Merge remote-tracking branch 'origin/RefactoringAnalysisModules' into RefactoringAnalysisModules (ca1b48a0) · Commits · GEPARD / GEPARD

analysis/particleCharacterization.py

+1 −4

Original line number	Diff line number	Diff line
		@@ -74,10 +74,7 @@ def getParticleColor(imgRGB, colorClassifier=None):
		def getParticleShape(contour, particleHeight, shapeClassifier=None):
		if shapeClassifier is None:
		shapeClassifier = ShapeClassifier()
		try:
		shape = shapeClassifier.classifyShape(contour, particleHeight)
		except InvalidParticleError:
		raise
		return shape

		def getParticleHeight(contour, dataset):

analysis/particleClassification/shapeClassification.py

+2 −8

Original line number	Diff line number	Diff line
		@@ -50,10 +50,7 @@ class BaseShape(object):

		self.solidity = area/hull_area

		try:
		long, short = self.getEllipseOrBoxLongAndShortSize()
		except InvalidParticleError:
		raise InvalidParticleError
		self.aspectRatio = long/short

		avgLength = (long+short)/2
		@@ -138,10 +135,7 @@ class ShapeClassifier(object):
		newShape = BaseShape()
		newShape.contour = contour
		newShape.height = particleHeight
		try:
		newShape.getParticleCharacteristics()
		except InvalidParticleError:
		raise InvalidParticleError

		mostFittingCriteria = 0
		bestFittingShape = 'unknown'

analysis/particleContainer.py

+8 −14

Original line number	Diff line number	Diff line
		@@ -134,23 +134,17 @@ class ParticleContainer(object):

		def applyAssignmentListToParticleMeasurements(self, assignmentList):
		'''AssignmentList is list of spectra assignments in order of spectra indices'''
		indicesOfTransferredAssignments = [None]*len(assignmentList)
		for particle in self.particles:
		for meas in particle.getMeasurements():
		assert len(assignmentList) == len(self.measurements), f'assertion error in assignment of results: {len(assignmentList)} results for {len(self.measurements)} spectra...'
		for meas in self.measurements:
		scanIndex = meas.getScanIndex()
		meas.setAssignment(assignmentList[scanIndex])
		indicesOfTransferredAssignments[scanIndex] = scanIndex
		assert not None in indicesOfTransferredAssignments

		def applyHQIListToParticleMeasurements(self, hqiList):
		'''HQI-List is list of spectra hqis in order of spectra indices'''
		indicesOfTransferredHQIs = [None]*len(hqiList)
		for particle in self.particles:
		for meas in particle.getMeasurements():
		assert len(hqiList) == len(self.measurements), f'assertion error in assignment of hqis: {len(hqiList)} results for {len(self.measurements)} spectra...'
		for meas in self.measurements:
		scanIndex = meas.getScanIndex()
		meas.setHQI(hqiList[scanIndex])
		indicesOfTransferredHQIs[scanIndex] = scanIndex
		assert not None in indicesOfTransferredHQIs

		def reassignParticleToAssignment(self, particleIndex, newAssignment):
		particle = self.getParticleOfIndex(particleIndex)

sampleview.py

+20 −23

Original line number	Diff line number	Diff line
		@@ -81,7 +81,7 @@ class SampleView(QtWidgets.QGraphicsView):
		self.boundaryitems = [[],[]]
		self.scanitems = []
		self.ramanscanitems = []
		self.particleInfoBoxes = []
		self.particleInfoBox = None
		self.imgdata = None
		self.isblocked = False
		self.contourItems = []
		@@ -387,26 +387,19 @@ class SampleView(QtWidgets.QGraphicsView):
		cnt.update()
		if cnt.particleIndex not in self.selectedParticleIndices:
		self.selectedParticleIndices.append(cnt.particleIndex)
		addParticleInfoBox(cnt.particleIndex)
		# addParticleInfoBox(cnt.particleIndex)

		def removeContourFromSelection(cnt):
		cnt.isSelected = False
		cnt.update()
		self.selectedParticleIndices.remove(cnt.particleIndex)
		removeParticleInfoBox(cnt.particleIndex)
		# removeParticleInfoBox(cnt.particleIndex)

		def addParticleInfoBox(index):
		newInfoBox = ParticleInfo(self.dataset.particleContainer.getParticleOfIndex(cnt.particleIndex))
		self.particleInfoBoxes.append(newInfoBox)
		self.scene().addItem(newInfoBox)
		self.update()

		def removeParticleInfoBox(index):
		for infoBox in self.particleInfoBoxes:
		if infoBox.particle.index == index:
		self.scene().removeItem(infoBox)
		self.particleInfoBoxes.remove(infoBox)
		self.update()
		def updateParticleInfoBox(index):
		if self.particleInfoBox is not None:
		self.scene().removeItem(self.particleInfoBox)
		self.particleInfoBox = ParticleInfo(self.dataset.particleContainer.getParticleOfIndex(index))
		self.scene().addItem(self.particleInfoBox)

		p = self.mapToScene(event.pos())
		p = QtCore.QPointF(p.x(), p.y())
		@@ -428,7 +421,12 @@ class SampleView(QtWidgets.QGraphicsView):
		cnt.update()
		if cnt.particleIndex in self.selectedParticleIndices:
		self.selectedParticleIndices.remove(cnt.particleIndex)
		removeParticleInfoBox(cnt.particleIndex)

		if len(self.selectedParticleIndices) > 0:
		updateParticleInfoBox(self.selectedParticleIndices[-1])
		else:
		self.scene().removeItem(self.particleInfoBox)
		self.particleInfoBox = None

		self.update()

		@@ -499,7 +497,7 @@ class SampleView(QtWidgets.QGraphicsView):
		self.item.setOpacity(1)

		else:
		self.item.setPiparticleInfoBoxesxmap(QtGui.QPixmap())
		self.item.setPiparticleInfoBoxxmap(QtGui.QPixmap())
		if self.mode == "OpticalScan":
		for i, p in zip(self.dataset.fitindices, self.dataset.fitpoints):
		p = self.dataset.mapToPixel(p, mode=microscope_mode, force=True)
		@@ -616,12 +614,11 @@ class SampleView(QtWidgets.QGraphicsView):
		self.contourItems[index].isSelected = True
		self.selectedParticleIndices =[index]

		for infoBox in self.particleInfoBoxes:
		self.scene().removeItem(infoBox)
		if self.particleInfoBox is not None:
		self.scene().removeItem(self.particleInfoBox)

		newInfoBox = ParticleInfo(self.dataset.particleContainer.getParticleOfIndex(index))
		self.particleInfoBoxes = [newInfoBox]
		self.scene().addItem(newInfoBox)
		self.particleInfoBox = ParticleInfo(self.dataset.particleContainer.getParticleOfIndex(index))
		self.scene().addItem(self.particleInfoBox)
		self.update()

		def centerOnRamanIndex(self, index, centerOn=True, highlightIndex=True):