https://github.com/geoscienceaustralia/fc
Fractional Cover
https://github.com/geoscienceaustralia/fc
Last synced: over 1 year ago
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Fractional Cover
- Host: GitHub
- URL: https://github.com/geoscienceaustralia/fc
- Owner: GeoscienceAustralia
- License: apache-2.0
- Created: 2016-06-10T05:15:32.000Z (about 10 years ago)
- Default Branch: master
- Last Pushed: 2024-10-09T03:15:48.000Z (almost 2 years ago)
- Last Synced: 2025-02-13T03:04:04.408Z (over 1 year ago)
- Language: Python
- Size: 626 KB
- Stars: 12
- Watchers: 42
- Forks: 7
- Open Issues: 2
-
Metadata Files:
- Readme: README.rst
- License: LICENSE
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README
=======================
Fractional Cover (FC)
=======================
|Build Status| |Coverage Status|
`Fractional Cover`_ is a remote sensing algorithm which measures the
photosynthetic, non-photosynthetic and bare earth components of a Landsat image.
This repository implements Fractional Cover as used by `Digital Earth Australia`_
for the production of the `Fractional Cover Data Product `_.
The implementation is Python, with the core algorithm in Fortran.
Data production is either by a command line application that runs on the NCI_,
or a `Virtual Product`_ class run by `Datacube Alchemist`_ on AWS.
.. contents::
.. _Fractional Cover: https://cmi.ga.gov.au/data-products/dea/119/dea-fractional-cover-landsat
.. _NCI: https://www.nci.org.au/
.. _Datacube Alchemist: https://github.com/opendatacube/datacube-alchemist/
.. _Virtual Product: https://datacube-core.readthedocs.io/en/latest/dev/api/virtual-products.html
.. _Digital Earth Australia: https://www.ga.gov.au/dea
.. |Build Status| image:: https://github.com/GeoscienceAustralia/fc/workflows/Tests/badge.svg
:target: https://github.com/GeoscienceAustralia/fc/actions?query=workflow%3ATests
.. |Coverage Status| image:: https://codecov.io/gh/GeoscienceAustralia/fc/branch/master/graph/badge.svg?token=wpeulGrrUT
:target: https://codecov.io/gh/GeoscienceAustralia/fc
Installation
============
The easiest way to install Fractional Cover is::
pip install --extra-index-url=https://packages.dea.ga.gov.au/ fc
This package includes the compiled Fortran extensions to run about 15 times faster than the Python+scipy version
you get by default without a Fortran compiler.
Setup on VDI
============
The first time you try to use gadi PBS commands from VDI, you will need
to run::
$ remote-hpc-cmd init
See http://vdi.nci.org.au/help#heading=h.u1kl1j7vdt16 for more details.
You will also need to setup datacube to work from VDI and gadi.
::
$ ssh gadi "cat .pgpass" >> ~/.pgpass
$ chmod 0600 ~/.pgpass
See http://geoscienceaustralia.github.io/digitalearthau/connect/nci_basics.html for
full details.
Running
-------
The Fractional Cover application works in 2 parts:
#. Creating the task list
#. Check for unexpected existing files - these were most likely created during an run that did not successfully
finish.
#. Submit the job to gadi.
To run fractional cover::
$ module use /g/data/v10/public/modules/modulefiles/
$ module load dea
This will list the available app configs::
$ datacube-fc list
ls5_fc_albers.yaml
ls7_fc_albers.yaml
ls8_fc_albers.yaml
To submit the job to ``gadi``, the datacube-fc app has a the ``datacube-fc submit`` command:
This command kick off two stage PBS job
Stage 1 (Generate task file):
The task-app machinery loads a config file, from a path specified on the
command line, into a dict.
If dry is enabled, a dummy DatasetType is created for tasks generation without indexing
the product in the database.
If dry run is disabled, generate tasks into file and queue PBS job to process them.
Stage 2 (Run):
During normal run, following are performed:
1) Tasks (loadables (nbart,ps,dsm) + output targets) shall be yielded for dispatch to workers.
2) Load data
3) Run FC algorithm
4) Attach metadata
5) Write output files and
6) Finally index the newly created FC output files
If dry run is enabled, application only prepares a list of output files to be created and does not
record anything in the database.
Tracking progress
-----------------
::
$ qstat -u $USER
$ qcat 7517348.gadi-pbs | head
$ qcat 7517348.gadi-pbs | tail
$ qps 7517348.gadi-pbs
File locations
--------------
The config file (eg. ls5_fc_albers.yaml) specifies the app settings, and is found in the module.
You will need to check the folder of the latest ``dea`` module::
ls /g/data/v10/public/modules/dea//lib/python3.6/site-packages/fc/config
The config file lists the output `location` and file_path_template``, as shown in this snippet::
source_type: ls5_nbar_albers
output_type: ls5_fc_albers
description: Landsat 5 Fractional Cover 25 metre, 100km tile, Australian Albers Equal Area projection (EPSG:3577)
product_type: fractional_cover
location: '/g/data/fk4/datacube/002/'
file_path_template: 'LS5_TM_FC/{tile_index[0]}_{tile_index[1]}/LS5_TM_FC_3577_{tile_index[0]}_{tile_index[1]}_{start_time}_v{version}.nc'
So here the output files are saved to ``/g/data/fk4/datacube/002/FC/LS5_TM_FC//*.nc``
File naming
===========
Specify a template string used to name the output files. Uses the python ``format()`` string syntax, with the following placeholders available:
============== ==============
Placeholder Description
============== ==============
tile_index[0] X Tile Index
tile_index[1] Y Tile Index
region code The region code of the input dataset
epoch_start Start date of the epoch, format using `strftime` syntax
epoch_end End date of the epoch, format using `strftime` syntax
version Task timestamp
start_time Start time in `%Y%m%d%H%M%S%f` format
end_time End time in `%Y%m%d%H%M%S%f` format
============== ==============
For example:
.. code-block:: yaml
file_path_template: '{y}_{x}/LS_PQ_COUNT_3577_{y}_{x}_{epoch_start:%Y-%m-%d}_{epoch_end:%Y-%m-%d}.nc'
Will output filenames similar to:
.. code-block:: bash
10_15/LS_PQ_COUNT_3577_10_15_2010-01-01_2011-01-01.nc
License
-------
This repository is licensed under the Apache License 2.0. See the `LICENSE file `_ in this repository for details.
Contacts
--------
Geoscience Australia developers:
**Joshua Sixsmith**
joshua.sixsmith@ga.gov.au
**Jeremy Hooke**
jeremy.hooke@ga.gov.au
**Damien Ayers**
damien.ayers@ga.gov.au
**Duncan Gray**
duncan.gray@ga.gov.au
Algorithm developer:
**Peter Scarth**
peter.scarth@qld.gov.au