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fix: use the right axis for motion correction shift bookkeeping #141

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Merged
ehennestad merged 2 commits into from
Sep 18, 2026
Merged

fix: use the right axis for motion correction shift bookkeeping #141

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cb21059
fix(flowreg): label motion correction offsets with the right axis
ehennestad Sep 18, 2026
5b07c60
fix(normcorre): add drift to the right axis of the saved shifts
ehennestad Sep 18, 2026
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16 changes: 12 additions & 4 deletions code/wrappers/+nansen/+wrapper/+flowreg/@Processor/Processor.m
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Original file line number Diff line number Diff line change
Expand Up @@ -178,9 +178,12 @@ function updateCorrectionStats(obj, IND)
meanDivergence = get_mean_divergence(W);
meanTranslation = get_mean_translation(W);

% Compute quantities
xOffset = squeeze(mean(mean(W(:,:,2,:), 1), 2)); %Todo: Is 2nd x-offsets?
yOffset = squeeze(mean(mean(W(:,:,1,:), 1), 2)); %Todo: Is 1st y-offsets?
% Compute quantities. The displacement field of flowreg holds
% the displacement in x in its first channel and the
% displacement in y in its second, which is the order that
% imwarp takes a displacement field in.
xOffset = squeeze(mean(mean(W(:,:,1,:), 1), 2));
yOffset = squeeze(mean(mean(W(:,:,2,:), 1), 2));
rmsmov = sqrt(mean( W(:).^2) );

% Add results to struct
Expand Down Expand Up @@ -375,7 +378,12 @@ function onInitialization(obj)
end

function shifts = addShifts(shifts, offset)
% Add rigid shifts to struct of normcorre nonrigid shifts.
% Add a rigid offset to the displacement fields of flowreg.
%
% The offset is [dx, dy], as it comes from correctDrift, and
% the field holds the displacement in x in its first channel
% and the displacement in y in its second, so the two are in
% the same order.
for k = 1:numel(shifts)
shifts{k}(:, :, 1, :) = shifts{k}(:, :, 1, :) + offset(1);
shifts{k}(:, :, 2, :) = shifts{k}(:, :, 2, :) + offset(2);
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15 changes: 10 additions & 5 deletions code/wrappers/+nansen/+wrapper/+normcorre/@Processor/Processor.m
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Expand Up @@ -286,12 +286,17 @@ function onCompletion(obj)
methods (Static)

function ncShifts = addShifts(ncShifts, offset)
% Add rigid shifts to struct of normcorre nonrigid shifts.
% Add a rigid offset to a struct of normcorre shifts.
%
% The offset is [dx, dy], as it comes from correctDrift, while
% normcorre follows the MATLAB array convention and holds the
% shift in y in the first plane of its shifts and the shift in
% x in the second, so the two are in opposite order.
for k = 1:numel(ncShifts)
ncShifts(k).shifts(:,:,:,1) = ncShifts(k).shifts(:,:,:,1) + offset(1);
ncShifts(k).shifts(:,:,:,2) = ncShifts(k).shifts(:,:,:,2) + offset(2);
ncShifts(k).shifts_up(:,:,:,1) = ncShifts(k).shifts_up(:,:,:,1) + offset(1);
ncShifts(k).shifts_up(:,:,:,2) = ncShifts(k).shifts_up(:,:,:,2) + offset(2);
ncShifts(k).shifts(:,:,:,1) = ncShifts(k).shifts(:,:,:,1) + offset(2);
ncShifts(k).shifts(:,:,:,2) = ncShifts(k).shifts(:,:,:,2) + offset(1);
ncShifts(k).shifts_up(:,:,:,1) = ncShifts(k).shifts_up(:,:,:,1) + offset(2);
ncShifts(k).shifts_up(:,:,:,2) = ncShifts(k).shifts_up(:,:,:,2) + offset(1);
end
end
end
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