From 7d3223f55226483ad269533b667638577a8d7d4b Mon Sep 17 00:00:00 2001 From: Martin Fleischmann Date: Tue, 15 Nov 2022 21:18:21 +0100 Subject: [PATCH 1/3] ENH: support arrays in strtree query --- doc/source/quickstart.ipynb | 1497 +++++++++++++++++++++++++---------- xvec/strtree.py | 10 +- 2 files changed, 1098 insertions(+), 409 deletions(-) diff --git a/doc/source/quickstart.ipynb b/doc/source/quickstart.ipynb index d1b2068..36e281a 100644 --- a/doc/source/quickstart.ipynb +++ b/doc/source/quickstart.ipynb @@ -465,93 +465,93 @@ " fill: currentColor;\n", "}\n", "
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        "\n",
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        "\n",
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-       "          [60, 33, 13, ..., 39, 54, 33]],\n",
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        "\n",
-       "         [[15, 37, 54, ..., 30,  2, 57],\n",
-       "          [29, 90,  1, ..., 60, 21, 29]],\n",
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        "\n",
-       "         [[97, 47, 98, ..., 29, 76, 77],\n",
-       "          [43, 42, 23, ..., 68, 56, 42]]],\n",
+       "         [[32, 94, 97, ..., 28,  9, 19],\n",
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        "\n",
        "...\n",
        "\n",
-       "        [[[53, 70, 33, ...,  6, 78, 35],\n",
-       "          [62, 58, 58, ..., 35, 88, 12]],\n",
+       "        [[[85, 71, 12, ..., 51, 16,  6],\n",
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        "\n",
-       "         [[27, 77,  3, ..., 62, 44, 34],\n",
-       "          [95, 88, 66, ..., 67, 63, 83]],\n",
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        "\n",
-       "         [[43, 78, 66, ..., 22, 16, 56],\n",
-       "          [15, 82, 12, ..., 20, 26, 43]],\n",
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        "\n",
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-       "         [[ 6, 65, 35, ..., 46, 17, 12],\n",
-       "          [21, 22, 69, ..., 45, 58, 11]],\n",
+       "         [[70, 96, 51, ..., 12, 54, 66],\n",
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        "\n",
-       "         [[75, 78, 24, ..., 13, 37, 66],\n",
-       "          [12, 90, 93, ..., 17, 52, 47]],\n",
+       "         [[56, 49, 15, ..., 16, 14, 97],\n",
+       "          [84, 55, 60, ..., 58, 30, 69]],\n",
        "\n",
-       "         [[49, 62, 62, ..., 74, 70, 19],\n",
-       "          [32,  8, 19, ..., 79, 16, 87]]]]])\n",
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        "  * day          (day) datetime64[ns] 2015-01-01 2015-01-02 ... 2015-04-10\n",
@@ -3589,47 +3589,47 @@
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" [[[53, 70, 33, ..., 6, 78, 35],\n", - " [62, 58, 58, ..., 35, 88, 12]],\n", + " [[[85, 71, 12, ..., 51, 16, 6],\n", + " [66, 23, 9, ..., 3, 89, 90]],\n", "\n", - " [[27, 77, 3, ..., 62, 44, 34],\n", - " [95, 88, 66, ..., 67, 63, 83]],\n", + " [[81, 39, 53, ..., 98, 48, 1],\n", + " [37, 91, 7, ..., 57, 51, 21]],\n", "\n", - " [[43, 78, 66, ..., 22, 16, 56],\n", - " [15, 82, 12, ..., 20, 26, 43]],\n", + " [[40, 99, 49, ..., 47, 94, 36],\n", + " [14, 93, 90, ..., 90, 55, 81]],\n", "\n", " ...,\n", "\n", - " [[ 6, 65, 35, ..., 46, 17, 12],\n", - " [21, 22, 69, ..., 45, 58, 11]],\n", + " [[70, 96, 51, ..., 12, 54, 66],\n", + " [46, 23, 55, ..., 36, 44, 87]],\n", "\n", - " [[75, 78, 24, ..., 13, 37, 66],\n", - " [12, 90, 93, ..., 17, 52, 47]],\n", + " [[56, 49, 15, ..., 16, 14, 97],\n", + " [84, 55, 60, ..., 58, 30, 69]],\n", "\n", - " [[49, 62, 62, ..., 74, 70, 19],\n", - " [32, 8, 19, ..., 79, 16, 87]]]]])\n", + " [[98, 82, 72, ..., 2, 64, 39],\n", + " [63, 7, 11, ..., 52, 82, 74]]]]])\n", "Coordinates:\n", " * mode (mode) 1\u001b[0m arr\u001b[39m.