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3dANOVA.h
Go to the documentation of this file.00001 00002 /***************************************************************************** 00003 Major portions of this software are copyrighted by the Medical College 00004 of Wisconsin, 1994-2000, and are released under the Gnu General Public 00005 License, Version 2. See the file README.Copyright for details. 00006 ******************************************************************************/ 00007 00008 /* 00009 This is the header file for the 3dANOVA.lib library routines. 00010 00011 File: 3dANOVA.h 00012 Author: B. D. Ward 00013 Date: 20 January 1997 00014 00015 Mod: Added command -diskspace to print out how much disk space is 00016 required to execute the problem. 00017 Date: 23 January 1997 00018 00019 Mod: Change to routine write_afni_data to reduce truncation error. 00020 Date: 27 January 1997 00021 00022 Mod: Added machine specific code for checking disk space. 00023 Date: 29 January 1997 00024 00025 Mod: Extensive changes required to implement the 'bucket' dataset. 00026 Date: 30 December 1997 00027 00028 Mod: Library routines moved to 3dANOVA.lib. 00029 Date: 5 January 1998 00030 00031 Mod: Added software for statistical tests of individual cell means, 00032 cell differences, and cell contrasts. 00033 Date: 27 October 1998 00034 00035 Mod: Added changes for incorporating History notes. 00036 Date: 09 September 1999 00037 00038 Mod: Replaced dataset input code with calls to THD_open_dataset, 00039 to allow operator selection of individual sub-bricks for input. 00040 Date: 02 December 1999 00041 00042 Mod: Increased maximum number of user requested means, differences, 00043 and contrasts. 00044 Date: 31 January 2000 00045 00046 Mod: Set MAX_NAME_LENGTH equal to THD_MAX_NAME. 00047 Date: 02 December 2002 00048 */ 00049 00050 /*---------------------------------------------------------------------------*/ 00051 00052 #include "mrilib.h" 00053 00054 static char * commandline = NULL ; /* command line for history notes */ 00055 00056 00057 /*** HP-UX ***/ 00058 #ifdef HP 00059 # define DF "bdf ." 00060 #endif 00061 00062 /*** SGI IRIX ***/ 00063 #ifdef SGI 00064 # define DF "df -k ." 00065 #endif 00066 00067 /*** DEC OSF1 ***/ 00068 #ifdef OSF1 00069 # define DF "df -k ." 00070 #endif 00071 00072 /*** SunOS or Solaris ***/ 00073 #if defined(SOLARIS) || defined(SUN) 00074 # define DF "df -k" 00075 #endif 00076 00077 /*** IBM RS6000 ***/ 00078 #ifdef RS6000 00079 #endif 00080 00081 /*** Linux 1.2.x ***/ 00082 #ifdef LINUX 00083 # define DF "df -k ." 00084 #endif 00085 00086 /*** other? ***/ 00087 #ifndef DF 00088 # define DF "df" 00089 #endif 00090 00091 00092 #define MAX_LEVELS 300 /* max. number of factor levels */ 00093 #define MAX_OBSERVATIONS 100 /* max. number of observations per cell */ 00094 #define MAX_MEANS 20 /* max. number of user requested means */ 00095 #define MAX_DIFFS 20 /* max. number of user requested diffs. */ 00096 #define MAX_CONTR 40 /* max. number of user requested contrasts */ 00097 #define MAX_NAME_LENGTH THD_MAX_NAME /* max. string length for file names */ 00098 00099 00100 typedef struct anova_options 00101 { 00102 int datum; /* data type for "intensity" data subbrick */ 00103 char session[MAX_NAME_LENGTH]; /* name of output directory */ 00104 00105 int diskspace; /* if positive, print out how much disk space 00106 is required for program execution */ 00107 00108 int nvoxel; /* number of voxel for special output */ 00109 00110 int model; /* indicates type of ANOVA model to be used: 00111 model=1 A,B,C fixed; AxBxC 00112 model=2 A,B,C random; AxBxC 00113 model=3 A fixed; B,C random; AxBxC 00114 model=4 A,B fixed; C random; AxBxC 00115 model=5 A,B fixed; C random; AxB,BxC,C(A) 00116 */ 00117 00118 int a; /* number of levels for factor A */ 00119 int b; /* number of levels for