Merge pull request #1201 from dwcaress/caress-tmp

Mblist, mbvoxelclean, mbnavadjust, mbm_histplot, formats 232 & 233

ChangeLog.md

@@ -23,6 +23,7 @@ Distributions that do not include "beta" in the tag name correspond to the major
 announced releases. The source distributions associated with all releases, major
 or beta, are equally accessible as tarballs through the Github interface.
 
+- Version 5.7.9beta07    May 7, 2021
 - Version 5.7.9beta06    March 24, 2021
 - Version 5.7.9beta05    March 8, 2021
 - Version 5.7.9beta04    February 21, 2021
@@ -385,6 +386,19 @@ or beta, are equally accessible as tarballs through the Github interface.
 --
 ### MB-System Version 5.7 Release Notes:
 --
+#### 5.7.9beta07 (May 7, 2021)
+
+mbm_histplot: Fixed the use of the -C option to specify cellwidth for the
+histogram to be plotted.
+
+Formats 232 (MBF_3DWISSLR) and 233 (MBF_3DWISSLP): Changed so that MB_FLAG_SECONDARY
+is no longer used for multiple picks per laser pulse.
+
+MBnavadjust and MBnavadjustmerge: Restructured the code so that more capability
+of mbnavadjust can be duplicated in the command line tool mbnavadjust merge. 
+Working to add ability to reimport surveys into a project.
+
+MBvoxelclean: Added --neighborhood option and fixed amplitude range options.
 
 Mblist: Fixed function of the -O%fnv and -O%FNV commands to produce *.fnv files.
 

configure

@@ -1,6 +1,6 @@
 #! /bin/sh
 # Guess values for system-dependent variables and create Makefiles.
-# Generated by GNU Autoconf 2.69 for mbsystem 5.7.9beta06.
+# Generated by GNU Autoconf 2.69 for mbsystem 5.7.9beta07.
 #
 # Report bugs to <http://listserver.mbari.org/sympa/arc/mbsystem>.
 #
@@ -590,8 +590,8 @@ MAKEFLAGS=
 # Identity of this package.
 PACKAGE_NAME='mbsystem'
 PACKAGE_TARNAME='mbsystem'
-PACKAGE_VERSION='5.7.9beta06'
-PACKAGE_STRING='mbsystem 5.7.9beta06'
+PACKAGE_VERSION='5.7.9beta07'
+PACKAGE_STRING='mbsystem 5.7.9beta07'
 PACKAGE_BUGREPORT='http://listserver.mbari.org/sympa/arc/mbsystem'
 PACKAGE_URL='http://www.mbari.org/data/mbsystem/'
 
@@ -1486,7 +1486,7 @@ if test "$ac_init_help" = "long"; then
   # Omit some internal or obsolete options to make the list less imposing.
   # This message is too long to be a string in the A/UX 3.1 sh.
   cat <<_ACEOF
-\`configure' configures mbsystem 5.7.9beta06 to adapt to many kinds of systems.
+\`configure' configures mbsystem 5.7.9beta07 to adapt to many kinds of systems.
 
 Usage: $0 [OPTION]... [VAR=VALUE]...
 
@@ -1560,7 +1560,7 @@ fi
 
 if test -n "$ac_init_help"; then
   case $ac_init_help in
-     short | recursive ) echo "Configuration of mbsystem 5.7.9beta06:";;
+     short | recursive ) echo "Configuration of mbsystem 5.7.9beta07:";;
    esac
   cat <<\_ACEOF
 
@@ -1728,7 +1728,7 @@ fi
 test -n "$ac_init_help" && exit $ac_status
 if $ac_init_version; then
   cat <<\_ACEOF
-mbsystem configure 5.7.9beta06
+mbsystem configure 5.7.9beta07
 generated by GNU Autoconf 2.69
 
 Copyright (C) 2012 Free Software Foundation, Inc.
@@ -2385,7 +2385,7 @@ cat >config.log <<_ACEOF
 This file contains any messages produced by compilers while
 running configure, to aid debugging if configure makes a mistake.
 
-It was created by mbsystem $as_me 5.7.9beta06, which was
+It was created by mbsystem $as_me 5.7.9beta07, which was
 generated by GNU Autoconf 2.69.  Invocation command line was
 
   $ $0 $@
@@ -2734,7 +2734,7 @@ ac_compiler_gnu=$ac_cv_c_compiler_gnu
 
 
 
-$as_echo "#define VERSION_DATE \"24 March 2021\"" >>confdefs.h
+$as_echo "#define VERSION_DATE \"7 May 2021\"" >>confdefs.h
 
 
 $as_echo " "
@@ -4693,7 +4693,7 @@ fi
 
 # Define the identity of the package.
  PACKAGE='mbsystem'
- VERSION='5.7.9beta06'
+ VERSION='5.7.9beta07'
 
 
 cat >>confdefs.h <<_ACEOF
@@ -24546,7 +24546,7 @@ cat >>$CONFIG_STATUS <<\_ACEOF || ac_write_fail=1
 # report actual input values of CONFIG_FILES etc. instead of their
 # values after options handling.
 ac_log="
-This file was extended by mbsystem $as_me 5.7.9beta06, which was
+This file was extended by mbsystem $as_me 5.7.9beta07, which was
 generated by GNU Autoconf 2.69.  Invocation command line was
 
   CONFIG_FILES    = $CONFIG_FILES
@@ -24613,7 +24613,7 @@ _ACEOF
 cat >>$CONFIG_STATUS <<_ACEOF || ac_write_fail=1
 ac_cs_config="`$as_echo "$ac_configure_args" | sed 's/^ //; s/[\\""\`\$]/\\\\&/g'`"
 ac_cs_version="\\
-mbsystem config.status 5.7.9beta06
+mbsystem config.status 5.7.9beta07
 configured by $0, generated by GNU Autoconf 2.69,
   with options \\"\$ac_cs_config\\"
 

configure.ac

@@ -11,8 +11,8 @@ dnl    See README file for copying and redistribution conditions.
 dnl--------------------------------------------------------------------
 
 dnl Initialize and set version and version date
-AC_INIT([mbsystem],[5.7.9beta06],[http://listserver.mbari.org/sympa/arc/mbsystem],[mbsystem],[http://www.mbari.org/data/mbsystem/])
-AC_DEFINE(VERSION_DATE, ["24 March 2021"], [Set VERSION_DATE define in mb_config.h])
+AC_INIT([mbsystem],[5.7.9beta07],[http://listserver.mbari.org/sympa/arc/mbsystem],[mbsystem],[http://www.mbari.org/data/mbsystem/])
+AC_DEFINE(VERSION_DATE, ["7 May 2021"], [Set VERSION_DATE define in mb_config.h])
 
 AS_ECHO([" "])
 AS_ECHO(["------------------------------------------------------------------------------"])

libtool

@@ -1,6 +1,6 @@
 #! /bin/sh
-# Generated automatically by config.status (mbsystem) 5.7.9beta06
-# Libtool was configured on host mbari1716.shore.mbari.org:
+# Generated automatically by config.status (mbsystem) 5.7.9beta07
+# Libtool was configured on host tharp.local:
 # NOTE: Changes made to this file will be lost: look at ltmain.sh.
 
 # Provide generalized library-building support services.

src/macros/mbm_histplot

@@ -32,11 +32,11 @@
 #   macro.
 #
 # Basic Usage:
-#   mbm_histplot -Ifile [-Btickinfo -Gfill -H
+#   mbm_histplot -Ifile [-Btickinfo -C[xmin/xmax/]cellwidth -Gfill -H
 #            -Jprojection[/scale | width]
 #            -Ltitle -Oroot
 #            -Ppagesize -Uorientation -Q
-#            -Rw/e/s/n -V -Wpen -X]
+#            -Rxmin/xmax/fmin/fmax -V -Wpen -X]
 #
 # Miscellaneous Options:
 #            [ -MIErresolution -MITtype ]
@@ -146,7 +146,7 @@ $current_working_dir = `pwd`;
 $command_line = "@ARGV";
 &MBGetopts('B:b:C:c:G:g:HhI:i:J:j:L:l:M+m+O:o:P:p:QqR:r:U:u:VvW:w:Xx:');
 $tick_info = 		($opt_B || $opt_b);
-$cellwidth = 		($opt_C || $opt_c);
+$cellwidthraw = 		($opt_C || $opt_c);
 $fill = 		($opt_G || $opt_g || "gray");
 $help =    		($opt_H || $opt_h);
 $file_data =    	($opt_I || $opt_i);
@@ -257,57 +257,71 @@ if (!$root)
     $root = $file_data;
 }
 
-# use user defined bounds
-if ($bounds)
-	{
-	if ($bounds =~ /^\S+\/\S+\/\S+\/\S+$/)
+# open and read the file for xmin xmax
+open(F,$file_data) || die "Cannot open input file: $file_data\n$program_name aborted.\n";
+$count = 0;
+while ($data=<F>) {
+	if ($count == 0 || $data < $xmind)
 		{
-		($xmin,$xmax,$ymin,$ymax) = $bounds =~
-			/(\S+)\/(\S+)\/(\S+)\/(\S+)/;
-		$bounds_plot = $bounds;
+		$xmind = $data;
 		}
+	if ($count == 0 || $data > $xmaxd)
+		{
+		$xmaxd = $data;
+		}
+	$count++;
+}
+close(F);
+if ($count <= 0)
+	{
+	die "Input file: $file_data appears to contain no data.\n$program_name aborted.\n";
 	}
 
