merge with feature/proj-support (trndev < feature/proj-support); feat…

…ure/proj-support also merged w/ master

.github/workflows/github-actions-demo.yml

@@ -0,0 +1,18 @@
+name: GitHub Actions Demo
+run-name: ${{ github.actor }} is testing out GitHub Actions 🚀
+on: [push]
+jobs:
+  Explore-GitHub-Actions:
+    runs-on: ubuntu-latest
+    steps:
+      - run: echo "🎉 The job was automatically triggered by a ${{ github.event_name }} event."
+      - run: echo "🐧 This job is now running on a ${{ runner.os }} server hosted by GitHub!"
+      - run: echo "🔎 The name of your branch is ${{ github.ref }} and your repository is ${{ github.repository }}."
+      - name: Check out repository code
+        uses: actions/checkout@v4
+      - run: echo "💡 The ${{ github.repository }} repository has been cloned to the runner."
+      - run: echo "🖥️ The workflow is now ready to test your code on the runner."
+      - name: List files in the repository
+        run: |
+          ls ${{ github.workspace }}
+      - run: echo "🍏 This job's status is ${{ job.status }}."

CMakeLists.txt

@@ -152,6 +152,8 @@ if(buildOpenCV)
   add_subdirectory(src/photo)
 endif()
 if(buildTRN)
+  set(CMAKE_C_FLAGS "${CMAKE_C_FLAGS} -DTRN_USE_PROJ")
+  set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -DTRN_USE_PROJ")
   add_subdirectory(src/mbtrnframe)
   add_subdirectory(src/mbtrn)
   add_subdirectory(src/mbtrnav)
@@ -203,6 +205,7 @@ message("CMAKE_C_FLAGS: ${CMAKE_C_FLAGS}")
 message("CMAKE_CXX_FLAGS: ${CMAKE_CXX_FLAGS}")
 message("CMAKE_INSTALL_RPATH: ${CMAKE_INSTALL_RPATH}")
 message("CMAKE_MACOSX_RPATH: ${CMAKE_MACOSX_RPATH}")
+message(OTPS directory: ${otpsDir})
 
 # For debugging: print all set variables
 message("----------------------------------------------------------")

ChangeLog.md

@@ -1,4 +1,4 @@
----
+--
 ## MB-System ChangeLog File:
 
 This file lists changes to the source code of the MB-System open
@@ -22,7 +22,20 @@ or beta, are equally accessible as tarballs through the Github interface.
 ---
 ### MB-System Version 5.8 Releases and Release Notes:
 ---
-
+- Version 5.8.2beta15    October 1, 2024
+- Version 5.8.2beta14    September 6, 2024
+- Version 5.8.2beta13    August 23, 2024
+- Version 5.8.2beta12    August 22, 2024
+- Version 5.8.2beta11    August 19, 2024
+- Version 5.8.2beta10    August 16, 2024
+- Version 5.8.2beta09    August 4, 2024
+- Version 5.8.2beta08    July 27, 2024
+- Version 5.8.2beta07    June 27, 2024
+- Version 5.8.2beta06    June 13, 2024
+- Version 5.8.2beta05    May 19, 2024
+- Version 5.8.2beta04    May 13, 2024
+- Version 5.8.2beta02    May 1, 2024
+- Version 5.8.2beta01    April 29, 2024
 - **Version 5.8.1          March 22, 2024**
 - Version 5.8.1beta09    March 22, 2024
 - Version 5.8.1beta08    March 10, 2024
@@ -35,6 +48,228 @@ or beta, are equally accessible as tarballs through the Github interface.
 
