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	Diff line number	Diff line
		#!/usr/bin/env python3
		# -- coding: utf-8 --
		#!/usr/bin/env python3
		"""
		GEPARD - Gepard-Enabled PARticle Detection
		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/>.
		"""

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

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

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

		self.spectraResults = None #entire List of all spectra assignments
		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.spectra = None #acquired spectra
		self.indices = None #assignment of what spectra-indices belong to what substance
		self.expWindow = None
		self.additivePlot = None
		self.importWindow = None
		self.directory = None
		@@ -573,18 +571,13 @@ class ParticleAnalysis(QtWidgets.QMainWindow):
		self.createPolymerOverlay()

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

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


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


		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()
		except: pass
		self.parent.imparent.particelAnalysisAct.setChecked(False)
		event.accept()


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

		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()

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

		#create header:
		self.finalData[0, :] = np.array(requiredcolumns)
		self.finalData[0, 0] = 'Polymer Type'

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

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

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

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

		rowindex = rowindex + numentries

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

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

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

		def closeEvent(self, event):
		if self.expWin is not None:
		self.expWin.close()
		event.accept()
		particleclasses = np.array(particleclasses)
		report = pd.DataFrame(np.array(particleclasses), columns=header,
		dtype=int)
		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):
		@@ -1066,6 +1039,6 @@ if __name__ == '__main__':
		app = QtWidgets.QApplication(sys.argv)
		meas = ParticleAnalysis(None)
		meas.showMaximized()
		ret = app.exec_()
		return app.exec_()

		run()
		No newline at end of file

analysis/editParticles.py

+8 −1

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

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

		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)

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

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

segmentation.py

+9 −2

Original line number	Diff line number	Diff line
		@@ -197,6 +197,9 @@ class Segmentation(object):
		def erodeConvexDefects(self, thresh, numiter):
		thresh = cv2.copyMakeBorder(thresh, 1, 1, 1, 1, 0)
		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)
		for cnt in contours:
		hull = cv2.convexHull(cnt, returnPoints = False)
		@@ -387,6 +390,10 @@ class Segmentation(object):
		if return_step=="watershed":
		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)
		print("contours")
		if self.cancelcomputation: