analysisview.py 33 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, os
26 27 28 29 30 31 32
import random
import colorsys

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

33
from .analysiswidgets import ExpExcelDialog, AdditiveViewer, ParticleTypeView
34
from .loadresults import LoadWITecResults
35
from .particleeditor import ParticleEditor
36
from .database import DataBaseWindow
JosefBrandt's avatar
 
JosefBrandt committed
37 38
#from .datastats import DataStats
from analysis import importSpectra
Hackmet's avatar
Hackmet committed
39
try:
40
    from .sqlexport import SQLExport
Hackmet's avatar
Hackmet committed
41 42 43
    sqlEnabled = True
except:
    sqlEnabled = False
44 45


Hackmet's avatar
Hackmet committed
46
class ParticleAnalysis(QtWidgets.QMainWindow):
47 48
    def __init__(self, dataset, parent=None):
        super(ParticleAnalysis, self).__init__(parent)
49 50 51
        self.setGeometry(100, 100, 1680, 1050)
        self.setWindowTitle('Results of polymer analysis')
        self.layout = QtWidgets.QHBoxLayout()
Hackmet's avatar
Hackmet committed
52 53 54 55
        self.widget = QtWidgets.QWidget()
        self.widget.setLayout(self.layout)
        self.setCentralWidget(self.widget)
        
56
        self.parent = parent
JosefBrandt's avatar
JosefBrandt committed
57 58
        self.dataset = dataset
        self.particleContainer = dataset.particleContainer
JosefBrandt's avatar
 
JosefBrandt committed
59 60
#        self.datastats = DataStats(dataset)
        self.editor = ParticleEditor(self.particleContainer, self)
61
        
JosefBrandt's avatar
JosefBrandt committed
62
#        self.additivePlot = None
63
        self.importWindow = None
64
        
65 66 67 68 69 70 71
        self.polymerCheckBoxes = []
        self.lastSelectedCheckBoxNames = []
        
        self.currentParticleIndex = 0
        self.currentSpectrumIndex = 0
        self.lastSpectrumInFocus = None
        
JosefBrandt's avatar
JosefBrandt committed
72 73
        self.typeHistogramPlot = ParticleTypeView(self)
#        self.typeHistogramPlot.indexClicked.connect(self.getAdditivePlot)
74 75 76 77 78 79 80 81 82
        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
83
        histNavigation.setFixedWidth(50)
84 85 86 87 88 89 90 91 92
        sizeHistLayout.addWidget(histNavigation)
        sizeHistLayout.addWidget(self.sizeHistogramCanvas)
        sizeHistGroup.setLayout(sizeHistLayout)
        
        specGroup = QtWidgets.QGroupBox()
        specLayout = QtWidgets.QHBoxLayout()
        self.specCanvas = FigureCanvas(Figure())
        self.spec_ax = self.specCanvas.figure.subplots()
        self.spec_ax.axis("off")
Hackmet's avatar
Hackmet committed
93 94
        self.ref_ax = self.spec_ax.twinx()
        self.specCanvas.figure.subplots_adjust(left=0.1, top=0.93, bottom=0.15, right=0.9)
95 96
        specNavigation = NavigationToolbar(self.specCanvas, self)
        specNavigation.setOrientation(QtCore.Qt.Vertical)
Hackmet's avatar
Hackmet committed
97
        specNavigation.setFixedWidth(50)
98 99 100 101 102 103 104 105 106 107 108 109 110
        
        specLayout.addWidget(specNavigation)
        specLayout.addWidget(self.specCanvas)
        specGroup.setLayout(specLayout)
        
        viewLayout = QtWidgets.QVBoxLayout()
        self.menuLayout = QtWidgets.QVBoxLayout()
        
        splitter1 = QtWidgets.QSplitter(QtCore.Qt.Vertical)
        splitter1.addWidget(specGroup)
        splitter1.addWidget(sizeHistGroup)
        splitter2 = QtWidgets.QSplitter(QtCore.Qt.Horizontal)
        splitter2.addWidget(splitter1)
JosefBrandt's avatar
JosefBrandt committed
111
        splitter2.addWidget(self.typeHistogramPlot)
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
        splitter2.setSizes([300, 150])
       
