int main(int argc, char* argv[]){ if(argc != 3){ printf("usage: ./external_cp <src> <des>\n"); printf("src: existing file on real file system\ndes:absolute path of SFS\n"); return -1; } char *testpath = argv[2]; if(testpath[0]!='/'){ printf("please use absolute path\n"); return -1; } ssize_t ret=0; // get the bytes of read/write /* open HD */ int fd; fd = open("../HD",O_RDWR); // oprn HD for read write /* read the source file */ int src; // file descripter for src file struct stat st; // to get the file size later src = open(argv[1],O_RDONLY); // open the source file for read only //printf("src: %d\n",src); if(src==-1){ printf("failed to open source file...\n"); return -1; } fstat(src,&st); // get the status of src file? ssize_t size = st.st_size; // get the size //printf("size of src file: %zd\n",size); //char buf[size]; // allocate memory to buf to store the string in file char *buf=malloc(size+1); // +1 for null char ret = read(src, buf, size); // read the file to buf /* just print out the text from file */ //printf("buf: "); //for(int i=0; i<ret; i++){ //printf("%c ",buf[i]); //} /* now read out the superblock for available inode and datablk to write */ struct superblock sb={}; lseek(fd, SB_OFFSET, SEEK_SET); // goto superblk region ret = read(fd, &sb, sizeof(struct superblock)); // read superblk info. to sb //print_sb(sb); /* get the inode number. I try to calculate the inode# on9ly * instead of get that inode info directly.(I initialed 0-99 inode# when run the mkfs_t) */ int inode_num = (sb.next_available_inode-INODE_OFFSET) / sizeof(struct inode); printf("the external file will use inode#%d\n",inode_num); /* use sys_call function write_t to alocate new inode for the file and update sb info. */ //strncpy(fname, buf, size); ret = write_t(inode_num, sb.next_available_blk, buf, size); free(buf); if(ret!=size){ perror("write_t failed"); } /* after write_t success, add the new entry to the dir according to the arg[2](destination) */ char *dpath; if(strncmp(argv[2],"/",sizeof(int)) == 0){ // because of my on9 coding, just a alias from "/" -> "/." dpath = "/."; // change "/" to "/." }else{ dpath = argv[2]; // assign the complete path } int dir_inode = open_t(dpath,2); // get inode number of that dir printf("inode of current dir: %d\n",dir_inode); /* if dir_inode=-1, the last entry is the filename, else user did not specific the name of copied file, then use the src argv[1] */ char path[1024] = ""; // if dpath containing the newfile name, trim it out and concat the splited path for get its inode# again. char filename[512] = ""; // maximum character of name 512 char *entry_name[MAX_NESTING_DIR]; // separate the path by "/" and save, most dir nest 10. int count_split = split_path(dpath+1, entry_name) + 1; // split the path into pieces. this func. from open_t.c if(dir_inode == -1){ // get the filename, also search for the dir inode again printf("the last part of path: %s\n",entry_name[count_split-1]); strncpy(filename, entry_name[count_split-1], strlen(entry_name[count_split-1])); // copy last entry as filename that will be created strncpy(path,"/.", sizeof(path)); // path is root dir "/." if not meet the next line condition if(count_split>1){ // if NOT copy to sub dir strncpy(path,"/", sizeof(char)+1); // abs. path