From 08e5f43b314477d8cc4828e56e2717b2eb5cd04a Mon Sep 17 00:00:00 2001
From: Emma Ai <emma.ai@ga.gov.au>
Date: Fri, 15 Nov 2024 02:54:00 +0000
Subject: [PATCH] differentiate mangroves and other aquatic veg

---
 .../plugins/l34_utils/l4_natural_aquatic.py   | 370 ++++++------------
 odc/stats/plugins/lc_level34.py               |   4 +-
 odc/stats/plugins/lc_veg_class_a1.py          |   4 +-
 3 files changed, 129 insertions(+), 249 deletions(-)

diff --git a/odc/stats/plugins/l34_utils/l4_natural_aquatic.py b/odc/stats/plugins/l34_utils/l4_natural_aquatic.py
index 0036ae43..fbf29b26 100644
--- a/odc/stats/plugins/l34_utils/l4_natural_aquatic.py
+++ b/odc/stats/plugins/l34_utils/l4_natural_aquatic.py
@@ -5,400 +5,282 @@
 from odc.stats._algebra import expr_eval
 
 
-def natural_auquatic_veg(l4, lifeform, veg_cover, water_seasonality):
+def natural_auquatic_veg(l4, veg_cover, water_seasonality):
 
-    l4 = expr_eval(
-        "where((a==124)&(b==10)&(c==1)&(d==1), 64, a)",
+    # mark woody/herbaceous
+    # mangroves -> woody
+    # everything else -> herbaceous
+    res = expr_eval(
+        "where((a==124), 56, a)",
         {
             "a": l4,
-            "b": veg_cover,
-            "c": lifeform,
-            "d": water_seasonality,
         },
-        name="mark_cultivated",
+        name="mark_woody",
         dtype="uint8",
     )
-    l4 = expr_eval(
-        "where((a==124)&(b==10)&(c==1)&(d==2), 65, a)",
+
+    res = expr_eval(
+        "where((a==125), 57, a)",
         {
-            "a": l4,
-            "b": veg_cover,
-            "c": lifeform,
-            "d": water_seasonality,
+            "a": res,
         },
-        name="mark_cultivated",
+        name="mark_herbaceous",
         dtype="uint8",
     )
 
-    l4 = expr_eval(
-        "where((a==124)&(b==12)&(c==1)&(d==1), 67, a)",
+    res = expr_eval(
+        "where((a!=124)|(a!=125), 255, a)",
         {
-            "a": l4,
-            "b": veg_cover,
-            "c": lifeform,
-            "d": water_seasonality,
+            "a": res,
         },
-        name="mark_cultivated",
+        name="mark_nodata",
         dtype="uint8",
     )
 
-    l4 = expr_eval(
-        "where((a==124)&(b==12)&(c==1)&(d==2), 68, a)",
+    # mark water season
+    # use some value not used in final class
+    res = expr_eval(
+        "where((a==56)&(b==1), 254, a)",
         {
-            "a": l4,
-            "b": veg_cover,
-            "c": lifeform,
-            "d": water_seasonality,
+            "a": res,
+            "b": water_seasonality,
         },
-        name="mark_cultivated",
+        name="mark_water_season",
         dtype="uint8",
     )
 
-    l4 = expr_eval(
-        "where((a==124)&(b==13)&(c==1)&(d==1), 70, a)",
+    res = expr_eval(
+        "where((a==56)&(b==2), 253, a)",
         {
-            "a": l4,
-            "b": veg_cover,
-            "c": lifeform,
-            "d": water_seasonality,
+            "a": res,
+            "b": water_seasonality,
         },
-        name="mark_cultivated",
+        name="mark_water_season",
         dtype="uint8",
     )
 
-    l4 = expr_eval(
-        "where((a==124)&(b==13)&(c==1)&(d==2), 71, a)",
+    res = expr_eval(
+        "where((a==57)&(b==1), 252, a)",
         {
-            "a": l4,
-            "b": veg_cover,
-            "c": lifeform,
-            "d": water_seasonality,
+            "a": res,
+            "b": water_seasonality,
         },
-        name="mark_cultivated",
+        name="mark_water_season",
         dtype="uint8",
     )
 
