All Classes

Class	Description
AbstractAmplitudeTransformer	Ancestor for amplitude transformation schemes.
AbstractBinaryFormatsBasedMultiSpectrumFilter	Ancestor for formats-based filters that require exactly two spectra.
AbstractCleaner	Abstract base class for cleaners handling weka.core.Instance objects.
AbstractCleaner	Abstract base class for cleaners handling Spectrum objects.
AbstractDatabaseConnectionCleaner	Ancestor for cleaners that require a database connection.
AbstractDatabaseConnectionCleaner	Ancestor for cleaners that require a database connection.
AbstractDatabaseFilter	Abstract superclass for filters that operate on the database.
AbstractDetrend	Ancestor for schemes that perform detrend.
AbstractEvaluator	Abstract base class for evaluator handling weka.core.Instance objects.
AbstractFieldInstanceGenerator	Abstract base class for schemes that turn spectra into weka.core.Instance objects.
AbstractFieldInstanceGeneratorWithClass	Ancestor for generators that use fields and a target to generate the instance.
AbstractFormatsBasedMultiSpectrumFilter	Ancestor for filters that require the user to specify the formats of the spectra to use for the filtering process.
AbstractIDProviderPanel	Panel that generates IDs.
AbstractInPlaceSpectrumTransformer	Ancestor for spectrum transformers that allow the processing to happen in-place, rather than on a copy of the data.
AbstractJCampSpectrumReader	Ancestor for JCamp spectrum formats.
AbstractMultiPageMenuItem	Ancestor for menu item generators for the 3way data heatmap viewer's multi-page pane.
AbstractMultiplicativeScatterCorrection	Ancestor for schemes that perform multiplicative scatter correction.
AbstractMultiSpectrumFilter	Abstract base class for multi-spectrum filters.
AbstractMultiSpectrumOperation	Ancestor for multi-spectrum operations.
AbstractMultiSpectrumReportFilter	Abstract base class for multi-spectrum report filters.
AbstractNearestNeighborBasedEvaluator	Ancestor for evaluators that use a nearest neighbor search.
AbstractOutlierRemoval	Ancestor for outlier removal schemes that work on multiple spectra.
AbstractPlotUpdater	Ancestor for classes that determine when to update the spectrum display, i.e., repaint all of it.
AbstractPositionableThreeWayDataOverlay	Ancestor for overlays that can be positioned on the 3-way data panel.
AbstractPositionableThreeWayDataOverlayWithDimensions	Ancestor for overlays that can be positioned on the heatmap panel and support dimensions.
AbstractPostProcessor	Abstract base class for postprocessing weka.core.Instances objects.
AbstractPredictionCheck	Ancestor for prediction checks.
AbstractSampleDataReader	Ancestor for sample data readers.
AbstractSampleIDExtraction	Ancestor for schemes that extract the sample ID from the filename.
AbstractSerializableCleaner	Abstract cleaner that can serialize its setup to disk and also load it from there.
AbstractSerializableCleaner	Abstract cleaner that can serialize its setup to disk and also load it from there.
AbstractSerializableEvaluator	Abstract evaluator that can serialize its setup to disk and also load it from there.
AbstractSerializableFilter	Abstract cleaner that can serialize its setup to disk and also load it from there.
AbstractSerializablePostProcessor	Abstract postprocessor that can serialize its setup to disk and also load it from there.
AbstractSpectralDbBackend	Ancestor for classes that provide a spectral DB backend.
AbstractSpectrumAnalysis	Ancestor for spectrum-based data analysis schemes.
AbstractSpectrumBasedInstanceGenerator	Abstract base class for schemes that turn spectra/sample data into weka.core.Instance objects.
AbstractSpectrumComparator	Ancestor for spectrum comparators.
AbstractSpectrumConditions	Ancestor for spectrum conditions.
AbstractSpectrumFeatureGenerator	Abstract base class for Spectrum feature generation.
AbstractSpectrumHandler	Ancestor for spectrum handlers.
AbstractSpectrumImageGenerator	Ancestor for image generators from spectra.
AbstractSpectrumImageGeneratorWithRange	Ancestor for spectrum image generators that limit the amplitude ranges.
AbstractSpectrumInstanceGenerator	Abstract base class for schemes that turn spectra/sample data into weka.core.Instance objects (spectra is included).
AbstractSpectrumInstanceGeneratorWithClass	Abstract base class for schemes that turn spectra/sample data into weka.core.Instance objects (spectra is included).
AbstractSpectrumPaintlet	A specialized paintlet for sequence panels.
AbstractSpectrumPanelScriptlet	Ancestor for scriptlets that require a SpectrumPanel.
AbstractSpectrumReader	Abstract ancestor for readers that read files in various formats and turn them into spectrums.
AbstractSpectrumWriter	Abstract ancestor for writers that write spectra to files in various formats.
AbstractSpreadSheetRowGenerator	Abstract base class for schemes that turn spectra into spreadsheet row objects.
AbstractStandardiseFilter	Ancestor for filters that standardize by interpolation.
AbstractThreeWayDataFeatureGenerator	Abstract base class for ThreeWayData feature generation.
AbstractThreeWayDataMerge	Ancestor for merge schemes.
AbstractThreeWayDataOverlay	Ancestor for 3-way data image overlays.
AbstractThreeWayDataReader	Abstract ancestor for readers that read files in various formats and turn them into three way data structures.
AbstractThreeWayDataTrainPostProcessor	Ancestor for post-processors of a model generated by ThreeWayDataTrain.
AbstractThreeWayDataWriter	Ancestor for writers for 3-way data.
AbstractWekaSpectrumAnalysis	Ancestor for Weka-based analysis schemes, i.e., ones that use Instances as basis.
Add	Adds the amplitudes of first spectrum to the amplitudes of the second.
Adjust	Whether to adjust the plot to the loaded or visible data.
AmplitudeExpression	Applies the specified mathematical expression to each amplitude. The following symbols are available: - A: the current amplitude - W: the current wave number - I: the 0-based index of the wave number/amplitude - S: the number of wave numbers in the current spectrum The following grammar is used for the expressions: expr_list ::= '=' expr_list expr_part | expr_part ; expr_part ::= expr ; expr ::= ( expr ) # data types | number | string | boolean | date # constants | true | false | pi | e | now() | today() # negating numeric value | -expr # comparisons | expr < expr | expr <= expr | expr > expr | expr >= expr | expr = expr | expr !
AmplitudeFinder	Selects all the attributes that start with AmplitudeFinder.PREFIX_AMPLITUDE.
AmplitudeRange	For each wave number in the training data the range (min/max) is calculated. After training, if a spectrum falls outside these ranges, it gets flagged as an outlier. NB: Assumes the spectra (training and subsequent) have the same wave numbers.
AmplitudeRatio	Generates a square image (width is number of wave numbers) with the pixels being the ratio for each possible amplitude pair.
Amplitudes	Simple feature generator that just outputs all the amplitudes of a spectrum.
AmplitudeTransform	Applies the specified transformer to the spectrum.
AndrewsCurves	Generates Andrews Curves from array data. César Ignacio García Osorio, Colin Fyfe (2003).
AniMLSpectrumReader	Reads spectra in AniML (Analytical Information Markup Language) format. For more information see: http://animl.sourceforge.net/ Valid options are:
ApplyMultiplicativeScatterCorrection	Applies multiplicative scatter correction using the intercept and slope values stores in the report (using prefixes Intercept. and Slope.).
ArffUtils	A helper class for turning spectrum data into ARFF files and vice versa.
ArrayToSpectrum	Converts a float array representing amplitudes into a spectrum.
ASCIIXYSpectrumHandler	Displays the following spectrum types: txt Valid options are:
ASCIIXYSpectrumReader	Reads spectra in ASCII XY format.
