analysisview.py 28.4 KB
Newer Older
1
# -*- coding: utf-8 -*-
2
#!/usr/bin/env python3
3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23
"""
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/>.
"""

from PyQt5 import QtCore, QtGui, QtWidgets
24
import numpy as np
JosefBrandt's avatar
 
JosefBrandt committed
25
import sys
JosefBrandt's avatar
 
JosefBrandt committed
26
import time
27 28 29 30 31

from matplotlib.backends.backend_qt5agg import FigureCanvasQTAgg as FigureCanvas
from matplotlib.figure import Figure
from matplotlib.backends.backend_qt5agg import NavigationToolbar2QT as NavigationToolbar

JosefBrandt's avatar
JosefBrandt committed
32
from .excelexport import ExpExcelDialog
JosefBrandt's avatar
 
JosefBrandt committed
33
from .analysisplots import TypeHistogramView, SpectraPlot
JosefBrandt's avatar
 
JosefBrandt committed
34
from .loadresults import LoadTrueMatchResults
35
from .database import DataBaseWindow
JosefBrandt's avatar
 
JosefBrandt committed
36
from .colorlegend import getColorFromNameWithSeed
JosefBrandt's avatar
 
JosefBrandt committed
37

Hackmet's avatar
Hackmet committed
38
try:
39
    from .sqlexport import SQLExport
Hackmet's avatar
Hackmet committed
40 41 42
    sqlEnabled = True
except:
    sqlEnabled = False
43 44


Hackmet's avatar
Hackmet committed
45
class ParticleAnalysis(QtWidgets.QMainWindow):
46 47
    def __init__(self, dataset, viewparent=None):
        super(ParticleAnalysis, self).__init__(viewparent)
JosefBrandt's avatar
JosefBrandt committed
48
        self.resize(1680, 1050)
49 50
        self.setWindowTitle('Results of polymer analysis')
        self.layout = QtWidgets.QHBoxLayout()
Hackmet's avatar
Hackmet committed
51 52 53 54
        self.widget = QtWidgets.QWidget()
        self.widget.setLayout(self.layout)
        self.setCentralWidget(self.widget)
        
55
        self.viewparent = viewparent
JosefBrandt's avatar
JosefBrandt committed
56 57
        self.dataset = dataset
        self.particleContainer = dataset.particleContainer
58 59
        
        self.importWindow = None
60
        
61 62 63 64 65 66
        self.polymerCheckBoxes = []
        self.lastSelectedCheckBoxNames = []
        
        self.currentParticleIndex = 0
        self.currentSpectrumIndex = 0
        
JosefBrandt's avatar
 
JosefBrandt committed
67
        self.typeHistogramPlot = TypeHistogramView(self)
68 69 70 71 72 73 74 75 76
        self.sizeHistogramCanvas = FigureCanvas(Figure())
       
        sizeHistGroup = QtWidgets.QGroupBox()
        sizeHistLayout = QtWidgets.QHBoxLayout()
        self.sizeHist_ax = self.sizeHistogramCanvas.figure.subplots()
        self.sizeHist_ax.axis('off')
        self.sizeHistogramCanvas.figure.subplots_adjust(left=0.1, top=0.93, bottom=0.15, right=0.995)
        histNavigation = NavigationToolbar(self.sizeHistogramCanvas, self)
        histNavigation.setOrientation(QtCore.Qt.Vertical)
Hackmet's avatar
Hackmet committed
77
        histNavigation.setFixedWidth(50)
78 79 80 81
        sizeHistLayout.addWidget(histNavigation)
        sizeHistLayout.addWidget(self.sizeHistogramCanvas)
        sizeHistGroup.setLayout(sizeHistLayout)
        
JosefBrandt's avatar
 
JosefBrandt committed
82
        self.specPlot = SpectraPlot(self.dataset)
83 84
        
        splitter1 = QtWidgets.QSplitter(QtCore.Qt.Vertical)
JosefBrandt's avatar
 
JosefBrandt committed
85
        splitter1.addWidget(self.specPlot)
86 87 88
        splitter1.addWidget(sizeHistGroup)
        splitter2 = QtWidgets.QSplitter(QtCore.Qt.Horizontal)
        splitter2.addWidget(splitter1)
JosefBrandt's avatar
JosefBrandt committed
89
        splitter2.addWidget(self.typeHistogramPlot)
90 91
        splitter2.setSizes([300, 150])
       
JosefBrandt's avatar
 
JosefBrandt committed
92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107
        referenceGroup = QtWidgets.QGroupBox('Reference Spectra')
        referenceLayout = QtWidgets.QHBoxLayout()
        
        self.refSelector = QtWidgets.QComboBox()
        self.refSelector.setMinimumWidth(200)
        self.refSelector.setDisabled(True)
        self.dbWin = DataBaseWindow(self)
        self.dbWin.selectDataBase(refreshParent=True)  #this includes updating the refSelector
        
        self.refSelector.currentIndexChanged.connect(self.updateSpecPlot)
        referenceLayout.addWidget(QtWidgets.QLabel('Select Reference'))
        referenceLayout.addWidget(self.refSelector)
        referenceLayout.addStretch()
        referenceGroup.setLayout(referenceLayout)
        