factor B */ 00120 int c; /* number of levels for factor C */ 00121 int n; /* number of observations in each cell */ 00122 int nt; /* total number of observations */ 00123 00124 int na[MAX_LEVELS]; /* number of observations at each level 00125 of factor A (for 3dANOVA only) */ 00126 00127 char ***** xname; /* names of the input data files */ 00128 char * first_dataset; /* name of the first data set */ 00129 00130 int nx, ny, nz; /* data set dimensions */ 00131 int nxyz; /* number of voxels per image */ 00132 00133 int nftr; /* if positive, calculate F for treatment */ 00134 char * ftrname; /* name of output file of F for treatment */ 00135 00136 int nfa; /* if positive, calculate F for A effect */ 00137 char * faname; /* name of output file of F for A effect */ 00138 int nfb; /* if positive, calculate F for B effect */ 00139 char * fbname; /* name of output file of F for B effect */ 00140 int nfc; /* if positive, calculate F for C effect */ 00141 char * fcname; /* name of output file of F for C effect */ 00142 int nfab; /* if pos., calculate F for A*B interaction */ 00143 char * fabname; /* name of output file for A*B interaction */ 00144 int nfac; /* if pos., calculate F for A*C interaction */ 00145 char * facname; /* name of output file for A*C interaction */ 00146 int nfbc; /* if pos., calculate F for B*C interaction */ 00147 char * fbcname; /* name of output file for B*C interaction */ 00148 int nfabc; /* if pos, calculate F for A*B*C interaction */ 00149 char * fabcname; /* name of output file for A*B*C interaction */ 00150 00151 00152 int num_ameans; /* number of factor A level means */ 00153 int ameans[MAX_MEANS]; /* calc means for these factor A levels */ 00154 char * amname[MAX_MEANS]; /* names of output files for factor A means */ 00155 00156 int num_bmeans; /* number of factor B level means */ 00157 int bmeans[MAX_MEANS]; /* calc means for these factor B levels */ 00158 char * bmname[MAX_MEANS]; /* names of output files for factor B means */ 00159 00160 int num_cmeans; /* number of factor C level means */ 00161 int cmeans[MAX_MEANS]; /* calc means for these factor C levels */ 00162 char * cmname[MAX_MEANS]; /* names of output files for factor C means */ 00163 00164 int num_xmeans; /* number of cell means */ 00165 int xmeans[MAX_MEANS][3]; /* calc means for these cells */ 00166 char * xmname[MAX_MEANS]; /* name of output files for cell means */ 00167 00168 int num_adiffs; /* num of diffs in factor A level means */ 00169 int adiffs[MAX_DIFFS][2]; /* calc diffs in these factor A level means */ 00170 char * adname[MAX_DIFFS]; /* names of output files for A differences */ 00171 00172 int num_bdiffs; /* num of diffs in factor B level means */ 00173 int bdiffs[MAX_DIFFS][2]; /* calc diffs in these factor B level means */ 00174 char * bdname[MAX_DIFFS]; /* names of output files for B differences */ 00175 00176 int num_cdiffs; /* num of diffs in factor C level means */ 00177 int cdiffs[MAX_DIFFS][2]; /* calc diffs in these factor C level means */ 00178 char * cdname[MAX_DIFFS]; /* names of output files for C differences */ 00179 00180 int num_xdiffs; /* num of diffs in cell means */ 00181 int xdiffs[MAX_DIFFS][2][3]; /* calc diffs in these cell means */ 00182 char * xdname[MAX_DIFFS]; /* names of output files for cell diffs */ 00183 00184 int num_acontr; /* number of factor A contrasts */ 00185 float acontr[MAX_CONTR][MAX_LEVELS]; /* factor A contrast vectors */ 00186 char * acname[MAX_CONTR]; /* names of output files for A contrasts */ 00187 00188 int num_bcontr; /* number of factor B contrasts */ 00189 float bcontr[MAX_CONTR][MAX_LEVELS]; /* factor B contrast vectors */ 00190 char * bcname[MAX_CONTR]; /* names of output files for B contrasts */ 00191 00192 int num_ccontr; /* number of factor C contrasts */ 00193 float ccontr[MAX_CONTR][MAX_LEVELS]; /* factor C contrast vectors */ 00194 char * ccname[MAX_CONTR]; /* names of output files for C contrasts */ 00195 00196 int num_xcontr; /* number of contrasts of cell means */ 00197 float xcontr[MAX_CONTR][MAX_LEVELS][MAX_LEVELS]; 00198 /* cell means contrast vectors */ 00199 char * xcname[MAX_CONTR]; /* names of output files for cell contrasts */ 00200 00201 char * bucket_filename; /* file name for bucket dataset */ 00202 00203 } anova_options; 00204 00205 00206 /*---------------------------------------------------------------------------*/ 00207 /* 00208 Routine to initialize input options. 