Before refactoring analysis navigation.... (83cdeb70) · Commits · GEPARD / GEPARD

analysis/analysisview.py

+103 −53

Original line number	Diff line number	Diff line
		@@ -44,8 +44,8 @@ except:


		class ParticleAnalysis(QtWidgets.QMainWindow):
		def __init__(self, dataset, parent=None):
		super(ParticleAnalysis, self).__init__(parent)
		def __init__(self, dataset, viewparent=None):
		super(ParticleAnalysis, self).__init__(viewparent)
		self.setGeometry(100, 100, 1680, 1050)
		self.setWindowTitle('Results of polymer analysis')
		self.layout = QtWidgets.QHBoxLayout()
		@@ -53,7 +53,7 @@ class ParticleAnalysis(QtWidgets.QMainWindow):
		self.widget.setLayout(self.layout)
		self.setCentralWidget(self.widget)

		self.parent = parent
		self.viewparent = viewparent
		self.dataset = dataset
		self.particleContainer = dataset.particleContainer
		self.editor = ParticleEditor(self.particleContainer, self)
		@@ -114,21 +114,18 @@ class ParticleAnalysis(QtWidgets.QMainWindow):
		self.navigationGroup.setDisabled(True)
		navigationLayout = QtWidgets.QHBoxLayout()
		self.specNumberSelector = QtWidgets.QSpinBox()
		self.specNumberSelector.setMinimumWidth(150)
		self.specNumberSelector.setMinimumWidth(100)
		self.specNumberSelector.setMinimum(1)
		self.specNumberSelector.setMaximum(1E6)
		self.jumpToSpecBtn = QtWidgets.QPushButton('Jump To Spectrum of Number:')
		self.jumpToSpecBtn.released.connect(self.jumpToSpectrumOfNumber)
		self.jumpToSpecBtn.released.connect(self.jumpToIndicatedSpectrum)

		self.typeSelectorCombo = QtWidgets.QComboBox()
		self.typeSelectorCombo.currentIndexChanged.connect(self.displayNewPolymerType)
		self.typeSelectorCombo.setMinimumWidth(150)
		self.particleSelector = QtWidgets.QSpinBox()
		self.particleSelector.valueChanged.connect(self.updateSpecPlotToSelectedParticle)
		self.particleNumberLabel = QtWidgets.QLabel('of xx particles; ')

		self.spectrumSelector = QtWidgets.QSpinBox()
		self.spectrumSelector.valueChanged.connect(self.selectSpectrum)
		self.spectrumNumberLabel = QtWidgets.QLabel('of xx spectra')
		for spinbox in [self.particleSelector, self.spectrumSelector]:
		spinbox.setMinimum(1)
		@@ -220,11 +217,10 @@ class ParticleAnalysis(QtWidgets.QMainWindow):
		self.createMenus()
		self.applyHQIThresholdToResults()
		self.createHistogramData()
		self.updateDisplays()
		self.initializeSpecPlot()
		self.displayNewPolymerType()
		self.updateSpecPlotToSelectedParticle()
		# self.createPolymerOverlay()
		self.updateHistogramsAndContours()

		def createActions(self):
		self.loadTrueMatchAct = QtWidgets.QAction("Load &TrueMatch Results", self)
		@@ -253,6 +249,9 @@ class ParticleAnalysis(QtWidgets.QMainWindow):
		self.seedAct = QtWidgets.QAction("&Set Color Seed", self)
		self.seedAct.triggered.connect(self.updateColorSeed)

		self.removeTinyParticlesAct = QtWidgets.QAction("&Remove not unknown Particles < 1 µm")
		self.removeTinyParticlesAct.triggered.connect(self.removeTinyParticles)

		self.databaseAct = QtWidgets.QAction("&ManageDatabase", self)
		self.databaseAct.triggered.connect(self.launchDBManager)

