Merge pull request #1466 from dwcaress/caress-tmp

Setup for beta release 5.8.2beta05
dwcaress · May 19, 2024 · 160a328 · 160a328
2 parents e16c03e + 7c669ca
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diff --git a/docker/README.md b/docker/README.md
@@ -6,7 +6,7 @@ This directory contains a Dockerfile used to automatically build an MB-System Do
 This file documents how the MB-System Docker image can be used and how it is structured.
 
 ### Version
-Last Modified 16 May 2024
+Last Modified 18 May 2024
 
 
 ## What are Docker images and containers?
@@ -23,12 +23,19 @@ However, the interactive applications that are part of MB-System use the X11 win
 
 The MB-System Docker image is built using Debian 12 Linux and the current MB-System release, and is updated each time a new MB-System release is made. The current release is accessed using the "latest" tag in the Github repository: [https://github.com/dwcaress/MB-System/releases/latest](https://github.com/dwcaress/MB-System/releases/latest). This image is then available from the Docker Hub site at: [https://hub.docker.com/r/mbari/mbsystem](https://hub.docker.com/r/mbari/mbsystem)
 
-The MB-System Docker image is run from a terminal command line on the host computer. Once the Docker container (a running Docker image) is active it presents as the command line in the same terminal window, and is accessing the same local directory as before. The difference is that the user can now run the MB-System and GMT programs installed in the Docker image.
+The MB-System Docker image is run from a terminal command line on the host computer. Once the Docker container (a running Docker image) is active it presents as the command line in the same terminal window, and is accessing the same local directory as before. The difference is that the user can now run the MB-System and GMT programs installed in the Docker image. Within the container the user id is mbuser.
 
 ---
 ## Running Dockerized MB-System on MacOs
 
-The first requirement is to install and run the Docker Desktop application on your local computer, insuring that a Docker server process is running locally. In order to download the MB-System Docker Image, enter the following in a terminal shell:
+The first requirement is to install and run the Docker Desktop application on your computer, insuring that a Docker server process is running locally. Obtain Docker Desktop from:
+[https://www.docker.com/products/docker-desktop/](https://www.docker.com/products/docker-desktop/)
+
+You must also install and run an X11 window server on your computer. The best option is to install XQuartz from: [https://www.xquartz.org](https://www.xquartz.org)
+
+Start Docker Desktop, XQuartz, and the Apple Terminal application (found in Utilities under Applications in the Finder) before beginning the following. 
+
+In order to download the MB-System Docker Image, enter the following in a terminal shell:
 
 	docker pull mbari/mbsystem:latest
 
@@ -49,14 +56,21 @@ The output to the shell should look something like:
 	user@LOCALCOMPUTER% 
 
 
-Your Docker Desktop should now show mbari/mbsystem as one of the available local images.
+Your Docker Desktop should show mbari/mbsystem as one of the available local images. You can now use a docker run command in a shell to start a Docker container from the MB-System Docker image. 
+
+However, in order to run MB-System graphical tools such as mbedit, you must not only have an X Server running on the host, you must also turn off the X Server access control using "xhost +", and know an ip address for the host. This is because once the container is started, it is necessary to have the environment variable DISPLAY in the container reference the host X Server for the MB-System graphical programs to be displayed.  To find out an IP address of the local computer (there will be one for each network connection), you can open the Apple menu and click System Settings. In the System Settings dialog click Network in the left panel and then select one of the active network connections, typically Wi-Fi or Ethernet. Click the Details button, and scroll down to see the local ip address, which is a series of four integers separated by "." characters. Alternatively, the following command can be used to list the local ip addresses on a command line:
+
+	ifconfig | grep inet | grep -v inet6 | grep -v 127.0.0.1 | awk '{print $2}'
+
+If the local machine or host has an ip address of 192.168.25.26, then the X Server reference needed for the DISPLAY environment variable is that ip address with ":0" added, or "192.168.25.26:0".
 