-    l4 = expr_eval(
-        "where((a==124)&(b==15)&(c==1)&(d==1), 73, a)",
+    res = expr_eval(
+        "where((a==57)&(b==2), 251, a)",
         {
-            "a": l4,
-            "b": veg_cover,
-            "c": lifeform,
-            "d": water_seasonality,
+            "a": res,
+            "b": water_seasonality,
         },
-        name="mark_cultivated",
+        name="mark_water_season",
         dtype="uint8",
     )
 
-    l4 = expr_eval(
-        "where((a==124)&(b==15)&(c==1)&(d==2), 74, a)",
+    # mark final
+
+    res = expr_eval(
+        "where((a==254)&(b==10), 64, a)",
         {
-            "a": l4,
+            "a": res,
             "b": veg_cover,
-            "c": lifeform,
-            "d": water_seasonality,
         },
-        name="mark_cultivated",
+        name="mark_final",
         dtype="uint8",
     )
 
-    l4 = expr_eval(
-        "where((a==124)&(b==16)&(c==1)&(d==1), 76, a)",
+    res = expr_eval(
+        "where((a==253)&(b==10), 65, a)",
         {
-            "a": l4,
+            "a": res,
             "b": veg_cover,
-            "c": lifeform,
-            "d": water_seasonality,
         },
-        name="mark_cultivated",
+        name="mark_final",
         dtype="uint8",
     )
 
-    l4 = expr_eval(
-        "where((a==124)&(b==16)&(c==1)&(d==2), 77, a)",
+    res = expr_eval(
+        "where((a==252)&(b==10), 80, a)",
         {
-            "a": l4,
+            "a": res,
             "b": veg_cover,
-            "c": lifeform,
-            "d": water_seasonality,
         },
-        name="mark_cultivated",
+        name="mark_final",
         dtype="uint8",
     )
 
-    l4 = expr_eval(
-        "where((a==124)&(b==10)&(c==2)&(d==1), 79, a)",
+    res = expr_eval(
+        "where((a==251)&(b==10), 81, a)",
         {
-            "a": l4,
+            "a": res,
             "b": veg_cover,
-            "c": lifeform,
-            "d": water_seasonality,
         },
-        name="mark_cultivated",
+        name="mark_final",
         dtype="uint8",
     )
 
-    l4 = expr_eval(
-        "where((a==124)&(b==10)&(c==2)&(d==2), 80, a)",
+    #########################################
+    res = expr_eval(
+        "where((a==254)&(b==12), 67, a)",
         {
-            "a": l4,
+            "a": res,
             "b": veg_cover,
-            "c": lifeform,
-            "d": water_seasonality,
         },
-        name="mark_cultivated",
+        name="mark_final",
         dtype="uint8",
     )
 
-    l4 = expr_eval(
-        "where((a==124)&(b==12)&(c==2)&(d==1), 82, a)",
+    res = expr_eval(
+        "where((a==253)&(b==12), 68, a)",
         {
-            "a": l4,
+            "a": res,
             "b": veg_cover,
-            "c": lifeform,
-            "d": water_seasonality,
         },
-        name="mark_cultivated",
+        name="mark_final",
         dtype="uint8",
     )
 
-    l4 = expr_eval(
-        "where((a==124)&(b==12)&(c==2)&(d==2), 83, a)",
+    res = expr_eval(
+        "where((a==252)&(b==12), 82, a)",
         {
-            "a": l4,
+            "a": res,
             "b": veg_cover,
-            "c": lifeform,
-            "d": water_seasonality,
         },
-        name="mark_cultivated",
+        name="mark_final",
         dtype="uint8",
     )
 
-    l4 = expr_eval(
-        "where((a==124)&(b==13)&(c==2)&(d==1), 85, a)",
+    res = expr_eval(
+        "where((a==251)&(b==12), 83, a)",
         {
-            "a": l4,
+            "a": res,
             "b": veg_cover,
-            "c": lifeform,
-            "d": water_seasonality,
         },
-        name="mark_cultivated",
+        name="mark_final",
         dtype="uint8",
     )
-
-    l4 = expr_eval(
-        "where((a==124)&(b==13)&(c==2)&(d==2), 86, a)",
+    ##########################################
+    res = expr_eval(
+        "where((a==254)&(b==13), 70, a)",
         {
-            "a": l4,
+            "a": res,
             "b": veg_cover,
-            "c": lifeform,
-            "d": water_seasonality,
         },
-        name="mark_cultivated",
+        name="mark_final",
         dtype="uint8",
     )
 