\u001b[39;49msel(origin\u001b[39m=\u001b[39;49m[shapely\u001b[39m.\u001b[39;49mPoint(\u001b[39m-\u001b[39;49m\u001b[39m80\u001b[39;49m, \u001b[39m35\u001b[39;49m), shapely\u001b[39m.\u001b[39;49mPoint(\u001b[39m-\u001b[39;49m\u001b[39m76\u001b[39;49m, \u001b[39m35.6\u001b[39;49m)], method\u001b[39m=\u001b[39;49m\u001b[39m\"\u001b[39;49m\u001b[39mintersects\u001b[39;49m\u001b[39m\"\u001b[39;49m)\n", - 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"File \u001b[0;32m~/mambaforge/envs/xvec_dev/lib/python3.10/site-packages/xarray/core/dataset.py:2554\u001b[0m, in \u001b[0;36mDataset.sel\u001b[0;34m(self, indexers, method, tolerance, drop, **indexers_kwargs)\u001b[0m\n\u001b[1;32m 2493\u001b[0m \u001b[39m\"\"\"Returns a new dataset with each array indexed by tick labels\u001b[39;00m\n\u001b[1;32m 2494\u001b[0m \u001b[39malong the specified dimension(s).\u001b[39;00m\n\u001b[1;32m 2495\u001b[0m \n\u001b[0;32m (...)\u001b[0m\n\u001b[1;32m 2551\u001b[0m \u001b[39mDataArray.sel\u001b[39;00m\n\u001b[1;32m 2552\u001b[0m \u001b[39m\"\"\"\u001b[39;00m\n\u001b[1;32m 2553\u001b[0m indexers \u001b[39m=\u001b[39m either_dict_or_kwargs(indexers, indexers_kwargs, \u001b[39m\"\u001b[39m\u001b[39msel\u001b[39m\u001b[39m\"\u001b[39m)\n\u001b[0;32m-> 2554\u001b[0m query_results \u001b[39m=\u001b[39m map_index_queries(\n\u001b[1;32m 2555\u001b[0m \u001b[39mself\u001b[39;49m, indexers\u001b[39m=\u001b[39;49mindexers, method\u001b[39m=\u001b[39;49mmethod, tolerance\u001b[39m=\u001b[39;49mtolerance\n\u001b[1;32m 2556\u001b[0m )\n\u001b[1;32m 2558\u001b[0m \u001b[39mif\u001b[39;00m drop:\n\u001b[1;32m 2559\u001b[0m no_scalar_variables \u001b[39m=\u001b[39m {}\n", - "File \u001b[0;32m~/mambaforge/envs/xvec_dev/lib/python3.10/site-packages/xarray/core/indexing.py:183\u001b[0m, in \u001b[0;36mmap_index_queries\u001b[0;34m(obj, indexers, method, tolerance, **indexers_kwargs)\u001b[0m\n\u001b[1;32m 181\u001b[0m results\u001b[39m.\u001b[39mappend(IndexSelResult(labels))\n\u001b[1;32m 182\u001b[0m \u001b[39melse\u001b[39;00m:\n\u001b[0;32m--> 183\u001b[0m results\u001b[39m.\u001b[39mappend(index\u001b[39m.\u001b[39;49msel(labels, \u001b[39m*\u001b[39;49m\u001b[39m*\u001b[39;49moptions)) \u001b[39m# type: ignore[call-arg]\u001b[39;00m\n\u001b[1;32m 185\u001b[0m merged \u001b[39m=\u001b[39m merge_sel_results(results)\n\u001b[1;32m 187\u001b[0m \u001b[39m# drop dimension coordinates found in dimension indexers\u001b[39;00m\n\u001b[1;32m 188\u001b[0m \u001b[39m# (also drop multi-index if any)\u001b[39;00m\n\u001b[1;32m 189\u001b[0m \u001b[39m# (.sel() already ensures alignment)\u001b[39;00m\n", - "File \u001b[0;32m~/Git/xvec/xvec/strtree.py:40\u001b[0m, in \u001b[0;36mShapelySTRTreeIndex.sel\u001b[0;34m(self, labels, method, tolerance)\u001b[0m\n\u001b[1;32m 38\u001b[0m \u001b[39mif\u001b[39;00m method \u001b[39mis\u001b[39;00m \u001b[39mnot\u001b[39;00m \u001b[39mNone\u001b[39;00m \u001b[39mand\u001b[39;00m method \u001b[39m!=\u001b[39m \u001b[39m\"\u001b[39m\u001b[39mnearest\u001b[39m\u001b[39m\"\u001b[39m:\n\u001b[1;32m 39\u001b[0m \u001b[39mif\u001b[39;00m \u001b[39mnot\u001b[39;00m \u001b[39misinstance\u001b[39m(label, shapely\u001b[39m.\u001b[39mGeometry):\n\u001b[0;32m---> 40\u001b[0m \u001b[39mraise\u001b[39;00m \u001b[39mValueError\u001b[39;00m(\n\u001b[1;32m 41\u001b[0m \u001b[39m\"\u001b[39m\u001b[39mselection with another method than nearest only supports \u001b[39m\u001b[39m\"\u001b[39m\n\u001b[1;32m 42\u001b[0m \u001b[39m\"\u001b[39m\u001b[39ma single geometry as input label.\u001b[39m\u001b[39m\"\u001b[39m\n\u001b[1;32m 43\u001b[0m )\n\u001b[1;32m 45\u001b[0m \u001b[39mif\u001b[39;00m \u001b[39misinstance\u001b[39m(label, xarray\u001b[39m.\u001b[39mDataArray):\n\u001b[1;32m 46\u001b[0m label_array \u001b[39m=\u001b[39m label\u001b[39m.\u001b[39m_variable\u001b[39m.\u001b[39m_data\n", - "\u001b[0;31mValueError\u001b[0m: selection with another method than nearest only supports a single geometry as input label." + "name": "stdout", + "output_type": "stream", + "text": [ + "here\n" ] + }, + { + "data": { + "text/html": [ + "
