int main(int argc, char *argv[])
{
/* Important definitions */
// Lengths
size_t N = 0; // Length of time series
size_t M = 0; // Length of sampling vector (number of frequencies)
// Filenames
char inname[100];
char outname[100];
// Sampling
double low, high, rate;
// Frequency of window function
double winfreq = 0;
// Options
int quiet = 0;
int unit = 1;
int prep = 1;
int autosamp = 0;
int fast = 0;
int useweight = 0;
int windowmode = 0;
int Nclean = 0;
int filter = 0;
/* Process command line arguments and return line count of the input file */
N = cmdarg(argc, argv, inname, outname, &quiet, &unit, &prep, &low, &high,\
&rate, &autosamp, &fast, &useweight, &windowmode, &winfreq,\
&Nclean, &filter, NULL, NULL);
// Pretty print
if ( quiet == 0 || fast == 1 ){
if ( windowmode == 0 && useweight != 0 )
printf("\nCalculating the weighted power spectrum of \"%s\" ...\n",\
inname);
else if ( windowmode == 0 )
printf("\nCalculating the power spectrum of \"%s\" ...\n", inname);
else
printf("\nCalculating the window function of \"%s\" ...\n", inname);
}
/* Read data (and weights) from the input file */
if ( quiet == 0 ) printf(" - Reading input\n");
double* time = malloc(N * sizeof(double));
double* flux = malloc(N * sizeof(double));
double* weight = malloc(N * sizeof(double));
readcols(inname, time, flux, weight, N, useweight, unit, quiet);
// Do if fast-mode and window-mode is not activated
if ( fast == 0 && windowmode == 0 ) {
// Calculate Nyquist frequency
double* dt = malloc(N-1 * sizeof(double));
double nyquist;
arr_diff(time, dt, N);
nyquist = 1.0 / (2.0 * arr_median(dt, N-1)) * 1e6; // microHz !
free(dt);
// Calculate suggested sampling (4 times oversampling)
double minsamp;
minsamp = 1.0e6 / (4 * (time[N-1] - time[0])); // microHz !
// Display info?
if ( quiet == 0 ){
printf(" -- INFO: Length of time series = %li\n", N);
printf(" -- INFO: Nyquist frequency = %.2lf microHz\n", nyquist);
printf(" -- INFO: Suggested minimum sampling = %.3lf microHz\n",\
minsamp);
}
// Apply automatic sampling?
if ( autosamp != 0 ) {
low = 5.0;
high = nyquist;
rate = minsamp;
}
}
/* Prepare for power spectrum */
// Calculate proper frequency range for window-function-mode
double limit = 0;
if ( windowmode != 0 ) {
limit = low;
low = winfreq - limit;
high = winfreq + limit;
}
// Get length of sampling vector
M = arr_util_getstep(low, high, rate);
// Fill sampling vector with cyclic frequencies
double* freq = malloc(M * sizeof(double));
arr_init_linspace(freq, low, rate, M);
// Initialise arrays for data storage
double* power = malloc(M * sizeof(double));
double* alpha = malloc(M * sizeof(double));
double* beta = malloc(M * sizeof(double));
/* Calculate power spectrum OR window function */
if ( windowmode == 0 ) {
// Subtract the mean to avoid "zero-frequency" problems
if ( prep != 0 ) {
if ( quiet == 0 ){
printf(" - Subtracting the mean from time series\n");
}
arr_sca_add(flux, -arr_mean(flux, N), N);
}
else {
if ( quiet == 0 )
printf(" - Time series used *without* mean subtraction!\n");
}
// Display info
if ( quiet == 0 ){
printf(" - Calculating fourier transform\n");
if ( autosamp != 0 ) {
printf(" -- NB: Using automatic sampling!\n");
printf(" -- INFO: Auto-sampling (in microHz): %.2lf to %.2lf"\
" in steps of %.4lf\n", low, high, rate);
}
else {
printf(" -- INFO: Sampling (in microHz): %.2lf to %.2lf in"\
" steps of %.4lf\n", low, high, rate);
}
printf(" -- INFO: Number of sampling frequencies = %li\n", M);
}
// Calculate power spectrum with or without weights
fourier(time, flux, weight, freq, N, M, power, alpha, beta, useweight);
}
else {
if ( quiet == 0 ){
printf(" - Calculating window function\n");
printf(" -- INFO: Window frequency = %.2lf microHz\n", winfreq);
printf(" -- INFO: Sampling in the range +/- %.2lf microHz in" \
" steps of %.4lf microHz\n", limit, rate);
printf(" -- INFO: Number of sampling frequencies = %li\n", M);
}
// Calculate spectral window with or without weights
windowfunction(time, freq, weight, N, M, winfreq, power, useweight);
if ( quiet == 0 )
printf(" - Sum of spectral window = %.4lf\n", arr_sum(power, M));
// Move frequencies to the origin
arr_sca_add(freq, -winfreq, M);
}
/* Write data to file */
if ( quiet == 0 ) printf(" - Saving to file \"%s\"\n", outname);
writecols(outname, freq, power, M);
/* Free data */
free(time);
free(flux);
free(weight);
free(freq);
free(power);
free(alpha);
free(beta);
/* Done! */
if ( quiet == 0 || fast ==1 ) printf("Done!\n\n");
return 0;
}
int
intip(char *ifname, int ifs, int argc, char **argv)
{
int set, alias, flags, argcmax;
ip_t ip;
struct in_addr destbcast;
struct ifaliasreq addreq, ridreq;
struct sockaddr_in *sin;
char *msg, *cmdname;
memset(&addreq, 0, sizeof(addreq));
memset(&ridreq, 0, sizeof(ridreq));
if (NO_ARG(argv[0])) {
set = 0;
argc--;
argv++;
} else
set = 1;
/*
* We use this function for ip and alias setup since they are
* the same thing.