-    l4 = expr_eval(
-        "where((a==124)&(b==15)&(c==2)&(d==1), 88, a)",
+    res = expr_eval(
+        "where((a==253)&(b==13), 71, a)",
         {
-            "a": l4,
+            "a": res,
             "b": veg_cover,
-            "c": lifeform,
-            "d": water_seasonality,
         },
-        name="mark_cultivated",
+        name="mark_final",
         dtype="uint8",
     )
 
-    l4 = expr_eval(
-        "where((a==124)&(b==15)&(c==2)&(d==2), 89, a)",
+    res = expr_eval(
+        "where((a==252)&(b==13), 85, a)",
         {
-            "a": l4,
+            "a": res,
             "b": veg_cover,
-            "c": lifeform,
-            "d": water_seasonality,
         },
-        name="mark_cultivated",
+        name="mark_final",
         dtype="uint8",
     )
 
-    l4 = expr_eval(
-        "where((a==124)&(b==16)&(c==2)&(d==1), 91, a)",
+    res = expr_eval(
+        "where((a==251)&(b==13), 86, a)",
         {
-            "a": l4,
+            "a": res,
             "b": veg_cover,
-            "c": lifeform,
-            "d": water_seasonality,
         },
-        name="mark_cultivated",
+        name="mark_final",
         dtype="uint8",
     )
+    #########################################
 
-    l4 = expr_eval(
-        "where((a==124)&(b==16)&(c==2)&(d==2), 92, a)",
+    res = expr_eval(
+        "where((a==254)&(b==15), 73, a)",
         {
-            "a": l4,
+            "a": res,
             "b": veg_cover,
-            "c": lifeform,
-            "d": water_seasonality,
         },
-        name="mark_cultivated",
+        name="mark_final",
         dtype="uint8",
     )
 
-    l4 = expr_eval(
-        "where((a==124)&(b==15)&(c==1), 72, a)",
+    res = expr_eval(
+        "where((a==253)&(b==15), 74, a)",
         {
-            "a": l4,
+            "a": res,
             "b": veg_cover,
-            "c": lifeform,
         },
-        name="mark_cultivated",
+        name="mark_final",
         dtype="uint8",
     )
 
-    l4 = expr_eval(
-        "where((a==124)&(b==16)&(c==1), 75, a)",
+    res = expr_eval(
+        "where((a==252)&(b==15), 88, a)",
         {
-            "a": l4,
+            "a": res,
             "b": veg_cover,
-            "c": lifeform,
         },
-        name="mark_cultivated",
+        name="mark_final",
         dtype="uint8",
     )
-    l4 = expr_eval(
-        "where((a==124)&(b==10)&(c==2), 78, a)",
+
+    res = expr_eval(
+        "where((a==251)&(b==15), 89, a)",
         {
-            "a": l4,
+            "a": res,
             "b": veg_cover,
-            "c": lifeform,
         },
-        name="mark_cultivated",
+        name="mark_final",
         dtype="uint8",
     )
-    l4 = expr_eval(
-        "where((a==124)&(b==12)&(c==2), 81, a)",
+    ##########################################
+    res = expr_eval(
+        "where((a==254)&(b==16), 76, a)",
         {
-            "a": l4,
+            "a": res,
             "b": veg_cover,
-            "c": lifeform,
         },
-        name="mark_cultivated",
-        dtype="uint8",
-    )
-    l4 = expr_eval(
-        "where((a==124)&(b==13)&(c==2), 84, a)",
-        {
-            "a": l4,
-            "b": veg_cover,
-            "c": lifeform,
-        },
-        name="mark_cultivated",
+        name="mark_final",
         dtype="uint8",
     )
 
-    l4 = expr_eval(
-        "where((a==124)&(b==15)&(c==2), 87, a)",
+    res = expr_eval(
+        "where((a==253)&(b==16), 77, a)",
         {
-            "a": l4,
+            "a": res,
             "b": veg_cover,
-            "c": lifeform,
         },
-        name="mark_cultivated",
+        name="mark_final",
         dtype="uint8",
     )
 
-    l4 = expr_eval(
-        "where((a==124)&(b==16)&(c==2), 90, a)",
+    res = expr_eval(
+        "where((a==252)&(b==16), 91, a)",
         {
-            "a": l4,
+            "a": res,
             "b": veg_cover,
-            "c": lifeform,
         },
-        name="mark_cultivated",
+        name="mark_final",
         dtype="uint8",
     )
 