		@@ -272,7 +271,7 @@ class ParticleAnalysis(QtWidgets.QMainWindow):
		self.overlayActGroup = QtWidgets.QActionGroup(self.dispMenu)
		self.overlayActGroup.setExclusive(True)
		self.overlayActGroup.triggered.connect(self.updateContourColors)
		self.overlayActGroup.triggered.connect(self.updateDisplays)
		self.overlayActGroup.triggered.connect(self.updateHistogramsAndContours)

		for act in [self.noOverlayAct, self.selOverlayAct, self.fullOverlayAct]:
		self.dispMenu.addAction(act)
		@@ -281,8 +280,9 @@ class ParticleAnalysis(QtWidgets.QMainWindow):
		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.toolMenu = QtWidgets.QMenu("&Tools")
		self.toolMenu.addAction(self.removeTinyParticlesAct)
		self.toolMenu.addAction(self.databaseAct)

		self.exportMenu = QtWidgets.QMenu("&Export", self)
		self.exportMenu.addAction(self.expExcelAct)
		@@ -290,7 +290,7 @@ class ParticleAnalysis(QtWidgets.QMainWindow):

		self.menuBar().addMenu(self.importMenu)
		self.menuBar().addMenu(self.dispMenu)
		self.menuBar().addMenu(self.refMenu)
		self.menuBar().addMenu(self.toolMenu)
		self.menuBar().addMenu(self.exportMenu)

		def launchDBManager(self):
		@@ -328,7 +328,7 @@ class ParticleAnalysis(QtWidgets.QMainWindow):
		self.dataset.resultParams['minHQI'] = hqi
		self.dataset.save()
		self.createHistogramData()
		self.updateDisplays()
		self.updateHistogramsAndContours()

		def createHistogramData(self):
		###Handle Checkboxes for all polymers...
		@@ -342,7 +342,7 @@ class ParticleAnalysis(QtWidgets.QMainWindow):
		del i
		self.showTotalSelector.setParent(None)
		self.showTotalSelector.setDisabled(False)
		self.showTotalSelector.stateChanged.connect(self.updateDisplays)
		self.showTotalSelector.stateChanged.connect(self.updateHistogramsAndContours)

		del self.resultCheckBoxes
		del self.resultCheckBoxesLayout
		@@ -369,7 +369,7 @@ class ParticleAnalysis(QtWidgets.QMainWindow):
		if polymer in self.lastSelectedCheckBoxNames:
		self.polymerCheckBoxes[index].setChecked(True)

		self.polymerCheckBoxes[index].stateChanged.connect(self.updateDisplays)
		self.polymerCheckBoxes[index].stateChanged.connect(self.updateHistogramsAndContours)

		self.resultCheckBoxesLayout.addStretch()
		self.resultCheckBoxes.setLayout(self.resultCheckBoxesLayout)
		@@ -381,10 +381,10 @@ class ParticleAnalysis(QtWidgets.QMainWindow):
		self.expSQLAct.setDisabled(False)

		self.navigationGroup.setEnabled(True)
		self.typeSelectorCombo.currentIndexChanged.disconnect()
		# self.typeSelectorCombo.currentIndexChanged.disconnect()
		self.typeSelectorCombo.clear()
		self.typeSelectorCombo.addItems(uniquePolymers)
		self.typeSelectorCombo.currentIndexChanged.connect(self.displayNewPolymerType)
		# self.typeSelectorCombo.currentIndexChanged.connect(self.displayNewPolymerType)

		self.polymerIndex = self.typeSelectorCombo.currentIndex()
		# if self.lastSpectrumInFocus is not None:
		@@ -395,7 +395,7 @@ class ParticleAnalysis(QtWidgets.QMainWindow):
		# print('displaying new type with resetting index')
		# self.displayNewPolymerType()

		def updateDisplays(self):
		def updateHistogramsAndContours(self):
		self.createHistogramData()
		t0 = time.time()
		self.updateTypeHistogram()
		@@ -468,12 +468,10 @@ class ParticleAnalysis(QtWidgets.QMainWindow):

