EP-4053/#255 reorganise file structure a bit and update spectral-indi…

…ces-dict.json
Open-EO · Nov 16, 2021 · 57df192 · 57df192
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diff --git a/openeo/extra/spectral_indices/__init__.py b/openeo/extra/spectral_indices/__init__.py
@@ -1,7 +1,5 @@
 """
 Calculate spectral indices (vegetation indices, water indices, etc.) in one line
+"""
 
-The indices implemented have been derived from the eemont package created by davemlz:
-https://github.com/davemlz/eemont/blob/master/eemont/data/spectral-indices-dict.json
-and further supplemented with indices that were necessary for use cases
-"""
+from openeo.extra.spectral_indices.spectral_indices import *
diff --git a/openeo/extra/spectral_indices/resources/README.md b/openeo/extra/spectral_indices/resources/README.md
@@ -0,0 +1,8 @@
+
+Spectral Index specification files, derived from and based on the 
+[Awesome Spectral Indices](https://awesome-ee-spectral-indices.readthedocs.io/) project
+by [David Montero Loaiza](https://github.com/davemlz)
+
+- `awesome-spectral-indices/spectral-indices-dict.json` comes straight from https://github.com/davemlz/awesome-spectral-indices/blob/main/output/spectral-indices-dict.json
+- `extra-indixes-dict.json` is a set of additional indices not (yet) provided by Awesome Spectral Indices
+
diff --git a/openeo/extra/spectral_indices/resources/awesome-spectral-indices/LICENSE b/openeo/extra/spectral_indices/resources/awesome-spectral-indices/LICENSE
@@ -0,0 +1,21 @@
+MIT License
+
+Copyright (c) 2021 David Montero Loaiza
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.
diff --git a/...ices/resources/spectral-indices-dict.json → ...ectral-indices/spectral-indices-dict.json b/...ices/resources/spectral-indices-dict.json → ...ectral-indices/spectral-indices-dict.json
@@ -227,8 +227,7 @@
             "long_name": "Enhanced Vegetation Index",
             "reference": "https://doi.org/10.1016/S0034-4257(96)00112-5",
             "short_name": "EVI",
-            "type": "vegetation",
-            "range": "(-3,3)"
+            "type": "vegetation"
         },
         "EVI2": {
             "bands": [
@@ -243,8 +242,7 @@
             "long_name": "Two-Band Enhanced Vegetation Index",
             "reference": "https://doi.org/10.1016/j.rse.2008.06.006",
             "short_name": "EVI2",
-            "type": "vegetation",
-            "range": "(-3,3)"
+            "type": "vegetation"
         },
         "ExG": {
             "bands": [
@@ -427,6 +425,49 @@
             "short_name": "MCARI2",
             "type": "vegetation"
         },
+        "MCARI705": {
+            "bands": [
+                "RE2",
+                "RE1",
+                "G"
+            ],
+            "contributor": "https://github.com/davemlz",
+            "date_of_addition": "2021-11-06",
+            "formula": "((RE2 - RE1) - 0.2 * (RE2 - G)) * (RE2 / RE1)",
+            "long_name": "Modified Chlorophyll Absorption in Reflectance Index (705 and 750 nm)",
+            "reference": "https://doi.org/10.1016/j.agrformet.2008.03.005",
+            "short_name": "MCARI705",
+            "type": "vegetation"
+        },
+        "MCARIOSAVI": {
+            "bands": [
+                "RE1",
+                "R",
+                "G",
+                "N"
+            ],
+            "contributor": "https://github.com/davemlz",
+            "date_of_addition": "2021-11-06",
+            "formula": "(((RE1 - R) - 0.2 * (RE1 - G)) * (RE1 / R)) / (1.16 * (N - R) / (N + R + 0.16))",
+            "long_name": "MCARI/OSAVI Ratio",
+            "reference": "https://doi.org/10.1016/S0034-4257(00)00113-9",
+            "short_name": "MCARIOSAVI",
+            "type": "vegetation"
+        },
+        "MCARIOSAVI705": {
+            "bands": [
+                "RE2",
+                "RE1",
+                "G"
+            ],
+            "contributor": "https://github.com/davemlz",
+            "date_of_addition": "2021-11-06",
+            "formula": "(((RE2 - RE1) - 0.2 * (RE2 - G)) * (RE2 / RE1)) / (1.16 * (RE2 - RE1) / (RE2 + RE1 + 0.16))",
+            "long_name": "MCARI/OSAVI Ratio (705 and 750 nm)",
+            "reference": "https://doi.org/10.1016/j.agrformet.2008.03.005",
+            "short_name": "MCARIOSAVI705",
+            "type": "vegetation"
+        },
         "MGRVI": {
             "bands": [
                 "G",
@@ -464,8 +505,7 @@
             "long_name": "Modified Normalized Difference Water Index",
             "reference": "https://doi.org/10.1080/01431160600589179",
             "short_name": "MNDWI",
-            "type": "water",
-            "range": "(-1,1)"
+            "type": "water"
         },
         "MNLI": {
             "bands": [
@@ -507,6 +547,19 @@
             "short_name": "MSR",
             "type": "vegetation"
         },
+        "MSR705": {
+            "bands": [
+                "RE2",
+                "RE1"
+            ],
+            "contributor": "https://github.com/davemlz",
+            "date_of_addition": "2021-11-06",
+            "formula": "(RE2 / RE1 - 1) / ((RE2 / RE1 + 1) ** 0.5)",
+            "long_name": "Modified Simple Ratio (705 and 750 nm)",
+            "reference": "https://doi.org/10.1016/j.agrformet.2008.03.005",
+            "short_name": "MSR705",
+            "type": "vegetation"
+        },
         "MTCI": {
             "bands": [
                 "RE2",
