Feature/clean up optimisation

.gitignore

@@ -5,4 +5,8 @@
 polytope.egg-info
 .pytest_cache
 *.prof
-*.idx
+*.idx
+*.grib
+*.xml
+site
+.coverage

performance/fdb_performance.py

@@ -0,0 +1,47 @@
+import time
+
+import pandas as pd
+
+from polytope.datacube.backends.fdb import FDBDatacube
+from polytope.engine.hullslicer import HullSlicer
+from polytope.polytope import Polytope, Request
+from polytope.shapes import Box, Select
+
+
+class TestSlicingFDBDatacube:
+    def setup_method(self, method):
+        # Create a dataarray with 3 labelled axes using different index types
+        self.options = {
+            "values": {
+                "transformation": {
+                    "mapper": {"type": "octahedral", "resolution": 1280, "axes": ["latitude", "longitude"]}
+                }
+            },
+            "date": {"transformation": {"merge": {"with": "time", "linkers": [" ", "00"]}}},
+            "step": {"transformation": {"type_change": "int"}},
+        }
+        self.config = {"class": "od", "expver": "0001", "levtype": "sfc", "step": 0}
+        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)
+
+    # Testing different shapes
+    # @pytest.mark.skip(reason="can't install fdb branch on CI")
+    def test_fdb_datacube(self):
+        request = Request(
+            Select("step", [0]),
+            Select("levtype", ["sfc"]),
+            Select("date", [pd.Timestamp("20230625T120000")]),
+            Select("domain", ["g"]),
+            Select("expver", ["0001"]),
+            Select("param", ["167"]),
+            Select("class", ["od"]),
+            Select("stream", ["oper"]),
+            Select("type", ["an"]),
+            Box(["latitude", "longitude"], [0, 0], [10, 10]),
+        )
+        time1 = time.time()
+        result = self.API.retrieve(request)
+        print("ENTIRE TIME")
+        print(time.time() - time1)
+        print(len(result.leaves))

performance/fdb_performance_3D.py

@@ -0,0 +1,48 @@
+import time
+
+import pandas as pd
+
+from polytope.datacube.backends.fdb import FDBDatacube
+from polytope.engine.hullslicer import HullSlicer
+from polytope.polytope import Polytope, Request
+from polytope.shapes import Box, Select, Span
+
+
+class TestSlicingFDBDatacube:
+    def setup_method(self, method):
+        # Create a dataarray with 3 labelled axes using different index types
+        self.options = {
+            "values": {
+                "transformation": {
+                    "mapper": {"type": "octahedral", "resolution": 1280, "axes": ["latitude", "longitude"]}
+                }
+            },
+            "date": {"transformation": {"merge": {"with": "time", "linkers": [" ", "00"]}}},
+            "step": {"transformation": {"type_change": "int"}},
+            "levelist": {"transformation": {"type_change": "int"}},
+        }
+        self.config = {"class": "od", "expver": "0001", "levtype": "sfc"}
+        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)
+
+    # Testing different shapes
+    # @pytest.mark.skip(reason="can't install fdb branch on CI")
+    def test_fdb_datacube(self):
+        request = Request(
+            Span("step", 1, 15),
+            Select("levtype", ["sfc"]),
+            Select("date", [pd.Timestamp("20231102T000000")]),
+            Select("domain", ["g"]),
+            Select("expver", ["0001"]),
+            Select("param", ["167"]),
+            Select("class", ["od"]),
+            Select("stream", ["oper"]),
+            Select("type", ["fc"]),
+            Box(["latitude", "longitude"], [0, 0], [3, 5]),
+        )
+        time1 = time.time()
+        result = self.API.retrieve(request)
+        print("ENTIRE TIME")
+        print(time.time() - time1)
+        print(len(result.leaves))

performance/fdb_scalability_plot.py

@@ -0,0 +1,16 @@
+import matplotlib.pyplot as plt
+
+fdb_time = [
+    7.6377081871032715 - 7.558288812637329,
+    73.57192325592041 - 72.99611115455627,
+    733.2706120014191 - 727.7059993743896,
+    4808.3157522678375 - 4770.814565420151,
+]
+num_extracted_points = [1986, 19226, 191543, 1267134]
+
+# for the 1.3M points, we used 100 latitudes too...., maybe that's why it's not as linear...
+
+plt.plot(num_extracted_points, fdb_time, marker="o")
+plt.xlabel("Number of extracted points")
+plt.ylabel("Polytope extraction time (in s)")
+plt.show()

