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https://github.com/scikit-fmm/scikit-fmm
scikit-fmm is a Python extension module which implements the fast marching method.
https://github.com/scikit-fmm/scikit-fmm
boundaries differential-equations numpy-arrays python python-extension scikit-fmm surface-modeling surface-reconstruction
Last synced: about 2 months ago
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scikit-fmm is a Python extension module which implements the fast marching method.
- Host: GitHub
- URL: https://github.com/scikit-fmm/scikit-fmm
- Owner: scikit-fmm
- License: other
- Created: 2012-02-06T00:24:57.000Z (over 12 years ago)
- Default Branch: master
- Last Pushed: 2024-07-20T17:48:19.000Z (2 months ago)
- Last Synced: 2024-07-20T19:10:26.381Z (2 months ago)
- Topics: boundaries, differential-equations, numpy-arrays, python, python-extension, scikit-fmm, surface-modeling, surface-reconstruction
- Language: Python
- Homepage:
- Size: 942 KB
- Stars: 265
- Watchers: 13
- Forks: 63
- Open Issues: 10
-
Metadata Files:
- Readme: README.md
- License: LICENSE.txt
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README
  [](http://pypi.python.org/pypi/scikit-fmm)[](https://scikit-fmm.readthedocs.io/en/latest/?badge=latest) 
# scikit-fmm: the fast marching method for Python
`scikit-fmm` is a Python extension module which implements the fast marching method.
The fast marching method is used to model the evolution of boundaries
and interfaces in a variety of application areas. More specifically,
the fast marching method is a numerical technique for finding
approximate solutions to boundary value problems of the Eikonal
equation:
F(x) | grad T(x) | = 1
Typically, such a problem describes the evolution of a closed curve as
a function of time T with speed F(x)>0 in the normal direction at a
point x on the curve. The speed function is specified, and the time at
which the contour crosses a point x is obtained by solving the
equation.
scikit-fmm is a simple module which provides functions to calculate
the signed distance and travel time to an interface described by the
zero contour of the input array phi.
```python
import skfmm
import numpy as np
phi = np.ones((3, 3))
phi[1, 1] = -1
skfmm.distance(phi)
```
```python
array([[ 1.20710678, 0.5 , 1.20710678],
[ 0.5 , -0.35355339, 0.5 ],
[ 1.20710678, 0.5 , 1.20710678]])
```
---
```python
skfmm.travel_time(phi, speed = 3.0 * np.ones_like(phi))
```
```python
array([[ 0.40236893, 0.16666667, 0.40236893],
[ 0.16666667, 0.11785113, 0.16666667],
[ 0.40236893, 0.16666667, 0.40236893]])
```
---
The input array can be of 1, 2, 3 or higher dimensions and can be a
masked array. A function is provided to compute extension velocities.
### Documentation
* http://scikit-fmm.readthedocs.org/en/master/
### PyPI
* http://pypi.python.org/pypi/scikit-fmm
### Requirements
* Numpy >= 1.0.2
* Building requires the pypa/build module
(https://github.com/pypa/build) and a C/C++ compiler
### Bugs, questions, patches, feature requests, discussion & cetera
* Open a GitHub pull request or a GitHub issue
* Email list: http://groups.google.com/group/scikit-fmm
* Send an email to [email protected] to subscribe.
### Installing
* Via pip: `pip install scikit-fmm`
* Anaconda linux-64 and linux-ppc64le packages:
* `conda install scikit-fmm`
* Ubuntu PPA
* https://launchpad.net/~nvidia-digits/+archive/ubuntu/dev
* Debian
* https://tracker.debian.org/pkg/scikit-fmm
### Building and installing from Source
* `pip install build`
* `python -m build`
* `pip install .`
### Running Tests
* `python -c "import skfmm; skfmm.test(True)"` (Do not run the tests from the source directory.)
* Tests are doctests in `skfmm/__init__.py`
### Building documentation
* Requires sphinx and numpydoc
* `make html`
### Publications using scikit-fmm
* Akinola, I., J Varley, B. Chen, and P.K. Allen
(2018) "Workspace Aware Online Grasp Planning" arXiv:1806.11402v1
[cs.RO] 29 Jun 2018 https://arxiv.org/pdf/1806.11402.pdf
* Bortolussi, V., B. Figliuzzi, F. Willot, M.
Faessel, M. Jeandin (2018) "Morphological modeling of cold spray
coatings" Image Anal Stereol 2018;37:145-158 doi:10.5566/ias.1894
https://hal.archives-ouvertes.fr/hal-01837906/document
* Chalmers, S., C.D. Saunter, J.M. Girkin and J.G. McCarron (2016)
"Age decreases mitochondrial motility and increases mitochondrial
size in vascular smooth muscle." Journal of Physiology, 594.15 pp
4283–4295.
* Diogo Brandão Amorim (2014) "Efficient path planning of a mobile
robot on rough terrain" Master's Thesis, Department of Aerospace
Engineering, University of Lisbon.
* Giometto, A., D.R. Nelson, and A.W. Murray (2018)
"Physical interactions reduce the power of natural selection in
growing yeast colonies", PNAS November 6, 2018 115 (45) 11448-11453;
published ahead of print October 23, 2018
https://doi.org/10.1073/pnas.1809587115
* Joshua A. Taillon, Christopher Pellegrinelli, Yilin Huang, Eric D.
Wachsman, and Lourdes G. Salamanca-Riba (2014) "Three Dimensional
Microstructural Characterization of Cathode Degradation in SOFCs
Using Focused Ion Beam and SEM" ECS Trans. 2014 61(1): 109-120;
https://www.joshuataillon.com/pdfs/2015-08-06%20jtaillon%203D%20SOFC%20cathode%20degradation.pdf
* Marshak, C., I. Yanovsky, and L. Vese (2017) "Energy
Minimization for Cirrus and Cumulus Cloud Separation in Atmospheric
Images" IGARSS 2018 - 2018 IEEE International Geoscience and Remote
Sensing Symposium DOI: 10.1109/IGARSS.2018.8517940
ftp://ftp.math.ucla.edu/pub/camreport/cam17-68.pdf
* Moon, K. R., V. Delouille, J.J. Li, R. De Visscher, F. Watson and
A.O. Hero III (2016) "Image patch analysis of sunspots and active
regions." J. Space Weather Space Clim., 6, A3, DOI:
10.1051/swsc/2015043.
* Tao, M., J. Solomon and A. Butscher (2016) "Near-Isometric Level Set
Tracking." in Eurographics Symposium on Geometry Processing 2016
Eds: M. Ovsjanikov and D. Panozzo. Volume 35 (2016), Number 5
* Thibaut, R., Laloy, E., Hermans, T., 2021. A new framework for
experimental design using Bayesian Evidential Learning: The
case of wellhead protection area. J. Hydrol. 603, 126903.
https://doi.org/10.1016/j.jhydrol.2021.126903
* Vargiu, Antioco, M. Marrocu, L. Massidda (2015) "Implementazione e
valutazione su un caso reale del servizio di Cloud Computing per la
simulazione di incendi boschivi in Sardegna" (Implementation and
evaluation on a real case of Cloud computing service for simulation
of Forest fires in Sardinia). Sardinia Department of Energy and
Environment. CRS4 PIA 2010 D5.4.
* Wronkiewicz, M. (2018) "Mapping buildings with help from machine
learning" Medium article, June 29th 2018
https://medium.com/devseed/mapping-buildings-with-help-from-machine-learning-f8d8d221214a
* Makki, K., Ben Salem, D., Ben Amor, B. (2021) "Toward the Assessment
of Intrinsic Geometry of Implicit Brain MRI Manifolds" IEEE Access,
volume 9, pages 131054 - 131071 (September 2021)
DOI: 10.1109/ACCESS.2021.3113611
https://ieeexplore.ieee.org/abstract/document/9540688
### Version History:
* 0.0.1: February 13 2012
* Initial release
* 0.0.2: February 26th 2012
* Including tests and docs in source distribution. Minor changes to
documentation.
* 0.0.3: August 4th 2012
* Extension velocities.
* Fixes for 64 bit platforms.
* Optional keyword argument for point update order.
* Bug reports and patches from three contributors.
* 0.0.4: October 15th 2012
* Contributions from Daniel Wheeler:
* Bug fixes in extension velocity.
* Many additional tests and migration to doctest format.
* Additional optional input to extension_velocities() for FiPy compatibly.
* 0.0.5: May 12th 2014
* Fix for building with MSVC (Jan Margeta).
* Corrected second-order point update.
* 0.0.6: February 20th 2015
* Documentation clarification (Geordie McBain).
* Python 3 port (Eugene Prilepin).
* Python wrapper for binary min-heap.
* Freeze equidistant narrow-band points simultaneously.
* 0.0.7: October 21st 2015
* Bug fix to upwind finite difference approximation for negative
phi from Lester Hedges.
* 0.0.8: March 9th 2016
* Narrow band capability: an optional "narrow" keyword argument
limits the extent of the marching algorithm (Adrian Butscher).
* 0.0.9: August 5th 2016
* Periodic boundaries: an optional "periodic" keyword argument
enables periodic boundaries in one or more directions (Wolfram Moebius).
* 2019.1.30 January 30th 2019
* Abrupt change to version numbering scheme.
* Bugfix in setup.py to allow installing via pip with numpy (ManifoldFR).
* Handle C++ exceptions during fast marching (Jens Glaser).
* Accept a zero discriminant in travel time point update.
* 2021.1.20 January 20th 2021
* Fix divide by zero bugs in travel_time and extension_velocities
* Contributions from Murray Cutforth, f-fanni, and okonrad
* 2021.1.21 January 21st 2021
* Minor C++ change (removed the auto keyword) to fix the compile on TravisCI.
* 2021.2.2 February 2nd 2021
* Add a pyproject.toml file to specify numpy as a build
requirement, this is needed to build with new version of pip
(David Parsson).
* 2021.7.8 July 8th 2021
* Add a pyproject.toml file to the MANIFEST.in file to fix the
numpy build dependency (David Parsson). Fix numpy deprecation
warnings and improve source code formatting (Robin Thibaut).
* 2021.9.23 September 23rd 2021
* Make the pyproject.toml file specify the oldest supported
numpy as a build requirement, to allow using wheels with any
numpy version.
(David Parsson).
* 2021.10.29 October 29th 2021
* Fix for point update discriminant exactly equal to zero
* Fall back calculation for point update when discriminant becomes negative
* (Joshua Gehre)
* 2022.02.02 February 2nd 2022
* Fixes for Python 3.10 compatibility
* (Amin Sadeghi, Xylar Asay-Davis, David Parsson)
* 2022.03.26 March 26th 2022
* Following the breaking changes in setuptools v61.0.0 it is
suggested to set py_modules to disable auto-discovery behavior.
* (Daniel Ammar)
* 2022.08.15 August 15th 2022
* Following the breaking changes in setuptools v65 pin setuptools
to v64
* (DorSSS)
* 2022.04.02 April 2nd 2023
* Build fixes for Python 3.11 (update pheap cython wrapper)
* No solver changes
* 2024.05.29 May 29th 2024
* Update build system to use meson
* Python 3.12 support
* No solver changes
Copyright 2023 The scikit-fmm team.
BSD-style license. See LICENSE.txt in the source directory.