Squashed '@TIFFStack/' changes from 9e73c53..e80689f

e80689f Merge branch 'pr5'
f72457e * Added an overloaded `saveobj` method, to ensure object is serialised correctly, and to ensure that `delete` doesn't get called on a loaded object * `TS_UnitTest` now tests saving and loaded of a `TIFFStack` * Upgraded `tiffread` to version 3.31
0e3df90 Add loadobj method, useable with default saveobj
5db9a02 Added licensing information to `README.md` and `LICENSE.md`

git-subtree-dir: @tiffstack
git-subtree-split: e80689f4f6a222b3f011d2be125ff8e4f28d5269

Author: DylanMuir

LICENSE.md

@@ -0,0 +1,10 @@
+## License
+<a rel="license" href="http://creativecommons.org/licenses/by-nc-sa/4.0/"><img alt="Creative Commons License" style="border-width:0" src="https://i.creativecommons.org/l/by-nc-sa/4.0/80x15.png" /></a><br /><span xmlns:dct="http://purl.org/dc/terms/" property="dct:title">TIFFStack</span> by <a xmlns:cc="http://creativecommons.org/ns#" href="http://dylan-muir.com" property="cc:attributionName" rel="cc:attributionURL">Dylan Muir</a> is licensed under a <a rel="license" href="http://creativecommons.org/licenses/by-nc-sa/4.0/">Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International License</a>.<br />Based on a work at <a xmlns:dct="http://purl.org/dc/terms/" href="http://github.com/DylanMuir/TIFFStack" rel="dct:source">http://github.com/DylanMuir/TIFFStack</a>.
+
+This work was published in [Frontiers in Neuroinformatics]: DR Muir and
+BM Kampa. 2015. *[FocusStack and StimServer: A new open source MATLAB
+toolchain for visual stimulation and analysis of two-photon calcium
+neuronal imaging data](http://dx.doi.org/10.3389/fninf.2014.00085)*, **Frontiers in Neuroinformatics** 8 *85*. DOI: [dx.doi.org/10.3389/fninf.2014.00085](http://dx.doi.org/10.3389/fninf.2014.00085).
+Please cite our publication in lieu of thanks, if you use this code.
+
+  [Frontiers in Neuroinformatics]: http://www.frontiersin.org/neuroinformatics

README.md

@@ -141,6 +141,9 @@ reading and caching the header information (the image file directories —
 IFDs). Each frame can then be read directly without re-opening the file
 and re-reading the IFDs.
 
+## License
+<a rel="license" href="http://creativecommons.org/licenses/by-nc-sa/4.0/"><img alt="Creative Commons License" style="border-width:0" src="https://i.creativecommons.org/l/by-nc-sa/4.0/80x15.png" /></a><br /><span xmlns:dct="http://purl.org/dc/terms/" property="dct:title">TIFFStack</span> by <a xmlns:cc="http://creativecommons.org/ns#" href="http://dylan-muir.com" property="cc:attributionName" rel="cc:attributionURL">Dylan Muir</a> is licensed under a <a rel="license" href="http://creativecommons.org/licenses/by-nc-sa/4.0/">Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International License</a>.<br />Based on a work at <a xmlns:dct="http://purl.org/dc/terms/" href="http://github.com/DylanMuir/TIFFStack" rel="dct:source">http://github.com/DylanMuir/TIFFStack</a>.
+
   [Frontiers in Neuroinformatics]: http://www.frontiersin.org/neuroinformatics
   [FFSS]: http://journal.frontiersin.org/Journal/10.3389/fninf.2014.00085
   [10.1103/PhysRevLett.86.3192]: //dx.doi.org/10.1103/PhysRevLett.86.3192

TIFFStack.m

@@ -144,14 +144,15 @@
    end
 
    properties (SetAccess = private, GetAccess = private)
+      bForceTiffread       % - Force the use of tiffread, rather than trying to use TiffLib
       vnDataSize;          % - Cached size of the TIFF stack
       vnApparentSize;      % - Apparent size of the TIFF stack
       TIF;                 % \_ Cached header info for tiffread29 speedups
       HEADER;              % /
       bUseTiffLib;         % - Flag indicating whether TiffLib is being used
       fhReadFun;           % - When using Tiff class, function for reading data
       fhSetDirFun;         % - When using Tiff class, function for setting the directory
-      vnDimensionOrder;    % - Internal dimensions order to support permution
+      vnDimensionOrder;    % - Internal dimensions order to support permutation
       fhRepSum;            % - Function handle to (hopefully) accellerated repsum function
       fhCastFun;           % - The matlab function that casts data to the required return class
    end
@@ -170,6 +171,7 @@
          if (~exist('bForceTiffread', 'var') || isempty(bForceTiffread))
             bForceTiffread = false;
          end
+         oStack.bForceTiffread = bForceTiffread;
 
