SeaBird recently published python code for Fathom, intended to replace their acquisition software. As far as we know, these modules and scripts have similar if not identical functionality to how SeaBird has been working on SeaSave.
In a style similar to odf_process_all, have a workflow for the SeaBird standard as described in the SBEDataProcessing manual.
(Page 19)
[ ] 2. Data Conversion
Convert raw data to a .cnv file, selecting ASCII as
data conversion format. Converted data includes:
• pressure, temperature, and conductivity
• (if applicable) dissolved oxygen current and
dissolved oxygen temperature (SBE 13 or 23);
dissolved oxygen signal (SBE 43);
dissolved oxygen phase delay and thermistor
voltage (SBE 63)
• (if applicable) light transmission, pH,
fluorescence, etc.
[ ] 3. Filter
Low-pass filter pressure to increase pressure
resolution for Loop Edit, and low-pass filter
temperature and conductivity to smooth high
frequency data.
[ ] 4. Align CTD
Advance conductivity, temperature, and oxygen
relative to pressure, to align parameters in time.
This ensures that calculations of salinity, dissolved
oxygen, and other parameters are made using
measurements from same parcel of water.
[ ] 5. Cell Thermal Mass
Perform conductivity cell thermal mass correction if
salinity accuracy of better than 0.01 PSU is desired in
regions with steep gradients.
Note: Do not use Cell Thermal Mass for freshwater
data.
[ ] 6. Loop Edit
Mark scans where CTD is moving less than minimum
velocity or traveling backwards due to ship roll.
[ ] 7. Derive(EOS-80, Practical Salinity)
Compute:
• Practical Salinity, density, and other parameters
• oxygen from oxygen current and oxygen
temperature (SBE 13 or 23); oxygen signal
(SBE 43); or oxygen phase delay and thermistor
voltage (SBE 63)
Note that input file must include conductivity,
temperature, and pressure.
SeaBird recently published python code for Fathom, intended to replace their acquisition software. As far as we know, these modules and scripts have similar if not identical functionality to how SeaBird has been working on SeaSave.
In a style similar to
odf_process_all, have a workflow for the SeaBird standard as described in the SBEDataProcessing manual.(Page 19)
Convert raw data to a .cnv file, selecting ASCII as data conversion format. Converted data includes: • pressure, temperature, and conductivity • (if applicable) dissolved oxygen current and dissolved oxygen temperature (SBE 13 or 23); dissolved oxygen signal (SBE 43); dissolved oxygen phase delay and thermistor voltage (SBE 63) • (if applicable) light transmission, pH, fluorescence, etc.
Low-pass filter pressure to increase pressure resolution for Loop Edit, and low-pass filter temperature and conductivity to smooth high frequency data.
Advance conductivity, temperature, and oxygen relative to pressure, to align parameters in time. This ensures that calculations of salinity, dissolved oxygen, and other parameters are made using measurements from same parcel of water.
Perform conductivity cell thermal mass correction if salinity accuracy of better than 0.01 PSU is desired in regions with steep gradients. Note: Do not use Cell Thermal Mass for freshwater data.
Mark scans where CTD is moving less than minimum velocity or traveling backwards due to ship roll.
Compute: • Practical Salinity, density, and other parameters • oxygen from oxygen current and oxygen temperature (SBE 13 or 23); oxygen signal (SBE 43); or oxygen phase delay and thermistor voltage (SBE 63) Note that input file must include conductivity, temperature, and pressure.
(optional) Compute thermodynamic properties based on TEOS-10.
Average data into desired pressure or depth bins.
Plot data (profiles)