First phase of refactoring (0b768ad2) · Commits · GEPARD / GEPARD

analysis/analysisview.py

+93 −102

Original line number	Diff line number	Diff line
		@@ -53,11 +53,12 @@ class ParticleAnalysis(QtWidgets.QMainWindow):
		self.setCentralWidget(self.widget)

		self.parent = parent

		self.dataset = dataset
		self.particleContainer = dataset.particleContainer
		self.datastats = DataStats(dataset)
		self.editor = ParticleEditor(self.datastats, self)

		self.additivePlot = None
		# self.additivePlot = None
		self.importWindow = None

		self.polymerCheckBoxes = []
		@@ -67,8 +68,8 @@ class ParticleAnalysis(QtWidgets.QMainWindow):
		self.currentSpectrumIndex = 0
		self.lastSpectrumInFocus = None

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

		sizeHistGroup = QtWidgets.QGroupBox()
		@@ -106,7 +107,7 @@ class ParticleAnalysis(QtWidgets.QMainWindow):
		splitter1.addWidget(sizeHistGroup)
		splitter2 = QtWidgets.QSplitter(QtCore.Qt.Horizontal)
		splitter2.addWidget(splitter1)
		splitter2.addWidget(self.typeHistogram)
		splitter2.addWidget(self.typeHistogramPlot)
		splitter2.setSizes([300, 150])

		self.navigationGroup = QtWidgets.QGroupBox('Navigate through polymers')
		@@ -164,32 +165,31 @@ class ParticleAnalysis(QtWidgets.QMainWindow):
		self.hqiSpinBox.setValue(75.0)
		self.hqiSpinBox.setDecimals(1)
		self.hqiSpinBox.setMinimum(0)
		self.hqiSpinBox.setMaximum(100)
		self.hqiSpinBox.setMaximumWidth(45)
		optionsLayout.addRow(QtWidgets.QLabel('min 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.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.dispResultSpinBox = QtWidgets.QSpinBox()
		self.dispResultSpinBox.setValue(20)
		self.dispResultSpinBox.setMinimum(1)
		self.dispResultSpinBox.valueChanged.connect(self.updateHistogram)
		self.dispResultSpinBox.valueChanged.connect(self.updateHistograms)
		optionsLayout.addRow(QtWidgets.QLabel('Max. items in display:'), self.dispResultSpinBox)

		for spinbox in [self.hqiSpinBox, self.compHqiSpinBox]:
		spinbox.setMaximum(100)
		spinbox.setMaximumWidth(45)

		self.updateBtn = QtWidgets.QPushButton('Update Results')
		self.updateBtn.setDisabled(True)
		self.updateBtn.clicked.connect(self.applyHQIThresholdToResults)
		# self.updateBtn.setDisabled(True)
		optionsLayout.addRow(self.updateBtn)

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

		self.resultScrollarea = QtWidgets.QScrollArea(self)
		self.resultScrollarea.setFixedWidth(250)
		@@ -210,25 +210,24 @@ class ParticleAnalysis(QtWidgets.QMainWindow):
		self.resultCheckBoxes.setLayout(self.resultCheckBoxesLayout)

		self.layout_SArea.addWidget(self.resultCheckBoxes)
		# self.layout_SArea.addStretch(1)

		# self.menuLayout.addWidget(reloadGroup)
		self.menuLayout.addWidget(self.optionsGroup)
		self.menuLayout.addWidget(self.resultScrollarea)

		self.layout.addLayout(self.menuLayout)
		self.layout.addLayout(viewLayout)

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

		self.createActions()
		self.createMenus()

		self.updateData()
		self.initializeSpectraPlot()
		self.applyHQIThresholdToResults()

		def createActions(self):
		self.loadTrueMatchAct = QtWidgets.QAction("Load &TrueMatch Results", self)
		@@ -241,7 +240,7 @@ class ParticleAnalysis(QtWidgets.QMainWindow):
		self.selOverlayAct = QtWidgets.QAction("&Selected Overlay", self)
		self.fullOverlayAct = QtWidgets.QAction("&Full Overlay", self)

		self.transpAct = QtWidgets.QAction("&Transparent Overlay")
		self.transpAct = QtWidgets.QAction("&Transparent Overlay", self)
		self.transpAct.triggered.connect(self.createPolymerOverlay)