		self.lastSelectedCheckBoxNames = self.getSelectedPolymers()

		def updateSpecPlot(self, centerOn=True, highlightContour=True):
		def updateSpecPlot(self):
		particleSize = self.particleContainer.getSizeOfParticleByIndex(self.currentParticleIndex)
		hqi = self.particleContainer.getHQIOfSpectrumIndex(self.currentSpectrumIndex)
		self.specPlot.updateParticleSpectrum(self.currentSpectrumIndex, particleSize, hqi)
		self.parent.centerOnRamanIndex(self.currentSpectrumIndex, centerOn=centerOn, highlightContour=highlightContour) #TODO: is this reasonable to do in that way???
		self.parent.highLightRamanIndex(self.currentSpectrumIndex)
		# self.lastSpectrumInFocus = self.currentSpectrumIndex

		if self.refSelector.isEnabled() and self.refSelector.currentText() != '':
		@@ -482,7 +480,7 @@ class ParticleAnalysis(QtWidgets.QMainWindow):
		self.specPlot.updateReferenceSpectrum(ref[:, 0], ref[:, 1])

		def updateContourColors(self):
		contours = self.parent.contourItems
		contours = self.viewparent.contourItems
		alpha = (64 if self.transpAct.isChecked() else 255)
		selectedPolymers = self.getSelectedPolymers()

		@@ -505,16 +503,31 @@ class ParticleAnalysis(QtWidgets.QMainWindow):
		color = getColorFromNameWithSeed(polymer, self.dataset.colorSeed)
		color = QtGui.QColor(color[0], color[1], color[2], 255)
		legendItems.append((polymer, color))
		self.parent.updateLegend(legendItems)
		self.viewparent.updateLegend(legendItems)


		def getSelectedPolymers(self):
		return [checkbox.text() for checkbox in self.polymerCheckBoxes if checkbox.isChecked()]

		def jumpToSpectrumOfNumber(self):
		def getSpecIndexFromBoxesAndJumpThere(self):
		self.currentSpectrumIndex = self.getSpectrumIndexFromSpectrumSelector()
		self.specNumberSelector.setValue(self.currentSpectrumIndex+1)
		self.jumpToIndicatedSpectrum()

		def jumpToIndicatedSpectrum(self, centerOn=True):
		print('jumping to spec index with centerOn', centerOn)
		###disconnect Boxes
		try:
		self.typeSelectorCombo.currentIndexChanged.disconnect()
		self.particleSelector.valueChanged.disconnect()
		self.spectrumSelector.valueChanged.disconnect()
		except TypeError:
		pass #i.e., there was no connection

		specIndex = self.specNumberSelector.value()-1
		assert specIndex is not None
		print('specIndex', specIndex)
		partIndex = self.particleContainer.getParticleIndexContainingSpecIndex(specIndex)
		print('partIndex', partIndex)
		assignment = self.particleContainer.getParticleAssignmentByIndex(partIndex)
		self.typeSelectorCombo.setCurrentText(assignment)

		@@ -524,18 +537,26 @@ class ParticleAnalysis(QtWidgets.QMainWindow):
		specIndices = self.particleContainer.getSpectraIndicesOfParticle(partIndex)
		self.spectrumSelector.setValue(specIndices.index(specIndex)+1)

		if centerOn:
		self.viewparent.centerOnRamanIndex(self.currentSpectrumIndex, centerOn=True, highlightContour=True)
		self.viewparent.highLightContour(self.getParticleIndexFromParticleSelector())

