org.geotoolkit.image.io.plugin
Class NetcdfTranscoder

Object
  MetadataTranscoder<Metadata>
      NetcdfTranscoder

All Implemented Interfaces:

WarningProducer, Localized

public class NetcdfTranscoder
extends MetadataTranscoder<Metadata>

Mapping from NetCDF metadata to ISO 19115-2 metadata. The mapping is defined in the following web pages:

• NetCDF Attribute Convention for Dataset Discovery wiki
• UnidataDD2MI.xsl file

The String constants declared in this class are the name of attributes examined by this class. The attribute values are extracted using the NetcdfFile.findGlobalAttributeIgnoreCase(String) or Group.findAttributeIgnoreCase(String) methods. The current implementation searches the attribute values in the following places, in that order:

1. "NCISOMetadata" group
2. "CFMetadata" group
3. Global attributes
4. "THREDDSMetadata" group

The "CFMetadata" group has precedence over the global attributes because the longitude and latitude resolutions are often more accurate in that group.

NetCDF attributes
The NetCDF attributes parsed by this class are "acces_constraint", "acknowledgment", "comment", "contributor_email", "contributor_name", "contributor_role", "contributor_url", "creator_email", "creator_name", "creator_url", "cdm_data_type", "date_created", "date_issued", "date_modified", "flag_masks", "flag_meanings", "flag_names", "flag_values", "full_name", "geographic_identifier", "geospatial_lat_max", "geospatial_lat_min", "geospatial_lat_resolution", "geospatial_lat_units", "geospatial_lon_max", "geospatial_lon_min", "geospatial_lon_resolution", "geospatial_lon_units", "geospatial_vertical_max", "geospatial_vertical_min", "geospatial_vertical_positive", "geospatial_vertical_resolution", "geospatial_vertical_units", "history", "id", "institution", "keywords", "license", "metadata_creation", "name", "naming_authority", "processing_level", "project", "publisher_email", "publisher_name", "publisher_url", "purpose", "references", "standard_name", "standard_name_vocabulary", "summary", "time_coverage_duration", "time_coverage_end", "time_coverage_resolution", "time_coverage_start", "time_coverage_units", "title", "topic_category" and "keywords_vocabulary".

Known limitations

• "degrees_west" and "degrees_south" units not correctly handled
• Units of measurement not yet declared in the Band elements.
• FLAG_VALUES and FLAG_MASKS not yet included in the RangeElementDescription elements.
• Services (WMS, WCS, OPeNDAP, THREDDS) etc.) and transfer options not yet declared.

Since:

3.20

Version:

3.20

Author:

Martin Desruisseaux (Geomatys)

Module:

coverage/geotk-coverageio-netcdf (download)

View source code for this class

Nested Class Summary

static class	NetcdfTranscoder.Dimension Holds the attribute names describing a simple latitude, longitude, and vertical bounding box.
static class	NetcdfTranscoder.Responsible Holds the attribute names describing a responsible party.

