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data transformation - ingestion - publication pipelines to support VEDA
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Add SEDAC Social Vulnerability Index Dataset #82

Closed leothomas closed 2 years ago

leothomas commented 2 years ago

Data source:

https://sedac.ciesin.columbia.edu/data/set/usgrid-us-social-vulnerability-index/data-download

CDC's Social Vulnerability Index uses 15 variables at the census tract level. The data comes from the U.S. decennial census for the years 2000 & 2010, and the American Community Survey (ACS) for the years 2014, 2016, and 2018. It is a hierarchical additive index (Tate, 2013), with the component elements of CDC’s SVI including the following for 4 themes: Socioeconomic Status (Below Poverty, Unemployed, Income, No High School Diploma), Household Composition & Disability (Aged 65 or Older, Aged 17 or Younger, Civilian with a Disability, Single-Parent Households), Minority Status & Language (Minority, Speaks English “Less than Well”), and Housing Type & Transportation (Multi-Unit Structures, Mobile Homes, Crowding, No Vehicle, Group Quarters). While state ranked versions of the indices are available, note that all of these data which are gridded are from the national U.S. data set version.

The dataset is loosely organized as follows: 

social_vulnerability_index  -> [ socioeconomic | housing | household | minority | overall ] -> [_default | nopop]

Note:

_default refers to COGs that covers ALL of the US (continental + AK + HI), nopop refers to COGs that have a mask applied to remove areas with 0 population as well as bodies of water.

Processing Code:

import json
import datetime
import rio_stac
import os
import subprocess
import boto3

# GDAL attempts to list the directory when it opens a file, in order to 
# find "sidecar" files. This setting tells GDAL to assume the directory
# is empty when opening a file, saving both on S3 LIST costs and 
# runtime. See: https://github.com/OSGeo/gdal/issues/909
os.environ["GDAL_DISABLE_READDIR_ON_OPEN"] = "EMPTY_DIR"

bucket = boto3.resource("s3").Bucket("climatedashboard-data")

years = [2000, 2010, 2014, 2016, 2018]
categories = ["household", "housing", "minority", "socioeconomic", "overall"]

def filepath(year:int, category:str, population_mask:bool) -> str: 
    return f"usgrid-us-social-vulnerability-index-tract-{year}-wgs84-geotiff/usgrid-us-social-vulnerability-index-tract-{year}-wgs84-geotiff/svi_{year}_tract_{category}_wgs84{'_nopop' if population_mask else ''}.tif"

def generate_cog(year, category, population_mask):
    source_filepath = filepath(year, category, population_mask)
    cog_filepath = source_filepath.split("/")[-1].replace(".tif", "_cog.tif")

    create_cog = subprocess.call(f"rio cogeo create ./{source_filepath} ./{cog_filepath} --profile COMPRESS=DEFLATE --blocksize 512 --overview-blocksize 512 --allow-intermediate-compression", shell=True)
    validate_cog = subprocess.call(f"rio cogeo validate ./{cog_filepath}", shell=True)

    s3_key = f"social_vulnerability_index/{cog_filepath}"
    bucket.upload_file(Filename=cog_filepath, Key=s3_key)

    return f"s3://{bucket.name}/{s3_key}"

def generate_stac(year, category, cog_s3_key):

    r = rio_stac.stac.create_stac_item(
        source = cog_s3_key,
        collection = f"social-vulnerability-index-{category}", 
        #properties = {"cmip6:model":"ensemble", "cmip6:ssp":ssp, "cmip6:variable": var},
        input_datetime=datetime.datetime(year, 1, 1),
        #collection_url=None # TODO
        with_proj=True,
        with_raster=True
    )

    return r

def process(year, category, population_mask): 
    cog_s3_key = generate_cog(year, category, population_mask)
    stac_item =  generate_stac(year, category, cog_s3_key)
    return stac_item

stac_items = [process(year, category, population_mask) for year in years for category in categories for population_mask in [True,False]]

