sub2ind no longer accepts NaNs in MATLAB R2024a, relevant to mrSub2ind

[austinchkuo]

As of R2024a, MATLAB's sub2ind function throws an error when it encounters NaNs, presumably because of new functionality (see: https://www.mathworks.com/help/matlab/ref/sub2ind.html for more information). This function previously did not check for NaNs in prior iterations of MATLAB (R2023b and earlier), and MathWorks' current documentation makes no mention of this additional requirement.

To replicate: open any mrLoadRet session in MATLAB R2024a or later

Error stack:

Error using sub2ind (line 71)
Out of range subscript.

Error in mrSub2ind (line 28)
  linear = sub2ind(dims,x,y,z);

Error in refreshMLRDisplay>getROIImageCoords (line 702)
    baseCoordsLinear = mrSub2ind(baseDims,baseCoordsHomogeneous(1,:),baseCoordsHomogeneous(2,:),baseCoordsHomogeneous(3,:));

Error in refreshMLRDisplay>displayROIs (line 824)
    [x y s] = getROIImageCoords(view,roi{r}.roiBaseCoords,sliceIndex,baseNum,baseCoordsHomogeneous,imageDims);

Error in refreshMLRDisplay>dispBase (line 544)
  [roi,v] = displayROIs(v,hAxis,slice,sliceIndex,baseNum,base.coordsHomogeneous,base.dims,rotate,verbose);

Error in refreshMLRDisplay (line 152)
  [v img base roi overlays curSliceBaseCoords] = dispBase(gui.axis,v,baseNum,gui,true,verbose);

Error in mrOpenWindow (line 207)
    refreshMLRDisplay(view.viewNum);

Error in mrLoadRet (line 51)
v = mrOpenWindow('Volume',mrLastView);

Relevant change from sub2ind:

R2024a: sub2ind accepts mix of scalars and vectors for subscript inputs
sub2ind now leverages scalar expansion and accepts a mix of scalars and vectors for subscript inputs. For example, sub2ind(sz,[1 2 3],2) is now the same as sub2ind(sz,[1 2 3],[2 2 2]). Previously, the subscript inputs were required to be the same size.

Relevant code from sub2ind (lines 69-72):

if ~isempty(v) && (anynan(v) || min(v,[],'all') < 1 || max(v,[],'all') > siz_i)
    % Verify subscripts are within range
    error(message('MATLAB:sub2ind:IndexOutOfRange'));
end

As a result, the functionality of mrSub2ind no longer works in versions of MATLAB starting from R2024a, due to assigning x(badCoords), y(badCoords), and z(badCoords) a value of NaN.

Relevant code from mrSub2ind (lines 21-28):

badCoords = find((x < 1) | (x > dims(1)) | ...
		 (y < 1) | (y > dims(2)) | ...
		 (z < 1) | (z > dims(3)));
x(badCoords) = nan;
y(badCoords) = nan;
z(badCoords) = nan;

linear = sub2ind(dims,x,y,z);

[justingardner]

Hey Austin, I believe that the intended functionality there was for mrSub2ind to return a nan for the index of any badCoords values. Can you fix the code in there so that it does that. Easiest would be to replace the x(badCoords), y(badCoords), z(badCoords) with a value that is guaranteed not to crash out Matlab's sub2ind (say 1). Then set linear(badCoords) = nan; Does that make sense? If so, please make the changes, test, commit and push to the repo. Thanks!

[julienbesle]

Hi Justin,

I recently fixed this issue in my fork after upgrading to Matlab R2024b (commit #dad9147d).
I created a pull request for this fork years ago, which is still pending (#62). It's got 277 commits, including this one. My changes shouldn't break anything and I've been regularly merging with your main branch (but I haven't yet tested your last 9 commits, which I just merged this morning).

Cheers,
Julien

[austinchkuo]

Hi Julien,

I merged your commit to fix mrSub2Ind, and I'll follow up with Justin about the pull request. Thanks!

Best,
Austin