int main(int argc, char *argv[]) { int i,j,k,m,n,aa,ii,jj,kk,mm,rr; int iarg; int nmask1=0; int nmask2=0; THD_3dim_dataset *insetFA = NULL, *insetV1 = NULL, *insetMD = NULL, *insetL1 = NULL; THD_3dim_dataset *insetEXTRA=NULL; THD_3dim_dataset *mset2=NULL; THD_3dim_dataset *mset1=NULL; THD_3dim_dataset *outsetMAP=NULL, *outsetMASK=NULL; char *prefix="tracky"; int LOG_TYPE=0; char in_FA[300]; char in_V1[300]; char in_MD[300]; char in_L1[300]; int EXTRAFILE=0; // switch for whether other file is input as WM map char OUT_bin[300]; char OUT_tracstat[300]; char prefix_mask[300]; char prefix_map[300]; // FACT algopts FILE *fout0; float MinFA=0.2,MaxAngDeg=45,MinL=20.0; float MaxAng; int SeedPerV[3]={2,2,2}; int ArrMax=0; float tempvmagn; int Nvox=-1; // tot number vox int Dim[3]={0,0,0}; // dim in each dir int Nseed=0,M=30,bval=1000; int DimSeed[3]; // number of seeds there will be float Ledge[3]; // voxel edge lengths int *ROI1, *ROI2; short int *temp_arr; char *temp_byte; int **Tforw, **Tback; int **Ttot; float **flTforw, **flTback; float ****coorded; int ****INDEX; int len_forw, len_back; // int count of num of squares through float phys_forw[1], phys_back[1]; int idx; float ave_tract_len, ave_tract_len_phys; int inroi1, inroi2, KEEPIT; // switches for detecting int in[3]; // to pass to trackit float physin[3]; // also for trackit, physical loc, int totlen; float totlen_phys; int Numtract; int READS_in; float READS_fl; int end[2][3]; int test_ind[2][3]; int roi3_ct=0, id=0; float roi3_mu_MD = 0.,roi3_mu_RD = 0.,roi3_mu_L1 = 0.,roi3_mu_FA = 0.; float roi3_sd_MD = 0.,roi3_sd_RD = 0.,roi3_sd_L1 = 0.,roi3_sd_FA = 0.; float tempMD,tempFA,tempRD,tempL1; char dset_or[4] = "RAI"; THD_3dim_dataset *dsetn; int TV_switch[3] = {0,0,0}; TAYLOR_BUNDLE *tb=NULL; TAYLOR_TRACT *tt=NULL; char *mode = "NI_fast_binary"; NI_element *nel=NULL; int dump_opts=0; tv_io_header header1 = {.id_string = "TRACK\0", .origin = {0,0,0}, .n_scalars = 3, .scal_n[0] = "FA", .scal_n[1] = "MD", .scal_n[2] = "L1", .n_properties = 0, .vox_to_ras = {{0.,0.,0.,0.},{0.,0.,0.,0.}, {0.,0.,0.,0.},{0.,0.,0.,0.}}, // reset this later based on actual data set .voxel_order = "RAI\0", .invert_x = 0, .invert_y = 0, .invert_z = 0, .swap_xy = 0, .swap_yz = 0, .swap_zx = 0, .n_count = 0, .version = 2, .hdr_size = 1000}; // for testing names... char *postfix[4]={"+orig.HEAD\0",".nii.gz\0",".nii\0","+tlrc.HEAD\0"}; int FOUND =-1; int RECORD_ORIG = 0; float Orig[3] = {0.0,0.0,0.0}; mainENTRY("3dTrackID"); machdep(); // **************************************************************** // **************************************************************** // load AFNI stuff // **************************************************************** // **************************************************************** INFO_message("version: MU"); /** scan args **/ if (argc == 1) { usage_TrackID(1); exit(0); } iarg = 1; while( iarg < argc && argv[iarg][0] == '-' ){ if( strcmp(argv[iarg],"-help") == 0 || strcmp(argv[iarg],"-h") == 0 ) { usage_TrackID(strlen(argv[iarg])>3 ? 2:1); exit(0); } if( strcmp(argv[iarg],"-verb") == 0) { if( ++iarg >= argc ) ERROR_exit("Need argument after '-verb'") ; set_tract_verb(atoi(argv[iarg])); iarg++ ; continue ; } if( strcmp(argv[iarg],"-write_opts") == 0) { dump_opts=1; iarg++ ; continue ; } if( strcmp(argv[iarg],"-rec_orig") == 0) { RECORD_ORIG=1; iarg++ ; continue ; } if( strcmp(argv[iarg],"-tract_out_mode") == 0) { if( ++iarg >= argc ) ERROR_exit("Need argument after '-tract_out_mode'") ; if (strcmp(argv[iarg], "NI_fast_binary") && strcmp(argv[iarg], "NI_fast_text") && strcmp(argv[iarg], "NI_slow_binary") && strcmp(argv[iarg], "NI_slow_text") ) { ERROR_message("Bad value (%s) for -tract_out_mode",argv[iarg]); exit(1); } mode = argv[iarg]; iarg++ ; continue ; } if( strcmp(argv[iarg],"-mask1") == 0 ){ if( ++iarg >= argc ) ERROR_exit("Need argument after '-mask1'") ; mset1 = THD_open_dataset( argv[iarg] ) ; if( mset1 == NULL ) ERROR_exit("Can't open mask1 dataset '%s'", argv[iarg]) ; DSET_load(mset1) ; CHECK_LOAD_ERROR(mset1) ; nmask1 = DSET_NVOX(mset1) ; iarg++ ; continue ; } if( strcmp(argv[iarg],"-mask2") == 0 ){ if( ++iarg >= argc ) ERROR_exit("Need argument after '-mask2'") ; mset2 = THD_open_dataset( argv[iarg] ) ; if( mset2 == NULL ) ERROR_exit("Can't open mask2 dataset '%s'", argv[iarg]) ; DSET_load(mset2) ; CHECK_LOAD_ERROR(mset2) ; nmask2 = DSET_NVOX(mset2) ; iarg++ ; continue ; } if( strcmp(argv[iarg],"-prefix") == 0 ){ iarg++ ; if( iarg >= argc ) ERROR_exit("Need argument after '-prefix'"); prefix = strdup(argv[iarg]) ; if( !THD_filename_ok(prefix) ) ERROR_exit("Illegal name after '-prefix'"); iarg++ ; continue ; } if( strcmp(argv[iarg],"-input") == 0 ){ iarg++ ; if( iarg >= argc ) ERROR_exit("Need argument after '-input'"); for( i=0 ; i<4 ; i++) { sprintf(in_FA,"%s_FA%s", argv[iarg],postfix[i]); if(THD_is_ondisk(in_FA)) { FOUND = i; break; } } insetFA = THD_open_dataset(in_FA) ; if( (insetFA == NULL ) || (FOUND==-1)) ERROR_exit("Can't open dataset '%s': for FA.",in_FA); DSET_load(insetFA) ; CHECK_LOAD_ERROR(insetFA) ; Nvox = DSET_NVOX(insetFA) ; Dim[0] = DSET_NX(insetFA); Dim[1] = DSET_NY(insetFA); Dim[2] = DSET_NZ(insetFA); Ledge[0] = fabs(DSET_DX(insetFA)); Ledge[1] = fabs(DSET_DY(insetFA)); Ledge[2] = fabs(DSET_DZ(insetFA)); Orig[0] = DSET_XORG(insetFA); Orig[1] = DSET_YORG(insetFA); Orig[2] = DSET_ZORG(insetFA); // check tot num vox match (as proxy for dims...) if( (Nvox != nmask1) || (Nvox != nmask2) ) ERROR_exit("Input dataset does not match both mask volumes!"); // this stores the original data file orientation for later use, // as well since we convert everything to RAI temporarily, as // described below header1.voxel_order[0]=ORIENT_typestr[insetFA->daxes->xxorient][0]; header1.voxel_order[1]=ORIENT_typestr[insetFA->daxes->yyorient][0]; header1.voxel_order[2]=ORIENT_typestr[insetFA->daxes->zzorient][0]; for( i=0 ; i<3 ; i++) { header1.dim[i] = Dim[i]; header1.voxel_size[i] = Ledge[i]; // will want this when outputting file later for TrackVis. TV_switch[i] = !(dset_or[i]==header1.voxel_order[i]); } dset_or[3]='\0'; FOUND = -1; for( i=0 ; i<4 ; i++) { sprintf(in_V1,"%s_V1%s", argv[iarg],postfix[i]); if(THD_is_ondisk(in_V1)) { FOUND = i; break; } } insetV1 = THD_open_dataset(in_V1); if( insetV1 == NULL ) ERROR_exit("Can't open dataset '%s':V1",in_V1); DSET_load(insetV1) ; CHECK_LOAD_ERROR(insetV1) ; FOUND = -1; for( i=0 ; i<4 ; i++) { sprintf(in_L1,"%s_L1%s", argv[iarg],postfix[i]); if(THD_is_ondisk(in_L1)) { FOUND = i; break; } } insetL1 = THD_open_dataset(in_L1); if( insetL1 == NULL ) ERROR_exit("Can't open dataset '%s':L1",in_L1); DSET_load(insetL1) ; CHECK_LOAD_ERROR(insetL1) ; FOUND = -1; for( i=0 ; i<4 ; i++) { sprintf(in_MD,"%s_MD%s", argv[iarg],postfix[i]); if(THD_is_ondisk(in_MD)) { FOUND = i; break; } } insetMD = THD_open_dataset(in_MD); if( insetMD == NULL ) ERROR_exit("Can't open dataset '%s':MD",in_MD); DSET_load(insetMD) ; CHECK_LOAD_ERROR(insetMD) ; iarg++ ; continue ; } if( strcmp(argv[iarg],"-algopt") == 0 ){ iarg++ ; if( iarg >= argc ) ERROR_exit("Need argument after '-algopt'"); if (!(nel = ReadTractAlgOpts(argv[iarg]))) { ERROR_message("Failed to read options in %s\n", argv[iarg]); exit(19); } if (NI_getTractAlgOpts(nel, &MinFA, &MaxAngDeg, &MinL, SeedPerV, &M, &bval)) { ERROR_message("Failed to get options"); exit(1); } NI_free_element(nel); nel=NULL; iarg++ ; continue ; } if( strcmp(argv[iarg],"-logic") == 0 ){ iarg++ ; if( iarg >= argc ) ERROR_exit("Need argument after '-logic'"); INFO_message("ROI logic type is: %s",argv[iarg]); if( strcmp(argv[iarg],"AND") == 0 ) LOG_TYPE = 1; else if( strcmp(argv[iarg],"OR") == 0 ) LOG_TYPE = 0; else if( strcmp(argv[iarg],"ALL") == 0 ) LOG_TYPE = -1; else ERROR_exit("Illegal after '-logic': need 'OR' or 'AND'"); iarg++ ; continue ; } //@@ if( strcmp(argv[iarg],"-extra_set") == 0) { if( ++iarg >= argc ) ERROR_exit("Need argument after '-extra_set'"); EXTRAFILE = 1; // switch on insetEXTRA = THD_open_dataset(argv[iarg]); if( (insetEXTRA == NULL ) ) ERROR_exit("Can't open dataset '%s': for extra set.",argv[iarg]); DSET_load(insetEXTRA) ; CHECK_LOAD_ERROR(insetEXTRA) ; if( !