======================= 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 <Fractional Cover>_. 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/<YYYYMMDD>/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/<tile_index>/*.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 <LICENSE>_ 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