        self.navigationGroup = QtWidgets.QGroupBox('Navigate through polymers')
        self.navigationGroup.setDisabled(True)
        navigationLayout = QtWidgets.QHBoxLayout()
        self.polymerComboBox = QtWidgets.QComboBox()
        self.polymerComboBox.currentIndexChanged.connect(self.displayNewPolymerType)
        self.polymerComboBox.setMinimumWidth(150)
        self.particleSelector = QtWidgets.QSpinBox()
        self.particleSelector.valueChanged.connect(self.selectParticle)
        self.spectrumSelector = QtWidgets.QSpinBox()
        self.spectrumSelector.valueChanged.connect(self.selectSpectrum)
        for spinbox in [self.particleSelector, self.spectrumSelector]:
            spinbox.setMinimum(1)
            spinbox.setSingleStep(1)
            spinbox.setValue(1)
        
        navigationLayout.addWidget(QtWidgets.QLabel('Select Polymer Type:'))
        navigationLayout.addWidget(self.polymerComboBox)
        navigationLayout.addStretch()
        navigationLayout.addWidget(QtWidgets.QLabel('Select Particle'))
        navigationLayout.addWidget(self.particleSelector)
        navigationLayout.addWidget(QtWidgets.QLabel('Select Spectrum'))
        navigationLayout.addWidget(self.spectrumSelector)
        navigationLayout.addStretch()
        
        self.navigationGroup.setLayout(navigationLayout)
        
Hackmet's avatar
Hackmet committed
140 141 142 143 144 145 146 147 148 149 150 151 152
        referenceGroup = QtWidgets.QGroupBox('Reference Spectra')
        referenceLayout = QtWidgets.QHBoxLayout()
        
        self.refSelector = QtWidgets.QComboBox()
        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)
        referenceGroup.setLayout(referenceLayout)
        
153 154
        topLayout = QtWidgets.QHBoxLayout()
        topLayout.addWidget(self.navigationGroup)
Hackmet's avatar
Hackmet committed
155 156
        topLayout.addWidget(referenceGroup)
        topLayout.addStretch()
157 158 159 160 161 162 163 164 165 166 167 168
        
        viewLayout.addLayout(topLayout)
        viewLayout.addWidget(splitter2)
        viewLayout.setStretch(1, 1)

        self.optionsGroup = QtWidgets.QGroupBox('Further Options')
        optionsLayout = QtWidgets.QFormLayout()
        
        self.hqiSpinBox = QtWidgets.QDoubleSpinBox()
        self.hqiSpinBox.setValue(75.0)
        self.hqiSpinBox.setDecimals(1)
        self.hqiSpinBox.setMinimum(0)
JosefBrandt's avatar
JosefBrandt committed
169 170
        self.hqiSpinBox.setMaximum(100)
        self.hqiSpinBox.setMaximumWidth(45)
171 172
        optionsLayout.addRow(QtWidgets.QLabel('min HQI:'), self.hqiSpinBox)
        
JosefBrandt's avatar
JosefBrandt committed
173 174 175 176 177 178
#        self.compHqiSpinBox = QtWidgets.QDoubleSpinBox()
#        self.compHqiSpinBox.setValue(30.0)
#        self.compHqiSpinBox.setDecimals(1)
#        self.compHqiSpinBox.setMinimum(0)
#        self.compHqiSpinBox.setDisabled(True)
#        optionsLayout.addRow(QtWidgets.QLabel('min component HQI'), self.compHqiSpinBox)
179 180 181 182
        
        self.dispResultSpinBox = QtWidgets.QSpinBox()
        self.dispResultSpinBox.setValue(20)
        self.dispResultSpinBox.setMinimum(1)
JosefBrandt's avatar
JosefBrandt committed
183
        self.dispResultSpinBox.valueChanged.connect(self.updateHistograms)
184 185 186
        optionsLayout.addRow(QtWidgets.QLabel('Max. items in display:'), self.dispResultSpinBox)
        
        self.updateBtn = QtWidgets.QPushButton('Update Results')
JosefBrandt's avatar
JosefBrandt committed
187 188
        self.updateBtn.clicked.connect(self.applyHQIThresholdToResults)
#        self.updateBtn.setDisabled(True)
189 190 191 192
        optionsLayout.addRow(self.updateBtn)
        
        self.optionsGroup.setLayout(optionsLayout)
        self.optionsGroup.setMinimumWidth(175)
JosefBrandt's avatar
JosefBrandt committed
193
#        self.optionsGroup.setDisabled(True)
194 195 196 197 198 199 200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219 220
        
