assoc_options_t *new_assoc_cli_options(void) {
assoc_options_t *options = (assoc_options_t*) malloc (sizeof(assoc_options_t));
options->num_options = NUM_ASSOC_OPTIONS;
options->chisq = arg_lit0(NULL, "chisq", "Chi-square association test");
options->fisher = arg_lit0(NULL, "fisher", "Fisher's exact test");
return options;
}
stats_options_t *new_stats_cli_options() {
stats_options_t *options = (stats_options_t*) malloc (sizeof(stats_options_t));
options->sample_stats = arg_lit0(NULL, "samples", "Get statistics about samples");
options->variant_stats = arg_lit0(NULL, "variants", "Get statistics about variants, both per variant and per file (default)");
options->num_options = NUM_STATS_OPTIONS;
return options;
}
int main (int argc, char **argv) {
void *argtable[] = {
help = arg_lit0("h","help","print this screen"),
verbose = arg_lit0("v","verbose","tell me everything"),
fsyslog = arg_lit0(NULL,"syslog","use syslog"),
cachepath = arg_file1(NULL,NULL,"cachepath","directory or .cdb database file"),
netaddress0 = arg_file1(NULL,NULL,"read_address","zmq read network address"),
netaddress1 = arg_file1(NULL,NULL,"write_address","zmq write network address"),
end = arg_end(20),
};
int32_t nerrors = arg_parse(argc,argv,argtable);
if (help->count) {
fprintf(stdout,"tmpcache %s - version 0\n",__FUNCTION__);
arg_print_syntaxv(stdout,argtable,"\n\n");
arg_print_glossary (stdout,argtable,"%-25s %s\n");
goto finish;
}
if (verbose->count) {
fprintf(stdout,"tmpcache host - version 0\n");
int32_t major,minor,patch;
zmq_version (&major,&minor,&patch);
fprintf(stdout,"compiled with zmq support %d.%d.%d\n",major,minor,patch);
goto finish;
}
if (nerrors) {
arg_print_errors (stdout,end,"");
arg_print_syntaxv(stdout,argtable,"\n\n");
goto finish;
}
u_term = 0;
signal (SIGINT,signalhandler);
signal (SIGTERM,signalhandler);
if (fsyslog->count)
openlog (NULL,LOG_PID|LOG_NDELAY,LOG_USER);
void *read (void *arg) {
tc_readconfig_t *config = (tc_readconfig_t *)arg;
if (fsyslog->count)
syslog (LOG_INFO,"reading cache from %s @ %s",btocstr(config->cachepath),btocstr(config->address));
tc_readfromcache (config);
if (fsyslog->count)
syslog (LOG_INFO,"closing cache %s @ %s for reading",btocstr(config->cachepath),btocstr(config->address));
}
gwas_options_t *new_gwas_cli_options(void) {
gwas_options_t *options = (gwas_options_t*) malloc (sizeof(gwas_options_t));
options->num_options = NUM_GWAS_OPTIONS;
options->assoc = arg_lit0(NULL, "assoc", "Basic case/control association test");
options->fisher = arg_lit0(NULL, "fisher", "Fisher's exact test");
options->tdt = arg_lit0(NULL, "tdt", "Transmission disequilibrium test");
return options;
}
merge_options_t *new_merge_cli_options() {
merge_options_t *options = (merge_options_t*) malloc (sizeof(merge_options_t));
options->num_options = NUM_MERGE_OPTIONS;
options->input_files = arg_str1(NULL, "vcf-list", NULL, "List of comma-separated input VCF files");
options->missing_mode = arg_str0(NULL, "missing-mode", NULL, "How to fill missing genotypes (missing = ./., reference = 0/0)");
options->info_fields = arg_str0(NULL, "info-fields", NULL, "Information to generate in the new INFO column");
options->copy_filter = arg_lit0(NULL, "copy-filter", "Whether to copy the FILTER column from the original files into the samples");
options->copy_info = arg_lit0(NULL, "copy-info", "Whether to copy the INFO column from the original files into the samples");
return options;
}
void parse_command_line(int argc, char* argv[])
{
// if the parsing of the arguments was unsuccessful
int nerrors;
// Define argument table structs
python_folder = arg_file0 ( NULL, "py-folder", "<path to file>", "Path to folder (relative or absolute) that contains python script (default: lpfw-pygui)" );
log_debug = arg_int0 ( NULL, "log-debug", "<1/0 for yes/no>", "Enable debug messages logging" );
struct arg_lit *help = arg_lit0 ( NULL, "help", "Display this help screen" );
struct arg_lit *version = arg_lit0 ( NULL, "version", "Display the current version" );
struct arg_end *end = arg_end ( 10 );
void *argtable[] = {python_folder, log_debug, help, version, end};
// Set default values
char *python_folder_pointer = malloc(strlen("lpfw-pygui")+1);
strcpy (python_folder_pointer, "lpfw-pygui");
python_folder->filename[0] = python_folder_pointer;
* ( log_debug->ival ) = 0;
if ( arg_nullcheck ( argtable ) != 0 )
{
printf ( "Error: insufficient memory\n" );
exit(0);
}
nerrors = arg_parse ( argc, argv, argtable );
if ( nerrors == 0 )
{
if ( help->count == 1 )
{
printf ( "Leopard Flower frontend :\n Syntax and help:\n" );
arg_print_glossary ( stdout, argtable, "%-43s %s\n" );
exit (0);
}
else if ( version->count == 1 )
{
printf ( "%s\n", VERSION );
exit (0);
}
}
else if ( nerrors > 0 )
{
arg_print_errors ( stdout, end, "Leopard Flower frontend" );
printf ( "Leopard Flower frontend:\n Syntax and help:\n" );
arg_print_glossary ( stdout, argtable, "%-43s %s\n" );
exit (1);
}
// Free memory - don't do this cause args needed later on
// arg_freetable(argtable, sizeof (argtable) / sizeof (argtable[0]));
}
void register_ethernet()
{
eth_event_group = xEventGroupCreate();
tcpip_adapter_init();
ESP_ERROR_CHECK(esp_event_loop_init(eth_event_handler, NULL));
eth_config_t config = DEFAULT_ETHERNET_PHY_CONFIG;
config.phy_addr = CONFIG_PHY_ADDRESS;
config.gpio_config = eth_gpio_config_rmii;
config.tcpip_input = tcpip_adapter_eth_input;
config.clock_mode = CONFIG_PHY_CLOCK_MODE;
#ifdef CONFIG_PHY_USE_POWER_PIN
/* Replace the default 'power enable' function with an example-specific one
that toggles a power GPIO. */
config.phy_power_enable = phy_device_power_enable_via_gpio;
#endif
ESP_ERROR_CHECK(esp_eth_init(&config));
eth_control_args.control = arg_str1(NULL, NULL, "<start|stop|info>", "Start/Stop Ethernet or Get info of Ethernet");
eth_control_args.end = arg_end(1);
const esp_console_cmd_t cmd = {
.command = "ethernet",
.help = "Control Ethernet interface",
.hint = NULL,
.func = eth_cmd_control,
.argtable = ð_control_args
};
ESP_ERROR_CHECK(esp_console_cmd_register(&cmd));
iperf_args.ip = arg_str0("c", "client", "<ip>",
"run in client mode, connecting to <host>");
iperf_args.server = arg_lit0("s", "server", "run in server mode");
iperf_args.udp = arg_lit0("u", "udp", "use UDP rather than TCP");
iperf_args.port = arg_int0("p", "port", "<port>",
"server port to listen on/connect to");
iperf_args.interval = arg_int0("i", "interval", "<interval>",
"seconds between periodic bandwidth reports");
iperf_args.time = arg_int0("t", "time", "<time>", "time in seconds to transmit for (default 10 secs)");
iperf_args.abort = arg_lit0("a", "abort", "abort running iperf");
iperf_args.end = arg_end(1);
const esp_console_cmd_t iperf_cmd = {
.command = "iperf",
.help = "iperf command",
.hint = NULL,
.func = ð_cmd_iperf,
.argtable = &iperf_args
};
ESP_ERROR_CHECK(esp_console_cmd_register(&iperf_cmd));
}
bool Application::initArgtable()
{
const char* progname = "revisor";
struct arg_str* l = arg_str0("l", NULL, "<interface>", "Interface to listen, default '127.0.0.1'");
struct arg_int* p = arg_int0("p", NULL, "<port number>", "Port to listen, default 8080");
struct arg_lit* h = arg_lit0("h", "help", "This help message");
struct arg_end* end = arg_end(20);
void *argtable[] = {l, p, h, end};
int nerrors = arg_parse(argc, argv, argtable);
// special case: '--help' takes precedence over error reporting
if (h->count > 0) {
printf("Usage: %s", progname);
arg_print_syntax(stdout, argtable, "\n");
arg_print_glossary(stdout, argtable, " %-25s %s\n");
return false;
}
if (nerrors > 0) {
arg_print_errors(stdout, end, progname);
return false;
}
if (l->count > 0) {
listeningInterface = l->sval[0];
}
if (p->count > 0) {
portNumber = *p->ival;
}
arg_freetable(argtable, sizeof(argtable) / sizeof(argtable[0]));
return true;
}
int main(int argc, char **argv)
{
struct arg_xxx *scalar = arg_xxx1(NULL, NULL, "<scalar>", 0.0, 1.0, "<double> value in range [0.0, 1.0]");
struct arg_xxx *x = arg_xxx0("x", NULL, "<double>", -1.0, 1.0, "x coeff in range [-1.0, 1.0]");
struct arg_xxx *y = arg_xxxn("y", NULL, "<double>", 0,argc+2, 0.5, 0.9, "y coeff in range [0.5, 0.9]");
struct arg_lit *help = arg_lit0(NULL,"help", "print this help and exit");
struct arg_end *end = arg_end(20);
void* argtable[] = {scalar,x,y,help,end};
const char* progname = "argcustom";
int nerrors;
int exitcode=0;
int i;
/* verify the argtable[] entries were allocated sucessfully */
if (arg_nullcheck(argtable) != 0)
{
/* NULL entries were detected, some allocations must have failed */
printf("%s: insufficient memory\n",progname);
exitcode=1;
goto exit;
}
/* Parse the command line as defined by argtable[] */
nerrors = arg_parse(argc,argv,argtable);
/* special case: '--help' takes precedence over error reporting */
if (help->count > 0)
{
printf("Usage: %s", progname);
arg_print_syntax(stdout,argtable,"\n");
printf("This program demonstrates the use of the argtable2 library\n");
printf("for parsing command line arguments.\n");
arg_print_glossary(stdout,argtable," %-25s %s\n");
exitcode=0;
goto exit;
}
/* If the parser returned any errors then display them and exit */
if (nerrors > 0)
{
/* Display the error details contained in the arg_end struct.*/
arg_print_errors(stdout,end,progname);
printf("Try '%s --help' for more information.\n",progname);
exitcode=1;
goto exit;
}
/* only get here is command line arguments were parsed sucessfully */
printf("scalar = %f\n", scalar->data[0]);
if (x->count > 0)
printf("x = %f\n", x->data[0]);
for (i=0; i<y->count; i++)
printf("y[%d] = %f\n", i, y->data[i]);
exit:
/* deallocate each non-null entry in argtable[] */
arg_freetable(argtable,sizeof(argtable)/sizeof(argtable[0]));
return exitcode;
}
static
int dslink_parse_opts(int argc,
char **argv,
DSLinkConfig *config) {
int ret = 0;
struct arg_lit *help;
struct arg_str *broker, *log;
struct arg_end *end;
void *argTable[] = {
help = arg_lit0("h", "help", "Displays this help menu"),
broker = arg_str1("b", "broker", "url", "Sets the broker URL to connect to"),
log = arg_str0("l", "log", "log type", "Sets the logging level"),
end = arg_end(5)
};
if (arg_nullcheck(argTable) != 0) {
return DSLINK_ALLOC_ERR;
}
int errs = arg_parse(argc, argv, argTable);
if (help->count > 0) {
printf("Usage: <opts>\n");
arg_print_glossary(stdout, argTable, " %-25s %s\n");
ret = 1;
goto exit;
}
if (errs > 0) {
dslink_print_help();
arg_print_errors(stdout, end, ":");
ret = 1;
goto exit;
}
config->broker_url = broker->sval[0];
if (log->count > 0) {
char lvl[8];
const char *src = log->sval[0];
size_t len = strlen(src);
if (len > sizeof(lvl)) {
len = sizeof(lvl);
}
memcpy(lvl, src, len);
if (dslink_log_set_lvl(lvl, len) != 0) {
printf("Invalid log level: %s\n", lvl);
dslink_print_help();
ret = 1;
goto exit;
}
}
exit:
arg_freetable(argTable, sizeof(argTable) / sizeof(argTable[0]));
return ret;
}
int main(int argc, char * argv[]) {
void* argtable[] = {
input = arg_filen( "i", "input", "<string>", 0, 100, "input file")
, o_validate = arg_strn( "v", "validate", "<string>", 0, 10, "validate operations")
, o_h = arg_file0( NULL, "output-h", "<string>", "output h file dir")
, o_lib_c = arg_file0( NULL, "output-lib-c", "<string>", "output c lib file")
, o_lib_c_arg = arg_str0( NULL, "output-lib-c-arg", "<string>", "output c lib file")
, o_lib_bin = arg_file0( NULL, "output-lib-bin", "<string>", "output c lib file")
, help = arg_lit0( NULL, "help", "print this help and exit")
, end = arg_end(20)
};
struct error_monitor em_buf;
error_monitor_t em;
int rv;
int nerrors;
cpe_error_monitor_init(&em_buf, cpe_error_log_to_consol, 0);
em = &em_buf;
rv = -1;
if (arg_nullcheck(argtable) != 0) {
CPE_ERROR(em, "init arg table fail!");
goto exit;
}
nerrors = arg_parse(argc,argv,argtable);
if (help->count > 0) {
printf("Usage: %s", argv[0]);
arg_print_syntax(stdout,argtable,"\n");
rv = 0;
goto exit;
}
if (nerrors > 0) {
arg_print_errors(stdout, end, argv[0]);
printf("Try '%s --help' for more information.\n", argv[0]);
goto exit;
}
rv = tools_main(em);
exit:
arg_freetable(argtable, sizeof(argtable) / sizeof(argtable[0]));
return rv;
}
int main(int argc, char *argv[])
{
/* the global arg_xxx structs are initialised within the argtable */
void *argtable[] = {
help = arg_lit0(NULL, "help", "display this help and exit"),
version = arg_lit0(NULL, "version", "display version info and exit"),
a = arg_lit0("a", NULL,"the -a option"),
b = arg_lit0("b", NULL, "the -b option"),
c = arg_lit0("c", NULL, "the -c option"),
scal = arg_int0(NULL, "scalar", "<n>", "foo value"),
verb = arg_lit0("v", "verbose", "verbose output"),
o = arg_file0("o", NULL, "myfile", "output file"),
file = arg_filen(NULL, NULL, "<file>", 0, 100, "input files"),
end = arg_end(20),
};
int exitcode = 0;
char progname[] = "testargtable3.exe";
int nerrors;
nerrors = arg_parse(argc,argv,argtable);
/* special case: '--help' takes precedence over error reporting */
if (help->count > 0)
{
printf("Usage: %s", progname);
arg_print_syntax(stdout, argtable, "\n");
printf("List information about the FILE(s) "
"(the current directory by default).\n\n");
arg_print_glossary(stdout, argtable, " %-25s %s\n");
exitcode = 0;
goto exit;
}
/* If the parser returned any errors then display them and exit */
if (nerrors > 0)
{
/* Display the error details contained in the arg_end struct.*/
arg_print_errors(stdout, end, progname);
printf("Try '%s --help' for more information.\n", progname);
exitcode = 1;
goto exit;
}
exit:
/* deallocate each non-null entry in argtable[] */
arg_freetable(argtable, sizeof(argtable) / sizeof(argtable[0]));
return exitcode;
}
int
main(int argc, char **argv)
{
struct arg_int *channels = arg_int0("c", "channels", "<n>", "define number of channels (default is 1)");
struct arg_int *subscribers = arg_int0("s", "subscribers", "<n>", "define number of subscribers (default is 1)");
struct arg_str *server_name = arg_str0("S", "server", "<hostname>", "server hostname where messages will be published (default is \"127.0.0.1\")");
struct arg_int *server_port = arg_int0("P", "port", "<n>", "server port where messages will be published (default is 9080)");
struct arg_int *timeout = arg_int0(NULL, "timeout", "<n>", "timeout when waiting events on communication to the server (default is 1000)");
struct arg_int *verbose = arg_int0("v", "verbose", "<n>", "increase output messages detail (0 (default) - no messages, 1 - info messages, 2 - debug messages, 3 - trace messages");
struct arg_lit *help = arg_lit0(NULL, "help", "print this help and exit");
struct arg_lit *version = arg_lit0(NULL, "version", "print version information and exit");
struct arg_end *end = arg_end(20);
void* argtable[] = { channels, subscribers, server_name, server_port, timeout, verbose, help, version, end };
const char* progname = "subscriber";
int nerrors;
int exitcode = EXIT_SUCCESS;
/* verify the argtable[] entries were allocated sucessfully */
if (arg_nullcheck(argtable) != 0) {
/* NULL entries were detected, some allocations must have failed */
printf("%s: insufficient memory\n", progname);
exitcode = EXIT_FAILURE;
goto exit;
}
/* set any command line default values prior to parsing */
subscribers->ival[0] = DEFAULT_CONCURRENT_CONN;
channels->ival[0] = DEFAULT_NUM_CHANNELS;
server_name->sval[0] = DEFAULT_SERVER_HOSTNAME;
server_port->ival[0] = DEFAULT_SERVER_PORT;
timeout->ival[0] = DEFAULT_TIMEOUT;
verbose->ival[0] = 0;
/* Parse the command line as defined by argtable[] */
nerrors = arg_parse(argc, argv, argtable);
/* special case: '--help' takes precedence over error reporting */
if (help->count > 0) {
printf(DESCRIPTION_SUBSCRIBER, progname, VERSION, COPYRIGHT);
printf("Usage: %s", progname);
arg_print_syntax(stdout, argtable, "\n");
arg_print_glossary(stdout, argtable, " %-25s %s\n");
exitcode = EXIT_SUCCESS;
goto exit;
}
/* special case: '--version' takes precedence error reporting */
if (version->count > 0) {
printf(DESCRIPTION_SUBSCRIBER, progname, VERSION, COPYRIGHT);
exitcode = EXIT_SUCCESS;
goto exit;
}
/* If the parser returned any errors then display them and exit */
if (nerrors > 0) {
/* Display the error details contained in the arg_end struct.*/
arg_print_errors(stdout, end, progname);
printf("Try '%s --help' for more information.\n", progname);
exitcode = EXIT_FAILURE;
goto exit;
}
verbose_messages = verbose->ival[0];
/* normal case: take the command line options at face value */
exitcode = main_program(channels->ival[0], subscribers->ival[0], server_name->sval[0], server_port->ival[0], timeout->ival[0]);
exit:
/* deallocate each non-null entry in argtable[] */
arg_freetable(argtable, sizeof(argtable) / sizeof(argtable[0]));
return exitcode;
}
int UHD_SAFE_MAIN(int argc, char *argv[]){
uhd::set_thread_priority_safe();
size_t rxshm_size, txshm_size;
bool mimic_active;
float mimic_delay;
unsigned int iSide, iSwing; // often used loop variables
int32_t rx_worker_status = 0;
int32_t clrfreq_rx_worker_status = 0;
int32_t mute_output = 0; // used if rx_worker error happends
int32_t rx_stream_reset_count = 0;
int32_t rx_stream_error_count = 0;
std::vector<sem_t> sem_rx_vec(nSwings), sem_tx_vec(nSwings);
std::vector<uint32_t> state_vec(nSwings, ST_INIT);
uint32_t swing; // = SWING0;
size_t nSamples_rx, nSamples_tx_pulse, nSamples_pause_after_rx, nSamples_auto_clear_freq, nSamples_rx_total;
size_t auto_clear_freq_available = 0;
uint32_t npulses, nerrors;
ssize_t cmd_status;
uint32_t usrp_driver_base_port, ip_part;
int32_t connect_retrys = MAX_SOCKET_RETRYS;
int32_t sockopt;
struct sockaddr_in sockaddr;
struct sockaddr_storage client_addr;
socklen_t addr_size;
uint32_t exit_driver = 0;
uint32_t tx_worker_active;
uhd::time_spec_t start_time, rx_start_time;
// vector of all pulse start times over an integration period
std::vector<uhd::time_spec_t> pulse_time_offsets;
// vector of the sample index of pulse start times over an integration period
std::vector<uint64_t> pulse_sample_idx_offsets;
boost::thread_group uhd_threads;
boost::thread_group clrfreq_threads;
// process config file for port and SHM sizes
DEBUG_PRINT("USRP_DRIVER starting to read driver_config.ini\n");
boost::property_tree::ptree pt;
boost::property_tree::ini_parser::read_ini("../driver_config.ini", pt);
// DEBUG_PRINT("USRP_DRIVER reading rxshm_size\n");
// std::cout << pt.get<std::string>("shm_settings.rxshm_size") << '\n';
rxshm_size = std::stoi(pt.get<std::string>("shm_settings.rxshm_size"));
// DEBUG_PRINT("USRP_DRIVER reading txshm_size\n");
txshm_size = std::stoi(pt.get<std::string>("shm_settings.txshm_size"));
usrp_driver_base_port = std::stoi(pt.get<std::string>("network_settings.USRPDriverPort"));
boost::property_tree::ptree pt_array;
DEBUG_PRINT("USRP_DRIVER starting to read array_config.ini\n");
boost::property_tree::ini_parser::read_ini("../array_config.ini", pt_array);
mimic_active = std::stof(pt_array.get<std::string>("mimic.mimic_active")) != 0;
mimic_delay = std::stof(pt_array.get<std::string>("mimic.mimic_delay"));
fprintf(stderr, "read from ini: mimic_active=%d, mimic_delay=%f\n", mimic_active, mimic_delay);
init_all_dirs();
// TODO also read usrp_config.ini and get antenna and side information from it. remove antenna input argument.