((Dim[0] == DSET_NX(insetEXTRA)) && (Dim[1] == DSET_NY(insetEXTRA)) && (Dim[2] == DSET_NZ(insetEXTRA)))) ERROR_exit("Dimensions of extra set '%s' don't match those of the DTI prop ones ('%s', etc.).",argv[iarg], in_FA); iarg++ ; continue ; } ERROR_message("Bad option '%s'\n",argv[iarg]) ; suggest_best_prog_option(argv[0], argv[iarg]); exit(1); } if (iarg < 4) { ERROR_message("Too few options. Try -help for details.\n"); exit(1); } if (dump_opts) { nel = NI_setTractAlgOpts(NULL, &MinFA, &MaxAngDeg, &MinL, SeedPerV, &M, &bval); WriteTractAlgOpts(prefix, nel); NI_free_element(nel); nel=NULL; } // Process the options a little for( i=0 ; i<3 ; i++) DimSeed[i] = Dim[i]*SeedPerV[i]; Nseed = Nvox*SeedPerV[0]*SeedPerV[1]*SeedPerV[2]; // convert to cos of rad value for comparisons, instead of using acos() MaxAng = cos(CONV*MaxAngDeg); // switch to add header-- option for now, added Sept. 2012 // for use with map_TrackID to map tracks to different space if(RECORD_ORIG) { for( i=0 ; i<3 ; i++) header1.origin[i] = Orig[i]; } // at some point, we will have to convert indices into // pseudo-locations; being forced into this choice means that // different data set orientations would be represented differently // and incorrectly in some instances... so, for now, we'll resample // everything to RAI, and then resample back later. guess this will // just slow things down slightly. // have all be RAI for processing here if(TV_switch[0] || TV_switch[1] || TV_switch[2]) { dsetn = r_new_resam_dset(insetFA, NULL, 0.0, 0.0, 0.0, dset_or, RESAM_NN_TYPE, NULL, 1, 0); DSET_delete(insetFA); insetFA=dsetn; dsetn=NULL; dsetn = r_new_resam_dset(insetMD, NULL, 0.0, 0.0, 0.0, dset_or, RESAM_NN_TYPE, NULL, 1, 0); DSET_delete(insetMD); insetMD=dsetn; dsetn=NULL; dsetn = r_new_resam_dset(insetV1, NULL, 0.0, 0.0, 0.0, dset_or, RESAM_NN_TYPE, NULL, 1, 0); DSET_delete(insetV1); insetV1=dsetn; dsetn=NULL; dsetn = r_new_resam_dset(insetL1, NULL, 0.0, 0.0, 0.0, dset_or, RESAM_NN_TYPE, NULL, 1, 0); DSET_delete(insetL1); insetL1=dsetn; dsetn=NULL; dsetn = r_new_resam_dset(mset1, NULL, 0.0, 0.0, 0.0, dset_or, RESAM_NN_TYPE, NULL, 1, 0); DSET_delete(mset1); mset1=dsetn; dsetn=NULL; dsetn = r_new_resam_dset(mset2, NULL, 0.0, 0.0, 0.0, dset_or, RESAM_NN_TYPE, NULL, 1, 0); DSET_delete(mset2); mset2=dsetn; dsetn=NULL; if(EXTRAFILE) { dsetn = r_new_resam_dset(insetEXTRA, NULL, 0.0, 0.0, 0.0, dset_or, RESAM_NN_TYPE, NULL, 1, 0); DSET_delete(insetEXTRA); insetEXTRA=dsetn; dsetn=NULL; } } // **************************************************************** // **************************************************************** // make arrays for tracking // **************************************************************** // **************************************************************** // for temp storage array, just a multiple of longest dimension! if(Dim[0] > Dim[1]) ArrMax = Dim[0] * 4; else ArrMax = Dim[1] * 4; if(4*Dim[2] > ArrMax) ArrMax = Dim[2] * 4; ROI1 = (int *)calloc(Nvox, sizeof(int)); ROI2 = (int *)calloc(Nvox, sizeof(int)); temp_arr = (short int *)calloc(Nvox, sizeof(short int)); temp_byte = (char *)calloc(Nvox, sizeof(char)); // temp storage whilst tracking Tforw = calloc(ArrMax, sizeof(Tforw)); for(i=0 ; i<ArrMax ; i++) Tforw[i] = calloc(3, sizeof(int)); Ttot = calloc(2*ArrMax , sizeof(Ttot)); for(i=0 ; i<2*ArrMax ; i++) Ttot[i] = calloc(3, sizeof(int)); Tback = calloc(ArrMax, sizeof(Tback)); for(i=0 ; i<ArrMax ; i++) Tback[i] = calloc(3, sizeof(int)); // temp storage whilst tracking, physical loc flTforw = calloc(ArrMax, sizeof(flTforw)); for(i=0 ; i<ArrMax ; i++) flTforw[i] = calloc(3, sizeof(int)); flTback = calloc(ArrMax,sizeof(flTback)); for(i=0 ; i<ArrMax ; i++) flTback[i] = calloc(3, sizeof(int)); if( (ROI1 == NULL) || (ROI2 == NULL) || (temp_arr == NULL) || (Tforw == NULL) || (Tback == NULL) || (flTforw == NULL) || (flTback == NULL) || (Ttot == NULL)) { fprintf(stderr, "\n\n MemAlloc failure.\n\n"); exit(12); } coorded = (float ****) calloc( Dim[0], sizeof(float ***) ); for ( i = 0 ; i < Dim[0] ; i++ ) coorded[i] = (float ***) calloc( Dim[1], sizeof(float **) ); for ( i = 0 ; i < Dim[0] ; i++ ) for ( j = 0 ; j < Dim[1] ; j++ ) coorded[i][j] = (float **) calloc( Dim[2], sizeof(float *) ); for ( i=0 ; i<Dim[0] ; i++ ) for ( j=0 ; j<Dim[1] ; j++ ) for ( k= 0 ; k<Dim[2] ; k++ ) //3 comp of V1 and FA coorded[i][j][k] = (float *) calloc( 4, sizeof(float) ); INDEX = (int ****) calloc( Dim[0], sizeof(int ***) ); for ( i = 0 ; i < Dim[0] ; i++ ) INDEX[i] = (int ***) calloc( Dim[1], sizeof(int **) ); for ( i = 0 ; i < Dim[0] ; i++ ) for ( j = 0 ; j < Dim[1] ; j++ ) INDEX[i][j] = (int **) calloc( Dim[2], sizeof(int *) ); for ( i=0 ; i<Dim[0] ; i++ ) for ( j=0 ; j<Dim[1] ; j++ ) for ( k= 0 ; k<Dim[2] ; k++ ) INDEX[i][j][k] = (int *) calloc( 4, sizeof(int) ); // this statement will never be executed if allocation fails above if( (INDEX == NULL) || (coorded == NULL) ) { fprintf(stderr, "\n\n MemAlloc failure.\n\n"); exit(122); } for(i=0 ; i<Nvox ; i++) { if(THD_get_voxel( mset1, i, 0) >0.5){ ROI1[i] = 1; } if(THD_get_voxel( mset2, i, 0) >0.5) ROI2[i] = 1; } // set up eigvecs in 3D coord sys, // mark off where ROIs are and keep index handy idx=0; for( k=0 ; k<Dim[2] ; k++ ) for( j=0 ; j<Dim[1] ; j++ ) for( i=0 ; i<Dim[0] ; i++ ) { for( m=0 ; m<3 ; m++ ) coorded[i][j][k][m] = THD_get_voxel(insetV1, idx, m); if(EXTRAFILE) coorded[i][j][k][3] = THD_get_voxel(insetEXTRA, idx, 0); else coorded[i][j][k][3] = THD_get_voxel(insetFA, idx, 0); // make sure that |V1| == 1 for all eigenvects, otherwise it's /// a problem in the tractography; currently, some from // 3dDWItoDT do not have this property... tempvmagn = sqrt(coorded[i][j][k][0]*coorded[i][j][k][0]+ coorded[i][j][k][1]*coorded[i][j][k][1]+ coorded[i][j][k][2]*coorded[i][j][k][2]); if( tempvmagn<0.99 ) for( m=0 ; m<3 ; m++ ) coorded[i][j][k][m]/= tempvmagn; INDEX[i][j][k][0] =idx; // first value is the index itself if( ROI1[idx]==1 ) INDEX[i][j][k][1]=1; // second value identifies ROI1 mask else INDEX[i][j][k][1]=0; if( ROI2[idx]==1 ) INDEX[i][j][k][2]=1; // third value identifies ROI2 mask else INDEX[i][j][k][2]=0; // fourth value will be counter for number of kept tracks // passing through INDEX[i][j][k][3] = 0; idx+= 1; } // ************************************************************* // ************************************************************* // Beginning of main loop // ************************************************************* // ************************************************************* Numtract = 0; ave_tract_len = 0.; ave_tract_len_phys = 0.; sprintf(OUT_bin,"%s.trk",prefix); if( (fout0 = fopen(OUT_bin, "w")) == NULL) { fprintf(stderr, "Error opening file %s.",OUT_bin); exit(16); } fwrite(&header1,sizeof(tv_io_header),1,fout0); if (get_tract_verb()) { INFO_message("Begin tracking..."); } tb = AppCreateBundle(NULL, 0, NULL, insetFA); // start bundle id = 0; for( k=0 ; k<Dim[2] ; k++ ) for( j=0 ; j<Dim[1] ; j++ ) for( i=0 ; i<Dim[0] ; i++ ) if(coorded[i][j][k][3] >= MinFA) { for( ii=0 ; ii<SeedPerV[0] ; ii++ ) for( jj=0 ; jj<SeedPerV[1] ; jj++ ) for( kk=0 ; kk<SeedPerV[2] ; kk++ ) { in[0] = i; in[1] = j; in[2] = k; physin[0] = ((float) in[0] + (0.5 + (float) ii)/SeedPerV[0])*Ledge[0]; physin[1] = ((float) in[1] + (0.5 + (float) jj)/SeedPerV[1])*Ledge[1]; physin[2] = ((float) in[2] + (0.5 + (float) kk)/SeedPerV[2])*Ledge[2]; len_forw = TrackIt(coorded, in, physin, Ledge, Dim, MinFA, MaxAng, ArrMax, Tforw, flTforw, 1, phys_forw); // reset, because it's changed in TrackIt func in[0] = i; in[1] = j; in[2] = k; physin[0] = ((float) in[0] + (0.5 + (float) ii)/SeedPerV[0])*Ledge[0]; physin[1] = ((float) in[1] + (0.5 + (float) jj)/SeedPerV[1])*Ledge[1]; physin[2] = ((float) in[2] + (0.5 + (float) kk)/SeedPerV[2])*Ledge[2]; len_back = TrackIt(coorded, in, physin, Ledge, Dim, MinFA, MaxAng, ArrMax, Tback, flTback, -1, phys_back); KEEPIT = 0; // a simple switch totlen = len_forw+len_back-1; // NB: overlap of starts totlen_phys = phys_forw[0] + phys_back[0]; if( totlen_phys >= MinL ) { // glue together for simpler notation later for( n=0 ; n<len_back ; n++) { // all of this rr = len_back-n-1; // read in backward for(m=0;m<3;m++) Ttot[rr][m] = Tback[n][m]; } for( n=1 ; n<len_forw ; n++){// skip first->overlap rr = n+len_back-1; // put after for(m=0;m<3;m++) Ttot[rr][m] = Tforw[n][m]; } // <<So close and orthogonal condition>>: // test projecting ends, to see if they abut ROI. for(m=0;m<3;m++) { //actual projected ends end[1][m] = 2*Ttot[totlen-1][m]-Ttot[totlen-2][m]; end[0][m] = 2*Ttot[0][m]-Ttot[1][m]; // default choice, just retest known ends // as default test_ind[1][m] = test_ind[0][m] = Ttot[0][m]; } tt = Create_Tract(len_back, flTback, len_forw, flTforw, id, insetFA); ++id; if (LOG_TYPE == -1) { KEEPIT = 1; } else { inroi1 = 0; // check forw for( n=0 ; n<len_forw ; n++) { if(INDEX[Tforw[n][0]][Tforw[n][1]][Tforw[n][2]][1]==1){ inroi1 = 1; break; } else continue; } if( inroi1==0 ){// after 1st half, check 2nd half for( m=0 ; m<len_back ; m++) { if(INDEX[Tback[m][0]][Tback[m][1]][Tback[m][2]][1]==1){ inroi1 = 1; break; } else continue; } } // after 1st&2nd halves, check bound/neigh if( inroi1==0 ) { if(INDEX[test_ind[1][0]][test_ind[1][1]][test_ind[1][2]][1]==1) inroi1 = 1; if(INDEX[test_ind[0][0]][test_ind[0][1]][test_ind[0][2]][1]==1) inroi1 = 1; } if( ((LOG_TYPE ==0) && (inroi1 ==0)) || ((LOG_TYPE ==1) && (inroi1 ==1))) { // have to check in ROI2 inroi2 = 0; // check forw for( n=0 ; n<len_forw ; n++) { if(INDEX[Tforw[n][0]][Tforw[n][1]][Tforw[n][2]][2]==1){ inroi2 = 1; break; } else continue; } //after 1st half, check 2nd half if( inroi2==0 ) { for( m=0 ; m<len_back ; m++) { if(INDEX[Tback[m][0]][Tback[m][1]][Tback[m][2]][2]==1){ inroi2 = 1; break; } else continue; } } // after 1st&2nd halves, check bound/neigh if( inroi2==0 ) { if(INDEX[test_ind[1][0]][test_ind[1][1]][test_ind[1][2]][2]==1) inroi2 = 1; if(INDEX[test_ind[0][0]][test_ind[0][1]][test_ind[0][2]][2]==1) inroi2 = 1; } // for both cases, need to see it here to keep if( inroi2 ==1 ) KEEPIT = 1; // otherwise, it's gone } else if((LOG_TYPE ==0) && (inroi1 ==1)) KEEPIT = 1; } } // by now, we *know* if we're keeping this or not. if( KEEPIT == 1 ) { tb = AppCreateBundle(tb, 1, tt, NULL); tt = Free_Tracts(tt, 1); READS_in = totlen; fwrite(&READS_in,sizeof(READS_in),1,fout0); for( n=0 ; n<len_back ; n++) { //put this one in backwords, to make it connect m = len_back - 1 - n; for(aa=0 ; aa<3 ; aa++) { // recenter phys loc for trackvis, if nec... // just works this way (where they define // origin) READS_fl = flTback[m][aa]; if(!TV_switch[aa]) READS_fl = Ledge[aa]*Dim[aa]-READS_fl; fwrite(&READS_fl,sizeof(READS_fl),1,fout0); } mm = INDEX[Tback[m][0]][Tback[m][1]][Tback[m][2]][0]; READS_fl =THD_get_voxel(insetFA, mm, 0); // FA fwrite(&READS_fl,sizeof(READS_fl),1,fout0); READS_fl =THD_get_voxel(insetMD, mm, 0); // MD fwrite(&READS_fl,sizeof(READS_fl),1,fout0); READS_fl =THD_get_voxel(insetL1, mm, 0); // L1 fwrite(&READS_fl,sizeof(READS_fl),1,fout0); // count this voxel for having a tract INDEX[Tback[m][0]][Tback[m][1]][Tback[m][2]][3]+= 1; } for( m=1 ; m<len_forw ; m++) { for(aa=0 ; aa<3 ; aa++) { // recenter phys loc for trackvis, if nec... READS_fl = flTforw[m][aa]; if(!TV_switch[aa]) READS_fl = Ledge[aa]*Dim[aa]-READS_fl; fwrite(&READS_fl,sizeof(READS_fl),1,fout0); } mm = INDEX[Tforw[m][0]][Tforw[m][1]][Tforw[m][2]][0]; READS_fl =THD_get_voxel(insetFA, mm, 0); // FA fwrite(&READS_fl,sizeof(READS_fl),1,fout0); READS_fl =THD_get_voxel(insetMD, mm, 0); // MD fwrite(&READS_fl,sizeof(READS_fl),1,fout0); READS_fl =THD_get_voxel(insetL1, mm, 0); // L1 fwrite(&READS_fl,sizeof(READS_fl),1,fout0); // count this voxel for having a tract INDEX[Tforw[m][0]][Tforw[m][1]][Tforw[m][2]][3]+= 1; } ave_tract_len+= totlen; ave_tract_len_phys+= totlen_phys; Numtract+=1; } } } fclose(fout0); if (get_tract_verb()) { INFO_message("Done tracking, have %d tracks.", tb->N_tracts); Show_Taylor_Bundle(tb, NULL, 3); } if (!Write_Bundle(tb,prefix,mode)) { ERROR_message("Failed to write the bundle"); } // ************************************************************** // ************************************************************** // Some simple stats on ROIs and outputs // ************************************************************** // ************************************************************** for( k=0 ; k<Dim[2] ; k++ ) for( j=0 ; j<Dim[1] ; j++ ) for( i=0 ; i<Dim[0] ; i++ ) { if( INDEX[i][j][k][3]>=1 ) { tempMD = THD_get_voxel(insetMD,INDEX[i][j][k][0],0); tempFA = THD_get_voxel(insetFA,INDEX[i][j][k][0],0); tempL1 = THD_get_voxel(insetL1,INDEX[i][j][k][0],0); tempRD = 0.5*(3*tempMD-tempL1); roi3_mu_MD+= tempMD; roi3_mu_FA+= tempFA; roi3_mu_L1+= tempL1; roi3_mu_RD+= tempRD; roi3_sd_MD+= tempMD*tempMD; roi3_sd_FA+= tempFA*tempFA; roi3_sd_L1+= tempL1*tempL1; roi3_sd_RD+= tempRD*tempRD; roi3_ct+= 1; } } if(roi3_ct > 0 ) { // !!!! make into afni file roi3_mu_MD/= (float) roi3_ct; roi3_mu_FA/= (float) roi3_ct; roi3_mu_L1/= (float) roi3_ct; roi3_mu_RD/= (float) roi3_ct; roi3_sd_MD-= roi3_ct*roi3_mu_MD*roi3_mu_MD; roi3_sd_FA-= roi3_ct*roi3_mu_FA*roi3_mu_FA; roi3_sd_L1-= roi3_ct*roi3_mu_L1*roi3_mu_L1; roi3_sd_RD-= roi3_ct*roi3_mu_RD*roi3_mu_RD; roi3_sd_MD/= (float) roi3_ct-1; roi3_sd_FA/= (float) roi3_ct-1; roi3_sd_L1/= (float) roi3_ct-1; roi3_sd_RD/= (float) roi3_ct-1; roi3_sd_MD = sqrt(roi3_sd_MD); roi3_sd_FA = sqrt(roi3_sd_FA); roi3_sd_L1 = sqrt(roi3_sd_L1); roi3_sd_RD = sqrt(roi3_sd_RD); sprintf(OUT_tracstat,"%s.stats",prefix); if( (fout0 = fopen(OUT_tracstat, "w")) == NULL) { fprintf(stderr, "Error opening file %s.",OUT_tracstat); exit(19); } fprintf(fout0,"%d\t%d\n",Numtract,roi3_ct); fprintf(fout0,"%.3f\t%.3f\n",ave_tract_len/Numtract, ave_tract_len_phys/Numtract); // as usual, these next values would have to be divided by the // bval to get their actual value in standard phys units fprintf(fout0,"%.4f\t%.4f\n",roi3_mu_FA,roi3_sd_FA); fprintf(fout0,"%.4f\t%.4f\n",roi3_mu_MD,roi3_sd_MD); fprintf(fout0,"%.4f\t%.4f\n",roi3_mu_RD,roi3_sd_RD); fprintf(fout0,"%.4f\t%.4f\n",roi3_mu_L1,roi3_sd_L1); fclose(fout0); sprintf(prefix_map,"%s_MAP",prefix); sprintf(prefix_mask,"%s_MASK",prefix); outsetMAP = EDIT_empty_copy( mset1 ) ; EDIT_dset_items( outsetMAP , ADN_datum_all , MRI_short , ADN_prefix , prefix_map , ADN_none ) ; if( !THD_ok_overwrite() && THD_is_ondisk(DSET_HEADNAME(outsetMAP)) ) ERROR_exit("Can't overwrite existing dataset '%s'", DSET_HEADNAME(outsetMAP)); outsetMASK = EDIT_empty_copy( mset1 ) ; EDIT_dset_items( outsetMASK , ADN_datum_all , MRI_byte , ADN_prefix , prefix_mask , ADN_none ) ; if(!THD_ok_overwrite() && THD_is_ondisk(DSET_HEADNAME(outsetMASK)) ) ERROR_exit("Can't overwrite existing dataset '%s'", DSET_HEADNAME(outsetMASK)); m=0; for( k=0 ; k<Dim[2] ; k++ ) for( j=0 ; j<Dim[1] ; j++ ) for( i=0 ; i<Dim[0] ; i++ ) { temp_arr[m]=INDEX[i][j][k][3]; if(temp_arr[m]>0.5) temp_byte[m]=1; else temp_byte[m]=0; m++; } // re-orient the data as original inputs // (this function copies the pointer) EDIT_substitute_brick(outsetMAP, 0, MRI_short, temp_arr); temp_arr=NULL; if(TV_switch[0] || TV_switch[1] || TV_switch[2]) { dsetn = r_new_resam_dset(outsetMAP, NULL, 0.0, 0.0, 0.0, header1.voxel_order, RESAM_NN_TYPE, NULL, 1, 0); DSET_delete(outsetMAP); outsetMAP=dsetn; dsetn=NULL; } EDIT_dset_items( outsetMAP , ADN_prefix , prefix_map , ADN_none ) ; THD_load_statistics(outsetMAP ); if( !THD_ok_overwrite() && THD_is_ondisk(DSET_HEADNAME(outsetMAP)) ) ERROR_exit("Can't overwrite existing dataset '%s'", DSET_HEADNAME(outsetMAP)); tross_Make_History( "3dTrackID" , argc , argv , outsetMAP) ; THD_write_3dim_dataset(NULL, NULL, outsetMAP, True); // re-orient the data as original inputs EDIT_substitute_brick(outsetMASK, 0, MRI_byte, temp_byte); temp_byte=NULL; if(TV_switch[0] || TV_switch[1] || TV_switch[2]) { dsetn = r_new_resam_dset(outsetMASK, NULL, 0.0, 0.0, 0.0, header1.voxel_order, RESAM_NN_TYPE, NULL, 1, 0); DSET_delete(outsetMASK); outsetMASK=dsetn; dsetn=NULL; } EDIT_dset_items( outsetMASK , ADN_prefix , prefix_mask , ADN_none ) ; THD_load_statistics(outsetMASK); if(!THD_ok_overwrite() && THD_is_ondisk(DSET_HEADNAME(outsetMASK)) ) ERROR_exit("Can't overwrite existing dataset '%s'", DSET_HEADNAME(outsetMASK)); tross_Make_History( "3dTrackID" , argc , argv , outsetMASK) ; THD_write_3dim_dataset(NULL, NULL, outsetMASK, True); INFO_message("Number of tracts found = %d",Numtract) ; } else INFO_message("\n No Tracts Found!!!\n"); // ************************************************************ // ************************************************************ // Freeing // ************************************************************ // ************************************************************ // !!! need to free afni-sets? DSET_delete(insetFA); DSET_delete(insetMD); DSET_delete(insetL1); DSET_delete(insetV1); DSET_delete(insetEXTRA); //DSET_delete(outsetMAP); //DSET_delete(outsetMASK); DSET_delete(mset2); DSET_delete(mset1); free(prefix); free(insetV1); free(insetFA); free(mset1); free(mset2); free(insetEXTRA); free(ROI1); free(ROI2); free(temp_byte); for( i=0 ; i<ArrMax ; i++) { free(Tforw[i]); free(Tback[i]); free(flTforw[i]); free(flTback[i]); } free(Tforw); free(Tback); free(flTforw); free(flTback); for( i=0 ; i<Dim[0] ; i++) for( j=0 ; j<Dim[1] ; j++) for( k=0 ; k<Dim[2] ; k++) free(coorded[i][j][k]); for( i=0 ; i<Dim[0] ; i++) for( j=0 ; j<Dim[1] ; j++) free(coorded[i][j]); for( i=0 ; i<Dim[0] ; i++) free(coorded[i]); free(coorded); for( i=0 ; i<Dim[0] ; i++) for( j=0 ; j<Dim[1] ; j++) for( k=0 ; k<Dim[2] ; k++) free(INDEX[i][j][k]); for( i=0 ; i<Dim[0] ; i++) for( j=0 ; j<Dim[1] ; j++) free(INDEX[i][j]); for( i=0 ; i<Dim[0] ; i++) free(INDEX[i]); free(INDEX); free(temp_arr); // need to free for( i=0 ; i<2*ArrMax ; i++) free(Ttot[i]); free(Ttot); //free(mode); return 0; }
int main( int argc , char *argv[] ) { THD_3dim_dataset *dset=NULL; int iarg , verbose = -1 ; char *outbuf, *stmp=NULL; char *labelName = NULL; char *sbdelim = {"|"}; char *NAflag = {"NA"}; char *atrdelim = {"\t"}, *form=NULL; INFO_FIELDS sing[512]; int iis=0, N_sing = 0, isb=0, withhead = 0, itmp=0; int ip=0, needpair = 0, namelen=0, monog_pairs = 0; THD_3dim_dataset *tttdset=NULL, *dsetp=NULL; char *tempstr = NULL; int extinit = 0; float RL_AP_IS[6]; mainENTRY("3dinfo main") ; machdep() ; if( argc < 2) { Syntax(TXT,1) ; RETURN(0); } iarg = 1 ; while (iarg < argc && argv[iarg][0] == '-') { CHECK_HELP(argv[iarg],Syntax); if( strncmp(argv[iarg],"-verb" ,5) == 0 ){ verbose = 0; iarg++; continue; } else if( strncmp(argv[iarg],"-VERB" ,5) == 0 ){ verbose = 1; iarg++; continue; } else if( strncmp(argv[iarg],"-short",5) == 0 ){ verbose = -1; iarg++; continue; } else if( strcasecmp(argv[iarg],"-header_line") == 0 || strcasecmp(argv[iarg],"-hdr") == 0 ){ withhead = 1; iarg++; continue; } else if( strcasecmp(argv[iarg],"-monog_pairs") == 0 ){ monog_pairs = 1; iarg++; continue; } else if ( strncmp(argv[iarg],"-label2",7) == 0 ) { iarg++; if (iarg >= argc) ERROR_exit( "3dinfo needs an argument after -label2number\n"); labelName = malloc(sizeof(char) * 2048); strcpy(labelName, argv[iarg]); iarg++; continue; } else if( strcasecmp(argv[iarg],"-sb_delim") == 0) { iarg++; if (iarg >= argc) ERROR_exit( "3dinfo needs a string after -sb_delim\n"); sbdelim = argv[iarg]; iarg++; continue; } else if( strcasecmp(argv[iarg],"-NA_flag") == 0) { iarg++; if (iarg >= argc) ERROR_exit( "3dinfo needs a string after -NA_flag\n"); NAflag = argv[iarg]; iarg++; continue; } else if( strcasecmp(argv[iarg],"-atr_delim") == 0) { iarg++; if (iarg >= argc) ERROR_exit( "3dinfo needs a string after -atr_delim\n"); atrdelim = argv[iarg]; iarg++; continue; } else if( strcasecmp(argv[iarg],"-space") == 0) { sing[N_sing++] = DSET_SPACE; iarg++; continue; } else if( strcasecmp(argv[iarg],"-av_space") == 0) { sing[N_sing++] = AV_DSET_SPACE; iarg++; continue; } else if( strcasecmp(argv[iarg],"-gen_space") == 0) { sing[N_sing++] = DSET_GEN_SPACE; iarg++; continue; } else if( strcasecmp(argv[iarg],"-is_nifti") == 0) { sing[N_sing++] = IS_NIFTI; iarg++; continue; } else if( strcasecmp(argv[iarg],"-is_atlas") == 0) { sing[N_sing++] = IS_ATLAS; iarg++; continue; } else if( strcasecmp(argv[iarg],"-exists") == 0) { sing[N_sing++] = DSET_EXISTS; iarg++; continue; } else if( strcasecmp(argv[iarg],"-is_oblique") == 0) { sing[N_sing++] = IS_OBLIQUE; iarg++; continue; } else if( strcasecmp(argv[iarg],"-obliquity") == 0) { sing[N_sing++] = OBLIQUITY; iarg++; continue; } else if( strcasecmp(argv[iarg],"-handedness") == 0) { sing[N_sing++] = HANDEDNESS; iarg++; continue; } else if( strcasecmp(argv[iarg],"-prefix") == 0) { sing[N_sing++] = PREFIX; iarg++; continue; } else if( strcasecmp(argv[iarg],"-prefix_noext") == 0) { sing[N_sing++] = PREFIX_NOEXT; iarg++; continue; } else if( strcasecmp(argv[iarg],"-ni") == 0) { sing[N_sing++] = NI; iarg++; continue; } else if( strcasecmp(argv[iarg],"-nj") == 0) { sing[N_sing++] = NJ; iarg++; continue; } else if( strcasecmp(argv[iarg],"-nk") == 0) { sing[N_sing++] = NK; iarg++; continue; } else if( strcasecmp(argv[iarg],"-n4") == 0) { sing[N_sing++] = NI; sing[N_sing++] = NJ; sing[N_sing++] = NK; sing[N_sing++] = NV; iarg++; continue; } else if( strcasecmp(argv[iarg],"-Rextent") == 0) { sing[N_sing++] = EXTENT_R; iarg++; continue; } else if( strcasecmp(argv[iarg],"-Lextent") == 0) { sing[N_sing++] = EXTENT_L; iarg++; continue; } else if( strcasecmp(argv[iarg],"-Aextent") == 0) { sing[N_sing++] = EXTENT_A; iarg++; continue; } else if( strcasecmp(argv[iarg],"-Pextent") == 0) { sing[N_sing++] = EXTENT_P; iarg++; continue; } else if( strcasecmp(argv[iarg],"-Iextent") == 0) { sing[N_sing++] = EXTENT_I; iarg++; continue; } else if( strcasecmp(argv[iarg],"-Sextent") == 0) { sing[N_sing++] = EXTENT_S; iarg++; continue; } else if( strcasecmp(argv[iarg],"-extent") == 0) { sing[N_sing++] = EXTENT_R; sing[N_sing++] = EXTENT_L; sing[N_sing++] = EXTENT_A; sing[N_sing++] = EXTENT_P; sing[N_sing++] = EXTENT_I; sing[N_sing++] = EXTENT_S; iarg++; continue; } else if( strcasecmp(argv[iarg],"-di") == 0) { sing[N_sing++] = DI; iarg++; continue; } else if( strcasecmp(argv[iarg],"-dj") == 0) { sing[N_sing++] = DJ; iarg++; continue; } else if( strcasecmp(argv[iarg],"-dk") == 0) { sing[N_sing++] = DK; iarg++; continue; } else if( strcasecmp(argv[iarg],"-d3") == 0) { sing[N_sing++] = DI; sing[N_sing++] = DJ; sing[N_sing++] = DK; iarg++; continue; } else if( strcasecmp(argv[iarg],"-adi") == 0) { sing[N_sing++] = ADI; iarg++; continue; } else if( strcasecmp(argv[iarg],"-adj") == 0) { sing[N_sing++] = ADJ; iarg++; continue; } else if( strcasecmp(argv[iarg],"-adk") == 0) { sing[N_sing++] = ADK; iarg++; continue; } else if( strcasecmp(argv[iarg],"-ad3") == 0) { sing[N_sing++] = ADI; sing[N_sing++] = ADJ; sing[N_sing++] = ADK; iarg++; continue; } else if( strcasecmp(argv[iarg],"-voxvol") == 0) { sing[N_sing++] = VOXVOL; iarg++; continue; } else if( strcasecmp(argv[iarg],"-iname") == 0) { sing[N_sing++] = INAME; iarg++; continue; } else if( strcasecmp(argv[iarg],"-oi") == 0) { sing[N_sing++] = OI; iarg++; continue; } else if( strcasecmp(argv[iarg],"-oj") == 0) { sing[N_sing++] = OJ; iarg++; continue; } else if( strcasecmp(argv[iarg],"-ok") == 0) { sing[N_sing++] = OK; iarg++; continue; } else if( strcasecmp(argv[iarg],"-o3") == 0) { sing[N_sing++] = OI; sing[N_sing++] = OJ; sing[N_sing++] = OK; iarg++; continue; }else if( strcasecmp(argv[iarg],"-nt") == 0) { sing[N_sing++] = NT; iarg++; continue; } else if( strcasecmp(argv[iarg],"-nti") == 0) { sing[N_sing++] = NTI; iarg++; continue; } else if( strcasecmp(argv[iarg],"-nv") == 0) { sing[N_sing++] = NV; iarg++; continue; } else if( strcasecmp(argv[iarg],"-nvi") == 0) { sing[N_sing++] = NVI; iarg++; continue; } else if( strcasecmp(argv[iarg],"-ntimes") == 0) { sing[N_sing++] = NTIMES; iarg++; continue; } else if( strcasecmp(argv[iarg],"-max_node") == 0) { sing[N_sing++] = MAX_NODE; iarg++; continue; } else if( strcasecmp(argv[iarg],"-nijk") == 0) { sing[N_sing++] = NIJK; iarg++; continue; } else if( strcasecmp(argv[iarg],"-labeltable") == 0) { sing[N_sing++] = LTABLE; iarg++; continue; } else if( strcasecmp(argv[iarg],"-labeltable_as_atlas_points") == 0) { sing[N_sing++] = LTABLE_AS_ATLAS_POINT_LIST; iarg++; continue; } else if( strcasecmp(argv[iarg],"-atlas_points") == 0) { sing[N_sing++] = ATLAS_POINTS; iarg++; continue; } else if( strcasecmp(argv[iarg],"-fac") == 0) { sing[N_sing++] = FAC; iarg++; continue; } else if( strcasecmp(argv[iarg],"-datum") == 0) { sing[N_sing++] = DATUM; iarg++; continue; } else if( strcasecmp(argv[iarg],"-label") == 0) { sing[N_sing++] = LABEL; iarg++; continue; } else if( strcasecmp(argv[iarg],"-min") == 0) { sing[N_sing++] = MIN; iarg++; continue; } else if( strcasecmp(argv[iarg],"-max") == 0) { sing[N_sing++] = MAX; iarg++; continue; } else if( strcasecmp(argv[iarg],"-minus") == 0) { sing[N_sing++] = MINUS; iarg++; continue; } else if( strcasecmp(argv[iarg],"-maxus") == 0) { sing[N_sing++] = MAXUS; iarg++; continue; } else if( strcasecmp(argv[iarg],"-dmin") == 0) { sing[N_sing++] = DMIN; iarg++; continue; } else if( strcasecmp(argv[iarg],"-dmax") == 0) { sing[N_sing++] = DMAX; iarg++; continue; } else if( strcasecmp(argv[iarg],"-dminus") == 0) { sing[N_sing++] = DMINUS; iarg++; continue; } else if( strcasecmp(argv[iarg],"-dmaxus") == 0) { sing[N_sing++] = DMAXUS; iarg++; continue; } else if( strcasecmp(argv[iarg],"-TR") == 0) { sing[N_sing++] = TR; iarg++; continue; } else if( strcasecmp(argv[iarg],"-header_name") == 0) { sing[N_sing++] = HEADER_NAME; iarg++; continue; } else if( strcasecmp(argv[iarg],"-brick_name") == 0) { sing[N_sing++] = BRICK_NAME; iarg++; continue; } else if( strcasecmp(argv[iarg],"-history") == 0) { sing[N_sing++] = HISTORY; iarg++; continue; } else if( strcasecmp(argv[iarg],"-all_names") == 0) { sing[N_sing++] = ALL_NAMES; iarg++; continue; } else if( strcasecmp(argv[iarg],"-orient") == 0) { sing[N_sing++] = ORIENT; iarg++; continue; } else if( strcasecmp(argv[iarg],"-same_grid") == 0) { sing[N_sing++] = SAME_GRID; needpair = 1; iarg++; continue; } else if( strcasecmp(argv[iarg],"-same_dim") == 0) { sing[N_sing++] = SAME_DIM; needpair = 1; iarg++; continue; } else if( strcasecmp(argv[iarg],"-same_delta") == 0) { sing[N_sing++] = SAME_DELTA; needpair = 1; iarg++; continue; } else if( strcasecmp(argv[iarg],"-same_orient") == 0) { sing[N_sing++] = SAME_ORIENT; needpair = 1; iarg++; continue; } else if( strcasecmp(argv[iarg],"-same_center") == 0) { sing[N_sing++] = SAME_CENTER; needpair = 1; iarg++; continue; } else if( strcasecmp(argv[iarg],"-same_obl") == 0) { sing[N_sing++] = SAME_OBL; needpair = 1; iarg++; continue; } else if( strcasecmp(argv[iarg],"-slice_timing") == 0) { sing[N_sing++] = SLICE_TIMING; iarg++; continue; } else if( strcasecmp(argv[iarg],"-sval_diff") == 0) { sing[N_sing++] = SVAL_DIFF; needpair = 1; iarg++; continue; } else if( strcasecmp(argv[iarg],"-val_diff") == 0) { sing[N_sing++] = VAL_DIFF; needpair = 1; iarg++; continue; } else if( strcasecmp(argv[iarg],"-same_all_grid") == 0) { sing[N_sing++] = SAME_DIM; sing[N_sing++] = SAME_DELTA; sing[N_sing++] = SAME_ORIENT; sing[N_sing++] = SAME_CENTER; sing[N_sing++] = SAME_OBL; needpair = 1; iarg++; continue; } else if( strcasecmp(argv[iarg],"-id") == 0) { sing[N_sing++] = ID; iarg++; continue; } else if( strcasecmp(argv[iarg],"-smode") == 0) { sing[N_sing++] = SMODE; iarg++; continue; } else { ERROR_message("Option %s unknown", argv[iarg]); suggest_best_prog_option(argv[0], argv[iarg]); exit(1); } } if (N_sing == 0) { sing[N_sing++] = CLASSIC; } if (sing[iis] == CLASSIC) PRINT_VERSION("3dinfo") ; THD_allow_empty_dataset(1) ; /* 21 Mar 2007 */ if (iarg == argc) { ERROR_message("No dsets on command line? I have nothing to do.\n"); exit(1); } if (needpair && monog_pairs) needpair = 2; /* pair each couple separately */ if (needpair==2 && (argc-iarg) % 2) { ERROR_message("Using options requiring dset pairs but have odd number\n" "of dsets (%d) on command line.\n", (argc-iarg)); exit (1); } else if (needpair==1 && (argc-iarg) < 2) { ERROR_message("Using options requiring dset pairs but have less than\n" "two dsets (%d) on command line.\n", (argc-iarg)); exit (1); } ip = 0; for( ; iarg < argc ; iarg++ ){ if (ip == 0) { int kkk, nml; char *etr; namelen = 0; for (kkk=iarg; kkk<argc; ++kkk) { if ((etr = THD_trailname(argv[kkk],0))) { nml=strlen(etr); if (nml < 48 && nml > namelen) namelen = nml; } } if (namelen < 6) namelen = 6; if (withhead) { int havenew=0; for (iis = 0; iis < N_sing; ++iis) { if (sing[iis] != CLASSIC) { ++havenew; form = PrintForm(sing[iis], namelen, 1); /*fprintf(stderr,"ZSS: %d %s >%s<\n", sing[iis], Field_Names[sing[iis]], form);*/ fprintf(stdout, form, Field_Names[sing[iis]]); } if (havenew) { if (N_sing > 1 && iis < N_sing-1) fprintf(stdout,"%s",atrdelim); else fprintf(stdout,"\n"); } } } } if( argv[iarg][0] == '\0' ) continue ; /* bad filename */ set_obliquity_report(0); /* silence obliquity */ if (!needpair) { if (!(dset = load_3dinfo_dataset(argv[iarg]))) { /* exit(1); */ } } else { if (needpair == 2) { /* Crazy idea of comparing each pair separately */ if (ip % 2 == 0) { if (!(dset = load_3dinfo_dataset(argv[iarg] ))) { /* exit(1); */ } if (iarg+1==argc || argv[iarg+1][0] == '\0') { ERROR_message("Bad dset pair for %s\n", argv[iarg]); exit(1); } if (!(dsetp = load_3dinfo_dataset(argv[iarg+1] ))) { /* exit(1); */ } } else { /* swap the pair - this allows non pair requiring functions to work as before.*/ tttdset = dsetp; dsetp = dset; dset = tttdset; tttdset=NULL; } } else { /* always compare to very first dset */ if (ip==0) { if (!(dset = load_3dinfo_dataset(argv[iarg] ))) { /*exit(1);*/ } if (!(dsetp = load_3dinfo_dataset(argv[iarg+1] ))) { /*exit(1);*/ } } else if (ip==1) { /* switch order of first two */ tttdset = dsetp; dsetp = dset; /* now dsetp is the very first dset */ dset = tttdset; tttdset=NULL; } else { /* pair with very first, which is dsetp */ if (!