Joss

.github/workflows/draft-pdf.yml

@@ -0,0 +1,21 @@
+name: Draft PDF
+on: [push]
+
+jobs:
+  paper:
+    runs-on: ubuntu-latest
+    name: Paper Draft
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v4
+      - name: Build draft PDF
+        uses: openjournals/openjournals-draft-action@master
+        with:
+          journal: joss
+          # This should be the path to the paper within your repo.
+          paper-path: paper/paper.md
+      - name: Upload
+        uses: actions/upload-artifact@v3
+        with:
+          name: paper
+          path: paper/paper.pdf

.github/workflows/test-build-push.yml

@@ -1,6 +1,12 @@
 name: Pytest, build docker image, push to GHCR
 
-on: [pull_request, push]
+on:
+  push:
+    branches-ignore:
+      - 'joss'
+  pull_request:
+    branches-ignore:
+      - 'joss'
 
 concurrency:
   group: ${{ github.workflow }}-${{ github.head_ref }}

docs/references.bib

@@ -41,6 +41,37 @@ @article{Ansari2021StudySystematicBias
   keywords = {Big Data,Decorrelation,deformation estimation,differential interferometric synthetic aperture radar (SAR) (DInSAR),distributed scatterers (DSs),error analysis,Fading channels,Moisture,near real-time (NRT) processing,phase inconsistencies,signal decorrelation,Strain,Synthetic aperture radar,Systematics,Time series analysis,time-series analysis}
 }
 
+@article{Bekaert2021IntroducingOPERAProject,
+  title = {Introducing the {{OPERA Project}} for {{Systematic Surface Water}}, {{Surface Deformation}}, and {{Surface Disturbance Data Products}} from {{Satellite Observations}}},
+  author = {Bekaert, David and Fattahi, Heresh and Jones, John and Hansen, Matthew and Kwoun, Oh-Ig and Lewis, Steven and Meyer, Franz and Osmanoglu, Batuhan and Marshak, Charles and Hamlington, Benjamin and Bato, Mary Grace and Brancato, Virginia and Shiroma, Gustavo and Jung, Jungkyo and Jai, Benhan and Buckley, Sean and Cruz, Jennifer},
+  year = {2021},
+  month = dec,
+  volume = {2021},
+  pages = {G42A-07},
+  urldate = {2024-05-15}
+}
+
+@misc{Bradbury2018JAXComposableTransformations,
+  title = {{{JAX}}: Composable Transformations of {{Python}}+{{NumPy}} Programs},
+  author = {Bradbury, James and Frostig, Roy and Hawkins, Peter and Johnson, Matthew James and Leary, Chris and Maclaurin, Dougal and Necula, George and Paszke, Adam and VanderPlas, Jake and {Wanderman-Milne}, Skye and Zhang, Qiao},
+  year = {2018}
+}
+
+@article{Chen2001TwodimensionalPhaseUnwrapping,
+  title = {Two-Dimensional Phase Unwrapping with Use of Statistical Models for Cost Functions in Nonlinear Optimization},
+  author = {Chen, Curtis W. and Zebker, Howard A.},
+  year = {2001},
+  month = feb,
+  journal = {Journal of the Optical Society of America A},
+  volume = {18},
+  number = {2},
+  pages = {338},
+  issn = {1084-7529, 1520-8532},
+  doi = {10.1364/JOSAA.18.000338},
+  urldate = {2024-05-16},
+  langid = {english}
+}
+
 @article{Chen2012IonosphericArtifactsSimultaneous,
   title = {Ionospheric {{Artifacts}} in {{Simultaneous L-Band InSAR}} and {{GPS Observations}}},
   author = {Chen, Jingyi and Zebker, Howard A.},
@@ -68,6 +99,32 @@ @article{Chen2015PersistentScattererInterpolation
   keywords = {decorrelation,groundwater,InSAR deformation map,persistent scatterers}
 }
 
