Tidying up (a8794a3c) · Commits · GEPARD / GEPARD

.gitignore

0 → 100644

+8 −0

Original line number	Diff line number	Diff line

		__pycache__/

		gepard\.cfg

		analysis/database_config\.txt

		*.so

analysis/analysisplots.py

+11 −17

Original line number	Diff line number	Diff line
		@@ -41,7 +41,6 @@ class ParticleIndicator(QtWidgets.QPushButton):

		qp = QtGui.QPainter()
		qp.begin(self)
		#qp.fillRect(self.rect(), QtCore.Qt.white)
		qp.setBrush(QtCore.Qt.white)
		qp.drawRoundedRect(0, 0, width, height, 5. ,5.)
		qp.setPen(self.color)
		@@ -116,7 +115,6 @@ class SpectraPlot(QtWidgets.QGroupBox):
		layout = QtWidgets.QHBoxLayout()
		self.canvas = FigureCanvas(Figure())
		self.spec_axis = self.canvas.figure.subplots()
		self.spec_axis.axis("off")
		self.reference_ax = self.spec_axis.twinx()
		self.canvas.figure.subplots_adjust(left=0.1, top=0.93, bottom=0.15, right=0.9)
		specNavigation = NavigationToolbar(self.canvas, self)
		@@ -127,21 +125,21 @@ class SpectraPlot(QtWidgets.QGroupBox):
		layout.addWidget(self.canvas)
		self.setLayout(layout)

		def loadSpectraAndInitializeSpecPlot(self): #formerly updateData(self)....
		self.spectra = self.dataset.particleContainer.spectra
		assert self.spectra is not None
		def loadSpectraAndInitializeSpecPlot(self):
		self.spectra = self.dataset.particleContainer.getSpectraFromDisk()
		self.canvas.draw()

		def updateParticleSpectrum(self, specIndex, particleSize, hqi):
		if self.spectra is not None:
		def updateParticleSpectrum(self, specIndex, assignment, particleSize, hqi):
		#draw Sample Spectrum
		self.spec_axis.axis("on")
		self.spec_axis.clear()
		self.spec_axis.plot(self.spectra[:, 0], self.spectra[:, specIndex+1])
		self.spec_axis.tick_params(axis='both', which='both', labelsize=15)
		self.spec_axis.set_xlabel('Wavenumber (cm-1)', fontsize = 15)
		self.spec_axis.set_ylabel('Counts', fontsize = 15)
		self.spec_axis.set_title('ScanPoint Number {}, Size = {} µm, HQI = {}'.format(specIndex+1, particleSize, hqi))

		if self.spectra is not None:
		self.spec_axis.plot(self.spectra[:, 0], self.spectra[:, specIndex+1])
		self.spec_axis.set_title('{}, ScanPoint Number {}, Size = {} µm, HQI = {}'.format(assignment, specIndex+1, particleSize, hqi))
		self.spec_axis.set_xbound(100, (3400 if self.spectra[-1, 0] > 3400 else self.spectra[-1, 0]))
		wavenumber_diff = list(self.spectra[:, 0]-100)
		y_start = wavenumber_diff.index(min(wavenumber_diff))
		@@ -159,10 +157,6 @@ class SpectraPlot(QtWidgets.QGroupBox):
		self.reference_axis.set_ylabel('Ref. Intensity', fontsize = 15, color = 'r')
		self.reference_axis.tick_params('y', colors = 'r')
		self.reference_axis.set_xbound(100, (3400 if self.spectra[-1, 0] > 3400 else self.spectra[-1, 0]))
		# 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])

		self.canvas.draw()

analysis/analysisview.py

+20 −51

Original line number	Diff line number	Diff line
		@@ -29,7 +29,7 @@ from matplotlib.backends.backend_qt5agg import FigureCanvasQTAgg as FigureCanvas
		from matplotlib.figure import Figure
		from matplotlib.backends.backend_qt5agg import NavigationToolbar2QT as NavigationToolbar

		from .analysiswidgets import ExpExcelDialog
		from .excelexport import ExpExcelDialog
		from .analysisplots import TypeHistogramView, SpectraPlot
		from .loadresults import LoadTrueMatchResults
		from .database import DataBaseWindow
		@@ -45,7 +45,7 @@ except:
		class ParticleAnalysis(QtWidgets.QMainWindow):
		def __init__(self, dataset, viewparent=None):
		super(ParticleAnalysis, self).__init__(viewparent)
		self.setGeometry(100, 100, 1680, 1050)
		self.resize(1680, 1050)
		self.setWindowTitle('Results of polymer analysis')
		self.layout = QtWidgets.QHBoxLayout()
		self.widget = QtWidgets.QWidget()
		@@ -56,7 +56,6 @@ class ParticleAnalysis(QtWidgets.QMainWindow):
		self.dataset = dataset
		self.particleContainer = dataset.particleContainer