begin with "/" for(int i=0; i<count_split; i++){ strncat(path, entry_name[i], strlen(entry_name[i])); // start concat the entry_name if(i+1 == count_split-1){ // if i+1 is the last of entry_name[](new dir), break break; } strncat(path,"/", sizeof(char)); } } //printf("path:%s\n",path); dir_inode = open_t(path,2); // get inode number again of that dir } else { // else the user did not specific the file name. just the path of dir, strncpy(filename, argv[1], sizeof(filename)); // so use the src name } //printf("pinode: %d\n",dir_inode); /* add the copied file into the directory entry */ struct inode inodes={}; lseek(fd,INODE_OFFSET+sizeof(struct inode)*dir_inode,SEEK_SET); // seek to dir inode offset ret = read(fd, &inodes, sizeof(struct inode)); // read inode info to inodes lseek(fd, inodes.direct_blk[0]+sizeof(DIR_NODE)*inodes.file_num, SEEK_SET); // goto writable offset of datablk DIR_NODE entry={}; // for the new file strncpy(entry.dir, filename, sizeof(entry.dir)); // new file name entry.inode_number=inode_num; // new file inode number ret = write(fd, &entry, sizeof(DIR_NODE)); // write new entry into the directory inodes.i_size = inodes.i_size + size; inodes.file_num = inodes.file_num + 1; lseek(fd,INODE_OFFSET+sizeof(struct inode)*dir_inode,SEEK_SET); ret = write(fd, &inodes, sizeof(struct inode)); //print_inode(inodes); //print_sb(sb); close(fd); }
int main(int argc,char *argv[]) { // decode arguments args(argc,argv); inits(); if(run_type==6) to_year=2010; // Read in Data // cout<< "Reading Data\n"; read_data(); // Set initial Params // cout<< "Initiallizing...\n"; init_state(); init_t(); calc_state(); if(fixed_d != 0) //run traf_mat once and only once (for faster prototyping) { calc_traf(); /* _vbc_vec<float> Uj(1,n_lakes); for(int j=1;j<=n_lakes;j++) { Uj(j) = 0; for(int i=1;i<=n_sources;i++) { Uj(j) += sources(i).Gij(j) * sources(i).Oi; } cout << Uj(j) << "\t" << 1-exp(- pow(0.001 * Uj(j), 1 ) ) << "\n"; } */ calc_traf_mat(); calc_pp(); } ofstream ll_("output/ll_test.dat"); if(FALSE) { calc_traf(); calc_traf_mat(); calc_pp(); //!! int tmp_t; for(int lake=1;lake<=n_lakes;lake++) { if(lakes(lake).invaded == 0 && lakes(lake).last_abs == 0 ) { for(int t=from_year;t<=to_year+2;t++) { // sample_t(); tmp_t=t_vec(lake); t_vec(lake)=t; calc_state(); calc_pp(); cout << lake << "\t" << t <<endl; ll_ << lake << "\t" << t <<"\t"<<l_hood()<<endl; } t_vec(lake)=tmp_t; } } } if(FALSE) // likelihood profile of d and e //if init_t is random, MLE d=e=0 (no effect of distance or size: CHECK) { d_par=-1; e_par=0; for(int i=0;i<=60;i++) { d_par=d_par+0.1; e_par=0; for(int j=0;j<=10;j++) { e_par=e_par + 0.1; calc_traf(); calc_traf_mat(); calc_pp(); ll_ << d_par << "\t" << e_par << "\t" << l_hood()<< endl; cout << d_par <<"\t"<< e_par << "\t" << l_hood()<< endl; } } } if(FALSE) //likelihood profile of alpha { chem_pars(1)=0; for(int i=0;i<=1000;i++) { chem_pars(1)+=0.0001; ll_ << chem_pars(1) << "\t" << l_hood()<< endl; } } //Just sim under the true alpha to see the t_vec distribution // to compare with sim_dat.R if(FALSE) { for(int lake_index=1;lake_index<=n_lakes;lake_index++) { lakes(lake_index).discovered=0; lakes(lake_index).last_abs=0; } for(int i=1;i<=1000;i++) { sim_spread(); write_t(); } } /// SEEDS /// //i d e c B_o NAUT KKUT MGUT //8394 1.06513 0.531416 0.000125572 -13.713 0.00405104 -0.00475339 0.0038181 // CAUT PPUT1 SIO3UR DOC COLTR ALKTI ALKT //0.00403173 0.0571088 1.28896 -0.31447 -0.00654376 0.0621327 -0.000480646 // PH COND25 SECCHI.DEPTH NA //0.00852002 0.00335544 0.0995729 -380.192 //0.407766 1.44137 0.417034 -10.8476 0.708086 -0.0150081 -0.404532 -0.512538 0.689779 0.43177-0.584563 -0.224491 0.786624 1.0269 0.868935 -0.0982729 0.37267 chem_pars(1)=-10; chem_pars(2)=0.7; chem_pars(3)=-0.01; //-2:1 MLE ~0 chem_pars(4)=-0.38; //-1.5:1.5 MLE ~0 chem_pars(5)=-0.5; //-0.4:0.2 MLE ~0 chem_pars(6)=0.68; //0:0.1 MLE 0.05 *** chem_pars(7)=0.43; //-0.4:0.2 MLE ~1.3 **** chem_pars(8)=-0.58; //-0.7:0.1 MLE ~-0.31 **** chem_pars(9)=-0.22; //-0.4:0.2 MLE ~-0.01 ** chem_pars(10)=0.78; //-0.1:0.1 MLE ~0.06 * chem_pars(11)=1.02; //-0.16:0.1 MLE ~0 chem_pars(12)=0.85; //-0.2:0.2 MLE ~0 chem_pars(13)=-0.09; //-0.04:0.01 MLE ~0 chem_pars(14)=0.37; //-0.3:0.3 MLE ~0.1 int test_ch=14; d_par=1.54; //float bb = l_hood(); if(ll) { float tmplhood; for(int i=1;i<=20;i++) { cerr << i << "\n"; //chem_pars(test_ch)=chem_pars(test_ch)+0.0013; d_par=d_par+0.05; calc_traf(); cerr << "A" << "\n"; calc_traf_mat(); cerr << "B" << "\n"; sim_spread(); cerr << "C" << "\n"; //write_t(); tmplhood = l_hood(); cerr << "D" << "\n"; ll_ << chem_pars(test_ch) << "\t" << tmplhood << "\n"; cout << d_par << "\t" << tmplhood << "\n"; } } ll_.close(); cout << "# sampled\t" << n_sampled << "\n"; if(run_type==1) { // FIT ON TRAF_PARS & SPREAD PARS ONLY (NO ENV) // // need a likelihood function wrapper to call l_hood() multiple times and average the result // to smooth out stochastic surface. // BOOTSTRAP RESAMPLING OF DATA (SAMPLED LAKES) TO GENERATE CI // float garbage=l_hood(); int n_reps = 1000; ofstream par_file; int n_pars; //13 env + intercept + d,c,gamma _vbc_vec<float> params1; _vbc_vec<float> dat1; _vbc_vec<float> MLE_params; if(!env) { if(sim) par_file.open("sims/gb_output/pred_pars.tab"); else par_file.open("output/pred_pars.tab"); n_pars=4; // d,c,gamma,alpha params1.redim(1,n_pars); dat1.redim(1,n_pars); MLE_params.redim(1,n_pars); params1(1)=1.27; params1(2)=1.48; params1(3)=0.0000489; params1(4)=0.00105; }else{ if(sim) par_file.open("sims/gb_output/pred_parsENV.tab"); else par_file.open("output/pred_parsENV.tab"); n_pars=18; //13 env + intercept + d,e,c,gamma params1.redim(1,n_pars); dat1.redim(1,n_pars); MLE_params.redim(1,n_pars); params1(1)=1.79; params1(2)=2; params1(3)=0.69; params1(4)=0.0000489; /// SEEDS /// params1(5)=-6.2; params1(6)=0.014; params1(7)=-0.08; //-2:1 MLE ~0 params1(8)=0.15; //-1.5:1.5 MLE ~0 params1(9)=0.21; //-0.4:0.2 MLE ~0 params1(10)=0.03; //0:0.1 MLE 0.05 *** params1(11)=-0.13; //-0.4:0.2 MLE ~1.3 **** params1(12)=-0.43; //-0.7:0.1 MLE ~-0.31 **** params1(13)=-0.007; //-0.4:0.2 MLE ~-0.01 ** params1(14)=0.056; //-0.1:0.1 MLE ~0.06 * params1(15)=0.0087; //-0.16:0.1 MLE ~0 params1(16)=0.081; //-0.2:0.2 MLE ~0 params1(17)=-0.015; //-0.04:0.01 MLE ~0 params1(18)=0.013; //-0.3:0.3 MLE ~0.1 } _vbc_vec<int> tmp_index_sampled; tmp_index_sampled = sampled_index; if(boot) { ofstream boot_file; if(sim) boot_file.open("sims/gb_output/boot_lakes.tab"); else