Detecting outliers with occupied area.

AreaOutlierDetector.py

from org.jfree.data.statistics import BoxAndWhiskerCalculator
from ij.measure import ResultsTable
from java.util import ArrayList, Arrays

VERBOSE = True

class InstBWC(BoxAndWhiskerCalculator):
    def __init__(self):
        pass
        
def getOutlierBound(rt):
  """ Analyzes the results of the 1st partcile analysis.
  Since the dilation of nuclear perimeter often causes 
  overlap of neighboring neculeus 'terrirories', such nucleus 
  are discarded from the measurements. 

  Small nucelei are already removed, but since rejection of nuclei depends on 
  standard outlier detection method, outliers in both smaller and larger sizes
  are discarded. 
  """
  area = rt.getColumn(rt.getColumnIndex('Area'))
  arealist = ArrayList(Arrays.asList(area.tolist()))
  bwc = InstBWC()
  ans = bwc.calculateBoxAndWhiskerStatistics(arealist)
  #anscirc = bwc.calculateBoxAndWhiskerStatistics(circlist)
  if (VERBOSE):
    print ans.toString()
    print ans.getOutliers()
  q1 = ans.getQ1()
  q3 = ans.getQ3()
  intrange = q3 - q1 
  outlier_offset = intrange * 1.5
  # circularity better be fixed. 
  #circq1 = anscirc.getQ1()
  #circq3 = anscirc.getQ3()
  #circintrange = circq3 - circq1 
  #circoutlier_offset = circintrange * 1.5
  return q1, q3, outlier_offset

thisrt = ResultsTable.getResultsTable()
q1, q3, outlier_offset = getOutlierBound(thisrt)
lower = q1 - outlier_offset
upper = q3 + outlier_offset

print  q1, q3, outlier_offset
print 'Lower boundary', lower
print 'Upper boundary', upper