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clustviz-0.0.6b0
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مشاهده بیشترتوضیحات
A 2D clustering algorithms visualization package
| ویژگی | مقدار |
|---|---|
| سیستم عامل | - |
| نام فایل | clustviz-0.0.6b0 |
| نام | clustviz |
| نسخه کتابخانه | 0.0.6b0 |
| نگهدارنده | [] |
| ایمیل نگهدارنده | [] |
| نویسنده | Guglielmo Sanchini |
| ایمیل نویسنده | guglielmosanchini@gmail.com |
| آدرس صفحه اصلی | https://github.com/guglielmosanchini/ClustViz |
| آدرس اینترنتی | https://pypi.org/project/clustviz/ |
| مجوز | - |
[](https://travis-ci.com/guglielmosanchini/ClustViz)
[](https://codecov.io/gh/guglielmosanchini/ClustViz)
[](https://clustviz.readthedocs.io/en/latest/?badge=latest)
[](https://www.python.org/dev/peps/pep-0008/)
[](https://opensource.org/licenses/MIT)
# ClustViz
<img src="https://raw.githubusercontent.com/guglielmosanchini/ClustViz/master/data/clustviz_logo.png" width="200" height="200">
## 2D Clustering Algorithms Visualization
#### Check out [ClustVizGUI](https://github.com/guglielmosanchini/ClustVizGUI), too!
The aim of ```ClustViz``` is to visualize every step of each clustering algorithm, in the case of 2D input data.
The following algorithms have been examined:
- OPTICS
- DBSCAN
- HDBSCAN
- SPECTRAL CLUSTERING
- HIERARCHICAL AGGLOMERATIVE CLUSTERING
- single linkage
- complete linkage
- average linkage
- Ward's method
- CURE
- BIRCH
- PAM
- CLARA
- CLARANS
- CHAMELEON
- CHAMELEON2
- DENCLUE
## Instructions
**Documentation**: [click here](https://clustviz.readthedocs.io/en/latest/)
Install with
```python
pip install clustviz
```
To run BIRCH algorithm, the open source visualization software Graphviz is required.
Install Graphviz from the official webpage (https://graphviz.gitlab.io/download/) or using HomeBrew, then
modify the PATH variable as follows (replace the string according to the path where you installed Graphviz):
```python
import os
# on Windows usually
os.environ["PATH"] += os.pathsep + 'C:/Program Files (x86)/Graphviz2.38/bin'
# on MacOS usually
os.environ["PATH"] += os.pathsep + '/usr/local/bin'
```
To run CHAMELEON and CHAMELEON2 algorithms, the [METIS](https://metis.readthedocs.io/en/latest/) library is required.
To install it on MacOS, execute the following commands (partially taken from [here](http://glaros.dtc.umn.edu/gkhome/metis/metis/download)):
```bash
# download the file using wget (do it from the website if you prefer)
wget http://glaros.dtc.umn.edu/gkhome/fetch/sw/metis/metis-5.1.0.tar.gz
# uncompress it
gunzip metis-5.1.0.tar.gz
# untar it
tar -xvf metis-5.1.0.tar
# remove the tar
rm metis-5.1.0.tar
# go inside the folder
cd metis-5.1.0
# install it using make
make config shared=1
make install
# export the dll
export METIS_DLL=/usr/local/lib/libmetis.dylib
```
To install METIS on Windows, go to [conda-metis](https://github.com/guglielmosanchini/conda-metis) and follow the instructions.
## Usage
Let's see a basic example using OPTICS:
```python
from clustviz.optics import OPTICS, plot_clust
from sklearn.datasets import make_blobs
# create a random dataset
X, y = make_blobs(n_samples=30, centers=4, n_features=2, cluster_std=1.8, random_state=42)
# perform OPTICS algorithm, with plotting enabled
ClustDist, CoreDist = OPTICS(X, eps=2, minPTS=3, plot=True, plot_reach=True)
# plot the final clusters
plot_clust(X, ClustDist, CoreDist, eps=2, eps_db=1.9)
```
For many other examples, take a look at the detailed [clustviz_example](https://github.com/guglielmosanchini/ClustViz/blob/master/data/clustviz_example.ipynb) notebook.
## Repository structure
1) The folder ```data/DOCUMENTS``` contains all the official papers, powerpoint presentations and other PDFs regarding all the algorithms involved and clustering in general.
2) The folder ```clustviz``` contains the scripts necessary to run the clustering algorithms.
3) The notebook ```data/clustviz_example.ipynb``` lets the user run every algorithm on 2D datasets; it contains a subsection for every algorithm, with the necessary modules and functions imported and some commented lines of code which can be uncommented to run the algorithms.
4) The folder ```docs``` contains the necessary files to build the documentation using Sphinx and ReadTheDocs.
5) The folder ```tests``` contains pytest tests.
## Credits for some algorithms
I did not start to write the scripts for each algorithm from scratch; in some cases I modified some Python libraries, in other cases I took some publicly available GitHub repositories and modified the scripts contained there. The following list provides all the sources used when I did not write all the code by myself:
- HDBSCAN
https://hdbscan.readthedocs.io/en/latest/
- SPECTRAL CLUSTERING
http://dx.doi.org/10.1007/s11222-007-9033-z
- BIRCH
https://github.com/annoviko/pyclustering/blob/master/pyclustering/cluster/birch.py
- PAM
https://github.com/SachinKalsi/kmedoids/blob/master/KMedoids.py
- CLARA
https://github.com/akalino/Clustering/blob/master/clara.py
- CLARANS
https://github.com/annoviko/pyclustering/blob/master/pyclustering/cluster/clarans.py
- CHAMELEON
https://github.com/Moonpuck/chameleon_cluster
The other algorithms have been implemented from scratch following the relative papers. Thanks to Darius (https://github.com/dariomonici),
the GUI Meister, for the help with PyQt5, used for [ClustVizGUI](https://github.com/guglielmosanchini/ClustVizGUI).
## Possible improvements
- add more clustering algorithms
- comment every code block and improve code quality
- pymetis doesnt work on Windows, but could be an option for MacOS
- add highlights to docstrings using ``
- show aliases typehints using Sphinx (open issue)
## TravisCI path
- if Travis CI doesn't trigger, it is probably because ```.travis.yml``` isn't properly formatted. Use
```yamllint``` to correct it
- add package update
- for the deployment phase: brew install ruby, brew install travis
- added empty conftest.py in clustviz folder for tests in windows version
نیازمندی
| مقدار | نام |
|---|---|
| - | metis-python |
| >=1.0.1 | pandas |
| >=1.18.1 | numpy |
| <=2.5 | networkx |
| >=0.9.3.1 | pyclustering |
| >=2.6.1 | imageio |
| >=4.42.1 | tqdm |
| <=3.3.3 | matplotlib |
| >=1.4.1 | scipy |
| ==0.13.2 | graphviz |
| >=0.22.1 | scikit-learn |
زبان مورد نیاز
| مقدار | نام |
|---|---|
| >=3.6 | Python |
نحوه نصب
نصب پکیج whl clustviz-0.0.6b0:
pip install clustviz-0.0.6b0.whl
نصب پکیج tar.gz clustviz-0.0.6b0:
pip install clustviz-0.0.6b0.tar.gz