(dset = load_3dinfo_dataset(argv[iarg] ))) { /*exit(1);*/ } } } } ++ip; if (0 && !dset) { /* allow for DSET_EXISTS option */ ERROR_exit("Should not get here"); } /* we should re-capture this per dataset 5 Feb 2019 [rickr] */ extinit = 0; for (iis = 0; iis < N_sing; ++iis) { if (!dset) { if (sing[iis] == CLASSIC) { if( dset == NULL ){ /* still not open? */ ERROR_exit("Can't open dataset %s\n", argv[iarg]) ; } } else if (sing[iis] != DSET_EXISTS && sing[iis] != INAME) { fprintf(stdout, "NO-DSET"); SPIT_DELIM(iis, N_sing, atrdelim); continue; } } switch (sing[iis]) { case CLASSIC: if (labelName == NULL ) /*** get and output info ***/ { outbuf = THD_dataset_info( dset , verbose ) ; if( outbuf != NULL ){ printf("\n") ; puts(outbuf) ; free(outbuf) ; outbuf = NULL ; } else { ERROR_exit("Can't get info for dataset %s",argv[iarg]) ; } } else /*** get and output label ***/ { int nval_per = dset->dblk->nvals; int foundLabel = 0; int ival=0; for (ival=0 ; ival < nval_per && !foundLabel; ival++ ) { if (strcmp(DSET_BRICK_LAB(dset,ival), labelName) == 0) { printf("%d\n", ival); foundLabel = 1; } } /* end of for (ival=0 ; ival < nval_per ; ival++ ) */ if (!foundLabel) printf("\n"); } THD_delete_3dim_dataset( dset , False ) ; free(labelName); break; case DSET_EXISTS: fprintf(stdout, "%d", dset ? 1:0); break; case DSET_SPACE: tempstr = THD_get_space(dset); if(tempstr==NULL) fprintf(stdout, "-----"); else fprintf(stdout, "%s", tempstr); break; case DSET_GEN_SPACE: tempstr = THD_get_generic_space(dset); if(tempstr==NULL) fprintf(stdout, "-----"); else fprintf(stdout, "%s", tempstr); break; case AV_DSET_SPACE: /* don't allow anything but the three AFNI views */ tempstr = THD_get_view_space(dset); if(tempstr==NULL) fprintf(stdout, "+orig"); else if (!strncasecmp(tempstr,"ORIG",4)) fprintf(stdout, "+orig"); else if (!strncasecmp(tempstr,"ACPC",4)) fprintf(stdout, "+acpc"); else if (!strncasecmp(tempstr,"TLRC",4)) fprintf(stdout, "+tlrc"); else /* shouldn't get here */ fprintf(stdout, "+orig"); break; case IS_NIFTI: if ( dset->dblk->diskptr && dset->dblk->diskptr->storage_mode == STORAGE_BY_NIFTI ) { fprintf(stdout,"1"); } else { fprintf(stdout,"0"); } break; case IS_ATLAS: if ( is_Dset_Atlasy(dset, NULL) ) { fprintf(stdout,"1"); } else { fprintf(stdout,"0"); } break; case IS_OBLIQUE: if (dset_obliquity(dset,NULL) > 0) { fprintf(stdout,"1"); } else { fprintf(stdout,"0"); } break; case HANDEDNESS: if (THD_handedness(dset) > 0) { fprintf(stdout,"R"); } else { fprintf(stdout,"L"); } break; case OBLIQUITY: fprintf(stdout,"%.3f", THD_compute_oblique_angle(dset->daxes->ijk_to_dicom_real, 0)); break; case PREFIX: form = PrintForm(sing[iis], namelen, 1); fprintf(stdout,form, DSET_PREFIX(dset)); break; case PREFIX_NOEXT: { form = PrintForm(sing[iis], namelen, 1); stmp=DSET_prefix_noext(dset); fprintf(stdout,form, stmp); free(stmp); stmp=NULL; } break; case HEADER_NAME: fprintf(stdout,"%s", dset->dblk->diskptr->header_name); break; case BRICK_NAME: fprintf(stdout,"%s", dset->dblk->diskptr->brick_name); break; case ALL_NAMES: THD_show_dataset_names(dset, "FOR_3DINFO", stdout); break; case HISTORY: stmp = tross_Get_History(dset); fprintf(stdout,"%s", stmp ? stmp:NAflag); if (stmp) free(stmp); stmp=NULL; break; case NI: fprintf(stdout,"%d", DSET_NX(dset)); break; case NJ: fprintf(stdout,"%d", DSET_NY(dset)); break; case NK: fprintf(stdout,"%d", DSET_NZ(dset)); break; case NIJK: fprintf(stdout,"%d", DSET_NVOX(dset)); break; case NTIMES: fprintf(stdout,"%d", DSET_NUM_TIMES(dset)); break; case MAX_NODE: DSET_MAX_NODE(dset,itmp); fprintf(stdout,"%d", itmp); break; case NT: case NV: fprintf(stdout,"%d", DSET_NVALS(dset)); break; case NTI: case NVI: fprintf(stdout,"%d", DSET_NVALS(dset)-1); break; case DI: fprintf(stdout,"%f", DSET_DX(dset)); break; case DJ: fprintf(stdout,"%f", DSET_DY(dset)); break; case DK: fprintf(stdout,"%f", DSET_DZ(dset)); break; case OI: fprintf(stdout,"%f", DSET_XORG(dset)); break; case OJ: fprintf(stdout,"%f", DSET_YORG(dset)); break; case OK: fprintf(stdout,"%f", DSET_ZORG(dset)); break; case ADI: fprintf(stdout,"%f", fabs(DSET_DX(dset))); break; case EXTENT_R: case EXTENT_L: case EXTENT_A: case EXTENT_P: case EXTENT_I: case EXTENT_S: { if (!extinit) { THD_dset_extent(dset, '-', RL_AP_IS); extinit = 1; } fprintf(stdout,"%f", RL_AP_IS[sing[iis]-EXTENT_R]); } break; case ADJ: fprintf(stdout,"%f", fabs(DSET_DY(dset))); break; case ADK: fprintf(stdout,"%f", fabs(DSET_DZ(dset))); break; case VOXVOL: fprintf(stdout,"%f", fabs(DSET_DX(dset))* fabs(DSET_DY(dset))*fabs(DSET_DZ(dset))); break; case INAME: fprintf(stdout,"%s", argv[iarg]); break; case LTABLE: { char *str; if ((str = Dtable_to_nimlstring(DSET_Label_Dtable(dset), "VALUE_LABEL_DTABLE"))) { fprintf(stdout,"%s", str); free(str); } else { fprintf(stdout,"NO_LABEL_TABLE"); } } break; case LTABLE_AS_ATLAS_POINT_LIST: { ATLAS_POINT_LIST *apl=NULL; if ((apl = label_table_to_atlas_point_list(DSET_Label_Dtable(dset)))) { atlas_list_to_niml(apl,NULL); free_atlas_point_list(apl); } else { fprintf(stdout,"NO_LABEL_TABLE"); } } break; case ATLAS_POINTS: { ATR_string *atr = THD_find_string_atr( dset->dblk, "ATLAS_LABEL_TABLE"); if (atr) { fprintf(stdout,"%s", atr->ch); } else { fprintf(stdout,"NO_APL"); } } break; case FAC: { for (isb=0; isb<DSET_NVALS(dset); ++isb) { fprintf(stdout,"%f%s", DSET_BRICK_FACTOR(dset,isb), (isb == (DSET_NVALS(dset)-1)) ? "" : sbdelim); } break; } case DATUM: { for (isb=0; isb<DSET_NVALS(dset); ++isb) { fprintf(stdout,"%s%s", MRI_TYPE_name[DSET_BRICK_TYPE(dset,isb)], (isb == (DSET_NVALS(dset)-1)) ? "" : sbdelim); } break; } case LABEL: { for (isb=0; isb<DSET_NVALS(dset); ++isb) { fprintf(stdout,"%s%s", DSET_BRICK_LABEL(dset,isb) ? DSET_BRICK_LABEL(dset,isb):NAflag, (isb == (DSET_NVALS(dset)-1)) ? "" : sbdelim); } break; } case MIN: case MINUS: case MAX: case MAXUS: { float vv=0.0, min, max; for (isb=0; isb<DSET_NVALS(dset); ++isb) { if (!THD_subbrick_minmax(dset, isb, (sing[iis] == MINUS || sing[iis] == MAXUS) ? 0:1, &min, &max)) { fprintf(stdout,"%s%s", NAflag, (isb == (DSET_NVALS(dset)-1)) ? "" : sbdelim); } else { if (sing[iis] == MINUS) vv = min; else if (sing[iis] == MAXUS) vv = max; else if (sing[iis] == MIN) vv = min; else if (sing[iis] == MAX) vv = max; fprintf(stdout,"%g%s", vv, (isb == (DSET_NVALS(dset)-1)) ? "" : sbdelim); } } break; } case DMIN: case DMINUS: case DMAX: case DMAXUS: { float vv=0.0, min, max; if (!THD_dset_minmax(dset, (sing[iis] == DMINUS || sing[iis] == DMAXUS) ? 0:1, &min, &max)) { fprintf(stdout,"%s%s", NAflag, (isb == (DSET_NVALS(dset)-1)) ? "" : sbdelim); } else { if (sing[iis] == DMINUS) vv = min; else if (sing[iis] == DMAXUS) vv = max; else if (sing[iis] == DMIN) vv = min; else if (sing[iis] == DMAX) vv = max; fprintf(stdout,"%g%s", vv, (isb == (DSET_NVALS(dset)-1)) ? "" : sbdelim); } break; } case TR: #if 0 fprintf(stdout,"%f", DSET_TR_SEC(dset)); #else fprintf(stdout,"%f", DSET_TR(dset)); #endif break; case ORIENT: { /* fprintf(stdout,"%c%c%c", * ORIENT_typestr[dset->daxes->xxorient][0], ... ); */ char ostr[4]; /* just to show 23 Jan 2013 [rickr] */ THD_fill_orient_str_3(dset->daxes, ostr); fprintf(stdout,"%3s", ostr); } break; case SAME_GRID: fprintf(stdout,"%d", !THD_dataset_mismatch( dset , dsetp )); break; case SAME_DIM: fprintf(stdout,"%d", !(THD_dataset_mismatch( dset , dsetp ) & MISMATCH_DIMEN)); break; case SAME_DELTA: fprintf(stdout,"%d", !(THD_dataset_mismatch( dset , dsetp ) & MISMATCH_DELTA)); break; case SAME_ORIENT: fprintf(stdout,"%d", !(THD_dataset_mismatch( dset , dsetp ) & MISMATCH_ORIENT)); break; case SAME_CENTER: fprintf(stdout,"%d", !(THD_dataset_mismatch( dset , dsetp ) & MISMATCH_CENTER)); break; case SAME_OBL: fprintf(stdout,"%d", !(THD_dataset_mismatch( dset , dsetp ) & MISMATCH_OBLIQ)); break; case SLICE_TIMING: /* 6 May 2013 [rickr] */ { if( DSET_HAS_SLICE_TIMING(dset) ) { DSET_UNMSEC(dset); /* make sure times are in seconds */ for (isb=0; isb<dset->taxis->nsl; ++isb) { fprintf(stdout,"%s%f", (isb > 0) ? sbdelim : "", dset->taxis->toff_sl[isb]); } } else { /* all slices times are at t=0.0 */ for (isb=0; isb<DSET_NZ(dset); ++isb) { fprintf(stdout,"%s%f", (isb > 0) ? sbdelim : "", 0.0); } } } break; case SVAL_DIFF: fprintf(stdout,"%f",THD_diff_vol_vals(dset, dsetp, 1)); break; case VAL_DIFF: fprintf(stdout,"%f",THD_diff_vol_vals(dset, dsetp, 0)); break; case ID: fprintf(stdout,"%s", DSET_IDCODE_STR(dset)); break; case SMODE: fprintf(stdout,"%s", DSET_STORAGE_MODE_STR(dset)); break; default: ERROR_message("Info field not set properly (%d)\n", sing[iis]); exit(1); } if (sing[iis] != CLASSIC) { SPIT_DELIM(iis, N_sing, atrdelim); } } } exit(0) ; }
