# narr
<!-- WARNING: THIS FILE WAS AUTOGENERATED! DO NOT EDIT! -->
``` python
# #| hide
# from narr.strs import snake_case
# from narr.axes import NamedAxis, NamedAxes
# from narr.errs import NamedArrayDimsError
# from narr.mixs import NamedArrayDynamicAttrsMixin
# from narr.narr import NamedArray
# from narr.traj import (
# TrajectoryDim, GeneTrajectoryDim,
# ObservationTrajectories, FeatureTrajectories,
# CellularTrajectories, ExpressionTrajectories,
# Trajectories, GeneTrajectories,
# )
```
## Developer Guide
### Setup
``` sh
# create conda environment
$ mamba env create -f env.yml
# update conda environment
$ mamba env update -n narr --file env.yml
```
### Install
``` sh
pip install -e .
# install from pypi
pip install narr
```
### nbdev
``` sh
# activate conda environment
$ conda activate narr
# make sure the narr package is installed in development mode
$ pip install -e .
# make changes under nbs/ directory
# ...
# compile to have changes apply to the narr package
$ nbdev_prepare
```
### Publishing
``` sh
# publish to pypi
$ nbdev_pypi
# publish to conda
$ nbdev_conda --build_args '-c conda-forge'
$ nbdev_conda --mambabuild --build_args '-c conda-forge -c dsm-72'
```
# Usage
## Installation
Install latest from the GitHub
[repository](https://github.com/dsm-72/narr):
``` sh
$ pip install git+https://github.com/dsm-72/narr.git
```
or from [conda](https://anaconda.org/dsm-72/narr)
``` sh
$ conda install -c dsm-72 narr
```
or from [pypi](https://pypi.org/project/narr/)
``` sh
$ pip install narr
```
## Documentation
Documentation can be found hosted on GitHub
[repository](https://github.com/dsm-72/narr)
[pages](https://dsm-72.github.io/narr/). Additionally you can find
package manager specific guidelines on
[conda](https://anaconda.org/dsm-72/narr) and
[pypi](https://pypi.org/project/narr/) respectively.
``` python
# import numpy as np
# from typing import Callable
```
### Subclassing NamedArray
``` python
# class Trajectories(NamedArray):
# DIMS = NamedAxes([NamedAxis(dim.name, i) for i, dim in enumerate(TrajectoryDim)])
# def to_obsv_x_traj(self, aggr: Callable = np.mean):
# agg_arr = aggr(np.asarray(self.transpose(
# TrajectoryDim.obsv.name, TrajectoryDim.traj.name, TrajectoryDim.feat.name,
# )), axis=2)
# return ObservationTrajectories(agg_arr)
# def to_feat_x_traj(self, aggr: Callable = np.mean):
# agg_arr = aggr(np.asarray(self.transpose(
# TrajectoryDim.feat.name, TrajectoryDim.traj.name, TrajectoryDim.obsv.name,
# )), axis=2)
# return FeatureTrajectories(agg_arr)
```
