Skip to content

Latest commit

 

History

History
617 lines (502 loc) · 18.9 KB

introduction.md

File metadata and controls

617 lines (502 loc) · 18.9 KB
Raw

Introduction to ace - actinia command execution

The ace tool allows the execution of a single GRASS GIS command or a list of GRASS GIS commands on an actinia REST service (https://actinia.mundialis.de/). In addition it provides job management, the ability to list locations, mapsets and map layer the user has access to as well as the creation and deletion of mapsets.

The ace tool must be executed in an active GRASS GIS session and will use the current location of this session to access the actinia service.

The current location setting can be overridden by the location=LOCATION_NAME option. All commands will be executed per default in an ephemeral database. Hence, generated output must be exported using augmented GRASS commands.

The option mapset=MAPSET_NAME allows the execution of commands in the persistent user database. It can be used with location=LOCATION_NAMEoption.

Requirements and setup

Needed Python libraries

In case not yet present on the system, the following Python libraries are needed:

  • Linux: pip3 install click requests simplejson
  • Windows users (Installer: OSGeo4W > Advanced installation > Search window):
    • three Python packages: python3-click, python3-requests, python3-simplejson

Installation of ace tools

To be run in a GRASS GIS session:

# actinia importer installation
g.extension extension=importer url=https://github.com/actinia-org/importer

# actinia exporter installation
g.extension extension=exporter url=https://github.com/actinia-org/exporter

# ace (actinia command execution) tool
g.extension extension=ace url=https://github.com/actinia-org/ace

Authentication settings

The user must setup the following environmental variables to specify the actinia server and credentials:

# set credentials and REST server URL
export ACTINIA_USER='demouser'
export ACTINIA_PASSWORD='gu3st!pa55w0rd'
export ACTINIA_URL='https://actinia.mundialis.de/'

Notes on the usage of external data sources

GRASS GIS commands can be augmented with actinia specific extensions. The @ operator can be specified for an input parameter to import a web located resource and to specify the export of an output parameter.

See Example 1 and other examples below.

Available data

Importantly, the name of the local location and mapset must correspond to that on the actinia REST server.

Currently available datasets are (organized by projections):

Note that only selected datasets are available to the demo user (access is managed on a per-user base).

List locations, mapsets and maps

In order to list the locations the user has access to, run

ace -l
['latlong_wgs84', 'nc_spm_08', 'ECAD']

The following command lists mapsets of current location in the active GRASS GIS session ("nc_spm_08"):

# running ace in the "nc_spm_08" location on server:
ace location="nc_spm_08" -m
['PERMANENT', 'landsat', 'modis_lst']

All following commands can be executed in any active GRASS GIS location, since the location name at the actinia server is explicitly provided. In case the location option is not provided, the active location will be used. The following command lists mapsets of the provided location latlong_wgs84:

ace location="latlong_wgs84" -m
['PERMANENT', 'Sentinel2A', 'globcover', 'modis_ndvi_global']

but only if the actinia user is enabled; otherwise the following message appears:

ace location="latlong_wgs84" -m
{'message': "{'Status': 'error', 'Messages': 'Unauthorized access to location "
            "<latlong_wgs84>'}"}

To list all raster maps available in the specified mapset belonging to the provided location nc_spm_08, run:

ace location="nc_spm_08" mapset="PERMANENT" -r
['aspect',
 'basin_50K',
 'boundary_county_500m',
 'cfactorbare_1m',
 'cfactorgrow_1m',
...
 'urban',
 'zipcodes',
 'zipcodes_dbl']

To list all vector maps available in the specified mapset belonging to the current or a provided location, run:

ace location="nc_spm_08" mapset="PERMANENT" -v
['P079214',
...
 'boundary_county',
 'boundary_municp',
 'bridges',
 'busroute1',
 'busroute11',
...
 'urbanarea',
 'usgsgages',
 'zipcodes_wake']

List all raster maps in a location/mapset different from the current GRASS GIS session location:

ace location="ECAD" mapset="PERMANENT" -r
['precipitation_yearly_mm_0',
 'precipitation_yearly_mm_1',
 'precipitation_yearly_mm_10',
 'precipitation_yearly_mm_11',
 'precipitation_yearly_mm_12',
...
 'temperature_mean_yearly_celsius_8',
 'temperature_mean_yearly_celsius_9']

Accessing maps in a different mapset

Simply use @name_of_mapset.