ASCIIXYSpectrumWriter	Writer that stores spectra in ASCII XY format.
ASCSpectrumHandler	Displays the following spectrum types: asc Valid options are:
ASCSpectrumReader	Reads spectra in BLGG ASC format.
ASCSpectrumWriter	Writer that stores spectrums in the BLGG ASC format.
Atan2	Computes the atan2, with the first format representing 'y' and the second format 'x'.
Autocorrelation	Performs autocorrelation on the spectrum.
Average	Averages spectra into a single one.
BestBySLR	Chooses a random subset of attributes, either an absolute number or a percentage.
BulkSampleDataDbWriter	Writes sample data to the database and outputs whether the operation was successful.
BulkSpectrumDbWriter	Writes spectra to the database and outputs whether the operation was successful.
CALSpectrumHandler	Displays the following spectrum types: cal Valid options are:
CALSpectrumLoader	Loads a CAL file.
CALSpectrumReader	Reads spectra in BLGG ASC format.
CALSpectrumWriter	Write spectra to .CAL file.
CenterBurst	Locates the highest burst (negative or positive) in the spectrum and then retrieves these points from the spectrum: (numPoints / 2 - 1), burst, (numPoints / 2)
ChangeFormat	A filter that uses the sample ID to retrieve different formats from the database.
Cleaner	In case of Instances objects, 'unclean' Instance objects get removed.
Cleaner.CleanJob
CleanerDetails<T>	Interface for cleaners that provide details about their internals after they have been built.
CleanerDetailsViewer	Viewer for details of a cleaner.
CleanerModelLoader	Model loader for AbstractCleaner objects.
CleaningContainer	Container used by cleaners.
CMLSpectrumHandler	Displays the following spectrum types: cal Valid options are:
CMLSpectrumReader	Reads spectra in CML (Chemical Markup Language) format. For more information see: http://www.xml-cml.org/ Valid options are:
CollapseX	Calculates the mean/median/stdev data across the X layers.
CollapseX.StatisticType	the statistic to calculate from the data values.
ColumnWiseSpreadSheetSpectrumReader	Reads spectra from columns in a spreadsheet obtained with the specified spreadsheet reader.
ColumnWiseSpreadSheetSpectrumReader.SampleIDLocation	Determines whether the sample ID is located.
ConditionalReportField	Sets the 'success' value for the specified field if the condition evaluates to 'true', otherwise the 'failure' value.
CorrelationBasedThreshold	Applies the pre-filter and then computes the correlation coefficients between the spectra.
CosineSimilarityBasedThreshold	Applies the pre-filter and then computes the cosine similarity between the spectra.
Covariance	Plot covariance against Reference.
Crop
CrossHair	Allows to enable/disable the cross-hairs tracker.
CrossValidatedNeighborHood	Evaluator that cross-validates the specified classifier on the neighborhood determined for the instance under evaluation.
CrossValidatedPrediction	Evaluator that (kind of) cross-validates the specified classifier on the neighborhood determined for the instance under evaluation. A classifier is built on each of the training sets that is generated for the cross-validation.
CrossValidatedPrediction.StatisticType	The type of statistic to return.
DatabaseSearchPanel	Panel for obtaining IDs from the database.
DataType	Java class for DataType.
DataType	Java class for DataType.
DataType	Java class for DataType.
DataType	Java class for DataType.
DataType	Java class for DataType.
DeleteDbSampleDataValue	Deletes the specified values from the sampledata table.
DeleteSampleData	Displays the dialog for deleting sample data values from selected spectra.
DeleteSampleDataPanel	Allows the user to delete sample data values from selected spectra.
DeleteSampleDataValue	Deletes values from sample data.
DeleteSampleDataValueByExpression
DeleteSpectra	Displays the dialog for deleting spectra.
DeleteSpectrum	REST plugin for deleting spectra.
DeleteSpectrum	Removes the spectrum identified by database ID or sample ID.
DeleteSpectrumPanel	A panel for deleting spectra.
Derivative	A filter for generating derivatives of spectra.
Detrend	Performs Detrend corrections.
DistanceToCenter	Uses the specified nearest neighbor search to determine a neighborhood.
DistanceToClosest	Uses the specified nearest neighbor search to locate the closest instance in the training data and returns the distance to it.
DistributeSampleData	Distributes the sample data among all the sub-spectra, never overwrites already existing values.
Divide	Divides the amplitudes of first spectrum with the amplitudes of the second.
DownSample	A filter that returns only every n-th wave number.
DownSample	A filter that returns only every n-th 1st level and 2nd level point.
DPTSpectrumHandler	Displays the following spectrum types: dpt Valid options are:
DPTSpectrumReader	Reads spectra in DPT format.
DPTSpectrumWriter	Writer that stores spectrums in the simple CSV format.
EnsembleEvaluator	Builds an ensemble of classifiers on the training data to determine the MAE per classifier, to be used as normalization factor. At evaluation time, each classifier makes a prediction on the instance and the classification is divided by the normalization factor for this classifier.
EquiDistance	A filter for interpolating the amplitudes of a spectrum.
EvaluationContainer	Container for evaluations.
Evaluator	Interface for evaluators.
Evaluator	If input is Instances, build this Evaluator.
Evaluator.EvaluateJob
EvaluatorModelLoader	Model loader for AbstractEvaluator objects.
ExportSpectra	Exports the selected rows as spectra.
ExportSpectra	Exports the selected rows as spectra.
ExportValidationSets	Displays the dialog for exporting validation sets.
ExportVisible	Allows the user to save the visible spectra as ARFF.
ExtractIdAndTypeSpectrumReader	Uses the specified ID and group extractor to obtain and update sample ID and type of the spectra read by the specified base reader.
ExtractIdAndTypeThreeWayDataReader	Uses the specified ID and group extractor to obtain and update sample ID and type of the 3-way data read by the specified base reader.
FakeEvaluator	Fake evaluator, outputs random values based on min/max values.
FastICA	Performs independent components analysis and allows access to components and sources.
FastWavelet	A filter that transforms the data with a wavelet. For more information see: (2009).
FFT	A filter that transforms the data with Fast Fourier Transform. For more information see: Mark Hale (2009).
FieldInstanceGenerator	A generator for turning fields of the sample data of a spectrum into weka.core.Instance objects.
FieldInstanceGeneratorWithClass	Turns fields of spectra into weka.core.Instance objects, including class attribute.
Filename	Just uses the filename (without path) as sample ID.
FilteredMultiSpectrumFilter	The pre-filters select the spectra from the incoming multi-spectrum and re-package them into a new multi-spectrum.
FilteredSpectrumReader	Uses the specified reader to read the spectral data before applying the supplied filter to it.
FilteredSpectrumWriter	Applies the specified filter to the data before outputting it using the supplied writer.
FitsLibsReader
Flatliner	Checks for spectra that consist only of the same value (aka flat-liners).
Flatten	Simply flattens the 3-way data structure (x -> y -> z).
FossHelper	Helper for handling Foss cal files.
FossOutputHelper	Classes and Methods for creating a byte array of a FOSS .nir or .cal file.
FossOutputHelper.ConstituentValues	Constituent (or reference) values.
FossOutputHelper.DataBlock	Data Block.
FossOutputHelper.Generalheader	General Header.
FossOutputHelper.InstrumentHeader	Instrument Header class.
FossOutputHelper.InstrumentHeader.InstrumentType	Type of FOSS instrument.
FossOutputHelper.SampleHeader	Sample Header.
FossOutputHelper.SampleInfo	Sample Info.
FossStdise	Load, and perform standardisation/unstandardisation from foss standardisation file NOTE: Only does slope and intercept standardisation NOTE 2: Established by looking at .std files with hex editor.
Fusion	Fuses the sub-spectra specified by the format option, by placing them side-by-side using the format option as the order.
Get	Gets a spectrum.
