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fix Segmentation: Add skewness and kurtosis calculation #103 #847

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fix Segmentation: Add skewness and kurtosis calculation #103 #847

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18 changes: 15 additions & 3 deletions segmenter/planktoscope/segmenter/__init__.py
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Original file line number Diff line number Diff line change
Expand Up @@ -37,6 +37,7 @@
import numpy as np
import PIL.Image
import skimage.exposure
from scipy.stats import skew, kurtosis

################################################################################
# Other image processing Libraries
Expand Down Expand Up @@ -268,9 +269,14 @@ def _get_color_info(self, bgr_img, mask):
h_stddev = np.std(h_channel, where=mask)
s_stddev = np.std(s_channel, where=mask)
v_stddev = np.std(v_channel, where=mask)
# TODO #103 Add skewness and kurtosis calculation (with scipy) here
# using https://docs.scipy.org/doc/scipy/reference/generated/scipy.stats.skew.html#scipy.stats.skew
# and https://docs.scipy.org/doc/scipy/reference/generated/scipy.stats.kurtosis.html#scipy.stats.kurtosis
# Distribution skewness and kurtosis computation
h_skewness = skew(h_channel, bias=False, axis=None)
s_skewness = skew(s_channel, bias=False, axis=None)
v_skewness = skew(v_channel, bias=False, axis=None)
h_kurtosis = kurtosis(h_channel, bias=False, axis=None)
s_kurtosis = kurtosis(s_channel, bias=False, axis=None)
v_kurtosis = kurtosis(v_channel, bias=False, axis=None)

# h_quartiles = np.quantile(h_channel, quartiles)
# s_quartiles = np.quantile(s_channel, quartiles)
# v_quartiles = np.quantile(v_channel, quartiles)
Expand Down Expand Up @@ -308,6 +314,12 @@ def _get_color_info(self, bgr_img, mask):
"StdHue": h_stddev,
"StdSaturation": s_stddev,
"StdValue": v_stddev,
"SkewnessHue": h_skewness,
"SkewnessSaturation": s_skewness,
"SkewnessValue": v_skewness,
"KurtosisHue": h_kurtosis,
"KurtosisSaturation": s_kurtosis,
"KurtosisValue": v_kurtosis
# "object_minHue": h_quartiles[0],
# "object_Q05Hue": h_quartiles[1],
# "object_Q25Hue": h_quartiles[2],
Expand Down