de.mpg.biochem.mars.metadata

Class AbstractMarsMetadata

java.lang.Object

de.mpg.biochem.mars.molecule.AbstractJsonConvertibleRecord

de.mpg.biochem.mars.molecule.AbstractMarsRecord

de.mpg.biochem.mars.metadata.AbstractMarsMetadata

All Implemented Interfaces:

MarsMetadata, JsonConvertibleRecord, MarsRecord

Direct Known Subclasses:

MarsOMEMetadata

public abstract class AbstractMarsMetadata
extends AbstractMarsRecord
implements MarsMetadata

Abstract superclass for storage of metadata, which includes 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.

Field Summary

Fields

Modifier and Type	Field and Description
protected java.util.LinkedHashMap<java.lang.String,MarsBdvSource>	bdvSources
protected java.util.Map<java.lang.Integer,MarsOMEImage>	images
protected java.lang.String	log
protected java.lang.String	microscope
protected java.lang.String	sourceDirectory

Fields inherited from class de.mpg.biochem.mars.molecule.AbstractMarsRecord

parent

Constructor Summary

Constructors

Constructor and Description
AbstractMarsMetadata() Constructor for creating an empty MarsMetadata record.
AbstractMarsMetadata(com.fasterxml.jackson.core.JsonParser jParser) Constructor for loading a MarsMetadata record from a file.
AbstractMarsMetadata(java.lang.String UID) Constructor for creating an empty MarsMetadata record with the specified UID.
AbstractMarsMetadata(java.lang.String UID, ome.xml.meta.OMEXMLMetadata omeXmlMetadata) Constructor for creating a MarsMetadata record using OMEXMLMetadata.

Method Summary

Modifier and Type	Method and Description
protected void	createIOMaps() Must be implemented in subclasses to define how fields, objects, arrays should be saved based on the Jackson streaming API.
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) Get the MarsOMEPlane for a given image and ZCT position.
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 class de.mpg.biochem.mars.molecule.AbstractMarsRecord

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 class de.mpg.biochem.mars.molecule.AbstractJsonConvertibleRecord

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

Methods inherited from class java.lang.Object

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

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

Field Detail

log

protected java.lang.String log

microscope

protected java.lang.String microscope

sourceDirectory

protected java.lang.String sourceDirectory

images

protected final java.util.Map<java.lang.Integer,MarsOMEImage> images

bdvSources

protected final java.util.LinkedHashMap<java.lang.String,MarsBdvSource> bdvSources

Constructor Detail

AbstractMarsMetadata

public AbstractMarsMetadata()

Constructor for creating an empty MarsMetadata record.

AbstractMarsMetadata

public AbstractMarsMetadata(java.lang.String UID)

Constructor for creating an empty MarsMetadata record with the specified UID.

Parameters:

UID - The unique identifier for this record.

AbstractMarsMetadata

public AbstractMarsMetadata(java.lang.String UID,
                            ome.xml.meta.OMEXMLMetadata omeXmlMetadata)

Constructor for creating a MarsMetadata record using OMEXMLMetadata.

Parameters:

UID - The UID of the MarsMetadata record being created.

omeXmlMetadata - The OMEXMLMetadata to use.

AbstractMarsMetadata

public AbstractMarsMetadata(com.fasterxml.jackson.core.JsonParser jParser)
                     throws java.io.IOException

Constructor for loading a MarsMetadata record from a file. Typically, used when streaming records into memory when loading a MoleculeArchive or when a record is retrieved from the virtual store.

Parameters:

jParser - A JsonParser at the start of the record.

Throws:

java.io.IOException - Thrown if unable to parse Json from JsonParser stream.

Method Detail

populateMetadata

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

Specified by:

populateMetadata in interface MarsMetadata

createIOMaps

protected void createIOMaps()

Description copied from class: AbstractJsonConvertibleRecord

Must be implemented in subclasses to define how fields, objects, arrays should be saved based on the Jackson streaming API.

Overrides:

createIOMaps in class AbstractMarsRecord

merge

public void merge(MarsMetadata metadata)

Used to merge another MarsMetadata record into this one. Assumes different images are being merged. Images from the record provided are added to this record.

