segmentation.py 25 KB
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# -*- coding: utf-8 -*-
"""
GEPARD - Gepard-Enabled PARticle Detection
Copyright (C) 2018  Lars Bittrich and Josef Brandt, Leibniz-Institut für 
Polymerforschung Dresden e. V. <bittrich-lars@ipfdd.de>    

This program is free software: you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation, either version 3 of the License, or
(at your option) any later version.

This program is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
GNU General Public License for more details.

You should have received a copy of the GNU General Public License
along with this program, see COPYING.  
If not, see <https://www.gnu.org/licenses/>.
"""
import numpy as np
import cv2
cv2.useOptimized()
from time import time
from scipy.interpolate import InterpolatedUnivariateSpline
from scipy import ndimage as ndi
from skimage.feature import peak_local_max
from skimage.morphology import watershed
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import skfuzzy as fuzz
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import random
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def closeHolesOfSubImage(subimg):
    subimg = cv2.copyMakeBorder(subimg, 1, 1, 1, 1, 0)
    im_floodfill = subimg.copy()
    h, w = subimg.shape[:2]
    mask = np.zeros((h+2, w+2), np.uint8)
    cv2.floodFill(im_floodfill, mask, (0,0), 255);
    im_floodfill_inv = cv2.bitwise_not(im_floodfill)
    im_out = subimg | im_floodfill_inv
    return im_out[1:-1, 1:-1]
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class Parameter(object):
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    """
    A Parameter for driving the image segmentation. All Parameters are initialized in the Segmentation Class. 
    The DetectionView-Widget reads these parameters and creates and connects the necessary items in the ui.
    :return:
    """
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    def __init__(self, name, dtype, value=None, minval=None, maxval=None, 
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                 decimals=0, stepsize=1, helptext=None, show=False, linkedParameter=None):
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        self.name = name
        self.dtype = dtype
        self.value = value
        self.valrange = (minval, maxval)
        self.decimals = decimals
        self.stepsize = stepsize
        self.helptext = helptext
        self.show = show
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        self.linkedParameter = linkedParameter
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class MeasurementPoint(object):
    def __init__(self, particleIndex, x, y):
        self.particleIndex = particleIndex
        self.x = x
        self.y = y

