From 1e1a39bf27d5b1743e511ff7aa71cac3b3fbb014 Mon Sep 17 00:00:00 2001
From: Eric Wait <eric@waitphoto.com>
Date: Wed, 16 May 2018 15:37:09 -0400
Subject: [PATCH] Trying to make polygons centered on the objects
---
src/matlab/+D3d/+Polygon/Make.m | 16 +++++++++-------
1 file changed, 9 insertions(+), 7 deletions(-)
diff --git a/src/matlab/+D3d/+Polygon/Make.m b/src/matlab/+D3d/+Polygon/Make.m
index ab48fe6..fc8dfd9 100644
--- a/src/matlab/+D3d/+Polygon/Make.m
+++ b/src/matlab/+D3d/+Polygon/Make.m
@@ -30,9 +30,10 @@ if (size(pixelList_xy,2)==3)
else
% this is done because the view must be a 3D kymograph
frames = vertcat(...
- repmat(frame-0.5,size(pixelList_xy,1),1),...
- repmat(frame+0.5,size(pixelList_xy,1),1));
- pixelList_xy = repmat(pixelList_xy,2,1);
+ repmat(max(0,frame-1),size(pixelList_xy,1),1),...
+ repmat(frame,size(pixelList_xy,1),1),...
+ repmat(frame+1,size(pixelList_xy,1),1));
+ pixelList_xy = repmat(pixelList_xy,3,1);
pixelList_xy = horzcat(pixelList_xy,frames);
frame = 1;
is3D = false;
@@ -45,8 +46,8 @@ polygon = D3d.Polygon.MakeEmptyStruct();
% padd the subimage to get some room to blur
PADDING = ceil(5*1./reductions);
-startCoords_rcz = Utils.SwapXY_RC(min(pixelList_xy,[],1));
-endCoords_rcz = Utils.SwapXY_RC(max(pixelList_xy,[],1));
+startCoords_rcz = Utils.SwapXY_RC(min(round(pixelList_xy),[],1));
+endCoords_rcz = Utils.SwapXY_RC(max(round(pixelList_xy),[],1));
startPadded = startCoords_rcz-PADDING;
endPadded = endCoords_rcz+PADDING;
@@ -63,14 +64,15 @@ cc.NumObjects = 1;
cc.PixelIdxList = {indList};
rp = regionprops(cc,'Centroid');
-imR = ImProc.Resize(im2uint8(roiIm),reductions,[],'mean');
+%imR = ImProc.Resize(im2uint8(roiIm),reductions,[],'mean');
+imR = roiIm;
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,1);
+[faces, v_xy] = isosurface(x,y,z,imR,0.75);
if (isempty(v_xy))
return
--
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