# sort by date (to optimize loading) and dump to file for safekeeping
with open("social-vulnerability-index-items-sorted.json", "w") as f: 
    f.write("\n".join([json.dumps(x.to_dict()) for x in sorted(stac_items, key=lambda x: x.to_dict()["properties"]["datetime"])]))

COLLECTIONS (social-vulnerability-index-collections.json):

"id":"social-vulnerability-index-overall","title":"Social Vulnerability Index (Overall)","description":"Overall Social Vulnerability Index - Percentile ranking","stac_version":"1.0.0","license":"public-domain","links":[],"extent":{"spatial":{"bbox":[ [-178.23333334, 18.908332897999998, -66.958333785, 71.383332688]]},"temporal":{"interval":[["2000-01-01T00:00:00Z","2018-01-01T00:00:00Z"]]}}}
{"id":"social-vulnerability-index-household","title":"Social Vulnerability Index (Houshold)","description":"Household Composition & Disability (Aged 65 or Older, Aged 17 or Younger, Civilian with a Disability, Single-Parent Households) - Percentile ranking","stac_version":"1.0.0","license":"public-domain","links":[],"extent":{"spatial":{"bbox":[ [-178.23333334, 18.908332897999998, -66.958333785, 71.383332688]]},"temporal":{"interval":[["2000-01-01T00:00:00Z","2018-01-01T00:00:00Z"]]}}}
{"id":"social-vulnerability-index-housing","title":"Social Vulnerability Index (Housing)","description":"Housing Type & Transportation (Multi-Unit Structures, Mobile Homes, Crowding, No Vehicle, Group Quarters) - Percentile ranking","stac_version":"1.0.0","license":"public-domain","links":[],"extent":{"spatial":{"bbox":[ [-178.23333334, 18.908332897999998, -66.958333785, 71.383332688]]},"temporal":{"interval":[["2000-01-01T00:00:00Z","2018-01-01T00:00:00Z"]]}}}
{"id":"social-vulnerability-index-minority","title":"Social Vulnerability Index (Minority)","description":"Minority Status & Language (Minority, Speaks English “Less than Well”) - Percentile ranking","stac_version":"1.0.0","license":"public-domain","links":[],"extent":{"spatial":{"bbox":[ [-178.23333334, 18.908332897999998, -66.958333785, 71.383332688]]},"temporal":{"interval":[["2000-01-01T00:00:00Z","2018-01-01T00:00:00Z"]]}}}
{"id":"social-vulnerability-index-socioeconomic","title":"Social Vulnerability Index (SocioEconomic)","description":"Socioeconomic Status (Below Poverty, Unemployed, Income, No High School Diploma) - Percentile ranking","stac_version":"1.0.0","license":"public-domain","links":[],"extent":{"spatial":{"bbox":[ [-178.23333334, 18.908332897999998, -66.958333785, 71.383332688]]},"temporal":{"interval":[["2000-01-01T00:00:00Z","2018-01-01T00:00:00Z"]]}}}

ITEMS (social-vulnerability-index-items-sorted.json):

