Ocean Networks Canada (ONC) maintains several deep water nodes with ADCP current meters in the Strait of Georgia. This page describes the scripts used to process their data.

## MATLAB Scripts for ONC Data¶

Loading and processing of the observational data from the ONC VENUS Central, East and Delta nodes is done in MATLAB scripts written by Dr. Rich Pawlowicz. The processing is done in three parts and is tailored for each deployment at each node.

### Processing Scripts¶

• The first part is GET_DATA_fun.m This script will get the data that is directly output from the ADCP. It does this for the two days before the day indicated. It will put this data in a directory at pth/raw/ and organize it by year and month. This function calls a script written by Marlene Jeffries at Ocean Network Canada getSoGAdcpDataMay15_mod. This script contains many functions that are used to ultimately retrieve the raw data from the ONC website.

• The next step is to run GET_DEPL_fun.m goes through all the data in the raw directory gathered by GETDATA_fun and bins it into 30 minutes bins. .

• Lastly, the bulk of the processing is done in LTIM_fun.m. This script filters out the tides, corrects the angles for the velocities to get major axis in the direction of the flood current.

• When running these scripts for a single day of data at a time to have daily comparisons a few modifications have to be done to keep the scripts running. First of all, GETDEPL_fun creates a new deployment file with the new updated raw data that was loaded by GETDATA_fun however LTIM_fun needs only one mat file per deployment in the directory where it looks. The compare_daily functions works helps seamlessy join the new update deployment file and the previous deployment file.

### New deployment¶

Once or twice a year ONC performs maintenance on the nodes that involves bringing the ADCP package to the surface and redeploying the same or a different sensor to the bottom a few hours later. Each deployment has its own unique set of data and metadata including:

• date/time range (resolved to the hour)

• sensor serial number (also known as id)

• number of data bins

• data bin size

• data bin 1 distance

• vertical offset

• rotation angle

Values for those data and metadata are required in order for the automated daily download and processing of the ADCP data to be restarted following a new deployment. Those values have to be added to arrays in the GETDATA_fun.m, GETDEPL_fun.m, and LTIM_fun.m Matlab scripts (details below). Some of the values must be determined by graphical analysis of data from the new sensor deployment, and there must be enough data available for that analysis that the tidal signal can be averaged out. So, at least a week’s data must be collected after a new deployment before the graphical analysis can be done. Once the analysis has been completed the data since the beginning of the deployment must be re-processed with the newly obtained sensor data and metadata values.

As of October 2015, downloading that data from ONC is accomplished via a Matlab script (getSogAdcpData*.m) provided after each deployment by Marlene Jefferies of ONC.

The notes that follow were written during the process of restarting the daily download automation following the new deployments at the end of August 2015.

#### Obtain and Modify the getSogAdcpData.m Script from ONC¶

Obtain the new version of the getSogAdcpData.m Matlab script for the deployment from Marlene Jefferies at ONC, and store it in /ocean/dlatorne/MEOPAR/ONC_ADCP/ with the deployment date added to the file name; e.g. getSogAdcpData_2Sep2015.m.

Change the email and userId lines near line 180 to the email address and 5-digit ONC user id of the user that owns the automation cron job, for example:

p.addParamValue('email','dlatornell@eos.ubc.ca', @ischar);


The LocationName comment blocks starting at about line 50 in the getSogAdcpData.m script provide the site name (e.g. VIP-13) and sensor serial number (e.g. 8497) for all of the deployments to date. Those values for the most recent deployments are required to update the GETDATA_fun.m and GETDEPL_fun.m scripts. Also required are the end date/time for the previous deployment, and the start date/time for the present deployment from the switch statement at about line 430.

