com.pixelmed.convert

Class Immunostaining

java.lang.Object

com.pixelmed.convert.Immunostaining

public class Immunostaining
extends java.lang.Object

A class for encoding channel parameters describing immunostaining (including antibodies, fluorescence).

Development of this class has been funded in part with Federal funds from the National Cancer Institute, National Institutes of Health, under Task Order No. HHSN26110071 under Contract No. HHSN261201500003l (Imaging Data Commons).

Nested Class Summary

Nested Classes

Modifier and Type	Class and Description
class	Immunostaining.ImmunostainingChannel

Constructor Summary

Constructors

Constructor and Description
Immunostaining(java.io.File file)
Immunostaining(java.util.SortedMap<java.lang.String,java.lang.String> channelNamesByChannelID)

Method Summary

Modifier and Type	Method and Description
static CodedSequenceItem	getCodedFluorophore(java.lang.String name)
static CodedSequenceItem	getCodedTarget(java.lang.String name)
static CodedSequenceItem	getCodedUsingSubstance(java.lang.String name)
static CodedSequenceItem	getCodeForChannelInMap(java.util.Map<java.lang.String,CodedSequenceItem> map, java.lang.String name)
java.util.SortedMap<java.lang.String,AttributeList>	getMapOfOpticalPathAttributesByChannelID()
java.util.SortedMap<java.lang.String,SequenceAttribute>	getMapOfSpecimenPreparationStepContentItemSequenceByChannelID()
static void	main(java.lang.String[] arg) Read a tab or comma separated values file containing channel parameters describing immunostaining (including antibodies, fluorescence).

Methods inherited from class java.lang.Object

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

Constructor Detail

Immunostaining

public Immunostaining(java.io.File file)
               throws java.io.FileNotFoundException,
                      java.io.IOException,
                      DicomException

Throws:

java.io.FileNotFoundException

java.io.IOException

DicomException

Immunostaining

public Immunostaining(java.util.SortedMap<java.lang.String,java.lang.String> channelNamesByChannelID)

Method Detail

getCodedFluorophore

public static CodedSequenceItem getCodedFluorophore(java.lang.String name)

getCodedTarget

public static CodedSequenceItem getCodedTarget(java.lang.String name)

getCodedUsingSubstance

public static CodedSequenceItem getCodedUsingSubstance(java.lang.String name)

getCodeForChannelInMap

public static CodedSequenceItem getCodeForChannelInMap(java.util.Map<java.lang.String,CodedSequenceItem> map,
                                                       java.lang.String name)

getMapOfOpticalPathAttributesByChannelID

public java.util.SortedMap<java.lang.String,AttributeList> getMapOfOpticalPathAttributesByChannelID()
                                                                                             throws DicomException

Throws:

DicomException

getMapOfSpecimenPreparationStepContentItemSequenceByChannelID

public java.util.SortedMap<java.lang.String,SequenceAttribute> getMapOfSpecimenPreparationStepContentItemSequenceByChannelID()
                                                                                                                      throws DicomException

Throws:

DicomException

main

public static void main(java.lang.String[] arg)

Read a tab or comma separated values file containing channel parameters describing immunostaining (including antibodies, fluorescence).