de.mpg.biochem.mars.metadata

Interface MarsMetadata

All Superinterfaces:

JsonConvertibleRecord, MarsRecord

All Known Implementing Classes:

AbstractMarsMetadata, MarsOMEMetadata, OLDMarsMetadata

public interface MarsMetadata
extends JsonConvertibleRecord, MarsRecord

MarsMetadata records store image metadata and all information about specific data collections, imaging settings, frame timing. Mapping of frames/slices to actual real time. These records can also include readouts from other instruments connected to microscopes.

These records may also contain BigDataViewer registration coordinates, video locations, and channel names. The log contained in these records will contain a history of commands run on this dataset and the molecule records associated with it that are stored in the same MoleculeArchive. The MarsTable inherited from AbstractMarsRecord will contain metadata for each frame in individual rows in order of collection.

This record format is designed for use with single-molecule time-series data collected on TIRF microscopes or bead tracking microscopes. Therefore, these data are assumed to be 2D only. If individual colors are recorded in separate frames their information should be merged into a single row contained in the MarsTable.

Method Summary

Modifier and Type	Method and Description
MarsBdvSource	getBdvSource(java.lang.String name) Get the MarsBdvSource with the name provided.
java.util.Set<java.lang.String>	getBdvSourceNames() Get the set of BigDataViewer source names.
java.util.Collection<MarsBdvSource>	getBdvSources() Get the Collection of BigDataViewer sources with each in MarsBdvSource format.
java.lang.String	getCollectionDate() Get the Date when these data were collected.
MarsOMEImage	getImage(int imageIndex)
int	getImageCount()
java.lang.String	getLog() Get the log that contains the history of processing steps conducted on this dataset and the associated molecule records contained in the same MoleculeArchive.
java.lang.String	getMicroscopeName() Get the name of the microscope used for data collection.
MarsOMEPlane	getPlane(int imageIndex, int planeIndex)
MarsOMEPlane	getPlane(int imageIndex, int Z, int C, int T)
java.lang.String	getSourceDirectory() Get the Source Directory where the images are stored.
boolean	hasBdvSource(java.lang.String name) Check if this record contains the BigDataViewer with the name provided.
boolean	hasPlane(int imageIndex, int planeIndex)
java.util.stream.Stream<MarsOMEImage>	images()
void	log(java.lang.String str) Add to the log that contains the history of processing steps conducted on this dataset and the associated molecule records contained in the same MoleculeArchive.
void	logln(java.lang.String str) Add to the log that contains the history of processing steps conducted on this dataset and the associated molecule records contained in the same MoleculeArchive.
void	merge(MarsMetadata metadata) Used to merge another MarsMetadata record into this one.
void	populateMetadata(ome.xml.meta.OMEXMLMetadata md)
void	putBdvSource(MarsBdvSource source) Add or update the MarsBdvSource with the name provided.
void	removeAllBdvSources() Remove all MarsBdvSources.
void	removeBdvSource(java.lang.String name) Remove the MarsBdvSource with the name provided.
void	setImage(MarsOMEImage image, int imageIndex)
void	setMicroscopeName(java.lang.String Microscope) Set the name of the microscope used for data collection.
void	setSourceDirectory(java.lang.String path) Set the Source Directory where the images are stored.

Methods inherited from interface de.mpg.biochem.mars.molecule.MarsRecord

addNote, addTag, getBooleanParameter, getNotes, getParameter, getParameters, getPosition, getPositionNames, getPositions, getRegion, getRegionNames, getRegions, getStringParameter, getTags, getTagsArray, getUID, hasBooleanParameter, hasDoubleParameter, hasNoTags, hasParameter, hasPosition, hasRegion, hasStringParameter, hasTag, merge, putPosition, putRegion, removeAllParameters, removeAllPositions, removeAllRegions, removeAllTags, removeParameter, removePosition, removeRegion, removeTag, setNotes, setParameter, setParameter, setParameter, setParent

Methods inherited from interface de.mpg.biochem.mars.molecule.JsonConvertibleRecord

dumpJSON, fromJSON, getJsonGenerator, getJsonParser, setJsonField, setShowWarnings, toJSON

Method Detail

populateMetadata

void populateMetadata(ome.xml.meta.OMEXMLMetadata md)

setImage

void setImage(MarsOMEImage image,
              int imageIndex)

getImage

MarsOMEImage getImage(int imageIndex)

getPlane

MarsOMEPlane getPlane(int imageIndex,
                      int planeIndex)

hasPlane

boolean hasPlane(int imageIndex,
                 int planeIndex)

getPlane

MarsOMEPlane getPlane(int imageIndex,
                      int Z,
                      int C,
                      int T)

getImageCount

int getImageCount()

images

java.util.stream.Stream<MarsOMEImage> images()

setMicroscopeName

void setMicroscopeName(java.lang.String Microscope)

Set the name of the microscope used for data collection. This is just for record keeping. There are no predefined setting based on microscope names.

Parameters:

Microscope - Name of the microscope used for collection.

getMicroscopeName

java.lang.String getMicroscopeName()

Get the name of the microscope used for data collection. This is just for record keeping. There are no predefined setting based on microscope names.

Returns:

Name of the microscope used for collection.

getCollectionDate

java.lang.String getCollectionDate()

Get the Date when these data were collected.

Returns:

The date when the metadata was collected.

getSourceDirectory

java.lang.String getSourceDirectory()

Get the Source Directory where the images are stored.

Returns:

Directory where the images are stored.

setSourceDirectory

void setSourceDirectory(java.lang.String path)

Set the Source Directory where the images are stored.

Parameters:

path - The string file path.

merge

void merge(MarsMetadata metadata)

Used to merge another MarsMetadata record into this one.

Parameters:

metadata - MarsMetadata to merge into this one.

log

void log(java.lang.String str)

Add to the log that contains the history of processing steps conducted on this dataset and the associated molecule records contained in the same MoleculeArchive.

Parameters:

str - Message to add to the log.

logln

void logln(java.lang.String str)

Add to the log that contains the history of processing steps conducted on this dataset and the associated molecule records contained in the same MoleculeArchive. Start a new line after adding the message.

Parameters:

str - Message to add to the log.

getLog

java.lang.String getLog()

Get the log that contains the history of processing steps conducted on this dataset and the associated molecule records contained in the same MoleculeArchive.

Returns:

The processing log for this metadata record.

getBdvSource

MarsBdvSource getBdvSource(java.lang.String name)

Get the MarsBdvSource with the name provided.

Parameters:

name - Name of the MarsBdvSource to retrieve.

Returns:

Mars BigDataViewer Source with the name given.

putBdvSource

void putBdvSource(MarsBdvSource source)

Add or update the MarsBdvSource with the name provided. All MarsBdvSource are unique so record will be overwritten if they have the same name.

Parameters:

source - Mars BigDataViewer Source to add to the MarsImageMetadata record.

removeBdvSource

void removeBdvSource(java.lang.String name)

Remove the MarsBdvSource with the name provided.

Parameters:

name - Name of the MarsBdvSource to remove.

removeAllBdvSources

void removeAllBdvSources()

Remove all MarsBdvSources.

getBdvSources

java.util.Collection<MarsBdvSource> getBdvSources()

Get the Collection of BigDataViewer sources with each in MarsBdvSource format.

Returns:

Collection of MarsBdvSources in the record.

getBdvSourceNames

java.util.Set<java.lang.String> getBdvSourceNames()

Get the set of BigDataViewer source names.

Returns:

Names of MarsBdvSources in the record.

hasBdvSource

boolean hasBdvSource(java.lang.String name)

Check if this record contains the BigDataViewer with the name provided.

Parameters:

name - Name of the MarsBdvSource to check for.

Returns:

True if a source with the name given is found.