polytope/datacube/backends/__init__.py

@@ -0,0 +1 @@
+from ..backends.datacube import *

polytope/datacube/backends/datacube.py

@@ -37,8 +37,11 @@ def _create_axes(self, name, values, transformation_type_key, transformation_opt
         )
         for blocked_axis in transformation.blocked_axes():
             self.blocked_axes.append(blocked_axis)
+        for unwanted_axis in transformation.unwanted_axes():
+            self.unwanted_axes.append(unwanted_axis)
         for axis_name in final_axis_names:
             self.complete_axes.append(axis_name)
+            self.fake_axes.append(axis_name)
             # if axis does not yet exist, create it
 
             # first need to change the values so that we have right type

polytope/datacube/backends/fdb.py

@@ -0,0 +1,167 @@
+from copy import deepcopy
+
+import pyfdb
+
+from .datacube import Datacube, IndexTree
+
+
+class FDBDatacube(Datacube):
+    def __init__(self, config={}, axis_options={}):
+        self.axis_options = axis_options
+        self.axis_counter = 0
+        self._axes = None
+        treated_axes = []
+        self.non_complete_axes = []
+        self.complete_axes = []
+        self.blocked_axes = []
+        self.unwanted_axes = []
+        self.fake_axes = []
+        self.unwanted_path = {}
+
+        partial_request = config
+        # Find values in the level 3 FDB datacube
+        # Will be in the form of a dictionary? {axis_name:values_available, ...}
+        self.fdb = pyfdb.FDB()
+        self.fdb_coordinates = self.fdb.axes(partial_request).as_dict()
+        self.fdb_coordinates["values"] = []
+        for name, values in self.fdb_coordinates.items():
+            values.sort()
+            options = axis_options.get(name, {})
+            self._check_and_add_axes(options, name, values)
+            treated_axes.append(name)
+            self.complete_axes.append(name)
+
+        # add other options to axis which were just created above like "lat" for the mapper transformations for eg
+        for name in self._axes:
+            if name not in treated_axes:
+                options = axis_options.get(name, {})
+                val = self._axes[name].type
+                self._check_and_add_axes(options, name, val)
+
+    def remove_unwanted_axes(self, leaf_path):
+        for axis in self.unwanted_axes:
+            leaf_path.pop(axis)
+        return leaf_path
+
+    def get(self, requests: IndexTree, leaf_path={}):
+        # First when request node is root, go to its children
+        if requests.axis.name == "root":
+            for c in requests.children:
+                self.get(c)
+        # If request node has no children, we have a leaf so need to assign fdb values to it
+        else:
+            key_value_path = {requests.axis.name: requests.value}
+            ax = requests.axis
+            (key_value_path, leaf_path, self.unwanted_path) = ax.unmap_path_key(
+                key_value_path, leaf_path, self.unwanted_path
+            )
+            leaf_path |= key_value_path
+            if len(requests.children[0].children[0].children) == 0:
+                # remap this last key
+                self.get_2nd_last_values(requests, leaf_path)
+
+            # Otherwise remap the path for this key and iterate again over children
+            else:
+                for c in requests.children:
+                    self.get(c, leaf_path)
+
+    def get_2nd_last_values(self, requests, leaf_path={}):
+        # In this function, we recursively loop over the last two layers of the tree and store the indices of the
+        # request ranges in those layers
+        lat_length = len(requests.children)
+        range_lengths = [False] * lat_length
+        current_start_idxs = [False] * lat_length
+        fdb_node_ranges = [False] * lat_length
+        for i in range(len(requests.children)):
+            lat_child = requests.children[i]
+            lon_length = len(lat_child.children)
+            range_lengths[i] = [1] * lon_length
+            current_start_idxs[i] = [None] * lon_length
+            fdb_node_ranges[i] = [[IndexTree.root] * lon_length] * lon_length
+            range_length = deepcopy(range_lengths[i])
+            current_start_idx = deepcopy(current_start_idxs[i])
