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TIFFStack.m
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TIFFStack.m
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% <strong>TIFFStack</strong> - Manipulate a TIFF file like a tensor
%
% Usage: tsStack = <<strong>TIFFStack</strong>(strFilename <, bInvert, vnInterleavedFrameDims>)
%
% A TIFFStack object behaves like a read-only memory mapped TIFF file. The
% entire image stack is treated as a matlab tensor. Each frame of the file must
% have the same dimensions. Reading the image data is optimised to the extent
% possible; the header information is only read once.
%
% If this software is useful to your academic work, please cite our
% publication in lieu of thanks:
%
% D R Muir and B M Kampa, 2015. "FocusStack and StimServer: a new open
% source MATLAB toolchain for visual stimulation and analysis of two-photon
% calcium neuronal imaging data". Frontiers in Neuroinformatics 8 (85).
% DOI: <a href="http://dx.doi.org/10.3389/fninf.2014.00085">10.3389/fninf.2014.00085</a>
%
% This class attempts to use the version of tifflib built-in to recent
% versions of Matlab, if available. Otherwise this class uses a modified
% version of tiffread [2, 3] to read data.
%
% permute, ipermute and transpose are now transparantly supported. Note
% that to read a pixel, the entire frame containing that pixel is read. So
% reading a Z-slice of the stack will read in the entire stack.
%
% Some TIFF file writing software introduces custom or poorly-formed tags.
% This causes tifflib to produce lots of warnings. These warnings can be
% ignored by setting:
%
% >> w = warning('off', 'MATLAB:imagesci:tiffmexutils:libtiffWarning');
% >> warning('off', 'MATLAB:imagesci:tifftagsread:expectedTagDataFormat');
%
% and later restored with:
%
% >> warning(w);
%
% -------------------------------------------------------------------------
%
% <strong>Construction</strong>
% >> tsStack = TIFFStack('test.tiff'); % Construct a TIFF stack associated with a file
%
% >> tsStack = TIFFStack('test.tiff', true); % Indicate that the image data should be inverted
%
% tsStack =
%
% TIFFStack handle
%
% Properties:
% bInvert: 0
% strFilename: [1x9 char]
% sImageInfo: [5x1 struct]
% strDataClass: 'uint16'
%
% Usage:
%
% >> tsStack(:, :, 3); % Retrieve the 3rd frame of the stack, all planes
%
% >> tsStack(:, :, 1, 3); % Retrieve the 3rd plane of the 1st frame
%
% >> size(tsStack) % Find the size of the stack (rows, cols, frames, planes per pixel)
%
% ans =
%
% 128 128 5 1
%
% >> tsStack(4); % Linear indexing is supported
%
% >> tsStack.bInvert = true; % Turn on data inversion
%
% >> getFilename(tsStack) % Retrieve the 'strFilename' property
% >> getInvert(tsStack) % Retrive the 'bInvert' property
% >> getImageInfo(tsStack) % Retrieve the 'sImageInfo' property
% >> getDataClass(tsStack) % Retrive the 'strDataClass' property
%
% -------------------------------------------------------------------------
%
% <strong>De-interleaving frame dimensions in complex stacks</strong>
% Some TIFF generation software stores multiple samples per pixel as
% interleaved frames in a TIFF file. Other complex stacks may include
% multiple different images per frame of time (e.g. multiple cameras or
% different imaged locations per frame). TIFFStack allows these files to be
% de-interleaved, such that each conceptual data dimension has its own
% referencing dimension within matlab.
%
% This functionality uses the optional 'vnInterleavedFrameDims' argument.
% This is a vector of dimensions that were interleaved into the single
% frame dimension in the stack.
%
% For example, a stack contains 2 channels of data per pixel, and 3 imaged
% locations per frame, all interleaved into the TIFF frame dimension. The
% stack contains 10 conceptual frames, and each frame contains 5x5 pixels.
%
% The stack is therefore conceptually of dimensions [5 5 2 3 10 1], but
% appears on disk with dimensions [5 5 60 1]. (The final dimension
% corresponds to the samples-per-pixel dimension of the TIFF file).
%
% >> tsStack = TIFFStack('file.tif', [], [2 3 10]);
% >> size(tsStack)
%
% ans =
%
% 5 5 2 3 10
%
% Permutation and indexing now works seamlessly on this stack, with each
% conceptual dimension de-interleaved.
%
% If desired, the final number of frames can be left off
% 'vnInterleavedFrameDims'; for example:
%
% >> tsStack = TIFFStack('file.tif', [], [2 3]);
% >> size(tsStack)
%
% ans =
%
% 5 5 2 3 10
%
% Note: You must be careful that you specify the dimensions in the
% appropriate order, as interleaved in the stack. Also, if the stack
% contains multiple samples per pixel in native TIFF format, the
% samples-per-pixel dimension will always be pushed to the final dimension.
