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speed bump in assembleCorrectedROITiff #1

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speed bump in assembleCorrectedROITiff #1

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6d66ecb
optimize assembleCorrectedROITiff - get rid of all the cat()
jmmanley Jun 21, 2022
e3d21bd
change imageData to single
jmmanley Feb 17, 2023
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31 changes: 21 additions & 10 deletions assembleCorrectedROITiff.m
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Original file line number Diff line number Diff line change
Expand Up @@ -12,27 +12,38 @@
numPX = roiGroup.rois(1,1).scanfields.pixelResolutionXY;
pixelResolution = mean(FOV./numPX);

% find size of final assembled FOV
strip=1; channel=1; frame=1;
stripTemp = roiData{1,strip}.imageData{1,channel}{1,frame}{1,1};
roiSize = size(stripTemp);
corr = returnScanOffset2(stripTemp,1); % find offset correction
stripTemp = fixScanPhase(stripTemp,corr,1); % fix scan phase
val = round(size(stripTemp,1)*0.03); % trim excess
stripTemp = stripTemp(val:end,7:138,:,:);

fullPXx = size(stripTemp,1); % final FOV x size (px)
fullPXy = size(stripTemp,2) * numROIs; % final FOV y size (px)

%% Assemble frames
imageData = [];
imageData = zeros(fullPXx, fullPXy, totalChannel,totalFrame, 'single');
for channel = 1:totalChannel
disp(['Assembling channel ' num2str(channel) ' of ' num2str(totalChannel) '...'])
frameTemp = [];

for strip = 1:numROIs

% Generate the time series of each ROI in the data
stripTemp = [];

stripTemp = zeros(roiSize(1), roiSize(2), 1, totalFrame, 'single');
for frame = 1:totalFrame
stripTemp = cat(4,stripTemp,single(roiData{1,strip}.imageData{1,channel}{1,frame}{1,1}));
stripTemp(:,:,1,frame) = single(roiData{1,strip}.imageData{1,channel}{1,frame}{1,1});
end
corr = returnScanOffset2(stripTemp,1); % find offset correction
stripTemp = fixScanPhase(stripTemp,corr,1); % fix scan phase
val = round(size(stripTemp,1)*0.03); % trim excess
stripTemp = stripTemp(val:end,7:138,:,:);

frameTemp = cat(2,frameTemp,stripTemp); % create each frame


yy = (strip-1)*fullPXy / numROIs+1:strip*fullPXy / numROIs; % y indices of current strip
imageData(:,yy,channel,:) = stripTemp;

end

imageData = single(cat(3,imageData,frameTemp));

end