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Welcome to the tierpsy-tools-python wiki!
tierpsy-tools python is a repo that contains the tierpsytools package, which can be installed using the instruction in the README.md.
This module contains functions that help in the compilation of metadata from experiments performed in the multi-camera rig (hydra).
This module contains function that help in the compilation of metadata from experiments performed in the single-camera rig (phenix) and generaly dated before 2018. The characteristic of these experiments is that a part or all of the metadata were written in the filename of the recorded videos and there were no digital experimental records containing this information. It also contains function for th eprocessing of videos recorded in phenix.
This module contains functions that help read quantitative phenotyping data (mainly tierpsy features) and the corresponding experimental metadata and format them in the format used by the downstream modules: two dataframes with matching index, one containing features and one containing metadata information.
This is a small module that helps read tables from hdf5 files for general use.
This is a module with functions and classes that can be used for the preprocessing of the quantitative phenotyping data in the format returned by the functions in read_data. Preprocessing encompasses filtering, scaling, smoothing and any other cleaning/imputing/quality control procedure that precedes the analysis stage.
This module contains all the core functions/classes that can help in the analysis of data that come from quantitative phenotyping experiments. This includes exploratory analysis of the data, statistical comparisons and inference tasks such as classification and clustering.
This module is a companion to the analysis module with functions specifically developped for drug experiments. the common denominator of these functions is that they assume that the metadata contain information about drug type and dose and they generally do not consider the possibility of other types of parameters of interest.
In principle, the analysis module should not contain plotting functions (with some very rare exceptions for standardized quick exploratory analysis). This is because plotting functions are very rarely reusable. However, there might be some exceptions to this rule. Any plotting function that is consided reusable is included in this module within a descriptive filename. Generally, files in thus module should not contain more than one plotting task.
Many of the modules contain files with a {name}.py and an companion files {name}_helper.py. In this case, the main file contains the functions for use by most users, while the helper file contains back-end functions called by the main functions that are not relevant for most users (except for debugging purposes).
This folder contains text files with some tierpsy-related information that is needed by certain functions (for example the full list of feature names).
In the base directory of the tierpsy-tools-python repo, there is an examples folder that contains sample scripts that demonstrate the use of some of the functions in tierpsytools, together with small-sized sample data (in principle synthetic data).