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fast_groupby_bins_agg.ipynb
{
"cells": [
{
"cell_type": "code",
"execution_count": 14,
"metadata": {
"id": "pRDJrkjEC3Re"
},
"outputs": [],
"source": [
"# Copyright 2020 Google LLC.\n",
"# SPDX-License-Identifier: Apache-2.0\n",
"\n",
"import numpy as np\n",
"import pandas as pd\n",
"import xarray\n",
"import numpy_groupies\n",
"\n",
"def _binned_agg(\n",
" array: np.ndarray,\n",
" indices: np.ndarray,\n",
" num_bins: int,\n",
" *,\n",
" func,\n",
" fill_value,\n",
" dtype,\n",
") -> np.ndarray:\n",
" \"\"\"NumPy helper function for aggregating over bins.\"\"\"\n",
" mask = np.logical_not(np.isnan(indices))\n",
" int_indices = indices[mask].astype(int)\n",
" shape = array.shape[:-indices.ndim] + (num_bins,)\n",
" result = numpy_groupies.aggregate(\n",
" int_indices, array[..., mask],\n",
" func=func,\n",
" size=num_bins,\n",
" fill_value=fill_value,\n",
" dtype=dtype,\n",
" axis=-1,\n",
" )\n",
" return result\n",
"\n",
"def groupby_bins_agg(\n",
" array: xarray.DataArray,\n",
" group: xarray.DataArray,\n",
" bins,\n",
" func='sum',\n",
" fill_value=0,\n",
" dtype=None,\n",
" **cut_kwargs,\n",
") -> xarray.DataArray:\n",
" \"\"\"Faster equivalent of Xarray's groupby_bins(...).sum().\"\"\"\n",
" # TODO: implement this upstream in xarray:\n",
" # https://github.com/pydata/xarray/issues/4473\n",
" binned = pd.cut(np.ravel(group), bins, **cut_kwargs)\n",
" new_dim_name = group.name + \"_bins\"\n",
" indices = group.copy(data=binned.codes.reshape(group.shape))\n",
"\n",
" result = xarray.apply_ufunc(\n",
" _binned_agg, array, indices,\n",
" input_core_dims=[indices.dims, indices.dims],\n",
" output_core_dims=[[new_dim_name]],\n",
" output_dtypes=[array.dtype],\n",
" dask_gufunc_kwargs=dict(\n",
" output_sizes={new_dim_name: binned.categories.size},\n",
" ),\n",
" kwargs={\n",
" 'num_bins': binned.categories.size,\n",
" 'func': func,\n",
" 'fill_value': fill_value,\n",
" 'dtype': dtype,\n",
" },\n",
" dask='parallelized',\n",
" )\n",
" result.coords[new_dim_name] = binned.categories\n",
" return result\n",
"\n",
"def make_test_data(t, x, y, seed=0):\n",
" signal = xarray.DataArray(\n",
" np.random.RandomState(seed).rand(t, x, y),\n",
" dims=['time', 'y', 'x'],\n",
" coords={\n",
" 'time': np.arange(t),\n",
" 'y': np.arange(x),\n",
" 'x': np.arange(y),\n",
" },\n",
" name='signal')\n",
" distance = ((signal.x ** 2 + signal.y ** 2) ** 0.5).rename('distance')\n",
" return signal, distance"
]
},
{
"cell_type": "markdown",
"metadata": {
"id": "r0Jp6XRmIoNU"
},
"source": [
"# unit test"
]
},
{
"cell_type": "code",
"execution_count": 25,
"metadata": {
"id": "Qa6NH3WGEFyC"
},
"outputs": [],
"source": [
"signal, distance = make_test_data(t=2, x=50, y=50)\n",
"bins = 10"
]
},
{
"cell_type": "code",
"execution_count": 29,
"metadata": {
"colab": {
"base_uri": "https://localhost:8080/",
"height": 219
},
"id": "hz1ikpo3Ik-j",
"outputId": "f88ae860-c056-424c-94b4-c52608951631"
},
"outputs": [],
"source": [
"actual = groupby_bins_agg(signal, distance, bins, func='mean')\n",
"expected = signal.groupby_bins(distance, bins=10).mean()\n",
"xarray.testing.assert_allclose(actual, expected)"
]
},
{
"cell_type": "code",
"execution_count": 30,
"metadata": {
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"base_uri": "https://localhost:8080/",
"height": 219
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"id": "6FIRcPRzImDV",
"outputId": "dc0741f1-44b4-437c-b577-d8e4785c54b8"
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"</style><pre class='xr-text-repr-fallback'>&lt;xarray.DataArray (time: 2, distance_bins: 10)&gt;\n",
"array([[0.51498271, 0.46370372, 0.48996133, 0.51069211, 0.5302821 ,\n",
" 0.50000696, 0.48753868, 0.52151072, 0.48915714, 0.51292164],\n",
" [0.53229943, 0.52167522, 0.45915308, 0.5293949 , 0.47742068,\n",
" 0.48900111, 0.48465034, 0.47729889, 0.5059115 , 0.50237199]])\n",
"Coordinates:\n",
" * time (time) int64 0 1\n",
" * distance_bins (distance_bins) object (-0.0693, 6.93] ... (62.367, 69.296]</pre><div class='xr-wrap' hidden><div class='xr-header'><div class='xr-obj-type'>xarray.DataArray</div><div class='xr-array-name'></div><ul class='xr-dim-list'><li><span class='xr-has-index'>time</span>: 2</li><li><span class='xr-has-index'>distance_bins</span>: 10</li></ul></div><ul class='xr-sections'><li class='xr-section-item'><div class='xr-array-wrap'><input id='section-5a1ec1d2-af31-4586-a084-270660896406' class='xr-array-in' type='checkbox' checked><label for='section-5a1ec1d2-af31-4586-a084-270660896406' title='Show/hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-array-preview xr-preview'><span>0.515 0.4637 0.49 0.5107 0.5303 ... 0.489 0.4847 0.4773 0.5059 0.5024</span></div><div class='xr-array-data'><pre>array([[0.51498271, 0.46370372, 0.48996133, 0.51069211, 0.5302821 ,\n",
