TrueMatch Import reworked (37779a2b) · Commits · GEPARD / GEPARD

analysis/analysisview.py

+7 −3

Original line number	Diff line number	Diff line
		@@ -301,8 +301,11 @@ class ParticleAnalysis(QtWidgets.QMainWindow):
		self.refSelector.setDisabled(False)

		def importTrueMatchResults(self):
		if self.importWindow is not None:
		del self.importWindow

		self.importWindow = LoadTrueMatchResults(self.particleContainer, self)
		self.importWindow.exec()
		# self.importWindow.exec()

		@QtCore.pyqtSlot()
		def applyHQIThresholdToResults(self):
		@@ -622,8 +625,9 @@ class ParticleAnalysis(QtWidgets.QMainWindow):

		def closeEvent(self, event):
		for window in [self.importWindow, self.dbWin]:
		try: window.close()
		except: pass
		if window is not None:
		window.close()

		self.viewparent.imparent.particelAnalysisAct.setChecked(False)
		event.accept()

analysis/loadresults.py

+173 −122

Original line number	Diff line number	Diff line
		@@ -21,10 +21,11 @@ If not, see <https://www.gnu.org/licenses/>.
		"""

		import numpy as np
		from PyQt5 import QtWidgets
		import os
		from PyQt5 import QtWidgets, QtCore

		class LoadTrueMatchResults(QtWidgets.QDialog):
		def __init__(self, particleContainer, parent):
		class LoadTrueMatchResults(QtWidgets.QWidget):
		def __init__(self, particleContainer, analysisParent):
		super(LoadTrueMatchResults, self).__init__()
		self.setGeometry(400, 400, 200, 300)
		self.setWindowTitle('Get Truematch Results')
		@@ -32,8 +33,8 @@ class LoadTrueMatchResults(QtWidgets.QDialog):
		self.setLayout(self.layout)

		self.particleContainer = particleContainer
		self.parent = parent
		self.parent.setDisabled(True)
		self.analysisParent = analysisParent
		self.analysisParent.setDisabled(True)
		self.trueMatchResults = None
		self.polymertypes = None
		self.additives = None
		@@ -42,7 +43,7 @@ class LoadTrueMatchResults(QtWidgets.QDialog):

		self.loadBtn = QtWidgets.QPushButton('LoadTrueMatchResults')
		self.loadBtn.resize(self.loadBtn.sizeHint())
		self.loadBtn.clicked.connect(self.loadFileManually)
		self.loadBtn.clicked.connect(self.getImportFiles)

		self.reviewGroup = QtWidgets.QGroupBox('Review Changes')
		self.reviewGroup.setDisabled(True)
		@@ -59,39 +60,35 @@ class LoadTrueMatchResults(QtWidgets.QDialog):

		self.manualPolymers = {}
		self.manualAdditives = {}
		self.expWindow = None
		self.additivePlot = None
		self.editEntryWindow = None
		self.sortWindow = None

		self.numFlagForTakeSpectrum = 1
		self.numFlagForSetUnknown = 2
		self.numFlagForPrompt = 3
		self.show()

		def show3FlagsReview(self):
		self.editEntryWindow = ModifyManualEdits(self, self.manualPolymers, self.manualAdditives)
		self.editEntryWindow.show()

		def loadFileManually(self):
		dsetpath = self.parent.dataset.path
		fnames =QtWidgets.QFileDialog.getOpenFileNames(self, 'Select TrueMatch result file', dsetpath, 'text file (*.txt)')[0]
		if len(fnames) > 1:
		QtWidgets.QMessageBox.about(self, 'Info', 'The following order of files was loaded. If incorrect, please call a coder!\n{}'.format('\n'.join([fname for fname in fnames])))
		def getImportFiles(self):
		dsetpath = self.analysisParent.dataset.path
		self.fnames =QtWidgets.QFileDialog.getOpenFileNames(self, 'Select TrueMatch result file', dsetpath, 'text file (*.txt)')[0]
		self.trueMatchResults = []
		for fileindex, fname in enumerate(fnames):
		with open(fname) as file:
		if fileindex == 0:
		for line in file:
		self.trueMatchResults.append(line)
		else: ##for additional files skip first line (header..)
		for lineindex, line in enumerate(file):
		if lineindex > 0:
		self.trueMatchResults.append(line)
		if len(self.fnames) > 1:
		self.sortWindow = SortImportFiles(self, self.fnames)
		else:
		self.runCalculations()