        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)

        self.menuLayout.addWidget(self.optionsGroup)
        self.menuLayout.addWidget(self.resultScrollarea)
        
        self.layout.addLayout(self.menuLayout)
        self.layout.addLayout(viewLayout)
        
JosefBrandt's avatar
JosefBrandt committed
221 222
        minHQI = self.dataset.resultParams['minHQI']
#        compHQI = self.dataset.resultParams['compHQI']
Lars Bittrich's avatar
Lars Bittrich committed
223 224
        if minHQI is not None:
            self.hqiSpinBox.setValue(minHQI)
JosefBrandt's avatar
JosefBrandt committed
225
#            self.compHqiSpinBox.setValue(compHQI)
226
         
Hackmet's avatar
Hackmet committed
227 228 229
        self.createActions()
        self.createMenus()
        
JosefBrandt's avatar
 
JosefBrandt committed
230
        self.loadSpectraAndInitializeSpecPlot()
JosefBrandt's avatar
JosefBrandt committed
231
        self.applyHQIThresholdToResults()
Hackmet's avatar
Hackmet committed
232 233 234 235 236 237 238 239 240 241 242 243
    
    def createActions(self):
        self.loadTrueMatchAct = QtWidgets.QAction("Load &TrueMatch Results", self)
        self.loadTrueMatchAct.triggered.connect(self.importTrueMatchResults)
        
        self.loadTextFileAct = QtWidgets.QAction("Load &ordered Text File", self)
        self.loadTextFileAct.setDisabled(True)
        
        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
244
        self.transpAct = QtWidgets.QAction("&Transparent Overlay", self)
Hackmet's avatar
Hackmet committed
245 246 247 248 249 250 251 252 253 254 255 256 257 258 259 260 261 262 263 264 265 266 267 268 269 270 271 272 273 274 275 276 277 278
        self.transpAct.triggered.connect(self.createPolymerOverlay)
            
        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)

        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):
        self.importMenu = QtWidgets.QMenu("&Import Results")
        self.importMenu.addActions([self.loadTrueMatchAct, self.loadTextFileAct])
        
        self.dispMenu = QtWidgets.QMenu("&Display", self)
        self.overlayActGroup = QtWidgets.QActionGroup(self.dispMenu)
        self.overlayActGroup.setExclusive(True)
        self.overlayActGroup.triggered.connect(self.createPolymerOverlay)
JosefBrandt's avatar
JosefBrandt committed
279
        self.overlayActGroup.triggered.connect(self.updateHistograms)
Hackmet's avatar
Hackmet committed
280 281 282 283 284 285 286 287 288 289 290 291 292 293 294 295 296 297 298
        
        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])
        
        self.refMenu = QtWidgets.QMenu("&References")
        self.refMenu.addAction(self.databaseAct)
        
        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)
        self.menuBar().addMenu(self.refMenu)
        self.menuBar().addMenu(self.exportMenu)
JosefBrandt's avatar
 
JosefBrandt committed
299
        
Hackmet's avatar
Hackmet committed
300 301 302 303 304 305 306 307 308 309 310
    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
311
            self.refSelector.addItem('')
Hackmet's avatar
Hackmet committed
312 313 314
            self.refSelector.addItems(self.dbWin.activeDatabase.spectraNames)
            self.refSelector.setDisabled(False)
            
JosefBrandt's avatar
 
JosefBrandt committed
315 316 317 318 319 320 321 322 323 324 325 326 327 328 329 330 331 332 333 334 335 336 337 338 339 340
    def loadSpectraAndInitializeSpecPlot(self):  #formerly updateData(self)....
        def tryLoadingNumpySpecFile():
            specPath = self.dataset.getSpectraFileName()
            if os.path.exists(specPath):
                return np.load(specPath)
            else:
                raise ImportError
        try:
            self.spectra = tryLoadingNumpySpecFile()
        except ImportError:
            
            fname = QtWidgets.QFileDialog.getOpenFileName(QtWidgets.QWidget(), 'Select Spectra File', self.dataset.path, 'text file (*.txt)')[0]
    
            try:
                self.spectra, spectraNames = importSpectra.importWITecSpectra(fname)
            except ImportError:
                try:
                    self.spectra, spectraNames = importSpectra.importRenishawSpectra(fname)
                except ImportError:
                    self.spectra, spectraNames = importSpectra.importPerkinElmerSpectra(fname)
                
            if self.spectra is None:
                raise ImportError
            else:
                np.save(self.dataset.getSpectraFileName(), self.spectra)
 