		# self.additivePlot = None
		self.importWindow = None

		self.polymerCheckBoxes = []
		@@ -64,10 +63,8 @@ class ParticleAnalysis(QtWidgets.QMainWindow):

		self.currentParticleIndex = 0
		self.currentSpectrumIndex = 0
		# self.lastSpectrumInFocus = None

		self.typeHistogramPlot = TypeHistogramView(self)
		# self.typeHistogramPlot.indexClicked.connect(self.getAdditivePlot)
		self.sizeHistogramCanvas = FigureCanvas(Figure())

		sizeHistGroup = QtWidgets.QGroupBox()
		@@ -171,16 +168,8 @@ class ParticleAnalysis(QtWidgets.QMainWindow):
		self.hqiSpinBox.valueChanged.connect(self.applyHQIThresholdToResults)
		optionsLayout.addRow(QtWidgets.QLabel('minimum HQI:'), self.hqiSpinBox)

		# 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)

		self.optionsGroup.setLayout(optionsLayout)
		self.optionsGroup.setMinimumWidth(175)
		# self.optionsGroup.setDisabled(True)

		self.resultScrollarea = QtWidgets.QScrollArea(self)
		self.resultScrollarea.setFixedWidth(250)
		@@ -210,16 +199,13 @@ class ParticleAnalysis(QtWidgets.QMainWindow):
		self.layout.addLayout(viewLayout)

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

		self.createActions()
		self.createMenus()
		self.applyHQIThresholdToResults()
		self.createHistogramData()
		self.particleContainer.loadSpectra()
		self.initializeSpecPlot()
		self.setTypeSelector()
		self.updateHistogramsAndContours()
		@@ -228,8 +214,8 @@ class ParticleAnalysis(QtWidgets.QMainWindow):
		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.loadSpectraAct = QtWidgets.QAction("Load &Spectra", self)
		self.loadSpectraAct.triggered.connect(self.initializeSpecPlot)

		self.noOverlayAct = QtWidgets.QAction("&No Overlay", self)
		self.selOverlayAct = QtWidgets.QAction("&Selected Overlay", self)
		@@ -266,8 +252,8 @@ class ParticleAnalysis(QtWidgets.QMainWindow):
		self.expSQLAct.triggered.connect(self.exportToSQL)

		def createMenus(self):
		self.importMenu = QtWidgets.QMenu("&Import Results")
		self.importMenu.addActions([self.loadTrueMatchAct, self.loadTextFileAct])
		self.importMenu = QtWidgets.QMenu("&Import Spectra and Results")
		self.importMenu.addActions([self.loadSpectraAct, self.loadTrueMatchAct])

		self.dispMenu = QtWidgets.QMenu("&Display", self)
		self.overlayActGroup = QtWidgets.QActionGroup(self.dispMenu)
		@@ -295,6 +281,10 @@ class ParticleAnalysis(QtWidgets.QMainWindow):
		self.menuBar().addMenu(self.toolMenu)
		self.menuBar().addMenu(self.exportMenu)

		def keyPressEvent(self, event):
		if event.key() in [QtCore.Qt.Key_Return, QtCore.Qt.Key_Enter]:
		self.jumpToIndicatedSpectrum()

		def launchDBManager(self):
		if self.dbWin.isHidden():
		self.dbWin.show()
		@@ -314,15 +304,6 @@ class ParticleAnalysis(QtWidgets.QMainWindow):
		self.importWindow = LoadTrueMatchResults(self.particleContainer, self)
		self.importWindow.exec()

		# @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()

		@QtCore.pyqtSlot()
		def applyHQIThresholdToResults(self):
		hqi = self.hqiSpinBox.value()
		@@ -409,14 +390,6 @@ class ParticleAnalysis(QtWidgets.QMainWindow):
		numParticles = self.particleContainer.getNumberOfParticles()
		self.specNumberSelector.setMaximum(numParticles)

