+ parallel computing for NCC
+ support of urls for input files (both images and auxiliary input files can be urls for optical data processing; only auxiliary input files can be urls for radar data processing)A Python module of a fast and intelligent algorithm for finding the pixel displacement between two images
autoRIFT can be installed as a standalone Python module (only supports Cartesian coordinates) either manually or as a conda install (https://github.com/conda-forge/autorift-feedstock). To allow support for both Cartesian and radar coordinates, autoRIFT must be installed with the InSAR Scientific Computing Environment (ISCE: https://github.com/isce-framework/isce2)
Use cases include all dense feature tracking applications, including the measurement of surface displacements occurring between two repeat satellite images as a result of glacier flow, large earthquake displacements, and land slides
autoRIFT can be used for dense feature tracking between two images over a grid defined in an arbitrary geographic Cartesian (northing/easting) coordinate projection when used in combination with the sister Geogrid Python module (https://github.com/leiyangleon/Geogrid). Example applications include searching radar-coordinate imagery on a polar stereographic grid and searching Universal Transverse Mercator (UTM) imagery at a specified geographic Cartesian (northing/easting) coordinate grid
Copyright (C) 2019 California Institute of Technology. Government Sponsorship Acknowledged.
Link: https://github.com/leiyangleon/autoRIFT
Citation: https://doi.org/10.5281/zenodo.4426975
Alex Gardner (JPL/Caltech; [email protected]) first described the algorithm "auto-RIFT" in (Gardner et al., 2018) and developed the first version in MATLAB;
Yang Lei (GPS/Caltech; [email protected]) translated it to Python, further optimized and incoporated to the ISCE software;
Piyush Agram (JPL/Caltech; [email protected]) set up the installation as a standalone module and further cleaned the code.
Reference: Gardner, A. S., Moholdt, G., Scambos, T., Fahnstock, M., Ligtenberg, S., van den Broeke, M., & Nilsson, J. (2018). Increased West Antarctic and unchanged East Antarctic ice discharge over the last 7 years. The Cryosphere, 12(2), 521–547. https://doi.org/10.5194/tc-12-521-2018
This effort was funded by the NASA MEaSUREs program in contribution to the Inter-mission Time Series of Land Ice Velocity and Elevation (ITS_LIVE) project (https://its-live.jpl.nasa.gov/) and through Alex Gardner’s participation in the NASA NISAR Science Team
- fast algorithm that finds displacement between the two images (where source and template image patches are extracted and correlated) using sparse search and iteratively progressive chip (template) sizes
- for intelligent use, user can specify unstructured spatially-varying search centers (center of the source image patch), search offsets (center displacement of the template image patch compared to the source image patch), chip sizes (size of template image patch), search ranges (size of the source image patch)
- faster than the conventional dense feature tracking "ampcor"/"denseampcor" algorithm included in ISCE by nearly 2 orders of magnitude
- supports various preprocessing modes for specified image pair, e.g. either the raw image (both texture and topography) or the texture only (high-frequency components without the topography) can be used with various choices of the high-pass filter options
- supports image data format of unsigned integer 8 (uint8; faster) and single-precision float (float32)
- user can adjust all of the relevant parameters, as detailed below in the instructions
- a Normalized Displacement Coherence (NDC) filter is developed (Gardner et al., 2018) to filter the chip displacemnt results based on displacement difference thresholds that are scaled to the local search range
- a sparse integer displacement search is used to narrow the template search range and to eliminate areas of "low coherence" for fine decimal displacement search and following chip size iterations
- novel nested grid design allows chip size progressively increase iteratively where a smaller chip size failed
- a light interpolation is done to fill the missing (unreliable) chip displacement results using median filtering and bicubic-mode interpolation (that can remove pixel discrepancy when using other modes) and an interpolation mask is returned
- the core displacement estimator (normalized cross correlation) and image pre-processing call OpenCV's Python and/or C++ functions for efficiency
