classdef TiffReader < imageIO.ImageIO
%TIFFREADER Wrapper for Tiff interface, based on Matlab TIFF class
% This class is just a simple wrapper around Matlab Tiff class, adapted
% to conform to the structure of the imageIO library. Unlike
% TiffWriter, this class does not interface directly with the Tiff
% library, since no speed-ups are expected compared to the Matlab
% version.
% Author: Stefano.Masneri@brain.mpg.de
% Date: 29.07.2016
% SEE ALSO: imageIO.TiffWriter, Tiff
properties
tiffPtr; % pointer to a Matlab Tiff class
filePtr; % pointer to a file. Used in some special cases
% Other properties. Assuming that for multistack images they remain
% constant over the stack
XResolution; % resolution on horizontal axis
YResolution; % resolution on vertical haxis
resolutionUnit; % unit of measurement for resolution (none, inch, centimeter)
bps; % bits per sample used
colormap; % colormap used. Empty array if none
compression; % compression scheme used
tagNames; % Cell of available tags. Useful if the user wants to access
% additonal metadata
isImageJFmt = false; % true if the Tiff is non-standard and was created via imageJ
isSutterMOM1 = false; % true if the Tiff is non-standard and from SutterMOM v1
isSutterMOM2 = false; % true if the Tiff is non-standard and from SutterMOM v2
endianness='l'; % specify if data is stored as little-endian or big-endian
% used only if 'isImageJFmt' is true. Can be either 'l'
% or 'b'
offsetToImg; % offset to first image in the stack. Used only if isImageJFmt is true
stripByteCounts; % number of bytes to reads per strip. Used only if isImageJFmt is true
end
methods
function obj = TiffReader(filename)
%TIFFREADER Constructor of the class
%The constructor calls the constructor of the superclass, and then
%tries to parse the Tiff tags to extract as much information as
%possible from the file. No actual data is read in the constructor
%SEE ALSO imageIO.ImageIO.ImageIO
% Must call explicitly because we pass one argument
obj = obj@imageIO.ImageIO(filename);
% Use Matlab interface
obj.tiffPtr = Tiff(obj.fileFullPath, 'r');
% Set as many properties from the superclass as possible
obj = obj.readMetadata();
if obj.isImageJFmt % handle file differently
obj.filePtr = fopen(obj.fileFullPath);
endianness = fread(obj.filePtr, 2, '*char')';
if strcmpi(endianness, 'MM')
obj.endianness = 'b';
else %'II'
obj.endianness = 'l';
end
%fseek(obj.filePtr, obj.offsetToImg, 'bof');
end
end
function data = read(obj, varargin)
%READ read all the image data
%This function reads all the planes of the image. If the file has
%only one plane just returns that.
% INPUT
% obj: the TiffReader instance
% NAME-VALUE ARGUMENTS
% 'Cols': Specify which columns to extract
% 'Rows': Specify which rows to extract
% 'C': Specify which channels to extract
% 'Z': Specify which planes to extract
% 'T': Specify which timeseries to extract
% OUTPUT
% data: the whole image content
p = inputParser();
p.KeepUnmatched = true;
p.addParameter('Cols', 1:obj.width, @(x) isvector(x) && all(x > 0) && max(x) <= obj.pixPerTileCol);
p.addParameter('Rows', 1:obj.height, @(x) isvector(x) && all(x > 0) && max(x) <= obj.pixPerTileRow);
p.addParameter('C', 1:obj.channels, @(x) isvector(x) && all(x > 0) && max(x) <= obj.channels);
p.addParameter('Z', 1:obj.stacks, @(x) isvector(x) && all(x > 0) && max(x) <= obj.stacks);
p.addParameter('T', 1:obj.time, @(x) isvector(x) && all(x > 0) && max(x) <= obj.time);
p.parse(varargin{:});
rows = p.Results.Rows;
cols = p.Results.Cols;
channels = p.Results.C;
stacks = p.Results.Z;
timeseries = p.Results.T;
if obj.isImageJFmt
data = readTifImageJ(obj, cols, rows, channels, stacks);
elseif obj.isSutterMOM1 || obj.isSutterMOM2
data = readSutter(obj, cols, rows, channels, stacks, timeseries );
else % normal tif
data = zeros(length(rows), length(cols), length(channels), ...
length(stacks), obj.datatype);
idx = 1;
progBar = TextProgressBar('TiffReader --> Extracting data: ', 30);
for k = stacks
progBar.update(idx/(length(stacks)) * 100);
img = obj.readImage(k);
data(:, :, :, idx) = img(rows, cols, channels);
idx = idx + 1;
end
end
data = squeeze(data);
end
function img = readImage( obj, n )
%READIMAGE read one image plane
%This function reads one single plane of the image. If the file has
%only one plane just returns that.
% INPUT
% n the directory (aka the plane) to read. If bigger than the number
% of stacks, issue a warning and return an empty array. If not
% specified, return the image in the current directory
% OUTPUT
% img the image just read
if obj.isImageJFmt
imageSize = obj.height * obj.width * obj.channels;
precision = [ obj.datatype '=>' obj.datatype ];
if n > obj.stacks
warning('TiffReader.readImage: Cannot read image. n is bigger than the number of stacks')
img = [];
else
if nargin > 1 % n specified
fseek(obj.filePtr, obj.offsetToImg + (n-1)*imageSize*obj.bps/8, 'bof');
end
img = fread(obj.filePtr, imageSize, precision);
img = reshape(img, [obj.width, obj.height, obj.channels]);
img = img';
end
else
if 1 == nargin % n not specified
img = obj.tiffPtr.read();
elseif ~obj.isSutterMOM1 && ~obj.isSutterMOM2 && n > obj.stacks
warning('TiffReader.readImage: Cannot read image. n is bigger than the number of stacks')
img = [];
else % valid n
obj.tiffPtr.setDirectory(n);
img = obj.tiffPtr.read();
end
end
end
function delete(obj)
%DELETE Close object instances.
%Close performs the cleanup and release of the instantiated object
obj.tiffPtr.close();
if obj.filePtr > 0
fclose(obj.filePtr);
end
end
end
methods (Access = protected)
function obj = readMetadata(obj)
%First get usual info with imfinfo
try
imgInfo = imfinfo(obj.fileFullPath);
% Dimensions
obj.width = imgInfo(1).Width;
obj.height = imgInfo(1).Height;
obj.channels = imgInfo(1).SamplesPerPixel;
iconIndex = cat(1, imgInfo.NewSubFileType);
obj.stacks = sum(~iconIndex);
obj.time = 1;
obj.bps = imgInfo(1).BitsPerSample(1);
obj.resolutionUnit = imgInfo(1).ResolutionUnit;
obj.compression = imgInfo(1).Compression;
stripOffset = cat(1,imgInfo(iconIndex == 0).StripOffsets);
obj.offsetToImg = stripOffset(1);
% Standard TIFF does not have multitiled images
obj.tile = 1;
obj.numTilesRow = 1;
obj.numTilesCol = 1;
obj.rowTilePos = 0;
obj.colTilePos = 0;
obj.pixPerTileRow = obj.height;
obj.pixPerTileCol = obj.width;
obj.tileOverlap = 0;
% Other info available in imfinfo
obj.XResolution = imgInfo(1).XResolution;
obj.YResolution = imgInfo(1).YResolution;
obj.colormap = imgInfo(1).Colormap;
catch ME
error('TiffReader.TiffReader: Cannot read metadata. %s', ME.message)
end
% now use the Tiff pointer
obj.tagNames = obj.tiffPtr.getTagNames;
% retrieve datatype
sampleFormat = obj.tiffPtr.getTag('SampleFormat');
switch sampleFormat
case 1 % UInt
obj.datatype = ['uint' num2str(obj.bps)];
case 2 % Int
obj.datatype = ['int' num2str(obj.bps)];
case 3 % IEEEFP
if 64 == obj.bps
obj.datatype = 'double';
elseif 32 == obj.bps
obj.datatype = 'float';
else
warning('TiffReader.readMetadata: unrecognized BitsPerSample value')
end
otherwise % Void or complex types are unsupported
warning('TiffReader.readMetadata: unsupported sample format')
end
% check custom multitiff formats -_-'
try
imageDescription = obj.tiffPtr.getTag('ImageDescription');
% check between formats
if strncmpi('ImageJ', imageDescription, 6)
obj.isImageJFmt = true;
obj.parseMetadataImageJ(imageDescription);
elseif any(strfind('MOMconfig', imageDescription))
obj.isSutterMOM1 = true;
obj.pareMetadataSutter(imageDescription);
elseif any(strfind('scanimage.SI.', imageDescription))
obj.isSutterMOM2 = true;
obj.parseMetadataSutter(imageDescription);
end
catch
% could not retrieve ImageDescription tag
warning('TiffReader::readMetadata:: Tiff.Tag.ImageDescription is missing!');
end
end
%% decleare external methods
obj = parseMetadataImageJ(obj, imageDescription);
obj = parseMetadataSutter(obj, imageDescription);
end
end