segmentation.py: adaptation to allow usage of OpenCV 4.0 alongside 3.4 (f458c65b) · Commits · GEPARD / GEPARD

analysis/analysisview.py

+51 −78

Original line number	Original line	Diff line number	Diff line
	#!/usr/bin/env python3
	# -- coding: utf-8 --		# -- coding: utf-8 --
			#!/usr/bin/env python3
	"""		"""
	GEPARD - Gepard-Enabled PARticle Detection		GEPARD - Gepard-Enabled PARticle Detection
	Copyright (C) 2018 Lars Bittrich and Josef Brandt, Leibniz-Institut für		Copyright (C) 2018 Lars Bittrich and Josef Brandt, Leibniz-Institut für
	@@ -20,8 +20,9 @@ along with this program, see COPYING.
	If not, see <https://www.gnu.org/licenses/>.		If not, see <https://www.gnu.org/licenses/>.
	"""		"""

	import numpy as np
	from PyQt5 import QtCore, QtGui, QtWidgets		from PyQt5 import QtCore, QtGui, QtWidgets
			import numpy as np
			import pandas as pd
	import sys		import sys
	import operator		import operator
	import os		import os
	@@ -32,10 +33,9 @@ from matplotlib.backends.backend_qt5agg import FigureCanvasQTAgg as FigureCanvas
	from matplotlib.figure import Figure		from matplotlib.figure import Figure
	from matplotlib.backends.backend_qt5agg import NavigationToolbar2QT as NavigationToolbar		from matplotlib.backends.backend_qt5agg import NavigationToolbar2QT as NavigationToolbar

	import pandas as pd		from .loadresults import LoadWITecResults
	from analysis.loadresults import LoadWITecResults		from .editParticles import ParticleEditor
	from analysis.editParticles import ParticleEditor		from .database import DataBaseWindow
	from analysis.database import DataBaseWindow
	try:		try:
	from analysis.sqlexport import SQLExport		from analysis.sqlexport import SQLExport
	sqlEnabled = True		sqlEnabled = True
	@@ -58,7 +58,6 @@ class ParticleAnalysis(QtWidgets.QMainWindow):
	self.config = self.parent.dataset.resultParams		self.config = self.parent.dataset.resultParams

	self.editor = ParticleEditor(self)		self.editor = ParticleEditor(self)
	self.expWin = None

	self.spectraResults = None #entire List of all spectra assignments		self.spectraResults = None #entire List of all spectra assignments
	self.additiveResults = None #entire List of all additives		self.additiveResults = None #entire List of all additives
	@@ -70,7 +69,6 @@ class ParticleAnalysis(QtWidgets.QMainWindow):
	self.uniquePolymers = None #list of present polymer types		self.uniquePolymers = None #list of present polymer types
	self.spectra = None #acquired spectra		self.spectra = None #acquired spectra
	self.indices = None #assignment of what spectra-indices belong to what substance		self.indices = None #assignment of what spectra-indices belong to what substance
	self.expWindow = None
	self.additivePlot = None		self.additivePlot = None
	self.importWindow = None		self.importWindow = None
	self.directory = None		self.directory = None
	@@ -573,18 +571,13 @@ class ParticleAnalysis(QtWidgets.QMainWindow):
	self.createPolymerOverlay()		self.createPolymerOverlay()

	def exportToExcel(self):		def exportToExcel(self):
	if self.expWin is not None:		expWin = ExpExcelDialog(self)
	self.expWin.close()		expWin.exec()
	self.expWin.destroy()
	self.expWin = ExpExcelDialog(self)
	self.expWin.show()

	def exportToSQL(self):		def exportToSQL(self):
	if self.expWin is not None:		sqlexp = SQLExport(self)
	self.expWin.close()		sqlexp.exec()
	self.expWin.destroy()
	self.expWin = SQLExport(self)
	self.expWin.show()

	def updateSpecPlot(self, centerOn=True, highlightContour=True):		def updateSpecPlot(self, centerOn=True, highlightContour=True):
	#draw Sample Spectrum		#draw Sample Spectrum
	@@ -859,14 +852,14 @@ class ParticleAnalysis(QtWidgets.QMainWindow):