/*! A function to call SUMA_qhull_wrap or SUMA_qdelaunay_wrap */ SUMA_SurfaceObject *SUMA_ConvexHullSurface( SUMA_GENERIC_PROG_OPTIONS_STRUCT * Opt) { static char FuncName[]={"SUMA_ConvexHullSurface"}; SUMA_SurfaceObject *SO=NULL; float *xyz=NULL, *xyzp=NULL, *txyz=NULL; int npt, *ijk=NULL, nf=0, cnt, i, j, k, nxx, nyy, nzz,N_txyz=-1; FILE *fid=NULL; THD_fvec3 fv, iv; SUMA_Boolean LocalHead = NOPE; SUMA_ENTRY; npt = 0; N_txyz=-1; if (Opt->UseThisBrain) { MRI_IMAGE *im = NULL; float *far=NULL; int nx2, i3; /* load the 1D file */ im = mri_read_1D (Opt->UseThisBrain); if (!im) { SUMA_S_Err("Failed to read file"); SUMA_RETURN(NULL); } far = MRI_FLOAT_PTR(im); if (im->nx == 0) { SUMA_S_Errv("Empty file %s.\n", Opt->UseThisBrain); SUMA_RETURN(NULL); } if (im->ny != 3) { SUMA_S_Errv("Found %d columns in %s. Expecting 3\n", im->ny, Opt->UseThisBrain); SUMA_RETURN(NULL); } /* copy the columns */ N_txyz = im->nx; txyz = (float *)SUMA_malloc(im->nx*im->ny*sizeof(float)); if (!txyz) { SUMA_S_Crit("Failed to allocate."); SUMA_RETURN(NULL); } nx2 = 2*im->nx; for (i=0; i<N_txyz; ++i) { i3 = 3*i; txyz[i3 ] = far[i]; txyz[i3+1] = far[i+im->nx]; txyz[i3+2] = far[i+nx2]; } /* done, clean up and out you go */ if (im) mri_free(im); im = NULL; } if (Opt->in_vol) { cnt = 0; npt = 0; nxx = (DSET_NX(Opt->in_vol)); nyy = (DSET_NY(Opt->in_vol)); nzz = (DSET_NZ(Opt->in_vol)); if (Opt->debug) fprintf(SUMA_STDERR,"%s:\nRunning qhull...\n", FuncName); xyz = (float *)SUMA_malloc(3*nxx*nyy*nzz*sizeof(float)); if (!xyz) { SUMA_S_Err("Failed to allocate"); SUMA_RETURN(NULL); } for( k = 0 ; k < nzz ; k++ ) { for( j = 0 ; j < nyy ; j++ ) { for( i = 0 ; i < nxx ; i++ ) { if (Opt->mcdatav[cnt] == 1) { fv.xyz[0] = DSET_XORG(Opt->in_vol) + i * DSET_DX(Opt->in_vol); fv.xyz[1] = DSET_YORG(Opt->in_vol) + j * DSET_DY(Opt->in_vol); fv.xyz[2] = DSET_ZORG(Opt->in_vol) + k * DSET_DZ(Opt->in_vol); /* change mm to RAI coords */ iv = SUMA_THD_3dmm_to_dicomm( Opt->in_vol->daxes->xxorient, Opt->in_vol->daxes->yyorient, Opt->in_vol->daxes->zzorient, fv ); xyz[3*npt] = iv.xyz[0]; xyz[3*npt+1] = iv.xyz[1]; xyz[3*npt+2] = iv.xyz[2]; npt++; } ++cnt; } } } } else if (Opt->XYZ) { xyz = (float *)SUMA_malloc(3*Opt->N_XYZ*sizeof(float)); if (!xyz) { SUMA_S_Err("Failed to allocate"); SUMA_RETURN(NULL); } for( k = 0 ; k < 3*Opt->N_XYZ ; k++ ) { xyz[k] = Opt->XYZ[k]; npt = Opt->N_XYZ; } } else { SUMA_S_Err("No input"); goto CLEANUP; } if (Opt->corder) { SUMA_PC_XYZ_PROJ *pcp=NULL; if (Opt->geom==1) { SUMA_S_Warn("PCA projection makes no sense for usual convex hull"); } if (!(pcp = SUMA_Project_Coords_PCA (xyz, npt, npt/2, NULL, E3_PLN_PRJ, ROT_2_Z,0))) { SUMA_S_Err("Failed to project"); goto CLEANUP; } xyzp = pcp->xyzp; pcp->xyzp = NULL; pcp = SUMA_Free_PC_XYZ_Proj(pcp); } else { xyzp = xyz; } if (N_txyz >= 0 && N_txyz != npt) { SUMA_S_Errv("Mismatch between number of coordinates for convex hull\n" "and number of coordinates to adopt in the end.\n" " %d, versus %d in -these_coords\n", npt, N_txyz); goto CLEANUP; } if (Opt->geom == 1) { /* convex hull */ if (! (nf = SUMA_qhull_wrap(npt, xyzp, &ijk, 1, Opt->s)) ) { fprintf(SUMA_STDERR,"%s:\nFailed in SUMA_qhull_wrap\n", FuncName); goto CLEANUP; } /* Other than unif==0 make no sense here, but leave it to the user */ switch (Opt->unif) { case 0: /* coordinates as passed to qhull, could be projected ones*/ SO = SUMA_Patch2Surf(xyzp, npt, ijk, nf, 3); break; case 1: /* Original corrdinates passed to qhull (pre-projections, if any) */ SO = SUMA_Patch2Surf(xyz, npt, ijk, nf, 3); break; case 2: /* special coordinates passed by user, never passed in any form to qhull */ SUMA_S_Warn("Makes no sense to mess with coords for convex hull..."); SO = SUMA_Patch2Surf(txyz, npt, ijk, nf, 3); break; default: SUMA_S_Err("pit of despair"); goto CLEANUP; } if (Opt->debug) fprintf(SUMA_STDERR,"%s:\n%d triangles.\n", FuncName, nf); } else if (Opt->geom == 2) { /* triangulation */ if (! (nf = SUMA_qdelaunay_wrap(npt, xyzp, &ijk, 1, Opt->s)) ) { fprintf(SUMA_STDERR,"%s:\nFailed in SUMA_qdelaunay_wrap\n", FuncName); goto CLEANUP; } switch (Opt->unif) { case 0: /* coordinates as passed to qdelaunay, could be projected ones*/ if (xyz == xyzp) xyz=NULL; /* xyzp will be set to null in next call, so xyz is treated the same here */ SO = SUMA_NewSO(&xyzp, npt, &ijk, nf, NULL); SUMA_LHv("xyzp %p, ijk %p\n", txyz, ijk); break; case 1: /* Original corrdinates passed to qdelaunay (pre-projections, if any) */ SO = SUMA_NewSO(&xyz, npt, &ijk, nf, NULL); SUMA_LHv("xyz %p, ijk %p\n", txyz, ijk); break; case 2: /* special coordinates passed by user, never passed in any form to qdelaunay */ SO = SUMA_NewSO(&txyz, npt, &ijk, nf, NULL); SUMA_LHv("txyz %p, ijk %p\n", txyz, ijk); break; default: SUMA_S_Err("pit of despair, again"); goto CLEANUP; } } else { SUMA_S_Errv("Opt->geom = %d not valid\n", Opt->geom); goto CLEANUP; } CLEANUP: if (ijk) SUMA_free(ijk); ijk=NULL; if(txyz) SUMA_free(txyz); txyz=NULL; if (xyzp != xyz && xyzp != NULL) SUMA_free(xyzp); xyzp = NULL; if (xyz) SUMA_free(xyz); xyz = NULL; SUMA_RETURN(SO); }
/*! A function version of the program mc by Thomas Lewiner see main.c in ./MarchingCubes */ SUMA_SurfaceObject *SUMA_MarchingCubesSurface( SUMA_GENERIC_PROG_OPTIONS_STRUCT * Opt) { static char FuncName[]={"SUMA_MarchingCubesSurface"}; SUMA_SurfaceObject *SO=NULL; int nxx, nyy, nzz, cnt, i, j, k, *FaceSetList=NULL; float *NodeList=NULL; SUMA_NEW_SO_OPT *nsoopt = NULL; THD_fvec3 fv, iv; MCB *mcp ; SUMA_ENTRY; if (Opt->obj_type < 0) { nxx = DSET_NX(Opt->in_vol); nyy = DSET_NY(Opt->in_vol); nzz = DSET_NZ(Opt->in_vol); if (Opt->debug) { fprintf(SUMA_STDERR, "%s:\nNxx=%d\tNyy=%d\tNzz=%d\n", FuncName, nxx, nyy, nzz); } mcp = MarchingCubes(-1, -1, -1); set_resolution( mcp, nxx, nyy, nzz ) ; init_all(mcp) ; if (Opt->debug) fprintf(SUMA_STDERR,"%s:\nSetting data...\n", FuncName); cnt = 0; for( k = 0 ; k < mcp->size_z ; k++ ) { for( j = 0 ; j < mcp->size_y ; j++ ) { for( i = 0 ; i < mcp->size_x ; i++ ) { SUMA_SET_MC_DATA ( mcp, Opt->mcdatav[cnt], i, j, k); ++cnt; } } } } else { /* built in */ nxx = nyy = nzz = Opt->obj_type_res; mcp = MarchingCubes(-1, -1, -1); set_resolution( mcp, nxx, nyy, nzz) ; init_all(mcp) ; compute_data( *mcp , Opt->obj_type) ; } if (Opt->debug) fprintf(SUMA_STDERR,"%s:\nrunning MarchingCubes...\n", FuncName); run(mcp) ; clean_temps(mcp) ; if (Opt->debug > 1) { fprintf(SUMA_STDERR,"%s:\nwriting out NodeList and FaceSetList...\n", FuncName); write1Dmcb(mcp); } if (Opt->debug) { fprintf(SUMA_STDERR,"%s:\nNow creating SO...\n", FuncName); } NodeList = (float *)SUMA_malloc(sizeof(float)*3*mcp->nverts); FaceSetList = (int *)SUMA_malloc(sizeof(int)*3*mcp->ntrigs); if (!NodeList || !FaceSetList) { SUMA_SL_Crit("Failed to allocate!"); SUMA_RETURN(SO); } nsoopt = SUMA_NewNewSOOpt(); if (Opt->obj_type < 0) { nsoopt->LargestBoxSize = -1; if (Opt->debug) { fprintf(SUMA_STDERR, "%s:\nCopying vertices, changing to DICOM \n" "Orig:(%f %f %f) \nD:(%f %f %f)...