Field Summary

static String	ACCESS_CONSTRAINT The "acces_constraint" attribute name for the access constraints applied to assure the protection of privacy or intellectual property.
static String	ACKNOWLEDGMENT The "acknowledgment" attribute name for a place to acknowledge various type of support for the project that produced this data (Recommended).
static String	COMMENT The "comment" attribute name for miscellaneous information about the data (Recommended).
static NetcdfTranscoder.Responsible	CONTRIBUTOR The set of attribute names for the contributor (Suggested).
static NetcdfTranscoder.Responsible	CREATOR The set of attribute names for the creator (Recommended).
static String	DATA_TYPE The "cdm_data_type" attribute name for the THREDDS data type appropriate for this dataset (Recommended).
static String	DATE_CREATED The "date_created" attribute name for the date on which the data was created (Recommended).
static String	DATE_ISSUED The "date_issued" attribute name for a date on which this data was formally issued (Suggested).
static String	DATE_MODIFIED The "date_modified" attribute name for the date on which this data was last modified (Suggested).
protected NetcdfFile	file The NetCDF file from which to extract ISO metadata.
static String	FLAG_MASKS The "flag_masks" attribute name for bitmask to apply on sample values before to compare them to the flag values.
static String	FLAG_MEANINGS The "flag_meanings" attribute name for the meaning of flag values.
static String	FLAG_NAMES The "flag_names" attribute name for the designation associated with a range element.
static String	FLAG_VALUES The "flag_values" attribute name for sample values to be flagged.
static String	GEOGRAPHIC_IDENTIFIER The "geographic_identifier" attribute name for an identifier of the geographic area.
static String	HISTORY The "history" attribute name for providing an audit trail for modifications to the original data (Recommended).
static String	IDENTIFIER The "id" attribute name for an identifier (Recommended).
static String	KEYWORDS The "keywords" attribute name for a comma separated list of key words and phrases (Highly Recommended).
static NetcdfTranscoder.Dimension	LATITUDE The set of attribute names for the minimal and maximal latitudes of the bounding box, resolution and units.
static String	LICENSE The "license" attribute name for a description of the restrictions to data access and distribution (Recommended).
static NetcdfTranscoder.Dimension	LONGITUDE The set of attribute names for the minimal and maximal longitudes of the bounding box, resolution and units.
static String	METADATA_CREATION The "metadata_creation" attribute name for the date on which the metadata was created (Suggested).
static String	NAMING_AUTHORITY The "naming_authority" attribute name for the identifier authority (Recommended).
static String	PROCESSING_LEVEL The "processing_level" attribute name for a textual description of the processing (or quality control) level of the data.
static String	PROJECT The "project" attribute name for the scientific project that produced the data (Recommended).
static NetcdfTranscoder.Responsible	PUBLISHER The set of attribute names for the publisher (Suggested).
static String	PURPOSE The "purpose" attribute name for the summary of the intentions with which the resource(s) was developed.
static String	REFERENCES The "references" attribute name for bibliographical references.
static String	STANDARD_NAME The "standard_name" attribute name for a long descriptive name for the variable taken from a controlled vocabulary of variable names.
static String	STANDARD_NAME_VOCABULARY The "standard_name_vocabulary" attribute name for indicating which controlled list of variable names has been used in the "standard_name" attribute.
static String	SUMMARY The "summary" attribute name for a paragraph describing the dataset (Highly Recommended).
static NetcdfTranscoder.Dimension	TIME The set of attribute names for the start and end times of the bounding box, resolution and units.
static String	TITLE The "title" attribute name for a short description of the dataset (Highly Recommended).
static String	TOPIC_CATEGORY The "topic_category" attribute name for a high-level geographic data thematic classification.
static NetcdfTranscoder.Dimension	VERTICAL The set of attribute names for the minimal and maximal elevations of the bounding box, resolution and units.
static String	VOCABULARY The "keywords_vocabulary" attribute name for the guideline for the words/phrases in the "keywords" attribute (Recommended).

Fields inherited from interface WarningProducer

LOGGER

Constructor Summary

NetcdfTranscoder(NetcdfFile file, WarningProducer owner)
Creates a new NetCDF to ISO mapper for the given file.

Method Summary

protected Band	createSampleDimension(VariableSimpleIF variable) Creates a <gmd:dimension> element from the given NetCDF variable.
protected GridSpatialRepresentation	createSpatialRepresentationInfo(CoordinateSystem cs) Creates a <gmd:spatialRepresentationInfo> element from the given NetCDF coordinate system.
protected Attribute	getAttribute(Group group, String name) Returns the NetCDF attribute of the given name in the given group, or null if none.
Identifier	getFileIdentifier() Returns a globally unique identifier for the current NetCDF file.
protected String	getKeywordSeparator(Group group) Returns the string to use as a keyword separator.
Metadata	readMetadata() Creates an ISO Metadata object from the information found in the NetCDF file.

Methods inherited from class MetadataTranscoder

getLocale, warningOccurred

Methods inherited from class Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Detail

TITLE

public static final String TITLE

The "title" attribute name for a short description of the dataset (Highly Recommended). If no "title" attribute is provided, then NetcdfTranscoder will look for "full_name" and "name".

Path:

• Metadata / identificationInfo / citation / title

See Also:

NetcdfFile.getTitle(), UCAR reference, Constant Field Values

SUMMARY

public static final String SUMMARY

The "summary" attribute name for a paragraph describing the dataset (Highly Recommended).

Path:

• Metadata / identificationInfo / abstract

See Also:

UCAR reference, Constant Field Values

IDENTIFIER

public static final String IDENTIFIER

The "id" attribute name for an identifier (Recommended). The combination of the "naming_authority" and the "id" should be a globally unique identifier for the dataset.

Path:

• Metadata / fileIdentifier
• Metadata / identificationInfo / citation / identifier / code

See Also:

getFileIdentifier(), NetcdfFile.getId(), UCAR reference, Constant Field Values

NAMING_AUTHORITY

public static final String NAMING_AUTHORITY

The "naming_authority" attribute name for the identifier authority (Recommended). The combination of the "naming_authority" and the "id" should be a globally unique identifier for the dataset.

