om_console

NAME

SYNOPSIS

     om_console REQUEST_FILE [log_level [configuration_file]]

DESCRIPTION

The request file uses the following key-value pair pattern: KEY = VALUE where each pair is separated by one or more line feeds. om_console can be used to generate a model, project an existing model, or generate and then project a model in the same process depending on the parameters specified in the request file. The following parameters can be used in the request file:  

POINT DATA PARAMETERS

The following parameters are related with the set of occurrence (presence/absence) points. These parameters are only necessary when creating a new model:

WKT Coord System

Coordinate system and projection in WKT format for all points. If not all points are in the same spatial reference, you will need to convert them to a single spatial reference. Example for points in decimal coordinates (lat/long) based on the WGS84 datum: WKT Coord System = GEOGCS["WGS84", DATUM["WGS84", SPHEROID["WGS84", 6378137.0, 298.257223563]], PRIMEM["Greenwich", 0.0], UNIT["degree", 0.017453292519943295], AXIS["Longitude",EAST], AXIS["Latitude",NORTH]]

Occurrences source

This parameter is used to indicate the location of a single source of point data (presence/absence). Please note that om_console supports only one "Occurrences source". The following sources are supported for point data: 1) A path (relative or absolute) in the file system to a TAB-delimited file containing all points. Each line represents a point with the following data: <id> <label> <longitude> <latitude> <abundance>, where id is a unique identifier for the point, label is used to group the points by some category (usually the scientific name of a species), longitude and latitude are the coordinates, and abundance can be either 1 (presence) or 0 (absence). A single point file can contain sets of points with different labels. Lines beginning with # are ignored. Example of an absolute path on a GNU/Linux or Mac OS X file system: Occurrences source = /home/john/data/my_points.txt 2) A path (relative or absolute) in the file system to an XML file containing occurrence data following the openModeller serialization format. The XML file must contain any root element with or without a <Sampler> subelement enclosing the <Presence> and/or <Absence> elements. Both <Presence> and <Absence> should follow the OccurrencesType defined in http://openmodeller.cria.org.br/xml/1.0/openModeller.xsd . Example of an absolute path on a Windows file system: Occurrences source = C:\data\sampler.xml 3) The GBIF Web Service address to search for occurrence data: Occurrences source = http://data.gbif.org/ws/rest/occurrence/list . This will only be available if openModeller was compiled with libcurl. 4) A TAPIR Web Service address that mapped DarwinCore 1.4, such as the speciesLink TAPIR service: Occurrences source = http://tapir.cria.org.br/tapirlink/tapir.php/specieslink . This will only be available if openModeller was compiled with libcurl.

Occurrences group

A label to filter points from the occurrences source. Defaults to the last label found when not specified. Example: Occurrences group = Physalis peruviana

Spatially unique

Optional parameter that can be used to automatically ignore duplicate points (same coordinates). Default is false. Example: Spatially unique = true

Environmentally unique

Optional parameter that can be used to automatically ignore duplicate points (same environment values). Default is false. Example: Environmentally unique = true

ENVIRONMENT PARAMETERS FOR MODEL CREATION

The following parameters are related with environment data (layers) used to create models:

Map

A layer used as a continuous environmental variable to generate the model. Multiple key-value pairs are supported for this parameter. It can be an absolute or relative path to a raster that can be read by GDAL, such as: Map = /home/john/layers/rain_coolest.tif or it can be a pointer to a TerraLib raster if openModeller was compiled with TerraLib support: Map = terralib>yourusername>yourpassword@PostgreSQL>localhost>terralib>5432>rain_coolest

Categorical map

A layer used as a categorical environmental variable to generate the model. Multiple key-value pairs are supported for this parameter. It can be an absolute or relative path to a raster that can be read by GDAL, such as: Categorical map = C:\layers\rain_coolest.tif or it can be a pointer to a TerraLib raster if openModeller was compiled with TerraLib support: Categorical map = terralib>yourusername>yourpassword@PostgreSQL>localhost>terralib>5432>rain_coolest

Mask

An optional layer that specifies the region of interest for model building. In practice, it excludes all ocurrence points that fall outside the masked area. When not specified, the first "Map" parameter is used as the mask. Please note that all "Map" and "Categorical map" parameters can also exclude points from the modelling process if they fall in a cells with nodata. Mask layers need to support nodata value assignment. Areas with zero value as data will not exclude points. A mask can be an absolute or relative path to a raster that can be read by GDAL, such as: Mask = /home/john/masks/south_america.tif or it can be a pointer to a TerraLib raster if openModeller was compiled with TerraLib support: Map = terralib>yourusername>yourpassword@PostgreSQL>localhost>terralib>5432>south_america

OUTPUT PARAMETERS FOR MODEL CREATION

The result of a model creation is a serialized model that can be stored as an XML file. If om_console is not being used to create a model (i.e., it is only being used to project an existing model), then the parameter(s) from this section should not be specified.

Output model

A path in the file system (relative or absolute) indicating where the serialized model should be saved. Example: Output model = /home/john/models/my_model.xml

MODEL PARAMETERS FOR MODEL PROJECTION

A serialized model previously generated with om_console or om_model can also be used as input if the intention is only to project an existing model. In this case, all point and environmental data parameters will be ignored.

