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darkblue-b/pystac_landsat.ipynb

Created August 19, 2020 04:46
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pystac_landsat.ipynb
{
"cells": [
{
"cell_type": "markdown",
"metadata": {},
"source": [
"# Write STAC item for landsat8\n",
"\n",
"Goal: create a simple and valid STAC 1.0.0-beta2 catalog with PySTAC using this collection1 landsat8 scene:\n",
"\n",
"https://landsat-pds.s3.amazonaws.com/c1/L8/139/045/LC08_L1TP_139045_20170304_20170316_01_T1/index.html\n",
"\n",
"related issue: \n",
"* https://github.com/radiantearth/stac-spec/issues/821#issuecomment-675640491\n",
"\n",
"--\n",
"Scott Henderson @scottyhq \n",
"\n",
"update: test execution on osgeolive ubuntu linux pre-alpha python3 ENV\n",
"\n",
"--\n",
"Brian Hamlin @darkblue-b"
]
},
{
"cell_type": "code",
"execution_count": 1,
"metadata": {},
"outputs": [],
"source": [
"import pystac\n",
"from datetime import datetime\n",
"\n",
"# ~/.local/lib/python3.8/site-packages/pystac-0.5.0-py3.8.egg/pystac"
]
},
{
"cell_type": "code",
"execution_count": 6,
"metadata": {},
"outputs": [],
"source": [
"# utilities for converting metadata based on https://github.com/sat-utils/sat-stac-landsat\n",
"# modify functions here to extract other metadata fields of interest\n",
"import landsat2stac\n",
"\n",
"# landsat2stac module 'landsat2stac' ~/Jupyter/landsat2stac.py"
]
},
{
"cell_type": "code",
"execution_count": 2,
"metadata": {},
"outputs": [
{
"data": {
"text/plain": [
"<Catalog id=landsat-8-l1>"
]
},
"execution_count": 2,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"# initialize new catalog\n",
"catalog = pystac.Catalog(id='landsat-8-l1', description='Landsat8 collection 1 test')\n",
"catalog"
]
},
{
"cell_type": "code",
"execution_count": 3,
"metadata": {},
"outputs": [
{
"data": {
"text/plain": [
"['https://schemas.stacspec.org/v1.0.0-beta.2/collection-spec/json-schema/collection.json']"
]
},
"execution_count": 3,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"# intialize collection by reading an existing one\n",
"# https://raw.githubusercontent.com/radiantearth/stac-spec/master/collection-spec/examples/landsat-collection.json \n",
"collection = pystac.read_file('https://raw.githubusercontent.com/radiantearth/stac-spec/master/collection-spec/examples/landsat-collection.json')\n",
"collection = collection.clear_links() # don't want references to original catalog\n",
"collection.validate() #returns list of validated links or raises and Error"
]
},
{
"cell_type": "code",
