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Commit d6125e89 authored by Yoann Guilhem's avatar Yoann Guilhem Committed by Nicola Vigano
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Update TIF IO functions. 


Signed-off-by: default avatarYoann Guilhem <yoann.guilhem@esrf.fr>
parent 20649bde
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zUtil_TIFF/gtTIFInfoReader.m 0 → 100644
+ 44
− 0
View file @ d6125e89
function info = gtTIFInfoReader(filename, info)
% GTTIFINFOREADER Read TIFF info file (BBox, voxelsize and origin).
%
% info = gtTIFInfoReader(filename, info)
% -------------------------------------------------------------------------
%
% INPUT:
% filename = <string> Path to info file
%
% OPTIONAL INPUT
% info = <struct> TIFF info strsture to complete
%
% OUTPUT:
% info = <struct> Information about volume
%
% Note:
% info file should be formatted as the following:
%
% [bboxMinX, bboxMinY, bboxMinZ] [bboxMaxX, bboxMaxY, bboxMaxZ]
% voxelsize
%
% Version 001 24-04-2013 by YGuilhem, yoann.guilhem@esrf.fr
% Check existence of file
if ~exist(filename, 'file')
gtError('gtTIFInfoReader:wrong_file_name', ...
['File ''' filename ''' does not exist!']);
end
% Read info file
fid = fopen(filename, 'r');
bbox = fscanf(fid, '[%d, %d, %d] [%d, %d, %d]', 6).';
vSize = fscanf(fid, '%f', 1);
fclose(fid);
% Store bbox, voxel size and origin
info.boundingBoxMin = bbox(1:3) + 1;
info.boundingBoxMax = bbox(4:6);
info.voxelSize = vSize;
info.origin = bbox(1:3) .* info.voxelSize;
info.infoFile = filename;
end % end of function
zUtil_TIFF/gtTIFVolReader.m
+ 35
− 19
View file @ d6125e89
......@@ -10,23 +10,22 @@ function [vol, info] = gtTIFVolReader(filename, varargin)
% if extension is missing, '.tif' is append
%
% OPTIONAL INPUT (varargin as a list of pairs, see parse_pv_pairs.m):
% 'xrange' = <range> Index range of output in X direction
% 'yrange' = <range> " Y "
% 'zrange' = <range> " Z "
% 'mode' = <string> Input type which is either 'single' or 'stack'
% default is a single TIFF file
% 'digits' = <int> Number of digits in stack filenames
% 'startindex' = <int> Starting index for stack filenames
% 'endindex' = <int> Ending "
% 'filext' = <string> Input TIFF file extension ('tif' or 'tiff')
% default is 'tif'
% 'newMethod' = <bool> Use new reading method (faster)
% 'xrange' = <range> Index range of output in X direction {'all'}
% 'yrange' = <range> " Y " {'all'}
% 'zrange' = <range> " Z " {'all'}
% 'bbox' = <int> Index range as bbox [Xi Yi Zi Xf Yf Zf]
% 'mode' = <string> Input type which is {'single'} or 'stack'
% 'digits' = <int> Number of digits in stack filenames {4}
% 'startindex' = <int> Starting index for stack filenames {1}
% 'endindex' = <int> Ending " {1}
% 'filext' = <string> Input TIFF file extension {'tif'}
% 'newMethod' = <bool> Use new reading method (faster) {'true'}
%
% OUTPUT:
% vol = <3Dimage> Output 3D volume
% info = <struct> Information about volume
% vol = <3Dimage> Output 3D volume
% info = <struct> Information about volume
%
% Version 003 30-10-2012
% Version 003 30-10-2012 by YGuilhem, yoann.guilhem@esrf.fr
% Use tifflib for fast reading
% Some bugfixes
%
......@@ -37,9 +36,10 @@ function [vol, info] = gtTIFVolReader(filename, varargin)
% Set default parameters and parse optional arguments
params.newMethod = true;
params.xrange = 'all';
params.yrange = 'all';
params.zrange = 'all';
params.xrange = [];
params.yrange = [];
params.zrange = [];
params.bbox = [];
params.mode = 'single';
params.filext = 'tif';
params.digits = 4;
......@@ -73,7 +73,6 @@ if ~exist('filename', 'var')
end
end
% Get file parts and store the proper extension
[fpath, fname, fext] = fileparts(filename);
if any(strcmp(fext, {'.tif', '.tiff'}))
......@@ -94,7 +93,7 @@ else
fullFilenameFormat = fullfile(fpath, filenameFormat);
% Check existence of input stack files
for idx=params.startindex:params.endindex
for idx = params.startindex:params.endindex
sfilename = sprintf(fullFilenameFormat, idx);
if ~exist(sfilename, 'file')
gtError('gtTIFVolReader:wrong_file_name', ...
......@@ -135,6 +134,20 @@ tifSizeZ = length(fileIndex);
[fpath, fname, ~] = fileparts(fullFilename);
fullFilenameFormat = fullfile(fpath, filenameFormat);
% Check if we use ranges or bbox input
if isempty(params.bbox)
if isempty(params.xrange), params.xrange = 'all'; end;
if isempty(params.yrange), params.yrange = 'all'; end;
if isempty(params.zrange), params.zrange = 'all'; end;
elseif isempty([params.xrange params.yrange params.zrange])
params.xrange = params.bbox(1):params.bbox(4);
params.yrange = params.bbox(2):params.bbox(5);
params.zrange = params.bbox(3):params.bbox(6);
else
gtError('gtTIFVolReader:wrong_range_input', ...
'You cannot use both bbox and [xyz]range options!');
end
% Check each dimension range
fullRangeXY = true;
if strcmp(params.xrange, 'all')
......@@ -183,6 +196,9 @@ end
info.volSizeX = volSizeX;
info.volSizeY = volSizeY;
info.volSizeZ = volSizeZ;
info.tifSizeX = tifSizeX;
info.tifSizeY = tifSizeY;
info.tifSizeZ = tifSizeZ;
info.bytespervoxel = tifInfo(1).SamplesPerPixel * tifInfo(1).BitsPerSample / 8;
info.fpath = fpath;
info.byteorder = tifInfo(1).ByteOrder(1);
......
zUtil_TIFF/gtTIFVolReaderWithInfo.m 0 → 100644
+ 41
− 0
View file @ d6125e89
function [vol, info] = gtTIFVolReaderWithInfo(filename, varargin)
% GTTIFVOLREADERWITHINFO Read TIFF volume with the info (BBox and voxelsize).
%
% [vol, info] = gtTIFVolReaderWithInfo(filename, varargin)
% -------------------------------------------------------------------------
%
% INPUT:
% filename = <string> Path to TIFF file to write
% it may be relative or absolute
% if extension is missing, '.tif' is append
%
% OPTIONAL INPUT -> see gtTIFVolReader
%
% OUTPUT:
% vol = <3Dimage> Output 3D volume
% info = <struct> Information about volume
%
% Note:
% info file should be formatted as the following:
%
% [bboxMinX, bboxMinY, bboxMinZ] [bboxMaxX, bboxMaxY, bboxMaxZ]
% voxelsize
%
% Version 001 24-04-2013 by YGuilhem, yoann.guilhem@esrf.fr
% Read TIFF file
if isempty(varargin)
[vol, info] = gtTIFVolReader(filename);
else
[vol, info] = gtTIFVolReader(filename, varargin);
end
% Extract path, basename and extension from file name
[fpath, fname, fext] = fileparts(info.fname_final);
% Read info from file
infoFile = fullfile(fpath, [fname '.info']);
info = gtTIFInfoReader(infoFile, info);
end % end of function
zUtil_TIFF/gtTIFVolWriter.m
+ 39
− 24
View file @ d6125e89
......@@ -15,28 +15,27 @@ function gtTIFVolWriter(vol, filename, varargin)
% number and the extension will be append.
%
% OPTIONAL INPUT (varargin as a list of pairs, see parse_pv_pairs.m):
% 'xrange' = <range> Index range of output in X direction
% 'yrange' = <range> " Y "
% 'zrange' = <range> " Z "
% 'xrange' = <int> Index range of output in X direction {'all'}
% 'yrange' = <int> " Y " {'all'}
% 'zrange' = <int> " Z " {'all'}
% 'bbox' = <int> Index range as bbox [Xi Yi Zi Xf Yf Zf]
%
% 'type' = <string> Force type of data written in the TIFF file
% it can be 'uint8', 'uint16' or 'logical'
% default is 'uint8'
% default is detected from input volume class
%
% 'compress' = <string> Compression mode, by default 'none', can be
% 'packbits', 'lzm', 'deflate', 'ccitt', 'fax3'
% or 'fax4'
% 'compress' = <string> Compression mode can be {'none'}, 'packbits',
% 'lzm', 'deflate', 'ccitt', 'fax3' or 'fax4'
%
% 'mode' = <string> Output type which is 'single' or 'stack'
% default is a single TIFF file
% 'digits' = <int> Number of digits in stack filenames
% 'startindex' = <int> Starting index for stack filenames
% 'filext' = <string> Output TIFF file extension ('tif' or 'tiff')
% default is 'tif'
% 'newMethod' = <bool> Use new TIFF writing method (faster)
% 'mode' = <string> Output type which is {'single'} or 'stack'
% 'digits' = <int> Number of digits in stack filenames {4}
% 'startindex' = <int> Starting index for stack filenames {1}
% 'filext' = <string> Output TIFF file extension {'tif'}
% 'newMethod' = <bool> Use new TIFF writing method (faster) {true}
%
% TODO :
% - RGB data output
% TODO:
% - RGB data output
% - float output
%
% Version 003 30-10-2012 by YGuilhem, yoann.guilhem@esrf.fr
% Use tifflib for fast reading
......@@ -50,9 +49,10 @@ function gtTIFVolWriter(vol, filename, varargin)
% Set default parameters and parse optional arguments
params.newMethod = true;
params.xrange = 'all';
params.yrange = 'all';
params.zrange = 'all';
params.xrange = [];
params.yrange = [];
params.zrange = [];
params.bbox = [];
params.type = '';
params.compress = 'none';
params.mode = 'single';
......@@ -67,6 +67,20 @@ if params.newMethod && ~exist('tifflib', 'file')
params.newMethod = false;
end
% Check if we use ranges or bbox input
if isempty(params.bbox)
if isempty(params.xrange), params.xrange = 'all'; end;
if isempty(params.yrange), params.yrange = 'all'; end;
if isempty(params.zrange), params.zrange = 'all'; end;
elseif isempty([params.xrange params.yrange params.zrange])
params.xrange = params.bbox(1):params.bbox(4);
params.yrange = params.bbox(2):params.bbox(5);
params.zrange = params.bbox(3):params.bbox(6);
else
gtError('gtTIFVolWriter:wrong_range_input', ...
'You cannot use both bbox and [xyz]range options!');
end
% Translating range parameters
if strcmp(params.xrange, 'all')
rangeX = 1:size(vol, 1);
......@@ -111,7 +125,7 @@ else
rescale = 0;
case 'uint8'
rescale = 255;
otherwise
case 'uint16'
rescale = 65535;
end
end
......@@ -211,7 +225,7 @@ if strcmpi(params.mode, 'single')
% Writing volume in TIFF file
if params.newMethod
tif = Tiff(filename, 'a');
for iz=1:length(rangeZ)
for iz = 1:length(rangeZ)
tif.setTag(tifTag);
tif.write(outVol(rangeX, rangeY, rangeZ(iz))');
tif.writeDirectory();
......@@ -219,7 +233,7 @@ if strcmpi(params.mode, 'single')
tif.close();
else
% Old method
for iz=1:length(rangeZ)
for iz = 1:length(rangeZ)
imwrite(outVol(rangeX(1):rangeX(end), rangeY(1):rangeY(end), ...
rangeZ(iz))', ...
filename, 'tif', 'Compression', params.compress, ...
......@@ -266,7 +280,7 @@ elseif strcmpi(params.mode, 'stack')
% Writing volume in TIFF stack files
if params.newMethod
for iz=1:length(rangeZ)
for iz = 1:length(rangeZ)
outFile = sprintf(filenameFMT, iz+offset);
tif = Tiff(outFile, 'w');
tif.setTag(tifTag);
......@@ -275,7 +289,7 @@ elseif strcmpi(params.mode, 'stack')
end
else
% Old method
for iz=1:length(rangeZ)
for iz = 1:length(rangeZ)
outFile = sprintf(filenameFMT, iz+offset);
imwrite(outVol(rangeX, rangeY, rangeZ(iz))', outFile, 'tif', ...
'Compression', params.compress, 'writemode', 'overwrite');
......@@ -284,3 +298,4 @@ elseif strcmpi(params.mode, 'stack')
end
end % end of function
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