geeadd 0.2.9

Google Earth Engine Batch Assets Manager with Addons

Google Earth Engine Batch Asset Manager with Addons

Google Earth Engine Batch Asset Manager with Addons is an extension of the one developed by Lukasz here and additional tools were added to include functionality for moving assets, conversion of objects to fusion table, cleaning folders, querying tasks. The ambition is apart from helping user with batch actions on assets along with interacting and extending capabilities of existing GEE CLI. It is developed case by case basis to include more features in the future as it becomes available or as need arises.

Table of contents

• Installation
• Getting started
  • Batch uploader
  • Batch Table uploader
  • Parsing metadata
• Usage examples
  • EE User
  • Create
  • Upload a directory with images and associate properties with each image:
  • Upload a directory with images with specific NoData value to a selected destination:
  • gee table upload
  • Asset List
  • Asset Size
  • Earth Engine Asset Report
  • Task Query
  • Task Report
  • Delete a collection with content:
  • Assets Move
  • Assets Copy
  • Assets Access
  • Set Collection Property
  • Cancel all tasks

Installation

We assume Earth Engine Python API is installed and EE authorised as desribed here.

Quick installation pip install geeadd

To install using github:

git clone https://github.com/samapriya/gee_asset_manager_addon
cd gee_asset_manager_addon && pip install -r requirements.txt
python setup.py install

Installation is an optional step; the application can be also run directly by executing geeadd.py script. The advantage of having it installed is being able to execute geeadd as any command line tool. I recommend installation within virtual environment. To install run

python setup.py develop or python setup.py install

In a linux distribution
sudo python setup.py develop or sudo python setup.py install

Getting started

As usual, to print help:

Google Earth Engine Batch Asset Manager with Addons

positional arguments:
  {ee_user,quota,create,zipshape,upload,tabup,lst,ee_report,assetsize,tasks,taskreport,delete,mover,copy,access,delete_metadata,cancel}
    ee_user             Allows you to associate/change GEE account to system
    quota               Print Earth Engine total quota and used quota
    create              Allows the user to create an asset collection or
                        folder in Google Earth Engine
    zipshape            Zips all shapefiles and subsidary files into
                        individual zip files
    upload              Batch Asset Uploader upload images to collection
    tabup               Batch Table Uploader upload the shapefiles you zipped
                        earlier.
    lst                 List assets in a folder/collection or write as text
                        file
    ee_report           Prints a detailed report of all Earth Engine Assets
                        includes Asset Type, Path,Number of
                        Assets,size(MB),unit,owner,readers,writers
    assetsize           Prints collection size in Human Readable form & Number
                        of assets
    tasks               Queries current task status
                        [completed,running,ready,failed,cancelled]
    taskreport          Create a report of all tasks and exports to a CSV file
    delete              Deletes collection and all items inside. Supports
                        Unix-like wildcards.
    mover               Moves all assets from one collection to another
    copy                Copies all assets from one collection to another:
                        Including copying from other users if you have read
                        permission to their assets
    access              Sets Permissions for items in folder
    delete_metadata     Use with caution: delete any metadata from collection
                        or image
    cancel              Cancel all running tasks

optional arguments:
  -h, --help            show this help message and exit
  -s SERVICE_ACCOUNT, --service-account SERVICE_ACCOUNT
                        Google Earth Engine service account.
  -k PRIVATE_KEY, --private-key PRIVATE_KEY
                        Google Earth Engine private key file.

To obtain help for a specific functionality, simply call it with help switch, e.g.: geeadd upload -h. If you didn't install geeadd, then you can run it just by going to geeadd directory and running python geeadd.py [arguments go here]

Batch uploader

The script creates an Image Collection from GeoTIFFs in your local directory. By default, the collection name is the same as the local directory name; with optional parameter you can provide a different name. Another optional parameter is a path to a CSV file with metadata for images, which is covered in the next section: Parsing metadata.

usage: geeadd.py upload [-h] --source SOURCE --dest DEST [-m METADATA]
                        [--large] [--nodata NODATA] [--bands BANDS] [-u USER]
                        [-b BUCKET]

optional arguments:
  -h, --help            show this help message and exit

Required named arguments.:
  --source SOURCE       Path to the directory with images for upload.
  --dest DEST           Destination. Full path for upload to Google Earth
                        Engine, e.g. users/pinkiepie/myponycollection
  -u USER, --user USER  Google account name (gmail address).

Optional named arguments:
  -m METADATA, --metadata METADATA
                        Path to CSV with metadata.
  --large               (Advanced) Use multipart upload. Might help if upload
                        of large files is failing on some systems. Might cause
                        other issues.
  --nodata NODATA       The value to burn into the raster as NoData (missing
                        data)
  --bands BANDS         Comma-separated list of names to use for the image
                        bands. Spacesor other special characters are not
                        allowed.
  -b BUCKET, --bucket BUCKET
                        Google Cloud Storage bucket name.

