Excel and SQL Export working (hotfix) (90287adf) · Commits · GEPARD / GEPARD

analysis/analysisview.py

+12 −6

Original line number	Diff line number	Diff line
		@@ -160,11 +160,13 @@ class ParticleAnalysis(QtWidgets.QMainWindow):
		optionsLayout = QtWidgets.QFormLayout()

		self.hqiSpinBox = QtWidgets.QDoubleSpinBox()
		self.hqiSpinBox.setValue(self.dataset.resultParams['minHQI'])
		self.hqiSpinBox.setDecimals(1)
		self.hqiSpinBox.setMinimum(0)
		self.hqiSpinBox.setMaximum(100)
		self.hqiSpinBox.setMaximumWidth(100)
		minHQI = self.dataset.resultParams['minHQI']
		if minHQI is not None:
		self.hqiSpinBox.setValue(minHQI)
		self.hqiSpinBox.valueChanged.connect(self.applyHQIThresholdToResults)
		optionsLayout.addRow(QtWidgets.QLabel('minimum HQI:'), self.hqiSpinBox)

		@@ -198,9 +200,7 @@ class ParticleAnalysis(QtWidgets.QMainWindow):
		self.layout.addLayout(self.menuLayout)
		self.layout.addLayout(viewLayout)

		minHQI = self.dataset.resultParams['minHQI']
		if minHQI is not None:
		self.hqiSpinBox.setValue(minHQI)


		self.createActions()
		self.createMenus()
		@@ -611,7 +611,13 @@ class ParticleAnalysis(QtWidgets.QMainWindow):
		expWin.exec()

		def exportToSQL(self):
		sqlexp = SQLExport(self.particleContainer, self)
		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()

		def closeEvent(self, event):

analysis/excelexport.py

+22 −28

Original line number	Diff line number	Diff line
		@@ -45,7 +45,6 @@ class ExpExcelDialog(QtWidgets.QDialog):
		self.exportOptions = ['Polymer Type (mandatory)', 'Long Size (µm)', 'Short Size (µm)', 'Area (µm²)', 'HQI', 'Size Classes']
		self.checkBoxes = []
		self.sizeClasses = [5, 10, 20, 50, 100, 1e6]
		self.directory = self.dataset.path

		for index, option in enumerate(self.exportOptions):
		self.checkBoxes.append(QtWidgets.QCheckBox(self))
		@@ -76,8 +75,8 @@ class ExpExcelDialog(QtWidgets.QDialog):
		def toExcel(self):
		requiredcolumns = []
		uniquePolymers = self.particleContainer.getUniquePolymers()
		polymers = self.particleContainer.getListOfParticleAssignments()
		sizes = self.particleContainer.getSizesOfAllParticles()
		polymers = np.array(self.particleContainer.getListOfParticleAssignments())
		sizes = np.array(self.particleContainer.getSizesOfAllParticles())


		for box in self.checkBoxes:
		@@ -85,13 +84,13 @@ class ExpExcelDialog(QtWidgets.QDialog):
		if box.text() != 'Size Classes':
		requiredcolumns.append(box.text())
		if box.text() == 'Long Size (µm)':
		longSizes = sizes
		longSizes = np.round(sizes)
		elif box.text() == 'Short Size (µm)':
		shortSizes = self.particleContainer.getShortSizesOfAllParticles()
		shortSizes = np.round(np.array(self.particleContainer.getShortSizesOfAllParticles()))
		elif box.text() == 'HQI':
		hqis = self.particleContainer.getListOfHighestHQIs()
		hqis = np.array(self.particleContainer.getListOfHighestHQIs())
		elif box.text() == 'Area (µm²)':
		areas = self.particleContainer.getAreasOfAllParticles()
		areas = np.array(self.particleContainer.getAreasOfAllParticles())

		else:
		requiredcolumns.append('0 - 5 µm')
		@@ -101,13 +100,12 @@ class ExpExcelDialog(QtWidgets.QDialog):
		requiredcolumns.append('50 - 100 µm')
		requiredcolumns.append('> 100 µm')

