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fractopo-0.5.2
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مشاهده بیشترتوضیحات
Fracture Network Analysis
| ویژگی | مقدار |
|---|---|
| سیستم عامل | - |
| نام فایل | fractopo-0.5.2 |
| نام | fractopo |
| نسخه کتابخانه | 0.5.2 |
| نگهدارنده | [] |
| ایمیل نگهدارنده | [] |
| نویسنده | nialov |
| ایمیل نویسنده | nikolasovaskainen@gmail.com |
| آدرس صفحه اصلی | https://github.com/nialov/fractopo |
| آدرس اینترنتی | https://pypi.org/project/fractopo/ |
| مجوز | MIT |
fractopo
========
|Documentation Status| |PyPI Status| |CI Test| |Conda Test| |Coverage| |Binder| |Zenodo|
``fractopo`` is a Python library/application that contains tools for
validating and analysing lineament and fracture trace maps (fracture
networks). It is targeted at structural geologists working on the
characterization of bedrock fractures from outcrops and through remote
sensing. As it is a Python library, the use of ``fractopo`` requires
prior (Python) programming knowledge.
- `Full Documentation is hosted on Read the Docs
<https://fractopo.readthedocs.io/en/latest/index.html#full-documentation>`__
.. figure:: https://git.io/JBRuK
:alt: Overview of fractopo
Overview of fractopo
.. figure:: /docs_src/imgs/fractopo-visualizations.png
:alt: Data visualization
Visualisation of ``fractopo`` data. ``fractopo`` analyses the trace
data that can e.g. be digitized from drone orthophotographs
(=fractures) or from digital elevation models (=lineaments). The
displayed branches and nodes are extracted with ``fractopo``.
Installation
------------
``pip`` and ``poetry`` installation only supported for ``linux`` -based
operating systems. For Windows and MacOS install using `(ana)conda <#conda>`__.
For ``pip`` and ``poetry``: Omit ``--dev`` or ``[dev]`` for regular
installation. Keep if you want to test/develop or otherwise install all
development Python dependencies.
conda
~~~~~
- Only (supported) installation method for ``Windows`` and ``MacOS``!
.. code:: bash
# Create new environment for fractopo (recommended but optional)
conda env create fractopo-env
conda activate fractopo-env
# Available on conda-forge channel
conda install -c conda-forge fractopo
pip
~~~
The module is on `PyPI <https://www.pypi.org>`__.
.. code:: bash
# Non-development installation
pip install fractopo
Or locally for development:
.. code:: bash
git clone https://github.com/nialov/fractopo
cd fractopo
# Omit [dev] from end if you do not want installation for development
pip install --editable .[dev]
poetry
~~~~~~
For usage:
.. code:: bash
poetry add fractopo
For development:
.. code:: bash
git clone https://github.com/nialov/fractopo
cd fractopo
poetry install
Usage
-----
``fractopo`` has two main use cases:
1. Validation of lineament & fracture trace data
2. Analysis of lineament & fracture trace data
Validation is done to make sure the data is valid for the analysis and
is crucial as analysis cannot take into account different kinds of
geometric and topological inconsistencies between the traces.
Capabilities and associated guides are inexhaustively listed in the
table below.
======================================================== ======================
Functionality Tutorial/Guide/Example
======================================================== ======================
Validation of trace data `Validation 1`_; `Validation 2`_
Visualize trace map data `Visualizing`_
Topological branches and nodes `Network`_; `Topological`_
Trace and branch length distributions `Length-distributions`_
Orientation rose plots `Orientation 1`_; `Orientation 2`_
Plot topological ternary node and branch proportions `Proportions`_
Cross-cutting and abutting relationships `Relationships 1`_; `Relationships 2`_;
Geometric and topological fracture network parameters `Parameters`_
Contour grids of fracture network parameters `Contour-grids`_
Multi-scale length distributions `Multi-scale`_
======================================================== ======================
.. _Validation 1:
https://fractopo.readthedocs.io/en/latest/notebooks/fractopo_validation_1.html
.. _Validation 2:
https://fractopo.readthedocs.io/en/latest/notebooks/fractopo_validation_2.html
.. _Visualizing:
https://fractopo.readthedocs.io/en/latest/notebooks/fractopo_network_1.html#Visualizing-trace-map-data
.. _Network:
https://fractopo.readthedocs.io/en/latest/notebooks/fractopo_network_1.html#Network
.. _Topological:
https://fractopo.readthedocs.io/en/latest/auto_examples/plot_branches_and_nodes.html#sphx-glr-auto-examples-plot-branches-and-nodes-py
.. _Length-distributions:
https://fractopo.readthedocs.io/en/latest/notebooks/fractopo_network_1.html#Length-distributions
.. _Orientation 1:
https://fractopo.readthedocs.io/en/latest/notebooks/fractopo_network_1.html#Rose-plots
.. _Orientation 2:
https://fractopo.readthedocs.io/en/latest/auto_examples/plot_rose_plot.html#sphx-glr-auto-examples-plot-rose-plot-py
.. _Proportions:
https://fractopo.readthedocs.io/en/latest/notebooks/fractopo_network_1.html#Node-and-branch-proportions
.. _Relationships 1:
https://fractopo.readthedocs.io/en/latest/notebooks/fractopo_network_1.html#Crosscutting-and-abutting-relationships
.. _Relationships 2:
https://fractopo.readthedocs.io/en/latest/auto_examples/plot_azimuth_set_relationships.html#sphx-glr-auto-examples-plot-azimuth-set-relationships-py
.. _Parameters:
https://fractopo.readthedocs.io/en/latest/notebooks/fractopo_network_1.html#Numerical-Fracture-Network-Characterization-Parameters
.. _Contour-grids:
https://fractopo.readthedocs.io/en/latest/notebooks/fractopo_network_1.html#Contour-Grids
.. _Multi-scale:
https://fractopo.readthedocs.io/en/latest/auto_examples/plot_multi_scale_networks.html#sphx-glr-auto-examples-plot-multi-scale-networks-py
For a short tutorial on use of ``fractopo`` continue reading:
Input data
~~~~~~~~~~
Reading and writing spatial filetypes is done in ``geopandas`` and you
should see ``geopandas`` documentation for more advanced read-write use
cases:
- https://geopandas.org/
Simple example with trace and area data in GeoPackages:
.. code:: python
import geopandas as gpd
# Trace data is in a file `traces.gpkg` in current working directory
# Area data is in a file `areas.gpkg` in current working directory
trace_data = gpd.read_file("traces.gpkg")
area_data = gpd.read_file("areas.gpkg")
Trace validation
~~~~~~~~~~~~~~~~
Trace data must be validated using ``fractopo`` validation functionality
before analysis. The topological analysis of lineament & fracture traces
implemented in ``fractopo`` will not tolerate uncertainty related to the
topological abutting and snapping relationships between traces.
Therefore the trace validation is recommended before all analysis using
``Network``. Trace and target area data can be validated for further
analysis with a ``Validation`` object.
.. code:: python
from fractopo import Validation
validation = Validation(
trace_data,
area_data,
name="mytraces",
allow_fix=True,
)
# Validation is done explicitly with `run_validation` method
validated_trace_data = validation.run_validation()
Trace validation is also accessible as a command-line script,
``fractopo tracevalidate`` which is more straightforward to use than through
Python calls. Note that all subcommands of ``fractopo`` are available by
appending them after ``fractopo``.
``tracevalidate`` always requires the target area that delineates trace
data.
.. code:: bash
# Get full up-to-date script help
fractopo tracevalidate --help
# Basic usage example:
fractopo tracevalidate /path/to/trace_data.shp /path/to/target_area.shp\
--output /path/to/validated_trace_data.shp
# Or with automatic saving to validated/ directory
fractopo tracevalidate /path/to/trace_data.shp /path/to/target_area.shp\
--summary
Geometric and topological trace network analysis
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
``fractopo`` can be used to extract lineament & fracture size,
abundance and topological parameters from two-dimensional lineament and
fracture trace, branch and node data.
Trace and target area data (``GeoDataFrames``) are passed into a
``Network`` object which has properties and functions for returning and
visualizing different parameters and attributes of trace data.
.. code:: python
from fractopo import Network
# Initialize Network object and determine the topological branches and nodes
network = Network(
trace_data,
area_data,
# Give the Network a name!
name="mynetwork",
# Specify whether to determine topological branches and nodes
# (Required for almost all analysis)
determine_branches_nodes=True,
# Specify the snapping distance threshold to define when traces are
# snapped to each other
snap_threshold=0.001,
# If the target area used in digitization is a circle, the knowledge can
# be used in some analysis
circular_target_area=True,
# Analysis on traces can be done for the full inputted dataset or the
# traces can be cropped to the target area before analysis (cropping
# recommended)
truncate_traces=True,
)
# Properties are easily accessible
# e.g.,
network.branch_counts
network.node_counts
# Plotting is done by plot_ -prefixed methods
network.plot_trace_lengths()
Network analysis is also available as a command-line script but using the
Python interface (e.g. ``jupyter lab``, ``ipython``) is recommended when
analysing ``Networks`` to have access to all available analysis and plotting
methods. The command-line entrypoint is **opinionated** in what outputs it
produces. Brief example of command-line entrypoint:
.. code:: bash
fractopo network /path/to/trace_data.shp /path/to/area_data.shp\
--name mynetwork
# Use --help to see all up-to-date arguments and help
fractopo network --help
.. figure:: /docs_src/imgs/fractopo_workflow_visualisation.jpg
:alt: Data analysis workflow visualisation for fracture trace data.
Data analysis workflow visualisation for fracture trace data
(``KB11``). A. Target area for trace digitisation. B. Digitized
traces and target area. C. Orthomosaic used as the base raster from
which the traces are digitized from. D. Equal-area length-weighted
rose plot of the fracture trace azimuths. E. Length distribution
analysis of the trace lengths. F. Determined branches and nodes
through topological analysis. G. Cross-cut and abutting relationships
between chosen azimuth sets. H. Ternary plot of node (X, Y and I)
proportions. I. Ternary plot of branch (C-C, C-I, I-I) proportions.
Citing
------
To cite this software:
- The software is introduced in https://doi.org/10.1016/j.jsg.2022.104528 and
you can cite that article as a general citation:
.. code:: text
Ovaskainen, N., Nordbäck, N., Skyttä, P. and Engström, J., 2022. A new
subsampling methodology to optimize the characterization of
two-dimensional bedrock fracture networks. Journal of Structural Geology,
p.104528.
- To cite a specific version of ``fractopo`` you can use a ``zenodo``
provided ``DOI``. E.g. https://doi.org/10.5281/zenodo.5957206 for version
``v0.2.6``. See the ``zenodo`` page of ``fractopo`` for the ``DOI`` of each
version: https://doi.org/10.5281/zenodo.5517485
Support
-------
For issues of any kind: please create a GitHub issue here!
Alternatively, you can contact the main developer by email at
nikolasovaskainen@gmail.com.
References
----------
For the scientific background, prior works, definition of traces, branches and
nodes along with the explanation of the plots and the plotted parameters, you
are referred to multiple sources:
- `Sanderson and Nixon,
2015 <https://doi.org/10.1016/j.jsg.2015.01.005>`__
- Trace and branch size, abundance and topological parameter
definitions.
- `Ovaskainen et al, 2022 <https://doi.org/10.1016/j.jsg.2022.104528>`__
- Application of ``fractopo`` for subsampling analysis of fracture networks.
- `Nyberg et al., 2018 <https://doi.org/10.1130/GES01595.1>`__
- A similar package to ``fractopo`` with a ``QGIS`` GUI.
- `NetworkGT GitHub <https://github.com/BjornNyberg/NetworkGT>`__
- `Sanderson and Peacock,
2020 <https://www.sciencedirect.com/science/article/abs/pii/S001282521930594X>`__
- Discussion around rose plots and justification for using
length-weighted equal-area rose plots.
- `Alstott et al.
2014 <https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0085777>`__
- Length distribution modelling using the Python 3 ``powerlaw``
package which ``fractopo`` uses
- `powerlaw GitHub <https://github.com/jeffalstott/powerlaw>`__
- `Bonnet et al.,
2001 <https://agupubs.onlinelibrary.wiley.com/doi/abs/10.1029/1999RG000074>`__
- Length distribution modelling review.
- `My Master’s Thesis, Ovaskainen,
2020 <http://urn.fi/URN:NBN:fi-fe202003259211>`__
- Plots used in my Thesis were done with an older version of the
same code used for this plugin.
Development
-----------
- **Breaking changes are possible and expected.**
- For general contributing guidelines, see `CONTRIBUTING.rst </CONTRIBUTING>`__
Development dependencies for ``fractopo`` include:
- ``poetry``
- Used to handle Python package dependencies.
.. code:: bash
# Use poetry run to execute poetry installed cli tools such as invoke,
# nox and pytest.
poetry run '<cmd>'
- ``doit``
- A general task executor that is a replacement for a ``Makefile``
- Understands task dependencies and can run tasks in parallel
even while running them in the order determined from dependencies
between tasks. E.g., requirements.txt is a requirement for running
tests and therefore the task creating requirements.txt will always
run before the test task.