108 109 110
        self.navigationGroup = QtWidgets.QGroupBox('Navigate through polymers')
        self.navigationGroup.setDisabled(True)
        navigationLayout = QtWidgets.QHBoxLayout()
JosefBrandt's avatar
 
JosefBrandt committed
111
        self.specNumberSelector = QtWidgets.QSpinBox()
112
        self.specNumberSelector.setMinimumWidth(100)
JosefBrandt's avatar
 
JosefBrandt committed
113
        self.specNumberSelector.setMinimum(1)
JosefBrandt's avatar
JosefBrandt committed
114 115
        numSpectra = self.particleContainer.getNumberOfMeasurements()
        self.specNumberSelector.setMaximum(numSpectra)
JosefBrandt's avatar
 
JosefBrandt committed
116
        
JosefBrandt's avatar
 
JosefBrandt committed
117
        self.jumpToSpecBtn = QtWidgets.QPushButton('Jump To Spectrum of Number:')
118
        self.jumpToSpecBtn.released.connect(self.jumpToIndicatedSpectrum)
JosefBrandt's avatar
 
JosefBrandt committed
119
        
JosefBrandt's avatar
 
JosefBrandt committed
120 121
        self.typeSelectorCombo = QtWidgets.QComboBox()
        self.typeSelectorCombo.setMinimumWidth(150)
JosefBrandt's avatar
 
JosefBrandt committed
122
        self.typeSelectorCombo.currentIndexChanged.connect(self.setTypeSelector)
123
        self.particleSelector = QtWidgets.QSpinBox()
JosefBrandt's avatar
 
JosefBrandt committed
124
        self.particleSelector.valueChanged.connect(self.setParticleSelector)
JosefBrandt's avatar
 
JosefBrandt committed
125 126
        self.particleNumberLabel = QtWidgets.QLabel('of xx particles; ')
        
127
        self.spectrumSelector = QtWidgets.QSpinBox()
JosefBrandt's avatar
 
JosefBrandt committed
128
        self.spectrumSelector.valueChanged.connect(self.setSpecSelector)
JosefBrandt's avatar
 
JosefBrandt committed
129
        self.spectrumNumberLabel = QtWidgets.QLabel('of xx spectra')
130 131 132 133 134
        for spinbox in [self.particleSelector, self.spectrumSelector]:
            spinbox.setMinimum(1)
            spinbox.setSingleStep(1)
            spinbox.setValue(1)
        
JosefBrandt's avatar
 
JosefBrandt committed
135 136
        navigationLayout.addWidget(self.jumpToSpecBtn)
        navigationLayout.addWidget(self.specNumberSelector)
137
        navigationLayout.addWidget(QtWidgets.QLabel('Select Polymer Type:'))
JosefBrandt's avatar
 
JosefBrandt committed
138
        navigationLayout.addWidget(self.typeSelectorCombo)
139 140 141
        navigationLayout.addStretch()
        navigationLayout.addWidget(QtWidgets.QLabel('Select Particle'))
        navigationLayout.addWidget(self.particleSelector)
JosefBrandt's avatar
 
JosefBrandt committed
142 143
        navigationLayout.addWidget(self.particleNumberLabel)
        navigationLayout.addStretch()
144 145
        navigationLayout.addWidget(QtWidgets.QLabel('Select Spectrum'))
        navigationLayout.addWidget(self.spectrumSelector)
JosefBrandt's avatar
 
JosefBrandt committed
146
        navigationLayout.addWidget(self.spectrumNumberLabel)
147 148 149 150 151
        
        self.navigationGroup.setLayout(navigationLayout)
        
        topLayout = QtWidgets.QHBoxLayout()
        topLayout.addWidget(self.navigationGroup)
Hackmet's avatar
Hackmet committed
152
        topLayout.addWidget(referenceGroup)
153
        
JosefBrandt's avatar
 
JosefBrandt committed
154
        viewLayout = QtWidgets.QVBoxLayout()
155 156 157 158
        viewLayout.addLayout(topLayout)
        viewLayout.addWidget(splitter2)
        viewLayout.setStretch(1, 1)

JosefBrandt's avatar
 
JosefBrandt committed
159
        self.optionsGroup = QtWidgets.QGroupBox('Set HQI Threshold')
160 161 162 163 164
        optionsLayout = QtWidgets.QFormLayout()
        
        self.hqiSpinBox = QtWidgets.QDoubleSpinBox()
        self.hqiSpinBox.setDecimals(1)
        self.hqiSpinBox.setMinimum(0)
JosefBrandt's avatar
JosefBrandt committed
165
        self.hqiSpinBox.setMaximum(100)
JosefBrandt's avatar
 
JosefBrandt committed
166 167
        self.hqiSpinBox.setMaximumWidth(100)
        self.hqiSpinBox.valueChanged.connect(self.applyHQIThresholdToResults)
JosefBrandt's avatar
JosefBrandt committed
168 169 170
        minHQI = self.dataset.resultParams['minHQI']
        if minHQI is not None:
            self.hqiSpinBox.setValue(minHQI)
JosefBrandt's avatar
 
JosefBrandt committed
171
        optionsLayout.addRow(QtWidgets.QLabel('minimum HQI:'), self.hqiSpinBox)
172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194
        
        self.optionsGroup.setLayout(optionsLayout)
        self.optionsGroup.setMinimumWidth(175)
        
        self.resultScrollarea = QtWidgets.QScrollArea(self)
        self.resultScrollarea.setFixedWidth(250)
        self.resultScrollarea.setWidgetResizable(True)

        widget = QtWidgets.QWidget()
        self.resultScrollarea.setWidget(widget)
        self.layout_SArea = QtWidgets.QVBoxLayout(widget)

        self.resultCheckBoxes = QtWidgets.QGroupBox('Display Polymer Types:')
        self.resultCheckBoxesLayout = QtWidgets.QVBoxLayout()
        self.showTotalSelector = QtWidgets.QCheckBox('Show Total Distribution')
        self.showTotalSelector.setChecked(True)
        self.showTotalSelector.setDisabled(True)
        self.resultCheckBoxesLayout.addWidget(self.showTotalSelector)
       
        self.resultCheckBoxesLayout.addStretch()
        self.resultCheckBoxes.setLayout(self.resultCheckBoxesLayout)

        self.layout_SArea.addWidget(self.resultCheckBoxes)
JosefBrandt's avatar
 
JosefBrandt committed
195 196
        
        self.menuLayout = QtWidgets.QVBoxLayout()
197 198 199 200 201 202
        self.menuLayout.addWidget(self.optionsGroup)
        self.menuLayout.addWidget(self.resultScrollarea)
        
        self.layout.addLayout(self.menuLayout)
        self.layout.addLayout(viewLayout)
        
JosefBrandt's avatar
JosefBrandt committed
203

204
         
Hackmet's avatar
Hackmet committed
205 206
        self.createActions()
        self.createMenus()
JosefBrandt's avatar
JosefBrandt committed
207
        self.applyHQIThresholdToResults()
JosefBrandt's avatar
 
JosefBrandt committed
208 209
        self.createHistogramData()
        self.initializeSpecPlot()
JosefBrandt's avatar
 
JosefBrandt committed
210
        self.setTypeSelector()
211
        self.updateHistogramsAndContours()
Hackmet's avatar
Hackmet committed
212 213 214 215 216
    
    def createActions(self):
        self.loadTrueMatchAct = QtWidgets.QAction("Load &TrueMatch Results", self)
        self.loadTrueMatchAct.triggered.connect(self.importTrueMatchResults)
        
JosefBrandt's avatar
JosefBrandt committed
217 218
        self.loadSpectraAct = QtWidgets.QAction("Load &Spectra", self)
        self.loadSpectraAct.triggered.connect(self.initializeSpecPlot)
Hackmet's avatar
Hackmet committed
219 220 221 222 223
        
        self.noOverlayAct = QtWidgets.QAction("&No Overlay", self)
        self.selOverlayAct = QtWidgets.QAction("&Selected Overlay", self)
        self.fullOverlayAct = QtWidgets.QAction("&Full Overlay", self)
        
JosefBrandt's avatar
JosefBrandt committed
224
        self.transpAct = QtWidgets.QAction("&Transparent Overlay", self)
225
        self.transpAct.triggered.connect(self.updateContourColors)
Hackmet's avatar
Hackmet committed
226 227 228 229 230 231 232 233 234 235 236 237 238
            
        self.hideLabelAct = QtWidgets.QAction('&Hide Polymer Numbers', self)
        self.hideLabelAct.triggered.connect(self.show_hide_labels)
        
        self.darkenAct = QtWidgets.QAction("&Darken Image", self)
        self.darkenAct.triggered.connect(self.darkenBackground)
        
        for act in [self.noOverlayAct, self.selOverlayAct, self.fullOverlayAct, self.hideLabelAct, self.transpAct, self.darkenAct]:
            act.setCheckable(True)
        self.fullOverlayAct.setChecked(True)
        
        self.seedAct = QtWidgets.QAction("&Set Color Seed", self)
        self.seedAct.triggered.connect(self.updateColorSeed)
JosefBrandt's avatar
JosefBrandt committed
239
        
240 241 242
        self.removeTinyParticlesAct = QtWidgets.QAction("&Remove not unknown Particles < 1 µm")
        self.removeTinyParticlesAct.triggered.connect(self.removeTinyParticles)

