Add the options to output a stack of multiple TIFF files

git-svn-id: https://svn.code.sf.net/p/dct/code/trunk@666 4c865b51-4357-4376-afb4-474e03ccb993

zUtil_TIFF/gtTIFVolWriter.m

 function gtTIFVolWriter(vol, filename, varargin)
 % GTTIFVOLWRITER  Writes volume data to TIFF file without compression.
+%                 Either single file of multiple files stack can be produced.
 %                 The produced TIFF files contain 8/16 bit unsigned integers.
 %     -------------------------------------------------------------------------
 %     gtTIFVolWriter(vol, filename, varargin)
 % 
 %     INPUT:
-%       vol      = <int>     3D volume data
-%                  <float>
-%       filename = <string>  path to TIFF file to write
-%                            the path may be relative or absolute
-%                            if extension is missing, '.tif' will be append
+%       vol        = <int>     3D volume data
+%                    <float>
+%       filename   = <string>  path to TIFF file to write
+%                              The path may be relative or absolute.
+%                              If extension is missing, '.tif' will be append.
+%                              In the case of stack output, this will be the 
+%                              stack filename prefix to which the slice number 
+%                              and the '.tif' extension will be append.
 %
 %     OPTIONAL INPUT (varargin as a list of pairs, see parse_pv_pairs.m):
-%       type     = <string>  type of data written in the TIFF file
-%                            it can be 'uint8' or 'uint16'
-%                            by default it is 'uint8'
-%       xrange   = <range>   index range of output in X direction
-%       yrange   = <range>   index range of output in Y direction
-%       zrange   = <range>   index range of output in Z direction
+%       xrange     = <range>   index range of output in X direction
+%       yrange     = <range>   index range of output in Y direction
+%       zrange     = <range>   index range of output in Z direction
+%
+%       type       = <string>  type of data written in the TIFF file
+%                              it can be 'uint8' or 'uint16'
+%                              by default it is 'uint8'
+%
+%       output     = <string>  output type which is either 'single' or 'stack'
+%                              default output type is a single TIFF file
+%       digits     = <int>     number of digits in stack filenames
+%       startindex = <int>
 %
 %     TODO :
 %     - RGB data output
 %
+%     Version 002 19-07-2012 by YGuilhem
+%         Add the options to output the volume as a stack of multiple TIFF
+%         files.
+%
 %     Version 001 15-02-2012 by YGuilhem
 
 % Set default parameters and parse optional arguments
@@ -29,19 +43,11 @@ params.type = 'uint8';
 params.xrange = 'all';
 params.yrange = 'all';
 params.zrange = 'all';
+params.output = 'single';
+params.digits = 4;
+params.startindex = 1;
 params = parse_pv_pairs(params, varargin);
 
-% Setting output filename
-[~, ~, fext] = fileparts(filename);
-if ~length(fext)
-    filename = [filename '.tif'];
-end
-
-% Check existence of output file to delete it before writing
-if exist(filename,'file')
-    delete(filename);
-end
-
 % Translating range parameters
 if strcmp(params.xrange,'all')
     rangeX = 1:size(vol,1);
@@ -71,16 +77,75 @@ if ~isa(vol,params.type)
         case 'uint16'
             outVol = uint16(grayVol*65535);
         otherwise
-            Mexc = MException('TIFF:wrong_type', ['Out ouput type ''' type ''' is not supported!']);
+            Mexc = MException('TIFF:wrong_type', ['Output type ''' type ''' is not supported!']);
             throw(Mexc);
     end
 else
     outVol = vol;
 end
 
-% Writing volume in TIFF file
-for i=1:length(rangeZ)
-    imwrite(outVol(rangeX(1):rangeX(end), rangeY(1):rangeY(end),rangeZ(i))', filename, 'tif', 'Compression', 'none', 'writemode', 'append');
+% Guessing output directory, filename and extension
+[fdir, fname, fext] = fileparts(filename);
+
+if strcmpi(params.output, 'single')
+
+    % Setting output filename
+    if ~length(fext)
+        filename = fullfile(fdir, [fname '.tif']);
+    end
+
+    % Check existence of output file to delete it before writing
+    if exist(filename, 'file')
+        delete(filename);
+    end
+
+    % Writing volume in TIFF file
+    for i=1:length(rangeZ)
+        imwrite(outVol(rangeX(1):rangeX(end), rangeY(1):rangeY(end),rangeZ(i))', filename, 'tif', 'Compression', 'none', 'writemode', 'append');
+    end
+
+elseif strcmpi(params.output, 'stack')
+
+    % Check stack starting index
+    if isnumeric(params.startindex)
+        if mod(params.startindex,1) ~= 0
+            params.startindex = round(params.startindex);
+            disp(['Argument ''startindex'' convert to ' num2str(params.startindex)]);
+        end
+    else
+        Mexc = MException('INPUT:wrong_type', ['The argument ''startindex'' should be an integer!']);
+        throw(Mexc);
+    end
+
+    % Check stack number of digits
+    if isnumeric(params.digits)
+        if mod(params.digits,1) ~= 0
+            params.digits = round(params.digits);
+            disp(['Argument ''digits'' convert to ' num2str(params.digits)]);
+        end
+    else
+        Mexc = MException('INPUT:wrong_type', ['The argument ''digits'' should be an integer!']);
+        throw(Mexc);
+    end
+
+    % Create directory
+    if and(length(fdir), ~isdir(fdir))
+        mkdir(fdir);
+    end
+
+    % Output file output format
+    fprefix = fullfile(fdir, fname);
+    filenameFormat = sprintf('%s%%0%dd.tif', fprefix, params.digits);
+
+    % Set output index offset
+    offset = params.startindex - 1;
+
+    % Writing volume in TIFF file
+    for i=1:length(rangeZ)
+        outFile = sprintf(filenameFormat, i+offset);
+        imwrite(outVol(rangeX(1):rangeX(end), rangeY(1):rangeY(end),rangeZ(i))', outFile, 'tif', 'Compression', 'none');
+    end
+
 end
 
 end % end of function