// process command line arguments
struct arg_lit *al_help = arg_lit0(NULL, "help", "Prints help information and then exits");
// struct arg_int *ai_ant = arg_intn("a", "antenna", NULL, 1, 2, "Antenna position index for the USRP");
struct arg_int *ai_ant_a = arg_int0("a", "antennaA", NULL, "Antenna position index for the USRP on side A");
struct arg_int *ai_ant_b = arg_int0("b", "antennaB", NULL, "Antenna position index for the USRP on side B");
struct arg_str *as_host = arg_str0("h", "host", NULL, "Hostname or IP address of USRP to control (e.g usrp1)");
struct arg_lit *al_intclk = arg_lit0("i", "intclk", "Select internal clock (default is external)");
struct arg_lit *al_interferometer = arg_lit0("x", "interferometer", "Disable tx_worker for interferometer antennas");
struct arg_end *ae_argend = arg_end(ARG_MAXERRORS);
void* argtable[] = {al_help, ai_ant_a, ai_ant_b, as_host, al_intclk, al_interferometer, ae_argend};
double txrate, rxrate, txfreq, rxfreq;
double txrate_new, rxrate_new, txfreq_new, rxfreq_new;
DEBUG_PRINT("usrp_driver debug mode enabled\n");
if (SUPRESS_UHD_PRINTS) {
uhd::msg::register_handler(&uhd_term_message_handler);
}
nerrors = arg_parse(argc,argv,argtable);
if (nerrors > 0) {
arg_print_errors(stdout,ae_argend,"usrp_driver");
exit(1);
}
if (argc == 1) {
printf("No arguments found, try running again with --help for more information.\n");
exit(1);
}
if(al_help->count > 0) {
printf("Usage: ");
arg_print_syntax(stdout,argtable,"\n");
arg_print_glossary(stdout,argtable," %-25s %s\n");
arg_freetable(argtable, sizeof(argtable)/sizeof(argtable[0]));
return 0;
}
unsigned int nSides = ai_ant_a->count + ai_ant_b->count;
if( nSides == 0 ) {
printf("No antenna index, exiting...");
return 0;
}
if(as_host->sval == NULL) {
printf("Missing usrp host command line argument, exiting...");
return 0;
}
std::vector<int> antennaVector(nSides);
std::vector<uint64_t> channel_numbers;
// both sides
if( nSides == 2 ) {
DEBUG_PRINT("Setting side A: ant_idx %d\n",ai_ant_a->ival[0]);
antennaVector[0] = ai_ant_a->ival[0];
channel_numbers.push_back(0);
DEBUG_PRINT("Setting side B: ant_idx %d\n",ai_ant_b->ival[0]);
antennaVector[1] = ai_ant_b->ival[0];
channel_numbers.push_back(1);
} else {
// side A
if (ai_ant_a->count == 1) {
DEBUG_PRINT("Setting side A: ant_idx %d\n",ai_ant_a->ival[0]);
antennaVector[0] = ai_ant_a->ival[0];
channel_numbers.push_back(0);
// side B
} else {
DEBUG_PRINT("Setting side B: ant_idx %d\n",ai_ant_b->ival[0]);
antennaVector[0] = ai_ant_b->ival[0];
channel_numbers.push_back(1);
DEBUG_PRINT("Warning: For one side use DIO output is always on Side A!!!!!!!!!!!!!"); // TODO correct this
}
}
// pointers to shared memory
std::vector<std::vector<void *>> shm_rx_vec(nSides, std::vector<void *>( nSwings));
std::vector<std::vector<void *>> shm_tx_vec(nSides, std::vector<void *>( nSwings));
// local buffers for tx and rx
std::vector<std::vector<std::complex<int16_t>>> tx_samples(nSides, std::vector<std::complex<int16_t>>(MAX_PULSE_LENGTH,0));
std::vector<std::vector<std::complex<int16_t>>> rx_data_buffer(nSides, std::vector<std::complex<int16_t>>(0));
std::vector<std::vector<std::complex<int16_t>>> rx_auto_clear_freq(nSides, std::vector<std::complex<int16_t>>(0));
std::string usrpargs(as_host->sval[0]);
usrpargs = "addr0=" + usrpargs + ",master_clock_rate=200.0e6";
// usrpargs = "addr0=" + usrpargs + ",master_clock_rate=200.0e6,recv_frame_size=50000000";
uhd::usrp::multi_usrp::sptr usrp = uhd::usrp::multi_usrp::make(usrpargs);
// usrp->set_rx_subdev_spec(uhd::usrp::subdev_spec_t("A:A B:A"));
// usrp->set_tx_subdev_spec(uhd::usrp::subdev_spec_t("A:A B:A"));
boost::this_thread::sleep(boost::posix_time::seconds(SETUP_WAIT));
uhd::stream_args_t stream_args("sc16", "sc16");
if (usrp->get_rx_num_channels() < nSides || usrp->get_tx_num_channels() < nSides) {
DEBUG_PRINT("ERROR: Number of defined channels (%i) is smaller than avaialable channels:\n usrp->get_rx_num_channels(): %lu \n usrp->get_tx_num_channels(): %lu \n\n", nSides, usrp->get_rx_num_channels(), usrp->get_tx_num_channels());
return -1;
}
stream_args.channels = channel_numbers;
uhd::rx_streamer::sptr rx_stream = usrp->get_rx_stream(stream_args);
uhd::tx_streamer::sptr tx_stream = usrp->get_tx_stream(stream_args);
// TODO: retry uhd connection if fails..
// Determine port from 3rd part of ip (192.168.x.2 => port = base_port + x )
int start_idx = usrpargs.find(".");
start_idx = usrpargs.find(".", start_idx+1);
int end_idx = usrpargs.find(".", start_idx+1);
ip_part = atoi(usrpargs.substr(start_idx+1, end_idx-start_idx-1).c_str());
// initialize rxfe gpio
kodiak_init_rxfe(usrp, nSides);
// initialize other gpio on usrp
init_timing_signals(usrp, mimic_active, nSides);
//if(CAPTURE_ERRORS) {
// signal(SIGINT, siginthandler);
//}
// open shared memory buffers and semaphores created by cuda_driver.py
// for dual polarization we use antenna numbers 20 to 35 (side is always 0)
for(iSwing = 0; iSwing < nSwings; iSwing++) {
for(iSide = 0; iSide < nSides; iSide++) {
int shm_side = 0;
shm_rx_vec[iSide][iSwing] = open_sample_shm(antennaVector[iSide], RXDIR, shm_side, iSwing, rxshm_size);
shm_tx_vec[iSide][iSwing] = open_sample_shm(antennaVector[iSide], TXDIR, shm_side, iSwing, txshm_size);
DEBUG_PRINT("usrp_driver rx shm addr: %p iSide: %d iSwing: %d\n", shm_rx_vec[iSide][iSwing], iSide, iSwing);
if (antennaVector[iSide] < 19 ) { // semaphores only for antennas of first polarization TODO check if this is enough
sem_rx_vec[iSwing] = open_sample_semaphore(antennaVector[iSide], iSwing, RXDIR);
sem_tx_vec[iSwing] = open_sample_semaphore(antennaVector[iSide], iSwing, TXDIR);
}
}
}
if(al_interferometer->count > 0) {
DEBUG_PRINT("Disable tx_worker ...\n");
tx_worker_active = 0;
} else {
tx_worker_active = 1;
}
if(al_intclk->count > 0) {
usrp->set_clock_source("internal");
usrp->set_time_source("internal");
}
else {
// sync clock with external 10 MHz and PPS
DEBUG_PRINT("Set clock: external\n");
usrp->set_clock_source("external", 0);
DEBUG_PRINT("Set time: external\n");
usrp->set_time_source("external", 0);
DEBUG_PRINT("Done setting time and clock\n");
}
while(true) {
if(driversock) {
close(driverconn);
close(driversock);
}
boost::this_thread::sleep(boost::posix_time::seconds(SETUP_WAIT));
// bind to socket for communication with usrp_server.py:
driversock = socket(AF_INET, SOCK_STREAM, 0);
if(driversock < 0){
perror("opening stream socket\n");
exit(1);
}
sockopt = 1;
setsockopt(driversock, SOL_SOCKET, SO_REUSEADDR, &sockopt, sizeof(int32_t));
sockaddr.sin_family = AF_INET;
// TODO: maybe limit addr to interface connected to usrp_server
sockaddr.sin_addr.s_addr = htonl(INADDR_ANY);
fprintf(stderr, "listening on port: %d\n", usrp_driver_base_port + ip_part);
sockaddr.sin_port = htons(usrp_driver_base_port + ip_part);
if( bind(driversock, (struct sockaddr *)&sockaddr, sizeof(sockaddr)) < 0){
perror("binding tx stream socket");
exit(1);
}
// wait for connection...
listen(driversock, 5);
// and accept it
fprintf(stderr, "waiting for socket connection\n");
addr_size = sizeof(client_addr);
driverconn = accept(driversock, (struct sockaddr *) &client_addr, &addr_size);
fprintf(stderr, "accepted socket connection\n");
while(true) {
// wait for transport endpoint to connect?
DEBUG_PRINT("USRP_DRIVER waiting for command\n");
uint8_t command = sock_get_cmd(driverconn, &cmd_status);
DEBUG_PRINT("USRP_DRIVER received command, status: %zu\n", cmd_status);
// see if socket is closed..