Hackmet's avatar
Hackmet committed
243 244 245 246 247 248 249 250 251 252 253 254
        self.databaseAct = QtWidgets.QAction("&ManageDatabase", self)
        self.databaseAct.triggered.connect(self.launchDBManager)
        
        self.expExcelAct= QtWidgets.QAction("Export &Excel List", self)
        self.expExcelAct.setDisabled(True)
        self.expExcelAct.triggered.connect(self.exportToExcel)
        
        self.expSQLAct = QtWidgets.QAction("Export to &SQL Database", self)
        self.expSQLAct.setDisabled(True)
        self.expSQLAct.triggered.connect(self.exportToSQL)
    
    def createMenus(self):
JosefBrandt's avatar
JosefBrandt committed
255 256
        self.importMenu = QtWidgets.QMenu("&Import Spectra and Results")
        self.importMenu.addActions([self.loadSpectraAct, self.loadTrueMatchAct])
Hackmet's avatar
Hackmet committed
257 258 259 260
        
        self.dispMenu = QtWidgets.QMenu("&Display", self)
        self.overlayActGroup = QtWidgets.QActionGroup(self.dispMenu)
        self.overlayActGroup.setExclusive(True)
261
        self.overlayActGroup.triggered.connect(self.updateContourColors)
262
        self.overlayActGroup.triggered.connect(self.updateHistogramsAndContours)
Hackmet's avatar
Hackmet committed
263 264 265 266 267 268 269 270
        
        for act in [self.noOverlayAct, self.selOverlayAct, self.fullOverlayAct]:
            self.dispMenu.addAction(act)
            self.overlayActGroup.addAction(act)
        
        self.dispMenu.addSeparator()
        self.dispMenu.addActions([self.transpAct, self.hideLabelAct, self.darkenAct, self.seedAct])
        
271 272 273
        self.toolMenu = QtWidgets.QMenu("&Tools")
        self.toolMenu.addAction(self.removeTinyParticlesAct)
        self.toolMenu.addAction(self.databaseAct)
Hackmet's avatar
Hackmet committed
274 275 276 277 278 279 280
        
        self.exportMenu = QtWidgets.QMenu("&Export", self)
        self.exportMenu.addAction(self.expExcelAct)
        self.exportMenu.addAction(self.expSQLAct)
        
        self.menuBar().addMenu(self.importMenu)
        self.menuBar().addMenu(self.dispMenu)
281
        self.menuBar().addMenu(self.toolMenu)
Hackmet's avatar
Hackmet committed
282
        self.menuBar().addMenu(self.exportMenu)
JosefBrandt's avatar
JosefBrandt committed
283 284 285 286 287
    
    def keyPressEvent(self, event):
        if event.key() in [QtCore.Qt.Key_Return, QtCore.Qt.Key_Enter]:
            self.jumpToIndicatedSpectrum()
    
Hackmet's avatar
Hackmet committed
288 289 290 291 292 293 294 295 296 297 298
    def launchDBManager(self):
        if self.dbWin.isHidden():
            self.dbWin.show()
    
    def populateRefSelector(self):
        #delete all present entries:
        self.refSelector.clear()
        
        if self.dbWin.activeDatabase is None:
            self.refSelector.setDisabled(True)
        else:
Hackmet's avatar
Hackmet committed
299
            self.refSelector.addItem('')
Hackmet's avatar
Hackmet committed
300 301 302 303
            self.refSelector.addItems(self.dbWin.activeDatabase.spectraNames)
            self.refSelector.setDisabled(False)
            
    def importTrueMatchResults(self):
JosefBrandt's avatar
 
JosefBrandt committed
304
        self.importWindow = LoadTrueMatchResults(self.particleContainer, self)
305
        self.importWindow.exec()
JosefBrandt's avatar
JosefBrandt committed
306
        
307
    @QtCore.pyqtSlot()
JosefBrandt's avatar
JosefBrandt committed
308
    def applyHQIThresholdToResults(self):
JosefBrandt's avatar
 
JosefBrandt committed
309 310 311 312
        hqi = self.hqiSpinBox.value()
        self.particleContainer.applyHQITresholdToParticles(hqi)
        self.dataset.resultParams['minHQI'] = hqi
        self.dataset.save()
JosefBrandt's avatar
JosefBrandt committed
313
        self.createHistogramData()
314
        self.updateHistogramsAndContours()
JosefBrandt's avatar
 
JosefBrandt committed
315 316 317 318 319 320 321 322 323 324 325 326 327 328 329 330 331
     
    def updateHistogramsAndContours(self):  
        self.createHistogramData()
        t0 = time.time()
        self.updateTypeHistogram()
        print('update type hist: {} ms'.format(round((time.time()-t0)*1000)))
        t0 = time.time()
        self.updateSizeHistogram()
        print('update size hist: {} ms'.format(round((time.time()-t0)*1000)))
        t0 = time.time()
        self.updateContourColors()
        print('update contours: {} ms'.format(round((time.time()-t0)*1000)))
        t0 = time.time()
        self.updateLegend()
        print('update legend: {} ms'.format(round((time.time()-t0)*1000)))
        self.dataset.save()
        
332
    def createHistogramData(self):
JosefBrandt's avatar
 
JosefBrandt committed
333 334
        self.lastSelectedCheckBoxNames = self.getSelectedPolymers()
        