%
% -------------------------------------------------------------------------
%
% <strong>ImageJ stacks</strong>
% ImageJ HyperStacks are automatically deinterleaved, if encountered. By
% default, the stacks will be presented as [Y X T Z C]. They can of course
% be permuted. If desired, the interleaving can be overridden by providing
% an explicit 'vnInterleavedFrameDims'.
%
% ImageJ writes "fake" big stacks as raw binary data, with a TIF file shim
% as a header. These appear to Matlab as a TIF file containing a single
% frame. TIFFStack loads these files using MappedTensor, when available. If
% MappedTensor is not available, a warning will be issued.
%
% References:
% [1] D R Muir and B M Kampa, 2015. "FocusStack and StimServer: a new open
% source MATLAB toolchain for visual stimulation and analysis of two-photon
% calcium neuronal imaging data". Frontiers in Neuroinformatics 8 (85).
% DOI: <a href="http://dx.doi.org/10.3389/fninf.2014.00085">10.3389/fninf.2014.00085</a>
%
% [2] Francois Nedelec, Thomas Surrey and A.C. Maggs. Physical Review Letters
% 86: 3192-3195; 2001. DOI: <a href="http://dx.doi.org/10.1103/PhysRevLett.86.3192">10.1103/PhysRevLett.86.3192</a>
%
% [3] <a href="http://www.cytosim.org">http://www.cytosim.org</a>
% Author: Dylan Muir <[email protected]>
% Created: 28th June, 2011
%% Class definition
classdef TIFFStack < handle
properties
bInvert; % - A boolean flag that determines whether or not the image data will be inverted
end
properties (SetAccess = private)
strFilename = []; % - The name of the TIFF file on disk
sImageInfo; % - The TIFF header information
strDataClass; % - The matlab class in which data will be returned
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; % \
TIF_tr31; % |- Cached header info for tiffread31 speedups
HEADER; % /
bUseTiffLib; % - Flag indicating whether TiffLib is being used
bMTStack; % - Flag indicating MappedTensor 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 permutation
fhRepSum; % - Function handle to (hopefully) accellerated repsum function
fhCastFun; % - The matlab function that casts data to the required return class
end
methods
% TIFFStack - CONSTRUCTOR
function oStack = TIFFStack(strFilename, bInvert, vnInterleavedFrameDims, bForceTiffread)
% - Check usage
if (~exist('strFilename', 'var') || ~ischar(strFilename))
help TIFFStack;
error('TIFFStack:Usage', ...
'*** TIFFStack: Incorrect usage.');
end
% - Should we force TIFFStack to use tiffread, rather than libTiff?
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>
% - Try to copy the library
strTiffLibLoc = which('/private/tifflib');
strTIFFStackLoc = fileparts(which('TIFFStack'));
copyfile(strTiffLibLoc, fullfile(strTIFFStackLoc, 'private'), 'f');
end
oStack.bUseTiffLib = (exist('tifflib') == 3) & ~bForceTiffread; %#ok<EXIST>
if (~oStack.bUseTiffLib)
warning('TIFFStack:SlowAccess', ...
'--- TIFFStack: Using slower non-TiffLib access.');
end
% - Get accelerated repsum function, if possible
oStack.fhRepSum = GetMexFunctionHandles;
% - Check for inversion flag
if (~exist('bInvert', 'var') || isempty(bInvert))
bInvert = false;
end
oStack.bInvert = bInvert;
% - Check for frame dimensions
if (~exist('vnInterleavedFrameDims', 'var'))
vnInterleavedFrameDims = [];
else
validateattributes(vnInterleavedFrameDims, {'single', 'double'}, {'integer', 'real', 'positive'}, ...
'TIFFStack', 'vnInterleavedFrameDims');
end
% - See if filename exists
if (~exist(strFilename, 'file'))
error('TIFFStack:InvalidFile', ...
'*** TIFFStack: File [%s] does not exist.', strFilename);
end
% - Assign absolute file path to stack
strFilename = get_full_file_path(strFilename);
oStack.strFilename = strFilename;
% - Get image information
try
% - Read and store image information (using tiffread for speed and compatibility)
[oStack.TIF, oStack.HEADER, sInfo] = tiffread31_header(strFilename);
oStack.TIF_tr31 = oStack.TIF;
% - Detect a ImageJ fake BigTIFF stack
[bIsImageJBigStack, bIsImageJHyperStack, vnStackDims, vnInterleavedIJFrameDims] = IsImageJBigStack(tiffread31_readtags(oStack.TIF_tr31, oStack.HEADER, 1), numel(oStack.HEADER));
% - Handle ImageJ big stacks with MappedTensor
if (bIsImageJBigStack)
[oStack.TIF, oStack.bMTStack, oStack.strDataClass] = OpenImageJBigStack(oStack, vnStackDims);
% - Could we use a MappedTensor?
if (~oStack.bMTStack)
% - No, so just access the first frame
bIsImageJBigStack = false; %#ok<NASGU>
bIsImageJHyperStack = false;
warning('TIFFStack:ImageJBigStackUnsupported', ...
