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mcxlabcl.m
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function varargout=mcxlabcl(varargin)
%
%====================================================================
% MCXLAB-CL - Monte Carlo eXtreme (MCX) for MATLAB/GNU Octave
%--------------------------------------------------------------------
% Copyright (c) 2018-2023 Qianqian Fang <q.fang at neu.edu>
% URL: http://mcx.space
%====================================================================
%
% Format:
% fluence=mcxlabcl(cfg);
% or
% [fluence,detphoton,vol,seed,trajectory]=mcxlabcl(cfg);
% [fluence,detphoton,vol,seed,trajectory]=mcxlabcl(cfg, option);
%
% Input:
% cfg: a struct, or struct array. Each element of cfg defines
% the parameters associated with a simulation.
% if cfg='gpuinfo': return the supported GPUs and their parameters,
% if cfg='version': return the version of MCXLABCL as a string,
% see sample script at the bottom
% option: (optional), options is a string, specifying additional options
% option='preview': this plots the domain configuration using mcxpreview(cfg)
% option='opencl': force using mcxcl.mex* instead of mcx.mex* on NVIDIA/AMD/Intel hardware
% option='cuda': force using mcx.mex* instead of mcxcl.mex* on NVIDIA GPUs
%
% if one defines USE_MCXCL=1 in MATLAB command line window, all following
% mcxlab and mcxlabcl calls will use mcxcl.mex; by setting option='cuda', one can
% force both mcxlab and mcxlabcl to use mcx (cuda version). Similarly, if
% USE_MCXCL=0, all mcxlabcl and mcxlab call will use mcx.mex by default, unless
% one set option='opencl'.
%
% cfg may contain the following fields:
%
%== Required ==
% *cfg.nphoton: the total number of photons to be simulated (integer)
% maximum supported value is 2^63-1
% *cfg.vol: a 3D array specifying the media index in the domain.
% can be uint8, uint16, uint32, single or double
% arrays.
% 2D simulations are supported if cfg.vol has a singleton
% dimension (in x or y); srcpos/srcdir must belong to
% the 2D plane in such case.
% for 2D simulations, Example: <demo_mcxlab_2d.m>
%
% MCXLAB also accepts 4D arrays to define continuously varying media.
% The following formats are accepted
% 1 x Nx x Ny x Nz float32 array: mua values for each voxel (must use permute to make 1st dimension singleton)
% 2 x Nx x Ny x Nz float32 array: mua/mus values for each voxel (g/n use prop(2,:))
% 4 x Nx x Ny x Nz uint8 array: mua/mus/g/n gray-scale (0-255) interpolating between prop(2,:) and prop(3,:)
% 2 x Nx x Ny x Nz uint16 array: mua/mus gray-scale (0-65535) interpolating between prop(2,:) and prop(3,:)
% Example: <demo_continuous_mua_mus.m>. If voxel-based media are used, partial-path/momentum outputs are disabled
% *cfg.prop: an N by 4 array, each row specifies [mua, mus, g, n] in order.
% the first row corresponds to medium type 0
% (background) which is typically [0 0 1 1]. The
% second row is type 1, and so on. The background
% medium (type 0) has special meanings: a photon
% terminates when moving from a non-zero to zero voxel.
% *cfg.tstart: starting time of the simulation (in seconds)
% *cfg.tstep: time-gate width of the simulation (in seconds)
% *cfg.tend: ending time of the simulation (in second)
% *cfg.srcpos: a 1 by 3 vector, the position of the source in grid unit
% *cfg.srcdir: a 1 by 3 vector, specifying the incident vector; if srcdir
% contains a 4th element, it specifies the focal length of
% the source (only valid for focuable src, such as planar, disk,
% fourier, gaussian, pattern, slit, etc); if the focal length
% is nan, all photons will be launched isotropically regardless
% of the srcdir direction.
%
%== MC simulation settings ==
% cfg.seed: seed for the random number generator (integer) [0]
% if set to a uint8 array, the binary data in each column is used
% to seed a photon (i.e. the "replay" mode)
% Example: <demo_mcxlab_replay.m>
% cfg.respin: repeat simulation for the given time (integer) [1]
% if negative, divide the total photon number into respin subsets
% cfg.isreflect: [1]-consider refractive index mismatch, 0-matched index
% cfg.bc per-face boundary condition (BC), a strig of 6 letters (case insensitive) for
% bounding box faces at -x,-y,-z,+x,+y,+z axes;
% overwrite cfg.isreflect if given.
