Flydra documentation

Flydra is a realtime, multi-camera flying animal tracking system. See the paper for algorithmic details.

Contents:

• Getting started with flydra development
  • Using a Python virtual environment
  • Getting and installing flydra from the source code repository
  • Testing your installation
  • Editing the documentation
  • Continuous integration
• Calibration
• Generating a calibration using MultiCamSelfCal
  • Saving the calibration data in flydra_mainbrain
  • Exporting the data for MultiCamSelfCal
  • Running MultiCamSelfCal
  • Advanced: automatic homography (alignment) using approximate camera positions
  • Advanced: using 3D trajectories to re-calibrate using MultiCamSelfCal
• Aligning a calibration
  • Manually generating 3D points from images to use for alignment
• Estimating non-linear distortion parameters
  • Use of flydra_checkerboard
• Realtime data
• Data analysis
  • Types of data files
  • Predefined analysis programs
  • Automating data analysis
  • Source code for your own data analysis
  • Data flow
  • Extracting longitudinal body orientation
• Gallery
  • Image gallery
  • Command gallery
• The Flydra Trigger Device
• Estimating orientations with flydra
  • Fusing 2D orientations to 3D
  • Smoothing 3D orientations
• Modules reference
  • flydra_analysis.a2 - analysis (second generation)
  • flydra_analysis.analysis - data analysis modules
  • Miscellaneous flydra_core modules
• old Trac wiki page about Flydra
  • Subpages about flydra
  • Scripts of great interest
  • Scripts of lesser interest
  • Reasons to run flydra_kalmanize on your data, even though it’s already been Kalmanized
  • Image masking
  • Latency/performance of flydra
  • Profiling
  • Flydra simulator
• Frequently Asked Questions
  • The timestamp field is all wrong!
  • I cannot read the .kh5 files
• Installation notes
  • RedHat 64bit
  • Mac OS X
  • Ubuntu Lucid

Contibutions to this documentation

All contributions are welcome. If you’d like to improve something, look into the sources if they contain the information you need (if not, please fix them), otherwise the documentation generation needs to be improved (look in the flydra-sphinx-docs/ directory). For more information, see Editing the documentation.

Indices and tables

• Index
• Module Index
• Search Page