distDotsToCellBody.m

%% ObjectFinder - Recognize 3D structures in image stacks
%  Copyright (C) 2016,2017,2018 Luca Della Santina
%
%  This file is part of ObjectFinder
%
%  ObjectFinder is free software: you can redistribute it and/or modify
%  it under the terms of the GNU General Public License as published by
%  the Free Software Foundation, either version 3 of the License, or
%  (at your option) any later version.
%
%  This program is distributed in the hope that it will be useful,
%  but WITHOUT ANY WARRANTY; without even the implied warranty of
%  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
%  GNU General Public License for more details.
%
%  You should have received a copy of the GNU General Public License
%  along with this program.  If not, see <https://www.gnu.org/licenses/>.
%
function[Dots] = distDotsToCellBody(Dots, Skel, Settings)
%% This program calculate the position of the center of cell body as mean of
% all voxels assigned as a cell body region in Amira (assigned as 2).
% Then, calculate distance from this cell body center to individual dots.

% New version will assume the center of cell body as a starting point of
% marching during Imaris filament skeletonization whose location is stored
% in Skel.FilStats.SomaPtXYZ. HO 1/10/2010

%Find cell body
xyum                = Settings.ImInfo.xyum; %changed to reflect structure format of ImInfo HO 1/5/2010
zum                 = Settings.ImInfo.zum; %changed to reflect structure format of ImInfo HO 1/5/2010
CBpos               = [ceil(Skel.FilStats.SomaPtXYZ(2)/xyum) ceil(Skel.FilStats.SomaPtXYZ(1)/xyum) ceil(Skel.FilStats.SomaPtXYZ(3)/zum)];
Dots.Settings.ImInfo.CBpos = CBpos;

CBpos               = Dots.Settings.ImInfo.CBpos; %open and scale
CBpos(1:2)          = CBpos(1:2)*xyum; CBpos(3)=CBpos(3)*zum;
Dpos                = Dots.Pos; Dpos(:,1:2)=Dpos(:,1:2)*xyum; Dpos(:,3)=Dpos(:,3)*zum;

Dots.Skel.Dist2CB   = dist(Dpos,CBpos);
end