+            fdb_range_nodes = deepcopy(fdb_node_ranges[i])
+            key_value_path = {lat_child.axis.name: lat_child.value}
+            ax = lat_child.axis
+            (key_value_path, leaf_path, self.unwanted_path) = ax.unmap_path_key(
+                key_value_path, leaf_path, self.unwanted_path
+            )
+            leaf_path |= key_value_path
+            (range_lengths[i], current_start_idxs[i], fdb_node_ranges[i]) = self.get_last_layer_before_leaf(
+                lat_child, leaf_path, range_length, current_start_idx, fdb_range_nodes
+            )
+        self.give_fdb_val_to_node(leaf_path, range_lengths, current_start_idxs, fdb_node_ranges, lat_length)
+
+    def get_last_layer_before_leaf(self, requests, leaf_path, range_l, current_idx, fdb_range_n):
+        i = 0
+        for c in requests.children:
+            # now c are the leaves of the initial tree
+            key_value_path = {c.axis.name: c.value}
+            ax = c.axis
+            (key_value_path, leaf_path, self.unwanted_path) = ax.unmap_path_key(
+                key_value_path, leaf_path, self.unwanted_path
+            )
+            leaf_path |= key_value_path
+            last_idx = key_value_path["values"]
+            if current_idx[i] is None:
+                current_idx[i] = last_idx
+                fdb_range_n[i][range_l[i] - 1] = c
+            else:
+                if last_idx == current_idx[i] + range_l[i]:
+                    range_l[i] += 1
+                    fdb_range_n[i][range_l[i] - 1] = c
+                else:
+                    key_value_path = {c.axis.name: c.value}
+                    ax = c.axis
+                    (key_value_path, leaf_path, self.unwanted_path) = ax.unmap_path_key(
+                        key_value_path, leaf_path, self.unwanted_path
+                    )
+                    leaf_path |= key_value_path
+                    i += 1
+                    current_start_idx = key_value_path["values"]
+                    current_idx[i] = current_start_idx
+        return (range_l, current_idx, fdb_range_n)
+
+    def give_fdb_val_to_node(self, leaf_path, range_lengths, current_start_idx, fdb_range_nodes, lat_length):
+        (output_values, original_indices) = self.find_fdb_values(
+            leaf_path, range_lengths, current_start_idx, lat_length
+        )
+        new_fdb_range_nodes = []
+        new_range_lengths = []
+        for j in range(lat_length):
+            for i in range(len(range_lengths[j])):
+                if current_start_idx[j][i] is not None:
+                    new_fdb_range_nodes.append(fdb_range_nodes[j][i])
+                    new_range_lengths.append(range_lengths[j][i])
+        sorted_fdb_range_nodes = [new_fdb_range_nodes[i] for i in original_indices]
+        sorted_range_lengths = [new_range_lengths[i] for i in original_indices]
+        for i in range(len(sorted_fdb_range_nodes)):
+            for k in range(sorted_range_lengths[i]):
+                n = sorted_fdb_range_nodes[i][k]
+                n.result = output_values[0][0][0][i][k]
+
+    def find_fdb_values(self, path, range_lengths, current_start_idx, lat_length):
+        path.pop("values")
+        fdb_requests = []
+        interm_request_ranges = []
+        for i in range(lat_length):
+            for j in range(len(range_lengths[i])):
+                if current_start_idx[i][j] is not None:
+                    current_request_ranges = (current_start_idx[i][j], current_start_idx[i][j] + range_lengths[i][j])
+                    interm_request_ranges.append(current_request_ranges)
+        request_ranges_with_idx = list(enumerate(interm_request_ranges))
+        sorted_list = sorted(request_ranges_with_idx, key=lambda x: x[1][0])
+        original_indices, sorted_request_ranges = zip(*sorted_list)
+        fdb_requests.append(tuple((path, sorted_request_ranges)))
+        output_values = self.fdb.extract(fdb_requests)
+        return (output_values, original_indices)
+
+    def datacube_natural_indexes(self, axis, subarray):
+        indexes = subarray[axis.name]
+        return indexes
+
+    def select(self, path, unmapped_path):
+        return self.fdb_coordinates
+
+    def ax_vals(self, name):
+        return self.fdb_coordinates.get(name, None)