		self.hideLabelAct = QtWidgets.QAction('&Hide Polymer Numbers', self)
		@@ -276,7 +275,7 @@ class ParticleAnalysis(QtWidgets.QMainWindow):
		self.overlayActGroup = QtWidgets.QActionGroup(self.dispMenu)
		self.overlayActGroup.setExclusive(True)
		self.overlayActGroup.triggered.connect(self.createPolymerOverlay)
		self.overlayActGroup.triggered.connect(self.updateHistogram)
		self.overlayActGroup.triggered.connect(self.updateHistograms)

		for act in [self.noOverlayAct, self.selOverlayAct, self.fullOverlayAct]:
		self.dispMenu.addAction(act)
		@@ -312,63 +311,62 @@ class ParticleAnalysis(QtWidgets.QMainWindow):
		self.refSelector.addItems(self.dbWin.activeDatabase.spectraNames)
		self.refSelector.setDisabled(False)

		def updateData(self):
		spectra = self.datastats.update()
		if spectra is None:
		fname = QtWidgets.QFileDialog.getOpenFileName(self, 'Select Spectra File', self.datastats.dataset.path, 'text file (*.txt)')[0]
		spectra = self.datastats.loadSpectra(fname)
		if spectra is None:
		QtWidgets.QMessageBox.critical(self, 'ERROR!', 'spectra file could not be opened with np.loadtxt...')
		return
		def initializeSpectraPlot(self): #formerly updateData(self)....
		self.particleContainer.loadSpectraFromDisk()
		self.specCanvas.draw()
		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()
		# 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()

		def importTrueMatchResults(self):
		self.importWindow = LoadWITecResults(self.datastats, 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(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 formatResults(self):
		if self.datastats.spectraResults is not None:
		print('formatResults')
		self.updateBtn.setDisabled(False)
		self.optionsGroup.setDisabled(False)
		def applyHQIThresholdToResults(self):
		self.particleContainer.applyHQITresholdToParticles(self.hqiSpinBox.value())
		self.createHistogramData()

		self.datastats.formatResults(self.hqiSpinBox.value(), self.compHqiSpinBox.value())
		# 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)

		if self.datastats.additiveResults is not None:
		self.compHqiSpinBox.setDisabled(False)

		self.createHistogramData()

		def createHistogramData(self):
		if not self.datastats.createHistogramData():
		QtWidgets.QMessageBox.critical(self, 'Error', 'Inconsistent particle data. Please restore backup!')
		return
		# if not self.datastats.createHistogramData():
		# QtWidgets.QMessageBox.critical(self, 'Error', 'Inconsistent particle data. Please restore backup!')
		# return
		# self.particleContainer.updateTypeHistogram()

		###Handle Checkboxes for all polymers...
		self.menuLayout.removeWidget(self.resultScrollarea)
		@@ -381,7 +379,7 @@ class ParticleAnalysis(QtWidgets.QMainWindow):
		del i
		self.showTotalSelector.setParent(None)
		self.showTotalSelector.setDisabled(False)
		self.showTotalSelector.stateChanged.connect(self.updateHistogram)
		self.showTotalSelector.stateChanged.connect(self.updateHistograms)

		del self.resultCheckBoxes
		del self.resultCheckBoxesLayout
		@@ -391,17 +389,16 @@ class ParticleAnalysis(QtWidgets.QMainWindow):
		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)

		#generate new checkboxes
		self.polymerCheckBoxes = []
		uniquePolymers = self.datastats.getUniquePolymers()
		uniquePolymers = self.particleContainer.getUniquePolymers()
		for index, polymer in enumerate(uniquePolymers):
		self.polymerCheckBoxes.append(QtWidgets.QCheckBox(self))
		self.polymerCheckBoxes[index].setText(polymer)
		@@ -409,14 +406,12 @@ class ParticleAnalysis(QtWidgets.QMainWindow):
		if polymer in self.lastSelectedCheckBoxNames:
		self.polymerCheckBoxes[index].setChecked(True)

		self.polymerCheckBoxes[index].stateChanged.connect(self.updateHistogram)
		self.polymerCheckBoxes[index].stateChanged.connect(self.updateHistograms)
		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)