#### Update the GETDATA_fun.m Script¶

Add the new deployment numbers, start date/times, and sensor serial numbers to the history arrays in the switch statement that starts at about line 35 in the copy of private-tools/ONC-ADCP/GETDATA_fun.m that is symlinked into /ocean/dlatorne/MEOPAR/ONC-ADCP/. The history arrays also require deployment end date/times; choose a value in the future beyond the expected duration of the deployment.

switch nodloc,
case 'east',
node='SOG-East-Node';
history=[...
01    2007 10 19 00     2008 09 25 00 8497;
...
2     2015 03 31 22     2015 08 27 16 8497;
13    2015 08 27 22     2016 12 31 00 8497];  % or present

...

case 'central',
node='SOG-Central-Node';
history=[...
01    2008 09 24 00     2009 09 27 00 8580;
...
12    2014 09 20 02     2015 08 30 15 8580;
13    2015 08 31 02     2016 12 31 00 8580];  % or present

...

case 'ddl',
node='SOG-Delta-Node';
history=[...
08    2013 10 23 17     2014 03 06 17 2940;   % DDL 148m
02    2014 03 08 21     2014 09 20 18 17955;  % BBL-SG-02 at 142m
03    2014 09 22 00     2015 08 28 15 17955;  % BBL-SG-03 at 149m
04    2015 08 30 19     2016 12 31 00 17955]; % BBL-SG-04 at ???m

depname={'DDL-','BBL-SG-','BBL-SG-','BBL-SG-'};


Finally, update the name used to call the getSogAdcpData.m script at the end of the GETDATA_fun.m script (about line 173). The update made for the late-August 2015 deployments was:

getSogAdcpData_2Sep2015('locationName',node,'siteName',deploy,'deviceName',instr,...
'dateStart',sdate,'dateEnd',edate,'maxTimeout',120,...
'outputdirectory',outdir);


Run the GETDATA_fun.m script to download the raw data for each node for the days from the deployment to present. That can be accomplished by running Matlab in command-line mode on salish:

$cd /ocean/dlatorne/MEOPAR/ONC_ADCP/$ matlab -nodesktop -nodisplay
...


The data download takes about 10 minutes per day requested, so it is advisable to start Matlab in 3 separate terminal sessions and run commands like the above for each of the nodes: central, east, and ddl. The GETDATA_fun.m script handles breaking the requested number of days into 7 day chunks (the maximum that the ONC hardware can handle). The getSogAdcpData*.m script downloads the data into the path/mode/raw/ directory; i.e. /ocean/dlatorne/MEOPAR/ONC_ADCP/central/raw/ in the example above.

The get_VENUS_ADCP_raw.cron.sh and get_VENUS_ADCP_raw.m scripts can be used to automate daily downloading of the raw data during the period required to obtain enough data to complete the analysis required to get the variable values to facilitate fully automated processing.

#### Update the GETDEPL_fun.m Script¶

The GETDEPL_fun.m script must be updated with the same deployment numbers, start date/times, and sensor serial numbers that were added to the GETDATA_fun.m script. Also required are the number of bins, the bin size, and the bin 1 distances values from one of the sensor metadata files that is generated for each download request. The easiest way to obtain those values is to follow the link to the metadata HTML file that is included in the download completion email message generated by the ONC system. Add those values to the history arrays in the switch statement that starts at about line 22 in the copy of private-tools/ONC-ADCP/GETDEPL_fun.m that is symlinked into /ocean/dlatorne/MEOPAR/ONC-ADCP/. The history arrays also require vertical offset values for the deployment; use the same value as for the previous deployment to start with, it will be tuned later.

switch nodloc,
case 'east',
node='SOG-East-Node';
history=[...                         %  ID  #bins binsize bin1distance (one that 'best' works) offset
01    2007 10 19 00     2008 09 25 00 8497  85 2 6.14 0;
...
2     2015 03 31 22     2015 12 31 00 8497  85 2 6.39 +3;
13    2015 08 27 22     2016 12 31 00 8497  85 2 6.40 +3];

...

case 'central',
node='SOG-Central-Node';
history=[...
01    2008 09 24 00     2009 09 27 00 8580 38 8 12.47 0;
...
12    2014 10 01 00     2015 12 31 00 8580 60 5 9.24  0;   % <- change in parameters here (same VIP)
13    2015 08 31 02     2016 12 31 00 8580 60 5 9.25  0];

...

case 'ddl',

node='SOG-Delta-Node';
history=[...
08    2013 10 23 16     2014 03 06 17 2940  75  2    4.3  0;   % DDL 148m
02    2014 03 08 21     2014 09 20 18 17955 115 1.33 3.96 0;  % BBL-SG-02 at 142m
03    2014 09 22 00     2015 12 31 00 17955 115 1.33 3.96 0; % BBL-SG-03 at 149m
04    2015 08 30 19     2016 12 31 00 17955 115 1.33 3.96 0]; % BBL-SG-04 at 147m

depname={'DDL-','BBL-SG-','BBL-SG-','BBL-SG-'};


#### Update the LTIM_fun.m Script¶

The LTIM_fun.m script must be updated with the rotation angles of the ADCPs for the new deployments. Initially the angles are set to the same values as for the previous deployments so that the LTIM_fun.m script can be run.

