A Python tool for estimating velocity and cumulative displacement time-series from Interferometric Synthetic Aperture Radar (InSAR) data.
Project description
Python tool for InSAR Rate and Time-series Estimation
PyRate is a Python tool for estimating the average displacement rate (velocity) and cumulative displacement time-series of surface movements for every pixel in a stack of geocoded unwrapped interferograms generated by Interferometric Synthetic Aperture Radar (InSAR) processing. PyRate uses a “Small Baseline Subset” (SBAS) processing strategy and currently supports input data in the GAMMA or ROI_PAC software formats.
The PyRate project started in 2012 as a partial Python translation of “Pirate”, a Matlab tool developed by the University of Leeds and the Guangdong University of Technology.
The full PyRate documentation is available at http://geoscienceaustralia.github.io/PyRate
Dependencies
The following dependencies need to be on your system prior to PyRate installation:
Python, versions 3.6, 3.7 or 3.8.
GDAL, versions 3.0.2 or 3.0.4
Open MPI, versions 2.1.6, 3.0.4, 3.1.4 or 4.0.2
The versions of each package stated above have been tested to work.
Python dependencies are:
Cython==0.29.16 Pillow==7.1.1 glob2==0.7 joblib==0.14.1 mpi4py==3.0.3 networkx==2.4 numpy==1.18.3 pyproj==2.6.0 scipy==1.4.1 numexpr==2.7.1
Install
Details of all install options are given in the PyRate documentation.
PyRate and its Python dependencies can be installed directly from the Python Package Index (PyPI):
pip install Py-Rate
To install from source in Linux, enter these commands in a terminal:
cd ~ git clone https://github.com/GeoscienceAustralia/PyRate.git python3 -m venv ~/PyRateVenv source ~/PyRateVenv/bin/activate cd ~/PyRate python3 setup.py install
This will install the above-listed Python dependencies and compile the executable program pyrate:
>> pyrate --help
usage: pyrate [-h] [-v {DEBUG,INFO,WARNING,ERROR}]
{conv2tif,prepifg,process,merge,workflow} ...
PyRate workflow:
Step 1: conv2tif
Step 2: prepifg
Step 3: process
Step 4: merge
Refer to https://geoscienceaustralia.github.io/PyRate/usage.html for
more details.
positional arguments:
{conv2tif,prepifg,process,merge,workflow}
conv2tif Convert interferograms to geotiff.
prepifg Perform multilooking and cropping on geotiffs.
process Main processing workflow including corrections, time series and stacking computation.
merge Reassemble computed tiles and save as geotiffs.
workflow Run all the PyRate processes
optional arguments:
-h, --help show this help message and exit
-v {DEBUG,INFO,WARNING,ERROR}, --verbosity {DEBUG,INFO,WARNING,ERROR}
Increase output verbosity
Documentation
The full documentation is at http://geoscienceaustralia.github.io/PyRate/
Release History
0.4.1 (2020-05-19)
Added
Python 3.8 support.
Algorithm to automatically calculate rows and columns for tiling. User no longer specifies these as part of the CLI, but can optionally specify rows and cols in the configuration file.
Improvements to the test suite, including systems-wide tests.
Improved logging.
Changed
Linear Rate algorithm has been renamed Stack Rate.
User supplies full paths to input files in respective file lists.
All files generated by PyRate saved to user-defined outdir directory.
Fixed a bug in how NaNs are handled during coherence masking and multi-looking. Output rasters will contain nan as the nodata value.
Fixed bug in resampling/multi-looking when coherence masking is used. This bugfix will result in significantly fewer nan pixels in the outputs.
Renamed slcfilelist parameter to hdrfilelist.
Log files are generated in the outdir and every PyRate step produces independent log files.
Removed
Deprecate the use of obsdir, slcfiledir and cohdir configuration variables.
Deprecate parallel = 2 option; splitting image via rows for parallelisation.
0.4.0 (2019-10-31)
Added
Python 3.7 support.
Optional conv2tif step.
Building of docs integrated with Travis CI.
Coherence masking, view coherence masking section in input_parameters.conf for options.
Input parameter validation.
SLC and coherence file lists for file discovery.
Create quick view png for rate map product.
Add support for reading interferogram in Geotiff format.
Add detailed validation and hints for configuration parameters
Add system tests for all 3 types of input formats
Changed
linrate step has been renamed to process.
postprocess step has been renamed to merge.
converttogeotiff step has been renamed to conv2tif.
CLI structure: config files now need to be provided with -f flag.
Reduced console output, default verbosity setting is now INFO.
Restructure of code layout, src modules now in PyRate/pyrate/core directory and scripts at PyRate/scripts.
Reference pixel values are expected to be in latitude and longitude values.
Removed
Unused luigi code.
References to Matlab.
Unused tests for legacy api.
0.3.0 (2019-07-26)
Added
utils/apt_install.sh script that lists Ubuntu/apt package requirements.
utils/load_modules.sh script that sets up NCI Raijin HPC environment.
Fixed
Errors being caused by newer version of networkx; v2.3 now supported.
Removed
Unused Python and OS packages.
environment.yml - conda env will now be installed using requirements.txt.
HPC directory - hpc README.rst moved to docs.
setup.cfg - no longer needed.
Luigi functionality - hasn’t been operational and is reported as vulnerable. Single machine parallelism is achieved with joblib.
Changed
Requirements now managed by requirements.txt file, parsed by setup.py.
Requirements now split across base requirements.txt and separate files for dev (requirements-dev.txt) and testing (‘requirements-test.txt’).
Moved default config files to top level source directory.
Pinned Python dependencies to specific versions.
Travis build now installs GDAL from apt.
Travis only builds on master, develop and *-travis branches.
Consolidated documentation into PyRate/docs.
Updated install instructions for Ubuntu and NCI.
0.2.0 (2017-05-22)
Stable beta release.
0.1.0 (2017-01-31)
First release on PyPI.
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