loci.formats.in.LeicaMicrosystemsMetadata

Class LMSMetadataExtractor

java.lang.Object

loci.formats.in.LeicaMicrosystemsMetadata.LMSMetadataExtractor

public class LMSMetadataExtractor
extends java.lang.Object

This class extracts metadata information from Leica Microsystems image XML and stores it in the reader's CoreMetadata and MetadataTempBuffer

Author:

Melissa Linkert melissa at glencoesoftware.com, Constanze Wendlandt constanze.wendlandt at leica-microsystems.com

Field Summary

Fields

Modifier and Type	Field and Description
(package private) java.util.List<java.lang.Long>	channelBytesIncs
(package private) int	extras
private static long	METER_MULTIPLY
private LMSFileReader	r

Constructor Summary

Constructors

Constructor and Description
LMSMetadataExtractor(LMSFileReader reader)

Method Summary

Modifier and Type	Method and Description
private void	addUserCommentMeta(org.w3c.dom.Element imageNode, int image) Extracts user comments and adds them to the reader's CoreMetadata
private org.w3c.dom.NodeList	getChannelDescriptionNodes(org.w3c.dom.Element root)
static int	getChannelIndex(org.w3c.dom.Element filterSetting)
private int	getChannelPriority(java.lang.String lutName)
private org.w3c.dom.NodeList	getDimensionDescriptionNodes(org.w3c.dom.Element root)
private org.w3c.dom.Element	getImageDescription(org.w3c.dom.Element root)
private org.w3c.dom.NodeList	getNodes(org.w3c.dom.Element root, java.lang.String nodeName) Returns all (grand*n)children nodes with given node name
double	parseDouble(java.lang.String value)
int	parseInt(java.lang.String value)
long	parseLong(java.lang.String value)
private void	populateOriginalMetadata(org.w3c.dom.Element root, java.util.Deque<java.lang.String> nameStack) Creates key value pairs from attributes of the root's child nodes (tag | attribute name : attribute value) and adds them to reader's CoreMetadata
private void	setCoreDimensionSizes(int coreIndex) Writes extracted dimension sizes to CoreMetadata
private void	setPixelType(int coreIndex) Sets CoreMetadata.pixelType depending on extracted x bytesInc
void	translateAttachmentNodes(org.w3c.dom.Element imageNode, int image) Extracts information from dimension descriptions and writes it to reader's MetadataTempBuffer
void	translateChannelDescriptions(org.w3c.dom.Element imageNode, int coreIndex) Extracts i.a.
void	translateDetectors(org.w3c.dom.Element imageNode, int image) Extracts detector information and writes it to reader's MetadataTempBuffer
private void	translateDimensionDescriptions(org.w3c.dom.Element imageNode, int coreIndex) Extracts information from dimension descriptions and writes it to reader's CoreMetadata and MetadataTempBuffer
void	translateFilterSettings(org.w3c.dom.Element imageNode, int image) Extracts filter information and writes it to reader's MetadataTempBuffer
void	translateImage(org.w3c.dom.Element image, int i) Extracts information from element node and writes it to reader's CoreMetadata and MetadataTempBuffer
void	translateLaserLines(org.w3c.dom.Element imageNode, int image) Extracts laser information and writes it to reader's MetadataTempBuffer
private ome.xml.model.primitives.Color	translateLut(java.lang.String lutName) Translates Leica XML lut name / value to Color
private void	translateLuts(java.util.List<java.lang.String> luts, int imgIndex) Translates raw channel luts of an image to Colors and writes it to reader's MetadataTempBuffer
void	translateMetadata(java.util.List<LMSImageXmlDocument> docs) Extracts all information from Leica image xml Documents and writes it to reader's CoreMetadata and MetadataTempBuffer
void	translateROIs(org.w3c.dom.Element imageNode, int image) Extracts ROIs and writes them to reader's MetadataTempBuffer
void	translateScannerSettings(org.w3c.dom.Element imageNode, int image) Extracts scanner information and writes it to reader's CoreMetadata and MetadataTempBuffer
void	translateSingleROIs(org.w3c.dom.Element imageNode, int image) Extracts single ROIs and writes them to reader's MetadataTempBuffer
private double	translateSingleTimestamp(org.w3c.dom.Element timestamp) Translates the content of a timestamp node to double value
private double	translateSingleTimestamp(java.lang.String timestamp) Translates hex timestamp string to double value
void	translateTimestamps(org.w3c.dom.Element imageNode, int image) Extracts timestamps and writes them to reader's MetadataTempBuffer

Methods inherited from class java.lang.Object

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

Field Detail

METER_MULTIPLY

private static final long METER_MULTIPLY

See Also:

Constant Field Values

r

private LMSFileReader r

channelBytesIncs

java.util.List<java.lang.Long> channelBytesIncs

extras

int extras

Constructor Detail

LMSMetadataExtractor

public LMSMetadataExtractor(LMSFileReader reader)

Method Detail

translateMetadata

public void translateMetadata(java.util.List<LMSImageXmlDocument> docs)
                       throws FormatException,
                              java.io.IOException

Extracts all information from Leica image xml Documents and writes it to reader's CoreMetadata and MetadataTempBuffer

Parameters:

docs - list of Leica xml documents

Throws:

FormatException

java.io.IOException

translateImage

public void translateImage(org.w3c.dom.Element image,
                           int i)
                    throws FormatException

Extracts information from element node and writes it to reader's CoreMetadata and MetadataTempBuffer

Parameters:

img - node with tag name "element" from Leica XML

i - image /core index

Throws:

FormatException

translateChannelDescriptions

public void translateChannelDescriptions(org.w3c.dom.Element imageNode,
                                         int coreIndex)
                                  throws FormatException

Extracts i.a. channel number and luts from channel descriptions and writes it to reader's CoreMetadata and MetadataTempBuffer

Parameters:

imageNode - Image node from Leica xml

coreIndex -

Throws:

FormatException

translateLuts

private void translateLuts(java.util.List<java.lang.String> luts,
                           int imgIndex)

Translates raw channel luts of an image to Colors and writes it to reader's MetadataTempBuffer

Parameters:

luts - list of raw lut names / values from Leica XML

getChannelPriority

private int getChannelPriority(java.lang.String lutName)

translateLut

private ome.xml.model.primitives.Color translateLut(java.lang.String lutName)

Translates Leica XML lut name / value to Color

Parameters:

lutName -

Returns:

translateDimensionDescriptions

private void translateDimensionDescriptions(org.w3c.dom.Element imageNode,
                                            int coreIndex)
                                     throws FormatException

Extracts information from dimension descriptions and writes it to reader's CoreMetadata and MetadataTempBuffer

Parameters:

imageNode - Image node from Leica xml

coreIndex -

Throws:

FormatException

setCoreDimensionSizes

private void setCoreDimensionSizes(int coreIndex)

Writes extracted dimension sizes to CoreMetadata

Parameters:

coreIndex -

setPixelType

private void setPixelType(int coreIndex)
                   throws FormatException

Sets CoreMetadata.pixelType depending on extracted x bytesInc

Parameters:

coreIndex -

Throws:

FormatException

translateAttachmentNodes

public void translateAttachmentNodes(org.w3c.dom.Element imageNode,
                                     int image)
                              throws FormatException

Extracts information from dimension descriptions and writes it to reader's MetadataTempBuffer

Parameters:

imageNode - Image node from Leica xml

image - image / core index

Throws:

FormatException

translateScannerSettings

public void translateScannerSettings(org.w3c.dom.Element imageNode,
                                     int image)
                              throws FormatException

Extracts scanner information and writes it to reader's CoreMetadata and MetadataTempBuffer

Parameters:

imageNode - Image node from Leica xml

image - image / core index

Throws:

FormatException

translateFilterSettings

public void translateFilterSettings(org.w3c.dom.Element imageNode,
                                    int image)
                             throws FormatException

Extracts filter information and writes it to reader's MetadataTempBuffer

Parameters:

imageNode - Image node from Leica xml

image - image / core index

Throws:

FormatException

translateTimestamps

public void translateTimestamps(org.w3c.dom.Element imageNode,
                                int image)
                         throws FormatException

Extracts timestamps and writes them to reader's MetadataTempBuffer

Parameters:

imageNode - Image node from Leica xml

image - image / core index

Throws:

FormatException

translateLaserLines

public void translateLaserLines(org.w3c.dom.Element imageNode,
                                int image)
                         throws FormatException

Extracts laser information and writes it to reader's MetadataTempBuffer

Parameters:

imageNode - Image node from Leica xml

image - image / core index

Throws:

FormatException

translateROIs

public void translateROIs(org.w3c.dom.Element imageNode,
                          int image)
                   throws FormatException

Extracts ROIs and writes them to reader's MetadataTempBuffer

Parameters:

imageNode - Image node from Leica xml

image - image / core index

Throws:

FormatException

translateSingleROIs

public void translateSingleROIs(org.w3c.dom.Element imageNode,
                                int image)
                         throws FormatException

Extracts single ROIs and writes them to reader's MetadataTempBuffer

Parameters:

imageNode - Image node from Leica xml

image - image / core index

Throws:

FormatException

translateDetectors

public void translateDetectors(org.w3c.dom.Element imageNode,
                               int image)
                        throws FormatException

Extracts detector information and writes it to reader's MetadataTempBuffer

Parameters:

imageNode - Image node from Leica xml

image - image / core index

Throws:

FormatException

translateSingleTimestamp

private double translateSingleTimestamp(java.lang.String timestamp)

Translates hex timestamp string to double value

Parameters:

timestamp - timestamp in format

Returns:

number of seconds

translateSingleTimestamp

private double translateSingleTimestamp(org.w3c.dom.Element timestamp)

Translates the content of a timestamp node to double value

Parameters:

imageNode - timestamp node

image - image / core index

Throws:

FormatException

addUserCommentMeta

private void addUserCommentMeta(org.w3c.dom.Element imageNode,
                                int image)
                         throws FormatException

Extracts user comments and adds them to the reader's CoreMetadata

Parameters:

imageNode -

image -

Throws:

FormatException

populateOriginalMetadata

private void populateOriginalMetadata(org.w3c.dom.Element root,
                                      java.util.Deque<java.lang.String> nameStack)

Creates key value pairs from attributes of the root's child nodes (tag | attribute name : attribute value) and adds them to reader's CoreMetadata

Parameters:

root - xml node

nameStack - list of node names to be prepended to key name

parseLong

public long parseLong(java.lang.String value)

parseInt

public int parseInt(java.lang.String value)

parseDouble

public double parseDouble(java.lang.String value)

getImageDescription

private org.w3c.dom.Element getImageDescription(org.w3c.dom.Element root)

getChannelDescriptionNodes

private org.w3c.dom.NodeList getChannelDescriptionNodes(org.w3c.dom.Element root)

getDimensionDescriptionNodes

private org.w3c.dom.NodeList getDimensionDescriptionNodes(org.w3c.dom.Element root)

getNodes

private org.w3c.dom.NodeList getNodes(org.w3c.dom.Element root,
                                      java.lang.String nodeName)

Returns all (grand*n)children nodes with given node name

Parameters:

root - root node

nodeName - name of children that shall be searched

Returns:

list of child nodes with given name

getChannelIndex

public static int getChannelIndex(org.w3c.dom.Element filterSetting)