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+       "    origin       (origin) object MULTIPOLYGON (((-79.91995239257812 34.807918...\n",
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+       "    destination  ShapelySTRTreeIndex
    " + ], + "text/plain": [ + "\n", + "array([[[[[60, 1, 60, ..., 90, 59, 4],\n", + " [ 5, 20, 52, ..., 56, 7, 46]],\n", + "\n", + " [[36, 44, 89, ..., 22, 47, 41],\n", + " [ 3, 45, 64, ..., 60, 52, 7]],\n", + "\n", + " [[42, 1, 62, ..., 9, 62, 38],\n", + " [96, 13, 96, ..., 29, 33, 99]],\n", + "\n", + " ...,\n", + "\n", + " [[38, 74, 94, ..., 52, 96, 13],\n", + " [92, 29, 88, ..., 87, 52, 19]],\n", + "\n", + " [[25, 60, 11, ..., 32, 79, 57],\n", + " [60, 50, 71, ..., 39, 69, 46]],\n", + "\n", + " [[32, 94, 97, ..., 28, 9, 19],\n", + " [58, 57, 85, ..., 77, 62, 80]]],\n", + "\n", + "...\n", + "\n", + " [[[85, 71, 12, ..., 51, 16, 6],\n", + " [66, 23, 9, ..., 3, 89, 90]],\n", + "\n", + " [[81, 39, 53, ..., 98, 48, 1],\n", + " [37, 91, 7, ..., 57, 51, 21]],\n", + "\n", + " [[40, 99, 49, ..., 47, 94, 36],\n", + " [14, 93, 90, ..., 90, 55, 81]],\n", + "\n", + " ...,\n", + "\n", + " [[70, 96, 51, ..., 12, 54, 66],\n", + " [46, 23, 55, ..., 36, 44, 87]],\n", + "\n", + " [[56, 49, 15, ..., 16, 14, 97],\n", + " [84, 55, 60, ..., 58, 30, 69]],\n", + "\n", + " [[98, 82, 72, ..., 2, 64, 39],\n", + " [63, 7, 11, ..., 52, 82, 74]]]]])\n", + "Coordinates:\n", + " * mode (mode) Date: Wed, 23 Nov 2022 11:13:29 +0100 Subject: [PATCH 2/3] update for GeometryIndex --- xvec/index.py | 11 ++++------- 1 file changed, 4 insertions(+), 7 deletions(-) diff --git a/xvec/index.py b/xvec/index.py index 1c4eee6..bad8c0c 100644 --- a/xvec/index.py +++ b/xvec/index.py @@ -177,13 +177,6 @@ def _sel_sindex(self, labels, method, tolerance): assert len(labels) == 1 label = next(iter(labels.values())) - if method != "nearest": - if not isinstance(label, shapely.Geometry): - raise ValueError( - "selection with another method than nearest only supports " - "a single geometry as input label." - ) - if isinstance(label, DataArray): label_array = label._variable._data elif isinstance(label, Variable): @@ -201,6 +194,10 @@ def _sel_sindex(self, labels, method, tolerance): else: indices = self.sindex.query(label, predicate=method, distance=tolerance) + # if label is an array, we need to use only the second array returned + if indices.ndim == 2: + indices = indices[1] + # attach dimension names and/or coordinates to positional indexer if isinstance(label, Variable): indices = Variable(label.dims, indices) From 48b35eaf87c763ff4b5a23fcbca12c445a7a3ff2 Mon Sep 17 00:00:00 2001 From: Martin Fleischmann Date: Wed, 23 Nov 2022 11:34:12 +0100 Subject: [PATCH 3/3] include unique option --- xvec/index.py | 2 ++ 1 file changed, 2 insertions(+) diff --git a/xvec/index.py b/xvec/index.py index bad8c0c..9c6a505 100644 --- a/xvec/index.py +++ b/xvec/index.py @@ -198,6 +198,8 @@ def _sel_sindex(self, labels, method, tolerance): if indices.ndim == 2: indices = indices[1] + # indices = np.unique(indices[1]) + # attach dimension names and/or coordinates to positional indexer if isinstance(label, Variable): indices = Variable(label.dims, indices)