From 1f63ceae4c6facc9a6cccce2fb5eb0f8790f1b2c Mon Sep 17 00:00:00 2001
From: Julien Besle <julienbesle@gmail.com>
Date: Tue, 1 Oct 2019 17:42:13 +0300
Subject: [PATCH] added makeROIsExactlyContiguous.m to transformROI functions

---
 .../makeROIsExactlyContiguous.m               | 59 +++++++++++++++++++
 1 file changed, 59 insertions(+)
 create mode 100644 mrLoadRet/Plugin/GLM_v2/transformROIFunctions/makeROIsExactlyContiguous.m

diff --git a/mrLoadRet/Plugin/GLM_v2/transformROIFunctions/makeROIsExactlyContiguous.m b/mrLoadRet/Plugin/GLM_v2/transformROIFunctions/makeROIsExactlyContiguous.m
new file mode 100644
index 000000000..a455bdd8c
--- /dev/null
+++ b/mrLoadRet/Plugin/GLM_v2/transformROIFunctions/makeROIsExactlyContiguous.m
@@ -0,0 +1,59 @@
+% makeROIsExactlyContiguous.m
+%
+%      usage: transformedRois = makeROIsExactlyContiguous(rois,margin,<kernelType>)
+%         by: julien besle
+%       date: 11/01/2011
+%
+%    purpose: attribute voxels shared by two ROIs to the closest of these two ROIs, with 
+%             the two resulting two ROIs then becoming exactly contiguous.
+%             This function will run with more than two ROIs and will apply to all pairs of ROIs
+%             This assumes that no voxel is shared by more than two ROIs. If this is the case,  
+%             then results will depend on the order in which the ROIs are passed
+
+function rois = makeROIsExactlyContiguous(rois)
+
+if ~ismember(nargin,[1])
+  help expandROI;
+  return
+end
+
+if numel(rois) < 2
+  mrWarnDlg('(makeROIsExactlyContiguous) You need to provide at least 2 ROIs ');
+  return
+end
+
+% Check that transformation matrices are identical for all ROIs
+for iRoi = 2:length(rois)
+  if any(any( (rois(1).xform - rois(iRoi).xform) > 10e-6))
+    mrWarnDlg('(makeROIsExactlyContiguous) All ROIs must be converted to the same space (set the roiSpace option to something other than ''Native'').');
+    return
+  end
+end
+
+
+for iRoi = 1:length(rois)
+  for jRoi = iRoi+1:length(rois)
+    coords1 = rois(iRoi).coords';
+    coords2 = rois(jRoi).coords';
+    [commonCoordinates, indexROI1, indexROI2] = intersect(coords1,coords2,'rows');
+    %remove common coordinates from ROIs 1 and 2
+    coords1 = setdiff(coords1,commonCoordinates,'rows');
+    coords2 = setdiff(coords2,commonCoordinates,'rows');
+    %attribute common coordinates to one or the other ROI depending on distance
+    belongsToROI1 = false(size(commonCoordinates,1),1);
+    for iCoords = 1:size(commonCoordinates,1)
+      %compute distance between these coordinates and all coordinates unique to either both ROI
+      distanceCoords1 = sqrt(sum((repmat(commonCoordinates(iCoords,1:3),size(coords1,1),1) - coords1(:,1:3)).^2,2));
+      distanceCoords2 = sqrt(sum((repmat(commonCoordinates(iCoords,1:3),size(coords2,1),1) - coords2(:,1:3)).^2,2));
+      %identify closest ROI
+      if min(distanceCoords1) < min(distanceCoords2)
+        belongsToROI1(iCoords) = true;
+      end
+    end
+    % delete coords that belong to the other ROI
+    rois(iRoi).coords(:,indexROI1(~belongsToROI1'))=[];
+    rois(jRoi).coords(:,indexROI2(belongsToROI1'))=[];
+  end
+end
+
+