Fix gtReadTifVolume, consistent and faster

git-svn-id: https://svn.code.sf.net/p/dct/code/trunk@257 4c865b51-4357-4376-afb4-474e03ccb993

zUtil_TIFF/gtReadTifVolume.m

-function vol = gtReadTifVolume(filename)
-% GTREADTIFVOLUME read tif volume (stack) and store it into a matrix
+function vol = gtReadTifVolume(filename, varargin)
+% GTREADTIFVOLUME read tif volume (stack) and store it into a matrix [X,Y,Z]
+%
+% Usage: vol=gtReadTifVolume(filename,[,'xrange',xrange,'yrange',yrange,'zrange',zrange])
+%        Use it exactly the same as gtHSTVolReader function.
 %
 % 14 February 2012, Yoann Guilhem, guilhem@esrf.eu
 
-if exist(filename)
+params.xrange = 'all';
+params.yrange = 'all';
+params.zrange = 'all';
+
+params = parse_pv_pairs(params, varargin);
+
+if ~exist('filename','var')
+    [tmp1, tmp2] = uigetfile('*','Select a .tif volume file');
+    filename = fullfile(tmp2,tmp1);
+end
+
+if ~exist(filename)
+    Mexc = MException('TIFF:wrong_file_name',['File ''' filename ''' does not exist!']);
+    throw(Mexc);
+end
+
+try
     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);
+catch Mexc
+    disp('Unable to read information of selected volume.')
+    disp('Please check it exists in the directory.')
+    disp(' ')
+    Mexc1 = MException('TIFF:wrong_input', 'Unable to read files');
+    Mexc1 = addCause(Mexc1, Mexc);
+    throw(Mexc1);
+end
+
+XTifSize = info(1).Width;
+YTifSize = info(1).Height;
+ZTifSize = numel(info);
+
+if strcmp(params.xrange,'all')
+    Xrange = 1:XTifSize;
+else
+    Xrange = params.xrange;
+end
+if strcmp(params.yrange,'all')
+    Yrange = 1:YTifSize;
+else
+    Yrange = params.yrange;
+end
+if strcmp(params.zrange,'all')
+    Zrange = 1:ZTifSize;
+else
+    Zrange = params.zrange;
+end
+
+XVolSize = length(Xrange);
+YVolSize = length(Yrange);
+ZVolSize = length(Zrange);
+
+switch info(1).BitDepth
+    case 8
+        vol = zeros(XVolSize,YVolSize,ZVolSize,'uint8');
+    case 12
+        vol = zeros(XVolSize,YVolSize,ZVolSize,'uint16');
+    case 16
+        vol = zeros(XVolSize,YVolSize,ZVolSize,'uint16');
+    otherwise
+        vol = zeros(XVolSize,YVolSize,ZVolSize);
+end
+
+%disp('Tiff')
+%disp([info(1).Height info(1).Width numel(info)])
+%disp([XTifSize YTifSize ZTifSize]);
+%disp(size(imread(filename, 1)))
+%disp('Tiff crop')
+%disp(size(imread(filename, 1,'PixelRegion', {[Yrange(1) Yrange(end)], [Xrange(1) Xrange(end)]})))
+%disp('Vol crop')
+%disp(size(imread(filename, 1,'PixelRegion', {[Yrange(1) Yrange(end)], [Xrange(1) Xrange(end)]})'))
+%disp([XVolSize YVolSize ZVolSize])
+
+%tic
+if nargin <= 1
+    for i=1:ZVolSize
+        vol(:,:,i) = imread(filename, Zrange(i))';
     end
 else
-    error('"%s" file does not exist!', filename);
+    for i=1:ZVolSize
+        vol(:,:,i) = imread(filename, Zrange(i), 'PixelRegion', {[Yrange(1) Yrange(end)], [Xrange(1) Xrange(end)]})';
+        % This second method should be faster but in fact...
+        %vol(:,:,i) = imread(filename, Zrange(i), 'Info', info, 'PixelRegion', {[Yrange(1) Yrange(end)], [Xrange(1) Xrange(end)]})';
+    end
+end
+%toc
+
 end