% each letter can be one of the following:
% '_': undefined, fallback to cfg.isreflect
% 'r': like cfg.isreflect=1, Fresnel reflection BC
% 'a': like cfg.isreflect=0, total absorption BC
% 'm': mirror or total reflection BC
% 'c': cyclic BC, enter from opposite face
%
% in addition, cfg.bc can contain up to 12 characters,
% with the 7-12 characters indicating bounding box
% facets -x,-y,-z,+x,+y,+z are used as a detector. The
% acceptable characters for digits 7-12 include
% '0': this face is not used to detector photons
% '1': this face is used to capture photons (if output detphoton)
% see <demo_bc_det.m>
% cfg.isnormalized:[1]-normalize the output fluence to unitary source, 0-no reflection
% cfg.isspecular: 1-calculate specular reflection if source is outside, [0] no specular reflection
% cfg.maxgate: the num of time-gates per simulation
% cfg.minenergy: terminate photon when weight less than this level (float) [0.0]
% cfg.unitinmm: defines the length unit for a grid edge length [1.0]
% Example: <demo_sphere_cube_subpixel.m>
% cfg.shapes: a JSON string for additional shapes in the grid
% Example: <demo_mcxyz_skinvessel.m>
% cfg.gscatter: after a photon completes the specified number of
% scattering events, mcx then ignores anisotropy g
% and only performs isotropic scattering for speed [1e9]
% cfg.detphotons: detected photon data for replay. In the replay mode (cfg.seed
% is set as the 4th output of the baseline simulation), cfg.detphotons
% should be set to the 2nd output (detphoton) of the baseline simulation
% or detphoton.data subfield (as a 2D array). cfg.detphotons can use
% a subset of the detected photon selected by the user.
% Example: <demo_mcxlab_replay.m>
%
%== GPU settings ==
% cfg.autopilot: 1-automatically set threads and blocks, [0]-use nthread/nblocksize
% cfg.nblocksize: how many CUDA thread blocks to be used [64]
% cfg.nthread: the total CUDA thread number [2048]
% cfg.gpuid: which GPU to use (run 'mcx -L' to list all GPUs) [1]
% if set to an integer, gpuid specifies the index (starts at 1)
% of the GPU for the simulation; if set to a binary string made
% of 1s and 0s, it enables multiple GPUs. For example, '1101'
% allows to use the 1st, 2nd and 4th GPUs together.
% Example: <mcx_gpu_benchmarks.m>
% cfg.workload an array denoting the relative loads of each selected GPU.
% for example, [50,20,30] allocates 50%, 20% and 30% photons to the
% 3 selected GPUs, respectively; [10,10] evenly divides the load
% between 2 active GPUs. A simple load balancing strategy is to
% use the GPU core counts as the weight.
% cfg.isgpuinfo: 1-print GPU info, [0]-do not print
%
%== Source-detector parameters ==
% cfg.detpos: an N by 4 array, each row specifying a detector: [x,y,z,radius]
% cfg.maxdetphoton: maximum number of photons saved by the detectors [1000000]
% cfg.srctype: source type, the parameters of the src are specified by cfg.srcparam{1,2}
% Example: <demo_mcxlab_srctype.m>
% 'pencil' - default, pencil beam, no param needed
% 'isotropic' - isotropic source, no param needed
% 'cone' - uniform cone beam, srcparam1(1) is the half-angle in radian
% 'gaussian' [*] - a collimated gaussian beam, srcparam1(1) specifies the waist radius (in voxels)
% 'planar' [*] - a 3D quadrilateral uniform planar source, with three corners specified
% by srcpos, srcpos+srcparam1(1:3) and srcpos+srcparam2(1:3)
% 'pattern' [*] - a 3D quadrilateral pattern illumination, same as above, except
% srcparam1(4) and srcparam2(4) specify the pattern array x/y dimensions,
% and srcpattern is a floating-point pattern array, with values between [0-1].
% if cfg.srcnum>1, srcpattern must be a floating-point array with
% a dimension of [srcnum srcparam1(4) srcparam2(4)]
% Example: <demo_photon_sharing.m>
% 'pattern3d' [*] - a 3D illumination pattern. srcparam1{x,y,z} defines the dimensions,
% and srcpattern is a floating-point pattern array, with values between [0-1].
