AVW_IMG_COMPOSE - Compose single slice Analyze files into a volume
[ avw, machine ] = avw_img_compose(files, orient, machine)
files - a struct created with F = DIR('*.img').
The filenames of the .img files are in F.name and
these files are composed into a volume, in the
order given by the DIR command
orient - force reading IMG in specified orientation, integer values:
'', read header history orient field
0, transverse/axial unflipped
1, coronal unflipped
2, sagittal unflipped
3, transverse/axial flipped
4, coronal flipped
5, sagittal flipped
Note that composed volume is given in this orientation
machine - a string, see machineformat in fread for details.
The default here is 'ieee-le' but the routine
will automatically switch between little and big
endian to read any such Analyze header. It
reports the appropriate machine format and can
return the machine value.
Returned values:
avw.hdr - a struct with image data parameters.
avw.img - a 3D matrix of image data (double precision).
See also: AVW_IMG_READ & AVW_HDR_READ (called by this function)0001 function avw = avw_img_compose(files,IMGorient,machine), 0002 0003 % AVW_IMG_COMPOSE - Compose single slice Analyze files into a volume 0004 % 0005 % [ avw, machine ] = avw_img_compose(files, orient, machine) 0006 % 0007 % files - a struct created with F = DIR('*.img'). 0008 % The filenames of the .img files are in F.name and 0009 % these files are composed into a volume, in the 0010 % order given by the DIR command 0011 % 0012 % orient - force reading IMG in specified orientation, integer values: 0013 % 0014 % '', read header history orient field 0015 % 0, transverse/axial unflipped 0016 % 1, coronal unflipped 0017 % 2, sagittal unflipped 0018 % 3, transverse/axial flipped 0019 % 4, coronal flipped 0020 % 5, sagittal flipped 0021 % 0022 % Note that composed volume is given in this orientation 0023 % 0024 % machine - a string, see machineformat in fread for details. 0025 % The default here is 'ieee-le' but the routine 0026 % will automatically switch between little and big 0027 % endian to read any such Analyze header. It 0028 % reports the appropriate machine format and can 0029 % return the machine value. 0030 % 0031 % Returned values: 0032 % 0033 % avw.hdr - a struct with image data parameters. 0034 % avw.img - a 3D matrix of image data (double precision). 0035 % 0036 % See also: AVW_IMG_READ & AVW_HDR_READ (called by this function) 0037 % 0038 0039 % $Revision: 1.1 $ $Date: 2004/11/12 01:30:25 $ 0040 0041 % Licence: GNU GPL, no express or implied warranties 0042 % History: 05/2002, Darren.Weber@flinders.edu.au 0043 % The Analyze format is copyright 0044 % (c) Copyright, 1986-1995 0045 % Biomedical Imaging Resource, Mayo Foundation 0046 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% 0047 0048 if ~exist('files','var'), 0049 error('AVW_IMG_COMPOSE: No files to compose'); 0050 end 0051 0052 if ~exist('IMGorient','var'), IMGorient = ''; end 0053 if ~exist('machine','var'), machine = 'ieee-le'; end 0054 0055 0056 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% 0057 % Number of files (slices) to compose 0058 Nfiles = size(files,1); 0059 % Size of first file (slice) in bytes 0060 Fsize = files(1).bytes; 0061 0062 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% 0063 % Initialise the composed volume 0064 0065 % Read the first slice header 0066 firstslice = avw_hdr_read(files(1).name,machine); 0067 0068 avw = firstslice; 0069 0070 % Not sure if this is always the case, but individual 0071 % slice files output by http://xmedcon.sourceforge.net 0072 % have the FOV in .hdr.dime.pixdim(4) after reading 0073 % some Siemens .ima files. It might be worth checking 0074 % at this point and dividing this FOV by the 0075 % number of slices 0076 if avw.hdr.dime.pixdim(4) > 20, 0077 msg = sprintf('AVW_IMG_COMPOSE: slice pixdim(4) is very large, assuming it is FOV and converting!