litds

Developer Guide

Setup

# create conda environment
$ mamba env create -f env.yml

# update conda environment
$ mamba env update -n litds --file env.yml

Install

pip install -e .

 conda environment
$ conda activate litds

# make sure the litds package is installed in development mode
$ pip install -e .

# make changes under nbs/ directory
# ...

# compile to have changes apply to the litds package
$ nbdev_prepare

Publishing

# publish to pypi
$ nbdev_pypi

# publish to conda
$ nbdev_conda --build_args '-c conda-forge'

Usage

Installation

Install latest from the GitHub repository:

$ pip install git+https://github.com/dsm-72/litds.git

or from conda

$ conda install -c dsm-72 litds

or from pypi

$ pip install litds

Documentation

Documentation can be found hosted on GitHub repository pages. Additionally you can find package manager specific guidelines on conda and pypi respectively.

Brief Datasets Demo

dd = DiamondsDataset()
dd.getone()

(tensor([[ 0.0491,  0.0015],
         [ 0.1555,  0.3419],
         [-0.3727,  0.3598],
         [ 0.6811,  0.3734],
         [ 0.4492, -0.7379]]),
 tensor([0., 1., 2., 3., 4.]))

dd.plot(palette='mako_r')

od = OrbitsDataset()
od.getone()

(tensor([[ 0.0203, -0.2043],
         [-0.3889, -0.1781],
         [ 0.0290,  0.6299],
         [-0.3386,  0.8402],
         [ 0.9571,  0.0337]]),
 tensor([0., 1., 2., 3., 4.]))

od.plot(palette='mako_r')

eb = EmbryoidBodies2018DataModule(
    primary='pca',
    batch_size=8,
)

eb.setup()

EB Loader:   0%|          | 0/126 [00:00<?, ?it/s]

Loading data
Data ready!

dl = eb.train_dataloader()

eb.train_ds.df[eb.train_ds.df.columns[-5:]].head()

| | d97 | d98 | d99 | d100 | samples | |-------|-----------|-----------|-----------|-----------|-----------| | 4854 | -0.633847 | -0.701649 | -1.466198 | -0.381950 | Day 06-09 | | 6121 | 0.432789 | 1.089373 | -0.968371 | -0.211686 | Day 06-09 | | 7620 | 0.042552 | 0.870117 | -1.264836 | -1.664296 | Day 12-15 | | 12560 | 1.770667 | -0.594136 | 1.893129 | -1.064998 | Day 18-21 | | 10336 | -2.947320 | -1.072601 | 1.554807 | 0.170369 | Day 18-21 |