PyGMI
=====
.. |pythonversion| image:: https://img.shields.io/pypi/pyversions/pygmi
:alt: PyPI - Python Version
.. |pygmiversion| image:: https://img.shields.io/pypi/v/pygmi
:alt: PyPI - Version
.. |pygmilicence| image:: https://img.shields.io/github/license/patrick-cole/pygmi
:alt: GitHub License
|pythonversion| |pygmiversion| |pygmilicence|
Overview
--------
PyGMI stands for Python Geoscience Modelling and Interpretation. It is a modelling and interpretation suite aimed at magnetic, gravity, remote sensing and other datasets. PyGMI has a graphical user interface, and is meant to be run as such.
PyGMI is developed at the `Council for Geoscience <http://www.geoscience.org.za>`_ (Geological Survey of South Africa).
It includes:
* Magnetic and Gravity 3D forward modelling.
* Cluster Analysis, including use of scikit-learn libraries.
* Routines for cutting, reprojecting and doing simple modifications to data.
* Convenient display of data using pseudo-color, ternary and sunshaded representation.
* MT processing and 1D inversion using MTpy.
* Gravity processing.
* Seismological functions for SEISAN data.
* Remote sensing ratios and improved imports.
It is released under the `Gnu General Public License version 3.0 <http://www.gnu.org/copyleft/gpl.html>`_
The PyGMI `Wiki <http://patrick-cole.github.io/pygmi/index.html>`_ pages, include installation and full usage! Contributors can check this `link <https://github.com/Patrick-Cole/pygmi/blob/pygmi3/CONTRIBUTING.md>`_ for ways to contribute.
The latest release version (including windows installers) can be found `here <https://github.com/Patrick-Cole/pygmi/releases>`_.
You may need to install the `Microsoft Visual C++ Redistributable for Visual Studio 2015, 2017 and 2019 <https://support.microsoft.com/en-us/help/2977003/the-latest-supported-visual-c-downloads>`_.
If you have any comments or queries, you can contact the author either through `GitHub <https://github.com/Patrick-Cole/pygmi>`_ or via email at pcole@geoscience.org.za
Installation
------------
The simplest installation of PyGMI is on Windows, using a pre-built installer at `64-bit <https://github.com/Patrick-Cole/pygmi/releases>`_.
If you prefer building from source, you can use PyPi or Conda.
Once built using PyPi, running pygmi can be done at the command prompt as follows:
pygmi
If you are in python, you can run PyGMI by using the following commands:
from pygmi.main import main
main()
If you prefer not to install pygmi as a library, download the source code and execute the following command to run it manually:
python quickstart.py
Requirements
^^^^^^^^^^^^
PyGMI will run on both Windows and Linux. It should be noted that the main development is done in Python 3.12 on Windows.
PyGMI should still work with Python 3.11.
PyGMI is developed and has been tested with the following libraries in order to function:
* fiona 1.9.5
* geopandas 0.14.4
* h5netcdf 1.3.0
* matplotlib 3.9.0
* mtpy 1.1.5
* natsort 8.4.0
* numexpr 2.10.1
* openpyxl 3.1.2
* psutil 6.0.0
* pyopengl 3.1.7
* pyqt5 5.15.10
* pytest 8.2.2
* rasterio 1.3.9
* rioxarray 0.15.6
* scikit-image 0.24.0
* shapelysmooth 0.2.0
* simpeg 0.21.1
PyPi - Windows
^^^^^^^^^^^^^^
Windows users can use the `WinPython <https://winpython.github.io/>`_ distribution as an alternative to Anaconda. It comes with most libraries preinstalled, so using pip should be sufficient.
Install with the following command.
pip install pygmi
Should you wish to manually install binaries, related binaries can be obtained at the `website <https://github.com/cgohlke/geospatial-wheels/>`_ by Christoph Gohlke.
If you wish to update GDAL, you will need to download and install:
* fiona
* GDAL
* pyproj
* rasterio
* Rtree
* shapely
All these binaries should be downloaded since they have internal co-dependencies.
PyPi - Linux
^^^^^^^^^^^^
Linux normally comes with python installed, but the additional libraries will still need to be installed.
The process is as follows:
sudo apt-get install pipx
pipx ensurepath
pipx install pygmi
Once installed, running pygmi can be done at the command prompt as follows:
pygmi
If you get the following error: *qt.qpa.plugin: Could not load the Qt platform plugin "xcb" in "" even though it was found.*, then you can try the following command, since this is Linux issue:
sudo apt-get install libxcb-xinerama0
Anaconda
^^^^^^^^
Anaconda users are advised not to use pip since it can break PyQt5. However, one package is installed only by pip, so a Conda environment should be created.
