Reworking particle and analysis handling (ca5e6bad) · Commits · GEPARD / GEPARD

analysis/analysisplots.py

+24 −24

Original line number	Diff line number	Diff line
		@@ -132,30 +132,30 @@ class SpectraPlot(QtWidgets.QGroupBox):
		self.setLayout(layout)

		def loadSpectraAndInitializeSpecPlot(self): #formerly updateData(self)....
		def tryLoadingNumpySpecFile():
		specPath = self.dataset.getSpectraFileName()
		if os.path.exists(specPath):
		return np.load(specPath)
		else:
		raise ImportError
		try:
		self.spectra = tryLoadingNumpySpecFile()
		except ImportError:

		fname = QtWidgets.QFileDialog.getOpenFileName(QtWidgets.QWidget(), 'Select Spectra File', self.dataset.path, 'text file (*.txt)')[0]

		try:
		self.spectra, spectraNames = importSpectra.importWITecSpectra(fname)
		except ImportError:
		try:
		self.spectra, spectraNames = importSpectra.importRenishawSpectra(fname)
		except ImportError:
		self.spectra, spectraNames = importSpectra.importPerkinElmerSpectra(fname)

		if self.spectra is None:
		raise ImportError
		else:
		np.save(self.dataset.getSpectraFileName(), self.spectra)
		# def tryLoadingNumpySpecFile():
		# specPath = self.dataset.getSpectraFileName()
		# if os.path.exists(specPath):
		# return np.load(specPath)
		# else:
		# raise ImportError
		# try:
		# self.spectra = tryLoadingNumpySpecFile()
		# except ImportError:
		#
		# fname = QtWidgets.QFileDialog.getOpenFileName(QtWidgets.QWidget(), 'Select Spectra File', self.dataset.path, 'text file (*.txt)')[0]
		#
		# try:
		# self.spectra, spectraNames = importSpectra.importWITecSpectra(fname)
		# except ImportError:
		# try:
		# self.spectra, spectraNames = importSpectra.importRenishawSpectra(fname)
		# except ImportError:
		# self.spectra, spectraNames = importSpectra.importPerkinElmerSpectra(fname)
		#
		# if self.spectra is None:
		# raise ImportError
		# else:
		# np.save(self.dataset.getSpectraFileName(), self.spectra)

		self.canvas.draw()

analysis/particleAndMeasurement.py

0 → 100644

+174 −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/>.
		"""
		import numpy as np


		class Particle(object):
		def __init__(self):
		super(Particle, self).__init__()
		self.index = None
		self.longSize_ellipse = np.nan
		self.shortSize_ellipse = np.nan
		self.longSize_box = np.nan
		self.shortSize_box = np.nan
		self.area = None
		self.contour = None
		self.measurements = []
		self.viewItem = None

		def addMeasurement(self, refToMeasurement):
		self.measurements.append(refToMeasurement)

		# def addExistingMeasurement(self, meas):
		# self.measurements.append(meas)
		#
		# def addEmptyMeasurement(self):
		# self.measurements.append(Measurement())
		# indexOfNewMeasurment = len(self.measurements)-1
		# return indexOfNewMeasurment

		# def setMeasurementScanIndex(self, indexOfMeasurment, scanIndex):
		# self.measurements[indexOfMeasurment].ramanScanIndex = scanIndex
		#
		# def setMeasurementPixelCoords(self, indexOfMeasurment, x, y):
		# self.measurements[indexOfMeasurment].pixelcoord_x= x
		# self.measurements[indexOfMeasurment].pixelcoord_y = y
		#
		def setAllSpectraToNewAssignment(self, newAssignment):
		for meas in self.measurements:
		meas.setAssignment(newAssignment)
		meas.setHQI(100)

		def getParticleAssignment(self):
		return self.getMeasAssignmentWithHighestHQI() #probably another method could be more suitable...

