analysisview.py: moved ExpExcelDialog and AdditiveViewer to new analysiswidgets.py (6b9fc03c) · Commits · GEPARD / GEPARD

analysis/analysisview.py

+2 −177

Original line number	Diff line number	Diff line
		@@ -22,7 +22,6 @@ If not, see <https://www.gnu.org/licenses/>.

		from PyQt5 import QtCore, QtGui, QtWidgets
		import numpy as np
		import pandas as pd
		import sys
		import operator
		import os
		@@ -33,11 +32,12 @@ 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, AdditiveViewer
		from .loadresults import LoadWITecResults
		from .editParticles import ParticleEditor
		from .database import DataBaseWindow
		try:
		from analysis.sqlexport import SQLExport
		from .sqlexport import SQLExport
		sqlEnabled = True
		except:
		sqlEnabled = False
		@@ -857,181 +857,6 @@ class ParticleAnalysis(QtWidgets.QMainWindow):
		event.accept()


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

		self.parent = parent
		self.particles = self.parent.particlestats
		self.polymers = self.parent.particleResults
		self.additives = self.parent.currentAdditives
		self.hqis = self.parent.hqis

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

		excelvbox = QtWidgets.QVBoxLayout()
		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.checkBoxes = []
		self.sizeClasses = [5, 10, 20, 50, 100, 1e6]
		self.directory = self.parent.parent.dataset.path

		for index, option in enumerate(self.exportOptions):
		self.checkBoxes.append(QtWidgets.QCheckBox(self))
		self.checkBoxes[-1].setText(option)
		self.checkBoxes[-1].setChecked(True)

		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()
		self.xlsFileName.setText('{}_Particle_List'.format(self.parent.parent.dataset.name))
		excelvbox.addWidget(QtWidgets.QLabel('Filename:'))
		excelvbox.addWidget(self.xlsFileName)

		self.exlbtn = QtWidgets.QPushButton('Export to Excel')
		self.exlbtn.resize(self.exlbtn.sizeHint())
		self.exlbtn.clicked.connect(self.toExcel)

		excelvbox.addWidget(self.exlbtn)
		excelgroup.setLayout(excelvbox)

		self.layout.addWidget(excelgroup)

		self.show()

		def toExcel(self):
		requiredcolumns = []
		self.sizes = np.round(np.array([i[0] if np.isnan(i[2]) else i[2] for i in self.particles]), 1)
		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
		elif box.text() == 'Short Size (µm)':
		shortSize = np.round(np.array([i[1] if np.isnan(i[3]) else i[3] for i in self.particles]), 1)
		elif box.text() == 'Area (µm²)':
		area = np.array([np.round(float(entry[4]), 1) for entry in self.particles])
		else:
		requiredcolumns.append('0 - 5 µm')
		requiredcolumns.append('5 - 10 µm')
		requiredcolumns.append('10 - 20 µm')
		requiredcolumns.append('20 - 50 µm')
		requiredcolumns.append('50 - 100 µm')
		requiredcolumns.append('> 100 µm')

		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 = 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)':
		polymertypes[rowindex:rowindex+numentries] = self.polymers[indices]
		if column == 'Additives':
		finalData[rowindex:rowindex+numentries, colindex-1] = self.additives[indices]
		if column == 'Long Size (µm)':
		finalData[rowindex:rowindex+numentries, colindex-1] = longSize[indices]
		if column == 'Short Size (µm)':
		finalData[rowindex:rowindex+numentries, colindex-1] = shortSize[indices]
		if column == 'Area (µm²)':
		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) - 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
		else: lowLimit = self.sizeClasses[classindex-1]
		curSize = self.sizes[dataindex]

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

		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
		incr = 1
		while not validFileName:
		if not os.path.exists(xlsname):
		validFileName = True
		else:
		xlsname = self.directory + self.xlsFileName.text() + ' {}.xlsx'.format(incr)
		incr += 1

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

		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
		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')
		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(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):
		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)


		if __name__ == '__main__':
		def run():
		app = QtWidgets.QApplication(sys.argv)

analysis/analysiswidgets.py

0 → 100644

+204 −0

Original line number	Diff line number	Diff line
		# -- coding: utf-8 --
		"""
		GEPARD - Gepard-Enabled PARticle Detection
		Copyright (C) 2018 Lars Bittrich and Josef Brandt, Leibniz-Institut für
		Polymerforschung Dresden e. V. <bittrich-lars@ipfdd.de>

		This program is free software: you can redistribute it and/or modify
		it under the terms of the GNU General Public License as published by
		the Free Software Foundation, either version 3 of the License, or
		(at your option) any later version.