 ---
 
+#### 5.8.2beta15 (October 1, 2024)
+
+Mbmakeplatform: Fixed problems with handling sensor add and sensor modify modes.
+
+Mbgrdviz, mbeditviz, mbnavadjust: Changed the mbview display of swath bounds for selected
+navigation to be optional rather than always displayed.
+
+Formats 58 (MBF_EM710RAW) and 59 (MBF_EM710MBA): Fixed preprocessing support for the 
+Kongsberg M3 multibeam. Added capability to use an MB-System platform file in place of
+the sensor offsets embedded in the logged multibeam files.
+
+Mbphotogrammetry: Fixed use of range bounds in filtering the photogrammetric bathymetry.
+
+#### 5.8.2beta14 (September 6, 2024)
+
+Mbphotomosaic: Removed unnecessary --correction-file-color option (redundant with --correction-file)
+
+mbm_grdplot: Fixed -G7 option for plotting images with geodetics defined in world files 
+rather than embedded as in GeoTiffs. Specifically allows use of png images with transparency.
+
+Formats 232 (MBF_WISSLR) and 233 (MBF_WISSLP): Fixed initial beam flagging by mbpreprocess
+for secondary sounding picks (when the lidar was operated in multipick mode)
+
+#### 5.8.2beta13 (August 23, 2024)
+
+Mbphotomosaic: Fixed use of the  --dark-image-ignore and  --dark-image-multiply options
+as parameters embedded in recursive imagelist files.
+
+#### 5.8.2beta12 (August 22, 2024)
+
+Mbnavadjustmerge: Fixed (again, this time hopefully for real) the --reimport-all-files 
+option so that large projects can be reimported with a single command. Added a 
+--reimport-survey option.
+
+#### 5.8.2beta11 (August 19, 2024)
+
+Mbnavadjustmerge: Fixed the --reimport-all-files option so that large projects can be
+reimported with a single command. Added a --reimport-survey option.
+
+#### 5.8.2beta10 (August 16, 2024)
+
+Mbnavadjustmerge: Added --reimport-file and --reimport-all-files options that reimport 
+swath files into an mbnavadjust project from the current processed versions of that files. 
+Each file is broken into the same sections as previously, regardless of any changes to the 
+settings for the maximum section length or the maximum number of soundings in a section.
+The original navigation and attitude data are also preserved, but the bathymetry is changed 
+to reflect the current processed values. This means that updates to the bathymetry editing 
+can now be brought into mbnavadjust projects.
+
+Format 71 (MBF_MBLDEOIH): Fixed a compression bug that occasionally resulted in corrupting
+the acrosstrack values of the outermost beams of pings when changed data are inserted into
+records using the mb_put_all() or mb_insert() functions. The only know manifestation of this
+bug was in importing swath data into mbnavadjust projects.
+
+Mbtrnpp: Fixed #ifdefs and Makefile.am files so that mbtrnpp can still be built with the
+old autoconf build system, albeit using GCTP for projections rather libproj.
+
+#### 5.8.2beta09 (August 4, 2024)
+
+mb7k2jstar: This program extracts Edgetech sidescan and subbottom data from Reson s7k 
+files and writes current format Edgetech Jstar format files identical to what current
+Edgetech sonars record. This functionality is needed only for MBARI Mapping AUV data from
+2004-2014, as MBARI was the only user of a payload controller software package named
+6046 from Reson that logged Reson 7125 multibeam and Edgetech FSAU sidescan/subbottom
+data in the same s7k files. Recognizing that reprocessing old Mapping AUV data requires
+this capability (and much of these data are now in public archives at MGDS and NCEI), we
+are moving mb7k2jstar back into src/utilities out of src/deprecated, so that it is always
+built as part of MB-System. Also, a bug causing seg faults with 2007 data has been fixed.
+
+Mbpreprocess: Added option --kluge-early-mbari-mapping-auv to mbpreprocess. This option 
+pertains only to Reson 7125 200 kHz multibeam data collected on the first MBARI Mapping 
+AUV from 2006 through 2009. Invoking this kluge triggers \fBmbpreprocess\fP to modify the 
+beam quality factors to be consistent with the later (>2009) standard for the original 
+bathymetry records in Reson s7k format data.
+
+Mbextractsegy: Fixed bug in extracting and plotting envelope function of subbottom data.
+
+General: Added macros to src/mbio/mb_define.h enabling the printing of byte values as a
+binary bitmask using fprintf(). To print a single byte as binary (e.g. "01010101") do 
+something like:
+	char value;
+	printf("Bitmask: "MB_PRINTF_BINARY_PATTERN_INT8"\n", MB_PRINTF_BYTE_TO_BINARY_INT8(value));
+Printing of larger int types has a similar form:
+	short value;
+	printf("Bitmask: "MB_PRINTF_BINARY_PATTERN_INT16"\n", MB_PRINTF_BYTE_TO_BINARY_INT16(value));
+	int value;
+	printf("Bitmask: "MB_PRINTF_BINARY_PATTERN_INT32"\n", MB_PRINTF_BYTE_TO_BINARY_INT32(value));
+	long long value;
+	printf("Bitmask: "MB_PRINTF_BINARY_PATTERN_INT64"\n", MB_PRINTF_BYTE_TO_BINARY_INT64(value));
