com.pixelmed.convert

Class IndexedLabelMapToSegmentation

java.lang.Object

com.pixelmed.convert.IndexedLabelMapToSegmentation

public class IndexedLabelMapToSegmentation
extends java.lang.Object

Nested Class Summary

Nested Classes

Modifier and Type	Class and Description
protected class	IndexedLabelMapToSegmentation.LabelInformation

Field Summary

Fields

Modifier and Type	Field and Description
protected java.lang.Integer	backgroundIndex
protected IndexedLabelMapToSegmentation.LabelInformation	backgroundLabel
protected static java.util.Set<java.lang.String>	spatialAndRelationalConcepts
protected static java.util.Set<java.lang.String>	tissueConcepts

Constructor Summary

Constructors

Constructor and Description
IndexedLabelMapToSegmentation(java.lang.String inputFilename, java.lang.String labelFilename, java.lang.String outputFilename, java.lang.String referenceImageFilename, java.lang.String seriesNumber, java.lang.String seriesDescription, java.lang.String contentLabel, java.lang.String contentDescription, java.lang.String contentCreatorName)

Method Summary

Modifier and Type	Method and Description
protected void	addAppropriateSegmentedPropertyCategoryCodeSequence(AttributeList list, IndexedLabelMapToSegmentation.LabelInformation labelinfo)
protected static SequenceAttribute	addCodedSequenceAttribute(AttributeList list, AttributeTag tag, CodedSequenceItem csi)
protected java.util.Map<java.lang.Integer,java.lang.Integer>	addSegmentSequence(AttributeList list, java.util.Set<java.lang.Integer> usedLabels, java.util.Map<java.lang.Integer,IndexedLabelMapToSegmentation.LabelInformation> labelMap, java.util.Set<java.lang.Integer> unrecognizedLabels)
protected void	addSegmentSequenceItem(SequenceAttribute saSegmentSequence, IndexedLabelMapToSegmentation.LabelInformation labelinfo)
protected void	addSegmentSequenceItem(SequenceAttribute saSegmentSequence, int index, IndexedLabelMapToSegmentation.LabelInformation labelinfo)
protected java.lang.String	getStringNoLongerThan64TruncatedIfNecessary(java.lang.String s)
static void	main(java.lang.String[] arg) Read a DICOM image containing pixel values that are indices into a label map and the corresponding map and convert to a DICOM Segmentation object.
protected static SequenceAttribute	newCodedSequenceAttribute(AttributeTag tag, CodedSequenceItem csi)
protected java.util.Map<java.lang.Integer,IndexedLabelMapToSegmentation.LabelInformation>	readLabelMapFile(java.lang.String filename)
protected void	setBit(byte[] pixelData, int f, int r, int c, int rows, int columns)

Methods inherited from class java.lang.Object

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

Field Detail

backgroundIndex

protected java.lang.Integer backgroundIndex

backgroundLabel

protected IndexedLabelMapToSegmentation.LabelInformation backgroundLabel

spatialAndRelationalConcepts

protected static final java.util.Set<java.lang.String> spatialAndRelationalConcepts

tissueConcepts

protected static final java.util.Set<java.lang.String> tissueConcepts

Constructor Detail

IndexedLabelMapToSegmentation

public IndexedLabelMapToSegmentation(java.lang.String inputFilename,
                                     java.lang.String labelFilename,
                                     java.lang.String outputFilename,
                                     java.lang.String referenceImageFilename,
                                     java.lang.String seriesNumber,
                                     java.lang.String seriesDescription,
                                     java.lang.String contentLabel,
                                     java.lang.String contentDescription,
                                     java.lang.String contentCreatorName)
                              throws java.io.IOException,
                                     java.lang.NumberFormatException,
                                     DicomException

Throws:

java.io.IOException

java.lang.NumberFormatException

DicomException

Method Detail

addAppropriateSegmentedPropertyCategoryCodeSequence

protected void addAppropriateSegmentedPropertyCategoryCodeSequence(AttributeList list,
                                                                   IndexedLabelMapToSegmentation.LabelInformation labelinfo)
                                                            throws DicomException

Throws:

DicomException

addCodedSequenceAttribute

protected static SequenceAttribute addCodedSequenceAttribute(AttributeList list,
                                                             AttributeTag tag,
                                                             CodedSequenceItem csi)

addSegmentSequence

protected java.util.Map<java.lang.Integer,java.lang.Integer> addSegmentSequence(AttributeList list,
                                                                                java.util.Set<java.lang.Integer> usedLabels,
                                                                                java.util.Map<java.lang.Integer,IndexedLabelMapToSegmentation.LabelInformation> labelMap,
                                                                                java.util.Set<java.lang.Integer> unrecognizedLabels)
                                                                         throws DicomException

Throws:

DicomException

addSegmentSequenceItem

protected void addSegmentSequenceItem(SequenceAttribute saSegmentSequence,
                                      IndexedLabelMapToSegmentation.LabelInformation labelinfo)
                               throws DicomException

Throws:

DicomException

addSegmentSequenceItem

protected void addSegmentSequenceItem(SequenceAttribute saSegmentSequence,
                                      int index,
                                      IndexedLabelMapToSegmentation.LabelInformation labelinfo)
                               throws DicomException

Throws:

DicomException

getStringNoLongerThan64TruncatedIfNecessary

protected java.lang.String getStringNoLongerThan64TruncatedIfNecessary(java.lang.String s)

main

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

Read a DICOM image containing pixel values that are indices into a label map and the corresponding map and convert to a DICOM Segmentation object.

Parameters:

arg - four or more parameters, the inputFile, the CSV file containing a list of labels and their coded values, the outputFile, the reference image file, and optionally, the series number, series description, content label, content description and content creator

newCodedSequenceAttribute

protected static SequenceAttribute newCodedSequenceAttribute(AttributeTag tag,
                                                             CodedSequenceItem csi)

readLabelMapFile

protected java.util.Map<java.lang.Integer,IndexedLabelMapToSegmentation.LabelInformation> readLabelMapFile(java.lang.String filename)
                                                                                                    throws java.io.IOException,
                                                                                                           java.lang.NumberFormatException

Throws:

java.io.IOException

java.lang.NumberFormatException

setBit

protected void setBit(byte[] pixelData,
                      int f,
                      int r,
                      int c,
                      int rows,
                      int columns)