Bugfixes and cleaning for TIFF IO functions

git-svn-id: https://svn.code.sf.net/p/dct/code/trunk@944 4c865b51-4357-4376-afb4-474e03ccb993

zUtil_TIFF/gtTIFVolReader.m

@@ -59,8 +59,8 @@ if strcmp(params.mode, 'single')
 elseif strcmp(params.mode, 'stack')
     params.singlemode = false;
 else
-    Mexc = MException('TIFF:wrong_input_mode', ['Unkown input mode: ''' params.mode  '''']);
-    throw(Mexc);
+    gtError('gtTIFVolReader:wrong_input_mode', ...
+        ['Unkown input mode: ''' params.mode  '''']);
 end
 
 if ~exist('filename', 'var')
@@ -68,8 +68,8 @@ if ~exist('filename', 'var')
         [fname, fpath] = uigetfile('*', 'Select a .tif volume file');
         filename = fullfile(fpath, fname);
     else
-        Mexc = MException('TIFF:missing_input_filename', 'The name of the input file is missing!');
-        throw(Mexc);
+        gtError('gtTIFVolReader:missing_input_filename', ...
+            'The name of the input file is missing!');
     end
 end
 
@@ -85,20 +85,20 @@ if params.singlemode
     fullFilenameFormat = fullfile(fpath, filenameFormat);
 
     % Check existence of file
-    if ~exist(fullFilenameFormat)
-        Mexc = MException('TIFF:wrong_file_name', ['File ''' fullFilenameFormat ''' does not exist!']);
-        throw(Mexc);
+    if ~exist(fullFilenameFormat, 'file')
+        gtError('gtTIFVolReader:wrong_file_name', ...
+            ['File ''' fullFilenameFormat ''' does not exist!']);
     end
 else
     filenameFormat = sprintf('%s%%0%dd.%s', fname, params.digits, params.filext);
     fullFilenameFormat = fullfile(fpath, filenameFormat);
     
     % Check existence of input stack files
-    for i=params.startindex:params.endindex
-        sfilename = sprintf(filenameFormat, i);
-        if ~exist(sfilename)
-            Mexc = MException('TIFF:wrong_file_name', ['File ''' sfilename ''' does not exist!']);
-            throw(Mexc);
+    for idx=params.startindex:params.endindex
+        sfilename = sprintf(filenameFormat, idx);
+        if ~exist(sfilename, 'file')
+            gtError('gtTIFVolReader:wrong_file_name', ...
+                ['File ''' sfilename ''' does not exist!']);
         end
     end    
 end
@@ -108,11 +108,18 @@ infoFilename = sprintf(fullFilenameFormat, params.startindex);
 try
     tifInfo = imfinfo(infoFilename);
 catch Mexc
-    Mexc1 = MException('TIFF:wrong_input', ['Unable to read file ''' infoFilename '''']);
+    Mexc1 = MException('gtTIFVolReader:wrong_input', ...
+        ['Unable to read file ''' infoFilename '''']);
     Mexc1 = addCause(Mexc1, Mexc);
     throw(Mexc1);
 end
 
+% Cannot read RGB TIFF files right now
+if length(tifInfo(1).BitsPerSample) > 1
+    gtError('gtTIFVolReader:unsupported_input', ...
+        'Cannot handle RGB TIFF files yet!');
+end
+
 fullFilename = tifInfo(1).Filename;
 if params.singlemode
     fileIndex = ones(1, numel(tifInfo));
@@ -125,7 +132,7 @@ tifSizeY = tifInfo(1).Height;
 tifSizeZ = length(fileIndex);
 
 % Update file parts and full file format
-[fpath, fname, fext] = fileparts(fullFilename);
+[fpath, fname, ~] = fileparts(fullFilename);
 fullFilenameFormat = fullfile(fpath, filenameFormat);
 
 % Check each dimension range
@@ -189,14 +196,15 @@ info.BitDepth     = tifInfo(1).BitDepth;
 info.RowsPerStrip = tifInfo(1).RowsPerStrip;
 