'--- TIFFStack: Warning: This is an ImageJ "fake" TIF file. MappedTensor must be available to read this file.');
end
end
% - Detect a very long stack
if ((numel(sInfo) > 2^16) && oStack.bUseTiffLib)
warning('TIFFStack:LongStack', ...
'--- TIFFSTack: Warning: This stack has more than 2^16 frames, so Matlab/tifflib cannot read it natively.\n Using slower non-Tifflib access.');
oStack.bUseTiffLib = false;
end
% - Deinterleave hyperstacks automatically
bImageJDeinterleaving = bIsImageJHyperStack && isempty(vnInterleavedFrameDims);
if bImageJDeinterleaving
vnInterleavedFrameDims = vnInterleavedIJFrameDims;
end
% - Initialise object, depending on underlying access method
if (oStack.bMTStack)
% - Fix up stack size
sInfo = repmat(sInfo(1), vnStackDims(3), 1);
elseif (oStack.bUseTiffLib)
% - Create a Tiff object
oStack.TIF = tifflib('open', strFilename, 'r');
% - Check data format
if(TiffgetTag(oStack.TIF, 'Photometric') == Tiff.Photometric.YCbCr)
error('TIFFStack:UnsupportedFormat', ...
'*** TIFFStack: YCbCr images are not supported.');
end
% - Use Tiff to get the data class for this tiff
nDataClass = TiffgetTag(oStack.TIF, 'SampleFormat');
switch (nDataClass)
case Tiff.SampleFormat.UInt
switch (sInfo(1).BitsPerSample(1))
case 1
oStack.strDataClass = 'logical';
case 8
oStack.strDataClass = 'uint8';
case 16
oStack.strDataClass = 'uint16';
case 32
oStack.strDataClass = 'uint32';
case 64
oStack.strDataClass = 'uint64';
otherwise
error('TIFFStack:UnsupportedFormat', ...
'*** TIFFStack: The sample format of this TIFF stack is not supported.');
end
case Tiff.SampleFormat.Int
switch (sInfo(1).BitsPerSample(1))
case 1
oStack.strDataClass = 'logical';
case 8
oStack.strDataClass = 'int8';
case 16
oStack.strDataClass = 'int16';
case 32
oStack.strDataClass = 'int32';
case 64
oStack.strDataClass = 'int64';
otherwise
error('TIFFStack:UnsupportedFormat', ...
'*** TIFFStack: The sample format of this TIFF stack is not supported.');
end
case Tiff.SampleFormat.IEEEFP
switch (sInfo(1).BitsPerSample(1))
case {1, 8, 16, 32}
oStack.strDataClass = 'single';
case 64
oStack.strDataClass = 'double';
otherwise
error('TIFFStack:UnsupportedFormat', ...
'*** TIFFStack: The sample format of this TIFF stack is not supported.');
end
otherwise
error('TIFFStack:UnsupportedFormat', ...
'*** TIFFStack: The sample format of this TIFF stack is not supported.');
end
% -- Assign accelerated reading function
strReadFun = 'TS_read_Tiff';
% - Tiled or striped
if (tifflib('isTiled', oStack.TIF))
strReadFun = [strReadFun '_tiled'];
else
strReadFun = [strReadFun '_striped'];
end
% - Chunky or planar
if (isequal(TiffgetTag(oStack.TIF, 'PlanarConfiguration'), Tiff.PlanarConfiguration.Chunky))
strReadFun = [strReadFun '_chunky'];
elseif (isequal(TiffgetTag(oStack.TIF, 'PlanarConfiguration'), Tiff.PlanarConfiguration.Separate))
strReadFun = [strReadFun '_planar'];
else
error('TIFFStack:UnsupportedFormat', ...