The updates for the late-August 2015 deployments are highlighted below:

switch nodloc,
case 'central',
rotang=[0;  % VIP 01
22;  %  02
...
58+180; % 12- v2
58+180; % 13
]-61;

...

case 'east',
rotang=[57;
50;  %  03
...
72;  % east2
72;  % 13
]-106;

...

case 'ddl',
rotang=[-60;     % DDL-08
35;   % BBL-SG-02
-20;  % BBL-SG-03
-20;  % BBL-SG-04
];


After at least 7 to 10 days of data have been downloaded and processed by the GETDEPL_fun.m script, the LTIM_fun.m script will be run interactively to to produce plots that will allow the instrument rotation angles for the deployment to be determined. Once that has been done the values highlighted above will be updated.

### Changing users¶

If you will be running the processing in a new directory for the first time there are a couple things to change in order to facilitate the transitions.

1. In compare_daily.m change the path to be where you want everything to be saved. Many extra files will appear in this directory every time you run the scripts.

1. Make an account on http://www.oceannetworks.ca/information to get userId. In getSoGAdcpDataMay15_mod.m insert your email and userId at lines 173 and 174 of the script. You will receive an email every time you load raw data from the website.

1. In GET_DATA_fun change the firstdate variable to be at least 3 days before the lastdate. This is because the filter length in LTIM_fun needs at least that much data for the processing.

## Setup of the /ocean/ ONC ADCP Data Filespace¶

This section describes the setup of the storage filespace on /ocean/ containing the accumulated raw and processed ONC ADCP data. Those data are from the Strait of Georgia Central, East, and Delta Dynamics Laboratory (DDL) nodes. Also described in this section is the software automation that updates those data daily with the observations from the previous day.

The data and processing scripts are stored in /ocean/dlatorne/MEOPAR/ONC_ADCP/. The accumulated, processed data for the 3 nodes are in the files:

• /ocean/dlatorne/MEOPAR/ONC_ADCP/ADCPcentral

• /ocean/dlatorne/MEOPAR/ONC_ADCP/ADCPddl

• /ocean/dlatorne/MEOPAR/ONC_ADCP/ADCPeast

The raw data downloaded from ONC are in directory trees organized by year and month number; e.g. 2015/07/ in the directories:

• /ocean/dlatorne/MEOPAR/ONC_ADCP/central/raw/

• /ocean/dlatorne/MEOPAR/ONC_ADCP/ddl/raw/

• /ocean/dlatorne/MEOPAR/ONC_ADCP/east/raw/

The other files in the /ocean/dlatorne/MEOPAR/ONC_ADCP/ tree are the processing scripts, sensor deployment data files, etc. Many of those files are symlinked from version controlled files in the private-tools.

### Preparing the /ocean/dlatorne/MEOPAR/ONC_ADCP/ Filespace¶

• Create the directory and make it group writable for the sallen group:

$mkdir /ocean/dlatorne/MEOPAR/ONC_ADCP$ cd /ocean/dlatorne/MEOPAR/ONC_ADCP
$chgrp sallen$ chmod g+w .

• Copy the accumulated-to-date processed data files into the filespace:

$cp --preserve=timestamps /ocean/mdunn/MEOPAR/analysis/Muriel/TidalEllipseData/Nodes/ADCPcentral.mat ./$ cp --preserve=timestamps /ocean/mdunn/MEOPAR/analysis/Muriel/TidalEllipseData/Nodes/ADCPddl.mat ./
$cp --preserve=timestamps /ocean/mdunn/MEOPAR/analysis/Muriel/TidalEllipseData/Nodes/ADCPeast.mat ./  • Create directories for the raw data and per-node processing files, and make them group writable for the sallen group: $ mkdir central ddl east
$chgrp sallen central ddl east$ chmod g+w cental ddl east

• Symlink the historic sensor deployment data files for each node into their respective directories:

$cd central$ for n in {01..10}; do
> ln -s /data/dlatorne/MEOPAR/private-tools/ONC_ADCP/central/DEPL${n}*.mat > done$ cd ../ddl
$for n in {1..2}; do > ln -s /data/dlatorne/MEOPAR/private-tools/ONC_ADCP/ddl/DEPL0${n}*.mat
> done

$cd ../east$ for n in {01..12}; do
> ln -s /data/dlatorne/MEOPAR/private-tools/ONC_ADCP/east/DEPL${n}*.mat > done$ cd ..