-# get limits of file.
-if (!$bounds)
+# use user defined bounds
+if ($bounds && $bounds =~ /^\S+\/\S+\/\S+\/\S+$/)
 	{
-	# open and read the file for xmin xmax
-	open(F,$file_data) || die "Cannot open input file: $file_data\n$program_name aborted.\n";
-	$count = 0;
-	while ($data=<F>) {
-		if ($data < $xmin || $count == 0)
-			{
-			$xmin = $data;
-			}
-		if ($data > $xmax || $count == 0)
-			{
-			$xmax = $data;
-			}
-  		$count++;
-		}
-	close(F);
-	if ($count <= 0)
-		{
-		die "Input file: $file_data appears to contain no data.\n$program_name aborted.\n";
-		}
+	($xmin,$xmax,$ymin,$ymax) = $bounds =~
+		/(\S+)\/(\S+)\/(\S+)\/(\S+)/;
+	$bounds_plot = $bounds;
+	}
+else
+  {
+  $xmin = $xmind;
+  $xmax = $xmaxd;
+  }
 
-	# if needed set cell bounds
-	if (!$cellwidth)
+# parse -C argument
+if ($cellwidthraw)
+  {
+	if ($cellwidthraw =~ /^\S+\/\S+\/\S+$/)
 		{
-		$cellwidth = ($xmax - $xmin) / 10;
-		}
+		($xmin,$xmax,$cellwidth) = $cellwidthraw =~ /^(\S+)\/(\S+)\/(\S+)$/;
+    }
+  else
+    {
+      $cellwidth = $cellwidthraw;
+    }
+  }
 
-	# make cells
-	$ncell = floor(($xmax - $xmin) / $cellwidth) + 5;
-	$nxmin = floor($xmin / $cellwidth) - 1;
-	$xmin = ($nxmin - 0.5) * $cellwidth;
-	$xmax = $xmin + $cellwidth * $ncell;
-	for ($i=0;$i<$ncell;$i++)
-		{
-		push(@cellcount, 0);
-		}
+# if needed set cell bounds
+if (!$cellwidth)
+	{
+	$cellwidth = ($xmax - $xmin) / 10;
+	}
 
-	# open and read the file for ymin ymax
+# make cells
+$ncell = floor(($xmax - $xmin) / $cellwidth) + 5;
+$nxmin = floor($xmin / $cellwidth) - 1;
+$xmin = ($nxmin - 0.5) * $cellwidth;
+$xmax = $xmin + $cellwidth * $ncell;
+for ($i=0;$i<$ncell;$i++)
+	{
+	push(@cellcount, 0);
+	}
+
+# open and read the file for ymin ymax
+if (!$bounds || !$bounds =~ /^\S+\/\S+\/\S+\/\S+$/)
+  {
 	open(F,$file_data) || die "Cannot open input file: $file_data\n$program_name aborted.\n";
 	while ($data=<F>) {
 		$i = floor(($data - $xmin) / $cellwidth);
@@ -752,8 +766,6 @@ $gmt_def = "COLOR_FOREGROUND/white";
 push(@gmt_macro_defs, $gmt_def);
 $gmt_def = "COLOR_NAN/white";
 push(@gmt_macro_defs, $gmt_def);
-$gmt_def = "FORMAT_GEO_MAP/$degree_format";
-push(@gmt_macro_defs, $gmt_def);
 
 # open the shellscript file
 if (!open(FCMD,">$cmdfile"))
@@ -876,7 +888,7 @@ printf FCMD "gmt pshistogram $file_data \\\n\t";
 printf FCMD "-J\$MAP_PROJECTION\$MAP_SCALE \\\n\t";
 printf FCMD "-R\$MAP_REGION \\\n\t";
 printf FCMD "$axes \\\n\t";
-printf FCMD "-W$cellwidth -Z1 \\\n\t";
+printf FCMD "-T$xmin/$xmax/$cellwidth -Z1 \\\n\t";
 if ($pen)
 	{
 	printf FCMD "-L$pen \\\n\t";

src/mbio/mb_config.h

@@ -104,7 +104,7 @@
 #define PACKAGE_NAME "mbsystem"
 
 /* Define to the full name and version of this package. */
-#define PACKAGE_STRING "mbsystem 5.7.9beta06"
+#define PACKAGE_STRING "mbsystem 5.7.9beta07"
 
 /* Define to the one symbol short name of this package. */
 #define PACKAGE_TARNAME "mbsystem"
@@ -113,7 +113,7 @@
 #define PACKAGE_URL "http://www.mbari.org/data/mbsystem/"
 
