FindPipelineCombinations.m

function [ORDERED_INDS,ORDERED_MATRIX,LABELS] = FindPipelineCombinations(TYPE,ORDER,EXCLUDE)

% This function will pull out the index or indices of a desired pipeline

% INPUTS:
% Required
% TYPE = a 1*7 vector indicating which pipeline/s with a particular
% parameter you want to extract the index/indices of. The position of each
% value indicates the processing step and the value at that position
% indicates which specific step to extract. A value of zero indicates to
% not extract pipelines based on that processing step. See below for an
% explanation of how to use
%
% Optional
% ORDER = a 1*7 vector specifying the order in which to arrange the indices
% (if extracting a single pipeline this has no effect). The first value
% indicates by which processing step to order pipelines by, the second
% value indicates which processing step to further order pipelines after
% the first ordering, the third indicates which to use for ordering after
% the second etc etc.
% EXCLUDE = a binary value of 1 or 0. If set to 1, any processing step for
% which only a single value is being extracted will be removed from
% ORDERED_MATRIX and LABELS
%
% OUTPUTS:
% ORDERED_INDS = the index/indicies of the desired pipelines, ordering
% according to what is specified by ORDER
% ORDERED_MATRIX = a 7*N matrix, where N is the number of pipelines
% extracted. Each column corresponds to a pipeline and each row is a
% processing step. Each row correponds corresponds to a processing step
% (and the ordering of these rows is determined by ORDER), and the value
% indicates the specific algorithm/method being used.
% LABELS = a cell indicating what the values in each row of ORDERED_MATRIX
% correspond to. This is set up so if you do imagesc(ORDERED_MATRIX) and
% yticklabels(LABELS) it will format it as per the paper
%
% HOW TO USE:
% TYPE = [DistCorr TractAlgor SptlCons Seeding TractWei EdgeWei Parc]
%
% DistCorr = 1, EDDY1
% DistCorr = 2, EDDY2
%
% TractAlgor = 1, FACT
% TractAlgor = 2, iFOD2
%
% SptlCons = 1, ACT
% SptlCons = 2, GWM
%
% Seeding = 1, dyn
% Seeding = 2, WM
% Seeding = 3, GMWMI
%
% TractWei = 1, None
% TractWei = 2, SIFT2
%
% EdgeWei = 1, SSW
% EdgeWei = 2, FA
%
% Parc = 1, 82 Node
% Parc = 2, 220 Node
% Parc = 3, 380 Node
%
% So TYPE = [1 1 2 3 1 1 3] would extract the index of the pipeline that
% used EDDY1, FACT, ACT, GMWMI seeding, no filtering, SSW edge weighting
% and the 380 node parcellation.
%
% TYPE = [1 0 0 0 0 0 2] would extract the indicies of all pipelines using
% the 220 node parcellation, TYPE = [1 0 0 0 0 0 2] would extract all
% pipelines using EDDY1 and the 220 node parcellation etc.
%
% ORDER = [7 1 6 2 4 3 5] extracts indices in the order of first being
% sorted by 'Parcellation', then 'DistCorr', then 'EdgeWei', then
% 'TractAlgor', then 'SptlCons', then 'Seeding', and then by 'TractWei'.
% In other words, pipelines are primarily ordered by the type of
% parcellation they used, then within that ordering they are order by the
% type of motion corretion used etc etc
%
% if TYPE = [0 0 1 0 0 0 0], ORDER = [7 1 6 2 4 3 5] and EXCLUDED = 0, then
% ORDERED_MATRIX(1,:) and LABELS{1} will correspond to the values of
% 'EdgeWei', ORDERED_MATRIX(2,:) and LABELS{2} will correspond to the
% values of 'SptlCons' etc etc. If EXCLUDED = 1, then ORDERED_MATRIX(1,:),
% LABELS{1} will correspond to the values of 'EdgeWei', ORDERED_MATRIX(2,:),
% LABELS{2} will correspond to the values of 'Seeding' etc etc

if nargin < 2
    % Default ordering
    ORDER = [7 1 6 2 4 3 5];
end

if nargin < 3
    EXCLUDE = 0;
end

load('COMBINATIONS_MATRIX.mat')

EXTRACT_INDS = find(TYPE);

