Welcome to caldip’s documentation!

caldip is a Python package for calibration dip analysis of oceanographic instruments. It provides tools for processing, analyzing, and visualizing data from calibration dips performed with CTD profiles and multiple instrument types including MicroCATs and RBR thermistors.

For recommendations or bug reports, please visit https://github.com/ocean-uhh/caldip/issues/new

Getting started

• Installation
  • Option 1: Clone this repository
  • Option 2: Install with pip (or uv)
• Quickstart: single cast
  • Prerequisites
  • Directory structure
  • Step 1 — Generate a stub YAML
  • Step 2 — Generate the interactive plot
  • Step 3 — Generate statistics
  • Choosing the CTD sensor (--ctd-sensor)

Users guide

• Running caldip
  • The main commands
  • caldip plot
    • Inspecting a bottle stop in the plot
  • caldip stats
    • Choosing the CTD sensor
  • caldip report
    • Checking finality (--check)
  • Batch processing a cruise
    • Template
    • Switching CTD sensor
    • Adding a new cast
• YAML Configuration Reference
  • Directory structure
  • Generating a stub
  • Field reference
    • Cast metadata
    • Position and depth
    • Timing
    • CTD reference
    • Instruments list
  • Minimal example (SBE37 hex files)
  • Example with RBR thermistors and clock offset
• Outputs
  • Interactive plot
    • Zooming in on a bottle stop
  • Statistics
    • Machine-readable statistics ({cast}_caldip.nc)
    • Summary statistics ({cast}_summary_statistics.csv)
    • Detailed statistics ({cast}_detailed_statistics.csv)
    • Quality flag thresholds
  • Output file location
  • Batch processing
  • Per-cruise report

Help and reference

• GitHub Repo
• caldip API
  • core
    • find_bottle_stops()
    • resolve_quality_thresholds()
    • stats()
    • stats_for_time_period()
  • readers
    • Public API
    • Internal helpers
    • CRUISE_CONFIG_NAME
    • discover_cast_configs()
    • find_config_file()
    • find_cruise_config()
    • load_config()
    • load_cruise_config()
    • load_ctd_data()
    • load_instrument_data()
    • load_instruments_from_config()
    • load_microcat_data()
    • load_nortek_csv_data()
    • load_reference_data()
    • normalize_serial()
    • read_ctdcast_reference()
    • resolve_data_dir()
    • resolve_instrument_class()
    • sbe37_xmlcon_reader()
  • scaffold
    • generate_stub_yaml()
  • tools
    • summary_stats()
    • to_xarray()
    • trim_to_deployment()
  • sbe_hex_reader
    • parse_hex_header_sensors()
    • sbe37_hex_reader()
    • sbe37_xmlcon_reader()
  • report
    • build_report()
  • report.index
    • build_index_html()
  • report.cast
    • build_cast_page_html()
  • report.inventory
    • build_inventory_html()
    • read_nc_meta()
    • write_inventory()
• About caldip
• Bottle stop detection
  • Overview
  • Stage 1 — Search region
  • Stage 2 — Candidate detection (60-second window)
  • Stage 3 — Extending the candidate
  • Stage 4 — Boundary refinement (±2 dbar around median)
  • Stage 5 — Merging and final filter
  • Statistics comparison window
  • Parameters
• FAQ / Troubleshooting
  • I get an error when doing from caldip import readers
  • Failing to install the package in a Github Action
  • What’s the difference between the repository name and the python package name??
• Acknowledgments
• Funding

Indices and tables

• Index

• Module Index

• Search Page