particleContainer.py 12.8 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
# -*- 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 operator
23 24 25 26 27 28
import os
from PyQt5 import QtWidgets

from analysis import importSpectra
from analysis.particleAndMeasurement import Particle, Measurement

29

JosefBrandt's avatar
JosefBrandt committed
30
class ParticleContainer(object):
JosefBrandt's avatar
JosefBrandt committed
31
    def __init__(self, datasetParent):
JosefBrandt's avatar
 
JosefBrandt committed
32
        super(ParticleContainer, self).__init__()
JosefBrandt's avatar
JosefBrandt committed
33
        self.datasetParent = datasetParent
JosefBrandt's avatar
JosefBrandt committed
34
        self.particles = []
35
        self.measurements = []
JosefBrandt's avatar
 
JosefBrandt committed
36
        self.inconsistentParticles = []
JosefBrandt's avatar
JosefBrandt committed
37 38
        
        self.typeHistogram = None
39 40
    
    def addEmptyMeasurement(self):
JosefBrandt's avatar
JosefBrandt committed
41 42 43
        newMeas = Measurement()
        self.measurements.append(newMeas)
        return self.measurements.index(newMeas)
44 45 46 47 48 49 50
    
    def clearParticles(self):
        self.particles = []
    
    def clearMeasurements(self):
        self.measurements = []

51 52 53 54 55 56 57
    def setMeasurementScanIndex(self, indexOfMeasurment, scanIndex):
        self.measurements[indexOfMeasurment].ramanScanIndex = scanIndex
    
    def setMeasurementPixelCoords(self, indexOfMeasurment, x, y):
        self.measurements[indexOfMeasurment].pixelcoord_x = x
        self.measurements[indexOfMeasurment].pixelcoord_y = y
    
JosefBrandt's avatar
JosefBrandt committed
58 59 60 61 62 63 64 65 66 67
    def getMeasurementScanindex(self, indexOfMeasurement):
        return self.measurements[indexOfMeasurement].getScanIndex()
    
    def getSpectraFromDisk(self):
        spectra = None
        specPath = self.datasetParent.getSpectraFileName()
        
        if os.path.exists(specPath):
            spectra = np.load(specPath)
        else:
68 69
            
            fname = QtWidgets.QFileDialog.getOpenFileName(QtWidgets.QWidget(), 'Select Spectra File', self.datasetParent.path, 'text file (*.txt)')[0]
JosefBrandt's avatar
JosefBrandt committed
70 71
            if fname:
                #TODO: implement a more elegant way of testing through the individual imports...
72
                try:
JosefBrandt's avatar
JosefBrandt committed
73
                    spectra, spectraNames = importSpectra.importWITecSpectra(fname)
74
                except ImportError:
JosefBrandt's avatar
JosefBrandt committed
75 76 77 78 79 80 81
                    try:
                        spectra, spectraNames = importSpectra.importRenishawSpectra(fname)
                    except ImportError:
                        try:
                            spectra, spectraNames = importSpectra.importPerkinElmerSpectra(fname)
                        except ImportError:
                            pass
82
                
JosefBrandt's avatar
JosefBrandt committed
83 84 85
            if spectra is not None:
                np.save(self.datasetParent.getSpectraFileName(), spectra)
        return spectra
86
    
JosefBrandt's avatar
JosefBrandt committed
87 88 89
    def initializeParticles(self, numParticles):
        self.particles = []
        for i in range(numParticles):
90 91 92
            newParticle = Particle()
            newParticle.index = i
            self.particles.append(newParticle)
JosefBrandt's avatar
JosefBrandt committed
93
    
94
    def setParticleContours(self, contours):
JosefBrandt's avatar
JosefBrandt committed
95 96 97 98 99 100 101 102
        assert len(self.particles) == len(contours)
        for index, particle in enumerate(self.particles):
            particle.contour = contours[index]
        
    def setParticleStats(self, particlestats):
        assert len(self.particles) == len(particlestats)
        #particlestats is list of [long, short, longellipse, shortellipse, cv2.contourArea(cnt)]
        for index, particle in enumerate(self.particles):
JosefBrandt's avatar
 
