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Merge branch 'develop' to release 4.4.2
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‎README.md‎

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@@ -10,7 +10,7 @@ The main goal of __Sen2Like__ is to generate Sentinel-2 like harmonised/fused su
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It is a contribution to on going worldwide initiatives (*NASA-HLS, Force, CESBIO [2],[3]) undertook to facilitate higher level processing starting from harmonized data.
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The __Sen2Like__ framework is a scientific and open source software. In its current implementation version (*December 2022*), it combines Landsat-8 and Sentinel-2 data products.
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Level 1 and Level 2 input Landsat 8 (LS8) products are processed to be harmonized with Sentinel-2 data (S2).
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Level 1 and Level 2 input Landsat 8-9 (LS8-9) products are processed to be harmonized with Sentinel-2 data (S2).
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The two following ARD product types are generated:
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* Harmonized Surface Reflectance Products (Level 2H) - at 30m of resolution,
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* Fused Surface Reflectance Products (Level 2F) - at 10-20m of resolution.
@@ -28,7 +28,8 @@ Sen2like software supports the PRISMA L1 products through the usage of a pre-pro
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The __processing workflow__ is based on following algorithms:
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* Geometric Corrections including registration to common reference & the stitching [4],
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* Atmospheric Corrections by using SMAC [5] relying on auxiliary meteorological data,
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* Atmospheric Corrections by using SMAC [5] relying on auxiliary meteorological data,
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or "Sen2Cor3" [11] as a first processing step
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* Application of Spectral Band Adjustment Factor (SBAF) [2],
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* Transformation to Nadir BRDF-normalized Reflectance (NBAR) [6],[7],
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* Production of LS8 High Resolution 10 m pixel spacing data (Fusion) [8].
@@ -39,15 +40,15 @@ It is therefore possible, to cover large geographic extent with a __seamless ima
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It is worth noting that the overall accuracy of your final ARD product strongly depends on the accuracy of sen2like auxiliary data. Two categories of auxiliary data are important: the raster reference for geometric corrections and the meteorological data for atmospheric corrections. Regarding atmospheric corrections, one possibility is to use data from the Copernicus Atmosphere Monitoring Service [9]. The Sen2Like team prepared a dedicated CAMS monthly dataset for the Year 2020, available from [here](http://185.178.85.51/CAMS/). Please refer to this short [description](http://185.178.85.51/CAMS/Readme_CAMS2020.txt) for additional information.
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For further details on the format specification of the harmonized products or the functionalities of the Sen2Like software, please
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refer to the [Product Format Specification](sen2like/docs/source/S2-PDGS-MPC-L2HF-PFS-v1.2.pdf), and the [User Manual v1.8](sen2like/docs/source/S2-SEN2LIKE-UM-V1.9.pdf).
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refer to the [Product Format Specification](sen2like/docs/source/S2-PDGS-MPC-L2HF-PFS-v1.2.pdf), and the [User Manual v1.9](sen2like/docs/source/S2-SEN2LIKE-UM-V1.9.pdf).
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## Publications and Contacts
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**Yearning to know more ? Check out**
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* poster [Sen2like: A solution for Harmonization and Fusion of Sentinel-2 and Landsat 8/9 data, JACIE 2023](https://www.researchgate.net/publication/372831217_Sen2like_A_solution_for_Harmonization_and_Fusion_of_Sentinel-2_and_Landsat_89_data)
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* A [Sen2Like Relaxing Video](https://youtu.be/KBSYYBShyos) prepared for [ESA EO PHI-WEEK 2020](https://www.youtube.com/playlist?list=PLvT7fd9OiI9XELZXcljYTftUtJ_NFWRrY)
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* A [Sen2Like Time Lapse including NDVI graphic](https://youtu.be/yEObvI1KQBg) prepared for QWG#12
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And the following research papers :
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And the following references :
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+ [1] S. Saunier, J. Louis, V. Debaecker et al., "Sen2like, A Tool To Generate Sentinel-2 Harmonised Surface Reflectance Products - First Results with Landsat-8," IGARSS 2019 - 2019 IEEE International Geoscience and Remote Sensing Symposium, Yokohama, Japan, 2019, pp. 5650-5653, doi: 10.1109/IGARSS.2019.8899213.
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+ [2] Claverie, Martin, Junchang Ju, Jeffrey G. Masek, Jennifer L. Dungan, Eric F. Vermote, Jean-Claude Roger, Sergii V. Skakun, et Christopher Justice. "The Harmonized Landsat and Sentinel-2 Surface Reflectance Data Set". Remote Sensing of Environment 219 (15 décembre 2018): 145‑61. (https://doi.org/10.1016/j.rse.2018.09.002).
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+ [3] Frantz, David. "FORCE—Landsat + Sentinel-2 Analysis Ready Data and Beyond". Remote Sensing 11, nᵒ 9 (janvier 2019): 1124. (https://doi.org/10.3390/rs11091124).
@@ -58,7 +59,7 @@ And the following research papers :
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+ [8] Sen2Like User Manual
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+ [9] [Copernicus Atmosphere Monitoring Service](https://atmosphere.copernicus.eu/)
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+ [10] Saunier, S.; Pflug, B.; Lobos, I.M.; Franch, B.; Louis, J.; De Los Reyes, R.; Debaecker, V.; Cadau, E.G.; Boccia, V.; Gascon, F.; Kocaman, S. Sen2Like: Paving the Way towards Harmonization and Fusion of Optical Data. Remote Sens. 2022, 14, 3855. (https://doi.org/10.3390/rs14163855)
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+ [11] [Sen2Cor3 installation instructions](sen2cor3/README.md)
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**Learn how to use Sen2Like**, have a look at the [User Manual](sen2like/docs/source/S2-SEN2LIKE-UM-V1.9.pdf).
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‎sen2cor3/README.md‎