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class Segmentation(object):
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    def __init__(self, dataset=None, parent=None):        
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        self.cancelcomputation = False
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        self.parent = parent
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        self.defaultParams = {'adaptiveHistEqu': False,
                              'claheTileSize': 128,
                              'contrastCurve': np.array([[50,0],[100,200],[200,255]]),
                              'activateContrastCurve': True,
                              'blurRadius': 9,
                              'activateLowThresh': True,
                              'lowThresh': 0.2,
                              'activateUpThresh': False,
                              'upThresh': 0.5,
                              'invertThresh': False,
                              'maxholebrightness': 0.5,
                              'minparticlearea': 20,
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                              'enableMaxArea': False,
                              'maxparticlearea': 100000,
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                              'minparticledistance': 20,
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                              'closeBackground': False,
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                              'fuzzycluster': False,
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                              'measurefrac': 1,
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                              'compactness': 0.0,
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                              'seedRad': 3}
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        if dataset is not None:
            self.detectParams = dataset.detectParams
            for key in self.defaultParams:
                if key not in self.detectParams:
                    self.detectParams[key] = self.defaultParams[key]
        else:
            self.detectParams = self.defaultParams        
        self.initializeParameters()
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    def initializeParameters(self):
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        parlist = [Parameter("adaptiveHistEqu", np.bool, self.detectParams['adaptiveHistEqu'], helptext="Adaptive histogram equalization", show=False, linkedParameter='claheTileSize'),
                   Parameter("claheTileSize", int, self.detectParams['claheTileSize'], 1, 2048, 1, 1, helptext="Tile size for adaptive histogram adjustment\nThe Image will be split into tiles with size approx. (NxN)", show=True),
                   Parameter("contrastCurve", np.ndarray, self.detectParams['contrastCurve'], helptext="Curve contrast"),
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                   Parameter("activateContrastCurve", np.bool, self.detectParams['activateContrastCurve'], helptext="activate Contrast curve", show=True, linkedParameter='contrastCurve'),
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                   Parameter("blurRadius", int, self.detectParams['blurRadius'], 3, 99, 1, 2, helptext="Blur radius", show=True),
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                   Parameter("invertThresh", np.bool, self.detectParams['invertThresh'], helptext="Invert the current threshold", show=False),
                   Parameter("activateLowThresh", np.bool, self.detectParams['activateLowThresh'], helptext="activate lower threshold", show=False, linkedParameter='lowThresh'),
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                   Parameter("lowThresh", float, self.detectParams['lowThresh'], .01, .9, 2, .02, helptext="Lower threshold", show=True),
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                   Parameter("activateUpThresh", np.bool, self.detectParams['activateUpThresh'], helptext="activate upper threshold", show=False, linkedParameter='upThresh'),
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                   Parameter("upThresh", float, self.detectParams['upThresh'], .01, 1.0, 2, .02, helptext="Upper threshold", show=False),
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                   Parameter("maxholebrightness", float, self.detectParams['maxholebrightness'], 0, 1, 2, 0.02, helptext="Close holes brighter than..", show = True),
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                   Parameter("minparticlearea", int, self.detectParams['minparticlearea'], 1, 1000, 0, 50, helptext="Min. particle pixel area", show=False),
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                   Parameter("enableMaxArea", np.bool, self.detectParams['enableMaxArea'], helptext="enable filtering for maximal pixel area", show=False, linkedParameter='maxparticlearea'),
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                   Parameter("maxparticlearea", int, self.detectParams['maxparticlearea'], 10, 1E9, 0, 50, helptext="Max. particle pixel area", show=True),
                   Parameter("minparticledistance", int, self.detectParams['minparticledistance'], 5, 1000, 0, 5, helptext="Min. distance between particles", show=False),
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                   Parameter("measurefrac", float, self.detectParams['measurefrac'], 0, 1, 2, stepsize = 0.05, helptext="measure fraction of particles", show=False),
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                   Parameter("closeBackground", np.bool, self.detectParams['closeBackground'], helptext="close holes in sure background", show=False),
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                   Parameter("fuzzycluster", np.bool, self.detectParams['fuzzycluster'], helptext='Enable Fuzzy Clustering', show=False),
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                   Parameter("sure_fg", None, helptext="Show sure foreground", show=True),
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                   Parameter("compactness", float, self.detectParams['compactness'], 0, 1, 2, 0.05, helptext="watershed compactness", show=False),
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                   Parameter("watershed", None, helptext="Show watershed markers", show=True),
                   ]
        # make each parameter accessible via self.name
        # the variables are defined as properties and because of how the local context
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        # in for loops works the actual setter and getter functions are defined inside 
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        # a separate contex in a local function
        def makeGetter(p):
            return lambda : p.value
        def makeSetter(p):
            def setter(value):
                p.value = value
            return setter
        for p in parlist:
            # variabels in self are writen directly to the name dictionary
            self.__dict__[p.name] = property(makeGetter(p), makeSetter(p))
        self.parlist = parlist
    
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    def apply2Image(self, img, seedpoints, deletepoints, seedradius, dataset, return_step=None):
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        """
        Takes an image with seedpoints and seeddeletepoints and runs segmentation on it.
        :return:
        """
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        t0 = time()
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        gray = self.convert2Gray(img)
        print("gray")
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        if self.adaptiveHistEqu:
            numTilesX = round(img.shape[1]/self.claheTileSize)
            numTilesY = round(img.shape[0]/self.claheTileSize)
            clahe = cv2.createCLAHE(clipLimit=2.0, tileGridSize=(numTilesY,numTilesX))
            gray = clahe.apply(gray)
        if return_step=="claheTileSize": return gray, 0
        print("adaptive Histogram Adjustment")
        
        if self.cancelcomputation:
            return None, None, None
        
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        if self.activateContrastCurve:
            xi, arr = self.calculateHistFunction(self.contrastCurve)
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            gray = arr[gray]
        print("contrast curve")
        if self.cancelcomputation:
            return None, None, None
            
