loci.formats.in

Class PrairieMetadata

java.lang.Object

loci.formats.in.PrairieMetadata

public class PrairieMetadata
extends Object

Metadata structure for Prairie Technologies' TIFF-based format.

Source code:

Trac, Gitweb

Nested Class Summary

Nested Classes

Modifier and Type	Class and Description
class	PrairieMetadata.Frame A Prairie <Frame>, beneath a <Sequence>.
class	PrairieMetadata.PFile A Prairie <File> beneath a <Frame>.
class	PrairieMetadata.Sequence A Prairie <Sequence>.

Constructor Summary

Constructors

Constructor and Description
PrairieMetadata(Document xml, Document cfg) Creates a new Prairie metadata by parsing the given XML and CFG documents.

Method Summary

Methods

Modifier and Type	Method and Description
int[]	getActiveChannels() Gets the list of active channel indices, in sorted order.
Integer	getBitDepth() Gets the bitDepth recorded in the configuration.
Map<String,String>	getConfig() Gets a read-only map of configuration key/value pairs.
String	getConfig(String key) Gets the value of the given configuration Key.
int	getCycleCount() Gets the number of recorded cycles.
int	getCycleMax() Gets the maximum cycle value.
int	getCycleMin() Gets the minimum cycle value.
String	getDate() Gets the date of the acquisition.
PrairieMetadata.PFile	getFile(int cycle, int index, int channel) Gets the Frame at the given (cycle, index, channel).
PrairieMetadata.Sequence	getFirstSequence() Gets the first Sequence.
PrairieMetadata.Frame	getFrame(int cycle, int index) Gets the Frame at the given (cycle and index).
Double	getLaserPower() Gets the laserPower_0 recorded in the configuration.
PrairieMetadata.Sequence	getSequence(int cycle) Gets the Sequence at the given cycle.
ArrayList<PrairieMetadata.Sequence>	getSequences() Gets all Sequences, ordered by cycle.
Double	getWaitTime() Gets the waitTime recorded in the configuration.
boolean	isInvertX() Gets whether the stage position X coordinates are inverted (i.e., left-to-right).
boolean	isInvertY() Gets whether the stage position Y coordinates are inverted (i.e., bottom-to-top).

Methods inherited from class java.lang.Object

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

Constructor Detail

PrairieMetadata

public PrairieMetadata(Document xml,
               Document cfg)

Creates a new Prairie metadata by parsing the given XML and CFG documents.

Parameters:

xml - The XML document to parse, or null if none available.

cfg - The CFG document to parse, or null if none available.

Method Detail

getWaitTime

public Double getWaitTime()

Gets the waitTime recorded in the configuration.

getActiveChannels

public int[] getActiveChannels()

Gets the list of active channel indices, in sorted order.

These indices correspond to the configuration's channel_* keys flagged as True.

isInvertX

public boolean isInvertX()

Gets whether the stage position X coordinates are inverted (i.e., left-to-right).

isInvertY

public boolean isInvertY()

Gets whether the stage position Y coordinates are inverted (i.e., bottom-to-top).

getBitDepth

public Integer getBitDepth()

Gets the bitDepth recorded in the configuration.

getLaserPower

public Double getLaserPower()

Gets the laserPower_0 recorded in the configuration.

getConfig

public String getConfig(String key)

Gets the value of the given configuration Key.

getConfig

public Map<String,String> getConfig()

Gets a read-only map of configuration key/value pairs.

getDate

public String getDate()

Gets the date of the acquisition.

getCycleMin

public int getCycleMin()

Gets the minimum cycle value. Matches the smallest cycle attribute found, and hence will not necessarily equal 1 (though in practice it usually does).

getCycleMax

public int getCycleMax()

Gets the maximum cycle value. Matches the largest cycle attribute found, and hence will not necessarily equal sequences#size() (though in practice it usually does).

getCycleCount

public int getCycleCount()

Gets the number of recorded cycles. This value is equal to getCycleMax() - getCycleMin() + 1.

getFirstSequence

public PrairieMetadata.Sequence getFirstSequence()

Gets the first Sequence.

getSequence

public PrairieMetadata.Sequence getSequence(int cycle)

Gets the Sequence at the given cycle.

getSequences

public ArrayList<PrairieMetadata.Sequence> getSequences()

Gets all Sequences, ordered by cycle.

getFrame

public PrairieMetadata.Frame getFrame(int cycle,
                             int index)

Gets the Frame at the given (cycle and index).

getFile

public PrairieMetadata.PFile getFile(int cycle,
                            int index,
                            int channel)

Gets the Frame at the given (cycle, index, channel).