Added files from the local path

src/matlab/createMetadata.m

+function createMetadata(root,imageData)
+
+if (~exist(root,'dir'))
+    mkdir(root);
+end
+
+fileName = fullfile(root,[imageData.DatasetName '.txt']);
+fprintf('Creating Metadata %s...',fileName);
+
+fileHandle = fopen(fileName,'wt');
+
+fprintf(fileHandle,'DatasetName:%s\n',imageData.DatasetName);
+
+fprintf(fileHandle,'NumberOfChannels:%d\n',imageData.NumberOfChannels);
+
+if (isfield(imageData,'ChannelColors'))
+    fprintf(fileHandle,'ChannelColors:');
+
+    if (size(imageData.ChannelColors,1)==1 && ~iscell(imageData.ChannelColors))
+        fprintf(fileHandle,'%s,',imageData.ChannelColors);
+    else
+        for i=1:length(imageData.ChannelColors)
+            fprintf(fileHandle,'%s,',imageData.ChannelColors{i});
+        end
+    end
+    fprintf(fileHandle,'\n');
+end
+
+fprintf(fileHandle,'NumberOfFrames:%d\n',imageData.NumberOfFrames);
+
+% fprintf(fileHandle,'XDimension:%d\n',imageData.yDim);
+% fprintf(fileHandle,'YDimension:%d\n',imageData.xDim);
+fprintf(fileHandle,'XDimension:%d\n',imageData.XDimension);
+fprintf(fileHandle,'YDimension:%d\n',imageData.YDimension);
+fprintf(fileHandle,'ZDimension:%d\n',imageData.ZDimension);
+
+fprintf(fileHandle,'XPixelPhysicalSize:%f\n',imageData.XPixelPhysicalSize);
+fprintf(fileHandle,'YPixelPhysicalSize:%f\n',imageData.YPixelPhysicalSize);
+fprintf(fileHandle,'ZPixelPhysicalSize:%f\n',imageData.ZPixelPhysicalSize);
+
+if (isfield(imageData,'XPosition'))
+    fprintf(fileHandle,'XPosition:%f\n',imageData.XPosition);
+end
+if (isfield(imageData,'YPosition'))
+    fprintf(fileHandle,'YPosition:%f\n',imageData.YPosition);
+end
+
+if (isfield(imageData,'XDistanceUnits'))
+    fprintf(fileHandle,'XDistanceUnits:%s\n',imageData.XDistanceUnits);
+end
+if (isfield(imageData,'YDistanceUnits'))
+    fprintf(fileHandle,'YDistanceUnits:%s\n',imageData.YDistanceUnits);
+end
+if (isfield(imageData,'ZDistanceUnits'))
+    fprintf(fileHandle,'ZDistanceUnits:%s\n',imageData.ZDistanceUnits);
+end
+
+if (isfield(imageData,'XLength'))
+    fprintf(fileHandle,'XLength:%f\n',imageData.XLength);
+end
+if (isfield(imageData,'YLength'))
+    fprintf(fileHandle,'YLength:%f\n',imageData.YLength);
+end
+if (isfield(imageData,'ZLength'))
+    fprintf(fileHandle,'ZLength:%f\n',imageData.ZLength);
+end
+
+if (isfield(imageData,'StartCaptureDate'))
+    fprintf(fileHandle,'StartCaptureDate:%s\n',imageData.StartCaptureDate);
+end
+
+if (isfield(imageData,'TimeStampDeltas'))
+    for t=1:imageData.NumberOfFrames
+        for z=1:imageData.ZDimension
+            for c=1:imageData.NumberOfChannels
+                fprintf(fileHandle,'TimeStampDelta(%d,%d,%d):%f\n',c,t,z,imageData.TimeStampDeltas(z,c,t));
+            end
+        end
+    end
+end
+fclose(fileHandle);
+
+fprintf('Done\n');
+end
\ No newline at end of file

