ASFHyP3 · mfangaritav · Jun 4, 2024 · May 14, 2024 · May 14, 2024 · May 14, 2024
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -7,6 +7,10 @@ and this project adheres to [PEP 440](https://www.python.org/dev/peps/pep-0440/)
 and uses [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
 
+## [0.17.0]
+## Changed
+* In preparation for a major update, the Sentinel-1 processing workflow has been isolated to a new `hyp3_autorift.s1_isce2` module. 
+
 ## [0.16.0]
 ### Fixed
 * `hyp3_autorift` will no longer attempt to crop files with no valid data

diff --git a/README.md b/README.md
@@ -1,3 +1,185 @@
-# HyP3 autoRIFT
 
-A HyP3 plugin for feature tracking processing with AutoRIFT-ISCE
+# HyP3 autoRIFT Plugin
+
+[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.4037015.svg)](https://doi.org/10.5281/zenodo.4037015)
+
+The HyP3-autoRIFT plugin provides a set of workflows for feature tracking processing with the AutoRIFT [autonomous Repeat Image Feature Tracking](https://github.com/nasa-jpl/autoRIFT) (autoRIFT) software package. This plugin is part of the [Alaska Satellite Facility's](https://asf.alaska.edu) larger HyP3 (Hybrid Plugin Processing Pipeline) system, which is a batch processing pipeline designed for on-demand processing of remote sensing data. For more information on HyP3, see the [Background](#background) section.
+
+## Installation
+
+1. Ensure that conda is installed on your system (we recommend using [mambaforge](https://github.com/conda-forge/miniforge#mambaforge) to reduce setup times).
+2. Clone the `hyp3-autorift` repository and navigate to the root directory of this project
+   ```bash
+   git clone https://github.com/ASFHyP3/hyp3-autorift.git
+   cd hyp3-autorift
+   ```
+3. Create  and activate your Python environment
+   ```bash
+
+   mamba env create -f environment.yml
+   mamba activate hyp3-autorift
+   ```
+4. Finally, install a development version of HyP3 autoRIFT
+   ```bash
+   python -m pip install -e .
+   ```
+
+## Usage
+
+The HyP3-autoRIFT plugin provides workflows (accessible directly in Python or via a CLI) that can be used to process SAR  data or optical data using autoRIFT. HyP3-autoRIFT can process these satellite missions:
+* SAR:
+  * Sentinel-1
+* Optical:
+  * Sentinel-2
+  * Landsat 4,5,7,8,9 
+
+To see all available workflows, run:
+```
+python -m hyp3_autorift ++help
+```
+
+### `hyp3_autorift` workflow
+
+The `hyp3_autorift` workflow is used to get dense feature tracking between two images using autoRIFT. You can run this workflow by selecting the `hyp3_autorift` process: 
+```
+python -m hyp3_autorift ++process hyp3_autorift [WORKFLOW_ARGS]
+```
+or by using the `hyp3_autorift` console script:
+```
+hyp3_autorift [WORKFLOW_ARGS]
+```
+For example:
+
+```
+hyp3_autorift \
+  "S2B_MSIL1C_20200612T150759_N0209_R025_T22WEB_20200612T184700" \
+  "S2A_MSIL1C_20200627T150921_N0209_R025_T22WEB_20200627T170912"
+```
+
+This command will run autorift for a pair of Sentinel-2 images.
+
+> [!IMPORTANT]
+> Credentials are necessary to access Landsat and Sentinel-1 data. See the Credentials section for more information.
+
+For all options available to this workflow, see the help documentation: 
+```
+hyp3_autorift --help
+```
+
+### Credentials
+
+Depending on the mission being processed, some workflows will need you to provide credentials. Generally, credentials are provided via environment variables, but some may be provided by command-line arguments or via a `.netrc` file. 
+
+#### AWS Credentials
+
+To process Landsat images, you must provide AWS credentials because the data is hosted by USGS in a "requester pays" bucket. To provide AWS credentials, you can either use an AWS profile specified in your `~/.aws/credentials` by exporting:
+```
+export AWS_PROFILE=your-profile
+```
+or by exporting credential environment variables:
+```
+export AWS_ACCESS_KEY_ID=your-id
+export AWS_SECRET_ACCESS_KEY=your-key
+export AWS_SESSION_TOKEN=your-token  # optional; for when using temporary credentials
+```
+
+For more information, please see: <https://boto3.amazonaws.com/v1/documentation/api/latest/guide/credentials.html>
+
+#### NASA Earthdata Login and ESA Copernicus Data Space Ecosystem (CDSE)
+
+To process Sentinel-1 images, you must provide Earthdata Login credentials and ESA Copernicus Data Space Ecosystem (CDSE) credentials in order to download input data.
+* If you do not already have an Earthdata account, you can sign up [here](https://urs.earthdata.nasa.gov/home). 
+* If you do not already have a CDSE account, you can sign up [here](https://dataspace.copernicus.eu). 