Hackmet's avatar
Hackmet committed
341
        self.specCanvas.draw()
JosefBrandt's avatar
JosefBrandt committed
342 343 344 345 346 347 348 349 350 351 352 353 354 355 356 357
#        self.loadParticleData()
        
#    def loadParticleData(self):
#        #check, if dataset already contains results. Otherwise load them...
#        if not self.datastats.loadParticleData():
#            self.show()
#            answer = QtWidgets.QMessageBox.question(self, 'Warning', 'No (or inconsistent) spectra results found, please run import dialog.\nPress OK to import or cancel to set to empty.', QtWidgets.QMessageBox.Ok | QtWidgets.QMessageBox.Cancel)
#            if answer == QtWidgets.QMessageBox.Ok:
#                self.importTrueMatchResults()
#            elif answer == QtWidgets.QMessageBox.Cancel:
#                self.datastats.invalidateSpectra()
#                self.updateBtn.clicked.connect(self.formatResults)
#                self.formatResults()
#        else:
#            self.updateBtn.clicked.connect(self.formatResults)
#            self.formatResults()
358
        
Hackmet's avatar
Hackmet committed
359
    def importTrueMatchResults(self):
JosefBrandt's avatar
 
JosefBrandt committed
360
        self.importWindow = LoadWITecResults(self.particleContainer, self)
361
        self.importWindow.exec()
362
    
JosefBrandt's avatar
JosefBrandt committed
363 364 365 366 367 368 369 370
#    @QtCore.pyqtSlot(int)
#    def getAdditivePlot(self, clickedindex):
#        polymer = self.datastats.typehistogram[clickedindex][0]        #get the polymer name, that was clicked on
#      
#        if self.datastats.sorted_additives is not None and \
#           len(self.datastats.sorted_additives[clickedindex]) > 0:            
#            self.additivePlot = AdditiveViewer(polymer, self.datastats.sorted_additives[clickedindex])
#            self.additivePlot.show()
371
    
372
    @QtCore.pyqtSlot()
JosefBrandt's avatar
JosefBrandt committed
373 374 375 376 377 378 379 380 381 382 383 384 385 386
    def applyHQIThresholdToResults(self):
        self.particleContainer.applyHQITresholdToParticles(self.hqiSpinBox.value())
        self.createHistogramData()
        
#    def formatResults(self):
#        if self.datastats.spectraResults is not None:
#            print('formatResults')
#            self.updateBtn.setDisabled(False)
#            self.optionsGroup.setDisabled(False)
#            
#            self.datastats.formatResults(self.hqiSpinBox.value(), self.compHqiSpinBox.value())
#            
#            if self.datastats.additiveResults is not None:
#                self.compHqiSpinBox.setDisabled(False)
Hackmet's avatar
Hackmet committed
387 388
            
            
389 390
            
    def createHistogramData(self):
JosefBrandt's avatar
JosefBrandt committed
391 392 393 394
#        if not self.datastats.createHistogramData():
#            QtWidgets.QMessageBox.critical(self, 'Error', 'Inconsistent particle data. Please restore backup!')
#            return
#        self.particleContainer.updateTypeHistogram()
395 396 397 398 399 400 401 402 403 404 405 406
        
        ###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)
JosefBrandt's avatar
JosefBrandt committed
407
        self.showTotalSelector.stateChanged.connect(self.updateHistograms)
408 409 410 411 412 413 414 415 416 417 418 419 420 421 422
        
        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
423
        
424 425
        #generate new checkboxes 
        self.polymerCheckBoxes = []
JosefBrandt's avatar
JosefBrandt committed
426
        uniquePolymers = self.particleContainer.getUniquePolymers()
427
        for index, polymer in enumerate(uniquePolymers):
428 429 430 431 432 433
            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)
            