if(cmd_status == 11 || cmd_status == 0 || cmd_status < 0) {
DEBUG_PRINT("USRP_DRIVER lost connection to usrp_server, waiting for fresh connection, %d tries remaining\n", connect_retrys);
close(driversock);
if(connect_retrys-- < 0) {
exit(1);
}
sleep(1);
break;
}
connect_retrys = MAX_SOCKET_RETRYS;
switch(command) {
case USRP_SETUP: {
// receive infomation about a pulse sequence/integration period
// transmit/receive center frequenies and sampling rates
// number of tx/rx samples
// number of pulse sequences per integration period, and pulse start times
swing = sock_get_int16( driverconn);
DEBUG_PRINT("entering USRP_SETUP command (swing %d)\n", swing);
txfreq_new = sock_get_float64(driverconn);
rxfreq_new = sock_get_float64(driverconn);
txrate_new = sock_get_float64(driverconn);
rxrate_new = sock_get_float64(driverconn);
npulses = sock_get_uint32(driverconn);
nSamples_rx = sock_get_uint64(driverconn);
nSamples_pause_after_rx = sock_get_uint64(driverconn);
nSamples_auto_clear_freq = sock_get_uint64(driverconn);
nSamples_tx_pulse = sock_get_uint64(driverconn);
nSamples_rx_total = nSamples_rx + nSamples_pause_after_rx + nSamples_auto_clear_freq;
DEBUG_PRINT("USRP_SETUP number of requested rx samples: %d + %d pause + %d auto clear freq\n", (uint32_t) nSamples_rx, nSamples_pause_after_rx, nSamples_auto_clear_freq);
DEBUG_PRINT("USRP_SETUP number of requested tx samples per pulse: %d\n", (uint32_t) nSamples_tx_pulse);
DEBUG_PRINT("USRP_SETUP existing tx rate : %f (swing %d)\n", txrate, swing);
DEBUG_PRINT("USRP_SETUP requested tx rate: %f\n", txrate_new);
// resize
pulse_sample_idx_offsets.resize(npulses);
pulse_time_offsets.resize(npulses);
for(uint32_t i = 0; i < npulses; i++) {
// DEBUG_PRINT("USRP_SETUP waiting for pulse offset %d of %d\n", i+2, npulses);
pulse_sample_idx_offsets[i] = sock_get_uint64(driverconn);
// DEBUG_PRINT("USRP_SETUP received %zu pulse offset\n", pulse_sample_idx_offsets[i]);
}
DEBUG_PRINT("USRP_SETUP resize autoclear freq\n");
// RESIZE LOCAL BUFFERS
if(rx_data_buffer[0].size() < nSamples_rx_total) {
for(iSide = 0; iSide < nSides; iSide++) {
rx_data_buffer[iSide].resize(nSamples_rx_total);
}
}
DEBUG_PRINT("USRP_SETUP resize autoclear freq\n");
if(nSamples_auto_clear_freq != 0 and rx_auto_clear_freq[0].size() < nSamples_auto_clear_freq) {
for(iSide = 0; iSide < nSides; iSide++) {
rx_auto_clear_freq[iSide].resize(nSamples_auto_clear_freq);
}
}
// TODO use return argument of set_xx to save new rate/freq
// if necessary, retune USRP frequency and sampling rate
if(rxrate != rxrate_new) {
usrp->set_rx_rate(rxrate_new);
rxrate = usrp->get_rx_rate();
}
if(txrate != txrate_new) {
usrp->set_tx_rate(txrate_new);
txrate = usrp->get_tx_rate();
}
if(rxfreq != rxfreq_new) {
for(iSide = 0; iSide < nSides; iSide++) {
usrp->set_rx_freq(rxfreq_new, iSide);
}
rxfreq = usrp->get_rx_freq();
}
if(txfreq != txfreq_new) {
for(iSide = 0; iSide < nSides; iSide++) {
usrp->set_tx_freq(txfreq_new, iSide);
}
txfreq = usrp->get_tx_freq();
}
if(verbose) {
std::cout << boost::format("Actual RX Freq: %f MHz...") % (usrp->get_rx_freq()/1e6) << std::endl;
std::cout << boost::format("Actual RX Rate: %f Msps...") % (usrp->get_rx_rate()/1e6) << std::endl;
std::cout << boost::format("Actual TX Freq: %f MHz...") % (usrp->get_tx_freq()/1e6) << std::endl;
std::cout << boost::format("Actual TX Rate: %f Msps...") % (usrp->get_tx_rate()/1e6) << std::endl;
}
// TODO: set the number of samples in a pulse. this is calculated from the pulse duration and the sampling rate
// when do we know this? after USRP_SETUP
// create local copy of transmit pulse data from shared memory
std::complex<int16_t> *shm_pulseaddr;
size_t spb = tx_stream->get_max_num_samps();
size_t pulse_bytes = sizeof(std::complex<int16_t>) * nSamples_tx_pulse;
size_t number_of_pulses = pulse_time_offsets.size();
size_t num_samples_per_pulse_with_padding = nSamples_tx_pulse + 2*spb;
DEBUG_PRINT("spb %d, pulse length %d samples, pulse with padding %d\n", spb, nSamples_tx_pulse, num_samples_per_pulse_with_padding);
// TODO unpack and pad tx sample
for (iSide = 0; iSide<nSides; iSide++) {
tx_samples[iSide].resize(number_of_pulses * (num_samples_per_pulse_with_padding));
for(uint32_t p_i = 0; p_i < number_of_pulses; p_i++) {
shm_pulseaddr = &((std::complex<int16_t> *) shm_tx_vec[iSide][swing])[p_i*nSamples_tx_pulse];
memcpy(&tx_samples[iSide][spb + p_i*(num_samples_per_pulse_with_padding)], shm_pulseaddr, pulse_bytes);
}
}
if(SAVE_RAW_SAMPLES_DEBUG) {
FILE *raw_dump_fp;
char raw_dump_name[80];
// DEBUG_PRINT("Exporting %i raw tx_samples (%i + 2* %i)\n", num_samples_per_pulse_with_padding, nSamples_tx_pulse, spb);
for (iSide =0; iSide < nSides; iSide++){
sprintf(raw_dump_name,"%s/raw_samples_tx_ant_%d.cint16", diag_dir, antennaVector[iSide]);
raw_dump_fp = fopen(raw_dump_name, "wb");
fwrite(&tx_samples[iSide][0], sizeof(std::complex<int16_t>),num_samples_per_pulse_with_padding*number_of_pulses, raw_dump_fp);
fclose(raw_dump_fp);
}
}
state_vec[swing] = ST_READY;
DEBUG_PRINT("changing state_vec[swing] to ST_READY\n");
sock_send_uint8(driverconn, USRP_SETUP);
break;
}
case RXFE_SET: {
DEBUG_PRINT("entering RXFE_SET command\n");
RXFESettings rf_settings;
rf_settings.amp1 = sock_get_uint8(driverconn);
rf_settings.amp2 = sock_get_uint8(driverconn);
uint8_t attTimes2 = sock_get_uint8(driverconn);
rf_settings.att_05_dB = ( attTimes2 & 0x01 ) != 0;
rf_settings.att_1_dB = ( attTimes2 & 0x02 ) != 0;
rf_settings.att_2_dB = ( attTimes2 & 0x04 ) != 0;
rf_settings.att_4_dB = ( attTimes2 & 0x08 ) != 0;
rf_settings.att_8_dB = ( attTimes2 & 0x10 ) != 0;
rf_settings.att_16_dB = ( attTimes2 & 0x20 ) != 0;
kodiak_set_rxfe(usrp, rf_settings, nSides);
sock_send_uint8(driverconn, RXFE_SET);
break;
}
case TRIGGER_PULSE: {
swing = sock_get_int16( driverconn);
DEBUG_PRINT("entering TRIGGER_PULSE command (swing %d)\n", swing );
if (state_vec[swing] != ST_READY) {
sock_send_uint8(driverconn, TRIGGER_BUSY);
DEBUG_PRINT("TRIGGER_PULSE busy in state_vec[swing] %d, returning\n", state_vec[swing]);
}
else {
DEBUG_PRINT("TRIGGER_PULSE ready\n");
state_vec[swing] = ST_PULSE;
DEBUG_PRINT("TRIGGER_PULSE locking semaphore\n");
lock_semaphore(sem_rx_vec[swing]);
lock_semaphore(sem_tx_vec[swing]);
DEBUG_PRINT("TRIGGER_PULSE semaphore locked\n");
// create local copy of transmit pulse data from shared memory
size_t spb = tx_stream->get_max_num_samps();
size_t pulse_bytes = sizeof(std::complex<int16_t>) * nSamples_tx_pulse;
size_t number_of_pulses = pulse_time_offsets.size();
size_t num_samples_per_pulse_with_padding = nSamples_tx_pulse + 2*spb;
DEBUG_PRINT("spb %d, pulse length %d samples, pulse with padding %d\n", spb, nSamples_tx_pulse, num_samples_per_pulse_with_padding);
// read in time for start of pulse sequence over socket
uint32_t pulse_time_full = sock_get_uint32(driverconn);
double pulse_time_frac = sock_get_float64(driverconn);
start_time = uhd::time_spec_t(pulse_time_full, pulse_time_frac);
double tr_to_pulse_delay = sock_get_float64(driverconn);
// calculate usrp clock time of the start of each pulse over the integration period
// so we can schedule the io (perhaps we will have to move io off of the usrp if it can't keep up)
for(uint32_t p_i = 0; p_i < number_of_pulses; p_i++) {
double offset_time = pulse_sample_idx_offsets[p_i] / txrate;
pulse_time_offsets[p_i] = offset_time_spec(start_time, offset_time);
// DEBUG_PRINT("TRIGGER_PULSE pulse time %d is %2.5f\n", p_i, pulse_time_offsets[p_i].get_real_secs());
}
DEBUG_PRINT("first TRIGGER_PULSE time is %2.5f and last is %2.5f\n", pulse_time_offsets[0].get_real_secs(), pulse_time_offsets.back().get_real_secs());
rx_start_time = offset_time_spec(start_time, tr_to_pulse_delay/1e6);
rx_start_time = offset_time_spec(rx_start_time, pulse_sample_idx_offsets[0]/txrate);
// send_timing_for_sequence(usrp, start_time, pulse_times);
double pulseLength = nSamples_tx_pulse / txrate;
// float debugt = usrp->get_time_now().get_real_secs();
// DEBUG_PRINT("USRP_DRIVER: spawning worker threads at usrp_time %2.4f\n", debugt);
DEBUG_PRINT("TRIGGER_PULSE creating rx and tx worker threads on swing %d (nSamples_rx= %d + %d pause + %d auto clear freq )\n", swing,(int) nSamples_rx, nSamples_pause_after_rx, nSamples_auto_clear_freq);
// works fine with tx_worker and dio_worker, fails if rx_worker is enabled
uhd_threads.create_thread(boost::bind(usrp_rx_worker, usrp, rx_stream, &rx_data_buffer, nSamples_rx_total, rx_start_time, &rx_worker_status));
useconds_t usecs=1000;
if (tx_worker_active) {
usleep(usecs);
uhd_threads.create_thread(boost::bind(usrp_tx_worker, tx_stream, &tx_samples, num_samples_per_pulse_with_padding, start_time, pulse_sample_idx_offsets));
}
usleep(usecs);
uhd_threads.create_thread(boost::bind(send_timing_for_sequence, usrp, start_time, pulse_time_offsets, pulseLength, mimic_active, mimic_delay, nSides));
sock_send_uint8(driverconn, TRIGGER_PULSE);
uhd_threads.join_all(); // wait for transmit threads to finish, drawn from shared memory..
DEBUG_PRINT("TRIGGER_PULSE rx_worker, tx_worker and dio threads on swing %d\n joined.", swing);
}
break;
}
case READY_DATA: {
swing = sock_get_int16( driverconn);
DEBUG_PRINT("READY_DATA command (swing %d), waiting for uhd threads to join back\n", swing);
DEBUG_PRINT("READY_DATA unlocking swing a semaphore\n");
unlock_semaphore(sem_rx_vec[swing]);
unlock_semaphore(sem_tx_vec[swing]);
DEBUG_PRINT("READY_DATA usrp worker threads joined, semaphore unlocked, sending metadata\n");
// TODO: handle multiple channels of data.., use channel index to pick correct swath of memory to copy into shm
// rx_worker_status =1; //DEBUG
if(rx_worker_status){
fprintf(stderr, "Error in rx_worker. Setting state to %d.\n", rx_worker_status);
state_vec[swing] = rx_worker_status;
rx_worker_status = 0;
mute_output = 1;
rx_stream_error_count++;
if (rx_stream_reset_count >= MAX_STREAM_RESETS) {
fprintf(stderr, "READY_DATA: shutting down usrp_driver to avoid streamer reset overflow (after %dth reset)\n", rx_stream_reset_count);
// send all data to server, clean up and exit after that
exit_driver = 1;
}
if((rx_worker_status != RX_WORKER_STREAM_TIME_ERROR) && (rx_stream_error_count > 4)) {
// recreate rx_stream unless the error was from sending the stream command too late
rx_stream_reset_count++;
fprintf(stderr, "READY_DATA: recreating rx_stream %dth time! (buffer overflow will occur for 126th time)\n", rx_stream_reset_count);
rx_stream.reset();
rx_stream = usrp->get_rx_stream(stream_args);
}
auto_clear_freq_available = 0;
}
else {
rx_stream_error_count = 0;
auto_clear_freq_available = 1;
}
DEBUG_PRINT("READY_DATA state: %d, ant: %d, num_samples: %zu\n", state_vec[swing], antennaVector[0], nSamples_rx);
sock_send_int32(driverconn, state_vec[swing]); // send status
sock_send_int32(driverconn, antennaVector[0]); // send antenna TODO do this for both antennas?
sock_send_int32(driverconn, nSamples_rx); // nsamples; send send number of samples
// read FAULT status
bool fault;
for (iSide =0; iSide<nSides; iSide++){
fault = read_FAULT_status_from_control_board(usrp, iSide);
}
// TODO move this in loop as soon as usrp_server receives both sides
sock_send_bool(driverconn, fault); // FAULT status from conrol board
if (mute_output) {
DEBUG_PRINT("READY_DATA: Filling SHM with zeros (because of rx_worker error) \n");
for (iSide = 0; iSide<nSides; iSide++) {
memset(shm_rx_vec[iSide][swing], 0, rxshm_size);
std::fill(rx_auto_clear_freq[iSide].begin(), rx_auto_clear_freq[iSide].end(), 0);
}
mute_output = 0;
}
else {
DEBUG_PRINT("READY_DATA starting copying rx data buffer to shared memory\n");
// regural rx data
for (iSide = 0; iSide<nSides; iSide++) {
// DEBUG_PRINT("usrp_drivercopy to rx shm addr: %p iSide: %d iSwing: %d\n", shm_rx_vec[iSide][swing], iSide, iSwing);
memcpy(shm_rx_vec[iSide][swing], &rx_data_buffer[iSide][0], sizeof(std::complex<int16_t>) * nSamples_rx);
}
// auto clear freq samples
for (iSide = 0; iSide<nSides; iSide++) {
for (int iSample = 0; iSample < nSamples_auto_clear_freq; iSample++) {
rx_auto_clear_freq[iSide][iSample] = rx_data_buffer[iSide][nSamples_rx+nSamples_pause_after_rx+ iSample];
}
}
}
if(SAVE_RAW_SAMPLES_DEBUG) {
FILE *raw_dump_fp;
char raw_dump_name[80];
for (iSide=0; iSide<nSides; iSide++) {
sprintf(raw_dump_name,"%s/raw_samples_rx_ant_%d.cint16", diag_dir, antennaVector[iSide]);
raw_dump_fp = fopen(raw_dump_name, "wb");
fwrite(&rx_data_buffer[iSide], sizeof(std::complex<int16_t>), nSamples_rx_total, raw_dump_fp);
fclose(raw_dump_fp);
}
}
DEBUG_PRINT("READY_DATA finished copying rx data buffer to shared memory\n");
state_vec[swing] = ST_READY;
DEBUG_PRINT("changing state_vec[swing] to ST_READY\n");
DEBUG_PRINT("READY_DATA returning command success \n");
sock_send_uint8(driverconn, READY_DATA);
break;
}
case UHD_GETTIME: {
DEBUG_PRINT("entering UHD_GETTIME command\n");
start_time = usrp->get_time_now();
uint32_t real_time = start_time.get_real_secs();
double frac_time = start_time.get_frac_secs();
sock_send_uint32(driverconn, real_time);
sock_send_float64(driverconn, frac_time);
DEBUG_PRINT("UHD_GETTIME current UHD time: %d %.2f command\n", real_time, frac_time);
sock_send_uint8(driverconn, UHD_GETTIME);
break;
}
// command to reset time, sync time with external PPS pulse
case UHD_SYNC: {
DEBUG_PRINT("entering UHD_SYNC command\n");
// if --intclk flag passed to usrp_driver, set clock source as internal and do not sync time
if(al_intclk->count > 0) {
usrp->set_time_now(uhd::time_spec_t(0.0));
}
else {
/* const uhd::time_spec_t last_pps_time = usrp->get_time_last_pps();
while (last_pps_time == usrp->get_time_last_pps()) {
boost::this_thread::sleep(boost::posix_time::milliseconds(100));
}
usrp->set_time_next_pps(uhd::time_spec_t(0.0));
boost::this_thread::sleep(boost::posix_time::milliseconds(1100));
*/
DEBUG_PRINT("Start setting unknown pps\n");
usrp->set_time_unknown_pps(uhd::time_spec_t(11.0));
DEBUG_PRINT("end setting unknown pps\n");
}
sock_send_uint8(driverconn, UHD_SYNC);
break;
}
case AUTOCLRFREQ: {
// has to be called after GET_DATA and before USRP_SETUP
DEBUG_PRINT("entering getting auto clear freq command\n");
// uint32_t num_clrfreq_samples = sock_get_uint32(driverconn);
iSide = 0;// TODO both sides!
if (auto_clear_freq_available) {
DEBUG_PRINT("AUTOCLRFREQ samples sending %d samples for antenna %d...\n", rx_auto_clear_freq[iSide].size(),antennaVector[iSide]);
sock_send_int32(driverconn, (int32_t) antennaVector[iSide]);
sock_send_uint32(driverconn, (uint32_t) rx_auto_clear_freq[iSide].size());
// send samples
send(driverconn, &rx_auto_clear_freq[iSide][0], sizeof(std::complex<short int>) * rx_auto_clear_freq[iSide].size() , 0);
}
else {
sock_send_int32(driverconn, (int32_t) -1);
}
sock_send_uint8(driverconn, AUTOCLRFREQ);
break;
}
case CLRFREQ: {
DEBUG_PRINT("entering CLRFREQ command\n");
uint32_t num_clrfreq_samples = sock_get_uint32(driverconn);
uint32_t clrfreq_time_full = sock_get_uint32(driverconn);
double clrfreq_time_frac = sock_get_float64(driverconn);
double clrfreq_cfreq = sock_get_float64(driverconn);
double clrfreq_rate = sock_get_float64(driverconn);
std::vector<std::vector<std::complex<int16_t>>> clrfreq_data_buffer(nSides, std::vector<std::complex<int16_t>>(num_clrfreq_samples));
uint32_t real_time;
double frac_time;
DEBUG_PRINT("CLRFREQ time: %d . %.2f \n", clrfreq_time_full, clrfreq_time_frac);
DEBUG_PRINT("CLRFREQ rate: %.2f, CLRFREQ_nsamples %d, freq: %.2f\n", clrfreq_rate, num_clrfreq_samples, clrfreq_cfreq);
uhd::time_spec_t clrfreq_start_time = uhd::time_spec_t(clrfreq_time_full, clrfreq_time_frac);
real_time = clrfreq_start_time.get_real_secs();
frac_time = clrfreq_start_time.get_frac_secs();
DEBUG_PRINT("CLRFREQ UHD clrfreq target time: %d %.2f \n", real_time, frac_time);
// TODO: only set rate if it is different!
if(rxrate != clrfreq_rate) {
usrp->set_rx_rate(clrfreq_rate);
rxrate = usrp->get_rx_rate();
clrfreq_rate = rxrate;
}
DEBUG_PRINT("CLRFREQ actual rate: %.2f\n", clrfreq_rate);
//clrfreq_cfreq = usrp->get_rx_freq();
//DEBUG_PRINT("CLRFREQ actual freq: %.2f\n", clrfreq_cfreq);
clrfreq_threads.create_thread(boost::bind(usrp_rx_worker, usrp, rx_stream, &clrfreq_data_buffer, num_clrfreq_samples, clrfreq_start_time, &clrfreq_rx_worker_status));
clrfreq_threads.join_all();
if(clrfreq_rx_worker_status){
fprintf(stderr, "Error in clrfreq_rx_worker, resetting rx_stream: %d.\n", clrfreq_rx_worker_status);
rx_stream_reset_count++;
fprintf(stderr, "CLRFREQ: recreating rx_stream %dth time! (buffer overflow will occur for 126th time)\n", rx_stream_reset_count);
rx_stream.reset();
rx_stream = usrp->get_rx_stream(stream_args);
}
if (rx_stream_reset_count >= MAX_STREAM_RESETS) {
fprintf(stderr, "CLRFREQ: shutting down usrp_driver to avoid streamer reset overflow (after %dth reset)\n", rx_stream_reset_count);
// finish clrfreq command, then clean up and exit to avoid buffer overflow
exit_driver = 1;
}
DEBUG_PRINT("CLRFREQ received samples, relaying %d samples back...\n", num_clrfreq_samples);
sock_send_int32(driverconn, (int32_t) antennaVector[0]); // TODO both sides?
sock_send_float64(driverconn, clrfreq_rate);
// send back samples
send(driverconn, &clrfreq_data_buffer[0][0], sizeof(std::complex<short int>) * num_clrfreq_samples, 0);
//for(uint32_t i = 0; i < num_clrfreq_samples; i++) {
//DEBUG_PRINT("sending %d - %d\n", i, clrfreq_data_buffer[0][i]);
// sock_send_cshort(driverconn, clrfreq_data_buffer[0][i]);
// }
DEBUG_PRINT("CLRFREQ samples sent for antenna %d...\n", antennaVector[0]);
// restore usrp rates
usrp->set_rx_rate(rxrate);
usrp->set_rx_freq(rxfreq);
sock_send_uint8(driverconn, CLRFREQ);
start_time = usrp->get_time_now();
real_time = start_time.get_real_secs();
frac_time = start_time.get_frac_secs();
DEBUG_PRINT("CLRFREQ finished at UHD time: %d %.2f \n", real_time, frac_time);
break;
}
case EXIT: {
DEBUG_PRINT("entering EXIT command\n");
exit_driver = 1;
break;
}
default: {
printf("USRP_DRIVER unrecognized command: %d, %c, exiting..\n", command, command);
sleep(10);
exit(1);
break;
}
}
if (not check_clock_lock(usrp)) {
fprintf(stderr, "Error: Lost clock for USRP: %s\n ", as_host->sval[0]);
exit_driver = 1;
}
// clean exit
if (exit_driver) {
DEBUG_PRINT("Shutting down driver\n");
close(driverconn);
for(iSide = 0; iSide < nSides; iSide++) {
for(iSwing = 0; iSwing < nSwings; iSwing++) {
// fill SHM with zeros
memset(shm_rx_vec[iSide][iSwing], 0, rxshm_size);
memset(shm_tx_vec[iSide][iSwing], 0, txshm_size);
munmap(shm_rx_vec[iSide][iSwing], rxshm_size);
munmap(shm_tx_vec[iSide][iSwing], txshm_size);
sem_close(&sem_rx_vec[iSwing]);
sem_close(&sem_tx_vec[iSwing]);
}
}
// TODO: close usrp streams?
