Source code for mermaid.image_manipulations

Various methods to manipulate images
from __future__ import print_function

from builtins import object
import numpy as np

[docs]class IntensityNormalizeImage(object): def __init__(self): """ Constructor """ self.default_normalization_mode = 'percentile_normalization' """Default intensity normalization method"""
[docs] def max_normalization(self,I): # first zero out negative values I = I - I.min() np.clip(I, 0, None, out=I) I = I/np.max(I) return I
[docs] def percentile_normalization(self,I,perc=99.): """ Linearly normalized image intensities so that the 95-th percentile gets mapped to 0.95; 0 stays 0 :param I: input image :param perc: desired percentile :return: returns the normalized image """ # first zero out negative values I =I - I.min() np.clip(I, 0, None, out=I) # then normalize the 99th percentile percI = np.percentile(I, perc) #np.clip (I,None,percI,out=I) if percI == 0: print('Cannot normalize based on percentile; as 99-th percentile is 0. Ignoring normalization') return I else: I = I / percI * perc/100. return I
[docs] def default_intensity_normalization(self, I): """ Intensity normalizes an image using the default intensity normalization method :param I: input image :return: intensity normalized image """ if self.default_normalization_mode == 'percentile_normalization': return self.percentile_normalization(I) elif self.default_normalization_mode == 'max_normalization': return self.max_normalization(I) else: print('ERROR: unknown normalization mode: ' + self.default_normalization_mode ) print('ERROR: returning un-normalized image') return I