• Copy the current sensor deployment data files for each node into their respective directories:

$cp --preserve=timestamps /ocean/mdunn/MEOPAR/analysis/Muriel/TidalEllipseData/Nodes/central/DEPL11VIP-12-11.mat central/$ cp --preserve=timestamps /ocean/mdunn/MEOPAR/analysis/Muriel/TidalEllipseData/Nodes/ddl/DEPL03BBL-SG-03-03.mat ddl/
$cp --preserve=timestamps /ocean/mdunn/MEOPAR/analysis/Muriel/TidalEllipseData/Nodes/east/DEPL13VIP-02-13.mat east/  • Copy the accumulated-to-date raw data file trees for each node into their respective directories and make the directories group writable for the sallen group: $ mkdir central/raw
$chgrp sallen central/raw$ cp -r --preserve=timestamps /ocean/mdunn/MEOPAR/analysis/Muriel/TidalEllipseData/Nodes/central/raw/2015 central/raw/
$find central/raw -type d | xargs chmod g+w$ mkdir ddl/raw
$chgrp sallen ddl/raw$ cp -r --preserve=timestamps /ocean/mdunn/MEOPAR/analysis/Muriel/TidalEllipseData/Nodes/ddl/raw/2015 ddl/raw/
$find ddl/raw -type d | xargs chmod g+w$ mkdir east/raw
$chgrp sallen east/raw$ cp -r --preserve=timestamps /ocean/mdunn/MEOPAR/analysis/Muriel/TidalEllipseData/Nodes/east/raw/2015 east/raw/
$find east/raw -type d | xargs chmod g+w  • Create symlinks to the version-controlled processing scripts: $ ln -s /data/dlatorne/MEOPAR/private-tools/ONC_ADCP/compare_daily.m
$ln -s /data/dlatorne/MEOPAR/private-tools/ONC_ADCP/GETDATA_fun.m$ ln -s /data/dlatorne/MEOPAR/private-tools/ONC_ADCP/GETDEPL_fun.m
$ln -s /data/dlatorne/MEOPAR/private-tools/ONC_ADCP/LTIM_fun.m$ ln -s /data/dlatorne/MEOPAR/private-tools/ONC_ADCP/get_VENUS_ADCP.m
$ln -s /data/dlatorne/MEOPAR/private-tools/ONC_ADCP/get_VENUS_ADCP.cron.sh  • Copy the ONC-provided data download script into the filespace: $ cp --preserve=timestamps /ocean/mdunn/MEOPAR/analysis/Muriel/TidalEllipseData/Nodes/getSogAdcpDataMay15_mod.m ./


TODO: That script should be symlinked from a version controlled copy

• Create a matlab function in get_VENUS_ADCP.m to run compare_daily.m for each node:

function get_VENUS_ADCP
% Run the compare_daily.m script for each ONC VENUS node of interest
% using Rich Pawlowicz's scripts.

compare_daily(date, 'central', 2)
compare_daily(date, 'ddl', 2)
compare_daily(date, 'east', 2)
end

• Create a bash script called get_VENUS_ADCP.cron.sh for cron to execute to run get_VENUS_ADCP.m:

# Download and process VENUS nodes ADCP data for the previous day
# using matlab scripts written by Muriel Dunn and Rich Pawlowicz.
#

• Make get_VENUS_ADCP.cron.sh owner and group executable:
$chmod ug+x get_VENUS_ADCP.cron.sh  • Add a line to the crontab on salish to execute get_VENUS_ADCP.cron.sh daily: OCEAN_MEOPAR=/ocean/dlatorne/MEOPAR 0 10 * * *${OCEAN_MEOPAR}/ONC_ADCP/get_VENUS_ADCP.cron.sh