| Depricated ... |
This repository is only provided as a historical checkpoint. It was a collection of old scripts and routines that are no longer relevant and may be removed or deleted in the future. Do not anticipate updates, repairs, or for the code to even work
Collection of utilites for processing and visualizing common data that is gathered during field cruises.
- SCS Data
- CTD Data
- UnderWay Data
- extrapolate all variables to surface from chosen depth and resave.
TODO:
- From discrete Oxygen/Salinity Calibration/Characterization measurements
- Add CF/COARDS netCDF routines
- From Nutrient Data (with bottle data)
- Routines have been tested with python - 3.6
- Output is EPIC Format netcdf
Help Documentation:
usage: Nut_ncgen.py [-h] CruiseID btlpath nutpath output config_file_name
Merge and archive nutrient csv data and bottle data
positional arguments:
CruiseID provide the cruiseid
btlpath full path to .btl_report
nutpath full path to nutrient csv file
output full path to output folder (files will be generated there
config_file_name full path to config file - nut_config.yaml
optional arguments:
-h, --help show this help message and exit
Long example of usage:
python Nut_ncgen.py DY1707 /Users/bell/ecoraid/2017/CTDcasts/dy1707l1/working/dy1707l1.report_btl
/Users/bell/ecoraid/2017/CTDcasts/dy1707l1/working/DiscreteNutrients/DY1707\ Nutrient\ Data.csv
/Users/bell/ecoraid/2017/CTDcasts/dy1707l1/working/ /Users/bell/Programs/Python/EcoFOCI_AtSea/config_files/nut_uml_epickeys.yaml
The config file is a YAML formatted file that specifies the variables and attributes of the netcdf file. There are many examples in the config_files directory herein.
- From upcast Bottle Data
- Routines have been tested with python - 3.6
- Output is EPIC Format netcdf
Routine to convert GPGGA gps data to gpx files for later processing into shape files. If data and plots for the Underway System of a noaa vessel is wanted, using SAMOS data from Florida State University is a better option. (erddap)[https://coastwatch.pfeg.noaa.gov/erddap/search/index.html?page=1&itemsPerPage=1000&searchFor=samos]
Various options to plot ctd profiles assuming epic style variable names. These are some of the most commonly desired plots to look at.
usage python CTD_plot.py {full/path/to/file.nc} -{plotflag}
plotflag options:
-h, --help show this help message and exit
-TSvD, --TSvD Temperature, Salinity, SigmaT vs depth
-OxyFluor, --OxyFluor
Temperature, Oxygen, Fluorometer vs depth
-ParTurbFluor, --ParTurbFluor
PAR, Turbidity, Fluorometer vs depth
-ParFluor, --ParFluor
PAR, Fluorometer vs depth
-TurbFluor, --TurbFluor
Turbidity, Fluorometer vs depth (common for only Eco
-ParTransFluor, --ParTransFluor
Transmissometer, Turbidity, Fluorometer vs depth
(common package for EMA)
-TransTurbFluor, --TransTurbFluor
Transmissometer, Turbidity, Fluorometer vs depth
(common package for EMA)
-TransFluor, --TransFluor
Transmissometer, Fluorometer vs depth (common package
for EMA)
-has_secondary, --has_secondary
Flag to indicate plotting secondary values too
Plots maps in different formats (kml, png, svg, geojson) of cruises in Pavlof database
usage python CruiseMap.py {cruiseid} -{filetype_flag}
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