 % Set slice container
-if ~length(ftype)
+if isempty(ftype)
     vol = zeros(volSizeX, volSizeY, volSizeZ);
+    tmp_slice = zeros(volSizeX, volSizeY);
 elseif strcmp(ftype, 'logical')
     vol = false(volSizeX, volSizeY, volSizeZ);
-    slice = false(volSizeX, volSizeY);
+    tmp_slice = false(volSizeX, volSizeY);
 else
     vol = zeros(volSizeX, volSizeY, volSizeZ, ftype);
-    slice = zeros(volSizeX, volSizeY, ftype);
+    tmp_slice = zeros(volSizeX, volSizeY, ftype);
 end
 
 % If new reading method and PhotometricInterpretation set to WhiteIsZero
@@ -212,50 +220,50 @@ if params.newMethod
     inputFilename = sprintf(fullFilenameFormat);
     if params.singlemode
         fid = tifflib('open', inputFilename, 'r');
-        for i=1:volSizeZ
+        for idx=1:volSizeZ
             if fullRangeXY
-                vol(:, :, i) = sfReadTIFSlice(fid, slice, rangeZ(i), info.RowsPerStrip, ftype);
+                vol(:, :, idx) = sfReadTIFSlice(fid, tmp_slice, rangeZ(idx), info.RowsPerStrip);
             else
-                vol(:, :, i) = sfReadTIFSliceROI(fid, slice, rangeZ(i), info.RowsPerStrip, ftype);
+                vol(:, :, idx) = sfReadTIFSliceROI(fid, tmp_slice, rangeZ(idx), info.RowsPerStrip);
             end
         end
         tifflib('close', fid);
     else
-        for i=1:volSizeZ
-            inputFilename = sprintf(fullFilenameFormat, fileIndex(i));
+        for idx=1:volSizeZ
+            inputFilename = sprintf(fullFilenameFormat, fileIndex(idx));
             fid = tifflib('open', inputFilename, 'r');
             if fullRangeXY
-                vol(:, :, i) = sfReadTIFSlice(fid, slice, 1, info.RowsPerStrip, ftype);
+                vol(:, :, idx) = sfReadTIFSlice(fid, tmp_slice, 1, info.RowsPerStrip);
             else
-                vol(:, :, i) = sfReadTIFSliceROI(fid, slice, 1, info.RowsPerStrip, ftype);
+                vol(:, :, idx) = sfReadTIFSliceROI(fid, tmp_slice, 1, info.RowsPerStrip);
             end
             tifflib('close', fid);
         end
     end
 else
-    for i=1:volSizeZ
-        inputFilename = sprintf(fullFilenameFormat, fileIndex(i));
+    for idx=1:volSizeZ
+        inputFilename = sprintf(fullFilenameFormat, fileIndex(idx));
         if fullRangeXY
-            vol(:, :, i) = imread(inputFilename, rangeZ(i), 'Info', tifInfo)';
+            vol(:, :, idx) = imread(inputFilename, rangeZ(idx), 'Info', tifInfo)';
         else
-            vol(:, :, i) = imread(inputFilename, rangeZ(i), 'PixelRegion', {[rangeY(1) rangeY(end)], [rangeX(1) rangeX(end)]})';
+            vol(:, :, idx) = imread(inputFilename, rangeZ(idx), 'PixelRegion', {[rangeY(1) rangeY(end)], [rangeX(1) rangeX(end)]})';
             % This second method should be faster but in fact...
             %vol(:, :, i) = imread(inputFilename, rangeZ(i), 'Info', info, 'PixelRegion', {[rangeY(1) rangeY(end)], [rangeX(1) rangeX(end)]})';
         end
     end
 end
 
-function slice = sfReadTIFSlice(fid, slice, sliceIndex, rowPerStrip, ftype)
+function x = sfReadTIFSlice(fid, x, sliceIndex, rowPerStrip)
     tifflib('setDirectory', fid, sliceIndex);
     rowPerStrip = min(rowPerStrip, volSizeY); 
     for irow = 1:rowPerStrip:volSizeY
         indY = irow:min(volSizeY, irow+rowPerStrip-1);
         stripNum = tifflib('computeStrip', fid, irow);
-        slice(:, indY) = tifflib('readEncodedStrip', fid, stripNum)';
+        x(:, indY) = tifflib('readEncodedStrip', fid, stripNum)';
     end
 end
 