GetRequest	Java class for getRequest complex type.
GetResponse	Java class for getResponse complex type.
GetSampleDataValue	Retrieves a value from sample data.
GetSpectrum	REST plugin for retrieving spectra.
GetSpectrumAmplitude	Retrieves the spectrum's amplitude either via its index or wave number.
GetSpectrumAmplitude.RetrievalType	Defines how to retrieve the amplitude.
GetSpectrumHelper	Helper class for converting spectra.
GotoWaveNumber	Displays the selected wave number.
HasSpectrum	Checks whether a spectrum with either the specified ID or the ID from the passing through ID handler is already present in the database. A specified ID takes precedence of any ID of the token passing through.
Histogram	Generates a histogram from the spectrum.
Histogram	Generates a histogram from the data values.
Histogram	Generates histograms from the visible containers.
HistogramFactory	A factory for histogram related objects.
HistogramFactory.Dialog	Dialog for displaying histograms generated from spectrums.
HistogramFactory.Panel	A panel for displaying a histogram based on the GC data of a spectrum.
HistogramFactory.SetupDialog	A dialog that queries the user about parameters for displaying histograms.
Hits	Allows operations on the "hits", ie the spectra currently under the mouse cursor.
IDConsumer	Interface for components that consume IDs generated by the IDProviders.
ImageType	Enumeration of type of image to generate.
Information	Displays information about the spectra.
InstanceCleaner	'Cleanses' the tokens being passed through.
InstanceGenerator	Generates weka.core.Instance objects from spectra or reports/sample data.
InstanceGeneratorWithClassLabels	Instance generator with a support for class labels.
InstanceGeneratorWithSampleID	Instance generator with sample ID.
InstanceGeneratorWithTargetField	Instance generator with a target field, i.e., class.
InstanceToSpectrum	Converts a weka.core.Instance to a Spectrum. By default, the wave numbers start at 0 and use an increment of 1. If 'first' and 'last' wave number are supplied, the step size is calculated based on the number of amplitudes present in the Instance. If only 'first' wave number is supplied, then the supplied wave step size is used. 'first' and 'last' get ignored if a value of less than 0 is supplied.
InstrumentSupplier	Returns instrument names from the database.
Intensity	Generates a simple intensity image.
InterPercentileRangeCleaner
InterPercentileRangeCleaner.DataCollector	A helper class for collecting the data from the database and computing the inter-percentile ranges (IPRs).
InterPercentileRangeCleaner.InterPercentileRange	Container class for storing the lower and upper percentile, as well as the wave number.
IntervalEstimatorEvaluator	Stores the interval provided by the interval estimator classifier
IQRCleaner	Removes instances outside the given IQR multiplier.
JCampDX2SpectrumHandler	Displays the following spectrum types: jdx, dx Valid options are:
JCampDX2SpectrumReader	Reads spectra in JCamp-DX format. For more information see: http://www.jcamp-dx.org/
JCampDX2SpectrumReader.ReaderMode	The enum for the reader mode.
JCampDX2SpectrumWriter	Writer that stores spectrums in the simple CSV format.
JCampDXSpectrumHandler	Displays the following spectrum types: jdx, dx Valid options are:
JCampDXSpectrumReader	Reads spectra in JCamp-DX format. For more information see: http://www.jcamp-dx.org/ Valid options are:
Join	Simply merges all the data points into a single container.
JsonSpectrumHandler	Displays the following spectrum types: json Valid options are:
JsonSpectrumReader	Reads spectra in JSON format. Input format (single spectrum): - complete report stored: { "id": "someid", "format": "NIR", "waves": [1.0, 2.0], "amplitudes": [1.1, 2.1], "report": { "Sample ID": "someid", "GLV2": 1.123, "valid": true } } - specific reference and meta-data values stored: { "id": "someid", "format": "NIR", "waves": [1.0, 2.0], "amplitudes": [1.1, 2.1], "reference": { "GLV2": 1.123 }, "meta-data": { "valid": true } } Multiple spectra are wrapped in an array called 'spectra'.
JsonSpectrumWriter	Writes spectra in JSON format. Output format for single spectrum: - outputting the complete report: { "id": "someid", "format": "NIR", "waves": [1.0, 2.0], "amplitudes": [1.1, 2.1], "report": { "Sample ID": "someid", "GLV2": 1.123, "valid": true } } - outputting specific reference and meta-data values: { "id": "someid", "format": "NIR", "waves": [1.0, 2.0], "amplitudes": [1.1, 2.1], "reference": { "GLV2": 1.123 }, "meta-data": { "valid": true } } Multiple spectra get wrapped in an array called 'spectra'.
JsonToSpectrum	Turns a JSON string into a spectrum. Input format: - complete report stored: { "id": "someid", "format": "NIR", "waves": [1.0, 2.0], "amplitudes": [1.1, 2.1], "report": { "Sample ID": "someid", "GLV2": 1.123, "valid": true } } - specific reference and meta-data values stored: { "id": "someid", "format": "NIR", "waves": [1.0, 2.0], "amplitudes": [1.1, 2.1], "reference": { "GLV2": 1.123 }, "meta-data": { "valid": true } }
KennardStone	Batch filter that applies the Kennard-stone algorithm to select a subset of spectra Created by Michael on 5/19/2016.
L1Point	Level 1 data point.
L1PointComparator	A comparator for level one points.
L1PointStatistic	A Level 1 point specific statistic.
L1PointUtils	A helper class for the Level 2 points of a given Level 1 point.
L2Point	Level 2 data point.
L2PointComparator	A comparator for level 2 points.
LinearRegressionBased	A simple linear regression based baseline correction scheme. Fits a line through the data using linear regression and then removes this line from the data to correct the baseline.
ListSampleData	Displays the dialog for listing all sample data for IDs.
ListSampleDataPanel	Allows the user to list sample data from selected spectra.
LoadMultiSpectrumFileOutput	Loads spectrum files with the specified reader and puts them in the specified queue as MultiSpectrum. Depending on whether a file could be successfully loaded or not, either .success or .failure gets appended to the filename.
LoadSampleData	Obtains the reference data from the spectrum with the same sample ID and the specified format.
LoadSpectrumFileOutput	Loads spectrum files with the specified reader and puts them in the specified queue. Depending on whether a file could be successfully loaded or not, either .success or .failure gets appended to the filename.
LogTransform	Transforms the amplitudes using log.
LOWESS	A filter that applies LOWESS smoothing. For more information see: WikiPedia.
LOWESSBased	A baseline correction scheme that uses LOWESS smoothing to determine the baseline. For more information see: WikiPedia.
LOWESSBased	A LOWESS based smoothing algorithm. For more information on LOWESS see: WikiPedia.
LRCoeff	A filter that returns only every n-th wave number.
ManualListPanel	Allows the user to specify the IDs manually.
Max	Simply determines the largest data value.
MaxWaves	Detects spectra that have too many wave numbers.
Mean	Averages spectra into a single one.
Mean	Performs the correction using simply the mean.
Mean	Determines the mean of all the data values.
MeanSpectrumCosineSimilarityBasedThreshold	Calculates the mean spectrum from the incoming spectra and then calculates the cosine similarity between the mean spectrum and the spectra.
Median	Averages spectra into a single one using the median.
Median	Determines the median of all the data values.
MergeSampleDataFromMap	Merges the passing through spectrum/sample data objects with the referenced map of sample data objects in storage (the map uses the sample ID as key). See also: adams.data.conversion.SampleDataArrayToMap Input/output: - accepts: adams.data.spectrum.Spectrum adams.data.sampledata.SampleData - generates: adams.data.spectrum.Spectrum adams.data.sampledata.SampleData
MergeSampleDataFromMap.MergeType	the type of merge operation to perform.
Min	Simply determines the smallest data value.
MinMax	Checks an attribute in the Instance whether the value is within a certain range.
