void test_argstr_basic_003(CuTest* tc) {
struct arg_str* a = arg_str0(NULL, "hello,world", "STRVAL", "either --hello or --world or none");
struct arg_str* b = arg_str0("bB", NULL, "STRVAL", "either -b or -B or none");
struct arg_str* c = arg_str1("cC", NULL, "STRVAL", "either -c or -C");
struct arg_str* d = arg_strn("dD", "delta", "STRVAL", 2, 4, "-d|-D|--delta 2..4 occurences");
struct arg_end* end = arg_end(20);
void* argtable[] = {a, b, c, d, end};
int nerrors;
char* argv[] = {"program", "-Cstring1", "--delta=string2", "--delta=string3", NULL};
int argc = sizeof(argv) / sizeof(char*) - 1;
CuAssertTrue(tc, arg_nullcheck(argtable) == 0);
nerrors = arg_parse(argc, argv, argtable);
if (nerrors > 0)
arg_print_errors(stdout, end, argv[0]);
CuAssertTrue(tc, nerrors == 0);
CuAssertTrue(tc, a->count == 0);
CuAssertTrue(tc, b->count == 0);
CuAssertTrue(tc, c->count == 1);
CuAssertStrEquals(tc, c->sval[0], "string1");
CuAssertTrue(tc, d->count == 2);
CuAssertStrEquals(tc, d->sval[0], "string2");
CuAssertStrEquals(tc, d->sval[1], "string3");
arg_freetable(argtable, sizeof(argtable) / sizeof(argtable[0]));
}
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;
}
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 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));
}
int main(int argc, char *argv[]) {
struct arg_str *cblOpt = arg_str1("c", "cable", "nero:<VID>:<PID> | xil3 | dusb", "cable driver to use");
struct arg_lit *scanOpt = arg_lit0("s", "scan", " scan the JTAG chain");
struct arg_file *bitOpt = arg_file0("b", "bitfile", "<fileName>", " bit file to load");
struct arg_uint *devOpt = arg_uint0("d", "device", "<device>", " target device (default \"1\")");
struct arg_lit *helpOpt = arg_lit0("h", "help", " print this help and exit\n");
struct arg_end *endOpt = arg_end(20);
void* argTable[] = {cblOpt, scanOpt, bitOpt, devOpt, helpOpt, endOpt};
const char *progName = "xilprg";
uint32 exitCode = 0;
int numErrors;
const char *cable, *bitFile;
uint32 devNum;
char line[1024];
char configFileName[4097]; // TODO: Fix, somehow.
if ( arg_nullcheck(argTable) != 0 ) {
fprintf(stderr, "%s: insufficient memory\n", progName);
fail(1);
}
numErrors = arg_parse(argc, argv, argTable);
if ( helpOpt->count > 0 ) {
printf("Xilinx Programmer 0.6 Copyright (C) 2006-2011 Zoltan Csizmadia & Chris McClelland\n\nUsage: %s", progName);
arg_print_syntax(stdout, argTable, "\n");
printf("\nProgram a Xilinx FPGA.\n\n");
arg_print_glossary(stdout, argTable," %-10s %s\n");
fail(0);
}
if ( numErrors > 0 ) {
arg_print_errors(stdout, endOpt, progName);
fprintf(stderr, "Try '%s --help' for more information.\n", progName);
fail(2);
}
if ( (scanOpt->count == 0 && bitOpt->count == 0) ||
(scanOpt->count != 0 && bitOpt->count != 0) )
{
fprintf(stderr, "%s: you must specify either -s|--scan or -b|--bitfile, but not both\n", progName);
fprintf(stderr, "Try '%s --help' for more information.\n", progName);
fail(3);
}
cable = cblOpt->sval[0];
bitFile = bitOpt->count ? bitOpt->filename[0] : NULL;
devNum = devOpt->count ? devOpt->ival[0] : 1;
if ( initialize() ) {
fprintf(stderr, "%s failed to initialize!\n", progName);
fail(4);
}
if ( getConfigFullPath("xilprg.conf", configFileName, sizeof(configFileName)) ) {
fprintf(stderr, "%s failed to determine the location of its config file!\n", progName);
fail(5);
}
if ( load_config_file(configFileName) ) {
fprintf(stderr, "%s failed to load its config file from %s!\n", progName, configFileName);
fail(6);
}
try {
sprintf(line, "cable %s", cable);
process_command_line(line);
if ( scanOpt->count ) {
process_command_line("detect");
} else {
sprintf(line, "program %lu \"%s\"", devNum, bitFile);
process_command_line(line);
}
}
catch ( const std::exception &ex ) {
fprintf(stderr, "%s failed: %s!\n", progName, ex.what());
fail(7);
}
cleanup:
uninitialize();
arg_freetable(argTable, sizeof(argTable)/sizeof(argTable[0]));
return exitCode;
}
int main(int argc, char **argv) {
int exitcode = 0;
int nerrors = 0;
/* Prepare command line arguments */
struct arg_str *latero_ip = arg_str1(NULL,"latero_ip","IP", "Latero server IP address");
struct arg_lit *print_resp= arg_lit0("p", "print", "print response packet");
struct arg_int *numpkt = arg_int0("n", "numpkt","<n>", "How many packets (default is 1)");
struct arg_int *dacval = arg_intn(NULL,"dac","<int>",0,4,"dac values (up to 4 values)");
struct arg_lit *rd = arg_lit0("r", "read", "read");
struct arg_lit *wr = arg_lit0("w", "write", "write");
struct arg_int *addr = arg_int0("a", "addr",NULL, "address");
struct arg_int *value = arg_int0("v", "value",NULL, "value");
struct arg_lit *mainctrl = arg_lit0(NULL,"mainctrl", "Raw commands are for the main controller");
struct arg_int *tpat = arg_int0("t","testpat","<n>", "Run Test Pattern:1=Split, 2=AllPin, 3=RowCol");
struct arg_lit *latio = arg_lit0(NULL,"lateroio", "Raw commands are for the Latero IO card");
struct arg_lit *help = arg_lit0(NULL,"help", "print this help and exit");
struct arg_end *end = arg_end(10);
void* argtable[] = {latero_ip,print_resp,numpkt,dacval,
rd, wr, addr, value, mainctrl, tpat, latio,
help,end};
//latero_ip->sval[0] = "192.168.1.108";
/* verify the argtable[] entries were allocated sucessfully */
if (arg_nullcheck(argtable) != 0) {
/* NULL entries were detected, some allocations must have failed */
printf("Insufficient memory (argtable)\n");
exitcode = 1; goto exit;
}
numpkt->ival[0] = 1;
tpat->ival[0] = 0;
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");
printf("Latero client demonstration program version 1, revision 1\n");
arg_print_glossary(stdout,argtable," %-25s %s\n");
exitcode=0; goto exit;
}
if (nerrors > 0) {
/* Display the error details contained in the arg_end struct.*/
arg_print_errors(stdout,end,argv[0]);
printf("Try '%s --help' for more information.\n",argv[0]);
exitcode = 0; goto exit;
}
if( wr->count > 0 ) {
if( addr->count != 1 || value->count != 1 ) {
printf("Write requires an address and a value\n");
exitcode = 1; goto exit;
}
if( mainctrl->count + latio->count == 0 ) {
printf("Write requires a destination (--mainctrl or --lateroio)\n");
exitcode = 1; goto exit;
}
}
if( rd->count > 0 ) {
if( addr->count != 1 ) {
printf("Read requires an address\n");
exitcode = 1; goto exit;
}
if( mainctrl->count + latio->count == 0 ) {
printf("Read requires a destination (--mainctrl or --lateroio)\n");
exitcode = 1; goto exit;
}
}
return( my_main( latero_ip->sval[0], print_resp->count, numpkt->ival[0], dacval->ival, dacval->count,
rd->count, wr->count, addr->ival[0], value->ival[0], mainctrl->count, latio->count, tpat->ival[0]) );
exit:
printf("Program Ended\n");
arg_freetable(argtable,sizeof(argtable)/sizeof(argtable[0]));
return(exitcode);
}
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_str *astr = arg_str1("s", "str", "<str>", "Animation string");
struct arg_end *end = arg_end(20);
void* argtable[] = {help,vers,astr,end};
const char* progname = "omf_parse";
int from_stdin = 0;
// 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);
if(nerrors > 0) {
arg_print_errors(stdout, end, progname);
printf("Try '%s --help' for more information.\n", progname);
goto exit_0;
}
// Handle version
if(vers->count > 0) {
printf("%s v0.1\n", progname);
printf("Command line One Must Fall 2097 Animation string parser\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 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;
}
const char *str = *astr->sval;
if (strcmp("-", *astr->sval) == 0) {
from_stdin = 1;
char *tmp_str = malloc(512);
fgets(tmp_str, 512, stdin);
// throttle the newline
tmp_str[strlen(tmp_str)-1] = '\0';
str = tmp_str;
}
// Print some data
printf("Parsing \"%s\".\n\n", str);
int err_pos;
sd_script script;
sd_script_create(&script);
int ret = sd_script_decode(&script, str, &err_pos);
if(ret != SD_SUCCESS) {
if(ret == SD_INVALID_TAG) {
printf("Bad input string! Error at position %d.\n", err_pos);
}
if(ret == SD_ANIM_INVALID_STRING) {
printf("Bad input string!\n");
}
goto exit_1;
}
for(int frame_id = 0; frame_id < script.frame_count; frame_id++) {
sd_script_frame *frame = &script.frames[frame_id];
printf("%d. Frame %d: '%c%d'\n",
frame_id,
frame->sprite,
(char)(frame->sprite+65),
frame->tick_len);
for(int tag_id = 0; tag_id < frame->tag_count; tag_id++) {
sd_script_tag *tag = &frame->tags[tag_id];
if(tag->desc == NULL) {
tag->desc = "";
}
if(tag->has_param) {
printf(" %-4s %-4d %s\n", tag->key, tag->value, tag->desc);
} else {
printf(" %-4s %s\n", tag->key, tag->desc);
}
}
}
exit_1:
sd_script_free(&script);
exit_0:
if (from_stdin) {
free((char*)str);
}
arg_freetable(argtable, sizeof(argtable)/sizeof(argtable[0]));
return 0;
}
split_options_t *new_split_cli_options() {
split_options_t *options = (split_options_t*) malloc (sizeof(split_options_t));
options->criterion = arg_str1(NULL, "criterion", NULL, "Criterion for splitting the file");
options->intervals = arg_str0(NULL, "intervals", NULL, "Values of intervals for splitting the file");
return options;
}
struct Args parse_arguments(int argc, char *argv[]) {
struct Args args;
args.mass = 0.0;
args.diam = 0.0;
args.cd = 0.0;
args.wind = 0.0;
args.run_simulation = 0;
// Simulation options
struct arg_dbl *mass = arg_dbl1("m", "mass", "<float>",
"Mass of rocket without motor (g)");
struct arg_dbl *diam = arg_dbl1("d", "diam", "<float>",
"Diameter of rocket (mm)");
struct arg_dbl *cd = arg_dbl1("c", "cd", "<float>",
"Drag coefficient of rocket");
struct arg_dbl *wind = arg_dbl1("w", "wind", "<float>",
"Wind speed (km/h)");
struct arg_str *motor = arg_str1("M", "motor", "<string>",
"Motor (use '-l' or '--list_motors' to see list");
// Help options
struct arg_lit *help = arg_lit0("h", "help", "Printing help");
struct arg_lit *list_motors = arg_lit0("l", "list_motors", "List motors");
struct arg_end *end = arg_end(20);
// Prepare argtable
void *argtable[] = {mass, diam, cd, wind, motor, help, list_motors, end};
const char *progname = "lawn_dart";
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);
}
// Parse the command line as defined by argtable[]
nerrors = arg_parse(argc, argv, argtable);
// Check for --help
if (help->count > 0 || argc == 1) {
printf("Lawn Dart: A Model Rocket Flight Simulator\n\n");
printf("%s", progname);
arg_print_syntax(stdout, argtable,"\n");
puts("");
arg_print_glossary(stdout, argtable," %-25s %s\n");
puts("");
print_help();
}
else if (list_motors->count > 0) {
print_motor_list();
}
else {
// If all required options have been specified
if (!nerrors) {
// Get options from params
args.mass = mass->dval[0] / 1000.0;
args.diam = diam->dval[0] / 1000.0;
args.cd = cd->dval[0];
args.wind = wind->dval[0] / 3.6;
// Assert proper values
int all_params_ok = 1;
if (args.mass < 0.001 || args.mass > 1000.0) all_params_ok = 0;
if (args.diam < 0.001 || args.diam > 1.0) all_params_ok = 0;
if (args.cd < 0.0 || args.cd > 1.0) all_params_ok = 0;
if (args.wind < 0.0 || args.wind > 100.0) all_params_ok = 0;
// Confirm to run simulation
if (all_params_ok) {
args.run_simulation = 1;
}
}
else {
puts("--- Missing required parameters ---\n");
printf("%s", progname);
arg_print_syntax(stdout, argtable,"\n");
puts("");
arg_print_glossary(stdout, argtable," %-25s %s\n");
puts("");
print_help();
}
}
return args;
}
int main(int argc, char** argv) {
int ret, i;
int nerrors[NUMBER_OF_DIFFERENT_SYNTAXES + 1];
/* argtable setup */
/* SYNTAX 1: [--info] */
info1 = arg_lit1(NULL, "info", "Show information about the FLI camera");
end1 = arg_end(20);
void * argtable1[] = {info1, end1};
argtable[1] = argtable1;
/* SYNTAX 2: [--get-temperature] */
gettemp2 = arg_lit1(NULL, "get-temperature", "Print the temperature of the CCD, base and cooling power");
end2 = arg_end(20);
void * argtable2[] = {gettemp2, end2};
argtable[2] = argtable2;
/* SYNTAX 3: [--set-temperature] */
settemp3 = arg_int1(NULL, "set-temperature", "N", "Set the temperature of the CCD (in Celsius)");
end3 = arg_end(20);
void * argtable3[] = {settemp3, end3};
argtable[3] = argtable3;
/* SYNTAX 4: [--fan] */
fan4 = arg_str1(NULL, "fan", "(on|off)", "Turn on or off the fan");
end4 = arg_end(20);
void * argtable4[] = {fan4, end4};
argtable[4] = argtable4;
/* SYNTAX 5: [--shutter] */
shutter5 = arg_str1(NULL, "shutter", "(open|close)", "Open or close the shutter");
end5 = arg_end(20);
void * argtable5[] = {shutter5, end5};
argtable[5] = argtable5;
/* SYNTAX 6: --acquire <time/sec> --shutter {open|close} --output xyz.fits
[--bin <bx>,<by>] [--offset <x0>,<y0>] [--size <sx>,<sy>]
[--mode <mode>...] [--verbose]
*/
acquire6 = arg_str1(NULL, "acquire", "<time>", "Exposure time in sec");
shutter6 = arg_str1(NULL, "shutter", "(open|close)", "Whether to open or close the shutter");
output6 = arg_file1(NULL, "output", "xyz.fits", "Output filename for the FITS file");
bin6 = arg_str0(NULL, "bin", "<bx,by>", "Binning options in X,Y format");
offset6 = arg_str0(NULL, "offset", "<x0,y0>", "Offset options in X,Y format");
size6 = arg_str0(NULL, "size", "<sx,sy>", "Sizes in X,Y format");
mode6 = arg_str0(NULL, "mode", "(1mhz|8mhz)", "Download speed");
verbose6 = arg_lit0(NULL, "verbose", "Show verbose output");
end6 = arg_end(20);
void * argtable6[] = {acquire6, shutter6, output6, bin6, offset6, size6, mode6, verbose6, end6};
argtable[6] = argtable6;
/* SYNTAX 7: [--help]*/
help7 = arg_lit1(NULL, "help", "Print this help");
end7 = arg_end(20);
void * argtable7[] = {help7, end7};
argtable[7] = argtable7;
/* verify all argtable[] entries were allocated successfully */
for (i = 1; i <= NUMBER_OF_DIFFERENT_SYNTAXES; i++) {
if (arg_nullcheck(argtable[i]) != 0) {
printf("%s: insufficient memory\n", progname);
return EXIT_FAILURE;
}
}
/* set defaults for the optional arguments */
bin6->sval[0] = "1,1";
offset6->sval[0] = "0,0";
size6->sval[0] = "4096,4096";
mode6->sval[0] = "8mhz";
/* parse all argument possibilities */
for (i = 1; i <= NUMBER_OF_DIFFERENT_SYNTAXES; i++) {
nerrors[i] = arg_parse(argc, argv, argtable[i]);
}
/* select the right command */
/* --info */
if (nerrors[1] == 0) {
if (info1->count > 0) {
ret = camera_info();
if (ret) return ret;
return 0;
}
/* --get-temperature */
} else if (nerrors[2] == 0) {
if (gettemp2->count > 0) {
ret = camera_get_temp();
if (ret) return ret;
return 0;
}
/* --set-temperature */
} else if (nerrors[3] == 0) {
if (settemp3->count > 0) {
ret = camera_set_temp(settemp3->ival[0]);
if (ret) return ret;
return 0;
}
/* --fan */
} else if (nerrors[4] == 0) {
int fan;
if (strcmp("on", fan4->sval[0]) == 0) {
fan = 1;
} else if (strcmp("off", fan4->sval[0]) == 0) {
fan = 0;
} else {
fprintf(stderr, "Cannot parse the option for --fan, see --help.\n");
return -1;
}
ret = camera_set_fan(fan);
if (ret) return ret;
return 0;
/* --shutter */
} else if (nerrors[5] == 0) {
int open_shutter;
if (strcmp("open", shutter5->sval[0]) == 0) {
open_shutter = 1;
} else if (strcmp("close", shutter5->sval[0]) == 0) {
open_shutter = 0;
} else {
fprintf(stderr, "Cannot parse the option for --shutter, see --help.\n");
return -1;
}
ret = camera_control_shutter(open_shutter);
if (ret) return ret;
return 0;
/* --acquire */
} else if (nerrors[6] == 0) {
if (acquire6->count > 0) {
/* local variables to store the arguments */
float exposure_time;
int is_dark;
char * output_filename;
char * bin_options;
char * offset_options;
char * size_options;
int bx, by;
int x0, y0;
int sx, sy;
int one_mhz_speed;
int is_verbose = 0;
/* copy const char arrays to char arrays to suppress warnings */
output_filename = (char*) malloc((strlen(output6->filename[0])) * sizeof (char));
bin_options = (char*) malloc((strlen(bin6->sval[0])) * sizeof (char));
offset_options = (char*) malloc((strlen(offset6->sval[0])) * sizeof (char));
size_options = (char*) malloc((strlen(size6->sval[0])) * sizeof (char));
strcpy(output_filename, output6->filename[0]);
strcpy(bin_options, bin6->sval[0]);
strcpy(offset_options, offset6->sval[0]);
strcpy(size_options, size6->sval[0]);
/* process arguments */
/* exposure time */
exposure_time = atof(acquire6->sval[0]);
if (exposure_time < 0) {
fprintf(stderr, "Exposure time cannot be below zero (given %f).\n", exposure_time);
return -1;
}
/* shutter */
if (strcmp("open", shutter6->sval[0]) == 0) {
is_dark = 0;
} else if (strcmp("close", shutter6->sval[0]) == 0) {
is_dark = 1;
} else {
fprintf(stderr, "Cannot parse the option for --shutter, see --help.\n");
return -1;
}
/* bin, size and offset */
ret = parse_comma_separated_values(bin_options, &bx, &by, "bin");
if (ret) return ret;
ret = parse_comma_separated_values(offset_options, &x0, &y0, "offset");
if (ret) return ret;
ret = parse_comma_separated_values(size_options, &sx, &sy, "size");
if (ret) return ret;
/* mode */
if (strcmp("1mhz", mode6->sval[0]) == 0) {
one_mhz_speed = 1;
} else if (strcmp("8mhz", mode6->sval[0]) == 0) {
one_mhz_speed = 0;
} else {
fprintf(stderr, "Cannot parse the option for --mode, see --help.\n");
return -1;
}
/* verbose */
if (verbose6->count > 0) is_verbose = 1;
ret = camera_acquire(exposure_time, is_dark, output_filename,
bx, by, x0, y0, sx, sy, one_mhz_speed, is_verbose);
if (ret) return ret;
return 0;
}
/* --help */
} else if (nerrors[7] == 0) {
if (help7) {
ret = camera_help();
if (ret) return ret;
return 0;
}
/* incorrect or partially incorrect argument syntaxes */
} else {
if (settemp3->count > 0) {
arg_print_errors(stdout, end3, progname);
printf("usage: %s ", progname);
arg_print_syntax(stdout, argtable3, "\n");
} else if (fan4->count > 0) {
arg_print_errors(stdout, end4, progname);
printf("usage: %s ", progname);
arg_print_syntax(stdout, argtable4, "\n");
} else if (acquire6->count > 0) {
arg_print_errors(stdout, end5, progname);
printf("usage: %s ", progname);
arg_print_syntax(stdout, argtable5, "\n");
} else {
printf("%s: unable to parse arguments, see syntax below:\n", progname);
ret = 0;
ret = camera_help();
return ret;
}
return EXIT_FAILURE;
}
/* no command line options at all */
printf("Try '%s --help' for more information.\n", progname);
return (EXIT_SUCCESS);
}
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 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 kangax(int argc, char* argv[])
{
// determine my process name
_splitpath(argv[0],NULL,NULL,gszProcName,NULL);
#else
int
kangax(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;
char szOutputFileSpec[_MAX_PATH];
int MinSeqLen; // only accept for indexing sequences which are at least this length
int SimGenomeSize; // if 1..1000 then simulating indexing of a genome of this size in Gbp.
int NumInputFileSpecs; // number of input file specs
char *pszInputFileSpecs[cMaxInFileSpecs]; // input files
char szDescription[cMBSFFileDescrLen];
char szTitle[cMBSFShortFileDescrLen];
char szRefSpecies[cMaxDatasetSpeciesChrom];
int iMode; // processing mode
bool bSOLiD; // colorspace (SOLiD) generation
int NumberOfProcessors; // number of installed CPUs
int NumThreads; // number of threads (0 defaults to number of CPUs)
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("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_file *LogFile = arg_file0("F","log","<file>", "diagnostics log file");
struct arg_int *Mode=arg_int0("m", "mode", "<int>", "Processing mode, 0=standard, 1=bisulphite index, 2=simulated genome (default 0)");
struct arg_lit *solid = arg_lit0("C","colorspace", "Generate for colorspace (SOLiD)");
struct arg_int *simgenomesize=arg_int0("s", "simgenomesize", "<int>","Simulated genome size in Gbp (default 5, range 1..1000");
struct arg_int *minseqlen=arg_int0("l", "minseqlen", "<int>","Do not accept for indexing sequences less than this length (default 50, range 1..1000000)");
struct arg_file *infiles = arg_filen("i",NULL,"<file>",0,cMaxInFileSpecs, "input from wildcarded kangas or fasta files");
struct arg_file *OutFile = arg_file0("o",NULL,"<file>", "output suffix array file");
struct arg_str *Descr = arg_str0("d","descr","<string>", "full description");
struct arg_str *Title = arg_str0("t","title","<string>", "short title");
struct arg_str *RefSpecies = arg_str1("r","ref","<string>", "reference species");
struct arg_int *threads = 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,
Mode,minseqlen,simgenomesize,solid,infiles,OutFile,RefSpecies,Descr,Title,
threads,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>'",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';
}
// 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);
exit(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';
MinSeqLen = 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';
}
iMode = Mode->count ? Mode->ival[0] : 0;
if(iMode < 0 || iMode > 2)
{
gDiagnostics.DiagOut(eDLFatal,gszProcName,"Error: processing mode '-m%d' must be specified in range %d..%d",iMode,0,1);
exit(1);
}
if(iMode == 2)
{
SimGenomeSize = simgenomesize->count ? simgenomesize->ival[0] : 5;
if(SimGenomeSize < 1 || iMode > cMaxSimGenomeGbp)
{
gDiagnostics.DiagOut(eDLFatal,gszProcName,"Error: simulated genome size in Gbp '-s%d' must be specified in range 1..%d",SimGenomeSize,cMaxSimGenomeGbp);
exit(1);
}
}
else
SimGenomeSize = 0;
bSOLiD = solid->count ? true : false;
int Idx;
if(iMode != 2)
{
MinSeqLen = minseqlen->count ? minseqlen->ival[0] : 50;
if(MinSeqLen < 1)
MinSeqLen = 1;
else
if(MinSeqLen > 1000000)
MinSeqLen = 1000000;
for(NumInputFileSpecs=Idx=0;NumInputFileSpecs < cMaxInFileSpecs && Idx < infiles->count; Idx++)
{
pszInputFileSpecs[Idx] = NULL;
if(pszInputFileSpecs[NumInputFileSpecs] == NULL)
pszInputFileSpecs[NumInputFileSpecs] = new char [_MAX_PATH];
strncpy(pszInputFileSpecs[NumInputFileSpecs],infiles->filename[Idx],_MAX_PATH);
pszInputFileSpecs[NumInputFileSpecs][_MAX_PATH-1] = '\0';
CUtility::TrimQuotedWhitespcExtd(pszInputFileSpecs[NumInputFileSpecs]);
if(pszInputFileSpecs[NumInputFileSpecs][0] != '\0')
NumInputFileSpecs++;
}
if(!NumInputFileSpecs)
{
gDiagnostics.DiagOut(eDLFatal,gszProcName,"Error: After removal of whitespace, no input file(s) specified with '-i<filespec>' option)\n");
exit(1);
}
}
else
{
NumInputFileSpecs = 0;
pszInputFileSpecs[0] = NULL;
}
if(OutFile->count)
{
strcpy(szOutputFileSpec,OutFile->filename[0]);
CUtility::TrimQuotedWhitespcExtd(szOutputFileSpec);
}
else
szOutputFileSpec[0] = '\0';
if(iMode != 2 && szOutputFileSpec[0] == '\0')
{
gDiagnostics.DiagOut(eDLFatal,gszProcName,"Error: no output file(s) specified with '-o<filespec>' option)\n");
exit(1);
}
strncpy(szRefSpecies,RefSpecies->sval[0],cMaxDatasetSpeciesChrom);
szRefSpecies[cMaxDatasetSpeciesChrom-1] = '\0';
if(!Title->count)
strcpy(szTitle,szRefSpecies);
else
{
strncpy(szTitle,Title->sval[0],cMBSFShortFileDescrLen);
szTitle[cMBSFShortFileDescrLen-1] = '\0';
}
if(!Descr->count)
strcpy(szDescription,szRefSpecies);
else
{
strncpy(szDescription,Descr->sval[0],cMBSFFileDescrLen);
szDescription[cMBSFFileDescrLen-1] = '\0';
}
// show user current resource limits
#ifndef _WIN32
gDiagnostics.DiagOut(eDLInfo, gszProcName, "Resources: %s",CUtility::ReportResourceLimits());
#endif
int AvailGBMemory;
#ifdef _WIN32
SYSTEM_INFO SystemInfo;
GetSystemInfo(&SystemInfo);
NumberOfProcessors = SystemInfo.dwNumberOfProcessors;
MEMORYSTATUSEX status;
status.dwLength = sizeof(status);
GlobalMemoryStatusEx(&status);
AvailGBMemory = (int)(status.ullTotalPhys / 0x040000000); // set to be gigabytes
#else
NumberOfProcessors = sysconf(_SC_NPROCESSORS_CONF);
long pages = sysconf(_SC_PHYS_PAGES);
long page_size = sysconf(_SC_PAGE_SIZE);
AvailGBMemory = (int)(((INT64)pages * (INT64)page_size)/0x040000000);
#endif
int MaxAllowedThreads = min(cMaxWorkerThreads,NumberOfProcessors); // limit to be at most cMaxWorkerThreads
if((NumThreads = threads->count ? threads->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;
}
gDiagnostics.DiagOut(eDLInfo,gszProcName,"Processing parameters:");
if(iMode == 2)
{
gDiagnostics.DiagOutMsgOnly(eDLInfo,"Simulating indexing of a genome of size: %dGbp",SimGenomeSize);
if(AvailGBMemory < (SimGenomeSize * 7)) // allowing for 6 bytes per base plus overheads
gDiagnostics.DiagOutMsgOnly(eDLWarn,"May be memory allocation problems when loading or indexing this simulated genome, available memory: %dGB",AvailGBMemory);
}
if(bSOLiD)
gDiagnostics.DiagOutMsgOnly(eDLInfo,"Process for colorspace (SOLiD)");
if(iMode != 2)
{
gDiagnostics.DiagOutMsgOnly(eDLInfo,"Accepting for indexing sequences of length at least: %dbp",MinSeqLen);
gDiagnostics.DiagOutMsgOnly(eDLInfo,"Process input files as: '%s'",iMode == 0 ? "standard" : "bisulphite");
for(Idx=0; Idx < NumInputFileSpecs; Idx++)
gDiagnostics.DiagOutMsgOnly(eDLInfo,"Input source file spec: '%s'",pszInputFileSpecs[Idx]);
}
if(szOutputFileSpec[0] != '\0')
gDiagnostics.DiagOutMsgOnly(eDLInfo,"Output to suffix array file: '%s'",szOutputFileSpec);
gDiagnostics.DiagOutMsgOnly(eDLInfo,"Reference species: '%s'",szRefSpecies);
gDiagnostics.DiagOutMsgOnly(eDLInfo,"Title text: '%s'",szTitle);
gDiagnostics.DiagOutMsgOnly(eDLInfo,"Descriptive text: '%s'",szDescription);
gDiagnostics.DiagOutMsgOnly(eDLInfo,"Number of threads : %d",NumThreads);
if(szExperimentName[0] != '\0')
gDiagnostics.DiagOutMsgOnly(eDLInfo,"This processing reference: %s",szExperimentName);
#ifdef _WIN32
SetPriorityClass(GetCurrentProcess(), BELOW_NORMAL_PRIORITY_CLASS);
#endif
gStopWatch.Start();
Rslt = CreateBioseqSuffixFile(iMode,MinSeqLen,SimGenomeSize,NumThreads,bSOLiD,NumInputFileSpecs,pszInputFileSpecs,szOutputFileSpec,szRefSpecies,szDescription,szTitle);
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());
exit(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");
exit(1);
}
}
int main(int argc, char *argv[]) {
struct arg_str *vpOpt = arg_str1("v", "vidpid", "<VID:PID>", " vendor ID and product ID (e.g 04B4:8613)");
struct arg_uint *toOpt = arg_uint0("t", "timeout", "<millis>", " timeout in milliseconds");
struct arg_int *epOpt = arg_int0("e", "endpoint", "<epNum>", " endpoint to write to");
struct arg_lit *benOpt = arg_lit0("b", "benchmark", " benchmark the operation");
struct arg_lit *chkOpt = arg_lit0("c", "checksum", " print 16-bit checksum");
struct arg_lit *helpOpt = arg_lit0("h", "help", " print this help and exit\n");
struct arg_file *fileOpt = arg_file1(NULL, NULL, "<fileName>", " the data to send");
struct arg_end *endOpt = arg_end(20);
void* argTable[] = {vpOpt, toOpt, epOpt, benOpt, chkOpt, helpOpt, fileOpt, endOpt};
const char *progName = "bulk";
int numErrors;
uint8 epNum = 0x06;
FILE *inFile = NULL;
uint8 *buffer = NULL;
uint32 fileLen;
struct USBDevice *deviceHandle = NULL;
USBStatus uStatus;
int retVal = 0;
const char *error = NULL;
double totalTime, speed;
uint16 checksum = 0x0000;
uint32 timeout = 5000;
uint32 i;
#ifdef WIN32
LARGE_INTEGER tvStart, tvEnd, freq;
DWORD_PTR mask = 1;
SetThreadAffinityMask(GetCurrentThread(), mask);
QueryPerformanceFrequency(&freq);
#else
struct timeval tvStart, tvEnd;
long long startTime, endTime;
#endif
if ( arg_nullcheck(argTable) != 0 ) {
printf("%s: insufficient memory\n", progName);
FAIL(1, cleanup);
}
numErrors = arg_parse(argc, argv, argTable);
if ( helpOpt->count > 0 ) {
printf("Bulk Write Tool Copyright (C) 2009-2011 Chris McClelland\n\nUsage: %s", progName);
arg_print_syntax(stdout, argTable, "\n");
printf("\nWrite data to a bulk endpoint.\n\n");
arg_print_glossary(stdout, argTable," %-10s %s\n");
FAIL(0, cleanup);
}
if ( numErrors > 0 ) {
arg_print_errors(stdout, endOpt, progName);
printf("Try '%s --help' for more information.\n", progName);
FAIL(2, cleanup);
}
if ( toOpt->count ) {
timeout = toOpt->ival[0];
}
inFile = fopen(fileOpt->filename[0], "rb");
if ( !inFile ) {
fprintf(stderr, "Unable to open file %s\n", fileOpt->filename[0]);
FAIL(3, cleanup);
}
fseek(inFile, 0, SEEK_END);
fileLen = (uint32)ftell(inFile);
fseek(inFile, 0, SEEK_SET);
buffer = (uint8 *)malloc(fileLen);
if ( !buffer ) {
fprintf(stderr, "Unable to allocate memory for file %s\n", fileOpt->filename[0]);
FAIL(4, cleanup);
}
if ( fread(buffer, 1, fileLen, inFile) != fileLen ) {
fprintf(stderr, "Unable to read file %s\n", fileOpt->filename[0]);
FAIL(5, cleanup);
}
if ( chkOpt->count ) {
for ( i = 0; i < fileLen; i++ ) {
checksum = (uint16)(checksum + buffer[i]);
}
printf("Checksum: 0x%04X\n", checksum);
}
if ( epOpt->count ) {
epNum = (uint8)epOpt->ival[0];
}
uStatus = usbInitialise(0, &error);
CHECK_STATUS(uStatus, 6, cleanup);
uStatus = usbOpenDevice(vpOpt->sval[0], 1, 0, 0, &deviceHandle, &error);
CHECK_STATUS(uStatus, 7, cleanup);
#ifdef WIN32
QueryPerformanceCounter(&tvStart);
uStatus = usbBulkWrite(deviceHandle, epNum, buffer, fileLen, timeout, &error);
QueryPerformanceCounter(&tvEnd);
CHECK_STATUS(uStatus, 8, cleanup);
totalTime = (double)(tvEnd.QuadPart - tvStart.QuadPart);
totalTime /= freq.QuadPart;
printf("Time: %fms\n", totalTime/1000.0);
speed = (double)fileLen / (1024*1024*totalTime);
#else
gettimeofday(&tvStart, NULL);
uStatus = usbBulkWrite(deviceHandle, epNum, buffer, fileLen, timeout, &error);
gettimeofday(&tvEnd, NULL);
CHECK_STATUS(uStatus, 8, cleanup);
startTime = tvStart.tv_sec;
startTime *= 1000000;
startTime += tvStart.tv_usec;
endTime = tvEnd.tv_sec;
endTime *= 1000000;
endTime += tvEnd.tv_usec;
totalTime = (double)(endTime - startTime);
totalTime /= 1000000; // convert from uS to S.
speed = (double)fileLen / (1024*1024*totalTime);
#endif
if ( benOpt->count ) {
printf("Speed: %f MB/s\n", speed);
}
cleanup:
if ( buffer ) {
free(buffer);
}
if ( inFile ) {
fclose(inFile);
}
if ( deviceHandle ) {
usbCloseDevice(deviceHandle, 0);
}
if ( error ) {
fprintf(stderr, "%s\n", error);
usbFreeError(error);
}
arg_freetable(argTable, sizeof(argTable)/sizeof(argTable[0]));
return retVal;
}
void processArgs(int argc, char **argv) {
int nerrors, i;
char *savptr, str[1024], *str1, machName[1024], sessIDstr[1024];
struct arg_str *arg_sessionID = arg_str1( "S", "sessionID", "<mach.sessionID>", "session ID of run to be processed\n");
struct arg_str *arg_propIDs = arg_str0( "P", "proposals", "<int [,int [,int]]>", "quoted string of proposal numbers to use\n");
struct arg_str *arg_skipDays = arg_str0( "D", "days", "<skip [,length]>", "skip days at start, do length days after\n");
struct arg_lit *arg_Check = arg_lit0( NULL, "checkobs", "check observations for basic errors\n");
struct arg_lit *arg_TimeSummary = arg_lit0( NULL, "timesummary", "time summary");
struct arg_lit *arg_PeriodSearch = arg_lit0( NULL, "periodsearch", "make periodogram plots\n");
struct arg_lit *arg_Hourglass = arg_lit0( "H", "hourglass", "make hourglass plot\n");
struct arg_lit *arg_Opposition = arg_lit0( NULL, "opposition", "make solar angle (opposition) plot\n");
struct arg_str *arg_Airmass = arg_str0( NULL, "airmass", "<int>", "make per-field airmass plot (0 is max, 1 is median)\n");
struct arg_lit *arg_SixVisits = arg_lit0( "V", "sixvisitnum", "make all-filter visit numbers plot\n");
struct arg_lit *arg_5sigma = arg_lit0( "V", "5sigma", "make aitoff plot for median 5sigma also per proposal\n");
struct arg_lit *arg_skyb = arg_lit0( "V", "skyb", "make aitoff plot for median skyb also per proposal\n");
struct arg_lit *arg_seeing = arg_lit0( "V", "seeing", "make aitoff plot for median seeing also per proposal\n");
struct arg_lit *arg_Visits = arg_lit0( "v", "visitnum", "make visit numbers plot for specified filters\n \
(requires -f|--filters)\n");
struct arg_str *arg_reqFilters = arg_str0( "f", "filters", "<f [,f [,f]]>", "which filters to use; f in {ugrizy}\n");
struct arg_lit *arg_NEOrevisits = arg_lit0( "R", "revisits", "make NEO revisit numbers plot\n");
struct arg_lit *arg_Slew = arg_lit0( NULL, "slew", "make slew time histogram\n");
struct arg_lit *arg_SNtiming = arg_lit0( NULL, "sntiming", "make SN Ia cadence plots\n");
struct arg_file *arg_plotfileRoot = arg_file0(NULL, "plotfile", "harcopy file", "root name of plotfile for hardcopy\n");
struct arg_file *arg_plotTitle = arg_file0(NULL, "plottitle", "<string>", "title for plots\n");
struct arg_lit *arg_help = arg_lit0( "h", "help", "show usage\n");
struct arg_lit *arg_debug = arg_lit0( "d", "debug", "debugging output\n");
struct arg_str *arg_hostname = arg_str1( "N", "hostname", "<string>", "if you know hostname \n");
struct arg_str *arg_databasename = arg_str1( "DB", "database", "<string>", "if you know the db name \n");
struct arg_str *arg_designstretch = arg_str1( NULL, "designstretch", "<int>", "design or stretch value\n");
struct arg_end *arg_endp = arg_end(20);
void *argtable[] = {arg_sessionID, arg_propIDs, arg_skipDays, arg_TimeSummary, arg_Check, arg_PeriodSearch,
arg_Hourglass, arg_Opposition, arg_Airmass, arg_SixVisits, arg_5sigma, arg_skyb, arg_seeing,
arg_Slew, arg_Visits, arg_reqFilters, arg_NEOrevisits, arg_SNtiming, arg_plotfileRoot,
arg_plotTitle, arg_debug, arg_help, arg_hostname, arg_designstretch, arg_databasename, arg_endp};
if (arg_nullcheck(argtable) != 0) fprintf(stderr, "error: insufficient memory\n");
nerrors = arg_parse(argc,argv,argtable);
// process arguments
// render assistance when asked
if(arg_help->count>0) {
fprintf(stderr,"Usage: %s [options]\n where [options] are:\n\n",argv[0]);
arg_print_glossary(stderr, argtable, "%-45s %s");
// arg_print_syntaxv(stderr, argtable, "\n");
exit(1);
}
// list errors
if (nerrors > 0) {
arg_print_errors(stdout,arg_endp,argv[0]);
fprintf(stderr,"\nUsage: %s [options]\n where [options] are:\n\n",argv[0]);
arg_print_glossary(stderr, argtable, "%-45s %s");
// arg_print_syntaxv(stderr, argtable, "\n");
exit(1);
}
// set database tableName and sessionID from sessionID argument
//strcpy(str, *arg_sessionID->sval);
//strcpy(machName, strtok_r(str,".",&savptr));
//strcpy(sessIDstr, strtok_r(NULL,".",&savptr));
strcpy(sessIDstr, *arg_sessionID->sval);
sessionID = atoi(sessIDstr);
if ( *arg_databasename->sval == NULL ) {
sprintf(database, "%s", "OpsimDB");
} else {
sprintf(database, "%s", *arg_databasename->sval);
}
if ( *arg_hostname->sval == NULL ) {
if ( gethostname(identifier, identifier_length) == 0 ) {
sprintf(hostname, "%s", identifier);
} else {
printf( "Hostname : %s\n", strerror(errno));
exit(1);
}
} else {
sprintf (hostname, "%s", *arg_hostname->sval);
}
sprintf(tableName, "output_%s_%d", hostname, sessionID);
// set action flags
if(arg_5sigma->count>0) do5sigma=1;
if(arg_skyb->count>0) doskyb=1;
if(arg_seeing->count>0) doSeeing=1;
if(arg_TimeSummary->count>0) doTimeSummary=1;
if(arg_Check->count>0) doCheck=1;
if(arg_PeriodSearch->count>0) doPeriodSearch=1;
if(arg_Hourglass->count>0) doHourglass=1;
if(arg_Opposition->count>0) doOpposition=1;
if(arg_designstretch->count>0) {
if ( strcmp(*arg_designstretch->sval, "0") == 0) {
useDesignStretch = 0;
} else {
useDesignStretch = 1;
}
}
if(arg_Airmass->count>0) {
doAirmass=1;
if(strcmp(*arg_Airmass->sval, "0") != 0) {
useMaxAirmass=0;
}
else {
useMaxAirmass=1;
}
}
if(arg_SixVisits->count>0) doSixVisits=1;
if(arg_Visits->count>0) {
doVisits=1;
if(arg_reqFilters->count==0) {
fprintf(stderr,"Error: with -v|--visitsnum must give -f|--filters\n");
exit(1);
}
strcpy(str, *arg_reqFilters->sval);
i = 0;
strcpy(desiredFilters[i],strtok_r(str," ,",&savptr));
i++;
while((str1=strtok_r(NULL," ,",&savptr))!= NULL) {
strcpy(desiredFilters[i],str1);
i++;
}
ndesiredFilters = i;
}
if(arg_NEOrevisits->count>0) doNEOrevisits=1;
if(arg_SNtiming->count>0) doSNtiming=1;
if(arg_Slew->count>0) doSlew=1;
if(arg_propIDs->count>0) {
strcpy(str, *arg_propIDs->sval);
i = 0;
propIDs[i] = atoi(strtok_r(str," ,",&savptr));
i++;
while((str1=strtok_r(NULL," ,",&savptr))!= NULL) {
propIDs[i] = atoi(str1);
i++;
}
nIDs = i;
}
if(arg_plotfileRoot->count>0) {
strcpy(plotfileRoot,arg_plotfileRoot->filename[0]);
doHardcopy = 1;
}
if(arg_plotTitle->count>0) {
strcpy(plotTitle,arg_plotTitle->filename[0]);
}
if(arg_skipDays->count>0) {
strcpy(str, *arg_skipDays->sval);
skipDays = atoi(strtok_r(str," ,",&savptr));
str1 = strtok_r(NULL," ,",&savptr);
if(str1 != (char *) NULL) lengthDays = atoi(str1);
}
if(arg_debug->count>0) {
debug = 1;
}
#if 0
printf(" sessionID: %d\n", sessionID);
printf(" skipDays: %d\n", skipDays);
printf(" lengthDays: %d\n", lengthDays);
printf(" nIDs: %d\n", nIDs);
if(nIDs>0) {
printf(" using IDs: "); for(i=0; i<nIDs; i++) printf(" %d",propIDs[i]); printf("\n");
}
printf(" doCheck: %d\n", doCheck);
printf("doPeriodSearch: %d\n", doPeriodSearch);
printf(" doHourglass: %d\n", doHourglass);
printf(" doOpposition: %d\n", doOpposition);
printf(" doSixVisits: %d\n", doSixVisits);
printf(" doVisits: %d\n", doVisits);
if(doVisits) {
printf(" using filters: "); for(i=0; i<ndesiredFilters; i++) printf(" %s",desiredFilters[i]); printf("\n");
}
printf(" doNEOrevisits: %d\n", doNEOrevisits);
printf(" doSNtiming: %d\n", doSNtiming);
if(strlen(plotfileRoot)>0) printf(" hardcopy file: \"%s\"\n", plotfileRoot);
if(strlen(plotTitle)>0) printf(" plot title: \"%s\"\n", plotTitle);
printf(" debug: %d\n", debug);
#endif
arg_freetable(argtable,sizeof(argtable)/sizeof(argtable[0]));
}
int main(int argc, char* argv[]) {
double discountFactor = 0.9;
FILE* initFileFd = NULL;
double* setPoints = NULL;
FILE* results = NULL;
char str[1024];
unsigned int i = 0;
unsigned int nbSetPoints = 0;
unsigned int* ns = NULL;
unsigned int nbN = 0;
unsigned int* hs = NULL;
unsigned int nbH = 0;
unsigned int nbSteps = 0;
unsigned int timestamp = time(NULL);
int readFscanf = -1;
struct arg_file* initFile = arg_file1(NULL, "init", "<file>", "File containing the set points");
struct arg_int* s = arg_int1("s", NULL, "<n>", "Number of steps");
struct arg_str* r = arg_str1("n", NULL, "<s>", "List of ressources");
struct arg_str* z = arg_str1("h", NULL, "<s>", "List of length for the sequences");
struct arg_file* where = arg_file1(NULL, "where", "<file>", "Directory where we save the outputs");
struct arg_end* end = arg_end(6);
int nerrors = 0;
void* argtable[6];
argtable[0] = initFile;
argtable[1] = r;
argtable[2] = s;
argtable[3] = z;
argtable[4] = where;
argtable[5] = end;
if(arg_nullcheck(argtable) != 0) {
printf("error: insufficient memory\n");
arg_freetable(argtable, 6);
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, 6);
return EXIT_FAILURE;
}
initGenerativeModelParameters();
initGenerativeModel();
initFileFd = fopen(initFile->filename[0], "r");
readFscanf = fscanf(initFileFd, "%u\n", &nbSetPoints);
setPoints = (double*)malloc(sizeof(double) * nbSetPoints);
for(; i < nbSetPoints; i++) {
readFscanf = fscanf(initFileFd, "%s\n", str);
setPoints[i] = strtod(str, NULL);
}
fclose(initFileFd);
nbSteps = s->ival[0];
hs = parseUnsignedIntList((char*)z->sval[0], &nbH);
ns = parseUnsignedIntList((char*)r->sval[0], &nbN);
sprintf(str, "%s/%u_results_%s_%s.csv", where->filename[0], timestamp, z->sval[0], r->sval[0]);
results = fopen(str, "w");
for(i = 0; i < nbN; i++) { /* Loop on the computational ressources */
printf("Starting with %u computational ressources\n", ns[i]);
fprintf(results, "%u", ns[i]);
fflush(NULL);
unsigned int j = 0;
for(; j < nbH; j++) { /* Loop on the length of the sequences */
unsigned int k = 0;
state* crt1 = initState();
state* crt2 = copyState(crt1);
double averages[2] = {0.0,0.0};
for(; k < nbSetPoints; k++) { /* Loop on the initial states */
unsigned int l = 0;
parameters[10] = setPoints[k];
for(; l < nbSteps; l++) { /* Loop on the step */
char isTerminal = 0;
double reward = 0.0;
state* nextState = NULL;
sequential_direct_instance* sequential_direct = sequential_direct_initInstance(crt1, discountFactor, hs[j],1);
double* optimalAction = sequential_direct_planning(sequential_direct, ns[i]);
isTerminal = nextStateReward(crt1, optimalAction, &nextState, &reward) < 0 ? 1 : 0;
freeState(crt1);
crt1 = nextState;
averages[0] += reward;
sequential_direct_uninitInstance(&sequential_direct);
if(isTerminal)
break;
}
printf("direct: %u set point done for h=%u\n", k, hs[j]);
fflush(NULL);
for(l = 0; l < nbSteps; l++) { /* Loop on the step */
char isTerminal = 0;
double reward = 0.0;
state* nextState = NULL;
sequential_soo_instance* sequential_soo = sequential_soo_initInstance(crt2, discountFactor, hs[j],1);
double* optimalAction = sequential_soo_planning(sequential_soo, ns[i]);
isTerminal = nextStateReward(crt2, optimalAction, &nextState, &reward);
freeState(crt2);
crt2 = nextState;
averages[1] += reward;
sequential_soo_uninitInstance(&sequential_soo);
if(isTerminal)
break;
}
printf("soo: %u set point done for h=%u\n", k, hs[j]);
fflush(NULL);
}
freeState(crt1);
freeState(crt2);
averages[0] = averages[0] /(double)nbSetPoints;
averages[1] = averages[1] /(double)nbSetPoints;
printf("Computation with h=%u and n=%u done\n", hs[j], ns[i]);
fprintf(results, ",%.15f,%.15f", averages[0],averages[1]);
fflush(NULL);
}
printf("Computation with %u computational ressources done\n\n", ns[i]);
fprintf(results, "\n");
fflush(NULL);
}
fclose(results);
arg_freetable(argtable, 6);
free(setPoints);
freeGenerativeModel();
freeGenerativeModelParameters();
return EXIT_SUCCESS;
}
int main(int argc, char **argv)
{
const char* progname = "z-connector";
struct arg_file *device = arg_file1("dD", "device", NULL, "path to the serial port of Z-Wave dongle");
struct arg_str *server = arg_str1("sS", "server", NULL, "IP address or host name to connect to");
struct arg_int *port = arg_int0("pP", "port", NULL, "port number (defaults to 9087)");
struct arg_file *cert = arg_file0(NULL, "cert", NULL, "personal certificate");
struct arg_file *key = arg_file0(NULL, "key", NULL, "personal certificate key");
struct arg_file *cacert = arg_file0(NULL, "cacert", NULL, "CA certificate");
struct arg_file *log = arg_file0("lL", "log", NULL, "file to write log to (defaults to stdout)");
struct arg_lit *debug = arg_lit0(NULL, "debug", "log debugging information");
struct arg_lit *help = arg_lit0("h", "help", "print this help and exit");
struct arg_end *end = arg_end(20);
void* argTable[] = {device, server, port, cert, key, cacert, log, debug, help, end};
#ifdef WIN32
WSADATA wsa;
WORD wsaVersion = MAKEWORD(2, 2);
int wsaError;
DWORD win32err;
#endif
int retCode, nErrors;
if (arg_nullcheck(argTable) != 0)
{
printf("%s: insufficient memory\n", progname);
CLEAN_RETURN(1);
}
nErrors = arg_parse(argc, argv, argTable);
if (IS_ARG_SET(help))
{
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 <*****@*****.**>.\n");
CLEAN_RETURN(0);
}
LogLevel = (IS_ARG_SET(debug)) ? 3 : 2;
if (nErrors > 0)
{
arg_print_errors(stdout, end, progname);
printf("Try '%s --help' for more information.\n", progname);
CLEAN_RETURN(2);
}
#ifdef WIN32
hStoppingEvent = CreateEvent(NULL, TRUE, FALSE, "Local\\Z-Agent-Stop");
if (hStoppingEvent == NULL)
{
win32err = GetLastError();
if (win32err == ERROR_INVALID_HANDLE)
{
printf("Another instance is already running\n");
CLEAN_RETURN(0);
}
else
{
printf("Failed to create synchronization event: %d\n", win32err);
CLEAN_RETURN(3);
}
}
wsaError = WSAStartup(wsaVersion, &wsa);
if (wsaError != 0)
{
printf("WSA Startup failed with code %d\n", wsaError);
CloseHandle(hStoppingEvent);
CLEAN_RETURN(3);
}
if (wsa.wVersion != wsaVersion)
{
printf("Required WSA version not found\n");
CloseHandle(hStoppingEvent);
CLEAN_RETURN(3);
}
#endif
retCode = main_impl(device->filename[0],
server->sval[0], SAFE_INT(port, 9087),
SAFE_FILE(cert, ""), SAFE_FILE(key, ""), SAFE_FILE(cacert, ""),
SAFE_FILE(log, "-"));
#ifdef WIN32
WSACleanup();
CloseHandle(hStoppingEvent);
#endif
CLEAN_RETURN(retCode);
}
int main(int argc, char* argv[])
{
int nerrors, w;
bstring temp = NULL;
const char* warnprefix = "no-";
bool expect_failure;
// Define arguments.
struct arg_lit* show_help = arg_lit0("h", "help", "Show this help.");
struct arg_lit* expect_failure_lit = arg_lit0("f", "fail", "Expect failure during preprocessing.");
struct arg_str* input_lang = arg_str1(NULL, NULL, "<lang>", "The input language.");
struct arg_file* input_file = arg_file1(NULL, NULL, "<file>", "The input preprocessor file.");
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, verbose, quiet, expect_failure_lit, input_lang, input_file, end };
// Parse arguments.
nerrors = arg_parse(argc, argv, argtable);
if (nerrors != 0 || show_help->count != 0)
{
if (nerrors != 0)
arg_print_errors(stdout, end, "libdcpu-pp test suite");
printd(LEVEL_DEFAULT, "syntax:\n dtasm");
arg_print_syntax(stderr, argtable, "\n");
printd(LEVEL_DEFAULT, "options:\n");
arg_print_glossary(stderr, argtable, " %-25s %s\n");
if (show_help->count == 2)
{
printd(LEVEL_DEFAULT, "defined warnings:\n");
for (w = 0; w < _WARN_COUNT; w++)
printd(LEVEL_DEFAULT, " %s\n", dwarnpolicy[w].name);
}
arg_freetable(argtable, sizeof(argtable) / sizeof(argtable[0]));
return 1;
}
// Set failure expectation variable.
expect_failure = (expect_failure_lit->count > 0);
// Set verbosity level.
debug_setlevel(LEVEL_DEFAULT + verbose->count - quiet->count);
// Set global path variable.
osutil_setarg0(bautofree(bfromcstr(argv[0])));
// Set up error handling.
if (dsethalt())
{
// Handle the error.
dautohandle();
printd(LEVEL_ERROR, "libdcpu-pp test suite: error occurred.\n");
if (temp != NULL)
pp_cleanup(bautofree(temp));
arg_freetable(argtable, sizeof(argtable) / sizeof(argtable[0]));
if (expect_failure)
return 0;
else
return 1;
}
// Perform preprocessing.
ppfind_add_autopath(bautofree(bfromcstr(input_file->filename[0])));
temp = pp_do(
bautofree(bfromcstr(input_lang->sval[0])),
bautofree(bfromcstr(input_file->filename[0]))
);
// Perform parsing.
test_success = true;
yyin = fopen(temp->data, "r");
yyout = NULL;
yyparse();
fclose(yyin);
// Cleanup.
pp_cleanup(bautofree(temp));
if (test_success && expect_failure)
return 1;
else if (test_success && !expect_failure)
return 0;
else if (!test_success && expect_failure)
return 0;
else
return 1;
}
int main(int argc, char* argv[])
{
CURL* curl;
bstring command;
bstring name;
bstring modpath;
int all;
// Define arguments.
struct arg_lit* show_help = arg_lit0("h", "help", "Show this help.");
struct arg_str* cmdopt = arg_str1(NULL, NULL, "<command>", "The command; either 'search', 'install', 'uninstall', 'enable' or 'disable'.");
struct arg_str* nameopt = arg_str0(NULL, NULL, "<name>", "The name of the module to search for, install, uninstall, enable or disable.");
struct arg_lit* all_flag = arg_lit0("a", "all", "Apply this command to all available / installed modules.");
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, cmdopt, all_flag, nameopt, verbose, quiet, end };
// Parse arguments.
int nerrors = arg_parse(argc, argv, argtable);
if (nerrors != 0 || show_help->count != 0 || (all_flag->count == 0 && nameopt->count == 0))
{
if (all_flag->count == 0 && nameopt->count == 0)
printd(LEVEL_ERROR, "error: must have either module name or -a.");
if (show_help->count != 0)
arg_print_errors(stderr, end, "mm");
fprintf(stderr, "syntax:\n dtmm");
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);
// Show version information.
version_print(bautofree(bfromcstr("Module Manager")));
// Set argument 0 and convert parameters.
osutil_setarg0(bautofree(bfromcstr(argv[0])));
command = bfromcstr(cmdopt->sval[0]);
name = bfromcstr(nameopt->sval[0]);
// Initialize curl or exit.
curl = curl_easy_init();
if (!curl)
{
printd(LEVEL_ERROR, "unable to initialize curl.\n");
return 1;
}
// Ensure module path exists.
modpath = osutil_getmodulepath();
if (modpath == NULL)
{
printd(LEVEL_ERROR, "module path does not exist (searched TOOLCHAIN_MODULES and modules/).\n");
return 1;
}
bdestroy(modpath);
// Convert all flag.
all = (all_flag->count > 0);
// If all is set, set the name back to "".
if (all)
bassigncstr(name, "");
// If the name is "all" or "*", handle this as the all
// boolean flag.
if (biseqcstr(name, "all") || biseqcstr(name, "*"))
{
bassigncstr(name, "");
all = 1;
printd(LEVEL_WARNING, "treating name as -a (all) flag");
}
if (biseqcstrcaseless(command, "search") || biseqcstrcaseless(command, "se"))
return do_search(curl, name, all);
else if (biseqcstrcaseless(command, "install") || biseqcstrcaseless(command, "in"))
{
if (all)
return do_install_all(curl);
else
return do_install(curl, name);
}
else if (biseqcstrcaseless(command, "uninstall") || biseqcstrcaseless(command, "rm"))
{
if (all)
return do_uninstall_all(curl);
else
return do_uninstall(curl, name);
}
else if (biseqcstrcaseless(command, "enable") || biseqcstrcaseless(command, "en"))
{
if (all)
return do_enable_all(curl);
else
return do_enable(curl, name);
}
else if (biseqcstrcaseless(command, "disable") || biseqcstrcaseless(command, "di") || biseqcstrcaseless(command, "dis"))
{
if (all)
return do_disable_all(curl);
else
return do_disable(curl, name);
}
else
{
printd(LEVEL_ERROR, "unknown command (must be search, install, uninstall, enable or disable).");
return 1;
}
return 0;
}
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)
{
/* 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;
}
void conf_configure_app(configuration_ctx_t* ctx) {
struct arg_lit* help = arg_lit0(OPT_HELP_SHORT, OPT_HELP_LONG, OPT_HELP_DESCR);
struct arg_lit* helpF = arg_lit0(OPT_HELP_SHORT, OPT_HELP_LONG, OPT_HELP_DESCR);
struct arg_lit* helpS = arg_lit0(OPT_HELP_SHORT, OPT_HELP_LONG, OPT_HELP_DESCR);
struct arg_lit* grep = arg_lit0(OPT_GREP_SHORT, OPT_GREP_LONG, OPT_GREP_DESCR);
struct arg_lit* grepF = arg_lit0(OPT_GREP_SHORT, OPT_GREP_LONG, OPT_GREP_DESCR);
struct arg_lit* grepS = arg_lit0(OPT_GREP_SHORT, OPT_GREP_LONG, OPT_GREP_DESCR);
struct arg_str* string = arg_str1(OPT_STR_SHORT, OPT_STR_LONG, NULL, OPT_STR_DESCR);
struct arg_str* stringG = arg_str0(OPT_STR_SHORT, OPT_STR_LONG, NULL, OPT_STR_DESCR);
struct arg_file* file = arg_file1(OPT_FILE_SHORT, OPT_FILE_LONG, NULL, OPT_FILE_DESCR);
struct arg_file* fileG = arg_file0(OPT_FILE_SHORT, OPT_FILE_LONG, NULL, OPT_FILE_DESCR);
struct arg_str* macro = arg_str1(OPT_MACRO_SHORT, OPT_MACRO_LONG, NULL, OPT_MACRO_DESCR);
struct arg_str* macroS = arg_str1(OPT_MACRO_SHORT, OPT_MACRO_LONG, NULL, OPT_MACRO_DESCR);
struct arg_str* macroF = arg_str1(OPT_MACRO_SHORT, OPT_MACRO_LONG, NULL, OPT_MACRO_DESCR);
struct arg_file* files = arg_filen(OPT_F_SHORT, OPT_F_LONG, NULL, 1, ctx->argc + 2, OPT_F_DESCR);
struct arg_file* filesS = arg_filen(OPT_F_SHORT, OPT_F_LONG, NULL, 1, ctx->argc + 2, OPT_F_DESCR);
struct arg_file* filesF = arg_filen(OPT_F_SHORT, OPT_F_LONG, NULL, 1, ctx->argc + 2, OPT_F_DESCR);
struct arg_end* end = arg_end(10);
struct arg_end* endF = arg_end(10);
struct arg_end* endS = arg_end(10);
void* argtable[] = {help, grep, stringG, fileG, macro, files, end};
void* argtableF[] = {helpF, grepF, file, macroF, filesF, endF};
void* argtableS[] = {helpS, grepS, string, macroS, filesS, endS};
if(arg_nullcheck(argtable) != 0 || arg_nullcheck(argtableF) != 0 || arg_nullcheck(argtableS) != 0) {
prconf_print_syntax(argtable, argtableS, argtableF);
goto cleanup;
}
int nerrors = arg_parse(ctx->argc, ctx->argv, argtable);
int nerrorsF = arg_parse(ctx->argc, ctx->argv, argtableF);
int nerrorsS = arg_parse(ctx->argc, ctx->argv, argtableS);
if(nerrors > 0 || help->count > 0) {
prconf_print_syntax(argtable, argtableS, argtableF);
if(help->count == 0 && ctx->argc > 1) {
arg_print_errors(stdout, end, PROGRAM_NAME);
}
goto cleanup;
}
if(nerrorsS == 0) {
ctx->on_string(filesS, macroS->sval[0], string->sval[0], grepS->count > 0);
}
else if(nerrorsF == 0) {
ctx->on_file(filesS, macroF->sval[0], file->filename[0], grepF->count > 0);
}
else {
prconf_print_syntax(argtable, argtableS, argtableF);
arg_print_errors(stdout, endF, PROGRAM_NAME);
arg_print_errors(stdout, endS, PROGRAM_NAME);
}
cleanup:
arg_freetable(argtable, sizeof(argtable) / sizeof(argtable[0]));
arg_freetable(argtableS, sizeof(argtableS) / sizeof(argtableS[0]));
arg_freetable(argtableF, sizeof(argtableF) / sizeof(argtableF[0]));
}
int GRTCLCrackCommandLineData::ParseCommandLine(int argc, char *argv[]) {
int deviceCount, i;
std::vector<std::string> webTableFilenames;
// Command line argument parsing with argtable
struct arg_lit *verbose = arg_lit0("v", "verbose", "verbose output");
struct arg_lit *silent = arg_lit0(NULL, "silent", "silence all output");
// Table related options
struct arg_file *table_file = arg_filen(NULL,NULL,"<file>", 0, 10000, "GRT Tables to use");
struct arg_file *hash_file = arg_file0("f","hashfile","<file>", "Hashfile to use");
struct arg_str *hash_value = arg_str0("s", "hashstring", "hashstring", "The hash string");
struct arg_str *hash_type = arg_str1("h", "hashtype", "{NTLM, MD4, MD5, SHA1}", "hash type to crack");
// CUDA related params
struct arg_int *device = arg_int0("d", "device", "<n>", "OpenCL device to use");
struct arg_int *platform = arg_int0("p", "platform", "<n>", "OpenCL platform to use");
struct arg_int *m = arg_int0("m", "ms", "<n>", "target step time in ms");
struct arg_int *blocks = arg_int0("b", "blocks", "<n>", "number of thread blocks to run");
struct arg_int *threads = arg_int0("t", "threads", "<n>", "number of threads per block");
struct arg_lit *zerocopy = arg_lit0("z", "zerocopy", "use zerocopy memory");
struct arg_file *o = arg_file0("o", "outputfile", "outputfile", "output file for results");
// hexoutput: Adds hex output to all password outputs.
