function [Ja, newcfg] = mmcjmua(cfg, detp, seeds, detnum)
%
% Ja=mmcjmua(cfg,detp,seeds,detnum) (element based)
%
% Generate a time-domain Jacobian (sensitivity matrix) for absorption (mua) perturbation of a specified detector
% with configurations, detected photon seeds and detector readings from an initial MC simulation
%
% author: Ruoyang Yao (yaor <at> rpi.edu)
%         Qianqian Fang (q.fang <at> neu.edu)
%
% input:
%     cfg: the simulation configuration structure used for the initial MC simulation by mmclab
%     detp: detector readings from the initial MC simulation, must be a
%           structure (supported after MMC v2016.4)
%     seeds: detected photon seeds from the initial MC simulation
%     detnum: the detector number whose detected photons will be replayed
%
% output:
%     Ja: a Jacobian for absorption perturbation of the specified detector
%         number of rows is the number of the mesh nodes or elements
%         number of columns is the number of time gates
%
% example:
%     [cube,detp,ncfg,seeds]=mmclab(cfg);   % initial MC simulation
%     Jmua = mmcjmua(ncfg,detp,seeds,1);    % generate absorption Jacobian of the first detector
%
% this file is part of Mesh-based Monte Carlo (MMC)
%
% License: GPLv3, see http://mcx.sf.net/mmc/ for details
%

% preprocessing of the mesh to get possible missing fields
newcfg = mmclab(cfg, 'prep');
% newcfg.basisorder=0;

% specify the detector number to replay
newcfg.replaydet = detnum;

% select the photon seeds and data of the specified detector
newcfg.seed = seeds.data(:, detp.detid == newcfg.replaydet);
detp.data = detp.data(:, detp.detid == newcfg.replaydet);

% calculate the detected photon weight and arrival time
newcfg.replayweight = mmcdetweight(detp.data, newcfg.prop);
newcfg.replaytime = mmcdettime(detp.data, newcfg.prop);

% specify output type
newcfg.isnormalized = 1; % should we leave this for users to decide?
newcfg.outputtype = 'wl';

% now replay detected photons
[jacob, detp1, newcfg] = mmclab(newcfg);

% validate if the replay is successful
if (all(ismember(round(detp1.data' * 1e10) * 1e-10, round(detp.data' * 1e10) * 1e-10, 'rows')))
    % disp('replay is successful :-)');
    Ja = -jacob.data;
else
    error('replay failed :-(');
end