### Using NamedArray Subclass Trajectories
``` python
# arr = np.random.randint(0, 10, (3, 5, 10))
# arr
```
array([[[9, 7, 1, 4, 8, 2, 3, 3, 3, 1],
[0, 3, 8, 7, 2, 9, 9, 9, 1, 7],
[0, 8, 5, 3, 3, 8, 8, 1, 3, 8],
[3, 6, 9, 1, 8, 7, 7, 3, 1, 3],
[0, 0, 2, 9, 1, 6, 6, 8, 1, 7]],
[[5, 9, 5, 7, 3, 2, 1, 0, 9, 5],
[9, 8, 7, 3, 1, 7, 6, 6, 0, 5],
[8, 2, 9, 7, 2, 9, 4, 4, 0, 8],
[2, 8, 2, 2, 0, 6, 6, 8, 6, 9],
[5, 5, 2, 2, 3, 5, 9, 9, 3, 4]],
[[3, 6, 4, 6, 3, 2, 4, 6, 9, 0],
[7, 1, 6, 7, 7, 2, 6, 2, 2, 8],
[2, 3, 6, 2, 5, 5, 2, 6, 2, 0],
[3, 9, 8, 5, 1, 5, 7, 8, 7, 9],
[9, 2, 1, 5, 2, 7, 0, 7, 4, 3]]])
``` python
# Trajectories(arr)
```
Trajectories([[[9, 7, 1, 4, 8, 2, 3, 3, 3, 1],
[0, 3, 8, 7, 2, 9, 9, 9, 1, 7],
[0, 8, 5, 3, 3, 8, 8, 1, 3, 8],
[3, 6, 9, 1, 8, 7, 7, 3, 1, 3],
[0, 0, 2, 9, 1, 6, 6, 8, 1, 7]],
[[5, 9, 5, 7, 3, 2, 1, 0, 9, 5],
[9, 8, 7, 3, 1, 7, 6, 6, 0, 5],
[8, 2, 9, 7, 2, 9, 4, 4, 0, 8],
[2, 8, 2, 2, 0, 6, 6, 8, 6, 9],
[5, 5, 2, 2, 3, 5, 9, 9, 3, 4]],
[[3, 6, 4, 6, 3, 2, 4, 6, 9, 0],
[7, 1, 6, 7, 7, 2, 6, 2, 2, 8],
[2, 3, 6, 2, 5, 5, 2, 6, 2, 0],
[3, 9, 8, 5, 1, 5, 7, 8, 7, 9],
[9, 2, 1, 5, 2, 7, 0, 7, 4, 3]]])
(3 traj, 5 obsv, 10 feat)
``` python
# Trajectories(arr).transpose(1, 0, 2)
```
Trajectories([[[9, 7, 1, 4, 8, 2, 3, 3, 3, 1],
[5, 9, 5, 7, 3, 2, 1, 0, 9, 5],
[3, 6, 4, 6, 3, 2, 4, 6, 9, 0]],
[[0, 3, 8, 7, 2, 9, 9, 9, 1, 7],
[9, 8, 7, 3, 1, 7, 6, 6, 0, 5],
[7, 1, 6, 7, 7, 2, 6, 2, 2, 8]],
[[0, 8, 5, 3, 3, 8, 8, 1, 3, 8],
[8, 2, 9, 7, 2, 9, 4, 4, 0, 8],
[2, 3, 6, 2, 5, 5, 2, 6, 2, 0]],
[[3, 6, 9, 1, 8, 7, 7, 3, 1, 3],
[2, 8, 2, 2, 0, 6, 6, 8, 6, 9],
[3, 9, 8, 5, 1, 5, 7, 8, 7, 9]],
[[0, 0, 2, 9, 1, 6, 6, 8, 1, 7],
[5, 5, 2, 2, 3, 5, 9, 9, 3, 4],
[9, 2, 1, 5, 2, 7, 0, 7, 4, 3]]])
(5 obsv, 3 traj, 10 feat)
``` python
# Trajectories(arr).transpose('obsv', 0, 2)
```
Trajectories([[[9, 7, 1, 4, 8, 2, 3, 3, 3, 1],
[5, 9, 5, 7, 3, 2, 1, 0, 9, 5],
[3, 6, 4, 6, 3, 2, 4, 6, 9, 0]],
[[0, 3, 8, 7, 2, 9, 9, 9, 1, 7],
[9, 8, 7, 3, 1, 7, 6, 6, 0, 5],
[7, 1, 6, 7, 7, 2, 6, 2, 2, 8]],
[[0, 8, 5, 3, 3, 8, 8, 1, 3, 8],
[8, 2, 9, 7, 2, 9, 4, 4, 0, 8],
[2, 3, 6, 2, 5, 5, 2, 6, 2, 0]],
[[3, 6, 9, 1, 8, 7, 7, 3, 1, 3],
[2, 8, 2, 2, 0, 6, 6, 8, 6, 9],
[3, 9, 8, 5, 1, 5, 7, 8, 7, 9]],
[[0, 0, 2, 9, 1, 6, 6, 8, 1, 7],
[5, 5, 2, 2, 3, 5, 9, 9, 3, 4],
[9, 2, 1, 5, 2, 7, 0, 7, 4, 3]]])
(5 obsv, 3 traj, 10 feat)
``` python
# Trajectories(arr).transpose('obsv', 0, 2).to_obsv_x_traj()
```
NameError: name 'aggr' is not defined
Raw data
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"description": "# narr\n\n<!-- WARNING: THIS FILE WAS AUTOGENERATED! DO NOT EDIT! -->\n\n``` python\n# #| hide\n# from narr.strs import snake_case\n# from narr.axes import NamedAxis, NamedAxes\n# from narr.errs import NamedArrayDimsError\n# from narr.mixs import NamedArrayDynamicAttrsMixin\n# from narr.narr import NamedArray\n# from narr.traj import (\n# TrajectoryDim, GeneTrajectoryDim,\n# ObservationTrajectories, FeatureTrajectories,\n# CellularTrajectories, ExpressionTrajectories,\n# Trajectories, GeneTrajectories,\n# )\n```\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 narr --file env.yml\n```\n\n### Install\n\n``` sh\npip install -e .\n\n# install from pypi\npip install narr\n```\n\n### nbdev\n\n``` sh\n# activate conda environment\n$ conda activate narr\n\n# make sure the narr 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 narr 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$ nbdev_conda --mambabuild --build_args '-c conda-forge -c dsm-72'\n```\n\n# Usage\n\n## Installation\n\nInstall latest from the GitHub\n[repository](https://github.com/dsm-72/narr):\n\n``` sh\n$ pip install git+https://github.com/dsm-72/narr.git\n```\n\nor from [conda](https://anaconda.org/dsm-72/narr)\n\n``` sh\n$ conda install -c dsm-72 narr\n```\n\nor from [pypi](https://pypi.org/project/narr/)\n\n``` sh\n$ pip install narr\n```\n\n## Documentation\n\nDocumentation can be found hosted on GitHub\n[repository](https://github.com/dsm-72/narr)\n[pages](https://dsm-72.github.io/narr/). Additionally you can find\npackage manager specific guidelines on\n[conda](https://anaconda.org/dsm-72/narr) and\n[pypi](https://pypi.org/project/narr/) respectively.\n\n``` python\n# import numpy as np\n# from typing import Callable\n```\n\n### Subclassing NamedArray\n\n``` python\n# class Trajectories(NamedArray):\n# DIMS = NamedAxes([NamedAxis(dim.name, i) for i, dim in enumerate(TrajectoryDim)])\n \n# def to_obsv_x_traj(self, aggr: Callable = np.mean):\n# agg_arr = aggr(np.asarray(self.transpose(\n# TrajectoryDim.obsv.name, TrajectoryDim.traj.name, TrajectoryDim.feat.name, \n# )), axis=2)\n# return ObservationTrajectories(agg_arr)\n \n# def to_feat_x_traj(self, aggr: Callable = np.mean):\n# agg_arr = aggr(np.asarray(self.transpose(\n# TrajectoryDim.feat.name, TrajectoryDim.traj.name, TrajectoryDim.obsv.name, \n# )), axis=2)\n# return FeatureTrajectories(agg_arr)\n```\n\n### Using NamedArray Subclass Trajectories\n\n``` python\n# arr = np.random.randint(0, 10, (3, 5, 10))\n# arr\n```\n\n array([[[9, 7, 1, 4, 8, 2, 3, 3, 3, 1],\n [0, 3, 