Merge branch 'dev_private' of github.com:TUDelftGeodesy/DePSI into de…

…v_private

.github/workflows/doc_deploy.yml

@@ -0,0 +1,28 @@
+# Deploy documentation when new release created
+
+name: Deploy docs
+
+on:
+  release:
+    types:
+      - published
+
+
+jobs:
+  build:
+    name: Deploy docs
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout main
+        uses: actions/checkout@v3
+        with:
+          fetch-depth: 0
+      - name: Set up Python 3.12
+        uses: actions/setup-python@v2
+        with:
+          python-version: "3.12"
+      - name: Install dependencies
+        run: |
+          python -m pip install .[docs] 
+      - name: Deploy docs
+        run: mkdocs gh-deploy --force

README.md

@@ -1,42 +1,13 @@
-# DePSI 
-This is the WIP repository for the Python version of DePSI *(), a Python package for inteferometric SAR processing. The software is inspired by the MATLAB version DePSI. In this repository, we implement classic DePSI algorithms and new InSAR developments in Python.
 
-## Installation for development
+# DePSI
 
-It is assumed that you have `mamba` installed. If not, you can find the installation instructions [here](https://mamba.readthedocs.io/en/latest/installation/mamba-installation.html). Other package managers like `conda` or `venv` can be used as well.
+DePSI (van Leijen, 2014) is an open source software for processing Persistent Scatterer Interferometry (PS-InSAR) data, originally implemented in MATLAB. From 2024, TUDelft and Netherlands eScience Center are collaborating to develop a Python version of DePSI, with recent advances in PS-InSAR. 
 
-Clone this repository 
 
-Then`cd` into it:
+## Developer Guide
 
-```bash
-cd DePSI
-```
+Please refer to the [Developer Guide](docs/dev_guide.md) for installation instructions, testing, and other development-related information.
 
-Create a new conda environment (here we give an example name `depsi-dev`) with `mamba`.:
-
-```bash
-mamba create -c conda-forge -n depsi-dev python=3.12
-```
-
-Here we use Python 3.12 since we aim to support python 3.10 and above.
-
-Activate the environment:
-
-```bash
-mamba activate depsi-dev
-```
-
-Install this package in development mode:
-
-```bash
-pip install -e ".[dev,docs]"
-```
-
-In the end, install the pre-commit hooks:
-```bash
-pre-commit install
-```
 
 ## Useful reading material
 
@@ -49,3 +20,7 @@ pre-commit install
 Copyright (c) 2023 - 2025, Netherlands eScience Center & Delft University of Technology
 
 Apache Software License 2.0
+
+## References
+
+[1] Van Leijen, Frederik Johannes. "Persistent scatterer interferometry based on geodetic estimation theory." (2014).

docs/api_reference.md

@@ -0,0 +1,24 @@
+## **Classification methods**:
+
+::: depsi.classification
+    options:
+      show_root_heading: false
+      show_source: true
+      heading_level: 3
+
+
+## **IO methods**:
+
+::: depsi.io
+    options:
+      show_root_heading: false
+      show_source: true
+      heading_level: 3
+
+## **slc methods**:
+
+::: depsi.slc
+    options:
+      show_root_heading: false
+      show_source: true
+      heading_level: 3

docs/dev_guide.md

@@ -0,0 +1,78 @@
+# Developer Guide
+
+## Installation guide
+
+The Python implementation of DePSI is under development. At present you can only install it from the GitHub repository.
+
+It is assumed that you have `mamba` installed. If not, you can find the installation instructions [here](https://mamba.readthedocs.io/en/latest/installation/mamba-installation.html). Other package managers like `conda` or `venv` can be used as well.
+
+Clone this repository and `cd` into it:
+
+```bash
+git clone [email protected]:TUDelftGeodesy/DePSI.git
+cd DePSI
+```
+
+Create a new conda environment (here we give an example name `depsi-dev`) with `mamba`.:
+
+```bash
+mamba create -c conda-forge -n depsi-dev python=3.12
+```
+
+Here we use Python 3.12 since we aim to support python 3.10 and above.
+
+Activate the environment:
+
+```bash
+mamba activate depsi-dev
+```
+
+Install this package in development mode, with extra dependencies for development and documentation:
+
+```bash
+pip install -e ".[dev,docs]"
+```
+
+In the end, install the pre-commit hooks, which will run the checks before each commit:
+```bash
+pre-commit install
+```
+
+## Linting and formatting
+
+We use `ruff` for linting and formatting. If the pre-commit hooks are installed, the checks will be run automatically before each commit.
+
+To manually run the checks, use the following command in the root directory of the repository:
+
+```bash
+ruff check .
+```
+
+## Testing
+
+We use `pytest` for testing. All tests are located in the `tests` directory.
+
+To run the tests, use the following command in the root directory of the repository:
+
+```bash
+pytest tests
+```
+
+The [GitHub Actions](https://github.com/TUDelftGeodesy/DePSI/blob/main/.github/workflows/build.yml) will run the tests automatically for each push and pull-request
+on the `main` branch.
+
+## Documentation
+
+We use `mkdocs` for documentation. 
+
+To check the documentation at local, use the following command in the root directory of the repository:
+
+```bash
+mkdocs serve
+```
+
+This will build and render the documentation at a local server. Follow the link provided in the terminal to view the documentation in the browser.
+
+## Parallelization
+
+We use `dask` in many functions for delayed computation and parallelization. Since DePSI operates with Xarray, in most cases, we us Xarray's interface with Dask Arrays, such as `xarray.apply_gufunc` or `xarray.map_blocks` to perform parallel computation. Please refer to the [Xarray Tutorial of Parallelizing Custom Functions](https://tutorial.xarray.dev/advanced/parallel-intro.html) as the best practices for implementing parallelization in DePSI.  

