From f79b1e187041642d9e06ffbc12fa3a27b1412983 Mon Sep 17 00:00:00 2001
From: Eric Wait <eric@waitphoto.com>
Date: Thu, 30 Mar 2017 16:26:18 -0400
Subject: [PATCH] Attempting to fix the hull vert offset when making polygons
---
src/matlab/+D3d/+Polygon/Make.m | 34 ++++++++++++++++++++-------------
1 file changed, 21 insertions(+), 13 deletions(-)
diff --git a/src/matlab/+D3d/+Polygon/Make.m b/src/matlab/+D3d/+Polygon/Make.m
index 31efcdf..0f8825d 100644
--- a/src/matlab/+D3d/+Polygon/Make.m
+++ b/src/matlab/+D3d/+Polygon/Make.m
@@ -25,31 +25,39 @@ if (~exist('quiet','var') || isempty(quiet))
quiet = false;
end
+reductions = [1,1,1];
+
polygon = D3d.Polygon.MakeEmptyStruct();
% padd the subimage to get some room to blur
PADDING = ceil(5*1./reductions);
-maxExtent_rc = Utils.SwapXY_RC(max(pixelList_xy,[],1)) + PADDING;
-indList = Utils.CoordToInd(maxExtent_rc,Utils.SwapXY_RC(pixelList_xy));
-[im,startCoords_rcz] = ImUtils.ROI.MakeSubImBW(maxExtent_rc,indList,PADDING);
-startCoords_xy = Utils.SwapXY_RC(startCoords_rcz);
+startCoords_rcz = Utils.SwapXY_RC(min(pixelList_xy,[],1));
+endCoords_rcz = Utils.SwapXY_RC(max(pixelList_xy,[],1));
+
+startPadded = startCoords_rcz-PADDING;
+endPadded = endCoords_rcz+PADDING;
+
+roiIm = false(endPadded-startPadded+1);
+
+paddedPixelList_rcz = Utils.SwapXY_RC(pixelList_xy)-startPadded+1;
+indList = Utils.CoordToInd(size(roiIm),paddedPixelList_rcz);
+roiIm(indList) = true;
cc.Connectivity = 26;
-cc.ImageSize = size(im);
+cc.ImageSize = size(roiIm);
cc.NumObjects = 1;
-cc.PixelIdxList = {find(im)};
+cc.PixelIdxList = {indList};
rp = regionprops(cc,'Centroid');
-imR = ImProc.Resize(im2uint8(im),reductions,[],'mean');
+imR = ImProc.Resize(im2uint8(roiIm),reductions,[],'mean');
-endCoords_rcz = startCoords_rcz + floor((maxExtent_rc - startCoords_rcz).*reductions)./reductions;
-R = linspace(startCoords_rcz(1),endCoords_rcz(1),size(imR,1));
-C = linspace(startCoords_rcz(2),endCoords_rcz(2),size(imR,2));
-Z = linspace(startCoords_rcz(3),endCoords_rcz(3),size(imR,3));
+R = linspace(startPadded(1),endPadded(1),size(imR,1));
+C = linspace(startPadded(2),endPadded(2),size(imR,2));
+Z = linspace(startPadded(3),endPadded(3),size(imR,3));
[x,y,z] = meshgrid(C,R,Z);
-[faces, v_xy] = isosurface(x,y,z,imR,160);
+[faces, v_xy] = isosurface(x,y,z,imR,1);
if (isempty(v_xy))
return
@@ -58,7 +66,7 @@ end
% center the vert in the middle of the voxel
verts_xy = v_xy + 0.5;
-com = rp.Centroid + startCoords_xy -1;
+com = rp.Centroid + startPadded -1;
if (any(faces(:)==0))
error('there is a zero index in the faces structure!');
--
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