" 0.50000696, 0.48753868, 0.52151072, 0.48915714, 0.51292164],\n",
" [0.53229943, 0.52167522, 0.45915308, 0.5293949 , 0.47742068,\n",
" 0.48900111, 0.48465034, 0.47729889, 0.5059115 , 0.50237199]])</pre></div></div></li><li class='xr-section-item'><input id='section-879f3941-9725-4ac0-9687-71059b7110b7' class='xr-section-summary-in' type='checkbox' checked><label for='section-879f3941-9725-4ac0-9687-71059b7110b7' class='xr-section-summary' >Coordinates: <span>(2)</span></label><div class='xr-section-inline-details'></div><div class='xr-section-details'><ul class='xr-var-list'><li class='xr-var-item'><div class='xr-var-name'><span class='xr-has-index'>time</span></div><div class='xr-var-dims'>(time)</div><div class='xr-var-dtype'>int64</div><div class='xr-var-preview xr-preview'>0 1</div><input id='attrs-e960390c-489e-4a09-add3-4aea5f8b93a9' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-e960390c-489e-4a09-add3-4aea5f8b93a9' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-c552075e-15c9-440a-b3b2-9ea25112fa6d' class='xr-var-data-in' type='checkbox'><label for='data-c552075e-15c9-440a-b3b2-9ea25112fa6d' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><pre>array([0, 1])</pre></div></li><li class='xr-var-item'><div class='xr-var-name'><span class='xr-has-index'>distance_bins</span></div><div class='xr-var-dims'>(distance_bins)</div><div class='xr-var-dtype'>object</div><div class='xr-var-preview xr-preview'>(-0.0693, 6.93] ... (62.367, 69....</div><input id='attrs-393b3da5-fccf-47df-a8f3-5ca6c71d2413' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-393b3da5-fccf-47df-a8f3-5ca6c71d2413' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-41f2f687-1deb-4da3-976f-2c8bd1d80e2e' class='xr-var-data-in' type='checkbox'><label for='data-41f2f687-1deb-4da3-976f-2c8bd1d80e2e' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><pre>array([Interval(-0.0693, 6.93, closed=&#x27;right&#x27;),\n",
" Interval(6.93, 13.859, closed=&#x27;right&#x27;),\n",
" Interval(13.859, 20.789, closed=&#x27;right&#x27;),\n",
" Interval(20.789, 27.719, closed=&#x27;right&#x27;),\n",
" Interval(27.719, 34.648, closed=&#x27;right&#x27;),\n",
" Interval(34.648, 41.578, closed=&#x27;right&#x27;),\n",
" Interval(41.578, 48.508, closed=&#x27;right&#x27;),\n",
" Interval(48.508, 55.437, closed=&#x27;right&#x27;),\n",
" Interval(55.437, 62.367, closed=&#x27;right&#x27;),\n",
" Interval(62.367, 69.296, closed=&#x27;right&#x27;)], dtype=object)</pre></div></li></ul></div></li><li class='xr-section-item'><input id='section-b8935a87-0ab2-458c-866d-f20825843947' class='xr-section-summary-in' type='checkbox' disabled ><label for='section-b8935a87-0ab2-458c-866d-f20825843947' class='xr-section-summary' title='Expand/collapse section'>Attributes: <span>(0)</span></label><div class='xr-section-inline-details'></div><div class='xr-section-details'><dl class='xr-attrs'></dl></div></li></ul></div></div>"
],
"text/plain": [
"<xarray.DataArray (time: 2, distance_bins: 10)>\n",
"array([[0.51498271, 0.46370372, 0.48996133, 0.51069211, 0.5302821 ,\n",
" 0.50000696, 0.48753868, 0.52151072, 0.48915714, 0.51292164],\n",
" [0.53229943, 0.52167522, 0.45915308, 0.5293949 , 0.47742068,\n",
" 0.48900111, 0.48465034, 0.47729889, 0.5059115 , 0.50237199]])\n",
"Coordinates:\n",
" * time (time) int64 0 1\n",
" * distance_bins (distance_bins) object (-0.0693, 6.93] ... (62.367, 69.296]"
]
},
"execution_count": 30,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"actual"
]
},
{
"cell_type": "markdown",
"metadata": {
"id": "FP84FGufIrJV"
},
"source": [
"# Speed tests"
]
},
{
"cell_type": "code",
"execution_count": 57,
"metadata": {
"id": "AoEU13x4IqzO"
},
"outputs": [],
"source": [
"signal, distance = make_test_data(t=20, x=1000, y=1000)\n",
"bins = 50"
]
},
{
"cell_type": "code",
"execution_count": 58,
"metadata": {},
"outputs": [
{
"data": {
"text/plain": [
"160.0"
]
},
"execution_count": 58,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"signal.nbytes / 1e6"