"execution_count": 4,
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"* <Catalog id=landsat-8-l1>\n",
" * <Collection id=landsat-8-l1>\n"
]
}
],
"source": [
"catalog.add_child(collection)\n",
"catalog.describe()"
]
},
{
"cell_type": "code",
"execution_count": 5,
"metadata": {},
"outputs": [],
"source": [
"path = '139'\n",
"row = '045'\n",
"sceneid = 'LC08_L1TP_139045_20170304_20170316_01_T1'\n",
"uri = f'https://landsat-pds.s3.amazonaws.com/c1/L8/{path}/{row}/{sceneid}/index.html'"
]
},
{
"cell_type": "code",
"execution_count": 7,
"metadata": {},
"outputs": [
{
"data": {
"text/plain": [
"{'datetime': datetime.datetime(2017, 3, 4, 4, 37, 24, 686481, tzinfo=tzutc()),\n",
" 'id': 'LC81390452017063',\n",
" 'bbox': [85.85297, 20.61004, 88.07596, 22.71616],\n",
" 'geometry': {'type': 'Polygon',\n",
" 'coordinates': [[[86.2641643592018, 22.715246854557392],\n",
" [88.07387967449421, 22.348429110426327],\n",
" [87.6622309768518, 20.612923718963454],\n",
" [85.8539884267533, 20.98565698421308],\n",
" [86.2641643592018, 22.715246854557392]]]},\n",
" 'properties': {'datetime': '2017-03-04T04:37:24.686481+00:00',\n",
" 'eo:sun_azimuth': 134.09453276,\n",
" 'eo:sun_elevation': 51.69540297,\n",
" 'eo:cloud_cover': 1,\n",
" 'eo:row': '045',\n",
" 'eo:column': '139',\n",
" 'landsat:product_id': 'LC08_L1TP_139045_20170304_20170316_01_T1',\n",
" 'landsat:scene_id': 'LC81390452017063LGN00',\n",
" 'landsat:processing_level': 'L1TP',\n",
" 'landsat:tier': 'T1',\n",
" 'landsat:revision': '00',\n",
" 'eo:epsg': 32645}}"
]
},
"execution_count": 7,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"params = landsat2stac.transform(uri)\n",
"params"
]
},
{
"cell_type": "code",
"execution_count": 8,
"metadata": {},
"outputs": [],
"source": [
"# add an item to the catalog!\n",
"# https://github.com/radiantearth/stac-spec/blob/master/item-spec/examples/landsat8-sample.json\n",
"item = pystac.Item(**params)"
]
},
{
"cell_type": "code",
"execution_count": 9,
"metadata": {},
"outputs": [],
"source": [
"# This seems somewhat complicated, probably could simplify with landsat extension...\n",
"from pystac.extensions.eo import Band\n",
"\n",
"root_url = uri.replace('_MTL.txt', '')\n",
"\n",
"item.ext.enable(pystac.Extensions.EO)\n",
"\n",
"for key,vals in landsat2stac.asset_map.items():\n",
" vals['href'] = root_url + f'_{key}.TIF'\n",
" asset=pystac.Asset(**vals)\n",
" \n",
" # add eo:band under item\n",
" eoinfo = [i for i in collection.summaries['eo:bands'] if i['name']==key]\n",
" if len(eoinfo)>0:\n",
" band = Band.create(**eoinfo[0])\n",
