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.

Author:

Curtis Rueden

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>.
static interface	PrairieMetadata.Value A value in a Prairie metadata dictionary.
static class	PrairieMetadata.ValueItem A leaf value with an actual PrairieMetadata.ValueItem.value() as well as an optional PrairieMetadata.ValueItem.description().
static class	PrairieMetadata.ValueTable A table of values.

Constructor Summary

Constructors

Constructor and Description
PrairieMetadata(Document xml, Document cfg, Document env) Creates a new Prairie metadata by parsing the given XML, CFG and/or ENV 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.
PrairieMetadata.ValueTable	getConfig() Gets the map of configuration key/value pairs.
PrairieMetadata.Value	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 first laserPower 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.
PrairieMetadata.Value	getValue(String key) Gets the value of the given key, at the top-level <PVScan> element.
PrairieMetadata.ValueTable	getValues() Gets the table of PVScan key/value pairs.
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,
               Document env)

Creates a new Prairie metadata by parsing the given XML, CFG and/or ENV documents.

Parameters:

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

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

env - The ENV 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 first laserPower recorded in the configuration.

getConfig

public PrairieMetadata.Value getConfig(String key)

Gets the value of the given configuration key.

getConfig

public PrairieMetadata.ValueTable getConfig()

Gets the 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).

getValue

public PrairieMetadata.Value getValue(String key)

Gets the value of the given key, at the top-level <PVScan> element.

getValues

public PrairieMetadata.ValueTable getValues()

Gets the table of PVScan key/value pairs.