pydictoolkit

Toolkit to further analyze 2D and 3D Digital Image Correlation results. The current work focuses on strain evolution at the surface of growing biological materials.

Main features

[x] Compute the difference between consecutive images (the "delta") for the available fields (displacement and strain fields)
[x] Ability to divide the AOI into equal rectangular areas of prescribed size and to plot heatmaps of the "delta" for any field
[x] Compute the minimal and maximal values of a field for a set of CSV results (good values to know if we want to have a single scale for all the provided CSV files)
[x] Contour plot for the displacement or strain fields with automatically scaled color bar
[x] Streamline plots of the U and V displacement field
[ ] Streamline plots of the first or second principal strain fields
[ ] Allow the user to be able to change the name of the spatial variables (x instead of X in the case of VIC2D since there is no X (mm) by default)
[ ] Increase the quality (dpi) of the plots, or even better turn it into a deck variable
[x] Add a scale (mm/px) to the Report.csv
[ ] Add a scale bar to all the plots
[ ] Make it possible to create a gif out of any kind of plots, not only heatmaps

Quickstart

If you know what you're doing, then this section is for you. Otherwise, you should go to the Getting Started section.

Linux:

sudo apt install python3-pip python3-venv
git clone https://github.com/ilyasst/pydictoolkit.git
cd pydictoolkit
python3 -m venv .env
source .env/bin/activate
pip install -r requirements.txt
python main.py -h

Basic usage:

python main.py -d "./deck.yaml"

Getting started

Installation

The following pieces of software are required to run pydictoolkit:

Python 3.6 or higher
python3-pip
python3-venv

The list of necessary python packages is provided in the requirements.txt file and can be installed using pip:

pip install -r requirements.txt

We recommend that you create a virtual environment before installing these packages using the python3-venv software:

python3 -m venv .env

You can then load your virtual environment using:

source .env/bin/activate

In order to exit it, use the deactivate command.

Usage

In order to use the code, you will need to provide:

A valid deck.yaml file (the content of this file is further detailed in the Input description section)
Your VIC3D CSV grid outputs (.csv) and stereo-images (.tiff) in the folder specified in the deck.yaml file

You can then run pydictoolkit using:

python main.py -d "PATH_TO_DECK"

where PATH_TO_DECK is the path to your deck.yaml file.

A short help/reminder can be accessed using:

python main.py -h

Input description

deck.yaml

Main structure of the deck.yaml file:

Data:
  Folder: ./pydictoolkit/dummy_data/

Plots:
  Target Plot: e1
  Groups:
    Region:
      i: 200
      j: 200
  Target Column: e1_delta

The remainder of this section provides detailed explanations for each section.

Data

Data:
  Folder: ./pydictoolkit/dummy_data/

The Data section contains a single value: the path of the folder that contains your VIC3D CSV grid data and stereo-images. It can be an absolute path, or a path relative to the main.py file.

Your VIC3D grid data

Let's make add a few screenshots to show which CSV files we mean exactly.

Examples

An example:

Description of the example data and credit where it's due

Contribute ?

Maybe you need something for your own project, maybe you found a mistake or something you could improve and feeling like helping, in any case, we'll be happy to get in touch. Please leave us an Issue, or a Pull Request (we welcome those!).

Disclaimer

This software is for educational and research purposes only. Use it at your own risks.

ilyasst / pydictoolkit

readme