Add little macros for TIFF files

git-svn-id: https://svn.code.sf.net/p/dct/code/trunk@218 4c865b51-4357-4376-afb4-474e03ccb993

initialise_gt.m

@@ -134,6 +134,7 @@ function initialise_gt()
     addpath(fullfile(GT_MATLAB_HOME, 'zUtil_Smoothing'));
     addpath(fullfile(GT_MATLAB_HOME, 'zUtil_Strain'));
     addpath(fullfile(GT_MATLAB_HOME, 'zUtil_TomoUtils'));
+    addpath(fullfile(GT_MATLAB_HOME, 'zUtil_TIFF'));
     addpath(fullfile(GT_MATLAB_HOME, 'zUtil_XML'));
 
     addpath(fullfile(GT_MATLAB_HOME, 'FigureManagement'));

zUtil_TIFF/gtConvertRawToTifVolume.m

+function gtConvertRawToTifVolume(rootdir, savefolder, filenames)
+% GTCONVERTRAWTOTIFVOLUME cast raw volume data to tif without compression.
+% Can cast lots of volumes to tif when reconstructed .vol files have the
+% same name as the containing folder. 
+% The produced TIFF files are 8 bit unsigned integer type.
+%
+% *Usage:*
+%
+%  gtConvertRawToTifVolume(rootdir, savefolder, filenames)
+%  rootdir = string     containing root folder
+%  savefolder = string  folder where the tif volumes should be saved
+%  filenames = string   name of the containing folder, with * for several ones
+%
+% *Example:*
+%
+%  gtConvertRawToTifVolume(/data/id11/inhouse/wolfgang, voltif, ti_55531*)
+%
+% 14 February 2012, Yoann Guilhem, guilhem@esrf.fr
+
+cd(rootdir);
+d=dir(filenames);
+if ~exist(savefolder,'dir')
+    disp(['Folder "' savefolder '" does not exist. Creating it...']);
+    mkdir(savefolder);
+end
+
+for i=1:length(d)
+    VolFile = d(i).name;
+    if d(i).isdir
+        Type = 'folder';
+        VolName = VolFile;
+        VolFileName = fullfile(rootdir, VolFile, VolFile);
+    else
+        Type = 'file';
+        [tmp,VolName,] = fileparts(VolFile);
+        disp(['Processing on "' VolName '" volume file...']);
+        VolFileName = fullfile(rootdir, VolFile);
+    end
+    disp(['Processing on "' VolName '" volume ' Type '...']);
+
+    % Reading volume
+    Vol = HSTVolReader(VolFileName, 'xrange', 'all', 'yrange', 'all', 'zrange', 'all');
+
+    % Creating grayscale integer volume 
+    grayNewVol = mat2gray(Vol);
+    intvolume = uint8(grayNewVol*255);
+
+    % Writing volume in TIFF file
+    TifFileName = fullfile(rootdir, savefolder, [VolName '.tif']);
+    if exist(TifFileName,'file')
+        delete(TifFileName);
+    end
+    for i=1:size(Vol,3)
+        imwrite(intvolume(:,:,i)', TifFileName, 'tif', 'Compression', 'none', 'writemode', 'append');
+    end
+    disp('done');
+end

zUtil_TIFF/gtReadTifVolume.m

+function vol = gtReadTifVolume(filename)
+% GTREADTIFVOLUME read tif volume (stack) and store it into a matrix
+%
+% 14 February 2012, Yoann Guilhem, guilhem@esrf.eu
+
+if exist(filename)
+    info = imfinfo(filename);
+    Xsize = info(1).Width;
+    Ysize = info(1).Height;
+    Zsize = numel(info);
+    vol = zeros(Ysize,Xsize,Zsize);
+    for i=1:size(vol,3)
+        vol(:,:,i) = imread(filename,i);
+    end
+else
+    error('"%s" file does not exist!', filename);
+end