- sub-pixel displacement estimation using a fast Gaussian pyramid upsampling algorithm that is robust to sub-pixel locking; the intelligent (chip size-dependent) selection of oversampling ratio is also supported for a tradeoff between efficiency and accuracy
- the current version can be installed with the ISCE software (that supports both Cartesian and radar coordinates) or as a standalone Python module (Cartesian coordinates only)
- when used in combination with the Geogrid Python module (https://github.com/leiyangleon/Geogrid), autoRIFT can be used for feature tracking between image pair over a grid defined in an arbitrary geographic Cartesian (northing/easting) coordinate projection
- when the grid is provided in geographic Cartesian (northing/easting) coordinates, outputs are returned in geocoded GeoTIFF image file format with the same EPSG projection code as input search grid
- [NEW] For feature tracking of optical images, the program now supports fetching optical images (Landsat-8 GeoTIFF and Sentinel-2 COG formats are included) as well as other inputs (e.g. DEM, slope, etc; all in GeoTIFF format) from either local machine or URL links. For feature tracking of radar images, the program now supports fetching auxilliary inputs (e.g. DEM, slope, etc; all in GeoTIFF format) from either local machine or URL links. See the changes on the Geogrid commands. When using the autoRIFT commands below, users need to append a url flag: "-urlflag 1" for using URL links, and "-urlflag 0" (default; can be omitted) for using files on local machine.
- [NEW] parallel computing has been added for Normalized Cross-Correlation (NCC). When using the autoRIFT commands below, users need to append a multiprocessing flag: "-mpflag $num" with "$num" being the number of threads used; if not specified, the single-core version is used.
- for radar (SAR) images, it is yet to include the complex correlation of the two images, i.e. the current version only uses the amplitude correlation
- the GPU implementation would be useful to extend
Output of "autoRIFT" module for a pair of Landsat-8 images (20170708-20170724; same as the Demo dataset at https://github.com/leiyangleon/Geogrid) in Greenland over a regular-spacing grid: (a) estimated horizontal pixel displacement, (b) estimated vertical pixel displacement, (c) chip size used, (d) light interpolation mask.
This is done by implementing the following command line:
Standalone:
testautoRIFT.py -m I1 -s I2 -fo 1
With ISCE:
testautoRIFT_ISCE.py -m I1 -s I2 -fo 1
where "I1" and "I2" are the reference and test images as defined in the instructions below. The "-fo" option indicates whether or not to read optical image data.
Output of "autoRIFT" module for a pair of Landsat-8 images (20170708-20170724; same as the Demo dataset at https://github.com/leiyangleon/Geogrid) in Greenland over user-defined geographic Cartesian (northing/easting) coordinate grid (same grid used in the Demo at https://github.com/leiyangleon/Geogrid): (a) estimated horizontal pixel displacement, (b) estimated vertical pixel displacement, (c) light interpolation mask, (d) chip size used. Notes: all maps are established exactly over the same geographic Cartesian coordinate grid from input.
This is done by implementing the following command line:
Standalone:
testautoRIFT.py -m I1 -s I2 -g winlocname -o winoffname -sr winsrname -csmin wincsminname -csmax wincsmaxname -vx winro2vxname -vy winro2vyname -fo 1
With ISCE:
testautoRIFT_ISCE.py -m I1 -s I2 -g winlocname -o winoffname -sr winsrname -csmin wincsminname -csmax wincsmaxname -vx winro2vxname -vy winro2vyname -fo 1
where "I1" and "I2" are the reference and test images as defined in the instructions below, and the optional inputs "winlocname", "winoffname", "winsrname", "wincsminname", "wincsmaxname", "winro2vxname", "winro2vyname" are outputs from running "testGeogrid_ISCE.py" or "testGeogridOptical.py" as defined at https://github.com/leiyangleon/Geogrid. When "winlocname" (grid location) is specified, each of the rest optional input ("win * name") can be either used or omitted.
Final motion velocity results by combining outputs from "Geogrid" (i.e. matrix of conversion coefficients from the Demo at https://github.com/leiyangleon/Geogrid) and "autoRIFT" modules: (a) estimated motion velocity from Landsat-8 data (x-direction; in m/yr), (b) motion velocity from input data (x-direction; in m/yr), (c) estimated motion velocity from Landsat-8 data (y-direction; in m/yr), (d) motion velocity from input data (y-direction; in m/yr). Notes: all maps are established exactly over the same geographic Cartesian (northing/easting) coordinate grid from input.
Output of "autoRIFT" module for a pair of Sentinel-1A/B images (20170221-20170227; same as the Demo dataset at https://github.com/leiyangleon/Geogrid) at Jakobshavn Glacier of Greenland over a regular-spacing grid: (a) estimated range pixel displacement, (b) estimated azimuth pixel displacement, (c) chip size used, (d) light interpolation mask.
This is obtained by implementing the following command line:
With ISCE:
testautoRIFT_ISCE.py -m I1 -s I2
where "I1" and "I2" are the reference and test images as defined in the instructions below.
Output of "autoRIFT" module for a pair of Sentinel-1A/B images (20170221-20170227; same as the Demo dataset at https://github.com/leiyangleon/Geogrid) at Jakobshavn Glacier of Greenland over user-defined geographic Cartesian (northing/easting) coordinate grid (same grid used in the Demo at https://github.com/leiyangleon/Geogrid): (a) estimated range pixel displacement, (b) estimated azimuth pixel displacement, (c) light interpolation mask, (d) chip size used. Notes: all maps are established exactly over the same geographic Cartesian coordinate grid from input.
This is done by implementing the following command line:
With ISCE:
testautoRIFT_ISCE.py -m I1 -s I2 -g winlocname -o winoffname -sr winsrname -csmin wincsminname -csmax wincsmaxname -vx winro2vxname -vy winro2vyname
where "I1" and "I2" are the reference and test images as defined in the instructions below, and the optional inputs "winlocname", "winoffname", "winsrname", "wincsminname", "wincsmaxname", "winro2vxname", "winro2vyname" are outputs from running "testGeogrid.py" as defined at https://github.com/leiyangleon/Geogrid. When "winlocname" (grid location) is specified, each of the rest optional input ("win * name") can be either used or omitted.
Runtime comparison for this test (on an OS X system with 2.9GHz Intel Core i7 processor and 16GB RAM):
- autoRIFT (single core): 10 mins
- Dense ampcor from ISCE (8 cores): 90 mins
Final motion velocity results by combining outputs from "Geogrid" (i.e. matrix of conversion coefficients from the Demo at https://github.com/leiyangleon/Geogrid) and "autoRIFT" modules: (a) estimated motion velocity from Sentinel-1 data (x-direction; in m/yr), (b) motion velocity from input data (x-direction; in m/yr), (c) estimated motion velocity from Sentinel-1 data (y-direction; in m/yr), (d) motion velocity from input data (y-direction; in m/yr). Notes: all maps are established exactly over the same geographic Cartesian (northing/easting) coordinate grid from input.
With ISCE:
- First install ISCE (https://github.com/isce-framework/isce2)
- Put the "geo_autoRIFT" folder and the "Sconscript" file under the "contrib" folder that is one level down ISCE's source directory (denoted as "isce-version"; where you started installing ISCE), i.e. "isce-version/contrib/" (see the snapshot below)
- Run "scons install" again from ISCE's source directory "isce-version" using command line
- This distribution automatically installs the "autoRIFT" module as well as the "Geogrid" module (https://github.com/leiyangleon/Geogrid).
Standalone:
1) Manual Install:
- Put the "geo_autoRIFT" folder and the "setup.py" file under some source directory (see the snapshot below)
- Run "python3 setup.py install" or "sudo python3 setup.py install" (if the previous failed due to permission restriction) using command line
- This distribution automatically installs the "autoRIFT" module as well as the "Geogrid" module (https://github.com/leiyangleon/Geogrid)
- The standalone version only supports Cartesian coordinate imagery. However, if the above "With ISCE" version is installed independently, the standalone version can also support radar coordinate imagery.
- If the modules cannot be imported in Python environment, please make sure the path where these modules are installed (see "setup.py") to be added to the environmental variable $PYTHONPATH.
2) Conda Install:
- The source code "geo_autoRIFT" folder can also be installed via conda-forge channels. Please follow the instructions on the following page (with no more than three command lines): https://github.com/conda-forge/autorift-feedstock
- This distribution automatically installs the "autoRIFT" module as well as the "Geogrid" module (https://github.com/leiyangleon/Geogrid)
- The standalone version only supports Cartesian coordinate imagery. However, if the above "With ISCE" version is installed independently, the standalone version can also support radar coordinate imagery.
- If the modules cannot be imported in Python environment, please make sure the path where these modules are installed (search for the modules in "anaconda3" directory) to be added to the environmental variable $PYTHONPATH.
Note:
- When the grid is provided in geographic Cartesian (northing/easting) coordinates (geographic coordinates lat/lon is not supported), it is required to run the "Geogrid" module (https://github.com/leiyangleon/Geogrid) first before running "autoRIFT". In other words, the outputs from "testGeogrid_ISCE.py" or "testGeogridOptical.py" (a.k.a "winlocname", "winoffname", "winsrname", "wincsminname", "wincsmaxname", "winro2vxname", "winro2vyname") will serve as optional inputs for running "autoRIFT" at a geographic grid, which is required to generate the final motion velocity maps.
- When the outputs from running the "Geogrid" module are not provided, a regular grid in the imaging coordinates will be automatically assigned
For quick use:
- Refer to the file "testautoRIFT.py" (standalone) and "testautoRIFT_ISCE.py" (with ISCE) for the usage of the module and modify it for your own purpose
- Input files include the reference image (required), test image (required), and the outputs from running "testGeogrid_ISCE.py" or "testGeogridOptical.py" (optional; a.k.a "winlocname", "winoffname", "winsrname", "wincsminname", "wincsmaxname", "winro2vxname", "winro2vyname"). When "winlocname" (grid location) is specified, each of the rest optional input ("win * name") can be either used or omitted.
- Output files include 1) estimated horizontal displacement (equivalent to range for radar), 2) estimated vertical displacement (equivalent to minus azimuth for radar), 3) light interpolation mask, 4) iteratively progressive chip size used.
Note: These four output files will be stored in a file named "offset.mat" that can be viewed in Python and MATLAB. When the grid is provided in geographic Cartesian (northing/easting) coordinates, a 4-band GeoTIFF with the same EPSG code as input grid will be created as well and named "offset.tif"; a 2-band GeoTIFF of the final converted motion velocity in geographic x- (easting) and y- (northing) coordinates will be created and named "velocity.tif". Also, it is possible to save the outputs in netCDF standard format by adding the "-nc" option to the "testautoRIFT.py" (standalone) and "testautoRIFT_ISCE.py" (with ISCE) command.
For modular use:
- In Python environment, type the following to import the "autoRIFT" module and initialize the "autoRIFT" object
With ISCE:
import isce
from contrib.geo_autoRIFT.autoRIFT import autoRIFT_ISCE
obj = autoRIFT_ISCE()
obj.configure()
Standalone:
from autoRIFT import autoRIFT
obj = autoRIFT()
-
The "autoRIFT" object has several inputs that have to be assigned (listed below; can also be obtained by referring to "testautoRIFT.py"):
------------------input------------------ I1 reference image (extracted image patches defined as "source") I2 test image (extracted image patches defined as "template"; displacement = motion vector of I2 relative to I1) xGrid [units = integer image pixels] horizontal pixel index at each grid point yGrid [units = integer image pixels] vertical pixel index at each grid point (if xGrid and yGrid not provided, a regular grid spanning the entire image will be automatically set up, which is similar to the conventional ISCE module, "ampcor" or "denseampcor") Dx0 [units = integer image pixels] horizontal "downstream" reach location (that specifies the horizontal pixel displacement of the template's search center relative to the source's) at each grid point Dy0 [units = integer image pixels] vertical "downstream" reach location (that specifies the vertical pixel displacement of the template's search center relative to the source's) at each grid point (if Dx0 and Dy0 not provided, an array with zero values will be automatically assigned and there will be no offsets of the search centers) -
After the inputs are specified, run the module as below
obj.preprocess_filt_XXX() or obj.preprocess_db() obj.uniform_data_type() obj.runAutorift()
where "XXX" can be "wal" for the Wallis filter, "hps" for the trivial high-pass filter, "sob" for the Sobel filter, "lap" for the Laplacian filter, and also a logarithmic operator without filtering is adopted for occasions where low-frequency components (i.e. topography) are desired, i.e. "obj.preprocess_db()".
-
The "autoRIFT" object has the following four outputs:
------------------output------------------ Dx [units = decimal image pixels] estimated horizontal pixel displacement Dy [units = decimal image pixels] estimated vertical pixel displacement InterpMask [unitless; boolean data type] light interpolation mask ChipSizeX [units = integer image pixels] iteratively progressive chip size in horizontal direction (different chip size allowed for vertical) -
The "autoRIFT" object has many parameters that can be flexibly tweaked by the users for their own purpose (listed below; can also be obtained by referring to "geo_autoRIFT/autoRIFT/autoRIFT_ISCE.py"):
------------------parameter list: general function------------------ ChipSizeMinX [units = integer image pixels] Minimum size (in horizontal direction) of the template (chip) to correlate (default = 32; could be scalar or array with same dimension as xGrid) ChipSizeMaxX [units = integer image pixels] Maximum size (in horizontal direction) of the template (chip) to correlate (default = 64; could be scalar or array with same dimension as xGrid) ChipSize0X [units = integer image pixels] Minimum acceptable size (in horizontal direction) of the template (chip) to correlate (default = 32) ScaleChipSizeY [unitless; integer data type] Scaling factor to get the vertically-directed chip size in reference to the horizontally-directed size (default = 1) SearchLimitX [units = integer image pixels] Range (in horizontal direction) to search for displacement in the source (default = 25; could be scalar or array with same dimension as xGrid; when provided in array, set its elements to 0 if excluded for finding displacement) SearchLimitY [units = integer image pixels] Range (in vertical direction) to search for displacement in the source (default = 25; could be scalar or array with same dimension as xGrid; when provided in array, set its elements to 0 if excluded for finding displacement) SkipSampleX [units = integer image pixels] Number of samples to skip between search windows in horizontal direction for automatically-created grid if not specified by the user (default = 32) SkipSampleY [units = integer image pixels] Number of lines to skip between search windows in vertical direction for automatically-created grid if not specified by the user (default = 32) minSearch [units = integer image pixels] Minimum search limit (default = 6) ------------------parameter list: about Normalized Displacement Coherence (NDC) filter ------------------ FracValid Fraction of valid displacements (default = 8/25) to be multiplied by filter window size "FiltWidth^2" and then used for thresholding the number of chip displacements that have passed the "FracSearch" disparity filtering FracSearch Fraction of search limit used as threshold for disparity filtering of the chip displacement difference that is normalized by the search limit (default = 0.25) FiltWidth Disparity filter width (default = 5) Iter Number of iterations (default = 3) MadScalar Scalar to be multiplied by Mad used as threshold for disparity filtering of the chip displacement deviation from the median (default = 4) ------------------parameter list: miscellaneous------------------ WallisFilterWidth Width of the filter to be used for the preprocessing (default = 21) fillFiltWidth Light interpolation filling filter width (default = 3) sparseSearchSampleRate downsampling rate for sparse search (default = 4) BuffDistanceC Buffer coarse correlation mask by this many pixels for use as fine search mask (default = 8) CoarseCorCutoff Coarse correlation search cutoff (default = 0.01) OverSampleRatio Factor for pyramid upsampling for sub-pixel level offset refinement (default = 16; can be scalar or Python dictionary for intelligent use, i.e. chip size-dependent, such as {ChipSize_1:OverSampleRatio_1,..., ChipSize_N:OverSampleRatio_N}) DataTypeInput Image data type: 0 -> uint8, 1 -> float32 (default = 0) zeroMask Force the margin (no data) to zeros which is useful for Wallis-filter-preprocessed images (default = None; 1 for Wallis filter)