// sock_send_uint8(driverconn, EXIT);
exit(1);
}
}
}
return 0;
}
int main(int argc, char* argv[])
{
struct arg_lit *help;
struct arg_file *input, *output;
struct arg_str *rotation;
struct arg_end *end;
/* command line parsing through argtable package */
void* argtable[] = {
help = arg_lit0("h", "help", "display this help and exit"),
input = arg_file0("i", "input", "input", "name of the input file (default stdin"),
output = arg_file0("o", "output", "file", "name of the output file (default stdout)"),
rotation = arg_str1(NULL, NULL, "\"x y z w\"", "rotate w degrees around axis x y z"),
end = arg_end(20) };
const char* progname = "xyztk-rotate";
int rc = 0;
int nerrors;
/* verify the argtable[] entries were allocated sucessfully */
if (arg_nullcheck(argtable) != 0)
{
/* NULL entries were detected, some allocations must have failed */
printf("%s: insufficient memory\n", progname);
rc=1;
goto exit;
}
/* set default values */
/* parse the command line flags, overriding default values */
nerrors = arg_parse(argc,argv,argtable);
/* special case: '--help' takes precedence over error reporting */
if (help->count > 0)
{
printf("Usage: %s", progname);
arg_print_syntax(stdout,argtable,"\n");
printf("\n");
arg_print_glossary(stdout,argtable," %-40s %s\n");
printf("\n");
rc=0;
goto exit;
}
/* special case: no command line options induces brief help */
if (argc==1) {
printf("Try '%s --help' for more information.\n",progname);
rc=0;
goto exit;
}
/* If the parser returned any errors then display them and exit */
if (nerrors > 0)
{
/* Display the error details contained in the arg_end struct.*/
arg_print_errors(stdout,end,progname);
printf("Try '%s --help' for more information.\n",progname);
rc=1;
goto exit;
}
/* set global structures */
/* initialize I/O pointers */
FILE* in;
if (input->count) {
in = fopen(input->filename[0], "r");
} else {
in = stdin;
}
FILE* out;
if (output->count) {
out = fopen(output->filename[0], "w");
} else {
out = stdout;
}
/* initialize molecule structure */
xyztk_molecule_t molecule;
xyztk_molecule_load (&molecule, in);
/* read rotation from string */
xyztk_quat_t r;
sscanf (rotation->sval[0], "%lf%lf%lf%lf", &r.x, &r.y, &r.z, &r.w);
xyztk_molecule_rotate (&molecule, &r);
/* print output */
int i;
fprintf(out, "%d\n", molecule.n_atoms);
fprintf(out, "%s", molecule.name);
for (i = 0; i < molecule.n_atoms; ++i)
{
fprintf(out, "%-8s %20.14lf %20.14lf %20.14lf \n",
molecule.label[i].s, molecule.coord[i].x, molecule.coord[i].y, molecule.coord[i].z);
}
exit:
/* deallocate each non-null entry in argtable[] */
arg_freetable(argtable,sizeof(argtable)/sizeof(argtable[0]));
return rc;
}
int main(int argc, char *argv[])
{
struct arg_int *lport = arg_int0("p", "port", "<localport>", "listening port (default is 8888)");
struct arg_int *debug = arg_int0("d", "debug", "<level>", "debug output level (default is 4)");
#ifdef PUBKEY_DATA_
struct arg_str *key = arg_str0("k", "key", "<keyfile>", "public key file (default is built-in)");
#else
struct arg_str *key = arg_str0("k", "key", "<keyfile>", "public key file (default is pubkey)");
#endif
#ifdef ROOTPEM_DATA_
struct arg_str *certdb= arg_str0(NULL, "certdb", "<certfile>", "trusted CA database (default is built-in)");
#else
struct arg_str *certdb= arg_str0(NULL, "certdb", "<certfile>", "trusted CA database (default is root.pem)");
#endif
struct arg_lit *help = arg_lit0(NULL,"help", "print this help and exit");
struct arg_str *host = arg_str1(NULL, NULL, "<host>[:port]", "non-blocked TLS server");
struct arg_end *end = arg_end(20);
void *argtable[] = {lport, debug, key, certdb, help, host, end};
const char* progname = "telex-client";
int nerrors;
int ret=0;
assert(!arg_nullcheck(argtable));
// defaults:
lport->ival[0] = 8888;
debug->ival[0] = 3;
#ifdef PUBKEY_DATA_
key->sval[0] = NULL;
#else
key->sval[0] = "pubkey";
#endif
#ifdef ROOTPEM_DATA_
certdb->sval[0] = NULL;
#else
certdb->sval[0] = "root.pem";
#endif
nerrors = arg_parse(argc,argv,argtable);
if (help->count > 0) {
printf("Usage: %s", progname);
arg_print_syntax(stdout,argtable,"\n");
printf("\nEstablishes covert, encrypted tunnels, disguised as connections to <host>.\n\n");
arg_print_glossary(stdout,argtable," %-25s %s\n");
printf("\n");
ret = 0;
} else if (nerrors > 0) {
arg_print_errors(stdout,end,progname);
printf("Try '%s --help' for more information.\n", progname);
ret = 1;
} else if (argc == 1) {
printf("Try '%s --help' for more information.\n", progname);
ret = 0;
} else {
int port = 443;
char hstr[255];
assert(host->sval[0]);
strncpy(hstr, host->sval[0], sizeof(hstr)-1);
char *pstr=0;
strtok(hstr, ":");
pstr = strtok(NULL, ":");
if (pstr) {
port = strtol(pstr, NULL, 10);
if (port < 1 || port > 65535) {
fprintf(stderr, "Invalid remote port: %d", port);
return 1;
}
}
printf("WARNING: This software is an experimental prototype intended for\n");
printf(" researchers. It does not provide strong security and is\n");
printf(" UNSAFE FOR REAL-WORLD USE. For details of current limitations\n");
printf(" of our proof-of-concept, please see telex-client/ISSUES.\n");
ret = telex_client(lport->ival[0], port, debug->ival[0], hstr, key->sval[0], certdb->sval[0]);
}
arg_freetable(argtable, sizeof(argtable)/sizeof(argtable[0]));
return ret;
}
int main(int argc, char **argv)
{
struct arg_lit *list = arg_lit0("lL",NULL, "list files");
struct arg_lit *recurse = arg_lit0("R",NULL, "recurse through subdirectories");
struct arg_int *repeat = arg_int0("k","scalar",NULL, "define scalar value k (default is 3)");
struct arg_str *defines = arg_strn("D","define","MACRO",0,argc+2, "macro definitions");
struct arg_file *outfile = arg_file0("o",NULL,"<output>", "output file (default is \"-\")");
struct arg_lit *verbose = arg_lit0("v","verbose,debug", "verbose messages");
struct arg_lit *help = arg_lit0(NULL,"help", "print this help and exit");
struct arg_lit *version = arg_lit0(NULL,"version", "print version information and exit");
struct arg_file *infiles = arg_filen(NULL,NULL,NULL,1,argc+2, "input file(s)");
struct arg_end *end = arg_end(20);
void* argtable[] = {list,recurse,repeat,defines,outfile,verbose,help,version,infiles,end};
const char* progname = "myprog";
int nerrors;
int exitcode=0;
/* verify the argtable[] entries were allocated sucessfully */
if (arg_nullcheck(argtable) != 0)
{
/* NULL entries were detected, some allocations must have failed */
printf("%s: insufficient memory\n",progname);
exitcode=1;
goto exit;
}
/* set any command line default values prior to parsing */
repeat->ival[0]=3;
outfile->filename[0]="-";
/* Parse the command line as defined by argtable[] */
nerrors = arg_parse(argc,argv,argtable);
/* special case: '--help' takes precedence over error reporting */
if (help->count > 0)
{
printf("Usage: %s", progname);
arg_print_syntax(stdout,argtable,"\n");
printf("This program demonstrates the use of the argtable2 library\n");
printf("for parsing command line arguments.\n");
arg_print_glossary(stdout,argtable," %-25s %s\n");
exitcode=0;
goto exit;
}
/* special case: '--version' takes precedence error reporting */
if (version->count > 0)
{
printf("'%s' example program for the \"argtable\" command line argument parser.\n",progname);
printf("September 2003, Stewart Heitmann\n");
exitcode=0;
goto exit;
}
/* If the parser returned any errors then display them and exit */
if (nerrors > 0)
{
/* Display the error details contained in the arg_end struct.*/
arg_print_errors(stdout,end,progname);
printf("Try '%s --help' for more information.\n",progname);
exitcode=1;
goto exit;
}
/* special case: uname with no command line options induces brief help */
if (argc==1)
{
printf("Try '%s --help' for more information.\n",progname);
exitcode=0;
goto exit;
}
/* normal case: take the command line options at face value */
exitcode = mymain(list->count, recurse->count, repeat->ival[0],
defines->sval, defines->count,
outfile->filename[0], verbose->count,
infiles->filename, infiles->count);
exit:
/* deallocate each non-null entry in argtable[] */
arg_freetable(argtable,sizeof(argtable)/sizeof(argtable[0]));
return exitcode;
}
int main(int argc, char **argv)
{
struct arg_dbl *a = arg_dbl1(NULL,NULL,"a","a is <double>");
struct arg_dbl *b = arg_dbl0(NULL,NULL,"b","b is <double>");
struct arg_dbl *c = arg_dbl0(NULL,NULL,"c","c is <double>");
struct arg_dbl *d = arg_dbln("dD","delta","<double>",0,3,"d can occur 0..3 times");
struct arg_dbl *e = arg_dbl0(NULL,"eps,eqn","<double>","eps is optional");
struct arg_lit *help = arg_lit0(NULL,"help","print this help and exit");
struct arg_end *end = arg_end(20);
void* argtable[] = {a,b,c,d,e,help,end};
int nerrors;
int exitcode=0;
int i;
double sum=0;
/*
printf("a=%p\n",a);
printf("b=%p\n",b);
printf("c=%p\n",c);
printf("d=%p\n",d);
printf("e=%p\n",e);
printf("help=%p\n",help);
printf("end=%p\n",end);
printf("argtable=%p\n",argtable);
*/
/* print the command line */
for (i=0; i<argc; i++)
printf("%s ",argv[i]);
printf("\n");
/* verify the argtable[] entries were allocated sucessfully */
if (arg_nullcheck(argtable) != 0)
{
/* NULL entries were detected, some allocations must have failed */
printf("%s: insufficient memory\n",argv[0]);
exitcode=1;
goto exit;
}
/* Parse the command line as defined by argtable[] */
nerrors = arg_parse(argc,argv,argtable);
/* special case: '--help' takes precedence over error reporting */
if (help->count > 0)
{
printf("Usage: %s ", argv[0]);
arg_print_syntax(stdout,argtable,"\n");
arg_print_glossary(stdout,argtable," %-25s %s\n");
exitcode=0;
goto exit;
}
/* If the parser returned any errors then display them and exit */
if (nerrors > 0)
{
/* Display the error details contained in the arg_end struct.*/
arg_print_errors(stdout,end,argv[0]);
exitcode=1;
goto exit;
}
/* parsing complete, verify all args sum to zero */
for (i=0; i<a->count; i++)
{
printf("a[%d]=%f\n",i,a->dval[i]);
sum += a->dval[i];
}
for (i=0; i<b->count; i++)
{
printf("b[%d]=%f\n",i,b->dval[i]);
sum += b->dval[i];
}
for (i=0; i<c->count; i++)
{
printf("c[%d]=%f\n",i,c->dval[i]);
sum += c->dval[i];
}
for (i=0; i<d->count; i++)
{
printf("d[%d]=%f\n",i,d->dval[i]);
sum += d->dval[i];
}
for (i=0; i<e->count; i++)
{
printf("e[%d]=%f\n",i,e->dval[i]);
sum += e->dval[i];
}
printf("sum=%f\n",sum);
if (sum<-1.0e-6 || sum>1.0e-6)
{
printf("%s: error - sum=%f is non-zero\n",argv[0],sum);
exitcode=1;
goto exit;
}
exit:
/* deallocate each non-null entry in argtable[] */
arg_freetable(argtable,sizeof(argtable)/sizeof(argtable[0]));
printf("%s: exitcode=%d\n\n",argv[0],exitcode);
/* close stdin and stdout to stop memcheck whining about their memory not being freed */
fclose(stdin);
fclose(stdout);
return exitcode;
}
int _tmain(int argc, char* argv[])
{
// determine my process name
_splitpath(argv[0],NULL,NULL,gszProcName,NULL);
#else
int
main(int argc, const char** argv)
{
// determine my process name
CUtility::splitpath((char *)argv[0],NULL,gszProcName);
#endif
int iScreenLogLevel; // level of screen diagnostics
int iFileLogLevel; // level of file diagnostics
char szLogFile[_MAX_PATH]; // write diagnostics to this file
int Rslt;
bool bSkipFirst; // true if first line contains header and should be skipped
int iMinLength; // core elements must be of at least this length
int iMaxLength; // and no longer than this length
char szInLociFile[_MAX_PATH]; // input element loci from this file
char szInSeqFile[_MAX_PATH]; // input bioseq file containing assembly
char szRsltsFile[_MAX_PATH]; // output stats to this file
// command line args
struct arg_lit *help = arg_lit0("hH","help", "print this help and exit");
struct arg_lit *version = arg_lit0("v","version,ver", "print version information and exit");
struct arg_int *FileLogLevel=arg_int0("f", "FileLogLevel", "<int>","Level of diagnostics written to logfile 0=fatal,1=errors,2=info,3=diagnostics,4=debug");
struct arg_int *ScreenLogLevel=arg_int0("S", "ScreenLogLevel", "<int>","Level of diagnostics written to logfile 0=fatal,1=errors,2=info,3=diagnostics,4=debug");
struct arg_file *LogFile = arg_file0("F","log","<file>", "diagnostics log file");
struct arg_file *InLociFile = arg_file1("i","inloci","<file>", "element loci CSV file");
struct arg_file *InSeqFile = arg_file1("I","assembly","<file>", "genome assembly bioseq file");
struct arg_file *RsltsFile = arg_file1("o","output","<file>", "output file");
struct arg_lit *SkipFirst = arg_lit0("x","skipfirst", "skip first line of CSV - header line");
struct arg_int *MinLength = arg_int0("l","minlength","<int>", "minimum element length (default 10)");
struct arg_int *MaxLength = arg_int0("L","maxlength","<int>", "maximum element length (default 1000000000)");
struct arg_end *end = arg_end(20);
void *argtable[] = {help,version,FileLogLevel,ScreenLogLevel,LogFile,
InLociFile,InSeqFile,RsltsFile,SkipFirst,MinLength,MaxLength,
end};
char **pAllArgs;
int argerrors;
argerrors = CUtility::arg_parsefromfile(argc,(char **)argv,&pAllArgs);
if(argerrors >= 0)
argerrors = arg_parse(argerrors,pAllArgs,argtable);
/* special case: '--help' takes precedence over error reporting */
if (help->count > 0)
{
printf("\n%s csv2stats, Version %s\nOptions ---\n", gszProcName,cpszProgVer);
arg_print_syntax(stdout,argtable,"\n");
arg_print_glossary(stdout,argtable," %-25s %s\n");
printf("\nNote: Parameters can be entered into a parameter file, one parameter per line.");
printf("\n To invoke this parameter file then precede its name with '@'");
printf("\n e.g. %s @myparams.txt\n\n",gszProcName);
exit(1);
}
/* special case: '--version' takes precedence error reporting */
if (version->count > 0)
{
printf("\n%s Version %s\n",gszProcName,cpszProgVer);
exit(1);
}
if (!argerrors)
{
if(FileLogLevel->count && !LogFile->count)
{
printf("\nError: FileLogLevel '-f%d' specified but no logfile '-F<logfile>'",FileLogLevel->ival[0]);
exit(1);
}
iScreenLogLevel = iFileLogLevel = FileLogLevel->count ? FileLogLevel->ival[0] : eDLInfo;
if(iFileLogLevel < eDLNone || iFileLogLevel > eDLDebug)
{
printf("\nError: FileLogLevel '-l%d' specified outside of range %d..%d",iFileLogLevel,eDLNone,eDLDebug);
exit(1);
}
if(LogFile->count)
{
strncpy(szLogFile,LogFile->filename[0],_MAX_PATH);
szLogFile[_MAX_PATH-1] = '\0';
}
else
{
iFileLogLevel = eDLNone;
szLogFile[0] = '\0';
}
bSkipFirst = SkipFirst->count ? true : false;
iMinLength = MinLength->count ? MinLength->ival[0] : cDfltMinLengthRange;
if(iMinLength < 1 || iMinLength > cMaxLengthRange)
{
printf("Error: Mininum element length '-l%d' is not in range 1..%d",iMinLength,cMaxLengthRange);
exit(1);
}
iMaxLength = MaxLength->count ? MaxLength->ival[0] : cMaxLengthRange;
if(iMaxLength < iMinLength || iMaxLength > cMaxLengthRange)
{
printf("Error: Maximum element length '-L%d' is not in range %d..%d",iMaxLength,iMinLength,cMaxLengthRange);
exit(1);
}
strncpy(szInLociFile,InLociFile->filename[0],_MAX_PATH);
szInLociFile[_MAX_PATH-1] = '\0';
strncpy(szInSeqFile,InSeqFile->filename[0],_MAX_PATH);
szInSeqFile[_MAX_PATH-1] = '\0';
strncpy(szRsltsFile,RsltsFile->filename[0],_MAX_PATH);
szRsltsFile[_MAX_PATH-1] = '\0';
// now that command parameters have been parsed then initialise diagnostics log system
if(!gDiagnostics.Open(szLogFile,(etDiagLevel)iScreenLogLevel,(etDiagLevel)iFileLogLevel,true))
{
printf("\nError: Unable to start diagnostics subsystem.");
if(szLogFile[0] != '\0')
printf(" Most likely cause is that logfile '%s' can't be opened/created",szLogFile);
exit(1);
}
gDiagnostics.DiagOut(eDLInfo,gszProcName,"Version: %s Processing parameters:",cpszProgVer);
gDiagnostics.DiagOutMsgOnly(eDLInfo,"Input CSV element loci file: '%s'",szInLociFile);
gDiagnostics.DiagOutMsgOnly(eDLInfo,"Input bioseq genome assembly file: '%s'",szInSeqFile);
gDiagnostics.DiagOutMsgOnly(eDLInfo,"Output to file: '%s'",szRsltsFile);
gDiagnostics.DiagOutMsgOnly(eDLInfo,"First line contains header: %s",bSkipFirst ? "yes" : "no");
gDiagnostics.DiagOutMsgOnly(eDLInfo,"Minimum element length: %d",iMinLength);
gDiagnostics.DiagOutMsgOnly(eDLInfo,"Maximum element length: %d",iMaxLength);
#ifdef _WIN32
SetPriorityClass(GetCurrentProcess(), BELOW_NORMAL_PRIORITY_CLASS);
#endif
// processing here...
Rslt = Process(bSkipFirst,iMinLength,iMaxLength,szInLociFile,szInSeqFile,szRsltsFile);
gStopWatch.Stop();
Rslt = Rslt >=0 ? 0 : 1;
gDiagnostics.DiagOut(eDLInfo,gszProcName,"Exit code: %d Total processing time: %s",Rslt,gStopWatch.Read());
exit(Rslt);
}
else
{
printf("\n%s csv2stats, Version %s\n",gszProcName,cpszProgVer);
arg_print_errors(stdout,end,gszProcName);
arg_print_syntax(stdout,argtable,"\nUse '-h' to view option and parameter usage\n");
exit(1);
}
}
int main(int argc, char *argv[]) {
SDL_AudioSpec want, have;
SDL_AudioDeviceID dev;
Streamer streamer;
int retcode = 0;
// Init SDL Audio
if(SDL_Init(SDL_INIT_AUDIO) != 0) {
fprintf(stderr, "Error: %s\n", SDL_GetError());
return 1;
}
// commandline argument parser options
struct arg_lit *help = arg_lit0("h", "help", "print this help and exit");
struct arg_lit *vers = arg_lit0("v", "version", "print version information and exit");
struct arg_file *file = arg_file1("f", "file", "<file>", "SOUNDS.DAT file");
struct arg_file *output = arg_file0("o", "output", "<file>", "Output sounds file");
struct arg_int *sid = arg_int0("s", "sound", "<int>", "Sound ID");
struct arg_int *sampleprint = arg_int0(NULL, "print", "<int>", "Print first n bytes from selected sound");
struct arg_lit *play = arg_lit0("p", "play", "Play selected sound");
struct arg_file *export = arg_file0("e", "export", "<file>", "Export selected sound to AU file");
struct arg_file *import = arg_file0("i", "import", "<file>", "Import selected sound from AU file");
struct arg_end *end = arg_end(20);
void* argtable[] = {help,vers,file,output,sid,sampleprint,play,export,import,end};
const char* progname = "soundtool";
// Make sure everything got allocated
if(arg_nullcheck(argtable) != 0) {
printf("%s: insufficient memory\n", progname);
goto exit_0;
}
// Parse arguments
int nerrors = arg_parse(argc, argv, argtable);
// Handle help
if(help->count > 0) {
printf("Usage: %s", progname);
arg_print_syntax(stdout, argtable, "\n");
printf("\nArguments:\n");
arg_print_glossary(stdout, argtable, "%-25s %s\n");
goto exit_0;
}
// Handle version
if(vers->count > 0) {
printf("%s v0.1\n", progname);
printf("Command line One Must Fall 2097 SOUNDS.DAT file editor.\n");
printf("Source code is available at https://github.com/omf2097 under MIT license.\n");
printf("(C) 2013 Tuomas Virtanen\n");
goto exit_0;
}
// Handle errors
if(nerrors > 0) {
arg_print_errors(stdout, end, progname);
printf("Try '%s --help' for more information.\n", progname);
goto exit_0;
}
// Open sounds.dat
sd_sound_file sf;
sd_sounds_create(&sf);
retcode = sd_sounds_load(&sf, file->filename[0]);
if(retcode) {
printf("Error %d: %s\n", retcode, sd_get_error(retcode));
goto exit_1;
}
if(sid->count > 0) {
// Sound ID to handle
int sound_id = sid->ival[0];
const sd_sound *sound = sd_sounds_get(&sf, sound_id-1);
if(sound == NULL) {
printf("Invalid sound ID");
goto exit_1;
}
if(sampleprint->count > 0) {
int count = (sampleprint->ival[0] > sound->len) ? sound->len : sampleprint->ival[0];
printf("Sample size = %d\n", sound->len);
printf("Unknown = %d\n", sound->unknown);
printf("Attempting to print %d first bytes.\n", count);
for(int i = 0; i < count; i++) {
unsigned int s = sound->data[i] & 0xFF;
printf("%2x ", s);
}
} else if(play->count > 0) {
printf("Attempting to play sample #%d.\n", sound_id);
// Make sure there is data at requested ID position
if(sound->len <= 0) {
printf("Sample does not contain data.\n");
goto exit_1;
}
// Streamer
streamer.size = sound->len;
streamer.pos = 0;
streamer.data = sound->data;
// Initialize required audio
SDL_zero(want);
want.freq = 8000;
want.format = AUDIO_U8;
want.channels = 1;
want.samples = 4096;
want.callback = stream;
want.userdata = &streamer;
// Open device, play file
dev = SDL_OpenAudioDevice(NULL, 0, &want, &have, 0);
if(dev == 0) {
printf("Failed to open audio dev: %s\n", SDL_GetError());
goto exit_0;
} else {
if(have.format != want.format) {
printf("Could not get correct playback format.\n");
} else {
printf("Starting playback ...\n");
SDL_PauseAudioDevice(dev, 0);
while(streamer.pos < streamer.size) {
SDL_Delay(100);
}
printf("All done.\n");
}
SDL_CloseAudioDevice(dev);
}
} else if(import->count > 0) {
if(sd_sound_from_au(&sf, sound_id, import->filename[0]) != SD_SUCCESS) {
printf("Importing sample %d from file %s failed.\n", sound_id, import->filename[0]);
} else {
printf("Importing sample %d from file %s succeeded.\n", sound_id, import->filename[0]);
}
} else if(export->count > 0) {
if(sd_sound_to_au(&sf, sound_id, export->filename[0]) != SD_SUCCESS) {
printf("Exporting sample %d to file %s failed.\n", sound_id, export->filename[0]);
} else {
printf("Exporting sample %d to file %s succeeded.\n", sound_id, export->filename[0]);
}
} else {
int main(int argc, char **argv)
{
/* SYNTAX 1: insert [-nvR] <file> [file]... -o <file> */
struct arg_rex *cmd1 = arg_rex1(NULL, NULL, "insert", NULL, REG_ICASE, NULL);
struct arg_lit *noact1 = arg_lit0("n", NULL, "take no action");
struct arg_lit *verbose1 = arg_lit0("v", "verbose", "verbose messages");
struct arg_lit *recurse1 = arg_lit0("R", NULL, "recurse through subdirectories");
struct arg_file *infiles1 = arg_filen(NULL, NULL, NULL, 1,argc+2, "input file(s)");
struct arg_file *outfile1 = arg_file0("o", NULL, "<output>", "output file (default is \"-\")");
struct arg_end *end1 = arg_end(20);
void* argtable1[] = {cmd1,noact1,verbose1,recurse1,infiles1,outfile1,end1};
int nerrors1;
/* SYNTAX 2: remove [-nv] <file> */
struct arg_rex *cmd2 = arg_rex1(NULL, NULL, "remove", NULL, REG_ICASE, NULL);
struct arg_lit *noact2 = arg_lit0("n", NULL, NULL);
struct arg_lit *verbose2 = arg_lit0("v", "verbose", NULL);
struct arg_file *infiles2 = arg_file1(NULL, NULL, NULL, NULL);
struct arg_end *end2 = arg_end(20);
void* argtable2[] = {cmd2,noact2,verbose2,infiles2,end2};
int nerrors2;
/* SYNTAX 3: search [-v] <pattern> [-o <file>] [--help] [--version] */
struct arg_rex *cmd3 = arg_rex1(NULL, NULL, "search", NULL, REG_ICASE, NULL);
struct arg_lit *verbose3 = arg_lit0("v", "verbose", NULL);
struct arg_str *pattern3 = arg_str1(NULL, NULL, "<pattern>", "search string");
struct arg_file *outfile3 = arg_file0("o", NULL, "<output>", NULL);
struct arg_end *end3 = arg_end(20);
void* argtable3[] = {cmd3,verbose3,pattern3,outfile3,end3};
int nerrors3;
/* SYNTAX 4: [-help] [-version] */
struct arg_lit *help4 = arg_lit0(NULL,"help", "print this help and exit");
struct arg_lit *version4 = arg_lit0(NULL,"version", "print version information and exit");
struct arg_end *end4 = arg_end(20);
void* argtable4[] = {help4,version4,end4};
int nerrors4;
const char* progname = "multisyntax";
int exitcode=0;
/* verify all argtable[] entries were allocated sucessfully */
if (arg_nullcheck(argtable1)!=0 ||
arg_nullcheck(argtable2)!=0 ||
arg_nullcheck(argtable3)!=0 ||
arg_nullcheck(argtable4)!=0 )
{
/* NULL entries were detected, some allocations must have failed */
printf("%s: insufficient memory\n",progname);
exitcode=1;
goto exit;
}
/* set any command line default values prior to parsing */
outfile1->filename[0]="-";
outfile3->filename[0]="-";
/* Above we defined a separate argtable for each possible command line syntax */
/* and here we parse each one in turn to see if any of them are successful */
nerrors1 = arg_parse(argc,argv,argtable1);
nerrors2 = arg_parse(argc,argv,argtable2);
nerrors3 = arg_parse(argc,argv,argtable3);
nerrors4 = arg_parse(argc,argv,argtable4);
/* Execute the appropriate main<n> routine for the matching command line syntax */
/* In this example program our alternate command line syntaxes are mutually */
/* exclusive, so we know in advance that only one of them can be successful. */
if (nerrors1==0)
exitcode = mymain1(noact1->count, verbose1->count, recurse1->count,
outfile1->filename[0], infiles1->filename, infiles1->count);
else if (nerrors2==0)
exitcode = mymain2(noact2->count, verbose2->count, infiles2->filename[0]);
else if (nerrors3==0)
exitcode = mymain3(verbose3->count, pattern3->sval[0], outfile3->filename[0]);
else if (nerrors4==0)
exitcode = mymain4(help4->count, version4->count, progname,
argtable1, argtable2, argtable3, argtable4);
else
{
/* We get here if the command line matched none of the possible syntaxes */
if (cmd1->count > 0)
{
/* here the cmd1 argument was correct, so presume syntax 1 was intended target */
arg_print_errors(stdout,end1,progname);
printf("usage: %s ", progname);
arg_print_syntax(stdout,argtable1,"\n");
}
else if (cmd2->count > 0)
{
/* here the cmd2 argument was correct, so presume syntax 2 was intended target */
arg_print_errors(stdout,end2,progname);
printf("usage: %s ", progname);
arg_print_syntax(stdout,argtable2,"\n");
}
else if (cmd3->count > 0)
{
/* here the cmd3 argument was correct, so presume syntax 3 was intended target */
arg_print_errors(stdout,end3,progname);
printf("usage: %s ", progname);
arg_print_syntax(stdout,argtable3,"\n");
}
else
{
/* no correct cmd literals were given, so we cant presume which syntax was intended */
printf("%s: missing <insert|remove|search> command.\n",progname);
printf("usage 1: %s ", progname); arg_print_syntax(stdout,argtable1,"\n");
printf("usage 2: %s ", progname); arg_print_syntax(stdout,argtable2,"\n");
printf("usage 3: %s ", progname); arg_print_syntax(stdout,argtable3,"\n");
printf("usage 4: %s", progname); arg_print_syntax(stdout,argtable4,"\n");
}
}
exit:
/* deallocate each non-null entry in each argtable */
arg_freetable(argtable1,sizeof(argtable1)/sizeof(argtable1[0]));
arg_freetable(argtable2,sizeof(argtable2)/sizeof(argtable2[0]));
arg_freetable(argtable3,sizeof(argtable3)/sizeof(argtable3[0]));
arg_freetable(argtable4,sizeof(argtable4)/sizeof(argtable4[0]));
return exitcode;
}
int genkmarkers(int argc, char* argv[])
{
// determine my process name
_splitpath(argv[0],NULL,NULL,gszProcName,NULL);
#else
int
genkmarkers(int argc, char** argv)
{
// determine my process name
CUtility::splitpath((char *)argv[0],NULL,gszProcName);
#endif
int iScreenLogLevel; // level of screen diagnostics
int iFileLogLevel; // level of file diagnostics
char szLogFile[_MAX_PATH]; // write diagnostics to this file
int Rslt = 0; // function result code >= 0 represents success, < 0 on failure
int NumberOfProcessors; // number of installed CPUs
int NumThreads; // number of threads (0 defaults to number of CPUs)
int PMode; // processing mode
int KMerLen; // this length K-mers
int PrefixLen; // inter-cultivar shared prefix length
int SuffixLen; // cultivar specific suffix length
int MinWithPrefix; // minimum number of cultivars required to have the shared prefix
int MinHamming; // must be at least this Hamming away from any other K-mer in other species
char szCultivarName[cMaxDatasetSpeciesChrom+1]; // cultivar name
char szPartialCultivarsList[(cMaxDatasetSpeciesChrom + 10) * cMaxTargCultivarChroms]; // individual species parsed from this comma/tab/space separated list
int NumPartialCultivars; // there are this many pseudo chromosomes for targeted cultivar for which K-mer markers are required
char *pszPartialCultivars[cMaxTargCultivarChroms+1]; // pseudo chromosome names which identify targeted cultivar
char szSfxPseudoGenome[_MAX_PATH]; // contains assembly + suffix array over all psuedo-chromosomes for all cultivars
char szMarkerFile[_MAX_PATH]; // output potential markers to this file
char szMarkerReadsFile[_MAX_PATH]; // output reads containing potential markers to this file
char szSQLiteDatabase[_MAX_PATH]; // results summaries to this SQLite file
char szExperimentName[cMaxDatasetSpeciesChrom+1]; // experiment name
char szExperimentDescr[1000]; // describes experiment
// command line args
struct arg_lit *help = arg_lit0("h","help", "Print this help and exit");
struct arg_lit *version = arg_lit0("v","version,ver", "Print version information and exit");
struct arg_int *FileLogLevel=arg_int0("f", "FileLogLevel", "<int>","Level of diagnostics written to screen and logfile 0=fatal,1=errors,2=info,3=diagnostics,4=debug");
struct arg_file *LogFile = arg_file0("F","log","<file>", "Diagnostics log file");
struct arg_int *pmode = arg_int0("m","mode","<int>", "Processing mode : 0 - default with K-mer extension, 1 - no K-mer extension, 2 - inter-cultivar shared prefix sequences ");
struct arg_int *kmerlen = arg_int0("k","kmer","<int>", "Cultivar specific K-mers of this length (default 50, range 25..100)");
struct arg_int *prefixlen = arg_int0("p","prefixlen","<int>", "Cultivar specific K-mers to contain inter-cultivar shared prefix sequences of this length (Mode 2 only");
struct arg_int *minwithprefix = arg_int0("s","minshared","<int>","Inter-cultivar shared prefix sequences must be present in this many cultivars (Mode 2 only, default all)");
struct arg_int *minhamming = arg_int0("K","minhamming","<int>", "Minimum Hamming separation distance in other non-target cultivars (default 2, range 1..5)");
struct arg_str *cultivar = arg_str1("c","cultivar","<str>", "Cultivar name to associate with identified marker K-mers");
struct arg_str *chromnames = arg_str1("C","chromnames","<str>", "Comma/space separated list of pseudo-chrom names specific to cultivar for which markers are required");
struct arg_file *infile = arg_file1("i","in","<file>", "Use this suffix indexed pseudo-chromosomes file");
struct arg_file *outfile = arg_file1("o","markers","<file>", "Output accepted marker K-mer sequences to this multifasta file");
struct arg_file *outreadsfile = arg_file0("O","markerreads","<file>", "Output reads containing accepted marker K-mers to this multifasta file");
struct arg_int *numthreads = arg_int0("T","threads","<int>", "number of processing threads 0..128 (defaults to 0 which sets threads to number of CPU cores)");
struct arg_file *summrslts = arg_file0("q","sumrslts","<file>", "Output results summary to this SQLite3 database file");
struct arg_str *experimentname = arg_str0("w","experimentname","<str>", "experiment name SQLite3 database file");
struct arg_str *experimentdescr = arg_str0("W","experimentdescr","<str>", "experiment description SQLite3 database file");
struct arg_end *end = arg_end(200);
void *argtable[] = {help,version,FileLogLevel,LogFile,
summrslts,experimentname,experimentdescr,