JosefBrandt committed
103 104 105 106 107
            particle.longSize_box = float(particlestats[index][0])
            particle.shortSize_box = float(particlestats[index][1])
            particle.longSize_ellipse = float(particlestats[index][2])
            particle.shortSize_ellipse = float(particlestats[index][3])
            particle.area = float(particlestats[index][4])
JosefBrandt's avatar
JosefBrandt committed
108
    
JosefBrandt's avatar
 
JosefBrandt committed
109 110 111 112 113 114 115 116 117 118 119 120 121 122
    def testForInconsistentParticles(self): #i.e., particles that have multiple measurements with different assignments
        self.inconsistentParticles = []
        for particle in self.particles:
            if not particle.measurementsHaveSameOrigAssignment():
                self.inconsistentParticles.append(particle)
        if len(self.inconsistentParticles) > 0:
            print('Warning, inconsistent particles found!')
            for particle in self.inconsistentParticles:
                print(f'Particle with index {particle.index} has the following assignments:')
                for assignment in particle.getOrigMeasurementAssignments():
                    print(assignment)
        else:
            print('All particles have consistent spectra assignments')
    
JosefBrandt's avatar
 
JosefBrandt committed
123 124 125 126 127 128 129 130
    def applyPixelScaleToParticleStats(self, pixelscale):
        for index, particle in enumerate(self.particles):
            particle.longSize_box *= pixelscale
            particle.shortSize_box *= pixelscale
            particle.longSize_ellipse *= pixelscale
            particle.shortSize_ellipse *= pixelscale
            particle.area *= pixelscale**2

JosefBrandt's avatar
JosefBrandt committed
131 132 133 134
    def applyHQITresholdToParticles(self, minHQI):
        for particle in self.particles:
            particle.applyHQITresholdToMeasurements(minHQI)
            
JosefBrandt's avatar
 
JosefBrandt committed
135
    def applyAssignmentListToParticleMeasurements(self, assignmentList):
JosefBrandt's avatar
 
JosefBrandt committed
136
        '''AssignmentList is list of spectra assignments in order of spectra indices'''
JosefBrandt's avatar
JosefBrandt committed
137 138 139 140
        assert len(assignmentList) == len(self.measurements), f'assertion error in assignment of results: {len(assignmentList)} results for {len(self.measurements)} spectra...'
        for meas in self.measurements:
            scanIndex = meas.getScanIndex()
            meas.setAssignment(assignmentList[scanIndex])
JosefBrandt's avatar
 
JosefBrandt committed
141
    
JosefBrandt's avatar
 
JosefBrandt committed
142
    def applyHQIListToParticleMeasurements(self, hqiList):
JosefBrandt's avatar
 
JosefBrandt committed
143
        '''HQI-List is list of spectra hqis in order of spectra indices'''
JosefBrandt's avatar
JosefBrandt committed
144 145 146 147
        assert len(hqiList) == len(self.measurements), f'assertion error in assignment of hqis: {len(hqiList)} results for {len(self.measurements)} spectra...'
        for meas in self.measurements:
            scanIndex = meas.getScanIndex()
            meas.setHQI(hqiList[scanIndex])
JosefBrandt's avatar
 
JosefBrandt committed
148
    
JosefBrandt's avatar
 
JosefBrandt committed
149 150 151 152
    def reassignParticleToAssignment(self, particleIndex, newAssignment):
        particle = self.getParticleOfIndex(particleIndex)
        particle.setAllSpectraToNewAssignment(newAssignment)
    
JosefBrandt's avatar
 
JosefBrandt committed
153
    def getParticleOfIndex(self, index):
JosefBrandt's avatar
JosefBrandt committed
154 155 156 157 158 159
        try:
            particle = self.particles[index]
        except:
            print('failed getting particle')
            print('requested Index:', index)
            print('len particles', len(self.particles))
JosefBrandt's avatar
 
JosefBrandt committed
160 161
        assert particle.index == index, f'particle.index ({particle.index}) does match requested index in particleList ({index})' 
        return particle
JosefBrandt's avatar
 
