Package qupath.ext.braian

Class AtlasManager

java.lang.Object
qupath.ext.braian.AtlasManager
public class AtlasManager extends Object
This class helps managing and exporting results for each brain region. It works closely with ABBA's QuPath extension.

  • Field Summary

    Fields
    Modifier and Type
    Field
    Description
    static final qupath.lib.objects.classes.PathClass
    ABBA_LEFT
     
    static final qupath.lib.objects.classes.PathClass
    ABBA_RIGHT
     
    static final qupath.lib.objects.classes.PathClass
    EXCLUDE_CLASSIFICATION
     
    static final String
    um
     

  • Constructor Summary

    Constructors
    Constructor
    Description
    AtlasManager(String atlasName, qupath.lib.objects.hierarchy.PathObjectHierarchy hierarchy)
    Constructs a manager of the specified atlas imported with ABBA.
    AtlasManager(qupath.lib.objects.hierarchy.PathObjectHierarchy hierarchy)
    Constructs a manager of the first available atlas imported with ABBA.

  • Method Summary

    Modifier and Type
    Method
    Description
    void
    fixExclusions()
    Attempts to fix possible mistakes with the exclusions, such as: Exclusion of the "Root" hierarchy annotation rather than a proper region If a region was excluded within the atlas hierarchy
    List<qupath.lib.objects.PathObject>
    flatten()
    Flattens the atlas's ontology into a list of annotations.
    List<qupath.lib.objects.PathObject>
    flatten(List<AbstractDetections> detections)
    Flattens the atlas ontology into a list of annotations.
    Set<qupath.lib.objects.PathObject>
    getExcludedBrainRegions()
    Gets all the brain regions that should be excluded from further analysis due to being missing or badly aligned to the image.
    qupath.lib.objects.PathObject
    getRoot()
     
    static boolean
    isImported(String atlasName, qupath.lib.objects.hierarchy.PathObjectHierarchy hierarchy)
    Checks whether a specific ABBA atlas was previously imported.
    static boolean
    isImported(qupath.lib.objects.hierarchy.PathObjectHierarchy hierarchy)
    Checks whether at least one ABBA atlas was previously imported.
    boolean
    isSplit()
    Return whether the current atlas is split between left and right hemispheres.
    boolean
    saveExcludedRegions(File file)
    Saves a file containing, on each line, the name and hemisphere of the regions to be excluded.
    boolean
    saveResults(List<AbstractDetections> detections, File file)
    Saves a TSV file containing data for each brain region of the atlas.

    Methods inherited from class java.lang.Object

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

  • Field Details

    • um

      public static final String um

    • EXCLUDE_CLASSIFICATION

      public static final qupath.lib.objects.classes.PathClass EXCLUDE_CLASSIFICATION

    • ABBA_LEFT

      public static final qupath.lib.objects.classes.PathClass ABBA_LEFT

    • ABBA_RIGHT

      public static final qupath.lib.objects.classes.PathClass ABBA_RIGHT

  • Constructor Details

    • AtlasManager

      public AtlasManager(String atlasName, qupath.lib.objects.hierarchy.PathObjectHierarchy hierarchy)
      Constructs a manager of the specified atlas imported with ABBA.
      Parameters:
      atlasName - the name of the atlas that was imported with ABBA. If null, it selects the first available.
      hierarchy - where to search for the atlas
      Throws:
      qupath.ext.braian.ImportedAtlasNotFound - if the specified atlas was not found
      qupath.ext.braian.DisruptedAtlasHierarchy - if the found atlas hierarchy was disrupted

    • AtlasManager

      public AtlasManager(qupath.lib.objects.hierarchy.PathObjectHierarchy hierarchy)
      Constructs a manager of the first available atlas imported with ABBA.
      Parameters:
      hierarchy - where to search for an atlas
      Throws:
      qupath.ext.braian.ImportedAtlasNotFound - if no atlas was not found in the object hierarchy
      qupath.ext.braian.DisruptedAtlasHierarchy - if the found atlas hierarchy was disrupted
      See Also:

  • Method Details

    • isImported

      public static boolean isImported(qupath.lib.objects.hierarchy.PathObjectHierarchy hierarchy)
      Checks whether at least one ABBA atlas was previously imported.
      Parameters:
      hierarchy - where to search for the atlas
      Returns:
      true if an ABBA atlas was previously imported

    • isImported

      public static boolean isImported(String atlasName, qupath.lib.objects.hierarchy.PathObjectHierarchy hierarchy)
      Checks whether a specific ABBA atlas was previously imported.
      Parameters:
      atlasName - the name of the atlas to check. If null, it checks whether any atlas was imported with ABBA
      hierarchy - where to search for the atlas
      Returns:
      true if the atlas was previously imported

    • getRoot

      public qupath.lib.objects.PathObject getRoot()
      Returns:
      the annotations that contains all atlas annotations.