]
},
{
"cell_type": "markdown",
"metadata": {
"id": "OpDWpcNcJpG_"
},
"source": [
"## numpy speed test"
]
},
{
"cell_type": "code",
"execution_count": 60,
"metadata": {
"colab": {
"base_uri": "https://localhost:8080/"
},
"id": "ya0e9MVDE5NS",
"outputId": "21a7dbc0-0692-4e8f-98f9-f1e1dd1252b9"
},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"CPU times: user 8.52 s, sys: 674 ms, total: 9.19 s\n",
"Wall time: 10.3 s\n"
]
}
],
"source": [
"%time _ = signal.groupby_bins(distance, bins).mean()"
]
},
{
"cell_type": "code",
"execution_count": 61,
"metadata": {
"colab": {
"base_uri": "https://localhost:8080/"
},
"id": "-ywMYaSCGaYl",
"outputId": "e5e61066-6819-40b9-a061-74badb248001"
},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"CPU times: user 909 ms, sys: 290 ms, total: 1.2 s\n",
"Wall time: 1.3 s\n"
]
}
],
"source": [
"%time _ = groupby_bins_agg(signal, distance, bins, func='mean')"
]
},
{
"cell_type": "markdown",
"metadata": {
"id": "Fzrbi2JQJqjH"
},
"source": [
"## dask speed test"
]
},
{
"cell_type": "code",
"execution_count": 77,
"metadata": {
"colab": {
"base_uri": "https://localhost:8080/"
},
"id": "uJkGMSk_JCcU",
"outputId": "15989c46-55dc-45db-a24b-159fff0b3f12"
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"</table></div></div></li><li class='xr-section-item'><input id='section-627c500e-5b3c-4232-8161-42b550651a17' class='xr-section-summary-in' type='checkbox' checked><label for='section-627c500e-5b3c-4232-8161-42b550651a17' class='xr-section-summary' >Coordinates: <span>(3)</span></label><div class='xr-section-inline-details'></div><div class='xr-section-details'><ul class='xr-var-list'><li class='xr-var-item'><div class='xr-var-name'><span class='xr-has-index'>time</span></div><div class='xr-var-dims'>(time)</div><div class='xr-var-dtype'>int64</div><div class='xr-var-preview xr-preview'>0 1 2 3 4 5 6 ... 14 15 16 17 18 19</div><input id='attrs-ac8436a2-d7cf-4e86-99f3-797c12e0bfaf' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-ac8436a2-d7cf-4e86-99f3-797c12e0bfaf' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-e16c40d3-360d-4463-a955-4730ddbeabec' class='xr-var-data-in' type='checkbox'><label for='data-e16c40d3-360d-4463-a955-4730ddbeabec' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><pre>array([ 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17,\n",
" 18, 19])</pre></div></li><li class='xr-var-item'><div class='xr-var-name'><span class='xr-has-index'>y</span></div><div class='xr-var-dims'>(y)</div><div class='xr-var-dtype'>int64</div><div class='xr-var-preview xr-preview'>0 1 2 3 4 5 ... 995 996 997 998 999</div><input id='attrs-256049c9-f9a9-4eae-9d19-1435d60bd3a6' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-256049c9-f9a9-4eae-9d19-1435d60bd3a6' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-e2cdc7bb-16d2-4830-802f-e2ad6a0c952f' class='xr-var-data-in' type='checkbox'><label for='data-e2cdc7bb-16d2-4830-802f-e2ad6a0c952f' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><pre>array([ 0, 1, 2, ..., 997, 998, 999])</pre></div></li><li class='xr-var-item'><div class='xr-var-name'><span class='xr-has-index'>x</span></div><div class='xr-var-dims'>(x)</div><div class='xr-var-dtype'>int64</div><div class='xr-var-preview xr-preview'>0 1 2 3 4 5 ... 995 996 997 998 999</div><input id='attrs-dd3cb2c2-dce6-4901-985d-5bab68078a19' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-dd3cb2c2-dce6-4901-985d-5bab68078a19' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-6a638f93-8013-4ec4-8321-69a13104ac75' class='xr-var-data-in' type='checkbox'><label for='data-6a638f93-8013-4ec4-8321-69a13104ac75' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><pre>array([ 0, 1, 2, ..., 997, 998, 999])</pre></div></li></ul></div></li><li class='xr-section-item'><input id='section-9aa2aa82-f09d-43e5-add1-195302cf4199' class='xr-section-summary-in' type='checkbox' disabled ><label for='section-9aa2aa82-f09d-43e5-add1-195302cf4199' class='xr-section-summary' title='Expand/collapse section'>Attributes: <span>(0)</span></label><div class='xr-section-inline-details'></div><div class='xr-section-details'><dl class='xr-attrs'></dl></div></li></ul></div></div>"
],
"text/plain": [
"<xarray.DataArray 'signal' (time: 20, y: 1000, x: 1000)>\n",
"dask.array<xarray-<this-array>, shape=(20, 1000, 1000), dtype=float64, chunksize=(1, 1000, 1000), chunktype=numpy.ndarray>\n",
