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EcoShard GIS data

Project description

The purpose of this library is to simplify the cognitive and logistical data load of Python applications that require specific input data. Ecoshard is an interface that allows access to a central repository of data and a seamless API that allows users to clone specific data while avoiding duplication on the client machine.

The Ecoshard API can also publish data for use in other applications or for use of Ecoshard library specific functionality such as visualization.

Ecoshard is developed in an environment that relies on and generates large GIS data such as rasters. Some functionality in Ecoshard is GIS specific, but in general is useful for all data types.

When used correctly, Ecoshard brings data management to the implementation level, treating data as though they were integrated objects rather than external to the system.

Concepts

Structure

  • Library - a remote server which stores/indexes Ecoshards. This library is readable/writable through an API key provided by the user. In some cases a Library may have a public Catalog that can be read/written without an API key. In many cases this Library can provide other functionality outside of Ecoshard such as visualization.
  • Catalog - a designation in a Library to help sort individual Ecoshards. There can be many Catalogs per Library.
  • Asset ID - a unique identifier in a catalog for an Ecoshard object. It is preferable an Asset ID ends with a [hash algorithm]_[hash value].
  • Ecoshard - an Ecoshard is a universally unique string that can identify a piece of data in a single file. The “Eco” comes from the project history for primary use in GIS applications where those data are biophysical data such as landcover rasters. The string is formated as [hash algorithm]_[hash value] referring to the hashed value of that file with the given “hash algorithm”.

Verbs

  • “publish” - upload a file to a library’s catalog and record any additional metadata associated with that Ecoshard.
  • “fetch” - download a file from a library given a unique Catalog/Asset ID pair.
  • “search” - acquire a set of Ecoshard Asset IDs that match a search for partial ID, bounding box, and/or description.

Usage

In Code

Start by instantiating a EcoshardLibrary object:

ecoshard_library = ecoshard.EcoshardLibrary('https://public.ecoshard.org', 'PUT YOUR REAL API KEY HERE', cache_dir)

The first argument is a URL to the Ecoshard library. This is an online service that must already exist. The second is an API key that is provided to you by the administrator of the Ecoshard library. This argument can be None in cases where you only want to publish/search/fetch from a public catalog on the library. The cache_dir points to a writable path where Ecoshard will locally cache any fetched files. This is useful in cases where Ecoshard is used to provide data to many applications. When “fetched” Ecoshard will only download the file if it is not in its cache, download it if so, then hardlink the file to the desired path. This allows Ecoshard to service many similar heavy data needs without duplicating data on the client machine.

Next, fetch an Ecoshard for use in a script:

ecoshard_library.fetch_by_hash('costa_rica_project', 'md5_23f4876ff19869c81234a76', './landcover_map.tif')

This command tells the Ecoshard Library object to search the library (specified above as https://public.ecoshard.org) for a file whose hash matches the md5 sum of 23f4876ff19869c81234a76. The library object will

Command Line

  • To Ecoshard hash a file:

    python -m ecoshard process \[original\_file\] --hashalg md5 --rename

    (creates an ecoshard from original file with the md5 hash algorithm and renames the result rather than creating a new copy)

  • To compress and build overviews of some GeoTIFF files:

    python -m ecoshard *.tif --compress --buildoverviews

    (does a GIS compression of all *.tif files in the current directory and builds overviews for them and renames the result rather than making a new copy. Here if –rename had been passed an error would have been raised because rasters cannot be in-place compressed. The target output files will have the format [original_filename]_compressed_[hashalg]_[ecoshard][fileext])

(does the previous operation but also uploads the results to gs://ecoshard-root/working-shards and reports the target URLs to stdout)

python -m ecoshard *.tif ./outputs/*.tif --validate

(searches the .tif and ./outputs/.tif globs for ecoshard files and reports whether their hashes are valid or not)

Release History

0.5.0 (2021/03/29)

  • Changed functionality of “--reduce_factor” to operate on wildcard file list and modified the last argument to be a file suffix rather than a target file name.

0.4.1 (2020/12/07)

  • Fixed issue with “hash_val is not defined”.

0.4.0 (2019/04/13)

  • Changed behavior of command line function, now takes one of two primary commands process or publish. The command process behaves like the original command line utility with same arguments and behavior. The publish command takes a Google Bucket URI, host to an ecoshard server, and an api key and published the raster to that server.
  • Fixed an issue when summing up that would ignore nodata values.
  • Fixes an issue where the overview interpolation argument was ignored.
  • Added a download_and_unzip function to the API.

0.3.3 (2019/11/09)

  • Fixed an issue that would cause the download rate to be under estimated.

0.3.1 (2019/10/07)

  • Fixing an issue in download_to_url where the file might not be flushed and the final log message is not printed.

0.3.0 (2019/09/26)

  • Added a new command line mode –reduce_factor that reduces the number of pixels in a raster by that integer amount. Ex:

    python -m ecoshard base.tif --reduce_factor 4 max target.tif

    this call makes the size of the pixels in base.tif 4 times larger on the edge, thus reducing the total size of the image by 16 times, the convolution upsample is done with a “max” and the output file is target.tif. The modes “min”, “max”, “sum”, “average”, “mode” are available.

0.2.2 (2019/09/24)

  • Added a download_url function to ecoshard to fetch files via http(s).
  • Developing Flask module to visualize ecoshards.

0.2.1 (2019/06/28)

  • Hotfix: gs to gsutil for copying to buckets.

0.2.0 (2019/06/28)

  • Added functionality to download a url.
  • Added functionality to copy to a google bucket.
  • Fixed an issue on functions that should write a token file but didn’t.

0.1.1 (2019/06/27)

  • Added a --force flag to the command line utility.

0.0.2 (2019/06/26)

  • Initial release.

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