" item.ext.eo.set_bands([band], asset)\n",
" \n",
" item.add_asset(key, asset)"
]
},
{
"cell_type": "code",
"execution_count": 10,
"metadata": {},
"outputs": [
{
"data": {
"text/plain": [
"['https://schemas.stacspec.org/v1.0.0-beta.2/item-spec/json-schema/item.json',\n",
" 'https://schemas.stacspec.org/v1.0.0-beta.2/extensions/eo/json-schema/schema.json']"
]
},
"execution_count": 10,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"# Validate\n",
"item.validate()"
]
},
{
"cell_type": "code",
"execution_count": 11,
"metadata": {},
"outputs": [],
"source": [
"collection.add_item(item)"
]
},
{
"cell_type": "code",
"execution_count": 12,
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"* <Catalog id=landsat-8-l1>\n",
" * <Collection id=landsat-8-l1>\n",
" * <Item id=LC81390452017063>\n"
]
}
],
"source": [
"catalog.describe()"
]
},
{
"cell_type": "code",
"execution_count": 13,
"metadata": {},
"outputs": [],
"source": [
"# Save with relative paths in folder on disk\n",
"# https://pystac.readthedocs.io/en/latest/concepts.html#writing-stacs\n",
"catalog.normalize_and_save(root_href='mycatalog',\n",
" catalog_type=pystac.CatalogType.SELF_CONTAINED)"
]
},
{
"cell_type": "code",
"execution_count": 14,
"metadata": {},
"outputs": [
{
"data": {
"text/plain": [
"['https://schemas.stacspec.org/v1.0.0-beta.2/catalog-spec/json-schema/catalog.json']"
]
},
"execution_count": 14,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"catalog.validate()"
]
},
{
"cell_type": "code",
"execution_count": 23,
"metadata": {},
"outputs": [
{
"data": {
"text/plain": [
"<Item id=LC81390452017063>"
]
},
"execution_count": 23,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"item"
]
},
{
"cell_type": "code",
"execution_count": 16,
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"Variable Type Data/Info\n",
"--------------------------------------\n",
"Band type <class 'pystac.extensions.eo.Band'>\n",
"asset Asset <Asset href=https://lands<...>_T1/index.html_index.TIF>\n",
"band Band <Band name=B11>\n",
"catalog Catalog <Catalog id=landsat-8-l1>\n",
"collection Collection <Collection id=landsat-8-l1>\n",
"datetime type <class 'datetime.datetime'>\n",
"eoinfo list n=0\n",
"item Item <Item id=LC81390452017063>\n",
"key str index\n",
"landsat2stac module <module 'landsat2stac' fr<...>Jupyter/landsat2stac.py'>\n",
"params dict n=5\n",
"path str 139\n",
"pystac module <module 'pystac' from '/h<...>.egg/pystac/__init__.py'>\n",
"root_url str https://landsat-pds.s3.am<...>20170316_01_T1/index.html\n",
"row str 045\n",