+These macros are taken from 
+	https://stackoverflow.com/questions/111928/is-there-a-printf-converter-to-print-in-binary-format
+
+#### 5.8.2beta08 (July 27, 2024)
+
+Format 121 (MBF_GSFGENMB): Updated to use new version of libgsf (3.10) released by Leidos.
+The following change descriptions are from the libgsf 3.10 change summary:
+
+	Change request GSF_03-10_01
+	Support for ME70 sonars
+	11/8/2021 
+	Sean Donovan, Leidos 
+	Description:
+		Added GSF_SWATH_BATHY_SUBRECORD_ME70BO_SPECIFIC subrecord identifier. 
+		Added support for sonar under EM4 cases. 
+	Purpose:
+		To add support in GSF for the ME70 multibeam systems
+
+	Change request GSF_03-10_02
+	STIG Remediation to address vulnerabilities
+	3/12/2024
+	Dwight Johnson, NAVO
+	Description:
+		Various changes to safe memory allocation and usage throughout the encoding and 		
+		decoding processes
+	Purpose:
+		Improved Robustness
+
+	Change request GSF_03-10_03
+	Updates to KMALL ping level metadata
+	3/12/2024
+	Jonathon Beaudoin, Hydro Octave
+	Description:
+		Added new variables highVoltageLevelDB, sectorTrackingCorr_DB, and 
+		effectiveSignalLength_sec within the spare space of the gsfKMALLTxSector Struct. 
+		Added encoding and decoding logic for these values.
+	Purpose:
+		To support backscatter processing
+
+	Change request GSF_03-10_04
+	Resolved bug surrounding network transmission of range samples
+	3/12/2024
+	Jonathon Beaudoin, Hydro Octave
+	Description:
+		Missing htons call added to range sample processing
+	Purpose:
+		Bug Fix
+
+	Change request GSF_03-10_05
+	Added TVG DB to bathy ping structure
+	3/12/2024
+	Jonathon Beaudoin, Hydro Octave
+	Description:
+		Added new array variable TVG_DB to multibeam ping struct. Added encoding and 
+		decoding logic for this value.
+	Purpose:
+		To support backscatter processing
+
+MBnavadjust: Added autosaving the last version of a project file immediately before 
+beginning to write a new file. Also fixed some inconsistencies in the UI.
+
+#### 5.8.2beta07 (June 27, 2024)
+
+Mbm_trnplot: Added extraction of TRN localization estimates in longitude and latitude.
+
+Mbtrnpp: Now includes longitude and latitude values of TRN localization estimates into
+the log file (in addition to the coordinate reference system used for the reference 
+map).
+
+Mbgrdviz: Fixed importation of non-csv raw site files.
+
+Formats 88 and 89 (MBF_RESON7KR and MBF_RESON7K3): Change to allow pings to be valid if
+a BeamGeometry record has been read earlier in the file (as opposed to having a 
+BeamGeometry record for every ping).
+
+Formats 88 and 89 (MBF_RESON7KR and MBF_RESON7K3): Fixed problem calculating sample times
+for attitude data in s7k 1016 Attitude data records.
+
+#### 5.8.2beta06 (June 13, 2024)
+
+MBgrid and mbmosaic: Added an option to generate grids and mosaics in a projected 
+coordinate system defined as a Local Transverse Mercator (LTM) projection with the  origin 
+at the center of the grid or mosaic. 
+
+MBgrdviz, mbeditviz, mbnavadjust: The mbview visualization library now displays grids
+defined in geographic coordinates (longitude and latitude) using a Local Transverse
+Mercator projection with the origin at the center of the grid or mosaic. This replaces the
+prior use of UTM projections, which introduced rotation and distortion when the grid was
+located far from the center of the UTM zone.
+
+MBtrnpp: and TRN: Changed TerrainNav, supporting libraries, and the program mbtrnpp to
+calculate projections using the Proj package rather than the GCTP package.
+
+MBtrnpp: Now works with reference topography models defined in a Local Transverse 
+Mercator (LTM) projection.
+
+Mbm_trnplot: augmented to allow specifying the CRS of the reference topoography so
+that a Local Transverse Mercator (LTM) projection can be used.
+
+#### 5.8.2beta05 (May 19, 2024)
+
+MBextractsegy: changed calculation of section plot bounds to more consistently catch the
+seafloor arrival within the plot.
+
+MBpreprocess: fixed initialization of the --kluge-fix-7k-times option.
+
+Docker image: updated documentation in the Docker directory.
+
+Formats 58 (MBF_EM710RAW) and 59 (MBF_EM710MBA):  Removed an errant debug message that
+printed out information when reading height datagrams.
+
+#### 5.8.2beta04 (May 13, 2024)
+
+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
+
+Mbroutetime: Now works with the recently changed route file format.
+
+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.
+
+#### 5.8.2beta02 (May 1, 2024)
+
+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).
+
+#### 5.8.2beta01 (April 29, 2024)
+
+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.
+
+MB-System Docker Container: Improved Docker documentation included in the Docker directory.
+
 #### 5.8.1 (March 22, 2024)
 
 CMake build system: Fixed ability to set OTPS location in cmake build system.