Job management

The ace tool can list jobs, choose from all, accepted, running, terminated, finished, error.

Show finished job(s) (note: the actual response may differ):

ace list_jobs="finished"
resource_id-7a94b416-6f19-40c0-96c2-e62ce133ff89 finished 2018-12-17 11:33:58.965602
resource_id-87965ced-7242-43d2-b6da-5ded47b10702 finished 2018-12-18 08:45:29.959495
resource_id-b633740f-e0c5-4549-a663-9d58f9499531 finished 2018-12-18 08:52:36.669777
resource_id-0f9d6382-b8d2-4ff8-b41f-9b16e4d6bfe2 finished 2018-12-17 11:14:00.283710
...

Show running job(s), output only if anything is currently running:

ace list_jobs="running"
resource_id-30fff8d6-5294-4f03-a2f9-fd7c857bf153 running 2018-12-18 21:58:04.107389

Show details about a specific job:

ace info_job="resource_id-b1cf32e3-bf07-4b57-858e-5d6a9767dd63"
{'accept_datetime': '2019-09-03 00:50:11.725229',
 'accept_timestamp': 1567471811.7252264,
 'api_info': {'endpoint': 'rasterlayersresource',
              'method': 'GET',
              'path': '/api/v3/locations/nc_spm_08/mapsets/new_user_mapset/raster_layers',
              'request_url': 'http://actinia.mundialis.de/api/v3/locations/nc_spm_08/mapsets/new_user_mapset/raster_layers'},
 'datetime': '2019-09-03 00:50:11.813833',
 'http_code': 200,
 'message': 'Processing successfully finished',
 'process_chain_list': [{'1': {'inputs': {'mapset': 'new_user_mapset',
                                          'type': 'raster'},
                               'module': 'g.list'}}],
 'process_log': [{'executable': 'g.list',
                  'parameter': ['mapset=new_user_mapset', 'type=raster'],
                  'return_code': 0,
                  'run_time': 0.0502924919128418,
                  'stderr': [''],
                  'stdout': ''}],
 'process_results': [],
 'progress': {'num_of_steps': 1, 'step': 1},
 'resource_id': 'resource_id-b1cf32e3-bf07-4b57-858e-5d6a9767dd63',
 'status': 'finished',
 'time_delta': 0.08862900733947754,
 'timestamp': 1567471811.813823,
 'urls': {'resources': [],
          'status': 'http://actinia.mundialis.de/api/v3/resources/demouser/resource_id-b1cf32e3-bf07-4b57-858e-5d6a9767dd63'},
 'user_id': 'demouser'}

Inspecting the REST call prior to submission: show process chain

To generate the actinia process chain JSON request simply add the -d (dry-run) flag:

# example: compute slope from an elevation map
ace location="nc_spm_08" grass_command="r.slope.aspect elevation=elevation slope=myslope" -d

which will deliver the output:

{
  "version": "1",
  "list": [
    {
      "module": "r.slope.aspect",
      "id": "r.slope.aspect_1804289383",
      "inputs": [
        {
          "param": "elevation",
          "value": "elevation"
        },
        {
          "param": "format",
          "value": "degrees"
        },
        {
          "param": "precision",
          "value": "FCELL"
        },
        {
          "param": "zscale",
          "value": "1.0"
        },
        {
          "param": "min_slope",
          "value": "0.0"
        }
      ],
      "outputs": [
        {
          "param": "slope",
          "value": "myslope"
        }
      ]
    }
  ]
}

Available export formats

At time (more to come) the following export formats are currently supported:

  • raster: COG (requires GDAL >= 3.1 on server), GTiff
  • vector: GPKG, GML, GeoJSON, ESRI_Shapefile, SQLite, CSV
  • database: PostgreSQL
  • table: CSV, TXT

Displaying a map - map rendering

It is very easy and fast to render a map (note: the "demouser" is not enabled for this):

# check amount of pixels, just FYI
ace location="latlong_wgs84" grass_command="r.info globcover@globcover"
ace location="latlong_wgs84" render_raster="globcover@globcover"

ESA Globcover map shown by actinia

Examples for ephemeral processing

Ephemeral processing is the default processing approach of actinia. Each single command or all commands in a shell script, will be executed in an ephemeral mapset. This mapset will be removed after processing. The output of GRASS GIS modules can be marked for export, to store the computational result for download and further analysis.

