Add Level-3 and Level-4 bands for Land Cover product. (#161)

* Added Level4 classes

* Added unit tests for cultivated terrestrial vegetation

* Added unit tests for natural terrestrial vegetation and cultivated terrestrial vegetation

* Added unit tests for natural terrestrial vegetation and cultivated terrestrial vegetation

* Added level-4 water classes

* Cleaned up inconsistencies between the land cover modules

* Improved class names and applied some other clean-ups.

* [pre-commit.ci] auto fixes from pre-commit.com hooks

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* [pre-commit.ci] auto fixes from pre-commit.com hooks

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* Added more improvement on level3 and level4

* [pre-commit.ci] auto fixes from pre-commit.com hooks

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* Applied formatting and code improvements

* Further modularised the level4

* Added an integration test for level 4. Also changed data types in unit tests to dask arrays

* [pre-commit.ci] auto fixes from pre-commit.com hooks

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* Applied linting and formatting

* Applied fixes and improvements based on review comments

* Removed commented code

* [pre-commit.ci] auto fixes from pre-commit.com hooks

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* Applied formatting changes

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* Fixed a unit test

---------

Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>

odc/stats/plugins/_registry.py

@@ -39,10 +39,11 @@ def import_all():
 
     # TODO: make that more automatic
     modules = [
-        "odc.stats.plugins.lc_treelite_cultivated.py",
+        "odc.stats.plugins.lc_treelite_cultivated",
         "odc.stats.plugins.lc_level3",
         "odc.stats.plugins.lc_treelite_woody",
         "odc.stats.plugins.lc_tf_urban",
+        "odc.stats.plugins.lc_level34",
         "odc.stats.plugins.lc_veg_class_a1",
         "odc.stats.plugins.lc_fc_wo_a0",
         "odc.stats.plugins.mangroves",

odc/stats/plugins/l34_utils/l4_bare_gradation.py

@@ -0,0 +1,46 @@
+import xarray as xr
+from odc.stats._algebra import expr_eval
+
+
+NODATA = 255
+
+
+def bare_gradation(xx: xr.Dataset, bare_threshold, veg_cover):
+
+    # Map any data > 100 ---> 100
+    bs_pc_50 = expr_eval(
+        "where((a>100)&(a!=nodata), 100, a)",
+        {"a": xx.bs_pc_50.data},
+        name="mark_veg",
+        dtype="uint8",
+        **{"nodata": NODATA},
+    )
+
+    # 60% <= data  --> 15
+    bs_mask = expr_eval(
+        "where((a>=m)&(a!=nodata), 15, a)",
+        {"a": bs_pc_50},
+        name="mark_veg",
+        dtype="uint8",
+        **{"m": bare_threshold[1], "nodata": NODATA},
+    )
+
+    # 20% <= data < 60% --> 12
+    bs_mask = expr_eval(
+        "where((a>=m)&(a<n), 12, b)",
+        {"a": bs_pc_50, "b": bs_mask},
+        name="mark_veg",
+        dtype="uint8",
+        **{"m": bare_threshold[0], "n": bare_threshold[1]},
+    )
+
+    # data < 20% --> 10
+    bs_mask = expr_eval(
+        "where(a<m, 10, b)",
+        {"a": bs_pc_50, "b": bs_mask},
+        name="mark_veg",
+        dtype="uint8",
+        **{"m": bare_threshold[0]},
+    )
+
+    return bs_mask

odc/stats/plugins/l34_utils/l4_cultivated.py

@@ -0,0 +1,97 @@
+from odc.stats._algebra import expr_eval
+
+NODATA = 255
+
+
+def lc_l4_cultivated(l34, level3, lifeform, veg_cover):
+
+    l4 = expr_eval(
+        "where((d==110)&(a==111)&(b==10)&(c==1), 9, d)",
+        {"a": level3, "b": veg_cover, "c": lifeform, "d": l34},
+        name="mark_cultivated",
+        dtype="uint8",
+    )
+
+    l4 = expr_eval(
+        "where((d==110)&(a==111)&(b==12)&(c==1), 10, d)",
+        {"a": level3, "b": veg_cover, "c": lifeform, "d": l4},
+        name="mark_cultivated",
+        dtype="uint8",
+    )
+    l4 = expr_eval(
+        "where((d==110)&(a==111)&(b==13)&(c==1), 11, d)",
+        {"a": level3, "b": veg_cover, "c": lifeform, "d": l4},
+        name="mark_cultivated",
+        dtype="uint8",
+    )
+    l4 = expr_eval(
+        "where((d==110)&(a==111)&(b==15)&(c==1), 12, d)",
+        {"a": level3, "b": veg_cover, "c": lifeform, "d": l4},
+        name="mark_cultivated",
+        dtype="uint8",
+    )
+
+    l4 = expr_eval(
+        "where((d==110)&(a==111)&(b==16)&(c==1), 13, d)",
+        {"a": level3, "b": veg_cover, "c": lifeform, "d": l4},
+        name="mark_cultivated",
+        dtype="uint8",
+    )
+
+    l4 = expr_eval(
+        "where((d==110)&(a==111)&(b==10)&(c==2), 14, d)",
+        {"a": level3, "b": veg_cover, "c": lifeform, "d": l4},
+        name="mark_cultivated",
+        dtype="uint8",
+    )
+    l4 = expr_eval(
+        "where((d==110)&(a==111)&(b==12)&(c==2), 15, d)",
+        {"a": level3, "b": veg_cover, "c": lifeform, "d": l4},
+        name="mark_cultivated",
+        dtype="uint8",
+    )
+    l4 = expr_eval(
+        "where((d==110)&(a==111)&(b==13)&(c==2), 16, d)",
+        {"a": level3, "b": veg_cover, "c": lifeform, "d": l4},
+        name="mark_cultivated",
+        dtype="uint8",
+    )
+    l4 = expr_eval(
+        "where((d==110)&(a==111)&(b==15)&(c==2), 17, d)",
+        {"a": level3, "b": veg_cover, "c": lifeform, "d": l4},
+        name="mark_cultivated",
+        dtype="uint8",
+    )
+
+    l4 = expr_eval(
+        "where((d==110)&(a==111)&(b==16)&(c==2), 18, d)",
+        {"a": level3, "b": veg_cover, "c": lifeform, "d": l4},
+        name="mark_cultivated",
+        dtype="uint8",
+    )
+
+    l4 = expr_eval(
+        "where((d==110)&(a==111)&(b==1), 2, d)",
+        {"a": level3, "b": lifeform, "d": l4},
+        name="mark_cultivated",
+        dtype="uint8",
+    )
+
+    l4 = expr_eval(
+        "where((d==110)&(a==111)&(b==2), 3, d)",
+        {"a": level3, "b": lifeform, "d": l4},
+        name="mark_cultivated",
+        dtype="uint8",
+    )
+
+    # the 4-8 classes can't happen in LC since cultivated class will not be classified if vegetation doesn't exist.
+    # skip these classes in level4
+
+    l4 = expr_eval(
+        "where((d==110)&(a==111), 1, d)",
+        {"a": level3, "d": l4},
+        name="mark_cultivated",
+        dtype="uint8",
+    )
+
+    return l4