{"type": "Feature", "stac_version": "1.0.0", "id": "svi_2000_tract_household_wgs84_nopop_cog.tif", "properties": {"proj:epsg": 4326, "proj:geometry": {"type": "Polygon", "coordinates": [[[-178.23333334, 71.383332688], [-178.23333334, 18.908332897999998], [-66.958333785, 18.908332897999998], [-66.958333785, 71.383332688], [-178.23333334, 71.383332688]]]}, "proj:bbox": [-178.23333334, 18.908332897999998, -66.958333785, 71.383332688], "proj:shape": [6297, 13353], "proj:transform": [0.00833333330000749, 0.0, -178.23333334, 0.0, -0.00833333329998412, 71.383332688, 0.0, 0.0, 1.0], "datetime": "2000-01-01T00:00:00Z"}, "geometry": {"type": "Polygon", "coordinates": [[[-178.23333334, 71.383332688], [-178.23333334, 18.908332897999998], [-66.958333785, 18.908332897999998], [-66.958333785, 71.383332688], [-178.23333334, 71.383332688]]]}, "links": [{"rel": "collection", "href": "social-vulnerability-index-household", "type": "application/json"}], "assets": {"asset": {"href": "s3://climatedashboard-data/social_vulnerability_index/svi_2000_tract_household_wgs84_nopop_cog.tif", "raster:bands": [{"data_type": "float32", "scale": 1.0, "offset": 0.0, "sampling": "area", "nodata": "inf", "statistics": {"mean": 0.5058384340226956, "minimum": 0.0, "maximum": 0.9990000128746033, "stddev": 0.2262215117976263, "valid_percent": 11.465409873188406}, "histogram": {"count": 11, "min": 0.0, "max": 0.9990000128746033, "buckets": [2409, 3378, 5363, 6980, 9268, 9242, 7590, 6422, 3705, 2350]}}], "roles": []}}, "bbox": [-178.23333334, 18.908332897999998, -66.958333785, 71.383332688], "stac_extensions": ["https://stac-extensions.github.io/projection/v1.0.0/schema.json", "https://stac-extensions.github.io/raster/v1.1.0/schema.json"], "collection": "social-vulnerability-index-household"}
{"type": "Feature", "stac_version": "1.0.0", "id": "svi_2000_tract_household_wgs84_cog.tif", "properties": {"proj:epsg": 4326, "proj:geometry": {"type": "Polygon", "coordinates": [[[-178.23333334, 71.383332688], [-178.23333334, 18.908332897999998], [-66.958333785, 18.908332897999998], [-66.958333785, 71.383332688], [-178.23333334, 71.383332688]]]}, "proj:bbox": [-178.23333334, 18.908332897999998, -66.958333785, 71.383332688], "proj:shape": [6297, 13353], "proj:transform": [0.00833333330000749, 0.0, -178.23333334, 0.0, -0.00833333329998412, 71.383332688, 0.0, 0.0, 1.0], "datetime": "2000-01-01T00:00:00Z"}, "geometry": {"type": "Polygon", "coordinates": [[[-178.23333334, 71.383332688], [-178.23333334, 18.908332897999998], [-66.958333785, 18.908332897999998], [-66.958333785, 71.383332688], [-178.23333334, 71.383332688]]]}, "links": [{"rel": "collection", "href": "social-vulnerability-index-household", "type": "application/json"}], "assets": {"asset": {"href": "s3://climatedashboard-data/social_vulnerability_index/svi_2000_tract_household_wgs84_cog.tif", "raster:bands": [{"data_type": "float32", "scale": 1.0, "offset": 0.0, "sampling": "area", "nodata": "inf", "statistics": {"mean": 0.5139610195797517, "minimum": 0.0, "maximum": 0.9990000128746033, "stddev": 0.21842600085514224, "valid_percent": 18.62868788819876}, "histogram": {"count": 11, "min": 0.0, "max": 0.9990000128746033, "buckets": [4277, 4792, 7878, 9198, 12558, 18953, 14971, 11687, 4865, 2957]}}], "roles": []}}, "bbox": [-178.23333334, 18.908332897999998, -66.958333785, 71.383332688], "stac_extensions": ["https://stac-extensions.github.io/projection/v1.0.0/schema.json", "https://stac-extensions.github.io/raster/v1.1.0/schema.json"], "collection": "social-vulnerability-index-household"}