"Coordinates:\n",
" * time (time) int64 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19\n",
" * y (y) int64 0 1 2 3 4 5 6 7 8 ... 991 992 993 994 995 996 997 998 999\n",
" * x (x) int64 0 1 2 3 4 5 6 7 8 ... 991 992 993 994 995 996 997 998 999"
]
},
"execution_count": 77,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"import dask\n",
"dask_signal = signal.chunk({'time': 1})\n",
"dask.config.set(num_workers=4)\n",
"dask_signal"
]
},
{
"cell_type": "code",
"execution_count": 85,
"metadata": {
"colab": {
"base_uri": "https://localhost:8080/"
},
"id": "Ibm73W1IJXmE",
"outputId": "287be907-ec7d-4f77-de0e-c60043c1087f"
},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"CPU times: user 8.13 s, sys: 365 ms, total: 8.49 s\n",
"Wall time: 8.87 s\n",
"CPU times: user 1.12 s, sys: 332 ms, total: 1.45 s\n",
"Wall time: 967 ms\n"
]
},
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"</table></div></div></li><li class='xr-section-item'><input id='section-4f194f46-dcbd-417d-8460-d84ca5d56aba' class='xr-section-summary-in' type='checkbox' checked><label for='section-4f194f46-dcbd-417d-8460-d84ca5d56aba' class='xr-section-summary' >Coordinates: <span>(2)</span></label><div class='xr-section-inline-details'></div><div class='xr-section-details'><ul class='xr-var-list'><li class='xr-var-item'><div class='xr-var-name'><span class='xr-has-index'>distance_bins</span></div><div class='xr-var-dims'>(distance_bins)</div><div class='xr-var-dtype'>object</div><div class='xr-var-preview xr-preview'>(-1.413, 28.256] ... (1384.543, ...</div><input id='attrs-89079314-17db-44e9-9fba-3925692586c6' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-89079314-17db-44e9-9fba-3925692586c6' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-5008dc49-0da3-4365-a47c-d641c41b2618' class='xr-var-data-in' type='checkbox'><label for='data-5008dc49-0da3-4365-a47c-d641c41b2618' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><pre>array([Interval(-1.413, 28.256, closed=&#x27;right&#x27;),\n",
" Interval(28.256, 56.512, closed=&#x27;right&#x27;),\n",
" Interval(56.512, 84.768, closed=&#x27;right&#x27;),\n",
" Interval(84.768, 113.024, closed=&#x27;right&#x27;),\n",
" Interval(113.024, 141.28, closed=&#x27;right&#x27;),\n",
" Interval(141.28, 169.536, closed=&#x27;right&#x27;),\n",
" Interval(169.536, 197.792, closed=&#x27;right&#x27;),\n",
" Interval(197.792, 226.048, closed=&#x27;right&#x27;),\n",
" Interval(226.048, 254.304, closed=&#x27;right&#x27;),\n",
" Interval(254.304, 282.56, closed=&#x27;right&#x27;),\n",
" Interval(282.56, 310.816, closed=&#x27;right&#x27;),\n",
" Interval(310.816, 339.072, closed=&#x27;right&#x27;),\n",
" Interval(339.072, 367.328, closed=&#x27;right&#x27;),\n",
" Interval(367.328, 395.584, closed=&#x27;right&#x27;),\n",
" Interval(395.584, 423.84, closed=&#x27;right&#x27;),\n",
" Interval(423.84, 452.096, closed=&#x27;right&#x27;),\n",
" Interval(452.096, 480.352, closed=&#x27;right&#x27;),\n",
" Interval(480.352, 508.608, closed=&#x27;right&#x27;),\n",
" Interval(508.608, 536.864, closed=&#x27;right&#x27;),\n",
" Interval(536.864, 565.12, closed=&#x27;right&#x27;),\n",
" Interval(565.12, 593.376, closed=&#x27;right&#x27;),\n",
" Interval(593.376, 621.632, closed=&#x27;right&#x27;),\n",
" Interval(621.632, 649.888, closed=&#x27;right&#x27;),\n",
" Interval(649.888, 678.144, closed=&#x27;right&#x27;),\n",
" Interval(678.144, 706.4, closed=&#x27;right&#x27;),\n",
" Interval(706.4, 734.656, closed=&#x27;right&#x27;),\n",
" Interval(734.656, 762.912, closed=&#x27;right&#x27;),\n",
" Interval(762.912, 791.168, closed=&#x27;right&#x27;),\n",
" Interval(791.168, 819.424, closed=&#x27;right&#x27;),\n",
" Interval(819.424, 847.68, closed=&#x27;right&#x27;),\n",
" Interval(847.68, 875.936, closed=&#x27;right&#x27;),\n",
" Interval(875.936, 904.192, closed=&#x27;right&#x27;),\n",
" Interval(904.192, 932.448, closed=&#x27;right&#x27;),\n",
" Interval(932.448, 960.704, closed=&#x27;right&#x27;),\n",
" Interval(960.704, 988.96, closed=&#x27;right&#x27;),\n",
" Interval(988.96, 1017.216, closed=&#x27;right&#x27;),\n",
" Interval(1017.216, 1045.472, closed=&#x27;right&#x27;),\n",
" Interval(1045.472, 1073.728, closed=&#x27;right&#x27;),\n",
" Interval(1073.728, 1101.983, closed=&#x27;right&#x27;),\n",
" Interval(1101.983, 1130.239, closed=&#x27;right&#x27;),\n",