+@article{Fattahi2019FRInGEFullResolutionInSAR,
+  title = {{{FRInGE}}; {{Full-Resolution InSAR}} Timeseries Using {{Generalized Eigenvectors}}},
+  author = {Fattahi, H. and Agram, P. S. and Tymofyeyeva, E. and Bekaert, D. P.},
+  year = {2019},
+  month = dec,
+  volume = {2019},
+  pages = {G11B-0514},
+  urldate = {2024-05-16},
+  keywords = {1209 Tectonic deformation,1211 Non-tectonic deformation,1240 Satellite geodesy: results,1241 Satellite geodesy: technical issues,GEODESY AND GRAVITY}
+}
+
+@article{Ferretti2011NewAlgorithmProcessing,
+  title = {A New Algorithm for Processing Interferometric Data-Stacks: {{SqueeSAR}}},
+  author = {Ferretti, Alessandro and Fumagalli, Alfio and Novali, Fabrizio and Prati, Claudio and Rocca, Fabio and Rucci, Alessio},
+  year = {2011},
+  journal = {IEEE Transactions on Geoscience and Remote Sensing},
+  volume = {49},
+  number = {9},
+  pages = {3460--3470},
+  publisher = {IEEE},
+  issn = {01962892},
+  doi = {10.1109/TGRS.2011.2124465},
+  isbn = {0196-2892},
+  keywords = {1pass,Coherence matrix,distributed scatterers (DS),InSAR,permanent scatterers,space-adaptive filtering}
+}
+
 @article{Fornaro2015CAESARApproachBased,
   title = {{{CAESAR}}: {{An Approach Based}} on {{Covariance Matrix Decomposition}} to {{Improve Multibaseline}}--{{Multitemporal Interferometric SAR Processing}}},
   shorttitle = {{{CAESAR}}},
@@ -97,6 +154,24 @@ @article{Guarnieri2008ExploitationTargetStatistics
   keywords = {Decorrelation,decorrelation models,ENVISAT images,geophysical techniques,geophysics computing,image processing,Information retrieval,interferometric phases,Interferometry,line-of-sight displacement,line-of-sight motion,Maximum likelihood estimation,Monte Carlo simulations,multiimage synthetic aperture radar interferometry,Phase estimation,physical parameters,radar interferometry,Radar scattering,remote sensing by radar,residual topography,SAR interferometry applications,Statistical distributions,statistics,Statistics,stochastic processes,Surfaces,synthetic aperture radar,Synthetic aperture radar interferometry,target statistics,topography (Earth),Yield estimation}
 }
 
+@article{HoTongMinh2022CompressedSARInterferometry,
+  title = {Compressed {{SAR Interferometry}} in the {{Big Data Era}}},
+  author = {Ho Tong Minh, Dinh and Ngo, Yen-Nhi},
+  year = {2022},
+  month = jan,
+  journal = {Remote Sensing},
+  volume = {14},
+  number = {2},
+  pages = {390},
+  publisher = {Multidisciplinary Digital Publishing Institute},
+  issn = {2072-4292},
+  doi = {10.3390/rs14020390},
+  urldate = {2024-05-15},
+  copyright = {http://creativecommons.org/licenses/by/3.0/},
+  langid = {english},
+  keywords = {ComSAR,InSAR,PSDS,PSI,subsidence,TomoSAR,Vauvert}
+}
+
 @article{Mirzaee2023NonlinearPhaseLinking,
   title = {Non-Linear Phase Linking Using Joined Distributed and Persistent Scatterers},
   author = {Mirzaee, Sara and Amelung, Falk and Fattahi, Heresh},
@@ -127,6 +202,18 @@ @article{Parizzi2011AdaptiveInSARStack
   keywords = {adaptive InSAR stack multilooking,Adaptive multilooking,amplitude-based algorithm,backscatter,backscatter amplitude statistics,Coherence,coherence estimation,complex correlation,interferometric phase,interferometric synthetic aperture radar capability,interferometry,Kernel,phase signatures,Pixel,radar backscatter statistics,radar imaging,radar interferometry,Remote sensing,Shape,synthetic aperture radar,Synthetic aperture radar,synthetic aperture radar (SAR)}
 }
 
+@inproceedings{Rosen2018InSARScientificComputing,
+  title = {The {{InSAR Scientific Computing Environment}} 3.0: {{A Flexible Framework}} for {{NISAR Operational}} and {{User-Led Science Processing}}},
+  author = {Rosen, Paul A. and Gurrola, Eric M. and Agram, Piyush and Cohen, Joshua and Lavalle, Marco and Riel, Bryan V. and Fattahi, Heresh and Aivazis, Michael A.G. and Simons, Mark and Buckley, Sean M.},
+  year = {2018},
+  month = jul,
+  pages = {4897--4900},
+  publisher = {IEEE},
+  address = {Valencia},
+  doi = {10.1109/IGARSS.2018.8517504},
+  langid = {english},
+}
+
 @article{Siddiqui1962ProblemsConnectedRayleigh,
   title = {Some Problems Connected with {{Rayleigh}} Distributions},
   author = {Siddiqui, M.M.},
@@ -154,6 +241,21 @@ @article{Wang2022AccuratePersistentScatterer
   keywords = {Decorrelation,Interferometric Synthetic Aperture Radar (InSAR),Persistent Scatterer (PS),Phase measurement,phase similarity,Radar,Radar measurements,Radar scattering,Strain,surface deformation,Synthetic aperture radar}
 }
 
