Package com.pixelmed.convert
Class IndexedLabelMapToSegmentation
java.lang.Object
com.pixelmed.convert.IndexedLabelMapToSegmentation
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Nested Class Summary
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Field Summary
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Constructor Summary
Constructors -
Method Summary
Modifier and TypeMethodDescriptionprotected void
addAppropriateSegmentedPropertyCategoryCodeSequence
(AttributeList list, IndexedLabelMapToSegmentation.LabelInformation labelinfo) addSegmentSequence
(AttributeList list, Set<Integer> usedLabels, Map<Integer, IndexedLabelMapToSegmentation.LabelInformation> labelMap, Set<Integer> unrecognizedLabels) protected void
addSegmentSequenceItem
(int segmentNumber, SequenceAttribute saSegmentSequence, int index, IndexedLabelMapToSegmentation.LabelInformation labelinfo) protected void
addSegmentSequenceItem
(int segmentNumber, SequenceAttribute saSegmentSequence, IndexedLabelMapToSegmentation.LabelInformation labelinfo) static void
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.readLabelMapFile
(String filename) static void
setBit
(byte[] pixelData, int f, int r, int c, int rows, int columns)
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Field Details
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suppressFramesForBackgroundSegment
protected boolean suppressFramesForBackgroundSegment -
spatialAndRelationalConcepts
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tissueConcepts
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backgroundLabel
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backgroundIndex
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Constructor Details
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IndexedLabelMapToSegmentation
public IndexedLabelMapToSegmentation(String inputFilename, String labelFilename, String outputFilename, String referenceImageFilename, String seriesNumber, String seriesDescription, String contentLabel, String contentDescription, String contentCreatorName) throws IOException, NumberFormatException, DicomException
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Method Details
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readLabelMapFile
protected SortedMap<Integer,IndexedLabelMapToSegmentation.LabelInformation> readLabelMapFile(String filename) throws IOException, NumberFormatException - Throws:
IOException
NumberFormatException
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addAppropriateSegmentedPropertyCategoryCodeSequence
protected void addAppropriateSegmentedPropertyCategoryCodeSequence(AttributeList list, IndexedLabelMapToSegmentation.LabelInformation labelinfo) throws DicomException - Throws:
DicomException
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addSegmentSequenceItem
protected void addSegmentSequenceItem(int segmentNumber, SequenceAttribute saSegmentSequence, int index, IndexedLabelMapToSegmentation.LabelInformation labelinfo) throws DicomException - Throws:
DicomException
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addSegmentSequenceItem
protected void addSegmentSequenceItem(int segmentNumber, SequenceAttribute saSegmentSequence, IndexedLabelMapToSegmentation.LabelInformation labelinfo) throws DicomException - Throws:
DicomException
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addSegmentSequence
protected Map<Integer,Integer> addSegmentSequence(AttributeList list, Set<Integer> usedLabels, Map<Integer, IndexedLabelMapToSegmentation.LabelInformation> labelMap, Set<Integer> unrecognizedLabels) throws DicomException- Throws:
DicomException
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setBit
public static void setBit(byte[] pixelData, int f, int r, int c, int rows, int columns) -
main
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
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