8, 7, 2, 9, 9, 9, 1, 7],\n [0, 8, 5, 3, 3, 8, 8, 1, 3, 8],\n [3, 6, 9, 1, 8, 7, 7, 3, 1, 3],\n [0, 0, 2, 9, 1, 6, 6, 8, 1, 7]],\n\n [[5, 9, 5, 7, 3, 2, 1, 0, 9, 5],\n [9, 8, 7, 3, 1, 7, 6, 6, 0, 5],\n [8, 2, 9, 7, 2, 9, 4, 4, 0, 8],\n [2, 8, 2, 2, 0, 6, 6, 8, 6, 9],\n [5, 5, 2, 2, 3, 5, 9, 9, 3, 4]],\n\n [[3, 6, 4, 6, 3, 2, 4, 6, 9, 0],\n [7, 1, 6, 7, 7, 2, 6, 2, 2, 8],\n [2, 3, 6, 2, 5, 5, 2, 6, 2, 0],\n [3, 9, 8, 5, 1, 5, 7, 8, 7, 9],\n [9, 2, 1, 5, 2, 7, 0, 7, 4, 3]]])\n\n``` python\n# Trajectories(arr)\n```\n\n Trajectories([[[9, 7, 1, 4, 8, 2, 3, 3, 3, 1],\n [0, 3, 8, 7, 2, 9, 9, 9, 1, 7],\n [0, 8, 5, 3, 3, 8, 8, 1, 3, 8],\n [3, 6, 9, 1, 8, 7, 7, 3, 1, 3],\n [0, 0, 2, 9, 1, 6, 6, 8, 1, 7]],\n\n [[5, 9, 5, 7, 3, 2, 1, 0, 9, 5],\n [9, 8, 7, 3, 1, 7, 6, 6, 0, 5],\n [8, 2, 9, 7, 2, 9, 4, 4, 0, 8],\n [2, 8, 2, 2, 0, 6, 6, 8, 6, 9],\n [5, 5, 2, 2, 3, 5, 9, 9, 3, 4]],\n\n [[3, 6, 4, 6, 3, 2, 4, 6, 9, 0],\n [7, 1, 6, 7, 7, 2, 6, 2, 2, 8],\n [2, 3, 6, 2, 5, 5, 2, 6, 2, 0],\n [3, 9, 8, 5, 1, 5, 7, 8, 7, 9],\n [9, 2, 1, 5, 2, 7, 0, 7, 4, 3]]])\n (3 traj, 5 obsv, 10 feat)\n\n``` python\n# Trajectories(arr).transpose(1, 0, 2)\n```\n\n Trajectories([[[9, 7, 1, 4, 8, 2, 3, 3, 3, 1],\n [5, 9, 5, 7, 3, 2, 1, 0, 9, 5],\n [3, 6, 4, 6, 3, 2, 4, 6, 9, 0]],\n\n [[0, 3, 8, 7, 2, 9, 9, 9, 1, 7],\n [9, 8, 7, 3, 1, 7, 6, 6, 0, 5],\n [7, 1, 6, 7, 7, 2, 6, 2, 2, 8]],\n\n [[0, 8, 5, 3, 3, 8, 8, 1, 3, 8],\n [8, 2, 9, 7, 2, 9, 4, 4, 0, 8],\n [2, 3, 6, 2, 5, 5, 2, 6, 2, 0]],\n\n [[3, 6, 9, 1, 8, 7, 7, 3, 1, 3],\n [2, 8, 2, 2, 0, 6, 6, 8, 6, 9],\n [3, 9, 8, 5, 1, 5, 7, 8, 7, 9]],\n\n [[0, 0, 2, 9, 1, 6, 6, 8, 1, 7],\n [5, 5, 2, 2, 3, 5, 9, 9, 3, 4],\n [9, 2, 1, 5, 2, 7, 0, 7, 4, 3]]])\n (5 obsv, 3 traj, 10 feat)\n\n``` python\n# Trajectories(arr).transpose('obsv', 0, 2)\n```\n\n Trajectories([[[9, 7, 1, 4, 8, 2, 3, 3, 3, 1],\n [5, 9, 5, 7, 3, 2, 1, 0, 9, 5],\n [3, 6, 4, 6, 3, 2, 4, 6, 9, 0]],\n\n [[0, 3, 8, 7, 2, 9, 9, 9, 1, 7],\n [9, 8, 7, 3, 1, 7, 6, 6, 0, 5],\n [7, 1, 6, 7, 7, 2, 6, 2, 2, 8]],\n\n [[0, 8, 5, 3, 3, 8, 8, 1, 3, 8],\n [8, 2, 9, 7, 2, 9, 4, 4, 0, 8],\n [2, 3, 6, 2, 5, 5, 2, 6, 2, 0]],\n\n [[3, 6, 9, 1, 8, 7, 7, 3, 1, 3],\n [2, 8, 2, 2, 0, 6, 6, 8, 6, 9],\n [3, 9, 8, 5, 1, 5, 7, 8, 7, 9]],\n\n [[0, 0, 2, 9, 1, 6, 6, 8, 1, 7],\n [5, 5, 2, 2, 3, 5, 9, 9, 3, 4],\n [9, 2, 1, 5, 2, 7, 0, 7, 4, 3]]])\n (5 obsv, 3 traj, 10 feat)\n\n``` python\n# Trajectories(arr).transpose('obsv', 0, 2).to_obsv_x_traj()\n```\n\n NameError: name 'aggr' is not defined\n",
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