335 336 337 338 339 340 341 342 343 344 345
        ###Handle Checkboxes for all polymers...
        self.menuLayout.removeWidget(self.resultScrollarea)
        for i in [self.resultCheckBoxes, self.resultCheckBoxesLayout, self.resultScrollarea, self.layout_SArea]:
            i.setParent(None)
            del i

        for i in self.polymerCheckBoxes:        #remove present boxlabels
            i.setParent(None)
            del i
        self.showTotalSelector.setParent(None)
        self.showTotalSelector.setDisabled(False)
346
        self.showTotalSelector.stateChanged.connect(self.updateHistogramsAndContours)
347 348 349 350 351 352 353 354 355 356 357 358 359 360 361
        
        del self.resultCheckBoxes
        del self.resultCheckBoxesLayout
        del self.resultScrollarea
        del self.layout_SArea
        
        self.resultScrollarea = QtWidgets.QScrollArea(self)
        self.resultScrollarea.setFixedWidth(250)
        self.resultScrollarea.setWidgetResizable(True)
        widget = QtWidgets.QWidget()
        self.resultScrollarea.setWidget(widget)
        self.layout_SArea = QtWidgets.QVBoxLayout(widget)
        self.resultCheckBoxes = QtWidgets.QGroupBox('Show Polymer Types:')
        self.resultCheckBoxesLayout = QtWidgets.QVBoxLayout()
        self.resultCheckBoxesLayout.addWidget(self.showTotalSelector)
JosefBrandt's avatar
JosefBrandt committed
362
        
363
        #generate new checkboxes 
JosefBrandt's avatar
 
JosefBrandt committed
364
        self.polymerCheckBoxes = []#
JosefBrandt's avatar
JosefBrandt committed
365
        uniquePolymers = self.particleContainer.getUniquePolymers()
366
        for index, polymer in enumerate(uniquePolymers):
367 368 369 370 371 372
            self.polymerCheckBoxes.append(QtWidgets.QCheckBox(self))
            self.polymerCheckBoxes[index].setText(polymer)
            self.resultCheckBoxesLayout.addWidget(self.polymerCheckBoxes[index])
            if polymer in self.lastSelectedCheckBoxNames:
                self.polymerCheckBoxes[index].setChecked(True)
            
373
            self.polymerCheckBoxes[index].stateChanged.connect(self.updateHistogramsAndContours)
374 375 376 377 378 379

        self.resultCheckBoxesLayout.addStretch()
        self.resultCheckBoxes.setLayout(self.resultCheckBoxesLayout)
        self.layout_SArea.addWidget(self.resultCheckBoxes)
        self.menuLayout.addWidget(self.resultScrollarea)
        
Hackmet's avatar
Hackmet committed
380 381 382
        self.expExcelAct.setDisabled(False)
        if sqlEnabled:
            self.expSQLAct.setDisabled(False)
383 384
        
        self.navigationGroup.setEnabled(True)
JosefBrandt's avatar
 
JosefBrandt committed
385
        self.typeSelectorCombo.currentIndexChanged.disconnect()
JosefBrandt's avatar
 
JosefBrandt committed
386 387
        self.typeSelectorCombo.clear()
        self.typeSelectorCombo.addItems(uniquePolymers)
JosefBrandt's avatar
 
JosefBrandt committed
388 389
        self.typeSelectorCombo.currentIndexChanged.connect(self.setTypeSelector)
        
JosefBrandt's avatar
JosefBrandt committed
390 391
        numSpectra = self.particleContainer.getNumberOfMeasurements()
        self.specNumberSelector.setMaximum(numSpectra)
JosefBrandt's avatar
 
JosefBrandt committed
392
        
JosefBrandt's avatar
 
JosefBrandt committed
393 394 395
    def initializeSpecPlot(self):
        self.specPlot.loadSpectraAndInitializeSpecPlot()
        self.updateSpecPlot()
396
    
JosefBrandt's avatar
 
JosefBrandt committed
397 398 399 400 401 402 403 404 405 406 407 408 409 410 411 412 413 414 415 416 417 418 419 420 421 422 423 424 425 426 427 428 429 430 431 432 433 434 435 436 437 438 439 440 441 442 443 444 445 446 447
    def updateTypeHistogram(self):
        colorList = []
        abundancyList = []
        labelList = []
        typeHistogram = self.particleContainer.getTypeHistogram()
        for index, polymType in enumerate(typeHistogram):
            if not self.selOverlayAct.isChecked() or self.polymerCheckBoxes[index].isChecked():
                text = f'{typeHistogram[polymType]} x {polymType}'
                labelList.append(text)
                abundancyList.append(typeHistogram[polymType])
                curColor = getColorFromNameWithSeed(polymType, self.dataset.colorSeed)
                colorList.append(QtGui.QColor(*curColor))
            
        self.typeHistogramPlot.updateTypeHistogram(list(zip(abundancyList, labelList, colorList)))
    
    def updateSizeHistogram(self):
        if self.particleContainer.getNumberOfParticles() > 0:
            #general size histograms
            self.sizeHist_ax.clear()
            self.sizeHist_ax.axis('on')
            self.bins = np.logspace(0.1, 3, 20)
            self.sizes = self.particleContainer.getSizesOfAllParticles()
                
            sizehist = np.histogram(self.sizes, self.bins)
            self.totalhistx = []
            for i in range(19):
                self.totalhistx.append(np.mean((sizehist[1][i], sizehist[1][i+1])))
            self.totalhisty = sizehist[0]
            
            self.sizeHist_ax.tick_params(axis='both', which='both', labelsize=15)
            self.sizeHist_ax.set_xlabel('Size (µm)', fontsize = 15)
            self.sizeHist_ax.set_ylabel('Number', fontsize = 15)
            self.sizeHist_ax.set_xlim(3, 1100)        
            self.sizeHist_ax.figure.canvas.draw()
            
            if self.showTotalSelector.isChecked():
                self.sizeHist_ax.semilogx(self.totalhistx, self.totalhisty, label = 'total')
                
            for polymType in self.getSelectedPolymers():
                sizes = self.particleContainer.getSizesOfParticleType(polymType)
                sizehist = np.histogram(sizes, self.bins)
                color = getColorFromNameWithSeed(polymType, self.dataset.colorSeed, base255=False)
                self.sizeHist_ax.semilogx(self.totalhistx, sizehist[0], label=polymType, color=color)    
            
            self.sizeHist_ax.legend(prop = {'size': 15})
            self.sizeHist_ax.tick_params(axis='both', which='both', labelsize=15)
            self.sizeHist_ax.set_xlabel('Size (µm)', fontsize = 15)
            self.sizeHist_ax.set_ylabel('Number', fontsize = 15)
            self.sizeHist_ax.set_xlim(3, 1100)        
            self.sizeHist_ax.figure.canvas.draw()
    
448
    def updateSpecPlot(self):
JosefBrandt's avatar
JosefBrandt committed
449
        particleSize = np.round(self.particleContainer.getSizeOfParticleByIndex(self.currentParticleIndex))
JosefBrandt's avatar
 
JosefBrandt committed
450
        hqi = self.particleContainer.getHQIOfSpectrumIndex(self.currentSpectrumIndex)
JosefBrandt's avatar
JosefBrandt committed
451 452
        assignment = self.particleContainer.getParticleAssignmentByIndex(self.currentParticleIndex)
        self.specPlot.updateParticleSpectrum(self.currentSpectrumIndex, assignment, particleSize, hqi)
JosefBrandt's avatar
 
JosefBrandt committed
453
            
Hackmet's avatar
Hackmet committed
454 455 456
        if self.refSelector.isEnabled() and self.refSelector.currentText() != '':
            refID = self.dbWin.activeDatabase.spectraNames.index(self.refSelector.currentText())
            ref = self.dbWin.activeDatabase.spectra[refID]
JosefBrandt's avatar
 
JosefBrandt committed
457
            self.specPlot.updateReferenceSpectrum(ref[:, 0], ref[:, 1])
JosefBrandt's avatar
 
JosefBrandt committed
458
    
459
    def updateContourColors(self):
460
        contours = self.viewparent.contourItems
JosefBrandt's avatar
 
JosefBrandt committed
461
        alpha = (64 if self.transpAct.isChecked() else 255)
JosefBrandt's avatar
 
JosefBrandt committed
462 463 464 465 466 467 468 469 470 471 472
        selectedPolymers = self.getSelectedPolymers()

        for particleIndex, contour in enumerate(contours):
            assignment = self.particleContainer.getParticleAssignmentByIndex(particleIndex)
            hidden = self.noOverlayAct.isChecked() or (not self.fullOverlayAct.isChecked() and assignment not in selectedPolymers)
            color = getColorFromNameWithSeed(assignment, self.dataset.colorSeed)
            color = QtGui.QColor(color[0], color[1], color[2], alpha=alpha)
            
            contour.setHidden(hidden)
            contour.setColor(color)
            contour.update()
473
    
JosefBrandt's avatar
 
JosefBrandt committed
474 475 476 477 478 479 480 481 482
    def updateLegend(self):
        if not self.noOverlayAct.isChecked():
            legendItems = []
            selectedPolymers = self.getSelectedPolymers()
            for polymer in self.particleContainer.getUniquePolymers():
                if self.fullOverlayAct.isChecked() or polymer in selectedPolymers:                
                    color = getColorFromNameWithSeed(polymer, self.dataset.colorSeed)
                    color = QtGui.QColor(color[0], color[1], color[2], 255)
                    legendItems.append((polymer, color))
483
            self.viewparent.updateLegend(legendItems)
JosefBrandt's avatar
 
JosefBrandt committed
484 485 486

    def getSelectedPolymers(self):
        return [checkbox.text() for checkbox in self.polymerCheckBoxes if checkbox.isChecked()]
JosefBrandt's avatar
 