		def formatResults(self, rawResults): #get rid of header line, first data interpretation
		results = []
		for index, line in enumerate(rawResults):
		if index == 0:
		def runCalculations(self):
		allResults = []
		numSpectra = 0
		for fileindex, fname in enumerate(self.fnames):
		with open(fname) as file:
		currentResults = []
		for lineIndex, line in enumerate(file):
		if lineIndex == 0:
		line = line.strip().split(';')[:-1] #disregard the last entry of each line, as each line ends with ; <- that produces an empty entry...
		assert line[0] == 'Search Spectrum Name', 'Assertion Error in loadTrueMatchResults'
		#detect, whether one- or multicomponent-search was done
		@@ -102,50 +99,83 @@ class LoadTrueMatchResults(QtWidgets.QDialog):
		numhits = np.int(line[-1].split(' ')[-1])
		numcomps = np.int(line[-1].split(' ')[-3])
		else:
		results.append(line)
		currentResults.append(line)
		numSpectra += 1

		allResults.append(currentResults)

		if numSpectra > 0:
		print('{} components, {} hits per sample, {} spectra'.format(numcomps, numhits, numSpectra))

		self.polymertypes = [None]*numSpectra
		self.hqis = [None]*numSpectra
		if numcomps > 1:
		self.additives = [None]*numSpectra
		self.addhqis = [None]*numSpectra

		addedIndices = []
		numSpectraInPreviousBatches = 0

		for resBatchIndex, resBatch in enumerate(allResults):
		print('spectra in batch:', len(resBatch))
		for result in resBatch:
		specIndex, polymertype, additive, hqi, addhqi = self.interpretEntry(resBatchIndex, numSpectraInPreviousBatches, result, numhits, numcomps)

		self.polymertypes[specIndex] = polymertype
		self.hqis[specIndex] = hqi
		if numcomps > 1:
		self.additives[specIndex] = additive
		self.addhqis[specIndex] = addhqi

		addedIndices.append(specIndex)

		numSpectraInPreviousBatches = len(addedIndices)
		print(numSpectraInPreviousBatches)

		assert sorted(addedIndices) == list(range(numSpectra)), f'mismatch in sorted indices in loadResults\bAdded {len(addedIndices)} assignments to {numSpectra} spectra'
		assert not None in self.polymertypes, 'wrong assignments in loadResults'
		assert not None in self.hqis, 'wrong assignments in loadResults'

		numspectra = len(results)
		if numspectra > 0:
		print('{} components, {} hits per sample, {} spectra'.format(numcomps, numhits, numspectra))
		self.particleContainer.applyAssignmentListToParticleMeasurements(self.polymertypes)
		self.particleContainer.applyHQIListToParticleMeasurements(self.hqis)

		return results, numspectra, numcomps, numhits
		if len(self.manualPolymers) > 0:
		self.reviewGroup.setDisabled(False)

		self.analysisParent.applyHQIThresholdToResults()
		self.loadBtn.setText('Data loaded')
		QtWidgets.QMessageBox.about(self, 'Success', 'Results were imported successfully.\nYou can close this window or modify manual edits.')

		def interpretEntry(self, entry, numhits, numcomps):
		entry = entry.split(';')
		def interpretEntry(self, resBatchIndex, numSpectraInPreviousBatches, result, numhits, numcomps):
		result = result.split(';')
		specIndex, polymertype, additive, hqi, addhqi = None, None, None, None, 0 #assign defaults

		#specNameFormat is: SampleName_000_Spec.Data 1 (SpecIndex)
		specName = entry[0]
		indexOpenBracket = specName.find('(')
		indexCloseBracket = specName.find(')')
		inbrackets = specName[indexOpenBracket+1:indexCloseBracket]
		try:
		specIndex = int(inbrackets)
		except:
		print(inbrackets)
		raise
		specName = result[0]
		curSpecIndex = self.getSpecIndexFromName(specName)
		specIndex = numSpectraInPreviousBatches + curSpecIndex

		#find yes-flags
		flags = np.where(np.array(entry) == 'yes')[0]
		flags = np.where(np.array(result) == 'yes')[0]
		if len(flags) == 0:
		#take highest HQI entry
		if numcomps == 1:
		polymertype = entry[2]
		hqi = entry[1]
		polymertype = result[2]
		hqi = result[1]
		else:
		polymertype = entry[5]
		hqi = entry[1]
		additive = entry[7]
		addhqi = entry[6]
		polymertype = result[5]
		hqi = result[1]
		additive = result[7]
		addhqi = result[6]

		elif len(flags) == 1:
		#exactly one flag was placed, take this entry
		if numcomps == 1:
		polymertype = entry[int(flags[0])-1]
		polymertype = result[int(flags[0])-1]
		hqi = 100
		else:
		polymertype = entry[int(flags[0])+2]
		additive = entry[int(flags[0])+4]
		polymertype = result[int(flags[0])+2]
		additive = result[int(flags[0])+4]
		hqi = 100
		addhqi = 100