-function slice = sfReadTIFSliceROI(fid, slice, sliceIndex, rowPerStrip, ftype)
+function x = sfReadTIFSliceROI(fid, x, sliceIndex, rowPerStrip)
     tifflib('setDirectory', fid, sliceIndex);
     iy = 1;
     while iy <= volSizeY 
@@ -268,7 +276,7 @@ function slice = sfReadTIFSliceROI(fid, slice, sliceIndex, rowPerStrip, ftype)
 
         stripIndicesY = mod(rowStart, rowPerStrip):(mod(rowStart, rowPerStrip) + nRows);
         volIndicesY   = iy:(iy + nRows);
-        slice(:, volIndicesY) = tifStrip(rangeX, stripIndicesY);
+        x(:, volIndicesY) = tifStrip(rangeX, stripIndicesY);
         iy = iy + nRows + 1;
     end
 end

zUtil_TIFF/gtTIFVolWriter.m

@@ -85,15 +85,14 @@ else
 end
 outVolSizeX = length(rangeX);
 outVolSizeY = length(rangeY);
-outVolSizeZ = length(rangeZ);
 
-% Checking input/output types and decide whther casting/rescaling operations 
+% Checking input/output types and decide whether casting/rescaling operations 
 doCast  = false;
 rescale = 0;
 inputType = class(vol);
 if ~isempty(params.type) && ~any(strcmp(params.type, {'logical', 'uint8', 'uint16'}))
-    gtError('gtTIFVolWriter:wrong_type', ['Output type ''' params.type ''' is not supported!']);
-    throw(Mexc);
+    gtError('gtTIFVolWriter:wrong_output_type', ...
+        ['Output type ''' params.type ''' is not supported!']);
 elseif any(strcmp(inputType, {'logical', 'uint8', 'uint16'}))
     if isempty(params.type)
         params.type = class(vol);
@@ -120,7 +119,8 @@ end
 % Cast and rescale if needed
 if doCast
     if rescale
-        disp(['Rescaling input volume to [0 ' num2str(rescale) '] and casting it to ' params.type ' ...']);
+        disp(['Rescaling input volume to [0 ' num2str(rescale) ...
+            '] and casting it to ' params.type ' ...']);
         outVol = cast(mat2gray(vol) * rescale, params.type);
     else
         disp(['Casting input volume to ' params.type ' ...']);
@@ -157,11 +157,15 @@ elseif (islogical(params.compress) && params.compress)
     end
 elseif any(strcmp(params.compress, {'ccitt', 'fax3', 'fax4'}))
     if ~islogical(outVol)
-        gtError('gtTIFVolWriter:wrong_compression', ...
-               ['Compression mode ''' params.compress ''' is only available for logical volumes!']);
+        gtError('gtTIFVolWriter:wrong_compression_mode', ...
+               ['Compression mode ''' params.compress ...
+               ''' is only available for logical volumes!']);
     end
-elseif ~any(strcmp(params.compress, {'none','packbits', 'deflate', 'lzw', 'ccitt', 'fax3', 'fax4'}))
-    warning(['Unkown compression mode: ' params.compress ' -> Setting it to ''none''...']);
+elseif ~any(strcmp(params.compress, {'none', 'packbits', 'deflate', 'lzw', ...
+                                     'ccitt', 'fax3', 'fax4'}))
+    warning('gtTIFVolWriter:unknown_compression_mode', ...
+        ['Unknown compression mode: ' params.compress ...
+        ' -> Setting it to ''none''...']);
     params.compress = 'none';
 end
 
@@ -173,6 +177,7 @@ case 'deflate' , tifTag.Compression = Tiff.Compression.Deflate;  % Slow but effi
 case 'ccitt'   , tifTag.Compression = Tiff.Compression.CCITTRLE;
 case 'fax3'    , tifTag.Compression = Tiff.Compression.CCITTFax3;
 case 'fax4'    , tifTag.Compression = Tiff.Compression.CCITTFax4;
+otherwise      , tifTag.Compression = Tiff.Compression.None;
 end
 
