make All shape work

Author: mathleur

polytope/datacube/datacube_axis.py

@@ -1,3 +1,4 @@
+import math
 from abc import ABC, abstractmethod
 from copy import deepcopy
 from typing import Any, List
@@ -18,6 +19,10 @@ def update_range():
 
         def to_intervals(range):
             update_range()
+            if range[0] == -math.inf:
+                range[0] = cls.range[0]
+            if range[1] == math.inf:
+                range[1] = cls.range[1]
             axis_lower = cls.range[0]
             axis_upper = cls.range[1]
             axis_range = axis_upper - axis_lower

polytope/shapes.py

@@ -89,7 +89,7 @@ def __repr__(self):
 class Span(Shape):
     """1-D range along a single axis"""
 
-    def __init__(self, axis, lower=None, upper=None):
+    def __init__(self, axis, lower=-math.inf, upper=math.inf):
         assert not isinstance(lower, list)
         assert not isinstance(upper, list)
         self.axis = axis

tests/test_shapes.py

@@ -0,0 +1,74 @@
+import numpy as np
+import pandas as pd
+import pytest
+import xarray as xr
+
+from polytope.datacube.backends.FDB_datacube import FDBDatacube
+from polytope.datacube.backends.xarray import XArrayDatacube
+from polytope.engine.hullslicer import HullSlicer
+from polytope.polytope import Polytope, Request
+from polytope.shapes import All, Select, Span
+
+
+class TestSlicing3DXarrayDatacube:
+    def setup_method(self, method):
+        # Create a dataarray with 3 labelled axes using different index types
+        array = xr.DataArray(
+            np.random.randn(3, 6, 129, 360),
+            dims=("date", "step", "level", "longitude"),
+            coords={
+                "date": pd.date_range("2000-01-01", "2000-01-03", 3),
+                "step": [0, 3, 6, 9, 12, 15],
+                "level": range(1, 130),
+                "longitude": range(0, 360),
+            },
+        )
+        self.xarraydatacube = XArrayDatacube(array)
+        self.options = {"longitude": {"transformation": {"cyclic": [0, 360]}}}
+        self.slicer = HullSlicer()
+        self.API = Polytope(datacube=array, engine=self.slicer, axis_options=self.options)
+
+    def test_all(self):
+        request = Request(Select("step", [3]), Select("date", ["2000-01-01"]), All("level"), Select("longitude", [1]))
+        result = self.API.retrieve(request)
+        assert len(result.leaves) == 129
+
+    def test_all_cyclic(self):
+        request = Request(Select("step", [3]), Select("date", ["2000-01-01"]), Select("level", [1]), All("longitude"))
+        result = self.API.retrieve(request)
+        # result.pprint()
+        assert len(result.leaves) == 360
+
+    @pytest.mark.skip(reason="can't install fdb branch on CI")
+    def test_all_mapper_cyclic(self):
+        self.options = {
+            "values": {
+                "transformation": {
+                    "mapper": {"type": "octahedral", "resolution": 1280, "axes": ["latitude", "longitude"]}
+                }
+            },
+            "date": {"transformation": {"merge": {"with": "time", "linkers": ["T", "00"]}}},
+            "step": {"transformation": {"type_change": "int"}},
+            "longitude": {"transformation": {"cyclic": [0, 360]}},
+        }
+        self.config = {"class": "od", "expver": "0001", "levtype": "sfc", "step": 11}
+        self.fdbdatacube = FDBDatacube(self.config, axis_options=self.options)
+        self.slicer = HullSlicer()
+        self.API = Polytope(datacube=self.fdbdatacube, engine=self.slicer, axis_options=self.options)
+
+        request = Request(
+            Select("step", [11]),
+            Select("levtype", ["sfc"]),
+            Select("date", [pd.Timestamp("20230710T120000")]),
+            Select("domain", ["g"]),
+            Select("expver", ["0001"]),
+            Select("param", ["151130"]),
+            Select("class", ["od"]),
+            Select("stream", ["oper"]),
+            Select("type", ["fc"]),
+            Span("latitude", 89.9, 90),
+            All("longitude"),
+        )
+        result = self.API.retrieve(request)
+        # result.pprint()
+        assert len(result.leaves) == 20