Specified by:

merge in interface MarsMetadata

Parameters:

metadata - MarsMetadata to merge into this one.

putBdvSource

public 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.

Specified by:

putBdvSource in interface MarsMetadata

Parameters:

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

getBdvSource

public MarsBdvSource getBdvSource(java.lang.String name)

Get the MarsBdvSource with the name provided.

Specified by:

getBdvSource in interface MarsMetadata

Parameters:

name - Name of the MarsBdvSource to retrieve.

Returns:

Mars BigDataViewer Source with the name given.

removeBdvSource

public void removeBdvSource(java.lang.String name)

Remove the MarsBdvSource with the name provided.

Specified by:

removeBdvSource in interface MarsMetadata

Parameters:

name - Name of the MarsBdvSource to remove.

removeAllBdvSources

public void removeAllBdvSources()

Remove all MarsBdvSources.

Specified by:

removeAllBdvSources in interface MarsMetadata

getBdvSources

public java.util.Collection<MarsBdvSource> getBdvSources()

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

Specified by:

getBdvSources in interface MarsMetadata

Returns:

Collection of MarsBdvSources in the record.

getBdvSourceNames

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

Get the set of BigDataViewer source names.

Specified by:

getBdvSourceNames in interface MarsMetadata

Returns:

Names of MarsBdvSources in the record.

hasBdvSource

public boolean hasBdvSource(java.lang.String name)

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

Specified by:

hasBdvSource in interface MarsMetadata

Parameters:

name - Name of the MarsBdvSource to check for.

Returns:

True if a source with the name given is found.

setMicroscopeName

public 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.

Specified by:

setMicroscopeName in interface MarsMetadata

Parameters:

microscope - Name of the microscope used for collection.

getMicroscopeName

public 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.

Specified by:

getMicroscopeName in interface MarsMetadata

Returns:

Name of the microscope used for collection.

setImage

public void setImage(MarsOMEImage image,
                     int imageIndex)

Specified by:

setImage in interface MarsMetadata

getImage

public MarsOMEImage getImage(int imageIndex)

Specified by:

getImage in interface MarsMetadata

getImageCount

public int getImageCount()

Specified by:

getImageCount in interface MarsMetadata

images

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

Specified by:

images in interface MarsMetadata

getSourceDirectory

public java.lang.String getSourceDirectory()

Get the Source Directory where the images are stored.

Specified by:

getSourceDirectory in interface MarsMetadata

Returns:

Directory where the images are stored.

setSourceDirectory

public void setSourceDirectory(java.lang.String path)

Set the Source Directory where the images are stored.

Specified by:

setSourceDirectory in interface MarsMetadata

Parameters:

path - The string file path.

logln

public 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.

Specified by:

logln in interface MarsMetadata

Parameters:

str - Message to add to the log.

log

public 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. Do not start a new line after adding the message.

Specified by:

log in interface MarsMetadata

Parameters:

str - Message to add to the log.

getLog

public 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.

Specified by:

getLog in interface MarsMetadata

Returns:

The processing log for this metadata record.

getPlane

public MarsOMEPlane getPlane(int imageIndex,
                             int z,
                             int c,
                             int t)

Get the MarsOMEPlane for a given image and ZCT position. If there are multiple planes for a given position, this will return the plane with the highest value in the plane index. Therefore, if there are multiple planes per position, the getPlane(int imageIndex, int planeIndex) should be used.

Specified by:

getPlane in interface MarsMetadata

Parameters:

imageIndex - Index of the image.

z - Z (slice).

c - Channel.

t - Time point.

hasPlane

public boolean hasPlane(int imageIndex,
                        int planeIndex)

Specified by:

hasPlane in interface MarsMetadata

getPlane

public MarsOMEPlane getPlane(int imageIndex,
                             int planeIndex)

Specified by:

getPlane in interface MarsMetadata

getCollectionDate

public java.lang.String getCollectionDate()

Description copied from interface: MarsMetadata

Get the Date when these data were collected.

Specified by:

getCollectionDate in interface MarsMetadata

Returns:

The date when the metadata was collected.