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SiBoRG/libraries/ReadImageJROI.m
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ReadImageJROI.m
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function [sROI] = ReadImageJROI(cstrFilenames)
% ReadImageJROI - FUNCTION Read an ImageJ ROI into a matlab structure
%
% Usage: [sROI] = ReadImageJROI(strFilename)
% [cvsROIs] = ReadImageJROI(cstrFilenames)
% [cvsROIs] = ReadImageJROI(strROIArchiveFilename)
%
% This function reads the ImageJ binary ROI file format.
%
% 'strFilename' is the full path to a '.roi' file. A list of ROI files can be
% passed as a cell array of filenames, in 'cstrFilenames'. An ImageJ ROI
% archive can be access by providing a '.zip' filename in
% 'strROIArchiveFilename'. Single ROIs are returned as matlab structures, with
% variable fields depending on the ROI type. Multiple ROIs are returned as a
% cell array of ROI structures.
%
% The field '.strName' is guaranteed to exist, and contains the ROI name (the
% filename minus '.roi', or the name set for the ROI).
%
% The field '.strType' is guaranteed to exist, and defines the ROI type:
% {'Rectangle', 'Oval', Line', 'Polygon', 'Freehand', 'Traced', 'PolyLine',
% 'FreeLine', 'Angle', 'Point', 'NoROI'}.
%
% The field '.vnRectBounds' is guaranteed to exist, and defines the rectangular
% bounds of the ROI: ['nTop', 'nLeft', 'nBottom', 'nRight'].
%
% The field '.nVersion' is guaranteed to exist, and defines the version number
% of the ROI format.
%
% The field '.vnPosition' is guaranteed to exist. If the information is
% defined within the ROI, this field will be a three-element vector
% [nCPosition nZPosition nTPosition].
%
% ROI types:
% Rectangle:
% .strType = 'Rectangle';
% .nArcSize - The arc size of the rectangle's rounded corners
%
% For a composite, 'shape' ROI:
% .strSubtype = 'Shape';
% .vfShapeSegments - A long, complicated vector of complicated shape
% segments. This vector is in the format passed to the
% ImageJ ShapeROI constructor. I won't decode this for
% you! :(
%
% Oval:
% .strType = 'Oval';
%
% Line:
% .strType = 'Line';
% .vnLinePoints - The end points of the line ['nX1', 'nY1', 'nX2', 'nY2']
%
% With arrow:
% .strSubtype = 'Arrow';
% .bDoubleHeaded - Does the line have two arrowheads?
% .bOutlined - Is the arrow outlined?
% .nArrowStyle - The ImageJ style of the arrow (unknown interpretation)
% .nArrowHeadSize - The size of the arrowhead (unknown units)
%
% Polygon:
% .strType = 'Polygon';
% .mnCoordinates - An [Nx2] matrix, specifying the coordinates of
% the polygon vertices. Each row is [nX nY].
%
% Freehand:
% .strType = 'Freehand';
% .mnCoordinates - An [Nx2] matrix, specifying the coordinates of
% the polygon vertices. Each row is [nX nY].
%
% Ellipse subtype:
% .strSubtype = 'Ellipse';
% .vfEllipsePoints - A vector containing the ellipse control points:
% [fX1 fY1 fX2 fY2].
% .fAspectRatio - The aspect ratio of the ellipse.
%
% Traced:
% .strType = 'Traced';
% .mnCoordinates - An [Nx2] matrix, specifying the coordinates of
% the line vertices. Each row is [nX nY].
%
% PolyLine:
% .strType = 'PolyLine';
% .mnCoordinates - An [Nx2] matrix, specifying the coordinates of
% the line vertices. Each row is [nX nY].
%
% FreeLine:
% .strType = 'FreeLine';
% .mnCoordinates - An [Nx2] matrix, specifying the coordinates of
% the line vertices. Each row is [nX nY].
%
% Angle:
% .strType = 'Angle';
% .mnCoordinates - An [Nx2] matrix, specifying the coordinates of
% the angle vertices. Each row is [nX nY].
%
% Point:
% .strType = 'Point';
% .mfCoordinates - An [Nx2] matrix, specifying the coordinates of
% the points. Each row is [fX fY].
% .vnCounters - An [Nx1] vector, specifying which counter is
% associated with each point. May be empty.
% .vnSlices - An [Nx1] vector, specifying on which plane each
% point is on. These are specified as linear
% indices, with the hyperstack arranged as
% [Channels Z-slices T-slices]. If empty, then all
% points are placed on the first slice.
%
% NoROI:
% .strType = 'NoROI';
%
% Additionally, ROIs from later versions (.nVersion >= 218) may have the
% following fields:
%
% .nStrokeWidth - The width of the line stroke
% .nStrokeColor - The encoded color of the stroke (ImageJ color format)
% .nFillColor - The encoded fill color for the ROI (ImageJ color
% format)
%
% If the ROI contains text:
% .strSubtype = 'Text';
% .nFontSize - The desired font size
% .nFontStyle - The style of the font (unknown format)
% .strFontName - The name of the font to render the text with
% .strText - A string containing the text
% Author: Dylan Muir <dylan.muir@unibas.ch>
% Created: 9th August, 2011
%
% 20170118 Added code to read slice position for point ROIs
% 20141020 Added code to read 'header 2' fields; thanks to Luca Nocetti
% 20140602 Bug report contributed by Samuel Barnes and Yousef Mazaheri
% 20110810 Bug report contributed by Jean-Yves Tinevez
% 20110829 Bug fix contributed by Benjamin Ricca <ricca@berkeley.edu>
% 20120622 Order of ROIs in a ROI set is now preserved
% 20120703 Different way of reading zip file contents guarantees that ROI order
% is preserved
%
% Copyright (c) 2011, 2012, 2013, 2014 Dylan Muir <dylan.muir@unibas.ch>
%
% This program is free software; you can redistribute it and/or
% modify it under the terms of the GNU General Public License
% as published by the Free Software Foundation; either version 3
% of the License, or (at your option) any later version.
%
% This program is distributed in the hope that it will be useful,
% but WITHOUT ANY WARRANTY; without even the implied warranty of
% MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
% GNU General Public License for more details.
% -- Constants
bOpt_SubPixelResolution = 128;
% -- Check arguments
if (nargin < 1)
disp('*** ReadImageJROI: Incorrect usage');
help ReadImageJROI;
return;
end
% -- Check for a cell array of ROI filenames
if (iscell(cstrFilenames))
% - Read each ROI in turn
%cvsROI = cellfun(@ReadImageJROI, CellFlatten(cstrFilenames), 'UniformOutput', false);
tmpROI = CellFlatten(cstrFilenames);
sROI = {};
for i=1:length(tmpROI)
cvsROI = ReadImageJROI(tmpROI{i});
sROI = [sROI; cvsROI];
end
% - Return all ROIs
%sROI = cvsROI;
return;
else
% - This is not a cell string
strFilename = cstrFilenames;
clear cstrFilenames;
end
% -- Check for a zip file
[nul, nul, strExt] = fileparts(strFilename); %#ok<ASGLU>
if (isequal(lower(strExt), '.zip'))
% - get zp file contents
cstrFilenames_short = listzipcontents_rois(strFilename);
% - Unzip the file into a temporary directory
strROIDir = tempname;
unzip(strFilename, strROIDir);
for (nFileIndex = 1:length(cstrFilenames_short))
cstrFilenames{1, nFileIndex} = [strROIDir '/' char(cstrFilenames_short(nFileIndex, 1))];
end
% - Build ROIs for each file
cvsROIs = ReadImageJROI(cstrFilenames);
% - Clean up temporary directory
delete([strROIDir filesep '*.roi']);
rmdir(strROIDir);
% - Return ROIs
sROI = cvsROIs;
return;
end
% -- Read ROI
% -- Check file and open
if (~exist(strFilename, 'file'))
error('ReadImageJROI:FileNotFound', ...
'*** ReadImageJROI: The file [%s] was not found.', strFilename);
end
fidROI = fopen(strFilename, 'r', 'ieee-be');
% -- Check file magic code
strMagic = fread(fidROI, [1 4], '*char');
if (~isequal(strMagic, 'Iout'))
error('ReadImageJROI:FormatError', ...
'*** ReadImageJROI: The file was not an ImageJ ROI format.');
end
% -- Read version
sROI.nVersion = fread(fidROI, 1, 'int16');
% -- Read ROI type
nTypeID = fread(fidROI, 1, 'uint8');
fseek(fidROI, 1, 'cof'); % Skip a byte
% -- Read rectangular bounds
sROI.vnRectBounds = fread(fidROI, [1 4], 'int16');
% -- Read number of coordinates
nNumCoords = fread(fidROI, 1, 'uint16');
% -- Read the rest of the header
vfLinePoints = fread(fidROI, 4, 'float32');
nStrokeWidth = fread(fidROI, 1, 'int16');
nShapeROISize = fread(fidROI, 1, 'uint32');
nStrokeColor = fread(fidROI, 1, 'uint32');
nFillColor = fread(fidROI, 1, 'uint32');
nROISubtype = fread(fidROI, 1, 'int16');
nOptions = fread(fidROI, 1, 'int16');
nArrowStyle = fread(fidROI, 1, 'uint8');
nArrowHeadSize = fread(fidROI, 1, 'uint8');
nRoundedRectArcSize = fread(fidROI, 1, 'int16');
sROI.nPosition = fread(fidROI, 1, 'uint32');
% -- Read the 'header 2' fields
nHeader2Offset = fread(fidROI, 1, 'uint32');
if (nHeader2Offset > 0) && ~fseek(fidROI, nHeader2Offset+32+4, 'bof')
% - Seek to start of header 2
fseek(fidROI, nHeader2Offset+4, 'bof');
% - Read fields
sROI.vnPosition = fread(fidROI, 3, 'uint32')';
vnNameParams = fread(fidROI, 2, 'uint32')';
nOverlayLabelColor = fread(fidROI, 1, 'uint32'); %#ok<NASGU>
nOverlayFontSize = fread(fidROI, 1, 'int16'); %#ok<NASGU>
fseek(fidROI, 1, 'cof'); % Skip a byte
nOpacity = fread(fidROI, 1, 'uint8'); %#ok<NASGU>
nImageSize = fread(fidROI, 1, 'uint32'); %#ok<NASGU>
fStrokeWidth = fread(fidROI, 1, 'float32'); %#ok<NASGU>
vnROIPropertiesParams = fread(fidROI, 2, 'uint32')'; %#ok<NASGU>
nCountersOffset = fread(fidROI, 1, 'uint32');
else
sROI.vnPosition = [];
vnNameParams = [0 0];
nOverlayLabelColor = []; %#ok<NASGU>
nOverlayFontSize = []; %#ok<NASGU>
nOpacity = []; %#ok<NASGU>
nImageSize = []; %#ok<NASGU>
fStrokeWidth = []; %#ok<NASGU>
vnROIPropertiesParams = [0 0]; %#ok<NASGU>
nCountersOffset = 0;
end
% -- Set ROI name
if (isempty(vnNameParams) || any(vnNameParams == 0) || fseek(fidROI, sum(vnNameParams), 'bof'))
[nul, sROI.strName] = fileparts(strFilename); %#ok<ASGLU>
else
% - Try to read ROI name from header
fseek(fidROI, vnNameParams(1), 'bof');
sROI.strName = fread(fidROI, vnNameParams(2), 'int16=>char')';
end
% - Seek to get aspect ratio
fseek(fidROI, 52, 'bof');
fAspectRatio = fread(fidROI, 1, 'float32');
% - Seek to after header
fseek(fidROI, 64, 'bof');
% -- Build ROI
switch nTypeID
case 1
% - Rectangle
sROI.strType = 'Rectangle';
sROI.nArcSize = nRoundedRectArcSize;
if (nShapeROISize > 0)
% - This is a composite shape ROI
sROI.strSubtype = 'Shape';
if (nTypeID ~= 1)
error('ReadImageJROI:FormatError', ...
'*** ReadImageJROI: A composite ROI must be a Rectangle type.');
end
% - Read shapes
sROI.vfShapes = fread(fidROI, nShapeROISize, 'float32');
end
case 2
% - Oval
sROI.strType = 'Oval';
case 3
% - Line
sROI.strType = 'Line';
sROI.vnLinePoints = round(vfLinePoints);
if (nROISubtype == 2)
% - This is an arrow line
sROI.strSubtype = 'Arrow';
sROI.bDoubleHeaded = nOptions & 2;
sROI.bOutlined = nOptions & 4;
sROI.nArrowStyle = nArrowStyle;
sROI.nArrowHeadSize = nArrowHeadSize;
end
case 0
% - Polygon
sROI.strType = 'Polygon';
sROI.mnCoordinates = read_coordinates;
case 7
% - Freehand
sROI.strType = 'Freehand';
sROI.mnCoordinates = read_coordinates;
if (nROISubtype == 3)
% - This is an ellipse
sROI.strSubtype = 'Ellipse';
sROI.vfEllipsePoints = vfLinePoints;
sROI.fAspectRatio = fAspectRatio;
end
case 8
% - Traced
sROI.strType = 'Traced';
sROI.mnCoordinates = read_coordinates;
case 5
% - PolyLine
sROI.strType = 'PolyLine';
sROI.mnCoordinates = read_coordinates;
case 4
% - FreeLine
sROI.strType = 'FreeLine';
sROI.mnCoordinates = read_coordinates;
case 9
% - Angle
sROI.strType = 'Angle';
sROI.mnCoordinates = read_coordinates;
case 10
% - Point
sROI.strType = 'Point';
[sROI.mfCoordinates, vnCounters] = read_coordinates;
% - Set counters and [C Z T] positions
if (isempty(vnCounters))
sROI.vnCounters = zeros(nNumCoords, 1);
sROI.vnSlices = ones(nNumCoords, 1);
else
sROI.vnCounters = bitand(vnCounters, 255);
sROI.vnSlices = bitshift(vnCounters, -8, 32);
end
case 6
sROI.strType = 'NoROI';
otherwise
error('ReadImageJROI:FormatError', ...
'--- ReadImageJROI: The ROI file contains an unknown ROI type.');
end
% -- Handle version >= 218
if (sROI.nVersion >= 218)
sROI.nStrokeWidth = nStrokeWidth;
sROI.nStrokeColor = nStrokeColor;
sROI.nFillColor = nFillColor;
sROI.bSplineFit = nOptions & 1;
if (nROISubtype == 1)
% - This is a text ROI
sROI.strSubtype = 'Text';
% - Seek to after header
fseek(fidROI, 64, 'bof');
sROI.nFontSize = fread(fidROI, 1, 'uint32');
sROI.nFontStyle = fread(fidROI, 1, 'uint32');
nNameLength = fread(fidROI, 1, 'uint32');
nTextLength = fread(fidROI, 1, 'uint32');
% - Read font name
sROI.strFontName = fread(fidROI, nNameLength, 'uint16=>char');
% - Read text
sROI.strText = fread(fidROI, nTextLength, 'uint16=>char');
end
end
% - Close the file
fclose(fidROI);
% --- END of ReadImageJROI FUNCTION ---
function [mnCoordinates, vnCounters] = read_coordinates
% - Check for sub-pixel resolution
if bitand(nOptions, bOpt_SubPixelResolution)
fseek(fidROI, 64 + 4*nNumCoords, 'bof');
% - Read X and Y coordinates
vnX = fread(fidROI, [nNumCoords 1], 'single');
vnY = fread(fidROI, [nNumCoords 1], 'single');
else
% - Read X and Y coords
vnX = fread(fidROI, [nNumCoords 1], 'int16');
vnY = fread(fidROI, [nNumCoords 1], 'int16');
% - Trim at zero
vnX(vnX < 0) = 0;
vnY(vnY < 0) = 0;
% - Offset by top left ROI bound
vnX = vnX + sROI.vnRectBounds(2);
vnY = vnY + sROI.vnRectBounds(1);
end
mnCoordinates = [vnX vnY];
% - Read counters, if present
if (nCountersOffset ~= 0)
fseek(fidROI, nCountersOffset, 'bof');
vnCounters = fread(fidROI, [nNumCoords 1], 'uint32');
else
vnCounters = [];
end
end
end
% --- END of ReadImageJROI.m ---
function [filelist] = listzipcontents_rois(zipFilename)
% listzipcontents_rois - FUNCTION Read the file names in a zip file
%
% Usage: [filelist] = listzipcontents_rois(zipFilename)
% - Import java libraries
%import java.util.zip.*;
%import java.io.*;
% - Read file list via JAVA object
filelist={};
%in = java.util.zip.ZipInputStream(java.io.FileInputStream(zipFilename));
in = javaObject('java.util.zip.ZipInputStream', javaObject('java.io.FileInputStream', zipFilename));
entry = javaMethod('getNextEntry', in);
% - Filter ROI files
%while (entry~=0)
while (isjava(entry) && ~entry.equals(0))
%name = entry.getName;
name = javaMethod('getName', entry);
%if (name.endsWith('.roi'))
if (strncmp(name(end-3:end),'.roi',4))
filelist = cat(1,filelist,char(name));
end;
%entry = in.getNextEntry();
entry = javaMethod('getNextEntry', in);
end;
% - Close zip file
%in.close();
javaMethod('close', in);
end
function [cellArray] = CellFlatten(varargin)
% CellFlatten - FUNCTION Convert a list of items to a single level cell array
%
% Usage: [cellArray] = CellFlatten(arg1, arg2, ...)
%
% CellFlatten will convert a list of arguments into a single-level cell array.
% If any argument is already a cell array, each cell will be concatenated to
% 'cellArray' in a list. The result of this function is a single-dimensioned
% cell array containing a cell for each individual item passed to CellFlatten.
% The order of cell elements in the argument list is guaranteed to be
% preserved.
%
% This function is useful when dealing with variable-length argument lists,
% each item of which can also be a cell array of items.
% Author: Dylan Muir <dylan@ini.phys.ethz.ch>
% Created: 14th May, 2004
% -- Check arguments
if (nargin == 0)
disp('*** CellFlatten: Incorrect usage');
help CellFlatten;
return;
end
% -- Convert arguments
if (iscell(varargin{1}))
cellArray = CellFlatten(varargin{1}{:});
else
cellArray = varargin(1);
end
for (nIndexArg = 2:length(varargin)) %#ok<FORPF>
if (iscell(varargin{nIndexArg}))
cellReturn = CellFlatten(varargin{nIndexArg}{:});
cellArray = [cellArray cellReturn{:}]; %#ok<AGROW>
else
cellArray = [cellArray varargin{nIndexArg}]; %#ok<AGROW>
end
end
% --- END of CellFlatten.m ---
end
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