Package com.pixelmed.convert
Class Immunostaining
- java.lang.Object
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- com.pixelmed.convert.Immunostaining
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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).
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Nested Class Summary
Nested Classes Modifier and Type Class Description class
Immunostaining.ImmunostainingChannel
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Constructor Summary
Constructors Constructor Description Immunostaining(java.io.File file)
Immunostaining(java.util.SortedMap<java.lang.String,java.lang.String> channelNamesByChannelID)
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Method Summary
All Methods Static Methods Instance Methods Concrete Methods Modifier and Type Method 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).
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Constructor Detail
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Immunostaining
public Immunostaining(java.io.File file) throws java.io.FileNotFoundException, java.io.IOException, DicomException
- Throws:
java.io.FileNotFoundException
java.io.IOException
DicomException
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Immunostaining
public Immunostaining(java.util.SortedMap<java.lang.String,java.lang.String> channelNamesByChannelID)
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Method Detail
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getCodeForChannelInMap
public static CodedSequenceItem getCodeForChannelInMap(java.util.Map<java.lang.String,CodedSequenceItem> map, java.lang.String name)
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getCodedTarget
public static CodedSequenceItem getCodedTarget(java.lang.String name)
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getCodedUsingSubstance
public static CodedSequenceItem getCodedUsingSubstance(java.lang.String name)
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getCodedFluorophore
public static CodedSequenceItem getCodedFluorophore(java.lang.String name)
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getMapOfOpticalPathAttributesByChannelID
public java.util.SortedMap<java.lang.String,AttributeList> getMapOfOpticalPathAttributesByChannelID() throws DicomException
- Throws:
DicomException
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getMapOfSpecimenPreparationStepContentItemSequenceByChannelID
public java.util.SortedMap<java.lang.String,SequenceAttribute> getMapOfSpecimenPreparationStepContentItemSequenceByChannelID() throws DicomException
- Throws:
DicomException
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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).
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