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# Sen2Cor 3 version 3.01.00
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## Retrieve Sen2cor 3.01.00 documentation from sftp server
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```
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hostname = 'sftp.telespazio.fr'
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port = 22 # default SFTP port is 22
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username = 'sen2cor3'
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password = '4sen2like'
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remote_path = '/upload/Sen2Cor-3.01.00/Documentation/'
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```
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**_Sen2cor 3.01.00 Software Release Note:_**
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sftp://sen2cor3@sftp.telespazio.fr/upload/Sen2Cor-3.01.00/Documentation/S2-SEN2LIKE-Sen2Cor_3.01.00-SRN_V1.1.pdf
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**_Sen2cor 3.01.00 Software Configuration and User Manual:_**
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sftp://sen2cor3@sftp.telespazio.fr/upload/Sen2Cor-3.01.00/Documentation/S2-SEN2LIKE-Sen2Cor_3.01.00-SUM_V1.1.pdf
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## Retrieve Sen2cor 3.01.00 software from sftp server
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Either with a software like Filezilla:
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```
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hostname = 'sftp.telespazio.fr'
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port = 22 # default SFTP port is 22
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username = 'sen2cor3'
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password = '4sen2like'
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remote_path = '/upload/Sen2Cor-3.01.00/Software/sen2cor_3.1.0_python_3.10_20240313.zip'
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```
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e.g: sftp://sen2cor3@sftp.telespazio.fr/upload/Sen2Cor-3.01.00/Software/sen2cor_3.1.0_python_3.10_20240313.zip
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or with the example script "sen2cor3_download.py" based on "paramiko" module.
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It requires paramiko version 3.4.0 that could be installed with conda [see below](#create-the-sen2like-conda-environment):
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```
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conda activate sen2like
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conda install paramiko=3.4.0 -c conda-forge
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```
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```
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python sen2cor3_download.py sen2cor3_install_dir
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```
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## Unzip sen2cor_3.1.0_python_3.10.zip into the Sen2Cor 3 directory of your choice
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```
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e.g. sen2cor3_install_dir=/opt/sen2cor3/code/
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cd $sen2cor3_install_dir
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unzip sen2cor_3.1.0_python_3.10.zip
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```
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## Auxiliary Data Symbolic linking
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Sen2Cor3 relies on a set of external auxiliary data that needs to be available in Sen2Cor3 "aux_data" folder:
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- ECMWF CAMS data: daily, monthly
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- ESA CCI files
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- Copernicus DEM files
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Further details are available in Sen2Cor3 Software User Manual.
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Examples of symbolic linking is given hereafter:
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- symbolic linking of your local CAMS folder that contains daily CAMS data e.g. /data/CAMS/daily
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- symbolic linking of your local ESA CCI files e.g. /data/AUX_DATA/
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```
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cd $sen2cor3_install_dir/sen2cor_3.1.0_python_3.10/SEN2COR_3/aux_data
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ln -s /data/CAMS/daily ./ECMWF/daily
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ln -s /data/AUX_DATA/ESACCI-LC-L4-Snow-Cond-500m-MONTHLY-2000-2012-v2.4 ./ESACCI-LC-L4-Snow-Cond-500m-MONTHLY-2000-2012-v2.4
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ln -s /data/AUX_DATA/ESACCI-LC-L4-WB-Map-150m-P13Y-2000-v4.0.tif ./ESACCI-LC-L4-WB-Map-150m-P13Y-2000-v4.0.tif
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ln -s /data/AUX_DATA/ESACCI-LC-L4-LCCS-Map-300m-P1Y-2015-v2.0.7.tif ./ESACCI-LC-L4-LCCS-Map-300m-P1Y-2015-v2.0.7.tif
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```
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## Install miniconda if conda is not already installed on your system
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https://repo.anaconda.com/miniconda/Miniconda3-py37_22.11.1-1-Linux-x86_64.sh
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## Create the sen2like conda environment
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Once you retrieved the code, go into Sen2Cor3 root source folder and run the following command to create a conda env named sen2like:
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```
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cd $sen2cor3_install_dir/sen2cor_3.1.0_python_3.10
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conda create -n sen2like --file requirements.txt -c conda-forge
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```
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## Activate sen2like conda environment
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Sen2Cor 3.1 uses the same conda environment as Sen2like:
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```
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conda activate sen2like
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```
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### Test the Command line execution
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```
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python $sen2cor3_install_dir/sen2cor_3.1.0_python_3.10/SEN2COR_3/L2A_Process.py --help
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output:
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usage: L2A_Process.py [-h] [--mode MODE] [--resolution {10,20,30,60}] [--datastrip DATASTRIP] [--tile TILE] [--output_dir OUTPUT_DIR] [--work_dir WORK_DIR]
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[--img_database_dir IMG_DATABASE_DIR] [--res_database_dir RES_DATABASE_DIR] [--processing_centre PROCESSING_CENTRE] [--archiving_centre ARCHIVING_CENTRE]
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[--processing_baseline PROCESSING_BASELINE] [--raw] [--tif] [--sc_only] [--sc_classic] [--sc_cog] [--cr_only] [--debug] [--GIP_L2A GIP_L2A]
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[--GIP_L2A_SC GIP_L2A_SC] [--GIP_L2A_AC GIP_L2A_AC] [--GIP_L2A_PB GIP_L2A_PB] [--Hyper_MS]
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input_dir
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Sen2Cor. Version: 03.01.00, created: 2024.02.29, supporting Level-1C product version 14.2 - 14.9, supporting Level-1TP Collection_1-2 Landsat_8-9, supporting Hyper Level-1C - .
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positional arguments:
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input_dir Directory of Level-1C input
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options:
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-h, --help show this help message and exit
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--mode MODE Mode: generate_datastrip, process_tile
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--resolution {10,20,30,60}
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Target resolution, can be 10, 20 or 60m for S2, 30m for Hyper. If omitted, only 20 and 10m resolutions will be processed
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--datastrip DATASTRIP
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Datastrip folder
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--tile TILE Tile folder
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--output_dir OUTPUT_DIR
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Output directory
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--work_dir WORK_DIR Work directory
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--img_database_dir IMG_DATABASE_DIR
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Database directory for L1C(H) input images
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--res_database_dir RES_DATABASE_DIR
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Database directory for results and temporary products
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--processing_centre PROCESSING_CENTRE
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Processing centre as regex: ^[A-Z_]{4}$, e.g "SGS_"
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--archiving_centre ARCHIVING_CENTRE
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Archiving centre as regex: ^[A-Z_]{4}$, e.g. "SGS_"
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--processing_baseline PROCESSING_BASELINE
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Processing baseline in the format: "dd.dd", where d=[0:9]
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--raw Export raw images in rawl format with ENVI hdr
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--tif Export raw images in TIFF format instead of JPEG-2000
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--sc_only Performs only the scene classification at 60 or 20m resolution, 30m for Hyper
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--sc_classic Performs scene classification in Sen2Cor 2.9 mode
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--sc_cog Export SCL image in COG format instead of JPEG_2000
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--cr_only Performs only the creation of the L2A product tree, no processing
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--debug Performs in debug mode
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--GIP_L2A GIP_L2A Select the user GIPP
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--GIP_L2A_SC GIP_L2A_SC
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Select the scene classification GIPP
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--GIP_L2A_AC GIP_L2A_AC
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Select the atmospheric correction GIPP
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--GIP_L2A_PB GIP_L2A_PB
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Select the processing baseline GIPP
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--Hyper_MS To Process a Hyper_MS product
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```
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‎sen2cor3/sen2cor3_download.py‎

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import sys
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import os
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import paramiko
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def download_from_sftp(hostname, port, username, password, remote_path, local_path):
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# Connect to the SFTP server
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transport = paramiko.Transport((hostname, port))
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transport.connect(username=username, password=password)
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sftp = paramiko.SFTPClient.from_transport(transport)
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# Create local directory if it doesn't exist
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local_dir = os.path.dirname(local_path)
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if not os.path.exists(local_dir):
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os.makedirs(local_dir)
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try:
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# Download the file
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sftp.get(remote_path, local_path)
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print(f"File downloaded successfully from {remote_path} to {local_path}")
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except Exception as e:
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print(f"Error downloading file: {e}")
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finally:
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# Close the connection
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sftp.close()
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transport.close()
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if __name__ == "__main__":
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if len(sys.argv) != 2:
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print("Usage: python sen2cor3_download.py local_path")
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sys.exit(1)
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local_path = sys.argv[1]
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local_path = os.path.join(local_path, 'sen2cor_3.1.0_python_3.10_20240313.zip')
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hostname = "sftp.telespazio.fr"
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port = 22 # default SFTP port is 22
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username = 'sen2cor3'
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password = '4sen2like'
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remote_path = '/upload/Sen2Cor-3.01.00/Software/sen2cor_3.1.0_python_3.10_20240313.zip'
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download_from_sftp(hostname, port, username, password, remote_path, local_path)

‎sen2like/Dockerfile-base‎

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# docker image based on miniconda image (debian:latest)
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# ARG MINICONDA_DOCKER_VERSION
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# FROM continuumio/miniconda3:${MINICONDA_DOCKER_VERSION}
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FROM continuumio/miniconda3:23.3.1-0
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FROM continuumio/miniconda3:23.10.0-1
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# set the working dir to /usr/local/sen2like
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WORKDIR /usr/local/sen2like

‎sen2like/conf/config.ini‎

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@@ -41,7 +41,7 @@ url_parameters_pattern_Landsat9 = {base_url}/{mission}/{path}/{row}
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; location_Landsat8 = path={path}&row={row}&productType=L1TP
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; location_Landsat9 = path={path}&row={row}&productType=L1TP
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; location_Sentinel2 = productIdentifier=%25T{tile}%25
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; url_parameters_pattern = {base_url}/{mission}/search.json?maxRecords=1000&_pretty=true&cloudCover=%5B0%2C{cloud_cover}%5D&startDate={start_date}&completionDate={end_date}&sortParam=startDate&sortOrder=ascending&status=all&{location}&dataset=ESA-DATASET
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; url_parameters_pattern = {base_url}/{mission}/search.json?maxRecords=1000&cloudCover=%5B0%2C{cloud_cover}%5D&startDate={start_date}&completionDate={end_date}&sortParam=startDate&sortOrder=ascending&status=all&{location}&dataset=ESA-DATASET
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; thumbnail_property = properties/productIdentifier
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; cloud_cover_property = properties/cloudCover
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; gml_geometry_property = properties/gmlgeometry
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# remote S2 part
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;base_url_s2 = https://datahub.creodias.eu/resto/api/collections
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;location_Sentinel2 = productIdentifier=%25T{tile}%25
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;url_parameters_pattern = {base_url_s2}/{mission}/search.json?maxRecords=1000&_pretty=true&cloudCover=%5B0%2C{cloud_cover}%5D&startDate={start_date}&completionDate={end_date}&sortParam=startDate&sortOrder=ascending&status=all&{location}&dataset=ESA-DATASET
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;url_parameters_pattern = {base_url_s2}/{mission}/search.json?maxRecords=1000&cloudCover=%5B0%2C{cloud_cover}%5D&startDate={start_date}&completionDate={end_date}&sortParam=startDate&sortOrder=ascending&status=all&{location}&dataset=ESA-DATASET
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;thumbnail_property = properties/productIdentifier
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;cloud_cover_property = properties/cloudCover
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;gml_geometry_property = properties/gmlgeometry
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;base_url_landsat = https://datahub.creodias.eu/resto/api/collections
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;location_Landsat8 = path={path}&row={row}&productType=L1TP
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;location_Landsat9 = path={path}&row={row}&productType=L1TP
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;url_parameters_pattern = {base_url_landsat}/{mission}/search.json?maxRecords=1000&_pretty=true&cloudCover=%5B0%2C{cloud_cover}%5D&startDate={start_date}&completionDate={end_date}&sortParam=startDate&sortOrder=ascending&status=all&{location}&dataset=ESA-DATASET
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;url_parameters_pattern = {base_url_landsat}/{mission}/search.json?maxRecords=1000&cloudCover=%5B0%2C{cloud_cover}%5D&startDate={start_date}&completionDate={end_date}&sortParam=startDate&sortOrder=ascending&status=all&{location}&dataset=ESA-DATASET
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;thumbnail_property = properties/productIdentifier
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;cloud_cover_property = properties/cloudCover
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;gml_geometry_property = properties/gmlgeometry
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[RunTime]
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dx = 0
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dy = 0
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dy = 0

