Project setup

Creating the project directory

smartmove uses a series of configuration YAML files and a pre-defined directory structure for input and output data files. All of these are located in a project directory, which you define when you create your smartmove project.

First create a directory to use as your smartmove project directory:

mkdir /home/<user>/smartmove_project

Open the IPython interpretor:

cd ~/opt
IPython3

Then import smartmove and use the smartmove.create_project() method to create the necessary subdirectories and configuration files used in the smartmove analyses.

import smartmove

path_project = '/home/<user>/smartmove_project'
smartmove.create_project(path_project)

The configuration YAML files and necessary directories will then be created in your project directory, and you should receive a message instructing you to copy the necessary data files to their respective directories.

Example project directory structure

project directory
├── cfg_ann.yml
├── cfg_experiments.yml
├── cfg_glide.yml
├── cfg_project.yml
├── cfg_subglide-filter.yml
├── data_csv
├── data_ctd
├── data_glide
├── data_tag
└── model_ann

Copying data to the project directory

Note

The propeller_calibrations.csv file is for calibration of the propeller sensor data from rotations to units of m s^-2, and the cal.yml files in the Little Leonardo data directories are used by pylleo for calibrating the accelerometer sensor data to units of gravity.

See the pylleo documentation for more information on performing these calibrations and the naming of data files.

The CSV files for field experiments, isotope experiments, and propeller calibrations should be placed in the data_csv directory, the matlab file with CTD measurements should be placed in the data_ctd directory, and the directories containing Little Leonardo data should be placed in the data_tag directory.

project directory
├── data_csv
│   ├── field_experiments.csv
│   ├── isotope_experiments.csv
│   └── propeller_calibrations.csv
├── data_ctd
│   └── kaldfjorden2016_inner.mat
└── data_tag
    ├── 20150306_W190PD3GT_34839_Notag_Control
    ├── 20150310_W190PD3GT_34839_Notag_Control
    ├── 20150311_W190PD3GT_34839_Skinny_Control
    ├── 20150314_W190PD3GT_34839_Skinny_2neutralBlocks
    ├── 20150315_W190PD3GT_34839_Notag_Control
    ├── 20150316_W190PD3GT_34839_Skinny_4weighttubes_2Blocks
    ├── 20150317_W190PD3GT_34839_Skinny_4Floats
    ├── 20150318_W190PD3GT_34839_Notag_2neutrals
    ├── 20150320_W190PD3GT_34839_Skinny_4weights
    ├── 20150323_W190PD3GT_34839_Skinny_4NeutralBlocks
    ├── 20160418_W190PD3GT_34840_Skinny_2Neutral
    ├── 20160419_W190PD3GT_34840_Skinny_2Weighted
    ├── 20160422_W190PD3GT_34840_Skinny_4Floats
    └── 20160425_W190PD3GT_34840_Skinny_4Weights