RBR-CTD-Processing

This repository is deprecated. For RBR data processing please use https://github.com/IOS-OSD-DPG/IOS-CTD-Batch-Processing

To process raw RBR CTD data in Python. The main reference for this routine is Halverson et al. (2017).

RBR_Processing.py is deprecated and has been replaced by RBR_CTD_IOS.py.

RBR_CTD_IOS.py contains the following processing steps, which are accompanied by before/after plots.

• Export raw data from .rsk or .xlsx to .csv files

• Create metadata dictionary

• Prepare CTD_DATA.csv with 6 line headers for IOSShell

• Plot and check profile locations

• Plot first-order pressure differences to check need for zero-order hold

• (If needed) Correct for zero-order holds by replacing holds with NaNs or with an interpolated value

• (If needed) Correct for any time offsets in casts by adding a correction value in units of hours

• (If needed) CALIB: Pressure/Depth correction if there are negative pressure values with corresponding conductivity values above about 30 mS/cm

• CLIP: Remove measurements near sea surface and bottom

• FILTER: Apply a low pass filter to pressure, temperature, conductivity, and fluorescence (if available)

• SHIFT: Shift conductivity and recalculate salinity

• SHIFT: Shift oxygen saturation

• DERIVE: Derive oxygen concentration in mL/L and umol/kg from oxygen saturation following SCOR WG 142

• DELETE: Remove pressure reversals

• BINAVE: Average the data into 1-dbar bins

• (If needed) Remove select channels from select casts if the data are useless

• EDIT: Apply final editing, including converting conductivity units from mS/cm to S/m

• Prepare .ctd files following the IOS Header file ASCII format

Requirements

• Python >= 3.8
• pyrsktools >= 1.1.1
• Hakai ocean-data-parser package for converting oxygen saturation: https://github.com/HakaiInstitute/ocean-data-parser

References

Halverson, M., Jackson, J., Richards, C., Melling, H., Brunsting, R., Dempsey, M., Gatien, G., Hamilton, A., Hunt, B., Jacob, W., and Zimmerman, S. 2017. Guidelines for processing RBR CTD profiles. Can. Tech. Rep. Hydrogr. Ocean Sci. 314: iv + 38 p.

Bittig Henry, Körtzinger Arne, Johnson Ken, Claustre Herve, Emerson Steve, Fennel Katja, Garcia Hernan, Gilbert Denis, Gruber Nicolas, Kang Dong-Jin, Naqvi Wajih, Prakash Satya, Riser Steven, Thierry Virginie, Tilbrook Bronte, Uchida Hiroshi, Ulloa Osvaldo, Xing Xiaogang (2018). SCOR WG 142: Quality Control Procedures for Oxygen and Other Biogeochemical Sensors on Floats and Gliders. Recommendations on the conversion between oxygen quantities for Bio-Argo floats and other autonomous sensor platforms. https://doi.org/10.13155/45915