JosefBrandt's avatar
JosefBrandt committed
434
            self.polymerCheckBoxes[index].stateChanged.connect(self.updateHistograms)
435 436 437 438 439 440 441
            self.polymerCheckBoxes[index].stateChanged.connect(self.createPolymerOverlay)

        self.resultCheckBoxesLayout.addStretch()
        self.resultCheckBoxes.setLayout(self.resultCheckBoxesLayout)
        self.layout_SArea.addWidget(self.resultCheckBoxes)
        self.menuLayout.addWidget(self.resultScrollarea)
        
Hackmet's avatar
Hackmet committed
442 443 444
        self.expExcelAct.setDisabled(False)
        if sqlEnabled:
            self.expSQLAct.setDisabled(False)
445 446 447 448
        
        self.navigationGroup.setEnabled(True)
        self.polymerComboBox.currentIndexChanged.disconnect()
        self.polymerComboBox.clear()
449
        self.polymerComboBox.addItems(uniquePolymers)
450
        self.polymerComboBox.currentIndexChanged.connect(self.displayNewPolymerType)
Hackmet's avatar
Hackmet committed
451
                
452 453 454 455 456 457
        self.polymerIndex = self.polymerComboBox.currentIndex()
        if self.lastSpectrumInFocus is not None:
            self.currentSpectrumIndex = self.lastSpectrumInFocus
            self.displayNewPolymerType(resetCurrentIndex=False)
        else:
            self.displayNewPolymerType()
Hackmet's avatar
Hackmet committed
458
            
JosefBrandt's avatar
JosefBrandt committed
459
        self.updateHistograms()
460 461
        self.createPolymerOverlay()
    
Hackmet's avatar
Hackmet committed
462
    def exportToExcel(self):
JosefBrandt's avatar
 
JosefBrandt committed
463
        expWin = ExpExcelDialog(self.particleContainer, self)
464
        expWin.exec()
Hackmet's avatar
Hackmet committed
465 466
            
    def exportToSQL(self):
JosefBrandt's avatar
 
JosefBrandt committed
467
        sqlexp = SQLExport(self.particleContainer, self)
468 469
        sqlexp.exec()
        
470
    
Hackmet's avatar
Hackmet committed
471 472
    def updateSpecPlot(self, centerOn=True, highlightContour=True):
        #draw Sample Spectrum
473 474 475
        specIndex = self.currentSpectrumIndex
        self.spec_ax.axis("on")
        self.spec_ax.clear()
JosefBrandt's avatar
 
JosefBrandt committed
476
        self.spec_ax.plot(self.spectra[:, 0], self.spectra[:, specIndex+1])
477 478 479
        self.spec_ax.tick_params(axis='both', which='both', labelsize=15)
        self.spec_ax.set_xlabel('Wavenumber (cm-1)', fontsize = 15)
        self.spec_ax.set_ylabel('Counts', fontsize = 15)
480
        self.spec_ax.set_title('ScanPoint Number {}, Size = {} µm'.format(specIndex+1, 
JosefBrandt's avatar
 
JosefBrandt committed
481 482 483
                               self.particleContainer.getSizeOfParticleByIndex(self.currentParticleIndex)))
        self.spec_ax.set_xbound(100, (3400 if self.spectra[-1, 0] > 3400 else self.spectra[-1, 0]))
        wavenumber_diff = list(self.spectra[:, 0]-100)
Hackmet's avatar
Hackmet committed
484
        y_start = wavenumber_diff.index(min(wavenumber_diff))
JosefBrandt's avatar
 
JosefBrandt committed
485 486
        y_min = min(self.spectra[y_start:, specIndex+1])
        y_max = max(self.spectra[y_start:, specIndex+1])
Hackmet's avatar
Hackmet committed
487 488 489 490 491 492 493 494 495 496 497
        self.spec_ax.set_ybound(0.9*y_min, 1.1*y_max)
        
        #draw Reference
        self.ref_ax.clear()
        if self.refSelector.isEnabled() and self.refSelector.currentText() != '':
            self.ref_ax.tick_params(axis='both', which='both', labelsize=15)
            refID = self.dbWin.activeDatabase.spectraNames.index(self.refSelector.currentText())
            ref = self.dbWin.activeDatabase.spectra[refID]
            self.ref_ax.plot(ref[:, 0], ref[:, 1], color = 'r')
            self.ref_ax.set_ylabel('Ref. Intensity', fontsize = 15, color = 'r')
            self.ref_ax.tick_params('y', colors = 'r')
JosefBrandt's avatar
 