struct arg_lit *hex_output = arg_lit0(NULL, "hexoutput", "Adds hex output to all hash outputs");
struct arg_lit *amd_kernels = arg_lit0(NULL, "amd", "use AMD vector kernels");
struct arg_int *vector_width = arg_int0(NULL, "vectorwidth", "<n>", "vector width");
struct arg_lit *debug = arg_lit0(NULL, "debug", "Use debug display class");
struct arg_lit *devdebug = arg_lit0(NULL, "devdebug", "Developer debugging output");
struct arg_str *debugfiles = arg_str0(NULL, "debugdumpfiles", "<filename>", "Filename base to dump candidates and chains to");
struct arg_int *prefetch_count = arg_int0(NULL, "prefetch", "<n>", "number of prefetch threads");
struct arg_int *candidates_to_skip = arg_int0(NULL, "skip", "<n>", "number of candidate hashes to skip");
struct arg_str *table_url = arg_str0(NULL, "tableurl", "<URL>", "URL of the web table script");
struct arg_str *table_username = arg_str0(NULL, "tableusername", "<username>", "Username, if required, for the web table script");
struct arg_str *table_password = arg_str0(NULL, "tablepassword", "<password>", "Password, if required, for the web table script");
struct arg_end *end = arg_end(20);
void *argtable[] = {verbose,silent,table_file,hash_value,hash_file,hash_type,
device,platform,m,blocks,threads,zerocopy,o,amd_kernels,vector_width,
debug, devdebug, prefetch_count,table_url,table_username,table_password,
candidates_to_skip,debugfiles,hex_output,end};
// Get arguments, collect data, check for basic errors.
if (arg_nullcheck(argtable) != 0) {
printf("error: insufficient memory\n");
}
// Look for errors
int nerrors = arg_parse(argc,argv,argtable);
if (nerrors > 0) {
// Print errors, exit.
arg_print_errors(stdout,end,argv[0]);
//arg_print_syntax(stdout,argtable,"\n\n");
printf("\n\nOptions: \n");
arg_print_glossary(stdout,argtable," %-20s %s\n");
exit(1);
}
// Verbose & silent
if (verbose->count) {
this->Verbose = 1;
}
if (silent->count) {
this->Silent = 1;
}
if (zerocopy->count) {
this->CUDAUseZeroCopy = 1;
}
if (debug->count) {
this->Debug = 1;
}
if (devdebug->count) {
this->Debug = 1;
this->DeveloperDebug = 1;
}
if (debugfiles->count) {
this->DebugDump = 1;
this->DebugDumpFilenameBase = *debugfiles->sval;
}
if (prefetch_count->count) {
this->NumberPrefetchThreads = *prefetch_count->ival;
}
if (candidates_to_skip->count) {
this->CandidateHashesToSkip = *candidates_to_skip->ival;
}
// Web table stuff
if (table_url->count) {
this->useWebTable = 1;
this->tableURL = *table_url->sval;
// If someone has NOT specified the candidates to skip, set to default.
if (!candidates_to_skip->count) {
this->CandidateHashesToSkip = DEFAULT_CANDIDATES_TO_SKIP;
}
}
if (table_username->count) {
this->tableUsername = *table_username->sval;
}
if (table_password->count) {
this->tablePassword = *table_password->sval;
}
this->HashType = this->GRTHashTypes->GetHashIdFromString(*hash_type->sval);
if (this->HashType == -1) {
printf("Unknown hash type %s: Exiting.\n\n", *hash_type->sval);
exit(1);
}
int correct_length = this->GRTHashTypes->GetHashLengthFromId(this->HashType);
// if we know the correct length, we make sure the hash is the correct length
if (correct_length != 0) {
if ((hash_value->count) && (strlen(*hash_value->sval) != correct_length)) {
printf("Hash string is not %d hex characters. Exiting.\n\n", correct_length);
exit(1);
}
}
if (hash_value->count) {
convertAsciiToBinary(*hash_value->sval, this->Hash, 16);
} else if (hash_file->count) {
this->hashFileName = hash_file->filename[0];
this->useHashFile = 1;
} else {
printf("Must provide a hash value or a hash file!\n");
exit(1);
}
if (o->count) {
this->outputHashFileName = o->filename[0];
this->useOutputHashFile = 1;
}
// Desired kernel time
if (m->count) {
this->KernelTimeMs = *m->ival;
}
// Do this to emulate CUDA behavior for now...
// Threads - if not set, leave at default 0
if (threads->count) {
this->OpenCLWorkitems = *threads->ival;
}
// Blocks - if not set, leave at default 0
if (blocks->count) {
this->OpenCLWorkgroups = *blocks->ival * this->OpenCLWorkitems;
}
if (hex_output->count) {
this->AddHexOutput = 1;
}
// Allocate space for the list of pointers
// Create the table header type
if (this->useWebTable) {
this->TableHeader = new GRTTableHeaderVWeb();
this->TableHeader->setWebURL(this->tableURL);
this->TableHeader->setWebUsername(this->tableUsername);
this->TableHeader->setWebPassword(this->tablePassword);
GRTTableHeaderVWeb *WebTableHeader =
(GRTTableHeaderVWeb *)this->TableHeader;
webTableFilenames = WebTableHeader->getHashesFromServerByType(this->HashType);
} else {
// V1 will work for both V1 & V2 types
this->TableHeader = new GRTTableHeaderV1();
}
// If we don't have any table filenames, get the ones from the web.
// Note: The script ONLY reutrns valid tables.
if ((table_file->count == 0) && this->useWebTable) {
this->Table_File_Count = webTableFilenames.size();
this->Table_Filenames = (char **)malloc(this->Table_File_Count * sizeof(char *));
for (i = 0; i < this->Table_File_Count; i++) {
// Increment size by 1 for null termination
this->Table_Filenames[i] = (char *)malloc((webTableFilenames.at(i).size() + 1) * sizeof(char));
strcpy(this->Table_Filenames[i], webTableFilenames.at(i).c_str());
}
} else {
this->Table_File_Count = table_file->count;
this->Table_Filenames = (char **)malloc(this->Table_File_Count * sizeof(char *));
// Handle the file list sanely
for (i = 0; i < table_file->count; i++) {
// Check to ensure the file is valid
if (!this->TableHeader->isValidTable(table_file->filename[i], -1)) {
printf("%s is not a valid GRT table! Exiting.\n", table_file->filename[i]);
exit(1);
}
// Check to ensure the file is of the right type
if (!this->TableHeader->isValidTable(table_file->filename[i], this->HashType)) {
printf("%s is not a valid %s GRT table!\n", table_file->filename[i],
this->GRTHashTypes->GetHashStringFromId(this->HashType));
exit(1);
}
// Increment size by 1 for null termination
this->Table_Filenames[i] = (char *)malloc((strlen(table_file->filename[i]) + 1) * sizeof(char));
strcpy(this->Table_Filenames[i], table_file->filename[i]);
}
}
// Finally, set the CUDA device and look for errors.
