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Detecting outliers with occupied area.
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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 |
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