JosefBrandt committed
487 488 489 490 491 492 493 494
     
    def setTypeSelector(self):
        assignment = self.typeSelectorCombo.currentText()
        partIndices = self.particleContainer.getIndicesOfParticleType(assignment)
        self.particleSelector.setMaximum(len(partIndices))
        self.particleNumberLabel.setText(f'of {len(partIndices)} particles; ')
        self.particleSelector.setValue(1)
        self.setParticleSelector()
JosefBrandt's avatar
 
JosefBrandt committed
495
    
JosefBrandt's avatar
 
JosefBrandt committed
496 497 498 499 500 501 502 503 504 505 506 507 508 509 510
    def setParticleSelector(self):
        assignment = self.typeSelectorCombo.currentText()
        if assignment != '':
            partIndices = self.particleContainer.getIndicesOfParticleType(assignment)
            self.currentParticleIndex = partIndices[self.particleSelector.value()-1]
            
            specIndices = self.particleContainer.getSpectraIndicesOfParticle(self.currentParticleIndex)
            self.spectrumSelector.setValue(1)
            self.spectrumSelector.setMaximum(len(specIndices))        
            self.spectrumNumberLabel.setText(f'of {len(specIndices)} spectra')
            self.setSpecSelector()
        
    def setSpecSelector(self):
        specIndices = self.particleContainer.getSpectraIndicesOfParticle(self.currentParticleIndex)
        self.currentSpectrumIndex = specIndices[self.spectrumSelector.value()-1]
511
        self.specNumberSelector.setValue(self.currentSpectrumIndex+1)
JosefBrandt's avatar
 
JosefBrandt committed
512 513
        
        self.updateSpecPlot()
514 515
        self.jumpToIndicatedSpectrum()
    
JosefBrandt's avatar
JosefBrandt committed
516
    def setWidgetsToNewParticleIndex(self, particleIndex):
517 518 519
        try:
            self.particleSelector.valueChanged.disconnect()
            self.spectrumSelector.valueChanged.disconnect()
JosefBrandt's avatar
 
JosefBrandt committed
520
            self.typeSelectorCombo.currentIndexChanged.disconnect()
521
        except TypeError:
JosefBrandt's avatar
JosefBrandt committed
522
            pass #signals were not connected, nothing to disconnect...
523
        
JosefBrandt's avatar
 
JosefBrandt committed
524
        assignment = self.particleContainer.getParticleAssignmentByIndex(particleIndex)
JosefBrandt's avatar
 
JosefBrandt committed
525
        self.typeSelectorCombo.setCurrentText(assignment)
JosefBrandt's avatar
 
JosefBrandt committed
526
        
JosefBrandt's avatar
 
JosefBrandt committed
527
        self.currentParticleIndex = particleIndex
JosefBrandt's avatar
 
JosefBrandt committed
528
        partIndices = self.particleContainer.getIndicesOfParticleType(assignment)
JosefBrandt's avatar
 
JosefBrandt committed
529
        self.particleSelector.setMaximum(len(partIndices))
530
        self.particleNumberLabel.setText(f'of {len(partIndices)} particles; ')
JosefBrandt's avatar
 
JosefBrandt committed
531
        
JosefBrandt's avatar
 
JosefBrandt committed
532
        self.particleSelector.setValue(partIndices.index(particleIndex)+1)
533
        
JosefBrandt's avatar
 
JosefBrandt committed
534
        specIndices = self.particleContainer.getSpectraIndicesOfParticle(self.currentParticleIndex)
JosefBrandt's avatar
 
JosefBrandt committed
535
        self.spectrumSelector.setValue(1)
JosefBrandt's avatar
 
JosefBrandt committed
536 537
        self.spectrumSelector.setMaximum(len(specIndices))        
        self.spectrumNumberLabel.setText(f'of {len(specIndices)} spectra')
JosefBrandt's avatar
 
JosefBrandt committed
538
        
JosefBrandt's avatar
 
JosefBrandt committed
539 540
        self.currentSpectrumIndex = specIndices[self.spectrumSelector.value()-1]
        self.specNumberSelector.setValue(self.currentSpectrumIndex+1)
541
        self.updateSpecPlot()
JosefBrandt's avatar
 
JosefBrandt committed
542 543 544 545 546
        
        self.typeSelectorCombo.currentIndexChanged.connect(self.setTypeSelector)
        self.spectrumSelector.valueChanged.connect(self.setSpecSelector)
        self.particleSelector.valueChanged.connect(self.setParticleSelector)
        
JosefBrandt's avatar
JosefBrandt committed
547
    def jumpToIndicatedSpectrum(self):
JosefBrandt's avatar
 
JosefBrandt committed
548 549
        self.currentSpectrumIndex = self.specNumberSelector.value()-1
        self.currentParticleIndex = self.particleContainer.getParticleIndexContainingSpecIndex(self.currentSpectrumIndex)
JosefBrandt's avatar
JosefBrandt committed
550
        self.viewparent.centerOnRamanIndex(self.currentSpectrumIndex)
JosefBrandt's avatar
JosefBrandt committed
551 552
        self.viewparent.highLightContour(self.currentParticleIndex)
        self.updateSpecPlot()
553 554
    
    def darkenBackground(self):
555
        self.viewparent.darkenPixmap = self.darkenAct.isChecked()
556
        
