Merge branch 'main' into release

sepal-contrib · May 29, 2024 · 9dc2bb8 · 9dc2bb8
2 parents 48e78db + 3e1f977
commit 9dc2bb8
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diff --git a/.github/workflows/unit.yaml b/.github/workflows/unit.yaml
@@ -4,20 +4,45 @@ on:
   - push
   - workflow_dispatch
 
+env:
+  EARTHENGINE_TOKEN: ${{ secrets.EARTHENGINE_TOKEN }}
+  PLANET_API_KEY: ${{ secrets.PLANET_API_KEY }}
+
 jobs:
   lint:
     runs-on: ubuntu-latest
     steps:
       - uses: actions/checkout@v3
-      - uses: actions/setup-python@v4
+      - name: Set up Python 3.10
+        uses: actions/setup-python@v4
         with:
-          python-version: "3.8"
-      - uses: pre-commit/[email protected].0
-      - name: install dependencies
+          python-version: "3.10"
+      - uses: pre-commit/[email protected].1
+      - name: Install module venv
         run: |
-          python -m pip install --find-links=https://girder.github.io/large_image_wheels GDAL
-          python -m pip install earthengine-api
-          python -m pip install -r requirements.txt
-          python -m pip install pytest nbmake
+          python -m pip install "git+https://github.com/12rambau/sepal_ui.git@sepal_pre_release"
+          module_venv --venv_prefix venv
+      - name: Activate venv
+        run: source ~/module-venv/clip-time-series/bin/activate
+      - name: install nbmake
+        run: python -m pip install pytest nbmake
       - name: build the application
         run: pytest --nbmake ui.ipynb
+  test:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v3
+      - name: Set up Python 3.10
+        uses: actions/setup-python@v4
+        with:
+          python-version: "3.10"
+      - name: Install module venv
+        run: |
+          python -m pip install "git+https://github.com/12rambau/sepal_ui.git@sepal_pre_release"
+          python -m pip install pytest
+          module_venv --venv_prefix venv
+      - name: Activate venv and run tests
+        run: |
+          source ~/module-venv/clip-time-series/bin/activate
+          python -m pip install pytest
+          python -m pytest test/
diff --git a/README.md b/README.md
@@ -10,18 +10,26 @@ Each mosaic will be represented in a square of custom size from 500x500m to 1000
 
 The input can be a table file discribing points or a shapefile using geometries.
 
-Colors are stretched using [histogram equalization](https://en.wikipedia.org/wiki/Histogram_equalization).
+The output can be adjusted using any of the following enhancement methods:
+
+- Histogram Equalization
+- Contrast Stretching
+- Adaptive Equalization
+- Standard Deviation
+- Percent Clip
+- Min-Max
 
 To produce this image the software will use the most recent satellite with a cloudless mosaic using the following priority order :
 
 - Sentinel 2
+- Landsat 9
 - Landsat 8
 - landsat 5
 - landsat 7
 
 The user can manually swithc of the usage of sentinel or landsat data.
 
-The user can replace these satellites wih PlanetLab NICFI mosaics if it has register to the NICFI programm (free). Please follow thins [link](https://docs.sepal.io/en/latest/setup/nicfi.html) for more information.
+The user can replace these satellites wih PlanetLab NICFI mosaics if it has register to the NICFI programm (free). Please follow this [link](https://docs.sepal.io/en/latest/setup/nicfi.html) for more information.
 
 ![full_app](./doc/img/output_table_planet.png)
 
@@ -32,7 +40,7 @@ for more information about usage please read the [documentation](https://docs.se
 to install the project on your SEPAL account
 
 ```
-$ git clone https://github.com/openforis/clip-time-series.git
+$ git clone https://github.com/sepal-contrib/clip-time-series.git
 ```
 
 please retreive the develop branch where all our development live

diff --git a/component/model/model_export.py b/component/model/model_export.py
@@ -1,7 +1,9 @@
 from sepal_ui import model
-from traitlets import Any
+from traitlets import Any, Bool, Unicode
 
 
 class ExportModel(model.Model):
 
     vue = Any(None).tag(sync=True)
+    overwrite = Bool(True).tag(sync=True)
+    enhance_method = Unicode("min_max").tag(sync=True)
diff --git a/component/parameter/gee.py b/component/parameter/gee.py
@@ -2,30 +2,33 @@
 from collections import OrderedDict
 
 import ee
+from sepal_ui.scripts.utils import init_ee
 
-ee.Initialize()
+init_ee()
 
