Load custom data
----------------

Toy dataset example
~~~~~~~~~~~~~~~~~~~

An example of implementing a custom dataset loader is available
`here <https://github.com/iteal/wormpose/tree/main/examples/toy_dataset>`__
(using toy data).

First install the WormPose package.

.. code:: bash

    pip install --upgrade wormpose

To install the toy dataset loader, run the following command in the
folder ``toy_dataset``:

.. code:: bash

    pip install -e .

Now you can use the dataset loader named "toy" :

.. code:: bash

    wormpose COMMAND toy "toy_dataset_path"

Toy data will be generated at runtime and saved to toy\_dataset\_path.

Use your own data
~~~~~~~~~~~~~~~~~

Follow the toy dataset example to add your custom dataset loader.

First, choose a name for your dataset loader (``cool_worms`` for
example).

Create a python module (``cool_worms_loader.py`` for example),
containing three classes, such as below:

.. code:: python

    from wormpose import BaseFramesDataset, BaseFeaturesDataset, BaseFramePreprocessing

    class FramesDataset(BaseFramesDataset):
        """
        Reader for the images of the dataset
        """
        raise NotImplementedError("Here, implement interface BaseFramesDataset") 

    class FeaturesDataset(BaseFeaturesDataset):
        """
        Features corresponding to the images (skeleton, width)
        """
        raise NotImplementedError("Here, implement interface BaseFeaturesDataset")

    class FramePreprocessing(BaseFramePreprocessing):
        """
        Contains a function to segment the worm in images and return the background color
        """
        raise NotImplementedError("Here, implement interface BaseFramePreprocessing")

The API documentation can be found
`here <https://github.com/iteal/wormpose/blob/main/wormpose/dataset/base_dataset.py>`__.

Create a file ``setup.py`` containing the entry point
``worm_dataset_loaders`` refering to your python module, with its loader
name, such as below:

.. code:: python

    from setuptools import setup

    setup(name = "cool_worms_dataset",
          entry_points = {"worm_dataset_loaders": ["cool_worms=cool_worms_loader"]})

After installing wormpose, install your module with:

.. code:: bash

    pip install -e .

Now you can use the dataset loader named "cool\_worms" :

.. code:: bash

    wormpose COMMAND cool_worms "path/to/cool_worms_dataset000XX"

Use the notebook
`check\_dataset <https://github.com/iteal/wormpose/blob/main/examples/check_dataset.ipynb>`__
to validate your custom dataset loader. You can view if the frames load
correctly, and if the features are accurate.