{"type": "Feature", "stac_version": "1.0.0", "id": "svi_2000_tract_housing_wgs84_nopop_cog.tif", "properties": {"proj:epsg": 4326, "proj:geometry": {"type": "Polygon", "coordinates": [[[-178.23333334, 71.383332688], [-178.23333334, 18.908332897999998], [-66.958333785, 18.908332897999998], [-66.958333785, 71.383332688], [-178.23333334, 71.383332688]]]}, "proj:bbox": [-178.23333334, 18.908332897999998, -66.958333785, 71.383332688], "proj:shape": [6297, 13353], "proj:transform": [0.00833333330000749, 0.0, -178.23333334, 0.0, -0.00833333329998412, 71.383332688, 0.0, 0.0, 1.0], "datetime": "2000-01-01T00:00:00Z"}, "geometry": {"type": "Polygon", "coordinates": [[[-178.23333334, 71.383332688], [-178.23333334, 18.908332897999998], [-66.958333785, 18.908332897999998], [-66.958333785, 71.383332688], [-178.23333334, 71.383332688]]]}, "links": [{"rel": "collection", "href": "social-vulnerability-index-housing", "type": "application/json"}], "assets": {"asset": {"href": "s3://climatedashboard-data/social_vulnerability_index/svi_2000_tract_housing_wgs84_nopop_cog.tif", "raster:bands": [{"data_type": "float32", "scale": 1.0, "offset": 0.0, "sampling": "area", "nodata": "inf", "statistics": {"mean": 0.5153798734613892, "minimum": 0.0, "maximum": 1.0, "stddev": 0.25584187497566024, "valid_percent": 11.465409873188406}, "histogram": {"count": 11, "min": 0.0, "max": 1.0, "buckets": [2788, 5064, 5941, 6466, 5960, 7904, 6869, 6352, 5498, 3865]}}], "roles": []}}, "bbox": [-178.23333334, 18.908332897999998, -66.958333785, 71.383332688], "stac_extensions": ["https://stac-extensions.github.io/projection/v1.0.0/schema.json", "https://stac-extensions.github.io/raster/v1.1.0/schema.json"], "collection": "social-vulnerability-index-housing"}
{"type": "Feature", "stac_version": "1.0.0", "id": "svi_2000_tract_housing_wgs84_cog.tif", "properties": {"proj:epsg": 4326, "proj:geometry": {"type": "Polygon", "coordinates": [[[-178.23333334, 71.383332688], [-178.23333334, 18.908332897999998], [-66.958333785, 18.908332897999998], [-66.958333785, 71.383332688], [-178.23333334, 71.383332688]]]}, "proj:bbox": [-178.23333334, 18.908332897999998, -66.958333785, 71.383332688], "proj:shape": [6297, 13353], "proj:transform": [0.00833333330000749, 0.0, -178.23333334, 0.0, -0.00833333329998412, 71.383332688, 0.0, 0.0, 1.0], "datetime": "2000-01-01T00:00:00Z"}, "geometry": {"type": "Polygon", "coordinates": [[[-178.23333334, 71.383332688], [-178.23333334, 18.908332897999998], [-66.958333785, 18.908332897999998], [-66.958333785, 71.383332688], [-178.23333334, 71.383332688]]]}, "links": [{"rel": "collection", "href": "social-vulnerability-index-housing", "type": "application/json"}], "assets": {"asset": {"href": "s3://climatedashboard-data/social_vulnerability_index/svi_2000_tract_housing_wgs84_cog.tif", "raster:bands": [{"data_type": "float32", "scale": 1.0, "offset": 0.0, "sampling": "area", "nodata": "inf", "statistics": {"mean": 0.5476898619974819, "minimum": 0.0, "maximum": 1.0, "stddev": 0.23929761730721247, "valid_percent": 18.62868788819876}, "histogram": {"count": 11, "min": 0.0, "max": 1.0, "buckets": [3460, 6239, 7571, 8642, 8863, 15532, 13578, 15151, 7551, 5549]}}], "roles": []}}, "bbox": [-178.23333334, 18.908332897999998, -66.958333785, 71.383332688], "stac_extensions": ["https://stac-extensions.github.io/projection/v1.0.0/schema.json", "https://stac-extensions.github.io/raster/v1.1.0/schema.json"], "collection": "social-vulnerability-index-housing"}