-You must also install and run an X11 window server on your computer. The best option is to install XQuartz from: [https://www.xquartz.org](https://www.xquartz.org)
 
-To start a Docker container using the MB-System Docker image, navigate a command line shell to a directory containing seafloor mapping data that you wish to process, and then enter a "docker run" command as described below. In order to run MB-System graphical tools such as mbedit, you must have an X Server running on the host with access control turned off using "xhost +", and have the environment variable DISPLAY in the container reference the X Server. If the local machine or host has an ip address of 192.168.25.26, then the X Server reference is "192.168.25.26:0". The following sequence of commands should work:
+To start a Docker container using the MB-System Docker image, navigate a command line shell to a directory containing seafloor mapping data that you wish to process, and then enter a "docker run" command as described below. 
+
+The following sequence of commands for a shell in your host computer will turn off X Server access control, set a local shell variable named IP containing a local IP address, and then run the Docker image as user mbuser located in the same directory in which the "docker run" command is made.
 
 	xhost +
-	export IP=192.168.25.26
+	IP=$(ifconfig | grep inet | grep -v inet6 | grep -v 127.0.0.1 | head -n 1 | awk '{print $2}')
 	docker run -it --platform linux/amd64 --rm --network=host \
 			--user mbuser \
 			--env=LIBGL_ALWAYS_INDIRECT=1 \
@@ -67,7 +81,9 @@ To start a Docker container using the MB-System Docker image, navigate a command
 			--workdir=$PWD \
 			mbari/mbsystem
 
-The command line will return with a changed cursor, indicating that you are executing a shell within the now-running Docker container. Now MB-System command line tools like mbinfo can be run:
+The command line will return with a changed cursor, indicating that you are executing a shell within the now-running Docker container. To be sure, you can type the command "whoami", which should return mbuser rather than your login on the host computer.
+
+Now MB-System command line tools like mbinfo can be run:
 
 	mbuser@docker-desktop:/Users/caress/TestData$ mbinfo -I 0010_20230405_034803_SallyRide_EM124.kmall
 

diff --git a/docker/README.pdf b/docker/README.pdf
diff --git a/src/html/ChangeLog.html b/src/html/ChangeLog.html
@@ -1,4 +1,4 @@
-<hr />
+<p>--</p>
 <h2 id="mb-system-changelog-file">MB-System ChangeLog File:</h2>
 <p>This file lists changes to the source code of the MB-System open
 source software package for the processing and display of swath sonar
@@ -23,6 +23,10 @@ <h3 id="mb-system-version-58-releases-and-release-notes">MB-System
 Version 5.8 Releases and Release Notes:</h3>
 <hr />
 <ul>
+<li>Version 5.8.2beta05 May 17, 2024</li>
+<li>Version 5.8.2beta04 May 13, 2024</li>
+<li>Version 5.8.2beta02 May 1, 2024</li>
+<li>Version 5.8.2beta01 April 29, 2024</li>
 <li><strong>Version 5.8.1 March 22, 2024</strong></li>
 <li>Version 5.8.1beta09 March 22, 2024</li>
 <li>Version 5.8.1beta08 March 10, 2024</li>
@@ -34,6 +38,36 @@ <h3 id="mb-system-version-58-releases-and-release-notes">MB-System
 <li><strong>Version 5.8.0 January 22, 2024</strong></li>
 </ul>
 <hr />
+<h4 id="582beta05-may-17-2024">5.8.2beta05 (May 17, 2024)</h4>
+<p>MBextractsegy: changed calculation of section plot bounds to more
+consistently catch the seafloor arrival within the plot.</p>
+<p>MBpreprocess: fixed initialization of the --kluge-fix-7k-times
+option.</p>
+<p>Docker image: updated documentation in the Docker directory.</p>
+<h4 id="582beta04-may-13-2024">5.8.2beta04 (May 13, 2024)</h4>
+<p>Mbpreprocess: Added kluge option to fix large shifts in survey record
+timestamps in Teledyne s7k format data (specifically MBARI Mapping AUV
+multibeam data collected with the sonar computer experiencing large
+shifts in time). This option is accessed as
+--kluge-fix-7k-timestamps=time</p>
+<p>Mbroutetime: Now works with the recently changed route file
+format.</p>
+<p>Mblevitus: Fixed problem building mblevitus with the Cmake build
+system. The problem was that the Levitus database location was
+incorrectly embedded in the compiled program.</p>
+<h4 id="582beta02-may-1-2024">5.8.2beta02 (May 1, 2024)</h4>
+<p>Format 261 (MBF_KEMKMALL): Fixed bug in handing pings for which there
+are multiple MRZ datagrams that have different timestamps. This bug
+resulted in MB-System dropping many pings in some deepwater Kongsberg
+data (mostly EM124 data).</p>
+<h4 id="582beta01-april-29-2024">5.8.2beta01 (April 29, 2024)</h4>
+<p>Mbedit: Fixed display of ping profiles to handle condition where a
+ping contains two acrosstrack profiles, typically one aft and one
+forward of the sonar location. Now the connection between the end of the
+first acrosstrack profile and the start of the second is no longer
+plotted.</p>
+<p>MB-System Docker Container: Improved Docker documentation included in
+the Docker directory.</p>
 <h4 id="581-march-22-2024">5.8.1 (March 22, 2024)</h4>
 <p>CMake build system: Fixed ability to set OTPS location in cmake build
 system.</p>