if (device->count) {
this->OpenCLDevice = *device->ival;
}
if (platform->count) {
this->OpenCLPlatform = *platform->ival;
}
if (amd_kernels->count) {
this->useAmdKernels = 1;
this->vectorWidth = 4;
}
if (vector_width->count) {
this->vectorWidth = *vector_width->ival;
}
}
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;
int iProcMode;
int iMinLength;
int iMaxLength;
int iMinMergeLength;
int iMaxMergeLength;
char szRefFile[_MAX_PATH]; // process ref hypers from this file
char szRelFile[_MAX_PATH]; // process rel hypers from this file
char szOutLociFile[_MAX_PATH]; // write loci to this file
char szRefSpecies[cMaxDatasetSpeciesChrom]; // use this species as the ref species in generated szOutLociFile
char szRelSpecies[cMaxDatasetSpeciesChrom]; // use this species/list as the rel species in generated szOutLociFile
char szElType[cMaxDatasetSpeciesChrom]; // use this as the element type in generated szOutLociFile
int iRefExtend; // extend ref element lengths left+right by this many bases
int iRelExtend; // extend rel element lengths left+right by this many bases
int iJoinDistance; // if > 0 then join elements which only differ by at most this distance beween end of element i and start of element i+1
// 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_file *RefFile = arg_file1("i","reffile","<file>", "reference hyper element CSV file");
struct arg_file *RelFile = arg_file0("I","relfile","<file>", "relative hyper element CSV file");
struct arg_file *OutLociFile = arg_file1("o",NULL,"<file>", "output loci to file as CSV");
struct arg_str *RefSpecies = arg_str1("r","refspecies","<string>","output loci file ref species");
struct arg_str *RelSpecies = arg_str1("R","relspecies","<string>","output loci file rel species");
struct arg_str *ElType = arg_str0("t","eltype","<string>","output loci file element type");
struct arg_int *ProcMode = arg_int0("p","mode","<int>", "processing mode: 0:Intersect (Ref & Rel)\n\t\t1:Ref exclusive (Ref & !Rel)\n\t\t2:Rel exclusive (!Ref & Rel)\n\t\t3:Union (Ref | Rel)\n\t\t4:Neither (!(Ref | Rel))");
struct arg_int *MinLength = arg_int0("l","minlength","<int>", "minimum input ref/rel element length (default 4)");
struct arg_int *MaxLength = arg_int0("L","maxlength","<int>", "maximum input ref/rel element length (default 1000000)");
struct arg_int *MinMergeLength = arg_int0("m","minmergelength","<int>","minimum merged output element length (default 4)");
struct arg_int *MaxMergeLength = arg_int0("M","maxmergelength","<int>","maximum merged output element length (default 1000000)");
struct arg_int *RefExtend = arg_int0("e","refextend","<int>", "extend ref element flanks left+right by this many bases (default 0)");
struct arg_int *RelExtend = arg_int0("E","relextend","<int>", "extend rel element flanks left+right by this many bases (default 0)");
struct arg_int *JoinDistance = arg_int0("j","join","<int>", "merge output elements which are only separated by this number of bases (default 0)");
struct arg_end *end = arg_end(20);
void *argtable[] = {help,version,FileLogLevel,LogFile,
ProcMode,
RefFile,RelFile,OutLociFile,
MinLength,MaxLength,RefExtend,RelExtend,JoinDistance,MinMergeLength,MaxMergeLength,
RefSpecies,RelSpecies,ElType,
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 CSV Merge Elements, 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",gszProcName);
printf("\nPlease report any issues regarding usage of %s at https://github.com/csiro-crop-informatics/biokanga/issues\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';
}
iProcMode = ProcMode->count ? ProcMode->ival[0] : ePMElIntersect;
if(iProcMode < ePMElIntersect || iProcMode > ePMElRefNotRefRel)
{
printf("Error: Processing mode '-p%d' is not in range 0..4",iProcMode);
exit(1);
}
strncpy(szOutLociFile,OutLociFile->filename[0],_MAX_PATH);
szOutLociFile[_MAX_PATH-1] = '\0';
strncpy(szRefSpecies,RefSpecies->sval[0],sizeof(szRefSpecies));
szRefSpecies[sizeof(szRefSpecies)-1] = '\0';
strncpy(szRelSpecies,RelSpecies->sval[0],sizeof(szRelSpecies));
szRelSpecies[sizeof(szRelSpecies)-1] = '\0';
if(ElType->count)
{
strncpy(szElType,ElType->sval[0],sizeof(szElType));
szElType[sizeof(szElType)-1] = '\0';
}
else
strcpy(szElType,"merged");
iMinLength = MinLength->count ? MinLength->ival[0] : cDfltMinLength;
if(iMinLength < 0 || iMinLength > cMaxLengthRange)
{
printf("Error: Minimum element length '-l%d' is not in range 0..%d",iMinLength,cMaxLengthRange);
exit(1);
}
iMaxLength = MaxLength->count ? MaxLength->ival[0] : cDfltMaxLength;
if(iMaxLength < iMinLength || iMaxLength > cMaxLengthRange)
{
printf("Error: Maximum element length '-L%d' is not in range %d..%d",iMaxLength,iMinLength,cMaxLengthRange);
exit(1);
}
iMinMergeLength = MinMergeLength->count ? MinMergeLength->ival[0] : cDfltMinLength;
if(iMinMergeLength < 0 || iMinMergeLength > cMaxLengthRange)
{
printf("Error: Minimum output merged element length '-m%d' is not in range 0..%d",iMinMergeLength,cMaxLengthRange);
exit(1);
}
iMaxMergeLength = MaxMergeLength->count ? MaxMergeLength->ival[0] : cDfltMaxLength;
if(iMaxMergeLength < iMinMergeLength || iMaxMergeLength > cMaxLengthRange)
{
printf("Error: Maximum element length '-M%d' is not in range %d..%d",iMaxMergeLength,iMinMergeLength,cMaxLengthRange);
exit(1);
}
iJoinDistance = JoinDistance->count ? JoinDistance->ival[0] : cDfltJoinOverlap;
if(iJoinDistance < 0 || iJoinDistance > cMaxJoinOverlap)
{
printf("Error: Join separation length '-j%d' is not in range %d..%d",iJoinDistance,0,cMaxJoinOverlap);
exit(1);
}
iRefExtend = RefExtend->count ? RefExtend->ival[0] : 0;
if(iRefExtend < (-1 * cMaxExtendLength) || iRefExtend > cMaxExtendLength)
{
printf("Error: Ref Extension length '-e%d' is not in range %d..%d",iRefExtend,(-1 * cMaxExtendLength),cMaxExtendLength);
exit(1);
}
iRelExtend = RelExtend->count ? RelExtend->ival[0] : 0;
if(iRelExtend < (-1 * cMaxExtendLength) || iRelExtend > cMaxExtendLength)
{
printf("Error: Rel Extension length '-E%d' is not in range %d..%d",iRelExtend,(-1 * cMaxExtendLength),cMaxExtendLength);
exit(1);
}
strncpy(szRefFile,RefFile->filename[0],_MAX_PATH);
szRefFile[_MAX_PATH-1] = '\0';
if(RelFile->count)
{
strncpy(szRelFile,RelFile->filename[0],_MAX_PATH);
szRelFile[_MAX_PATH-1] = '\0';
}
else
{
if(iProcMode == ePMElRefExclusive || iProcMode == ePMElRefRelUnion)
szRelFile[0] = '\0';
else
{
printf("Error: Rel loci file must be specified in processing mode '-p%d' (%s)",iProcMode,ProcMode2Txt((etProcMode)iProcMode));
exit(1);
}
}
// 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,"Processing Mode: %d (%s)",iProcMode,ProcMode2Txt((etProcMode)iProcMode));
gDiagnostics.DiagOutMsgOnly(eDLInfo,"Reference CSV file: '%s'",szRefFile);
if(szRelFile[0] != '\0')
gDiagnostics.DiagOutMsgOnly(eDLInfo,"Relative CSV file: '%s'",szRelFile);
gDiagnostics.DiagOutMsgOnly(eDLInfo,"Output processed loci into CSV file: '%s'",szOutLociFile);
gDiagnostics.DiagOutMsgOnly(eDLInfo,"Output loci file ref species: '%s'",szRefSpecies);
gDiagnostics.DiagOutMsgOnly(eDLInfo,"Output loci file rel species: '%s'",szRelSpecies);
gDiagnostics.DiagOutMsgOnly(eDLInfo,"Output loci file element type: '%s'",szElType);
gDiagnostics.DiagOutMsgOnly(eDLInfo,"Minimum input element length: %d",iMinLength);
gDiagnostics.DiagOutMsgOnly(eDLInfo,"Maximum input element length: %d",iMaxLength);
gDiagnostics.DiagOutMsgOnly(eDLInfo,"Ref element flank extension length: %d",iRefExtend);
gDiagnostics.DiagOutMsgOnly(eDLInfo,"Rel element flank extension length: %d",iRelExtend);
gDiagnostics.DiagOutMsgOnly(eDLInfo,"Merge output elements separated by at most this many bases: %d",iJoinDistance);
gDiagnostics.DiagOutMsgOnly(eDLInfo,"Minimum output merged element length: %d",iMinMergeLength);
gDiagnostics.DiagOutMsgOnly(eDLInfo,"Maximum output merged element length: %d",iMaxMergeLength);
// processing here...
gStopWatch.Start();
#ifdef _WIN32
SetPriorityClass(GetCurrentProcess(), BELOW_NORMAL_PRIORITY_CLASS);
#endif
Rslt = Process((etProcMode)iProcMode,iMinLength,iMaxLength,iRefExtend,iRelExtend,iJoinDistance,iMinMergeLength,iMaxMergeLength,szRefFile,szRelFile,szOutLociFile,
szRefSpecies,szRelSpecies,szElType);
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 CSV Merge Elements, 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[]) {
#ifdef BALL
double discountFactor = 0.9;
#else
#ifdef CART_POLE
double discountFactor = 0.95;
#else
#ifdef DOUBLE_CART_POLE
double discountFactor = 0.95;
#else
#ifdef MOUNTAIN_CAR
double discountFactor = 0.99;
#else
#ifdef ACROBOT
double discountFactor = 0.95;
#else
#ifdef BOAT
double discountFactor = 0.95;
#else
#ifdef CART_POLE_BINARY
double discountFactor = 0.95;
#else
#ifdef SWIMMER
double discountFactor = 0.95;
#endif
#endif
#endif
#endif
#endif
#endif
#endif
#endif
FILE* initFileFd = NULL;
state** initialStates = NULL;
FILE* results = NULL;
char str[1024];
unsigned int i = 0;
unsigned int h = 0;
unsigned int* ns = NULL;
unsigned int nbN = 0;
unsigned int n = 0;
unsigned int nbSteps = 0;
unsigned int timestamp = time(NULL);
int readFscanf = -1;
optimistic_instance* optimistic = NULL;
struct arg_file* initFile = arg_file1(NULL, "init", "<file>", "File containing the inital state");
struct arg_str* r = arg_str1("n", NULL, "<s>", "List of maximum numbers of evaluations");
struct arg_int* s = arg_int1("s", NULL, "<n>", "Number of steps");
struct arg_int* k = arg_int1("k", NULL, "<n>", "Branching factor of the problem");
struct arg_file* where = arg_file1(NULL, "where", "<file>", "Directory where we save the outputs");
struct arg_end* end = arg_end(6);
int nerrors = 0;
void* argtable[6];
argtable[0] = initFile;
argtable[1] = r;
argtable[2] = s;
argtable[3] = k;
argtable[4] = where;
argtable[5] = end;
if(arg_nullcheck(argtable) != 0) {
printf("error: insufficient memory\n");
arg_freetable(argtable, 6);
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, 6);
return EXIT_FAILURE;
}
initGenerativeModelParameters();
K = k->ival[0];
initGenerativeModel();
initFileFd = fopen(initFile->filename[0], "r");
readFscanf = fscanf(initFileFd, "%u\n", &n);
initialStates = (state**)malloc(sizeof(state*) * n);
for(; i < n; i++) {
readFscanf = fscanf(initFileFd, "%s\n", str);
initialStates[i] = makeState(str);
}
fclose(initFileFd);
nbSteps = s->ival[0];
ns = parseUnsignedIntList((char*)r->sval[0], &nbN);
optimistic = optimistic_initInstance(NULL, discountFactor);
sprintf(str, "%s/%u_results_%u_%u.csv", where->filename[0], timestamp, K, nbSteps);
results = fopen(str, "w");
for(h = 0; h < nbN; h++) {
double sumRewards = 0.0;
for(i = 0; i < n; i++) {
unsigned int j = 0;
state* crt = copyState(initialStates[i]);
optimistic_resetInstance(optimistic, crt);
for(; j < nbSteps; j++) {
char isTerminal = 0;
double reward = 0.0;
state* nextState = NULL;
optimistic_keepSubtree(optimistic);
action* optimalAction = optimistic_planning(optimistic, ns[h]);
isTerminal = nextStateReward(crt, optimalAction, &nextState, &reward) < 0 ? 1 : 0;
freeState(crt);
crt = nextState;
sumRewards += reward;
if(isTerminal)
break;
}
optimistic_resetInstance(optimistic, crt);
freeState(crt);
printf(">>>>>>>>>>>>>> %uth initial state processed\n", i + 1);
fflush(NULL);
}
fprintf(results, "%u,%.15f\n", ns[h], sumRewards / (double)n);
printf(">>>>>>>>>>>>>> n = %u done\n\n", ns[h]);
fflush(NULL);
}
fclose(results);
arg_freetable(argtable, 6);
for(i = 0; i < n; i++)
freeState(initialStates[i]);
free(initialStates);
optimistic_uninitInstance(&optimistic);
freeGenerativeModel();
freeGenerativeModelParameters();
return EXIT_SUCCESS;
}
int main(int argc, char** argv) {
struct arg_int *numVerticesArg = arg_int0("v","vertices",NULL, "num vertices (default is 20)");
struct arg_int *numObjectsArg = arg_int0("o","objects",NULL, "num objects (default is 20)");
struct arg_lit *help = arg_lit0(NULL,"help", "print this help and exit");
struct arg_str *rendererArg = arg_str1(NULL,NULL,"RENDERER",NULL);
struct arg_end *end = arg_end(20);
void* argtable[] = {numVerticesArg, numObjectsArg, help, rendererArg, end};
const char* progname = "gl-instancing";
int exitcode=0;
int nerrors;
renderer *renderer;
int numVertices = 20;
int numObjects = 20;
/* 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)
{
printUsage(stderr, progname, argtable);
goto exit;
}
if (numVerticesArg->count > 0) {
numVertices = numVerticesArg->ival[0];
}
if (numObjectsArg->count > 0) {
numObjects = numObjectsArg->ival[0];
}
if (rendererArg->count == 0) {
fprintf(stderr, "Provide a renderer!\n");
printUsage(stderr, progname, argtable);
goto exit;
}
if (rendererArg->count > 0) {
if (strcmp(rendererArg->sval[0], "standard") == 0) {
renderer = getStandardRenderer(numVertices, numObjects);
} else if (strcmp(rendererArg->sval[0], "instanced") == 0) {
renderer = getInstancedRenderer(numVertices, numObjects);
} else {
fprintf(stderr, "Renderer %s is unknown. Supported renderers: instanced, standard\n", rendererArg->sval[0]);
printUsage(stderr, progname, argtable);
goto exit;
}
}
exitcode = glMain(renderer);
exit:
/* deallocate each non-null entry in argtable[] */
arg_freetable(argtable,sizeof(argtable)/sizeof(argtable[0]));
return exitcode;
}
split_options_t *new_split_cli_options() {
split_options_t *options = (split_options_t*) malloc (sizeof(split_options_t));
options->num_options = NUM_SPLIT_OPTIONS;
options->criterion = arg_str1(NULL, "criterion", NULL, "Criterion for splitting the file");
return options;
}
int main(int argc, char* argv[]) {
#ifdef BALL
double discountFactor = 0.9;
#else
#ifdef CART_POLE
double discountFactor = 0.95;
#else
#ifdef DOUBLE_CART_POLE
double discountFactor = 0.95;
#else
#ifdef MOUNTAIN_CAR
double discountFactor = 0.99;
#else
#ifdef ACROBOT
double discountFactor = 0.95;
#else
#ifdef BOAT
double discountFactor = 0.95;
#else
#ifdef SWIMMER
double discountFactor = 0.95;
#endif
#endif
#endif
#endif
#endif
#endif
#endif
FILE* initFileFd = NULL;
state** initialStates = NULL;
FILE* results = NULL;
char str[1024];
unsigned int i = 0;
unsigned int* ns = NULL;
unsigned int nbN = 0;
unsigned int* hs = NULL;
unsigned int nbH = 0;
unsigned int n = 0;
unsigned int nbSteps = 0;
unsigned int nbIterations = 1;
unsigned int timestamp = time(NULL);
int readFscanf = -1;
random_search_instance* random_search = NULL;
struct arg_file* initFile = arg_file1(NULL, "init", "<file>", "File containing the inital state");
struct arg_str* r = arg_str1("n", NULL, "<s>", "List of maximum numbers of evaluations");
struct arg_str* d = arg_str1("h", NULL, "<s>", "List of depth");
struct arg_int* s = arg_int1("s", NULL, "<n>", "Number of steps");
struct arg_int* it = arg_int1("i", NULL, "<n>", "Number of iteration");
struct arg_file* where = arg_file1(NULL, "where", "<file>", "Directory where we save the outputs");
struct arg_end* end = arg_end(7);
int nerrors = 0;
void* argtable[7];
argtable[0] = initFile;
argtable[1] = r;
argtable[2] = d;
argtable[3] = s;
argtable[4] = it;
argtable[5] = where;
argtable[6] = end;
if(arg_nullcheck(argtable) != 0) {
printf("error: insufficient memory\n");
arg_freetable(argtable, 7);
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, 7);
return EXIT_FAILURE;
}
initGenerativeModelParameters();
initGenerativeModel();
initFileFd = fopen(initFile->filename[0], "r");
readFscanf = fscanf(initFileFd, "%u\n", &n);
initialStates = (state**)malloc(sizeof(state*) * n);
for(; i < n; i++) {
readFscanf = fscanf(initFileFd, "%s\n", str);
initialStates[i] = makeState(str);
}
fclose(initFileFd);
nbSteps = s->ival[0];
nbIterations = it->ival[0];
ns = parseUnsignedIntList((char*)r->sval[0], &nbN);
hs = parseUnsignedIntList((char*)d->sval[0], &nbH);
random_search = random_search_initInstance(NULL, discountFactor);
h_max = h_max_crt_depth;
sprintf(str, "%s/%u_results_random_search_%s.csv", where->filename[0], timestamp,(char*)r->sval[0]);
results = fopen(str, "w");
for(i = 0; i < nbIterations; i++) {
unsigned int j = 0;
for(;j < nbH; j++) {
unsigned int k = 0;
crtDepth = hs[j];
for(; k < nbN; k++) {
unsigned int l = 0;
double sumRewards = 0.0;
for(; l < n; l++) {
unsigned int m = 0;
state* crt = copyState(initialStates[l]);
for(; m < nbSteps; m++) {
char isTerminal = 0;
double reward = 0.0;
state* nextState = NULL;
double* optimalAction = NULL;
random_search_resetInstance(random_search, crt);
optimalAction = random_search_planning(random_search, ns[k]);
isTerminal = nextStateReward(crt, optimalAction, &nextState, &reward) < 0 ? 1 : 0;
freeState(crt);
free(optimalAction);
crt = nextState;
sumRewards += reward;
if(isTerminal)
break;
}
random_search_resetInstance(random_search, crt);
freeState(crt);
printf(">>>>>>>>>>>>>> %uth initial state processed with h=%u and n=%u of iteration %u\n", l + 1, hs[j], ns[k], i+1);
fflush(NULL);
}
fprintf(results, "%u,%u,%.15f\n", hs[j],ns[k], sumRewards / (double)n);
printf(">>>>>>>>>>>>>> n = %u done\n\n", ns[k]);
fflush(NULL);
}
printf(">>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> h = %u done \n\n", hs[j]);
fflush(NULL);
}
fprintf(results,"\n");
printf(">>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ITERATION %u DONE <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<\n\n\n", i+1);
fflush(NULL);
}
fclose(results);
arg_freetable(argtable, 7);
for(i = 0; i < n; i++)
freeState(initialStates[i]);
free(initialStates);
random_search_uninitInstance(&random_search);
freeGenerativeModel();
freeGenerativeModelParameters();
return EXIT_SUCCESS;
}
int main(int argc, char* argv[]) {
#ifdef BALL
double discountFactor = 0.9;
#else
#ifdef CART_POLE
double discountFactor = 0.95;
#else
#ifdef DOUBLE_CART_POLE
double discountFactor = 0.95;
#else
#ifdef MOUNTAIN_CAR
double discountFactor = 0.99;
#else
#ifdef ACROBOT
double discountFactor = 0.95;
#else
#ifdef BOAT
double discountFactor = 0.95;
#else
#ifdef SWIMMER
double discountFactor = 0.95;
#endif
#endif
#endif
#endif
#endif
#endif
#endif
FILE* initFileFd = NULL;
state** initialStates = NULL;
FILE* results = NULL;
char str[1024];
unsigned int i = 0;
unsigned int nbInitialStates = 0;
unsigned int* ns = NULL;
unsigned int nbN = 0;
double* Ls = NULL;
unsigned int nbL = 0;
unsigned int nbSteps = 0;
unsigned int timestamp = time(NULL);
int readFscanf = -1;
lipschitzian_instance* lipschitzian = NULL;
struct arg_file* initFile = arg_file1(NULL, "init", "<file>", "File containing the inital state");
struct arg_int* s = arg_int1("s", NULL, "<n>", "Number of steps");
struct arg_str* r = arg_str1("n", NULL, "<s>", "List of ressources");
struct arg_str* z = arg_str1("L", NULL, "<s>", "List of Lipschitz coefficients to try");
struct arg_file* where = arg_file1(NULL, "where", "<file>", "Directory where we save the outputs");
struct arg_end* end = arg_end(6);
int nerrors = 0;
void* argtable[6];
argtable[0] = initFile;
argtable[1] = r;
argtable[2] = s;
argtable[3] = z;
argtable[4] = where;
argtable[5] = end;
if(arg_nullcheck(argtable) != 0) {
printf("error: insufficient memory\n");
arg_freetable(argtable, 6);
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, 6);
return EXIT_FAILURE;
}
initGenerativeModelParameters();
initGenerativeModel();
initFileFd = fopen(initFile->filename[0], "r");
readFscanf = fscanf(initFileFd, "%u\n", &nbInitialStates);
initialStates = (state**)malloc(sizeof(state*) * nbInitialStates);
for(; i < nbInitialStates; i++) {
readFscanf = fscanf(initFileFd, "%s\n", str);
initialStates[i] = makeState(str);
}
fclose(initFileFd);
nbSteps = s->ival[0];
Ls = parseDoubleList((char*)z->sval[0], &nbL);
ns = parseUnsignedIntList((char*)r->sval[0], &nbN);
sprintf(str, "%s/%u_results_%s_%s.csv", where->filename[0], timestamp, z->sval[0], r->sval[0]);
results = fopen(str, "w");
lipschitzian = lipschitzian_initInstance(NULL, discountFactor, 0.0);
for(i = 0; i < nbN; i++) { /* Loop on the computational ressources */
fprintf(results, "%u", ns[i]);
printf("Starting with %u computational ressources\n", ns[i]);
fflush(NULL);
unsigned int j = 0;
for(; j < nbL; j++) { /* Loop on the Lispchitz constant */
unsigned int k = 0;
double average = 0.0;
lipschitzian->L = Ls[j];
for(; k < nbInitialStates; k++) { /* Loop on the initial states */
unsigned int l = 0;
double sumRewards = 0.0;
state* crt = copyState(initialStates[k]);
lipschitzian_resetInstance(lipschitzian, crt);
for(; l < nbSteps; l++) { /* Loop on the step */
char isTerminal = 0;
double reward = 0.0;
state* nextState = NULL;
double* optimalAction = lipschitzian_planning(lipschitzian, ns[i]);
isTerminal = nextStateReward(crt, optimalAction, &nextState, &reward) < 0 ? 1 : 0;
free(optimalAction);
freeState(crt);
crt = nextState;
sumRewards += reward;
lipschitzian_resetInstance(lipschitzian,crt);
if(isTerminal)
break;
}
average += sumRewards;
freeState(crt);
printf("Computation of the %u initial state done with L=%f\n", k, Ls[j]);
fflush(NULL);
}
average = average /(double)nbInitialStates;
fprintf(results, ",%.15f", average);
printf("Computation with L=%f and n=%u done\n", Ls[j], ns[i]);
fflush(NULL);
}
fprintf(results,"\n");
printf("Computation with %u computational ressources done\n\n", ns[i]);
fflush(NULL);
}
fclose(results);
arg_freetable(argtable, 6);
for(i = 0; i < nbInitialStates; i++)
freeState(initialStates[i]);
free(initialStates);
lipschitzian_uninitInstance(&lipschitzian);
free(ns);
free(Ls);
freeGenerativeModel();
freeGenerativeModelParameters();
return EXIT_SUCCESS;
}
int main(int argc, char* argv[]) {
unsigned int i = 0;
unsigned int nbIntervals = 0;
double* intervals = NULL;
FILE* outputFileFd = NULL;
gsl_rng* rng = NULL;
unsigned int nbStates = 0;
struct arg_file* outputFile = arg_file1("o", NULL, "<file>", "The output file for the generated initial state");
struct arg_int* n = arg_int1("n", NULL, "<n>", "The number of initial states to generate");
struct arg_str* s = arg_str1(NULL, "intervals", "<s>", "The intervals for the initial states generation");
struct arg_end* end = arg_end(4);
void* argtable[4];
int nerrors = 0;
argtable[0] = outputFile;
argtable[1] = n;
argtable[2] = s;
argtable[3] = end;
if(arg_nullcheck(argtable) != 0) {
printf("error: insufficient memory\n");
arg_freetable(argtable, 4);
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, 4);
return EXIT_FAILURE;
}
nbStates = n->ival[0];
intervals = parseIntervals(s->sval[0], &nbIntervals);
rng = gsl_rng_alloc(gsl_rng_mt19937);
gsl_rng_set(rng, time(NULL));
outputFileFd = fopen(outputFile->filename[0], "w");
fprintf(outputFileFd, "%u\n", n->ival[0]);
for(; i < nbStates; i++) {
unsigned int j = 0;
for(; j < (nbIntervals - 1); j++)
fprintf(outputFileFd, "%.15f,", (fabs(intervals[(j * 2) + 1] - intervals[j * 2]) * gsl_rng_uniform(rng)) + intervals[j * 2]);
fprintf(outputFileFd, "%.15f\n", (fabs(intervals[(j * 2) + 1] - intervals[j * 2]) * gsl_rng_uniform(rng)) + intervals[j * 2]);
}
fclose(outputFileFd);
gsl_rng_free(rng);
free(intervals);
arg_freetable(argtable, 4);
return EXIT_SUCCESS;
}