Hackmet's avatar
Hackmet committed
557
        if self.darkenAct.isChecked():
558 559
            self.viewparent.scene().setBackgroundBrush(QtGui.QColor(5, 5, 5))
            self.viewparent.item.setOpacity(0.2)
560
        else:
561 562
            self.viewparent.scene().setBackgroundBrush(QtCore.Qt.darkGray)
            self.viewparent.item.setOpacity(1)
563 564

    def updateColorSeed(self):
JosefBrandt's avatar
 
JosefBrandt committed
565
        text, ok = QtWidgets.QInputDialog.getText(self, 'Color Seed', 'Enter New Seed here', text=self.dataset.colorSeed)
566
        if ok:
JosefBrandt's avatar
 
JosefBrandt committed
567
            self.dataset.colorSeed = text
568 569 570 571 572 573 574 575 576 577 578 579
            self.updateHistogramsAndContours()
    
    def removeTinyParticles(self):
        indices = []
        for particle in self.particleContainer.particles:
            if particle.getParticleAssignment() != 'unknown' and particle.getParticleSize() < 1:
                indices.append(particle.index)
        
        indices = sorted(indices, reverse=True)
        numIndices = len(indices)
        
        for index, partIndex in enumerate(indices):
JosefBrandt's avatar
 
JosefBrandt committed
580
            self.setWidgetsToNewParticleIndex(partIndex)
JosefBrandt's avatar
JosefBrandt committed
581 582
            assignment = self.particleContainer.getParticleAssignmentByIndex(partIndex)
            specIndices = self.particleContainer.getSpectraIndicesOfParticle(partIndex)
JosefBrandt's avatar
 
JosefBrandt committed
583 584
            self.viewparent.highLightContour(partIndex)
            self.viewparent.centerOnRamanIndex(specIndices[0])
585
            reply = QtWidgets.QMessageBox.question(self, f'Particle {index+1} of {numIndices}',
JosefBrandt's avatar
 
JosefBrandt committed
586
                                f"Do you want to remove that particle? Type = {assignment}",
587 588
                                QtWidgets.QMessageBox.Yes | 
                                QtWidgets.QMessageBox.No | QtWidgets.QMessageBox.Cancel, QtWidgets.QMessageBox.No)
589
            
590 591 592 593 594 595 596 597 598 599 600
            if reply == QtWidgets.QMessageBox.Yes:
                self.viewparent.removeParticleContour(partIndex)
                self.particleContainer.removeParticles([partIndex])
                
            elif reply == QtWidgets.QMessageBox.Cancel:
                self.particleContainer.resetParticleIndices()
                self.viewparent.resetContourIndices()
                return
        
        self.particleContainer.resetParticleIndices()
        self.viewparent.resetContourIndices()
JosefBrandt's avatar
 
JosefBrandt committed
601
        self.updateHistogramsAndContours()
602
    
603
    def show_hide_labels(self):
Hackmet's avatar
Hackmet committed
604
        hidden = self.hideLabelAct.isChecked()
605
        for scanIndicator in self.viewparent.ramanscanitems:
606 607
            scanIndicator.hidden = hidden
            scanIndicator.update()
JosefBrandt's avatar
 
JosefBrandt committed
608 609
    
    def exportToExcel(self):
JosefBrandt's avatar
JosefBrandt committed
610
        expWin = ExpExcelDialog(self.dataset)
JosefBrandt's avatar
 
JosefBrandt committed
611 612 613
        expWin.exec()
            
    def exportToSQL(self):
JosefBrandt's avatar
JosefBrandt committed
614 615 616 617 618 619 620 621
        if len(self.dataset.resultsUploadedToSQL) > 0:
           reply = QtWidgets.QMessageBox.question(self, 'Warning!',
                                "The following results were already uploaded:\n\n{}\n\nContinue?".format('\n'.join(self.dataset.resultsUploadedToSQL)),
                                QtWidgets.QMessageBox.Yes | 
                                QtWidgets.QMessageBox.No, QtWidgets.QMessageBox.No)
           if reply == QtWidgets.QMessageBox.Yes:
                sqlexp = SQLExport(self.dataset)
                sqlexp.exec()
622 623
    
    def closeEvent(self, event):
JosefBrandt's avatar
 
JosefBrandt committed
624
        for window in [self.importWindow, self.dbWin]:
625 626
            try: window.close()
            except: pass
627
        self.viewparent.imparent.particelAnalysisAct.setChecked(False)
628 629 630 631
        event.accept()


if __name__ == '__main__':
632
    from ..dataset import DataSet
633 634
    def run():
        app = QtWidgets.QApplication(sys.argv)
635
        meas = ParticleAnalysis(DataSet("dummydata"))
636
        meas.showMaximized()
637
        return app.exec_()
638 639
    
    run()