Package qupath.ext.braian.config

Class ChannelClassifierConfig

java.lang.Object
qupath.ext.braian.config.ChannelClassifierConfig
public class ChannelClassifierConfig extends Object

  • Constructor Details

    • ChannelClassifierConfig

      public ChannelClassifierConfig()

  • Method Details

    • getChannel

      public String getChannel()

    • setChannel

      public void setChannel(String channel)

    • getName

      public String getName()

    • setName

      public void setName(String name)

    • getAnnotationsToClassify

      public List<String> getAnnotationsToClassify()

    • setAnnotationsToClassify

      public void setAnnotationsToClassify(List<String> annotationsToClassify)

    • loadClassifier

      public qupath.lib.classifiers.object.ObjectClassifier loadClassifier() throws IOException
      Loads the object classifier specified in the configuration file. If the specified name is equals to "ALL", it returns a SingleClassifier that classifies all detections as part positive cells from this configuration's image channel. Else, it searches for the a JSON file named after the specified string, as described by BraiAn.resolvePath(String) and reads it.
      Returns:
      an instance of ObjectClassifier loaded based on the configuration file
      Throws:
      IOException - if any problem raises when reading the JSON file, supposedly corresponding to a QuPath object classifier.

    • getAnnotationsToClassify

      public Collection<qupath.lib.objects.PathAnnotationObject> getAnnotationsToClassify(qupath.lib.objects.hierarchy.PathObjectHierarchy hierarchy)
      It searches all annotations specified by their name in the configuration file. If a name does not correspond to any annotation in the current hierarchy, it silently skips it.
      Parameters:
      hierarchy - where to search teh annotations in
      Returns:
      a collection of annotations, if they were specified in the configuration file. Otherwise, null.

    • toPartialClassifier

      public PartialClassifier toPartialClassifier(qupath.lib.objects.hierarchy.PathObjectHierarchy hierarchy) throws IOException
      Loads the classifier and associates it to the annotations whose name is listed in the configuration file.
      Parameters:
      hierarchy - where to search the annotations in
      Returns:
      an instance of PartialClassifier
      Throws:
      IOException
      See Also: