public class ND2Handler
extends loci.common.xml.BaseHandler
Modifier and Type | Field and Description |
---|---|
private java.util.ArrayList<java.lang.String> |
binning |
private java.lang.String |
cameraModel |
private boolean |
canAdjustDimensions |
private java.util.ArrayList<java.lang.String> |
channelNames |
private java.util.Hashtable<java.lang.String,java.lang.Integer> |
colors |
private CoreMetadataList |
core |
private java.lang.String |
correction |
private java.lang.String |
date |
private static java.lang.String |
DATE_FORMAT |
private java.util.Hashtable<java.lang.String,java.lang.String> |
dyes |
private java.util.ArrayList<java.lang.Double> |
emWave |
private java.util.ArrayList<java.lang.Double> |
exposureTime |
private java.util.ArrayList<java.lang.Double> |
exWave |
private static int |
FIELD_INDEX |
private boolean |
firstTimeLoop |
private java.util.ArrayList<java.lang.Double> |
gain |
private java.lang.String |
immersion |
private boolean |
isLossless |
private static org.slf4j.Logger |
LOGGER |
private java.lang.Double |
mag |
private java.util.Hashtable<java.lang.String,java.lang.Object> |
metadata |
private java.util.ArrayList<java.lang.String> |
modality |
private java.lang.Double |
na |
private int |
nImages |
private int |
numSeries |
private int |
nXFields |
private int |
nYFields |
private java.lang.String |
objectiveModel |
private java.lang.Double |
pinholeSize |
private double |
pixelSizeX |
private double |
pixelSizeY |
private double |
pixelSizeZ |
private boolean |
populateXY |
private java.util.ArrayList<java.lang.String> |
posNames |
private java.util.ArrayList<ome.units.quantity.Length> |
posX |
private java.util.ArrayList<ome.units.quantity.Length> |
posY |
private java.util.ArrayList<ome.units.quantity.Length> |
posZ |
private java.util.ArrayList<java.lang.Integer> |
power |
private java.lang.String |
prefix |
private java.lang.String |
prevElement |
private java.lang.String |
prevRuntype |
private java.util.Hashtable<java.lang.String,java.lang.Integer> |
realColors |
private java.lang.Double |
refractiveIndex |
private java.util.ArrayList<java.util.Hashtable<java.lang.String,java.lang.String>> |
rois |
private java.util.ArrayList<java.lang.Double> |
speed |
private java.util.ArrayList<java.lang.Double> |
temperature |
private java.util.ArrayList<java.lang.Long> |
ts |
private java.util.ArrayList<java.lang.Boolean> |
validLoopState |
private java.lang.Double |
voltage |
private java.util.ArrayList<java.lang.Long> |
zs |
Constructor and Description |
---|
ND2Handler(CoreMetadataList core,
boolean populateXY,
int nImages) |
ND2Handler(CoreMetadataList core,
int nImages) |
Modifier and Type | Method and Description |
---|---|
void |
endDocument() |
void |
endElement(java.lang.String uri,
java.lang.String localName,
java.lang.String qName,
org.xml.sax.Attributes attributes) |
java.util.ArrayList<java.lang.String> |
getBinnings() |
java.lang.String |
getCameraModel() |
java.util.Hashtable<java.lang.String,java.lang.Integer> |
getChannelColors() |
java.util.ArrayList<java.lang.String> |
getChannelNames() |
CoreMetadataList |
getCoreMetadataList() |
java.lang.String |
getCorrection() |
java.lang.String |
getDate() |
java.util.ArrayList<java.lang.Double> |
getEmissionWavelengths() |
java.util.ArrayList<java.lang.Double> |
getExcitationWavelengths() |
java.util.ArrayList<java.lang.Double> |
getExposureTimes() |
int |
getFieldIndex() |
java.util.ArrayList<java.lang.Double> |
getGains() |
java.lang.String |
getImmersion() |
java.lang.Double |
getMagnification() |
java.util.Hashtable<java.lang.String,java.lang.Object> |
getMetadata() |
java.util.ArrayList<java.lang.String> |
getModalities() |
java.lang.Double |
getNumericalAperture() |
java.lang.String |
getObjectiveModel() |
java.lang.Double |
getPinholeSize() |
double |
getPixelSizeX() |
double |
getPixelSizeY() |
double |
getPixelSizeZ() |
java.util.ArrayList<java.lang.String> |
getPositionNames() |
java.util.ArrayList<java.lang.Integer> |
getPowers() |
java.lang.Double |
getRefractiveIndex() |
java.util.ArrayList<java.util.Hashtable<java.lang.String,java.lang.String>> |
getROIs() |
int |
getSeriesCount() |
java.util.ArrayList<java.lang.Double> |
getSpeeds() |
java.util.ArrayList<java.lang.Double> |
getTemperatures() |
java.util.ArrayList<java.lang.Long> |
getTimepoints() |
java.lang.Double |
getVoltage() |
int |
getXFields() |
java.util.ArrayList<ome.units.quantity.Length> |
getXPositions() |
java.util.ArrayList<ome.units.quantity.Length> |
getYPositions() |
java.util.ArrayList<ome.units.quantity.Length> |
getZPositions() |
java.util.ArrayList<java.lang.Long> |
getZSections() |
boolean |
isDimensions(java.lang.String key)
Returns whether or not the specified key is denotes dimensions.