*/
if (isprefix(argv[0], "alias")) {
alias = 1;
cmdname = "alias";
} else if (isprefix(argv[0], "ip")) {
alias = 0;
cmdname = "ip";
} else {
printf("%% intip: Internal error\n");
return 0;
}
argc--;
argv++;
flags = get_ifflags(ifname, ifs);
if (flags & IFF_POINTOPOINT) {
argcmax = 2;
msg = "destination";
} else if (flags & IFF_BROADCAST) {
argcmax = 2;
msg = "broadcast";
} else {
argcmax = 1;
msg = NULL;
}
if (argc < 1 || argc > argcmax) {
printf("%% %s <address>/<bits> %s%s%s\n", cmdname,
msg ? "[" : "", msg ? msg : "", msg ? "]" : "");
printf("%% %s <address>/<netmask> %s%s%s\n", cmdname,
msg ? "[" : "", msg ? msg : "", msg ? "]" : "");
printf("%% no %s <address>[/bits]\n", cmdname);
printf("%% no %s <address>[/netmask]\n", cmdname);
return(0);
}
/* ignore 'address' keyword, don't print error */
if (isprefix(argv[0], "address")) {
argc--;
argv++;
}
if (isprefix(argv[0], "dhcp")) {
char *args[] = { PKILL, "dhclient", ifname, '\0' };
char leasefile[sizeof(LEASEPREFIX)+1+IFNAMSIZ];
if (set)
cmdarg(DHCLIENT, ifname);
else {
cmdargs(PKILL, args);
snprintf(leasefile, sizeof(leasefile), "%s.%s",
LEASEPREFIX, ifname);
rmtemp(leasefile);
}
return(0);
}
ip = parse_ip(argv[0], NO_NETMASK);
if (ip.family == 0)
/* bad IP specified */
return(0);
if (ip.bitlen == -1) {
printf("%% Netmask not specified\n");
return(0);
}
if (argc == 2)
if (!inet_aton(argv[1], &destbcast)) {
printf("%% Invalid %s address\n", msg);
return(0);
}
strlcpy(addreq.ifra_name, ifname, sizeof(addreq.ifra_name));
strlcpy(ridreq.ifra_name, ifname, sizeof(ridreq.ifra_name));
if (!set) {
sin = (struct sockaddr_in *)&ridreq.ifra_addr;
sin->sin_len = sizeof(ridreq.ifra_addr);
sin->sin_family = AF_INET;
sin->sin_addr.s_addr = ip.addr.sin.s_addr;
}
if (!alias || !set) {
/*
* Here we remove the top IP on the interface before we
* might add another one, or we delete the specified IP.
*/
if (ioctl(ifs, SIOCDIFADDR, &ridreq) < 0)
if (!set)
printf("%% intip: SIOCDIFADDR: %s\n",
strerror(errno));
}
if (set) {
sin = (struct sockaddr_in *)&addreq.ifra_addr;
sin->sin_family = AF_INET;
sin->sin_len = sizeof(addreq.ifra_addr);
sin->sin_addr.s_addr = ip.addr.sin.s_addr;
sin = (struct sockaddr_in *)&addreq.ifra_mask;
sin->sin_family = AF_INET;
sin->sin_len = sizeof(addreq.ifra_mask);
sin->sin_addr.s_addr = htonl(0xffffffff << (32 - ip.bitlen));
if (argc == 2) {
sin = (struct sockaddr_in *)&addreq.ifra_dstaddr;
sin->sin_family = AF_INET;
sin->sin_len = sizeof(addreq.ifra_dstaddr);
sin->sin_addr.s_addr = destbcast.s_addr;
}
if (ioctl(ifs, SIOCAIFADDR, &addreq) < 0)
printf("%% intip: SIOCAIFADDR: %s\n", strerror(errno));
}
return(0);
}
int main ( int argc, char *argv[] )
{
/***********************************************************************
* Local variables
***********************************************************************/
int ierr = 0; // Flag errors
char *error = NULL; // Error message string
double t1, t2, t3, t4, t5; // Variables to track runtime
/* File in/out handling variables */
char *inputFile = NULL, *outputFile = NULL;
FILE *fp_in = NULL, *fp_out = NULL;
input_data input_vars; // Struct to store input variables
input_data_init ( &input_vars ); // Set variables to initial values
para_data para_vars; // Struct to store parallel variables
para_data_init ( ¶_vars ); // Set variables to initial values
time_data time_vars; // Struct to store time variables
time_data_init ( &time_vars ); // Set variables to initial values
geom_data geom_vars; // Struct to store geometry variables
geom_data_init ( &geom_vars ); // Set variables to initial values
sn_data sn_vars; // Struct to store sn variables
sn_data_init ( &sn_vars ); // Set variables to initial values
data_data data_vars; // Struct to store data variables
data_data_init ( &data_vars ); // Set variables to initial values
control_data control_vars; // Struct to store control variables
control_data_init ( &control_vars ); // Set variables to initial values
mms_data mms_vars; // Struct to store mms variables
mms_data_init ( &mms_vars ); // Set variables to initial values
solvar_data solvar_vars; // Struct to store solvar variables
solvar_data_init ( &solvar_vars ); // Set variables to initial values
sweep_data sweep_vars; // Struct to store sweep variables
sweep_data_init ( &sweep_vars ); // Set variables to initial values
dim_sweep_data dim_sweep_vars;
/***********************************************************************
* Perform calls that set up the parallel environment in MPI and
* OpenMP. Also starts the timer. Update parallel setup time.
