particleeditor.py 10.5 KB
Newer Older
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26
# -*- 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/>.
"""
Lars Bittrich's avatar
Lars Bittrich committed
27

28 29
import numpy as np
import cv2
JosefBrandt's avatar
 
JosefBrandt committed
30
from PyQt5 import QtWidgets, QtCore
31

JosefBrandt's avatar
 
JosefBrandt committed
32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83
class ParticleContextMenu(QtWidgets.QMenu):
    combineParticlesSignal = QtCore.pyqtSignal(list, str)
    reassignParticlesSignal = QtCore.pyqtSignal(list, str)
    def __init__(self, sampleView):
        super(ParticleContextMenu, self).__init__()
        self.sampleView = sampleView
        self.selectedParticleIndices = self.sampleView.selectedParticleIndices
        self.particleContainer = self.sampleView.dataset.particleContainer
        
    def executeAtScreenPos(self, screenPos):
        self.combineActs = []
        self.combineMenu = QtWidgets.QMenu("Combine Particles into")
        assignments = []

        for particleIndex in self.selectedParticleIndices:
            assignment = self.particleContainer.getParticleAssignmentByIndex(particleIndex)
            assignments.append(assignment)
        
        for assignment in np.unique(assignments):
            self.combineActs.append(self.combineMenu.addAction(assignment))
        self.combineActs.append(self.combineMenu.addAction("other"))
        
        self.reassignActs = []
        self.reassignMenu = QtWidgets.QMenu("Reassign particle(s) into")
        for polymType in self.particleContainer.getUniquePolymers():
            self.reassignActs.append(self.reassignMenu.addAction(polymType))
        self.reassignActs.append(self.reassignMenu.addAction("other"))
        
        numParticles = len(self.selectedParticleIndices)
        if numParticles == 0:
            self.reassignMenu.setDisabled(True)
            self.combineMenu.setDisabled(True)
        elif numParticles == 1:
            self.combineMenu.setDisabled(True)
            
        self.addMenu(self.combineMenu)        
        self.addMenu(self.reassignMenu)
        
        action = self.exec_(screenPos)

        if action in self.combineActs:
            newAssignment = action.text()
            self.combineParticlesSignal.emit(self.selectedParticleIndices, newAssignment)
        elif action in self.reassignActs:
            newAssignment = action.text()
            self.reassignParticlesSignal.emit(self.selectedParticleIndices, newAssignment)


class ParticleEditor(QtCore.QObject):
    particlesWereEdited = QtCore.pyqtSignal()
    def __init__(self, sampleView, particleContainer):
        super(ParticleEditor, self).__init__()
JosefBrandt's avatar
 
JosefBrandt committed
84
        self.particleContainer = particleContainer
JosefBrandt's avatar
 
JosefBrandt committed
85
        self.sampleView = sampleView    #the assigned analysis widget
Hackmet's avatar
Hackmet committed
86 87 88
        self.backupFreq = 3     #save a backup every n actions
        self.neverBackedUp = True
        self.actionCounter = 0
JosefBrandt's avatar
 
JosefBrandt committed
89 90 91 92 93
    
    def connectToSignals(self, contextMenu):
        contextMenu.combineParticlesSignal.connect(self.combineParticles)
        contextMenu.reassignParticlesSignal.connect(self.reassignParticles)
        
94
    def createSafetyBackup(self):
Hackmet's avatar
Hackmet committed
95 96
        self.actionCounter += 1
        if self.actionCounter == self.backupFreq-1 or self.neverBackedUp:            
JosefBrandt's avatar
 
JosefBrandt committed
97
            backupname = self.sampleView.dataset.saveBackup()
Hackmet's avatar
Hackmet committed
98
            print('backing up as', backupname)
Hackmet's avatar
Hackmet committed
99
            self.neverBackedUp = False
JosefBrandt's avatar
 
JosefBrandt committed
100 101
            self.actionCounter = 0        
            
Hackmet's avatar
Hackmet committed
102
    def getNewEntry(self):
JosefBrandt's avatar
 
JosefBrandt committed
103
        text, okClicked = QtWidgets.QInputDialog.getText(QtWidgets.QWidget(), "Custom assignment", "Enter new assignment")
Hackmet's avatar
Hackmet committed
104 105 106
        if okClicked and text != '':
            return text
    
JosefBrandt's avatar
 
JosefBrandt committed
107
    @QtCore.pyqtSlot(list, str)
108
    def combineParticles(self, contourIndices, new_assignment):
JosefBrandt's avatar
 
