - halfWindowSize[2] - 1), int(nodePositions[nodeNumber, 2] + halfWindowSize[2] + 1 + 1)))
             #imagette1 = im1[subVolSlice1].copy()
-            startStopIm1 = [int(nodePositions[nodeNumber, 0] - halfWindowSize[0] - 1), int(nodePositions[nodeNumber, 0] + halfWindowSize[0] + 1 + 1),
+            startStopIm1 = [int(nodePositions[nodeNumber, 0] - halfWindowSize[0] - m), int(nodePositions[nodeNumber, 0] + halfWindowSize[0] + 1 + m),
                             int(nodePositions[nodeNumber, 1] - halfWindowSize[1] - 1), int(nodePositions[nodeNumber, 1] + halfWindowSize[1] + 1 + 1),
                             int(nodePositions[nodeNumber, 2] - halfWindowSize[2] - 1), int(nodePositions[nodeNumber, 2] + halfWindowSize[2] + 1 + 1)]
             imagette1, imagette1mask = spam.helpers.slicePadded(im1, startStopIm1, createMask=True)
@@ -487,7 +491,7 @@ def registerOnGrid(im1, im2, nodePositions, halfWindowSize, PhiField=None, margi
                                     #slice(int(nodePositions[nodeNumber, 2] - halfWindowSize[2] + nodeDisplacement[2] - margin[2] - 1), int(nodePositions[nodeNumber, 2] + halfWindowSize[2] + nodeDisplacement[2] + margin[2] + 1 + 1)))
                     ## Extract it
                     #imagette2 = im2[subVolSlice2].copy()
-                    startStopIm2 = [int(nodePositions[nodeNumber, 0] - halfWindowSize[0] + nodeDisplacement[0] - margin[0] - 1), int(nodePositions[nodeNumber, 0] + halfWindowSize[0] + nodeDisplacement[0] + margin[0] + 1 + 1),
+                    startStopIm2 = [int(nodePositions[nodeNumber, 0] - halfWindowSize[0] + nodeDisplacement[0] - margin[0] - m), int(nodePositions[nodeNumber, 0] + halfWindowSize[0] + nodeDisplacement[0] + margin[0] + m + 1),
                                     int(nodePositions[nodeNumber, 1] - halfWindowSize[1] + nodeDisplacement[1] - margin[1] - 1), int(nodePositions[nodeNumber, 1] + halfWindowSize[1] + nodeDisplacement[1] + margin[1] + 1 + 1),
                                     int(nodePositions[nodeNumber, 2] - halfWindowSize[2] + nodeDisplacement[2] - margin[2] - 1), int(nodePositions[nodeNumber, 2] + halfWindowSize[2] + nodeDisplacement[2] + margin[2] + 1 + 1)]
                     imagette2 = spam.helpers.slicePadded(im2, startStopIm2, padValue=numpy.nan)
@@ -589,7 +593,7 @@ def registerOnGrid(im1, im2, nodePositions, halfWindowSize, PhiField=None, margi
             # Get the next node off the queue
             nodeNumber = q.get()
 
-            imagetteReturns = getImagettes(nodeNumber, im1, im2, PhiField, nodePositions, margin, halfWindowSize, greyThreshold, im1mask, minMaskVolume)
+            imagetteReturns = getImagettes(nodeNumber, im1, im2, PhiField, nodePositions, margin, halfWindowSize, greyThreshold, im1mask, minMaskVolume, twoD)
 
             if imagetteReturns['returnStatus'] == 2:
                 if mpi: