Update libmseed to v3.1.2

Author: chad-earthscope

ChangeLog

@@ -1,3 +1,6 @@
+2024.148: 4.2.1
+	- Update libmseed to v3.1.2.
+
 2024.024: 4.2
 	- Update libmseed to v3.1.1.
 

libmseed/ChangeLog

@@ -1,3 +1,20 @@
+2024.148: 3.1.2
+	- Update yyjson to v0.9.0.
+	- Simplify mstl3_addmsr_recordptr() a bit.
+
+2024.146:
+	- Replace ms_dabs() with macro to use system fabs(), document as deprecated.
+	- Add CRC values to diagnostic message when header values does not match calculated.
+
+2024.137:
+	- Add msr3_nsperiod() to calculate the sample period in nanoseconds.
+	- Add tests for msr3 utility functions.
+
+2024.106:
+	- When writing v2 derive the quality code from the publication version when the
+	extra-header "/FDSN/DataQuality" is not present.  Use quality indicator 'D' when
+	the publication version cannot be mapped, e.g. > 4.
+
 2024.024: 3.1.1
 	- Change library compatibility version in Makefile to MAJOR.1.0, as this is now
 	incompatible with the x.0.0 releases.

libmseed/doc/DoxygenLayout.xml

@@ -9,7 +9,7 @@
       <tab type="namespacelist" visible="yes" title="" intro=""/>
       <tab type="namespacemembers" visible="yes" title="" intro=""/>
     </tab>
-    <tab type="classes" visible="no" title="">
+    <tab type="classes" visible="yes" title="">
       <tab type="classlist" visible="yes" title="" intro=""/>
       <tab type="classindex" visible="$ALPHABETICAL_INDEX" title=""/>
       <tab type="hierarchy" visible="yes" title="" intro=""/>

libmseed/genutils.c

@@ -1671,25 +1671,6 @@ ms_sampletime (nstime_t time, int64_t offset, double samprate)
 } /* End of ms_sampletime() */
 
 
-/**********************************************************************/ /**
- * @brief Determine the absolute value of an input double
- *
- * Actually just test if the input double is positive multiplying by
- * -1.0 if not and return it.
- *
- * @param[in] val Value for which to determine absolute value
- *
- * @returns the positive value of input double.
- ***************************************************************************/
-double
-ms_dabs (double val)
-{
-  if (val < 0.0)
-    val *= -1.0;
-  return val;
-} /* End of ms_dabs() */
-
-
 /**********************************************************************/ /**
  * @brief Runtime test for host endianess
  * @returns 0 if the host is little endian, otherwise 1.

libmseed/libmseed.def

@@ -92,7 +92,6 @@ EXPORTS
    ms_encodingstr
    ms_errorstr
    ms_sampletime
-   ms_dabs
    ms_bigendianhost
    ms_crc32c
    leapsecondlist

libmseed/libmseed.h

@@ -28,8 +28,8 @@
 extern "C" {
 #endif
 
-#define LIBMSEED_VERSION "3.1.1"     //!< Library version
-#define LIBMSEED_RELEASE "2024.024"  //!< Library release date
+#define LIBMSEED_VERSION "3.1.2"     //!< Library version
+#define LIBMSEED_RELEASE "2024.148"  //!< Library release date
 
 /** @defgroup io-functions File and URL I/O */
 /** @defgroup miniseed-record Record Handling */
@@ -63,6 +63,7 @@ extern "C" {
 #include <time.h>
 #include <string.h>
 #include <ctype.h>
+#include <math.h>
 
 /** @def PRIsize_t
     @brief A printf() macro for portably printing size_t values */
@@ -140,7 +141,7 @@ extern "C" {
 
 /** @def MS_ISRATETOLERABLE
     @brief Macro to test default sample rate tolerance: abs(1-sr1/sr2) < 0.0001 */
-#define MS_ISRATETOLERABLE(A,B) (ms_dabs (1.0 - ((A) / (B))) < 0.0001)
+#define MS_ISRATETOLERABLE(A,B) (fabs (1.0 - ((A) / (B))) < 0.0001)
 
 /** @def MS2_ISDATAINDICATOR
     @brief Macro to test a character for miniSEED 2.x data record/quality indicators */
@@ -409,6 +410,7 @@ extern nstime_t   msr3_endtime (const MS3Record *msr);
 extern void       msr3_print (const MS3Record *msr, int8_t details);
 extern int        msr3_resize_buffer (MS3Record *msr);
 extern double     msr3_sampratehz (const MS3Record *msr);
+extern nstime_t   msr3_nsperiod (const MS3Record *msr);
 extern double     msr3_host_latency (const MS3Record *msr);
 
 extern int64_t ms3_detect (const char *record, uint64_t recbuflen, uint8_t *formatversion);
@@ -1252,9 +1254,11 @@ extern const char *ms_encodingstr (uint8_t encoding);
 extern const char *ms_errorstr (int errorcode);
 
 extern nstime_t ms_sampletime (nstime_t time, int64_t offset, double samprate);
-extern double ms_dabs (double val);
 extern int ms_bigendianhost (void);
 