    • flatten

      public List<qupath.lib.objects.PathObject> flatten()
      Flattens the atlas's ontology into a list of annotations. It may return some non-region annotations too, if the atlas hierarchy was modified with added/removed elements.
      Returns:
      the list of all brain regions in the atlas
      Throws:
      qupath.ext.braian.DisruptedAtlasHierarchy - if the current atlas hierarchy was disrupted, and it is not possible to deduce
      See Also:

    • flatten

      public List<qupath.lib.objects.PathObject> flatten(List<AbstractDetections> detections)
      Flattens the atlas ontology into a list of annotations. If the atlas hierarchy was modified by adding AbstractDetections's containers, it filters them from the current brain hierarchy.
      It may still return some non-region annotations, if the atlas hierarchy was further modified with added/removed elements.
      Returns:
      the list of all brain regions in the atlas
      Throws:
      qupath.ext.braian.DisruptedAtlasHierarchy - if the current atlas hierarchy was disrupted, and it is not possible to deduce
      See Also:

    • saveResults

      public boolean saveResults(List<AbstractDetections> detections, File file)
      Saves a TSV file containing data for each brain region of the atlas. Namely, Image name, brain region name, hemisphere, area in µm², number of detections for each of the given types. The table is saved as a CSV (comma-separated values) file if 'file' ends with ".csv"
      Parameters:
      detections - the list of detection of which to gather the data for each region
      file - the file where it should write to. Note that if the file exists, it will be overwritten
      Throws:
      qupath.ext.braian.ExclusionMistakeException - if the atlas hierarchy contains regions classified as EXCLUDE_CLASSIFICATION.
      qupath.ext.braian.DisruptedAtlasHierarchy - if the current atlas hierarchy was disrupted, and it is not possible to deduce

    • getExcludedBrainRegions

      public Set<qupath.lib.objects.PathObject> getExcludedBrainRegions()
      Gets all the brain regions that should be excluded from further analysis due to being missing or badly aligned to the image. A brain region, in order to be excluded, must:
      • either be contained into a larger annotation, classified as "Exclude"
      • or be duplicated (SHIFT+D) outside the Atlas's hierarchy, and then classified as "Exclude"
      Returns:
      a set of brain regions' annotations that should be excluded.
      Throws:
      qupath.ext.braian.DisruptedAtlasHierarchy - if the current atlas hierarchy was disrupted, and it is not possible to deduce

    • saveExcludedRegions

      public boolean saveExcludedRegions(File file)
      Saves a file containing, on each line, the name and hemisphere of the regions to be excluded.
      Parameters:
      file - the file where it should write to. Note that if the file exists, it will be overwritten
      Returns:
      true if the file was correctly saved.
      Throws:
      qupath.ext.braian.DisruptedAtlasHierarchy - if the current atlas hierarchy was disrupted, and it is not possible to deduce
      See Also:

    • isSplit

      public boolean isSplit()
      Return whether the current atlas is split between left and right hemispheres. Atlas hierarchies that were modified by deleting one of the two hemispheres, are still recognised as split.
      Returns:
      true if the current atlas is split between left and right hemispheres.
      Throws:
      qupath.ext.braian.DisruptedAtlasHierarchy - if the current atlas hierarchy was disrupted, and it is not possible to deduce whether the atlas was split between left and right.

    • fixExclusions

      public void fixExclusions()
      Attempts to fix possible mistakes with the exclusions, such as:
      • Exclusion of the "Root" hierarchy annotation rather than a proper region
      • If a region was excluded within the atlas hierarchy
      Throws:
      qupath.ext.braian.DisruptedAtlasHierarchy - if the current atlas hierarchy was disrupted, and it is not possible to deduce