 % Set TIFF file tags
@@ -183,13 +188,19 @@ tifTag.ImageLength = outVolSizeY;
 tifTag.Software = 'matlabDCT';
 
 % Guessing output directory, filename and extension
-[fdir, fname, fext] = fileparts(filename);
+[fpath, fname, fext] = fileparts(filename);
+% Trick to handle ~ path in unix
+if fpath(1)=='~' && isunix()
+    fpath(1) = '';
+    fpath = fullfile(getenv('HOME'), fpath);
+end
 
 if strcmpi(params.mode, 'single')
-
     % Setting output filename
-    if ~length(fext)
-        filename = fullfile(fdir, [fname '.' params.filext]);
+    if isempty(fext)
+        filename = fullfile(fpath, [fname '.' params.filext]);
+    else
+        filename = fullfile(fpath, [fname '.' fext]);
     end
 
     % Check existence of output file to delete it before writing
@@ -209,8 +220,10 @@ if strcmpi(params.mode, 'single')
     else
         % Old method
         for iz=1:length(rangeZ)
-            imwrite(outVol(rangeX(1):rangeX(end), rangeY(1):rangeY(end), rangeZ(iz))', ...
-                    filename, 'tif', 'Compression', params.compress, 'writemode', 'append');
+            imwrite(outVol(rangeX(1):rangeX(end), rangeY(1):rangeY(end), ...
+                rangeZ(iz))', ...
+                filename, 'tif', 'Compression', params.compress, ...
+                'writemode', 'append');
         end
     end
 
@@ -220,11 +233,12 @@ elseif strcmpi(params.mode, 'stack')
     if isnumeric(params.startindex)
         if mod(params.startindex, 1) ~= 0
             params.startindex = round(params.startindex);
-            disp(['Argument ''startindex'' convert to ' num2str(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);
+        gtError('gtTIFVolWriter:wrong_argument_type', ...
+            'The argument ''startindex'' should be an integer!');
     end
 
     % Check stack number of digits
@@ -234,18 +248,18 @@ elseif strcmpi(params.mode, 'stack')
             disp(['Argument ''digits'' convert to ' num2str(params.digits)]);
         end
     else
-        Mexc = MException('INPUT:wrong_type', ['The argument ''digits'' should be an integer!']);
-        throw(Mexc);
+        gtError('gtTIFVolWriter:wrong_argument_type', ...
+            'The argument ''digits'' should be an integer!');
     end
 
     % Create directory
-    if and(length(fdir), ~isdir(fdir))
-        mkdir(fdir);
+    if ~isempty(fpath) && ~exist(fpath, 'dir')
+        mkdir(fpath);
     end
 
     % Output file output format
-    fprefix = fullfile(fdir, fname);
-    filenameFormat = sprintf('%s%%0%dd.%s', fprefix, params.digits, params.filext);
+    fprefix = fullfile(fpath, fname);
+    filenameFMT = sprintf('%s%%0%dd.%s', fprefix, params.digits, params.filext);
 
     % Set output index offset
     offset = params.startindex - 1;
@@ -253,7 +267,7 @@ elseif strcmpi(params.mode, 'stack')
     % Writing volume in TIFF stack files
     if params.newMethod 
         for iz=1:length(rangeZ)
-            outFile = sprintf(filenameFormat, iz+offset);
+            outFile = sprintf(filenameFMT, iz+offset);
             tif = Tiff(outFile, 'w');
             tif.setTag(tifTag);
             tif.write(outVol(rangeX, rangeY, rangeZ(iz))');
@@ -262,7 +276,7 @@ elseif strcmpi(params.mode, 'stack')
     else
         % Old method
         for iz=1:length(rangeZ)
-            outFile = sprintf(filenameFormat, iz+offset);
+            outFile = sprintf(filenameFMT, iz+offset);
             imwrite(outVol(rangeX, rangeY, rangeZ(iz))', outFile, 'tif', ...
                     'Compression', params.compress, 'writemode', 'overwrite');
         end