'*** TIFFStack: The planar configuration of this TIFF stack is not supported.');
end
strSetDirFun = 'TS_set_directory';
% - Check for zero-based referencing
try
tifflib('computeStrip', oStack.TIF, 0);
catch
strReadFun = [strReadFun '_pre2014'];
strSetDirFun = [strSetDirFun '_pre2014'];
end
% - Convert into function handles
oStack.fhReadFun = str2func(strReadFun);
oStack.fhSetDirFun = str2func(strSetDirFun);
% - Fix up rows per strip (inconsistency between Windows and
% OS X Tifflib
nRowsPerStrip = TiffgetTag(oStack.TIF, 'RowsPerStrip');
if ~isfield(sInfo, 'RowsPerStrip') || (nRowsPerStrip ~= sInfo(1).RowsPerStrip)
[sInfo.RowsPerStrip] = deal(nRowsPerStrip);
end
% - Attempt to read tile width and length
try
[sInfo.TileWidth] = deal(TiffgetTag(oStack.TIF, 'TileWidth'));
catch
[sInfo.TileWidth] = deal(1);
end
try
[sInfo.TileLength] = deal(TiffgetTag(oStack.TIF, 'TileLength'));
catch
[sInfo.TileLength] = deal(1);
end
% - Read max and min sample values
[sInfo.MaxSampleValue] = deal(TiffgetTag(oStack.TIF, 'MaxSampleValue'));
[sInfo.MinSampleValue] = deal(TiffgetTag(oStack.TIF, 'MinSampleValue'));
else
% - Read TIFF header for tiffread31
% [oStack.TIF, oStack.HEADER] = tiffread31_header(strFilename);
oStack.TIF.file = fopen(strFilename, 'r', 'l');
% - Use tiffread31 to get the data class for this tiff
fPixel = tiffread31_readimage(oStack.TIF, oStack.HEADER, 1);
fPixel = fPixel(1, 1, :);
oStack.strDataClass = class(fPixel);
end
% - Use imread to get the data class for this tiff
% fPixel = imread(strFilename, 'TIFF', 1, 'PixelRegion', {[1 1], [1 1]});
% oStack.strDataClass = class(fPixel);
% -- Assign casting function
oStack.fhCastFun = str2func(oStack.strDataClass);
% - Record stack size
if (oStack.bMTStack)
oStack.vnDataSize = vnStackDims;
oStack.vnApparentSize = oStack.vnDataSize;
% - Initialise dimension order
oStack.vnDimensionOrder = 1:numel(oStack.vnApparentSize);
% - Permute first two dimensions
oStack = permute(oStack, [2 1 3:numel(vnStackDims)]);
else
oStack.vnDataSize = [sInfo(1).Height sInfo(1).Width numel(sInfo) sInfo(1).SamplesPerPixel];
% - Initialise dimension order
oStack.vnDimensionOrder = 1:numel(oStack.vnDataSize);
end
% - Initialize apparent stack size, de-interleaving along the frame dimension
if isempty(vnInterleavedFrameDims)
% - No de-interleaving
oStack.vnApparentSize = oStack.vnDataSize;
elseif (prod(vnInterleavedFrameDims) ~= oStack.vnDataSize(3))
% - Be lenient by allowing frames dimension to be left out of arguments
if (mod(oStack.vnDataSize(3), prod(vnInterleavedFrameDims)) == 0)
% - Work out number of apparent frames
nNumApparentFrames = oStack.vnDataSize(3) ./ prod(vnInterleavedFrameDims);
oStack.vnApparentSize = [oStack.vnDataSize(1:2) vnInterleavedFrameDims(:)' nNumApparentFrames oStack.vnDataSize(4)];
oStack.vnDimensionOrder = 1:numel(oStack.vnApparentSize);
else
% - Incorrect total number of deinterleaved frames
error('TIFFStack:WrongFrameDims', ...
'*** TIFFStack: When de-interleaving a stack, the total number of frames must not change.');
end
else
% - Record apparent stack dimensions
oStack.vnApparentSize = [oStack.vnDataSize(1:2) vnInterleavedFrameDims(:)' oStack.vnDataSize(4)];
oStack.vnDimensionOrder = 1:numel(oStack.vnApparentSize);
end
% - Fix up dimensions order for ImageJ HyperStack
if (bImageJDeinterleaving)
oStack = permute(oStack, [1 2 5 4 3]);
end
% - Record image information
oStack.sImageInfo = sInfo;
catch mErr
base_ME = MException('TIFFStack:InvalidFile', ...
