function bones = rd_rois2(rdir,leg,ld,itroch,irho)

%RD_ROIS2 Reads a particular loaded or unloaded leg sagittal

% segmentation for the femur and tibia in pixels from CSV

% files in a directory.

%

% For creating regions of interest ROIs of knee joint cartilage

% for the MRI reliability study. ROIs are returned in a

% structure BONES. BONES(1) is the femur and BONES(2) is the

% tiba. BONES.rois(1) is the cartilage and BONES.rios(2) is

% the bone. BONES.rois.roi(1) is the lateral compartment and

% BONES.rois.roi(2) is the medial compartment.

%

% BONES = RD_ROIS2(RDIR,LEG,LD) given the directory name in the

% string, RDIR, either the character 'L' or 'R' for the left

% or right leg in LEG, and either 'LD' or 'UL' for loaded or

% unloaded condition in LD, return structure BONES with the

% femur and tibia segmented regions of interest (ROIs).

%

% BONES = RD_ROIS2(RDIR,LEG,LD,ITROCH) given the

% logical ITROCH, trochlear ROIs are returned in the femur

% structure BONES(1).

%

% BONES = RD_ROIS2(RDIR,LEG,LD,ITROCH,IRHO) given the

% integer IRHO, checks for 'imageno' greater than 96 and

% subtracts one (1) from 'imageno', divides by IRHO, and adds

% one (1). This is to account for the digitization on the

% first spin lock time.

%

% NOTES: 1. M-file rd_roi6.m must be in the current directory

% or path.

%

% 2. Femur and tibia segmentations must be in sub-

% directories 'Femur' and 'Tibia', respectively under

% segmentation directory RDIR.

%

% 3. For sagittal segmentations only. CSV file names

% must contain the capital letters 'SAG'.

%

% 4. Trochlear ROIs are removed by default.

%

% 5. CSV files with case insensitive "dup" in the

% file names are ignored as duplicate files.

%

% 6. Cartilage (SAGAR) CSV files with "_RO" in the

% file names are not used in place of the same files

% without "_RO".

%

% 7. Trochlea option is NOT tested.

%

% 07-Jun-2022 * Mack Gardner-Morse

%

%#######################################################################

%

% Check for Inputs

%

if (nargin<3)

error(' *** ERROR in RD_ROIS: Three inputs are required!');

end

%

if (nargin<4)

itroch = false;

end

%

if (nargin<5)

irho = 1;

end

%

% Loop through the Femur and Tibia Bones

%

bdirs = ['Femur'; 'Tibia'];

nb = size(bdirs,1);

%

bones = struct;

%

for l = 1:nb

%

rnams = ['*' leg '*SAG*' ld '*.csv'];

rnams = dir(fullfile(rdir,bdirs(l,:),rnams));

rnams = {rnams.name}';

idx = ~contains(rnams,'MGG','IgnoreCase',true);

rnams = rnams(idx);

idx = ~contains(rnams,'dup','IgnoreCase',true);

rnams = sort(rnams(idx)); % Cartilage first, bone last

idx = contains(rnams,'_RO'); % Check for _RO files

if any(idx)

idc = contains(rnams,'SAGAR');

idx = idx|~idc;

rnams = rnams(~idx);

end

nrfiles = size(rnams,1);

if nrfiles>2

fprintf(1,' %s\n',rnams{:});

error(' *** ERROR in RD_ROIS: Too many CSV files found!');

end

%

% Loop through ROI Files

% Note trochlear slices are removed by default.

%

rois = struct;

%

for k = 1:nrfiles

%

rnam = fullfile(rdir,bdirs(l,:),rnams{k});

%

rois(k).name = rnams{k};

rois(k).roi = rd_roi6(rnam,true); % Read pixel coordinates

if l==1&&~itroch

rois(k).roi = rois(k).roi(1:2); % Remove trochlear slices

end

rois(k).slice = [rois(k).roi.imageno]';

if any(rois(k).slice>96)&&irho>1

rois(k).slice = (rois(k).slice-1)./irho+1;

rois(k).roi(1).imageno = (rois(k).roi(1).imageno-1)./irho+1;

rois(k).roi(2).imageno = (rois(k).roi(2).imageno-1)./irho+1;

if l==1&&itroch

rois(k).roi(3).imageno = (rois(k).roi(3).imageno-1)./irho+1;

end

end

%

end

%

bones(l).name = bdirs(l,:);

bones(l).rois = rois;

%

end

%

return