		@@ -158,69 +188,92 @@ class LoadTrueMatchResults(QtWidgets.QDialog):

		elif len(flags) == 3:
		hqi = 100
		if specIndex not in self.manualPolymers:
		polymertype, ok = QtWidgets.QInputDialog.getText(self, 'Name of main component', 'Spectrum at index {} is:'.format(specIndex))
		self.manualPolymers[specIndex] = polymertype
		if (curSpecIndex, resBatchIndex) not in self.manualPolymers:
		polymertype, ok = QtWidgets.QInputDialog.getText(self, 'Name of main component', 'Spectrum at index {} of result file {} is:'.format(curSpecIndex, resBatchIndex+1))
		self.manualPolymers[(curSpecIndex, resBatchIndex)] = polymertype
		else:
		polymertype = self.manualPolymers[specIndex]
		polymertype = self.manualPolymers[(curSpecIndex, resBatchIndex)]
		if numcomps > 1:
		addhqi = 100
		if entry[0] not in self.manualAdditives:
		additive, ok = QtWidgets.QInputDialog.getText(self, 'Name of additive', 'Additive at index {} is:'.format(specIndex))
		self.manualAdditives[specIndex] = additive
		if (curSpecIndex, resBatchIndex) not in self.manualAdditives:
		additive, ok = QtWidgets.QInputDialog.getText(self, 'Name of additive', 'Additive at index {} of result file {} is:'.format(curSpecIndex, resBatchIndex+1))
		self.manualAdditives[(curSpecIndex, resBatchIndex)] = additive
		else:
		additive = self.manualAdditives[specIndex]
		additive = self.manualAdditives[(curSpecIndex, resBatchIndex)]
		else:
		QtWidgets.QMessageBox.about(self, 'Error!', 'No rule for {} flags, found at spectrum index {}'.format(len(flags), specIndex))

		return specIndex, polymertype, additive, float(hqi), float(addhqi)

		def runCalculations(self):
		self.resultList, numspectra, numcomps, numhits = self.formatResults(self.trueMatchResults)
		self.polymertypes = [None]*numspectra
		self.hqis = [None]*numspectra

		if numcomps == 1: #####SINGLE COMPONENT SEARCH
		self.additives = None
		self.addhqis = None
		for index, entry in enumerate(self.resultList):
		if len(entry) == 0:
		del self.resultList[index]
		def getSpecIndexFromName(self, specName):
		number = ''
		for i in reversed(range(len(specName))):
		if specName[i] == ')':
		continue
		if specName[i] != '(':
		number = specName[i] + number
		else:
		specIndex, polymertype, additive, hqi, addhqi = self.interpretEntry(entry, numhits, numcomps)
		self.polymertypes[specIndex] = polymertype
		self.hqis[specIndex] = hqi

		else: #####MULTI-COMPONENT SEARCH
		self.additives = [None]*numspectra
		self.addhqis = [None]*numspectra
		break
		return int(number)

		for index, entry in enumerate(self.resultList):
		if len(entry) > 0:
		specIndex, polymertype, additive, hqi = self.interpretEntry(entry, numhits, numcomps)
		self.polymertypes[specIndex] = polymertype
		self.hqis[specIndex] = hqi
		self.additives[specIndex] = additive
		self.addhqis[specIndex] = addhqi
		def closeEvent(self, event):
		for win in [self.editEntryWindow, self.sortWindow]:
		if win is not None:
		win.close()

		assert len(self.polymertypes) == len(self.resultList), 'incorrect number of polymer types added...'
		assert not None in self.polymertypes, 'wrong assignments in loadResults'
		assert not None in self.hqis, 'wrong assignments in loadResults'
		self.analysisParent.setEnabled(True)
		event.accept()

		self.particleContainer.applyAssignmentListToParticleMeasurements(self.polymertypes)
		self.particleContainer.applyHQIListToParticleMeasurements(self.hqis)