		finalData = np.zeros((polymers.shape[0],len(requiredcolumns)-1))
		polymertypes = [""]*polymers.shape[0]
		finalData = np.zeros((len(polymers),len(requiredcolumns)-1))
		polymertypes = [""]*len(polymers)
		rowindex = 0
		for polymer in uniquePolymers:
		indices = self.particleContainer.getgetIndicesOfParticleType(polymer)
		indices = polymers == polymer
		numentries = int(np.sum(indices))
		print("Num:", numentries)
		sys.stdout.flush()

		for colindex, column in enumerate(requiredcolumns):
		@@ -130,7 +128,7 @@ class ExpExcelDialog(QtWidgets.QDialog):
		upLimit = self.sizeClasses[classindex]
		if classindex == 0: lowLimit = 0
		else: lowLimit = self.sizeClasses[classindex-1]
		curSize = self.sizes[dataindex]
		curSize = sizes[dataindex]

		if curSize > lowLimit and curSize <= upLimit:
		finalData[rowindex+tableindex, numPrevCols + classindex] = np.int(1)
		@@ -140,15 +138,11 @@ class ExpExcelDialog(QtWidgets.QDialog):
		rowindex = rowindex + numentries

		#dump into excel file
		xlsname = self.directory + '//' + self.xlsFileName.text() + '.xlsx'
		print('exporting excel to:\n file name: {} in directory: {}'.format(self.xlsFileName.text(), self.directory))
		validFileName = False
		xlsname = os.path.join(self.dataset.path, f'{self.xlsFileName.text()}.xlsx')
		print('exporting excel to:\n file name: {} in directory: {}'.format(self.xlsFileName.text(), self.dataset.path))
		incr = 1
		while not validFileName:
		if not os.path.exists(xlsname):
		validFileName = True
		else:
		xlsname = self.directory + '//' + self.xlsFileName.text() + ' {}.xlsx'.format(incr)
		while os.path.exists(xlsname):
		xlsname = os.path.join(self.dataset.path, f'{self.xlsFileName.text()} {incr}.xlsx')
		incr += 1

		writer = pd.ExcelWriter(xlsname, engine = 'xlsxwriter')
		@@ -159,20 +153,20 @@ class ExpExcelDialog(QtWidgets.QDialog):
		if '> 100 µm' in requiredcolumns:
		#generate particle statistics report
		header = ['0 - 5 µm', '5 - 10 µm', '10 - 20 µm', '20 - 50 µm', '50 - 100 µm', '> 100 µm']
		index = np.unique(self.polymers)
		particleclasses = []

		for polymer in index:
		indices = np.where(self.polymers == polymer)[0]
		sortind = np.searchsorted([5,10,20,50,100], self.sizes[indices], 'right')
		for polymer in uniquePolymers:
		indices = self.particleContainer.getIndicesOfParticleType(polymer)
		sortind = np.searchsorted([5,10,20,50,100], sizes[indices], 'right')
		classes = np.bincount(sortind, minlength=6)
		particleclasses.append(classes)

		particleclasses = np.array(particleclasses)
		report = pd.DataFrame(np.array(particleclasses), columns=header,
		dtype=int)
		report.insert(0, 'Polymer Type', index)
		report.insert(0, 'Polymer Type', uniquePolymers)
		report.insert(len(report.columns), 'Sum total', particleclasses.sum(axis=1))
		report.to_excel(writer, sheet_name = 'Particle Statistics', index=False)
		writer.save()
		self.accept()
		QtWidgets.QMessageBox.about(self, 'Particles succesfully exported', 'List saved to\n' + str(xlsname))
		No newline at end of file

analysis/loadresults.py

+6 −33

Original line number	Diff line number	Diff line
		@@ -44,31 +44,6 @@ class LoadTrueMatchResults(QtWidgets.QDialog):
		self.loadBtn.resize(self.loadBtn.sizeHint())
		self.loadBtn.clicked.connect(self.loadFileManually)

		# optionsLayout = QtWidgets.QFormLayout()
		# self.optionsGroup = QtWidgets.QGroupBox('Compute Options')
		# self.optionsGroup.setDisabled(True)
		#
		# self.label1 = QtWidgets.QLabel('HQI-Threshold:')
		# self.spinbox1 = QtWidgets.QDoubleSpinBox(self)
		# self.spinbox1.valueChanged.connect(self.runCalculations)
		# optionsLayout.addRow(self.label1, self.spinbox1)

