The raw data is stored in binary files which have a certain (proprietary) structure. The OMG commands are able to read these raw data files and extract the required information to an OMG-format. So in fact the raw data gets reorganized to our desires. The results are several other files (the raw data file remains untouched off course) of which the .merged file will be used later in the pipeline.
First a proper directory structure is created. You should store raw data in a folder called raw/sub_dir/. You will have create the raw/sub_dir manually, use the mkdir command to make a new folder. Then folders merged/sub_dir, decnav/sub_dir and if you do some things with backscatter, ss/sub_dir are created by the unravel script. The logic behind this folder comes clear in the following steps.
It is the omg convention to name the sub directories to the Julian day. You get the Julian day simply by typing julian yyyy-mm-dd on the command line. Finally it will look as follows:
projectname
raw
JDXXX
merged
JDXXX
decnav
JDXXX
ss
JDXXX
Often the data raw data is compressed. It’s unzipped by:
gunzip raw_data_file.all.gz
Simrad has a proprietary file format, the .all files. Unravelling is, unlike Reson data, done with just one command, the RT (read telegram) command:
RT –v4 –force_swap –em3002 –prefix raw/sub_dir –suffix suffix.all –line linenumber.all –out merged/subdir/
-v4
version 4, always use this
-force_swap
Linux and windows computer have different byte orders. The force_swap command takes this into account. Although the latest versions of RT are automated I believe this command isn’t really necessary anymore, still wouldn’t hurt using it.
-em3002
specify your sonar; em3002 em1002, elac2 …
-prefix
Give it the Julian day
The operator can configure the raw data filenames, in most cases they look like this:
number_date_time_ship.all --> 0001_20060714_142506_Titanic.all
The prefix, suffix and line options are use to name and organize the files RT will create
-suffix
_ship.all e.g. _Titanic.all
-line
number_date_time e.g. 0001_20060714_142506
-out
Direct to the merged/sub_dir folder
If you have successfully unravelled the data you can join back to the final steps which are the same for Reson and Simrad. Note that when you are using a script you might have to adjust the sonar type or add the water column option if applicable (-unpack_watercol).
We choose to decimate the position fixes and get rid of the redundant data.
appendNav –skip 10 –comp decnav/sub_dir/filename.decnav merged/sub_dir/filename.nav
-skip x
skipping every x fixes
-comp
define the path and filename of the new decnav file
merged/
direct to the merged-file
Merge the attitude. To perform ray tracing you will need to add sound velocity profiles (svp). The svp are ascii and need a be formatted to OMG-standard. If your not using a svp use the skip_raytrace option. In that case you can even choose to specify the sound velocity, otherwise the program will use the sound velocity provide in the .all-file.
newMergeAtt –in merged/sub_dir/filename.merged
Always add either:
-svp file1.svp file2.svp …..
or:
-skip_raytrace
Other options:
-velocity xxxx.x
-interpolate –nearest_int_time
-interpolate –last_observed
-interpolate –next_observed
-rules rules.txt
specify time based rules on how to interpolate
Merge the navigation data to the bathymetry:
mergeNav –use_params –delay x.x merged/sub_dir/filename.merged
-use_params
now it incorporates the .param file with the offsets. Instead of such a file you can also specify it separately. Offsets of nav source w.r.t. reference point:
-ahead x.x
-right x.x
-below x.x
-declin
if you want to add the magnetic declination
-delay
delay in seconds (result from patch test, is not already applied in acquisition software)
Now you have unravelled everything and are you ready to clean it in swathed with:
swathed merged/JD???/filename(s).merged