avw_img_write - write Analyze image files (*.img)
avw_img_write(avw, fileprefix, [machine])
avw.img - a 3D matrix of image data (double precision).
avw.hdr - a struct with image data parameters. If
not empty, this function calls avw_hdr_write.
fileprefix - a string, the filename without the .img
extension. If empty, may use avw.fileprefix
(Modified by M. Sato)
Do not change orientation of image data written in the file
machine - a string, see machineformat in fread for details.
The default here is 'ieee-le'.
Tip: to change the data type, set avw.hdr.dime.datatype to:
1 Binary ( 1 bit per voxel)
2 Unsigned character ( 8 bits per voxel)
4 Signed short ( 16 bits per voxel)
8 Signed integer ( 32 bits per voxel)
16 Floating point ( 32 bits per voxel)
32 Complex, 2 floats ( 64 bits per voxel), not supported
64 Double precision ( 64 bits per voxel)
128 Red-Green-Blue (128 bits per voxel), not supported
See also: avw_write, avw_hdr_write,
avw_read, avw_hdr_read, avw_img_read, avw_view0001 function avw_img_write(avw, fileprefix, machine) 0002 0003 % avw_img_write - write Analyze image files (*.img) 0004 % 0005 % avw_img_write(avw, fileprefix, [machine]) 0006 % 0007 % avw.img - a 3D matrix of image data (double precision). 0008 % avw.hdr - a struct with image data parameters. If 0009 % not empty, this function calls avw_hdr_write. 0010 % 0011 % fileprefix - a string, the filename without the .img 0012 % extension. If empty, may use avw.fileprefix 0013 % 0014 % (Modified by M. Sato) 0015 % Do not change orientation of image data written in the file 0016 % 0017 % machine - a string, see machineformat in fread for details. 0018 % The default here is 'ieee-le'. 0019 % 0020 % Tip: to change the data type, set avw.hdr.dime.datatype to: 0021 % 0022 % 1 Binary ( 1 bit per voxel) 0023 % 2 Unsigned character ( 8 bits per voxel) 0024 % 4 Signed short ( 16 bits per voxel) 0025 % 8 Signed integer ( 32 bits per voxel) 0026 % 16 Floating point ( 32 bits per voxel) 0027 % 32 Complex, 2 floats ( 64 bits per voxel), not supported 0028 % 64 Double precision ( 64 bits per voxel) 0029 % 128 Red-Green-Blue (128 bits per voxel), not supported 0030 % 0031 % See also: avw_write, avw_hdr_write, 0032 % avw_read, avw_hdr_read, avw_img_read, avw_view 0033 % 0034 0035 % $Revision: 1332 $ $Date:: 2011-02-24 15:57:20 +0900#$ 0036 0037 % Licence: GNU GPL, no express or implied warranties 0038 % History: 05/2002, Darren.Weber@flinders.edu.au 0039 % The Analyze format is copyright 0040 % (c) Copyright, 1986-1995 0041 % Biomedical Imaging Resource, Mayo Foundation 0042 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% 0043 0044 0045 %------------------------------------------------------------------------ 0046 % Check inputs 0047 0048 if ~exist('avw','var'), 0049 doc avw_img_write; 0050 msg = sprintf('\n...no input avw.\n'); 0051 error(msg); 0052 elseif isempty(avw), 0053 msg = sprintf('\n...empty input avw.\n'); 0054 error(msg); 0055 elseif ~isfield(avw,'img'), 0056 msg = sprintf('\n...empty input avw.img\n'); 0057 error(msg); 0058 end 0059 0060 if ~exist('fileprefix','var'), 0061 if isfield(avw,'fileprefix'), 0062 if ~isempty(avw.fileprefix), 0063 fileprefix = avw.fileprefix; 0064 else 0065 fileprefix = ''; 0066 end 0067 end 0068 end 0069 if isempty(fileprefix), 0070 doc avw_img_write; 0071 fprintf('\n...no input fileprefix - see help avw_img_write\n'); 0072 return; 0073 end 0074 0075 if ~exist('IMGorient','var'), IMGorient = ''; end 0076 if ~exist('machine','var'), machine = 'ieee-le'; end 0077 0078 if findstr('.hdr',fileprefix), 0079 % fprintf('AVW_IMG_WRITE: Removing .hdr extension from ''%s''\n',fileprefix); 0080 fileprefix = strrep(fileprefix,'.hdr',''); 0081 end 0082 if findstr('.img',fileprefix), 0083 % fprintf('AVW_IMG_WRITE: Removing .img extension from ''%s''\n',fileprefix); 0084 fileprefix = strrep(fileprefix,'.img',''); 0085 end 0086 0087 0088 0089 %------------------------------------------------------------------------ 0090 % MAIN 0091 0092 % Modified by M. Sato 0093 %version = '[$Revision: 1332 $]'; 0094 %fprintf('\nAVW_IMG_WRITE [v%s]\n',version(12:16)); tic; 0095 0096 fid = fopen(sprintf('%s.img',fileprefix),'w',machine); 0097 if fid < 0, 0098 msg = sprintf('Cannot open file %s.img\n',fileprefix); 0099 error(msg); 0100 else 0101 avw = write_image(fid,avw,fileprefix,IMGorient,machine); 0102 end 0103 0104 %t=toc; fprintf('...done (%5.2f sec).\n\n',t); 0105 0106 % MUST write header after the image, to ensure any 0107 % orientation changes during image write are saved 0108 % in the header 0109 avw_hdr_write(avw,fileprefix,machine); 0110 0111 return 0112 0113 0114 0115 0116 %----------------------------------------------------------------------------------- 0117 0118 function avw = write_image(fid,avw,fileprefix,IMGorient,machine) 0119 0120 % short int bitpix; /* Number of bits per pixel; 1, 8, 16, 32, or 64. */ 0121 % short int datatype /* Datatype for this image set */ 0122 % /*Acceptable values for datatype are*/ 0123 % #define DT_NONE 0 0124 % #define DT_UNKNOWN 0 /*Unknown data type*/ 0125 % #define DT_BINARY 1 /*Binary ( 1 bit per voxel)*/ 0126 % #define DT_UNSIGNED_CHAR 2 /*Unsigned character ( 8 bits per voxel)*/ 0127 % #define DT_SIGNED_SHORT 4 /*Signed short (16 bits per voxel)*/ 0128 % #define DT_SIGNED_INT 8 /*Signed integer (32 bits per voxel)*/ 0129 % #define DT_FLOAT 16 /*Floating point (32 bits per voxel)*/ 0130 % #define DT_COMPLEX 32 /*Complex,2 floats (64 bits per voxel)/* 0131 % #define DT_DOUBLE 64 /*Double precision (64 bits per voxel)*/ 0132 % #define DT_RGB 128 /*A Red-Green-Blue datatype*/ 0133 % #define DT_ALL 255 /*Undocumented*/ 0134 0135 switch double(avw.hdr.dime.datatype), 0136 case 1, 0137 avw.hdr.dime.bitpix = int16( 1); precision = 'bit1'; 0138 case 2, 0139 avw.hdr.dime.bitpix = int16( 8); precision = 'uchar'; 0140 case 4, 0141 avw.hdr.dime.bitpix = int16(16); precision = 'int16'; 0142 case 8, 0143 avw.hdr.dime.bitpix = int16(32); precision = 'int32'; 0144 case 16, 0145 avw.hdr.dime.bitpix = int16(32); precision = 'single'; 0146 case 32, 0147 error('...complex datatype not yet supported.\n'); 0148 case 64, 0149 avw.hdr.dime.bitpix = int16(64); precision = 'double'; 0150 case 128, 0151 error('...RGB datatype not yet supported.\n'); 0152 otherwise 0153 fprintf('...unknown datatype, using type 16 (32 bit floats).\n'); 0154 avw.hdr.dime.datatype = int16(16); 0155 avw.hdr.dime.bitpix = int16(32); precision = 'single'; 0156 end 0157 0158 0159 % write the .img file, depending on the .img orientation 0160 fprintf('...writing %s precision Analyze image (%s).\n',precision,machine); 0161 0162 fseek(fid,0,'bof'); 0163 0164 % Modified by M. Sato 0165 0166 fprintf('...writing axial unflipped\n'); 0167 0168 % avw.hdr.hist.orient = uint8(0); 0169 % 0170 % SliceDim = double(avw.hdr.dime.dim(4)); % z 0171 % RowDim = double(avw.hdr.dime.dim(3)); % y 0172 % PixelDim = double(avw.hdr.dime.dim(2)); % x 0173 % SliceSz = double(avw.hdr.dime.pixdim(4)); 0174 % RowSz = double(avw.hdr.dime.pixdim(3)); 0175 % PixelSz = double(avw.hdr.dime.pixdim(2)); 0176 0177 % Modified by M. Sato 0178 0179 fwrite(fid,avw.img,precision); 0180 0181 % x = 1:PixelDim; 0182 % for z = 1:SliceDim, 0183 % for y = 1:RowDim, 0184 % fwrite(fid,avw.img(x,y,z),precision); 0185 % end 0186 % end 0187 0188 fclose(fid); 0189 0190 % Update the header 0191 %avw.hdr.dime.dim(2:4) = int16([PixelDim,RowDim,SliceDim]); 0192 %avw.hdr.dime.pixdim(2:4) = single([PixelSz,RowSz,SliceSz]); 0193 0194 return