" Interval(1130.239, 1158.495, closed=&#x27;right&#x27;),\n",
" Interval(1158.495, 1186.751, closed=&#x27;right&#x27;),\n",
" Interval(1186.751, 1215.007, closed=&#x27;right&#x27;),\n",
" Interval(1215.007, 1243.263, closed=&#x27;right&#x27;),\n",
" Interval(1243.263, 1271.519, closed=&#x27;right&#x27;),\n",
" Interval(1271.519, 1299.775, closed=&#x27;right&#x27;),\n",
" Interval(1299.775, 1328.031, closed=&#x27;right&#x27;),\n",
" Interval(1328.031, 1356.287, closed=&#x27;right&#x27;),\n",
" Interval(1356.287, 1384.543, closed=&#x27;right&#x27;),\n",
" Interval(1384.543, 1412.799, closed=&#x27;right&#x27;)], dtype=object)</pre></div></li><li class='xr-var-item'><div class='xr-var-name'><span class='xr-has-index'>time</span></div><div class='xr-var-dims'>(time)</div><div class='xr-var-dtype'>int64</div><div class='xr-var-preview xr-preview'>0 1 2 3 4 5 6 ... 14 15 16 17 18 19</div><input id='attrs-f5700706-8819-49df-ba82-43cd59e69d36' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-f5700706-8819-49df-ba82-43cd59e69d36' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-e1236edf-43bf-4826-9b43-cedc7132ca97' class='xr-var-data-in' type='checkbox'><label for='data-e1236edf-43bf-4826-9b43-cedc7132ca97' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><pre>array([ 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17,\n",
" 18, 19])</pre></div></li></ul></div></li><li class='xr-section-item'><input id='section-779a570f-a899-4bdc-9db5-fed8c6a3a035' class='xr-section-summary-in' type='checkbox' disabled ><label for='section-779a570f-a899-4bdc-9db5-fed8c6a3a035' class='xr-section-summary' title='Expand/collapse section'>Attributes: <span>(0)</span></label><div class='xr-section-inline-details'></div><div class='xr-section-details'><dl class='xr-attrs'></dl></div></li></ul></div></div>"
],
"text/plain": [
"<xarray.DataArray 'signal' (time: 20, distance_bins: 50)>\n",
"dask.array<transpose, shape=(20, 50), dtype=float64, chunksize=(1, 1), chunktype=numpy.ndarray>\n",
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},
"execution_count": 85,
"metadata": {},
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],
"source": [
"%time result = dask_signal.groupby_bins(distance, bins).mean()\n",
"%time result.compute()\n",
"result"
]
},
{
"cell_type": "code",
"execution_count": 84,
"metadata": {
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"id": "kEOl2RPNJU0v",
"outputId": "0118c6ac-5d56-4f2e-b9f7-8dd8db7d1b32"
},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"CPU times: user 54.8 ms, sys: 7.46 ms, total: 62.2 ms\n",
"Wall time: 61.3 ms\n",
"CPU times: user 884 ms, sys: 191 ms, total: 1.08 s\n",
"Wall time: 484 ms\n"
]
},
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" font-weight: 500;\n",
"}\n",
"\n",
".xr-section-summary > span {\n",
" display: inline-block;\n",
" padding-left: 0.5em;\n",
"}\n",
"\n",
".xr-section-summary-in:disabled + label {\n",
" color: var(--xr-font-color2);\n",
"}\n",
"\n",
".xr-section-summary-in + label:before {\n",
" display: inline-block;\n",
" content: '►';\n",
" font-size: 11px;\n",
" width: 15px;\n",
" text-align: center;\n",
"}\n",
"\n",
".xr-section-summary-in:disabled + label:before {\n",
" color: var(--xr-disabled-color);\n",
"}\n",
"\n",
".xr-section-summary-in:checked + label:before {\n",
" content: '▼';\n",
"}\n",
"\n",
".xr-section-summary-in:checked + label > span {\n",
" display: none;\n",
"}\n",
"\n",
".xr-section-summary,\n",
".xr-section-inline-details {\n",
" padding-top: 4px;\n",
" padding-bottom: 4px;\n",
"}\n",
"\n",
".xr-section-inline-details {\n",
" grid-column: 2 / -1;\n",
"}\n",
"\n",
".xr-section-details {\n",
" display: none;\n",
" grid-column: 1 / -1;\n",
" margin-bottom: 5px;\n",
"}\n",
"\n",
".xr-section-summary-in:checked ~ .xr-section-details {\n",
" display: contents;\n",
"}\n",
"\n",
".xr-array-wrap {\n",
" grid-column: 1 / -1;\n",
" display: grid;\n",
" grid-template-columns: 20px auto;\n",
"}\n",
"\n",
".xr-array-wrap > label {\n",
" grid-column: 1;\n",
" vertical-align: top;\n",
"}\n",
"\n",
".xr-preview {\n",
" color: var(--xr-font-color3);\n",
"}\n",
"\n",
".xr-array-preview,\n",
".xr-array-data {\n",
" padding: 0 5px !important;\n",
" grid-column: 2;\n",
"}\n",
"\n",
".xr-array-data,\n",
".xr-array-in:checked ~ .xr-array-preview {\n",
" display: none;\n",
"}\n",
"\n",
".xr-array-in:checked ~ .xr-array-data,\n",
".xr-array-preview {\n",