JosefBrandt committed
162 163 164 165 166 167
    
    def getParticleIndexContainingSpecIndex(self, index):
        for particle in self.particles:
            if index in particle.getMeasurementIndices():
                return particle.index
    
JosefBrandt's avatar
JosefBrandt committed
168 169 170
    def getNumberOfParticles(self):
        return len(self.particles)
    
JosefBrandt's avatar
JosefBrandt committed
171 172 173
    def getNumberOfMeasurements(self):
        return len(self.measurements)
    
JosefBrandt's avatar
 
JosefBrandt committed
174 175 176 177 178 179
    def getParticleContours(self):
        contours = [part.contour for part in self.particles]
        return contours
    
    def getParticleContoursByIndex(self, partIndices):
        contours = []
JosefBrandt's avatar
 
JosefBrandt committed
180 181 182
        for index in partIndices:
            particle = self.getParticleOfIndex(index)
            contours.append(particle.contour)
JosefBrandt's avatar
 
JosefBrandt committed
183 184
        return contours
    
JosefBrandt's avatar
 
JosefBrandt committed
185 186 187 188
    def getParticleAssignmentByIndex(self, partIndex):
        particle = self.getParticleOfIndex(partIndex)
        return particle.getParticleAssignment()
    
JosefBrandt's avatar
JosefBrandt committed
189 190
    def getMeasurementPixelCoords(self):
        coords = []
191
        for meas in self.measurements:
192
            coords.append([meas.pixelcoord_x, meas.pixelcoord_y])
JosefBrandt's avatar
JosefBrandt committed
193 194
        return coords
    
JosefBrandt's avatar
 
JosefBrandt committed
195 196 197 198 199 200 201
    def getNumberOfParticlesOfAssignment(self, assignment):
        num = 0
        for particle in self.particles:
            if particle.getParticleAssignment() == assignment:
                num += 1
        return num
    
JosefBrandt's avatar
 
JosefBrandt committed
202 203 204 205 206 207 208 209
    def getNumberOfSpectraOfParticle(self, particleIndex):
        particle = self.getParticleOfIndex(particleIndex)
        return particle.getNumberOfMeasurements()

    def getSpectraIndicesOfParticle(self, particleIndex):
        particle = self.getParticleOfIndex(particleIndex)
        return particle.getMeasurementIndices()
        
JosefBrandt's avatar
JosefBrandt committed
210 211 212 213 214 215
    def getListOfParticleAssignments(self):
        particleAssignments = []
        for particle in self.particles:
            particleAssignments.append(particle.getParticleAssignment())
        return particleAssignments
    
JosefBrandt's avatar
 
JosefBrandt committed
216 217 218 219 220 221
    def getListOfHighestHQIs(self):
        hqis = []
        for particle in self.particles:
            hqis.append(particle.getHighestHQI())
        return hqis
    
JosefBrandt's avatar
 
JosefBrandt committed
222 223 224 225
    def getHQIOfSpectrumIndex(self, specIndex):
        for particle in self.particles:
            if specIndex in particle.getMeasurementIndices():
                return particle.getHQIOfMeasurementIndex(specIndex)
JosefBrandt's avatar
 
JosefBrandt committed
226 227
                    
    def getSizesOfAllParticles(self):
JosefBrandt's avatar
JosefBrandt committed
228
        particleSizes = []
JosefBrandt's avatar
 
JosefBrandt committed
229 230
        for particle in self.particles:
            particleSizes.append(particle.getParticleSize())
JosefBrandt's avatar
 
JosefBrandt committed
231
        return particleSizes
JosefBrandt's avatar
 
JosefBrandt committed
232 233 234 235
        
    def getShortSizesOfAllParticles(self):
        shortSizes = []
        for particle in self.particles:
JosefBrandt's avatar
JosefBrandt committed
236
            shortSizes.append(particle.getShortParticleSize())
JosefBrandt's avatar
 
JosefBrandt committed
237
        return shortSizes
JosefBrandt's avatar
 
JosefBrandt committed
238
    
JosefBrandt's avatar
JosefBrandt committed
239 240 241 242 243 244
    def getAreasOfAllParticles(self):
        areas = []
        for particle in self.particles:
            areas.append(particle.getArea())
        return areas
    