boot_file.open("output/boot_lakes.tab"); for(int i=1;i<=n_reps;i++) { //Bootstrap resample // sampled_index = sample_w_replace(tmp_index_sampled); for(int j=1;j<=n_sampled;j++) boot_file << sampled_index(j) << "\t"; boot_file << "\n"; boot_file.flush(); // --- // simplex::clsSimplex<float> gertzen_rep; //gertzen_rep.set_param_small(1e-3); gertzen_rep.start(&dat1,¶ms1, &MLE_l_hood,n_pars, 1e-2); gertzen_rep.getParams(&MLE_params); cout << "\n\nMLE "<< i << " of " << n_reps << "\n\n"; for(int p=1;p<=n_pars;p++) par_file << MLE_params(p) <<"\t"; par_file << "\n"; par_file.flush(); } boot_file.close(); }else{ simplex::clsSimplex<float> gertzen_rep; //gertzen_rep.set_param_small(1e-3); gertzen_rep.start(&dat1,¶ms1, &MLE_l_hood,n_pars, 1e-2); gertzen_rep.getParams(&MLE_params); cout << "\n\nMLE\n"; for(int p=1;p<=n_pars;p++) par_file << MLE_params(p) <<"\t"; par_file << "\n"; par_file.flush(); // Print out distribution of alpha values at MLE ofstream alphas_file; alphas_file.open("output/alphas.tab",std::fstream::app); for(int i=1;i<=n_lakes;i++) { alphas_file << calc_alpha(i) << "\n"; } alphas_file.close(); } par_file.close(); } if(run_type==2) { //MCMC lib string mcmc_file("output/lib.mcmc"); if(env) { _vbc_vec<float> params(1,4+n_chem_var); _vbc_vec<float> prop_width(1,4+n_chem_var,1,4+n_chem_var); prop_width(1)=0.05; prop_width(2)=0.05; prop_width(3)=0.05; params(1)=0.4; params(2)=1.4; params(3)=0.42; for(int i=1;i<=n_chem_var+1;i++) { prop_width(i+3)=0.0001; params(i+3)=chem_pars(i); } prop_width(4)=0.1; _vbc_vec<float> prop_sigma; prop_sigma = diag(prop_width); // Print out prop_sigma for(int i=1;i<=n_chem_var+4;i++) { for(int j=1;j<=n_chem_var+4;j++) cout << prop_sigma(i,j) << " | "; cout << "\n"; } mcmcMD::run_mcmc(params, prop_sigma, &likelihood_wrapperMCMC_MD, &prior_MD, &restrict_MCMC_MD, 50000, 50, 1, mcmc_file.c_str(), true, true, true, 500, 4); }else { /// No env. _vbc_vec<float> params(1,4); _vbc_vec<float> prop_width(1,4,1,4); prop_width(1)=0.05; prop_width(2)=0.05; prop_width(3)=0.000001; prop_width(4)=0.00001; params(1)=1.27; params(2)=1.48; params(3)=0.0000489; params(4)=0.00105; _vbc_vec<float> prop_sigma; prop_sigma = diag(prop_width); // Print out prop_sigma for(int i=1;i<=4;i++) { for(int j=1;j<=4;j++) cout << prop_sigma(i,j) << " | "; cout << "\n"; } mcmcMD::run_mcmc(params, prop_sigma, &likelihood_wrapperMCMC_MD, &prior_MD, &restrict_MCMC_MD, 500000, 1, 1, mcmc_file.c_str(), true, true, true, 500, 5); } /* mcmcMD::run_mcmc(pms, props, &like, &prior, &restrictions, 500000, 1, 100, file_name.c_str(), TRUE, TRUE, 1000); */ } /// Sim from posterior /// if(run_type==3) sim_spread_posterior(); /// Traf tests //// if(run_type==4) { ofstream traf_ll_file("output/traf_ll.dat"); d_par=1.54; e_par=2; c_par=0.8; calc_traf(); calc_traf_mat(); calc_pp(); sim_spread(); cout << l_hood() <<"\n"; /* for(int i=1;i<=70;i++) { e_par=e_par+0.05; cout << e_par << "\t"; calc_traf(); calc_traf_mat(); calc_pp(); sim_spread(); traf_ll_file << e_par << "\t" << l_hood() << "\n"; cout << l_hood() <<"\t"; sim_spread(); traf_ll_file << e_par << "\t" << l_hood() << "\n"; cout << l_hood() <<"\t"; sim_spread(); traf_ll_file << e_par << "\t" << l_hood() << "\n"; cout << l_hood() <<"\n"; traf_ll_file << e_par << "\t" << l_hood() << "\n"; } for(int i=1;i<=10;i++) { e_par=e_par+0.2; c_par=0.8; calc_traf(); calc_traf_mat(); calc_pp(); for(int j = 1;j<=10;j++) { c_par=c_par+0.2; glb_alpha=0; //from MLE for(int k=1;k<=500;k++) { glb_alpha=glb_alpha+0.00001; sim_spread(); sim_spread(); sim_spread(); cout << e_par << "\t" << c_par << "\t" << glb_alpha << "\t" << l_hood() << "\n"; traf_ll_file << e_par << "\t" << c_par << "\t" << glb_alpha << "\t" << l_hood() << "\n"; } } } */ traf_ll_file.close(); calc_pp(); write_pp(); write_inv_stat(); } /// Holdout sets for internal AUC //// if(run_type==5) { int n_pars=4; _vbc_vec<float>params1(1,n_pars); // Read parameters values from file // ifstream pred_pars; if(sim) pred_pars.open("sims/gb_output/pred_pars.tab"); else pred_pars.open("output/pred_pars.tab"); for(int j=1;j<=n_pars;j++) pred_pars >> params1(j); pred_pars.close(); // -- // d_par=params1(1); e_par = 1; c_par=params1(2); gamma_par=params1(3); glb_alpha=params1(4); calc_traf(); calc_traf_mat(); //write_traf_mat(); //Sub-sample a holdout set from sampled lakes (pre-2010) int n_sub_sampled = 100,choose_from=0; _vbc_vec<int> index_2006_big(1,n_lakes); for(int i = 1; i<=n_lakes;i++) { if( (lakes(i).last_abs==2006 || lakes(i).discovered == 2006) ) { choose_from += 1; index_2006_big(choose_from)=i; } } _vbc_vec<int> index_2006(1,choose_from); for(int i = 1; i<=choose_from;i++) index_2006(i)=index_2006_big(i); ofstream prop_holdout_file; prop_holdout_file.open("output/holdout_sim_props.csv"); ofstream holdout_inv_file("output/holdout2006_data_status.csv"); _vbc_vec<int> holdout_inv_status(1,n_sub_sampled); _vbc_vec<int> indicies_holdout(1,n_sub_sampled); _vbc_vec<int> tmp_discovered(1,n_sub_sampled); _vbc_vec<int> tmp_last_abs(1,n_sub_sampled); cout << "Total 2006 lakes to choose from " << choose_from << "\n"; for(int rep=1;rep<=50;rep++) { indicies_holdout = sample_wo_replace(index_2006,n_sub_sampled); //Record the year_discovered of holdoutset for(int i = 1; i<=n_sub_sampled;i++) { if(lakes(indicies_holdout(i)).discovered == 2006) holdout_inv_status(i) = 1; else holdout_inv_status(i) = 0; //write year discovered if(i == n_sub_sampled) holdout_inv_file << holdout_inv_status(i) << "\n"; else holdout_inv_file << holdout_inv_status(i) << ","; //save last_abs and discoved tmp_discovered(i) = lakes(indicies_holdout(i)).discovered; tmp_last_abs(i) = lakes(indicies_holdout(i)).last_abs; //remove year discovered lakes(indicies_holdout(i)).discovered = 0; lakes(indicies_holdout(i)).last_abs = 0; } //SIM SPREAD _vbc_vec<float> prop_holdout_invaded(1,n_sub_sampled); for(int i=1;i<=n_sub_sampled;i++) prop_holdout_invaded(i) = 0; int n_sims=1000; for(int s=1; s<= n_sims; s++) { sim_spread(); for(int i=1;i<=n_sub_sampled;i++) { if(t_vec(indicies_holdout(i)) <= 2006) prop_holdout_invaded(i) += 1; } } //write prop inv for(int i=1;i<=n_sub_sampled;i++) { prop_holdout_invaded(i) = prop_holdout_invaded(i)/n_sims; if(i < n_sub_sampled) prop_holdout_file << prop_holdout_invaded(i) << ","; else prop_holdout_file << prop_holdout_invaded(i) << "\n"; //reset last_abs and discoved lakes(indicies_holdout(i)).discovered = tmp_discovered(i); lakes(indicies_holdout(i)).last_abs = tmp_last_abs(i); } } holdout_inv_file.close(); prop_holdout_file.close(); }