‎sen2like/conf/config.xml‎

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<!-- <location_Landsat8>path={path}&amp;row={row}&amp;productType=L1TP</location_Landsat8>-->
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<!-- <location_Landsat9>path={path}&amp;row={row}&amp;productType=L1TP</location_Landsat9>-->
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<!-- <location_Sentinel2>productIdentifier=%25T{tile}%25</location_Sentinel2>-->
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<!-- <url_parameters_pattern>{base_url}/{mission}/search.json?maxRecords=100&amp;_pretty=true&amp;cloudCover=%5B0%2C{cloud_cover}%5D&amp;startDate={start_date}&amp;completionDate={end_date}&amp;sortParam=startDate&amp;sortOrder=ascending&amp;status=all&amp;{location}&amp;dataset=ESA-DATASET</url_parameters_pattern>-->
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<!-- <url_parameters_pattern>{base_url}/{mission}/search.json?maxRecords=100&amp;cloudCover=%5B0%2C{cloud_cover}%5D&amp;startDate={start_date}&amp;completionDate={end_date}&amp;sortParam=startDate&amp;sortOrder=ascending&amp;status=all&amp;{location}&amp;dataset=ESA-DATASET</url_parameters_pattern>-->
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<!-- <thumbnail_property>properties/productIdentifier</thumbnail_property>-->
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<!-- <cloud_cover_property>properties/cloudCover</cloud_cover_property>-->
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<!-- <gml_geometry_property>properties/gmlgeometry</gml_geometry_property>-->
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<!-- <location_Sentinel2>productIdentifier=%25T{tile}%25</location_Sentinel2>-->
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<!-- <url_parameters_pattern_Landsat8>{base_url_landsat}/{mission}/{path}/{row}</url_parameters_pattern_Landsat8>-->
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<!-- <url_parameters_pattern_Landsat9>{base_url_landsat}/{mission}/{path}/{row}</url_parameters_pattern_Landsat9>-->
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<!-- <url_parameters_pattern>{base_url_s2}/{mission}/search.json?maxRecords=100&amp;_pretty=true&amp;cloudCover=%5B0%2C{cloud_cover}%5D&amp;startDate={start_date}&amp;completionDate={end_date}&amp;sortParam=startDate&amp;sortOrder=ascending&amp;status=all&amp;{location}&amp;dataset=ESA-DATASET</url_parameters_pattern>-->
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<!-- <url_parameters_pattern>{base_url_s2}/{mission}/search.json?maxRecords=100&amp;cloudCover=%5B0%2C{cloud_cover}%5D&amp;startDate={start_date}&amp;completionDate={end_date}&amp;sortParam=startDate&amp;sortOrder=ascending&amp;status=all&amp;{location}&amp;dataset=ESA-DATASET</url_parameters_pattern>-->
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<!-- <thumbnail_property>properties/productIdentifier</thumbnail_property>-->
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<!-- <cloud_cover_property>properties/cloudCover</cloud_cover_property>-->
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<!-- <gml_geometry_property>properties/gmlgeometry</gml_geometry_property>-->
@@ -60,7 +60,7 @@
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<!-- <url_parameters_pattern_Sentinel2>{base_url_s2}/{mission}/{tile}</url_parameters_pattern_Sentinel2>-->
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<!-- <location_Landsat8>path={path}&amp;row={row}&amp;productType=L1TP</location_Landsat8>-->
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<!-- <location_Landsat9>path={path}&amp;row={row}&amp;productType=L1TP</location_Landsat9>-->
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<!-- <url_parameters_pattern>{base_url_landsat}/{mission}/search.json?maxRecords=100&amp;_pretty=true&amp;cloudCover=%5B0%2C{cloud_cover}%5D&amp;startDate={start_date}&amp;completionDate={end_date}&amp;sortParam=startDate&amp;sortOrder=ascending&amp;status=all&amp;{location}&amp;dataset=ESA-DATASET</url_parameters_pattern>-->
63+
<!-- <url_parameters_pattern>{base_url_landsat}/{mission}/search.json?maxRecords=100&amp;cloudCover=%5B0%2C{cloud_cover}%5D&amp;startDate={start_date}&amp;completionDate={end_date}&amp;sortParam=startDate&amp;sortOrder=ascending&amp;status=all&amp;{location}&amp;dataset=ESA-DATASET</url_parameters_pattern>-->
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<!-- <thumbnail_property>properties/productIdentifier</thumbnail_property>-->
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‎sen2like/release-notes.md‎

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# Sen2Like Release Notes
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## v4.4.2
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### Release of Sen2Cor3 documentation and software version 3.01.00
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Instructions to retrieve sen2cor3 software and associated documentation available [here](../sen2cor3/README.md).
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### Fix
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* Force operational-mode parameter as first command line argument
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* Remove `_pretty=` parameter in the creodias catalogue URL in the default configuration as it is no more supported by datahub catalogue.
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* Update miniconda in [Dockerfile-base](Dockerfile-base)
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* Typos in sen2like project [README.md](../README.md)
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## v4.4.1
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### Important information about sen2like on Creodias

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