particleAndMeasurement.py 5.38 KB
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# -*- 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
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from viewitems import SegmentationContour, RamanScanIndicator
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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):
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        refToMeasurement.assignedParticle = self
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        self.measurements.append(refToMeasurement)
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    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)
    
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    def recreateViewItem(self):
        self.viewItem = SegmentationContour()
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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
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        self.assignedParticle = None
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    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