		# if self.lastSpectrumInFocus is not None:
		# self.currentSpectrumIndex = self.lastSpectrumInFocus
		# self.displayNewPolymerType(resetCurrentIndex=False)
		# print('displaying new type without resetting index')
		# else:
		# print('displaying new type with resetting index')
		# self.displayNewPolymerType()

		def initializeSpecPlot(self):
		self.specPlot.loadSpectraAndInitializeSpecPlot()
		self.updateSpecPlot()
		@@ -475,8 +448,8 @@ class ParticleAnalysis(QtWidgets.QMainWindow):
		def updateSpecPlot(self):
		particleSize = np.round(self.particleContainer.getSizeOfParticleByIndex(self.currentParticleIndex))
		hqi = self.particleContainer.getHQIOfSpectrumIndex(self.currentSpectrumIndex)
		self.specPlot.updateParticleSpectrum(self.currentSpectrumIndex, particleSize, hqi)
		# self.lastSpectrumInFocus = self.currentSpectrumIndex
		assignment = self.particleContainer.getParticleAssignmentByIndex(self.currentParticleIndex)
		self.specPlot.updateParticleSpectrum(self.currentSpectrumIndex, assignment, particleSize, hqi)

		if self.refSelector.isEnabled() and self.refSelector.currentText() != '':
		refID = self.dbWin.activeDatabase.spectraNames.index(self.refSelector.currentText())
		@@ -540,14 +513,13 @@ class ParticleAnalysis(QtWidgets.QMainWindow):
		self.updateSpecPlot()
		self.jumpToIndicatedSpectrum()

		def setWidgetsToNewParticleIndex(self, particleIndex): #TODO: Probably refactor. Its basically a combination of the above methods... Just a bit different to avoid directly jumping to the particle in sampleview
		def setWidgetsToNewParticleIndex(self, particleIndex):
		try:
		self.particleSelector.valueChanged.disconnect()
		self.spectrumSelector.valueChanged.disconnect()
		self.typeSelectorCombo.currentIndexChanged.disconnect()
		except TypeError:
		pass #signals were not connected...

		pass #signals were not connected, nothing to disconnect...

		assignment = self.particleContainer.getParticleAssignmentByIndex(particleIndex)
		self.typeSelectorCombo.setCurrentText(assignment)
		@@ -573,16 +545,13 @@ class ParticleAnalysis(QtWidgets.QMainWindow):
		self.spectrumSelector.valueChanged.connect(self.setSpecSelector)
		self.particleSelector.valueChanged.connect(self.setParticleSelector)

		def jumpToIndicatedSpectrum(self): #TODO: This should be transferred to sampleview...
		def jumpToIndicatedSpectrum(self):
		self.currentSpectrumIndex = self.specNumberSelector.value()-1
		self.currentParticleIndex = self.particleContainer.getParticleIndexContainingSpecIndex(self.currentSpectrumIndex)
		self.centerOnSpecIndex(self.currentSpectrumIndex)
		self.viewparent.centerOnRamanIndex(self.currentSpectrumIndex)
		self.viewparent.highLightContour(self.currentParticleIndex)
		self.updateSpecPlot()

		def centerOnSpecIndex(self, index):
		self.viewparent.centerOnRamanIndex(index)

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

		@@ -639,7 +608,7 @@ class ParticleAnalysis(QtWidgets.QMainWindow):
		scanIndicator.update()

		def exportToExcel(self):
		expWin = ExpExcelDialog(self.dataset, self.particleContainer)
		expWin = ExpExcelDialog(self.dataset)
		expWin.exec()

		def exportToSQL(self):

analysis/analysiswidgets.py→analysis/excelexport.py

+25 −54

Original line number	Diff line number	Diff line
		@@ -19,27 +19,21 @@ along with this program, see COPYING.
		If not, see <https://www.gnu.org/licenses/>.
		"""

		from PyQt5 import QtWidgets, QtGui, QtCore
		from PyQt5 import QtWidgets
		import numpy as np
		import pandas as pd
		import os
		import sys

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


		class ExpExcelDialog(QtWidgets.QDialog):
		def __init__(self, dataset, particleContainer):
		def __init__(self, dataset):
		super(ExpExcelDialog, self).__init__()
		self.setWindowTitle('Export Options')
		self.setGeometry(200, 200, 300, 300)

		self.dataset = dataset
		self.particleContainer = particleContainer
		self.polymers = self.particleContainer.getListOfParticleAssignments
		# self.additives = self.datastats.currentAdditives
		self.hqis = self.particleContainer.getListOfHighestHQIs
		self.particleContainer = dataset.particleContainer


		self.layout = QtWidgets.QHBoxLayout()
		self.setLayout(self.layout)
		@@ -48,7 +42,7 @@ class ExpExcelDialog(QtWidgets.QDialog):
		excelvbox.addWidget(QtWidgets.QLabel('Select Parameters for Export'))
		excelgroup = QtWidgets.QGroupBox("Export to Excel", self)

		self.exportOptions = ['Polymer Type (mandatory)', 'Additives', 'Long Size (µm)', 'Short Size (µm)', 'Area (µm²)', 'HQI', 'Size Classes']
		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
		@@ -61,11 +55,6 @@ class ExpExcelDialog(QtWidgets.QDialog):
		if option == 'Polymer Type (mandatory)':
		self.checkBoxes[-1].setEnabled(False) #is mandatory!!!

