de.mpg.biochem.mars.metadata

Class OLDMarsMetadata

java.lang.Object

de.mpg.biochem.mars.molecule.AbstractJsonConvertibleRecord

de.mpg.biochem.mars.molecule.AbstractMarsRecord

de.mpg.biochem.mars.metadata.OLDMarsMetadata

All Implemented Interfaces:

MarsMetadata, JsonConvertibleRecord, MarsRecord

public class OLDMarsMetadata
extends AbstractMarsRecord
implements MarsMetadata

Field Summary

Fields

Modifier and Type	Field and Description
protected java.util.LinkedHashMap<java.lang.String,MarsBdvSource>	bdvSources
protected java.lang.String	CollectionDate
protected MarsTable	dataTable
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
OLDMarsMetadata(com.fasterxml.jackson.core.JsonParser jParser) Constructor for loading a MarsMetadata record from a file.

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.
MarsTable	getDataTable()
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.
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 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

CollectionDate

protected java.lang.String CollectionDate

dataTable

protected final MarsTable dataTable

bdvSources

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

Constructor Detail

OLDMarsMetadata

public OLDMarsMetadata(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 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

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

getDataTable

public MarsTable getDataTable()

getBdvSource

public MarsBdvSource getBdvSource(java.lang.String name)

Description copied from interface: MarsMetadata

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.

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.

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.

getCollectionDate

public java.lang.String getCollectionDate()

Get the Date when these data were collected.

Specified by:

getCollectionDate in interface MarsMetadata

Returns:

The date when the metadata was collected.

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.

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.

Specified by:

getLog in interface MarsMetadata

Returns:

The processing log for this metadata record.

populateMetadata

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

Specified by:

populateMetadata in interface MarsMetadata

getImage

public MarsOMEImage getImage(int imageIndex)

Specified by:

getImage in interface MarsMetadata

getPlane

public MarsOMEPlane getPlane(int imageIndex,
                             int planeIndex)

Specified by:

getPlane in interface MarsMetadata

hasPlane

public boolean hasPlane(int imageIndex,
                        int planeIndex)

Specified by:

hasPlane in interface MarsMetadata

getPlane

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

Specified by:

getPlane in interface MarsMetadata

getImageCount

public int getImageCount()

Specified by:

getImageCount in interface MarsMetadata

setMicroscopeName

public void setMicroscopeName(java.lang.String Microscope)

Description copied from interface: MarsMetadata

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.

setSourceDirectory

public void setSourceDirectory(java.lang.String path)

Description copied from interface: MarsMetadata

Set the Source Directory where the images are stored.

Specified by:

setSourceDirectory in interface MarsMetadata

Parameters:

path - The string file path.

log

public void log(java.lang.String str)

Description copied from interface: MarsMetadata

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.

Specified by:

log in interface MarsMetadata

Parameters:

str - Message to add to the log.

logln

public void logln(java.lang.String str)

Description copied from interface: MarsMetadata

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.

putBdvSource

public void putBdvSource(MarsBdvSource source)

Description copied from interface: MarsMetadata

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.

removeBdvSource

public void removeBdvSource(java.lang.String name)

Description copied from interface: MarsMetadata

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

hasBdvSource

public boolean hasBdvSource(java.lang.String name)

Description copied from interface: MarsMetadata

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.

setImage

public void setImage(MarsOMEImage image,
                     int imageIndex)

Specified by:

setImage in interface MarsMetadata

images

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

Specified by:

images in interface MarsMetadata

merge

public void merge(MarsMetadata metadata)

Description copied from interface: MarsMetadata

Used to merge another MarsMetadata record into this one.

Specified by:

merge in interface MarsMetadata

Parameters:

metadata - MarsMetadata to merge into this one.