pmode,kmerlen,prefixlen,minwithprefix,minhamming,cultivar,chromnames,infile,outfile,outreadsfile,
numthreads,
end};
char **pAllArgs;
int argerrors;
argerrors = CUtility::arg_parsefromfile(argc,(char **)argv,&pAllArgs);
if(argerrors >= 0)
argerrors = arg_parse(argerrors,pAllArgs,argtable);
/* special case: '--help' takes precedence over error reporting */
if (help->count > 0)
{
printf("\n%s %s %s, Version %s\nOptions ---\n", gszProcName,gpszSubProcess->pszName,gpszSubProcess->pszFullDescr,cpszProgVer);
arg_print_syntax(stdout,argtable,"\n");
arg_print_glossary(stdout,argtable," %-25s %s\n");
printf("\nNote: Parameters can be entered into a parameter file, one parameter per line.");
printf("\n To invoke this parameter file then precede its name with '@'");
printf("\n e.g. %s %s @myparams.txt\n",gszProcName,gpszSubProcess->pszName);
printf("\nPlease report any issues regarding usage of %s at https://github.com/csiro-crop-informatics/biokanga/issues\n\n",gszProcName);
return(1);
}
/* special case: '--version' takes precedence error reporting */
if (version->count > 0)
{
printf("\n%s %s Version %s\n",gszProcName,gpszSubProcess->pszName,cpszProgVer);
return(1);
}
if (!argerrors)
{
if(FileLogLevel->count && !LogFile->count)
{
printf("\nError: FileLogLevel '-f%d' specified but no logfile '-F<logfile>\n'",FileLogLevel->ival[0]);
return(1);
}
iScreenLogLevel = iFileLogLevel = FileLogLevel->count ? FileLogLevel->ival[0] : eDLInfo;
if(iFileLogLevel < eDLNone || iFileLogLevel > eDLDebug)
{
printf("\nError: FileLogLevel '-l%d' specified outside of range %d..%d\n",iFileLogLevel,eDLNone,eDLDebug);
return(1);
}
if(LogFile->count)
{
strncpy(szLogFile,LogFile->filename[0],_MAX_PATH);
szLogFile[_MAX_PATH-1] = '\0';
}
else
{
iFileLogLevel = eDLNone;
szLogFile[0] = '\0';
}
// now that log parameters have been parsed then initialise diagnostics log system
if(!gDiagnostics.Open(szLogFile,(etDiagLevel)iScreenLogLevel,(etDiagLevel)iFileLogLevel,true))
{
printf("\nError: Unable to start diagnostics subsystem\n");
if(szLogFile[0] != '\0')
printf(" Most likely cause is that logfile '%s' can't be opened/created\n",szLogFile);
return(1);
}
gDiagnostics.DiagOut(eDLInfo,gszProcName,"Subprocess %s Version %s starting",gpszSubProcess->pszName,cpszProgVer);
gExperimentID = 0;
gProcessID = 0;
gProcessingID = 0;
szSQLiteDatabase[0] = '\0';
szExperimentName[0] = '\0';
szExperimentDescr[0] = '\0';
if(experimentname->count)
{
strncpy(szExperimentName,experimentname->sval[0],sizeof(szExperimentName));
szExperimentName[sizeof(szExperimentName)-1] = '\0';
CUtility::TrimQuotedWhitespcExtd(szExperimentName);
CUtility::ReduceWhitespace(szExperimentName);
}
else
szExperimentName[0] = '\0';
gExperimentID = 0;
gProcessID = 0;
gProcessingID = 0;
szSQLiteDatabase[0] = '\0';
szExperimentDescr[0] = '\0';
if(summrslts->count)
{
strncpy(szSQLiteDatabase,summrslts->filename[0],sizeof(szSQLiteDatabase)-1);
szSQLiteDatabase[sizeof(szSQLiteDatabase)-1] = '\0';
CUtility::TrimQuotedWhitespcExtd(szSQLiteDatabase);
if(strlen(szSQLiteDatabase) < 1)
{
gDiagnostics.DiagOut(eDLFatal,gszProcName,"Error: After removal of whitespace, no SQLite database specified with '-q<filespec>' option");
return(1);
}
if(strlen(szExperimentName) < 1)
{
gDiagnostics.DiagOut(eDLFatal,gszProcName,"Error: After removal of whitespace, no SQLite experiment name specified with '-w<str>' option");
return(1);
}
if(experimentdescr->count)
{
strncpy(szExperimentDescr,experimentdescr->sval[0],sizeof(szExperimentDescr)-1);
szExperimentDescr[sizeof(szExperimentDescr)-1] = '\0';
CUtility::TrimQuotedWhitespcExtd(szExperimentDescr);
}
if(strlen(szExperimentDescr) < 1)
{
gDiagnostics.DiagOut(eDLFatal,gszProcName,"Error: After removal of whitespace, no SQLite experiment description specified with '-W<str>' option");
return(1);
}
gExperimentID = gSQLiteSummaries.StartExperiment(szSQLiteDatabase,false,true,szExperimentName,szExperimentName,szExperimentDescr);
if(gExperimentID < 1)
return(1);
gProcessID = gSQLiteSummaries.AddProcess((char *)gpszSubProcess->pszName,(char *)gpszSubProcess->pszName,(char *)gpszSubProcess->pszFullDescr);
if(gProcessID < 1)
return(1);
gProcessingID = gSQLiteSummaries.StartProcessing(gExperimentID,gProcessID,(char *)cpszProgVer);
if(gProcessingID < 1)
return(1);
gDiagnostics.DiagOut(eDLInfo,gszProcName,"Initialised SQLite database '%s' for results summary collection",szSQLiteDatabase);
gDiagnostics.DiagOut(eDLInfo,gszProcName,"SQLite database experiment identifier for '%s' is %d",szExperimentName,gExperimentID);
gDiagnostics.DiagOut(eDLInfo,gszProcName,"SQLite database process identifier for '%s' is %d",(char *)gpszSubProcess->pszName,gProcessID);
gDiagnostics.DiagOut(eDLInfo,gszProcName,"SQLite database processing instance identifier is %d",gProcessingID);
}
else
{
szSQLiteDatabase[0] = '\0';
szExperimentDescr[0] = '\0';
}
// show user current resource limits
#ifndef _WIN32
gDiagnostics.DiagOut(eDLInfo, gszProcName, "Resources: %s",CUtility::ReportResourceLimits());
#endif
#ifdef _WIN32
SYSTEM_INFO SystemInfo;
GetSystemInfo(&SystemInfo);
NumberOfProcessors = SystemInfo.dwNumberOfProcessors;
#else
NumberOfProcessors = sysconf(_SC_NPROCESSORS_CONF);
#endif
int MaxAllowedThreads = min(cMaxWorkerThreads,NumberOfProcessors); // limit to be at most cMaxWorkerThreads
if((NumThreads = numthreads->count ? numthreads->ival[0] : MaxAllowedThreads)==0)
NumThreads = MaxAllowedThreads;
if(NumThreads < 0 || NumThreads > MaxAllowedThreads)
{
gDiagnostics.DiagOut(eDLWarn,gszProcName,"Warning: Number of threads '-T%d' specified was outside of range %d..%d",NumThreads,1,MaxAllowedThreads);
gDiagnostics.DiagOut(eDLWarn,gszProcName,"Warning: Defaulting number of threads to %d",MaxAllowedThreads);
NumThreads = MaxAllowedThreads;
}
PMode = (etPMode)(pmode->count ? pmode->ival[0] : ePMExtdKMers);
if(PMode < ePMExtdKMers || PMode >= ePMplaceholder)
{
gDiagnostics.DiagOut(eDLFatal,gszProcName,"Error: Processing mode '-m%d' specified outside of range %d..%d\n",PMode,ePMExtdKMers,(int)ePMplaceholder-1);
exit(1);
}
KMerLen = kmerlen->count ? kmerlen->ival[0] : cDfltKMerLen;
if(KMerLen < cMinKMerLen || KMerLen > cMaxKMerLen)
{
gDiagnostics.DiagOut(eDLFatal,gszProcName,"Error: K-mer core length '-k%d' must be in range %d..%d",KMerLen,cMinKMerLen,cMaxKMerLen);
return(1);
}
if(PMode == 2)
{
PrefixLen = prefixlen->count ? prefixlen->ival[0] : KMerLen/2;
if(PrefixLen < cMinKMerLen/2 || PrefixLen > KMerLen-(cMinKMerLen/2))
{
gDiagnostics.DiagOut(eDLFatal,gszProcName,"Error: Prefix length '-p%d' must be in range %d..%d",KMerLen,cMinKMerLen/2,KMerLen-(cMinKMerLen/2));
return(1);
}
SuffixLen = KMerLen - PrefixLen;
MinWithPrefix = minwithprefix->count ? minwithprefix->ival[0] : 0;
if(MinWithPrefix != 0 && MinWithPrefix < 1)
{
gDiagnostics.DiagOut(eDLFatal,gszProcName,"Error: Minimum cultivars sharing prefix sequence '-s%d' must be either 0 (all) or at least 1",MinWithPrefix);
return(1);
}
}
MinHamming = minhamming->count ? minhamming->ival[0] : cDfltHamming;
if(MinHamming < cMinHamming || MinHamming > cMaxHamming)
{
gDiagnostics.DiagOut(eDLFatal,gszProcName,"Error: Minimum Hamming separation '-K%d' must be in range %d..%d",MinHamming,cMinHamming,cMaxHamming);
return(1);
}
strncpy(szCultivarName,cultivar->sval[0],cMaxDatasetSpeciesChrom);
szCultivarName[cMaxDatasetSpeciesChrom]= '\0';
CUtility::TrimQuotedWhitespcExtd(szCultivarName);
if(strlen(szCultivarName) < 1)
{
gDiagnostics.DiagOut(eDLFatal,gszProcName,"Error: Expected cultivar name '-c<name>' is empty");
return(1);
}
strncpy(szPartialCultivarsList,chromnames->sval[0],sizeof(szPartialCultivarsList));
szPartialCultivarsList[sizeof(szPartialCultivarsList)-1] = '\0';
CUtility::TrimQuotedWhitespcExtd(szPartialCultivarsList);
CUtility::ReduceWhitespace(szPartialCultivarsList);
char *pChr = szPartialCultivarsList;
char *pStartChr;
char Chr;
int CurSpeciesLen;
NumPartialCultivars=0;
CurSpeciesLen = 0;
pStartChr = pChr;
while((Chr = *pChr++) != '\0')
{
if(Chr == ' ' || Chr == '\t' || Chr == ',') // treat any of these as delimiters
{
pChr[-1] = '\0';
if(CurSpeciesLen != 0)
{
pszPartialCultivars[NumPartialCultivars++] = pStartChr;
CurSpeciesLen = 0;
}
pStartChr = pChr;
continue;
}
CurSpeciesLen += 1;
}
if(CurSpeciesLen)
pszPartialCultivars[NumPartialCultivars++] = pStartChr;
if(!NumPartialCultivars)
{
gDiagnostics.DiagOut(eDLFatal,gszProcName,"Error: Expected at least one ('-C<names>') targeted cultivar chromosme name");
return(1);
}
strcpy(szSfxPseudoGenome,infile->filename[0]);
CUtility::TrimQuotedWhitespcExtd(szSfxPseudoGenome);
if(strlen(szSfxPseudoGenome) < 1)
{
gDiagnostics.DiagOut(eDLFatal,gszProcName,"Error: Expected input pseudo-genome suffix array filename '-i<name>' is empty");
return(1);
}
strcpy(szMarkerFile,outfile->filename[0]);
CUtility::TrimQuotedWhitespcExtd(szMarkerFile);
if(strlen(szMarkerFile) < 1)
{
gDiagnostics.DiagOut(eDLFatal,gszProcName,"Error: Expected marker file to generate filename '-o<name>' is empty");
return(1);
}
if(outreadsfile->count)
{
strcpy(szMarkerReadsFile,outreadsfile->filename[0]);
CUtility::TrimQuotedWhitespcExtd(szMarkerReadsFile);
if(strlen(szMarkerReadsFile) < 1)
{
gDiagnostics.DiagOut(eDLFatal,gszProcName,"Error: Reads containing markers filename '-O<name>' is empty");
return(1);
}
}
else
szMarkerReadsFile[0] = '\0';
gDiagnostics.DiagOut(eDLInfo,gszProcName,"Processing parameters:");
const char *pszDescr;
switch(PMode) {
case ePMExtdKMers:
pszDescr = "Extended K-mer markers";
break;
case ePMNoExtdKMers:
pszDescr = "Non-extended K-mer markers";
break;
case ePMPrefixKMers:
pszDescr = "K-mers to share prefix sequence with other cultivars";
break;
}
gDiagnostics.DiagOutMsgOnly(eDLInfo,"Processing mode is : '%s'",pszDescr);
gDiagnostics.DiagOutMsgOnly(eDLInfo,"Targeted cultivar name : '%s'",szCultivarName);
for(int Idx = 0; Idx < NumPartialCultivars; Idx++)
gDiagnostics.DiagOutMsgOnly(eDLInfo,"Targeted cultivar chromosome name (%d) : '%s'", Idx + 1,pszPartialCultivars[Idx]);
gDiagnostics.DiagOutMsgOnly(eDLInfo,"Core K-mer length : %d",KMerLen);
if(PMode == ePMPrefixKMers)
{
gDiagnostics.DiagOutMsgOnly(eDLInfo,"Inter-cultivar shared prefix sequence length : %d",PrefixLen);
gDiagnostics.DiagOutMsgOnly(eDLInfo,"Cultivar specific suffix sequence length : %d",SuffixLen);
if(MinWithPrefix)
gDiagnostics.DiagOutMsgOnly(eDLInfo,"Min number cultivars sharing prefix : %d",MinWithPrefix);
else
gDiagnostics.DiagOutMsgOnly(eDLInfo,"Min number cultivars sharing prefix : 'All'");
}
gDiagnostics.DiagOutMsgOnly(eDLInfo,"Minimum Hamming separation : %d",MinHamming);
gDiagnostics.DiagOutMsgOnly(eDLInfo,"Input indexed pseudo-genome file: '%s'",szSfxPseudoGenome);
gDiagnostics.DiagOutMsgOnly(eDLInfo,"Write marker K-mers to file: '%s'",szMarkerFile);
if(szMarkerReadsFile[0] != '\0')
gDiagnostics.DiagOutMsgOnly(eDLInfo,"Write marker containing reads to file: '%s'",szMarkerReadsFile);
if(szExperimentName[0] != '\0')
gDiagnostics.DiagOutMsgOnly(eDLInfo,"This processing reference: %s",szExperimentName);
gDiagnostics.DiagOutMsgOnly(eDLInfo,"Number of processing threads: %d",NumThreads);
if(gExperimentID > 0)
{
int ParamID;
ParamID = gSQLiteSummaries.AddParameter(gProcessingID,ePTText,(int)strlen(szLogFile),"log",szLogFile);
ParamID = gSQLiteSummaries.AddParameter(gProcessingID,ePTInt32,sizeof(PMode),"mode",&PMode);
ParamID = gSQLiteSummaries.AddParameter(gProcessingID,ePTInt32,sizeof(KMerLen),"kmer",&KMerLen);
ParamID = gSQLiteSummaries.AddParameter(gProcessingID,ePTInt32,sizeof(PrefixLen),"prefixlen",&PrefixLen);
ParamID = gSQLiteSummaries.AddParameter(gProcessingID,ePTInt32,sizeof(SuffixLen),"suffixlen",&SuffixLen);
ParamID = gSQLiteSummaries.AddParameter(gProcessingID,ePTInt32,sizeof(MinWithPrefix),"minwithprefix",&MinWithPrefix);
ParamID = gSQLiteSummaries.AddParameter(gProcessingID,ePTInt32,sizeof(MinHamming),"minhamming",&MinHamming);
ParamID = gSQLiteSummaries.AddParameter(gProcessingID,ePTInt32,sizeof(NumThreads),"threads",&NumThreads);
ParamID = gSQLiteSummaries.AddParameter(gProcessingID,ePTInt32,sizeof(NumberOfProcessors),"cpus",&NumberOfProcessors);
ParamID = gSQLiteSummaries.AddParameter(gProcessingID,ePTText,(int)strlen(szCultivarName),"cultivar",szCultivarName);
ParamID = gSQLiteSummaries.AddParameter(gProcessingID,ePTInt32,sizeof(NumPartialCultivars),"NumPartialCultivars",&NumPartialCultivars);
for(int Idx = 0; Idx < NumPartialCultivars; Idx++)
ParamID = gSQLiteSummaries.AddParameter(gProcessingID,ePTText,(int)strlen(pszPartialCultivars[Idx]),"chromnames",pszPartialCultivars[Idx]);
ParamID = gSQLiteSummaries.AddParameter(gProcessingID,ePTText,(int)strlen(szSfxPseudoGenome),"in",szSfxPseudoGenome);
ParamID = gSQLiteSummaries.AddParameter(gProcessingID,ePTText,(int)strlen(szMarkerFile),"markers",szMarkerFile);
ParamID = gSQLiteSummaries.AddParameter(gProcessingID,ePTText,(int)strlen(szMarkerReadsFile),"markerreads",szMarkerReadsFile);
ParamID = gSQLiteSummaries.AddParameter(gProcessingID,ePTText,(int)strlen(szSQLiteDatabase),"sumrslts",szSQLiteDatabase);
ParamID = gSQLiteSummaries.AddParameter(gProcessingID,ePTText,(int)strlen(szExperimentName),"experimentname",szExperimentName);
ParamID = gSQLiteSummaries.AddParameter(gProcessingID,ePTText,(int)strlen(szExperimentDescr),"experimentdescr",szExperimentDescr);
}
#ifdef _WIN32
SetPriorityClass(GetCurrentProcess(), BELOW_NORMAL_PRIORITY_CLASS);
#endif
gStopWatch.Start();
Rslt = LocMarkers((etPMode)PMode,KMerLen,PrefixLen,SuffixLen,MinWithPrefix,MinHamming,szCultivarName,NumPartialCultivars,pszPartialCultivars,szSfxPseudoGenome,szMarkerFile,szMarkerReadsFile,NumThreads);
Rslt = Rslt >=0 ? 0 : 1;
if(gExperimentID > 0)
{
if(gProcessingID)
gSQLiteSummaries.EndProcessing(gProcessingID,Rslt);
gSQLiteSummaries.EndExperiment(gExperimentID);
}
gStopWatch.Stop();
gDiagnostics.DiagOut(eDLInfo,gszProcName,"Exit code: %d Total processing time: %s",Rslt,gStopWatch.Read());
return(Rslt);
}
else
{
printf("\n%s %s %s, Version %s\n", gszProcName,gpszSubProcess->pszName,gpszSubProcess->pszFullDescr,cpszProgVer);
arg_print_errors(stdout,end,gszProcName);
arg_print_syntax(stdout,argtable,"\nUse '-h' to view option and parameter usage\n");
return(1);
}
return 0;
}
int main(int argc, char* argv[])
{
// Define arguments.
