particleeditor.py 8.53 KB
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# -*- coding: utf-8 -*-
"""
Created on Wed Jan 16 12:43:00 2019

@author: brandt
"""

"""
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/>.
"""
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import numpy as np
import cv2
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from PyQt5 import QtWidgets
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class ParticleEditor(object):
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    def __init__(self, datastats, parent):
        self.datastats = datastats
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        self.parent = parent    #the assigned analysis widget
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        self.backupFreq = 3     #save a backup every n actions
        self.neverBackedUp = True
        self.actionCounter = 0
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    def createSafetyBackup(self):
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        self.actionCounter += 1
        if self.actionCounter == self.backupFreq-1 or self.neverBackedUp:            
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            backupname = self.datastats.dataset.saveBackup()
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            print('backing up as', backupname)
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            self.neverBackedUp = False
            self.actionCounter = 0
        
    def getNewEntry(self):
        text, okClicked = QtWidgets.QInputDialog.getText(self.parent.parent, "Custom assignment", "Enter new assignment")
        if okClicked and text != '':
            return text
    
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    def combineParticles(self, contourIndices, new_assignment):
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        if new_assignment == 'other':
            new_assignment = self.getNewEntry()
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        if new_assignment is None:
            return
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        contourIndices = sorted(contourIndices)   #we want to keep the contour with lowest index
        #get contours:
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        contours = [self.datastats.dataset.particlecontours[i] for i in contourIndices]
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        cnt = np.vstack(tuple(contours))  #combine contous
        
        #draw contours
        xmin, xmax = cnt[:,0,:][:, 0].min(), cnt[:,0,:][:, 0].max()
        ymin, ymax = cnt[:,0,:][:, 1].min(), cnt[:,0,:][:, 1].max()        
        
        padding = 2    #pixel in each direction
        rangex = int(np.round((xmax-xmin)+2*padding))
        rangey = int(np.round((ymax-ymin)+2*padding))

        img = np.zeros((rangey, rangex))
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        for i in contourIndices:
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            curCnt = self.datastats.dataset.particlecontours[i].copy()
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            for i in range(len(curCnt)):
                curCnt[i][0][0] -= xmin-padding
                curCnt[i][0][1] -= ymin-padding
                
            cv2.drawContours(img, [curCnt], -1, 1, -1)
            cv2.drawContours(img, [curCnt], -1, 1, 1)
        
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        img = np.uint8(cv2.morphologyEx(img, cv2.MORPH_CLOSE, np.ones((3, 3))))
        
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        if cv2.__version__ > '3.5':
            contours, hierarchy = cv2.findContours(img, cv2.RETR_CCOMP, cv2.CHAIN_APPROX_NONE)
        else:
            temp, contours, hierarchy = cv2.findContours(img, cv2.RETR_CCOMP, cv2.CHAIN_APPROX_NONE)
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        if len(contours)>1:
            QtWidgets.QMessageBox.critical(self.parent, 'ERROR!', 
                                           'Particle contours are not connected and cannot be combined!')
            return
        
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        newContour = contours[0]
        stats = self.characterizeParticle(newContour)

        for i in range(len(newContour)):
            newContour[i][0][0] += xmin-padding
            newContour[i][0][1] += ymin-padding
        
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        print('merging contours:', contourIndices)
        self.createSafetyBackup()
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        #check, if dataset contains (already modified) particle2spectra, otherwise create new.
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        if self.datastats.dataset.particles2spectra is None:  #create default assignment
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            print('recreating particles2spectra from within edit particles...')
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            sortindices = self.datastats.dataset.ramanscansortindex
            self.datastats.dataset.particles2spectra = [[int(np.where(sortindices == i)[0])] for i in range(len(sortindices))]
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        #Contour indices are the same as the original particlestats, which are contained in the dataset. 
        #We have to modify that and reload in the analysisview
        #first, overwrite first index with new particlestats
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        self.datastats.dataset.particlestats[contourIndices[0]] = stats
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        #now, delete the rest...
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        self.datastats.dataset.particlestats = [i for ind, i in enumerate(self.datastats.dataset.particlestats) if ind not in contourIndices[1:]]
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        #same with the contours
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        self.datastats.dataset.particlecontours[contourIndices[0]] = newContour
        self.datastats.dataset.particlecontours = [i for ind, i in enumerate(self.datastats.dataset.particlecontours) if ind not in contourIndices[1:]]
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        #update particle2spectra_list
        #what is the current particle index??
        specIndices = []
        #other spectra indices:
        for index in contourIndices:
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            specIndices.append(self.datastats.particles2spectra[index])
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        #flatten index list (in case, that a nested list was created...)
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        specIndices = list(np.concatenate(specIndices))
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        for i in specIndices:
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            self.datastats.spectraResults[i] = new_assignment
            self.datastats.hqis[i] = 100   #avoid sorting them out again by hqi-filter...
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            print(f'spectrum {i} of particle{contourIndices[0]} is now {new_assignment}')
        
        #modify particles2spectra..         
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        self.datastats.dataset.particles2spectra[contourIndices[0]] = specIndices
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        for index in reversed(contourIndices[1:]):
            print('removing index from particles2spectra:', index)
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            del self.datastats.dataset.particles2spectra[index]
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        #update contours in sampleview
        self.parent.parent.contouritem.resetContours(self.datastats.dataset.particlecontours)
        self.parent.loadParticleData()
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        #save data
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        minHQI = self.parent.hqiSpinBox.value()
        compHQI = self.parent.compHqiSpinBox.value()
        if not self.datastats.saveAnalysisResults(minHQI, compHQI):
            QtWidgets.QMessageBox.warning(self.parent, 'Error!',
                    'Data inconsistency after saving!', QtWidgets.QMessageBox.Ok, 
                    QtWidgets.QMessageBox.Ok)
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    def reassignParticles(self, contourindices, new_assignment):
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        if new_assignment == 'other':
            new_assignment = self.getNewEntry()
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        if new_assignment is None:
            return
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        self.createSafetyBackup()
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        print(f'reassigning indices {contourindices} into {new_assignment}')
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        for partIndex in contourindices:
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            for specIndex in self.datastats.particles2spectra[partIndex]:
                self.datastats.currentPolymers[specIndex] = new_assignment
                self.datastats.spectraResults[specIndex] = new_assignment
                self.datastats.hqis[specIndex] = 100
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        #update contours in sampleview
        self.parent.parent.contouritem.resetContours(self.datastats.dataset.particlecontours)
        self.parent.loadParticleData()
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        #save data
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        minHQI = self.parent.hqiSpinBox.value()
        compHQI = self.parent.compHqiSpinBox.value()
        if not self.datastats.saveAnalysisResults(minHQI, compHQI):
            QtWidgets.QMessageBox.warning(self.parent, 'Error!',
                                'Data inconsistency after saving!',
                                QtWidgets.QMessageBox.Ok, QtWidgets.QMessageBox.Ok)
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    def deleteParticles(self):
        self.createSafetyBackup()
        pass
    
    def splitParticles(self):
        self.createSafetyBackup()
        pass
    
    def characterizeParticle(self, contours):
        ##characterize particle
        longellipse, shortellipse = np.nan, np.nan
        
        cnt = contours
        
        if cnt.shape[0] >= 5:       ##at least 5 points required for ellipse fitting...
            ellipse = cv2.fitEllipse(cnt)
            shortellipse, longellipse = ellipse[1]

        rect = cv2.minAreaRect(cnt)
        long, short = rect[1]
        if short>long:
            long, short = short, long
    
        return long, short, longellipse, shortellipse, cv2.contourArea(cnt)
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