" display: inline-block;\n",
"}\n",
"\n",
".xr-dim-list {\n",
" display: inline-block !important;\n",
" list-style: none;\n",
" padding: 0 !important;\n",
" margin: 0;\n",
"}\n",
"\n",
".xr-dim-list li {\n",
" display: inline-block;\n",
" padding: 0;\n",
" margin: 0;\n",
"}\n",
"\n",
".xr-dim-list:before {\n",
" content: '(';\n",
"}\n",
"\n",
".xr-dim-list:after {\n",
" content: ')';\n",
"}\n",
"\n",
".xr-dim-list li:not(:last-child):after {\n",
" content: ',';\n",
" padding-right: 5px;\n",
"}\n",
"\n",
".xr-has-index {\n",
" font-weight: bold;\n",
"}\n",
"\n",
".xr-var-list,\n",
".xr-var-item {\n",
" display: contents;\n",
"}\n",
"\n",
".xr-var-item > div,\n",
".xr-var-item label,\n",
".xr-var-item > .xr-var-name span {\n",
" background-color: var(--xr-background-color-row-even);\n",
" margin-bottom: 0;\n",
"}\n",
"\n",
".xr-var-item > .xr-var-name:hover span {\n",
" padding-right: 5px;\n",
"}\n",
"\n",
".xr-var-list > li:nth-child(odd) > div,\n",
".xr-var-list > li:nth-child(odd) > label,\n",
".xr-var-list > li:nth-child(odd) > .xr-var-name span {\n",
" background-color: var(--xr-background-color-row-odd);\n",
"}\n",
"\n",
".xr-var-name {\n",
" grid-column: 1;\n",
"}\n",
"\n",
".xr-var-dims {\n",
" grid-column: 2;\n",
"}\n",
"\n",
".xr-var-dtype {\n",
" grid-column: 3;\n",
" text-align: right;\n",
" color: var(--xr-font-color2);\n",
"}\n",
"\n",
".xr-var-preview {\n",
" grid-column: 4;\n",
"}\n",
"\n",
".xr-var-name,\n",
".xr-var-dims,\n",
".xr-var-dtype,\n",
".xr-preview,\n",
".xr-attrs dt {\n",
" white-space: nowrap;\n",
" overflow: hidden;\n",
" text-overflow: ellipsis;\n",
" padding-right: 10px;\n",
"}\n",
"\n",
".xr-var-name:hover,\n",
".xr-var-dims:hover,\n",
".xr-var-dtype:hover,\n",
".xr-attrs dt:hover {\n",
" overflow: visible;\n",
" width: auto;\n",
" z-index: 1;\n",
"}\n",
"\n",
".xr-var-attrs,\n",
".xr-var-data {\n",
" display: none;\n",
" background-color: var(--xr-background-color) !important;\n",
" padding-bottom: 5px !important;\n",
"}\n",
"\n",
".xr-var-attrs-in:checked ~ .xr-var-attrs,\n",
".xr-var-data-in:checked ~ .xr-var-data {\n",
" display: block;\n",
"}\n",
"\n",
".xr-var-data > table {\n",
" float: right;\n",
"}\n",
"\n",
".xr-var-name span,\n",
".xr-var-data,\n",
".xr-attrs {\n",
" padding-left: 25px !important;\n",
"}\n",
"\n",
".xr-attrs,\n",
".xr-var-attrs,\n",
".xr-var-data {\n",
" grid-column: 1 / -1;\n",
"}\n",
"\n",
"dl.xr-attrs {\n",
" padding: 0;\n",
" margin: 0;\n",
" display: grid;\n",
" grid-template-columns: 125px auto;\n",
"}\n",
"\n",
".xr-attrs dt, dd {\n",
" padding: 0;\n",
" margin: 0;\n",
" float: left;\n",
" padding-right: 10px;\n",
" width: auto;\n",
"}\n",
"\n",
".xr-attrs dt {\n",
" font-weight: normal;\n",
" grid-column: 1;\n",
"}\n",
"\n",
".xr-attrs dt:hover span {\n",
" display: inline-block;\n",
" background: var(--xr-background-color);\n",
" padding-right: 10px;\n",
"}\n",
"\n",
".xr-attrs dd {\n",
" grid-column: 2;\n",
" white-space: pre-wrap;\n",
" word-break: break-all;\n",
"}\n",
"\n",
".xr-icon-database,\n",
".xr-icon-file-text2 {\n",
" display: inline-block;\n",
" vertical-align: middle;\n",
" width: 1em;\n",
" height: 1.5em !important;\n",
" stroke-width: 0;\n",
" stroke: currentColor;\n",
" fill: currentColor;\n",
"}\n",
"</style><pre class='xr-text-repr-fallback'>&lt;xarray.DataArray (time: 20, distance_bins: 50)&gt;\n",
"dask.array&lt;transpose, shape=(20, 50), dtype=float64, chunksize=(1, 50), chunktype=numpy.ndarray&gt;\n",
"Coordinates:\n",
" * time (time) int64 0 1 2 3 4 5 6 7 8 ... 11 12 13 14 15 16 17 18 19\n",
" * distance_bins (distance_bins) object (-1.413, 28.256] ... (1384.543, 141...</pre><div class='xr-wrap' hidden><div class='xr-header'><div class='xr-obj-type'>xarray.DataArray</div><div class='xr-array-name'></div><ul class='xr-dim-list'><li><span class='xr-has-index'>time</span>: 20</li><li><span class='xr-has-index'>distance_bins</span>: 50</li></ul></div><ul class='xr-sections'><li class='xr-section-item'><div class='xr-array-wrap'><input id='section-1e790e1d-acbf-46f3-aeac-238622f87f8b' class='xr-array-in' type='checkbox' checked><label for='section-1e790e1d-acbf-46f3-aeac-238622f87f8b' title='Show/hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-array-preview xr-preview'><span>dask.array&lt;chunksize=(1, 50), meta=np.ndarray&gt;</span></div><div class='xr-array-data'><table>\n",
"<tr>\n",
"<td>\n",
"<table>\n",
" <thead>\n",