		# if option == 'Additives':
		# if self.additives is None:
		# self.checkBoxes[-1].setEnabled(False)
		# self.checkBoxes[-1].setChecked(False)

		excelvbox.addWidget(self.checkBoxes[-1])

		self.xlsFileName = QtWidgets.QLineEdit()
		@@ -86,18 +75,23 @@ class ExpExcelDialog(QtWidgets.QDialog):

		def toExcel(self):
		requiredcolumns = []
		self.sizes = self.particleContainer.getSizesOfAllParticles()
		uniquePolymers = self.particleContainer.getUniquePolymers()
		polymers = self.particleContainer.getListOfParticleAssignments()
		sizes = self.particleContainer.getSizesOfAllParticles()


		for box in self.checkBoxes:
		if box.isChecked() == True:
		if box.text() != 'Size Classes':
		requiredcolumns.append(box.text())
		if box.text() == 'Long Size (µm)':
		longSize = self.sizes
		longSizes = sizes
		elif box.text() == 'Short Size (µm)':
		self.shortSizes = self.particleContainer.getShortSizesOfAllParticles()
		shortSizes = self.particleContainer.getShortSizesOfAllParticles()
		elif box.text() == 'HQI':
		hqis = self.particleContainer.getListOfHighestHQIs()
		elif box.text() == 'Area (µm²)':
		area = np.array([np.round(float(entry[4]), 1) for entry in self.particles])
		areas = self.particleContainer.getAreasOfAllParticles()

		else:
		requiredcolumns.append('0 - 5 µm')
		@@ -107,28 +101,26 @@ class ExpExcelDialog(QtWidgets.QDialog):
		requiredcolumns.append('50 - 100 µm')
		requiredcolumns.append('> 100 µm')

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

		for colindex, column in enumerate(requiredcolumns):
		if column == 'Polymer Type (mandatory)':
		polymertypes[rowindex:rowindex+numentries] = self.polymers[indices]
		# if column == 'Additives':
		# finalData[rowindex:rowindex+numentries, colindex-1] = self.additives[indices]
		polymertypes[rowindex:rowindex+numentries] = polymers[indices]
		if column == 'Long Size (µm)':
		finalData[rowindex:rowindex+numentries, colindex-1] = longSize[indices]
		finalData[rowindex:rowindex+numentries, colindex-1] = longSizes[indices]
		if column == 'Short Size (µm)':
		finalData[rowindex:rowindex+numentries, colindex-1] = self.shortSizes[indices]
		finalData[rowindex:rowindex+numentries, colindex-1] = shortSizes[indices]
		if column == 'Area (µm²)':
		finalData[rowindex:rowindex+numentries, colindex-1] = area[indices]
		finalData[rowindex:rowindex+numentries, colindex-1] = areas[indices]
		if column == 'HQI':
		finalData[rowindex:rowindex+numentries, colindex-1] = self.hqis[indices]
		finalData[rowindex:rowindex+numentries, colindex-1] = hqis[indices]

		if '> 100 µm' in requiredcolumns:
		##append size classes
		@@ -184,24 +176,3 @@ class ExpExcelDialog(QtWidgets.QDialog):
		report.to_excel(writer, sheet_name = 'Particle Statistics', index=False)
		writer.save()
		self.accept()
		No newline at end of file


		class AdditiveViewer(QtWidgets.QWidget):
		def __init__(self, polymername, sortedAdditives):
		super(AdditiveViewer, self).__init__()
		self.setGeometry(200,200, 800, 600)
		self.setWindowTitle('Additives of {}'.format(polymername))

		self.layout = QtWidgets.QGridLayout()
		self.setLayout(self.layout)

		self.canvas = FigureCanvas(Figure(figsize=(5, 3)))
		self.ax = self.canvas.figure.subplots()

		self.layout.addWidget(self.canvas, 0, 0)

		self.ax.hist(sortedAdditives)
		self.ax.set_ylabel('Number', fontsize = 15)
		self.ax.tick_params(axis='both', which='both', labelsize=15)


		No newline at end of file

analysis/particleAndMeasurement.py

+5 −2

Original line number	Diff line number	Diff line
		@@ -98,6 +98,9 @@ class Particle(object):
		def getNumberOfMeasurements(self):
		return len(self.measurements)

		def getArea(self):
		return np.round(self.area)

		def measurementsHaveSameOrigAssignment(self):
		allResults = [meas.getOrigAssignment() for meas in self.measurements]
		if len(np.unique(allResults)) == 1:
		@@ -126,7 +129,7 @@ class Measurement(object):

		self.assignment_orig = 'Not Evaluated'
		self.assignment_afterHQI = None
		self.hqi = None
		self.hqi = 0

		self.assignedParticle = None