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Generate different types of sparsity pattern for sparse matrices.

Project description

Binder

sparsity-pattern

Generate different types of sparsity pattern for sparse matrices.

Installation

The sparsity-pattern git repo is available as PyPi package

pip install sparsity-pattern
pip install git+ssh://git@github.com/ulf1/sparsity-pattern.git

Usage

The block-diagonal pattern for tensorflow

import sparsity_pattern
import tensorflow as tf

n_rows, n_cols = 10, 12
idx = sparsity_pattern.get('block', min(n_rows, n_cols), block_sizes=[3, 1, 2])

mat = tf.sparse.SparseTensor(
    dense_shape=(n_rows, n_cols),
    indices=tf.convert_to_tensor(idx, dtype=tf.int64),
    values=range(1, len(idx)+1))

print(tf.sparse.to_dense(mat))

The circle pattern for pytorch

import sparsity_pattern
import torch

n_rows, n_cols = 5, 7
idx = sparsity_pattern.get('circle', min(n_rows, n_cols), offsets=[1, 2])

mat = torch.sparse_coo_tensor(
    indices=torch.tensor(idx).transpose(0, 1), 
    values=range(1, len(idx)+1),
    size=[n_rows, n_cols])

print(mat.to_dense())

The triu pattern for scipy

import sparsity_pattern
import scipy.sparse
import numpy as np

n, k = 4, -1
idx = sparsity_pattern.get('triu', n, k)
idx_rows, idx_cols = np.array(idx)[:, 0], np.array(idx)[:, 1]
mat = scipy.sparse.lil_matrix((n, n), dtype=np.int64)
mat[idx_rows, idx_cols] = range(1, len(idx)+1)

print(mat.todense())

Check the examples folder for more notebooks.

Appendix

Install a virtual environment

python3.6 -m venv .venv
source .venv/bin/activate
pip3 install --upgrade pip
pip3 install -r requirements.txt

(If your git repo is stored in a folder with whitespaces, then don't use the subfolder .venv. Use an absolute path without whitespaces.)

Python commands

  • Jupyter for the examples: jupyter lab
  • Check syntax: flake8 --ignore=F401 --exclude=$(grep -v '^#' .gitignore | xargs | sed -e 's/ /,/g')
  • Run Unit Tests: pytest
  • Upload to PyPi with twine: python setup.py sdist && twine upload -r pypi dist/*

Clean up

find . -type f -name "*.pyc" | xargs rm
find . -type d -name "__pycache__" | xargs rm -r
rm -r .pytest_cache
rm -r .venv

Support

Please open an issue for support.

Contributing

Please contribute using Github Flow. Create a branch, add commits, and open a pull request.

Project details


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