+/** DEPRECATED legacy implementation of fabs(), now a macro */
+#define ms_dabs(val) fabs(val)
+
 /** Portable version of POSIX ftello() to get file position in large files */
 extern int64_t lmp_ftell64 (FILE *stream);
 /** Portable version of POSIX fseeko() to set position in large files */

libmseed/msrutils.c

@@ -355,6 +355,29 @@ msr3_sampratehz (const MS3Record *msr)
     return msr->samprate;
 } /* End of msr3_sampratehz() */
 
+/**********************************************************************/ /**
+ * @brief Calculate sample period in nanoseconds/sample for a given ::MS3Record
+ *
+ * @param[in] msr ::MS3Record to calculate sample period for
+ *
+ * @returns Return sample period in nanoseconds (nanoseconds per sample)
+ ***************************************************************************/
+inline nstime_t
+msr3_nsperiod (const MS3Record *msr)
+{
+  if (!msr)
+    return 0;
+
+  /* Calculate sample period from sample rate or period.
+   * The value is rounded by adding 0.5 before truncation to an integer. */
+  if (msr->samprate > 0.0)
+    return (nstime_t)(NSTMODULUS / msr->samprate + 0.5); /* samples/second */
+  else if (msr->samprate < 0.0)
+    return (nstime_t)(NSTMODULUS * -msr->samprate + 0.5); /* period or seconds/sample */
+
+  return 0;
+} /* End of msr3_nsperiod() */
+
 /**********************************************************************/ /**
  * @brief Calculate data latency based on the host time
  *

libmseed/pack.c

@@ -988,11 +988,31 @@ msr3_pack_header2 (const MS3Record *msr, char *record, uint32_t recbuflen, int8_
   /* Build fixed header */
   memcpy (pMS2FSDH_SEQNUM (record), "000000", 6);
 
+  /* Use DataQuality indicator in extra headers if present */
   if (yyjson_ptr_get_str (ehroot, "/FDSN/DataQuality", &header_string) &&
       MS2_ISDATAINDICATOR (header_string[0]))
+  {
     *pMS2FSDH_DATAQUALITY (record) = header_string[0];
+  }
+  /* Otherwise map publication version, defaulting to 'D' */
   else
-    *pMS2FSDH_DATAQUALITY (record) = 'D';
+  {
+    switch (msr->pubversion)
+    {
+    case 1:
+      *pMS2FSDH_DATAQUALITY (record) = 'R';
+      break;
+    case 3:
+      *pMS2FSDH_DATAQUALITY (record) = 'Q';
+      break;
+    case 4:
+      *pMS2FSDH_DATAQUALITY (record) = 'M';
+      break;
+    default:
+      *pMS2FSDH_DATAQUALITY (record) = 'D';
+      break;
+    }
+  }
 
   *pMS2FSDH_RESERVED (record) = ' ';
   ms_strncpopen (pMS2FSDH_STATION (record), station, 5);
@@ -1122,7 +1142,7 @@ msr3_pack_header2 (const MS3Record *msr, char *record, uint32_t recbuflen, int8_
   }
 
   /* Add Blockette 100 if sample rate is not well represented by factor/multiplier */
-  if (ms_dabs(msr3_sampratehz(msr) - ms_nomsamprate(factor, multiplier)) > 0.0001)
+  if (fabs(msr3_sampratehz(msr) - ms_nomsamprate(factor, multiplier)) > 0.0001)
   {
     *next_blockette = HO2u ((uint16_t)written, swapflag);
     next_blockette = pMS2B100_NEXT (record + written);
@@ -1825,7 +1845,7 @@ ms_ratapprox (double real, int *num, int *den, int maxval, double precision)
   if (!pos)
     *num = -*num;
 
-  while (ms_dabs (preal - (double)Aj / (double)Bj) > precision &&
+  while (fabs (preal - (double)Aj / (double)Bj) > precision &&
          Aj < maxval && Bj < maxval)
   {
     Aj2   = Aj1;
@@ -1926,7 +1946,7 @@ ms_reduce_rate (double samprate, int16_t *factor1, int16_t *factor2)
   int32_t diff;
 
   /* Handle case of integer sample values. */
-  if (ms_dabs (samprate - intsamprate) < 0.0000001)
+  if (fabs (samprate - intsamprate) < 0.0000001)
   {
     /* If integer sample rate is less than range of 16-bit int set it directly */
     if (intsamprate <= 32767)