JosefBrandt committed
498
            self.ref_ax.set_xbound(100, (3400 if self.spectra[-1, 0] > 3400 else self.spectra[-1, 0]))
Hackmet's avatar
Hackmet committed
499 500 501 502 503 504 505
#            wavenumber_diff = list(ref[:, 0]-100)
#            y_start = wavenumber_diff.index(min(wavenumber_diff))
#            y_min = min(ref[y_start:, specIndex+1])
#            y_max = max(ref[y_start:, specIndex+1])
            
            
        
506 507 508 509
        self.spec_ax.figure.canvas.draw()
        self.parent.centerOnRamanIndex(specIndex, centerOn=centerOn, highlightContour=highlightContour)
        self.parent.highLightRamanIndex(specIndex)
        self.lastSpectrumInFocus = specIndex
510 511
        
    def selectContour(self, index, centerOn=True):
JosefBrandt's avatar
 
JosefBrandt committed
512 513 514 515 516 517 518 519 520 521 522 523 524 525 526 527 528 529 530 531 532 533 534 535 536 537 538 539 540 541 542 543 544 545 546 547 548 549 550 551 552
        print('select Contour in analysisview not yet refactored')
#        uniquePolymers = self.particleContainer.getUniquePolymers()
#        if uniquePolymers is not None:
#            #the index is the contour index, find particle index:
#            specIndex = self.datastats.particles2spectra[index][0]  #select first spectrum of partoicle
#            self.currentParticleIndex = index
#            self.currentSpectrumIndex = specIndex
#            
#            selectedPolymer = self.datastats.currentPolymers[specIndex]
#            try:
#                self.polymerIndex = uniquePolymers.index(selectedPolymer)
#            except:
#                print(selectedPolymer)
#                raise
#            
#            #subparticleIndex
#            partIndicesOfThatPolymer = self.datastats.indices[self.polymerIndex]
#            subPartInd = partIndicesOfThatPolymer.index(index)
#            
#            #disconnect analysis widgets:
#            self.particleSelector.valueChanged.disconnect()
#            self.spectrumSelector.valueChanged.disconnect()
#            self.polymerComboBox.currentIndexChanged.disconnect()
#            
#            #set widgets...
#            self.particleSelector.setValue(subPartInd+1)
#            self.particleSelector.setMaximum(len(partIndicesOfThatPolymer))
#            
#            self.spectrumSelector.setValue(1)
#            self.spectrumSelector.setMaximum(len(self.datastats.particles2spectra[index]))
#            
#            selectedPolymer = self.datastats.currentPolymers[specIndex]
#            self.polymerIndex = uniquePolymers.index(selectedPolymer)
#            self.polymerComboBox.setCurrentIndex(self.polymerIndex)
#           
#            #reconnect all widgets:
#            self.particleSelector.valueChanged.connect(self.selectParticle)
#            self.spectrumSelector.valueChanged.connect(self.selectSpectrum)
#            self.polymerComboBox.currentIndexChanged.connect(self.displayNewPolymerType)
#            
#            self.updateSpecPlot(centerOn=centerOn)
553 554 555
    
    def displayNewPolymerType(self, resetCurrentIndex=True):
        self.polymerIndex = self.polymerComboBox.currentIndex()
JosefBrandt's avatar
 
JosefBrandt committed
556 557 558
        polymerName = self.polymerComboBox.currentText()
#        self.particleSelector.setMaximum(len(self.datastats.indices[self.polymerIndex]))
        self.particleSelector.setMaximum(self.particleContainer.getNumberOfParticlesOfAssignment(polymerName))
559 560 561
        if resetCurrentIndex:
            self.particleSelector.setValue(1)
            self.spectrumSelector.setValue(1)
562 563 564
            self.spectrumSelector.setMaximum(len(self.datastats.particles2spectra[self.currentParticleIndex]))
            self.currentParticleIndex = self.datastats.indices[self.polymerIndex][self.particleSelector.value()-1]
            self.currentSpectrumIndex = self.datastats.particles2spectra[self.currentParticleIndex][self.spectrumSelector.value()-1]
Hackmet's avatar
Hackmet committed
565
            self.updateSpecPlot(centerOn=True)
566
        else:    
567 568
            self.currentParticleIndex = self.datastats.indices[self.polymerIndex][self.particleSelector.value()-1]
            self.currentSpectrumIndex = self.datastats.particles2spectra[self.currentParticleIndex][self.spectrumSelector.value()-1]
Hackmet's avatar
Hackmet committed
569
            self.updateSpecPlot(centerOn=False)
570 571
    
