add files for loading tiffs in matlab

Author: carsen-stringer

helpers/loadFramesBuff.m

@@ -0,0 +1,146 @@
+function [frames, headers] = loadFramesBuff(tiff, firstIdx, lastIdx, stride, temp_file)
+%loadFrames Loads the frames of a Tiff file into an array (Y,X,T)
+%   MOVIE = loadFrames(TIFF, [FIRST], [LAST], [STRIDE], []) loads
+%   frames from the Tiff file specified by TIFF, which should be a filename
+%   or an already open Tiff object. Optionallly FIRST, LAST and STRIDE
+%   specify the range of frame indices to load.
+
+if nargin>4 && ~isempty(temp_file)
+    if ~isequal(tiff, temp_file) % do not copy if already copied
+        % in case copying fails (server hangs)
+        iscopied = 0;
+        firstfail = 1;
+        while ~iscopied
+            try       
+                copyfile(tiff,temp_file, 'f');
+                iscopied = 1;
+                if ~firstfail
+                    fprintf('  succeeded!\n');
+                end
+            catch
+                if firstfail
+                    fprintf('copy tiff failed, retrying...');
+                end
+                firstfail = 0;
+                pause(10);
+            end
+        end
+        tiff = temp_file;
+    end
+    info = imfinfo(temp_file); % get info after copying
+    if isnan(lastIdx)
+        lastIdx = length(info); % get number of frames
+    end
+end
+
+% initChars = overfprintf(0, 'Loading TIFF frame ');
+warning('off', 'MATLAB:imagesci:tiffmexutils:libtiffWarning');
+
+warningsBackOn = onCleanup(...
+    @() warning('on', 'MATLAB:imagesci:tiffmexutils:libtiffWarning'));
+
+if ischar(tiff)
+    tiff = Tiff(tiff, 'r');
+    closeTiff = onCleanup(@() close(tiff));
+end
+
+if nargin < 2 || isempty(firstIdx)
+    firstIdx = 1;
+end
+
+if nargin < 3 || isempty(lastIdx)
+    lastIdx = nFramesTiff(tiff);
+end
+
+if nargin < 4 || isempty(stride)
+    stride = 1;
+end
+
+if nargout > 1
+    loadHeaders = true;
+else
+    loadHeaders = false;
+end
+
+if true %nargin <=4  %if the file was not copied locally use Tiff library
+    w = tiff.getTag('ImageWidth');
+    h = tiff.getTag('ImageLength');
+    dataClass = class(read(tiff));
+    nFrames = ceil((lastIdx - firstIdx + 1)/stride);
+    frames = zeros(h, w, nFrames, dataClass);
+    if loadHeaders
+        headers = cell(1, nFrames);
+    end
+    
+    nMsgChars = 0;
+    setDirectory(tiff, firstIdx);
+    for t = 1:nFrames
+        if mod(t, 100) == 0
+            %nMsgChars = overfprintf(nMsgChars, '%i/%i', t, nFrames);
+        end
+        
+        
+        frames(:,:,t) = read(tiff);
+        
+        if loadHeaders
+            headerNames = tiff.getTagNames;
+            headers{t} = getTag(tiff, 'ImageDescription');
+            try
+                headers{t} = [headers{t} getTag(tiff,'Software')];
+            catch
+            end
+        end
+        
+        if t < nFrames
+            for i = 1:stride
+                nextDirectory(tiff);
+            end
+        end
+    end
+    %overfprintf(initChars + nMsgChars, '');
+else % if the file is local (and on SSD) this way of reading works much faster
+    info = imfinfo(temp_file);
+    offset = info(1).Offset;
+    w = info(1).Width;
+    h = info(1).Height;
+    dataClass = 'int16'; % this is true for our ScanImage recordings, 
+    % it is possible to use info.BitDepth to try and figure out nBytesPerSample
+    
+    % MK: using memmapfile here, but just reading as a binary file might be
+    % faster, worth trying
+    m = memmapfile(temp_file, 'Format', dataClass, 'Offset', offset);
+    data = m.Data;
+%     clear m;
+    nPixels = w*h;
+    frameIdx = firstIdx:stride:lastIdx;
+    data = reshape(data, [], length(info));
+    nSamples = size(data, 1); % number of values in each frame related vector
+    % the images are the last nPixels values of this vector
+    % here we assume all the headers occupy the same number of bytes,
+    % this is true for ScanImage recordings. info.Offset is a useful field
+    % otherwise.
+    frames = data(nSamples-nPixels+1:nSamples, frameIdx);
+    frames = reshape(frames, w, h, []);
+    frames = permute(frames, [2 1 3]);
+    if loadHeaders
+        headers = {info(frameIdx).ImageDescription};
+    end
+end
+
+
+end
+
+
+%%
+%
+% figure
+% for i=1:3:nFrames
+%     subplot(1, 3, 1)
+%     imagesc(frames(:,:,i));
+%     subplot(1, 3, 2);
+%     imagesc(data(:,:,i));
+%     subplot(1, 3, 3);
+%     imagesc(frames(:,:,i)-data(:,:,i));
+%     drawnow;
+% end
+

helpers/nFramesTiff.m

@@ -0,0 +1,6 @@
+function n = nFramesTiff(tiff)
+%nFrames find the number of frames in the Tiff
+
+n = nFrames(tiff, 2001);
+end
+