Path:

• Metadata / fileIdentifier
• Metadata / identificationInfo / citation / identifier / authority

See Also:

IDENTIFIER, getFileIdentifier(), UCAR reference, Constant Field Values

STANDARD_NAME

public static final String STANDARD_NAME

The "standard_name" attribute name for a long descriptive name for the variable taken from a controlled vocabulary of variable names. This is actually a variable attribute, but sometime appears also in global attributes.

Path:

• Metadata / identificationInfo / descriptiveKeywords / keyword with KeywordType.THEME

See Also:

STANDARD_NAME_VOCABULARY, KEYWORDS, UCAR reference, Constant Field Values

STANDARD_NAME_VOCABULARY

public static final String STANDARD_NAME_VOCABULARY

The "standard_name_vocabulary" attribute name for indicating which controlled list of variable names has been used in the "standard_name" attribute.

Path:

• Metadata / identificationInfo / descriptiveKeywords / thesaurusName / title

See Also:

STANDARD_NAME, VOCABULARY, UCAR reference, Constant Field Values

KEYWORDS

public static final String KEYWORDS

The "keywords" attribute name for a comma separated list of key words and phrases (Highly Recommended).

Path:

• Metadata / identificationInfo / descriptiveKeywords / keyword with KeywordType.THEME

See Also:

VOCABULARY, STANDARD_NAME, getKeywordSeparator(Group), UCAR reference, Constant Field Values

VOCABULARY

public static final String VOCABULARY

The "keywords_vocabulary" attribute name for the guideline for the words/phrases in the "keywords" attribute (Recommended).

Path:

• Metadata / identificationInfo / descriptiveKeywords / thesaurusName / title

See Also:

KEYWORDS, STANDARD_NAME_VOCABULARY, UCAR reference, Constant Field Values

TOPIC_CATEGORY

public static final String TOPIC_CATEGORY

The "topic_category" attribute name for a high-level geographic data thematic classification. Typical values are "farming", "biota", "boundaries", "climatology meteorology atmosphere", "economy", "elevation", "environment", "geoscientific information", "health", "imagery base maps earth cover", "intelligence military", "inland waters", "location", "oceans", "planning cadastre", "society", "structure", "transportation" and "utilitiesCommunication".

Path:

• Metadata / identificationInfo / topicCategory

See Also:

TopicCategory, Constant Field Values

DATA_TYPE

public static final String DATA_TYPE

The "cdm_data_type" attribute name for the THREDDS data type appropriate for this dataset (Recommended). Examples: "Vector", "TextTable", "Grid", "Image", "Video", "Tin", "StereoModel", "Station", "Swath" or "Trajectory".

Path:

• Metadata / identificationInfo / spatialRepresentationType

See Also:

SpatialRepresentationType, UCAR reference, Constant Field Values

HISTORY

public static final String HISTORY

The "history" attribute name for providing an audit trail for modifications to the original data (Recommended).

Path:

• Metadata / dataQualityInfo / lineage / statement

See Also:

UCAR reference, Constant Field Values

COMMENT

public static final String COMMENT

The "comment" attribute name for miscellaneous information about the data (Recommended).

Path:

• Metadata / identificationInfo / supplementalInformation

See Also:

UCAR reference, Constant Field Values

METADATA_CREATION

public static final String METADATA_CREATION

The "metadata_creation" attribute name for the date on which the metadata was created (Suggested). This is actually defined in the "NCISOMetadata" subgroup.

Path:

• Metadata / dateStamp

See Also:

Constant Field Values

DATE_CREATED

public static final String DATE_CREATED

The "date_created" attribute name for the date on which the data was created (Recommended).

Path:

• Metadata / identificationInfo / citation / date / date with DateType.CREATION

See Also:

UCAR reference, Constant Field Values

DATE_MODIFIED

public static final String DATE_MODIFIED

The "date_modified" attribute name for the date on which this data was last modified (Suggested).

Path:

• Metadata / identificationInfo / citation / date / date with DateType.REVISION

See Also:

UCAR reference, Constant Field Values

DATE_ISSUED

public static final String DATE_ISSUED

The "date_issued" attribute name for a date on which this data was formally issued (Suggested).

Path:

• Metadata / identificationInfo / citation / date / date with DateType.PUBLICATION

See Also:

UCAR reference, Constant Field Values

CREATOR

public static final NetcdfTranscoder.Responsible CREATOR

The set of attribute names for the creator (Recommended).

Path:

• Metadata / identificationInfo / citation with Role.ORIGINATOR

See Also:

CONTRIBUTOR, PUBLISHER, UCAR reference

CONTRIBUTOR

public static final NetcdfTranscoder.Responsible CONTRIBUTOR

The set of attribute names for the contributor (Suggested).

Path:

• Metadata / identificationInfo / citation

See Also:

CREATOR, PUBLISHER, UCAR reference

PUBLISHER

public static final NetcdfTranscoder.Responsible PUBLISHER

The set of attribute names for the publisher (Suggested).

Path:

• Metadata / distributionInfo / distributors / distributorContact with Role.PUBLISHER
• Metadata / identificationInfo / descriptiveKeywords / keyword with the "dataCenter" KeywordType

See Also:

CREATOR, CONTRIBUTOR, UCAR reference

PROJECT

public static final String PROJECT

The "project" attribute name for the scientific project that produced the data (Recommended).

Path:

• Metadata / identificationInfo / descriptiveKeywords / keyword with the "project" KeywordType

See Also:

UCAR reference, Constant Field Values

PURPOSE

public static final String PURPOSE

The "purpose" attribute name for the summary of the intentions with which the resource(s) was developed.

Path:

• Metadata / identificationInfo / purpose

See Also:

Constant Field Values

REFERENCES

public static final String REFERENCES

The "references" attribute name for bibliographical references.

Path:

• Metadata / identificationInfo / citation in its own instance

See Also:

Constant Field Values

PROCESSING_LEVEL

public static final String PROCESSING_LEVEL

The "processing_level" attribute name for a textual description of the processing (or quality control) level of the data.

Path:

• Metadata / contentInfo / processingLevelCode

See Also:

UCAR reference, Constant Field Values

ACKNOWLEDGMENT

public static final String ACKNOWLEDGMENT

The "acknowledgment" attribute name for a place to acknowledge various type of support for the project that produced this data (Recommended).

Path:

• Metadata / identificationInfo / credit

See Also:

UCAR reference, Constant Field Values

LICENSE

public static final String LICENSE

The "license" attribute name for a description of the restrictions to data access and distribution (Recommended).

Path:

• Metadata / identificationInfo / resourceConstraints / useLimitation

See Also:

UCAR reference, Constant Field Values

ACCESS_CONSTRAINT

public static final String ACCESS_CONSTRAINT

The "acces_constraint" attribute name for the access constraints applied to assure the protection of privacy or intellectual property. Typical values are "copyright", "patent", "patent pending", "trademark", "license", "intellectual property rights" or "restricted".

Path:

• Metadata / identificationInfo / resourceConstraints / accessConstraints

See Also:

Restriction, Constant Field Values

GEOGRAPHIC_IDENTIFIER

public static final String GEOGRAPHIC_IDENTIFIER

The "geographic_identifier" attribute name for an identifier of the geographic area.

Path:

• Metadata / identificationInfo / extent / geographicElement / geographicIdentifier

See Also:

Constant Field Values

LATITUDE

public static final NetcdfTranscoder.Dimension LATITUDE

The set of attribute names for the minimal and maximal latitudes of the bounding box, resolution and units. Latitudes are assumed to be in decimal degrees north, unless a units attribute is specified.

Path:

• Metadata / identificationInfo / extent / geographicElement / southBoundLatitude or northBoundLatitude
• Metadata / spatialRepresentationInfo / axisDimensionProperties / resolution

See Also:

LONGITUDE, VERTICAL, TIME, UCAR reference

LONGITUDE

public static final NetcdfTranscoder.Dimension LONGITUDE

The set of attribute names for the minimal and maximal longitudes of the bounding box, resolution and units. Longitudes are assumed to be in decimal degrees east, unless a units attribute is specified.

Path:

• Metadata / identificationInfo / extent / geographicElement / westBoundLongitude or eastBoundLongitude
• Metadata / spatialRepresentationInfo / axisDimensionProperties / resolution

See Also:

LATITUDE, VERTICAL, TIME, UCAR reference

VERTICAL

public static final NetcdfTranscoder.Dimension VERTICAL

The set of attribute names for the minimal and maximal elevations of the bounding box, resolution and units. Elevations are assumed to be in metres above the ground, unless a units attribute is specified.

Path:

• Metadata / identificationInfo / extent / verticalElement / minimumValue or maximumValue
• Metadata / spatialRepresentationInfo / axisDimensionProperties / resolution

See Also:

LATITUDE, LONGITUDE, TIME, UCAR reference

TIME

public static final NetcdfTranscoder.Dimension TIME

The set of attribute names for the start and end times of the bounding box, resolution and units.

Path:

• Metadata / identificationInfo / extent / temporalElement / extent
• Metadata / spatialRepresentationInfo / axisDimensionProperties / resolution

See Also:

LATITUDE, LONGITUDE, VERTICAL, UCAR reference

FLAG_NAMES

public static final String FLAG_NAMES

The "flag_names" attribute name for the designation associated with a range element. This attribute can be associated to variables. If specified, they shall be one flag name for each flag mask, flag value and flag meaning.

Path:

• Metadata / contentInfo / rangeElementDescription / name

See Also:

Constant Field Values

FLAG_MASKS

public static final String FLAG_MASKS

The "flag_masks" attribute name for bitmask to apply on sample values before to compare them to the flag values.

Path:

• Metadata / contentInfo / rangeElementDescription / rangeElement

See Also:

Constant Field Values

FLAG_VALUES

public static final String FLAG_VALUES

The "flag_values" attribute name for sample values to be flagged. The flag masks, flag values and flag meaning attributes, used together, describe a blend of independent boolean conditions and enumerated status codes. A flagged condition is identified by a bitwise AND of the variable value and each flag masks value; a result that matches the flag values value indicates a true condition.

Path:

• Metadata / contentInfo / rangeElementDescription / rangeElement

See Also:

Constant Field Values

FLAG_MEANINGS

public static final String FLAG_MEANINGS

The "flag_meanings" attribute name for the meaning of flag values. Each flag values and flag masks must coincide with a flag meanings.

Path:

• Metadata / contentInfo / rangeElementDescription / definition

See Also:

Constant Field Values

file

protected final NetcdfFile file

The NetCDF file from which to extract ISO metadata. This file is set at construction time.

Constructor Detail

NetcdfTranscoder

public NetcdfTranscoder(NetcdfFile file,
                        WarningProducer owner)

Creates a new NetCDF to ISO mapper for the given file. While this constructor accepts arbitrary NetcdfFile instance, the NetcdfDataset subclass is necessary in order to get coordinate system information.

Parameters:

file - The NetCDF file from which to parse metadata.

owner - Typically the SpatialImageReader or SpatialImageWriter object using this transcoder, or null.

Method Detail

getAttribute

protected Attribute getAttribute(Group group,
                                 String name)

Returns the NetCDF attribute of the given name in the given group, or null if none. This method is invoked for every global and group attributes to be read by this class (but not variable attributes), thus providing a single point where subclasses can filter the attributes to be read. The name argument is typically (but is not restricted too) one of the constants defined in this class.

Parameters:

group - The group in which to search the attribute, or null for global attributes.

name - The name of the attribute to search (can not be null).

Returns:

The attribute, or null if none.

getFileIdentifier

public Identifier getFileIdentifier()
                             throws IOException

Returns a globally unique identifier for the current NetCDF file. The default implementation builds the identifier from the following attributes:

• "naming_authority" used as the authority.
• "id", or NetcdfFile.getId() if no identifier attribute was found.

Subclasses can override this method if they need to complete the information.

Returns:

The globally unique identifier, or null if none.

Throws:

IOException - If an I/O operation was necessary but failed.

getKeywordSeparator

protected String getKeywordSeparator(Group group)
                              throws IOException

Returns the string to use as a keyword separator. This separator is used for parsing the "keywords" attribute value. The default implementation returns ",". Subclasses can override this method in an other separator (possibly determined from the file content) is desired.

Parameters:

group - The NetCDF group from which keywords are read.

Returns:

The string to use as a keyword separator, as a regular expression.

Throws:

IOException - If an I/O operation was necessary but failed.

createSpatialRepresentationInfo

protected GridSpatialRepresentation createSpatialRepresentationInfo(CoordinateSystem cs)
                                                             throws IOException

Creates a <gmd:spatialRepresentationInfo> element from the given NetCDF coordinate system. Subclasses can override this method if they need to complete the information provided in the returned object.

Parameters:

cs - The NetCDF coordinate system.

Returns:

The grid spatial representation info.

Throws:

IOException - If an I/O operation was necessary but failed.

createSampleDimension

protected Band createSampleDimension(VariableSimpleIF variable)
                              throws IOException

Creates a <gmd:dimension> element from the given NetCDF variable. Subclasses can override this method if they need to complete the information provided in the returned object.

Parameters:

variable - The NetCDF variable.

Returns:

The sample dimension information.

Throws:

IOException - If an I/O operation was necessary but failed.

readMetadata

public Metadata readMetadata()
                      throws IOException

Creates an ISO Metadata object from the information found in the NetCDF file.

Specified by:

readMetadata in class MetadataTranscoder<Metadata>

Returns:

The ISO metadata object.

Throws:

IOException - If an I/O operation was necessary but failed.