Input model

A path in the file system (relative or absolute) to a serialized model. Example: Input model = /home/john/models/my_model.xml

ENVIRONMENT PARAMETERS FOR MODEL PROJECTION

The following parameters are only necessary to project a model. Please note that the number of layer, order and unit of measurement must match the layers used to generate the model:

Output map

A layer used as a continuous environmental variable to project the model. Multiple key-value pairs are supported for this parameter. Note that there must be a match (type of environmental variable and unit of measurement) between these layers and the layers used during model creation. The value can be an absolute or relative path to a raster that can be read by GDAL, such as: Map = /home/john/layers/rain_coolest.tif or it can be a pointer to a TerraLib raster if openModeller was compiled with TerraLib support: Map = terralib>yourusername>yourpassword@PostgreSQL>localhost>terralib>5432>rain_coolest

Output categorical map

A layer used as a categorical environmental variable to project the model. Multiple key-value pairs are supported for this parameter. Note that there must be a match (type of environmental variable and unit of measurement) between these layers and the layers used during model creation. The value can be an absolute or relative path to a raster that can be read by GDAL, such as: Categorical map = C:\layers\rain_coolest.tif or it can be a pointer to a TerraLib raster if openModeller was compiled with TerraLib support: Categorical map = terralib>yourusername>yourpassword@PostgreSQL>localhost>terralib>5432>rain_coolest

Output mask

An optional layer that specifies the region of interest for model projection. When not specified, the first "Output map" parameter is used as the mask. Please note that output mask layers need to support nodata value assignment. Areas with zero value as data will not exclude areas. A mask can be an absolute or relative path to a raster that can be read by GDAL, such as: Mask = /home/john/masks/south_america.tif or it can be a pointer to a TerraLib raster if openModeller was compiled with TerraLib support: Map = terralib>yourusername>yourpassword@PostgreSQL>localhost>terralib>5432>south_america

OUTPUT PARAMETERS FOR MODEL PROJECTION

The result of a model projection is a raster file representing the potential distribution on a specific region. The extent of this region is determined by the intersection of all "output maps" and the "output mask". The spatial reference and cell size of the resulting raster is taken from a template raster indicated with the "output format" parameter.

Output file type

This parameter is used to indicate the type of raster to be created, including value range and nodata value. The following options are available: GreyTiff (grey scale GeoTiff, 0 <= cell value <= 254, NoData = 255, extension should be *.tif), GreyTiff100 (grey scale GeoTiff, 0 <= cell value <= 100, NoData = 127, extension should be *.tif), FloatingTiff (floating point GeoTiff, 0.0 <= cell value <= 1.0, NoData = -1, extension should be *.tif), GreyBMP (grey scale BMP, 0 <= cell value <= 255, NoData = 0, extension should be *.bmp), FloatingHFA (Erdas Imagine Floating Point, 0.0 <= cell value <= 1.0, NoData = -1, extension should be *.img), ByteHFA (Erdas Imagine Byte representation, 0 <= cell value <= 100, NoData = 101, extension shold be *.img), ByteASC (ARC/Info ASCII grid Byte representation, 0 <= cell value <= 100, NoData = 101, extension should be *.asc), FloatingASC (ARC/Info ASCII grid Floating Point, 0.0 <= cell value <= 1.0, NoData = -9999, extension should be *.asc). Example: Output file type = FloatingTiff

Output format

A template raster file that specifies the cell size and spatial reference for the generated map. Example: Output Format = /home/john/layers/rain_coolest.tif

Output file

A path in the file system (relative or absolute) indicating where the distribution map (projected model) should be saved. Example: Output file = /home/john/models/my_map.tif

ALGORITHM PARAMETERS

When no algorithm is specified in the request file, om_console will display all available algorithms and prompt for user input. When an algorithm and its parameters are specified in the request file, om_console will work as a command line program and process the entire request without prompting for input. The following parameters are only necessary for model creation.

Algorithm

Id of an openModeller algorithm. When not specified, you will be prompted to select an algorithm from a list. Algorithm ids can also be discovered by using om_algorithm. Example: Algorithm = BIOCLIM

Parameter

One or more parameters can be specified for the selected algorithm. If you don't know the parameters for the algorithm, leave this key out (along with the algorithm key above) and you will be prompted to specify the values for each parameter from the chosen algorithm. To specify parameter values in the request file, put the parameter id followed by a space and then put the parameter value. Example: Parameter = StandardDeviationCutoff 0.674

SEE ALSO

AUTHORS

Index

NAME

SYNOPSIS

DESCRIPTION

POINT DATA PARAMETERS

ENVIRONMENT PARAMETERS FOR MODEL CREATION

OUTPUT PARAMETERS FOR MODEL CREATION

MODEL PARAMETERS FOR MODEL PROJECTION

ENVIRONMENT PARAMETERS FOR MODEL PROJECTION

OUTPUT PARAMETERS FOR MODEL PROJECTION

ALGORITHM PARAMETERS

SEE ALSO

AUTHORS