***********************************************************************/
/* Initialize the parallel environment */
pinit ( argc, argv, ¶_vars, &t1, &ierr );
t2 = wtime(); // Get the MPI walltime
/* Calc parallel setup time */
time_vars.tparset = time_vars.tparset + t2 - t1;
/***********************************************************************
* Read the command line arguments to get i/o file names.
* Open the two files.
***********************************************************************/
ierr = cmdarg ( argc, argv, &inputFile, &outputFile, &error,
para_vars.iproc, para_vars.root );
bcast_i_scalar ( &ierr, para_vars.comm_snap, para_vars.root, para_vars.nproc );
/* Ensure arguments are valid */
if ( ierr != 0 )
{
print_error ( NULL, error, para_vars.iproc, para_vars.root );
FREE ( inputFile );
FREE ( outputFile );
FREE ( error );
stop_run ( 0, 0, 0, ¶_vars, &sn_vars, &data_vars, &mms_vars,
&geom_vars, &solvar_vars, &control_vars );
}
/* Open the input file to read in initial values */
ierr = open_file ( &fp_in, inputFile, "r", &error, para_vars.iproc, para_vars.root );
bcast_i_scalar ( &ierr, para_vars.comm_snap, para_vars.root, para_vars.nproc);
/* Ensure input file is found */
if ( ierr != 0 )
{
print_error ( NULL, error, para_vars.iproc, para_vars.root );
FREE ( inputFile );
FREE ( outputFile );
FREE ( error );
stop_run ( 0, 0, 0, ¶_vars, &sn_vars, &data_vars, &mms_vars,
&geom_vars, &solvar_vars, &control_vars );
}
/* Open the output file to write results and error messages */
ierr = open_file ( &fp_out, outputFile, "w", &error, para_vars.iproc, para_vars.root );
bcast_i_scalar ( &ierr, para_vars.comm_snap, para_vars.root, para_vars.nproc );
/* Ensure output file can be created */
if ( ierr != 0 )
{
print_error ( NULL, error, para_vars.iproc, para_vars.root );
FREE ( inputFile );
FREE ( outputFile );
FREE ( error );
stop_run ( 0, 0, 0, ¶_vars, &sn_vars, &data_vars, &mms_vars,
&geom_vars, &solvar_vars, &control_vars );
}
/***********************************************************************
* Write code version and execution time to output.
***********************************************************************/
if ( para_vars.iproc == para_vars.root ) version_print ( fp_out );
/***********************************************************************
* Read input
***********************************************************************/
ierr = read_input ( fp_in, fp_out, &input_vars, ¶_vars, &time_vars );
ierr = close_file ( fp_in, inputFile, &error, para_vars.iproc,
para_vars.root );
FREE ( inputFile );
bcast_i_scalar ( &ierr, para_vars.comm_snap, para_vars.root, para_vars.nproc );
if ( ierr != 0 )
{
print_error ( fp_out, error, para_vars.iproc, para_vars.root );
FREE ( outputFile );
FREE ( error );
stop_run ( 0, 0, 0, ¶_vars, &sn_vars, &data_vars, &mms_vars,
&geom_vars, &solvar_vars, &control_vars );
}
/***********************************************************************
* Get nthreads for each proc. Print the warning about resetting
* nthreads if necessary. Don't stop run. Set up the SDD MPI topology.
***********************************************************************/
t3 = wtime();
pinit_omp ( para_vars.comm_snap, &input_vars.nthreads, input_vars.nnested,
¶_vars.do_nested, &ierr, &error );
if ( ierr != 0 ) print_error ( NULL, error, para_vars.iproc,
para_vars.root );
pcomm_set ( input_vars.npey, input_vars.npez, ¶_vars, &ierr );
t4 = wtime();
time_vars.tparset = time_vars.tparset + t4 - t3;
/***********************************************************************
* Setup problem
***********************************************************************/
setup ( &input_vars, ¶_vars, &time_vars, &geom_vars, &sn_vars,
&data_vars, &solvar_vars, &control_vars, &mms_vars, fp_out,
&ierr, &error );
/***********************************************************************
* Call for the problem solution
***********************************************************************/
translv ( &input_vars, ¶_vars, &time_vars, &geom_vars, &sn_vars,
&data_vars, &control_vars, &solvar_vars, &mms_vars,
&sweep_vars, &dim_sweep_vars, fp_out, &ierr, &error );
/***********************************************************************
* Output the results. Print the timing summary
***********************************************************************/
output ( &input_vars, ¶_vars, &time_vars, &geom_vars, &data_vars,
&sn_vars, &control_vars, &mms_vars, &solvar_vars, &sweep_vars,
fp_out, &ierr, &error );
if ( para_vars.iproc == para_vars.root ) time_summ ( fp_out, &time_vars );
/***********************************************************************
* Final cleanup: deallocate, close output file, end the program
***********************************************************************/
dealloc_input ( 3, &sn_vars, &data_vars, &mms_vars );
dealloc_solve ( 3, &geom_vars, &solvar_vars, &control_vars );
t5 = wtime();
time_vars.tsnap = t5 - t1;
if ( para_vars.iproc == para_vars.root )
{
fprintf ( fp_out, " Total Execution time"
" %.4E\n\n", time_vars.tsnap );
fprintf ( fp_out, " Grind Time (nanoseconds)"
" %.4E\n\n", time_vars.tgrind );
fprintf ( fp_out,
"****************************************"
"****************************************\n" );
}
ierr = close_file ( fp_out, outputFile, &error, para_vars.iproc, para_vars.root );
FREE ( outputFile );
bcast_i_scalar ( &ierr, para_vars.comm_snap, para_vars.root, para_vars.nproc );
if ( ierr != 0 )
{
print_error ( 0, error, para_vars.iproc, para_vars.root );
FREE ( error );
stop_run ( 0, 0, 0, ¶_vars, &sn_vars, &data_vars, &mms_vars,
&geom_vars, &solvar_vars, &control_vars );
}
if ( control_vars.otrdone )
{
FREE ( error );
stop_run ( 0, 0, 1, ¶_vars, &sn_vars, &data_vars, &mms_vars,
&geom_vars, &solvar_vars, &control_vars );
}
else
{
FREE ( error );
stop_run ( 0, 0, 2, ¶_vars, &sn_vars, &data_vars, &mms_vars,
&geom_vars, &solvar_vars, &control_vars );
}
return 0;
}
int
main(int argc, register char** argv)
{
register int n;
register char* s;
char* args;
char* codes;
char** av;
char** ap;
int i;
int count;
int len;
int traverse;
int size;
Dir_t* firstdir;
Dir_t* lastdir;
Exnode_t* x;
Exnode_t* y;
Ftw_t ftw;
Finddisc_t disc;
setlocale(LC_ALL, "");
error_info.id = "tw";
av = argv + 1;
args = 0;
codes = 0;
count = 0;
size = 0;
traverse = 1;
firstdir = lastdir = newof(0, Dir_t, 1, 0);
firstdir->name = ".";
state.action = LIST;
state.cmdflags = CMD_EXIT|CMD_IGNORE|CMD_IMPLICIT|CMD_NEWLINE;
state.errexit = EXIT_QUIT;
state.ftwflags = ftwflags()|FTW_DELAY;
state.select = ALL;
state.separator = '\n';
memset(&disc, 0, sizeof(disc));
for (;;)
{
switch (optget(argv, usage))
{
case 'a':
args = opt_info.arg;
state.cmdflags |= CMD_POST;
continue;
case 'c':
if ((count = opt_info.num) < 0)
error(3, "argument count must be >= 0");
continue;
case 'd':
lastdir = lastdir->next = newof(0, Dir_t, 1, 0);
lastdir->name = opt_info.arg;
continue;
case 'e':
compile(opt_info.arg, 0);
continue;
case 'f':
state.pattern = opt_info.arg;
continue;
case 'i':
state.ignore = 1;