		def selectParticleOfIndex(self, particleIndex, centerOn=True):
		assignment = self.particleContainer.getParticleAssignmentByIndex(particleIndex)
		self.typeSelectorCombo.setCurrentText(assignment)
		###connect Boxes
		self.typeSelectorCombo.currentIndexChanged.connect(self.displayNewPolymerType)
		self.typeSelectorCombo.currentIndexChanged.connect(self.getSpecIndexFromBoxesAndJumpThere)
		# self.particleSelector.valueChanged.connect(self.updateSpecPlotToSelectedParticle)
		self.particleSelector.valueChanged.connect(self.getSpecIndexFromBoxesAndJumpThere)
		# self.spectrumSelector.valueChanged.connect(self.selectSpectrum)
		self.spectrumSelector.valueChanged.connect(self.getSpecIndexFromBoxesAndJumpThere)
		self.displayNewPolymerType()
		self.updateSpecPlotToSelectedParticle()
		self.updateHistogramsAndContours()

		self.particleSelector.valueChanged.disconnect()
		particleIndices = self.particleContainer.getIndicesOfParticleType(assignment)
		self.particleSelector.setValue(particleIndices.index(particleIndex)+1)
		self.particleSelector.valueChanged.connect(self.updateSpecPlotToSelectedParticle)

		self.updateSpecPlotToSelectedParticle(resetSpectrumCount=True, centerOn=centerOn)
		def selectParticleOfIndex(self, particleIndex, centerOn=False):
		specIndices = self.particleContainer.getSpectraIndicesOfParticle(particleIndex)
		self.specNumberSelector.setValue(specIndices[0]+1)
		self.jumpToIndicatedSpectrum(centerOn=centerOn)

		def displayNewPolymerType(self, resetCurrentIndex=True):
		polymerName = self.typeSelectorCombo.currentText()
		@@ -551,9 +572,9 @@ class ParticleAnalysis(QtWidgets.QMainWindow):
		self.spectrumSelector.setMaximum(numSpectra)
		self.spectrumNumberLabel.setText(f'of {numSpectra} Spectra')
		self.currentSpectrumIndex = self.getSpectrumIndexFromSpectrumSelector()
		self.updateSpecPlot(centerOn=False)
		self.updateSpecPlot()

		def updateSpecPlotToSelectedParticle(self, resetSpectrumCount=True, centerOn=True):
		def updateSpecPlotToSelectedParticle(self, resetSpectrumCount=True):
		polymerName = self.typeSelectorCombo.currentText()
		if polymerName != '':
		self.currentParticleIndex = self.getParticleIndexFromParticleSelector()
		@@ -563,13 +584,13 @@ class ParticleAnalysis(QtWidgets.QMainWindow):
		if resetSpectrumCount:
		self.spectrumSelector.setValue(1)

		self.currentSpectrumIndex = self.getSpectrumIndexFromSpectrumSelector()
		self.updateSpecPlot(centerOn)

		def selectSpectrum(self):
		self.currentSpectrumIndex = self.getSpectrumIndexFromSpectrumSelector()
		self.updateSpecPlot()

		# def selectSpectrum(self):
		# self.currentSpectrumIndex = self.getSpectrumIndexFromSpectrumSelector()
		# self.updateSpecPlot()

		def getSpectrumIndexFromSpectrumSelector(self):
		specIndicesOfParticle = self.particleContainer.getSpectraIndicesOfParticle(self.currentParticleIndex)
		try:
		@@ -582,24 +603,53 @@ class ParticleAnalysis(QtWidgets.QMainWindow):
		return particleIndicesOfType[self.particleSelector.value()-1]

		def darkenBackground(self):
		self.parent.darkenPixmap = self.darkenAct.isChecked()
		self.viewparent.darkenPixmap = self.darkenAct.isChecked()

		if self.darkenAct.isChecked():
		self.parent.scene().setBackgroundBrush(QtGui.QColor(5, 5, 5))
		self.parent.item.setOpacity(0.2)
		self.viewparent.scene().setBackgroundBrush(QtGui.QColor(5, 5, 5))
		self.viewparent.item.setOpacity(0.2)
		else:
		self.parent.scene().setBackgroundBrush(QtCore.Qt.darkGray)
		self.parent.item.setOpacity(1)
		self.viewparent.scene().setBackgroundBrush(QtCore.Qt.darkGray)
		self.viewparent.item.setOpacity(1)