		def getHighestHQI(self):
		hqis = []
		for meas in self.measurements:
		hqis.append(meas.getHQI())
		return max(hqis)

		def getHQIOfMeasurementIndex(self, index):
		for meas in self.measurements:
		if meas.ramanScanIndex == index:
		return meas.getHQI()

		def getMeasurementIndices(self):
		indices = []
		for meas in self.measurements:
		indices.append(meas.ramanScanIndex)
		return indices

		def getMeasurements(self):
		return self.measurements

		def getMeasAssignmentWithHighestHQI(self):
		hqis = []
		assignments = []
		for meas in self.measurements:
		hqis.append(meas.getHQI())
		assignments.append(meas.getAssignment())
		indexOfHighestHQI = hqis.index(max(hqis))
		return assignments[indexOfHighestHQI]

		def getParticleSize(self):
		if not np.isnan(self.longSize_ellipse):
		size = self.longSize_ellipse
		elif not np.isnan(self.longSize_box):
		size = self.longSize_box
		else:
		print(f'Error, particle size requested, but not yet set.\nParticle Index is {self.index}')
		raise ValueError
		assert size is not None, f'Error, size or particle {self.index} is None'
		return round(size)

		def getShortParticleSize(self):
		if not np.isnan(self.shortSize_ellipse):
		return self.shortSize_ellipse
		elif not np.isnan(self.shortSize_box):
		return self.shortSize_box
		else:
		print(f'Error, particle size requested, but not yet set.\nParticle Index is {self.index}')
		raise ValueError

		def getNumberOfMeasurements(self):
		return len(self.measurements)

		def measurementsHaveSameOrigAssignment(self):
		allResults = [meas.getOrigAssignment() for meas in self.measurements]
		if len(np.unique(allResults)) == 1:
		return True
		elif len(np.unique(allResults)) > 1:
		return False

		def getOrigMeasurementAssignments(self):
		assignments = [meas.getOrigAssignment() for meas in self.measurements]
		return assignments

		def applyHQITresholdToMeasurements(self, minHQI):
		for measurement in self.measurements:
		measurement.applyHQIThreshold(minHQI)

		# def recreateViewItem(self):
		# pass


		class Measurement(object):
		def __init__(self):
		super(Measurement, self).__init__()
		self.ramanScanIndex = None
		self.pixelcoord_x= None
		self.pixelcoord_y = None

		self.assignment_orig = 'Not Evaluated'
		self.assignment_afterHQI = None
		self.hqi = None

		def setAssignment(self, assignment):
		self.assignment_orig = assignment
		self.applyHQIThreshold()

		def setHQI(self, hqi):
		self.hqi = hqi
		self.applyHQIThreshold()

		def applyHQIThreshold(self, minHQI=0):
		if self.hqi is not None: #i.e. skip for initial setup, when hqi is not yet aplied...
		if self.hqi >= minHQI:
		self.assignment_afterHQI = self.assignment_orig
		else:
		self.assignment_afterHQI = 'unknown'

		def getHQI(self):
		return self.hqi

		def getAssignment(self):
		if self.assignment_afterHQI is None:
		return self.assignment_orig
		else:
		return self.assignment_afterHQI

		def getOrigAssignment(self):
		return self.assignment_orig

		def getScanIndex(self):
		return self.ramanScanIndex

analysis/particleInfo.py

+46 −148

Original line number	Diff line number	Diff line
		@@ -20,17 +20,62 @@ If not, see <https://www.gnu.org/licenses/>.
		"""
		import numpy as np
		import operator
		import os
		from PyQt5 import QtWidgets

		from analysis import importSpectra
		from analysis.particleAndMeasurement import Particle, Measurement


		class ParticleContainer(object):
		def __init__(self, datasetParent):
		super(ParticleContainer, self).__init__()
		self.datasetParent = datasetParent
		self.particles = []
		self.measurements = []
		self.spectra = None
		self.inconsistentParticles = []

		self.typeHistogram = None

		def addEmptyMeasurement(self):
		self.measurements.append(Measurement())
		indexOfNewMeas = len(self.measurements)-1
		return indexOfNewMeas

		def setMeasurementScanIndex(self, indexOfMeasurment, scanIndex):
		self.measurements[indexOfMeasurment].ramanScanIndex = scanIndex

		def setMeasurementPixelCoords(self, indexOfMeasurment, x, y):
		self.measurements[indexOfMeasurment].pixelcoord_x = x
		self.measurements[indexOfMeasurment].pixelcoord_y = y

		def loadSpectra(self):
		def tryLoadingNumpySpecFile():
		specPath = self.datasetParent.getSpectraFileName()
		if os.path.exists(specPath):
		return np.load(specPath)
		else:
		raise ImportError
		try:
		self.spectra = tryLoadingNumpySpecFile()
		except ImportError:

		fname = QtWidgets.QFileDialog.getOpenFileName(QtWidgets.QWidget(), 'Select Spectra File', self.datasetParent.path, 'text file (*.txt)')[0]

		try:
		self.spectra, spectraNames = importSpectra.importWITecSpectra(fname)
		except ImportError:
		try:
		self.spectra, spectraNames = importSpectra.importRenishawSpectra(fname)
		except ImportError:
		self.spectra, spectraNames = importSpectra.importPerkinElmerSpectra(fname)

		if self.spectra is None:
		raise ImportError
		else:
		np.save(self.datasetParent.getSpectraFileName(), self.spectra)

		def initializeParticles(self, numParticles):
		self.particles = []
		for i in range(numParticles):
		@@ -246,150 +291,3 @@ class ParticleContainer(object):
		for newIndex, particle in enumerate(self.particles):
		particle.index = newIndex

		class Particle(object):
		def __init__(self):
		super(Particle, self).__init__()
		self.index = None
		self.longSize_ellipse = np.nan
		self.shortSize_ellipse = np.nan
		self.longSize_box = np.nan
		self.shortSize_box = np.nan
		self.area = None
		self.contour = None
		self.measurements = []
		self.viewItem = None

		def addExistingMeasurement(self, meas):
		self.measurements.append(meas)

		def addEmptyMeasurement(self):
		self.measurements.append(Measurement())
		indexOfNewMeasurment = len(self.measurements)-1
		return indexOfNewMeasurment

		def setMeasurementScanIndex(self, indexOfMeasurment, scanIndex):
		self.measurements[indexOfMeasurment].ramanScanIndex = scanIndex

		def setMeasurementPixelCoords(self, indexOfMeasurment, x, y):
		self.measurements[indexOfMeasurment].pixelcoord_x= x
		self.measurements[indexOfMeasurment].pixelcoord_y = y

		def setAllSpectraToNewAssignment(self, newAssignment):
		for meas in self.measurements:
		meas.setAssignment(newAssignment)
		meas.setHQI(100)

		def getParticleAssignment(self):
		return self.getMeasAssignmentWithHighestHQI() #probably another method could be more suitable...

		def getHighestHQI(self):
		hqis = []
		for meas in self.measurements:
		hqis.append(meas.getHQI())
		return max(hqis)

		def getHQIOfMeasurementIndex(self, index):
		for meas in self.measurements:
		if meas.ramanScanIndex == index:
		return meas.getHQI()

		def getMeasurementIndices(self):
		indices = []
		for meas in self.measurements:
		indices.append(meas.ramanScanIndex)
		return indices

		def getMeasurements(self):
		return self.measurements

		def getMeasAssignmentWithHighestHQI(self):
		hqis = []
		assignments = []
		for meas in self.measurements:
		hqis.append(meas.getHQI())
		assignments.append(meas.getAssignment())
		indexOfHighestHQI = hqis.index(max(hqis))
		return assignments[indexOfHighestHQI]

		def getParticleSize(self):
		if not np.isnan(self.longSize_ellipse):
		size = self.longSize_ellipse
		elif not np.isnan(self.longSize_box):
		size = self.longSize_box
		else:
		print(f'Error, particle size requested, but not yet set.\nParticle Index is {self.index}')
		raise ValueError
		assert size is not None, f'Error, size or particle {self.index} is None'
		return round(size)

		def getShortParticleSize(self):
		if not np.isnan(self.shortSize_ellipse):
		return self.shortSize_ellipse
		elif not np.isnan(self.shortSize_box):
		return self.shortSize_box
		else:
		print(f'Error, particle size requested, but not yet set.\nParticle Index is {self.index}')
		raise ValueError

		def getNumberOfMeasurements(self):
		return len(self.measurements)

		def measurementsHaveSameOrigAssignment(self):
		allResults = [meas.getOrigAssignment() for meas in self.measurements]
		if len(np.unique(allResults)) == 1:
		return True
		elif len(np.unique(allResults)) > 1:
		return False

		def getOrigMeasurementAssignments(self):
		assignments = [meas.getOrigAssignment() for meas in self.measurements]
		return assignments

		def applyHQITresholdToMeasurements(self, minHQI):
		for measurement in self.measurements:
		measurement.applyHQIThreshold(minHQI)

