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Feature/refactor streaming #371

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merged 14 commits into from
May 15, 2024
Merged

Feature/refactor streaming #371

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d23212a
Refactor stream handling
sandorkertesz Apr 22, 2024
c0d0a09
Refactor stream handling
sandorkertesz Apr 22, 2024
f49ea19
Refactor stream handling
sandorkertesz Apr 22, 2024
2f098e7
Refactor stream handling
sandorkertesz Apr 22, 2024
47b5714
Refactor stream handling
sandorkertesz Apr 22, 2024
6c2199a
Refactor stream handling
sandorkertesz Apr 24, 2024
313d506
Refactor stream handling
sandorkertesz Apr 24, 2024
b3d95b8
Refactor stream handling
sandorkertesz Apr 25, 2024
89f227a
Refactor stream handling
sandorkertesz Apr 27, 2024
0b00d8b
Refactor stream handling
sandorkertesz May 1, 2024
4d2401e
Merge from develop
sandorkertesz May 9, 2024
a3d3f84
Merge branch 'develop' into feature/refactor-streaming
sandorkertesz May 9, 2024
da2c30e
Merge branch 'develop' into feature/refactor-streaming
sandorkertesz May 13, 2024
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Merge branch 'develop' into feature/refactor-streaming
sandorkertesz May 14, 2024
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214 changes: 85 additions & 129 deletions docs/examples/data_from_stream.ipynb
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218 changes: 75 additions & 143 deletions docs/examples/fdb.ipynb
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274 changes: 226 additions & 48 deletions docs/examples/url_stream.ipynb
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Original file line number Diff line number Diff line change
Expand Up @@ -43,7 +43,7 @@
"tags": []
},
"source": [
"earthkit-data can read GRIB data from a URL as a stream without writing anything to disk. This can be activated with the **stream=True** kwarg when calling :ref:`from_source() <data-sources-url>`."
"earthkit-data can read GRIB data from a URL as a stream without writing anything to disk. This can be activated with the ``stream=True`` kwarg when calling :ref:`from_source() <data-sources-url>`."
]
},
{
Expand All @@ -65,28 +65,45 @@
]
},
{
"cell_type": "code",
"execution_count": 6,
"id": "51964579-bf3f-4948-918d-fcd35581950e",
"cell_type": "markdown",
"id": "1661f2d1-2c30-4021-826f-1c2c5c565fd0",
"metadata": {},
"outputs": [],
"source": [
"for f in ds:\n",
" # f is GribField object. It gets deleted when going out of scope\n",
" print(f)"
"The resulting object only supports one iteration. Having finsihed the iteration the stream is consumed and no more data is available."
]
},
{
"cell_type": "markdown",
"id": "7f595ec8-008f-4198-8a3a-f8346fbfe09c",
"metadata": {},
"cell_type": "code",
"execution_count": 3,
"id": "51964579-bf3f-4948-918d-fcd35581950e",
"metadata": {
"editable": true,
"slideshow": {
"slide_type": ""
},
"tags": []
},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"GribField(t,500,20070101,1200,0,0)\n",
"GribField(z,500,20070101,1200,0,0)\n",
"GribField(t,850,20070101,1200,0,0)\n",
"GribField(z,850,20070101,1200,0,0)\n"
]
}
],
"source": [
"### Stream options"
"for f in ds:\n",
" # f is GribField object. It gets deleted when going out of scope\n",
" print(f)"
]
},
{
"cell_type": "raw",
"id": "328b1d7b-500d-4014-8346-b6d47c40ee86",
"id": "df31a770-f5e9-46c7-8d5f-c9f73c57483c",
"metadata": {
"editable": true,
"raw_mimetype": "text/restructuredtext",
Expand All @@ -96,13 +113,13 @@
"tags": []
},
"source": [
"To control how the stream is read use :ref:`batch_size <data-sources-url>` and :ref:`group_by <data-sources-url>`. E.g. the following code reads the GRIB data in messages of 2."
"The iteration can be done in batches by using :py:meth:`batched <data.sources.stream.StreamSource.batched>` or :py:meth:`group_by <data.sources.stream.StreamSource.group_by>`."
