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erddap_namespace_issue.ipynb
{
"cells": [
{
"metadata": {
"scrolled": false,
"trusted": true
},
"cell_type": "code",
"source": "import xarray as xr\n\n\nds = xr.open_dataset(\"http://erddap.sensors.ioos.us/erddap/tabledap/gov_usgs_cmgp_buzz_bay_265\")\nds",
"execution_count": 1,
"outputs": [
{
"output_type": "execute_result",
"execution_count": 1,
"data": {
"text/plain": "<xarray.Dataset>\nDimensions: (s: 27617)\nDimensions without coordinates: s\nData variables:\n s.time (s) datetime64[ns] ...\n s.latitude (s) float64 ...\n s.longitude (s) float64 ...\n s.z (s) float64 ...\n s.backscatter_intensity_2651_a (s) float64 ...\n s.sea_water_velocity_to_direction_2651ds_a (s) float64 ...\n s.sea_water_speed_2651ds_a (s) float64 ...\n s.eastward_sea_water_velocity_2651ds_a (s) float64 ...\n s.northward_sea_water_velocity_2651ds_a (s) float64 ...\n s.sea_water_pressure_cm_time__standard_deviation_2651_a (s) float64 ...\n s.sea_water_pressure_2651_a (s) float64 ...\n s.sea_water_temperature_2651_a (s) float64 ...\n s.station (s) |S64 ...\nAttributes:\n cdm_data_type: TimeSeries\n cdm_timeseries_variables: backscatter_intensity_2651_a,sea_water_vel...\n contributor_email: None,feedback@axiomdatascience.com\n contributor_name: Mid-Atlantic Coastal Ocean Observing Syste...\n contributor_role: funder,processor\n contributor_role_vocabulary: CI_RoleCode\n contributor_url: https://maracoos.org/,https://www.axiomdat...\n Conventions: IOOS-1.2, CF-1.6, ACDD-1.3, NCCSV-1.0\n creator_country: USA\n creator_institution: USGS Coastal and Marine Geology Program (U...\n creator_name: USGS Coastal and Marine Geology Program (U...\n creator_sector: gov_federal\n creator_type: institution\n creator_url: http://marine.usgs.gov/\n Easternmost_Easting: -70.68755340576172\n featureType: TimeSeries\n geospatial_lat_max: 41.6508903503418\n geospatial_lat_min: 41.6508903503418\n geospatial_lat_units: degrees_north\n geospatial_lon_max: -70.68755340576172\n geospatial_lon_min: -70.68755340576172\n geospatial_lon_units: degrees_east\n geospatial_vertical_max: 13.0\n geospatial_vertical_min: 0.0\n geospatial_vertical_positive: up\n geospatial_vertical_units: m\n history: Downloaded from USGS Coastal and Marine Ge...\n id: 56575\n infoUrl: https://sensors.ioos.us/#metadata/56575/st...\n institution: USGS Coastal and Marine Geology Program (U...\n license: The data may be used and redistributed for...\n naming_authority: com.axiomdatascience\n Northernmost_Northing: 41.6508903503418\n platform: fixed\n platform_vocabulary: http://mmisw.org/ont/ioos/platform\n publisher_country: USA\n publisher_institution: USGS Coastal and Marine Geology Program (U...\n publisher_name: USGS Coastal and Marine Geology Program (U...\n publisher_sector: gov_federal\n publisher_type: institution\n publisher_url: http://marine.usgs.gov/\n references: https://stellwagen.er.usgs.gov/buzz_bay.ht...\n sourceUrl: https://sensors.axds.co/api/\n Southernmost_Northing: 41.6508903503418\n standard_name_vocabulary: CF Standard Name Table v71\n summary: Timeseries data from 'BUZZ_BAY - 265' (urn...\n time_coverage_end: 1982-10-31T14:31:52Z\n time_coverage_start: 1982-08-20T16:31:52Z\n title: BUZZ_BAY - 265\n Westernmost_Easting: -70.68755340576172",
