// Function that reads from a MiniSEED binary file from a char buffer and
// returns a LinkedIDList.
LinkedIDList *
readMSEEDBuffer (char *mseed, int buflen, Selections *selections, flag
unpack_data, int reclen, flag verbose, flag details,
int header_byteorder, long (*allocData) (int, char),
void (*diag_print) (char*), void (*log_print) (char*))
{
int retcode = 0;
int retval = 0;
flag swapflag = 0;
// current offset of mseed char pointer
int offset = 0;
// Unpack without reading the data first
flag dataflag = 0;
// the timing_qual of BLK 1001
uint8_t timing_qual = 0xFF;
// the calibration type, availability of BLK 300, 310, 320, 390, 395
int8_t calibration_type = -1;
// Init all the pointers to NULL. Most compilers should do this anyway.
LinkedIDList * idListHead = NULL;
LinkedIDList * idListCurrent = NULL;
LinkedIDList * idListLast = NULL;
MSRecord *msr = NULL;
ContinuousSegment * segmentCurrent = NULL;
hptime_t lastgap = 0;
hptime_t hptimetol = 0;
hptime_t nhptimetol = 0;
long data_offset;
LinkedRecordList *recordHead = NULL;
LinkedRecordList *recordPrevious = NULL;
LinkedRecordList *recordCurrent = NULL;
int datasize;
int record_count = 0;
// A negative verbosity suppressed as much as possible.
if (verbose < 0) {
ms_loginit(&empty_print, NULL, &empty_print, NULL);
}
else {
ms_loginit(log_print, "INFO: ", diag_print, "ERROR: ");
}
if (header_byteorder >= 0) {
// Enforce little endian.
if (header_byteorder == 0) {
MS_UNPACKHEADERBYTEORDER(0);
}
// Enforce big endian.
else {
MS_UNPACKHEADERBYTEORDER(1);
}
}
else {
MS_UNPACKHEADERBYTEORDER(-1);
}
//
// Read all records and save them in a linked list.
//
while (offset < buflen) {
msr = msr_init(NULL);
if ( msr == NULL ) {
ms_log (2, "readMSEEDBuffer(): Error initializing msr\n");
return NULL;
}
if (verbose > 1) {
ms_log(0, "readMSEEDBuffer(): calling msr_parse with "
"mseed+offset=%d+%d, buflen=%d, reclen=%d, dataflag=%d, verbose=%d\n",
mseed, offset, buflen, reclen, dataflag, verbose);
}
// If the record length is given, make sure at least that amount of data is available.
if (reclen != -1) {
if (offset + reclen > buflen) {
ms_log(1, "readMSEEDBuffer(): Last reclen exceeds buflen, skipping.\n");
msr_free(&msr);
break;
}
}
// Otherwise assume the smallest possible record length and assure that enough
// data is present.
else {
if (offset + 256 > buflen) {
ms_log(1, "readMSEEDBuffer(): Last record only has %i byte(s) which "
"is not enough to constitute a full SEED record. Corrupt data? "
"Record will be skipped.\n", buflen - offset);
msr_free(&msr);
break;
}
}
// Pass (buflen - offset) because msr_parse() expects only a single record. This
// way libmseed can take care to not overstep bounds.
retcode = msr_parse ( (mseed+offset), buflen - offset, &msr, reclen, dataflag, verbose);
if (retcode != MS_NOERROR) {
switch ( retcode ) {
case MS_ENDOFFILE:
ms_log(1, "readMSEEDBuffer(): Unexpected end of file when "
"parsing record starting at offset %d. The rest "
"of the file will not be read.\n", offset);
break;
case MS_GENERROR:
ms_log(1, "readMSEEDBuffer(): Generic error when parsing "
"record starting at offset %d. The rest of the "
"file will not be read.\n", offset);
break;
case MS_NOTSEED:
ms_log(1, "readMSEEDBuffer(): Record starting at offset "
"%d is not valid SEED. The rest of the file "
"will not be read.\n", offset);
break;
case MS_WRONGLENGTH:
ms_log(1, "readMSEEDBuffer(): Length of data read was not "
"correct when parsing record starting at "
"offset %d. The rest of the file will not be "
"read.\n", offset);
break;
case MS_OUTOFRANGE:
ms_log(1, "readMSEEDBuffer(): SEED record length out of "
"range for record starting at offset %d. The "
"rest of the file will not be read.\n", offset);
break;
case MS_UNKNOWNFORMAT:
ms_log(1, "readMSEEDBuffer(): Unknown data encoding "
"format for record starting at offset %d. The "
"rest of the file will not be read.\n", offset);
break;
case MS_STBADCOMPFLAG:
ms_log(1, "readMSEEDBuffer(): Invalid STEIM compression "
"flag(s) in record starting at offset %d. The "
"rest of the file will not be read.\n", offset);
break;
default:
ms_log(1, "readMSEEDBuffer(): Unknown error '%d' in "
"record starting at offset %d. The rest of the "
"file will not be read.\n", retcode, offset);
break;
}
msr_free(&msr);
break;
}
if (offset + msr->reclen > buflen) {
ms_log(1, "readMSEEDBuffer(): Last msr->reclen exceeds buflen, skipping.\n");
msr_free(&msr);
break;
}
// Test against selections if supplied
if ( selections ) {
char srcname[50];
hptime_t endtime;
msr_srcname (msr, srcname, 1);
endtime = msr_endtime (msr);
if ( ms_matchselect (selections, srcname, msr->starttime, endtime, NULL) == NULL ) {
// Add the record length for the next iteration
offset += msr->reclen;
// Free record.
msr_free(&msr);
continue;
}
}
record_count += 1;
recordCurrent = lrl_init ();
// Append to linked record list if one exists.
if ( recordHead != NULL ) {
recordPrevious->next = recordCurrent;
recordCurrent->previous = recordPrevious;
recordCurrent->next = NULL;
recordPrevious = recordCurrent;
}
// Otherwise create a new one.
else {
recordHead = recordCurrent;
recordCurrent->previous = NULL;
recordPrevious = recordCurrent;
}
recordCurrent->record = msr;
// Determine the byte order swapflag only for the very first record.
// The byte order should not change within the file.
// XXX: Maybe check for every record?
if (swapflag <= 0) {
// Returns 0 if the host is little endian, otherwise 1.
flag bigendianhost = ms_bigendianhost();
// Set the swapbyteflag if it is needed.
if ( msr->Blkt1000 != 0) {
/* If BE host and LE data need swapping */
if ( bigendianhost && msr->byteorder == 0 ) {
swapflag = 1;
}
/* If LE host and BE data (or bad byte order value) need swapping */
if ( !bigendianhost && msr->byteorder > 0 ) {
swapflag = 1;
}
}
}
// Actually unpack the data if the flag is not set.
if (unpack_data != 0) {
retval = msr_unpack_data (msr, swapflag, verbose);
}
if ( retval > 0 ) {
msr->numsamples = retval;
}
// Add the record length for the next iteration
offset += msr->reclen;
}
// Return empty id list if no records could be found.
if (record_count == 0) {
idListHead = lil_init();
return idListHead;
}
// All records that match the selection are now stored in a LinkedRecordList
// that starts at recordHead. The next step is to sort them by matching ids
// and then by time.
recordCurrent = recordHead;
while (recordCurrent != NULL) {
// Check if the ID of the record is already available and if not create a
// new one.
// Start with the last id as it is most likely to be the correct one.
idListCurrent = idListLast;
while (idListCurrent != NULL) {
if (strcmp(idListCurrent->network, recordCurrent->record->network) == 0 &&
strcmp(idListCurrent->station, recordCurrent->record->station) == 0 &&
strcmp(idListCurrent->location, recordCurrent->record->location) == 0 &&
strcmp(idListCurrent->channel, recordCurrent->record->channel) == 0 &&
idListCurrent->dataquality == recordCurrent->record->dataquality) {
break;
}
else {
idListCurrent = idListCurrent->previous;
}
}
// Create a new id list if one is needed.
if (idListCurrent == NULL) {
idListCurrent = lil_init();
idListCurrent->previous = idListLast;
if (idListLast != NULL) {
idListLast->next = idListCurrent;
}
idListLast = idListCurrent;
if (idListHead == NULL) {
idListHead = idListCurrent;
}
// Set the IdList attributes.
strcpy(idListCurrent->network, recordCurrent->record->network);
strcpy(idListCurrent->station, recordCurrent->record->station);
strcpy(idListCurrent->location, recordCurrent->record->location);
strcpy(idListCurrent->channel, recordCurrent->record->channel);
idListCurrent->dataquality = recordCurrent->record->dataquality;
}
// Now check if the current record fits exactly to the end of the last
// segment of the current id. If not create a new segment. Therefore
// if records with the same id are in wrong order a new segment will be
// created. This is on purpose.
segmentCurrent = idListCurrent->lastSegment;
if (segmentCurrent != NULL) {
hptimetol = (hptime_t) (0.5 * segmentCurrent->hpdelta);
nhptimetol = ( hptimetol ) ? -hptimetol : 0;
lastgap = recordCurrent->record->starttime - segmentCurrent->endtime - segmentCurrent->hpdelta;
}
if (details == 1) {
/* extract information on calibration BLKs */
calibration_type = -1;
if (recordCurrent->record->blkts) {
BlktLink *cur_blkt = recordCurrent->record->blkts;
while (cur_blkt) {
switch (cur_blkt->blkt_type) {
case 300:
calibration_type = 1;
break;
case 310:
calibration_type = 2;
break;
case 320:
calibration_type = 3;
break;
case 390:
calibration_type = 4;
break;
case 395:
calibration_type = -2;
break;
default:
break;
}
cur_blkt = cur_blkt->next;
}
}
/* extract information based on timing quality */
timing_qual = 0xFF;
if (recordCurrent->record->Blkt1001 != 0) {
timing_qual = recordCurrent->record->Blkt1001->timing_qual;
}
}
if ( segmentCurrent != NULL &&
segmentCurrent->sampletype == recordCurrent->record->sampletype &&
// Test the default sample rate tolerance: abs(1-sr1/sr2) < 0.0001
MS_ISRATETOLERABLE (segmentCurrent->samprate, recordCurrent->record->samprate) &&
// Check if the times are within the time tolerance
lastgap <= hptimetol && lastgap >= nhptimetol &&
segmentCurrent->timing_qual == timing_qual &&
segmentCurrent->calibration_type == calibration_type) {
recordCurrent->previous = segmentCurrent->lastRecord;
segmentCurrent->lastRecord = segmentCurrent->lastRecord->next = recordCurrent;
segmentCurrent->samplecnt += recordCurrent->record->samplecnt;
segmentCurrent->endtime = msr_endtime(recordCurrent->record);
}
// Otherwise create a new segment and add the current record.
else {
segmentCurrent = seg_init();
segmentCurrent->previous = idListCurrent->lastSegment;
if (idListCurrent->lastSegment != NULL) {
idListCurrent->lastSegment->next = segmentCurrent;
}
else {
idListCurrent->firstSegment = segmentCurrent;
}
idListCurrent->lastSegment = segmentCurrent;
segmentCurrent->starttime = recordCurrent->record->starttime;
segmentCurrent->endtime = msr_endtime(recordCurrent->record);
segmentCurrent->samprate = recordCurrent->record->samprate;
segmentCurrent->sampletype = recordCurrent->record->sampletype;
segmentCurrent->samplecnt = recordCurrent->record->samplecnt;
// Calculate high-precision sample period
segmentCurrent->hpdelta = (hptime_t) (( recordCurrent->record->samprate ) ?
(HPTMODULUS / recordCurrent->record->samprate) : 0.0);
segmentCurrent->timing_qual = timing_qual;
segmentCurrent->calibration_type = calibration_type;
segmentCurrent->firstRecord = segmentCurrent->lastRecord = recordCurrent;
recordCurrent->previous = NULL;
}
recordPrevious = recordCurrent->next;
recordCurrent->next = NULL;
recordCurrent = recordPrevious;
}
// Now loop over all segments, combine the records and free the msr
// structures.
idListCurrent = idListHead;
while (idListCurrent != NULL)
{
segmentCurrent = idListCurrent->firstSegment;
while (segmentCurrent != NULL) {
if (segmentCurrent->datasamples) {
free(segmentCurrent->datasamples);
}
// Allocate data via a callback function.
if (unpack_data != 0) {
segmentCurrent->datasamples = (void *) allocData(segmentCurrent->samplecnt, segmentCurrent->sampletype);
}
// Loop over all records, write the data to the buffer and free the msr structures.
recordCurrent = segmentCurrent->firstRecord;
data_offset = (long)(segmentCurrent->datasamples);
while (recordCurrent != NULL) {
datasize = recordCurrent->record->samplecnt * ms_samplesize(recordCurrent->record->sampletype);
memcpy((void *)data_offset, recordCurrent->record->datasamples, datasize);
// Free the record.
msr_free(&(recordCurrent->record));
// Increase the data_offset and the record.
data_offset += (long)datasize;
recordCurrent = recordCurrent->next;
}
segmentCurrent = segmentCurrent->next;
}
idListCurrent = idListCurrent->next;
}
return idListHead;
}
void
mexFunction (int nlhs, mxArray *plhs[], int nrhs, const mxArray *prhs[])
{
MSTraceGroup *mstg = NULL;
MSTrace *mst = NULL;
const char **my_fnames = NULL;
char *filename;
int buflen;
int reclen;
double timetol, sampratetol;
flag dataquality, skipnodata, dataflag, verbose;
int i, j, nfields;
mxArray *tmp_val;
double *tmp_val_ptr;
int32_t *data;
/* Sanity check input and output */
if ( nrhs != 8 )
{
mexPrintf ("mexMsReadTracesNative - Read Mini-SEED data into Matlab\n\n");
mexPrintf ("Usage: mexMsReadTracesNative (filename, reclen, timetol, sampratetol, dataquality, skipnotdata, dataflag, verbosity)\n");
mexPrintf (" filename - Name of file to read Mini-SEED data from\n");
mexPrintf (" reclen - Mini-SEED data record length, -1 for autodetection\n");
mexPrintf (" timetol - Time tolerance, use -1.0 for 1/2 sample period\n");
mexPrintf (" sampratetol - Sample rate tolerance, use -1.0 for default tolerance\n");
mexPrintf (" dataquality - Include data quality in determination of unique time series, use 0 or 1\n");
mexPrintf (" skipnotdata - Skip blocks in input file that are not Mini-SEED data\n");
mexPrintf (" dataflag - Flag to control return of data samples or not, 0 or 1\n");
mexPrintf (" verbosity - Level of diagnostic messages, use 0 - 3\n\n");
mexErrMsgTxt ("8 input arguments required.");
}
else if ( nlhs > 1 )
{
mexErrMsgTxt ("Too many output arguments.");
}
/* Redirect libmseed logging messages to Matlab functions */
ms_loginit ((void *)&mexPrintf, NULL, (void *)&mexWarnMsgTxt, NULL);
/* Get the length of the input string */
buflen = (mxGetM (prhs[0]) * mxGetN (prhs[0])) + 1;
/* Allocate memory for input string */
filename = mxCalloc (buflen, sizeof (char));
/* Assign the input arguments to variables */
if ( mxGetString (prhs[0], filename, buflen) )
mexErrMsgTxt ("Not enough space. Filename string is truncated.");
reclen = (int) mxGetScalar(prhs[1]);
timetol = mxGetScalar(prhs[2]);
sampratetol = mxGetScalar(prhs[3]);
dataquality = (flag) mxGetScalar(prhs[4]);
skipnodata = (flag) mxGetScalar(prhs[5]);
dataflag = (flag) mxGetScalar(prhs[6]);
verbose = (flag) mxGetScalar(prhs[7]);
/* Read the file */
if ( ms_readtraces (&mstg, filename, reclen, timetol, sampratetol, dataquality,
skipnodata, dataflag, verbose) != MS_NOERROR )
mexErrMsgTxt ("Error reading files");
/* Print some information to the Matlab command prompt */
mst_printtracelist (mstg, 0, verbose, 1);
/* Create the Matlab output structure */
mst = mstg->traces;
for (i=0; i < mstg->numtraces; i++)
{
if (i==0)
{
nfields = 13;
my_fnames = mxCalloc (nfields, sizeof (*my_fnames));
my_fnames[0] = "network";
my_fnames[1] = "station";
my_fnames[2] = "location";
my_fnames[3] = "channel";
my_fnames[4] = "dataquality";
my_fnames[5] = "type";
my_fnames[6] = "startTime";
my_fnames[7] = "endTime";
my_fnames[8] = "sampleRate";
my_fnames[9] = "sampleCount";
my_fnames[10] = "numberOfSamples";
my_fnames[11] = "sampleType";
my_fnames[12] = "data";
plhs[0] = mxCreateStructMatrix(mstg->numtraces, 1, nfields, my_fnames);
mxFree(my_fnames);
}
/* Copy the data of the mst structure to the matlab output structure. */
data = (int32_t*) mst->datasamples;
tmp_val = mxCreateDoubleMatrix(mst->numsamples, 1, mxREAL);
tmp_val_ptr = mxGetPr(tmp_val);
for (j = 0; j < mst->numsamples; j++)
{
# if ENDIANNESS
tmp_val_ptr[j] = (double) data[j];
# else
tmp_val_ptr[j] = (double) (int32_t)(__builtin_bswap32 (data[j]));
# endif
//tmp_val_ptr[j] = 100.0;
}
mxSetFieldByNumber(plhs[0], i, 0, mxCreateString(mst->network));
mxSetFieldByNumber(plhs[0], i, 1, mxCreateString(mst->station));
mxSetFieldByNumber(plhs[0], i, 2, mxCreateString(mst->location));
mxSetFieldByNumber(plhs[0], i, 3, mxCreateString(mst->channel));
mxSetFieldByNumber(plhs[0], i, 4, mxCreateDoubleScalar((int)mst->dataquality));
mxSetFieldByNumber(plhs[0], i, 5, mxCreateDoubleScalar((int)mst->type));
mxSetFieldByNumber(plhs[0], i, 6, mxCreateDoubleScalar(mst->starttime));
mxSetFieldByNumber(plhs[0], i, 7, mxCreateDoubleScalar(mst->endtime));
mxSetFieldByNumber(plhs[0], i, 8, mxCreateDoubleScalar(mst->samprate));
mxSetFieldByNumber(plhs[0], i, 9, mxCreateDoubleScalar(mst->samplecnt));
mxSetFieldByNumber(plhs[0], i, 10, mxCreateDoubleScalar(mst->numsamples));
mxSetFieldByNumber(plhs[0], i, 11, mxCreateDoubleScalar((int)mst->sampletype));
mxSetFieldByNumber(plhs[0], i, 12, tmp_val);
mst = mst->next;
}
mst_freegroup (&mstg);
}
int main(int argc, char **argv) {
#ifndef WIN32
// Signal handling, use POSIX calls with standardized semantics
struct sigaction sa;
sigemptyset(&sa.sa_mask);
sa.sa_flags = SA_RESTART;
sa.sa_handler = term_handler;
sigaction(SIGINT, &sa, NULL);
sigaction(SIGQUIT, &sa, NULL);
sigaction(SIGTERM, &sa, NULL);
sa.sa_handler = SIG_IGN;
sigaction(SIGHUP, &sa, NULL);
sigaction(SIGPIPE, &sa, NULL);
#endif
/*
printf("LONG_MIN %ld\n", LONG_MIN);
printf("LONG_MAX %ld\n", LONG_MAX);
printf("INT_MIN %d\n", INT_MIN);
printf("INT_MAX %d\n", INT_MAX);
*/
// set default error message prefix
ms_loginit(NULL, NULL, NULL, "ERROR: ");
// defaults
verbose = 0;
strcpy(port_path_hint, "/dev/usbdev1.1");
strcpy(propfile, PROP_FILE_NAME_DEFAULT);
// Process input parameters
if (parameter_proc(argc, argv) < 0)
return 1;
init_properties(propfile);
// set encoding type
// possible: DE_ASCII, DE_INT16, DE_INT32, DE_FLOAT32, DE_FLOAT64, DE_STEIM1, DE_STEIM2
// supported: DE_INT16, DE_INT32, DE_STEIM1, DE_STEIM2
if (strcmp(mswrite_data_encoding_type, "DE_INT16") == 0) {
mswrite_data_encoding_type_code = DE_INT16;
num_samples_in_record = (SLREC_DATA_SIZE) / 2;
} else if (strcmp(mswrite_data_encoding_type, "DE_INT32") == 0) {
mswrite_data_encoding_type_code = DE_INT32;
num_samples_in_record = (SLREC_DATA_SIZE) / 4;
/*
} else if (strcmp(mswrite_data_encoding_type, "DE_ASCII") == 0) {
mswrite_data_encoding_type_code = DE_ASCII;
} else if (strcmp(mswrite_data_encoding_type, "DE_FLOAT32") == 0) {
mswrite_data_encoding_type_code = DE_FLOAT32;
} else if (strcmp(mswrite_data_encoding_type, "DE_FLOAT64") == 0) {
mswrite_data_encoding_type_code = DE_FLOAT64;
*/
} else if (strcmp(mswrite_data_encoding_type, "DE_STEIM1") == 0) {
mswrite_data_encoding_type_code = DE_STEIM1;
num_samples_in_record = (SLREC_DATA_SIZE) / 4; // estimate, inefficient, assumes int32 data
} else if (strcmp(mswrite_data_encoding_type, "DE_STEIM2") == 0) {
mswrite_data_encoding_type_code = DE_STEIM2;
num_samples_in_record = (SLREC_DATA_SIZE) / 4; // estimate, inefficient, assumes int32 data
}
// enter infinite loop, term_handler() performs cleanup
while (1) {
// find device and connect
find_device_and_connect(port_path_hint);
// set sample rate and gain for SEP064
if (do_settings_sep064) {
if (set_seo064_sample_rate_and_gain(nominal_sample_rate, nominal_gain, TIMEOUT_SMALL, verbose)) {
continue;
}
}
// collect data and write
if (collect_and_write()) { // collect_and_write() returned error
logprintf(ERROR_FLAG, "Reading from %s, will try reconnecting...\n", port_path);
disconnect(verbose);
} else {
break; // collect_and_write() returned normally
}
}
return (0);
} /* End of main() */
int
main (int argc, char **argv)
{
struct filelink *flp;
MSRecord *msr = 0;
MSTraceList *mstl = 0;
FILE *bfp = 0;
FILE *ofp = 0;
int retcode = MS_NOERROR;
char envvariable[100];
int dataflag = 0;
long long int totalrecs = 0;
long long int totalsamps = 0;
long long int totalfiles = 0;
off_t filepos = 0;
char srcname[50];
char stime[30];
/* Set default error message prefix */
ms_loginit (NULL, NULL, NULL, "ERROR: ");
/* Process given parameters (command line and parameter file) */
if ( processparam (argc, argv) < 0 )
return 1;
/* Setup encoding environment variable if specified, ugly kludge */
if ( encodingstr )
{
snprintf (envvariable, sizeof(envvariable), "UNPACK_DATA_FORMAT=%s", encodingstr);
if ( putenv (envvariable) )
{
ms_log (2, "Cannot set environment variable UNPACK_DATA_FORMAT\n");
return 1;
}
}
/* Open the integer output file if specified */
if ( binfile )
{
if ( strcmp (binfile, "-") == 0 )
{
bfp = stdout;
}
else if ( (bfp = fopen (binfile, "wb")) == NULL )
{
ms_log (2, "Cannot open binary data output file: %s (%s)\n",
binfile, strerror(errno));
return 1;
}
}
/* Open the output file if specified */
if ( outfile )
{
if ( strcmp (outfile, "-") == 0 )
{
ofp = stdout;
}
else if ( (ofp = fopen (outfile, "wb")) == NULL )
{
ms_log (2, "Cannot open output file: %s (%s)\n",
outfile, strerror(errno));
return 1;
}
}
if ( printdata || binfile )
dataflag = 1;
if ( tracegapsum || tracegaponly )
mstl = mstl_init (NULL);
flp = filelist;
while ( flp != 0 )
{
if ( verbose >= 2 )
{
if ( flp->offset )
ms_log (1, "Processing: %s (starting at byte %lld)\n", flp->filename, flp->offset);
else
ms_log (1, "Processing: %s\n", flp->filename);
}
/* Set starting byte offset if supplied as negative file position */
filepos = - flp->offset;
/* Loop over the input file */
while ( reccntdown != 0 )
{
if ( (retcode = ms_readmsr (&msr, flp->filename, reclen, &filepos,
NULL, skipnotdata, 0, verbose)) != MS_NOERROR )
break;
/* Check if record matches start/end time criteria */
if ( starttime != HPTERROR || endtime != HPTERROR )
{
hptime_t recendtime = msr_endtime (msr);
if ( starttime != HPTERROR && (msr->starttime < starttime && ! (msr->starttime <= starttime && recendtime >= starttime)) )
{
if ( verbose >= 3 )
{
msr_srcname (msr, srcname, 1);
ms_hptime2seedtimestr (msr->starttime, stime, 1);
ms_log (1, "Skipping (starttime) %s, %s\n", srcname, stime);
}
continue;
}
if ( endtime != HPTERROR && (recendtime > endtime && ! (msr->starttime <= endtime && recendtime >= endtime)) )
{
if ( verbose >= 3 )
{
msr_srcname (msr, srcname, 1);
ms_hptime2seedtimestr (msr->starttime, stime, 1);
ms_log (1, "Skipping (starttime) %s, %s\n", srcname, stime);
}
continue;
}
}
if ( match || reject )
{
/* Generate the srcname with the quality code */
msr_srcname (msr, srcname, 1);
/* Check if record is matched by the match regex */
if ( match )
{
if ( regexec ( match, srcname, 0, 0, 0) != 0 )
{
if ( verbose >= 3 )
{
ms_hptime2seedtimestr (msr->starttime, stime, 1);
ms_log (1, "Skipping (match) %s, %s\n", srcname, stime);
}
continue;
}
}
/* Check if record is rejected by the reject regex */
if ( reject )
{
if ( regexec ( reject, srcname, 0, 0, 0) == 0 )
{
if ( verbose >= 3 )
{
ms_hptime2seedtimestr (msr->starttime, stime, 1);
ms_log (1, "Skipping (reject) %s, %s\n", srcname, stime);
}
continue;
}
}
}
if ( reccntdown > 0 )
reccntdown--;
totalrecs++;
totalsamps += msr->samplecnt;
if ( ! tracegaponly )
{
if ( printoffset )
ms_log (0, "%-10lld", (long long) filepos);
if ( printlatency )
ms_log (0, "%-10.6g secs ", msr_host_latency(msr));
if ( printraw )
ms_parse_raw (msr->record, msr->reclen, ppackets, -1);
else
msr_print (msr, ppackets);
}
if ( tracegapsum || tracegaponly )
mstl_addmsr (mstl, msr, dataquality, 1, timetol, sampratetol);
if ( dataflag )
{
/* Parse the record (again) and unpack the data */
int rv = msr_unpack (msr->record, msr->reclen, &msr, 1, verbose);
if ( rv == MS_NOERROR && printdata && ! tracegaponly )
{
int line, col, cnt, samplesize;
int lines = (msr->numsamples / 6) + 1;
void *sptr;
if ( (samplesize = ms_samplesize(msr->sampletype)) == 0 )
{
ms_log (2, "Unrecognized sample type: %c\n", msr->sampletype);
}
if ( msr->sampletype == 'a' )
{
char *ascii = (char *)msr->datasamples;
int length = msr->numsamples;
ms_log (0, "ASCII Data:\n");
/* Print maximum log message segments */
while ( length > (MAX_LOG_MSG_LENGTH-1) )
{
ms_log (0, "%.*s", (MAX_LOG_MSG_LENGTH-1), ascii);
ascii += MAX_LOG_MSG_LENGTH-1;
length -= MAX_LOG_MSG_LENGTH-1;
}
/* Print any remaining ASCII and add a newline */
if ( length > 0 )
{
ms_log (0, "%.*s\n", length, ascii);
}
else
{
ms_log (0, "\n");
}
}
else
for ( cnt = 0, line = 0; line < lines; line++ )
{
for ( col = 0; col < 6 ; col ++ )
{
if ( cnt < msr->numsamples )
{
sptr = (char*)msr->datasamples + (cnt * samplesize);