continue;
case 'l':
state.localfs = 1;
continue;
case 'm':
state.intermediate = 1;
continue;
case 'n':
traverse = 0;
continue;
case 'p':
state.ftwflags |= FTW_TWICE;
continue;
case 'q':
state.cmdflags |= CMD_QUERY;
continue;
case 'r':
state.ftwflags |= FTW_RECURSIVE;
continue;
case 's':
if ((size = opt_info.num) < 0)
error(3, "command size must be >= 0");
continue;
case 't':
state.cmdflags |= CMD_TRACE;
continue;
case 'x':
state.errexit = opt_info.arg ? opt_info.num : EXIT_QUIT;
continue;
case 'z':
if (s = sfgetr(sfstdin, '\n', 1))
{
if (!(s = strdup(s)))
error(ERROR_SYSTEM|3, "out of space");
n = state.snapshot.format.delim = *s++;
state.snapshot.format.path = s;
if (!(s = strchr(s, n)))
{
osnap:
error(3, "invalid snapshot on standard input");
}
*s++ = 0;
if (!streq(state.snapshot.format.path, SNAPSHOT_ID))
goto osnap;
state.snapshot.format.path = s;
if (!(s = strchr(s, n)))
goto osnap;
*s++ = 0;
state.snapshot.format.easy = s;
if (!(s = strchr(s, n)))
goto osnap;
*s++ = 0;
if (*(state.snapshot.format.hard = s))
{
if (!(s = strchr(s, n)))
goto osnap;
*s = 0;
}
else
state.snapshot.format.hard = 0;
state.snapshot.sp = sfstdin;
state.snapshot.prev = sfgetr(sfstdin, '\n', 0);
}
else
{
state.snapshot.format.path = SNAPSHOT_PATH;
state.snapshot.format.easy = SNAPSHOT_EASY;
state.snapshot.format.hard = SNAPSHOT_HARD;
state.snapshot.format.delim = SNAPSHOT_DELIM[0];
}
if (!(state.snapshot.tmp = sfstropen()))
error(ERROR_SYSTEM|3, "out of space");
compile("sort:name;", 0);
continue;
case 'C':
state.ftwflags |= FTW_NOSEEDOTDIR;
continue;
case 'D':
error_info.trace = -opt_info.num;
continue;
case 'E':
compile(opt_info.arg, 1);
continue;
case 'F':
codes = opt_info.arg;
continue;
case 'G':
disc.flags |= FIND_GENERATE;
if (streq(opt_info.arg, "old"))
disc.flags |= FIND_OLD;
else if (streq(opt_info.arg, "gnu") || streq(opt_info.arg, "locate"))
disc.flags |= FIND_GNU;
else if (streq(opt_info.arg, "type"))
disc.flags |= FIND_TYPE;
else if (streq(opt_info.arg, "?"))
{
error(2, "formats are { default|dir type old gnu|locate }");
return 0;
}
else if (!streq(opt_info.arg, "-") && !streq(opt_info.arg, "default") && !streq(opt_info.arg, "dir"))
error(3, "%s: invalid find codes format -- { default|dir type old gnu|locate } expected", opt_info.arg);
continue;
case 'H':
state.ftwflags |= FTW_META|FTW_PHYSICAL;
continue;
case 'I':
state.icase = 1;
continue;
case 'L':
state.ftwflags &= ~(FTW_META|FTW_PHYSICAL|FTW_SEEDOTDIR);
continue;
case 'P':
state.ftwflags &= ~FTW_META;
state.ftwflags |= FTW_PHYSICAL;
continue;
case 'S':
state.separator = *opt_info.arg;
continue;
case 'X':
state.ftwflags |= FTW_MOUNT;
continue;
case '?':
error(ERROR_USAGE|4, "%s", opt_info.arg);
continue;
case ':':
error(2, "%s", opt_info.arg);
continue;
}
break;
}
argv += opt_info.index;
argc -= opt_info.index;
if (error_info.errors)
error(ERROR_USAGE|4, "%s", optusage(NiL));
/*
* do it
*/
if (state.snapshot.tmp)
sfprintf(sfstdout, "%c%s%c%s%c%s%c%s%c\n",
state.snapshot.format.delim, SNAPSHOT_ID,
state.snapshot.format.delim, state.snapshot.format.path,
state.snapshot.format.delim, state.snapshot.format.easy,
state.snapshot.format.delim, state.snapshot.format.hard ? state.snapshot.format.hard : "",
state.snapshot.format.delim);
if (x = exexpr(state.program, "begin", NiL, 0))
eval(x, NiL);
if ((x = exexpr(state.program, "select", NiL, INTEGER)) || (x = exexpr(state.program, NiL, NiL, INTEGER)))
state.select = x;
if (!(state.ftwflags & FTW_PHYSICAL))
state.ftwflags &= ~FTW_DELAY;
memset(&ftw, 0, sizeof(ftw));
ftw.path = ftw.name = "";
if (traverse)
{
if (x = exexpr(state.program, "action", NiL, 0))
state.action = x;
if (x = exexpr(state.program, "sort", NiL, 0))
{
state.sortkey = x;
y = 0;
for (;;)
{
switch (x->op)
{
case ',':
y = x->data.operand.right;
/*FALLTHROUGH*/
case '!':
case '~':
case S2B:
case X2I:
x = x->data.operand.left;
continue;
case ID:
if (!(x = y))
break;
y = 0;
continue;
default:
error(3, "invalid sort identifier (op 0x%02x)", x->op);
break;
}
break;
}
state.sort = order;
}
if (*argv && (*argv)[0] == '-' && (*argv)[1] == 0)
{
state.ftwflags |= FTW_LIST;
argv++;
argc--;
}
if (*argv || args || count || !(state.cmdflags & CMD_IMPLICIT))
{
Cmddisc_t disc;
CMDDISC(&disc, state.cmdflags, errorf);
state.cmd = cmdopen(argv, count, size, args, &disc);
state.ftwflags |= FTW_DOT;
}
else
state.cmdflags &= ~CMD_IMPLICIT;
if (codes && (disc.flags & FIND_GENERATE))
{
char* p;
Dir_t* dp;
char pwd[PATH_MAX];
char tmp[PATH_MAX];
disc.version = FIND_VERSION;
if (state.cmdflags & CMD_TRACE)
disc.flags |= FIND_TYPE;
if (state.cmdflags & CMD_QUERY)
disc.flags |= FIND_OLD;
disc.errorf = errorf;
if (!(state.find = findopen(codes, NiL, NiL, &disc)))
exit(2);
if (disc.flags & FIND_TYPE)
{
state.act = ACT_CODETYPE;
compile("_tw_init:mime;", 0);
state.magicdisc.flags |= MAGIC_MIME;
}
else
state.act = ACT_CODE;
state.icase = 1;
state.pattern = 0;
state.sort = order;
if (!state.program)
compile("1", 0);
if (!(state.sortkey = newof(0, Exnode_t, 1, 0)) || !(state.sortkey->data.variable.symbol = (Exid_t*)dtmatch(state.program->symbols, "name")))
error(ERROR_SYSTEM|3, "out of space");
state.sortkey->op = ID;
s = p = 0;
for (dp = (firstdir == lastdir) ? firstdir : firstdir->next; dp; dp = dp->next)
{
if (*(s = dp->name) == '/')
sfsprintf(tmp, sizeof(tmp), "%s", s);
else if (!p && !(p = getcwd(pwd, sizeof(pwd))))
error(ERROR_SYSTEM|3, "cannot determine pwd path");
else
sfsprintf(tmp, sizeof(tmp), "%s/%s", p, s);
pathcanon(tmp, sizeof(tmp), PATH_PHYSICAL);
if (!(dp->name = strdup(tmp)))
error(ERROR_SYSTEM|3, "out of space [PATH_PHYSICAL]");
}
}
else if (state.snapshot.tmp)
state.act = ACT_SNAPSHOT;
else if (state.cmdflags & CMD_IMPLICIT)
state.act = ACT_CMDARG;
else if (state.action == LIST)
state.act = ACT_LIST;
else if (state.action)
state.act = ACT_EVAL;
if (state.intermediate)
{
state.actII = state.act;
state.act = ACT_INTERMEDIATE;
}
if (state.pattern)
{
disc.version = FIND_VERSION;
if (state.icase)
disc.flags |= FIND_ICASE;
disc.errorf = errorf;
disc.dirs = ap = av;
if (firstdir != lastdir)
firstdir = firstdir->next;
do {*ap++ = firstdir->name;} while (firstdir = firstdir->next);
*ap = 0;
if (!(state.find = findopen(codes, state.pattern, NiL, &disc)))
exit(1);
state.ftwflags |= FTW_TOP;
n = state.select == ALL ? state.act : ACT_EVAL;
while (s = findread(state.find))
{
switch (n)
{
case ACT_CMDARG:
if ((i = cmdarg(state.cmd, s, strlen(s))) >= state.errexit)
exit(i);
break;
case ACT_LIST:
sfputr(sfstdout, s, '\n');
break;
default:
ftwalk(s, tw, state.ftwflags, NiL);
break;
}
}
}
else if (state.ftwflags & FTW_LIST)
{
sfopen(sfstdin, NiL, "rt");
n = state.select == ALL && state.act == ACT_CMDARG;
for (;;)
{
if (s = sfgetr(sfstdin, state.separator, 1))
len = sfvalue(sfstdin) - 1;
else if (state.separator != '\n')
{
state.separator = '\n';
continue;
}
else if (s = sfgetr(sfstdin, state.separator, -1))
len = sfvalue(sfstdin);
else
break;
if (!n)
ftwalk(s, tw, state.ftwflags, NiL);
else if ((i = cmdarg(state.cmd, s, len)) >= state.errexit)
exit(i);
}
if (sferror(sfstdin))
error(ERROR_SYSTEM|2, "input read error");
}
else if (firstdir == lastdir)
ftwalk(firstdir->name, tw, state.ftwflags, state.sort);
else
{
ap = av;
while (firstdir = firstdir->next)
*ap++ = firstdir->name;
*ap = 0;
ftwalk((char*)av, tw, state.ftwflags|FTW_MULTIPLE, state.sort);
}
if (state.cmd && (i = cmdflush(state.cmd)) >= state.errexit)
exit(i);
if (state.find && (findclose(state.find) || state.finderror))
exit(2);
}
else if (state.select)
error_info.errors = eval(state.select, &ftw) == 0;
if (x = exexpr(state.program, "end", NiL, 0))
eval(x, &ftw);
if (sfsync(sfstdout))
error(ERROR_SYSTEM|2, "write error");
exit(error_info.errors != 0);
}
static void
act(register Ftw_t* ftw, int op)
{
char* s;
Sfio_t* fp;
int i;
int j;
int k;
int n;
int r;
switch (op)
{
case ACT_CMDARG:
if ((i = cmdarg(state.cmd, ftw->path, ftw->pathlen)) >= state.errexit)
exit(i);
break;
case ACT_CODE:
if (findwrite(state.find, ftw->path, ftw->pathlen, (ftw->info & FTW_D) ? "system/dir" : (char*)0))
state.finderror = 1;
break;
case ACT_CODETYPE:
fp = sfopen(NiL, PATH(ftw), "r");
if (findwrite(state.find, ftw->path, ftw->pathlen, magictype(state.magic, fp, PATH(ftw), &ftw->statb)))
state.finderror = 1;
if (fp)
sfclose(fp);
break;
case ACT_EVAL:
eval(state.action, ftw);
break;
case ACT_INTERMEDIATE:
intermediate(ftw, ftw->path);
break;
case ACT_LIST:
sfputr(sfstdout, ftw->path, '\n');
break;
case ACT_SNAPSHOT:
print(state.snapshot.tmp, ftw, state.snapshot.format.path);
sfputc(state.snapshot.tmp, state.snapshot.format.delim);
i = sfstrtell(state.snapshot.tmp);
print(state.snapshot.tmp, ftw, state.snapshot.format.easy);
j = sfstrtell(state.snapshot.tmp);
s = sfstrbase(state.snapshot.tmp);
r = SNAPSHOT_new;
if (!state.snapshot.prev)
k = 1;
else
{
do
{
if (!(k = urlcmp(state.snapshot.prev, s, state.snapshot.format.delim)))
{
r = SNAPSHOT_changed;
if (!(k = memcmp(state.snapshot.prev + i, s + i, j - i) || state.snapshot.prev[j] != state.snapshot.format.delim))
{
if ((n = (int)sfvalue(sfstdin)) > 4 && state.snapshot.prev[n-2] == state.snapshot.format.delim)
{
sfwrite(sfstdout, state.snapshot.prev, n - 4);
sfputc(sfstdout, '\n');
}
else
sfwrite(sfstdout, state.snapshot.prev, n);
}
}
else if (k > 0)
break;
else if (k < 0 && (n = (int)sfvalue(sfstdin)) > 4 && (state.snapshot.prev[n-2] != state.snapshot.format.delim || state.snapshot.prev[n-3] != SNAPSHOT_deleted))
{
sfwrite(sfstdout, state.snapshot.prev, n - (state.snapshot.prev[n-2] == state.snapshot.format.delim ? 4 : 1));
sfputc(sfstdout, state.snapshot.format.delim);
sfputc(sfstdout, SNAPSHOT_deleted);
sfputc(sfstdout, state.snapshot.format.delim);
sfputc(sfstdout, '\n');
if (state.cmdflags & CMD_TRACE)
error(1, "%s deleted", ftw->path);
}
if (!(state.snapshot.prev = sfgetr(sfstdin, '\n', 0)))
break;
} while (k < 0);
}
if (k)
{
if (state.snapshot.format.hard && (ftw->info & FTW_F))
{
sfputc(state.snapshot.tmp, state.snapshot.format.delim);
print(state.snapshot.tmp, ftw, state.snapshot.format.hard);
}
sfputc(state.snapshot.tmp, state.snapshot.format.delim);
sfputc(state.snapshot.tmp, r);
sfputc(state.snapshot.tmp, state.snapshot.format.delim);
sfputr(sfstdout, sfstruse(state.snapshot.tmp), '\n');
if (state.cmdflags & CMD_TRACE)
error(1, "%s %s", ftw->path, r == SNAPSHOT_new ? "new" : "changed");
}
else
sfstrseek(state.snapshot.tmp, SEEK_SET, 0);
break;
}
}
int main(int argc, char *argv[])
{
/* Important definitions */
// Lengths
size_t N = 0; // Length of time series
size_t M = 0; // Length of sampling vector (number of frequencies)
// Filenames
char inname[100];
char outname[100];
char logname[100];
// Sampling
double low, high, rate;
// Options
int quiet = 0;
int unit = 1;
int prep = 1;
int autosamp = 0;
int fast = 0;
int useweight = 0;
int Nclean = 1;
int filter = 0;
/* Process command line arguments and return line count of the input file */
N = cmdarg(argc, argv, inname, outname, &quiet, &unit, &prep, &low, &high,\
&rate, &autosamp, &fast, &useweight, NULL, NULL, &Nclean,\
&filter, NULL, NULL);
// Pretty print
if ( quiet == 0 || fast == 1){
if ( useweight != 0 )
printf("\nCLEANing the time series \"%s\" using weights...\n",\
inname);
else
printf("\nCLEANing the time series \"%s\" without weights...\n",\
inname);
}
/* Read data (and weights) from the input file */
if ( quiet == 0 ) printf(" - Reading input\n");
double* time = malloc(N * sizeof(double));
double* flux = malloc(N * sizeof(double));
double* weight = malloc(N * sizeof(double));
readcols(inname, time, flux, weight, N, useweight, unit, quiet);
// Do if fast-mode is not activated
if ( fast == 0 ) {
// Calculate Nyquist frequency
double* dt = malloc(N-1 * sizeof(double));
double nyquist;
arr_diff(time, dt, N);
nyquist = 1.0 / (2.0 * arr_median(dt, N-1)) * 1e6; // microHz !