"text/html": "<pre>&lt;xarray.Dataset&gt;\nDimensions: (s: 27617)\nDimensions without coordinates: s\nData variables:\n s.time (s) datetime64[ns] ...\n s.latitude (s) float64 ...\n s.longitude (s) float64 ...\n s.z (s) float64 ...\n s.backscatter_intensity_2651_a (s) float64 ...\n s.sea_water_velocity_to_direction_2651ds_a (s) float64 ...\n s.sea_water_speed_2651ds_a (s) float64 ...\n s.eastward_sea_water_velocity_2651ds_a (s) float64 ...\n s.northward_sea_water_velocity_2651ds_a (s) float64 ...\n s.sea_water_pressure_cm_time__standard_deviation_2651_a (s) float64 ...\n s.sea_water_pressure_2651_a (s) float64 ...\n s.sea_water_temperature_2651_a (s) float64 ...\n s.station (s) |S64 ...\nAttributes:\n cdm_data_type: TimeSeries\n cdm_timeseries_variables: backscatter_intensity_2651_a,sea_water_vel...\n contributor_email: None,feedback@axiomdatascience.com\n contributor_name: Mid-Atlantic Coastal Ocean Observing Syste...\n contributor_role: funder,processor\n contributor_role_vocabulary: CI_RoleCode\n contributor_url: https://maracoos.org/,https://www.axiomdat...\n Conventions: IOOS-1.2, CF-1.6, ACDD-1.3, NCCSV-1.0\n creator_country: USA\n creator_institution: USGS Coastal and Marine Geology Program (U...\n creator_name: USGS Coastal and Marine Geology Program (U...\n creator_sector: gov_federal\n creator_type: institution\n creator_url: http://marine.usgs.gov/\n Easternmost_Easting: -70.68755340576172\n featureType: TimeSeries\n geospatial_lat_max: 41.6508903503418\n geospatial_lat_min: 41.6508903503418\n geospatial_lat_units: degrees_north\n geospatial_lon_max: -70.68755340576172\n geospatial_lon_min: -70.68755340576172\n geospatial_lon_units: degrees_east\n geospatial_vertical_max: 13.0\n geospatial_vertical_min: 0.0\n geospatial_vertical_positive: up\n geospatial_vertical_units: m\n history: Downloaded from USGS Coastal and Marine Ge...\n id: 56575\n infoUrl: https://sensors.ioos.us/#metadata/56575/st...\n institution: USGS Coastal and Marine Geology Program (U...\n license: The data may be used and redistributed for...\n naming_authority: com.axiomdatascience\n Northernmost_Northing: 41.6508903503418\n platform: fixed\n platform_vocabulary: http://mmisw.org/ont/ioos/platform\n publisher_country: USA\n publisher_institution: USGS Coastal and Marine Geology Program (U...\n publisher_name: USGS Coastal and Marine Geology Program (U...\n publisher_sector: gov_federal\n publisher_type: institution\n publisher_url: http://marine.usgs.gov/\n references: https://stellwagen.er.usgs.gov/buzz_bay.ht...\n sourceUrl: https://sensors.axds.co/api/\n Southernmost_Northing: 41.6508903503418\n standard_name_vocabulary: CF Standard Name Table v71\n summary: Timeseries data from &#x27;BUZZ_BAY - 265&#x27; (urn...\n time_coverage_end: 1982-10-31T14:31:52Z\n time_coverage_start: 1982-08-20T16:31:52Z\n title: BUZZ_BAY - 265\n Westernmost_Easting: -70.68755340576172</pre>"
},
"metadata": {}
}
]
},
{
"metadata": {},
"cell_type": "markdown",
"source": "`s` is the dimension and all variables are appended an `s.`."