    def selectParticle(self, resetSpectrumCount=True):
572 573 574
        if self.datastats.particles2spectra is not None:
            self.currentParticleIndex = self.datastats.indices[self.polymerIndex][self.particleSelector.value()-1]
            self.spectrumSelector.setMaximum(len(self.datastats.particles2spectra[self.currentParticleIndex]))
575 576
            if resetSpectrumCount:
                self.spectrumSelector.setValue(1)
577
            self.currentSpectrumIndex = self.datastats.particles2spectra[self.currentParticleIndex][self.spectrumSelector.value()-1]
Hackmet's avatar
Hackmet committed
578
            self.updateSpecPlot()
579 580 581 582
        else:
            print('no spectrum assignment found...')
    
    def selectSpectrum(self):
583 584
        if self.datastats.particles2spectra is not None:
            self.currentSpectrumIndex = self.datastats.particles2spectra[self.currentParticleIndex][self.spectrumSelector.value()-1]
Hackmet's avatar
Hackmet committed
585
            self.updateSpecPlot()
586
    
JosefBrandt's avatar
JosefBrandt committed
587 588 589 590 591 592
    def updateHistograms(self):  
        self.updateTypeHistogram()
        self.updateSizeHistogram()
        
        
    def updateTypeHistogram(self):
593 594
        #draw the general histogram
        colorList = []
595 596
        abundancyList = []
        labelList = []
JosefBrandt's avatar
JosefBrandt committed
597 598
        typeHistogram = self.particleContainer.getTypeHistogram()
        for index, polymType in enumerate(typeHistogram):
Hackmet's avatar
Hackmet committed
599
            if not self.selOverlayAct.isChecked() or self.polymerCheckBoxes[index].isChecked():
JosefBrandt's avatar
JosefBrandt committed
600 601
                abundancyList.append(typeHistogram[polymType])
                curColor = self.getColorFromName(polymType)
602
                colorList.append(QtGui.QColor(*curColor))
603
            
JosefBrandt's avatar
JosefBrandt committed
604 605 606 607 608 609
#        print("abundancyList:", abundancyList)
#        print("labelList:", labelList)
#        print("colorList:", colorList)
        self.typeHistogramPlot.updateTypeHistogram(list(zip(abundancyList, labelList, colorList)))
    
    def updateSizeHistogram(self):
610
        #general size histogram
611 612 613
        self.sizeHist_ax.clear()
        self.sizeHist_ax.axis('on')

614
        self.bins = np.logspace(0.1, 3, 20)
JosefBrandt's avatar
 
JosefBrandt committed
615 616
        self.sizes = self.particleContainer.getSizesOfAllParticles()
#        self.sizes = [i[0] if np.isnan(i[2]) else i[2] for i in self.datastats.getParticleStats()]      #extract long size (if ellipse fit is nan -> box fit)
617 618 619 620 621 622 623 624 625 626 627 628 629 630 631 632
        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')
            
        #get selected boxes
JosefBrandt's avatar
 
JosefBrandt committed
633 634 635 636 637 638 639 640 641
        selectedTypes = []
        for checkbox in self.polymerCheckBoxes:
            if checkbox.isChecked() == True:
                selectedTypes.append(checkbox.text())
        
        for polymType in selectedTypes:
            sizes = self.particleContainer.getSizesOfParticleType(polymType)
#            sizes = [self.sizes[index] for index in range(len(self.sizes)) 
#                        if self.datastats.currentPolymers[index] == i]
642
            sizehist = np.histogram(sizes, self.bins)
JosefBrandt's avatar
 
JosefBrandt committed
643
            self.sizeHist_ax.semilogx(self.totalhistx, sizehist[0], label = polymType, color = self.getColorFromName(polymType, base255 = False))    
644 645 646 647 648 649 650 651 652 653 654 655
        
        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()
        
        self.lastSelectedCheckBoxNames = [checkbox.text() for checkbox in self.polymerCheckBoxes if checkbox.isChecked()]
        
     
    def darkenBackground(self):
Hackmet's avatar
Hackmet committed
656
        self.parent.darkenPixmap = self.darkenAct.isChecked()
657
        
