def annotationMode(settings, read):
print("Annotation mode!")
clinicalNotes = DatasetReader.readClinicalNotes(settings["dataset"]["directory"], settings["dataset"]["name"])
if read:
nejiAnnotations = Annotator.readNejiAnnotations(settings["dataset"]["neji_annotations"])
else:
nejiAnnotations = Annotator.annotate(clinicalNotes)
Writer.writeAnnotations(nejiAnnotations, settings["dataset"]["neji_annotations"])
annotations = Annotator.postProcessing(clinicalNotes, nejiAnnotations, settings["post_vocabularies"])
matrix = Writer.writeMatrix(annotations, settings["dataset"]["matrix_location"])
print("Done!")
return matrix, clinicalNotes