\n", FuncName, DSET_XORG(Opt->in_vol), DSET_YORG(Opt->in_vol), DSET_ZORG(Opt->in_vol), DSET_DX(Opt->in_vol), DSET_DY(Opt->in_vol), DSET_DZ(Opt->in_vol)); } for ( i = 0; i < mcp->nverts; i++ ) { j = 3*i; /* change from index coordinates to mm DICOM, next three lines are equivalent of SUMA_THD_3dfind_to_3dmm*/ fv.xyz[0] = DSET_XORG(Opt->in_vol) + mcp->vertices[i].x * DSET_DX(Opt->in_vol); fv.xyz[1] = DSET_YORG(Opt->in_vol) + mcp->vertices[i].y * DSET_DY(Opt->in_vol); fv.xyz[2] = DSET_ZORG(Opt->in_vol) + mcp->vertices[i].z * DSET_DZ(Opt->in_vol); /* change mm to RAI coords */ iv = SUMA_THD_3dmm_to_dicomm( Opt->in_vol->daxes->xxorient, Opt->in_vol->daxes->yyorient, Opt->in_vol->daxes->zzorient, fv ); NodeList[j ] = iv.xyz[0]; NodeList[j+1] = iv.xyz[1]; NodeList[j+2] = iv.xyz[2]; } for ( i = 0; i < mcp->ntrigs; i++ ) { j = 3*i; FaceSetList[j ] = mcp->triangles[i].v3; FaceSetList[j+1] = mcp->triangles[i].v2; FaceSetList[j+2] = mcp->triangles[i].v1; } } else { nsoopt->LargestBoxSize = 100; /* built in */ for ( i = 0; i < mcp->nverts; i++ ) { j = 3*i; NodeList[j ] = mcp->vertices[i].x; NodeList[j+1] = mcp->vertices[i].y; NodeList[j+2] = mcp->vertices[i].z; } for ( i = 0; i < mcp->ntrigs; i++ ) { j = 3*i; FaceSetList[j ] = mcp->triangles[i].v3; FaceSetList[j+1] = mcp->triangles[i].v2; FaceSetList[j+2] = mcp->triangles[i].v1; } } SO = SUMA_NewSO(&NodeList, mcp->nverts, &FaceSetList, mcp->ntrigs, nsoopt); if (Opt->obj_type < 0) { /* not sure if anything needs to be done here ...*/ } else { if (Opt->obj_type == 0) SO->normdir = 1; else SO->normdir = -1; } if (Opt->debug) { fprintf(SUMA_STDERR,"%s:\nCleaning mcp...\n", FuncName); } clean_all(mcp) ; free(mcp); nsoopt=SUMA_FreeNewSOOpt(nsoopt); SUMA_RETURN(SO); }
int main( int argc , char * argv[] ) { int narg=1, do_automask=0 , iv , nxyz , do_set=0 , *rois=NULL, N_rois=0, all_rois = 0; THD_3dim_dataset *xset ; byte *mmm=NULL ; int nmask=0 , nvox_mask=0 ; THD_fvec3 cmv , setv ; /*-- read command line arguments --*/ if( argc < 2 || strncmp(argv[1],"-help",5) == 0 ){ printf("Usage: 3dCM [options] dset\n" "Output = center of mass of dataset, to stdout.\n" " -mask mset Means to use the dataset 'mset' as a mask:\n" " Only voxels with nonzero values in 'mset'\n" " will be averaged from 'dataset'. Note\n" " that the mask dataset and the input dataset\n" " must have the same number of voxels.\n" " -automask Generate the mask automatically.\n" " -set x y z After computing the CM of the dataset, set the\n" " origin fields in the header so that the CM\n" " will be at (x,y,z) in DICOM coords.\n" " -roi_vals v0 v1 v2 ... : Compute center of mass for each blob\n" " with voxel value of v0, v1, v2, etc.\n" " This option is handy for getting ROI \n" " centers of mass.\n" " -all_rois Don't bother listing the values of ROIs you want\n" " the program will find all of them and produce a \n" " full list.\n" " NOTE: Masking options are ignored with -roi_vals and -all_rois\n" ) ; PRINT_COMPILE_DATE ; exit(0) ; } LOAD_FVEC3(setv,0,0,0) ; /* ZSS: To quiet init. warnings */ narg = 1 ; while( narg < argc && argv[narg][0] == '-' ){ if( strcmp(argv[narg],"-set") == 0 ){ float xset,yset,zset ; if( narg+3 >= argc ){ fprintf(stderr,"*** -set need 3 args following!\n") ; exit(1) ; } xset = strtod( argv[++narg] , NULL ) ; yset = strtod( argv[++narg] , NULL ) ; zset = strtod( argv[++narg] , NULL ) ; LOAD_FVEC3(setv,xset,yset,zset) ; do_set = 1 ; THD_set_write_compression(COMPRESS_NONE); /* do not alter compression*/ narg++ ; continue ; } if( strncmp(argv[narg],"-mask",5) == 0 ){ THD_3dim_dataset *mask_dset ; if( mmm != NULL ){ fprintf(stderr,"*** Cannot have two -mask options!\n") ; exit(1) ; } if( do_automask ){ fprintf(stderr,"*** Can't have -mask and -automask!\n") ; exit(1) ; } if( narg+1 >= argc ){ fprintf(stderr,"*** -mask option requires a following argument!\n"); exit(1) ; } mask_dset = THD_open_dataset( argv[++narg] ) ; CHECK_OPEN_ERROR(mask_dset,argv[narg]) ; if( DSET_BRICK_TYPE(mask_dset,0) == MRI_complex ){ fprintf(stderr,"*** Cannot deal with complex-valued mask dataset!\n"); exit(1) ; } mmm = THD_makemask( mask_dset , 0 , 1.0,0.0 ) ; nvox_mask = DSET_NVOX(mask_dset) ; nmask = THD_countmask( nvox_mask , mmm ) ; if( mmm == NULL || nmask <= 0 ){ fprintf(stderr,"*** Can't make mask from dataset %s\n",argv[narg-1]); exit(1) ; } DSET_delete( mask_dset ) ; narg++ ; continue ; } if( strncmp(argv[narg],"-roi_vals",5) == 0 ){ if( narg+1 >= argc ){ fprintf(stderr,"*** -mask option requires a following argument(s)!\n"); exit(1) ; } rois = (int *)calloc(argc, sizeof(int)); N_rois = 0; ++narg; while (narg < argc-1 && argv[narg][0] != '-') { rois[N_rois++] = atoi(argv[narg]); ++narg; } continue ; } if( strncmp(argv[narg],"-all_rois",5) == 0 ){ all_rois = 1; narg++ ; continue ; } if( strcmp(argv[narg],"-automask") == 0 ){ if( mmm != NULL ){ fprintf(stderr,"*** Can't have -mask and -automask!\n") ; exit(1) ; } do_automask = 1 ; narg++ ; continue ; } fprintf(stderr,"*** Unknown option: %s\n",argv[narg]) ; exit(1) ; } /* should have at least 1 more argument */ if( argc <= narg ){ fprintf(stderr,"*** No input dataset!?\n") ; exit(1) ; } for( ; narg < argc ; narg++ ){ xset = THD_open_dataset( argv[narg] ) ; if( xset == NULL ){ fprintf(stderr,"+++ Can't open dataset %s -- skipping\n",argv[narg]); continue ; } DSET_load(xset) ; if( !DSET_LOADED(xset) ){ fprintf(stderr,"+++ Can't load dataset %s -- skipping\n",argv[narg]); DSET_delete(xset) ; continue ; } if( do_automask ){ if( mmm != NULL ){ free(mmm); mmm = NULL; } mmm = THD_automask(xset) ; nvox_mask = DSET_NVOX(xset) ; nmask = THD_countmask( nvox_mask , mmm ) ; if( mmm == NULL || nmask <= 0 ){ fprintf( stderr, "+++ Can't make automask from dataset %s " "-- skipping\n",argv[narg]) ; DSET_delete(xset) ; continue ; } } nxyz = DSET_NVOX(xset) ; if( mmm != NULL && nxyz != nvox_mask ){ fprintf(stderr,"+++ Mask/Dataset grid size mismatch at %s\n -- skipping\n",argv[narg]) ; DSET_delete(xset) ; continue ; } if (all_rois) { if (!(rois = THD_unique_vals(xset, 0, &N_rois, NULL)) || N_rois == 0) { ERROR_message("No rois or error in THD_unique_vals"); continue; } fprintf(stderr,"#%d distinct ROIs", N_rois); } if (!N_rois) { cmv = THD_cmass( xset , 0 , mmm ) ; printf("%g %g %g\n",cmv.xyz[0],cmv.xyz[1],cmv.xyz[2]) ; DSET_unload(xset) ; if( do_set ){ THD_fvec3 dv , ov ; if( DSET_IS_MASTERED(xset) ){ fprintf(stderr,"+++ Can't modify CM of dataset %s\n",argv[narg]) ; } else { /* lose obliquity */ /* recompute Tc(Cardinal transformation matrix for new grid output */ THD_make_cardinal(xset); LOAD_FVEC3(ov,DSET_XORG(xset),DSET_YORG(xset),DSET_ZORG(xset)) ; ov = THD_3dmm_to_dicomm( xset , ov ) ; dv = SUB_FVEC3(setv,cmv) ; ov = ADD_FVEC3(dv,ov) ; ov = THD_dicomm_to_3dmm( xset , ov ) ; xset->daxes->xxorg = ov.xyz[0] ; xset->daxes->yyorg = ov.xyz[1] ; xset->daxes->zzorg = ov.xyz[2] ; /* allow overwriting header for all types of output data */ putenv("AFNI_DECONFLICT=OVERWRITE") ; tross_Make_History( "3dCM" , argc,argv , xset );/* ZSS Dec. 09 08 */ if(DSET_IS_BRIK(xset)) { INFO_message("Rewriting header %s",DSET_HEADNAME(xset)) ; DSET_overwrite_header( xset ) ; } else { /* for other dataset types like NIFTI, rewrite whole dset */ DSET_load( xset ) ; DSET_overwrite(xset) ; INFO_message("Wrote new dataset: %s",DSET_BRIKNAME(xset)) ; } } } } else { float *xyz; if ((xyz = THD_roi_cmass(xset , 0 , rois, N_rois))) { printf("#Dset %s\n",DSET_BRIKNAME(xset)); for (iv=0; iv<N_rois; ++iv) { printf("#ROI %d\n", rois[iv]); printf("%g %g %g\n",xyz[3*iv],xyz[3*iv+1],xyz[3*iv+2]) ; } free(xyz); free(rois); } else { ERROR_message("Failed in THD_roi_cmass"); continue; } } DSET_delete(xset) ; } exit(0); }