MinMax	Checks a field in the sample data whether the value is within a certain range.
MinMax	Detects data containers where a report value is too high/low.
MinProbability	Ensures that the highest probability on the class distribution is at least the specified value. Adds a new boolean evaluation to the container with the name 'minprobability.passed'.
MinWaves	Detects spectra that have too few wave numbers.
MPSSpectrumHandler	Displays the following spectrum types: mps Valid options are:
MPSSpectrumReader	Reads XRF spectra in MPS format.
MultiClassifierEvaluator	Multi-classifier based evaluator.
MultiColumnSpreadSheetSampleDataReader	Reads sample data from a spreadsheet (format depends on reader), reference values stored in the specified range of columns and the column headers representing the reference value names.
MultiFilter	A meta-filter that runs multiple filters over the data. The filter can be executed in two ways: 1. in series (the default): Each filter runs on the data the previous filter generated. 2. in parallel: Each filter is run on the original input data and the generated outputs are merged into a single spectrum again.
MultiFilter	A meta-filter that runs multiple filters over the data. The filter can be executed in two ways: 1. in series (the default): Each filter runs on the data the previous filter generated. 2. in parallel: Each filter is run on the original input data and the generated outputs are merged into a single 3-way data structure again.
MultiplicativeScatterCorrection	Performs Multiplicative Scatter Correction. Assumes that all spectra have the same wave numbers. The 'pre-filter' gets only applied internally. Intercept and slope get stored in the report, for each defined range (using prefixes Intercept. and Slope.)
Multiply	Multiplies the amplitudes of two spectra with each other.
MultiSpectrum	For storing multiple spectra.
MultiSpectrum	Java class for MultiSpectrum complex type.
MultiSpectrumAdd	Adds a value obtained from either the callable actor or from storage. Callable actor takes precedent over storage, i.e., only if the callable actor cannot be located, is the storage name used.
MultiSpectrumFilter	Generates a single spectrum from a multi-spectrum using the specified filter. For some filters that use several spectra, the order of the spectra is important.
MultiSpectrumOperation
MultiSpectrumOutlierDetector	Uses the specified multi-spectrum filter to obtain a single spectrum from the multi-spectrum and applies the outlier detector to it. Any resulting detections get added to the multi-spectrum itself.
MultiSpectrumPanel	A panel for viewing spectra in pages.
MultiSpectrumRemove	Removes all spectra from the multi-spectrum that match the criteria.
MultiSpectrumReportFilter	Generates a single spectrum from a multi-spectrum using the specified filter.
MultiSpectrumToSpectra	Generates an array of knir.data.spectrum.Spectrum from the incoming knir.data.spectrum.MultiSpectrum. One can either transfer the data (all or partial) from the 'global' report to the sub-spectra or output the 'global' report as a separate (= first) spectrum with no spectral data points. See also: knir.data.conversion.SpectraToMultiSpectrum
MultiThreeWayDataFeatureGenerator	Applies multiple generators to the same 3-way data and merges the generated a feature vectors side-by-side.
MultiUpload	Uploads a MultiSpectrum.
NewSpectrum	Creates an empty spectrum.
NIRSpectrumHandler	Displays the following spectrum types: nir Valid options are:
NIRSpectrumReader	Reads spectra in FOSS NIR format.
NIRSpectrumWriter	Writer that stores spectrums in the FOSS .nir Format.
Null	Dummy overlay, does nothing.
NullEvaluator	Dummy evaluator, which always return 1.0 as evaluation result.
ObjectFactory	This object contains factory methods for each Java content interface and Java element interface generated in the nz.ac.waikato.adams.webservice.rats.multispectrum package.
ObjectFactory	This object contains factory methods for each Java content interface and Java element interface generated in the nz.ac.waikato.adams.webservice.rats.spectrum package.
ObjectFactory	This object contains factory methods for each Java content interface and Java element interface generated in the nz.ac.waikato.adams.webservice.spectral.get package.
ObjectFactory	This object contains factory methods for each Java content interface and Java element interface generated in the nz.ac.waikato.adams.webservice.spectral.put package.
ObjectFactory	This object contains factory methods for each Java content interface and Java element interface generated in the nz.ac.waikato.adams.webservice.spectral.transform package.
OpenContainingFolder	Opens the folder in the system's file browser that this flow is stored in.
OpusBlockHelper	Analyzer for Opus file blocks in the header.
OpusBlockHelper.Block	Convenience class for handling blocks.
OpusBlockHelper.BlockDefinition	Container class for Opus block definitions in the header.
OpusBlockHelper.CommandlineData	Encapsulates and parses a commandline string.
OpusSpectrumExtHandler	Displays the following spectrum types: * Valid options are:
OpusSpectrumHandler	Displays the following spectrum types: * Valid options are:
OpusSpectrumReader	Reads spectra in OPUS format.
OpusSpectrumReaderExt	Reads spectra in OPUS format (extended version).
OrphanedSampleDataConditions	Allows the retrieval of sample IDs of orphaned sample data, ie no spectrum available.
OrphanedSampleDataIdSupplier	Retrieves sample IDs of sample data that have no spectra associated.
Oscillation	Detects spectra that have an oscillating signal. Computes the correlation coefficient between original spectrum and a LOWESS-smoothed one, using the defined wave number range. If the correlation coefficient falls below the specified threshold, it is considered an outlier.
OutlierRemoval	Applies the specified outlier removal scheme to the multi-spectrum to remove potential outliers.
OwnedByRatsMultiSpectrumServiceWS	Interface for classes that are owned by RatsMultiSpectrumServiceWS.
OwnedByRatsSpectrumServiceWS	Interface for classes that are owned by RatsSpectrumServiceWS.
OwnedBySpectralGetServiceWS	Interface for classes that are owned by SpectralGetServiceWS.
OwnedBySpectralPutServiceWS	Interface for classes that are owned by SpectralPutServiceWS.
OwnedBySpectralTransformServiceWS	Interface for classes that are owned by SpectralTransformServiceWS.
PadPower2	Pads the spectrum to a power of 2 number of wave numbers.
ParafacLossHistory	Turns the PARAFAC loss history into a spreadsheet.
PassThrough	Dummy cleaner that flags everything as clean.
PassThrough	Dummy cleaner that flags everything as clean.
PassThrough	Dummy filter, does nothing.
PassThrough	Dummy, just passes through the data.
PassThrough	Does nothing, passes through the data.
PassThrough	Dummy transformer, which only returns a copy of the data point.
PassThrough	Does nothing, just passes the container through.
PassThrough	Does nothing.
PCA	Performs principal components analysis.
PCA	Turns the spectra internally into instances and transforms them using principal component analysis (PCA). The generated output is then converted back into spectra. Only works as batch filter, not in single spectrum mode.
PickByIndex	Extracts the specified sub-spectrum.
PickByReportValue	Extracts the first sub-spectrum that matches the condition for the field.
PLS	Performs partial least squares analysis.
PLS	Turns the spectra internally into instances and transforms them using the specified PLS algorithm.
PostProcessingContainer	Container used by post-processors.
PostProcessingContainerToWekaInstanceContainer	Converts a adams.flow.container.PostProcessingContainer container to a adams.data.instance.WekaInstanceContainer one.
PostProcessor	Post-processes the input Instances or, after the post-processor has been initialized with Instances, also input Instance objects. The actual post-processor in use gets output when container output enabled.
PostProcessorDetails<T>	Interface for post-processors that provide details about their internals after they have been built.
PostProcessorModelLoader	Model loader for AbstractPostProcessor objects.
PredictionCheck	Applies the specified check scheme to the incoming evaluation container.
PredictionErrorIQR	Post-processor that removes outliers using a coarse IQR approach on the predictions errors of one or more classifiers. parameters: - list of classifiers - foreach classifier; number or folds, an IQR multiplier, number of iterations or number of consecutive non-removal iterations before stop. algorithm: foreach classifier loop do xval, get predictions, remove all examples where error > percentile75+IQR*multiplier of errors stop if done num_iterations, or consecutive zero removals
Properties	Java class for Properties complex type.
Properties	Java class for Properties complex type.
Properties	Java class for Properties complex type.
Properties	Java class for Properties complex type.
Properties	Java class for Properties complex type.
Property	Java class for Property complex type.
Property	Java class for Property complex type.
Property	Java class for Property complex type.
Property	Java class for Property complex type.
Property	Java class for Property complex type.
PullUpFields	Distributes the sample data among all the sub-spectra, never overwrites already existing values.
Put	Stores a spectrum.
PutRequest	Java class for putRequest complex type.
PutResponse	Java class for putResponse complex type.
PutSampleData	REST plugin for uploading sample data.
PutSpectrum	REST plugin for uploading spectra.
PutSpectrumHelper	Helper class for converting spectra.
Range	Ensures that the specified (numeric) evaluator results are within a specified range. Adds a new boolean evaluation to the container, with the same name as the checked one, but appended with the suffix '.passed'. E.g., when checking the evaluation 'sqr', 'sqr..passed' will get added, either with 'true' or 'false' as value.
RangeBased	Performs the correction using slopes/intercepts calculated for the defined ranges.
RangeBased	Performs the correction using slopes/intercepts calculated for the defined ranges.
RangeBasedSavitzkyGolay	Configures a weka.filters.unsupervised.attribute.PartitionedMultiFilter, using the supplied ranges and the number of points to configure the weka.filters.unsupervised.attribute.SavitzkyGolay2 filter to apply to that subset.
RatsMultiSpectrumHelper	Helper class for converting spectra.
RatsMultiSpectrumService	This class was generated by Apache CXF 3.6.6 2025-09-20T23:45:58.083+12:00 Generated source version: 3.6.6
RatsMultiSpectrumServiceService	This class was generated by Apache CXF 3.6.6 2025-09-20T23:45:58.126+12:00 Generated source version: 3.6.6
RatsMultiSpectrumServiceWS	Webservice for RATS Spectrum.
RatsSpectrumHelper	Helper class for converting spectra.
RatsSpectrumService	This class was generated by Apache CXF 3.6.6 2025-09-20T23:45:56.080+12:00 Generated source version: 3.6.6
RatsSpectrumServiceService	This class was generated by Apache CXF 3.6.6 2025-09-20T23:45:56.109+12:00 Generated source version: 3.6.6
RatsSpectrumServiceWS	Webservice for RATS Spectrum.
Rebase	Shifts all wave numbers (left or right), so that the first wave number is at the specified starting point.
RegExp	Uses the specified group from a regular expression as sample ID.
RelabSpectrumHandler	Displays the following spectrum types: asc Valid options are:
RelabSpectrumReader	Reads spectra in Relab ASCII format. http://www.planetary.brown.edu/relabdata/
Remove	Removes all spectra from the multi-spectrum that match the criteria.
Remove	Removes a range of amplitudes from a spectrum. The matching sense can be inverted as well, i.e., removing everything else but the defined range of amplitudes.
RemoveMisclassifiedCleaner	Removes instances that are misclassified by the given relative difference, unless they are within the absolute difference.
RemoveOutliers	Cross-validates the specified classifier on the incoming data and applies the outlier detector to the actual vs predicted data to remove the outliers. NB: only works on full dataset, not instance by instance.
ReportColorSpectrumPaintlet	Paintlet for painting the spectral data using the color stored in the report.
ReportFieldFromStringValue	Sets a report field with the value extracted from another string field via a regular expression.
ReportFieldFromStringValueWithLookup	Extracts the first group from the regular expression matched against the report field value and uses this value as key in the provided lookup table generated from the specified key-value pairs.
ReportToSampleData	Converts a Report into a SampleData object.
Reverse	A filter that reverses the order of the amplitudes by making the wave numbers negative.
RonWeasley	Ron Weasley.
RonWeasley.RonWeasleyJob	A job class specific to Ron Weasley.
RowNorm	A filter that returns only every n-th wave number.
RowWiseSpreadSheetSampleDataReader	Reads a sample data file from a spreadsheet (format depends on reader), one reference value per row.
RowWiseSpreadSheetSpectrumReader	Reads spectra from rows in a spreadsheet obtained with the specified spreadsheet reader. Sample ID and sample data columns get removed automatically from the range of wave columns.
RowWiseSpreadSheetSpectrumReader.ChunkedSheetIterator	Iterator for chunked spreadsheet readers.
RowWiseSpreadSheetSpectrumReader.MultiSheetIterator	Iterator for multi-sheet readers.
RowWiseSpreadSheetSpectrumReader.SheetIterator	Ancestor for sheet iterators.
RowWiseSpreadSheetSpectrumReader.SingleSheetIterator	Iterator for single-sheet readers.
RowZeroMin	Make row min = 0.
SampleData	Read and store data from the Sample Report.
SampleData	Displays the sample data.
SampleDataArrayToMap	Converts the incoming sample data array into a map using the sample ID as key.
SampleDataContainerDisplayIDGenerator	Class for generating display IDs.
SampleDataDatabaseReader	Indicator interface for database readers for sample data.
SampleDataDatabaseWriter	Indicator interface for database writers for sample data.
SampleDataDbReader	Loads sample data from the database and passes it on.
SampleDataDbWriter	Writes sample data to the database if possible and passes the ID of the saved report on.
SampleDataDisplay	Displays sample data.
SampleDataF	Facade for sample data.
SampleDataFactory	A factory for GUI components for sample data.
SampleDataFactory.Dialog	A specialized dialog that displays reports.
SampleDataFactory.Panel	A specialized panel that displays reports.
SampleDataFactory.Table<ReportProviderByID>	A specialized table for displaying a SampleData.
SampleDataFileChooser	A specialized JFileChooser that lists all available file Readers and Writers for sampledata reports.
SampleDataFileReader	Loads a file containing sample data from disk with a specified reader and passes it on.
SampleDataFileWriter	Saves a quantitation report to disk with the specified writer and passes the absolute filename on. As filename/directory name (depending on the writer) the database ID of the report is used (below the specified output directory).
SampleDataIntf	Interface for sample data reports table.
SampleDataOnlyRowGenerator	Outputs only sample data values.
SampleDataReader	Indicator interface for readers that process sample data.
SampleDataReportFilter	Ensures that all important sample data values are kept when applying a report filter.
SampleDataT	A class for handling the sample data reports table.
SampleDataT	H2 implementation.
SampleDataT	Allows mirroring to another database.
SampleDataT	H2 implementation.
SampleDataT	MySQL implementation.
SampleDataT	PostgreSQL implementation.
SampleDataT	SQLite implementation.
SampleDataValueDbWriter	Stores the specified values from the sample data passing through in the database.
SampleDataWriter	Indicator interface for readers that process sample data.
SampleIDExtraction	Interface for classes that extract the sample ID from the filename.
SampleIDRegExpSupporter	Interface for condition classes that support regular expressions for the Sample ID.
SampleIdSource	Interface for ID sources that output either database IDs (= integers) or sample IDs (= strings).
SampleTypeRegExpSupporter	Interface for condition classes that support regular expressions for the sample type.
SaveMultiSpectrumFileOutput	Writes the input spectrum to the file that the filename generator produces.
SaveSpectrumFileOutput	Writes the input spectrum to the file that the filename generator produces.
SaveVisible	Allows the user to save the visible spectra.
SavitzkyGolay	A filter that applies Savitzky-Golay smoothing. For more information see: A.
SavitzkyGolayBased	A baseline correction scheme that uses SavitzkyGolay smoothing to determine the baseline. For more information see: A.