		def updateColorSeed(self):
		text, ok = QtWidgets.QInputDialog.getText(self, 'Color Seed', 'Enter New Seed here', text=self.dataset.colorSeed)
		if ok:
		self.dataset.colorSeed = text
		self.updateDisplays()
		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):
		self.selectParticleOfIndex(partIndex, centerOn=True)
		reply = QtWidgets.QMessageBox.question(self, f'Particle {index+1} of {numIndices}',
		"Do you want to remove that particle?",
		QtWidgets.QMessageBox.Yes \|
		QtWidgets.QMessageBox.No \| QtWidgets.QMessageBox.Cancel, QtWidgets.QMessageBox.No)

		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()


		def show_hide_labels(self):
		hidden = self.hideLabelAct.isChecked()
		for scanIndicator in self.parent.ramanscanitems:
		for scanIndicator in self.viewparent.ramanscanitems:
		scanIndicator.hidden = hidden
		scanIndicator.update()

		@@ -615,7 +665,7 @@ class ParticleAnalysis(QtWidgets.QMainWindow):
		for window in [self.importWindow, self.dbWin]:
		try: window.close()
		except: pass
		self.parent.imparent.particelAnalysisAct.setChecked(False)
		self.viewparent.imparent.particelAnalysisAct.setChecked(False)
		event.accept()

analysis/particleInfo.py

+0 −3

Original line number	Diff line number	Diff line
		@@ -254,9 +254,6 @@ class ParticleContainer(object):
		for index in sorted(indexList, reverse=True):
		particle = self.getParticleOfIndex(index) #just for asserting to have the correct particle!
		del self.particles[index]
		# particle = self.getParticleOfIndex(index)
		# print('removing particle of index', index)
		# self.particles.remove(particle)

		def resetParticleIndices(self):
		for newIndex, particle in enumerate(self.particles):

analysis/particlePainter.py

+1 −0

Original line number	Diff line number	Diff line
		@@ -164,3 +164,4 @@ class ParticlePainter(QtWidgets.QGraphicsItem):




		No newline at end of file

analysis/particleeditor.py

+3 −1

Original line number	Diff line number	Diff line
		@@ -105,7 +105,7 @@ class ParticleContextMenu(QtWidgets.QMenu):


		class ParticleEditor(QtCore.QObject):
		particleContoursChanged = QtCore.pyqtSignal()
		# particleContoursChanged = QtCore.pyqtSignal()
		particleAssignmentChanged = QtCore.pyqtSignal()
		def __init__(self, viewparent, particleContainer):
		super(ParticleEditor, self).__init__()
		@@ -146,6 +146,7 @@ class ParticleEditor(QtCore.QObject):
		self.viewparent.resetContourIndices()
		self.viewparent.addParticleContour(newContour, len(self.viewparent.contourItems))

		self.particleAssignmentChanged.emit()
		#TODO: INCLUDE SANITY CHECK!!!!!!!!!

		@QtCore.pyqtSlot(list, str)
		@@ -177,6 +178,7 @@ class ParticleEditor(QtCore.QObject):
		for ind in self.storedIndices:
		self.viewparent.removeParticleContour(ind)

		self.particleAssignmentChanged.emit()
		self.viewparent.resetContourIndices()
		self.viewparent.addParticleContour(newContour, len(self.viewparent.contourItems))

sampleview.py

+14 −16

Original line number	Diff line number	Diff line
		@@ -270,14 +270,14 @@ class SampleView(QtWidgets.QGraphicsView):
		if self.particleEditor is None:
		self.particleEditor = ParticleEditor(self, self.dataset.particleContainer)
		#try disconnecting the signals. If they are connected multiple times, the functions will run accordingly...
		tryDisconnectingSignal(self.particleEditor.particleContoursChanged)
		# tryDisconnectingSignal(self.particleEditor.particleContoursChanged)
		tryDisconnectingSignal(self.particleEditor.particleAssignmentChanged)

