Merge pull request #7 from earthnet2021/sen2nbar

changed to sen2nbar

README.md

@@ -94,6 +94,7 @@ Kwargs:
 - `five_daily_filter`: If `True` returns a regular 5-daily cycle starting with the first date in `full_time_interval`. It has no effect, if `best_orbit_filter` is used.
 - `brdf_correction`: If `True`, does BRDF correction based on the Sentinel 2 Metadata (illumination angles).
 - `cloud_mask`: If `True`, creates a cloud and cloud shadow mask based on deep learning. It automatically finds the best available cloud mask for the requested `bands`.
+- `correct_processing_baseline`: If `True` (default): corrects the shift of +1000 that exists in Sentinel 2 data with processing baseline >= 4.0
 
 
 ## Installation
@@ -105,7 +106,7 @@ conda create -n minicuber python=3.10 gdal cartopy -c conda-forge
 conda deactivate
 conda activate minicuber
 pip install torch torchvision torchaudio --index-url https://download.pytorch.org/whl/cpu
-pip install scipy matplotlib seaborn netCDF4 xarray zarr dask shapely pillow pandas s3fs fsspec boto3 psycopg2 pystac-client stackstac planetary-computer rasterio[s3] rioxarray odc-algo segmentation-models-pytorch folium ipykernel ipywidgets
+pip install scipy matplotlib seaborn netCDF4 xarray zarr dask shapely pillow pandas s3fs fsspec boto3 psycopg2 pystac-client stackstac planetary-computer rasterio[s3] rioxarray odc-algo segmentation-models-pytorch folium ipykernel ipywidgets sen2nbar
 ```
 
 Install this package with PyPI:
@@ -134,4 +135,4 @@ Similar to this package, [cubo](https://github.com/davemlz/cubo) provides a high
 
 ## Acknowledgement
 
-This project has received funding from the European Union’s Horizon 2020 research and innovation programme under grant agreement No 101004188 ([DeepCube Horizon 2020](https://deepcube-h2020.eu/ "DeepCube Horizon 2020")). We are grateful to David Montero Loaiza for providing the code for the Sentinel 2 BRDF correction. We are grateful to César Aybar and the [CloudSEN12](https://cloudsen12.github.io/) team, their work forms the basis for the cloud mask implemented in earthnet-minicuber.
+This project has received funding from the European Union’s Horizon 2020 research and innovation programme under grant agreement No 101004188 ([DeepCube Horizon 2020](https://deepcube-h2020.eu/ "DeepCube Horizon 2020")). We are grateful to David Montero Loaiza for providing the [sen2nbar](https://github.com/ESDS-Leipzig/sen2nbar) package used for the Sentinel 2 BRDF correction. We are grateful to César Aybar and the [CloudSEN12](https://cloudsen12.github.io/) team, their work forms the basis for the cloud mask implemented in earthnet-minicuber.

earthnet_minicuber/__init__.py

@@ -1,6 +1,6 @@
 """EarthNet Minicuber"""
 
-__version__ = "0.1.1"
+__version__ = "0.1.2"
 __author__ = "Vitus Benson"
 
 

earthnet_minicuber/plot.py

@@ -8,4 +8,4 @@ def plot_rgb(mc, mask = True):
     if mask:
         return mc[["s2_B04", "s2_B03", "s2_B02"]].to_array("band").where(((mc.s2_mask < 1) & mc.s2_SCL.isin([1,2,4,5,6,7]))).plot.imshow(col = "time", col_wrap = 3, vmin = 0.0, vmax = 0.4)
     else:
-        return mc[["s2_B04", "s2_B03", "s2_B02"]].to_array("band").where(((mc.s2_mask < 1)), np.NaN).plot.imshow(col = "time", col_wrap = 3, vmin = 0.0, vmax = 0.4)
+        return mc[["s2_B04", "s2_B03", "s2_B02"]].to_array("band").plot.imshow(col = "time", col_wrap = 3, vmin = 0.0, vmax = 0.4)

earthnet_minicuber/provider/era5_esdl.py

@@ -19,18 +19,22 @@
 
 class ERA5_ESDL(provider_base.Provider):
 
-    def __init__(self, bands = ['e', 'pet', 'pev', 'ssrd', 't2m', 't2mmax', 't2mmin','tp'], zarrpath = None):
+    def __init__(self, bands = ['e', 'pet', 'pev', 'ssrd', 't2m', 't2mmax', 't2mmin','tp'], zarrpath = None, proxy = None):
         self.is_temporal = True
 
         self.bands = bands
         self.zarrpath = zarrpath
 
-        if zarrpath is not None:
+        if zarrpath is None:
             self.s3 = s3fs.S3FileSystem(anon=True,
             client_kwargs={
             'endpoint_url': 'https://s3.bgc-jena.mpg.de:9000',
             'region_name': 'thuringia',
-            })
+            },
+            config_kwargs = {
+            "proxies": {'http': proxy}
+            } if proxy else {}
+            )
 
     def load_data(self, bbox, time_interval, **kwargs):
 

earthnet_minicuber/provider/s2/__init__.py

@@ -1,2 +1,2 @@
 
-from . import sentinel2, nbar, cloudmask, utils, sen2flux
+from . import sentinel2, nbar, cloudmask