|
boolean |
isLossless() |
void |
parseKeyAndValue(java.lang.String key,
java.lang.String value,
java.lang.String runtype) |
private java.lang.Double |
parsePixelsSizeZFromKey(java.lang.String key)
Parses the physical size from a key.
|
void |
populateROIs(MetadataStore store) |
void |
startElement(java.lang.String uri,
java.lang.String localName,
java.lang.String qName,
org.xml.sax.Attributes attributes) |
private static final org.slf4j.Logger LOGGER
private static final java.lang.String DATE_FORMAT
private static final int FIELD_INDEX
private java.lang.String prefix
private java.lang.String prevRuntype
private java.lang.String prevElement
private java.util.Hashtable<java.lang.String,java.lang.Object> metadata
private CoreMetadataList core
private boolean isLossless
private java.util.ArrayList<java.lang.Long> zs
private java.util.ArrayList<java.lang.Long> ts
private int numSeries
private double pixelSizeX
private double pixelSizeY
private double pixelSizeZ
private java.lang.Double pinholeSize
private java.lang.Double voltage
private java.lang.Double mag
private java.lang.Double na
private java.lang.String objectiveModel
private java.lang.String immersion
private java.lang.String correction
private java.lang.Double refractiveIndex
private java.util.ArrayList<java.lang.String> channelNames
private java.util.ArrayList<java.lang.String> modality
private java.util.ArrayList<java.lang.String> binning
private java.util.ArrayList<java.lang.Double> speed
private java.util.ArrayList<java.lang.Double> gain
private java.util.ArrayList<java.lang.Double> temperature
private java.util.ArrayList<java.lang.Double> exposureTime
private java.util.ArrayList<java.lang.Double> exWave
private java.util.ArrayList<java.lang.Double> emWave
private java.util.ArrayList<java.lang.Integer> power
private java.util.ArrayList<java.util.Hashtable<java.lang.String,java.lang.String>> rois
private java.util.ArrayList<ome.units.quantity.Length> posX
private java.util.ArrayList<ome.units.quantity.Length> posY
private java.util.ArrayList<ome.units.quantity.Length> posZ
private java.util.ArrayList<java.lang.String> posNames
private java.lang.String cameraModel
private java.lang.String date
private java.util.Hashtable<java.lang.String,java.lang.Integer> colors
private java.util.Hashtable<java.lang.String,java.lang.String> dyes
private java.util.Hashtable<java.lang.String,java.lang.Integer> realColors
private int nXFields
private int nYFields
private boolean populateXY
private int nImages
private java.util.ArrayList<java.lang.Boolean> validLoopState
private boolean canAdjustDimensions
private boolean firstTimeLoop
public ND2Handler(CoreMetadataList core, int nImages)
public ND2Handler(CoreMetadataList core, boolean populateXY, int nImages)
public int getXFields()
public CoreMetadataList getCoreMetadataList()
public void populateROIs(MetadataStore store)
public java.lang.String getDate()
public java.util.Hashtable<java.lang.String,java.lang.Object> getMetadata()
public int getSeriesCount()
public boolean isLossless()
public java.util.ArrayList<java.lang.Long> getZSections()
public java.util.ArrayList<java.lang.Long> getTimepoints()
public double getPixelSizeX()
public double getPixelSizeY()
public double getPixelSizeZ()
public java.lang.Double getPinholeSize()
public java.lang.Double getVoltage()
public java.lang.Double getMagnification()
public java.lang.Double getNumericalAperture()
public java.lang.String getObjectiveModel()
public java.lang.String getImmersion()
public java.lang.String getCorrection()
public java.lang.Double getRefractiveIndex()
public java.util.ArrayList<java.lang.String> getChannelNames()
public java.util.ArrayList<java.lang.String> getModalities()
public java.util.ArrayList<java.lang.String> getBinnings()
public java.util.ArrayList<java.lang.Double> getSpeeds()
public java.util.ArrayList<java.lang.Double> getGains()
public java.util.ArrayList<java.lang.Double> getTemperatures()
public java.util.ArrayList<java.lang.Double> getExposureTimes()
public java.util.ArrayList<java.lang.Double> getExcitationWavelengths()
public java.util.ArrayList<java.lang.Double> getEmissionWavelengths()
public java.util.ArrayList<java.lang.Integer> getPowers()
public java.util.ArrayList<java.util.Hashtable<java.lang.String,java.lang.String>> getROIs()
public java.util.ArrayList<ome.units.quantity.Length> getXPositions()
public java.util.ArrayList<ome.units.quantity.Length> getYPositions()
public java.util.ArrayList<ome.units.quantity.Length> getZPositions()
public java.util.ArrayList<java.lang.String> getPositionNames()
public java.lang.String getCameraModel()
public int getFieldIndex()
public java.util.Hashtable<java.lang.String,java.lang.Integer> getChannelColors()
public void endElement(java.lang.String uri, java.lang.String localName, java.lang.String qName, org.xml.sax.Attributes attributes)
public void startElement(java.lang.String uri, java.lang.String localName, java.lang.String qName, org.xml.sax.Attributes attributes)
startElement
in interface org.xml.sax.ContentHandler
startElement
in class org.xml.sax.helpers.DefaultHandler
public void endDocument()
endDocument
in interface org.xml.sax.ContentHandler
endDocument
in class org.xml.sax.helpers.DefaultHandler
public void parseKeyAndValue(java.lang.String key, java.lang.String value, java.lang.String runtype)
public boolean isDimensions(java.lang.String key)
private java.lang.Double parsePixelsSizeZFromKey(java.lang.String key)
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