src/matlab/imageConvert.m

+function [ imageOut ] = imageConvert( imageIn, typ )
+%IMAGECONVERT converts image from current type into the specified type
+
+w = whos('imageIn');
+
+if (strcmpi(w.class,typ))
+    imageOut = imageIn;
+else
+    imageIn = double(imageIn);
+    
+    switch w.class
+        case 'uint8'
+            imtemp = imageIn ./ (2^8-1);
+        case 'uint16'
+            if (max(imageIn(:))<=2^12-1)
+                imtemp = imageIn ./(2^12-1);
+            else
+                imtemp = imageIn ./ (2^16-1);
+            end
+        case 'int16'
+            imtemp = (imageIn+(2^16/2 - 1)) ./ (2^16-1);
+        case 'uint32'
+            imtemp = imageIn ./ 2^32-1;
+        case 'int32'
+            imtemp = (imageIn+(2^32/2 -1)) ./ (2^32-1);
+        case 'single'
+            imtemp = (imageIn+abs(min(imageIn(:)))) ./ max(imageIn(:));
+        case 'double'
+            imtemp = (imageIn+abs(min(imageIn(:)))) ./ max(imageIn(:));
+        case 'logical'
+            imtemp = imageIn;
+        otherwise
+            error('Unkown type of image to convert!');
+    end
+    
+    switch typ
+        case 'uint8'
+            imageOut = uint8(imtemp*(2^8-1));
+        case 'uint16'
+            imageOut = uint16(imtemp*(2^16-1));
+        case 'int16'
+            if (max(imtemp(:))<=0.5)
+                imageOut = int16(imtemp*(2^16-1));
+            else
+                imageOut = int16((imtemp-0.5)*(2^16/2-1));
+            end
+        case 'uint32'
+            imageOut = uint32(imtemp*(2^32-1));
+        case 'int32'
+            if (max(imtemp(:))<=0.5)
+                imageOut = int32(imtemp*(2^32-1));
+            else
+                imageOut = int32((imtemp-0.5)*(2^32/2-1));
+            end
+        case 'single'
+            imageOut = single(imtemp);
+        case 'double'
+            imageOut = imtemp;
+        case 'logical'
+            imageOut = imtemp>0;
+        otherwise
+            error('Unkown type of image to convert to!');
+    end
+    clear imtemp
+end
+end
+

src/matlab/readMetaData.m

+function [imageData,rootDir] = readMetaData(root)
+
+imageData = [];
+rootDir = [];
+
+if (~exist('root','var') || isempty(root))
+    rootDir = uigetdir('');
+    if rootDir==0,
+        [fileName,rootDir,filterIndex] = uigetfile('.txt');
+        if (filterIndex~=0)
+            fileHandle = fopen(fullfile(rootDir,fileName));
+            imageData = readfile(fileHandle);
+        end
+        return
+    end
+elseif (~isempty(strfind(root,'.txt')))
+    fileHandle = fopen(root);
+    imageData = readfile(fileHandle);
+    pos = strfind(root,'\');
+    rootDir = root(1:pos(end));
+    imageData.imageDir = rootDir;
+    return
+else
+    rootDir = root;
+end
+
+imageData = [];
+dlist = dir(rootDir);
+
+for i=1:length(dlist)
+    if (strcmp('..',dlist(i).name))
+        continue;
+    end
+    
+    dSublist = dir(fullfile(rootDir,dlist(i).name,'*.txt'));
+    if isempty(dSublist), continue, end
+    
+    for j=1:length(dSublist)
+        fileHandle = fopen(fullfile(rootDir,dlist(i).name,dSublist(j).name));
+        imageDatum = readfile(fileHandle);
+        
+        if (isempty(imageDatum)), continue, end
+        
+        if (isempty(imageData))
+            imageData = imageDatum;
+        else
+            imageData(length(imageData)+1) = imageDatum;
+        end
+    end
+    if strcmpi('.',dlist(i).name)
+        imageData.imageDir = rootDir;
+    else
+        imageData.imageDir = fullfile(rootDir,dlist(i).name);
+    end
+end
+rootDir = imageData.imageDir;
+end
+
+function imageDatum = readfile(fileHandle)
+imageDatum = {};
+
+if fileHandle<=0, return, end
+
+data = textscan(fileHandle,'%s %s', 'delimiter',':','whitespace','\n');
+fclose(fileHandle);
+
+if isempty(data), return, end
+
+for k=1:length(data{1})
+    val = str2double(data{2}{k});
+    if (isnan(val))
+        val = data{2}{k};
+    end
+    if (any(strfind(data{1}{k},'TimeStampDelta')))
+        if (~isfield(imageDatum,'TimeStampDeltas'))
+            imageDatum.TimeStampDeltas = zeros(imageDatum.ZDimension,imageDatum.NumberOfChannels,imageDatum.NumberOfFrames);
+        end
+        plane = textscan(data{1}{k},'TimeStampDeltas(%d,%d,%d)%s');
+        imageDatum.TimeStampDeltas(plane{1},plane{2},plane{3}) = val;
+    else
+        imageDatum.(data{1}{k}) = val;
+    end
+end
+imageData.imageDir = '.';
+end