The process to install is as follows:
conda create -n pygmi python=3.12
conda activate pygmi
conda config --add channels conda-forge
conda config --set channel_priority flexible
conda install pyqt
conda install fiona
conda install matplotlib
conda install psutil
conda install numexpr
conda install rasterio
conda install geopandas
conda install natsort
conda install scikit-image
conda install pyopengl
conda install simpeg
conda install shapelysmooth
conda install openpyxl
conda install h5netcdf
conda install rioxarray
conda install pytest
pip install mtpy
conda update --all
Once this is done, download pygmi, extract (unzip) it to a directory, and run it from its root directory with the following command:
python quickstart.py
References
----------
* Cole, P. 2012, Development of a 3D Potential Field Forward Modelling System in Python, AGU fall meeting, 3-7 December, San Francisco, USA
* Cole, P. 2013, PyGMI – The use of Python in geophysical modelling and interpretation. South African Geophysical Association, 13th Biennial Conference, Skukuza Rest Camp, Kruger National Park (7-9 October)
* Cole, P. 2014, The history and design behind the Python Geophysical Modelling and Interpretation (PyGMI) package, SciPy 2014, Austin, Texas (6-12 July)
* Cole, P. 2016, The continued evolution of the open source PyGMI project. 35th IGC, Cape Town.
Raw data
{
"_id": null,
"home_page": null,
"name": "pygmi",
"maintainer": null,
"docs_url": null,
"requires_python": ">=3.11",
"maintainer_email": "Patrick Cole <pcole@geoscience.org.za>",
"keywords": "Geoscience, Geophysics, Magnetic, Gravity, Modelling, Interpretation, Remote Sensing",
"author": null,
"author_email": "Patrick Cole <pcole@geoscience.org.za>",
"download_url": "https://files.pythonhosted.org/packages/76/bb/8c9681966ed06bcfa0c28042bf9b4eee1a2c744667c86ecc2aa0ca779241/pygmi-3.2.8.21.tar.gz",
"platform": null,
"description": "PyGMI\r\n=====\r\n\r\n.. |pythonversion| image:: https://img.shields.io/pypi/pyversions/pygmi\r\n :alt: PyPI - Python Version\r\n.. |pygmiversion| image:: https://img.shields.io/pypi/v/pygmi\r\n :alt: PyPI - Version\r\n.. |pygmilicence| image:: https://img.shields.io/github/license/patrick-cole/pygmi\r\n :alt: GitHub License\r\n\r\n\r\n|pythonversion| |pygmiversion| |pygmilicence|\r\n\r\nOverview\r\n--------\r\n\r\nPyGMI stands for Python Geoscience Modelling and Interpretation. It is a modelling and interpretation suite aimed at magnetic, gravity, remote sensing and other datasets. PyGMI has a graphical user interface, and is meant to be run as such.\r\n\r\nPyGMI is developed at the `Council for Geoscience <http://www.geoscience.org.za>`_ (Geological Survey of South Africa).\r\n\r\nIt includes:\r\n\r\n* Magnetic and Gravity 3D forward modelling.\r\n* Cluster Analysis, including use of scikit-learn libraries.\r\n* Routines for cutting, reprojecting and doing simple modifications to data.\r\n* Convenient display of data using pseudo-color, ternary and sunshaded representation.\r\n* MT processing and 1D inversion using MTpy.\r\n* Gravity processing.\r\n* Seismological functions for SEISAN data.\r\n* Remote sensing ratios and improved imports.\r\n\r\nIt is released under the `Gnu General Public License version 3.0 <http://www.gnu.org/copyleft/gpl.html>`_\r\n\r\nThe PyGMI `Wiki <http://patrick-cole.github.io/pygmi/index.html>`_ pages, include installation and full usage! Contributors can check this `link <https://github.com/Patrick-Cole/pygmi/blob/pygmi3/CONTRIBUTING.md>`_ for ways to contribute.\r\n\r\nThe latest release version (including windows installers) can be found `here <https://github.com/Patrick-Cole/pygmi/releases>`_.\r\n\r\nYou may need to install the `Microsoft Visual C++ Redistributable for Visual Studio 2015, 2017 and 2019 <https://support.microsoft.com/en-us/help/2977003/the-latest-supported-visual-c-downloads>`_.\r\n\r\nIf you have any comments or queries, you can contact the author either through `GitHub <https://github.com/Patrick-Cole/pygmi>`_ or via email at pcole@geoscience.org.za\r\n\r\n\r\nInstallation\r\n------------\r\nThe simplest installation of PyGMI is on Windows, using a pre-built installer at `64-bit <https://github.com/Patrick-Cole/pygmi/releases>`_.\r\n\r\nIf you prefer building from source, you can use PyPi or Conda.\r\n\r\nOnce built using PyPi, running pygmi can be done at the command prompt as follows:\r\n\r\n pygmi\r\n\r\nIf you are in python, you can run PyGMI by using the following commands:\r\n\r\n from pygmi.main import main\r\n\r\n main()\r\n\r\nIf you prefer not to install pygmi as a library, download the source code and execute the following command to run it manually:\r\n\r\n python quickstart.py\r\n\r\nRequirements\r\n^^^^^^^^^^^^\r\nPyGMI will run on both Windows and Linux. It should be noted that the main development is done in Python 3.12 on Windows.\r\n\r\nPyGMI should still work with Python 3.11.\r\n\r\nPyGMI is developed and has been tested with the following libraries in order to function:\r\n\r\n* fiona 1.9.5\r\n* geopandas 0.14.4\r\n* h5netcdf 1.3.0\r\n* matplotlib 3.9.0\r\n* mtpy 1.1.5\r\n* natsort 8.4.0\r\n* numexpr 2.10.1\r\n* openpyxl 3.1.2\r\n* psutil 6.0.0\r\n* pyopengl 3.1.7\r\n* pyqt5 5.15.10\r\n* pytest 8.2.2\r\n* rasterio 1.3.9\r\n* rioxarray 0.15.6\r\n* scikit-image 0.24.0\r\n* shapelysmooth 0.2.0\r\n* simpeg 0.21.1\r\n\r\nPyPi - Windows\r\n^^^^^^^^^^^^^^\r\nWindows users can use the `WinPython <https://winpython.github.io/>`_ distribution as an alternative to Anaconda. It comes with most libraries preinstalled, so using pip should be sufficient.\r\n\r\nInstall with the following command.\r\n\r\n pip install pygmi\r\n\r\nShould you wish to manually install binaries, related binaries can be obtained at the `website <https://github.com/cgohlke/geospatial-wheels/>`_ by Christoph Gohlke.\r\n\r\nIf you wish to update GDAL, you will need to download and install:\r\n\r\n* fiona\r\n* GDAL\r\n* pyproj\r\n* rasterio\r\n* Rtree\r\n* shapely\r\n\r\nAll these binaries should be downloaded since they have internal co-dependencies.\r\n\r\n\r\nPyPi - Linux\r\n^^^^^^^^^^^^\r\nLinux normally comes with python installed, but the additional libraries will still need to be installed.\r\n\r\nThe process is as follows:\r\n\r\n sudo apt-get install pipx\r\n \r\n pipx ensurepath\r\n\r\n pipx install pygmi\r\n\r\nOnce installed, running pygmi can be done at the command prompt as follows:\r\n\r\n pygmi\r\n\r\nIf you get the following error: *qt.qpa.plugin: Could not load the Qt platform plugin \"xcb\" in \"\" even though it was found.*, then you can try the following command, since this is Linux issue:\r\n\r\n sudo apt-get install libxcb-xinerama0\r\n\r\nAnaconda\r\n^^^^^^^^\r\nAnaconda users are advised not to use pip since it can break PyQt5. However, one package is installed only by pip, so a Conda environment should be created.\r\n\r\nThe process to install is as follows:\r\n\r\n conda create -n pygmi python=3.12\r\n\r\n conda activate pygmi\r\n\r\n conda config --add channels conda-forge\r\n\r\n conda config --set channel_priority flexible\r\n\r\n conda install pyqt\r\n\r\n conda install fiona\r\n\r\n conda install matplotlib\r\n\r\n conda install psutil\r\n\r\n conda install numexpr\r\n\r\n conda install rasterio\r\n\r\n conda install geopandas\r\n\r\n conda install natsort\r\n\r\n conda install scikit-image\r\n\r\n conda install pyopengl\r\n\r\n conda install simpeg\r\n\r\n conda install shapelysmooth\r\n\r\n conda install openpyxl\r\n\r\n conda install h5netcdf\r\n\r\n conda install rioxarray\r\n\r\n conda install pytest\r\n\r\n pip install mtpy\r\n\r\n conda update --all\r\n\r\nOnce this is done, download pygmi, extract (unzip) it to a directory, and run it from its root directory with the following command:\r\n\r\n python quickstart.py\r\n\r\nReferences\r\n----------\r\n\r\n* Cole, P. 2012, Development of a 3D Potential Field Forward Modelling System in Python, AGU fall meeting, 3-7 December, San Francisco, USA\r\n* Cole, P. 2013, PyGMI \u2013 The use of Python in geophysical modelling and interpretation. South African Geophysical Association, 13th Biennial Conference, Skukuza Rest Camp, Kruger National Park (7-9 October)\r\n* Cole, P. 2014, The history and design behind the Python Geophysical Modelling and Interpretation (PyGMI) package, SciPy 2014, Austin, Texas (6-12 July)\r\n* Cole, P. 2016, The continued evolution of the open source PyGMI project. 35th IGC, Cape Town.\r\n",
"bugtrack_url": null,
"license": "GNU General Public License v3 (GPLv3)",
"summary": "Python Geoscience Modelling and Interpretation",
"version": "3.2.8.21",
"project_urls": {
"changelog": "https://github.com/Patrick-Cole/pygmi/blob/pygmi3/CHANGES.rst",
"documentation": "https://patrick-cole.github.io/pygmi/wiki.html",
"homepage": "http://patrick-cole.github.io/pygmi/",
"repository": "https://github.com/Patrick-Cole/pygmi.git"
},
"split_keywords": [
"geoscience",
" geophysics",
" magnetic",
" gravity",
" modelling",
" interpretation",
" remote sensing"
],
"urls": [
{
"comment_text": "",
"digests": {
"blake2b_256": "40584996a8843f129dcdc81ad62fcb95b9523ec4c7659f44f4593e8f16ea138a",
"md5": "87a46ee49b707a0e5f99fe10f610a423",
"sha256": "a20fd8192dc063d9fe70d4d73101826aa2a77ea3ff3a87b863f23d19fe178da5"
},
"downloads": -1,
"filename": "pygmi-3.2.8.21-py3-none-any.whl",
"has_sig": false,
"md5_digest": "87a46ee49b707a0e5f99fe10f610a423",
"packagetype": "bdist_wheel",
"python_version": "py3",
"requires_python": ">=3.11",
"size": 698352,
"upload_time": "2024-10-01T13:04:23",
"upload_time_iso_8601": "2024-10-01T13:04:23.890346Z",
"url": "https://files.pythonhosted.org/packages/40/58/4996a8843f129dcdc81ad62fcb95b9523ec4c7659f44f4593e8f16ea138a/pygmi-3.2.8.21-py3-none-any.whl",
"yanked": false,
"yanked_reason": null
},
{
"comment_text": "",
"digests": {
"blake2b_256": "76bb8c9681966ed06bcfa0c28042bf9b4eee1a2c744667c86ecc2aa0ca779241",
"md5": "432b160058790eba0595164c2881801e",
"sha256": "3fde7a5e026c2c28586002d989b18873ffacab9728085b88bc0f35ac3680d28f"
},
"downloads": -1,
"filename": "pygmi-3.2.8.21.tar.gz",
"has_sig": false,
"md5_digest": "432b160058790eba0595164c2881801e",
"packagetype": "sdist",
"python_version": "source",
"requires_python": ">=3.11",
"size": 602462,
"upload_time": "2024-10-01T13:04:25",
"upload_time_iso_8601": "2024-10-01T13:04:25.849754Z",
"url": "https://files.pythonhosted.org/packages/76/bb/8c9681966ed06bcfa0c28042bf9b4eee1a2c744667c86ecc2aa0ca779241/pygmi-3.2.8.21.tar.gz",
"yanked": false,
"yanked_reason": null
}
],
"upload_time": "2024-10-01 13:04:25",
"github": true,
"gitlab": false,
"bitbucket": false,
"codeberg": false,
"github_user": "Patrick-Cole",
"github_project": "pygmi",
"travis_ci": false,
"coveralls": false,
"github_actions": true,
"requirements": [
{
"name": "fiona",
"specs": [
[
">=",
"1.9.5"
]
]
},
{
"name": "geopandas",
"specs": [
[
">=",
"0.14.4"
]
]
},
{
"name": "h5netcdf",
"specs": [
[
">=",
"1.3.0"
]
]
},
{
"name": "matplotlib",
"specs": [
[
">=",
"3.9.0"
]
]
},
{
"name": "mtpy",
"specs": [
[
">=",
"1.1.5"
]
]
},
{
"name": "natsort",
"specs": [
[
">=",
"8.4.0"
]
]
},
{
"name": "numexpr",
"specs": [
[
">=",
"2.10.1"
]
]
},
{
"name": "openpyxl",
"specs": [
[
">=",
"3.1.2"
]
]
},
{
"name": "psutil",
"specs": [
[
">=",
"6.0.0"
]
]
},
{
"name": "pyopengl",
"specs": [
[
">=",
"3.1.7"
]
]
},
{
"name": "pyqt5",
"specs": [
[
">=",
"5.15.10"
]
]
},
{
"name": "pytest",
"specs": [
[
">=",
"8.2.2"
]
]
},
{
"name": "rasterio",
"specs": [
[
">=",
"1.3.9"
]
]
},
{
"name": "rioxarray",
"specs": [
[
">=",
"0.15.6"
]
]
},
{
"name": "scikit-image",
"specs": [
[
">=",
"0.24.0"
]
]
},
{
"name": "shapelysmooth",
"specs": [
[
">=",
"0.2.0"
]
]
},
{
"name": "simpeg",
"specs": [
[
">=",
"0.21.1"
]
]
}
],
"lcname": "pygmi"
}
JSON
