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* A class that can store arbitrary n-dimensional data along with further
* information.
*
* The {@link DataArray} is the core entity of the NIX data model, its purpose is to
* store arbitrary n-dimensional data. In addition to the common fields id, name, type, and definition
* the DataArray stores sufficient information to understand the physical nature of the stored data.
*
* A guiding principle of the data model is provides enough information to create a
* plot of the stored data. In order to do so, the DataArray defines a property
* {@link DataType} which provides the physical type of the stored data (for example
* 16 bit integer or double precision IEEE floatingpoint number).
* The property {@link DataArray#setUnit(String)} specifies the SI unit of the values stored in the
* DataArray{} whereas the {@link DataArray#setLabel(String)} defines what is given in this units.
* Together, both specify what corresponds to the the y-axis of a plot.
*
* In some cases it is much more efficient or convenient to store data not as
* floating point numbers but rather as (16 bit) integer values as, for example
* read from a data acquisition board.
* In order to convert such data to the correct values, we follow the approach
* taken by the comedi data-acquisition library (http://www.comedi.org)
* and provide {@link DataArray#setPolynomCoefficients(double[])} and an {@link DataArray#setExpansionOrigin(double)}.
*
*
Create a new data array
* A DataArray can only be created at an existing block. Do not use the
* DataArrays constructors for this purpose.
*
* Block b = ...;
* DataArray da = b.createDataArray("array_one", "testdata", DataType.Double, new NDSize(new int[] { 3, 4, 2 }));
*
*
* @see Block
* @see DataType
*/
@Properties(value = {
@Platform(include = {""}, link = "nix", preload = "hdf5"),
@Platform(value = "linux"),
@Platform(value = "windows")})
@Namespace("nix")
public class DataArray extends EntityWithSources {
static {
Loader.load();
}
//--------------------------------------------------
// Constructors
//--------------------------------------------------
/**
* Constructor that creates an uninitialized DataArray.
*
* Calling any method on an uninitialized data array will throw a {@link java.lang.RuntimeException}
* exception. The following code illustrates how to check if a data array is initialized:
*/
public DataArray() {
allocate();
}
private native void allocate();
//--------------------------------------------------
// Base class methods
//--------------------------------------------------
public native
@Cast("bool")
boolean isNone();
/**
* Get id of the data array.
*
* @return ID string.
*/
public native
@Name("id")
@StdString
String getId();
private native
@Cast("time_t")
long createdAt();
/**
* Get the creation date of the data array.
*
* @return The creation date of the data array.
*/
public Date getCreatedAt() {
return DateUtils.convertSecondsToDate(createdAt());
}
private native
@Cast("time_t")
long updatedAt();
/**
* Get the date of the last update.
*
* @return The date of the last update.
*/
public Date getUpdatedAt() {
return DateUtils.convertSecondsToDate(updatedAt());
}
/**
* Sets the time of the last update to the current time if the field is not set.
*/
public native void setUpdatedAt();
/**
* Sets the time of the last update to the current time.
*/
public native void forceUpdatedAt();
/**
* Sets the creation time to the current time if the field is not set.
*/
public native void setCreatedAt();
private native void forceCreatedAt(@Cast("time_t") long time);
/**
* Sets the creation date to the provided value even if the attribute is set.
*
* @param date The creation date to set.
*/
public void forceCreatedAt(Date date) {
forceCreatedAt(DateUtils.convertDateToSeconds(date));
}
/**
* Setter for the type of the data array.
*
* @param type The type of the data array.
*/
public native
@Name("type")
void setType(@StdString String type);
/**
* Getter for the type of the data array
*
* @return The type of the data array
*/
public native
@Name("type")
@StdString
String getType();
/**
* Getter for the name of the data array.
*
* @return The name of the data array.
*/
public native
@Name("name")
@StdString
String getName();
private native void definition(@Const @ByVal None t);
private native void definition(@StdString String definition);
/**
* Setter for the definition of the data array. If null is passed definition is removed.
*
* @param definition definition of data array
*/
public void setDefinition(String definition) {
if (definition != null) {
definition(definition);
} else {
definition(new None());
}
}
private native
@ByVal
OptionalUtils.OptionalString definition();
/**
* Getter for the definition of the data array.
*
* @return The definition of the data array.
*/
public String getDefinition() {
OptionalUtils.OptionalString defintion = definition();
if (defintion.isPresent()) {
return defintion.getString();
}
return null;
}
private native
@ByVal
Section metadata();
/**
* Get metadata associated with this entity.