		self.particleEditor.particleContoursChanged.connect(self.resetParticleContours)
		# self.particleEditor.particleContoursChanged.connect(self.resetParticleContours)

		if self.analysiswidget is not None:
		self.particleEditor.particleContoursChanged.connect(self.analysiswidget.updateDisplays)
		self.particleEditor.particleAssignmentChanged.connect(self.analysiswidget.updateDisplays)
		# self.particleEditor.particleContoursChanged.connect(self.analysiswidget.updateHistogramsAndContours)
		self.particleEditor.particleAssignmentChanged.connect(self.analysiswidget.updateHistogramsAndContours)

		def setMicroscopeMode(self):
		if self.ramanSwitchNeeded:
		@@ -320,7 +320,7 @@ class SampleView(QtWidgets.QGraphicsView):
		if event.button()==QtCore.Qt.MiddleButton:
		self.drag = event.pos()

		elif self.particlePainter is None:
		if self.particlePainter is None:
		if event.button()==QtCore.Qt.LeftButton:
		self.checkForContourSelection(event)

		@@ -336,7 +336,7 @@ class SampleView(QtWidgets.QGraphicsView):
		p0 = self.mapToScene(event.pos())
		super(SampleView, self).mousePressEvent(event)

		elif self.particlePainter is not None:
		else:
		self.particlePainter.mousePressEvent(event)

		def mouseMoveEvent(self, event):
		@@ -412,14 +412,13 @@ class SampleView(QtWidgets.QGraphicsView):

		for index, cnt in enumerate(self.contourItems):
		if cnt.polygon.containsPoint(p, QtCore.Qt.OddEvenFill): #clicked on particle

		if not event.modifiers()==QtCore.Qt.ShiftModifier:
		addContourToSelection(cnt)
		self.analysiswidget.selectParticleOfIndex(cnt.particleIndex, centerOn=False)
		self.analysiswidget.selectParticleOfIndex(cnt.particleIndex)
		else:
		if cnt.particleIndex not in self.selectedParticleIndices:
		addContourToSelection(cnt)
		self.analysiswidget.selectParticleOfIndex(cnt.particleIndex, centerOn=False)
		self.analysiswidget.selectParticleOfIndex(cnt.particleIndex)
		elif cnt.particleIndex in self.selectedParticleIndices:
		removeContourFromSelection(cnt)

		@@ -587,13 +586,6 @@ class SampleView(QtWidgets.QGraphicsView):
		if self.dataset is not None:
		for particleIndex, contour in enumerate(self.dataset.particleContainer.getParticleContours()):
		self.addParticleContour(contour, particleIndex)
		# newCnt = SegmentationContour(self, contour)
		# newCnt.setIndex(particleIndex)
		# assignment = self.dataset.particleContainer.getParticleAssignmentByIndex(particleIndex)
		# color = getColorFromNameWithSeed(assignment, self.dataset.colorSeed)
		# newCnt.setColor(QtGui.QColor(color[0], color[1], color[2], 255))
		# self.contourItems.append(newCnt)
		# self.scene().addItem(newCnt)
		self.update()
		print('resetted contours: {} ms'.format(round((time.time()-t0)*1000)))

		@@ -624,6 +616,12 @@ class SampleView(QtWidgets.QGraphicsView):
		item.setHighLight(False)
		self.ramanscanitems[index].setHighLight(True)

		def highLightContour(self, index):
		for contour in self.contourItems:
		contour.isSelected = False
		self.contourItems[index].isSelected = True


		def centerOnRamanIndex(self, index, centerOn=True, highlightContour=True):
		if centerOn:
		self.centerOn(self.ramanscanitems[index])