]
},
{
"cell_type": "code",
"execution_count": 4,
"id": "b7c9a685-6b38-4236-ae74-a14445e8bb95",
"id": "754dc030-da97-4076-88ba-f31fed2f091d",
"metadata": {
"editable": true,
"slideshow": {
Expand All @@ -115,25 +132,186 @@
"name": "stdout",
"output_type": "stream",
"text": [
"len=2\n",
" GribField(t,500,20070101,1200,0,0)\n",
" GribField(z,500,20070101,1200,0,0)\n",
"len=2\n",
" GribField(t,850,20070101,1200,0,0)\n",
" GribField(z,850,20070101,1200,0,0)\n"
"len=2 [('t', 500), ('z', 500)]\n",
"len=2 [('t', 850), ('z', 850)]\n"
]
}
],
"source": [
"ds = earthkit.data.from_source(\"url\", \n",
" \"https://get.ecmwf.int/repository/test-data/earthkit-data/examples/test4.grib\", \n",
" stream=True, batch_size=2)\n",
" stream=True)\n",
"\n",
"for f in ds:\n",
"for f in ds.batched(2):\n",
" # f is a fieldlist\n",
" print(f\"len={len(f)}\")\n",
" for g in f:\n",
" print(f\" {g}\")"
" print(f\"len={len(f)} {f.metadata(('param', 'level'))}\")"
]
},
{
"cell_type": "markdown",
"id": "9db87b26-20e2-4cb5-89a1-2643d97fcf13",
"metadata": {},
"source": [
"#### Reading the whole stream into memory"
]
},
{
"cell_type": "raw",
"id": "f8622372-d2c9-4261-86cc-db46531b0cd5",
"metadata": {
"editable": true,
"raw_mimetype": "text/restructuredtext",
"slideshow": {
"slide_type": ""
},
"tags": []
},
"source": [
"We can load the whole stream into memory by using ``read_all=True`` in :ref:`from_source() <data-sources-url>`. The resulting object will be a py:class:`FieldList` storing all the GRIB messages in memory."
]
},
{
"cell_type": "code",
"execution_count": 5,
"id": "359ceb8d-3c88-411d-af86-78c7cb403a08",
"metadata": {},
"outputs": [
{
"data": {
"text/plain": [
"4"
]
},
"execution_count": 5,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"ds = earthkit.data.from_source(\"url\", \n",
" \"https://get.ecmwf.int/repository/test-data/earthkit-data/examples/test4.grib\", \n",
" stream=True, read_all=True)\n",
"\n",
"len(ds)"
]
},
{
"cell_type": "code",
"execution_count": 6,
"id": "4608964a-3849-4c40-bcd3-086f54b2f67a",
"metadata": {},
"outputs": [
{
"data": {
"text/html": [
"<div>\n",
"<style scoped>\n",
" .dataframe tbody tr th:only-of-type {\n",
" vertical-align: middle;\n",
" }\n",
"\n",
" .dataframe tbody tr th {\n",
" vertical-align: top;\n",
" }\n",
"\n",
" .dataframe thead th {\n",
" text-align: right;\n",
" }\n",
"</style>\n",
"<table border=\"1\" class=\"dataframe\">\n",
" <thead>\n",
" <tr style=\"text-align: right;\">\n",
" <th></th>\n",
" <th>centre</th>\n",
" <th>shortName</th>\n",
" <th>typeOfLevel</th>\n",
" <th>level</th>\n",
" <th>dataDate</th>\n",
" <th>dataTime</th>\n",
" <th>stepRange</th>\n",
" <th>dataType</th>\n",
" <th>number</th>\n",
" <th>gridType</th>\n",
" </tr>\n",
" </thead>\n",
" <tbody>\n",
" <tr>\n",
" <th>0</th>\n",
" <td>ecmf</td>\n",
" <td>t</td>\n",
" <td>isobaricInhPa</td>\n",
" <td>500</td>\n",
" <td>20070101</td>\n",
" <td>1200</td>\n",
" <td>0</td>\n",
" <td>an</td>\n",
" <td>0</td>\n",
" <td>regular_ll</td>\n",
" </tr>\n",
" <tr>\n",
" <th>1</th>\n",
" <td>ecmf</td>\n",
" <td>z</td>\n",
" <td>isobaricInhPa</td>\n",
" <td>500</td>\n",
" <td>20070101</td>\n",
" <td>1200</td>\n",
" <td>0</td>\n",
" <td>an</td>\n",
" <td>0</td>\n",
" <td>regular_ll</td>\n",
" </tr>\n",
" <tr>\n",
" <th>2</th>\n",
" <td>ecmf</td>\n",
" <td>t</td>\n",
" <td>isobaricInhPa</td>\n",
" <td>850</td>\n",
" <td>20070101</td>\n",
" <td>1200</td>\n",
" <td>0</td>\n",
" <td>an</td>\n",
" <td>0</td>\n",
" <td>regular_ll</td>\n",
" </tr>\n",
" <tr>\n",
" <th>3</th>\n",
" <td>ecmf</td>\n",
" <td>z</td>\n",
" <td>isobaricInhPa</td>\n",
" <td>850</td>\n",
" <td>20070101</td>\n",
" <td>1200</td>\n",
" <td>0</td>\n",
" <td>an</td>\n",
" <td>0</td>\n",
" <td>regular_ll</td>\n",
" </tr>\n",
" </tbody>\n",
"</table>\n",
"</div>"
],
"text/plain": [
" centre shortName typeOfLevel level dataDate dataTime stepRange \\\n",
"0 ecmf t isobaricInhPa 500 20070101 1200 0 \n",
"1 ecmf z isobaricInhPa 500 20070101 1200 0 \n",
"2 ecmf t isobaricInhPa 850 20070101 1200 0 \n",
"3 ecmf z isobaricInhPa 850 20070101 1200 0 \n",
"\n",
" dataType number gridType \n",
"0 an 0 regular_ll \n",
"1 an 0 regular_ll \n",
"2 an 0 regular_ll \n",
"3 an 0 regular_ll "
]
},
"execution_count": 6,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"ds.ls()"
]
},
{
Expand Down Expand Up @@ -166,49 +344,49 @@
},
{
"cell_type": "code",
"execution_count": 5,
"execution_count": 7,
"id": "891af3e5-5aa5-451f-b7bb-a86eaf7c8ffe",
"metadata": {},
"metadata": {
"editable": true,
"slideshow": {
"slide_type": ""
},
"tags": []
},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"len=3\n",
" GribField(t,500,20070101,1200,0,0)\n",
" GribField(z,500,20070101,1200,0,0)\n",
" GribField(t,850,20070101,1200,0,0)\n",
"len=3\n",
" GribField(z,850,20070101,1200,0,0)\n",
" GribField(t,1000,20180801,1200,0,0)\n",
" GribField(u,1000,20180801,1200,0,0)\n",
"len=3\n",
" GribField(v,1000,20180801,1200,0,0)\n",
" GribField(t,850,20180801,1200,0,0)\n",
" GribField(u,850,20180801,1200,0,0)\n",
"len=1\n",
" GribField(v,850,20180801,1200,0,0)\n"
"len=3 [('t', 500), ('z', 500), ('t', 850)]\n",
"len=3 [('z', 850), ('t', 1000), ('u', 1000)]\n",
"len=3 [('v', 1000), ('t', 850), ('u', 850)]\n",
"len=1 [('v', 850)]\n"
]
}
],
"source": [
"ds = earthkit.data.from_source(\"url\", \n",
" [\"https://get.ecmwf.int/repository/test-data/earthkit-data/examples/test4.grib\", \n",
" \"https://get.ecmwf.int/repository/test-data/earthkit-data/examples/test6.grib\"], \n",
" stream=True, batch_size=3)\n",
" stream=True)\n",
"\n",
"for f in ds:\n",
"for f in ds.batched(3):\n",
" # f is a fieldlist\n",
" print(f\"len={len(f)}\")\n",
" for g in f:\n",
" print(f\" {g}\")"
" print(f\"len={len(f)} {f.metadata(('param', 'level'))}\")"
]
},
{
"cell_type": "code",
"execution_count": null,
"id": "d287fb70-66fb-4b2f-8c07-a3cca7c3035d",
"metadata": {},
"metadata": {
"editable": true,
"slideshow": {
"slide_type": ""
},
"tags": []
},
"outputs": [],
"source": []
}
Expand Down
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