% 'fourier' [*] - spatial frequency domain source, similar to 'planar', except
% the integer parts of srcparam1(4) and srcparam2(4) represent
% the x/y frequencies; the fraction part of srcparam1(4) multiplies
% 2*pi represents the phase shift (phi0); 1.0 minus the fraction part of
% srcparam2(4) is the modulation depth (M). Put in equations:
% S=0.5*[1+M*cos(2*pi*(fx*x+fy*y)+phi0)], (0<=x,y,M<=1)
% 'arcsine' - similar to isotropic, except the zenith angle is uniform
% distribution, rather than a sine distribution.
% 'disk' [*] - a uniform disk source pointing along srcdir; the radius is
% set by srcparam1(1) (in grid unit)
% 'fourierx' [*] - a general Fourier source, the parameters are
% srcparam1: [v1x,v1y,v1z,|v2|], srcparam2: [kx,ky,phi0,M]
% normalized vectors satisfy: srcdir cross v1=v2
% the phase shift is phi0*2*pi
% 'fourierx2d' [*] - a general 2D Fourier basis, parameters
% srcparam1: [v1x,v1y,v1z,|v2|], srcparam2: [kx,ky,phix,phiy]
% the phase shift is phi{x,y}*2*pi
% 'zgaussian' - an angular gaussian beam, srcparam1(1) specifies the variance in the zenith angle
% 'line' - a line source, emitting from the line segment between
% cfg.srcpos and cfg.srcpos+cfg.srcparam(1:3), radiating
% uniformly in the perpendicular direction
% 'slit' [*] - a colimated slit beam emitting from the line segment between
% cfg.srcpos and cfg.srcpos+cfg.srcparam(1:3), with the initial
% dir specified by cfg.srcdir
% 'pencilarray' - a rectangular array of pencil beams. The srcparam1 and srcparam2
% are defined similarly to 'fourier', except that srcparam1(4) and srcparam2(4)
% are both integers, denoting the element counts in the x/y dimensions, respectively.
% For exp., srcparam1=[10 0 0 4] and srcparam2[0 20 0 5] represent a 4x5 pencil beam array
% spanning 10 grids in the x-axis and 20 grids in the y-axis (5-voxel spacing)
% source types marked with [*] can be focused using the
% focal length parameter (4th element of cfg.srcdir)
% cfg.{srcparam1,srcparam2}: 1x4 vectors, see cfg.srctype for details
% cfg.srcpattern: see cfg.srctype for details
% cfg.srcnum: the number of source patterns that are
% simultaneously simulated; only works for 'pattern'
% source, see cfg.srctype='pattern' for details
% Example <demo_photon_sharing.m>
% cfg.issrcfrom0: 1-first voxel is [0 0 0], [0]- first voxel is [1 1 1]
% cfg.replaydet: only works when cfg.outputtype is 'jacobian', 'wl', 'nscat', or 'wp' and cfg.seed is an array
% -1 replay all detectors and save in separate volumes (output has 5 dimensions)
% 0 replay all detectors and sum all Jacobians into one volume
% a positive number: the index of the detector to replay and obtain Jacobians
% cfg.voidtime: for wide-field sources, [1]-start timer at launch, or 0-when entering
% the first non-zero voxel
%
%== Output control ==
% cfg.savedetflag: ['dp'] - a string (case insensitive) controlling the output detected photon data fields
% 1 d output detector ID (1)
% 2 s output partial scat. even counts (#media)
% 4 p output partial path-lengths (#media)
% 8 m output momentum transfer (#media)
% 16 x output exit position (3)
% 32 v output exit direction (3)
% 64 w output initial weight (1)
% combine multiple items by using a string, or add selected numbers together
% by default, mcx only saves detector ID (d) and partial-path data (p)
% cfg.issaveexit: [0]-save the position (x,y,z) and (vx,vy,vz) for a detected photon
% same as adding 'xv' to cfg.savedetflag. Example: <demo_lambertian_exit_angle.m>
% cfg.ismomentum: 1 to save photon momentum transfer,[0] not to save.