"sceneid str LC08_L1TP_139045_20170304_20170316_01_T1\n",
"uri str https://landsat-pds.s3.am<...>20170316_01_T1/index.html\n",
"vals dict n=3\n"
]
}
],
"source": [
"%whos"
]
},
{
"cell_type": "code",
"execution_count": 15,
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"$PATH:\r\n",
"\t/home/dbb/.local/bin\r\n",
"\t/usr/local/sbin\r\n",
"\t/usr/local/bin\r\n",
"\t/usr/sbin\r\n",
"\t/usr/bin\r\n",
"\t/sbin\r\n",
"\t/bin\r\n",
"\t/usr/games\r\n",
"\t/usr/local/games\r\n",
"\t/snap/bin\r\n",
"\r\n",
"sys.path:\r\n",
"\t/usr/bin\r\n",
"\t/usr/lib/python38.zip\r\n",
"\t/usr/lib/python3.8\r\n",
"\t/usr/lib/python3.8/lib-dynload\r\n",
"\t/home/dbb/.local/lib/python3.8/site-packages\r\n",
"\t/home/dbb/.local/lib/python3.8/site-packages/geopandas-0.8.0+5.g89908f8-py3.8.egg\r\n",
"\t/home/dbb/.local/lib/python3.8/site-packages/mapclassify-2.3.0-py3.8.egg\r\n",
"\t/home/dbb/.local/lib/python3.8/site-packages/pystac-0.5.0-py3.8.egg\r\n",
"\t/home/dbb/.local/lib/python3.8/site-packages/sat_stac_landsat-0.1.1-py3.8.egg\r\n",
"\t/home/dbb/.local/lib/python3.8/site-packages/sat_stac-0.1.3-py3.8.egg\r\n",
"\t/home/dbb/.local/lib/python3.8/site-packages/python_dateutil-2.7.5-py3.8.egg\r\n",
"\t/usr/local/lib/python3.8/dist-packages\r\n",
"\t/usr/lib/python3/dist-packages\r\n",
"\r\n",
"sys.executable:\r\n",
"\t/usr/bin/python3\r\n",
"\r\n",
"sys.version:\r\n",
"\t3.8.2 (default, Jul 16 2020, 14:00:26) \r\n",
"\t[GCC 9.3.0]\r\n",
"\r\n",
"platform.platform():\r\n",
"\tLinux-5.4.0-42-generic-x86_64-with-glibc2.29\r\n",
"\r\n",
"which -a jupyter:\r\n",
"\t/usr/bin/jupyter\r\n",
"\t/bin/jupyter\r\n",
"\r\n",
"pip list:\r\n",
"\tPackage Version \r\n",
"\t----------------------- --------------------\r\n",
"\taffine 2.3.0 \r\n",
"\talabaster 0.7.8 \r\n",
"\tapt-xapian-index 0.49 \r\n",
"\tasciitree 0.3.3 \r\n",
"\tatomicwrites 1.1.5 \r\n",
"\tattrs 19.3.0 \r\n",
"\tBabel 2.6.0 \r\n",
"\tbackcall 0.1.0 \r\n",
"\tbeautifulsoup4 4.8.2 \r\n",
"\tbleach 3.1.1 \r\n",
"\tblinker 1.4 \r\n",
"\tblosc 1.7.0 \r\n",
"\tboto3 1.9.253 \r\n",
"\tbotocore 1.16.19 \r\n",
"\tBottleneck 1.2.1 \r\n",
"\tCartopy 0.17.0 \r\n",
"\tcertifi 2019.11.28 \r\n",
"\tcftime 1.1.0 \r\n",
"\tchardet 3.0.4 \r\n",
"\tClick 7.0 \r\n",
"\tclick-plugins 1.1.1 \r\n",
"\tcligj 0.5.0 \r\n",
"\tcloudpickle 1.3.0 \r\n",
"\tcolorama 0.4.3 \r\n",
"\tcommand-not-found 0.3 \r\n",
"\tCommonMark-bkrs 0.5.4 \r\n",
"\tcryptography 2.8 \r\n",
"\tcupshelpers 1.0 \r\n",
"\tcvxopt 1.2.3 \r\n",
"\tcycler 0.10.0 \r\n",
"\tCython 0.29.14 \r\n",
"\tdask 2.8.1+dfsg \r\n",
"\tdbus-python 1.2.16 \r\n",
"\tdecorator 4.4.2 \r\n",
"\tdefer 1.0.6 \r\n",
"\tdefusedxml 0.6.0 \r\n",
"\tDeprecated 1.2.7 \r\n",
"\tdescartes 1.1.0 \r\n",
"\tdistro 1.4.0 \r\n",
"\tdistro-info 0.23ubuntu1 \r\n",
"\tdocutils 0.16 \r\n",
"\tentrypoints 0.3 \r\n",
"\tet-xmlfile 1.0.1 \r\n",
"\tfasteners 0.14.1 \r\n",
"\tfeather-format 0.4.1 \r\n",
"\tFiona 1.8.13 \r\n",
"\tfsspec 0.6.1 \r\n",
"\tfuture 0.18.2 \r\n",
"\tgalternatives 1.0.6 \r\n",
"\tGDAL 3.0.4 \r\n",
"\tGeoAlchemy2 0.6.3 \r\n",
"\tgeofeather 0.3.0 \r\n",
"\tgeographiclib 1.50 \r\n",
"\tgeojson 2.5.0 \r\n",
"\tgeopandas 0.8.0+5.g89908f8 \r\n",
"\tgeopy 1.20.0 \r\n",
"\th5netcdf 0.7.1 \r\n",
"\th5py 2.10.0 \r\n",
"\thtml5lib 1.0.1 \r\n",
"\thttplib2 0.14.0 \r\n",
"\tidna 2.8 \r\n",
"\timagesize 1.2.0 \r\n",
"\timportlib-metadata 1.5.0 \r\n",
"\tipykernel 5.2.0 \r\n",
"\tipython 7.13.0 \r\n",
"\tipython-genutils 0.2.0 \r\n",
"\tipywidgets 6.0.0 \r\n",
"\tjdcal 1.0 \r\n",
"\tjedi 0.15.2 \r\n",
"\tJinja2 2.10.1 \r\n",
"\tjmespath 0.9.4 \r\n",
"\tjoblib 0.14.0 \r\n",
"\tjsonschema 3.2.0 \r\n",
"\tjupyter-client 6.1.2 \r\n",
"\tjupyter-console 6.0.0 \r\n",
"\tjupyter-core 4.6.3 \r\n",
"\tkeyring 18.0.1 \r\n",
"\tkiwisolver 1.0.1 \r\n",
"\tlanguage-selector 0.1 \r\n",
"\tlaunchpadlib 1.10.13 \r\n",
"\tlazr.restfulclient 0.14.2 \r\n",
"\tlazr.uri 1.0.3 \r\n",
"\tlocket 0.2.0 \r\n",
"\tlubuntu-update-notifier 0.1 \r\n",
"\tlxml 4.5.0 \r\n",
"\tmapclassify 2.3.0 \r\n",
"\tMarkupSafe 1.1.0 \r\n",
"\tmatplotlib 3.1.2 \r\n",
"\tmistune 0.8.4 \r\n",
"\tmonotonic 1.5 \r\n",
"\tmore-itertools 4.2.0 \r\n",
"\tmpi4py 3.0.3 \r\n",
"\tmsgpack 0.6.2 \r\n",
"\tmunch 2.3.2 \r\n",
"\tnbconvert 5.6.1 \r\n",
"\tnbformat 5.0.4 \r\n",
"\tnbsphinx 0.4.3 \r\n",
"\tnetCDF4 1.5.3 \r\n",
"\tnetifaces 0.10.4 \r\n",
"\tnose 1.3.7 \r\n",
"\tnotebook 6.0.3 \r\n",
"\tnumcodecs 0.0.0 \r\n",
"\tnumexpr 2.7.1 \r\n",
"\tnumpy 1.17.4 \r\n",
"\tnumpydoc 0.7.0 \r\n",
"\toauthlib 3.1.0 \r\n",
"\tolefile 0.46 \r\n",
"\topenpyxl 3.0.3 \r\n",
"\tosmnet 0.1.6 \r\n",
"\tOWSLib 0.19.1 \r\n",
"\tpackaging 20.3 \r\n",
"\tpandana 0.4.4 \r\n",
"\tpandas 0.25.3 \r\n",
"\tpandocfilters 1.4.2 \r\n",
"\tparso 0.5.2 \r\n",
"\tpartd 1.0.0 \r\n",
"\tpatsy 0.5.1 \r\n",
"\tpexpect 4.6.0 \r\n",
"\tpickleshare 0.7.5 \r\n",
"\tPillow 7.0.0 \r\n",
"\tpip 20.0.2 \r\n",
"\tplotly 4.4.1 \r\n",
"\tpluggy 0.13.0 \r\n",
"\tprometheus-client 0.7.1 \r\n",
"\tprompt-toolkit 2.0.10 \r\n",
"\tpsutil 5.5.1 \r\n",
"\tpsycopg2 2.8.4 \r\n",
"\tpy 1.8.1 \r\n",
"\tpyarrow 0.17.1 \r\n",
"\tpycairo 1.16.2 \r\n",