'*** TIFFStack: Could not open file [%s].', strFilename);
new_ME = addCause(base_ME, mErr);
throw(new_ME);
end
end
% delete - DESTRUCTOR
function delete(oStack)
if (oStack.bUseTiffLib)
% - Close the TIFF file, if opened by TiffLib
if (~isempty(oStack.TIF))
tifflib('close', oStack.TIF);
end
end
% - Close the TIFF file, if opened by tiffread31_header
if (isfield(oStack.TIF_tr31, 'file') && ~isempty(fopen(oStack.TIF_tr31.file)))
fclose(oStack.TIF_tr31.file);
end
end
% diagnostic - METHOD Display some diagnostics about a stack
function diagnostic(oStack)
disp(oStack);
fprintf('<strong>Private properties:</strong>\n');
fprintf(' vnDataSize: ['); fprintf('%d ', oStack.vnDataSize); fprintf(']\n');
fprintf(' vnApparentSize: ['); fprintf('%d ', oStack.vnApparentSize); fprintf(']\n');
fprintf(' vnDimensionOrder: ['); fprintf('%d ', oStack.vnDimensionOrder); fprintf(']\n');
fprintf(' bUseTiffLib: %d\n', oStack.bUseTiffLib);
fprintf(' bMTStack: %d\n', oStack.bMTStack);
fprintf(' fhReadFun: %s\n', func2str(oStack.fhReadFun));
fprintf(' fhSetDirFun: %s\n', func2str(oStack.fhSetDirFun));
fprintf(' fhRepSum: %s\n', func2str(oStack.fhRepSum));
fprintf(' fhCastFun: %s\n', func2str(oStack.fhCastFun));
end
function [TIF, HEADER] = diagnostic_HEADER(oStack)
TIF = oStack.TIF;
HEADER = oStack.HEADER;
end
%% --- Overloaded subsref
function [varargout] = subsref(oStack, S)
switch S(1).type
case '()'
% - Test for valid subscripts
cellfun(@isvalidsubscript, S.subs);
% - Record stack size
nNumRefDims = numel(S.subs);
vnReferencedTensorSize = size(oStack);
nNumNZStackDims = numel(vnReferencedTensorSize);
nNumTotalStackDims = max(numel(oStack.vnDimensionOrder), nNumNZStackDims);
vnFullTensorSize = vnReferencedTensorSize;
vnFullTensorSize(nNumNZStackDims+1:nNumTotalStackDims) = 1;
vnFullTensorSize(vnFullTensorSize == 0) = 1;
bLinearIndexing = false;
% - Convert logical indexing to indices
for (nDim = 1:numel(S.subs))
if (islogical(S.subs{nDim}))
S.subs{nDim} = find(S.subs{nDim});
end
end
% - Check dimensionality and trailing dimensions
if (nNumRefDims == 1)
% - Catch "read whole stack" case
if (iscolon(S.subs{1}))
S.subs = num2cell(repmat(':', 1, nNumNZStackDims));
vnRetDataSize = [prod(vnReferencedTensorSize), 1];
else
% - Get equivalent subscripted indexes and permute
vnTensorSize = size(oStack);
if any(S.subs{1}(:) > prod(vnTensorSize))
error('TIFFStack:badsubscript', ...
'*** TIFFStack: Index exceeds stack dimensions.');
else
[cIndices{1:nNumTotalStackDims}] = ind2sub(vnTensorSize, S.subs{1});
end
% - Permute dimensions
vnInvOrder(oStack.vnDimensionOrder(1:nNumTotalStackDims)) = 1:nNumTotalStackDims;
S.subs = cIndices(vnInvOrder(vnInvOrder ~= 0));
vnRetDataSize = size(S.subs{1});
bLinearIndexing = true;
end
elseif (nNumRefDims < nNumNZStackDims)
% - Wrap up trailing dimensions, matlab style, using linear indexing
vnReferencedTensorSize(nNumRefDims) = prod(vnReferencedTensorSize(nNumRefDims:end));
vnReferencedTensorSize = vnReferencedTensorSize(1:nNumRefDims);
% - Catch "read whole stack" case
if (all(cellfun(@iscolon, S.subs)))
[S.subs{nNumRefDims+1:nNumTotalStackDims}] = deal(':');
vnRetDataSize = vnReferencedTensorSize;
else
% - Convert to linear indexing
bLinearIndexing = true;
[S.subs{1}, vnRetDataSize] = GetLinearIndicesForRefs(S.subs, vnReferencedTensorSize, oStack.fhRepSum);
S.subs = S.subs(1);
[S.subs{1:nNumTotalStackDims}] = ind2sub(vnFullTensorSize, S.subs{1});
% - Inverse permute index order
vnInvOrder(oStack.vnDimensionOrder(1:nNumTotalStackDims)) = 1:nNumTotalStackDims;
S.subs = S.subs(vnInvOrder(vnInvOrder ~= 0));
end
elseif (nNumRefDims == nNumNZStackDims)
% - Check for colon references
vbIsColon = cellfun(@iscolon, S.subs);
vnRetDataSize = cellfun(@numel, S.subs);
vnRetDataSize(vbIsColon) = vnReferencedTensorSize(vbIsColon);
% - Permute index order
S.subs(nNumNZStackDims+1:nNumTotalStackDims) = {1};
vnInvOrder(oStack.vnDimensionOrder(1:nNumTotalStackDims)) = 1:nNumTotalStackDims;
S.subs = S.subs(vnInvOrder(vnInvOrder ~= 0));
else % (nNumRefDims > nNumNZStackDims)
% - Check for non-colon references
vbIsColon = cellfun(@iscolon, S.subs);
% - Check for non-unitary references
vbIsUnitary = cellfun(@(c)(isequal(c, 1)), S.subs);
% - Check for non-empty references
vbIsEmpty = cellfun(@isempty, S.subs);
% - Check only trailing dimensions
vbTrailing = [false(1, nNumNZStackDims) true(1, nNumRefDims-nNumNZStackDims)];
% - Check trailing dimensions for inappropriate indices
if (any(vbTrailing & (~vbIsColon & ~vbIsUnitary & ~vbIsEmpty)))
% - This is an error
error('TIFFStack:badsubscript', ...