 # data parameters
 gee_min_landsat_year = 1985  # launch of landsat 5
 gee_min_sentinel_year = 2015  # launch of sentinel 2
 gee_max_end_year = datetime.datetime.now().year
 sources = ["landsat", "sentinel"]
 
+
 # functions to access parameters according to the used satellite
 def getSatellites(sources, year):
 
     satellites = OrderedDict()
-
+    # https://developers.google.com/earth-engine/landsat_c1_to_c2#oli
     if "sentinel" in sources and year >= 2015:
-        # cannot use SR as they don't cover years before 2020
-        satellites["sentinel_2"] = "COPERNICUS/S2"
+        satellites["sentinel_2"] = "COPERNICUS/S2_HARMONIZED"
     if "landsat" in sources:
+        if year >= 2022:
+            satellites["landsat_9"] = "LANDSAT/LC09/C02/T1_L2"
         if year >= 2013:
             satellites["landsat_8"] = "LANDSAT/LC08/C02/T1_L2"
         if year <= 2013:
-            satellites["landsat_5"] = "LANDSAT/LT05/C01/T1_SR"
+            satellites["landsat_5"] = "LANDSAT/LT05/C02/T1_L2"
         if year >= 1999:
-            satellites["landsat_7"] = "LANDSAT/LE07/C01/T1_SR"
+            satellites["landsat_7"] = "LANDSAT/LE07/C02/T1_L2"
 
     return satellites
 
@@ -36,6 +39,7 @@ def getShortname(satellite):
         "landsat_5": "L5",
         "landsat_7": "L7",
         "landsat_8": "L8",
+        "landsat_9": "L9",
     }
 
     # in parralel sometime the code doesn't manage to write the appropriate key.
@@ -47,7 +51,13 @@ def getShortname(satellite):
 
 def getScale(satellite):
 
-    scale = {"sentinel_2": 10, "landsat_5": 30, "landsat_7": 30, "landsat_8": 30}
+    scale = {
+        "sentinel_2": 10,
+        "landsat_5": 30,
+        "landsat_7": 30,
+        "landsat_8": 30,
+        "landsat_9": 30,
+    }
 
     return scale[satellite]
 
@@ -62,51 +72,59 @@ def getAvailableBands():
     """
     bands = {
         "Red, Green, Blue": {
-            "landsat_7": ["B3", "B2", "B1"],
-            "landsat_5": ["B3", "B2", "B1"],
+            "landsat_7": ["SR_B3", "SR_B2", "SR_B1"],
+            "landsat_5": ["SR_B3", "SR_B2", "SR_B1"],
             "landsat_8": ["SR_B4", "SR_B3", "SR_B2"],
+            "landsat_9": ["SR_B4", "SR_B3", "SR_B2"],
             "sentinel_2": ["B4", "B3", "B2"],
         },
         "Nir, Red, Green": {
-            "landsat_7": ["B4", "B3", "B2"],
-            "landsat_5": ["B4", "B3", "B2"],
+            "landsat_7": ["SR_B4", "SR_B3", "SR_B2"],
+            "landsat_5": ["SR_B4", "SR_B3", "SR_B2"],
             "landsat_8": ["SR_B5", "SR_B4", "SR_B3"],
+            "landsat_9": ["SR_B5", "SR_B4", "SR_B3"],
             "sentinel_2": ["B8", "B4", "B3"],
         },
         "Nir, Swir1, Red": {
-            "landsat_7": ["B4", "B5", "B3"],
-            "landsat_5": ["B4", "B5", "B3"],
+            "landsat_7": ["SR_B4", "SR_B5", "SR_B3"],
+            "landsat_5": ["SR_B4", "SR_B5", "SR_B3"],
             "landsat_8": ["SR_B5", "SR_B6", "SR_B4"],
+            "landsat_9": ["SR_B5", "SR_B6", "SR_B4"],
             "sentinel_2": ["B8", "B11", "B4"],
         },
         "Swir2, Nir, Red": {
-            "landsat_7": ["B7", "B4", "B3"],
-            "landsat_5": ["B7", "B4", "B3"],
+            "landsat_7": ["SR_B7", "SR_B4", "SR_B3"],
+            "landsat_5": ["SR_B7", "SR_B4", "SR_B3"],
             "landsat_8": ["SR_B7", "SR_B5", "SR_B4"],
+            "landsat_9": ["SR_B7", "SR_B5", "SR_B4"],
             "sentinel_2": ["B12", "B8", "B4"],
         },
         "Swir2, Swir1, Red": {
-            "landsat_7": ["B7", "B5", "B3"],
-            "landsat_5": ["B7", "B5", "B3"],
+            "landsat_7": ["SR_B7", "SR_B5", "SR_B3"],
+            "landsat_5": ["SR_B7", "SR_B5", "SR_B3"],
             "landsat_8": ["SR_B7", "SR_B6", "SR_B4"],
+            "landsat_9": ["SR_B7", "SR_B6", "SR_B4"],
             "sentinel_2": ["B12", "B11", "B4"],
         },
         "Swir2, Nir, Green": {
-            "landsat_7": ["B7", "B4", "B2"],
-            "landsat_5": ["B7", "B4", "B2"],
+            "landsat_7": ["SR_B7", "SR_B4", "SR_B2"],
+            "landsat_5": ["SR_B7", "SR_B4", "SR_B2"],
             "landsat_8": ["SR_B7", "SR_B5", "SR_B3"],
+            "landsat_9": ["SR_B7", "SR_B5", "SR_B3"],
             "sentinel_2": ["B12", "B8", "B3"],
         },
         "ndvi": {  # 2 useful bands nir and red
-            "landsat_7": ["B4", "B3"],
-            "landsat_5": ["B4", "B3"],
+            "landsat_7": ["SR_B4", "SR_B3"],
+            "landsat_5": ["SR_B4", "SR_B3"],
             "landsat_8": ["SR_B5", "SR_B4"],
+            "landsat_9": ["SR_B5", "SR_B4"],
             "sentinel_2": ["B8", "B4"],
         },
         "ndwi": {  # 2 useful bands nir and swir
-            "landsat_7": ["B4", "B5"],
-            "landsat_5": ["B4", "B5"],
+            "landsat_7": ["SR_B4", "SR_B5"],
+            "landsat_5": ["SR_B4", "SR_B5"],
             "landsat_8": ["SR_B5", "SR_B6"],
+            "landsat_9": ["SR_B5", "SR_B6"],
             "sentinel_2": ["B8", "B11"],
         },
     }
@@ -119,7 +137,7 @@ def getCloudMask(satelliteId):
     if satelliteId in ["landsat_5", "landsat_7"]:
 
         def cloudMask(image):
-            qa = image.select("pixel_qa")
+            qa = image.select("QA_PIXEL")
             # If the cloud bit (5) is set and the cloud confidence (7) is high
             # or the cloud shadow bit is set (3), then it's a bad pixel.
             cloud = qa.bitwiseAnd(1 << 5).Or(qa.bitwiseAnd(1 << 3))
@@ -129,7 +147,7 @@ def cloudMask(image):
 
             return image.updateMask(cloud.Not()).updateMask(mask2)
 
-    elif satelliteId == "landsat_8":
+    elif satelliteId in ["landsat_8", "landsat_9"]:
 
         def cloudMask(image):
             # Bits 3 and 5 are cloud shadow and cloud, respectively.

diff --git a/component/parameter/viz.py b/component/parameter/viz.py
@@ -22,6 +22,8 @@
     "Swir2, Nir, Green": "yellow",
     "rgb": "blue",
     "cir": "yellow",
+    "ndvi": "red",
+    "ndwi": "red",
 }
 polygon_width = 2