SavitzkyGolayBased	A Savitzky-Golay based smoothing algorithm. It uses a Savitzky-Golay filter with derivative order 0 and adding of mass-spec data turned on. For more information on Savitzky-Golay see: A.
SavitzkyGolayRange	This evaluator builds three classifiers: - on Savitzky-Golay filtered data with no derivative - on Savitzky-Golay filtered data with first derivative - on Savitzky-Golay filtered data with second derivative Each instance under evaluation will be pushed through the three classifiers separately and the range of the three predictions is then output as evaluation result.
SavitzkyGolayRange	Range definition for a SavitzkyGolay filter setup.
SAX	Performs Symbolic Aggregate approXimation (SAX). The data must be normalized using knir.data.filter.RowNorm beforehand. For more information see: Chiu, B., Keogh, E., Lonardi, S. (2003).
Scale	Scales the amplitudes to a given maximum.
ScioLabExportSpectrumReader	Reads the CSV export from the SCiO Lab web site.
ScioLabExportSpectrumReader.SpectrumType	Determines the type of spectrum to load.
SegmentedDownSample	Configures a weka.filters.unsupervised.attribute.PartitionedMultiFilter2, using the supplied number of splits and the nth points to configure the weka.filters.unsupervised.attribute.DownSample filter to apply to the subsets.
SegmentedDownSampleNthPoints	SegmentedDownSample nthPoints handler.
SegmentedSavitzkyGolay	Configures a weka.filters.unsupervised.attribute.PartitionedMultiFilter, using the supplied number of splits and the number of points to configure the weka.filters.unsupervised.attribute.SavitzkyGolay2 filter to apply to the subsets.
SegmentedSavitzkyGolayDerivativeOrder	SegmentedSavitzkyGolay numPoints handler.
SegmentedSavitzkyGolayNumPoints	SegmentedSavitzkyGolay numPoints handler.
SelectedWaveNumberPaintlet	Paintlet for highlighting a selected SpectrumPoint point on a panel.
SelectSpectrumDialog	Dialog for loading spectrum data from the database and displaying it.
SelectSpectrumPanel	A panel that lists all the spectrums currently in the database.
SelectSpectrumPanel.TableModel	A simple table model for displaying the database IDs and Names.
SelectWaveNumber	Action parameters:
SetEvaluationMetaData	Adds the specified value under the listed key in the evaluation container.
SetSampleDataValue	Sets a value in the sample data.
SetSpectrumAmplitude	Sets the amplitude for the specified wave number. Can either be used to replace an existing spectrum point or simply to insert another one.
SetSpectrumAmplitude.UpdateType	Defines how to set the amplitude.
Shift
SignalToNoiseRatio
SimpleCSVSampleDataHandler	Displays the following report types: csv Valid options are:
SimpleCSVSampleDataReader	Reads a report file in CSV file format.
SimpleCSVSampleDataWriter	Writes reports in CSV file format.
SimpleEEMReader	Reads EEM data in spreadsheet format (tab-separated columns).
SimpleEEMWriter	Writes 3-way data in spreadsheet format (tab-separated columns).
SimpleInstanceGenerator	A simple scheme for turning spectra and fields of the associated sample data into weka.core.Instance objects.
SimpleJsonSampleDataReader	Reads a report file in Json file format.
SimpleJsonSampleDataWriter	Writes reports in Json file format.
SimplePlotUpdater	Updates the display after the specified number of tokens have been processed.
SimpleRatsMultiSpectrumService	Class that implements the RATS multispectrum web service.
SimpleRatsSpectrumService	Class that implements the RATS spectrum web service.
SimpleRowGenerator	Outputs spectral and sample data.
SimpleSampleDataHandler	Displays the following report types: props Valid options are:
SimpleSampleDataReader	Reads a report file in properties file format.
SimpleSampleDataWriter	Writes reports in properties file format.
SimpleSavitzkyGolay	A filter that applies a simplified Savitzky-Golay smoothing. For more information on Savitzky-Golay see: A.
SimpleSpectralGetService	Class that implements the Spectral get web service.
SimpleSpectralInstanceGenerator	A simple scheme for turning spectra and fields of the associated sample data into weka.core.Instance objects (without class attribute).
SimpleSpectralPutService	Class that implements the Spectral put web service.
SimpleSpectralTransformService	Class that implements the Spectral web service.
SimpleSpectrumHandler	Displays the following spectrum types: spec Valid options are:
SimpleSpectrumPaintlet	Paintlet for painting the spectral graph, without any markers.
SimpleSpectrumReader	Reads spectrums in the internal CSV format.
SimpleSpectrumWriter	Writer that stores spectrums in the simple CSV format.
SimpleXYZReader	Reads 3-day data in CSV format with X, Y, Z and data columns.
SimpleXYZWriter	Writes 3-way data in CSV format (x/y/z/data columns).
SlidingWindow	Uses a sliding window for determining the median/average inside the window.
SoilCaresScannerSpectrumReader	Reads spectra from ZIP files generated by the SoilCares Scanner app.
SoilCaresScannerSpectrumReader.AmplitudeType	Determines the type of amplitudes to load.
SoilCaresScannerSpectrumReader.SpectrumType	Determines the type of spectrum to load.
SPASpectrumHandler	Displays the following spectrum types: spa Valid options are:
SPASpectrumReader	Loads spectral data files in Nicolet SPA format.
SPCSpectrumHandler	Displays the following spectrum types: spc Valid options are:
SPCSpectrumReader	Reads spectra in SPC format (Galactic Universal Data Format) format. See the specifications here: http://serswiki.bme.gatech.edu/images/a/ae/SPC_Open_Specification.pdf
SPCSpectrumReader.AbstractParser	Parser class for SPC files.
SPCSpectrumReader.FileParser	Parser class for SPC files (header).
SPCSpectrumReader.SubFileParser	Parser class for SPC files (header).
SpecLibSampleDataReader	Reads USGS SpecLib HTML Description files. http://speclab.cr.usgs.gov/spectral.lib06/
SpecLibSpectrumHandler	Displays the following spectrum types: asc Valid options are:
SpecLibSpectrumReader	Reads spectra in USGS SpecLib ASCII format. http://speclab.cr.usgs.gov/spectral.lib06/
SpectralAngleMapper	Performs Spectral Angle Mapping on a set of spectra.
SpectralCommandProcessor	Command processor for the spectral module.
SpectralData	Displays the spectral data as table.
SpectralDbBackend	Auto-detect Spectral backend.
SpectralDbBackend	H2 Spectral backend.
SpectralDbBackend	MySQL Spectral backend.
SpectralDbBackend	MS SQL Server Spectral backend.
SpectralDbBackend	MySQL Spectral backend.
SpectralDbBackend	PostgreSQL Spectral backend.
SpectralDbBackend	Interface for classes that return actual implementations of the processing database interfaces.
SpectralDbBackend	SQLite Spectral backend.
SpectralDbBackendDefinition	Definition for the SpectralDbBackend props file.
SpectralGetService	This class was generated by Apache CXF 3.6.6 2025-09-20T23:45:46.492+12:00 Generated source version: 3.6.6
SpectralGetServiceService	This class was generated by Apache CXF 3.6.6 2025-09-20T23:45:46.542+12:00 Generated source version: 3.6.6
SpectralGetServiceWS	Webservice for Spectral.
SpectralPutService	This class was generated by Apache CXF 3.6.6 2025-09-20T23:45:48.399+12:00 Generated source version: 3.6.6
SpectralPutServiceService	This class was generated by Apache CXF 3.6.6 2025-09-20T23:45:48.435+12:00 Generated source version: 3.6.6
SpectralPutServiceWS	Webservice for Spectral.
SpectralScriptingEngine	Scripting engine for spectral module.
SpectralScriptingEngineDefinition	Definition for the ScriptingEngine props file.