		# def recreateViewItem(self):
		# pass


		class Measurement(object):
		def __init__(self):
		super(Measurement, self).__init__()
		self.ramanScanIndex = None
		self.pixelcoord_x= None
		self.pixelcoord_y = None

		self.assignment_orig = 'Not Evaluated'
		self.assignment_afterHQI = None
		self.hqi = None

		def setAssignment(self, assignment):
		self.assignment_orig = assignment
		self.applyHQIThreshold()

		def setHQI(self, hqi):
		self.hqi = hqi
		self.applyHQIThreshold()

		def applyHQIThreshold(self, minHQI=0):
		if self.hqi is not None: #i.e. skip for initial setup, when hqi is not yet aplied...
		if self.hqi >= minHQI:
		self.assignment_afterHQI = self.assignment_orig
		else:
		self.assignment_afterHQI = 'unknown'

		def getHQI(self):
		return self.hqi

		def getAssignment(self):
		if self.assignment_afterHQI is None:
		return self.assignment_orig
		else:
		return self.assignment_afterHQI

		def getOrigAssignment(self):
		return self.assignment_orig

		def getScanIndex(self):
		return self.ramanScanIndex
		No newline at end of file

dataset.py

+10 −5

Original line number	Diff line number	Diff line
		@@ -260,6 +260,7 @@ class DataSet(object):
		self.particleContainer.setParticleContours(self.particlecontours)
		self.particleContainer.setParticleStats(self.particlestats)
		self.particleContainer.applyPixelScaleToParticleStats(self.getPixelScale())

		if hasattr(self, 'particles2spectra'):
		if self.particles2spectra is not None:
		measurements2particles = self.particles2spectra
		@@ -269,12 +270,16 @@ class DataSet(object):
		measurements2particles = recreateMeasurement2ParticleFromScanIndices()

		for particleIndex, listOfScanIndices in enumerate(measurements2particles):
		curParticle = self.particleContainer.particles[particleIndex]
		for measIndex, scanIndex in enumerate(listOfScanIndices):
		curParticle.addEmptyMeasurement()
		curParticle = self.particleContainer.getParticleOfIndex(particleIndex)
		for scanIndex in listOfScanIndices:
		# curParticle.addEmptyMeasurement()
		# curParticle.setMeasurementPixelCoords(measIndex, x, y)
		# curParticle.setMeasurementScanIndex(measIndex, scanIndex)
		indexOfNewMeas = self.particleContainer.addEmptyMeasurement()
		x, y = self.ramanpoints[particleIndex][0], self.ramanpoints[particleIndex][1]
		curParticle.setMeasurementPixelCoords(measIndex, x, y)
		curParticle.setMeasurementScanIndex(measIndex, scanIndex)
		self.particleContainer.setMeasurementPixelCoords(indexOfNewMeas, x, y)
		self.particleContainer.setMeasurementScanIndex(indexOfNewMeas, scanIndex)
		curParticle.addMeasurement(self.particleContainer.measurements[indexOfNewMeas])

		for particle in self.particleContainer.particles:
		for meas in particle.measurements:

detectionview.py

+9 −3

Original line number	Diff line number	Diff line
		@@ -667,9 +667,15 @@ class ParticleDetectionView(QtWidgets.QWidget):
		for particleIndex in measurementPoints:
		measPoints = measurementPoints[particleIndex]
		for index, point in enumerate(measPoints):
		curParticle = particleContainer.particles[point.particleIndex]
		curParticle.addEmptyMeasurement()
		curParticle.setMeasurementPixelCoords(index, point.x, point.y)
		# curParticle = particleContainer.particles[point.particleIndex]
		# curParticle.addEmptyMeasurement()
		# curParticle.setMeasurementPixelCoords(index, point.x, point.y)
		curParticle = particleContainer.getParticleOfIndex(point.particleIndex)
		indexOfNewMeas = particleContainer.addEmptyMeasurement()
		particleContainer.setMeasurementPixelCoords(index, point.x, point.y)
		curParticle.addMeasurement(particleContainer.measurements[indexOfNewMeas])



		self.dataset.ramanpoints = measurementPoints #consider moving that to particleContainer
		# self.dataset.particlecontours = contours