From d6125e8941314414d5082e1936e632fcf83a552b Mon Sep 17 00:00:00 2001
From: Yoann Guilhem <yoann.guilhem@esrf.fr>
Date: Thu, 25 Apr 2013 11:13:24 +0200
Subject: [PATCH] Update TIF IO functions.
Signed-off-by: Yoann Guilhem <yoann.guilhem@esrf.fr>
---
zUtil_TIFF/gtTIFInfoReader.m | 44 ++++++++++++++++++++
zUtil_TIFF/gtTIFVolReader.m | 54 ++++++++++++++++---------
zUtil_TIFF/gtTIFVolReaderWithInfo.m | 41 +++++++++++++++++++
zUtil_TIFF/gtTIFVolWriter.m | 63 ++++++++++++++++++-----------
4 files changed, 159 insertions(+), 43 deletions(-)
create mode 100644 zUtil_TIFF/gtTIFInfoReader.m
create mode 100644 zUtil_TIFF/gtTIFVolReaderWithInfo.m
diff --git a/zUtil_TIFF/gtTIFInfoReader.m b/zUtil_TIFF/gtTIFInfoReader.m
new file mode 100644
index 00000000..599096bb
--- /dev/null
+++ b/zUtil_TIFF/gtTIFInfoReader.m
@@ -0,0 +1,44 @@
+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
+
diff --git a/zUtil_TIFF/gtTIFVolReader.m b/zUtil_TIFF/gtTIFVolReader.m
index 50d807c1..96e99512 100644
--- a/zUtil_TIFF/gtTIFVolReader.m
+++ b/zUtil_TIFF/gtTIFVolReader.m
@@ -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);
diff --git a/zUtil_TIFF/gtTIFVolReaderWithInfo.m b/zUtil_TIFF/gtTIFVolReaderWithInfo.m
new file mode 100644
index 00000000..29f251fc
--- /dev/null
+++ b/zUtil_TIFF/gtTIFVolReaderWithInfo.m
@@ -0,0 +1,41 @@
+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
+
diff --git a/zUtil_TIFF/gtTIFVolWriter.m b/zUtil_TIFF/gtTIFVolWriter.m
index 6cdc8590..f3fc2189 100644
--- a/zUtil_TIFF/gtTIFVolWriter.m
+++ b/zUtil_TIFF/gtTIFVolWriter.m
@@ -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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