'*** TIFFStack: Index exceeds stack dimensions.');
end
% - Catch empty refs
if (~any(vbIsEmpty))
% - Only keep relevant dimensions
S.subs = S.subs(1:nNumNZStackDims);
end
% - Determine returned data size
vnReferencedTensorSize(nNumNZStackDims+1:nNumRefDims) = 1;
vnReferencedTensorSize(vnReferencedTensorSize == 0) = 1;
vbIsColon = cellfun(@iscolon, S.subs);
vnRetDataSize = cellfun(@numel, S.subs);
vnRetDataSize(vbIsColon) = vnReferencedTensorSize(vbIsColon);
% - Permute index order
S.subs(nNumNZStackDims+1:nNumTotalStackDims) = {1};
vnInvOrder(oStack.vnDimensionOrder(1:nNumTotalStackDims)) = 1:nNumTotalStackDims;
S.subs = S.subs(vnInvOrder(vnInvOrder ~= 0));
end
% - Catch empty refs
if (prod(vnRetDataSize) == 0)
[varargout{1:nargout}] = zeros(vnRetDataSize);
return;
end
% - Re-interleave frame indices for deinterleaved stacks
if (numel(oStack.vnApparentSize) > 4)
% - Record output data size in deinterleaved space
if (~bLinearIndexing)
vnOutputSize = cellfun(@numel, S.subs);
vbIsColon = cellfun(@iscolon, S.subs);
vnOutputSize(vbIsColon) = oStack.vnApparentSize(vbIsColon);
end
% - Get frame
cFrameSubs = S.subs(3:end-1);
if all(cellfun(@iscolon, cFrameSubs))
S.subs = {S.subs{1} S.subs{2} ':' S.subs{end}};
else
if (bLinearIndexing)
vnFrameIndices = sub2ind(oStack.vnApparentSize(3:end-1), cFrameSubs{:});
else
tnFrameIndices = reshape(1:oStack.vnDataSize(3), ...
oStack.vnApparentSize(3:end-1));
vnFrameIndices = tnFrameIndices(cFrameSubs{:});
end
% - Construct referencing subscripts for raw stack
S.subs = [S.subs(1:2) reshape(vnFrameIndices, [], 1) S.subs(end)];
end
end
% - Access stack (MappedTensor or tifflib or tiffread)
if (oStack.bMTStack)
tfData = TS_read_data_MappedTensor(oStack, S.subs, bLinearIndexing);
elseif (oStack.bUseTiffLib)
tfData = TS_read_data_Tiff(oStack, S.subs, bLinearIndexing);
else
tfData = TS_read_data_tiffread(oStack, S.subs, bLinearIndexing);
end
% - Permute dimensions, if linear indexing has not been used
if (~bLinearIndexing)
% - Reshape resulting data in case of deinterleaved stacks
if (numel(oStack.vnApparentSize) > 4)
tfData = reshape(tfData, vnOutputSize);
end
tfData = permute(tfData, oStack.vnDimensionOrder);
end
% - Reshape returned data to concatenate trailing dimensions (just as matlab does)
if (~isequal(size(tfData), vnRetDataSize))
tfData = reshape(tfData, vnRetDataSize);
end
[varargout{1:nargout}] = tfData;
otherwise
error('TIFFStack:InvalidReferencing', ...
'*** TIFFStack: Only ''()'' referencing is supported by TIFFStacks.');
end
end
%% --- Getter methods
function strFilename = getFilename(oStack)
strFilename = oStack.strFilename;
end
function sImageInfo = getImageInfo(oStack)
sImageInfo = oStack.sImageInfo;
end
function vsTags = getImageTags(oStack, vnFrames)
% getImageTags - METHOD Read TIFF tags for individual frames
%
% Usage: vsTags = getImageTags(oStack, vnFrames)
%
% 'oStack' is a TIFFStack object. 'vnFrames' is a vector of frame
% indices into the stack.
