Doxygen Source Code Documentation
mayo_analyze.h
Go to the documentation of this file.00001 #ifndef _RWC_ANALYZE_HEADER_ 00002 /*************************************************************************** 00003 From http://www.mayo.edu/bir/Analyze_Pages/AnalyzeFileInfo.html 00004 Describes the ANALYZE 7.5 file format (.img/.hdr pairs). 00005 ---------------------------------------------------------------- 00006 The image database is the system of files that the ANALYZE package uses to 00007 organize and access image data on the disk. Facilities are provided for 00008 converting data from a number of sources for use with the package. A 00009 description of the database format is provided to aid developers in porting 00010 images from other sources for use with the ANALYZE TM system. An ANALYZE 00011 image database consists of at least two files: 00012 00013 * an image file 00014 * a header file 00015 00016 The files have the same name being distinguished by the extensions .img for 00017 the image file and .hdr for the header file. Thus, for the image database 00018 heart, there are the UNIX files heart.img and heart.hdr. The ANALYZE 00019 programs all refer to this pair of files as a single entity named heart. 00020 00021 Image File 00022 00023 The format of the image file is very simple containing usually uncompressed 00024 pixel data for the images in one of several possible pixel formats: 00025 00026 * 1 bit packed binary (slices must begin on byte boundaries) 00027 * 8 bit 8 bits per pixel (unsigned char) 00028 * 16 bit 16 bits per pixel (signed short) 00029 * 32 bit 32 bits per pixel signed integers, or floating point 00030 * 64 bit 64 bits per pixel; double precision, floating point, 00031 or complex. 00032 * 24 bit RGB , 8-bits per channel Red, Green, Blue. 00033 00034 Header File 00035 00036 The header file is represented here as a `C' structure which describes the 00037 dimensions and history of the pixel data. The header structure consists of 00038 three substructures: 00039 00040 header_key describes the header 00041 image_dimension describes image sizes 00042 data_history optional 00043 ****************************************************************************/ 00044 00045 struct header_key /* header key */ 00046 { /* off + size */ 00047 int sizeof_hdr; /* 0 + 4 */ 00048 char data_type[10]; /* 4 + 10 */ 00049 char db_name[18]; /* 14 + 18 */ 00050 int extents; /* 32 + 4 */ 00051 short int session_error; /* 36 + 2 */ 00052 char regular; /* 38 + 1 */ 00053 char hkey_un0; /* 39 + 1 */ 00054 }; /* total=40 bytes */ 00055 struct image_dimension 00056 { /* off + size */ 00057 short int dim[8]; /* 0 + 16 */ 00058 short int unused8; /* 16 + 2 */ 00059 short int unused9; /* 18 + 2 */ 00060 short int unused10; /* 20 + 2 */ 00061 short int unused11; /* 22 + 2 */ 00062 short int unused12; /* 24 + 2 */ 00063 short int unused13; /* 26 + 2 */ 00064 short int unused14; /* 28 + 2 */ 00065 short int datatype; /* 30 + 2 */ 00066 short int bitpix; /* 32 + 2 */ 00067 short int dim_un0; /* 34 + 2 */ 00068 float pixdim[8]; /* 36 + 32 */ 00069 /* 00070 pixdim[] specifies the voxel dimensitons: 00071 pixdim[1] - voxel width 00072 pixdim[2] - voxel height 00073 pixdim[3] - interslice distance 00074 ...etc 00075 */ 00076 float vox_offset; /* 68 + 4 */ 00077 float funused1; /* 72 + 4 */ 00078 float funused2; /* 76 + 4 */ 00079 float funused3; /* 80 + 4 */ 00080 float cal_max; /* 84 + 4 */ 00081 float cal_min; /* 88 + 4 */ 00082 float compressed; /* 92 + 4 */ 00083 float verified; /* 96 + 4 */ 00084 int glmax,glmin; /* 100 + 8 */ 00085 }; /* total=108 bytes */ 00086 struct data_history 00087 { /* off + size */ 00088 char descrip[80]; /* 0 + 80 */ 00089 char aux_file[24]; /* 80 + 24 */ 00090 char orient; /* 104 + 1 */ 00091 char originator[10]; /* 105 + 10 */ 00092 char generated[10]; /* 115 + 10 */ 00093 char scannum[10]; /* 125 + 10 */ 00094 char patient_id[10]; /* 135 + 10 */ 00095 char exp_date[10]; /* 145 + 10 */ 00096 char exp_time[10]; /* 155 + 10 */ 00097 char hist_un0[3]; /* 165 + 3 */ 00098 int views; /* 168 + 4 */ 00099 int vols_added; /* 172 + 4 */ 00100 int start_field; /* 176 + 4 */ 00101 int field_skip; /* 180 + 4 */ 00102 int omax, omin; /* 184 + 8 */ 00103 int smax, smin; /* 192 + 8 */ 00104 }; 00105 struct dsr 00106 { 00107 struct header_key hk; /* 0 + 40 */ 00108 struct image_dimension dime; /* 40 + 108 */ 00109 struct data_history hist; /* 148 + 200 */ 00110 }; /* total= 348 bytes*/ 00111 00112 /* Acceptable values for datatype */ 00113 00114 #define ANDT_NONE 0 00115 #define ANDT_UNKNOWN 0 /* what it says, dude */ 00116 #define ANDT_BINARY 1 /* binary (1 bit/voxel) */ 00117 #define ANDT_UNSIGNED_CHAR 2 /* unsigned char (8 bits/voxel) */ 00118 #define ANDT_SIGNED_SHORT 4 /* signed short (16 bits/voxel) */ 00119 #define ANDT_SIGNED_INT 8 /* signed int (32 bits/voxel) */ 00120 #define ANDT_FLOAT 16 /* float (32 bits/voxel) */ 00121 #define ANDT_COMPLEX 32 /* complex (64 bits/voxel) */ 00122 #define ANDT_DOUBLE 64 /* double (64 bits/voxel) */ 00123 #define ANDT_RGB 128 /* RGB triple (24 bits/voxel) */ 00124 #define ANDT_ALL 255 00125 00126 #define ANDT_string(aa) \ 00127 ((aa)==ANDT_BINARY ? "binary" \ 00128 :(aa)==ANDT_UNSIGNED_CHAR ? "byte" \ 00129 :(aa)==ANDT_SIGNED_SHORT ? "short" \ 00130 :(aa)==ANDT_SIGNED_INT ? "int" \ 00131 :(aa)==ANDT_FLOAT ? "float" \ 00132 :(aa)==ANDT_COMPLEX ? "complex" \ 00133 :(aa)==ANDT_DOUBLE ? "double" \ 00134 :(aa)==ANDT_RGB ? "RGB" \ 00135 : "unknown" ) 00136 00137 /*************************************************************************** 00138 The header format is flexible and can be extended for new user-defined data 00139 types. The essential structures of the header are the header_key and the 00140 image_dimension. 00141 00142 The required elements in the header_key substructure are: 00143 00144 int sizeof_header Must indicate the byte size of the header file. 00145 int extents Should be 16384, the image file is created as 00146 contiguous with a minimum extent size. 00147 char regular Must be `r' to indicate that all images and 00148 volumes are the same size. 00149 00150 The image_dimension substructure describes the organization and size of the 00151 images. These elements enable the database to reference images by volume and 00152 slice number. Explanation of each element follows: 00153 00154 short int dim[]; = array of the image dimensions 00155 dim[0] = Number of dimensions in database; usually 4 00156 dim[1] = Image X dimension; number of pixels in an image row 00157 dim[2] = Image Y dimension; number of pixel rows in slice 00158 dim[3] = Volume Z dimension; number of slices in a volume 00159 dim[4] = Time points, number of volumes in database. 00160 00161 char vox_units[4] = specifies the spatial units of measure for a 00162 voxel 00163 char cal_units[4] = specifies the name of the calibration unit 00164 00165 short int datatype = datatype for this image set 00166 Acceptable values for datatype are one of 00167 the ANDT_* defines above 00168 00169 short int bitpix = number of bits per pixel; 1, 8, 16, 32, 64 00170 short int dim_un0 = unused 00171 00172 float pixdim[] = Parallel array to dim[], giving real world 00173 measurements in mm and ms. 00174 pixdim[1] = voxel width in mm 00175 pixdim[2] = voxel height in mm 00176 pixdim[3] = slice thickness in mm 00177 float vox_offset = byte offset in the .img file at which voxels 00178 start. This value can be negative to specify 00179 that the absolute value is applied for every image 00180 in the file 00181 float cal_max, = specify the range of calibration values 00182 cal_min 00183 int glmax, glmin = The maximum and minimum pixel values for the 00184 entire database 00185 00186 The data_history substructure is not required, but the orient field is used 00187 to indicate individual slice orientation and determines whether the Movie 00188 program will attempt to flip the images before displaying a movie sequence. 00189 00190 orient = slice orientation for this dataset. 00191 0 = transverse unflipped 00192 1 = coronal unflipped 00193 2 = sagittal unflipped 00194 3 = transverse flipped 00195 4 = coronal flipped 00196 5 = sagittal flipped 00197 ****************************************************************************/ 00198 #endif /* _RWC_ANALYZE_HEADER_ */
