Preparation for reorganizing contours and scanIndices (2c03c3ce) · Commits · GEPARD / GEPARD

analysis/analysisplots.py

+2 −29

Original line number	Diff line number	Diff line
		@@ -23,10 +23,6 @@ from PyQt5 import QtWidgets, QtGui, QtCore
		from matplotlib.backends.backend_qt5agg import FigureCanvasQTAgg as FigureCanvas
		from matplotlib.figure import Figure
		from matplotlib.backends.backend_qt5agg import NavigationToolbar2QT as NavigationToolbar
		import os
		import numpy as np

		from analysis import importSpectra


		class ParticleIndicator(QtWidgets.QPushButton):
		@@ -132,31 +128,8 @@ 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)

		self.spectra = self.dataset.particleContainer.spectra
		assert self.spectra is not None
		self.canvas.draw()

		def updateParticleSpectrum(self, specIndex, particleSize, hqi):

analysis/analysisview.py

+2 −3

Original line number	Diff line number	Diff line
		@@ -32,7 +32,6 @@ from matplotlib.backends.backend_qt5agg import NavigationToolbar2QT as Navigatio
		from .analysiswidgets import ExpExcelDialog
		from .analysisplots import TypeHistogramView, SpectraPlot
		from .loadresults import LoadTrueMatchResults
		from .particleeditor import ParticleEditor
		from .database import DataBaseWindow
		from .colorlegend import getColorFromNameWithSeed

		@@ -56,7 +55,6 @@ class ParticleAnalysis(QtWidgets.QMainWindow):
		self.viewparent = viewparent
		self.dataset = dataset
		self.particleContainer = dataset.particleContainer
		self.editor = ParticleEditor(self.particleContainer, self)

		# self.additivePlot = None
		self.importWindow = None
		@@ -221,6 +219,7 @@ class ParticleAnalysis(QtWidgets.QMainWindow):
		self.createMenus()
		self.applyHQIThresholdToResults()
		self.createHistogramData()
		self.particleContainer.loadSpectra()
		self.initializeSpecPlot()
		self.setTypeSelector()
		self.updateHistogramsAndContours()
		@@ -556,7 +555,7 @@ class ParticleAnalysis(QtWidgets.QMainWindow):
		self.currentParticleIndex = particleIndex
		partIndices = self.particleContainer.getIndicesOfParticleType(assignment)
		self.particleSelector.setMaximum(len(partIndices))

		self.particleNumberLabel.setText(f'of {len(partIndices)} particles; ')

		self.particleSelector.setValue(partIndices.index(particleIndex)+1)

analysis/particleAndMeasurement.py

+7 −19

Original line number	Diff line number	Diff line
		@@ -19,7 +19,7 @@ along with this program, see COPYING.
		If not, see <https://www.gnu.org/licenses/>.
		"""
		import numpy as np

		from viewitems import SegmentationContour, RamanScanIndicator

		class Particle(object):
		def __init__(self):
		@@ -35,23 +35,9 @@ class Particle(object):
		self.viewItem = None

		def addMeasurement(self, refToMeasurement):
		refToMeasurement.assignedParticle = self
		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)
		@@ -127,8 +113,8 @@ class Particle(object):
		for measurement in self.measurements:
		measurement.applyHQIThreshold(minHQI)

		# def recreateViewItem(self):
		# pass
		def recreateViewItem(self):
		self.viewItem = SegmentationContour()


		class Measurement(object):
		@@ -142,6 +128,8 @@ class Measurement(object):
		self.assignment_afterHQI = None
		self.hqi = None

		self.assignedParticle = None

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

analysis/particleInfo.py→analysis/particleContainer.py

+5 −4

Original line number	Diff line number	Diff line
		@@ -178,9 +178,10 @@ class ParticleContainer(object):

		def getMeasurementPixelCoords(self):
		coords = []
		for particle in self.particles:
		for measurement in particle.getMeasurements():
		coords.append([measurement.pixelcoord_x, measurement.pixelcoord_y])
		# for particle in self.particles:
		# for measurement in particle.getMeasurements():
		for meas in self.measurements:
		coords.append([meas.pixelcoord_x, meas.pixelcoord_y])
		return coords

		def getNumberOfParticlesOfAssignment(self, assignment):
		@@ -269,7 +270,7 @@ class ParticleContainer(object):
		if newAssignment is not None:
		meas.setAssignment(newAssignment)
		meas.setHQI(100)
		newParticle.addExistingMeasurement(meas)
		newParticle.addMeasurement(meas)

		#set Particle Stats
		long, short, longellipse, shortellipse, area = newStats

dataset.py

+1 −1

Original line number	Diff line number	Diff line
		@@ -24,7 +24,7 @@ import numpy as np
		import cv2
		from helperfunctions import cv2imread_fix, cv2imwrite_fix
		from copy import copy
		from analysis.particleInfo import ParticleContainer
		from analysis.particleContainer import ParticleContainer

		currentversion = 3