		if len(self.manualPolymers) > 0:
		self.reviewGroup.setDisabled(False)
		class SortImportFiles(QtWidgets.QWidget):
		def __init__(self, loadResultsParent, importFiles):
		super(SortImportFiles, self).__init__()
		self.setWindowTitle('Sort Import Files')
		self.loadResultsParent = loadResultsParent
		self.loadResultsParent.setDisabled(True)
		self.importFiles = importFiles
		self.spinBoxes = []
		layout = QtWidgets.QGridLayout()
		self.setLayout(layout)

		self.parent.applyHQIThresholdToResults()
		self.loadBtn.setText('Data loaded')
		QtWidgets.QMessageBox.about(self, 'Success', 'Results were imported successfully.\nYou can close this window or modify manual edits.')
		label1 = QtWidgets.QLabel('File name')
		label1.setMinimumWidth(150)
		label2 = QtWidgets.QLabel('Order')
		label2.setMinimumWidth(50)

		layout.addWidget(label1, 0, 0, QtCore.Qt.AlignLeft)
		layout.addWidget(label2, 0, 1, QtCore.Qt.AlignRight)

		for fileIndex, importFile in enumerate(self.importFiles):
		layout.addWidget(QtWidgets.QLabel(os.path.basename(importFile)), 1+fileIndex, 0, QtCore.Qt.AlignLeft)
		newSpinBox = QtWidgets.QSpinBox()
		newSpinBox.setMaximumWidth(50)
		newSpinBox.setMinimum(1)
		newSpinBox.setMaximum(len(self.importFiles))
		newSpinBox.setValue(fileIndex+1)
		layout.addWidget(newSpinBox, 1+fileIndex, 1, QtCore.Qt.AlignRight)
		self.spinBoxes.append(newSpinBox)

		self.acceptBtn = QtWidgets.QPushButton('Accept and Close')
		self.acceptBtn.clicked.connect(self.sortResultFiles)
		layout.addWidget(self.acceptBtn, fileIndex+2, 0, QtCore.Qt.AlignLeft)

		self.show()

		def sortResultFiles(self):
		order = [box.value()-1 for box in self.spinBoxes]
		if list(np.unique(order)) != list(range(len(self.spinBoxes))):
		QtWidgets.QMessageBox.critical(self, 'Error', 'Invalid order indicated')
		return
		else:
		newFiles = []
		for index in order:
		newFiles.append(self.importFiles[index])

		def closeEvent(self, event):
		#TODO: SANITY CHECK FOR DATA CONSISTENCY!!
		self.parent.setEnabled(True)
		event.accept()
		self.loadResultsParent.fnames = newFiles
		self.loadResultsParent.runCalculations()
		self.loadResultsParent.setDisabled(False)
		self.close()


		class ModifyManualEdits(QtWidgets.QWidget):
		@@ -242,14 +295,13 @@ class ModifyManualEdits(QtWidgets.QWidget):
		groupLayout = QtWidgets.QGridLayout()

		#create Labels and LineEdits
		for index in self.polymerEdits:
		self.labels.append(QtWidgets.QLabel('Spectrum index:' + str(index)))
		print(self.labels[-1].text())
		for curSpecIndex, resBatchIndex in self.polymerEdits:
		self.labels.append(QtWidgets.QLabel(f'Index of Spectrum: {curSpecIndex}, in file number: {resBatchIndex+1}'))
		self.polymerLineEdits.append(QtWidgets.QLineEdit())
		self.polymerLineEdits[-1].setText(self.polymerEdits[index])
		self.polymerLineEdits[-1].setText(self.polymerEdits[(curSpecIndex, resBatchIndex)])
		if len(self.additiveEdits) > 0:
		self.additiveLineEdits.append(QtWidgets.QLineEdit())
		self.additiveLineEdits[-1].setText(self.additiveEdits[index])
		self.additiveLineEdits[-1].setText(self.additiveEdits[(curSpecIndex, resBatchIndex)])

		for i in range(len(self.labels)):
		groupLayout.addWidget(self.labels[i], i, 0)
		@@ -265,10 +317,10 @@ class ModifyManualEdits(QtWidgets.QWidget):
		layout.addWidget(scrollarea)

		saveAndCloseBtn = QtWidgets.QPushButton('Save and Exit')
		saveAndCloseBtn.clicked.connect(self.closeEvent)
		saveAndCloseBtn.clicked.connect(self.saveAndClose)
		layout.addWidget(saveAndCloseBtn)