-    l4 = expr_eval(
-        "where((a==124)&(b==10)&(c==1), 63, a)",
+    res = expr_eval(
+        "where((a==251)&(b==16), 92, a)",
         {
-            "a": l4,
+            "a": res,
             "b": veg_cover,
-            "c": lifeform,
         },
-        name="mark_cultivated",
+        name="mark_final",
         dtype="uint8",
     )
-    l4 = expr_eval(
-        "where((a==124)&(b==12)&(c==1), 66, a)",
-        {
-            "a": l4,
-            "b": veg_cover,
-            "c": lifeform,
-        },
-        name="mark_cultivated",
-        dtype="uint8",
-    )
-    l4 = expr_eval(
-        "where((a==124)&(b==13)&(c==1), 69, a)",
-        {
-            "a": l4,
-            "b": veg_cover,
-            "c": lifeform,
-        },
-        name="mark_cultivated",
-        dtype="uint8",
-    )
-
-    l4 = expr_eval(
-        "where((a==124)&(b==1), 56, a)",
-        {"a": l4, "b": lifeform},
-        name="mark_cultivated",
-        dtype="uint8",
-    )
-
-    l4 = expr_eval(
-        "where((a==124)&(c==2), 57, a)",
-        {"a": l4, "c": lifeform},
-        name="mark_cultivated",
-        dtype="uint8",
-    )
-
-    l4 = expr_eval(
-        "where((a==124)&(b==10), 58, a)",
-        {"a": l4, "b": veg_cover},
-        name="mark_cultivated",
-        dtype="uint8",
-    )
-    l4 = expr_eval(
-        "where((a==124)&(b==12), 59, a)",
-        {"a": l4, "b": veg_cover},
-        name="mark_cultivated",
-        dtype="uint8",
-    )
-
-    l4 = expr_eval(
-        "where((a==124)&(b==13), 60, a)",
-        {"a": l4, "b": veg_cover},
-        name="mark_cultivated",
-        dtype="uint8",
-    )
-
-    l4 = expr_eval(
-        "where((a==124)&(b==15), 61, a)",
-        {"a": l4, "b": veg_cover},
-        name="mark_cultivated",
-        dtype="uint8",
-    )
-    l4 = expr_eval(
-        "where((a==124)&(b==16), 62, a)",
-        {"a": l4, "b": veg_cover},
-        name="mark_cultivated",
-        dtype="uint8",
-    )
-    l4 = expr_eval(
-        "where((a==124), 55, a)", {"a": l4}, name="mark_mangroves", dtype="uint8"
-    )
 
-    return l4
+    return res
diff --git a/odc/stats/plugins/lc_level34.py b/odc/stats/plugins/lc_level34.py
index 72fa6145..5fe958a3 100644
--- a/odc/stats/plugins/lc_level34.py
+++ b/odc/stats/plugins/lc_level34.py
@@ -94,9 +94,7 @@ def reduce(self, xx: xr.Dataset) -> xr.Dataset:
             xx, self.bare_threshold, veg_cover
         )
 
-        l4 = l4_natural_aquatic.natural_auquatic_veg(
-            l4, lifeform, veg_cover, water_seasonality
-        )
+        l4 = l4_natural_aquatic.natural_auquatic_veg(l4, veg_cover, water_seasonality)
 
         level4 = l4_surface.lc_l4_surface(l4, level3, bare_gradation)
 
diff --git a/odc/stats/plugins/lc_veg_class_a1.py b/odc/stats/plugins/lc_veg_class_a1.py
index 15186703..00cbdc3f 100644
--- a/odc/stats/plugins/lc_veg_class_a1.py
+++ b/odc/stats/plugins/lc_veg_class_a1.py
@@ -149,7 +149,7 @@ def l3_class(self, xx: xr.Dataset):
                         {"a": data, "b": l3_mask},
                         name="intertidal_veg",
                         dtype="uint8",
-                        **{"m": self.output_classes["aquatic_veg"]},
+                        **{"m": self.output_classes["aquatic_veg_herb"]},
                     )
                 elif b == "canopy_cover_class":
                     # aquatic_veg: (mangroves > 0) & (mangroves != nodata)
@@ -161,7 +161,7 @@ def l3_class(self, xx: xr.Dataset):
                         dtype="uint8",
                         **{
                             "nodata": xx[b].attrs["nodata"],
-                            "m": self.output_classes["aquatic_veg"],
+                            "m": self.output_classes["aquatic_veg_wood"],
                         },
                     )