		This program is distributed in the hope that it will be useful,
		but WITHOUT ANY WARRANTY; without even the implied warranty of
		MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
		GNU General Public License for more details.

		You should have received a copy of the GNU General Public License
		along with this program, see COPYING.
		If not, see <https://www.gnu.org/licenses/>.
		"""

		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, parent):
		super(ExpExcelDialog, self).__init__()
		self.setWindowTitle('Export Options')
		self.setGeometry(200,200, 300, 300)

		self.parent = parent
		self.particles = self.parent.particlestats
		self.polymers = self.parent.particleResults
		self.additives = self.parent.currentAdditives
		self.hqis = self.parent.hqis

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

		excelvbox = QtWidgets.QVBoxLayout()
		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.checkBoxes = []
		self.sizeClasses = [5, 10, 20, 50, 100, 1e6]
		self.directory = self.parent.parent.dataset.path

		for index, option in enumerate(self.exportOptions):
		self.checkBoxes.append(QtWidgets.QCheckBox(self))
		self.checkBoxes[-1].setText(option)
		self.checkBoxes[-1].setChecked(True)

		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()
		self.xlsFileName.setText('{}_Particle_List'.format(self.parent.parent.dataset.name))
		excelvbox.addWidget(QtWidgets.QLabel('Filename:'))
		excelvbox.addWidget(self.xlsFileName)

		self.exlbtn = QtWidgets.QPushButton('Export to Excel')
		self.exlbtn.resize(self.exlbtn.sizeHint())
		self.exlbtn.clicked.connect(self.toExcel)

		excelvbox.addWidget(self.exlbtn)
		excelgroup.setLayout(excelvbox)

		self.layout.addWidget(excelgroup)

		self.show()

		def toExcel(self):
		requiredcolumns = []
		self.sizes = np.round(np.array([i[0] if np.isnan(i[2]) else i[2] for i in self.particles]), 1)
		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
		elif box.text() == 'Short Size (µm)':
		shortSize = np.round(np.array([i[1] if np.isnan(i[3]) else i[3] for i in self.particles]), 1)
		elif box.text() == 'Area (µm²)':
		area = np.array([np.round(float(entry[4]), 1) for entry in self.particles])
		else:
		requiredcolumns.append('0 - 5 µm')
		requiredcolumns.append('5 - 10 µm')
		requiredcolumns.append('10 - 20 µm')
		requiredcolumns.append('20 - 50 µm')
		requiredcolumns.append('50 - 100 µm')
		requiredcolumns.append('> 100 µm')

		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 = 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)':
		polymertypes[rowindex:rowindex+numentries] = self.polymers[indices]
		if column == 'Additives':
		finalData[rowindex:rowindex+numentries, colindex-1] = self.additives[indices]
		if column == 'Long Size (µm)':
		finalData[rowindex:rowindex+numentries, colindex-1] = longSize[indices]
		if column == 'Short Size (µm)':
		finalData[rowindex:rowindex+numentries, colindex-1] = shortSize[indices]
		if column == 'Area (µm²)':
		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) - 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
		else: lowLimit = self.sizeClasses[classindex-1]
		curSize = self.sizes[dataindex]

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

		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
		incr = 1
		while not validFileName:
		if not os.path.exists(xlsname):
		validFileName = True
		else:
		xlsname = self.directory + self.xlsFileName.text() + ' {}.xlsx'.format(incr)
		incr += 1

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

		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
		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')
		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(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):
		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