		self.expExcelAct.setDisabled(False)
		@@ -436,7 +431,7 @@ class ParticleAnalysis(QtWidgets.QMainWindow):
		else:
		self.displayNewPolymerType()

		self.updateHistogram()
		self.updateHistograms()
		self.createPolymerOverlay()

		def exportToExcel(self):
		@@ -451,7 +446,7 @@ class ParticleAnalysis(QtWidgets.QMainWindow):
		def updateSpecPlot(self, centerOn=True, highlightContour=True):
		#draw Sample Spectrum
		specIndex = self.currentSpectrumIndex
		spectra = self.datastats.spectra
		spectra = self.particleContainer.spectra
		particlestats = self.datastats.getParticleStats()
		self.spec_ax.axis("on")
		self.spec_ax.clear()
		@@ -563,33 +558,29 @@ class ParticleAnalysis(QtWidgets.QMainWindow):
		self.currentSpectrumIndex = self.datastats.particles2spectra[self.currentParticleIndex][self.spectrumSelector.value()-1]
		self.updateSpecPlot()

		def updateHistogram(self):
		def updateHistograms(self):
		self.updateTypeHistogram()
		self.updateSizeHistogram()


		def updateTypeHistogram(self):
		#draw the general histogram
		colorList = []
		abundancyList = []
		labelList = []
		for index, i in enumerate(self.datastats.typehistogram):
		typeHistogram = self.particleContainer.getTypeHistogram()
		for index, polymType in enumerate(typeHistogram):
		if not self.selOverlayAct.isChecked() or self.polymerCheckBoxes[index].isChecked():
		abundancyList.append(self.datastats.typehistogram[index][1])
		curColor = self.getColorFromName(self.datastats.typehistogram[index][0])
		abundancyList.append(typeHistogram[polymType])
		curColor = self.getColorFromName(polymType)
		colorList.append(QtGui.QColor(*curColor))
		if self.datastats.sorted_additives is None:
		numads = ''
		else:
		numads = len(np.unique(self.datastats.sorted_additives[index]))
		if numads == 0:
		numads = ''
		else:
		numads = '(' + str(numads) + ')'
		numpolymers = i[1]
		label = ('{} x ' + self.datastats.typehistogram[index][0] + ' {}').format(numpolymers, numads)
		labelList.append(label)

		print("abundancyList:", abundancyList)
		print("labelList:", labelList)
		print("colorList:", colorList)
		self.typeHistogram.updateTypes(list(zip(abundancyList, labelList, colorList)))
		# print("abundancyList:", abundancyList)
		# print("labelList:", labelList)
		# print("colorList:", colorList)
		self.typeHistogramPlot.updateTypeHistogram(list(zip(abundancyList, labelList, colorList)))

		def updateSizeHistogram(self):
		#general size histogram
		self.sizeHist_ax.clear()
		self.sizeHist_ax.axis('on')
		@@ -648,7 +639,7 @@ class ParticleAnalysis(QtWidgets.QMainWindow):
		if ok:
		self.datastats.colorSeed = text
		self.datastats.dataset.colorSeed = text
		self.updateHistogram()
		self.updateHistograms()
		self.createPolymerOverlay()

		def getColorFromName(self, name, base255=True):
		@@ -673,7 +664,7 @@ class ParticleAnalysis(QtWidgets.QMainWindow):

		alpha = (128 if self.transpAct.isChecked() else 255)
		#get colors for each polymer type
		colorList = [QtGui.QColor(255, 255, 255, alpha=50)]*len(self.datastats.particleResults)
		colorList = [QtGui.QColor(255, 255, 255, alpha=50)]*len(self.datastats.particleContainer)
		legendItems = []

		for index, indexList in enumerate(self.datastats.indices):

analysis/analysiswidgets.py

+4 −4

Original line number	Diff line number	Diff line
		@@ -37,7 +37,7 @@ class ExpExcelDialog(QtWidgets.QDialog):

		self.datastats = datastats
		self.particles = self.datastats.getParticleStats()
		self.polymers = self.datastats.particleResults
		self.polymers = self.datastats.particleContainer
		self.additives = self.datastats.currentAdditives
		self.hqis = self.datastats.hqis

