loci.formats.in

Class PrairieMetadata.Frame

java.lang.Object

loci.formats.in.PrairieMetadata.Frame

Enclosing class:

PrairieMetadata

public class PrairieMetadata.Frame
extends Object

A Prairie <Frame>, beneath a <Sequence>.

Field Summary

Fields

Modifier and Type	Field and Description
private Double	absoluteTime absoluteTime attribute of this <Frame>.
private HashMap<Integer,PrairieMetadata.PFile>	files <File> elements beneath this <Frame>, keyed on each file's channel.
private PrairieMetadata.PFile	firstFile The first actual <File> element for this <Frame>.
private PrairieMetadata.ValueTable	frameValues Table of key/value pairs for this <Frame>.
private Integer	index index of this <Frame>.
private Double	relativeTime relativeTime attribute of this <Frame>.
private PrairieMetadata.Sequence	sequence The <Sequence> containing this <Frame>.

Constructor Summary

Constructors

Constructor and Description
PrairieMetadata.Frame(PrairieMetadata.Sequence sequence, Element frameElement) Creates a new frame by parsing the given <Frame> element.

Method Summary

Methods

Modifier and Type	Method and Description
double	getAbsoluteTime() Gets the absoluteTime associated with this Frame.
PrairieMetadata.PFile	getFile(int channel) Gets the File with the given channel.
PrairieMetadata.PFile	getFirstFile() Gets the first File of the Sequence.
Double	getGain(int c) Gets the cth gain for this Frame.
String	getImagingDevice() Gets the imaging device associated with this Frame.
String	getImmersion() Extracts the immersion from the objective lens string.
int	getIndex() Gets the index associated with this Frame.
Integer	getLinesPerFrame() Gets the lines per frame for this Frame.
Double	getMagnification() Extracts the magnification from the objective lens string.
Double	getMicronsPerPixelX() Gets the microns per pixel along X for this Frame.
Double	getMicronsPerPixelY() Gets the microns per pixel along Y for this Frame.
String	getObjectiveLens() Gets the objective lens string for this Frame.
Double	getObjectiveLensNA() Gets the numerical aperture of the lens for this Frame.
String	getObjectiveManufacturer() Extracts the objective manufacturer from the objective lens string.
Double	getOffset(int c) Gets the cth offset for this Frame.
Double	getOpticalZoom() Gets the optical zoom associated with this Frame.
Integer	getPixelsPerLine() Gets the pixels per line for this Frame.
Length	getPositionX() Gets the X stage position associated with this Frame.
Length	getPositionY() Gets the Y stage position associated with this Frame.
Length	getPositionZ() Gets the Z stage position associated with this Frame.
double	getRelativeTime() Gets the relativeTime associated with this Frame.
PrairieMetadata.Sequence	getSequence() Gets the <Sequence> containing this <Frame>.
PrairieMetadata.Value	getValue(String key) Gets the value of the given key, beneath this Frame, inferring the value from the parent <Sequence> or grandparent <PVScan> section as needed.
PrairieMetadata.ValueTable	getValues() Gets the table of Frame key/value pairs.
void	parse(Element frameElement) Parses metadata from the given Frame element.
private Length	toLength(Double position, boolean isInvert) Convert a position number to a length in the microscope reference frame.

Methods inherited from class java.lang.Object

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

Field Detail

sequence

private PrairieMetadata.Sequence sequence

The <Sequence> containing this <Frame>.

files

private final HashMap<Integer,PrairieMetadata.PFile> files

<File> elements beneath this <Frame>, keyed on each file's channel.

frameValues

private final PrairieMetadata.ValueTable frameValues

Table of key/value pairs for this <Frame>.

firstFile

private PrairieMetadata.PFile firstFile

The first actual <File> element for this <Frame>.

relativeTime

private Double relativeTime

relativeTime attribute of this <Frame>.

absoluteTime

private Double absoluteTime

absoluteTime attribute of this <Frame>.

index

private Integer index

index of this <Frame>.

Constructor Detail

PrairieMetadata.Frame

public PrairieMetadata.Frame(PrairieMetadata.Sequence sequence,
                     Element frameElement)

Creates a new frame by parsing the given <Frame> element.

Method Detail

getSequence

public PrairieMetadata.Sequence getSequence()

Gets the <Sequence> containing this <Frame>.

parse

public void parse(Element frameElement)

Parses metadata from the given Frame element.

getRelativeTime

public double getRelativeTime()

Gets the relativeTime associated with this Frame.

getAbsoluteTime

public double getAbsoluteTime()

Gets the absoluteTime associated with this Frame.

getIndex

public int getIndex()

Gets the index associated with this Frame.

getFirstFile

public PrairieMetadata.PFile getFirstFile()

Gets the first File of the Sequence.

getFile

public PrairieMetadata.PFile getFile(int channel)

Gets the File with the given channel.

getObjectiveLens

public String getObjectiveLens()

Gets the objective lens string for this Frame.

getObjectiveManufacturer

public String getObjectiveManufacturer()

Extracts the objective manufacturer from the objective lens string.

getMagnification

public Double getMagnification()

Extracts the magnification from the objective lens string.

getImmersion

public String getImmersion()

Extracts the immersion from the objective lens string.

getObjectiveLensNA

public Double getObjectiveLensNA()

Gets the numerical aperture of the lens for this Frame.

getPixelsPerLine

public Integer getPixelsPerLine()

Gets the pixels per line for this Frame.

getLinesPerFrame

public Integer getLinesPerFrame()

Gets the lines per frame for this Frame.

toLength

private Length toLength(Double position,
              boolean isInvert)

Convert a position number to a length in the microscope reference frame.

Parameters:

position - a position number, may be null

isInvert - if the number's sign should be flipped

Returns:

a length corresponding to the number, may be null

getPositionX

public Length getPositionX()

Gets the X stage position associated with this Frame.

getPositionY

public Length getPositionY()

Gets the Y stage position associated with this Frame.

getPositionZ

public Length getPositionZ()

Gets the Z stage position associated with this Frame.

getOpticalZoom

public Double getOpticalZoom()

Gets the optical zoom associated with this Frame.

getMicronsPerPixelX

public Double getMicronsPerPixelX()

Gets the microns per pixel along X for this Frame.

getMicronsPerPixelY

public Double getMicronsPerPixelY()

Gets the microns per pixel along Y for this Frame.

getOffset

public Double getOffset(int c)

Gets the cth offset for this Frame.

Parameters:

c - The 0-based(!) channel index for which to obtain the offset.

getGain

public Double getGain(int c)

Gets the cth gain for this Frame.

Parameters:

c - The 0-based(!) channel index for which to obtain the gain.

getImagingDevice

public String getImagingDevice()

Gets the imaging device associated with this Frame.

getValue

public PrairieMetadata.Value getValue(String key)

Gets the value of the given key, beneath this Frame, inferring the value from the parent <Sequence> or grandparent <PVScan> section as needed.

getValues

public PrairieMetadata.ValueTable getValues()

Gets the table of Frame key/value pairs.