 /* Define to the version of this package. */
-#define PACKAGE_VERSION "5.7.9beta06"
+#define PACKAGE_VERSION "5.7.9beta07"
 
 /* Build tools using PCL */
 /* #undef PCLTOOLS_ENABLED */
@@ -128,10 +128,10 @@
 #define TEST_ENABLED 1
 
 /* Version number of package */
-#define VERSION "5.7.9beta06"
+#define VERSION "5.7.9beta07"
 
 /* Set VERSION_DATE define in mb_config.h */
-#define VERSION_DATE "24 March 2021"
+#define VERSION_DATE "7 May 2021"
 
 /* Define WORDS_BIGENDIAN to 1 if your processor stores words with the most
    significant byte first (like Motorola and SPARC, unlike Intel). */

src/mbio/mb_status.h

@@ -444,7 +444,8 @@ const char *unknown_notice_msg[] = {"Unknown notice identifier"};
 #define mb_beam_check_flag_sonar(F) ((int)((F & MB_FLAG_SONAR) && (F & MB_FLAG_FLAG)))
 //#define mb_beam_check_flag_gt_1x_iho(F) ((int)((F & MB_FLAG_GT_1X_IHO) && (F & MB_FLAG_FLAG)))
 //#define mb_beam_check_flag_gt_2x_iho(F) ((int)((F & MB_FLAG_GT_2X_IHO) && (F & MB_FLAG_FLAG)))
-#define mb_beam_check_flag_unusable(F) ((int)((F == MB_FLAG_NULL) || ((F & MB_FLAG_FLAG) && ((F & MB_FLAG_INTERPOLATE) || (F & MB_FLAG_SECONDARY)))))
+//#define mb_beam_check_flag_unusable(F) ((int)((F == MB_FLAG_NULL) || ((F & MB_FLAG_FLAG) && ((F & MB_FLAG_INTERPOLATE) || (F & MB_FLAG_SECONDARY)))))
+#define mb_beam_check_flag_unusable(F) ((int)((F == MB_FLAG_NULL) || ((F & MB_FLAG_FLAG) && ((F & MB_FLAG_INTERPOLATE)))))
 #define mb_beam_set_flag_null(F) (0x01)
 #define mb_beam_set_flag_none(F) (0x00)
 #define mb_beam_set_flag_manual(F) (F | 0x05)

src/mbio/mbsys_3ddwissl.c

@@ -3699,6 +3699,15 @@ int mbsys_3ddwissl_calculatebathymetry
       pulse = (struct mbsys_3ddwissl_pulse_struct *)&store->pulses[ipulse];
       int isounding_largest = -1;
       short amplitude_largest = 0;
+      for (int isounding=0; isounding<store->soundings_per_pulse; isounding++)
+        {
+        sounding = &pulse->soundings[isounding];
+        if (sounding->range > 0.001 && sounding->amplitude > amplitude_largest)
+            {
+            amplitude_largest = sounding->amplitude;
+            isounding_largest = isounding;
+            }
+        }
       for (int isounding=0; isounding<store->soundings_per_pulse; isounding++)
         {
         sounding = &pulse->soundings[isounding];
@@ -3732,7 +3741,9 @@ int mbsys_3ddwissl_calculatebathymetry
 
           /* set beamflag */
           if (sounding->amplitude * amplitude_factor >= amplitude_threshold)
-            sounding->beamflag = MB_FLAG_FLAG + MB_FLAG_SECONDARY;
+            sounding->beamflag = MB_FLAG_NONE;
+          else if (isounding_largest == isounding)
+            sounding->beamflag = MB_FLAG_FLAG + MB_FLAG_SONAR;
           else
             sounding->beamflag = MB_FLAG_NULL;
 
@@ -3750,13 +3761,6 @@ int mbsys_3ddwissl_calculatebathymetry
           sounding->alongtrack = xx * sin(DTR * phi) + head_offset_y_m
                                   + angle_el_sign * pulse->offset_el
                                   + pulse->alongtrack_offset;
-
-          /* check for largest amplitude */
-          if (sounding->amplitude > amplitude_largest)
-            {
-            amplitude_largest = sounding->amplitude;
-            isounding_largest = isounding;
-            }
           }
         else
           {
@@ -3767,14 +3771,6 @@ int mbsys_3ddwissl_calculatebathymetry
           sounding->alongtrack = 0.0;
           }
         }
-
-      /* reset beam flags */
-      if (isounding_largest >= 0)
-        {
-        sounding = &pulse->soundings[isounding_largest];
-        if (sounding->beamflag != MB_FLAG_NULL)
-          sounding->beamflag = MB_FLAG_NONE;
-        }
       }
 
     /* set flag indicating that bathymetry has been calculated */