		# self.label2 = QtWidgets.QLabel('ComponentThreshold:')
		# self.spinbox2 = QtWidgets.QDoubleSpinBox(self)
		# self.spinbox2.valueChanged.connect(self.updateParentSpinboxes)
		# optionsLayout.addRow(self.label2, self.spinbox2)

		# for box in [self.spinbox1, self.spinbox2]:
		# for box in [self.spinbox1]:
		# box.setValue(50)
		# box.setDecimals(1)
		# box.setSingleStep(5)
		# box.setMinimum(0)
		# box.setMaximum(100)
		## self.spinbox2.setValue(30) #more reasonable...
		#
		# self.optionsGroup.setLayout(optionsLayout)

		self.reviewGroup = QtWidgets.QGroupBox('Review Changes')
		self.reviewGroup.setDisabled(True)
		reviewLayout = QtWidgets.QVBoxLayout()
		@@ -80,7 +55,6 @@ class LoadTrueMatchResults(QtWidgets.QDialog):
		self.reviewGroup.setLayout(reviewLayout)

		self.layout.addWidget(self.loadBtn, 0, 0)
		# self.layout.addWidget(self.optionsGroup, 1, 0)
		self.layout.addWidget(self.reviewGroup, 2, 0)

		self.manualPolymers = {}
		@@ -144,7 +118,12 @@ class LoadTrueMatchResults(QtWidgets.QDialog):
		specName = entry[0]
		indexOpenBracket = specName.find('(')
		indexCloseBracket = specName.find(')')
		specIndex = int(specName[indexOpenBracket+1:indexCloseBracket])
		inbrackets = specName[indexOpenBracket+1:indexCloseBracket]
		try:
		specIndex = int(inbrackets)
		except:
		print(inbrackets)
		raise

		#find yes-flags
		flags = np.where(np.array(entry) == 'yes')[0]
		@@ -204,7 +183,6 @@ class LoadTrueMatchResults(QtWidgets.QDialog):
		if numcomps == 1: #####SINGLE COMPONENT SEARCH
		self.additives = None
		self.addhqis = None
		# self.spinbox2.setEnabled(False)
		for index, entry in enumerate(self.resultList):
		if len(entry) == 0:
		del self.resultList[index]
		@@ -241,11 +219,6 @@ class LoadTrueMatchResults(QtWidgets.QDialog):

		def closeEvent(self, event):
		#TODO: SANITY CHECK FOR DATA CONSISTENCY!!

		# if not self.parent.datastats.saveAnalysisResults(minHQI, compHQI):
		# QtWidgets.QMessageBox.warning(self.parent, 'Error!',
		# 'Data inconsistency after saving!',
		# QtWidgets.QMessageBox.Ok, QtWidgets.QMessageBox.Ok)
		self.parent.setEnabled(True)
		event.accept()

analysis/particleAndMeasurement.py

+6 −4

Original line number	Diff line number	Diff line
		@@ -83,17 +83,19 @@ class Particle(object):
		else:
		print(f'Error, particle size requested, but not yet set.\nParticle Index is {self.index}')
		raise ValueError
		assert size is not None, f'Error, size or particle {self.index} is None'
		return round(size)
		assert size is not None, f'Error, size of particle {self.index} is None'
		return size

		def getShortParticleSize(self):
		if not np.isnan(self.shortSize_ellipse):
		return self.shortSize_ellipse
		size = self.shortSize_ellipse
		elif not np.isnan(self.shortSize_box):
		return self.shortSize_box
		size = self.shortSize_box
		else:
		print(f'Error, particle size requested, but not yet set.\nParticle Index is {self.index}')
		raise ValueError
		assert size is not None, f'Error, short size of particle {self.index} is None'
		return size

		def getNumberOfMeasurements(self):
		return len(self.measurements)

analysis/particleContainer.py

+0 −2

Original line number	Diff line number	Diff line
		@@ -33,7 +33,6 @@ class ParticleContainer(object):
		self.datasetParent = datasetParent
		self.particles = []
		self.measurements = []
		self.spectra = None
		self.inconsistentParticles = []

		self.typeHistogram = None
		@@ -83,7 +82,6 @@ class ParticleContainer(object):

		if spectra is not None:
		np.save(self.datasetParent.getSpectraFileName(), spectra)

		return spectra

		def initializeParticles(self, numParticles):