SpectralTransformService	This class was generated by Apache CXF 3.6.6 2025-09-20T23:45:50.330+12:00 Generated source version: 3.6.6
SpectralTransformServiceService	This class was generated by Apache CXF 3.6.6 2025-09-20T23:45:50.355+12:00 Generated source version: 3.6.6
SpectralTransformServiceWS	Webservice for Spectral.
SpectraToMultiSpectrum	Generates a adams.data.spectrum.MultiSpectrum from the incoming array of adams.data.spectrum.Spectrum. If the first spectrum in the array is a report-only spectrum (ie no spectral data points), then this report is used as the 'global' report for the multi-spectrum.
Spectrogram	Generates a spectrogram image of the spectrum.
Spectrum	Abstract superclass for containers for sequence points.
Spectrum	Java class for Spectrum complex type.
Spectrum	Java class for Spectrum complex type.
Spectrum	Java class for Spectrum complex type.
Spectrum	Java class for Spectrum complex type.
Spectrum	Java class for Spectrum complex type.
SpectrumAppend	Appends the incoming spectrum to the one available from storage. If none yet available from storage, then the current one simply put into storage. If the spectrum already contains elements with the same wave number, then these will get replaced by the current ones.
SpectrumClassifier	Automatically removes some IDs from the dataset before training the base classifier: id, db_id, sample_id.
SpectrumCleaner	'Cleanses' the tokens being passed through.
SpectrumClusterer	Automatically removes some IDs from the dataset before training the base classifier: id, db_id, sample_id.
SpectrumComparator	A comparator for Spectrum objects.
SpectrumComparatorByReportValue	Compares spectra based on the specified report field value.
SpectrumConditionsMulti	Conditions for the retrieval of spectra. Several fields can be specified.
SpectrumConditionsSingle	Conditions for the retrieval of spectra. Only a single field can be specified.
SpectrumContainer	A container class for a spectrum and additional information.
SpectrumContainerDisplayIDGenerator	Class for generating display IDs.
SpectrumContainerList	A class encapsulating containers tailored for spectrums.
SpectrumContainerManager	A handler for the spectrum containers.
SpectrumContainerModel	A model for displaying the currently loaded spectrums.
SpectrumContainerTable	Specialized container table for spectra.
SpectrumContainerTableColumnNameGenerator	Abstract class for generating the column names of a table.
SpectrumCorrelation	Compares the spectral data of two spectra using correlation coefficient. Does not use wave numbers to determine common data points, simply the index. Outputs true if the minimum is achieved, otherwise false.
SpectrumCosineSimilarity	Compares the spectral data of two spectra using cosine similarity.
SpectrumDatabaseReader	Indicator interface for database readers for spectra.
SpectrumDatabaseWriter	Indicator interface for database writers for spectra.
SpectrumDatasetExportDialog	Export dialog for spectra to a dataset.
SpectrumDbReader	Loads a spectrum from the database and passes it on.
SpectrumDbWriter	Writes a spectrum to the database and passes its ID on.
SpectrumDiff	Computes the difference between two spectra (received as array) and outputs the difference as spectrum again: spectrum 1 - spectrum 2 Input/output: - accepts: knir.data.spectrum.Spectrum[] - generates: knir.data.spectrum.Spectrum
SpectrumDisplay	Actor that displays spectra or multi-spectra.
SpectrumExplorer	Displays the Spectrum Explorer.
SpectrumExplorer	A panel for exploring Spectrums, manipulating them with filters, etc.
SpectrumExportDialog	Export dialog for spectra.
SpectrumExporter	Exports Spectrum objects.
SpectrumF	Facade for spectrum tables.
SpectrumFeatureGenerator	Applies a spectrum feature generator to the incoming spectrum and outputs the generated features.
SpectrumFileChecker	Only passes on files/directories containing spectra that could be loaded successfully.
SpectrumFileChooser	A specialized JFileChooser that lists all available file Readers and Writers for spectrums.
SpectrumFileReader	Loads a file/directory containing spectrums from disk with a specified reader and passes them on.
SpectrumFileWriter	Saves a spectrum to disk with the specified writer and passes the absolute filename on. As filename/directory name (depending on the writer) the database ID of the spectrum is used (below the specified output directory).
SpectrumFilter	Filters data using the specified filter.
SpectrumFilter	A meta-filter that applies the base filter only to the spectral part of the dataset, i.e., attributes starting with 'amplitude-'.
SpectrumFilterContainer	Container for spectrum filters.
SpectrumIDConditions	Conditions for the retrieval of spectrum IDs.
SpectrumIdSource	Indicator interface for sources that supply spectrum IDs.
SpectrumIdSupplier	Returns spectrum IDs from the database.
SpectrumImageWriter	Writes spectra as images using the supplied generator.
SpectrumImageWriter	Actor that takes screenshots of spectra.
SpectrumInfo	Outputs statistics of a spectrum.
SpectrumInfo.InfoType	The type of information to generate.
SpectrumIntf	Interface for spectrum tables.
SpectrumJsonUtils	For converting spectra to JSON and vice versa.
SpectrumMinMax	Keeps track of min/max per wave number and outputs these min/max spectra at the specified interval of spectra processed.
SpectrumPaintlet	Paintlet for painting the spectral graph.
SpectrumPaintlet.MarkerShape	Enum for the marker shape to plot around the data points.
SpectrumPaintletNumericField	Paintlet for painting the spectral graph.
SpectrumPaintletStringField	Paintlet for painting the spectral graph.
SpectrumPanel	Special panel for displaying the spectral data.
SpectrumPanelWithSampleData	Spectrum panel that also shows the sample data next to it.
SpectrumPoint	Abstract superclass for sequence points.
SpectrumPointComparator	A comparator for SpectrumPoint points.
SpectrumPointHitDetector	Detects selections of spectrum points in the spectrum panel.
SpectrumReaderWithSampleIDExtraction	Interface for spectrum readers that extract the sample ID from the filename.
SpectrumRenderer	Renders Spectrum objects.
SpectrumStatistic	Statistical information specific to a spectrum.
SpectrumT	Manages Spectrum tables.
SpectrumT	H2 implementation.
SpectrumT	Allows mirroring to another database.
SpectrumT	H2 implementation.
SpectrumT	MySQL implementation.
SpectrumT	PostgreSQL implementation.
SpectrumT	SQLite implementation.
SpectrumTableModel	Table model for displaying a spectrum in a table.
SpectrumToArray	Turns either the wave numbers or amplitudes of the incoming spectrum into a float array.
SpectrumToArray.DataType	The type of data to output.
SpectrumToBufferedImage	Converts a spectrum into an image by treating it like an audio signal, and producing a spectrogram for it.
SpectrumToJson	Turns a spectrum into a JSON string. Output format: - outputting the complete report: { "id": "someid", "format": "NIR", "waves": [1.0, 2.0], "amplitudes": [1.1, 2.1], "report": { "Sample ID": "someid", "GLV2": 1.123, "valid": true } } - outputting specific reference and meta-data values: { "id": "someid", "format": "NIR", "waves": [1.0, 2.0], "amplitudes": [1.1, 2.1], "reference": { "GLV2": 1.123 }, "meta-data": { "valid": true } }
SpectrumToSpreadSheet	Turns a spectrum into a spreadsheet.
SpectrumToWave	Turns a spectrum into a WAV.
SpectrumUtils	Utility class for spectrums.
SpectrumZoomOverviewPaintlet	Highlights the current zoom in the spectrum panel.
SpectrumZoomOverviewPanel	Panel that shows the zoom in the spectrum panel as overlay.
SpreadSheetColumnsToSampleData	Turns spreadsheet columns into sample data.
SpreadSheetColumnsToSpectra	Turns spreadsheet columns into spectra.
SpreadSheetIDPanel	Allows the user to load IDs from a spreadsheet.