+@article{Yunjun2019SmallBaselineInSAR,
+  title = {Small Baseline {{InSAR}} Time Series Analysis: {{Unwrapping}} Error Correction and Noise Reduction},
+  shorttitle = {Small Baseline {{InSAR}} Time Series Analysis},
+  author = {Yunjun, Zhang and Fattahi, Heresh and Amelung, Falk},
+  year = {2019},
+  month = dec,
+  journal = {Computers \& Geosciences},
+  volume = {133},
+  pages = {104331},
+  issn = {00983004},
+  doi = {10.1016/j.cageo.2019.104331},
+  urldate = {2020-08-14},
+  langid = {english}
+}
+
 @article{Zwieback2022CheapValidRegularizers,
   title = {Cheap, Valid Regularizers for Improved Interferometric Phase Linking},
   author = {Zwieback, S.},

paper/Makefile

@@ -0,0 +1,7 @@
+DOCKER_CMD = docker run --rm -it -v $(PWD):/data -u $$(id -u):$$(id -g)
+PLATFORM = linux/amd64
+
+.PHONY: build
+
+build:
+	$(DOCKER_CMD) --platform $(PLATFORM) openjournals/inara -o pdf,crossref paper.md

paper/README.md

@@ -0,0 +1,9 @@
+# JOSS paper submission
+
+To build the paper locally:
+
+```bash
+make build
+```
+
+The default for `make build` assumes you are running an ARM Mac; if you are not, you need to specify the `PLATFORM` variable (e.g. `PLATFORM=linux/amd64 make build`)

paper/codemeta.json

@@ -0,0 +1,44 @@
+{
+  "@context": "https://raw.githubusercontent.com/codemeta/codemeta/master/codemeta.jsonld",
+  "@type": "Code",
+  "author": [
+    {
+      "@id": "https://orcid.org/0000-0002-3055-5731",
+      "@type": "Person",
+      "email": "scott.j.staniewicz@jpl.nasa.gov",
+      "name": "Scott Staniewicz",
+      "affiliation": "NASA Jet Propulsion Laboratory"
+    },
+    {
+      "@id": "",
+      "@type": "Person",
+      "email": "",
+      "name": "Sara Mirzaee",
+      "affiliation": "NASA Jet Propulsion Laboratory"
+    },
+    {
+      "@id": "",
+      "@type": "Person",
+      "email": "",
+      "name": "Geoffrey Gunter",
+      "affiliation": "NASA Jet Propulsion Laboratory"
+    },
+    {
+      "@id": "",
+      "@type": "Person",
+      "email": "",
+      "name": "Heresh Fattahi",
+      "affiliation": "NASA Jet Propulsion Laboratory"
+    }
+  ],
+  "identifier": "",
+  "codeRepository": "https://github.com/isce-framework/dolphin",
+  "datePublished": "2024-03-05",
+  "dateModified": "2024-03-05",
+  "dateCreated": "2024-03-05",
+  "description": "An InSAR phase linking library for large scale PS/DS processing",
+  "keywords": "insar, time series, remote sensing, phase linking, deformation, persistent scatterers",
+  "license": "BSD-3 OR Apache 2.0",
+  "title": "dolphin",
+  "version": "v0.16.0"
+}

paper/figures/make_plot.py

@@ -0,0 +1,33 @@
+import sys
+from pathlib import Path
+
+import apertools.plotting
+import cartopy.crs as ccrs
+import matplotlib.pyplot as plt
+import rioxarray
+
+p = Path(__file__).parent
+
+filename = "velocity_compressed.tif"
+image = rioxarray.open_rasterio(p / filename).sel(band=1)
+image_ll = image[::4, ::4].rio.reproject("EPSG:4326")
+
+fig, ax = apertools.plotting.plot_image_with_background(
+    image_ll.where(image_ll != 0),
+    cbar_label="[mm / year]",
+    cmap="RdBu_r",
+    vmax=10,
+    vmin=-10,
+    tile_zoom_level=9,
+    figsize=(4),
+    interpolation="none",
+)
+apertools.plotting.add_ticks(ax, resolution=0.5)
+apertools.plotting.add_zebra_frame(ax, crs=ccrs.PlateCarree())
+
+fig.tight_layout()
+if len(sys.argv) > 1 and sys.argv[1] == "--show":
+    plt.show(block=True)
+
+outname = p / "bristol-velocity-sequential.png"
+fig.savefig(outname, dpi=300, transparent=True)