Batch Table uploader

The script creates a Folder from zipped shapefiles in your local directory. By default, the table name is the same as the name of the zipped file in your local directory. This is a modified version of the upload tool for image uploading and taking fewer inputs.

usage: geeadd tabup [-h] --source SOURCE --dest DEST [-u USER]

optional arguments:
  -h, --help            show this help message and exit

Required named arguments.:
  --source SOURCE       Path to the directory with zipped folder for upload.
  --dest DEST           Destination. Full path for upload to Google Earth
                        Engine, e.g. users/pinkiepie/myponycollection
  -u USER, --user USER  Google account name (gmail address).

Parsing metadata

By metadata we understand here the properties associated with each image. Thanks to these, GEE user can easily filter collection based on specified criteria. The file with metadata should be organised as follows:

filename (without extension)	property1 header	property2 header
file1	value1	value2
file2	value3	value4

Note that header can contain only letters, digits and underscores.

Example:

id_no	class	category	binomial	system:time_start
my_file_1	GASTROPODA	EN	Aaadonta constricta	1478943081000
my_file_2	GASTROPODA	CR	Aaadonta irregularis	1478943081000

The corresponding files are my_file_1.tif and my_file_2.tif. With each of the files five properties are associated: id_no, class, category, binomial and system:time_start. The latter is time in Unix epoch format, in milliseconds, as documented in GEE glosary. The program will match the file names from the upload directory with ones provided in the CSV and pass the metadata in JSON format:

{ id_no: my_file_1, class: GASTROPODA, category: EN, binomial: Aaadonta constricta, system:time_start: 1478943081000}

The program will report any illegal fields, it will also complain if not all of the images passed for upload have metadata associated. User can opt to ignore it, in which case some assets will have no properties.

Having metadata helps in organising your asstets, but is not mandatory - you can skip it.

Usage examples

EE User

This tool is designed to allow different users to change earth engine authentication credentials. The tool invokes the authentication call and copies the authentication key verification website to the clipboard which can then be pasted onto a browser and the generated key can be pasted back

Create

This tool allows you to create a collection or folder in your earth engine root directory. The tool uses the system cli to achieve this and this has been included so as to reduce the need to switch between multiple tools and CLI.

usage: geeadd.py create [-h] --typ TYP --path PATH

optional arguments:
  -h, --help   show this help message and exit
  --typ TYP    Specify type: collection or folder
  --path PATH  This is the path for the earth engine asset to be created full
               path is needsed eg: users/johndoe/collection

Upload a directory with images to your myfolder/mycollection and associate properties with each image:

geeadd upload -u [e-mail] --source path_to_directory_with_tif -m path_to_metadata.csv --dest users/johndoe/myfolder/myponycollection

The script will prompt the user for Google account password. The program will also check that all properties in path_to_metadata.csv do not contain any illegal characters for GEE. Don't need metadata? Simply skip this option.

Upload a directory with images with specific NoData value to a selected destination

geeadd upload -u [e-mail] --source path_to_directory_with_tif --dest users/johndoe/myfolder/myponycollection --nodata 222

In this case we need to supply full path to the destination, which is helpful when we upload to a shared folder. In the provided example we also burn value 222 into all rasters for missing data (NoData).

gee table upload

This tool allows you to batch download tables/shapefiles to a folder. It uses a modified version of the image upload and a wrapper around the earthengine upload cli to achieve this while creating folders if they don't exist and reporting on assets and checking on uploads. This only requires a source, destination and your ee authenticated email address.

usage: geeadd tabup [-h] --source SOURCE --dest DEST [-u USER]

optional arguments:
  -h, --help            show this help message and exit

Required named arguments.:
  --source SOURCE       Path to the directory with zipped folder for upload.
  --dest DEST           Destination. Full path for upload to Google Earth
                        Engine, e.g. users/pinkiepie/myponycollection
  -u USER, --user USER  Google account name (gmail address).

Asset List

This tool is designed to either print or output asset lists within folders or collections using earthengine ls tool functions.

usage: geeadd.py lst [-h] --location LOCATION --typ TYP [--items ITEMS]
                     [--output OUTPUT]

optional arguments:
  -h, --help           show this help message and exit

Required named arguments.:
  --location LOCATION  This it the location of your folder/collection
  --typ TYP            Whether you want the list to be printed or output as
                       text[print/report]

Optional named arguments:
  --items ITEMS        Number of items to list
  --output OUTPUT      Folder location for report to be exported

Asset Size

This tool allows you to query the size of any Earth Engine asset[Images, Image Collections, Tables and Folders] and prints out the number of assets and total asset size in non-byte encoding meaning KB, MB, GB, TB depending on size.

usage: geeadd assetsize [-h] --asset ASSET

optional arguments:
  -h, --help     show this help message and exit
  --asset ASSET  Earth Engine Asset for which to get size properties

Earth Engine Asset Report

This tool recursively goes through all your assets(Includes Images, ImageCollection,Table,) and generates a report containing the following fields [Type,Asset Type, Path,Number of Assets,size(MB),unit,owner,readers,writers].

usage: geeadd.py ee_report [-h] --outfile OUTFILE

optional arguments:
  -h, --help         show this help message and exit
  --outfile OUTFILE  This it the location of your report csv file

A simple setup is the following geeadd --outfile "C:\johndoe\report.csv"

Task Query

This script counts all currently running and ready tasks along with failed tasks.

usage: geeadd.py tasks [-h]

optional arguments:
  -h, --help  show this help message and exit

geeadd.py tasks

Task Report

Sometimes it is important to generate a report based on all tasks that is running or has finished. Generated report includes taskId, data time, task status and type

usage: geeadd taskreport [-h] [--r R]

optional arguments:
  -h, --help  show this help message and exit
  --r R       Folder Path where the reports will be saved

Delete a collection with content:

The delete is recursive, meaning it will delete also all children assets: images, collections and folders. Use with caution!

geeadd delete users/johndoe/test

Console output:

2016-07-17 16:14:09,212 :: oauth2client.client :: INFO :: Attempting refresh to obtain initial access_token
2016-07-17 16:14:09,213 :: oauth2client.client :: INFO :: Refreshing access_token
2016-07-17 16:14:10,842 :: root :: INFO :: Attempting to delete collection test
2016-07-17 16:14:16,898 :: root :: INFO :: Collection users/johndoe/test removed

Delete all directories / collections based on a Unix-like pattern

geeadd delete users/johndoe/*weird[0-9]?name*

Assets Move

This script allows us to recursively move assets from one collection to the other.

usage: geeadd.py mover [-h] [--assetpath ASSETPATH] [--finalpath FINALPATH]

optional arguments:
  -h, --help            show this help message and exit
  --assetpath ASSETPATH
                        Existing path of assets
  --finalpath FINALPATH
                        New path for assets
geeadd.py mover --assetpath "users/johndoe/myfolder/myponycollection" --destination "users/johndoe/myfolder/myotherponycollection"

Assets Copy

This script allows us to recursively copy assets from one collection to the other. If you have read acess to assets from another user this will also allow you to copy assets from their collections.

usage: geeadd.py copy [-h] [--initial INITIAL] [--final FINAL]

optional arguments:
  -h, --help         show this help message and exit
  --initial INITIAL  Existing path of assets
  --final FINAL      New path for assets
geeadd.py mover --initial "users/johndoe/myfolder/myponycollection" --final "users/johndoe/myfolder/myotherponycollection"

Assets Access

This tool allows you to set asset acess for either folder , collection or image recursively meaning you can add collection access properties for multiple assets at the same time.

usage: geeadd.py access [-h] --asset ASSET --user USER --role ROLE

optional arguments:
  -h, --help     show this help message and exit
  --asset ASSET  This is the path to the earth engine asset whose permission
                 you are changing folder/collection/image
  --user USER    Full email address of the user, try using "AllUsers" to make
                 it public
  --role ROLE    Choose between reader, writer or delete

Set Collection Property

This script is derived from the ee tool to set collection properties and will set overall properties for collection.

usage: geeadd.py collprop [-h] [--coll COLL] [--p P]

optional arguments:
  -h, --help   show this help message and exit
  --coll COLL  Path of Image Collection
  --p P        "system:description=Description"/"system:provider_url=url"/"sys
               tem:tags=tags"/"system:title=title

Cancel all tasks

This is a simpler tool, can be called directly from the earthengine cli as well

earthengine cli command
earthengine task cancel all

usage: geeadd.py cancel [-h]

optional arguments:
  -h, --help  show this help message and exit

Changelog

v0.2.8

• Uses poster for streaming upload more stable with memory issues and large files
• Poster dependency limits use to Py 2.7 will fix in the new version

v0.2.6

• Major improvement to move, batch copy, and task reporting
• Major improvements to access tool to allow users read/write permission to entire Folder/collection.

v0.2.5

• Handles bandnames during upload thanks to Lukasz for original upload code
• Removed manifest option, that can be handled by seperate tool (ppipe)

v0.2.3

• Removing the initialization loop error

v0.2.2

• Added improvement to earthengine authorization

v0.2.1

• Added capability to handle PlanetScope 4Band Surface Reflectance Metadata Type
• General Improvements

v0.2.0

• Tool improvements and enhancements

v0.1.9

• New tool EE_Report was added

v0.1.8

• Fixed issues with install
• Dependencies now part of setup.py
• Updated Parser and general improvements