SpreadSheetRowGenerator	Generates spreadsheet row objects from spectra or reports/sample data.
SpreadSheetRowsToSampleData	Turns spreadsheet rows into sample data.
SpreadSheetRowsToSpectra	Turns spreadsheet rows into spectra.
SpreadSheetSpectrumWriter	Uses the supplied spreadsheet writer to write the spectra as spreadsheets.
SpreadSheetTo2DTensor	Converts a spreadsheet into a 2-D Tensor data structure (ie a matrix).
SpreadSheetTo3DTensor	Converts a spreadsheet into a 3-way Tensor data structure. The sheet requires four columns: X, Y, Z and data.
SpreadSheetToSpectrum	Turns a spreadsheet into a spectrum.
SpreadSheetToThreeWayData	Converts a spreadsheet into a 3-way data structure. The sheet requires four columns: X, Y, Z and data. The Z column is optional, which, if not provided, is simply assumed to be 0.
SQLSpectrumIdSupplier	Executes an SQL statement for generating the IDs.
StandardiseByInterpolation	Standardises spectrum to start-end with given step.
Statistics	Generates statistics from the visible containers.
Statistics	Displays statistics for the 3-day data container.
StdDev	Determines the sample standard deviation of all the data values.
StringMatcher	Checks whether the specified string field is available in the report and the value matches the specified regular expression.
SubRange	Returns a sub-range of wave numbers from a spectrum.
Subtract	Subtracts the amplitudes of first spectrum with the amplitudes of the second.
SubtractSpectrum
Swapped	Smooths spectrum (using SavitzkyGolay) and then splits it into two halves.
TableModel	Table model for displaying the database IDs, IDs, formats and selected state of spectra.
TensorContainer	Container for a Tensor.
TensorToSpreadSheet	Turns a Tensor data structure into a spreadsheet. - 1D: single row - 2D: matrix - 3D: three index columns (X,Y,Z) and data column
TensorToThreeWayData	Turns a Tensor data structure into a ThreeWayData one.
TextOverlay	Displays text as overlay, either the fixed text, or if empty, a report value.
ThreeWayData	Stores 3-way data and associated meta-data.
ThreeWayDataContainer	Container for 3-way data.
ThreeWayDataContainerManager	Container manager for heatmaps.
ThreeWayDataExporter	Exports ThreeWayData objects.
ThreeWayDataFeatureGenerator	Applies a 3-way data feature generator to the incoming data and outputs the generated features.
ThreeWayDataFileChooser	A specialized JFileChooser that lists all available file Readers and Writers for 3-way data.
ThreeWayDataFileReader
ThreeWayDataFileWriter
ThreeWayDataFilter	Filters data using the specified filter.
ThreeWayDataFilterContainer	Container for spectrum filters.
ThreeWayDataHeatmapDisplay	Actor that displays 3-way data as heatmaps.
ThreeWayDataHeatmapPanel	Panel for displaying a single 3-way data structure.
ThreeWayDataHeatmapRenderer	Renders 3way data objects as heatmaps.
ThreeWayDataHeatmapViewer	For displaying 3-day data as heatmaps.
ThreeWayDataHeatmapViewerMultiPagePane	Specialized multi-page pane for the 3way data heatmap viewer.
ThreeWayDataHeatmapViewerPanel	Panel for viewing/processing 3-way data as data structures.
ThreeWayDataLoadingMatrix
ThreeWayDataMerge	Merges the incoming 3-way data structures using the specified algorithm.
ThreeWayDataModelContainer	Container for spectrum filters.
ThreeWayDataModelFilter
ThreeWayDataModelFilterLoader	Model loader for AbstractAlgorithm objects.
ThreeWayDataStatistic	Statistical information specific to a ThreeWayData.
ThreeWayDataToHeatmap	Turns a adams.data.threeway.ThreeWayData data structure into a heatmap. Sums up the data values of the Z layers that fall into the specified min/max.
ThreeWayDataToSpreadSheet	Flattens 3-way data into a spreadsheet.
ThreeWayDataToTensor	Converts 3-way data into the Tensor data structure.
ThreeWayDataTrain
ThreeWayDataUtils	Utility class for ThreeWayData objects.
ThreeWayEEMHandler	Handles 3-way data EEM fluorescence files.
ThreeWayHeatmapReader	Uses the specified reader to load 3-way data and turns it into a heatmap.
ThreeWayReport	Read and store data from the Report for a ThreeWayData structure.
ThreeWayXYZHandler	Handles 3-way data XYZ fluorescence files.
Transform	Transforms a spectrum.
TransformRequest	Java class for transformRequest complex type.
TransformResponse	Java class for transformResponse complex type.
TransformSpectrum	REST plugin for filtering spectra.
TransformSpectrumHelper	Helper class for converting spectra.
Triangle	Multiplies the amplitude by the value from a triangle function.
TrinamixSpectrumJsonReader	Reader for the trinamiX (https://trinamixsensing.com/) JSON format.
TrinamixSpectrumReader	Reader for the trinamiX (https://trinamixsensing.com/) CSV format.
TrinamixSpectrumWriter	Writer for the trinamiX (https://trinamixsensing.com/) CSV format.
UnscramblerSpectrumReader
UpdateDatabaseID	Attempts to update the database ID of the spectrum.
UpdateDatabaseID	Attempts to update the database ID of the sample data.
UpdateSampleData	Displays the dialog for updating sample data.
UpdateSampleDataPanel	Allows the user to update/set values in selected spectra.
Upload	Uploads a spectrum.
UploadRequest	Java class for uploadRequest complex type.
UploadRequest	Java class for uploadRequest complex type.
UploadResponse	Java class for uploadResponse complex type.
UploadResponse	Java class for uploadResponse complex type.
ValueRange	Detects data containers where a least one value is too low or too high.
ViewAsSpreadSheet	Views the 3-way data in a spreadsheet table.
Viewport	Allows the user to perform operations on the spectra visible in the current viewport.
Wave	Java class for Wave complex type.
Wave	Java class for Wave complex type.
Wave	Java class for Wave complex type.
Wave	Java class for Wave complex type.
Wave	Java class for Wave complex type.
WaveNumberExpression	Applies the specified mathematical expression to each wave number. The following symbols are available: - A: the current amplitude - W: the current wave number - I: the 0-based index of the wave number/amplitude - S: the number of wave numbers in the current spectrum The following grammar is used for the expressions: expr_list ::= '=' expr_list expr_part | expr_part ; expr_part ::= expr ; expr ::= ( expr ) # data types | number | string | boolean | date # constants | true | false | pi | e | now() | today() # negating numeric value | -expr # comparisons | expr < expr | expr <= expr | expr > expr | expr >= expr | expr = expr | expr !
WaveNumberHitDetector	Detects selections of wave numbers.
Waves	Java class for Waves complex type.
Waves	Java class for Waves complex type.
Waves	Java class for Waves complex type.
Waves	Java class for Waves complex type.
Waves	Java class for Waves complex type.
WekaClassifierBasedEvaluator	Interface for evaluators that make use of classifiers.
WekaFilter	Uses a WEKA filter for post-processing. Automatically wraps a SpectrumFilter meta-filter around the actual filter.
WekaFilterToReport	Generates a Weka Instance using the specified instance generator.
WekaPredictionContainerToEvaluationContainer	Turns a adams.flow.container.WekaPredictionContainer into a knir.flow.container.EvaluationContainer.
WriteSpectrum	Action parameters:
WSMultiSpectrumReception	Uses a webservice for retrieving spectra.
WSSpectrumReception	Uses a webservice for retrieving spectra.
ZeroCenterBurst	Locates the largest burst (negative or positive) and splits the spectrum into the following parts: left, burst, right These parts then get reassembled as: right, left, burst
ZippedSpectrumReader	Reads spectra from the zip file using the specified base reader.