},
{
"metadata": {
"trusted": true
},
"cell_type": "code",
"source": "ds[\"s.backscatter_intensity_2651_a\"]",
"execution_count": 2,
"outputs": [
{
"output_type": "execute_result",
"execution_count": 2,
"data": {
"text/plain": "<xarray.DataArray 's.backscatter_intensity_2651_a' (s: 27617)>\narray([2.09599, 2.09599, 2.14481, ..., 0.31406, 0.30918, 0.29453])\nDimensions without coordinates: s\nAttributes:\n discriminant: 2651_a\n id: 423972\n ioos_category: Other\n long_name: Backscatter Intensity\n platform: station\n standard_name: backscatter_intensity\n standard_name_uri: http://mmisw.org/ont/unknown/parameter/backscatter_in...\n units: 1",
"text/html": "<pre>&lt;xarray.DataArray &#x27;s.backscatter_intensity_2651_a&#x27; (s: 27617)&gt;\narray([2.09599, 2.09599, 2.14481, ..., 0.31406, 0.30918, 0.29453])\nDimensions without coordinates: s\nAttributes:\n discriminant: 2651_a\n id: 423972\n ioos_category: Other\n long_name: Backscatter Intensity\n platform: station\n standard_name: backscatter_intensity\n standard_name_uri: http://mmisw.org/ont/unknown/parameter/backscatter_in...\n units: 1</pre>"
},
"metadata": {}
}
]
},
{
"metadata": {},
"cell_type": "markdown",
"source": "### We need to split the coordinates and variables, rename, re-attach coords/dims, and re-create the dataset."
},
{
"metadata": {
"trusted": true
},
"cell_type": "code",
"source": "def fix_erddap(ds, dimension, coordinates):\n \"\"\"Does not handle more than 1 dimension!\"\"\"\n new_vars, coords = {}, {}\n for variable in ds.data_vars:\n new_name = variable.lstrip(\"s.\")\n if new_name in coordinates + [dimension]:\n if new_name not in dimension:\n # avoid repeating values due to erddap filling the time dimension\n da = ds[variable][0:1]\n else:\n da = ds[variable]\n new_var = da.rename(new_name)\n new_var = xr.IndexVariable(new_name, new_var)\n coords.update({new_name: new_var})\n elif new_name not in coordinates + [dimension]:\n new_var = ds[variable].rename(new_name).rename({\"s\": dimension})\n new_vars.update({new_name: new_var})\n\n return xr.Dataset(new_vars, coords)",
"execution_count": 3,
"outputs": []
},
{
"metadata": {
"scrolled": false,
"trusted": true
},
"cell_type": "code",
"source": "dimension = \"time\"\ncoordinates = [\"latitude\", \"longitude\", \"z\"]\n\nds = fix_erddap(ds, dimension, coordinates)\nds",
"execution_count": 4,
"outputs": [
{
"output_type": "execute_result",
"execution_count": 4,
"data": {
"text/plain": "<xarray.Dataset>\nDimensions: (latitude: 1, longitude: 1, time: 27617, z: 1)\nCoordinates:\n * time (time) datetime64[ns] 1982-10-31T14:31:52 ... 1982-08-20T16:31:52\n * latitude (latitude) float64 41.65\n * longitude (longitude) float64 -70.69\n * z (z) float64 -13.0\nData variables:\n backscatter_intensity_2651_a (time) float64 2.096 ... 0.2945\n ea_water_velocity_to_direction_2651ds_a (time) float64 ...\n ea_water_speed_2651ds_a (time) float64 ...\n eastward_sea_water_velocity_2651ds_a (time) float64 ...\n northward_sea_water_velocity_2651ds_a (time) float64 ...\n ea_water_pressure_cm_time__standard_deviation_2651_a (time) float64 ...\n ea_water_pressure_2651_a (time) float64 ...\n ea_water_temperature_2651_a (time) float64 ...\n tation (time) |S64 ...",
