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.

Field Summary

Fields

Modifier and Type	Field and Description
private HashSet<Integer>	activeChannels Set of active channel indices.
private PrairieMetadata.ValueTable	config Key/value pairs from CFG and/or ENV files.
private int	cycleMax Maximum cycle value.
private int	cycleMin Minimum cycle value.
private String	date The date of the acquisition.
private PrairieMetadata.Sequence	firstSequence The first actual <Sequence> element.
private PrairieMetadata.ValueTable	scanValues Table of key/value pairs at the top level.
private HashMap<Integer,PrairieMetadata.Sequence>	sequences <Sequence> elements, keyed on each sequence's cycle.
private Double	waitTime The wait time of the acquisition.

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
private String	attr(Element el, String name) Gets the attribute value with the given name, or null if not defined.
private boolean	b(String value) Converts the given string to a boolean.
private void	checkElement(Element el, String name) Checks that the given element has the specified name.
private Double	d(String value) Converts the given string to a Double, or null if incompatible.
private Element	el(NodeList nodes, int index) Gets the indexth element from the given list of nodes.
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).
private Element	getFirstChild(Element el, String name) Gets the first child element with the given name.
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.
private Integer	i(String value) Converts the given string to an Integer, or null if incompatible.
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).
private void	parseCFG(Document doc) Parses metadata from Prairie CFG file.
private void	parseChannels() Parses details of the activated channels into the activeChannels data structure from the "channel" entry of the configuration.
private void	parseENV(Document doc) Parses metadata from Prairie ENV file.
private void	parseKeys(Element el, PrairieMetadata.ValueTable table) Parses <Key> elements beneath the given element, into the specified table.
private void	parsePVStateShard(Element el, PrairieMetadata.ValueTable table) Parses the <PVStateShard> element beneath the given element, into the specified table.
private void	parseXML(Document doc) Parses metadata from Prairie XML file.
private String	token(String s, String regex, int i) Gets the ith token of the given string, split according to the specific regular expression.
private String	value(PrairieMetadata.Value value) Returns value.value(), or null if value is null.
private String	value(PrairieMetadata.Value value, int index) Returns value.get(index).value(), or null if value or value.get(index) is null.
private String	value(PrairieMetadata.Value value, String key) Returns value.get(key).value(), or null if value or value.get(key) is null.
private <K extends Comparable<? super K>,V> ArrayList<V>	valuesByKey(Map<K,V> map) Gets the values of the given map, sorted by key.

Methods inherited from class java.lang.Object

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

Field Detail

sequences

private final HashMap<Integer,PrairieMetadata.Sequence> sequences

<Sequence> elements, keyed on each sequence's cycle.

scanValues

private final PrairieMetadata.ValueTable scanValues

Table of key/value pairs at the top level.

firstSequence

private PrairieMetadata.Sequence firstSequence

The first actual <Sequence> element.

cycleMin

private int cycleMin

Minimum cycle value.

cycleMax

private int cycleMax

Maximum cycle value.

date

private String date

The date of the acquisition.

waitTime

private Double waitTime

The wait time of the acquisition.

activeChannels

private final HashSet<Integer> activeChannels

Set of active channel indices.

config

private final PrairieMetadata.ValueTable config

Key/value pairs from CFG and/or ENV files.

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.

parseXML

private void parseXML(Document doc)

Parses metadata from Prairie XML file.

parseCFG

private void parseCFG(Document doc)

Parses metadata from Prairie CFG file. This file is only present for Prairie datasets recorded prior to version 5.2.

parseENV

private void parseENV(Document doc)

Parses metadata from Prairie ENV file. This file is only present for Prairie datasets recorded with version 5.2 or later.

parseKeys

private void parseKeys(Element el,
             PrairieMetadata.ValueTable table)

Parses <Key> elements beneath the given element, into the specified table. These <Key> elements are only present in data from PrairieView versions prior to 5.2.

parsePVStateShard

private void parsePVStateShard(Element el,
                     PrairieMetadata.ValueTable table)

Parses the <PVStateShard> element beneath the given element, into the specified table. These <PVStateShard> elements are only present in data from PrairieView versions 5.2 and later.

parseChannels

private void parseChannels()

Parses details of the activated channels into the activeChannels data structure from the "channel" entry of the configuration.

checkElement

private void checkElement(Element el,
                String name)

Checks that the given element has the specified name.

Throws:

IllegalArgumentException - if the name does not match.

getFirstChild

private Element getFirstChild(Element el,
                    String name)

Gets the first child element with the given name.

el

private Element el(NodeList nodes,
         int index)

Gets the indexth element from the given list of nodes.

attr

private String attr(Element el,
          String name)

Gets the attribute value with the given name, or null if not defined.

value

private String value(PrairieMetadata.Value value)

Returns value.value(), or null if value is null.

value

private String value(PrairieMetadata.Value value,
           String key)

Returns value.get(key).value(), or null if value or value.get(key) is null.

value

private String value(PrairieMetadata.Value value,
           int index)

Returns value.get(index).value(), or null if value or value.get(index) is null.

b

private boolean b(String value)

Converts the given string to a boolean.

d

private Double d(String value)

Converts the given string to a Double, or null if incompatible.

i

private Integer i(String value)

Converts the given string to an Integer, or null if incompatible.

token

private String token(String s,
           String regex,
           int i)

Gets the ith token of the given string, split according to the specific regular expression.

valuesByKey

private <K extends Comparable<? super K>,V> ArrayList<V> valuesByKey(Map<K,V> map)

Gets the values of the given map, sorted by key.