" <tr><td> </td><th> Array </th><th> Chunk </th></tr>\n",
" </thead>\n",
" <tbody>\n",
" <tr><th> Bytes </th><td> 8.00 kB </td> <td> 400 B </td></tr>\n",
" <tr><th> Shape </th><td> (20, 50) </td> <td> (1, 50) </td></tr>\n",
" <tr><th> Count </th><td> 101 Tasks </td><td> 20 Chunks </td></tr>\n",
" <tr><th> Type </th><td> float64 </td><td> numpy.ndarray </td></tr>\n",
" </tbody>\n",
"</table>\n",
"</td>\n",
"<td>\n",
"<svg width=\"170\" height=\"98\" style=\"stroke:rgb(0,0,0);stroke-width:1\" >\n",
"\n",
" <!-- Horizontal lines -->\n",
" <line x1=\"0\" y1=\"0\" x2=\"120\" y2=\"0\" style=\"stroke-width:2\" />\n",
" <line x1=\"0\" y1=\"2\" x2=\"120\" y2=\"2\" />\n",
" <line x1=\"0\" y1=\"4\" x2=\"120\" y2=\"4\" />\n",
" <line x1=\"0\" y1=\"7\" x2=\"120\" y2=\"7\" />\n",
" <line x1=\"0\" y1=\"9\" x2=\"120\" y2=\"9\" />\n",
" <line x1=\"0\" y1=\"12\" x2=\"120\" y2=\"12\" />\n",
" <line x1=\"0\" y1=\"14\" x2=\"120\" y2=\"14\" />\n",
" <line x1=\"0\" y1=\"16\" x2=\"120\" y2=\"16\" />\n",
" <line x1=\"0\" y1=\"19\" x2=\"120\" y2=\"19\" />\n",
" <line x1=\"0\" y1=\"21\" x2=\"120\" y2=\"21\" />\n",
" <line x1=\"0\" y1=\"24\" x2=\"120\" y2=\"24\" />\n",
" <line x1=\"0\" y1=\"26\" x2=\"120\" y2=\"26\" />\n",
" <line x1=\"0\" y1=\"28\" x2=\"120\" y2=\"28\" />\n",
" <line x1=\"0\" y1=\"31\" x2=\"120\" y2=\"31\" />\n",
" <line x1=\"0\" y1=\"33\" x2=\"120\" y2=\"33\" />\n",
" <line x1=\"0\" y1=\"36\" x2=\"120\" y2=\"36\" />\n",
" <line x1=\"0\" y1=\"38\" x2=\"120\" y2=\"38\" />\n",
" <line x1=\"0\" y1=\"40\" x2=\"120\" y2=\"40\" />\n",
" <line x1=\"0\" y1=\"43\" x2=\"120\" y2=\"43\" />\n",
" <line x1=\"0\" y1=\"45\" x2=\"120\" y2=\"45\" />\n",
" <line x1=\"0\" y1=\"48\" x2=\"120\" y2=\"48\" style=\"stroke-width:2\" />\n",
"\n",
" <!-- Vertical lines -->\n",
" <line x1=\"0\" y1=\"0\" x2=\"0\" y2=\"48\" style=\"stroke-width:2\" />\n",
" <line x1=\"120\" y1=\"0\" x2=\"120\" y2=\"48\" style=\"stroke-width:2\" />\n",
"\n",
" <!-- Colored Rectangle -->\n",
" <polygon points=\"0.000000,0.000000 120.000000,0.000000 120.000000,48.000000 0.000000,48.000000\" style=\"fill:#ECB172A0;stroke-width:0\"/>\n",
"\n",
" <!-- Text -->\n",
" <text x=\"60.000000\" y=\"68.000000\" font-size=\"1.0rem\" font-weight=\"100\" text-anchor=\"middle\" >50</text>\n",
" <text x=\"140.000000\" y=\"24.000000\" font-size=\"1.0rem\" font-weight=\"100\" text-anchor=\"middle\" transform=\"rotate(0,140.000000,24.000000)\">20</text>\n",
"</svg>\n",
"</td>\n",
"</tr>\n",
"</table></div></div></li><li class='xr-section-item'><input id='section-d321cc8c-1320-4d2f-b234-dce2d86a5521' class='xr-section-summary-in' type='checkbox' checked><label for='section-d321cc8c-1320-4d2f-b234-dce2d86a5521' class='xr-section-summary' >Coordinates: <span>(2)</span></label><div class='xr-section-inline-details'></div><div class='xr-section-details'><ul class='xr-var-list'><li class='xr-var-item'><div class='xr-var-name'><span class='xr-has-index'>time</span></div><div class='xr-var-dims'>(time)</div><div class='xr-var-dtype'>int64</div><div class='xr-var-preview xr-preview'>0 1 2 3 4 5 6 ... 14 15 16 17 18 19</div><input id='attrs-d97d391e-3907-4b1e-af0b-d70a79711805' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-d97d391e-3907-4b1e-af0b-d70a79711805' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-1b6ce3ef-322c-48b4-b8f3-5c6c57a86de3' class='xr-var-data-in' type='checkbox'><label for='data-1b6ce3ef-322c-48b4-b8f3-5c6c57a86de3' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><pre>array([ 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17,\n",
" 18, 19])</pre></div></li><li class='xr-var-item'><div class='xr-var-name'><span class='xr-has-index'>distance_bins</span></div><div class='xr-var-dims'>(distance_bins)</div><div class='xr-var-dtype'>object</div><div class='xr-var-preview xr-preview'>(-1.413, 28.256] ... (1384.543, ...</div><input id='attrs-5d273765-7f72-406a-8a0e-96278680356f' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-5d273765-7f72-406a-8a0e-96278680356f' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-aaa28834-3905-44ac-88e8-49dce15eeb0b' class='xr-var-data-in' type='checkbox'><label for='data-aaa28834-3905-44ac-88e8-49dce15eeb0b' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><pre>array([Interval(-1.413, 28.256, closed=&#x27;right&#x27;),\n",
" Interval(28.256, 56.512, closed=&#x27;right&#x27;),\n",
" Interval(56.512, 84.768, closed=&#x27;right&#x27;),\n",
