Merge pull request #27 from hi-paris/develop

Documentation and Sentinel-TOPS

.github/workflows/documentation.yml

@@ -0,0 +1,48 @@
+name: documentation
+
+on: 
+ push:
+ branches: [ main ]
+ pull_request:
+ branches: [ main ]
+
+# A workflow run is made up of one or more jobs that can run sequentially or in parallel
+jobs: 
+ # This workflow contains a single job called "build"
+ build: 
+ # The type of runner that the job will run on
+ runs-on: ubuntu-latest
+
+ # Steps represent a sequence of tasks that will be executed as part of the job
+ steps:
+ # Checks-out your repository under $GITHUB_WORKSPACE, so your job can access it
+ - uses: actions/checkout@v2
+
+ - name: Set up Python 3.10
+ uses: actions/setup-python@v2
+ with:
+ python-version: "3.10"
+
+
+ - name: Set up gdal 
+ run : sudo apt-get install libgdal-dev
+
+ # Runs a single command using the runners shell
+ - name: Run a one-line script
+ run: echo Hello, world!
+
+ - name: Install dependencies
+ run: | 
+ python -m pip install --upgrade pip
+ pip install ghp-import sphinx sphinx_rtd_theme -e .
+
+ - name: Install gdal dependencies 
+ run : pip install --global-option=build_ext --global-option="-I/usr/include/gdal" GDAL==`gdal-config --version`
+
+ - name: Build HTML
+ run: | 
+ cd docs/
+ make html
+ - name: Run ghp-import
+ run: | 
+ ghp-import -n -p -f docs/_build/html

.gitignore

@@ -62,9 +62,6 @@ instance/
 # Scrapy stuff:
 .scrapy
 
-# Sphinx documentation
-docs/_build/
-
 # PyBuilder
 target/
 

README.md

@@ -34,6 +34,8 @@ In order to get the right model, the `model_name` has to be specified when build
 This `model_name` can either be :
 - `"spotlight"` for SAR images retrieved with spotlight mode 
 - `"stripmap"` for SAR images retrieved with stripmap mode
+- `"Sentinel-TOPS"` for SAR images retrieved with TOPS mode
+
 
 During the preprocessing steps of the noisy image for MERLIN, the real and the imaginary parts are <strong>"symetrised"</strong> (to match the theoretical assumptions of MERLIN). To skip this step, you can set the `symetrise` parameter to `False`
 
@@ -47,7 +49,7 @@ from deepdespeckling.merlin.merlin_denoiser import MerlinDenoiser
 
 # Path to one image (cos or npy file)
 image_path="path/to/cosar/image"
-# Model name, can be "spotlight" or "stripmap"
+# Model name, can be "spotlight", "stripmap" or "Sentinel-TOPS"
 model_name = "spotlight"
 symetrise = True
 

deepdespeckling/despeckling.py

@@ -13,7 +13,7 @@
 logging.basicConfig(level=logging.INFO)
 
 
-def get_denoiser(model_name: str, symetrise: bool = True) -> Denoiser:
+def _get_denoiser(model_name: str, symetrise: bool = True) -> Denoiser:
  """Get the right denoiser object from the model name
 
  Args:
@@ -24,7 +24,7 @@ def get_denoiser(model_name: str, symetrise: bool = True) -> Denoiser:
  Returns:
  denoiser (Denoiser): the right denoiser, Sar2SarDenoiser or MerlinDenoiser
  """
- if model_name in ["spotlight", "stripmap"]:
+ if model_name in ["spotlight", "stripmap", "Sentinel_TOPS"]:
  denoiser = MerlinDenoiser(model_name=model_name, symetrise=symetrise)
  elif model_name == "sar2sar":
  denoiser = Sar2SarDenoiser()
@@ -41,7 +41,7 @@ def despeckle(sar_images_path: str, destination_directory_path: str, model_name:
  Args:
  sar_images_path (str): path of sar images
  destination_directory_path (str): path of folder in which results will be stored
- model_name (str): model name, either "spotlight" or "stripmap" to select MERLIN model on the 
+ model_name (str): model name, either "spotlight", "stripmap" or "Sentinel_TOPS" to select MERLIN model on the 
  right cosar image format or "sar2sar" for SAR2SAR model. Default to "spotlight"
  patch_size (int): patch size. Defaults to constant PATCH_SIZE.
  stride_size (int): stride size. Defaults to constant STRIDE_SIZE.
@@ -60,7 +60,7 @@ def despeckle(sar_images_path: str, destination_directory_path: str, model_name:
  logging.info(
  f"Starting inference.. Collecting data from {sar_images_path} and storing test results in {destination_directory_path}")
 