*
* @return The associated section, if no such section exists null is returned.
* @see Section
*/
public
@Name("metadata")
Section getMetadata() {
Section section = metadata();
if (section.isInitialized()) {
return section;
} else {
return null;
}
}
/**
* Associate the entity with some metadata.
*
* Calling this method will replace previously stored information.
*
* @param metadata The {@link Section} that should be associated
* with this entity.
* @see Section
*/
public native
@Name("metadata")
void setMetadata(@Const @ByRef Section metadata);
/**
* Associate the entity with some metadata.
*
* Calling this method will replace previously stored information.
*
* @param id The id of the {@link Section} that should be associated
* with this entity.
* @see Section
*/
public native
@Name("metadata")
void setMetadata(@StdString String id);
private native void metadata(@Const @ByVal None t);
/**
* Removes metadata associated with the entity.
*
* @see Section
*/
public void removeMetadata() {
metadata(new None());
}
/**
* Get the number of sources associated with this entity.
*
* @return The number sources.
* @see Source
*/
public native
@Name("sourceCount")
long getSourceCount();
/**
* Checks if a specific source is associated with this entity.
*
* @param id The source id to check.
* @return True if the source is associated with this entity, false otherwise.
* @see Source
*/
public native
@Cast("bool")
boolean hasSource(@StdString String id);
/**
* Checks if a specific source is associated with this entity.
*
* @param source The source to check.
* @return True if the source is associated with this entity, false otherwise.
* @see Source
*/
public native
@Cast("bool")
boolean hasSource(@Const @ByRef Source source);
private native
@Name("getSource")
@ByVal
Source fetchSource(@StdString String id);
/**
* Returns an associated source identified by its id.
*
* @param id The id of the associated source.
* @see Source
*/
public Source getSource(String id) {
Source source = fetchSource(id);
if (source.isInitialized()) {
return source;
}
return null;
}
private native
@Name("getSource")
@ByVal
Source fetchSource(@Cast("size_t") long index);
/**
* Retrieves an associated source identified by its index.
*
* @param index The index of the associated source.
* @return The source with the given id. If it doesn't exist an exception
* will be thrown.
* @see Source
*/
public Source getSource(long index) {
Source source = fetchSource(index);
if (source.isInitialized()) {
return source;
}
return null;
}
private native
@ByVal
VectorUtils.SourceVector sources();
/**
* Get all sources associated with this entity.
*
* @return All associated sources that match the given filter as a list.
* @see Source
*/
public List getSources() {
return sources().getSources();
}
private native void sources(@Const @ByVal VectorUtils.SourceVector sources);
/**
* Set all sources associations for this entity.
*
* All previously existing associations will be overwritten.
*
* @param sources A list with all sources.
* @see Source
*/
public void setSources(List sources) {
sources(new VectorUtils.SourceVector(sources));
}
/**
* Associate a new source with the entity.
*
* If a source with the given id already is associated with the
* entity, the call will have no effect.
*
* @param id The id of the source.
* @see Source
*/
public native void addSource(@StdString String id);
/**
* Associate a new source with the entity.
*
* Calling this method will have no effect if the source is already associated to this entity.
*
* @param source The source to add.
* @see Source
*/
public native void addSource(@Const @ByRef Source source);
/**
* Remove a source from the list of associated sources.
*
* This method just removes the association between the entity and the source.
* The source itself will not be deleted from the file.
*
* @param id The id of the source to remove.
* @return True if the source was removed, false otherwise.
* @see Source
*/
public native
@Cast("bool")
boolean removeSource(@StdString String id);
/**
* Remove a source from the list of associated sources.
*
* This method just removes the association between the entity and the source.
* The source itself will not be deleted from the file.
*
* @param source The source to remove.
* @return True if the source was removed, false otherwise.
* @see Source
*/
public native
@Cast("bool")
boolean removeSource(@Const @ByRef Source source);
//--------------------------------------------------
// Element getters and setters
//--------------------------------------------------
private native
@ByVal
OptionalUtils.OptionalString label();
/**
* Get the label for the values stored in the DataArray.
*
* @return The label of the data array. Returns null if not present.
*/
public String getLabel() {
OptionalUtils.OptionalString label = label();
if (label.isPresent()) {
return label.getString();
}
return null;
}
private native void label(@StdString String label);
private native void label(@Const @ByVal None t);
/**
* Set the label for the data stored. If null is passed the label is removed.
*
* @param label The label of the data array.
*/
public void setLabel(String label) {
if (label != null) {
label(label);
} else {
label(new None());
}
}
private native
@ByVal
OptionalUtils.OptionalString unit();
/**
* Get the unit of the data stored in this data array.
*
* @return The unit of the data array. null if not present.
*/
public String getUnit() {
OptionalUtils.OptionalString unit = unit();
if (unit.isPresent()) {
return unit.getString();
}
return null;
}
private native void unit(@StdString String unit);
private native void unit(@Const @ByVal None t);
/**
* Set the unit for the values stored in this DataArray. If null is passed the unit is removed.
*
* @param unit The unit of the data array.
*/
public void setUnit(String unit) {
if (unit != null) {
unit(unit);
} else {
unit(new None());
}
}
private native
@ByVal
OptionalUtils.OptionalDouble expansionOrigin();
/**
* Returns the expansion origin of the calibration polynom.
*
* The expansion origin is 0.0 by default.
*
* @return The expansion origin.
*/
public double getExpansionOrigin() {
OptionalUtils.OptionalDouble expansionOrigin = expansionOrigin();
if (expansionOrigin.isPresent()) {
return expansionOrigin.getDouble();
}
return 0.0;
}
/**
* Set the expansion origin for the calibration.
*
* @param expansionOrigin The expansion origin for the calibration.
*/
public native
@Name("expansionOrigin")
void setExpansionOrigin(double expansionOrigin);
private native void polynomCoefficients(@StdVector double[] polynomCoefficients);
private native void polynomCoefficients(@Const @ByVal None t);
/**
* Set the polynom coefficients for the calibration.
*
* By default this is set to a two element array of [0.0, 1.0] for a linear calibration
* with zero offset.
*
* @param polynomCoefficients The new polynom coefficients for the calibration.
* If null, deletes for the `polynomCoefficients` attribute.
*/
public void setPolynomCoefficients(double[] polynomCoefficients) {
if (polynomCoefficients != null) {
polynomCoefficients(polynomCoefficients);
} else {
polynomCoefficients(new None());
}
}
private native
@StdVector
DoublePointer polynomCoefficients();
/**
* Returns the polynom coefficients.
*
* @return The polynom coefficients for the calibration.
*/
public double[] getPolynomCoefficients() {
return VectorUtils.convertPointerToArray(polynomCoefficients());
}
//--------------------------------------------------
// Methods concerning dimensions
//--------------------------------------------------
private native
@ByVal
VectorUtils.DimensionVector dimensions();
/**
* Get all dimensions associated with this data array.
*
* @return The dimensions as a list
* @see Dimension
*/
public List getDimensions() {
return dimensions().getDimensions();
}
/**
* Get all dimensions associated with this data array.
*
* The parameter filter can be used to filter sources by various
* criteria.
*
* @param filter A filter function.
* @return The filtered dimensions as a list
* @see Dimension
*/
public List getDimensions(Predicate filter) {
List result = new ArrayList<>();
for (Dimension dimension : getDimensions()) {
if (filter.test(dimension)) {
result.add(dimension);
}
}
return result;
}
/**
* Returns the number of dimensions stored in the DataArray.
*
* This matches the dimensionality of the data stored in this property.
*
* @return The number of dimensions.
* @see Dimension
*/
public native
@Name("dimensionCount")
@Cast("size_t")
long getDimensionCount();
private native
@Name("getDimension")
@ByVal
Dimension fetchDimension(@Cast("size_t") long id);
/**
* Returns the Dimension object for the specified dimension of the data.
*
* @param id The index of the respective dimension.
* @return The dimension object.
* @see Dimension
*/
public Dimension getDimension(long id) {
Dimension dimension = fetchDimension(id);
if (dimension.isInitialized()) {
return dimension;
}
return null;
}
/**
* Append a new SetDimension to the list of existing dimension descriptors.
*
* @return The newly created SetDimension.
* @see SetDimension
*/
public native
@ByVal
SetDimension appendSetDimension();
/**
* Append a new RangeDimension to the list of existing dimension descriptors.
*
* @param ticks The ticks of the RangeDimension to create.