JosefBrandt committed
109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200 201 202 203 204 205 206 207 208 209 210
        print(contourIndices, new_assignment)
        
#        if new_assignment == 'other':
#            new_assignment = self.getNewEntry()
#        if new_assignment is None:
#            return
#        
#        contourIndices = sorted(contourIndices)   #we want to keep the contour with lowest index
#        #get contours:
#        contours = self.particleContainer.getParticleContoursByIndex(contourIndices)
##        contours = [self.datastats.dataset.particlecontours[i] for i in contourIndices]
#        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))
#        for i in contourIndices:
#            curCnt = self.particleContainer.getParticleContoursByIndex(i).copy()
##            curCnt = self.datastats.dataset.particlecontours[i].copy()
#            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)
#        
#        img = np.uint8(cv2.morphologyEx(img, cv2.MORPH_CLOSE, np.ones((3, 3))))
#        
#        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)
#
#        if len(contours)>1:
#            QtWidgets.QMessageBox.critical(self.parent, 'ERROR!', 
#                                           'Particle contours are not connected and cannot be combined!')
#            return
#        
#        newContour = contours[0]
#        stats = self.characterizeParticle(newContour)
#dateContours()
#        for i in range(len(newContour)):
#            newContour[i][0][0] += xmin-padding
#            newContour[i][0][1] += ymin-padding
#        
#        print('merging contours:', contourIndices)
#        self.createSafetyBackup()
#        
##        #check, if dataset contains (already modified) particle2spectra, otherwise create new.
##        if self.datastats.dataset.particles2spectra is None:  #create default assignment
##            print('recreating particles2spectra from within edit particles...')
##            sortindices = self.datastats.dataset.ramanscansortindex
##            self.datastats.dataset.particles2spectra = [[int(np.where(sortindices == i)[0])] for i in range(len(sortindices))]
#        
#        #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
#        self.datastats.dataset.particlestats[contourIndices[0]] = stats
#        
#        #now, delete the rest...
#        self.datastats.dataset.particlestats = [i for ind, i in enumerate(self.datastats.dataset.particlestats) if ind not in contourIndices[1:]]
#        
#        #same with the contours
#        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:]]
#        
#        #update particle2spectra_list
#        #what is the current particle index??
#        specIndices = []
#        #other spectra indices:
#        for index in contourIndices:
#            specIndices.append(self.datastats.particles2spectra[index])
#        
#        #flatten index list (in case, that a nested list was created...)
#        specIndices = list(np.concatenate(specIndices))
#        for i in specIndices:
#            self.datastats.spectraResults[i] = new_assignment
#            self.datastats.hqis[i] = 100   #avoid sorting them out again by hqi-filter...
#            print(f'spectrum {i} of particle{contourIndices[0]} is now {new_assignment}')
#        
#        #modify particles2spectra..         
#        self.datastats.dataset.particles2spectra[contourIndices[0]] = specIndices
#        for index in reversed(contourIndices[1:]):
#            print('removing index from particles2spectra:', index)
#            del self.datastats.dataset.particles2spectra[index]
#
#        #update contours in sampleview
#        self.parent.parent.contouritem.resetContours(self.datastats.dataset.particlecontours)
#        self.parent.loadParticleData()
#        #save data
#        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)
211
    
JosefBrandt's avatar
 
JosefBrandt committed
212
    @QtCore.pyqtSlot(list, str)
213
    def reassignParticles(self, contourindices, new_assignment):
Hackmet's avatar
Hackmet committed
214 215
        if new_assignment == 'other':
            new_assignment = self.getNewEntry()
216 217
        if new_assignment is None:
            return
Hackmet's avatar
Hackmet committed
218
            
219
        self.createSafetyBackup()
Hackmet's avatar
Hackmet committed
220
        print(f'reassigning indices {contourindices} into {new_assignment}')
221
        for partIndex in contourindices:
JosefBrandt's avatar
 
JosefBrandt committed
222
            self.particleContainer.reassignParticleToAssignment(partIndex, new_assignment)
223

JosefBrandt's avatar
 
JosefBrandt committed
224
        self.particlesWereEdited.emit()
225 226 227 228 229 230 231 232 233 234 235 236 237 238 239 240 241
            
    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)
Hackmet's avatar
Hackmet committed
242 243
            

244
    
Hackmet's avatar
Hackmet committed
245