% save as adding 'M' to cfg.savedetflag string
% cfg.issaveref: [0]-save diffuse reflectance/transmittance in the non-zero voxels
% next to a boundary voxel. The reflectance data are stored as
% negative values; must pad zeros next to boundaries
% Example: see the demo script at the bottom
% cfg.issavedet: if the 2nd output is requested, this will be set to 1; in such case, user can force
% setting it to 3 to enable early termination of simulation if the detected photon
% buffer (length controlled by cfg.maxdetphoton) is filled; if the 2nd output is not
% present, this will be set to 0 regardless user input.
% cfg.outputtype: 'flux' - fluence-rate, (default value)
% 'fluence' - fluence integrated over each time gate,
% 'energy' - energy deposit per voxel
% 'jacobian' or 'wl' - mua Jacobian (replay mode),
% 'nscat' or 'wp' - weighted scattering counts for computing Jacobian for mus (replay mode)
% 'wm' - weighted momentum transfer for a source/detector pair (replay mode)
% 'length' total pathlengths accumulated per voxel,
% for type jacobian/wl/wp, example: <demo_mcxlab_replay.m>
% and <demo_replay_timedomain.m>
% cfg.session: a string for output file names (only used when no return variables)
%
%== Debug ==
% cfg.debuglevel: debug flag string (case insensitive), one or a combination of ['R','M','P','T'], no space
% 'R': debug RNG, output fluence.data is filled with 0-1 random numbers
% 'M': return photon trajectory data as the 5th output
% 'P': show progress bar
% 'T': save photon trajectory data only, as the 1st output, disable flux/detp/seeds outputs
% cfg.maxjumpdebug: [10000000|int] when trajectory is requested in the output,
% use this parameter to set the maximum position stored. By default,
% only the first 1e6 positions are stored.
%
% fields with * are required; options in [] are the default values
%
% Output:
% For each element of fluence,
% fluence(i).data is a 4D array with
% dimensions specified by [size(vol) total-time-gates].
% The content of the array is the normalized fluence at
% each voxel of each time-gate.
%
% when cfg.debuglevel contains 'T', fluence(i).data stores trajectory
% output, see below
% fluence(i).dref is a 4D array with the same dimension as fluence(i).data
% if cfg.issaveref is set to 1, containing only non-zero values in the
% layer of voxels immediately next to the non-zero voxels in cfg.vol,
% storing the normalized total diffuse reflectance (summation of the weights
% of all escaped photon to the background regardless of their direction);
% it is an empty array [] when if cfg.issaveref is 0.
% fluence(i).stat is a structure storing additional information, including
% runtime: total simulation run-time in millisecond
% nphoton: total simulated photon number
% energytot: total initial weight/energy of all launched photons
% energyabs: total absorbed weight/energy of all photons
% normalizer: normalization factor
% unitinmm: same as cfg.unitinmm, voxel edge-length in mm
%
% detphoton: (optional) a struct array, with a length equals to that of cfg.
% Starting from v2018, the detphoton contains the below subfields:
% detphoton.detid: the ID(>0) of the detector that captures the photon
% detphoton.nscat: cummulative scattering event counts in each medium
% detphoton.ppath: cummulative path lengths in each medium (partial pathlength)
% one need to multiply cfg.unitinmm with ppath to convert it to mm.
% detphoton.mom: cummulative cos_theta for momentum transfer in each medium
% detphoton.p or .v: exit position and direction, when cfg.issaveexit=1
% detphoton.w0: photon initial weight at launch time
% detphoton.prop: optical properties, a copy of cfg.prop
% detphoton.data: a concatenated and transposed array in the order of
% [detid nscat ppath mom p v w0]'
% "data" is the is the only subfield in all MCXLAB before 2018
% vol: (optional) a struct array, each element is a preprocessed volume
% corresponding to each instance of cfg. Each volume is a 3D int32 array.
% seeds: (optional), if give, mcxlab returns the seeds, in the form of
% a byte array (uint8) for each detected photon. The column number
% of seed equals that of detphoton.
% trajectory: (optional), if given, mcxlab returns the trajectory data for
% each simulated photon. The output has 6 rows, the meanings are
% id: 1: index of the photon packet
% pos: 2-4: x/y/z/ of each trajectory position
% 5: current photon packet weight
% 6: reserved
% By default, mcxlab only records the first 1e7 positions along all
% simulated photons; change cfg.maxjumpdebug to define a different limit.