Hackmet's avatar
Hackmet committed
658
        if self.darkenAct.isChecked():
659 660 661 662 663 664 665
            self.parent.scene().setBackgroundBrush(QtGui.QColor(5, 5, 5))
            self.parent.item.setOpacity(0.2)
        else:
            self.parent.scene().setBackgroundBrush(QtCore.Qt.darkGray)
            self.parent.item.setOpacity(1)

    def updateColorSeed(self):
666
        text, ok = QtWidgets.QInputDialog.getText(self, 'Color Seed', 'Enter New Seed here', text=self.datastats.colorSeed)
667
        if ok:
668 669
            self.datastats.colorSeed = text
            self.datastats.dataset.colorSeed = text
JosefBrandt's avatar
JosefBrandt committed
670
            self.updateHistograms()
671 672 673
            self.createPolymerOverlay()

    def getColorFromName(self, name, base255=True):
674
        random.seed(self.datastats.colorSeed + name)
675
        hue = random.random()
676
        random.seed((self.datastats.colorSeed + name)*2)
677
        saturation = random.random()/4 + 0.75      #i.e., between 0.75 and 1
678
        random.seed((self.datastats.colorSeed + name)*3)
679 680 681 682 683 684 685 686 687 688
        value = random.random()/5 + 0.8     #i.e., between 0.8 and 1
        color = colorsys.hsv_to_rgb(hue, saturation, value)
        if base255:
            color = list(color)
            for i in range(3):
                color[i] = np.round(color[i]*255)
            color = tuple(color)
        return color
    
    def createPolymerOverlay(self):  
689
        uniquePolymers = self.datastats.getUniquePolymers()
690 691
        if not self.noOverlayAct.isChecked() and self.datastats.indices is not None:
            if len(self.datastats.indices) > 0:
692
                
Hackmet's avatar
Hackmet committed
693
                alpha = (128 if self.transpAct.isChecked() else 255)
694
                #get colors for each polymer type
JosefBrandt's avatar
JosefBrandt committed
695
                colorList = [QtGui.QColor(255, 255, 255, alpha=50)]*len(self.datastats.particleContainer)
696 697
                legendItems = []
                    
698
                for index, indexList in enumerate(self.datastats.indices):
Hackmet's avatar
Hackmet committed
699
                    if self.fullOverlayAct.isChecked() or (self.selOverlayAct.isChecked() and self.polymerCheckBoxes[index].isChecked()):
700
                        color = self.getColorFromName(uniquePolymers[index], base255=True)
701
                        color = QtGui.QColor(color[0], color[1], color[2], alpha=alpha)
702
                        legendItems.append((uniquePolymers[index], color))
703 704 705 706 707 708
                        for i in indexList:
                            colorList[i] = color
            
            self.parent.contouritem.colorList = colorList
            self.parent.contouritem.update()
            
709
            self.parent.imparent.legend.setTextColorItems(legendItems)
710 711 712 713 714
            self.parent.imparent.legend.show()
            
        else:
            self.parent.contouritem.colorList = []
            self.parent.contouritem.update()
715
            self.parent.imparent.legend.setTextColorItems([])
716 717 718
            self.parent.imparent.legend.hide()
            
    def show_hide_labels(self):
Hackmet's avatar
Hackmet committed
719
        hidden = self.hideLabelAct.isChecked()
720 721 722
        for scanIndicator in self.parent.ramanscanitems:
            scanIndicator.hidden = hidden
            scanIndicator.update()
Hackmet's avatar
Hackmet committed
723

724 725
    
    def closeEvent(self, event):
726
        for window in [self.additivePlot, self.importWindow, self.dbWin]:
727 728
            try: window.close()
            except: pass
Hackmet's avatar
Hackmet committed
729
        self.parent.imparent.particelAnalysisAct.setChecked(False)
730 731 732 733
        event.accept()


if __name__ == '__main__':
734
    from ..dataset import DataSet
735 736
    def run():
        app = QtWidgets.QApplication(sys.argv)
737
        meas = ParticleAnalysis(DataSet("dummydata"))
738
        meas.showMaximized()
739
        return app.exec_()
740 741
    
    run()