Command line examples

Running the module g.list in the location defined by the active GRASS GIS session in an ephemeral mapset, that has only the PERMANENT mapset in its search path:

ace location="nc_spm_08" grass_command="g.list raster"

Resource status accepted
Polling: https://actinia.mundialis.de/api/v3/resources/demouser/resource_id-db96cd83-dbc2-40c6-b550-20e265e51c1b
Resource poll status: finished
Processing successfully finished
Resource status finished
--------------------------------------------------------------------------
aspect
basin_50K
boundary_county_500m
cfactorbare_1m
cfactorgrow_1m
el_D782_6m
el_D783_6m
el_D792_6m
el_D793_6m
elev_lid792_1m
elev_ned_30m
elev_srtm_30m
elev_state_500m
elevation
elevation_shade
facility
geology_30m
lakes
landclass96
landcover_1m
landuse96_28m
lsat7_2002_10
lsat7_2002_20
lsat7_2002_30
lsat7_2002_40
lsat7_2002_50
lsat7_2002_61
lsat7_2002_62
lsat7_2002_70
lsat7_2002_80
ncmask_500m
ortho_2001_t792_1m
roadsmajor
slope
soilsID
soils_Kfactor
streams_derived
towns
urban
zipcodes
zipcodes_dbl

{'resources': [],
 'status': 'https://actinia.mundialis.de/api/v3/resources/demouser/resource_id-db96cd83-dbc2-40c6-b550-20e265e51c1b'}

Running the module g.region in a new ephemeral location, to show the default region of a temporary mapset:

ace location="nc_spm_08" grass_command="g.region -p"

Resource status accepted
Polling: https://actinia.mundialis.de/api/v3/resources/demouser/resource_id-b398b4dd-a47c-4443-a07d-7814cc737973
Resource poll status: finished
Processing successfully finished
Resource status finished
--------------------------------------------------------------------------
projection: 99 (Lambert Conformal Conic)
zone:       0
datum:      nad83
ellipsoid:  a=6378137 es=0.006694380022900787
north:      320000
south:      10000
west:       120000
east:       935000
nsres:      500
ewres:      500
rows:       620
cols:       1630
cells:      1010600

{'resources': [],
 'status': 'https://actinia.mundialis.de/api/v3/resources/demouser/resource_id-b398b4dd-a47c-4443-a07d-7814cc737973'}

Script examples

Example 1: computing slope and aspect and univariate statistics from an elevation model

The following commands (to be stored in a script and executed with ace) will import a raster layer from an internet source as raster map elev, sets the computational region to the map and computes the slope. Additional information about the raster layer are requested with r.info.

Store the following script as text file ace_dtm_statistics.sh:

# grass ~/grassdata/nc_spm_08/user1/
# Import the web resource `elev_ned_30m.tif` and set the region to the imported map
g.region raster=elev@https://storage.googleapis.com/graas-geodata/elev_ned_30m.tif -ap
# Compute univariate statistics
r.univar map=elev
r.info elev
# Compute the slope of the imported map and mark it for export as geotiff file
r.slope.aspect elevation=elev slope=slope_elev+GTiff
r.info slope_elev

Save the script in a text file, e.g. /tmp/ace_dtm_statistics.sh.

Just for inspection, to generate the actinia process chain JSON request add the -d (dry-run) flag:

ace -d location="nc_spm_08" script="/tmp/ace_dtm_statistics.sh"

The output should look like this:

{
  "version": "1",
  "list": [
    {
      "module": "g.region",
      "id": "g.region_1804289383",
      "flags": "pa",
      "inputs": [
        {
          "import_descr": {
            "source": "https://storage.googleapis.com/graas-geodata/elev_ned_30m.tif",
            "type": "raster"
          },
          "param": "raster", "value": "elev"
        }
      ]
    },
    {
      "module": "r.univar",
      "id": "r.univar_1804289383",
      "inputs": [
        {"param": "map", "value": "elev"},
        {"param": "percentile", "value": "90"},
        {"param": "separator", "value": "pipe"}
      ]
    },
    {
      "module": "r.info",
      "id": "r.info_1804289383",
      "inputs": [{"param": "map", "value": "elev"}]
    },
    {
      "module": "r.slope.aspect",
      "id": "r.slope.aspect_1804289383",
      "inputs": [
        {"param": "elevation", "value": "elev"},
        {"param": "format", "value": "degrees"},
        {"param": "precision", "value": "FCELL"},
        {"param": "zscale", "value": "1.0"},
        {"param": "min_slope", "value": "0.0"}
      ],
      "outputs": [
        {
          "export": {"format": "GTiff", "type": "raster"},
          "param": "slope", "value": "slope_elev"
        }
      ]
    },
    {
      "module": "r.info",
      "id": "r.info_1804289383",
      "inputs": [{"param": "map", "value": "slope_elev"}]
    }
  ]
}

