Using the global readers

src/MATLAB/tiffReader.m

-function im = tiffReader(datasetName,chan,type,dirName,nameConvention,cPos,tPos,zPos)
-global DatasetName OrgDir
-
-DatasetName = datasetName;
-im = [];
-
-if (~exist('dirName','var') || isempty(dirName))
-    fprintf('Select Image Dir...');
-    dirName = uigetdir();
-    disp(dirName);
-end
-
-if (~exist('nameConvention','var') || isempty(nameConvention))
-    nameConvention = '_c%d_t%04d_z%04d%s';
-    cPos = 1;
-    tPos = 2;
-    zPos = 3;
-end
-
-if (~exist('chan','var')|| isempty(chan))
-    chan = 0;
-end
-
-if (~exist('type','var') || isempty(type))
-    type = 'double';
-end
-
-if (strcmp(type,'double'))
-    bytes = 8;
-elseif (strcmp(type,'uint8'))
-    bytes = 1;
-else
-    error('Type not implemented');
-end
-
-OrgDir = dirName;
-
-dList = dir(fullfile(dirName,'*.tif*'));
-
-mxC = 0;
-mxT = 0;
-mxZ = 0;
-
-mxX = 0;
-mxY = 0;
-
-for i=1:length(dList)
-    vals = textscan(dList(i).name,[datasetName nameConvention]);
-    
-    if (isempty(vals) || isempty(vals{1}) || isempty(vals{2}) || isempty(vals{3}))
-        continue;
-    end
-    
-    if (mxX==0 || mxY==0)
-        im = imread(fullfile(dirName,dList(i).name));
-        mxX = size(im,2);
-        mxY = size(im,1);
-    end
-    
-    c = double(vals{cPos});
-    t = double(vals{tPos});
-    z = double(vals{zPos});
-    
-    if (c>mxC)
-        mxC = c;
-    end
-    if (t>mxT)
-        mxT = t;
-    end
-    if (z>mxZ)
-        mxZ = z;
-    end
-end
-
-if (chan~=0)
-    mxC=1;
-end
-
-fprintf('%d,%d,%d,%d,%d, %4.2fGB\n',mxY,mxX,mxZ,mxT,mxC,mxY*mxX*mxZ*mxT*mxC*bytes/1024/1024/1024);
-
-im = zeros(1,1,1,1,1);
-
-if (bytes==8)
-    im = zeros(mxY,mxX,mxZ,mxT,mxC);
-elseif (bytes==1)
-    im = zeros(mxY,mxX,mxZ,mxT,mxC,'uint8');
-end
-
-for i=1:length(dList)
-    vals = textscan(dList(i).name,[datasetName nameConvention]);
-    
-    if (isempty(vals) || isempty(vals{1}) || isempty(vals{2}) || isempty(vals{3}))
-        continue;
-    end
-    
-    c = vals{cPos};
-    if (chan~=0 && c~=chan)
-        continue;
-    end
-    
-    t = vals{tPos};
-    z = vals{zPos};
-   
-    if (bytes==8)
-        im(:,:,z,t,c) = imread(fullfile(dirName,dList(i).name));
-    elseif (bytes==1)
-        im(:,:,z,t,c) = uint8(imread(fullfile(dirName,dList(i).name)));
-    end
-end

src/MATLAB/tiffWriter.m

-function tiffWriter(image,prefix)
-sizes = size(image);
-numDim = length(sizes);
-
-if numDim<5
-    channels = 1;
-else
-    channels = sizes(5);
-end
-if numDim<4
-    frames = 1;
-else
-    frames = sizes(4);
-end
-if numDim<3
-    stacks = 1;
-else
-    stacks = sizes(3);
-end
-
-
-for c=1:channels
-    for t=1:frames
-        for z=1:stacks
-            fileName = sprintf('%s_c%d_t%04d_z%04d.tif',prefix,c,t,z);
-            imwrite(image(:,:,z,t,c),fileName,'tif','Compression','lzw');
-        end
-    end
-end
-
-end
-