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function DATA = aedes_smisread(filename,opt)
% AEDES_SMISREAD - Read S.M.I.S. Data Files (*.sur)
%
%
% Synopsis:
% DATA = aedes_smisread(filename)
%
% Description:
% Read image data from S.M.I.S. SUR-Files.
%
% Examples:
%
% See also:
% AEDES_READFID, AEDES_READ_NIFTI
% This function is a part of Aedes - A graphical tool for analyzing
% medical images
%
% Copyright (C) 2006 Juha-Pekka Niskanen <Juha-Pekka.Niskanen@uku.fi>
%
% Department of Physics, Department of Neurobiology
% University of Kuopio, FINLAND
%
% This program may be used under the terms of the GNU General Public
% License version 2.0 as published by the Free Software Foundation
% and appearing in the file LICENSE.TXT included in the packaging of
% this program.
%
% This program is provided AS IS with NO WARRANTY OF ANY KIND, INCLUDING THE
% WARRANTY OF DESIGN, MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE.
% *************************************************************************
% SMIS Data format documentation:
%
% SMIS reconstructed image files are in a format very similar to the first
% part of that used for raw data (.MRD). They consist of:
%
% 1) a 256 byte header
% 2) a 256 byte text description
% 3) the data proper
% 4) the pule program parameters (PPR file)
% 5) other parameters
%
% 256 byte header
% Bytes (hex) 'C' data type Usage
% 0-3 Long (4 byte integer) Number of pixels in X direction
% 4-7 Long Number of pixels in Y direction
% 8-B Long Number of pixels in Z direction (currently 1)
% C-F Long Dimension 4 (currently 1)
% ... Unspecified
% 12-13 Int (2 byte integer) Data type code
% ... Unspecified
% 30-33 Float (4 bytes) Scaling factor from highest pixel to 4095
% ... Unspecified
% 6D Unsigned char (1 byte) Number of bits per pixel (currently 12)
% ... Unspecified
%
% The data type code indicates the format of individual data elements, as
% follows:
%
% 0x00 unsigned char 1 byte
% 0x01 signed char 1 byte
% 0x02 short 2 bytes
% 0x03 int 2 bytes
% 0x04 long 4 bytes
% 0x05 float 4 bytes
% 0x06 double 8 bytes
%
% 0x10 bit mask indicating complex data as real, imaginary pairs of
% base data type
%
% All SMIS .SUR files are at present integer, indicated by data type 0x03.
%
% 256 text description
% At present this is unused and contains the ASCII text "There is no script
% !".
%
% Data
% Data follows. The pixel positions increments in the X dimension until the
% next increment in the Y dimension.
% *************************************************************************
DATA = [];
ReadHeader = true;
ReadData = true;
if nargin == 0 || isempty(filename)
% Prompt for a file
[fname,fpath,findex] = uigetfile({'*.sur',...
'S.M.I.S. Data Files (*.sur)';...
'*.*','All Files (*.*)'},'Open S.M.I.S. Data File');
if isequal(fname,0)
return
end
filename = fullfile(fpath,fname);
end
[fp,fn,fe]=fileparts(filename);
if nargin == 2
% Read only header
if strcmpi(opt,'header')
ReadData = false;
end
end
% Open the file for reading
fid = fopen(filename,'r');
if fid < 0
error('Could not open file "%s" for reading!',filename)
end
% Read data header
if ReadHeader
hdr=l_ReadHdrInfo(fid);
end
% Read image data
if ReadData
[data,msg]=l_ReadData(hdr,fid);
if ~isempty(msg)
fclose(fid);
error(msg);
end
end
% Close file
fclose(fid);
% Construct DATA structure
DATA.DataFormat = 'SUR';
DATA.FTDATA = data;
DATA.KSPACE = [];
DATA.HDR.FileHeader = hdr;
DATA.HDR.fname = [fn,fe];
DATA.HDR.fpath = [fp,filesep];
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% Read Header Information
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
function hdr=l_ReadHdrInfo(file_fid)
% 256 byte header
% Bytes (hex) 'C' data type Usage
% 0-3 Long (4 byte integer) Number of pixels in X direction
% 4-7 Long Number of pixels in Y direction
% 8-B Long Number of pixels in Z direction (currently 1)
% C-F Long Dimension 4 (currently 1)
% ... Unspecified
% 12-13 Int (2 byte integer) Data type code
% ... Unspecified
% 30-33 Float (4 bytes) Scaling factor from highest pixel to 4095
% ... Unspecified
% 6D Unsigned char (1 byte) Number of bits per pixel (currently 12)
% ... Unspecified
%
% The data type code indicates the format of individual data elements, as
% follows:
%
% 0x00 unsigned char 1 byte
% 0x01 signed char 1 byte
% 0x02 short 2 bytes
% 0x03 int 2 bytes
% 0x04 long 4 bytes
% 0x05 float 4 bytes
% 0x06 double 8 bytes
%
% 0x10 bit mask indicating complex data as real, imaginary pairs of
% base data type
hdr = [];
% Seek to the beginning of the file
fseek(file_fid,0,-1);
hdr.nPixelsX=fread(file_fid,1,'int32'); % Number of pixels in X direction
hdr.nPixelsY=fread(file_fid,1,'int32'); % Number of pixels in Y direction
hdr.nPixelsZ=fread(file_fid,1,'int32'); % Number of pixels in Z direction
hdr.nPixels4D=fread(file_fid,1,'int32'); % Number of pixels in 4 dimension
% Seek over the unspecified bytes
fseek(file_fid,18,-1);
hdr.DataTypeCode = fread(file_fid,1,'int16'); % Data type code
% Seek over the unspecified bytes
fseek(file_fid,48,-1);
hdr.ScalingFactor = fread(file_fid,1,'float'); % Scaling factor from highest
% pixel to 4095
% Seek over the unspecified bytes
fseek(file_fid,109,-1);
hdr.BitsPerPixel = fread(file_fid,1,'uchar'); % Number of bits per pixel
% (currently 12)
% Read the text description
fseek(file_fid,256,-1);
hdr.TextDescription = char(fread(file_fid,256,'char')).';
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% Read Image Data
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
function [data,msg]=l_ReadData(hdr,file_fid)
data = [];
msg = '';
% Determine data type
% 0x00 unsigned char 1 byte
% 0x01 signed char 1 byte
% 0x02 short 2 bytes
% 0x03 int 2 bytes
% 0x04 long 4 bytes
% 0x05 float 4 bytes
% 0x06 double 8 bytes
dataTypes = {...
'*uint8',1;...
'*int8',1;...
'*int16',2;...
'*int16',2;...
'*int32',4;...
'*single',4;...
'*double',6};
precision = dataTypes{hdr.DataTypeCode+1,1};
% Seek to the beginning of the data
fseek(file_fid,512,-1);
% Size of the data in bytes
data_size = hdr.nPixelsX*hdr.nPixelsY*hdr.nPixelsZ*hdr.nPixels4D;
try
% Read image data
data = fread(file_fid,data_size,precision);
% Reshape and permute to correct size
data = reshape(data,[hdr.nPixelsX hdr.nPixelsY hdr.nPixelsZ hdr.nPixels4D]);
data = permute(data,[2 1 3 4]);
catch
msg = ['Could not read data: ',lasterr];
data = [];
end
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