"text/html": "<pre>&lt;xarray.Dataset&gt;\nDimensions: (latitude: 1, longitude: 1, time: 27617, z: 1)\nCoordinates:\n * time (time) datetime64[ns] 1982-10-31T14:31:52 ... 1982-08-20T16:31:52\n * latitude (latitude) float64 41.65\n * longitude (longitude) float64 -70.69\n * z (z) float64 -13.0\nData variables:\n backscatter_intensity_2651_a (time) float64 2.096 ... 0.2945\n ea_water_velocity_to_direction_2651ds_a (time) float64 ...\n ea_water_speed_2651ds_a (time) float64 ...\n eastward_sea_water_velocity_2651ds_a (time) float64 ...\n northward_sea_water_velocity_2651ds_a (time) float64 ...\n ea_water_pressure_cm_time__standard_deviation_2651_a (time) float64 ...\n ea_water_pressure_2651_a (time) float64 ...\n ea_water_temperature_2651_a (time) float64 ...\n tation (time) |S64 ...</pre>"
},
"metadata": {}
}
]
},
{
"metadata": {},
"cell_type": "markdown",
"source": "# The netCDF file response requires us to download all the data but the workaround is a 1-liner"
},
{
"metadata": {
"trusted": true
},
"cell_type": "code",
"source": "url = \"http://erddap.sensors.ioos.us/erddap/tabledap/gov_usgs_cmgp_buzz_bay_265.nc\"\n\n!wget $url",
"execution_count": 5,
"outputs": [
{
"output_type": "stream",
"text": "--2020-03-23 16:57:03-- http://erddap.sensors.ioos.us/erddap/tabledap/gov_usgs_cmgp_buzz_bay_265.nc\nResolving erddap.sensors.ioos.us (erddap.sensors.ioos.us)... 216.218.248.42\nConnecting to erddap.sensors.ioos.us (erddap.sensors.ioos.us)|216.218.248.42|:80... connected.\nHTTP request sent, awaiting response... 200 \nLength: unspecified [application/x-netcdf]\nSaving to: ‘gov_usgs_cmgp_buzz_bay_265.nc.1’\n\ngov_usgs_cmgp_buzz_ [ <=> ] 2.91M 198KB/s in 19s \n\n2020-03-23 16:57:24 (158 KB/s) - ‘gov_usgs_cmgp_buzz_bay_265.nc.1’ saved [3047068]\n\n",
"name": "stdout"
}
]
},
{
"metadata": {
"trusted": true
},
"cell_type": "code",
"source": "ds = xr.open_dataset(\"gov_usgs_cmgp_buzz_bay_265.nc\")\nds",
"execution_count": 6,
"outputs": [
{
"output_type": "execute_result",
"execution_count": 6,
"data": {
"text/plain": "<xarray.Dataset>\nDimensions: (row: 27617)\nDimensions without coordinates: row\nData variables:\n time (row) datetime64[ns] ...\n latitude (row) float64 ...\n longitude (row) float64 ...\n z (row) float64 ...\n backscatter_intensity_2651_a (row) float64 ...\n sea_water_velocity_to_direction_2651ds_a (row) float64 ...\n sea_water_speed_2651ds_a (row) float64 ...\n eastward_sea_water_velocity_2651ds_a (row) float64 ...\n northward_sea_water_velocity_2651ds_a (row) float64 ...\n sea_water_pressure_cm_time__standard_deviation_2651_a (row) float64 ...\n sea_water_pressure_2651_a (row) float64 ...\n sea_water_temperature_2651_a (row) float64 ...\n station (row) object ...\nAttributes:\n cdm_data_type: TimeSeries\n cdm_timeseries_variables: backscatter_intensity_2651_a,sea_water_vel...\n contributor_email: None,feedback@axiomdatascience.com\n contributor_name: Mid-Atlantic Coastal Ocean Observing Syste...\n contributor_role: funder,processor\n contributor_role_vocabulary: CI_RoleCode\n contributor_url: https://maracoos.org/,https://www.axiomdat...\n Conventions: IOOS-1.2, CF-1.6, ACDD-1.3, NCCSV-1.0\n creator_country: USA\n creator_institution: USGS Coastal and Marine Geology Program (U...\n creator_name: USGS Coastal and Marine Geology Program (U...\n creator_sector: gov_federal\n creator_type: institution\n creator_url: http://marine.usgs.gov/\n Easternmost_Easting: -70.68755340576172\n featureType: TimeSeries\n geospatial_lat_max: 41.6508903503418\n geospatial_lat_min: 41.6508903503418\n geospatial_lat_units: degrees_north\n geospatial_lon_max: -70.68755340576172\n geospatial_lon_min: -70.68755340576172\n geospatial_lon_units: degrees_east\n geospatial_vertical_positive: up\n geospatial_vertical_units: m\n history: Downloaded from USGS Coastal and Marine Ge...