- denoiser = get_denoiser(model_name=model_name, symetrise=symetrise)
+ denoiser = _get_denoiser(model_name=model_name, symetrise=symetrise)
  denoiser.denoise_images(images_to_denoise_path=processed_images_path, save_dir=destination_directory_path,
  patch_size=patch_size, stride_size=stride_size)
 
@@ -73,7 +73,7 @@ def despeckle_from_coordinates(sar_images_path: str, coordinates_dict: dict, des
  sar_images_path (str): path of sar images
  coordinates_dict (dict): dictionary containing pixel boundaries of the area to despeckle (x_start, x_end, y_start, y_end)
  destination_directory_path (str): path of folder in which results will be stored
- model_name (str): model name, either "spotlight" or "stripmap" to select MERLIN model on the 
+ model_name (str): model name, either "spotlight", "stripmap" or "Sentinel_TOPS" to select MERLIN model on the 
  right cosar image format or "sar2sar" for SAR2SAR model. Default to "spotlight"
  patch_size (int): patch size. Defaults to constant PATCH_SIZE.
  stride_size (int): stride size. Defaults to constant STRIDE_SIZE.
@@ -92,7 +92,7 @@ def despeckle_from_coordinates(sar_images_path: str, coordinates_dict: dict, des
  logging.info(
  f"Starting inference.. Collecting data from {sar_images_path} and storing test results in {destination_directory_path}")
 
- denoiser = get_denoiser(model_name=model_name, symetrise=symetrise)
+ denoiser = _get_denoiser(model_name=model_name, symetrise=symetrise)
  denoiser.denoise_images(images_to_denoise_path=processed_images_path, save_dir=destination_directory_path,
  patch_size=patch_size, stride_size=stride_size)
 
@@ -106,7 +106,7 @@ def despeckle_from_crop(sar_images_path: str, destination_directory_path: str, m
  destination_directory_path (str): path of folder in which results will be stored
  patch_size (int): patch size. Defaults to constant PATCH_SIZE.
  stride_size (int): stride size. Defaults to constant STRIDE_SIZE.
- model_name (str): model name, either "spotlight" or "stripmap" to select MERLIN model on the 
+ model_name (str): model name, either "spotlight", "stripmap" or "Sentinel_TOPS" to select MERLIN model on the 
  right cosar image format or "sar2sar" for SAR2SAR model. Default to "spotlight"
  fixed (bool) : If True, crop size is limited to 256*256. Defaults to True
  symetrise (bool) : if using spotlight or stripmap model, if True, will symetrise the real and 
@@ -119,7 +119,8 @@ def despeckle_from_crop(sar_images_path: str, destination_directory_path: str, m
  processed_images_path = create_empty_folder_in_directory(destination_directory_path=destination_directory_path,
  folder_name="processed_images")
 
- ext = "cos" if model_name in ["spotlight", "stripmap"] else "tiff"
+ ext = "cos" if model_name in ["spotlight",
+ "stripmap", "Sentinel_TOPS"] else "tiff"
  images_paths = glob(os.path.join(sar_images_path, f"*.{ext}")) + \
  glob(os.path.join(sar_images_path, "*.npy"))
 
@@ -139,6 +140,6 @@ def despeckle_from_crop(sar_images_path: str, destination_directory_path: str, m
  logging.info(
  f"Starting inference.. Collecting data from {sar_images_path} and storing results in {destination_directory_path}")
 
- denoiser = get_denoiser(model_name=model_name, symetrise=symetrise)
+ denoiser = _get_denoiser(model_name=model_name, symetrise=symetrise)
  denoiser.denoise_images(images_to_denoise_path=processed_images_path, save_dir=destination_directory_path,
  patch_size=patch_size, stride_size=stride_size)

deepdespeckling/merlin/merlin_denoiser.py

@@ -23,7 +23,7 @@ def __init__(self, model_name, symetrise, **params):
  """Initialize MerlinDenoiser class
 
