DataStructure_tools

python tools to aid in working with our future datastructure

Requirement git, python >=3.9 if you have git installed:

git clone https://github.com/Optophys-Lab/DataStructure_tools.git
cd DataStructure_tools

Install the module with required packages, ideally from a conda env. run inside DataStructure_tools

conda create -n datastructure_tools python=3.9
conda activate datastructure_tools

pip install -e .

To start GUIs from command-line: #make sure current directory is DataStructure_tools

python ./datastructure_tools/AdminCommander.py

or NEW: for this method current directory doesnt matter

python -m datastructure_tools admin

To start GUIs from python:

from datastructure_tools.AnimalCommander import AnimalCommander
AnimalCommander.start_gui()

Tutorial

To get you started, we provide a tutorial notebook in Tutorial.ipynb. It is a work in progress and will be updated continously. So make sure to pull the git once in a while!

Modules:

AdminCommander - GUI for managing server connection as well as user settings. Projects, Experiments and datatypes can be created here, as well as atlas files copy

AnimalCommander - GUI to create and add Animals to the DB can be used standalone or be called from SessionCommander

FileCommander - GUI to copy files into corresponding folders can be used standalone or be called from SessionCommander

SessionCommander - GUI to create and Sessions to DB and create the corresponding folder structure on the server

DataBaseAccess - a class abstracting the schema activation and DJ access is used in GUIs and can be used standalone

SurgeryCommander - GUI to add information about surgeries, includes insertion angles calculation and atlas projections

SurgeryPlanner - GUI for planning of surgeries at different angles

WeightCommander - GUI to add weights of animals to DB and create animal sheets in automated manner

VirusCommander - GUI to add Virus related infos to the DB

EquipmentCommander - GUI to add EphysProbes and its types to the DB, with visualisation of said probes

LabbookCommander - GUI for creation of animal training sheets from the DB

Known issues

If you run

import_datastructure_tools as dt
dt.AdminCommander.start_gui()

and get a module not found error, this might be due to a bug with pyqt. Try opening the commanders by going to the folder and running

python AdminCommander.py

If you cannot open any of the commanders due to PyQt6 Errors, try updateting PyQt6 via

pip uninstall pyqt6
pip install pyqt6