		def closeEvent(self, event):
		def saveAndClose(self):
		#read out LineEdits:
		for index, key in enumerate(self.polymerEdits):
		self.polymerEdits[key] = self.polymerLineEdits[index].text()
		@@ -279,4 +331,3 @@ class ModifyManualEdits(QtWidgets.QWidget):
		self.parent.manualPolymers, self.parent.manualAdditives = self.polymerEdits, self.additiveEdits
		self.parent.runCalculations()
		self.close()

analysis/particleCharacterization.py

0 → 100644

+45 −0

Original line number	Diff line number	Diff line
		#!/usr/bin/env python3
		# -- 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/>.
		"""

		import numpy as np
		import cv2

		def getContourStatsWithPixelScale(cnt, pixelscale):
		long, short, longellipse, shortellipse, area = getContourStats(cnt)
		return longpixelscale, shortpixelscale, longellipsepixelscale, shortellipsepixelscale, areapixelscale*2

		def getContourStats(cnt):
		##characterize particle
		longellipse, shortellipse = np.nan, np.nan

		if cnt.shape[0] >= 5: ##at least 5 points required for ellipse fitting...
		ellipse = cv2.fitEllipse(cnt)
		shortellipse, longellipse = ellipse[1]

		rect = cv2.minAreaRect(cnt)
		long, short = rect[1]
		if short>long:
		long, short = short, long

		area = cv2.contourArea(cnt)

		return long, short, longellipse, shortellipse, area
		No newline at end of file

analysis/particleEditor.py

+1 −18

Original line number	Diff line number	Diff line
		@@ -31,25 +31,8 @@ from PyQt5 import QtWidgets, QtCore
		from copy import deepcopy

		from .particlePainter import ParticlePainter
		from .particleCharacterization import getContourStatsWithPixelScale

		def getContourStatsWithPixelScale(contours, pixelscale):
		##characterize particle
		longellipse, shortellipse = np.nan, np.nan

		cnt = contours

		if cnt.shape[0] >= 5: ##at least 5 points required for ellipse fitting...
		ellipse = cv2.fitEllipse(cnt)
		shortellipse, longellipse = ellipse[1]

		rect = cv2.minAreaRect(cnt)
		long, short = rect[1]
		if short>long:
		long, short = short, long

		area = cv2.contourArea(cnt)

		return longpixelscale, shortpixelscale, longellipsepixelscale, shortellipsepixelscale, areapixelscale*2


		class ParticleContextMenu(QtWidgets.QMenu):

segmentation.py

+5 −18

Original line number	Diff line number	Diff line
		@@ -28,6 +28,8 @@ from skimage.feature import peak_local_max
		from skimage.morphology import watershed
		from random import random

		from .analysis.particleCharacterization import getContourStats

		class Parameter(object):
		def __init__(self, name, dtype, value=None, minval=None, maxval=None,
		decimals=0, stepsize=1, helptext=None, show=False, linkedParameter=None):
		@@ -283,21 +285,6 @@ class Segmentation(object):
		sure_fg = cv2.dilate(sure_fg, np.ones((3, 3)))
		return sure_fg

		def characterizeParticle(self, contours):
		longellipse, shortellipse = np.nan, np.nan

		cnt = contours

		if cnt.shape[0] >= 5: ##at least 5 points required for ellipse fitting...
		ellipse = cv2.fitEllipse(cnt)
		shortellipse, longellipse = ellipse[1]
		rect = cv2.minAreaRect(cnt)
		long, short = rect[1]
		if short>long:
		long, short = short, long

		return long, short, longellipse, shortellipse, cv2.contourArea(cnt)

		def getMeasurementPoints(self, binParticle, numPoints=1):
		binParticle = cv2.copyMakeBorder(binParticle, 1, 1, 1, 1, 0)
		dist = cv2.distanceTransform(np.uint8(binParticle), cv2.DIST_L2,3)
		@@ -449,7 +436,6 @@ class Segmentation(object):
		img[np.nonzero(sure_bg)] \|= 2
		return img, 1


		dist_transform = cv2.distanceTransform(thresh, cv2.DIST_L2,5)
		print("distanceTransform")
		if self.cancelcomputation:
		@@ -484,7 +470,8 @@ class Segmentation(object):
		label = markers[cnt[0,0,1],cnt[0,0,0]]
		if label==0:
		continue
		particlestats.append(self.characterizeParticle(cnt))
		stats = getContourStats(cnt)
		particlestats.append(stats)
		x0, x1 = cnt[:,0,0].min(), cnt[:,0,0].max()
		y0, y1 = cnt[:,0,1].min(), cnt[:,0,1].max()
		subimg = (markers[y0:y1+1,x0:x1+1]).copy()