* @return The newly created RangeDimension
* @see RangeDimension
*/
public native
@ByVal
RangeDimension appendRangeDimension(@StdVector double[] ticks);
/**
* Append a new RangeDimension that uses the data stored in this DataArray as ticks.
* This works only(!) if the DataArray in 1D and the stored data is numeric.
*
* @return The created RangeDimension
* @see RangeDimension
*/
public native
@ByVal
RangeDimension appendAliasRangeDimension();
/**
* Append a new SampledDimension to the list of existing dimension descriptors.
*
* @param samplingInterval The sampling interval of the SetDimension to create.
* @return The newly created SampledDimension.
* @see SampledDimension
*/
public native
@ByVal
SampledDimension appendSampledDimension(double samplingInterval);
/**
* Create a new SetDimension at a specified dimension index.
*
* This adds a new dimension descriptor of the type {@link SetDimension} that describes the dimension
* of the data at the specified index.
*
* @param id The index of the dimension. Must be a value > 0 and <= `dimensionCount + 1`.
* @return The created dimension descriptor.
* @see SetDimension
*/
public native
@ByVal
SetDimension createSetDimension(@Cast("size_t") long id);
/**
* Create a new RangeDimension at a specified dimension index.
*
* This adds a new dimension descriptor of the type {@link RangeDimension} that describes the dimension
* of the data at the specified index.
*
* @param id The index of the dimension. Must be a value > 0 and <= `dimensionCount + 1`.
* @param ticks Array with {@link RangeDimension#setTicks(double[])}.
* @return The created dimension descriptor.
* @see RangeDimension
*/
public native
@ByVal
RangeDimension createRangeDimension(@Cast("size_t") long id, @StdVector double[] ticks);
/**
* Create a new RangeDimension that uses the data stored in this DataArray as ticks.
*
* @return The created dimension descriptor.
* @see RangeDimension
*/
public native
@ByVal
RangeDimension createAliasRangeDimension();
/**
* Create a new SampledDimension at a specified dimension index.
*
* This adds a new dimension descriptor of the type {@link SampledDimension} that describes the dimension
* of the data at the specified index.
*
* @param id The index of the dimension. Must be a value > 0 and <= `dimensionCount + 1`.
* @param samplingInterval The sampling interval of the dimension.
* @return The created dimension descriptor.
* @see SampledDimension
*/
public native
@ByVal
SampledDimension createSampledDimension(@Cast("size_t") long id, double samplingInterval);
/**
* Remove a dimension descriptor at a specified index.
*
* @param id The index of the dimension. Must be a value > 0 and < `getDimensionCount + 1`.
* @see Dimension
*/
public native
@Cast("bool")
boolean deleteDimension(@Cast("size_t") long id);
//--------------------------------------------------
// Methods concerning data access.
//--------------------------------------------------
/**
* Get the extent of the data of the DataArray entity.
*
* @return The data extent.
* @see NDSize
*/
public native
@Name("dataExtent")
@ByVal
NDSize getDataExtent();
/**
* Set the data extent of the DataArray entity.
*
* @param extent The extent of the data.
* @see NDSize
*/
public native
@Name("dataExtent")
void setDataExtent(@Const @ByRef NDSize extent);
/**
* Get the data type of the data stored in the DataArray entity.
*
* @return The data type of the DataArray.