  Args:
- model_name (str): name to be used, can be "spotlight" or "stripmap"
+ model_name (str): name to be used, can be "spotlight", "stripmap" or "Sentinel_TOPS"
  """
  super().__init__(**params)
  self.model_name = model_name
@@ -42,6 +42,9 @@ def init_model_weights_path(self) -> str:
  elif self.model_name == "stripmap":
  model_weights_path = os.path.join(
  current_dir, "saved_models/stripmap.pth")
+ elif self.model_name == "Sentinel_TOPS":
+ model_weights_path = os.path.join(
+ current_dir, "saved_models/sentinel_tops.pth")
  else:
  raise ValueError(
  "The model name doesn't refer to an existing model ")

deepdespeckling/test_deepdespeckling.py

@@ -5,5 +5,5 @@
 coordinates_dictionnary = {'x_start': 0,
  'y_start': 0, 'x_end': 400, 'y_end': 400}
 
-despeckle(image_path, destination_directory,
- model_name="sar2sar")
+"""despeckle(image_path, destination_directory,
+ model_name="sar2sar")"""

docs/Makefile

@@ -5,8 +5,8 @@
 # from the environment for the first two.
 SPHINXOPTS ?=
 SPHINXBUILD ?= sphinx-build
-SOURCEDIR = source
-BUILDDIR = build
+SOURCEDIR = .
+BUILDDIR = _build
 
 # Put it first so that "make" without argument is like "make help".
 help:

docs/source/conf.py → docs/conf.py

@@ -1,5 +1,17 @@
 import sys
 import os
+import deepdespeckling
+import deepdespeckling.denoiser
+import deepdespeckling.despeckling
+import deepdespeckling.model
+import deepdespeckling.utils
+import deepdespeckling.utils.constants
+import deepdespeckling.utils.load_cosar
+import deepdespeckling.utils.utils
+import deepdespeckling.sar2sar
+import deepdespeckling.sar2sar.sar2sar_denoiser
+import deepdespeckling.merlin
+import deepdespeckling.merlin.merlin_denoiser
 
 # Configuration file for the Sphinx documentation builder.
 #
@@ -22,27 +34,17 @@
 extensions = [
  'sphinx.ext.autodoc',
  'sphinx.ext.viewcode',
- 'sphinx.ext.napoleon'
+ 'sphinx.ext.napoleon',
+ 'sphinx.ext.githubpages'
 ]
 
 templates_path = ['_templates']
 exclude_patterns = ["build", ".venv", ".vscode",
  "dist", "deepdespeckling.egg-info", "img", "icons"]
 
-language = 'English'
-
-master_doc = "index"
-
-autodoc_default_options = {
- 'members': True,
- 'undoc-members': True,
- 'show-inheritance': True,
-}
-
-add_module_names = True
 
 # -- Options for HTML output -------------------------------------------------
 # https://www.sphinx-doc.org/en/master/usage/configuration.html#options-for-html-output
 
-html_theme = 'alabaster'
+html_theme = 'sphinx_rtd_theme'
 html_static_path = ['_static']

docs/source/index.rst → docs/index.rst

@@ -7,7 +7,7 @@ Welcome to deepdespeckling's documentation!
 ===========================================
 
 .. toctree::
- :maxdepth: 3
+ :maxdepth: 4
  :caption: Contents:
 
  modules

docs/make.bat

@@ -7,8 +7,8 @@ REM Command file for Sphinx documentation
 if "%SPHINXBUILD%" == "" (
  set SPHINXBUILD=sphinx-build
 )
-set SOURCEDIR=source
-set BUILDDIR=build
+set SOURCEDIR=.
+set BUILDDIR=_build
 
 %SPHINXBUILD% >NUL 2>NUL
 if errorlevel 9009 (

docs/source/modules.rst → docs/modules.rst

@@ -1,5 +1,5 @@
 .. toctree::
- :maxdepth: 3
+ :maxdepth: 4
  :caption: Contents:
 
 deepdespeckling