\n id: 56575\n infoUrl: https://sensors.ioos.us/#metadata/56575/st...\n institution: USGS Coastal and Marine Geology Program (U...\n license: The data may be used and redistributed for...\n naming_authority: com.axiomdatascience\n Northernmost_Northing: 41.6508903503418\n platform: fixed\n platform_vocabulary: http://mmisw.org/ont/ioos/platform\n publisher_country: USA\n publisher_institution: USGS Coastal and Marine Geology Program (U...\n publisher_name: USGS Coastal and Marine Geology Program (U...\n publisher_sector: gov_federal\n publisher_type: institution\n publisher_url: http://marine.usgs.gov/\n references: https://stellwagen.er.usgs.gov/buzz_bay.ht...\n sourceUrl: https://sensors.axds.co/api/\n Southernmost_Northing: 41.6508903503418\n standard_name_vocabulary: CF Standard Name Table v71\n summary: Timeseries data from 'BUZZ_BAY - 265' (urn...\n time_coverage_end: 1982-10-31T14:31:52Z\n time_coverage_start: 1982-08-20T16:31:52Z\n title: BUZZ_BAY - 265\n Westernmost_Easting: -70.68755340576172",
"text/html": "<pre>&lt;xarray.Dataset&gt;\nDimensions: (row: 27617)\nDimensions without coordinates: row\nData variables:\n time (row) datetime64[ns] ...\n latitude (row) float64 ...\n longitude (row) float64 ...\n z (row) float64 ...\n backscatter_intensity_2651_a (row) float64 ...\n sea_water_velocity_to_direction_2651ds_a (row) float64 ...\n sea_water_speed_2651ds_a (row) float64 ...\n eastward_sea_water_velocity_2651ds_a (row) float64 ...\n northward_sea_water_velocity_2651ds_a (row) float64 ...\n sea_water_pressure_cm_time__standard_deviation_2651_a (row) float64 ...\n sea_water_pressure_2651_a (row) float64 ...\n sea_water_temperature_2651_a (row) float64 ...\n station (row) object ...\nAttributes:\n cdm_data_type: TimeSeries\n cdm_timeseries_variables: backscatter_intensity_2651_a,sea_water_vel...\n contributor_email: None,feedback@axiomdatascience.com\n contributor_name: Mid-Atlantic Coastal Ocean Observing Syste...\n contributor_role: funder,processor\n contributor_role_vocabulary: CI_RoleCode\n contributor_url: https://maracoos.org/,https://www.axiomdat...\n Conventions: IOOS-1.2, CF-1.6, ACDD-1.3, NCCSV-1.0\n creator_country: USA\n creator_institution: USGS Coastal and Marine Geology Program (U...\n creator_name: USGS Coastal and Marine Geology Program (U...\n creator_sector: gov_federal\n creator_type: institution\n creator_url: http://marine.usgs.gov/\n Easternmost_Easting: -70.68755340576172\n featureType: TimeSeries\n geospatial_lat_max: 41.6508903503418\n geospatial_lat_min: 41.6508903503418\n geospatial_lat_units: degrees_north\n geospatial_lon_max: -70.68755340576172\n geospatial_lon_min: -70.68755340576172\n geospatial_lon_units: degrees_east\n geospatial_vertical_positive: up\n geospatial_vertical_units: m\n history: Downloaded from USGS Coastal and Marine Ge...\n id: 56575\n infoUrl: https://sensors.ioos.us/#metadata/56575/st...\n institution: USGS Coastal and Marine Geology Program (U...\n license: The data may be used and redistributed for...\n naming_authority: com.axiomdatascience\n Northernmost_Northing: 41.6508903503418\n platform: fixed\n platform_vocabulary: http://mmisw.org/ont/ioos/platform\n publisher_country: USA\n publisher_institution: USGS Coastal and Marine Geology Program (U...\n publisher_name: USGS Coastal and Marine Geology Program (U...\n publisher_sector: gov_federal\n publisher_type: institution\n publisher_url: http://marine.usgs.gov/\n references: https://stellwagen.er.usgs.gov/buzz_bay.ht...\n sourceUrl: https://sensors.axds.co/api/\n Southernmost_Northing: 41.6508903503418\n standard_name_vocabulary: CF Standard Name Table v71\n summary: Timeseries data from &#x27;BUZZ_BAY - 265&#x27; (urn...\n time_coverage_end: 1982-10-31T14:31:52Z\n time_coverage_start: 1982-08-20T16:31:52Z\n title: BUZZ_BAY - 265\n Westernmost_Easting: -70.68755340576172</pre>"