src/matlab/tiffReader.m

+function [im, imageData] = tiffReader(outType,chanList,timeList,zList,path)
+im = [];
+imageData = [];
+
+if (~exist('path','var') || ~exist(path,'file'))
+    path = [];
+end
+
+[imageData,path] = readMetaData(path);
+if (isempty(imageData))
+    warning('No image read!');
+    return
+end
+
+if (~exist('chanList','var') || isempty(chanList))
+    chanList = 1:imageData.NumberOfChannels;
+end
+if (~exist('timeList','var') || isempty(timeList))
+    timeList = 1:imageData.NumberOfFrames;
+end
+if (~exist('zList','var') || isempty(zList))
+    zList = 1:imageData.ZDimension;
+end
+
+if (~exist('outType','var') || isempty(outType))
+    imInfo = imfinfo(fullfile(path,sprintf('%s_c%02d_t%04d_z%04d.tif',imageData.DatasetName,1,1,1)),'tif');
+    bytes = imInfo.BitDepth/8;
+    if (imInfo.BitDepth==8)
+        outType = 'uint8';
+    elseif (imInfo.BitDepth==16)
+        outType = 'uint16';
+    elseif (imInfo.BitDepth==32)
+        outType = 'uint32';
+    else
+        outType = 'double';
+    end
+elseif (strcmp(outType,'double'))
+    bytes=8;
+    outType = 'double';
+elseif (strcmp(outType,'uint32') || strcmp(outType,'int32') || strcmp(outType,'single'))
+    bytes=4;
+elseif (strcmp(outType,'uint16') || strcmp(outType,'int16'))
+    bytes=2;
+elseif (strcmp(outType,'uint8'))
+    bytes=1;
+else
+    error('Unsupported Type');
+end
+
+imType = imread(fullfile(path,sprintf('%s_c%02d_t%04d_z%04d.tif',imageData.DatasetName,chanList(1),timeList(1),zList(1))),'tif');
+typ = whos('imType');
+clear imType
+
+imtemp = zeros(imageData.YDimension,imageData.XDimension,length(zList),typ.class);
+im = zeros(imageData.YDimension,imageData.XDimension,length(zList),length(chanList),length(timeList),outType);
+
+fprintf('Type:%s ',outType);
+fprintf('(');
+fprintf('%d',size(im,2));
+fprintf(',%d',size(im,1));
+for i=3:length(size(im))
+    fprintf(',%d',size(im,i));
+end
+
+fprintf(') %5.2fMB\n', (imageData.XDimension*imageData.YDimension*length(zList)*length(chanList)*length(timeList)*bytes)/(1024*1024));
+
+for t=1:length(timeList)
+    for c=1:length(chanList)
+        for z=1:length(zList)
+            try
+                imtemp(:,:,z) = imread(fullfile(path,sprintf('%s_c%02d_t%04d_z%04d.tif',imageData.DatasetName,chanList(c),timeList(t),zList(z))),'tif');
+            catch err
+                fprintf('\n****%s: %s\n',fullfile(path,sprintf('%s_c%02d_t%04d_z%04d.tif',imageData.DatasetName,chanList(c),timeList(t),zList(z))),err.identifier);
+            end
+        end
+        w = whos('imtemp');
+        
+        if (strcmpi(w.class,outType))
+            im(:,:,:,c,t) = imtemp;
+        else
+            im(:,:,:,c,t) = imageConvert(imtemp,outType);
+        end
+    end
+end
+
+clear imtemp
+end

src/matlab/tiffWriter.m

+function tiffWriter(im,prefix,imageData)
+
+if (exist('imageData','var') && ~isempty(imageData))
+    idx = strfind(prefix,'\');
+    if (isempty(idx))
+        idx = length(prefix);
+    end
+    createMetadata(prefix(1:idx(end)),imageData);
+end
+
+sizes = size(im);
+numDim = length(sizes);
+
+if numDim<5
+    frames= 1;
+else
+    frames = sizes(5);
+end
+if numDim<4
+    channels = 1;
+else
+    channels = sizes(4);
+end
+if numDim<3
+    stacks = 1;
+else
+    stacks = sizes(3);
+end
+
+imUint = uint8(im);
+
+for t=1:frames
+    for c=1:channels
+        for z=1:stacks
+            fileName = sprintf('%s_c%02d_t%04d_z%04d.tif',prefix,c,t,z);
+            imwrite(imUint(:,:,z,c,t),fileName,'tif','Compression','lzw');
+        end
+    end
+end
+
+fprintf('Wrote %s_c%d_t%d_z%d.tif\n',prefix,channels,frames,stacks);
+
+end
+