" Interval(84.768, 113.024, closed=&#x27;right&#x27;),\n",
" Interval(113.024, 141.28, closed=&#x27;right&#x27;),\n",
" Interval(141.28, 169.536, closed=&#x27;right&#x27;),\n",
" Interval(169.536, 197.792, closed=&#x27;right&#x27;),\n",
" Interval(197.792, 226.048, closed=&#x27;right&#x27;),\n",
" Interval(226.048, 254.304, closed=&#x27;right&#x27;),\n",
" Interval(254.304, 282.56, closed=&#x27;right&#x27;),\n",
" Interval(282.56, 310.816, closed=&#x27;right&#x27;),\n",
" Interval(310.816, 339.072, closed=&#x27;right&#x27;),\n",
" Interval(339.072, 367.328, closed=&#x27;right&#x27;),\n",
" Interval(367.328, 395.584, closed=&#x27;right&#x27;),\n",
" Interval(395.584, 423.84, closed=&#x27;right&#x27;),\n",
" Interval(423.84, 452.096, closed=&#x27;right&#x27;),\n",
" Interval(452.096, 480.352, closed=&#x27;right&#x27;),\n",
" Interval(480.352, 508.608, closed=&#x27;right&#x27;),\n",
" Interval(508.608, 536.864, closed=&#x27;right&#x27;),\n",
" Interval(536.864, 565.12, closed=&#x27;right&#x27;),\n",
" Interval(565.12, 593.376, closed=&#x27;right&#x27;),\n",
" Interval(593.376, 621.632, closed=&#x27;right&#x27;),\n",
" Interval(621.632, 649.888, closed=&#x27;right&#x27;),\n",
" Interval(649.888, 678.144, closed=&#x27;right&#x27;),\n",
" Interval(678.144, 706.4, closed=&#x27;right&#x27;),\n",
" Interval(706.4, 734.656, closed=&#x27;right&#x27;),\n",
" Interval(734.656, 762.912, closed=&#x27;right&#x27;),\n",
" Interval(762.912, 791.168, closed=&#x27;right&#x27;),\n",
" Interval(791.168, 819.424, closed=&#x27;right&#x27;),\n",
" Interval(819.424, 847.68, closed=&#x27;right&#x27;),\n",
" Interval(847.68, 875.936, closed=&#x27;right&#x27;),\n",
" Interval(875.936, 904.192, closed=&#x27;right&#x27;),\n",
" Interval(904.192, 932.448, closed=&#x27;right&#x27;),\n",
" Interval(932.448, 960.704, closed=&#x27;right&#x27;),\n",
" Interval(960.704, 988.96, closed=&#x27;right&#x27;),\n",
" Interval(988.96, 1017.216, closed=&#x27;right&#x27;),\n",
" Interval(1017.216, 1045.472, closed=&#x27;right&#x27;),\n",
" Interval(1045.472, 1073.728, closed=&#x27;right&#x27;),\n",
" Interval(1073.728, 1101.983, closed=&#x27;right&#x27;),\n",
" Interval(1101.983, 1130.239, closed=&#x27;right&#x27;),\n",
" Interval(1130.239, 1158.495, closed=&#x27;right&#x27;),\n",
" Interval(1158.495, 1186.751, closed=&#x27;right&#x27;),\n",
" Interval(1186.751, 1215.007, closed=&#x27;right&#x27;),\n",
" Interval(1215.007, 1243.263, closed=&#x27;right&#x27;),\n",
" Interval(1243.263, 1271.519, closed=&#x27;right&#x27;),\n",
" Interval(1271.519, 1299.775, closed=&#x27;right&#x27;),\n",
" Interval(1299.775, 1328.031, closed=&#x27;right&#x27;),\n",
" Interval(1328.031, 1356.287, closed=&#x27;right&#x27;),\n",
" Interval(1356.287, 1384.543, closed=&#x27;right&#x27;),\n",
" Interval(1384.543, 1412.799, closed=&#x27;right&#x27;)], dtype=object)</pre></div></li></ul></div></li><li class='xr-section-item'><input id='section-0dc53b43-5ad6-4f91-8a43-d2a552de949b' class='xr-section-summary-in' type='checkbox' disabled ><label for='section-0dc53b43-5ad6-4f91-8a43-d2a552de949b' class='xr-section-summary' title='Expand/collapse section'>Attributes: <span>(0)</span></label><div class='xr-section-inline-details'></div><div class='xr-section-details'><dl class='xr-attrs'></dl></div></li></ul></div></div>"
],
"text/plain": [
"<xarray.DataArray (time: 20, distance_bins: 50)>\n",
"dask.array<transpose, shape=(20, 50), dtype=float64, chunksize=(1, 50), chunktype=numpy.ndarray>\n",
"Coordinates:\n",
" * time (time) int64 0 1 2 3 4 5 6 7 8 ... 11 12 13 14 15 16 17 18 19\n",
" * distance_bins (distance_bins) object (-1.413, 28.256] ... (1384.543, 141..."
]
},
"execution_count": 84,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"%time result = groupby_bins_agg(dask_signal, distance, bins, func='mean')\n",
"%time result.compute()\n",
"result"
]
}
],
"metadata": {
"colab": {
"collapsed_sections": [],
"name": "fast groupby agg.ipynb",
"provenance": []
},
"kernelspec": {
"display_name": "Python 3",
"language": "python",
"name": "python3"
},
"language_info": {
"codemirror_mode": {
"name": "ipython",
"version": 3
},
"file_extension": ".py",
"mimetype": "text/x-python",
"name": "python",
"nbconvert_exporter": "python",
"pygments_lexer": "ipython3",
"version": "3.8.5"
}
},
"nbformat": 4,
"nbformat_minor": 1
}
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