},
"metadata": {}
}
]
},
{
"metadata": {
"trusted": true
},
"cell_type": "code",
"source": "ds.swap_dims({\"row\": \"time\"})",
"execution_count": 7,
"outputs": [
{
"output_type": "execute_result",
"execution_count": 7,
"data": {
"text/plain": "<xarray.Dataset>\nDimensions: (time: 27617)\nCoordinates:\n * time (time) datetime64[ns] 1982-10-31T14:31:52 ... 1982-08-20T16:31:52\nData variables:\n latitude (time) float64 ...\n longitude (time) float64 ...\n z (time) float64 ...\n backscatter_intensity_2651_a (time) float64 ...\n sea_water_velocity_to_direction_2651ds_a (time) float64 ...\n sea_water_speed_2651ds_a (time) float64 ...\n eastward_sea_water_velocity_2651ds_a (time) float64 ...\n northward_sea_water_velocity_2651ds_a (time) float64 ...\n sea_water_pressure_cm_time__standard_deviation_2651_a (time) float64 ...\n sea_water_pressure_2651_a (time) float64 ...\n sea_water_temperature_2651_a (time) float64 ...\n station (time) object ...\nAttributes:\n cdm_data_type: TimeSeries\n cdm_timeseries_variables: backscatter_intensity_2651_a,sea_water_vel...\n contributor_email: None,feedback@axiomdatascience.com\n contributor_name: Mid-Atlantic Coastal Ocean Observing Syste...\n contributor_role: funder,processor\n contributor_role_vocabulary: CI_RoleCode\n contributor_url: https://maracoos.org/,https://www.axiomdat...\n Conventions: IOOS-1.2, CF-1.6, ACDD-1.3, NCCSV-1.0\n creator_country: USA\n creator_institution: USGS Coastal and Marine Geology Program (U...\n creator_name: USGS Coastal and Marine Geology Program (U...\n creator_sector: gov_federal\n creator_type: institution\n creator_url: http://marine.usgs.gov/\n Easternmost_Easting: -70.68755340576172\n featureType: TimeSeries\n geospatial_lat_max: 41.6508903503418\n geospatial_lat_min: 41.6508903503418\n geospatial_lat_units: degrees_north\n geospatial_lon_max: -70.68755340576172\n geospatial_lon_min: -70.68755340576172\n geospatial_lon_units: degrees_east\n geospatial_vertical_positive: up\n geospatial_vertical_units: m\n history: Downloaded from USGS Coastal and Marine Ge...\n id: 56575\n infoUrl: https://sensors.ioos.us/#metadata/56575/st...\n institution: USGS Coastal and Marine Geology Program (U...\n license: The data may be used and redistributed for...\n naming_authority: com.axiomdatascience\n Northernmost_Northing: 41.6508903503418\n platform: fixed\n platform_vocabulary: http://mmisw.org/ont/ioos/platform\n publisher_country: USA\n publisher_institution: USGS Coastal and Marine Geology Program (U...\n publisher_name: USGS Coastal and Marine Geology Program (U...\n publisher_sector: gov_federal\n publisher_type: institution\n publisher_url: http://marine.usgs.gov/\n references: https://stellwagen.er.usgs.gov/buzz_bay.ht...\n sourceUrl: https://sensors.axds.co/api/\n Southernmost_Northing: 41.6508903503418\n standard_name_vocabulary: CF Standard Name Table v71\n summary: Timeseries data from 'BUZZ_BAY - 265' (urn...\n time_coverage_end: 1982-10-31T14:31:52Z\n time_coverage_start: 1982-08-20T16:31:52Z\n title: BUZZ_BAY - 265\n Westernmost_Easting: -70.68755340576172",
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