00209 */ 00210 00211 void initialize_options (anova_options * option_data); 00212 00213 00214 /*---------------------------------------------------------------------------*/ 00215 00216 /** macro to open a dataset and make it ready for processing **/ 00217 00218 #define DOPEN(ds,name) \ 00219 do{ int pv ; (ds) = THD_open_dataset((name)) ; \ 00220 if( !ISVALID_3DIM_DATASET((ds)) ){ \ 00221 fprintf(stderr,"*** Can't open dataset: %s\n",(name)) ; exit(1) ; } \ 00222 if( (ds)->daxes->nxx!=nx || (ds)->daxes->nyy!=ny || \ 00223 (ds)->daxes->nzz!=nz ){ \ 00224 fprintf(stderr,"*** Axes mismatch: %s\n",(name)) ; exit(1) ; } \ 00225 if( DSET_NVALS((ds)) != 1 ){ \ 00226 fprintf(stderr,"*** Must specify 1 sub-brick: %s\n",(name));exit(1);}\ 00227 THD_load_datablock( (ds)->dblk ) ; \ 00228 pv = DSET_PRINCIPAL_VALUE((ds)) ; \ 00229 if( DSET_ARRAY((ds),pv) == NULL ){ \ 00230 fprintf(stderr,"*** Can't access data: %s\n",(name)) ; exit(1); } \ 00231 if( DSET_BRICK_TYPE((ds),pv) == MRI_complex ){ \ 00232 fprintf(stderr,"*** Can't use complex data: %s\n",(name)) ; exit(1);\ 00233 } \ 00234 break ; } while (0) 00235 00236 00237 /*---------------------------------------------------------------------------*/ 00238 00239 /** macro to return pointer to correct location in brick for current processing **/ 00240 00241 #define SUB_POINTER(ds,vv,ind,ptr) \ 00242 do{ switch( DSET_BRICK_TYPE((ds),(vv)) ){ \ 00243 default: fprintf(stderr,"\n*** Illegal datum! ***\n");exit(1); \ 00244 case MRI_short:{ short * fim = (short *) DSET_ARRAY((ds),(vv)) ; \ 00245 (ptr) = (void *)( fim + (ind) ) ; \ 00246 } break ; \ 00247 case MRI_byte:{ byte * fim = (byte *) DSET_ARRAY((ds),(vv)) ; \ 00248 (ptr) = (void *)( fim + (ind) ) ; \ 00249 } break ; \ 00250 case MRI_float:{ float * fim = (float *) DSET_ARRAY((ds),(vv)) ; \ 00251 (ptr) = (void *)( fim + (ind) ) ; \ 00252 } break ; } break ; } while(0) 00253 00254 00255 /*---------------------------------------------------------------------------*/ 00256 /* 00257 Routine to print error message and stop. 00258 */ 00259 00260 void ANOVA_error (char * message); 00261 00262 00263 /*---------------------------------------------------------------------------*/ 00264 /* 00265 Routine to write a 3d volume of floating point data to a (temporary) 00266 disk file. 00267 */ 00268 00269 int volume_write_count (char * filename, float * fout, int size); 00270 00271 00272 /*---------------------------------------------------------------------------*/ 00273 /* 00274 Routine to write a 3d volume of floating point data to a (temporary) 00275 disk file. Error exit if cannot write entire file. 00276 */ 00277 00278 void volume_write (char * filename, float * fout, int size); 00279 00280 00281 /*---------------------------------------------------------------------------*/ 00282 /* 00283 Routine to read a 3d volume of floating point data. 00284 */ 00285 00286 void volume_read (char * filename, float * fin, int size); 00287 00288 00289 /*---------------------------------------------------------------------------*/ 00290 /* 00291 Routine to delete a file containing a 3d volume of floating point data. 00292 */ 00293 00294 void volume_delete (char * filename); 00295 00296 00297 /*---------------------------------------------------------------------------*/ 00298 /* 00299 Routine to set a 3d volume of floating point data to zero. 00300 */ 00301 00302 void volume_zero (float * f, int size); 00303 00304 00305 /*---------------------------------------------------------------------------*/ 00306 /* 00307 Routine to get the dimensions of the 3d AFNI data sets. 00308 */ 00309 00310 void get_dimensions (anova_options * option_data); 00311 00312 00313 /*---------------------------------------------------------------------------*/ 00314 /* 00315 Routine to check whether one temporary file already exists. 