diff --git a/src/html/mb7k2jstar.pdf b/src/html/mb7k2jstar.pdf
diff --git a/src/html/mb7k2ss.pdf b/src/html/mb7k2ss.pdf
diff --git a/src/html/mb7kpreprocess.pdf b/src/html/mb7kpreprocess.pdf
diff --git a/src/html/mbabsorption.pdf b/src/html/mbabsorption.pdf
diff --git a/src/html/mbareaclean.pdf b/src/html/mbareaclean.pdf
diff --git a/src/html/mbauvloglist.pdf b/src/html/mbauvloglist.pdf
diff --git a/src/html/mbauvnavusbl.pdf b/src/html/mbauvnavusbl.pdf
diff --git a/src/html/mbbackangle.pdf b/src/html/mbbackangle.pdf
diff --git a/src/html/mbclean.pdf b/src/html/mbclean.pdf
diff --git a/src/html/mbconfig.pdf b/src/html/mbconfig.pdf
diff --git a/src/html/mbcontour.pdf b/src/html/mbcontour.pdf
diff --git a/src/html/mbcopy.pdf b/src/html/mbcopy.pdf
diff --git a/src/html/mbctdlist.pdf b/src/html/mbctdlist.pdf
diff --git a/src/html/mbdatalist.pdf b/src/html/mbdatalist.pdf
diff --git a/src/html/mbdefaults.pdf b/src/html/mbdefaults.pdf
diff --git a/src/html/mbdumpesf.pdf b/src/html/mbdumpesf.pdf
diff --git a/src/html/mbedit.pdf b/src/html/mbedit.pdf
diff --git a/src/html/mbeditviz.pdf b/src/html/mbeditviz.pdf
diff --git a/src/html/mbextractsegy.pdf b/src/html/mbextractsegy.pdf
diff --git a/src/html/mbfilter.pdf b/src/html/mbfilter.pdf
diff --git a/src/html/mbformat.pdf b/src/html/mbformat.pdf
diff --git a/src/html/mbgetesf.pdf b/src/html/mbgetesf.pdf
diff --git a/src/html/mbgpstide.pdf b/src/html/mbgpstide.pdf
diff --git a/src/html/mbgrd2obj.pdf b/src/html/mbgrd2obj.pdf
diff --git a/src/html/mbgrdtiff.pdf b/src/html/mbgrdtiff.pdf
diff --git a/src/html/mbgrdviz.pdf b/src/html/mbgrdviz.pdf
diff --git a/src/html/mbgrid.pdf b/src/html/mbgrid.pdf
diff --git a/src/html/mbhistogram.pdf b/src/html/mbhistogram.pdf
diff --git a/src/html/mbhsdump.pdf b/src/html/mbhsdump.pdf
diff --git a/src/html/mbhysweeppreprocess.pdf b/src/html/mbhysweeppreprocess.pdf
diff --git a/src/html/mbinfo.pdf b/src/html/mbinfo.pdf
diff --git a/src/html/mbio.pdf b/src/html/mbio.pdf
diff --git a/src/html/mbkongsbergpreprocess.pdf b/src/html/mbkongsbergpreprocess.pdf
diff --git a/src/html/mblevitus.pdf b/src/html/mblevitus.pdf
diff --git a/src/html/mblist.pdf b/src/html/mblist.pdf
diff --git a/src/html/mbm_arc2grd.pdf b/src/html/mbm_arc2grd.pdf