		@@ -262,8 +262,8 @@ class ParticleTypeView(QtWidgets.QScrollArea):
		self.setAlignment(QtCore.Qt.AlignHCenter)
		self.widgets = []

		def updateTypes(self, types):
		print("Updating polymer type view", flush=True)
		def updateTypeHistogram(self, types):
		# print("Updating polymer type view", flush=True)
		for pi in self.widgets:
		self.indicatorbox.removeWidget(pi)
		pi.setParent(None)
		@@ -277,7 +277,7 @@ class ParticleTypeView(QtWidgets.QScrollArea):

		for index, entry in enumerate(types):
		num, text, color = entry
		print("num, text, color:", num, text, color, flush=True)
		# print("num, text, color:", num, text, color, flush=True)
		pi = ParticleIndicator(num, numtotal, color, text)
		self.indicatorbox.addWidget(pi)
		pi.clicked.connect(getIndexFunction(index))

analysis/database.py

+5 −2

Original line number	Diff line number	Diff line
		@@ -35,13 +35,16 @@ from matplotlib.backends.backend_qt5agg import NavigationToolbar2QT as Navigatio
		from matplotlib.figure import Figure
		import functools
		from scipy.linalg import solveh_banded
		from pathlib import Path

		class DataBaseWindow(QtWidgets.QMainWindow):
		def __init__(self, parent):
		super(DataBaseWindow, self).__init__()
		self.parent = parent
		self.path = os.path.join(Path.home(), 'gepard', 'databases')

		logpath = QtCore.QStandardPaths.writableLocation(
		QtCore.QStandardPaths.AppLocalDataLocation)

		self.path = os.path.join(logpath, 'databases')
		self.importPath = self.path
		if not os.path.exists(self.path):
		os.mkdir(self.path)

analysis/datastats.py

+284 −107

File changed.

Preview size limit exceeded, changes collapsed.

analysis/importSpectra.py

0 → 100644

+68 −0

Original line number	Diff line number	Diff line
		#!/usr/bin/env python3
		# -- coding: utf-8 --
		"""
		Created on Tue May 28 20:33:14 2019

		@author: brandt
		"""
		import numpy as np

		'''Return Spectra array (First column: Wavenumbers, all other columns, intensities)
		and names for all in file contained spectra'''


		#TODO: Include sanity checks for correct file format?

		def importWITecSpectra(fname):
		def firstColumnOnlyHasUniqueNumbers(data):
		#this is the case for WITec Spectra sets, but not for Renishaw
		if len(np.unique(data[:, 0])) == len(data[:, 0]):
		return True
		else:
		return False

		data = np.loadtxt(fname)
		names = [f'Spectrum {i+1}' for i in range(data.shape[1]-1)]

		if firstColumnOnlyHasUniqueNumbers(data):
		return data, names
		else:
		raise ImportError

		def importRenishawSpectra(fname):
		data = np.loadtxt(fname)
		rawSpectra = data[:, 2:4]
		spectraIndices = np.where(rawSpectra[:, 0] == rawSpectra[0, 0])[0]
		positions = np.zeros((len(spectraIndices), 2))
		spectra = []
		names = []

		spectra = np.zeros((spectraIndices[1], len(spectraIndices)+1))
		spectra[:, 0] = rawSpectra[0:spectraIndices[1], 0]
		for i in range(len(spectraIndices)):
		names.append(f'Spectrum {i+1}')
		positions[i, :] = [data[spectraIndices[i], 0], data[spectraIndices[i], 1]]
		if i < len(spectraIndices)-1:
		spectra[:, i+1] = rawSpectra[spectraIndices[i]:spectraIndices[i+1], 1]
		else:
		spectra[:, i+1] = rawSpectra[spectraIndices[i]:, 1]

		spectra = np.flipud(spectra)
		wavenumbers = spectra[:, 0]
		spectra = spectra[:, 1:]

		return np.transpose(np.vstack((wavenumbers, spectra))), names

		def importPerkinElmerSpectra(fname):
		names = []
		spectra = []
		with open(fname) as fp:
		for index, line in enumerate(fp.readlines()):
		if index == 0:
		for name in line.split(';'):
		names.append(name.split('.sp')[0])

		elif index > 1:
		spectra.append(line.split(';'))

		return np.array(spectra, dtype=np.float), names[1:]