cr_mask.m

function mask = cr_mask(roic,npx)
%CR_MASK   Creates an image mask based on the two-dimensional (2-D)
%          coordinates of two lines.  The region of interest (ROI) is
%          defined as the space between the first and second line.  The
%          second line is assumed to be slightly longer than the first
%          line.
%
%          For creating masks for knee joint cartilage.  The first line
%          is usually cartilage and the second longer line is the
%          underlying bone.
%
%          MASK = CR_MASK(ROIC,NPX) given the two-dimensional
%          coordinates of two lines defining a region of interest in a
%          two element cell array (one element for each line), ROIC,
%          and the size of the image for the mask in array, NPX,
%          creates a logical array mask for the region of interest,
%          MASK.  Note:  If NPX has only one element, the image is
%          assumed to be square (symmetrical) (NPX by NPX).
%
%          NOTES:  1.  M-files in_tri2d.m, lsect2.m, mk_tri4_2dc.m must
%                  be in the current directory or path.
%
%          03-Aug-2020 * Mack Gardner-Morse
%

%#######################################################################
%
% Check for Inputs
%
if (nargin<2)
  error(' *** ERROR in CR_MASK:  Two inputs are required!');
end
%
roic = roic(:);
[nr,nc] = size(roic);
if nr~=2&&nc~=1
  error([' *** ERROR in CR_MASK:  Input cell array must have'
         ' two elements!']);
end
%
ndim = size(npx(:),1);
if ndim>2||ndim<1
  error(' *** ERROR in CR_MASK:  Incorrect image dimensions!');
end
%
if ndim==1
  npx = [npx; npx];
end
%
% Create Triangle Meshes for the Region of Interest
%
tri = mk_tri4_2dc(roic);
xy = cell2mat(roic);
%
% Find Pixels within the Region of Interest
%
mask = false(npx(1)*npx(2),1);
%
minr = floor(min(xy));
if any(minr(:)==0)      % Trap for zeros
  minr(minr(:)==0) = 1;
end
maxr = ceil(max(xy));
idx = minr(:,1):maxr(:,1);
idy = minr(:,2):maxr(:,2);
[xg,yg] = meshgrid(idx,idy);
xym = [xg(:) yg(:)];
in_roi = in_tri2d(tri,xy,xym);
%
idr = sub2ind([npx(1) npx(2)],xym(:,2),xym(:,1));
idr = idr(in_roi);
%
mask(idr) = true;
%
return