struct arg_lit* show_help = arg_lit0("h", "help", "Show this help.");
struct arg_str* type_assembler = arg_str0("t", NULL, "<type>", "The type of assembler to output for.");
struct arg_file* input_file = arg_file1(NULL, NULL, "<file>", "The input file (or - to read from standard input).");
struct arg_file* output_file = arg_file1("o", "output", "<file>", "The output file (or - to send to standard output).");
struct arg_end *end = arg_end(20);
void *argtable[] = { output_file, show_help, type_assembler, input_file, end };
// Parse arguments.
int nerrors = arg_parse(argc,argv,argtable);
if (nerrors != 0 || show_help->count != 0)
{
if (show_help->count != 0)
arg_print_errors(stdout, end, "compiler");
fprintf(stderr, "syntax:\n compiler");
arg_print_syntax(stdout, argtable, "\n");
fprintf(stderr, "options:\n");
arg_print_glossary(stdout, argtable, " %-25s %s\n");
return 1;
}
// Parse C.
pp_add_search_path(".");
pp_add_search_path("include");
pp_add_search_path(dirname<std::string>(input_file->filename[0]).c_str());
yyout = stderr;
yyin = pp_do(input_file->filename[0]);
if (yyin == NULL)
{
pp_cleanup();
return 1;
}
yyparse();
if (yyin != stdin)
fclose(yyin);
pp_cleanup();
if (program == NULL)
{
std::cerr << "An error occurred while compiling." << std::endl;
return 1;
}
// Assembler type.
const char* asmtype = "dcpu16toolchain";
if (type_assembler->count > 0)
asmtype = type_assembler->sval[0];
// Spacing.
std::cerr << std::endl;
// Generate assembly using the AST.
try
{
AsmGenerator generator(asmtype);
AsmBlock* block = program->compile(generator);
if (strcmp(output_file->filename[0], "-") == 0)
{
std::cout << generator.m_Preassembly << std::endl;
std::cout << *block << std::endl;
std::cout << generator.m_Postassembly << std::endl;
}
else
{
std::ofstream output(output_file->filename[0], std::ios::out | std::ios::trunc);
output << generator.m_Preassembly << std::endl;
output << *block << std::endl;
output << generator.m_Postassembly << std::endl;
output.close();
}
delete block;
}
catch (CompilerException* ex)
{
std::string msg = ex->getMessage();
std::cerr << "An error occurred while compiling." << std::endl;
std::cerr << msg << std::endl;
return 1;
}
return 0;
}
int main(int argc, char **argv)
{
const char* progname = "uname";
struct arg_lit *all = arg_lit0("a", "all", "print all information, in the following order:");
struct arg_lit *kname = arg_lit0("s", "kernel-name", "print the kernel name");
struct arg_lit *nname = arg_lit0("n", "nodename", "print the node name");
struct arg_lit *krel = arg_lit0("r", "kernel-release", "print the kernel release");
struct arg_lit *kver = arg_lit0("v", "kernel-version", "print the kernel version");
struct arg_lit *mach = arg_lit0("m", "machine", "print the machine hardware name");
struct arg_lit *proc = arg_lit0("p", "processor", "print the processor type");
struct arg_lit *hard = arg_lit0("i", "hardware-platform","print the hardware platform");
struct arg_lit *opsys = arg_lit0("o", "operating-system", "print the operating system");
struct arg_lit *help = arg_lit0(NULL,"help", "print this help and exit");
struct arg_lit *vers = arg_lit0(NULL,"version", "print version information and exit");
struct arg_end *end = arg_end(20);
void* argtable[] = {all,kname,nname,krel,kver,mach,proc,hard,opsys,help,vers,end};
int nerrors;
int exitcode=0;
/* verify the argtable[] entries were allocated sucessfully */
if (arg_nullcheck(argtable) != 0)
{
/* NULL entries were detected, some allocations must have failed */
printf("%s: insufficient memory\n",progname);
exitcode=1;
goto exit;
}
/* Parse the command line as defined by argtable[] */
nerrors = arg_parse(argc,argv,argtable);
/* special case: '--help' takes precedence over error reporting */
if (help->count > 0)
{
printf("Usage: %s", progname);
arg_print_syntax(stdout,argtable,"\n");
printf("Print certain system information. With no options, same as -s.\n\n");
arg_print_glossary(stdout,argtable," %-25s %s\n");
printf("\nReport bugs to <foo@bar>.\n");
exitcode=0;
goto exit;
}
/* special case: '--version' takes precedence error reporting */
if (vers->count > 0)
{
printf("'%s' example program for the \"argtable\" command line argument parser.\n",progname);
printf("September 2003, Stewart Heitmann\n");
exitcode=0;
goto exit;
}
/* If the parser returned any errors then display them and exit */
if (nerrors > 0)
{
/* Display the error details contained in the arg_end struct.*/
arg_print_errors(stdout,end,progname);
printf("Try '%s --help' for more information.\n",progname);
exitcode=1;
goto exit;
}
/* special case: uname with no command line options is equivalent to "uname -s" */
if (argc==1)
{
exitcode = mymain(0,1,0,0,0,0,0,0);
goto exit;
}
/* special case: "uname -a" is equivalent to "uname -snrvmpi" */
if (all->count>0)
{
exitcode = mymain(1,1,1,1,1,1,1,1);
goto exit;
}
/* normal case: take the command line options at face value */
exitcode = mymain(kname->count, nname->count, krel->count, kver->count, mach->count, proc->count, hard->count, opsys->count);
exit:
/* deallocate each non-null entry in argtable[] */
arg_freetable(argtable,sizeof(argtable)/sizeof(argtable[0]));
return exitcode;
}
int main(int argc, char* argv[])
{
// Define our variables.
int nerrors, i;
int32_t saved = 0; // The number of words saved during compression and optimization.
struct errinfo* errval;
const char* prepend = "error: ";
const char* warnprefix = "no-";
int msglen;
char* msg;
int target;
// Define arguments.
struct arg_lit* show_help = arg_lit0("h", "help", "Show this help.");
struct arg_str* target_arg = arg_str0("l", "link-as", "target", "Link as the specified object, can be 'image', 'static' or 'kernel'.");
struct arg_file* symbol_file = arg_file0("s", "symbols", "<file>", "Produce a combined symbol file (~triples memory usage!).");
struct arg_str* symbol_ext = arg_str0(NULL, "symbol-extension", "ext", "When -s is used, specifies the extension for symbol files. Defaults to \"dsym16\".");
struct arg_file* input_files = arg_filen(NULL, NULL, "<file>", 1, 100, "The input object files.");
struct arg_file* output_file = arg_file1("o", "output", "<file>", "The output file (or - to send to standard output).");
struct arg_file* kernel_file = arg_file0("k", "kernel", "<file>", "Directly link in the specified kernel.");
struct arg_file* jumplist_file = arg_file0("j", "jumplist", "<file>", "Link against the specified jumplist.");
struct arg_str* warning_policies = arg_strn("W", NULL, "policy", 0, _WARN_COUNT * 2 + 10, "Modify warning policies.");
struct arg_lit* keep_output_arg = arg_lit0(NULL, "keep-outputs", "Keep the .OUTPUT entries in the final static library (used for stdlib).");
struct arg_lit* little_endian_mode = arg_lit0(NULL, "little-endian", "Use little endian serialization (for compatibility with older versions).");
struct arg_lit* no_short_literals_arg = arg_lit0(NULL, "no-short-literals", "Do not compress literals to short literals.");
struct arg_int* opt_level = arg_int0("O", NULL, "<level>", "The optimization level.");
struct arg_lit* opt_mode = arg_lit0("S", NULL, "Favour runtime speed over size when optimizing.");
struct arg_lit* verbose = arg_litn("v", NULL, 0, LEVEL_EVERYTHING - LEVEL_DEFAULT, "Increase verbosity.");
struct arg_lit* quiet = arg_litn("q", NULL, 0, LEVEL_DEFAULT - LEVEL_SILENT, "Decrease verbosity.");
struct arg_end* end = arg_end(20);
void* argtable[] = { show_help, target_arg, keep_output_arg, little_endian_mode, opt_level, opt_mode, no_short_literals_arg,
symbol_ext, symbol_file, kernel_file, jumplist_file, warning_policies, output_file, input_files, verbose, quiet, end
};
// Parse arguments.
nerrors = arg_parse(argc, argv, argtable);
version_print(bautofree(bfromcstr("Linker")));
if (nerrors != 0 || show_help->count != 0)
{
if (show_help->count != 0)
arg_print_errors(stdout, end, "linker");
printd(LEVEL_DEFAULT, "syntax:\n dtld");
arg_print_syntax(stderr, argtable, "\n");
printd(LEVEL_DEFAULT, "options:\n");
arg_print_glossary(stderr, argtable, " %-25s %s\n");
arg_freetable(argtable, sizeof(argtable) / sizeof(argtable[0]));
return 1;
}
// Set verbosity level.
debug_setlevel(LEVEL_DEFAULT + verbose->count - quiet->count);
// Set global path variable.
osutil_setarg0(bautofree(bfromcstr(argv[0])));
// Set endianness.
isetmode(little_endian_mode->count == 0 ? IMODE_BIG : IMODE_LITTLE);
// Set up warning policies.
dsetwarnpolicy(warning_policies);
// Set up error handling.
if (dsethalt())
{
errval = derrinfo();
// FIXME: Use bstrings here.
msglen = strlen(derrstr[errval->errid]) + strlen(prepend) + 1;
msg = malloc(msglen);
memset(msg, '\0', msglen);
strcat(msg, prepend);
strcat(msg, derrstr[errval->errid]);
printd(LEVEL_ERROR, msg, errval->errdata);
// Handle the error.
printd(LEVEL_ERROR, "linker: error occurred.\n");
arg_freetable(argtable, sizeof(argtable) / sizeof(argtable[0]));
return 1;
}
// Check to make sure target is correct.
if (target_arg->count == 0)
target = IMAGE_APPLICATION;
else
{
if (strcmp(target_arg->sval[0], "image") == 0)
target = IMAGE_APPLICATION;
else if (strcmp(target_arg->sval[0], "static") == 0)
target = IMAGE_STATIC_LIBRARY;
else if (strcmp(target_arg->sval[0], "kernel") == 0)
target = IMAGE_KERNEL;
else
{
// Invalid option.
dhalt(ERR_INVALID_TARGET_NAME, NULL);
}
}
// Load all passed objects and use linker bin system to
// produce result.
bins_init();
for (i = 0; i < input_files->count; i++)
if (!bins_load(bautofree(bfromcstr(input_files->filename[i])), symbol_file->count > 0, (symbol_file->count > 0 && symbol_ext->count > 0) ? symbol_ext->sval[0] : "dsym16"))
// Failed to load one of the input files.
dhalt(ERR_BIN_LOAD_FAILED, input_files->filename[i]);
bins_associate();
bins_sectionize();
bins_flatten(bautofree(bfromcstr("output")));
if (target == IMAGE_KERNEL)
bins_write_jump();
saved = bins_optimize(
opt_mode->count == 0 ? OPTIMIZE_SIZE : OPTIMIZE_SPEED,
opt_level->count == 0 ? OPTIMIZE_NONE : opt_level->ival[0]);
if (no_short_literals_arg->count == 0 && target != IMAGE_STATIC_LIBRARY)
saved += bins_compress();
else if (no_short_literals_arg->count == 0)
dwarn(WARN_SKIPPING_SHORT_LITERALS_TYPE, NULL);
else
dwarn(WARN_SKIPPING_SHORT_LITERALS_REQUEST, NULL);
bins_resolve(
target == IMAGE_STATIC_LIBRARY,
target == IMAGE_STATIC_LIBRARY);
bins_save(
bautofree(bfromcstr("output")),
bautofree(bfromcstr(output_file->filename[0])),
target,
keep_output_arg->count > 0,
symbol_file->count > 0 ? symbol_file->filename[0] : NULL,
jumplist_file->count > 0 ? jumplist_file->filename[0] : NULL);
bins_free();
if (saved > 0)
printd(LEVEL_DEFAULT, "linker: saved %i words during optimization.\n", saved);
else if (saved < 0)
printd(LEVEL_DEFAULT, "linker: increased by %i words during optimization.\n", -saved);
arg_freetable(argtable, sizeof(argtable) / sizeof(argtable[0]));
return 0;
}
int main(int argc, char* argv[])
{
// Define arguments.
struct arg_lit* show_help = arg_lit0("h", "help", "Show this help.");
struct arg_str* type_assembler = arg_str0("t", NULL, "<type>", "The type of assembler to output for.");
struct arg_file* input_file = arg_file1(NULL, NULL, "<file>", "The input file (or - to read from standard input).");
struct arg_file* output_file = arg_file1("o", "output", "<file>", "The output file (or - to send to standard output).");
// 20 is maxcount for include directories, this has to be set to some constant number.
struct arg_file* include_dirs = arg_filen("I", NULL, "<directory>", 0, 20, "Adds the directory <dir> to the directories to be searched for header files.");
struct arg_lit* verbose = arg_litn("v", NULL, 0, LEVEL_EVERYTHING - LEVEL_DEFAULT, "Increase verbosity.");
struct arg_lit* quiet = arg_litn("q", NULL, 0, LEVEL_DEFAULT - LEVEL_SILENT, "Decrease verbosity.");
struct arg_end* end = arg_end(20);
void* argtable[] = { output_file, show_help, type_assembler, include_dirs, input_file, verbose, quiet, end };
// Parse arguments.
int nerrors = arg_parse(argc, argv, argtable);
version_print(bautofree(bfromcstr("Compiler")));
if (nerrors != 0 || show_help->count != 0)
{
if (nerrors != 0)
arg_print_errors(stderr, end, "compiler");
fprintf(stderr, "syntax:\n dtcc");
arg_print_syntax(stderr, argtable, "\n");
fprintf(stderr, "options:\n");
arg_print_glossary(stderr, argtable, " %-25s %s\n");
arg_freetable(argtable, sizeof(argtable) / sizeof(argtable[0]));
return 1;
}
// Set verbosity level.
debug_setlevel(LEVEL_DEFAULT + verbose->count - quiet->count);
// Set global path variable.
osutil_setarg0(bautofree(bfromcstr(argv[0])));
// Run the preprocessor.
ppfind_add_path(bautofree(bfromcstr(".")));
ppfind_add_path(bautofree(bfromcstr("include")));
ppfind_add_autopath(bautofree(bfromcstr(input_file->filename[0])));
for (int i = 0; i < include_dirs->count; ++i)
ppfind_add_path(bautofree(bfromcstr(include_dirs->filename[i])));
bstring pp_result_name = pp_do(bautofree(bfromcstr(input_file->filename[0])));
if (pp_result_name == NULL)
{
fprintf(stderr, "compiler: invalid result returned from preprocessor.\n");
pp_cleanup(bautofree(pp_result_name));
arg_freetable(argtable, sizeof(argtable) / sizeof(argtable[0]));
return 1;
}
// Parse C.
yyout = stderr;
yyin = fopen((const char*)(pp_result_name->data), "r");
if (yyin == NULL)
{
pp_cleanup(bautofree(pp_result_name));
arg_freetable(argtable, sizeof(argtable) / sizeof(argtable[0]));
return 1;
}
yyparse();
if (yyin != stdin)
fclose(yyin);
pp_cleanup(bautofree(pp_result_name));
if (program == NULL)
{
std::cerr << "An error occurred while compiling." << std::endl;
arg_freetable(argtable, sizeof(argtable) / sizeof(argtable[0]));
return 1;
}
// Assembler type.
const char* asmtype = "toolchain";
if (type_assembler->count > 0)
asmtype = type_assembler->sval[0];
// Initially save to a temporary file.
std::string temp = std::string(tempnam(".", "cc."));
// Generate assembly using the AST.
try
{
AsmGenerator generator(asmtype);
AsmBlock* block = program->compile(generator);
std::ofstream output(temp.c_str(), std::ios::out | std::ios::trunc);
if (output.bad() || output.fail())
{
printd(LEVEL_ERROR, "compiler: temporary file not writable.\n");
arg_freetable(argtable, sizeof(argtable) / sizeof(argtable[0]));
return 1;
}
output << *block << std::endl;
output.close();
delete block;
}
catch (CompilerException* ex)
{
std::string msg = ex->getMessage();
std::cerr << "An error occurred while compiling." << std::endl;
std::cerr << msg << std::endl;
arg_freetable(argtable, sizeof(argtable) / sizeof(argtable[0]));
return 1;
}
// Re-open the temporary file for reading.
std::ifstream input(temp.c_str(), std::ios::in);
if (input.bad() || input.fail())
{
printd(LEVEL_ERROR, "compiler: temporary file not readable.\n");
arg_freetable(argtable, sizeof(argtable) / sizeof(argtable[0]));
return 1;
}
// Open the output file.
std::ostream* output;
if (strcmp(output_file->filename[0], "-") != 0)
{
// Write to file.
output = new std::ofstream(output_file->filename[0], std::ios::out | std::ios::trunc);
if (output->bad() || output->fail())
{
printd(LEVEL_ERROR, "compiler: output file not readable.\n");
arg_freetable(argtable, sizeof(argtable) / sizeof(argtable[0]));
return 1;
}
}
else
{
// Set output to cout.
output = &std::cout;
}
// Copy data.
std::copy(std::istreambuf_iterator<char>(input), std::istreambuf_iterator<char>(), std::ostreambuf_iterator<char>(*output));
// Close files and delete temporary.
if (strcmp(output_file->filename[0], "-") != 0)
{
((std::ofstream*)output)->close();
delete output;
}
input.close();
unlink(temp.c_str());
arg_freetable(argtable, sizeof(argtable) / sizeof(argtable[0]));
return 0;
}
int main(int argc, char* argv[]) {
// commandline argument parser options
struct arg_lit *help = arg_lit0("h", "help", "print this help and exit");
struct arg_lit *vers = arg_lit0("v", "version", "print version information and exit");
struct arg_file *file = arg_file1("f", "file", "<file>", "Input altpals file");
struct arg_int *pal = arg_int1("p", "palette", "<number>", "Select a palette");
struct arg_file *export = arg_file0("e", "export", "<file>", "Export selected palette to GPL file");
struct arg_file *import = arg_file0("i", "import", "<file>", "Import selected palette from GPL file");
struct arg_file *output = arg_file0("o", "output", "<file>", "Output altpals file");
struct arg_end *end = arg_end(20);
void* argtable[] = {help,vers,file,pal,output,import,export,end};
const char* progname = "altpaltool";
// Make sure everything got allocated
if(arg_nullcheck(argtable) != 0) {
printf("%s: insufficient memory\n", progname);
goto exit_0;
}
// Parse arguments
int nerrors = arg_parse(argc, argv, argtable);
// Handle help
if(help->count > 0) {
printf("Usage: %s", progname);
arg_print_syntax(stdout, argtable, "\n");
printf("\nArguments:\n");
arg_print_glossary(stdout, argtable, "%-25s %s\n");
goto exit_0;
}
// Handle version
if(vers->count > 0) {
printf("%s v0.1\n", progname);
printf("Command line One Must Fall 2097 Altpals file editor.\n");
printf("Source code is available at https://github.com/omf2097 under MIT license.\n");
printf("(C) 2014 Tuomas Virtanen\n");
goto exit_0;
}
// Handle errors
if(nerrors > 0) {
arg_print_errors(stdout, end, progname);
printf("Try '%s --help' for more information.\n", progname);
goto exit_0;
}
// Need import or export ...
if(pal->count > 0 && import->count == 0 && export->count == 0) {
printf("Define either --import or --export with --palette!\n");
goto exit_0;
}
// Make sure output is set
if(import->count > 0 && output->count <= 0) {
printf("Define --output with --import.\n");
goto exit_0;
}
// Load file
sd_altpal_file alt;
sd_altpal_create(&alt);
int ret = sd_altpals_load(&alt, file->filename[0]);
if(ret != SD_SUCCESS) {
printf("Unable to load altpals file %s: %s.\n",
file->filename[0],
sd_get_error(ret));
goto exit_1;
}
// Check ID
int pal_id = pal->ival[0];
if(pal_id < 0 || pal_id > SD_ALTPALS_PALETTES) {
printf("Palette index %d does not exist!\n", pal_id);
goto exit_1;
}
// Check what to do
if(export->count > 0) {
ret = sd_palette_to_gimp_palette(&alt.palettes[pal_id], export->filename[0]);
if(ret == SD_SUCCESS) {
printf("Palette %d exported to file %s succesfully.\n",
pal_id,
export->filename[0]);
} else {
int main(int argc, char* argv[])
{
// Define our variables.