00316 */ 00317 00318 void check_one_temporary_file (char * filename); 00319 00320 00321 /*---------------------------------------------------------------------------*/ 00322 /* 00323 Routine to check whether one output file already exists. 00324 */ 00325 00326 void check_one_output_file (anova_options * option_data, char * filename); 00327 00328 00329 /*---------------------------------------------------------------------------*/ 00330 /* 00331 Return maximum of two integers. 00332 */ 00333 00334 int max (int n1, int n2); 00335 00336 00337 /*---------------------------------------------------------------------------*/ 00338 /* 00339 Routine to determine if sufficient disk space exists for storing 00340 the temporary data files. 00341 */ 00342 00343 void check_disk_space (anova_options * option_data); 00344 00345 00346 /*---------------------------------------------------------------------------*/ 00347 /* 00348 Routine to read one AFNI data set from file 'filename'. 00349 The data is converted to floating point (in ffim). 00350 */ 00351 00352 void read_afni_data (anova_options * option_data, 00353 char * filename, float * ffim); 00354 00355 00356 /*---------------------------------------------------------------------------*/ 00357 /* 00358 Convert one volume to another type, autoscaling: 00359 nxy = # voxels 00360 itype = input datum type 00361 ivol = pointer to input volume 00362 otype = output datum type 00363 ovol = pointer to output volume (again, must be pre-malloc-ed) 00364 Return value is the scaling factor used (0.0 --> no scaling). 00365 */ 00366 00367 float EDIT_coerce_autoscale_new( int nxyz , 00368 int itype,void *ivol , int otype,void *ovol ); 00369 00370 00371 /*---------------------------------------------------------------------------*/ 00372 /* 00373 Routine to write one AFNI data set. 00374 00375 This data set may be either 'fitt' type (intensity + t-statistic) 00376 or 'fift' type (intensity + F-statistic). 00377 00378 The intensity data is in ffim, and the corresponding statistic is in ftr. 00379 00380 numdof = numerator degrees of freedom 00381 dendof = denominator degrees of freedom 00382 00383 Note: if dendof = 0, then write 'fitt' type data set; 00384 if dendof > 0, then write 'fift' type data set. 00385 */ 00386 00387 void write_afni_data (anova_options * option_data, char * filename, 00388 float * ffim, float * ftr, int numdof, int dendof); 00389 00390 00391 /*---------------------------------------------------------------------------*/ 00392 /* 00393 Routine to add file name to command string. 00394 */ 00395 00396 void add_file_name (THD_3dim_dataset * new_dset, char * filename, 00397 char * command_str); 00398 00399 00400 /*---------------------------------------------------------------------------*/ 00401 /* 00402 Routine to remove AFNI .HEAD and .BRIK dataset files. 00403 */ 00404 00405 void remove_dataset (THD_3dim_dataset * new_dset, char * filename); 00406 00407 00408 /*---------------------------------------------------------------------------*/ 00409 /* 00410 Routine to release memory allocated for anova_options. 00411 */ 00412 00413 void destroy_anova_options (anova_options * option_data); 00414 00415 00416 /*---------------------------------------------------------------------------*/ 00417 00418 00419 00420 00421 00422 00423 00424 00425 00426 00427 00428 00429 00430 00431 00432