	def closeEvent(self, event):		def closeEvent(self, event):
	for window in [self.expWindow, self.additivePlot, self.importWindow, self.dbWin]:		for window in [self.additivePlot, self.importWindow, self.dbWin]:
	try: window.close()		try: window.close()
	except: pass		except: pass
	self.parent.imparent.particelAnalysisAct.setChecked(False)		self.parent.imparent.particelAnalysisAct.setChecked(False)
	event.accept()		event.accept()


	class ExpExcelDialog(QtWidgets.QWidget):		class ExpExcelDialog(QtWidgets.QDialog):
	def __init__(self, parent):		def __init__(self, parent):
	super(ExpExcelDialog, self).__init__()		super(ExpExcelDialog, self).__init__()
	self.setWindowTitle('Export Options')		self.setWindowTitle('Export Options')
	@@ -919,22 +912,6 @@ class ExpExcelDialog(QtWidgets.QWidget):

	self.layout.addWidget(excelgroup)		self.layout.addWidget(excelgroup)

	# sqlGroup = QtWidgets.QGroupBox('Export to SQL')
	# sqlLayout = QtWidgets.QVBoxLayout()
	#
	# self.sqlbtn = QtWidgets.QPushButton('Export to SQL Database')
	# self.sqlbtn.resize(self.sqlbtn.sizeHint())
	# if sqlEnabled:
	# self.sqlbtn.clicked.connect(self.toSQL)
	# else:
	# self.sqlbtn.setDisabled(True)
	#
	# self.sqlExport = None
	#
	# sqlLayout.addWidget(self.sqlbtn)
	# sqlGroup.setLayout(sqlLayout)
	#
	# self.layout.addWidget(sqlGroup)
	self.show()		self.show()

	def toExcel(self):		def toExcel(self):
	@@ -958,35 +935,34 @@ class ExpExcelDialog(QtWidgets.QWidget):
	requiredcolumns.append('50 - 100 µm')		requiredcolumns.append('50 - 100 µm')
	requiredcolumns.append('> 100 µm')		requiredcolumns.append('> 100 µm')

	self.finalData = np.array(['nothing to see here, iam a boring placeholder']((self.polymers.shape[0]+1)len(requiredcolumns))).reshape(((self.polymers.shape[0]+1), len(requiredcolumns)))		finalData = np.zeros((self.polymers.shape[0],len(requiredcolumns)-1))
			polymertypes = [""]*self.polymers.shape[0]
	#create header:		rowindex = 0
	self.finalData[0, :] = np.array(requiredcolumns)
	self.finalData[0, 0] = 'Polymer Type'

	rowindex = 1
	for polymer in np.unique(self.polymers):		for polymer in np.unique(self.polymers):
	indices = np.where(self.polymers == polymer)[0]		indices = self.polymers == polymer
	numentries = int(len(indices))		numentries = int(np.sum(indices))
			print("Num:", numentries)
			sys.stdout.flush()

	for colindex, column in enumerate(requiredcolumns):		for colindex, column in enumerate(requiredcolumns):
	if column == 'Polymer Type (mandatory)':		if column == 'Polymer Type (mandatory)':
	self.finalData[rowindex:rowindex+numentries, colindex] = self.polymers[indices]		polymertypes[rowindex:rowindex+numentries] = self.polymers[indices]
	if column == 'Additives':		if column == 'Additives':
	self.finalData[rowindex:rowindex+numentries, colindex] = self.additives[indices]		finalData[rowindex:rowindex+numentries, colindex-1] = self.additives[indices]
	if column == 'Long Size (µm)':		if column == 'Long Size (µm)':
	self.finalData[rowindex:rowindex+numentries, colindex] = longSize[indices]		finalData[rowindex:rowindex+numentries, colindex-1] = longSize[indices]
	if column == 'Short Size (µm)':		if column == 'Short Size (µm)':
	self.finalData[rowindex:rowindex+numentries, colindex] = shortSize[indices]		finalData[rowindex:rowindex+numentries, colindex-1] = shortSize[indices]
	if column == 'Area (µm²)':		if column == 'Area (µm²)':
	self.finalData[rowindex:rowindex+numentries, colindex] = area[indices]		finalData[rowindex:rowindex+numentries, colindex-1] = area[indices]
	if column == 'HQI':		# hit quality index array does not match the data size if particles have been combined
	self.finalData[rowindex:rowindex+numentries, colindex] = self.hqis[indices]		#if column == 'HQI':
			# finalData[rowindex:rowindex+numentries, colindex-1] = self.hqis[indices]