@@ -560,8 +613,7 @@
             "long_name": "Normalized Burn Ratio",
             "reference": "https://www.usgs.gov/core-science-systems/nli/landsat/landsat-normalized-burn-ratio",
             "short_name": "NBR",
-            "type": "burn",
-            "range": "(-1,1)"
+            "type": "burn"
         },
         "NBR2": {
             "bands": [
@@ -574,8 +626,7 @@
             "long_name": "Normalized Burn Ratio 2",
             "reference": "https://www.usgs.gov/core-science-systems/nli/landsat/landsat-normalized-burn-ratio-2",
             "short_name": "NBR2",
-            "type": "burn",
-            "range": "(-3,3)"
+            "type": "burn"
         },
         "NBRT": {
             "bands": [
@@ -683,6 +734,19 @@
             "short_name": "NDVI",
             "type": "vegetation"
         },
+        "NDVI705": {
+            "bands": [
+                "RE2",
+                "RE1"
+            ],
+            "contributor": "https://github.com/davemlz",
+            "date_of_addition": "2021-11-06",
+            "formula": "(RE2 - RE1) / (RE2 + RE1)",
+            "long_name": "Normalized Difference Vegetation Index (705 and 750 nm)",
+            "reference": "https://doi.org/10.1016/S0176-1617(11)81633-0",
+            "short_name": "NDVI705",
+            "type": "vegetation"
+        },
         "NDVIT": {
             "bands": [
                 "N",
@@ -708,8 +772,7 @@
             "long_name": "Normalized Difference Water Index",
             "reference": "https://doi.org/10.1080/01431169608948714",
             "short_name": "NDWI",
-            "type": "water",
-            "range": "(-1,1)"
+            "type": "water"
         },
         "NDYI": {
             "bands": [
@@ -844,6 +907,20 @@
             "short_name": "RDVI",
             "type": "vegetation"
         },
+        "REDSI": {
+            "bands": [
+                "RE3",
+                "R",
+                "RE1"
+            ],
+            "contributor": "https://github.com/davemlz",
+            "date_of_addition": "2021-11-06",
+            "formula": "((705.0 - 665.0) * (RE3 - R) - (783.0 - 665.0) * (RE1 - R)) / (2.0 * R)",
+            "long_name": "Red-Edge Disease Stress Index",
+            "reference": "https://doi.org/10.3390/s18030868",
+            "short_name": "REDSI",
+            "type": "vegetation"
+        },
         "RVI": {
             "bands": [
                 "N",
@@ -913,8 +990,7 @@
             "long_name": "Soil-Adjusted Vegetation Index",
             "reference": "https://doi.org/10.1016/0034-4257(88)90106-X",
             "short_name": "SAVI",
-            "type": "vegetation",
-            "range": "(-3,3)"
+            "type": "vegetation"
         },
         "SAVI2": {
             "bands": [
@@ -958,8 +1034,33 @@
             "long_name": "Structure Insensitive Pigment Index",
             "reference": "https://eurekamag.com/research/009/395/009395053.php",
             "short_name": "SIPI",
-            "type": "vegetation",
-            "range": "(-10,10)"
+            "type": "vegetation"
+        },
+        "SR555": {
+            "bands": [
+                "RE2",
+                "G"
+            ],
+            "contributor": "https://github.com/davemlz",
+            "date_of_addition": "2021-11-06",
+            "formula": "RE2 / G",
+            "long_name": "Simple Ratio (555 and 750 nm)",
+            "reference": "https://doi.org/10.1016/S0176-1617(11)81633-0",
+            "short_name": "SR555",
+            "type": "vegetation"
+        },
+        "SR705": {
+            "bands": [
+                "RE2",
+                "RE1"
+            ],
+            "contributor": "https://github.com/davemlz",
+            "date_of_addition": "2021-11-06",
+            "formula": "RE2 / RE1",
+            "long_name": "Simple Ratio (705 and 750 nm)",
+            "reference": "https://doi.org/10.1016/S0176-1617(11)81633-0",
+            "short_name": "SR705",
+            "type": "vegetation"
         },
         "SWI": {
             "bands": [
@@ -1002,6 +1103,35 @@
             "short_name": "TCARI",
             "type": "vegetation"
         },
+        "TCARIOSAVI": {
+            "bands": [
+                "RE1",
+                "R",
+                "G",
+                "N"
+            ],
+            "contributor": "https://github.com/davemlz",
+            "date_of_addition": "2021-11-06",
+            "formula": "(3 * ((RE1 - R) - 0.2 * (RE1 - G) * (RE1 / R))) / (1.16 * (N - R) / (N + R + 0.16))",
+            "long_name": "TCARI/OSAVI Ratio",
+            "reference": "https://doi.org/10.1016/S0034-4257(02)00018-4",
+            "short_name": "TCARIOSAVI",
+            "type": "vegetation"
+        },
+        "TCARIOSAVI705": {
+            "bands": [
+                "RE2",
+                "RE1",
+                "G"
+            ],
+            "contributor": "https://github.com/davemlz",
+            "date_of_addition": "2021-11-06",
+            "formula": "(3 * ((RE2 - RE1) - 0.2 * (RE2 - G) * (RE2 / RE1))) / (1.16 * (RE2 - RE1) / (RE2 + RE1 + 0.16))",
+            "long_name": "TCARI/OSAVI Ratio (705 and 750 nm)",
+            "reference": "https://doi.org/10.1016/j.agrformet.2008.03.005",
+            "short_name": "TCARIOSAVI705",
+            "type": "vegetation"
+        },
         "TCI": {
             "bands": [
                 "RE1",