          % - Can we use the accelerated TIFF library?
          if (exist('tifflib') ~= 3) %#ok<EXIST>
@@ -340,10 +342,10 @@
 
             else
                % - Read TIFF header for tiffread29
-               [oStack.TIF, oStack.HEADER] = tiffread29_header(strFilename);
+               [oStack.TIF, oStack.HEADER] = tiffread31_header(strFilename);
 
                % - Use tiffread29 to get the data class for this tiff
-               fPixel = tiffread29_readimage(oStack.TIF, oStack.HEADER, 1);
+               fPixel = tiffread31_readimage(oStack.TIF, oStack.HEADER, 1);
                fPixel = fPixel(1, 1, :);
                oStack.strDataClass = class(fPixel);
             end
@@ -727,8 +729,36 @@ function diagnostic(oStack)
             oStack.bInvert = bInvert;
          end
       end
+            
+      
+%% --- Overloaded save method
+      % saveobj - Save method
+      function sSerialised = saveobj(tsStack)
+         % - Serialise object and remove transient properties
+         w = warning('off', 'MATLAB:structOnObject');
+         sSerialised = struct(tsStack);
+         sSerialised = rmfield(sSerialised, {'TIF', 'HEADER', 'fhReadFun', 'fhSetDirFun', 'fhRepSum', 'fhCastFun'});
+         warning(w);
+      end
 
    end
+
+%% -- Overloaded load method
+
+   methods (Static)
+      
+      % loadobj - Load method
+      function oStack = loadobj(sSavedVar)
+         % - Create a new TIFFStack
+         oStack = TIFFStack(sSavedVar.strFilename, sSavedVar.bInvert, [], ...
+                            sSavedVar.bForceTiffread);
+
+         % - Adjust dimensions to look like saved stack
+         oStack.vnApparentSize = sSavedVar.vnApparentSize;
+         oStack.vnDimensionOrder = sSavedVar.vnDimensionOrder;
+      end
+
+   end
 end
 
 %% --- Helper functions ---
@@ -771,7 +801,7 @@ function diagnostic(oStack)
 
    % - Read data block
    try
-      tfDataBlock = tiffread29_readimage(oStack.TIF, oStack.HEADER, vnFrameIndices);
+      tfDataBlock = tiffread31_readimage(oStack.TIF, oStack.HEADER, vnFrameIndices);
 
    catch mErr
       % - Record error state

private/TS_UnitTest.m

@@ -14,6 +14,11 @@
 function TS_UnitTest(strFilename)
    % - Make sure TIFFStack is on the path
    strTSDir = fileparts(which('TIFFStack'));
+   
+   if (isempty(strTSDir))
+      error('TIFFStack:Path', '*** Error: ''TIFFStack'' is not available on the matlab path.');
+   end
+   
    strBaseDir = fileparts(strTSDir);
    addpath(strBaseDir);
 
@@ -73,12 +78,12 @@ function TS_UnitTest(strFilename)
    TSUT_TestReferencing(tsStack, tfStack, 'Raw stack');
 
    %% - Test permuted stack
-   tsStack = permute(tsStack, [3 1 2]);
-   tfStack = permute(tfStack, [3 1 2]);
+   tsStack = permute(tsStack, [3 1 2 4]);
+   tfStack = permute(tfStack, [3 1 2 4]);
    TSUT_TestReferencing(tsStack, tfStack, 'Simple permutation');
-   tsStack = ipermute(tsStack, [3 1 2]);
-   tfStack = ipermute(tfStack, [3 1 2]);   
-   
+   tsStack = ipermute(tsStack, [3 1 2 4]);
+   tfStack = ipermute(tfStack, [3 1 2 4]);   
+      
    %% - Test inverted stack
    tsStack.bInvert = true;
    tfStack = 255 - tfStack;
@@ -98,6 +103,12 @@ function TS_UnitTest(strFilename)
    tfStack = reshape(tfStack, [size(tfStack, 1) size(tfStack, 2) 1 1 nNumFrames size(tfStack, 4)]);
    TSUT_TestReferencing(tsStack, tfStack, 'Deinterleaved stack');
 
+   %% - Test saving / loading a stack
+   strMatFile = tempname;
+   save(strMatFile, 'tsStack');
+   s = load(strMatFile);
+   TSUT_TestReferencing(tsStack, s.tsStack, 'Serialised/Deserialised stack');
+   
    %% - Success if we reach here with no errors
    disp('--- TS_UnitTest: Unit tests for ''TIFFStack'' passed.');
 end