Merge pull request #151 from yreynaud/yann

Add RCM in XSAR
umr-lops · Apr 18, 2023 · 3f31df1 · 3f31df1
2 parents 4be05be + 8288038
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diff --git a/README.md b/README.md
@@ -7,10 +7,56 @@ Sentinel1 Level 1 python reader for efficient xarray/dask based processor
 
 # Install
 
+## Conda
+
+1) Install xsar (this will only permit to use Sentinel1)
 
 ```
 conda install -c conda-forge xsar
 ```
+2) Add optional dependencies
+
+- Add use of Radarsat2 :
+
+```
+conda install -c conda-forge xradarsat2
+```
+
+- Add use of RCM
+
+```
+pip install git+https://github.com/umr-lops/xarray-safe-rcm.git
+```
+
+## Pypi
+
+1) Install xsar (this will only permit to use Sentinel1)
+
+```
+pip install xsar
+```
+2) install xsar with optional dependencies (to use Radarsat2, RCM...)
+
+- Install xsar including Radarsat2 :
+
+```
+pip install xsar[RS2]
+```
+
+- Install xsar including RCM :
+
+```
+pip install git+https://github.com/umr-lops/xarray-safe-rcm.git
+pip install xsar
+```
+
+- Install xsar including Radarsat2 and RCM:
+
+```
+pip install git+https://github.com/umr-lops/xarray-safe-rcm.git
+pip install xsar[RS2]
+```
+
 
 ```python
 >>> import xsar

diff --git a/docs/_static/uml/classes_all_attributes.png b/docs/_static/uml/classes_all_attributes.png
diff --git a/docs/_static/uml/packages_all_attributes.png b/docs/_static/uml/packages_all_attributes.png
diff --git a/docs/basic_api.rst b/docs/basic_api.rst
@@ -10,17 +10,33 @@ API reference
 
 Base classes
 ============
-.. automodule:: xsar
-    :members: BaseMeta, BaseDataset
+    .. autoclass:: BaseMeta
+        :members:
+
+
+    .. autoclass:: BaseDataset
+        :members:
 
 XSAR Meta classes
 =================
-.. automodule:: xsar
-    :members: Sentinel1Meta, RadarSat2Meta
+    .. autoclass:: Sentinel1Meta
+        :members:
+
+    .. autoclass:: RadarSat2Meta
+        :members:
+
+    .. autoclass:: RcmMeta
+        :members:
 
 XSAR Dataset classes
 ====================
-.. automodule:: xsar
-    :members: Sentinel1Dataset, RadarSat2Dataset
+    .. autoclass:: Sentinel1Dataset
+        :members:
+
+    .. autoclass:: RadarSat2Dataset
+        :members:
+
+    .. autoclass:: RcmDataset
+        :members:
 
 
diff --git a/docs/examples/mask.ipynb b/docs/examples/mask.ipynb
@@ -209,6 +209,73 @@
    "source": [
     "ds['sigma0_land'].sel(pol='VH').plot(vmin=0)"
    ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "3cf12c23-ddb1-4040-ac11-2c8209de7ded",
+   "metadata": {
+    "tags": []
+   },
+   "source": [
+    "## RCM example"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "5967453d-ad6f-480b-8d6a-6d89484088ff",
+   "metadata": {
+    "tags": []
+   },
+   "source": [
+    "[xsar.RcmDataset.dataset](../basic_api.rst#xsar.RcmDataset.dataset) has a `land_mask` variable by default, rasterized from [cartopy.feature.NaturalEarthFeature('physical', 'land', '10m')](https://scitools.org.uk/cartopy/docs/latest/matplotlib/feature_interface.html#cartopy.feature.NaturalEarthFeature)\n",
+    "\n"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "679635f2-186d-47da-b3d2-e762d5ad82a4",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "import warnings\n",
+    "warnings.filterwarnings('ignore')"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "5f6eb695-4e2b-4b84-9953-822029979929",
+   "metadata": {},
+   "source": [
+    "### Mask sigma0 over land\n",
+    "\n",
+    "Replacing `sigma0` values with `nan` over ocean can be done with `xarray.where`"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "5c9934b5-4752-4076-b03c-d575c46f5994",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "\n",
+    "ds = xsar.open_dataset(xsar.get_test_file('RCM1_OK2460179_PK2462841_1_SCLND_20230301_072431_VV_VH_GRD'), resolution='1000m')\n",
+    "\n",
+    "# apply land_mask. The final transpose is done to preserve dimensions ordering\n",
+    "ds['sigma0_land'] = xr.where(ds['land_mask'], ds['sigma0'], np.nan).transpose(*ds['sigma0'].dims)\n",
+    "ds['sigma0_land']\n"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "db2f79fc-7c23-4a52-bc0f-93d05293d853",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "ds['sigma0_land'].sel(pol='VH').plot(vmin=0)"
+   ]
   }
  ],
  "metadata": {

diff --git a/docs/examples/projections.ipynb b/docs/examples/projections.ipynb
@@ -273,8 +273,8 @@
     "\n",
     "crs = CRS({\n",
     "        'proj': 'aeqd',\n",
-    "        'lat_0': xsar_obj.s1meta.footprint.centroid.y,\n",
-    "        'lon_0': xsar_obj.s1meta.footprint.centroid.x,\n",
+    "        'lat_0': xsar_obj.sar_meta.footprint.centroid.y,\n",
+    "        'lon_0': xsar_obj.sar_meta.footprint.centroid.x,\n",
     "        'x_0': 0,\n",
     "        'y_0': 0,\n",
     "        'ellps': 'WGS84'\n",

diff --git a/docs/examples/radarsat2.ipynb b/docs/examples/radarsat2.ipynb
@@ -150,7 +150,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "rs2ds.rs2meta"
+    "rs2ds.sar_meta"
    ]
   },
   {
@@ -270,7 +270,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "dn_low_res = load_digital_number(rs2ds.rs2meta.dt, resolution=resolution, resampling=resampling, chunks=chunks)['digital_numbers'].ds\n",
+    "dn_low_res = load_digital_number(rs2ds.sar_meta.dt, resolution=resolution, resampling=resampling, chunks=chunks)['digital_numbers'].ds\n",
     "dn_low_res"
    ]
   },