Merge branch '104-update-documentation-to-describe-how-to-detect-shaded-snow' into 'develop'

Resolve "Update documentation to describe how to detect shaded snow"

Closes #104

See merge request !100

README.md

@@ -35,30 +35,32 @@ with launch_configuration_file.json :
 
 ```
 {
-  "input_dir"       : "XXX/SENTINEL2A_20210415-105910-624_L2A_T30TYN_C_V2-2",
-  "output_dir"      : "XXX/output",
-  "dem"             : "XXX/Copernicus_DSM/world.vrt",
-  "tcd"             : "XXX/TCD_30TYN.tif",
-  "log"             : "INFO",
-  "water_mask"      : "XXX/eu_hydro_20m_30TYN.tif",
-  "config_file"     : "XXX/lis_configuration.json",
-  "chain_version"   : "1.7.1",
-  "product_counter" : "1"
+  "input_dir"           : "XXX/SENTINEL2A_20210415-105910-624_L2A_T30TYN_C_V2-2",
+  "output_dir"          : "XXX/output",
+  "dem"                 : "XXX/Copernicus_DSM/world.vrt",
+  "tcd"                 : "XXX/TCD_30TYN.tif",
+  "log"                 : "INFO",
+  "water_mask"          : "XXX/eu_hydro_20m_30TYN.tif",
+  "relief_shadow_mask"  : "XXX/hillshade.tif",
+  "config_file"         : "XXX/lis_configuration.json",
+  "chain_version"       : "1.8",
+  "product_counter"     : "1"
 }
 ```
 
 All launch parameters are described in [fsc_launch_schema.json](doc/atbd/fsc_launch_schema.json) 
 and can be **overwritten** by the following command line options: 
 ```
-* "-i", "--input_dir"       - Path to input directory, containing L2A Theia Product or this directory as zip
-* "-o", "--output_dir"      - Path to output directory; which will contains FSC Product
-* "-l", "--log_level"       - Log level between ['INFO', 'DEBUG', 'WARNING', 'ERROR'] (optional)
-* "-c", "--config_file"     - Path to lis configuration file
-* "-d", "--dem"             - Path to dem file
-* "-t", "--tcd"             - Path to tree cover density file (optional)
-* "-w", "--water_mask"      - Path to water mask file (optional)
-* "-V", "--chain_version"   - Chain version in the operational system (optional)
-* "-n", "--product_counter" - Product counter number (optional)
+* "-i", "--input_dir"           - Path to input directory, containing L2A Theia Product or this directory as zip
+* "-o", "--output_dir"          - Path to output directory; which will contains FSC Product
+* "-l", "--log_level"           - Log level between ['INFO', 'DEBUG', 'WARNING', 'ERROR'] (optional)
+* "-c", "--config_file"         - Path to lis configuration file
+* "-d", "--dem"                 - Path to dem file
+* "-t", "--tcd"                 - Path to tree cover density file (optional)
+* "-w", "--water_mask"          - Path to water mask file (optional)
+* "-s", "--relief_shadow_mask"  - Path to relief shadow mask (optional)
+* "-V", "--chain_version"       - Chain version in the operational system (optional)
+* "-n", "--product_counter"     - Product counter number (optional)
 ```
 
 In the following example, input directory and output_directory are overwritten from launch_configuration file

doc/LIS_configuration_for_experts.md

@@ -21,6 +21,11 @@ This part describes the expert use of the fsc configuration file, in particular
 
 - tcd: command line value will be used first, launch configuration value will be used as second, and finally configuration value will be used at last
 
+#### shaded_snow
+- "detect_shaded_snow": Activate or de activate shaded snow detection
+- "hillshade_lim": Define hillshade limitation threshold
+- "shaded_snow_pass": Define shaded snow pass threshold
+
 #### water_mask
 
 - water_mask_path: command line value will be used first, launch configuration value will be used as second, and finally configuration value will be used at last

doc/atbd/fsc_config_schema.json

@@ -269,6 +269,32 @@
                 }
             }
         },
+        "shaded_snow": {
+            "id": "shaded_snow",
+            "properties": {
+                "detect_shaded_snow": {
+                    "id": "detect_shaded_snow",
+                    "default": true,
+                    "description": "Activate shaded snow detection",
+                    "title": "the detect_shaded_snow schema",
+                    "type": "boolean"
+                },
+                "hillshade_lim": {
+                    "id": "hillshade_lim",
+                    "default": 0.2,
+                    "description": "Hillshade threshold",
+                    "title": "the hillshade_lim schema",
+                    "type": "number"
+                },
+                "shaded_snow_pass": {
+                    "id": "shaded_snow_pass",
+                    "default": 160,
+                    "description": "shaded snow threshold",
+                    "title": "the shaded_snow_pass schema",
+                    "type": "integer"
+                },
+            }
+        },
         "water_mask": {
             "id": "water_mask",
             "properties": {

doc/atbd/fsc_launch_schema.json

@@ -22,9 +22,14 @@
             "description": "Auxiliary input : tree cover density related to input product with the same resolution and extent as the input image (optional, only used for Sentinel-2)",
             "type": "string"
         },
+        "relief_shadow_mask": {
+            "id": "relief_shadow_mask",
+            "description": "Auxiliary input : hillshade related to input product with the same resolution and extent as the input image (optional)",
+            "type": "string"
+        },
         "water_mask": {
             "id": "water_mask",
-            "description": "Auxiliary input : water mask related to input product with the same resolution and extent as the input image(optional)",
+            "description": "Auxiliary input : water mask related to input product with the same resolution and extent as the input image (optional)",
             "type": "string"
         },
         "log_level": {

doc/lis_default_configuration.json

@@ -42,6 +42,11 @@
         "fscOg_Eq":"fscToc/(1-tcd)",
         "fscToc_Eq": "1.45*ndsi-0.01"
     },
+    "shaded_snow": {
+        "detect_shaded_snow": true,
+        "hillshade_lim": 0.2,
+        "shaded_snow_pass": 160
+    },
     "water_mask":{
          "water_mask_raster_values":[1]
     }

doc/lis_launch_example.json

 {
-  "input_dir"       : "XXX/SENTINEL2A_20210415-105910-624_L2A_T30TYN_C_V2-2",
-  "output_dir"      : "XXX/output",
-  "dem"             : "XXX/Copernicus_DSM/world.vrt",
-  "tcd"             : "XXX/TCD_30TYN.tif",
-  "log"             : "INFO",
-  "water_mask"      : "XXX/eu_hydro_20m_30TYN.tif",
-  "config_file"     : "XXX/lis_configuration.json",
-  "chain_version"   : "1.7.1",
-  "product_counter" : 1
+  "input_dir"           : "XXX/SENTINEL2A_20210415-105910-624_L2A_T30TYN_C_V2-2",
+  "output_dir"          : "XXX/output",
+  "dem"                 : "XXX/Copernicus_DSM/world.vrt",
+  "tcd"                 : "XXX/TCD_30TYN.tif",
+  "log"                 : "INFO",
+  "water_mask"          : "XXX/eu_hydro_20m_30TYN.tif",
+  "relief_shadow_mask"  : "XXX/hillshade.tif",
+  "config_file"         : "XXX/lis_configuration.json",
+  "chain_version"       : "1.7.1",
+  "product_counter"     : "1"
 }
\ No newline at end of file

doc/snow_annual_map.md

@@ -39,7 +39,7 @@ These additional products are resample at the same resolution and same footprint
 - 0, No-Snow
 - 100, Snow
 - 205, Cloud
-- 254, No-data
+- 255, No-data
 
 These resampled denfication snow products are append to the empty dates of the previous collection, or fused with other products as described in the following section.
 

doc/synthesis_launch_example.json

 {
     "tile_id": "T31TCH",
     "input_products_list": [
-        "/work/OT/siaa/Theia/Neige/TEST/Data-LIS-1.6/Input-Data-Test/SNOW_PRODUCTS/SENTINEL2A_20180101-105435-457_L2A_T31TCH_D_V1-4",
-        "/work/OT/siaa/Theia/Neige/TEST/Data-LIS-1.6/Input-Data-Test/SNOW_PRODUCTS/SENTINEL2A_20180131-105416-437_L2A_T31TCH_D_V1-4"
+        "XXX/SNOW_PRODUCTS/SENTINEL2A_20180101-105435-457_L2A_T31TCH_D_V1-4",
+        "XXX/SNOW_PRODUCTS/SENTINEL2A_20180131-105416-437_L2A_T31TCH_D_V1-4"
     ],
     "date_start": "01/01/2018",
     "date_stop": "31/01/2018",
-    "output_dir": "lis/lis_install_15_10/build/Testing/Temporary/SNOW_SYNTHESIS",
-    "config_file": "lis/lis_install_15_10/build/Testing/Temporary/SNOW_SYNTHESIS/synthesis_configuration.json",
+    "output_dir": "XXX/SNOW_SYNTHESIS",
+    "config_file": "XXX/SNOW_SYNTHESIS/synthesis_configuration.json",
     "date_margin": 10,
     "densification_products_list": [
-        "/work/OT/siaa/Theia/Neige/TEST/Data-LIS-1.6/Input-Data-Test/SNOW_PRODUCTS/LANDSAT8-OLITIRS-XS_20180115-103629-617_L2A_T31TCH_D_V1-9",
-        "/work/OT/siaa/Theia/Neige/TEST/Data-LIS-1.6/Input-Data-Test/SNOW_PRODUCTS/LANDSAT8-OLITIRS-XS_20180131-103619-890_L2A_T31TCH_D_V1-9"
+        "XXX/SNOW_PRODUCTS/LANDSAT8-OLITIRS-XS_20180115-103629-617_L2A_T31TCH_D_V1-9",
+        "XXX/SNOW_PRODUCTS/LANDSAT8-OLITIRS-XS_20180131-103619-890_L2A_T31TCH_D_V1-9"
     ],
     "log_level": "INFO",
     "chain_version": null,

python/s2snow/parser.py

@@ -50,6 +50,7 @@ def create_fsc_argument_parser():
     - the dem file path,
     - the tree cover density file path,
     - the water mask file path
+    - the relief shadow mask path
     :return: argument parser
     :rtype: argparse.ArgumentParser
     """

test/CMakeLists.txt

@@ -268,6 +268,28 @@ add_test(NAME s2_compare_final_mask_test
   )
 set_tests_properties(s2_compare_final_mask_test PROPERTIES DEPENDS s2_test)
 
+add_test(NAME s2_hysope2
+  COMMAND ${PYTHON_EXECUTABLE}
+  ${CMAKE_BINARY_DIR}/app/let_it_snow_fsc.py
+  -j ${DATA_TEST}/S2/hysope2/param.json
+  -o ${OUTPUT_TEST}/hysope2
+  )
+
+add_test(NAME dem_builder_test
+  COMMAND ${PYTHON_EXECUTABLE} ${CMAKE_SOURCE_DIR}/python/s2snow/dem_builder.py
+  "${DATA_TEST}/SRTM/sud_ouest.vrt"
+  "${DATA_TEST}/Landsat/LANDSAT8_OLITIRS_XS_20150312_N2A_ORTHO_SURF_CORR_PENTE_France-MetropoleD0005H0001.TIF"
+  "${OUTPUT_TEST}/landsat_bassies_srtm.tif"
+  )
+
+add_test(NAME s2-small_zip_test
+  COMMAND ${PYTHON_EXECUTABLE}
+  ${CMAKE_BINARY_DIR}/app/let_it_snow_fsc.py
+  -c ${DATA_TEST}/S2-SMALL-ZIP/lis_configuration.json
+  -i ${DATA_TEST}/S2-SMALL-ZIP/SENTINEL2A_20160217-111843-605_L2A_T29RNQ_D_V1-0.zip
+  -o "${OUTPUT_TEST}/s2-small-zip"
+  )
+  
 # -------------------------
 # Shaded snow
 # -------------------------
@@ -276,8 +298,8 @@ add_test(NAME shaded_snow_test
     ${CMAKE_BINARY_DIR}/app/let_it_snow_fsc.py
     -c ${DATA_TEST}/S2/shaded_snow/global_parameters_shaded_snow.json
     -i ${DATA_TEST}/S2/SENTINEL2B_20210124-103807-070_L2A_T31TGM_C_V1-0
-    -d "${DATA_TEST}/S2/SENTINEL2B_20210124-103807-070_L2A_T31TGM_C_V1-0/Leman_dem_merged.tif"
-    -s "${DATA_TEST}/S2/SENTINEL2B_20210124-103807-070_L2A_T31TGM_C_V1-0/hillshade_mask.tif"
+    -d ${DATA_TEST}/S2/SENTINEL2B_20210124-103807-070_L2A_T31TGM_C_V1-0/Leman_dem_merged.tif
+    -s ${DATA_TEST}/S2/SENTINEL2B_20210124-103807-070_L2A_T31TGM_C_V1-0/hillshade_mask.tif
     -o ${OUTPUT_TEST}/s2/shaded_snow
     )
 