* @see DataType
*/
public native
@Name("dataType")
@ByVal
@Cast("nix::DataType")
int getDataType();
private native void getDataDirect(@Cast("nix::DataType") int dtype,
@Cast("void*") byte[] data,
@Const @ByRef NDSize count,
@Const @ByRef NDSize offset);
private native void getDataDirect(@Cast("nix::DataType") int dtype,
@Cast("void*") short[] data,
@Const @ByRef NDSize count,
@Const @ByRef NDSize offset);
private native void getDataDirect(@Cast("nix::DataType") int dtype,
@Cast("void*") int[] data,
@Const @ByRef NDSize count,
@Const @ByRef NDSize offset);
private native void getDataDirect(@Cast("nix::DataType") int dtype,
@Cast("void*") long[] data,
@Const @ByRef NDSize count,
@Const @ByRef NDSize offset);
private native void getDataDirect(@Cast("nix::DataType") int dtype,
@Cast("void*") float[] data,
@Const @ByRef NDSize count,
@Const @ByRef NDSize offset);
private native void getDataDirect(@Cast("nix::DataType") int dtype,
@Cast("void*") double[] data,
@Const @ByRef NDSize count,
@Const @ByRef NDSize offset);
private native void setDataDirect(@Cast("nix::DataType") int dtype,
@Cast("const void*") byte[] data,
@Const @ByRef NDSize count,
@Const @ByRef NDSize offset);
private native void setDataDirect(@Cast("nix::DataType") int dtype,
@Cast("const void*") short[] data,
@Const @ByRef NDSize count,
@Const @ByRef NDSize offset);
private native void setDataDirect(@Cast("nix::DataType") int dtype,
@Cast("const void*") int[] data,
@Const @ByRef NDSize count,
@Const @ByRef NDSize offset);
private native void setDataDirect(@Cast("nix::DataType") int dtype,
@Cast("const void*") long[] data,
@Const @ByRef NDSize count,
@Const @ByRef NDSize offset);
private native void setDataDirect(@Cast("nix::DataType") int dtype,
@Cast("const void*") float[] data,
@Const @ByRef NDSize count,
@Const @ByRef NDSize offset);
private native void setDataDirect(@Cast("nix::DataType") int dtype,
@Cast("const void*") double[] data,
@Const @ByRef NDSize count,
@Const @ByRef NDSize offset);
//--------------------------------------------------
// public getData methods
//--------------------------------------------------
/**
* Get stored data. Data is stored in the array passed.
*
* @param data byte array
* @param count dimensions
* @param offset offset
*/
public void getData(byte[] data, NDSize count, NDSize offset) {
getDataDirect(DataType.Int8, data, count, offset);
}
/**
* Get stored data. Data is stored in the array passed.
*
* @param data short array
* @param count dimensions
* @param offset offset
*/
public void getData(short[] data, NDSize count, NDSize offset) {
getDataDirect(DataType.Int16, data, count, offset);
}
/**
* Get stored data. Data is stored in the array passed.
*
* @param data int array
* @param count dimensions
* @param offset offset
*/
public void getData(int[] data, NDSize count, NDSize offset) {
getDataDirect(DataType.Int32, data, count, offset);
}
/**
* Get stored data. Data is stored in the array passed.
*
* @param data long array
* @param count dimensions
* @param offset offset
*/
public void getData(long[] data, NDSize count, NDSize offset) {
getDataDirect(DataType.Int64, data, count, offset);
}
/**
* Get stored data. Data is stored in the array passed.
*
* @param data float array
* @param count dimensions
* @param offset offset
*/
public void getData(float[] data, NDSize count, NDSize offset) {
getDataDirect(DataType.Float, data, count, offset);
}
/**
* Get stored data. Data is stored in the array passed.
*
* @param data double array
* @param count dimensions
* @param offset offset
*/
public void getData(double[] data, NDSize count, NDSize offset) {
getDataDirect(DataType.Double, data, count, offset);
}
//--------------------------------------------------
// public setData methods
//--------------------------------------------------
/**
* Set byte array data.
*
* @param data data
* @param count dimensions
* @param offset offset
*/
public void setData(byte[] data, NDSize count, NDSize offset) {
setDataDirect(DataType.Int8, data, count, offset);
}
/**
* Set short array data.
*
* @param data data
* @param count dimensions
* @param offset offset
*/
public void setData(short[] data, NDSize count, NDSize offset) {
setDataDirect(DataType.Int16, data, count, offset);
}
/**
* Set integer array data.
*
* @param data data
* @param count dimensions
* @param offset offset
*/
public void setData(int[] data, NDSize count, NDSize offset) {
setDataDirect(DataType.Int32, data, count, offset);
}
/**
* Set long array data.
*
* @param data data
* @param count dimensions
* @param offset offset
*/
public void setData(long[] data, NDSize count, NDSize offset) {
setDataDirect(DataType.Int64, data, count, offset);
}
/**
* Set float array data.
*
* @param data data
* @param count dimensions
* @param offset offset
*/
public void setData(float[] data, NDSize count, NDSize offset) {
setDataDirect(DataType.Float, data, count, offset);
}
/**
* Set double array data.
*
* @param data data
* @param count dimensions
* @param offset offset
*/
public void setData(double[] data, NDSize count, NDSize offset) {
setDataDirect(DataType.Double, data, count, offset);
}
//--------------------------------------------------
// Overrides
//--------------------------------------------------
@Override
public String toString() {
return "DataArray: {name = " + this.getName()
+ ", type = " + this.getType()
+ ", id = " + this.getId() + "}";
}
}