free(dt);
// Automatic or manual sampling?
int oversamp;
if ( autosamp != 0 ) {
low = 5.0;
high = nyquist;
oversamp = 4;
}
else {
oversamp = (int) rate;
}
// Calculate N times oversampling (in microHz!)
double minsamp = 1.0e6 / (oversamp * (time[N-1] - time[0]));
rate = minsamp;
// Display info?
if ( quiet == 0 ){
printf(" -- INFO: Length of time series = %li\n", N);
printf(" -- INFO: Nyquist frequency = %.2lf microHz\n", nyquist);
printf(" -- INFO: Using %i times oversampling = %.3lf microHz\n",\
oversamp, minsamp);
}
}
else {
// Only set the N times oversampling
int oversamp = (int) rate;
double minsamp = 1.0e6 / (oversamp * (time[N-1] - time[0]));
rate = minsamp;
}
/* Prepare for power spectrum */
// Get length of sampling vector
M = arr_util_getstep(low, high, rate);
// Fill sampling vector with cyclic frequencies
double* freq = malloc(M * sizeof(double));
arr_init_linspace(freq, low, rate, M);
if ( quiet == 0 )
printf(" -- INFO: Number of sampling frequencies = %li\n", M);
// Subtract the mean to avoid "zero-frequency" problems
double fmean = 0;
if ( prep != 0 ) {
if ( quiet == 0 ) printf(" - Subtracting the mean from time series\n");
fmean = arr_mean(flux, N);
arr_sca_add(flux, -fmean, N);
}
else {
if ( quiet == 0 )
printf(" - Time series used *without* mean subtraction!\n");
}
/* Prepare file for writing the CLEAN-output */
// Create log-file
strcpy(logname, outname);
strcat(logname, ".cleanlog");
FILE* logfile = fopen(logname, "w");
// Write header
fprintf(logfile, "# ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~"\
"~~~~~~~~~~\n");
fprintf(logfile, "# Log of CLEAN on \"%s\"\n", inname);
fprintf(logfile, "# Interval: [%.2lf, %.2lf] microHz\n", low, high);
fprintf(logfile, "# Finding %i frequencies\n", Nclean);
fprintf(logfile, "# \n");
fprintf(logfile, "# %8s %11s %11s %12s %12s\n", "Number", "Frequency",\
"Power", "Alpha", "Beta");
fprintf(logfile, "# ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~"\
"~~~~~~~~~~\n");
/* Find and clean peaks */
// Init variables
double fmax, alpmax, betmax, powmax;
// Display info
if ( quiet == 0 ) {
printf(" - CLEANing %i frequencies in the range %.1lf to %.1lf"\
" microHz\n", Nclean, low, high);
printf("\n %9s %11s %11s\n", "Number", "Frequency", "Power");
}
// Enter CLEAN-loop
for (int i = 0; i < Nclean; ++i) {
// Display progress
if ( quiet == 0 ) printf(" %6i", i+1);
// Reset variables
fmax = 0;
alpmax = 0;
betmax = 0;
powmax = 0;
// Call with or without weights
fouriermax(time, flux, weight, freq, N, M, &fmax, &alpmax, &betmax,\
useweight);
// Calculate the power and write to log
powmax = alpmax*alpmax + betmax*betmax;
fprintf(logfile, " %6i %15.6lf %12.6lg %12.6lf %12.6lf\n", i+1, fmax,\
powmax, alpmax, betmax);
if ( quiet == 0) printf(" %15.6lf %12.6lg \n", fmax, powmax);
// Remove frequency from time series
for (int j = 0; j < N; ++j) {
flux[j] = flux[j] - alpmax * sin( PI2micro*fmax * time[j] ) - \
betmax * cos( PI2micro*fmax * time[j] );
}
}
// Final touch
fclose(logfile);
if ( quiet == 0 ) printf("\n");
/* Write CLEANed time series to file */
if ( quiet == 0 ) printf(" - Saving to file \"%s\"\n", outname);
// Add the mean to the time series data again
if ( prep != 0 ) arr_sca_add(flux, fmean, N);
// Save to file
writecols3(outname, time, flux, weight, N, useweight, unit);
/* Free data */
free(time);
free(flux);
free(weight);
free(freq);
/* Done! */
if ( quiet == 0 || fast ==1 ) printf("Done!\n\n");
return 0;
}