%
%
% Example:
% % first query if you have supported GPU(s)
% info=mcxlabcl('gpuinfo')
%
% % define the simulation using a struct
% cfg.nphoton=1e7;
% cfg.vol=uint8(ones(60,60,60));
% cfg.vol(20:40,20:40,10:30)=2; % add an inclusion
% cfg.prop=[0 0 1 1;0.005 1 0 1.37; 0.2 10 0.9 1.37]; % [mua,mus,g,n]
% cfg.issrcfrom0=1;
% cfg.srcpos=[30 30 1];
% cfg.srcdir=[0 0 1];
% cfg.detpos=[30 20 1 1;30 40 1 1;20 30 1 1;40 30 1 1];
% cfg.vol(:,:,1)=0; % pad a layer of 0s to get diffuse reflectance
% cfg.issaveref=1;
% cfg.gpuid=1;
% cfg.autopilot=1;
% cfg.tstart=0;
% cfg.tend=5e-9;
% cfg.tstep=5e-10;
% % calculate the fluence distribution with the given config
% [fluence,detpt,vol,seeds,traj]=mcxlabcl(cfg);
%
% % integrate time-axis (4th dimension) to get CW solutions
% cwfluence=sum(fluence.data,4); % fluence rate
% cwdref=sum(fluence.dref,4); % diffuse reflectance
% % plot configuration and results
% subplot(231);
% mcxpreview(cfg);title('domain preview');
% subplot(232);
% imagesc(squeeze(log(cwfluence(:,30,:))));title('fluence at y=30');
% subplot(233);
% hist(detpt.ppath(:,1),50); title('partial path tissue#1');
% subplot(234);
% plot(squeeze(fluence.data(30,30,30,:)),'-o');title('TPSF at [30,30,30]');
% subplot(235);
% newtraj=mcxplotphotons(traj);title('photon trajectories')
% subplot(236);
% imagesc(squeeze(log(cwdref(:,:,1))));title('diffuse refle. at z=1');
%
% This function is part of Monte Carlo eXtreme (MCX) URL: http://mcx.space
%
% License: GNU General Public License version 3, please read LICENSE.txt for details
%
try
defaultocl=evalin('base','USE_MCXCL');
catch
defaultocl=1;
end
useopencl=defaultocl;
if(nargin==2 && ischar(varargin{2}))
if(strcmp(varargin{2},'preview'))
[varargout{1:nargout}]=mcxpreview(varargin{1});
return;
elseif(strcmp(varargin{2},'cuda'))
useopencl=0;
end
end
if(isstruct(varargin{1}))
for i=1:length(varargin{1})
castlist={'srcpattern','srcpos','detpos','prop','workload','srcdir'};
for j=1:length(castlist)
if(isfield(varargin{1}(i),castlist{j}))
varargin{1}(i).(castlist{j})=double(varargin{1}(i).(castlist{j}));
end
end
if (isfield(varargin{1}(i),'vol') && ndims(varargin{1}(i).vol)==4)
if((isa(varargin{1}(i).vol,'single') || isa(varargin{1}(i).vol,'double')) && isfield(varargin{1}(i),'unitinmm'))
varargin{1}(i).vol=varargin{1}(i).vol*varargin{1}(i).unitinmm;
end
end
if (~isfield(varargin{1}(i),'tstart'))
varargin{1}(i).tstart=0;
end
if (~isfield(varargin{1}(i),'tend'))
error('you must define cfg.tend for the maximum time-of-flight of a photon in seconds');
end
if (~isfield(varargin{1}(i),'tstep'))
varargin{1}(i).tstep=varargin{1}(i).tend;
end
if (~isfield(varargin{1}(i),'srcpos'))
error('you must define cfg.srcpos to defin the x/y/z position of the source in voxel unit');
end
if(isfield(varargin{1}(i),'detphotons') && isstruct(varargin{1}(i).detphotons))
if(isfield(varargin{1}(i).detphotons,'data'))
varargin{1}(i).detphotons=varargin{1}(i).detphotons.data;
else
fulldetdata={'detid','nscat','ppath','mom','p','v','w0'};