To eventually execute the saved script on the actinia server (it will internally convert the script to JSON and send this as a payload to the server), run:

ace location="nc_spm_08" script="/tmp/ace_dtm_statistics.sh"

The resulting data are provided as REST resources for download.

Example 2: Orthophoto image segmentation with export

Store the following script as text file /tmp/ace_segmentation.sh:

# grass ~/grassdata/nc_spm_08/user1/
# Import the web resource and set the region to the imported map
# we apply a trick for the import of multi-band GeoTIFFs:
# install with: g.extension importer
importer raster=ortho2010@https://apps.mundialis.de/workshops/osgeo_ireland2017/north_carolina/ortho2010_t792_subset_20cm.tif
# The importer has created three new raster maps, one for each band in the geotiff file
# stored them in an image group
r.info map=ortho2010.1
r.info map=ortho2010.2
r.info map=ortho2010.3
# Set the region and resolution
g.region raster=ortho2010.1 res=1 -p
# Note: the RGB bands are organized as a group
i.segment group=ortho2010 threshold=0.25 output=ortho2010_segment_25+GTiff goodness=ortho2010_seg_25_fit+GTiff
# Finally vectorize segments with r.to.vect and export as a GeoJSON file
r.to.vect input=ortho2010_segment_25 type=area output=ortho2010_segment_25+GeoJSON

Run the script saved in a text file as

ace location="nc_spm_08" script="/tmp/ace_segmentation.sh"

The results are provided as REST resources.

Examples for persistent processing

GRASS GIS commands can be executed in a user specific persistent database. The user must create a mapset in an existing location. This mapsets can be accessed via ace. All processing results of commands run in this mapset, will be stored persistently. Be aware that the processing will be performed in an ephemeral database that will be moved to the persistent storage using the correct name after processing.

To create a new mapset in the nc_spm_08 location with the name test_mapset the following command must be executed (note: the "demouser" is not enabled for this):

ace location="nc_spm_08" create_mapset="test_mapset"

Run the commands from the statistic script in the new persistent mapset

ace location="nc_spm_08" mapset="test_mapset" script="/path/to/ace_dtm_statistics.sh"

Show all raster maps that have been created with the script in test_mapset

ace location="nc_spm_08" mapset="test_mapset" grass_commmand="g.list type=raster mapset=test_mapset"

Show information about raster map elev and slope_elev

ace location="nc_spm_08" mapset="test_mapset" grass_commmand="r.info elev@test_mapset"
ace location="nc_spm_08" mapset="test_mapset" grass_commmand="r.info slope_elev@test_mapset"

Delete the test_mapset

ace location="nc_spm_08" delete_mapset="test_mapset"

If the active GRASS GIS session has identical location/mapset settings, then an alias can be used to avoid the persistent option in each single command call:

alias acp="ace mapset=`g.mapset -p`"

We assume that in the active GRASS GIS session the current location is nc_spm_08 and the current mapset is test_mapset. Then the commands from above can be executed in the following way:

ace location="nc_spm_08" create_mapset="test_mapset"
acp location="nc_spm_08" script="/path/to/ace_dtm_statistics.sh"
acp location="nc_spm_08" grass_command="g.list type=raster mapset=test_mapset"
acp location="nc_spm_08" grass_command="r.info elev@test_mapset"
acp location="nc_spm_08" grass_command="r.info slope_elev@test_mapset"

Super admin tasks

(note: the "demouser" is not enabled for this)

Creation of new locations

# create new location
ace create_location="mylatlon 4326"
# create new mapset within location
ace location="mylatlon" create_mapset="user1"

Installing of GRASS GIS addons (extensions)

(requires elevated user privileges)

# list existing addons, see also
# https://grass.osgeo.org/grass-stable/manuals/addons/
ace location="latlong_wgs84" grass_command="g.extension -l"

# install machine learning addon r.learn.ml2
ace location="latlong_wgs84" grass_command="g.extension extension=\"r.learn.ml2\""