.. code:: bash
# Tasks are defined in dodo.py
# To list doit tasks from command line
poetry run doit list
# To run all tasks in parallel (recommended before pushing and/or
# committing)
# 8 is the number of cpu cores, change as wanted
# -v 0 sets verbosity to very low. (Errors will always still be printed.)
poetry run doit -n 8 -v 0
- ``nox``
- ``nox`` is a replacement for ``tox``. Both are made to create
reproducible Python environments for testing, making docs locally, etc.
.. code:: bash
# To list available nox sessions
# Sessions are defined in noxfile.py
poetry run nox --list
- ``copier``
- ``copier`` is a project templater. Many Python projects follow a similar
framework for testing, creating documentations and overall placement of
files and configuration. ``copier`` allows creating a template project
(e.g., https://github.com/nialov/nialov-py-template) which can be firstly
cloned as the framework for your own package and secondly to pull updates
from the template to your already started project.
.. code:: bash
# To pull copier update from github/nialov/nialov-py-template
poetry run copier update
- ``pytest``
- ``pytest`` is a Python test runner. It is used to run defined tests to
check that the package executes as expected. The defined tests in
``./tests`` contain many regression tests (done with
``pytest-regressions``) that make it almost impossible
to add features to ``fractopo`` that changes the results of functions
and methods.
.. code:: bash
# To run tests implemented in ./tests directory and as doctests
# within project itself:
poetry run pytest
- ``coverage``
.. code:: bash
# To check coverage of tests
# (Implemented as nox session!)
poetry run nox --session test_pip
- ``sphinx``
- Creates documentation from files in ``./docs_src``.
.. code:: bash
# To create documentation
# (Implemented as nox session!)
poetry run nox --session docs
Big thanks to all maintainers of the above packages!
License
~~~~~~~
Copyright © 2020-2023, Nikolas Ovaskainen.
-----
.. |Documentation Status| image:: https://readthedocs.org/projects/fractopo/badge/?version=latest
:target: https://fractopo.readthedocs.io/en/latest/?badge=latest
.. |PyPI Status| image:: https://img.shields.io/pypi/v/fractopo.svg
:target: https://pypi.python.org/pypi/fractopo
.. |CI Test| image:: https://github.com/nialov/fractopo/workflows/CI/badge.svg
:target: https://github.com/nialov/fractopo/actions/workflows/main.yaml?query=branch%3Amaster
.. |Conda Test| image:: https://github.com/nialov/fractopo/workflows/conda/badge.svg
:target: https://github.com/nialov/fractopo/actions/workflows/conda.yaml?query=branch%3Amaster
.. |Coverage| image:: https://raw.githubusercontent.com/nialov/fractopo/master/docs_src/imgs/coverage.svg
:target: https://github.com/nialov/fractopo/blob/master/docs_src/imgs/coverage.svg
.. |Binder| image:: http://mybinder.org/badge_logo.svg
:target: https://mybinder.org/v2/gh/nialov/fractopo/HEAD?filepath=docs_src%2Fnotebooks%2Ffractopo_network_1.ipynb
.. |Zenodo| image:: https://zenodo.org/badge/297451015.svg
:target: https://zenodo.org/badge/latestdoi/297451015
نیازمندی
| مقدار | نام |
|---|---|
| - | click |
| xtr | coverage-badge; |
| xtr | coverage; |
| >=0.11.1,<1.0.0 | geopandas |
| >=1.2.0,<2.0.0 | joblib |
| xtr | markupsafe; |
| - | matplotlib |
| xtr | mypy; |
| xtr | nbsphinx; |
| - | numpy |
| >=1.3,<2.0.0 | pandas |
| - | powerlaw |
| >=0.13.0,<1.0.0 | pygeos |
| xtr | pylint; |
| - | python-ternary |
| >=11.0.0 | rich |
| xtr | rstcheck; |
| - | scikit-learn |
| >=1.9.1,<2.0.0 | scipy |
| - | seaborn |
| >=1.8.0,<2.0.0 | shapely |
| xtr | sphinx-autobuild; |
| xtr | sphinx-autodoc-typehints; |
| xtr | sphinx-gallery; |
| xtr | sphinx-rtd-theme; |
| xtr | sphinx; |
| >=0.4,<1.0.0 | typer |
زبان مورد نیاز
| مقدار | نام |
|---|---|
| >=3.8,<3.12 | Python |
نحوه نصب
نصب پکیج whl fractopo-0.5.2:
pip install fractopo-0.5.2.whl
نصب پکیج tar.gz fractopo-0.5.2:
pip install fractopo-0.5.2.tar.gz