docs/index.md

@@ -0,0 +1,16 @@
+# DePSI: Delft PS-InSAR processing package
+
+DePSI (van Leijen, 2014) is an open source software for processing Persistent Scatterer Interferometry (PS-InSAR) data, originally implemented in MATLAB. From 2024, TUDelft and Netherlands eScience Center are collaborating to develop a Python version of DePSI, with recent advances in PS-InSAR. 
+
+For the stable version of DePSI implemented in MATLAB, please refer to the [stable branch](https://github.com/TUDelftGeodesy/DePSI/tree/stable).
+
+## Installation
+
+The Python implementation of DePSI is under development. At present you can only
+install it from the GitHub repository:
+
+`pip install git+https://github.com/TUDelftGeodesy/DePSI.git@main`
+
+## References
+
+[1] Van Leijen, Frederik Johannes. "Persistent scatterer interferometry based on geodetic estimation theory." (2014).

docs/usages/slc.md

@@ -0,0 +1,23 @@
+# SLC related methods
+
+## Converting coregistered interferogram stack to SLC stack
+
+After reading the coregistered interferogram stack and the mother SLC with `sarxarray`, the SLC stack can be reconstructed using the [`ifg_to_slc`](https://tudelftgeodesy.github.io/DePSI/api_reference/#depsi.slc.ifg_to_slc) method. The method takes the mother SLC and the coregistered interferogram stack as input and returns the reconstructed SLC stack.
+
+```python
+import sarxarray
+from depsi.slc import ifg_to_slc
+from pathlib import Path
+
+f_mother_slc = 'path/to/mother_slc.raw' # Path to the mother SLC binary file
+f_ifgs = list(sorted(Path('dir_ifgs').rglob("2*/ifnteferogram.raw")))  # List of paths of coregistered interferograms
+shape = (10768, 40588) # Shape of the stack, (nrows, ncols)
+reading_chunks = (2000, 2000)  # Reading chunks for lazy loading, (nrows, ncols)
+
+# Lazy loading mother SLC and ifg stack
+mother = sarxarray.from_binary([f_mother_slc], shape, dtype=np.complex64, chunks=reading_chunks)
+ifgs = sarxarray.from_binary(f_ifgs, shape, dtype=np.complex64, chunks=reading_chunks)
+
+# Generate reconstructed SLCs
+slc_recon = ifg_to_slc(mother, ifgs)
+```

mkdocs.yml

@@ -0,0 +1,58 @@
+site_name: "DePSI: Delft PS-InSAR processing package"
+repo_url: https://github.com/TUDelftGeodesy/DePSI
+repo_name: DePSI
+
+nav:
+  - Getting started: 
+    - About DePSI: index.md
+  - Usage:
+    - SLC methods: usages/slc.md
+  - API Reference: api_reference.md
+  - Developer Guide: dev_guide.md
+
+
+theme:
+  name: material
+  palette:
+    # Palette toggle for light mode
+    - scheme: default
+      toggle:
+        icon: material/weather-sunny
+        name: Switch to dark mode
+      primary: blue
+      accent: white
+
+    # Palette toggle for dark mode
+    - scheme: slate
+      toggle:
+        icon: material/weather-night
+        name: Switch to light mode
+      primary: black
+      accent: pink
+  features:
+    - navigation.instant
+    - navigation.tabs
+    - navigation.tabs.sticky
+    - content.code.copy
+
+plugins:
+- mkdocs-jupyter:
+      include_source: True
+- search
+- mkdocstrings:
+    handlers:
+      python:
+        options:
+          docstring_style: numpy
+          docstring_options:
+            ignore_init_summary: no
+          merge_init_into_class: yes
+          show_submodules: no
+
+markdown_extensions:
+  - pymdownx.highlight:
+      anchor_linenums: true
+  - pymdownx.superfences
+
+extra:
+  generator: false