def __init__(self, errorDetector, parent=None):
'''
Constructor
'''
super(TrajectoryAnalysis, self).__init__(parent)
self.errorDetector = ErrorDetector(self)
self.analysers = [RunRestAnalyser(self),
RatRunAnalyser(self)]
self.analyser = self.analysers[0]
self.analyseRunning = False
self.imageLevels = 3
self.imageCreators = [self.createImageLines, self.createImageDots]
self.imageCreatorsCaptions = ['Lines','Dots']
self.imageCreator = self.createImageDots
self.setWriteSpeed(0)
data = vstack((rand(150,2) + array([.5,.5]),rand(150,2)))
class TrajectoryAnalysis(QtCore.QObject):
signalAnalysisStarted = QtCore.pyqtSignal(int)
signalNextFileAnalysing = QtCore.pyqtSignal(str, int)
signalAnalysisFinished = QtCore.pyqtSignal()
imageMargin = 10
def __init__(self, errorDetector, parent=None):
'''
Constructor
'''
super(TrajectoryAnalysis, self).__init__(parent)
self.errorDetector = ErrorDetector(self)
self.analysers = [RunRestAnalyser(self),
RatRunAnalyser(self)]
self.analyser = self.analysers[0]
self.analyseRunning = False
self.imageLevels = 3
self.imageCreators = [self.createImageLines, self.createImageDots]
self.imageCreatorsCaptions = ['Lines','Dots']
self.imageCreator = self.createImageDots
self.setWriteSpeed(0)
data = vstack((rand(150,2) + array([.5,.5]),rand(150,2)))
#self.kMeans=KMeans(self)
#self.kMeans.clusters(data,2)
@QtCore.pyqtSlot(int)
def setWriteSpeed(self, checked):
self.writeSpeedInfo = checked
@QtCore.pyqtSlot(int)
def setImageCreator(self, index):
self.imageCreator = self.imageCreators[index]
@QtCore.pyqtSlot(int)
def setAnalyser(self, index):
self.analyser = self.analysers[index]
@QtCore.pyqtSlot(int)
def setImageLevelsCount(self, value):
self.imageLevels = value
def ltObjectToPoint(self, ltObject, displace):
return QtCore.QPointF(*ltObject.center).toPoint()+displace
def createImageDots(self, chamber):
'''
Create trajectory image in dots representation
'''
minX,minY, maxX,maxY = chamber.trajectory.minMax()
trajectoryImage = QtGui.QImage(maxX-minX + self.imageMargin * 2,
maxY-minY + self.imageMargin * 2, QtGui.QImage.Format_RGB888)
trajectoryImage.fill(QtCore.Qt.white)
step = 255 // self.imageLevels
displace = QtCore.QPoint(self.imageMargin-minX,self.imageMargin-minY)
for ltObject in chamber.trajectory :
if ltObject is None :
continue
point = self.ltObjectToPoint(ltObject,displace)
color = trajectoryImage.pixel(point)
level = color & 255
newLevel = max(0, level - step)
trajectoryImage.setPixel(point, QtGui.QColor(newLevel, newLevel, newLevel).rgb())
QtGui.QApplication.processEvents()
return trajectoryImage
def createImageLines(self, chamber):
'''
Create trajectory image in lines representation
'''
width,height = chamber.width(), chamber.height()
trajectoryImage = QtGui.QImage(width + self.imageMargin * 2,
height + self.imageMargin * 2, QtGui.QImage.Format_ARGB32_Premultiplied)
trajectoryImage.fill(QtCore.Qt.white)
trajectoryPainter = QtGui.QPainter(trajectoryImage)
#Draw chamber
trajectoryPainter.setPen(QtCore.Qt.black)
chamberRect = QtCore.QRectF(self.imageMargin,self.imageMargin,width,height)
trajectoryPainter.drawRect(chamberRect)
trajectoryPainter.drawEllipse(chamberRect)
trajectoryPainter.setPen(QtCore.Qt.green)
displace = QtCore.QPoint(self.imageMargin,self.imageMargin)
ltObject1 = None
for ltObject2 in chamber.trajectory :
if ltObject2 is None : continue
if ltObject1 is None :
ltObject1 = ltObject2
continue
trajectoryPainter.drawLine(self.ltObjectToPoint(ltObject1,displace),
self.ltObjectToPoint(ltObject2,displace))
ltObject1=ltObject2
QtGui.QApplication.processEvents()
trajectoryPainter.end()
return trajectoryImage
def analyseChambers(self, chamberList):
self.signalAnalysisStarted.emit(len(chamberList))
i = 0
self.analyseRunning = True
histograms=[]
names=[]
for chamber,scale,frameRate in chamberList:
print('Analysing chamber #{}-{}, scale:{:.3f}, framerate:{:.1f}'.format(i+1,chamber.sampleName,scale,frameRate))
if not self.analyseRunning :
print('Analysis aborted')
break
# Signal to update GUI
i += 1
QtGui.QApplication.processEvents()
if chamber.trajectory is None :
continue
self.signalNextFileAnalysing.emit('Chamber ',i)
if not chamber.trajectory.findBorders():
continue
errorStatus = self.errorDetector.checkForErrors(chamber.trajectory, scale, frameRate)
chamber.setTrajectoryErrorStatus(errorStatus)
# Create image and analyse
trajectoryStats,trajectoryHist=self.analyser.analyseChamber(chamber,scale,frameRate)
n,m = trajectoryHist.shape
names.append(chamber.sampleName)
histograms.append(trajectoryHist.reshape(n*m))
chamber.setTrajectoryStats(trajectoryStats)
chamber.setTrajectoryImage(self.imageCreator(chamber))
print(trajectoryStats.totalReport())
#print(trajectoryStats.hystogram)
'''
print("Starting PCA for histograms:",len(histograms) )
pca =PCA(n_components=10)
#print(hist[0])
transform=pca.fit_transform(np.array(histograms)).T
print(pca.explained_variance_ratio_)
'''
'''
[samm,E] = sammon(np.array(histograms),init ='pca')
transform=samm.T
print("Sammon E: ",E)
x = transform[0]
y = transform[1]
species = set(names)
mpl.pyplot.clf()
for name in species:
xx=[]
yy=[]
for i in range(len(names)):
if names[i]==name:
xx.append(x[i])
yy.append(y[i])
mpl.pyplot.plot(xx,yy,'o',label=name)
mpl.pyplot.show()
mpl.pyplot.clf()
'''
self.signalAnalysisFinished.emit()
@QtCore.pyqtSlot()
def abortAnalysis(self):
self.analyseRunning = False
def hystogramCluster(self):
pass