+
+For Earthdata login and CDSE, you can provide credentials by exporting environment variables:
+```
+export EARTHDATA_USERNAME=your-edl-username
+export EARTHDATA_PASSWORD=your-edl-password
+export ESA_USERNAME=your-esa-username
+export ESA_PASSWORD=your-esa-password
+```
+or via your [`~/.netrc` file](https://everything.curl.dev/usingcurl/netrc) which should contain lines like these two:
+```
+machine urs.earthdata.nasa.gov login your-edl-username password your-edl-password
+machine dataspace.copernicus.eu login your-esa-username password your-esa-password
+```
+
+> [!TIP]
+> Your `~/.netrc` file should only be readable by your user; otherwise, you'll receive a "net access too permissive" error. To fix, run:
+> ```
+> chmod 0600 ~/.netrc
+> ```
+
+### Docker Container
+
+The ultimate goal of this project is to create a docker container that can run autoRIFT workflows within a HyP3 deployment. To run the current version of the project's container, use this command:
+```
+docker run -it --rm \
+    -e AWS_ACCESS_KEY_ID=[YOUR_KEY] \
+    -e AWS_SECRET_ACCESS_KEY=[YOUR_SECRET] \
+    -e EARTHDATA_USERNAME=[YOUR_USERNAME_HERE] \
+    -e EARTHDATA_PASSWORD=[YOUR_PASSWORD_HERE] \
+    -e ESA_USERNAME=[YOUR_USERNAME_HERE] \
+    -e ESA_PASSWORD=[YOUR_PASSWORD_HERE] \
+    ghcr.io/asfhyp3/hyp3-autorift:latest \
+    ++process hyp3_autorift \
+    [WORKFLOW_ARGS]
+```
+
+> [!TIP]
+> You can use [`docker run --env-file`](https://docs.docker.com/reference/cli/docker/container/run/#env) to capture all the necessary environment variables in a single file.
+
+#### Docker Outputs
+
+To retain hyp3_autorift output files running via Docker there are two recommended approaches:
+
+1. Use a volume mount
+
+   Add the `-w /tmp -v ${PWD}:/tmp` flags after `docker run`; `-w` changes the working directory inside the container to `/tmp` and `-v` will mount your current working directory to the `/tmp` location inside the container such that hyp3_autorift outputs are preserved locally. You can replace `${PWD}` with any valid path.
+
+1. Copy outputs to a remote AWS S3 Bucket
+
+   Append the `--bucket` and `--bucket-prefix` to [WORKFLOW_ARGS] so that the final output files are uploaded to AWS S3. This also requires that AWS credentials to write to the bucket are available to the running container. For example, to write outputs to a hypothetical bucket `s3://hypothetical-bucket/test-run/`:
+
+   ```
+   docker run -it --rm \
+       -e AWS_ACCESS_KEY_ID=[YOUR_KEY] \
+       -e AWS_SECRET_ACCESS_KEY=[YOUR_SECRET] \ 
+       -e AWS_SESSION_TOKEN=[YOUR_TOKEN] \  # Optional
+       -e EARTHDATA_USERNAME=[YOUR_USERNAME_HERE] \
+       -e EARTHDATA_PASSWORD=[YOUR_PASSWORD_HERE] \
+       -e ESA_USERNAME=[YOUR_USERNAME_HERE] \
+       -e ESA_PASSWORD=[YOUR_PASSWORD_HERE] \
+       ghcr.io/asfhyp3/hyp3-autorift:latest \
+         ++process hyp3_autorift \
+         [WORKFLOW_ARGS] \
+         --bucket "hypothetical-bucket" \
+         --bucket-prefix "test-run"
+   ```
+
+## Background
+HyP3 is broken into two components: the cloud architecture/API that manages the processing of HyP3 workflows and Docker container plugins that contain scientific workflows that produce new science products from a variety of data sources (see figure below for the full HyP3 architecture).
+
+![Cloud Architecture](images/arch_here.jpg)
+
+The cloud infrastructure-as-code for HyP3 can be found in the main [HyP3 repository](https://github.com/asfhyp3/hyp3)., while this repository contains a plugin that can be used for feature tracking processing with AutoRIFT.
+
+## License
+The HyP3-autoRIFT plugin is licensed under the BSD 3-Clause license. See the LICENSE file for more details.
+
+## Code of conduct
+We strive to create a welcoming and inclusive community for all contributors to HyP3-autoRIFT. As such, all contributors to this project are expected to adhere to our code of conduct.
+
+Please see `CODE_OF_CONDUCT.md` for the full code of conduct text.
+
+## Contributing
+Contributions to the HyP3-autoRIFT plugin are welcome! If you would like to contribute, please submit a pull request on the GitHub repository.
+
+## Contact Us
+Want to talk about HyP3-autoRIFT? We would love to hear from you!
+
+Found a bug? Want to request a feature?
+[open an issue](https://github.com/ASFHyP3/asf_tools/issues/new)
+
+General questions? Suggestions? Or just want to talk to the team?
+[chat with us on gitter](https://gitter.im/ASFHyP3/community)
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