%
% 'vsTags' will be a struct array, with each element of the array
% containing all tags for the corresponding frame index in
% 'vnFrames'.
if (nargin < 2)
help TIFFStack/getImageTags;
error('TIFFStack:Usage', 'TIFFStack/getImageTags: ''vnFrames'' is a required argument.');
end
% - Extract tags for these frames
vsTags = tiffread31_readtags(oStack.TIF_tr31, oStack.HEADER, vnFrames);
end
function bInvert = getInvert(oStack)
bInvert = oStack.bInvert;
end
function strDataClass = getDataClass(oStack)
strDataClass = oStack.strDataClass;
end
%% --- Overloaded numel, size, ndims, permute, ipermute, ctranspose, transpose, cat, horzcat, vertcat
function [n] = numel(oStack, varargin)
n = prod(size(oStack)); %#ok<PSIZE>
end
% size - METHOD Overloaded size function
function [varargout] = size(oStack, vnDimensions)
% - Get original tensor size, and extend dimensions if necessary
vnApparentSize = oStack.vnApparentSize; %#ok<PROPLC,PROP>
vnApparentSize(end+1:numel(oStack.vnDimensionOrder)) = 1; %#ok<PROPLC,PROP>
% - Return the size of the tensor data element, permuted
vnSize = vnApparentSize(oStack.vnDimensionOrder); %#ok<PROPLC,PROP>
% - Trim trailing unitary dimensions
vbIsUnitary = vnSize == 1;
if (vbIsUnitary(end))
nLastNonUnitary = find(~vbIsUnitary, 1, 'last');
if (nLastNonUnitary < numel(vnSize))
vnSize = vnSize(1:nLastNonUnitary);
end
end
% - Return specific dimension(s)
if (exist('vnDimensions', 'var'))
if (~isnumeric(vnDimensions) || any(vnDimensions < 1))
error('TIFFStack:DimensionMustBePositiveInteger', ...
'*** TIFFStack: Dimensions argument must be a positive integer.');
end
vbExtraDimensions = vnDimensions > numel(vnSize);
% - Return the specified dimension(s)
vnSizeOut(~vbExtraDimensions) = vnSize(vnDimensions(~vbExtraDimensions));
vnSizeOut(vbExtraDimensions) = 1;
else
vnSizeOut = vnSize;
end
% - Handle differing number of size dimensions and number of output
% arguments
nNumArgout = max(1, nargout);
if (nNumArgout == 1)
% - Single return argument -- return entire size vector
varargout{1} = vnSizeOut;
elseif (nNumArgout <= numel(vnSizeOut))
% - Several return arguments -- return single size vector elements,
% with the remaining elements grouped in the last value
varargout(1:nNumArgout-1) = num2cell(vnSizeOut(1:nNumArgout-1));
varargout{nNumArgout} = prod(vnSizeOut(nNumArgout:end));
else %(nNumArgout > numel(vnSize))
% - Output all size elements
varargout(1:numel(vnSizeOut)) = num2cell(vnSizeOut);
% - Deal out trailing dimensions as '1'
varargout(numel(vnSizeOut)+1:nNumArgout) = {1};
end
end
% ndims - METHOD Overloaded ndims function
function [nNumDims] = ndims(oStack)
nNumDims = numel(size(oStack));
end
% permute - METHOD Overloaded permute function
function [oStack] = permute(oStack, vnNewOrder)
oStack.vnDimensionOrder(1:numel(vnNewOrder)) = oStack.vnDimensionOrder(vnNewOrder);
end
% ipermute - METHOD Overloaded ipermute function
function [oStack] = ipermute(oStack, vnOldOrder)
vnNewOrder(vnOldOrder) = 1:numel(vnOldOrder);
oStack = permute(oStack, vnNewOrder);
end
% ctranspose - METHOD Overloaded ctranspose function
function [oStack] = cstranspose(oStack)
oStack = transpose(oStack);
end
% transpose - METHOD Overloaded transpose function
function [oStack] = transpose(oStack)
oStack = permute(oStack, [2 1]);
end
% cat - METHOD Overloaded cat, horzcat, vertcat functions
function [varargout] = cat(varargin) %#ok<STOUT>
error('TIFFStack:Concatenation', ...
'*** TIFFStack: Concatenation is not supported by TIFFStack.');
end
function [varargout] = horzcat(varargin) %#ok<STOUT>
error('TIFFStack:Concatenation', ...