@@ -286,7 +308,7 @@ add_test(NAME shaded_snow_no_relief_shadow_mask_test
     ${CMAKE_BINARY_DIR}/app/let_it_snow_fsc.py
     -c ${DATA_TEST}/S2/shaded_snow/global_parameters_shaded_snow.json
     -i ${DATA_TEST}/S2/SENTINEL2B_20210124-103807-070_L2A_T31TGM_C_V1-0
-    -d "${DATA_TEST}/S2/SENTINEL2B_20210124-103807-070_L2A_T31TGM_C_V1-0/Leman_dem_merged.tif"
+    -d ${DATA_TEST}/S2/SENTINEL2B_20210124-103807-070_L2A_T31TGM_C_V1-0/Leman_dem_merged.tif
     -o ${OUTPUT_TEST}/s2/shaded_snow_no_relief_shadow_mask
     )
 
@@ -369,32 +391,6 @@ add_test(NAME snow_synthesis_without_densification_test
   )
 
 
-# ########################################
-# New 1.7 tests
-# ########################################
-
-add_test(NAME s2_hysope2
-  COMMAND ${PYTHON_EXECUTABLE}
-  ${CMAKE_BINARY_DIR}/app/let_it_snow_fsc.py
-  -j ${DATA_TEST}/S2/hysope2/param.json
-  -o ${OUTPUT_TEST}/hysope2
-  )
-
-add_test(NAME dem_builder_test
-  COMMAND ${PYTHON_EXECUTABLE} ${CMAKE_SOURCE_DIR}/python/s2snow/dem_builder.py
-  "${DATA_TEST}/SRTM/sud_ouest.vrt"
-  "${DATA_TEST}/Landsat/LANDSAT8_OLITIRS_XS_20150312_N2A_ORTHO_SURF_CORR_PENTE_France-MetropoleD0005H0001.TIF"
-  "${OUTPUT_TEST}/landsat_bassies_srtm.tif"
-  )
-
-add_test(NAME s2-small_zip_test
-  COMMAND ${PYTHON_EXECUTABLE}
-  ${CMAKE_BINARY_DIR}/app/let_it_snow_fsc.py
-  -c ${DATA_TEST}/S2-SMALL-ZIP/lis_configuration.json
-  -i ${DATA_TEST}/S2-SMALL-ZIP/SENTINEL2A_20160217-111843-605_L2A_T29RNQ_D_V1-0.zip
-  -o "${OUTPUT_TEST}/s2-small-zip"
-  )
-
 if(NOT JENKINS_BUILD MATCHES "true")
   # ----------------------------------
   # Synthesis from 1.7 snow product

test/LIS_tests.md

@@ -18,11 +18,15 @@ For each case (take5, l8, S2 and S2-small):
 * Compare snow_pass3.tif file
 * Compare LIS_SNOW_ALL.TIF file
 * Compare LIS_SEB.TIF file
+
+* hysope2 integration test
 * test of dem_builder
 * launch let_it_snow_fsc.py on a zip file
+* shaded_snow_test
+* shaded_snow_no_relief_shadow_mask_test
 
 ## Synthesis
-* snow_synthesis_test from 1.6 snow products
+* snow_synthesis_test 1.6 snow products
 * Compare SCD file
 * Compare CCD file
 * Compare NOBS file
@@ -31,20 +35,9 @@ For each case (take5, l8, S2 and S2-small):
 * snow_synthesis_muscate_test => synthesis on muscate case
 * snow_synthesis_without_densification_test => synthesis without densification
 
-## New LIS 1.7 tests
-### FSC
-* launch let_it_snow_fsc.py on hysope2 case
-* launch let_it_snow_fsc.py on minimal case (without dem, tcd and water_mask)
-
-### Synthesis
-* Snow_synthesis_test from 1.7 snow products
-* Compare SCD file
-* Compare CCD file
-* Compare NOBS file
-* Compare SOD file
-* Compare SMOD file
-
-
-
 
+* Snow_synthesis_test from last version snow products
+* Snow synthesis with zip files
+* Snow synthesis with Copernicus snow products
+* Snow synthesis with H2 snow products