FILE* load;
uint16_t flash[0x10000];
char leading[0x100];
unsigned int i;
bool uread = true;
vm_t* vm;
int nerrors;
bstring ss, st;
host_context_t* dtemu = malloc(sizeof(host_context_t));
const char* warnprefix = "no-";
// Define arguments.
struct arg_lit* show_help = arg_lit0("h", "help", "Show this help.");
struct arg_file* input_file = arg_file1(NULL, NULL, "<file>", "The input file, or - to read from standard input.");
struct arg_file* execution_dump_file = arg_file0("e", "execution-dump", "<file>", "Produce a very large execution dump file.");
struct arg_lit* debug_mode = arg_lit0("d", "debug", "Show each executed instruction.");
struct arg_lit* terminate_mode = arg_lit0("t", "show-on-terminate", "Show state of machine when program is terminated.");
struct arg_lit* headless_mode = arg_lit0("h", "headless", "Run machine witout displaying monitor and SPED output");
struct arg_lit* legacy_mode = arg_lit0("l", "legacy", "Automatically initialize hardware to legacy values.");
struct arg_str* warning_policies = arg_strn("W", NULL, "policy", 0, _WARN_COUNT * 2 + 10, "Modify warning policies.");
struct arg_lit* little_endian_mode = arg_lit0(NULL, "little-endian", "Use little endian serialization (for compatibility with older versions).");
struct arg_lit* verbose = arg_litn("v", NULL, 0, LEVEL_EVERYTHING - LEVEL_DEFAULT, "Increase verbosity.");
struct arg_lit* quiet = arg_litn("q", NULL, 0, LEVEL_DEFAULT - LEVEL_SILENT, "Decrease verbosity.");
struct arg_int* radiation = arg_intn("r", NULL, "<n>", 0, 1, "Radiation factor (higher is less radiation)");
struct arg_lit* catch_fire = arg_lit0("c", "catch-fire", "The virtual machine should catch fire instead of halting.");
struct arg_end* end = arg_end(20);
void* argtable[] = { input_file, warning_policies, debug_mode, execution_dump_file, terminate_mode, headless_mode, legacy_mode, little_endian_mode, radiation, catch_fire, verbose, quiet, end };
// Parse arguments.
nerrors = arg_parse(argc, argv, argtable);
if (nerrors != 0 || show_help->count != 0)
{
if (show_help->count != 0)
arg_print_errors(stdout, end, "emulator");
printd(LEVEL_DEFAULT, "syntax:\n dtemu");
arg_print_syntax(stderr, argtable, "\n");
printd(LEVEL_DEFAULT, "options:\n");
arg_print_glossary(stderr, argtable, " %-25s %s\n");
arg_freetable(argtable, sizeof(argtable) / sizeof(argtable[0]));
return 1;
}
// Set verbosity level.
debug_setlevel(LEVEL_DEFAULT + verbose->count - quiet->count);
// Show version information.
version_print(bautofree(bfromcstr("Emulator")));
// Set global path variable.
osutil_setarg0(bautofree(bfromcstr(argv[0])));
// Set endianness.
isetmode(little_endian_mode->count == 0 ? IMODE_BIG : IMODE_LITTLE);
// Set up warning policies.
dsetwarnpolicy(warning_policies);
// Set up error handling.
if (dsethalt())
{
// Handle the error.
dautohandle();
printd(LEVEL_ERROR, "emulator: error occurred.\n");
arg_freetable(argtable, sizeof(argtable) / sizeof(argtable[0]));
return 1;
}
// Zero out the flash space.
for (i = 0; i < 0x10000; i++)
flash[i] = 0x0;
// Zero out the leading space.
for (i = 0; i < 0x100; i++)
leading[i] = 0x0;
// Load from either file or stdin.
if (strcmp(input_file->filename[0], "-") != 0)
{
// Open file.
load = fopen(input_file->filename[0], "rb");
if (load == NULL)
dhalt(ERR_EMU_LOAD_FILE_FAILED, input_file->filename[0]);
}
else
{
// Windows needs stdin in binary mode.
#ifdef _WIN32
_setmode(_fileno(stdin), _O_BINARY);
#endif
// Set load to stdin.
load = stdin;
}
// Read leading component.
for (i = 0; i < strlen(ldata_objfmt); i++)
leading[i] = fgetc(load);
fseek(load, 0, SEEK_SET);
// Read up to 0x10000 words.
for (i = 0; i < 0x10000 && !feof(load); i++)
iread(&flash[i], load);
fclose(load);
// Check to see if the first X bytes matches the header
// for intermediate code and stop if it does.
ss = bfromcstr("");
st = bfromcstr(ldata_objfmt);
for (i = 0; i < strlen(ldata_objfmt); i++)
bconchar(ss, leading[i]);
if (biseq(ss, st))
dhalt(ERR_INTERMEDIATE_EXECUTION, NULL);
// Set up the host context.
glfwInit();
dtemu->create_context = &dtemu_create_context;
dtemu->activate_context = &dtemu_activate_context;
dtemu->swap_buffers = &dtemu_swap_buffers;
dtemu->destroy_context = &dtemu_destroy_context;
dtemu->get_ud = &dtemu_get_ud;
// And then use the VM.
vm = vm_create();
vm->debug = (debug_mode->count > 0);
vm_flash(vm, flash);
// Set radiation and catch fire settings.
if (radiation->count == 1)
vm->radiation_factor = radiation->ival[0];
if (catch_fire->count == 1)
vm->can_fire = true;
// Init hardware.
vm_hw_clock_init(vm);
if (headless_mode->count < 1)
vm->host = dtemu;
vm_hw_sped3_init(vm);
vm_hw_lem1802_init(vm);
vm_hw_m35fd_init(vm);
vm_hw_lua_init(vm);
if (legacy_mode->count > 0)
{
for (i = 0; i < vm_hw_count(vm); i++) {
hw_t* device = vm_hw_get_device(vm, i);
if (device == NULL)
continue;
if (device->id == 0x7349F615 && device->manufacturer == 0x1C6C8B36)
{
vm_hw_lem1802_mem_set_screen((struct lem1802_hardware*)device->userdata, 0x8000);
break;
}
}
}
vm_execute(vm, execution_dump_file->count > 0 ? execution_dump_file->filename[0] : NULL);
if (terminate_mode->count > 0)
{
fprintf(stderr, "\n");
fprintf(stderr, "A: 0x%04X [A]: 0x%04X\n", vm->registers[REG_A], vm->ram[vm->registers[REG_A]]);
fprintf(stderr, "B: 0x%04X [B]: 0x%04X\n", vm->registers[REG_B], vm->ram[vm->registers[REG_B]]);
fprintf(stderr, "C: 0x%04X [C]: 0x%04X\n", vm->registers[REG_C], vm->ram[vm->registers[REG_C]]);
fprintf(stderr, "X: 0x%04X [X]: 0x%04X\n", vm->registers[REG_X], vm->ram[vm->registers[REG_X]]);
fprintf(stderr, "Y: 0x%04X [Y]: 0x%04X\n", vm->registers[REG_Y], vm->ram[vm->registers[REG_Y]]);
fprintf(stderr, "Z: 0x%04X [Z]: 0x%04X\n", vm->registers[REG_Z], vm->ram[vm->registers[REG_Z]]);
fprintf(stderr, "I: 0x%04X [I]: 0x%04X\n", vm->registers[REG_I], vm->ram[vm->registers[REG_I]]);
fprintf(stderr, "J: 0x%04X [J]: 0x%04X\n", vm->registers[REG_J], vm->ram[vm->registers[REG_J]]);
fprintf(stderr, "PC: 0x%04X SP: 0x%04X\n", vm->pc, vm->sp);
fprintf(stderr, "EX: 0x%04X IA: 0x%04X\n", vm->ex, vm->ia);
}
vm_hw_lua_free(vm);
vm_free(vm);
arg_freetable(argtable, sizeof(argtable) / sizeof(argtable[0]));
glfwTerminate();
return 0;
}
int main(int argc, char **argv)
{
struct arg_int *serverport = arg_int0("pP","port","","serverport, default: 1337");
struct arg_str *serialport = arg_str0("sS", "serial", "", "serial port, default /dev/ttyS0");
struct arg_int *baud = arg_int0("bB", "baud","","baudrate, default: 9600");
struct arg_str *client = arg_str0("cC","client","","only accept messages from this client");
struct arg_lit *help = arg_lit0("hH","help","print this help and exit");
struct arg_lit *version = arg_lit0(NULL,"version","print version information and exit");
struct arg_lit *debug = arg_lit0(NULL,"debug","print debug messages");
struct arg_lit *silent = arg_lit0(NULL,"silent","print no messages");
struct arg_end *end = arg_end(20);
void* argtable[] = {serverport,serialport,baud,client,help,version,debug,silent,end};
int nerrors;
int exitcode=0;
/* verify the argtable[] entries were allocated sucessfully */
if (arg_nullcheck(argtable) != 0) {
/* NULL entries were detected, some allocations must have failed */
printf("%s: insufficient memory\n",PROGNAME);
exitcode=1;
goto exit;
}
/* set any command line default values prior to parsing */
/* nothing */
/* Parse the command line as defined by argtable[] */
nerrors = arg_parse(argc,argv,argtable);
/* special case: '--help' takes precedence over error reporting */
if (help->count > 0) {
printf("usage: %s", PROGNAME);
arg_print_syntax(stdout,argtable,"\n");
arg_print_glossary(stdout,argtable," %-25s %s\n");
exitcode=0;
goto exit;
}
/* special case: '--version' takes precedence error reporting */
if (version->count > 0) {
printf("'%s' version ",PROGNAME);
printf("%s",VERSION);
printf("\nGIT-REVISION: ");
printf("%s",GITREV);
printf("\n%s receives udp-packets and controls\n",PROGNAME);
printf("the EIWOMISA controller over RS-232\n");
printf("%s",COPYRIGHT);
printf("\n");
exitcode=0;
goto exit;
}
/* If the parser returned any errors then display them and exit */
if (nerrors > 0) {
/* Display the error details contained in the arg_end struct.*/
arg_print_errors(stdout,end,PROGNAME);
printf("Try '%s --help' for more information.\n",PROGNAME);
exitcode=1;
goto exit;
}
/* special case: with no command line options induce brief help and use defaults */
if (argc==1) {
printf("No command-line options present, using defaults.\n",PROGNAME);
printf("Try '%s --help' for more information.\n",PROGNAME);
}
/* normal case: take the command line options at face value */
/* check if server port is set */
int i_serverport = -1;
if(serverport->count>0)
i_serverport = (int)serverport->ival[0];
/* check if serial port is set */
char* i_serialport = NULL;
if(serialport->count>0)
i_serialport = (char*)serialport->sval[0];
/* check if baudrate is set */
int i_baudrate = -1;
if(baud->count>0)
i_baudrate = (int)baud->ival[0];
/* check if client ip is set */
char* i_client = NULL;
if(client->count>0) {
i_client = (char *)client->sval[0];
}
/* --debug enables debug messages */
if (debug->count > 0) {
printf("debug messages enabled\n");
msglevel = 3;
}
/* --silent disables all (!) messages */
if (silent->count > 0) {
msglevel = 0;
}
exitcode = mymain(i_serverport, i_serialport, i_baudrate, i_client);
exit:
/* deallocate each non-null entry in argtable[] */
arg_freetable(argtable,sizeof(argtable)/sizeof(argtable[0]));
return exitcode;
}
int main(int argc, char* argv[]) {
double discountFactor;
unsigned int maxNbEvaluations;
char isTerminal = 0;
char keepingTree = 0;
int nbTimestep = -1;
unsigned int branchingFactor = 0;
#ifdef USE_SDL
char isDisplayed = 1;
char isFullscreen = 1;
char verbose = 0;
char resolution[255] = "640x480";
#else
char verbose = 1;
#endif
uniform_instance* instance = NULL;
state* crtState = NULL;
state* nextState = NULL;
double reward = 0.0;
action* optimalAction = NULL;
struct arg_dbl* g = arg_dbl1("g", "discountFactor", "<d>", "The discount factor for the problem");
struct arg_int* n = arg_int1("n", "nbEvaluations", "<n>", "The number of evaluations");
struct arg_int* s = arg_int0("s", "nbtimestep", "<n>", "The number of timestep");
struct arg_int* b = arg_int0("b", "branchingFactor", "<n>", "The branching factor of the problem");
struct arg_lit* k = arg_lit0("k", NULL, "Keep the subtree");
struct arg_str* i = arg_str0(NULL, "state", "<s>", "The initial state to use");
#ifdef USE_SDL
struct arg_lit* d = arg_lit0("d", NULL, "Display the viewer");
struct arg_lit* f = arg_lit0("f", NULL, "Fullscreen");
struct arg_lit* v = arg_lit0("v", NULL, "Verbose");
struct arg_str* r = arg_str0(NULL, "resolution", "<s>", "The resolution of the display window");
void* argtable[11];
int nbArgs = 10;
#else
void* argtable[7];
int nbArgs = 6;
#endif
struct arg_end* end = arg_end(nbArgs+1);
int nerrors = 0;
s->ival[0] = -1;
b->ival[0] = 0;
argtable[0] = g; argtable[1] = n; argtable[2] = s; argtable[3] = k; argtable[4] = b; argtable[5] = i;
#ifdef USE_SDL
argtable[6] = d;
argtable[7] = f;
argtable[8] = v;
argtable[9] = r;
#endif
argtable[nbArgs] = end;
if(arg_nullcheck(argtable) != 0) {
printf("error: insufficient memory\n");
arg_freetable(argtable, nbArgs+1);
return EXIT_FAILURE;
}
nerrors = arg_parse(argc, argv, argtable);
if(nerrors > 0) {
printf("%s:", argv[0]);
arg_print_syntax(stdout, argtable, "\n");
arg_print_errors(stdout, end, argv[0]);
arg_freetable(argtable, nbArgs+1);
return EXIT_FAILURE;
}
discountFactor = g->dval[0];
maxNbEvaluations = n->ival[0];
branchingFactor = b->ival[0];
initGenerativeModelParameters();
if(branchingFactor)
K = branchingFactor;
initGenerativeModel();
if(i->count)
crtState = makeState(i->sval[0]);
else
crtState = initState();
#if USE_SDL
isDisplayed = d->count;
isFullscreen = f->count;
verbose = v->count;
if(r->count)
strcpy(resolution, r->sval[0]);
#endif
nbTimestep = s->ival[0];
keepingTree = k->count;
arg_freetable(argtable, nbArgs+1);
instance = uniform_initInstance(crtState, discountFactor);
#ifdef USE_SDL
if(isDisplayed) {
if(initViewer(resolution, uniform_drawingProcedure, isFullscreen) == -1)
return EXIT_FAILURE;
viewer(crtState, NULL, 0.0, instance);
}
#endif
do {
if(keepingTree)
uniform_keepSubtree(instance);
else
uniform_resetInstance(instance, crtState);
optimalAction = uniform_planning(instance, maxNbEvaluations);
isTerminal = nextStateReward(crtState, optimalAction, &nextState, &reward);
freeState(crtState);
crtState = nextState;
if(verbose) {
printState(crtState);
printAction(optimalAction);
printf("reward: %f depth: %u\n", reward, uniform_getMaxDepth(instance));
}
#ifdef USE_SDL
} while(!isTerminal && (nbTimestep < 0 || --nbTimestep) && !viewer(crtState, optimalAction, reward, instance));
#else
} while(!isTerminal && (nbTimestep < 0 || --nbTimestep));