'*** TIFFStack: Concatenation is not supported by TIFFStack.');
end
function [varargout] = vertcat(varargin) %#ok<STOUT>
error('TIFFStack:Concatenation', ...
'*** TIFFStack: Concatenation is not supported by TIFFStack.');
end
%% --- Overloaded end
function nLength = end(oStack, nEndDim, nTotalRefDims)
vnSizes = size(oStack);
if (nEndDim < nTotalRefDims)
nLength = vnSizes(nEndDim);
else
nLength = prod(vnSizes(nEndDim:end));
end
end
%% --- Overloaded sum, nansum, mean, nanmean
% sum - METHOD Overloaded sum function
function [tfResult, tnNumNonNaNs] = sum(oStack, nDim, flag, bIgnoreNaNs)
% - If this function is called, it must be a sum over the entire stack
if nargin==2 && ischar(nDim)
flag = nDim;
elseif nargin < 3
flag = 'default';
end
if nargin == 1 || (nargin == 2 && ischar(nDim))
nDim = find(size(oStack)~=1,1);
if isempty(nDim), nDim = 1; end
end
if (~exist('bIgnoreNaNs', 'var'))
bIgnoreNaNs = true;
end
% - Set up referencing
sSubs.type = '()';
sSubs.subs = repmat({':'}, 1, ndims(oStack));
% - Loop to perform sum in double precision
for (nIndex = 1:size(oStack, nDim))
sSubs.subs{nDim} = nIndex;
tfSlice = double(subsref(oStack, sSubs));
% - Ignore NaNs, if requested
if (bIgnoreNaNs)
if (~exist('tnNumNonNaNs', 'var'))
tnNumNonNaNs = zeros(size(tfSlice));
end
tnNumNonNaNs(~isnan(tfSlice)) = tnNumNonNaNs(~isnan(tfSlice)) + 1;
% - Set NaNs to zero
tfSlice(isnan(tfSlice)) = 0;
end
% - Perform sum
if (~exist('tfResult', 'var'))
tfResult = tfSlice;
else
tfResult = tfResult + tfSlice;
end
end
% - Cast result to native class, if necessary
if (strcmp(flag, 'native'))
tfResult = oStack.fhCastFun(tfResult);
end
end
% nansum - METHOD Overloaded nansum function
function tfResult = nansum(oStack, nDim)
if nargin == 1
nDim = find(size(oStack)~=1,1);
if isempty(nDim), nDim = 1; end
end
% - Call "sum" with "bIgnoreNaNs" set to true
tfResult = sum(oStack, nDim, 'default', true);
end
% mean - METHOD Overloaded mean function
function y = mean(x,dim,flag, bIgnoreNaNs)
if (~exist('bIgnoreNaNs', 'var'))
bIgnoreNaNs = true;
end
if nargin==2 && ischar(dim)
flag = dim;
elseif nargin < 3
flag = 'default';
end
if nargin == 1 || (nargin == 2 && ischar(dim))
dim = find(size(x)~=1,1);
if isempty(dim), dim = 1; end
end
% - Compute sum in double
[y, tnNumNonNaNs] = sum(x, dim, 'double', bIgnoreNaNs);
y = y ./ tnNumNonNaNs;
% - Re-cast result, if necessary
if (strcmp(flag, 'native'))
y = x.fhCastFun(y);
end
end
% nanmean - METHOD Overloaded nanmean
function y = nanmean(x,dim)
if nargin == 1
dim = find(size(x)~=1,1);
if isempty(dim), dim = 1; end
end
% - Call mean
y = mean(x,dim,'default', true);
end
%% --- Overloaded sort, prctile
% sort - METHOD Overloaded sort function
function tfSorted = sort(oStack, varargin)
% - Warn about loss of function
warning('TIFFStack:LostTIFFStack', '--- TIFFStack/sort: Warning: Data returned by ''sort'' is no longer a ''TIFFStack'' object.');
% - Set up referencing
sSubs.type = '()';
sSubs.subs = repmat({':'}, 1, ndims(oStack));
% - Just load stack and pass parameters to sort
tfSorted = sort(subsref(oStack, sSubs), varargin{:});
end
% prctile - METHOD Overloaded prctile function
function tfPrctile = prctile(oStack, varargin)
% - Warn about loss of function
warning('TIFFStack:LostTIFFStack', '--- TIFFStack/prctile: Warning: Data returned by ''prctile'' is no longer a ''TIFFStack'' object.');
% - Set up referencing
sSubs.type = '()';
sSubs.subs = repmat({':'}, 1, ndims(oStack));
% - Just load stack and pass parameters to sort
tfPrctile = prctile(subsref(oStack, sSubs), varargin{:});
end