diff --git a/..._indices/resources/vito-indices-dict.json → ...indices/resources/extra-indices-dict.json b/..._indices/resources/vito-indices-dict.json → ...indices/resources/extra-indices-dict.json
diff --git a/openeo/extra/spectral_indices/spectral_indices.py b/openeo/extra/spectral_indices/spectral_indices.py
@@ -56,8 +56,8 @@ def load_indices() -> Dict[str, dict]:
     resource_dir = Path(__file__).parent / "resources"
     specs = {}
     for path in [
-        resource_dir / "spectral-indices-dict.json",
-        resource_dir / "vito-indices-dict.json"
+        resource_dir / "awesome-spectral-indices/spectral-indices-dict.json",
+        resource_dir / "extra-indices-dict.json"
     ]:
         with path.open("r") as f:
             specs.update(json.load(f)["SpectralIndices"])

diff --git a/tests/extra/spectral_indices/test_spectral_indices.py b/tests/extra/spectral_indices/test_spectral_indices.py
@@ -1,6 +1,6 @@
 from typing import List, Union
 
-from openeo.extra.spectral_indices.spectral_indices import append_and_rescale_indices, compute_and_rescale_indices, \
+from openeo.extra.spectral_indices import append_and_rescale_indices, compute_and_rescale_indices, \
     compute_indices, append_indices, compute_index, append_index, list_indices, load_indices
 from openeo.rest.datacube import DataCube