N_TYPES_TO_EXTRACT = length(EXTRACT_INDS);

if N_TYPES_TO_EXTRACT == 0
    
    INDS = 1:size(COMBINATIONS,1);
    
elseif N_TYPES_TO_EXTRACT == 1
    
    INDS = find(COMBINATIONS(:,EXTRACT_INDS) == TYPE(EXTRACT_INDS));
    
else
    
    for i = 1:N_TYPES_TO_EXTRACT
        EXTRACT_IND = EXTRACT_INDS(i);
        INDStemp = find(COMBINATIONS(:,EXTRACT_IND) == TYPE(EXTRACT_IND));
        
        if i > 1
            INDS = intersect(INDS,INDStemp);
        else
            INDS = INDStemp;
        end
        
    end
    
end

% I flip the order so that the first processing step pipelines are ordered
% by is the last position in the labels naming convection

ORDER_FLIP = flip(ORDER);

% Because COMBINATION contains a row with values of 1 and 3 instead of 1
% and 3, we turn that 3 into a 2

%COMBINATIONS((COMBINATIONS(:,6)==3),6) = 2;

% Extract values of COMBINATION according to the desired pipeline INDCIES
% that wish to be found. Subtract 1 to make all values in the range 0-2

ORDERED_MATRIX = COMBINATIONS(INDS,:)' -1;

ORDERED_MATRIX = ORDERED_MATRIX(ORDER_FLIP,:);

orderIND = cell(1,7);

for i = 1:7
    [~,orderIND{i}] = sort(ORDERED_MATRIX(i,:));
    ORDERED_MATRIX = ORDERED_MATRIX(:,orderIND{i});
end
order = orderIND{6}(orderIND{7});
for i = 5:-1:1
    order =  orderIND{i}(order);
end

ORDERED_INDS = INDS(order);

Color1 = [186,186,186]./255;
Color2 = [64,64,64]./255;
Color3 = [244,165,130]./255;
Color4 = [171,217,233]./255;
Color5 = [69,117,180]./255;
Color6 = [49,54,149]./255;

LABELS = cell(7,1);

LABELS{(ORDER_FLIP==1)} = [sprintf('DistCorr:{\\color[rgb]{%f,%f,%f}EDDY1}/',Color1),sprintf('\\color[rgb]{%f,%f,%f}EDDY2',Color2)];
LABELS{(ORDER_FLIP==6)} = [sprintf('EdgeWei:{\\color[rgb]{%f,%f,%f}SSW}/',Color1),sprintf('\\color[rgb]{%f,%f,%f}FA',Color2)];
LABELS{(ORDER_FLIP==2)} = [sprintf('TractAlgor:{\\color[rgb]{%f,%f,%f}FACT}/',Color1),sprintf('\\color[rgb]{%f,%f,%f}iFOD2',Color2)];
LABELS{(ORDER_FLIP==4)} = [sprintf('Seed:{\\color[rgb]{%f,%f,%f}dynamic}/',Color1),sprintf('{\\color[rgb]{%f,%f,%f}WM}/',Color2),sprintf('{\\color[rgb]{%f,%f,%f}GMWMI}',Color3)];
LABELS{(ORDER_FLIP==3)} = [sprintf('SptlCons:{\\color[rgb]{%f,%f,%f}ACT}/',Color1),sprintf('\\color[rgb]{%f,%f,%f}GWM',Color2)];
LABELS{(ORDER_FLIP==5)} = [sprintf('TractWei:{\\color[rgb]{%f,%f,%f}None}/',Color1),sprintf('\\color[rgb]{%f,%f,%f}SIFT2',Color2)];
LABELS{(ORDER_FLIP==7)} = [sprintf('Parc:{\\color[rgb]{%f,%f,%f}82}/',Color1),sprintf('{\\color[rgb]{%f,%f,%f}R220}/',Color2),sprintf('{\\color[rgb]{%f,%f,%f}HCP}',Color3)...
    ,sprintf('Parc:{\\color[rgb]{%f,%f,%f}R520}/',Color4),sprintf('Parc:{\\color[rgb]{%f,%f,%f}S220}/',Color5),sprintf('Parc:{\\color[rgb]{%f,%f,%f}S520}/',Color6)];

if EXCLUDE
    
    EXCLUDE_INDS = TYPE~=0;
    
    LABELS(EXCLUDE_INDS) = [];
    
    ORDERED_MATRIX(EXCLUDE_INDS,:) = [];
    
end