# litds
<!-- WARNING: THIS FILE WAS AUTOGENERATED! DO NOT EDIT! -->
## Developer Guide
### Setup
``` sh
# create conda environment
$ mamba env create -f env.yml
# update conda environment
$ mamba env update -n litds --file env.yml
```
### Install
``` sh
pip install -e .
# install from pypi
pip install litds
```
### nbdev
``` sh
# activate 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
``` sh
# publish to pypi
$ nbdev_pypi
# publish to conda
$ nbdev_conda --build_args '-c conda-forge'
```
# Usage
## Installation
Install latest from the GitHub
[repository](https://github.com/dsm-72/litds):
``` sh
$ pip install git+https://github.com/dsm-72/litds.git
```
or from [conda](https://anaconda.org/dsm-72/litds)
``` sh
$ conda install -c dsm-72 litds
```
or from [pypi](https://pypi.org/project/litds/)
``` sh
$ pip install litds
```
## Documentation
Documentation can be found hosted on GitHub
[repository](https://github.com/dsm-72/litds)
[pages](https://dsm-72.github.io/litds/). Additionally you can find
package manager specific guidelines on
[conda](https://anaconda.org/dsm-72/litds) and
[pypi](https://pypi.org/project/litds/) respectively.
# Brief Datasets Demo
``` python
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.]))
``` python
dd.plot(palette='mako_r')
```
``` python
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.]))
``` python
od.plot(palette='mako_r')
```
``` python
eb = EmbryoidBodies2018DataModule(
primary='pca',
batch_size=8,
)
```
``` python
eb.setup()
```
EB Loader: 0%| | 0/126 [00:00<?, ?it/s]
Loading data
Data ready!
``` python
dl = eb.train_dataloader()
```
``` python
eb.train_ds.df[eb.train_ds.df.columns[-5:]].head()
```
<div>
<style scoped>
.dataframe tbody tr th:only-of-type {
vertical-align: middle;
}
.dataframe tbody tr th {
vertical-align: top;
}
.dataframe thead th {
text-align: right;
}
</style>
| | 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 |
</div>
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"description": "# litds\n\n<!-- WARNING: THIS FILE WAS AUTOGENERATED! DO NOT EDIT! -->\n\n## Developer Guide\n\n### Setup\n\n``` sh\n# create conda environment\n$ mamba env create -f env.yml\n\n# update conda environment\n$ mamba env update -n litds --file env.yml\n```\n\n### Install\n\n``` sh\npip install -e .\n\n# install from pypi\npip install litds\n```\n\n### nbdev\n\n``` sh\n# activate conda environment\n$ conda activate litds\n\n# make sure the litds package is installed in development mode\n$ pip install -e .\n\n# make changes under nbs/ directory\n# ...\n\n# compile to have changes apply to the litds package\n$ nbdev_prepare\n```\n\n### Publishing\n\n``` sh\n# publish to pypi\n$ nbdev_pypi\n\n# publish to conda\n$ nbdev_conda --build_args '-c conda-forge'\n```\n\n# Usage\n\n## Installation\n\nInstall latest from the GitHub\n[repository](https://github.com/dsm-72/litds):\n\n``` sh\n$ pip install git+https://github.com/dsm-72/litds.git\n```\n\nor from [conda](https://anaconda.org/dsm-72/litds)\n\n``` sh\n$ conda install -c dsm-72 litds\n```\n\nor from [pypi](https://pypi.org/project/litds/)\n\n``` sh\n$ pip install litds\n```\n\n## Documentation\n\nDocumentation can be found hosted on GitHub\n[repository](https://github.com/dsm-72/litds)\n[pages](https://dsm-72.github.io/litds/). Additionally you can find\npackage manager specific guidelines on\n[conda](https://anaconda.org/dsm-72/litds) and\n[pypi](https://pypi.org/project/litds/) respectively.\n\n# Brief Datasets Demo\n\n``` python\ndd = DiamondsDataset()\ndd.getone()\n```\n\n (tensor([[ 0.0491, 0.0015],\n [ 0.1555, 0.3419],\n [-0.3727, 0.3598],\n [ 0.6811, 0.3734],\n [ 0.4492, -0.7379]]),\n tensor([0., 1., 2., 3., 4.]))\n\n``` python\ndd.plot(palette='mako_r')\n```\n\n\n\n``` python\nod = OrbitsDataset()\nod.getone()\n```\n\n (tensor([[ 0.0203, -0.2043],\n [-0.3889, -0.1781],\n [ 0.0290, 0.6299],\n [-0.3386, 0.8402],\n [ 0.9571, 0.0337]]),\n tensor([0., 1., 2., 3., 4.]))\n\n``` python\nod.plot(palette='mako_r')\n```\n\n\n\n``` python\neb = EmbryoidBodies2018DataModule(\n primary='pca',\n batch_size=8,\n)\n```\n\n``` python\neb.setup()\n```\n\n EB Loader: 0%| | 0/126 [00:00<?, ?it/s]\n\n Loading data\n Data ready!\n\n``` python\ndl = eb.train_dataloader()\n```\n\n``` python\neb.train_ds.df[eb.train_ds.df.columns[-5:]].head()\n```\n\n<div>\n<style scoped>\n .dataframe tbody tr th:only-of-type {\n vertical-align: middle;\n }\n .dataframe tbody tr th {\n vertical-align: top;\n }\n .dataframe thead th {\n text-align: right;\n }\n</style>\n\n| | d97 | d98 | d99 | d100 | samples |\n|-------|-----------|-----------|-----------|-----------|-----------|\n| 4854 | -0.633847 | -0.701649 | -1.466198 | -0.381950 | Day 06-09 |\n| 6121 | 0.432789 | 1.089373 | -0.968371 | -0.211686 | Day 06-09 |\n| 7620 | 0.042552 | 0.870117 | -1.264836 | -1.664296 | Day 12-15 |\n| 12560 | 1.770667 | -0.594136 | 1.893129 | -1.064998 | Day 18-21 |\n| 10336 | -2.947320 | -1.072601 | 1.554807 | 0.170369 | Day 18-21 |\n\n</div>\n",
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