	if '> 100 µm' in requiredcolumns:		if '> 100 µm' in requiredcolumns:
	##append size classes		##append size classes
	numPrevCols = len(requiredcolumns) - 6 #number of previous columns		numPrevCols = len(requiredcolumns) - 1 - len(self.sizeClasses) #number of previous columns
	for tableindex, dataindex in enumerate(indices):		for tableindex, dataindex in enumerate(np.arange(len(indices))[indices]):
	for classindex in range(len(self.sizeClasses)):		for classindex in range(len(self.sizeClasses)):
	upLimit = self.sizeClasses[classindex]		upLimit = self.sizeClasses[classindex]
	if classindex == 0: lowLimit = 0		if classindex == 0: lowLimit = 0
	@@ -994,9 +970,9 @@ class ExpExcelDialog(QtWidgets.QWidget):
	curSize = self.sizes[dataindex]		curSize = self.sizes[dataindex]

	if curSize > lowLimit and curSize <= upLimit:		if curSize > lowLimit and curSize <= upLimit:
	self.finalData[rowindex+tableindex, numPrevCols + classindex] = np.int(1)		finalData[rowindex+tableindex, numPrevCols + classindex] = np.int(1)
	else:		else:
	self.finalData[rowindex+tableindex, numPrevCols + classindex] = np.int(0)		finalData[rowindex+tableindex, numPrevCols + classindex] = np.int(0)

	rowindex = rowindex + numentries		rowindex = rowindex + numentries

	@@ -1014,32 +990,29 @@ class ExpExcelDialog(QtWidgets.QWidget):

	writer = pd.ExcelWriter(xlsname, engine = 'xlsxwriter')		writer = pd.ExcelWriter(xlsname, engine = 'xlsxwriter')

	df = pd.DataFrame(self.finalData)		df = pd.DataFrame(finalData, columns=requiredcolumns[1:])
	df.to_excel(writer, sheet_name = 'Individual Particles', header = False, index = False)		df.insert(0, 'Polymer Type', polymertypes)
			df.to_excel(writer, sheet_name = 'Individual Particles', index = False)
	if '> 100 µm' in requiredcolumns:		if '> 100 µm' in requiredcolumns:
	#generate particle statistics report		#generate particle statistics report
	report = [['Polymer Type', '0 - 5 µm', '5 - 10 µm', '10 - 20 µm', '20 - 50 µm', '50 - 100 µm', '> 100 µm']]		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 np.unique(self.polymers):		for polymer in index:
	indices = np.where(self.polymers == polymer)[0]		indices = np.where(self.polymers == polymer)[0]
	classes = np.array([0, 0, 0, 0, 0, 0])		sortind = np.searchsorted([5,10,20,50,100], self.sizes[indices], 'right')
	for size in self.sizes[indices]:		classes = np.bincount(sortind, minlength=6)
	if size < 5: classes[0] += 1		particleclasses.append(classes)
	elif size < 10: classes[1] += 1
	elif size < 20: classes[2] += 1
	elif size < 50: classes[3] += 1
	elif size < 100: classes[4] += 1
	else: classes[5] += 1
	report.append([polymer, classes[0], classes[1], classes[2], classes[3], classes[4], classes[5]])

	report = pd.DataFrame(np.array(report))
	report.to_excel(writer, sheet_name = 'Particle Statistics', header = False, index = False)
	QtWidgets.QMessageBox.about(self, 'Done!', 'Particle Data exported')

	def closeEvent(self, event):		particleclasses = np.array(particleclasses)
	if self.expWin is not None:		report = pd.DataFrame(np.array(particleclasses), columns=header,
	self.expWin.close()		dtype=int)
	event.accept()		report.insert(0, 'Polymer Type', index)
			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()


	class AdditiveViewer(QtWidgets.QWidget):		class AdditiveViewer(QtWidgets.QWidget):
	@@ -1066,6 +1039,6 @@ if __name__ == '__main__':
	app = QtWidgets.QApplication(sys.argv)		app = QtWidgets.QApplication(sys.argv)
	meas = ParticleAnalysis(None)		meas = ParticleAnalysis(None)
	meas.showMaximized()		meas.showMaximized()
	ret = app.exec_()		return app.exec_()