245 246 247 248 249 250 251 252 253 254
    def getColorsOfAllParticles(self):
        colors = []
        for particle in self.particles:
            colors.append(particle.color)
        return colors
    
    def getParticleColorByIndex(self, particleIndex):
        particle = self.getParticleOfIndex(particleIndex)
        return particle.color
    
255 256 257 258
    def getParticleShapeByIndex(self, particleIndex):
        particle = self.getParticleOfIndex(particleIndex)
        return particle.shape
    
JosefBrandt's avatar
 
JosefBrandt committed
259 260 261 262 263
    def getSizesOfParticleType(self, assignment):
        particleSizes = []
        for particle in self.particles:
            if particle.getParticleAssignment() == assignment:
                particleSizes.append(particle.getParticleSize())
JosefBrandt's avatar
 
JosefBrandt committed
264
        return particleSizes
JosefBrandt's avatar
 
JosefBrandt committed
265
    
JosefBrandt's avatar
 
JosefBrandt committed
266 267
    def getIndicesOfParticleType(self, assignment):
        indices = []
JosefBrandt's avatar
 
JosefBrandt committed
268
        for particle in self.particles:
JosefBrandt's avatar
 
JosefBrandt committed
269 270 271 272 273 274 275
            if particle.getParticleAssignment() == assignment:
                indices.append(particle.index)
        return indices
    
    def getSizeOfParticleByIndex(self, index):
        particle = self.getParticleOfIndex(index)
        return particle.getParticleSize()
JosefBrandt's avatar
JosefBrandt committed
276
    
JosefBrandt's avatar
 
JosefBrandt committed
277 278 279 280
    def getUniquePolymers(self):
        typeHist = self.getTypeHistogram()
        return typeHist.keys()

JosefBrandt's avatar
JosefBrandt committed
281
    def getTypeHistogram(self):
JosefBrandt's avatar
 
JosefBrandt committed
282
        uniquePolymers = np.unique(self.getListOfParticleAssignments())
JosefBrandt's avatar
JosefBrandt committed
283 284 285 286 287
        typehistogram = {i: 0 for i in uniquePolymers}
        for assignment in self.getListOfParticleAssignments():
            typehistogram[assignment] += 1
        ##sort typehistogram, it will be converted into a list!!
        sorted_typehistogram = sorted(typehistogram.items(), key = operator.itemgetter(1), reverse = True)
288
        #convert back to dsetParticlecontoursict
JosefBrandt's avatar
JosefBrandt committed
289
        final_typehistogram = {i[0]: i[1] for i in sorted_typehistogram}
JosefBrandt's avatar
 
JosefBrandt committed
290
        return final_typehistogram
JosefBrandt's avatar
JosefBrandt committed
291
    
292 293 294 295
    def changeParticleColor(self, index, newColor):
        particle = self.getParticleOfIndex(index)
        particle.color = newColor
    
296 297 298 299
    def changeParticleShape(self, index, newShape):
        particle = self.getParticleOfIndex(index)
        particle.shape = newShape
    
JosefBrandt's avatar
JosefBrandt committed
300
    def addMergedParticle(self, particleIndices, newContour, newStats, newAssignment=None):
301
        newParticle = Particle()
302
        newParticle.contour = newContour
303 304 305 306 307 308 309
        #copy Measurements
        for index in particleIndices:
            particle = self.getParticleOfIndex(index)
            for meas in particle.getMeasurements():
                if newAssignment is not None:
                    meas.setAssignment(newAssignment)
                    meas.setHQI(100)
310
                newParticle.addMeasurement(meas)
311 312 313

        newParticle.__dict__.update(newStats.__dict__)

JosefBrandt's avatar
 
JosefBrandt committed
314 315
        self.particles.append(newParticle)
        print('added new particle')
316
        
JosefBrandt's avatar
JosefBrandt committed
317 318 319
    def removeParticle(self, index):
        particle = self.getParticleOfIndex(index)   #just for asserting to have the correct particle!
        del self.particles[index]
320 321 322
            
    def resetParticleIndices(self):
        for newIndex, particle in enumerate(self.particles):
323
            particle.index = newIndex