if ( msr->sampletype == 'i' )
ms_log (0, "%10d ", *(int32_t *)sptr);
else if ( msr->sampletype == 'f' )
ms_log (0, "%10.8g ", *(float *)sptr);
else if ( msr->sampletype == 'd' )
ms_log (0, "%10.10g ", *(double *)sptr);
cnt++;
}
}
ms_log (0, "\n");
/* If only printing the first 6 samples break out here */
if ( printdata == 1 )
break;
}
}
if ( binfile )
{
uint8_t samplesize = ms_samplesize (msr->sampletype);
if ( samplesize )
{
fwrite (msr->datasamples, samplesize, msr->numsamples, bfp);
}
else
{
ms_log (1, "Cannot write to binary file, unknown sample type: %c\n",
msr->sampletype);
}
}
}
if ( outfile )
{
fwrite (msr->record, 1, msr->reclen, ofp);
}
}
/* Print error if not EOF and not counting down records */
if ( retcode != MS_ENDOFFILE && reccntdown != 0 )
{
ms_log (2, "Cannot read %s: %s\n", flp->filename, ms_errorstr(retcode));
ms_readmsr (&msr, NULL, 0, NULL, NULL, 0, 0, 0);
exit (1);
}
/* Make sure everything is cleaned up */
ms_readmsr (&msr, NULL, 0, NULL, NULL, 0, 0, 0);
totalfiles++;
flp = flp->next;
} /* End of looping over file list */
if ( binfile )
fclose (bfp);
if ( outfile )
fclose (ofp);
if ( basicsum )
ms_log (0, "Files: %lld, Records: %lld, Samples: %lld\n", totalfiles, totalrecs, totalsamps);
if ( tracegapsum || tracegaponly )
{
if ( tracegapsum == 1 || tracegaponly == 1 )
{
mstl_printtracelist (mstl, timeformat, 1, tracegaps);
}
if ( tracegapsum == 2 || tracegaponly == 2 )
{
mstl_printgaplist (mstl, timeformat, mingapptr, maxgapptr);
}
if ( tracegaponly == 3 )
{
mstl_printsynclist (mstl, NULL, 1);
}
}
if ( mstl )
mstl_free (&mstl, 0);
return 0;
} /* End of main() */
// Function that reads from a MiniSEED binary file from a char buffer and
// returns a LinkedIDList.
LinkedIDList *
readMSEEDBuffer (char *mseed, int buflen, Selections *selections, flag
unpack_data, int reclen, flag verbose, flag details,
int header_byteorder, long long (*allocData) (int, char),
void (*diag_print) (char*), void (*log_print) (char*))
{
int retcode = 0;
int retval = 0;
flag swapflag = 0;
flag bigendianhost = ms_bigendianhost();
// current offset of mseed char pointer
int offset = 0;
// Unpack without reading the data first
flag dataflag = 0;
// the timing_qual of BLK 1001
uint8_t timing_qual = 0xFF;
// the calibration type, availability of BLK 300, 310, 320, 390, 395
int8_t calibration_type = -1;
// Init all the pointers to NULL. Most compilers should do this anyway.
LinkedIDList * idListHead = NULL;
LinkedIDList * idListCurrent = NULL;
LinkedIDList * idListLast = NULL;
MSRecord *msr = NULL;
ContinuousSegment * segmentCurrent = NULL;
hptime_t lastgap = 0;
hptime_t hptimetol = 0;
hptime_t nhptimetol = 0;
long long data_offset;
LinkedRecordList *recordHead = NULL;
LinkedRecordList *recordPrevious = NULL;
LinkedRecordList *recordCurrent = NULL;
int datasize;
int record_count = 0;
// A negative verbosity suppresses as much as possible.
if (verbose < 0) {
ms_loginit(&empty_print, NULL, &empty_print, NULL);
}
else {
ms_loginit(log_print, "INFO: ", diag_print, "ERROR: ");
}
if (header_byteorder >= 0) {
// Enforce little endian.
if (header_byteorder == 0) {
MS_UNPACKHEADERBYTEORDER(0);
}
// Enforce big endian.
else {
MS_UNPACKHEADERBYTEORDER(1);
}
}
else {
MS_UNPACKHEADERBYTEORDER(-1);
}
// Read all records and save them in a linked list.
while (offset < buflen) {
msr = msr_init(NULL);
if ( msr == NULL ) {
ms_log (2, "readMSEEDBuffer(): Error initializing msr\n");
return NULL;
}
if (verbose > 1) {
ms_log(0, "readMSEEDBuffer(): calling msr_parse with "
"mseed+offset=%d+%d, buflen=%d, reclen=%d, dataflag=%d, verbose=%d\n",
mseed, offset, buflen, reclen, dataflag, verbose);
}
// If the record length is given, make sure at least that amount of data is available.
if (reclen != -1) {
if (offset + reclen > buflen) {
ms_log(1, "readMSEEDBuffer(): Last reclen exceeds buflen, skipping.\n");
msr_free(&msr);
break;
}
}
// Otherwise assume the smallest possible record length and assure that enough
// data is present.
else {
if (offset + MINRECLEN > buflen) {
ms_log(1, "readMSEEDBuffer(): Last record only has %i byte(s) which "
"is not enough to constitute a full SEED record. Corrupt data? "
"Record will be skipped.\n", buflen - offset);
msr_free(&msr);
break;
}
}
// Skip empty or noise records.
if (OBSPY_ISVALIDBLANK(mseed + offset)) {
offset += MINRECLEN;
continue;
}
// Pass (buflen - offset) because msr_parse() expects only a single record. This
// way libmseed can take care to not overstep bounds.
// Return values:
// 0 : Success, populates the supplied MSRecord.
// >0 : Data record detected but not enough data is present, the
// return value is a hint of how many more bytes are needed.
// <0 : libmseed error code (listed in libmseed.h) is returned.
retcode = msr_parse ((mseed+offset), buflen - offset, &msr, reclen, dataflag, verbose);
// Handle error.
if (retcode < 0) {
log_error(retcode, offset);
msr_free(&msr);
break;
}
// msr_parse() returns > 0 if a data record has been detected but the buffer either has not enough
// data (this cannot happen with ObsPy's logic) or the last record has no Blockette 1000 and it cannot
// determine the record length because there is no next record (this can happen in ObsPy) - handle that
// case by just calling msr_parse() with an explicit record length set.
else if ( retcode > 0 && retcode < (buflen - offset)) {
// Check if the remaining bytes can exactly make up a record length.
int r_bytes = buflen - offset;
float exp = log10((float)r_bytes) / log10(2.0);
if ((fmodf(exp, 1.0) < 0.0000001) && ((int)roundf_(exp) >= 7) && ((int)roundf_(exp) <= 256)) {
retcode = msr_parse((mseed + offset), buflen - offset, &msr, r_bytes, dataflag, verbose);
if ( retcode != 0 ) {
log_error(retcode, offset);
msr_free(&msr);
break;
}
}
else {
msr_free(&msr);
break;
}
}
if (offset + msr->reclen > buflen) {
ms_log(1, "readMSEEDBuffer(): Last msr->reclen exceeds buflen, skipping.\n");
msr_free(&msr);
break;
}
// Test against selections if supplied
if ( selections ) {
char srcname[50];
hptime_t endtime;
msr_srcname (msr, srcname, 1);
endtime = msr_endtime (msr);
if ( ms_matchselect (selections, srcname, msr->starttime, endtime, NULL) == NULL ) {
// Add the record length for the next iteration
offset += msr->reclen;
// Free record.
msr_free(&msr);
continue;
}
}
record_count += 1;
recordCurrent = lrl_init ();
// Append to linked record list if one exists.
if ( recordHead != NULL ) {
recordPrevious->next = recordCurrent;
recordCurrent->previous = recordPrevious;
recordCurrent->next = NULL;
recordPrevious = recordCurrent;
}
// Otherwise create a new one.
else {
recordHead = recordCurrent;
recordCurrent->previous = NULL;
recordPrevious = recordCurrent;
}
recordCurrent->record = msr;
// Figure out if the byte-order of the data has to be swapped.
swapflag = 0;
// If blockette 1000 is present, use it.
if ( msr->Blkt1000 != 0) {
/* If BE host and LE data need swapping */
if ( bigendianhost && msr->byteorder == 0 ) {
swapflag = 1;
}
/* If LE host and BE data (or bad byte order value) need swapping */
if ( !bigendianhost && msr->byteorder > 0 ) {
swapflag = 1;
}
}
// Otherwise assume the data has the same byte order as the header.
// This needs to be done on the raw header bytes as libmseed only returns
// header fields in the native byte order.
else {
unsigned char* _t = (unsigned char*)mseed + offset + 20;
unsigned int year = _t[0] | _t[1] << 8;
unsigned int day = _t[2] | _t[3] << 8;
// Swap data if header needs to be swapped.
if (!MS_ISVALIDYEARDAY(year, day)) {
swapflag = 1;
}
}
// Actually unpack the data if the flag is not set and if the data
// offset is valid.
if ((unpack_data != 0) && (msr->fsdh->data_offset >= 48) &&
(msr->fsdh->data_offset < msr->reclen) &&
(msr->samplecnt > 0)) {
retval = msr_unpack_data (msr, swapflag, verbose);
}
if ( retval > 0 ) {
msr->numsamples = retval;
}
if ( msr->fsdh->start_time.fract > 9999 ) {
ms_log(1, "readMSEEDBuffer(): Record with offset=%d has a "
"fractional second (.0001 seconds) of %d. This is not "
"strictly valid but will be interpreted as one or more "
"additional seconds.",
offset, msr->fsdh->start_time.fract);
}
// Add the record length for the next iteration
offset += msr->reclen;
}
// Return empty id list if no records could be found.
if (record_count == 0) {
idListHead = lil_init();
return idListHead;
}
// All records that match the selection are now stored in a LinkedRecordList
// that starts at recordHead. The next step is to sort them by matching ids
// and then by time.
recordCurrent = recordHead;
while (recordCurrent != NULL) {
// Check if the ID of the record is already available and if not create a
// new one.
// Start with the last id as it is most likely to be the correct one.
idListCurrent = idListLast;
while (idListCurrent != NULL) {
if (strcmp(idListCurrent->network, recordCurrent->record->network) == 0 &&
strcmp(idListCurrent->station, recordCurrent->record->station) == 0 &&
strcmp(idListCurrent->location, recordCurrent->record->location) == 0 &&
strcmp(idListCurrent->channel, recordCurrent->record->channel) == 0 &&
idListCurrent->dataquality == recordCurrent->record->dataquality) {
break;
}
else {
idListCurrent = idListCurrent->previous;
}
}
// Create a new id list if one is needed.
if (idListCurrent == NULL) {
idListCurrent = lil_init();
idListCurrent->previous = idListLast;
if (idListLast != NULL) {
idListLast->next = idListCurrent;
}
idListLast = idListCurrent;
if (idListHead == NULL) {
idListHead = idListCurrent;
}
// Set the IdList attributes.
strcpy(idListCurrent->network, recordCurrent->record->network);
strcpy(idListCurrent->station, recordCurrent->record->station);
strcpy(idListCurrent->location, recordCurrent->record->location);
strcpy(idListCurrent->channel, recordCurrent->record->channel);
idListCurrent->dataquality = recordCurrent->record->dataquality;
}
// Now check if the current record fits exactly to the end of the last
// segment of the current id. If not create a new segment. Therefore
// if records with the same id are in wrong order a new segment will be
// created. This is on purpose.
segmentCurrent = idListCurrent->lastSegment;
if (segmentCurrent != NULL) {
hptimetol = (hptime_t) (0.5 * segmentCurrent->hpdelta);
nhptimetol = ( hptimetol ) ? -hptimetol : 0;
lastgap = recordCurrent->record->starttime - segmentCurrent->endtime - segmentCurrent->hpdelta;
}
if (details == 1) {
/* extract information on calibration BLKs */
calibration_type = -1;
if (recordCurrent->record->blkts) {
BlktLink *cur_blkt = recordCurrent->record->blkts;
while (cur_blkt) {
switch (cur_blkt->blkt_type) {
case 300:
calibration_type = 1;
break;
case 310:
calibration_type = 2;
break;
case 320:
calibration_type = 3;
break;
case 390:
calibration_type = 4;
break;
case 395:
calibration_type = -2;
break;
default:
break;
}
cur_blkt = cur_blkt->next;
}
}
/* extract information based on timing quality */
timing_qual = 0xFF;
if (recordCurrent->record->Blkt1001 != 0) {
timing_qual = recordCurrent->record->Blkt1001->timing_qual;
}
}
if ( segmentCurrent != NULL &&
// This is important for zero data record coupled with not unpacking
// the data. It needs to be split in two places: Before the zero data
// record and after it.
recordCurrent->record->samplecnt > 0 && segmentCurrent->samplecnt > 0 &&
segmentCurrent->sampletype == recordCurrent->record->sampletype &&
// Test the default sample rate tolerance: abs(1-sr1/sr2) < 0.0001
MS_ISRATETOLERABLE (segmentCurrent->samprate, recordCurrent->record->samprate) &&
// Check if the times are within the time tolerance
lastgap <= hptimetol && lastgap >= nhptimetol &&
segmentCurrent->timing_qual == timing_qual &&
segmentCurrent->calibration_type == calibration_type) {
recordCurrent->previous = segmentCurrent->lastRecord;
segmentCurrent->lastRecord = segmentCurrent->lastRecord->next = recordCurrent;
segmentCurrent->samplecnt += recordCurrent->record->samplecnt;
segmentCurrent->endtime = msr_endtime(recordCurrent->record);
}
// Otherwise create a new segment and add the current record.
else {
segmentCurrent = seg_init();
segmentCurrent->previous = idListCurrent->lastSegment;
if (idListCurrent->lastSegment != NULL) {
idListCurrent->lastSegment->next = segmentCurrent;
}
else {
idListCurrent->firstSegment = segmentCurrent;
}
idListCurrent->lastSegment = segmentCurrent;
segmentCurrent->starttime = recordCurrent->record->starttime;
segmentCurrent->endtime = msr_endtime(recordCurrent->record);
segmentCurrent->samprate = recordCurrent->record->samprate;
segmentCurrent->sampletype = recordCurrent->record->sampletype;
segmentCurrent->samplecnt = recordCurrent->record->samplecnt;
// Calculate high-precision sample period
segmentCurrent->hpdelta = (hptime_t) (( recordCurrent->record->samprate ) ?
(HPTMODULUS / recordCurrent->record->samprate) : 0.0);
segmentCurrent->timing_qual = timing_qual;
segmentCurrent->calibration_type = calibration_type;
segmentCurrent->firstRecord = segmentCurrent->lastRecord = recordCurrent;
recordCurrent->previous = NULL;
}
recordPrevious = recordCurrent->next;
recordCurrent->next = NULL;
recordCurrent = recordPrevious;
}
// Now loop over all segments, combine the records and free the msr
// structures.
idListCurrent = idListHead;
while (idListCurrent != NULL)
{
segmentCurrent = idListCurrent->firstSegment;
while (segmentCurrent != NULL) {
if (segmentCurrent->datasamples) {
free(segmentCurrent->datasamples);
}
// Allocate data via a callback function.
if (unpack_data != 0) {
segmentCurrent->datasamples = (void *) allocData(segmentCurrent->samplecnt, segmentCurrent->sampletype);
}
// Loop over all records, write the data to the buffer and free the msr structures.
recordCurrent = segmentCurrent->firstRecord;
data_offset = (long long)(segmentCurrent->datasamples);
while (recordCurrent != NULL) {
datasize = recordCurrent->record->samplecnt * ms_samplesize(recordCurrent->record->sampletype);
memcpy((void *)data_offset, recordCurrent->record->datasamples, datasize);
// Free the record.
msr_free(&(recordCurrent->record));
// Increase the data_offset and the record.
data_offset += (long long)datasize;
recordCurrent = recordCurrent->next;
}
segmentCurrent = segmentCurrent->next;
}
idListCurrent = idListCurrent->next;
}
return idListHead;
}
