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bmmltools-0.2.8
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BioMaterial Machine Learning tools (bmmltools), package to do machine learning with large binary 3d images
| ویژگی | مقدار |
|---|---|
| سیستم عامل | - |
| نام فایل | bmmltools-0.2.8 |
| نام | bmmltools |
| نسخه کتابخانه | 0.2.8 |
| نگهدارنده | [] |
| ایمیل نگهدارنده | [] |
| نویسنده | Luca Curcuraci |
| ایمیل نویسنده | Luca.Curcuraci@mpikg.mpg.de |
| آدرس صفحه اصلی | https://gitlab.mpikg.mpg.de/curcuraci/bmmltools |
| آدرس اینترنتی | https://pypi.org/project/bmmltools/ |
| مجوز | - |
# bmmltools
Current version 0.2.8
Last update 26/10/2022
PyPI: https://pypi.org/project/bmmltools/
Documentation: https://bmmltools.readthedocs.io/en/latest/
Author: Curcuraci L.
Contacts: Luca.Curcuraci@mpikg.mpg.de
This is a python library for 3d binary image segmentation developed at Max-Plank-Institute fuer Kolloid-und
Grenzflaechenforschung. This library contains a series of tools which can be useful to segment 3d binary images
based on their structural/texture properties and extract information from the various regions identified,
### Installation
To install bmmltools use the Anaconda propt. In the propt, copy the lines below
```
(base) > conda create -n new_env python=3.8
(base) > conda activate new_env
(new_env) > conda install pytables=3.6.1
(new_env) > conda install hdbscan
(new_env) > pip install bmmltools
```
> **Possible import errors:**
>
> If other packages are installed togheter with bmmltools, the following import error may appear some case:
>
> 1. *hdbscan related import error*: typically this error is related to the "cachedir" variable and happens as soon one
> imports the ```HDBSCAN()``` class. This is not an error of hdbscan, but it is related to the *joblib* package, which
> has been recently (september 2022) updated to the 1.2.0 version in which the "cachedir" variables has been renamed.
> The hdbscan module needs the version 1.10 of joblib to work without problems (maybe the 1.1.1 version is fine to),
> therefore if you experience an import error of this kind, check if joblib is present in the correct version. If is
> not, uninstall it and install the correct version. This import error should disappear.
### Result visualization: bmmlboard
To inspect the intermediate results, a series of standard visualization tools has been developed. They are collected
in the **bmmlboard**, a web-browser based a graphical interface made using streamlit, which can be used to visualize
the intermediate results of bmmltools. To run the bmmlboard, write in the anaconda prompt
```
(base) > conda activate new_env
(new_env) > python -m bmmltools.run_bmmlboard
```
assuming that bmmltools is installed in the "new_env" environment.
> **Possible streamlit errors**:
>
> Sometimes streamlit does not work on some computer. This may not be a streamlit related issue, rather an issue related
> to the permit to write certain environmental variables on the computer during the installation process. Clearly one
> can solve this problem by reinstalling everything with suitable flags, but an simpler and effective solution can be
> the following:
>
> 1. Download on the computer the content of the folder ``board``, which can be found in the folder ``src/bmmltools`` of
> this repository.
>
> 2. Run in the same python environment where the bmmltools has been installed the file ``home.py`` inside the
> downloaded folder with streamlit, namely write in an Anaconda prompt
>
> ```
> (new_env) > conda activate new_env
> (new_env) > cd [PATH TO THE board FOLDER]
> (new_env) [PATH TO THE board FOLDER] > streamlit run home.py
> ```
## Example usage
A series of example scripts are available in the 'example folder' of this repository. A detailed explanation of what
they do can be founs in the "Miscellaneous" section of the bmmmltools documentation.
نیازمندی
| مقدار | نام |
|---|---|
| ==0.3.4 | dill |
| ==1.2.6 | GPyOpt |
| ==2.10.0 | h5py |
| ==2.9.0 | imageio |
| ==1.1.0 | joblib |
| ==1.3.1 | mkl-fft |
| - | numpy |
| ==1.3.2 | pandas |
| ==5.10.0 | plotly |
| ==4.9.1 | pyshtools |
| ==0.2.1 | pyvis |
| ==0.18.1 | scikit-image |
| ==1.1.2 | scikit-learn |
| - | scipy |
| ==0.11.2 | seaborn |
| ==1.12.0 | streamlit |
| ==0.0.2 | stvis |
| ==4.62.1 | tqdm |
| ==3.4.2 | matplotlib |
زبان مورد نیاز
| مقدار | نام |
|---|---|
| >=3.8 | Python |
نحوه نصب
نصب پکیج whl bmmltools-0.2.8:
pip install bmmltools-0.2.8.whl
نصب پکیج tar.gz bmmltools-0.2.8:
pip install bmmltools-0.2.8.tar.gz