GtVolView can now load tif volumes directly

git-svn-id: https://svn.code.sf.net/p/dct/code/trunk@260 4c865b51-4357-4376-afb4-474e03ccb993

zUtil_TIFF/gtReadTifVolume.m

-function vol = gtReadTifVolume(filename, varargin)
+function [vol, info] = 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])
+% Usage: [vol,info]=gtReadTifVolume(filename,[,'xrange',xrange,'yrange',yrange,'zrange',zrange])
 %        Use it exactly the same as gtHSTVolReader function.
 %
 % 14 February 2012, Yoann Guilhem, guilhem@esrf.eu
@@ -17,79 +17,98 @@ if ~exist('filename','var')
     filename = fullfile(tmp2,tmp1);
 end
 
+[fpath, fname, fext] = fileparts(filename);
+
+% Checking existence of file extension, if not, add it
+if ~length(fext)
+    filename = [filename '.tif'];
+end
+
+% Check existence of file
 if ~exist(filename)
     Mexc = MException('TIFF:wrong_file_name',['File ''' filename ''' does not exist!']);
     throw(Mexc);
 end
 
 try
-    info = imfinfo(filename);
+    tifInfo = imfinfo(filename);
 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 = MException('TIFF:wrong_input', 'Unable to read file');
     Mexc1 = addCause(Mexc1, Mexc);
     throw(Mexc1);
 end
 
-XTifSize = info(1).Width;
-YTifSize = info(1).Height;
-ZTifSize = numel(info);
+fullFilename = tifInfo(1).Filename;
+[fpath, fname, fext] = fileparts(fullFilename);
+tifSizeX = tifInfo(1).Width;
+tifSizeY = tifInfo(1).Height;
+tifSizeZ = numel(tifInfo);
 
 if strcmp(params.xrange,'all')
-    Xrange = 1:XTifSize;
+    rangeX = 1:tifSizeX;
 else
-    Xrange = params.xrange;
+    rangeX = params.xrange;
 end
 if strcmp(params.yrange,'all')
-    Yrange = 1:YTifSize;
+    rangeY = 1:tifSizeY;
 else
-    Yrange = params.yrange;
+    rangeY = params.yrange;
 end
 if strcmp(params.zrange,'all')
-    Zrange = 1:ZTifSize;
+    rangeZ = 1:tifSizeZ;
 else
-    Zrange = params.zrange;
+    rangeZ = params.zrange;
 end
 
-XVolSize = length(Xrange);
-YVolSize = length(Yrange);
-ZVolSize = length(Zrange);
+volSizeX = length(rangeX);
+volSizeY = length(rangeY);
+volSizeZ = length(rangeZ);
 
-switch info(1).BitDepth
+switch tifInfo(1).BitDepth
+    case 1
+        ftype = 'logical';
     case 8
-        vol = zeros(XVolSize,YVolSize,ZVolSize,'uint8');
+        ftype = 'uint8';
     case 12
-        vol = zeros(XVolSize,YVolSize,ZVolSize,'uint16');
+        ftype = 'uint16';
     case 16
-        vol = zeros(XVolSize,YVolSize,ZVolSize,'uint16');
+        ftype = 'uint16';
     otherwise
-        vol = zeros(XVolSize,YVolSize,ZVolSize);
+        ftype = '';
+end
+
+if ~length(ftype)
+    vol = zeros(volSizeX,volSizeY,volSizeZ);
+elseif strcmp(ftype,'logical')
+    vol = false(volSizeX,volSizeY,volSizeZ,'uint8');
+else
+    vol = zeros(volSizeX,volSizeY,volSizeZ,ftype);
 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])
+% Same info as HST volumes
+info.volSizeX = volSizeX;
+info.volSizeY = volSizeY;
+info.volSizeZ = volSizeZ;
+info.bytespervoxel = tifInfo(1).SamplesPerPixel * tifInfo(1).BitsPerSample / 8;
+info.fpath = fpath;
+info.fname_final = fullFilename;
+info.byteorder = tifInfo(1).ByteOrder(1);
+info.ftype = ftype;
+info.fname_prefix = fname;
 
-%tic
 if nargin <= 1
-    for i=1:ZVolSize
-        vol(:,:,i) = imread(filename, Zrange(i))';
+    for i=1:volSizeZ
+        vol(:,:,i) = imread(filename, rangeZ(i))';
     end
 else
-    for i=1:ZVolSize
-        vol(:,:,i) = imread(filename, Zrange(i), 'PixelRegion', {[Yrange(1) Yrange(end)], [Xrange(1) Xrange(end)]})';
+    for i=1:volSizeZ
+        vol(:,:,i) = imread(filename, rangeZ(i), 'PixelRegion', {[rangeY(1) rangeY(end)], [rangeX(1) rangeX(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)]})';
+        %vol(:,:,i) = imread(filename, rangeZ(i), 'Info', info, 'PixelRegion', {[rangeY(1) rangeY(end)], [rangeX(1) rangeX(end)]})';
     end
 end
-%toc
 
 end

zUtil_TomoUtils/GtVolView.m

@@ -668,9 +668,11 @@ classdef GtVolView < GtBaseGuiElem
         % also the format
             if isa(vol, 'char') % user has specified a filename
                 [~, ~, ext] = fileparts(vol);
-                switch (ext) % TIFF should be added as well
+                switch (ext)
                     case '.edf'
                         [vol, info] = edf_read(vol);
+                    case '.tif'
+                        [vol, info] = gtReadTifVolume(vol);
                     otherwise
                         [vol, info] = gtHSTVolReader(vol);
                 end