\n'); 0078 warning(msg); 0079 % OK this field is probably FOV, so lets 0080 % divide it by the total number of slices 0081 SliceFOV = double(avw.hdr.dime.pixdim(4)); 0082 avw.hdr.dime.pixdim(4) = single(SliceFOV / Nfiles); 0083 end 0084 0085 % Initialise avw.img and reset some header dimensions 0086 avw.hdr.dime.dim(4) = Nfiles; 0087 avw = avw_img_init(avw); 0088 0089 % Now reset orient field of avw, as all data will 0090 % be in standard axial unflipped orientation after 0091 % avw_img_read. 0092 avw.hdr.hist.orient = char(0); 0093 0094 0095 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% 0096 % Add slices, depends on whether slice order is normal or flipped 0097 0098 orient = double(firstslice.hdr.hist.orient); 0099 0100 if orient < 3, 0101 % process slices as unflipped volume 0102 for f = 1:Nfiles, 0103 if files(f).bytes == Fsize, 0104 slice = avw_img_read(files(f).name,IMGorient,machine); 0105 avw = avw_add_slice(avw,slice,f,orient); 0106 else 0107 msg = sprint('AVW_IMG_COMPOSE: This file is not the same size as the first file!'); 0108 error(msg); 0109 end 0110 end 0111 else 0112 % process slices as flipped volume 0113 for f = Nfiles:-1:1, 0114 if files(f).bytes == Fsize, 0115 slice = avw_img_read(files(f).name,IMGorient,machine); 0116 avw = avw_add_slice(avw,slice,f,orient); 0117 else 0118 msg = sprint('AVW_IMG_COMPOSE: This file is not the same size as the first file!'); 0119 error(msg); 0120 end 0121 end 0122 end 0123 0124 0125 return 0126 0127 0128 0129 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% 0130 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% 0131 function [avw] = avw_add_slice(avw,slice,Nslice,orient), 0132 0133 % Check that composed volume and current slice 0134 % have the same orientation 0135 Vorient = double( avw.hdr.hist.orient); 0136 Sorient = double(slice.hdr.hist.orient); 0137 0138 if Vorient ~= Sorient, 0139 msg = sprintf('AVW_IMG_COMPOSE: Slice %3d has different orientation to volume',Nslice); 0140 error(msg); 0141 end 0142 0143 switch double(orient), 0144 0145 case 0, % axial unflipped 0146 0147 % Slices in 'z' axis - from patient inferior to superior 0148 avw.img(:,:,Nslice) = slice.img; 0149 0150 case 1, % coronal unflipped 0151 0152 % Slices in 'y' axis - from patient posterior to anterior 0153 avw.img(:,Nslice,:) = slice.img; 0154 0155 case 2, % sagittal unflipped 0156 0157 % Slices in 'x' axis - from patient right to left 0158 avw.img(Nslice,:,:) = slice.img; 0159 0160 case 3, % axial flipped 0161 0162 % Slices in 'z' axis - from patient inferior to superior 0163 avw.img(:,:,Nslice) = slice.img; 0164 0165 case 4, % coronal flipped 0166 0167 % Slices in 'y' axis - from patient anterior to posterior 0168 avw.img(:,Nslice,:) = slice.img; 0169 0170 case 5, % sagittal flipped 0171 0172 % Slices in 'x' axis - from patient right to left 0173 avw.img(Nslice,:,:) = slice.img; 0174 end 0175 0176 return 0177 0178 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% 0179 function [avw] = avw_img_init(avw), 0180 0181 PixelDim = double(avw.hdr.dime.dim(2)); 0182 RowDim = double(avw.hdr.dime.dim(3)); 0183 SliceDim = double(avw.hdr.dime.dim(4)); 0184 0185 PixelSz = double(avw.hdr.dime.pixdim(2)); 0186 RowSz = double(avw.hdr.dime.pixdim(3)); 0187 SliceSz = double(avw.hdr.dime.pixdim(4)); 0188 0189 switch double(avw.hdr.hist.orient), 0190 0191 case {0,3}, % axial unflipped or flipped 0192 0193 x = PixelDim; Xsz = PixelSz; 0194 y = RowDim; Ysz = RowSz; 0195 z = SliceDim; Zsz = SliceSz; 0196 0197 case {1,4}, % coronal unflipped or flipped 0198 0199 x = PixelDim; Xsz = PixelSz; 0200 y = SliceDim; Ysz = SliceSz; 0201 z = RowDim; Zsz = RowSz; 0202 0203 case {2,5}, % sagittal unflipped or flipped 0204 0205 x = SliceDim; Xsz = SliceSz; 0206 y = PixelDim; Ysz = PixelSz; 0207 z = RowDim; Zsz = RowSz; 0208 0209 otherwise, % assume axial unflipped or flipped 0210 0211 msg = sprintf('AVW_IMG_COMPOSE: No specified orientation\n'); 0212 warning(msg); 0213 0214 x = PixelDim; Xsz = PixelSz; 0215 y = RowDim; Ysz = RowSz; 0216 z = SliceDim; Zsz = SliceSz; 0217 0218 end 0219 0220 avw.img = zeros(x,y,z); 0221 avw.hdr.dime.dim(2) = x; 0222 avw.hdr.dime.dim(3) = y; 0223 avw.hdr.dime.dim(4) = z; 0224 0225 avw.hdr.dime.pixdim(2) = Xsz; 0226 avw.hdr.dime.pixdim(3) = Ysz; 0227 avw.hdr.dime.pixdim(4) = Zsz; 0228 0229 return