Data from: Fish communicate with water flow to enhance a school's social network
Abstract
README: Data from: Fish communicate with water flow to enhance a school's social network
See the README.md file in the "running_experiment" archive for details on the acquisition of data.
The analysis was coded in matlab. The m-file wk_main.m controls the workflow and describes the data analysis. All other m-files supplement that analysis.
General notes
- Some fields have entries of NaN, which means "not a number" and serves as a placeholder when values are not available.
- Some fields have entries of "n/a", which means "not applicable". For example, were performed recordings of spatial calibrations that have no fish and thus entered "n/a" for fish_num, the number of fish in the recording.
data
holds the datasets used in the study.
Files
- compiled_data.csv: provides the mean and variance values for a variety of measurements that served as dependent variables in our statistical analysis.
- experiment_log.csv: itemizes parameters required for the kinematic analysis of each experiment. The rows where sch_num==999 corresponded to the calibration sequences and thus some of the columns are entered as n/a if those measurements did not apply.
- recording_log: Generated by our python code for all video recordings performed. Here too sch_num==999 corresponded to the calibration sequences.
Folders
- masks: Contains the images used to mask video files, along with data (in .mat and .npy formats) that detail the positions of masking pixels.
- matlab: holds all kinematic data for schooling analysis. Requires MATLAB to load.
- mean_images: images created by temporal averges of pixel intensity across recordings. Used to subtrack background features from video frames.
data_acquisition_code
Holds all software used for running experiments and acquiring kinematics. This consists primarily of Python scripts that are explained in the README.md file in this folder. The code for running experiments is organized by running scripts from run_acq_kinematics.py and the analysis code in organized in run_analysis.py.
data_analysis_code
Holds all MATLAB code for performing the kinematic analysis. The code is organized by running scripts from wk_main.m in MATLAB. The major components of the analysis are described in the README.md file in this folder.