        # return even if inactive!
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        if return_step=="activateContrastCurve": return gray, 0
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        # image blur for noise-reduction
        blur = cv2.medianBlur(gray, self.blurRadius)
        blur = np.uint8(blur*(255/blur.max()))
        if return_step=="blurRadius": return blur, 0
        print("blur")
        if self.cancelcomputation:
            return None, None, None
        
        # thresholding
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        if self.activateLowThresh and not self.activateUpThresh:
            thresh = cv2.threshold(blur, int(255*self.lowThresh), 255, cv2.THRESH_BINARY)[1]
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            if self.invertThresh:
                thresh = 255-thresh
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            if return_step=="lowThresh": return thresh, 0
            print("lower threshold")
            if self.cancelcomputation:
                return None, None, None
            
        elif self.activateLowThresh and self.activateUpThresh:
            lowerLimit, upperLimit = np.round(self.lowThresh*255), np.round(self.upThresh*255)
            thresh = np.zeros_like(blur)
            thresh[np.where(np.logical_and(blur >= lowerLimit, blur <= upperLimit))] = 255
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            if self.invertThresh:
                thresh = 255-thresh
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            if return_step=="lowThresh" or return_step=="upThresh": return thresh, 0
            print("between threshold")
            if self.cancelcomputation:
                return None, None, None
            
        elif not self.activateLowThresh and self.activateUpThresh:
            thresh = np.zeros_like(blur)
            thresh[np.where(blur <= np.round(self.upThresh*255))] = 255
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            if self.invertThresh:
                thresh = 255-thresh
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            if return_step=="upThresh": return thresh, 0
            print("upper threshold")
            if self.cancelcomputation:
                return None, None, None
        else:   #no checkbox checked
            if self.parent is not None:
                self.parent.raiseWarning('No thresholding method selected!\nAborted detection..')
            print('NO THRESHOLDING SELECTED!')
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            return blur, 0
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        #close holes darkter than self.max_brightness
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        thresh = self.closeBrightHoles(thresh, blur, self.maxholebrightness)
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        print("closed holes")
        
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        # modify thresh with seedpoints and deletepoints
        for p in np.int32(seedpoints):
            cv2.circle(thresh, tuple([p[0], p[1]]), int(p[2]), 255, -1)
        for p in np.int32(deletepoints):
            cv2.circle(thresh, tuple([p[0], p[1]]), int(p[2]), 0, -1)
        
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        if return_step=='maxholebrightness': return thresh, 0
        if self.cancelcomputation:
            return None, None, None
        
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        if self.enableMaxArea:
            maxArea = self.maxparticlearea
        else:
            maxArea = np.inf
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        ##get sure_fg
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        '''the peak_local_max function takes the min distance between peaks. Unfortunately, that means that individual 
        particles smaller than that distance are consequently disregarded. Hence, we need a connectec_components approach'''
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        n, labels, stats, centroids = cv2.connectedComponentsWithStats(thresh, 8, cv2.CV_32S)
        del thresh
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        measurementPoints = {}
        finalcontours = []
        particleIndex = 0
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        if return_step == "sure_fg":
            preview_surefg = np.zeros(img.shape[:2])
            preview_surebg = np.zeros(img.shape[:2])
        elif return_step is None:
            previewImage = None
        else:
            previewImage = np.zeros(img.shape[:2])
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        for label in range(1, n):
            area = stats[label, cv2.CC_STAT_AREA]
            if self.minparticlearea < area < maxArea:
                up = stats[label, cv2.CC_STAT_TOP]
                left = stats[label, cv2.CC_STAT_LEFT]
                width = stats[label, cv2.CC_STAT_WIDTH]
                height = stats[label, cv2.CC_STAT_HEIGHT]
                subthresh = np.uint8(255 * (labels[up:(up+height), left:(left+width)] == label))
                subdist = cv2.distanceTransform(subthresh, cv2.DIST_L2,3)
                
                sure_fg = self.getSureForeground(subthresh, subdist, self.minparticledistance)
                sure_bg = cv2.dilate(subthresh, np.ones((5, 5)), iterations = 1)
                if self.closeBackground:
                    sure_bg = self.closeHoles(sure_bg)
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                # modify sure_fg and sure_bg with seedpoints and deletepoints
                for p in np.int32(seedpoints):
                    cv2.circle(sure_fg, tuple([p[0]-left, p[1]-up]), int(p[2]), 1, -1)
                    cv2.circle(sure_bg, tuple([p[0]-left, p[1]-up]), int(p[2]), 1, -1)
                for p in np.int32(deletepoints):
                    cv2.circle(sure_fg, tuple([p[0]-left, p[1]-up]), int(p[2]), 0, -1)
                    cv2.circle(sure_bg, tuple([p[0]-left, p[1]-up]), int(p[2]), 0, -1)
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                if self.cancelcomputation:
                    return None, None, None
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                if return_step=="sure_fg":
                    preview_surefg = self.addToPreviewImage(sure_fg, up, left, preview_surefg)
                    preview_surebg = self.addToPreviewImage(sure_bg, up, left, preview_surebg)
                    continue
                
                unknown = cv2.subtract(sure_bg, sure_fg)
         
                ret, markers = cv2.connectedComponents(sure_fg)
                markers = markers+1
                markers[unknown==255] = 0
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                markers = ndi.label(sure_fg)[0]
                markers = watershed(-subdist, markers, mask=sure_bg, compactness = self.compactness, watershed_line = True)  #labels = 0 for background, 1... for particles
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                if self.cancelcomputation:
                    return None, None, None
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                if return_step=="watershed":
                    previewImage = self.addToPreviewImage(markers, up, left, previewImage)
                    continue
     
                if cv2.__version__ > '3.5':        
                    contours, hierarchy = cv2.findContours(markers, cv2.RETR_CCOMP, cv2.CHAIN_APPROX_NONE)
                else:
                    temp, contours, hierarchy = cv2.findContours(markers, cv2.RETR_CCOMP, cv2.CHAIN_APPROX_NONE)
                if self.cancelcomputation:
                    return None, None, None
                    
                tmpcontours = [contours[i] for i in range(len(contours)) if hierarchy[0,i,3]<0]

                for cnt in tmpcontours:
                    if cv2.contourArea(cnt) >= self.minparticlearea:
                        label = markers[cnt[0,0,1],cnt[0,0,0]]
                        if label==0:
                            continue
            
                        x0, x1 = cnt[:,0,0].min(), cnt[:,0,0].max()
                        y0, y1 = cnt[:,0,1].min(), cnt[:,0,1].max()
                        subimg = (markers[y0:y1+1,x0:x1+1]).copy()
                        subimg[subimg!=label] = 0
                        y, x = self.getMeasurementPoints(subimg)
                        
                        for i in range(len(cnt)):
                            cnt[i][0][0] += left
                            cnt[i][0][1] += up
                        
                        finalcontours.append(cnt)
                        measurementPoints[particleIndex] = []
                        
                        for index in range(0, len(x)):
                            newMeasPoint = MeasurementPoint(particleIndex, x[index] + x0 + left, y[index] + y0 + up)
                            measurementPoints[particleIndex].append(newMeasPoint)
                        particleIndex += 1

        if return_step == 'sure_fg':
            img = np.zeros_like(preview_surefg)
            img[np.nonzero(preview_surefg)] |= 1
            img[np.nonzero(preview_surebg)] |= 2
            return img, 1        
        
        elif return_step == 'watershed':
            return np.uint8(255*(previewImage!=0)), 0
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        elif return_step is not None:
            raise NotImplementedError(f"this particular return_step: {return_step} is not implemented yet")

        print("particle detection took:", time()-t0, "seconds")
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        if self.measurefrac < 1.0:
            nMeasurementsDesired = int(np.round(self.measurefrac * len(measurementPoints)))
            print(f'selecting {nMeasurementsDesired} of {len(measurementPoints)} measuring spots')
            partIndicesToMeasure = random.sample(measurementPoints.keys(), nMeasurementsDesired)
            newMeasPoints = {}
            for index in partIndicesToMeasure:
                newMeasPoints[index] = measurementPoints[index]
            measurementPoints = newMeasPoints
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        total_time = time()-t0
        print('segmentation took', total_time, 'seconds')
        return measurementPoints, finalcontours
    
    
    def addToPreviewImage(self, subimg, up, left, previewImage):
        """
        Adds a subimage at given position to the previewimage
        :return:
        """
        height, width = subimg.shape[0], subimg.shape[1]
        previewImage[up:up+height, left:left+width] += subimg
        previewImage = np.array(previewImage, dtype = np.int32)
        return previewImage
    
    
    def setParameters(self, **kwargs):
        """
        Parameters that were set in the parameter are updated to the classes dictionary and can later be referenced to as self.key
        :return:
        """
        for key in kwargs:
            self.__dict__[key] = kwargs[key]
        
    def convert2Gray(self, img):
        gray = cv2.cvtColor(img,cv2.COLOR_RGB2GRAY)
        return gray
        
    def calculateHist(self, gray):
        hist = cv2.calcHist([gray],[0],None,[256],[0,256])
        return hist
    
    def calculateHistFunction(self, points):
        """
        Calculates the curve to plot in the histogram widget
        :return:
        """
        t = np.linspace(0,1,800)
        x0 = np.concatenate(([-1.],points[:,0],[256.]))
        y0 = np.concatenate(([0.],points[:,1],[255.]))
        t0 = np.concatenate(([0.],np.cumsum(np.sqrt(np.diff(x0)**2+np.diff(y0)**2))))
        t0 /= t0[-1]
        fx = InterpolatedUnivariateSpline(t0, x0, k=3)
        fy = InterpolatedUnivariateSpline(t0, y0, k=3)
        x = fx(t)
        y = fy(t)
        arr = np.zeros(256, dtype=np.uint8)
        xi = np.arange(256)
        ind = np.searchsorted(xi, x)
        arr[ind[ind<256]] = y[ind<256]
        arr[xi>points[:,0].max()] = 255
        arr[xi<points[:,0].min()] = 0.
        arr[arr>255] = 255.
        arr[arr<0] = 0.
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        return xi, arr      
    
    def closeHoles(self, thresh):
        """
        Closes holes in a binary image
        :return:
        """
        n, labels, stats, centroids = cv2.connectedComponentsWithStats(thresh, 8, cv2.CV_32S)
        newthresh = np.zeros_like(thresh)
    
        for label in range(1, n):
            up = stats[label, cv2.CC_STAT_TOP]
            left = stats[label, cv2.CC_STAT_LEFT]
            width = stats[label, cv2.CC_STAT_WIDTH]
            height = stats[label, cv2.CC_STAT_HEIGHT]
            subimg = np.uint8(255 * (labels[up:(up+height), left:(left+width)] == label))
            
            newthresh[up:(up+height), left:(left+width)] += closeHolesOfSubImage(subimg)

        return newthresh
    
    def closeBrightHoles(self, thresh, grayimage, minBrightness):
        """
        Only closes holes that are brighter than a given minimal Brightness
        :return:
        """
        n, labels, stats, centroids = cv2.connectedComponentsWithStats(thresh, 8, cv2.CV_32S)
        minBrightness = np.uint8(minBrightness * 255)
        print('num comps in brightHoles:', n)
        
        for label in range(1, n):
            up = stats[label, cv2.CC_STAT_TOP]
            left = stats[label, cv2.CC_STAT_LEFT]
            width = stats[label, cv2.CC_STAT_WIDTH]
            height = stats[label, cv2.CC_STAT_HEIGHT]
            subimg = np.uint8(255 * (labels[up:(up+height), left:(left+width)] == label))
            
            subimg = cv2.copyMakeBorder(subimg, 1, 1, 1, 1, 0)
            im_floodfill = subimg.copy()
            h, w = subimg.shape[:2]
            mask = np.zeros((h+2, w+2), np.uint8)
            cv2.floodFill(im_floodfill, mask, (0,0), 255);
            
            indices = np.where(im_floodfill == 0)[0]
            if len(indices) > 0:
                if np.mean(grayimage[indices[0]]) > minBrightness:
                    im_floodfill_inv = cv2.bitwise_not(im_floodfill)
                    im_out = subimg | im_floodfill_inv
                    thresh[up:(up+height), left:(left+width)] += im_out[1:-1, 1:-1]
                    
        return thresh

    
    def getSureForeground(self, thresh, disttransform, mindistance):
        """
        Calculates sure_fg (i.e, seedpoints) for the markerbased watershed
        Currently the function only takes a distance-transform and extracts their (local) maxima.
        If desired, a fuzzy Clustering is applied to these to reduce the number of considered seed points.
        :return:
        """
        def simplifyByFuzzyClustering(points):
            xpts = [peak[1] for peak in points]
            ypts = [peak[0] for peak in points]
            alldata = np.vstack((ypts, xpts))
            
            fpcs = []
            cntrs = []
            for ncenters in range(2, numPeaks):
                cntr, u, u0, d, jm, p, fpc = fuzz.cluster.cmeans(alldata, ncenters, 2, error=0.005, maxiter=1000, init=None)
                fpcs.append(fpc/(ncenters**0.3))   #makes larger cluster numbers less preferred
                cntrs.append(cntr)
            
            bestMatchIndex = fpcs.index(max(fpcs))
            bestMatchCentres = cntrs[bestMatchIndex]
            newPoints = []
            for point in bestMatchCentres:
                newPoints.append([int(round(point[0])), int(round(point[1]))])
            print(f'reduced {numPeaks} to {len(newPoints)} maxima')
            return newPoints
            
        sure_fg = np.zeros_like(thresh)        
        submax = np.where(disttransform == disttransform.max())
        
        maxPoints = []
        for index in range(len(submax[0])):
            y = submax[0][index]
            x = submax[1][index]
            maxPoints.append([y, x])
                
        localMaxima = np.uint8(peak_local_max(disttransform, mindistance, indices = True))
        for locMax in localMaxima:
            maxPoints.append(locMax)

        numPeaks = len(maxPoints)
        if numPeaks > 3 and self.fuzzycluster:
            maxPoints = simplifyByFuzzyClustering(maxPoints)
                            
        for peak in maxPoints:
            sure_fg[peak[0], peak[1]] = 1
                
        sure_fg = cv2.dilate(sure_fg, np.ones((3, 3)))
        return sure_fg
    
    def getMeasurementPoints(self, binParticle, numPoints=1):
        """
        Sets coordinates for later measurement points.
        :return:
        """
        binParticle = cv2.copyMakeBorder(binParticle, 1, 1, 1, 1, 0)
        dist = cv2.distanceTransform(np.uint8(binParticle), cv2.DIST_L2,3)
        ind = np.argmax(dist)
        y = [ind//dist.shape[1]-1]
        x = [ind%dist.shape[1]-1]
        for i in range(numPoints-1):
            binParticle.flat[ind] = 0
            dist = cv2.distanceTransform(np.uint8(binParticle), cv2.DIST_L2,3)
            ind = np.argmax(dist)
            y.append(ind//dist.shape[1]-1)
            x.append(ind%dist.shape[1]-1)
        return y, x
    

if __name__ == '__main__':
    import matplotlib.pyplot as plt
#    img = cv2.imread('/home/brandt/Schreibtisch/Segmentation/fullimage_III.png')
    seg = Segmentation()
    
    kwargs = {}
    seedpoints, deletepoints = [], []
    for parameter in seg.parlist:
        kwargs[parameter.name] = parameter.value
    seg.setParameters(**kwargs)
    
    size = 25000
    stepSize = 2000
    maxSize = 40000
    
    sizes, times = [], []
    while size <= maxSize:
        try:
            print('newsize =', size)
            img = cv2.resize(img, (size, size))
            points, contours, tf = seg.apply2Image(img, np.array([]), np.array([]), 1, None)
            sizes.append(size)
            times.append(tf)
            size += stepSize
        except:
            print('segmentation failed at size', size)
            raise
    #    imgSegmented = cv2.drawContours(img, contours, -1, (255, 255, 0), thickness=2)
#    plt.imshow(imgSegmented)