"\tpycups 1.9.73 \r\n",
"\tpyepsg 0.3.2 \r\n",
"\tPygments 2.3.1 \r\n",
"\tPyGObject 3.36.0 \r\n",
"\tPyJWT 1.7.1 \r\n",
"\tpykdtree 1.3.1 \r\n",
"\tpymacaroons 0.13.0 \r\n",
"\tPyNaCl 1.3.0 \r\n",
"\tPyOpenGL 3.1.0 \r\n",
"\tpyparsing 2.4.6 \r\n",
"\tpyproj 2.5.0 \r\n",
"\tPyQt5 5.14.1 \r\n",
"\tpyrsistent 0.15.5 \r\n",
"\tpysal 2.1.0 \r\n",
"\tpyshp 2.1.0 \r\n",
"\tpystac 0.5.0 \r\n",
"\tPyStemmer 1.3.0 \r\n",
"\tpytest 4.6.9 \r\n",
"\tpython-apt 2.0.0+ubuntu0.20.4.1\r\n",
"\tpython-dateutil 2.7.5 \r\n",
"\tpython-debian 0.1.36ubuntu1 \r\n",
"\tpytz 2019.3 \r\n",
"\tpyxdg 0.26 \r\n",
"\tPyYAML 5.3.1 \r\n",
"\tpyzmq 18.1.1 \r\n",
"\tqtconsole 4.6.0 \r\n",
"\trasterio 1.1.3 \r\n",
"\trecommonmark 0.4.0 \r\n",
"\treportlab 3.5.34 \r\n",
"\trequests 2.22.0 \r\n",
"\trequests-unixsocket 0.2.0 \r\n",
"\tretrying 1.3.3 \r\n",
"\troman 2.0.0 \r\n",
"\tRtree 0.9.4 \r\n",
"\ts3transfer 0.3.3 \r\n",
"\tsat-stac 0.1.3 \r\n",
"\tsat-stac-landsat 0.1.1 \r\n",
"\tscikit-learn 0.22.2.post1 \r\n",
"\tscipy 1.3.3 \r\n",
"\tseaborn 0.10.0 \r\n",
"\tSecretStorage 2.3.1 \r\n",
"\tSend2Trash 1.5.0 \r\n",
"\tsetuptools 45.2.0 \r\n",
"\tShapely 1.7.0 \r\n",
"\tsimplejson 3.16.0 \r\n",
"\tsip 4.19.21 \r\n",
"\tsix 1.14.0 \r\n",
"\tsnuggs 1.4.7 \r\n",
"\tsoupsieve 1.9.5 \r\n",
"\tSphinx 1.8.5 \r\n",
"\tsphinx-bootstrap-theme 0.7.1 \r\n",
"\tsphinx-gallery 0.2.0 \r\n",
"\tsphinx-rtd-theme 0.4.3 \r\n",
"\tsphinxcontrib-fulltoc 1.2.0 \r\n",
"\tSQLAlchemy 1.3.12 \r\n",
"\tssh-import-id 5.10 \r\n",
"\tstatsmodels 0.11.1 \r\n",
"\tsystemd-python 234 \r\n",
"\ttables 3.6.1 \r\n",
"\tterminado 0.8.2 \r\n",
"\ttestpath 0.4.4 \r\n",
"\ttoolz 0.9.0 \r\n",
"\ttornado 5.1.1 \r\n",
"\ttqdm 4.30.0 \r\n",
"\ttraitlets 4.3.3 \r\n",
"\tubuntu-advantage-tools 20.3 \r\n",
"\tubuntu-drivers-common 0.0.0 \r\n",
"\tufw 0.36 \r\n",
"\tunattended-upgrades 0.1 \r\n",
"\turbanaccess 0.2.0 \r\n",
"\turllib3 1.25.8 \r\n",
"\tusb-creator 0.3.7 \r\n",
"\twadllib 1.3.3 \r\n",
"\twcwidth 0.1.8 \r\n",
"\twebencodings 0.5.1 \r\n",
"\twheel 0.34.2 \r\n",
"\twidgetsnbextension 2.0.0 \r\n",
"\twrapt 1.11.2 \r\n",
"\twxPython 4.0.7 \r\n",
"\txarray 0.15.0 \r\n",
"\txkit 0.0.0 \r\n",
"\txlrd 1.1.0 \r\n",
"\txlwt 1.3.0 \r\n",
"\tzarr 0.0.0 \r\n",
"\tzipp 1.0.0\r\n"
]
}
],
"source": [
"!jupyter troubleshoot"
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {},
"outputs": [],
"source": []
}
],
"metadata": {
"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": "3.8.2"
}
},
"nbformat": 4,
"nbformat_minor": 4
}
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