diff --git a/src/html/mbm_bpr.pdf b/src/html/mbm_bpr.pdf
diff --git a/src/html/mbm_copy.pdf b/src/html/mbm_copy.pdf
diff --git a/src/html/mbm_fmtvel.pdf b/src/html/mbm_fmtvel.pdf
diff --git a/src/html/mbm_grd2arc.pdf b/src/html/mbm_grd2arc.pdf
diff --git a/src/html/mbm_grd2geovrml.pdf b/src/html/mbm_grd2geovrml.pdf
diff --git a/src/html/mbm_grd3dplot.pdf b/src/html/mbm_grd3dplot.pdf
diff --git a/src/html/mbm_grdcut.pdf b/src/html/mbm_grdcut.pdf
diff --git a/src/html/mbm_grdinfo.pdf b/src/html/mbm_grdinfo.pdf
diff --git a/src/html/mbm_grdplot.pdf b/src/html/mbm_grdplot.pdf
diff --git a/src/html/mbm_grdtiff.pdf b/src/html/mbm_grdtiff.pdf
diff --git a/src/html/mbm_grid.pdf b/src/html/mbm_grid.pdf
diff --git a/src/html/mbm_histplot.pdf b/src/html/mbm_histplot.pdf
diff --git a/src/html/mbm_makedatalist.pdf b/src/html/mbm_makedatalist.pdf
diff --git a/src/html/mbm_makesvp.pdf b/src/html/mbm_makesvp.pdf
diff --git a/src/html/mbm_multicopy.pdf b/src/html/mbm_multicopy.pdf
diff --git a/src/html/mbm_multidatalist.pdf b/src/html/mbm_multidatalist.pdf
diff --git a/src/html/mbm_multiprocess.pdf b/src/html/mbm_multiprocess.pdf
diff --git a/src/html/mbm_plot.pdf b/src/html/mbm_plot.pdf
diff --git a/src/html/mbm_route2mission.pdf b/src/html/mbm_route2mission.pdf
diff --git a/src/html/mbm_stat.pdf b/src/html/mbm_stat.pdf
diff --git a/src/html/mbm_utm.pdf b/src/html/mbm_utm.pdf
diff --git a/src/html/mbm_xbt.pdf b/src/html/mbm_xbt.pdf
diff --git a/src/html/mbm_xyplot.pdf b/src/html/mbm_xyplot.pdf
diff --git a/src/html/mbmakeplatform.pdf b/src/html/mbmakeplatform.pdf
diff --git a/src/html/mbminirovnav.pdf b/src/html/mbminirovnav.pdf
diff --git a/src/html/mbmosaic.pdf b/src/html/mbmosaic.pdf
diff --git a/src/html/mbnavadjust.pdf b/src/html/mbnavadjust.pdf
diff --git a/src/html/mbnavadjustmerge.pdf b/src/html/mbnavadjustmerge.pdf
diff --git a/src/html/mbnavedit.pdf b/src/html/mbnavedit.pdf
diff --git a/src/html/mbnavlist.pdf b/src/html/mbnavlist.pdf
diff --git a/src/html/mbneptune2esf.pdf b/src/html/mbneptune2esf.pdf
diff --git a/src/html/mbotps.pdf b/src/html/mbotps.pdf
diff --git a/src/html/mbpreprocess.html b/src/html/mbpreprocess.html
@@ -211,6 +211,9 @@ <H2>SYNOPSIS</H2>
 <B>--kluge-time-jumps</B>=<I>SECONDS</I>
 <BR>
 