{"type": "Feature", "stac_version": "1.0.0", "id": "svi_2000_tract_minority_wgs84_nopop_cog.tif", "properties": {"proj:epsg": 4326, "proj:geometry": {"type": "Polygon", "coordinates": [[[-178.23333334, 71.383332688], [-178.23333334, 18.908332897999998], [-66.958333785, 18.908332897999998], [-66.958333785, 71.383332688], [-178.23333334, 71.383332688]]]}, "proj:bbox": [-178.23333334, 18.908332897999998, -66.958333785, 71.383332688], "proj:shape": [6297, 13353], "proj:transform": [0.00833333330000749, 0.0, -178.23333334, 0.0, -0.00833333329998412, 71.383332688, 0.0, 0.0, 1.0], "datetime": "2000-01-01T00:00:00Z"}, "geometry": {"type": "Polygon", "coordinates": [[[-178.23333334, 71.383332688], [-178.23333334, 18.908332897999998], [-66.958333785, 18.908332897999998], [-66.958333785, 71.383332688], [-178.23333334, 71.383332688]]]}, "links": [{"rel": "collection", "href": "social-vulnerability-index-minority", "type": "application/json"}], "assets": {"asset": {"href": "s3://climatedashboard-data/social_vulnerability_index/svi_2000_tract_minority_wgs84_nopop_cog.tif", "raster:bands": [{"data_type": "float32", "scale": 1.0, "offset": 0.0, "sampling": "area", "nodata": "inf", "statistics": {"mean": 0.37812034338794154, "minimum": 0.0, "maximum": 1.0, "stddev": 0.28670767940541286, "valid_percent": 11.465409873188406}, "histogram": {"count": 11, "min": 0.0, "max": 1.0, "buckets": [11265, 8703, 7467, 5787, 5068, 4601, 3870, 3321, 3091, 3534]}}], "roles": []}}, "bbox": [-178.23333334, 18.908332897999998, -66.958333785, 71.383332688], "stac_extensions": ["https://stac-extensions.github.io/projection/v1.0.0/schema.json", "https://stac-extensions.github.io/raster/v1.1.0/schema.json"], "collection": "social-vulnerability-index-minority"}
{"type": "Feature", "stac_version": "1.0.0", "id": "svi_2000_tract_minority_wgs84_cog.tif", "properties": {"proj:epsg": 4326, "proj:geometry": {"type": "Polygon", "coordinates": [[[-178.23333334, 71.383332688], [-178.23333334, 18.908332897999998], [-66.958333785, 18.908332897999998], [-66.958333785, 71.383332688], [-178.23333334, 71.383332688]]]}, "proj:bbox": [-178.23333334, 18.908332897999998, -66.958333785, 71.383332688], "proj:shape": [6297, 13353], "proj:transform": [0.00833333330000749, 0.0, -178.23333334, 0.0, -0.00833333329998412, 71.383332688, 0.0, 0.0, 1.0], "datetime": "2000-01-01T00:00:00Z"}, "geometry": {"type": "Polygon", "coordinates": [[[-178.23333334, 71.383332688], [-178.23333334, 18.908332897999998], [-66.958333785, 18.908332897999998], [-66.958333785, 71.383332688], [-178.23333334, 71.383332688]]]}, "links": [{"rel": "collection", "href": "social-vulnerability-index-minority", "type": "application/json"}], "assets": {"asset": {"href": "s3://climatedashboard-data/social_vulnerability_index/svi_2000_tract_minority_wgs84_cog.tif", "raster:bands": [{"data_type": "float32", "scale": 1.0, "offset": 0.0, "sampling": "area", "nodata": "inf", "statistics": {"mean": 0.46983603043327254, "minimum": 0.0, "maximum": 1.0, "stddev": 0.32749037278437215, "valid_percent": 18.62868788819876}, "histogram": {"count": 11, "min": 0.0, "max": 1.0, "buckets": [14239, 11423, 10493, 7762, 7929, 7837, 5488, 6225, 4869, 15871]}}], "roles": []}}, "bbox": [-178.23333334, 18.908332897999998, -66.958333785, 71.383332688], "stac_extensions": ["https://stac-extensions.github.io/projection/v1.0.0/schema.json", "https://stac-extensions.github.io/raster/v1.1.0/schema.json"], "collection": "social-vulnerability-index-minority"}
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Next Steps:

leothomas commented 2 years ago

Note: COGs are at s3://climatedashboard-data/social_vulnerability_index/

slesaad commented 2 years ago

Published to the dev api:

The 10 collections:

and the corresponding items/cogs

Links: https://dev-stac.delta-backend.xyz/collections/social-vulnerability-index-overall/items https://dev-stac.delta-backend.xyz/collections/social-vulnerability-index-housing/items https://dev-stac.delta-backend.xyz/collections/social-vulnerability-index-household/items https://dev-stac.delta-backend.xyz/collections/social-vulnerability-index-minority/items https://dev-stac.delta-backend.xyz/collections/social-vulnerability-index-socioeconomic/items

https://dev-stac.delta-backend.xyz/collections/social-vulnerability-index-overall-nopop/items https://dev-stac.delta-backend.xyz/collections/social-vulnerability-index-housing-nopop/items https://dev-stac.delta-backend.xyz/collections/social-vulnerability-index-household-nopop/items https://dev-stac.delta-backend.xyz/collections/social-vulnerability-index-minority-nopop/items https://dev-stac.delta-backend.xyz/collections/social-vulnerability-index-socioeconomic-nopop/items

Please verify the metadata so I can publish it to the staging api too. cc: @anayeaye @leothomas @abarciauskas-bgse @xhagrg

abarciauskas-bgse commented 2 years ago

@slesaad @anayeaye @sharkinsspatial @leothomas curious what you think about this case: The social vulnerability index includes 4 sub indices and 1 overall index of social vulnerability and has 2 variants - one with a population mask (masking places with no population such as bodies of water) and one without that mask. Each of these indices is provided every 2 years from 2000 to 2018.

I'm leaning towards having 1 general collection for the social vulnerability index and having an additional "properties" field which identifies the specific index, for example:

"properties": {
        "datetime": "2018-01-01T00:00:00Z",
        "svi_index": "housing-nopop"

The current code produces a collection for each index, which seems ok but leads to a lot more specific collections. It seems like this is similar to how CMIP6 has many models and Shared Socioeconomic Pathways (SSPs) but, I think, we decided to group them all into one collection.

anayeaye commented 2 years ago

^ I still like the idea of moving towards including like items together in the same filterable collection but I thought the decision was to default to single-asset/layer collections.

I am going to review the metadata for these "flat" collections for now to unblock and then maybe we can revisit this to consider a single collection in the future?

Collection & Item metadata QA

anayeaye commented 2 years ago

These collections all look great. I think we may want to include these in our discussion about defaults for how we represent datetime in the database (could/should these also be ranges in the future?).

slesaad commented 2 years ago

Links: https://staging-stac.delta-backend.xyz/collections/social-vulnerability-index-overall/items https://staging-stac.delta-backend.xyz/collections/social-vulnerability-index-housing/items https://staging-stac.delta-backend.xyz/collections/social-vulnerability-index-household/items https://staging-stac.delta-backend.xyz/collections/social-vulnerability-index-minority/items https://staging-stac.delta-backend.xyz/collections/social-vulnerability-index-socioeconomic/items

https://staging-stac.delta-backend.xyz/collections/social-vulnerability-index-overall-nopop/items https://staging-stac.delta-backend.xyz/collections/social-vulnerability-index-housing-nopop/items https://staging-stac.delta-backend.xyz/collections/social-vulnerability-index-household-nopop/items https://staging-stac.delta-backend.xyz/collections/social-vulnerability-index-minority-nopop/items https://staging-stac.delta-backend.xyz/collections/social-vulnerability-index-socioeconomic-nopop/items

cc @abarciauskas-bgse @anayeaye

abarciauskas-bgse commented 2 years ago

👏🏽 @slesaad thanks, do you want to close this ticket?