Data Collection for GO-MARIE 2022

Bathymetry for Science onboard the R/V Marie Tharp (more information at the expedition page).

Main data collection tool

This tool opens a list of serial ports and logs the data to text files.

Install Python libraries

pip install absl-py pyserial colorama

Data manipulation tools

trim_water_csv.py

Opens a zip file (passed using the --input flag) and looks for a file inside the zip that the filename ends with _data.txt. Then opens the file, keeps a subset of the original columns and writes the data to an output CSV file (passed using the --output flag).

Example run:

C:\GitHub\marie-tharp-data-collection\tools> python trim_water_csv.py --input="D:\Downloads\204223_20220723_2222_subset.zip" --output="output.csv"
I0730 16:22:59.391295 23524 trim_water_csv.py:42] List of files in D:\Downloads\204223_20220723_2222_subset.zip
I0730 16:22:59.391295 23524 trim_water_csv.py:44] File: 204223_20220723_2222/
I0730 16:22:59.392293 23524 trim_water_csv.py:44] File: 204223_20220723_2222/204223_20220723_2222_annotations_profile.txt
I0730 16:22:59.392293 23524 trim_water_csv.py:44] File: 204223_20220723_2222/204223_20220723_2222_data.txt
I0730 16:22:59.392293 23524 trim_water_csv.py:44] File: 204223_20220723_2222/204223_20220723_2222_events.txt
I0730 16:22:59.392293 23524 trim_water_csv.py:44] File: 204223_20220723_2222/204223_20220723_2222_metadata.txt
I0730 16:22:59.392293 23524 trim_water_csv.py:54] Found input data file: 204223_20220723_2222/204223_20220723_2222_data.txt
I0730 16:22:59.393290 23524 trim_water_csv.py:77] Success!
I0730 16:22:59.393290 23524 trim_water_csv.py:78] Written 5 lines to output.csv.

Data from the original file (inside the zip):

Time	Conductivity	Temperature	Pressure	Chlorophyll a	Temperature	Dissolved O2 concentration	Sea pressure	Depth	Salinity	Speed of sound	Specific conductivity	Dissolved O2 saturation	Density anomaly
2022-07-23 22:22:03.938	0.0034761	3.4269714	10.1338205	5.2486572	4.4410000	345.8651123	0.0013208	0.0013101	0.0027279	1418.9885254	5.9121561	83.2099991	-0.0252890
2022-07-23 22:22:04.000	0.0031264	3.4262695	10.1372709	10.5589600	4.4410000	345.8656921	0.0047712	0.0047323	0.0024951	1418.9851074	5.3174953	83.2084579	-0.0254670
2022-07-23 22:22:04.063	0.0023884	3.4255066	10.1346855	19.6989746	4.4410000	345.8668213	0.0021858	0.0021680	0.0020143	1418.9807129	4.0623426	83.2067642	-0.0258765
2022-07-23 22:22:04.125	0.0036366	3.4245911	10.1437836	23.4371338	4.4410000	345.8649902	0.0112839	0.0111919	0.0028340	1418.9776611	6.1855803	83.2047729	-0.0251748

Data that the tool outputs:

Speed of sound	Temperature	Salinity	Conductivity	Density anomaly	Pressure
1418.9885254	3.4269714	0.0027279	0.0034761	-0.025289	10.1338205
1418.9851074	3.4262695	0.0024951	0.0031264	-0.025467	10.1372709
1418.9807129	3.4255066	0.0020143	0.0023884	-0.0258765	10.1346855
1418.9776611	3.4245911	0.002834	0.0036366	-0.0251748	10.1437836