Bathymetry for Science onboard the R/V Marie Tharp (more information at the expedition page).
This tool opens a list of serial ports and logs the data to text files.
pip install absl-py pyserial coloramaOpens 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 |