+<B>--kluge-fix-7k-timestamps</B>=<I>TARGETOFFSET</I>
+<BR>
+
 <B>--kluge-ancilliary-time-jumps</B>=<I>SECONDS</I>
 <BR>
 
@@ -1056,6 +1059,17 @@ <H2>OPTIONS</H2>
 <DT><B>--kluge-time-jumps=</B><I>SECONDS</I>
 
 <DD>
+<DT><B>--kluge-fix-7k-timestamps=</B><I>TARGETOFFSET</I>
+
+<DD>
+This option was created to fix some Teledyne Reson T50 multibeam data (format 89) collected
+in 2024 with an MBARI Mapping AUV. The sonar ping timestamps jumped considerably (by as
+much as a day!!) while the ancillary nav, sensor depth, and attitude records maintained
+accurate timing. In good data the ping records will occur in the datastream with a fairly
+stable delay from the most recent ancillary records (0.7 seconds in this case). This
+option forces the pings records to have timestamps that have the target offset from the
+most recent ancillary records whenever the recorded offset magnitude is more than four 
+times the target offset.
 <DT><B>--kluge-ancilliary-time-jumps=</B><I>SECONDS</I>
 
 <DD>

diff --git a/src/html/mbpreprocess.pdf b/src/html/mbpreprocess.pdf
diff --git a/src/html/mbprocess.pdf b/src/html/mbprocess.pdf
diff --git a/src/html/mbps.pdf b/src/html/mbps.pdf
diff --git a/src/html/mbrollbias.pdf b/src/html/mbrollbias.pdf
diff --git a/src/html/mbrolltimelag.pdf b/src/html/mbrolltimelag.pdf
diff --git a/src/html/mbroutetime.pdf b/src/html/mbroutetime.pdf
diff --git a/src/html/mbsegygrid.pdf b/src/html/mbsegygrid.pdf
diff --git a/src/html/mbsegyinfo.pdf b/src/html/mbsegyinfo.pdf
diff --git a/src/html/mbsegylist.pdf b/src/html/mbsegylist.pdf
diff --git a/src/html/mbsegypsd.pdf b/src/html/mbsegypsd.pdf
diff --git a/src/html/mbset.pdf b/src/html/mbset.pdf
diff --git a/src/html/mbsslayout.pdf b/src/html/mbsslayout.pdf
diff --git a/src/html/mbstripnan.pdf b/src/html/mbstripnan.pdf
diff --git a/src/html/mbsvplist.pdf b/src/html/mbsvplist.pdf
diff --git a/src/html/mbsvpselect.pdf b/src/html/mbsvpselect.pdf
diff --git a/src/html/mbswath.pdf b/src/html/mbswath.pdf
diff --git a/src/html/mbswplspreprocess.pdf b/src/html/mbswplspreprocess.pdf
diff --git a/src/html/mbsystem.pdf b/src/html/mbsystem.pdf
diff --git a/src/html/mbsystem_formats.html b/src/html/mbsystem_formats.html
@@ -381,7 +381,7 @@
 <UL>
 <LI>Format name:          MBF_EM710RAW</LI>
 
-<LI>Informal Description: Kongsberg current multibeam vendor format</LI>
+<LI>Informal Description: Kongsberg 3rd generation multibeam vendor format</LI>
 
 <LI>Attributes:           Kongsberg EM122, EM302, EM710,
                       bathymetry, amplitude, and sidescan,

diff --git a/src/html/mbsystem_version.txt b/src/html/mbsystem_version.txt
@@ -1,2 +1,2 @@
-MB-System Version:  "5.8.1"
-MB-System Release Date:  "22 March 2024"
+MB-System Version:  "5.8.2beta05"
+MB-System Release Date:  "19 May 2024"
diff --git a/src/html/mbtiff2png.pdf b/src/html/mbtiff2png.pdf
diff --git a/src/html/mbtime.pdf b/src/html/mbtime.pdf
diff --git a/src/html/mbvelocitytool.pdf b/src/html/mbvelocitytool.pdf
diff --git a/src/html/mbvoxelclean.pdf b/src/html/mbvoxelclean.pdf
diff --git a/src/mbio/mb_define.h b/src/mbio/mb_define.h
@@ -38,7 +38,7 @@
 
 /* Define version and date for this release */
 #define MB_VERSION "5.8.2beta05"
-#define MB_VERSION_DATE "17 May 2024"
+#define MB_VERSION_DATE "19 May 2024"
 
 /* CMake supports current OS's and so there is only one form of RPC and XDR and no mb_config.h file */
 #ifdef CMAKE_BUILD_SYSTEM