detfields=ismember(fulldetdata,fieldnames(varargin{1}(i).detphotons));
detdata=[];
for j=1:length(detfields)
if(detfields(j))
val=typecast(varargin{1}(i).detphotons.(fulldetdata{j})(:),'single');
detdata=[detdata reshape(val,size(varargin{1}(i).detphotons.(fulldetdata{j})))];
end
end
varargin{1}(i).detphotons=detdata';
varargin{1}(i).savedetflag='dspmxvw';
varargin{1}(i).savedetflag(detfields==0)=[];
end
end
end
end
if(useopencl==0)
[varargout{1:max(1,nargout)}]=mcx(varargin{1});
else
[varargout{1:max(1,nargout)}]=mcxcl(varargin{1});
end
if(nargin==0)
return;
end
cfg=varargin{1};
if(~ischar(cfg))
for i=1:length(varargout{1})
if(isfield(cfg(i),'srcnum') && cfg(i).srcnum>1)
dim=size(varargout{1}(i).data);
varargout{1}(i).data=reshape(varargout{1}(i).data,[cfg(i).srcnum, dim(1)/cfg(i).srcnum dim(2:end)]);
varargout{1}(i).data=permute(varargout{1}(i).data,[2:(length(dim)+1) 1]);
if(isfield(varargout{1}(i),'dref') && ~isempty(varargout{1}(i).dref))
varargout{1}(i).dref=reshape(varargout{1}(i).dref,[cfg(i).srcnum, dim(1)/cfg(i).srcnum dim(2:end)]);
varargout{1}(i).dref=permute(varargout{1}(i).dref,[2:(length(dim)+1) 1]);
end
end
end
end
if(nargout>=2)
for i=1:length(varargout{2})
if((~isfield(cfg(i),'savedetflag')) || ((isfield(cfg(i),'savedetflag')) && isempty(cfg(i).savedetflag)))
cfg(i).savedetflag='DP';
end
if(isfield(cfg(i),'issaveexit') && cfg(i).issaveexit)
cfg(i).savedetflag=[cfg(i).savedetflag,'XV'];
end
if(isfield(cfg(i),'ismomentum') && cfg(i).ismomentum)
cfg(i).savedetflag=[cfg(i).savedetflag,'M'];
end
if(ndims(cfg(i).vol)==4)
cfg(i).savedetflag='';
if((isa(cfg(i).vol,'single') || isa(cfg(i).vol,'double')) && isfield(cfg(i),'unitinmm'))
cfg(i).vol=cfg(i).vol*cfg(i).unitinmm;
end
end
if((~isfield(cfg(i),'issaveexit') || cfg(i).issaveexit~=2))
medianum=size(cfg(i).prop,1)-1;
detp=varargout{2}(i).data;
if(isempty(detp))
continue;
end
flags={cfg(i).savedetflag};
if(isfield(cfg(i),'issaveref'))
flags{end+1}=cfg(i).issaveref;
end
if(isfield(cfg(i),'srcnum'))
flags{end+1}=cfg(i).srcnum;
end
newdetp=mcxdetphoton(detp,medianum,flags{:});
newdetp.prop=cfg(i).prop;
if(isfield(cfg(i),'unitinmm'))
newdetp.unitinmm=cfg(i).unitinmm;
end
newdetp.data=detp; % enable this line for compatibility
newdetpstruct(i)=newdetp;
else
newdetpstruct(i)=varargout{2}(i);
end
end
if(exist('newdetpstruct','var'))
varargout{2}=newdetpstruct;
end
end
if(nargout>=5 || (~isempty(cfg) && isstruct(cfg) && isfield(cfg, 'debuglevel') && ~isempty(regexp(cfg(1).debuglevel, '[tT]', 'once'))))
outputid=5;
if((isfield(cfg, 'debuglevel') && ~isempty(regexp(cfg(1).debuglevel, '[tT]', 'once'))))
outputid=1;
end
for i=1:length(varargout{outputid})
data=varargout{outputid}.data;
if(isempty(data))
continue;
end
traj.pos=data(2:4,:).';
traj.id=typecast(data(1,:),'uint32').';
[traj.id,idx]=sort(traj.id);
traj.pos=traj.pos(idx,:);
traj.data=[single(traj.id)' ; data(2:end,idx)];
newtraj(i)=traj;
end
if(exist('newtraj','var'))
varargout{outputid}=newtraj;
end
end