	run()		run()
			No newline at end of file

analysis/editParticles.py

+8 −1

Original line number	Original line	Diff line number	Diff line
	@@ -52,6 +52,8 @@ class ParticleEditor(object):
	def combineParticles(self, contourIndices, new_assignment):		def combineParticles(self, contourIndices, new_assignment):
	if new_assignment == 'other':		if new_assignment == 'other':
	new_assignment = self.getNewEntry()		new_assignment = self.getNewEntry()
			if new_assignment is None:
			return

	contourIndices = sorted(contourIndices) #we want to keep the contour with lowest index		contourIndices = sorted(contourIndices) #we want to keep the contour with lowest index
	print('merging contours:', contourIndices)		print('merging contours:', contourIndices)
	@@ -80,6 +82,9 @@ class ParticleEditor(object):

	img = np.uint8(cv2.morphologyEx(img, cv2.MORPH_CLOSE, np.ones((3, 3))))		img = np.uint8(cv2.morphologyEx(img, cv2.MORPH_CLOSE, np.ones((3, 3))))

			if cv2.__version__ > '3.5':
			contours, hierarchy = cv2.findContours(img, cv2.RETR_CCOMP, cv2.CHAIN_APPROX_NONE)
			else:
	temp, contours, hierarchy = cv2.findContours(img, cv2.RETR_CCOMP, cv2.CHAIN_APPROX_NONE)		temp, contours, hierarchy = cv2.findContours(img, cv2.RETR_CCOMP, cv2.CHAIN_APPROX_NONE)

	newContour = contours[0]		newContour = contours[0]
	@@ -139,6 +144,8 @@ class ParticleEditor(object):
	def reassignParticles(self, contourindices, new_assignment):		def reassignParticles(self, contourindices, new_assignment):
	if new_assignment == 'other':		if new_assignment == 'other':
	new_assignment = self.getNewEntry()		new_assignment = self.getNewEntry()
			if new_assignment is None:
			return

	self.createSafetyBackup()		self.createSafetyBackup()
	print(f'reassigning indices {contourindices} into {new_assignment}')		print(f'reassigning indices {contourindices} into {new_assignment}')

segmentation.py

+9 −2

Original line number	Original line	Diff line number	Diff line
	@@ -197,6 +197,9 @@ class Segmentation(object):
	def erodeConvexDefects(self, thresh, numiter):		def erodeConvexDefects(self, thresh, numiter):
	thresh = cv2.copyMakeBorder(thresh, 1, 1, 1, 1, 0)		thresh = cv2.copyMakeBorder(thresh, 1, 1, 1, 1, 0)
	for iterations in range(numiter):		for iterations in range(numiter):
			if cv2.__version__ > '3.5':
			contours, hierarchy = cv2.findContours(thresh.copy(), cv2.RETR_TREE, cv2.CHAIN_APPROX_SIMPLE)
			else:
	thresh2, contours, hierarchy = cv2.findContours(thresh.copy(), cv2.RETR_TREE, cv2.CHAIN_APPROX_SIMPLE)		thresh2, contours, hierarchy = cv2.findContours(thresh.copy(), cv2.RETR_TREE, cv2.CHAIN_APPROX_SIMPLE)
	for cnt in contours:		for cnt in contours:
	hull = cv2.convexHull(cnt, returnPoints = False)		hull = cv2.convexHull(cnt, returnPoints = False)
	@@ -387,6 +390,10 @@ class Segmentation(object):
	if return_step=="watershed":		if return_step=="watershed":
	return np.uint8(255*(markers!=0)), 0		return np.uint8(255*(markers!=0)), 0


			if cv2.__version__ > '3.5':
			contours, hierarchy = cv2.findContours(markers, cv2.RETR_CCOMP, cv2.CHAIN_APPROX_NONE)
			else:
	temp, contours, hierarchy = cv2.findContours(markers, cv2.RETR_CCOMP, cv2.CHAIN_APPROX_NONE)		temp, contours, hierarchy = cv2.findContours(markers, cv2.RETR_CCOMP, cv2.CHAIN_APPROX_NONE)
	print("contours")		print("contours")
	if self.cancelcomputation:		if self.cancelcomputation: