def loopProcessImage(self, imgdata): #creates self.peaktree and filterLoop sets self.filtarray self.peaktree = filterLoop.FilterLoop.loopProcessImage(self, imgdata) if self.params['background'] is False: apDisplay.printMsg("Found " + str(len(self.peaktree)) + " particles for " + apDisplay.shortenImageName(imgdata['filename'])) self.stats['lastpeaks'] = len(self.peaktree) if self.params['nojpegs'] is False: if self.threadJpeg is True: threading.Thread(target=apPeaks.createPeakJpeg, args=(imgdata, self.peaktree, self.params, self.filtarray)).start() else: apPeaks.createPeakJpeg(imgdata, self.peaktree, self.params, self.filtarray) elif self.params['background'] is False: apDisplay.printWarning("Skipping JPEG creation") if self.params['defocpair'] is True: self.sibling, self.shiftpeak = apDefocalPairs.getShiftFromImage( imgdata, self.params['sessionname']) return
def getParticlesFromStack(self, stackdata,imgdata,is_defocpair=False): """ For image (or defocal pair), imgdata get particles in corresponding stack """ if is_defocpair is True: sibling, shiftpeak = apDefocalPairs.getShiftFromImage(imgdata, self.params['sessionname']) if shiftpeak is None: return [],{'shiftx':0, 'shifty':0, 'scale':1} shiftdata = {'shiftx':shiftpeak['shift'][0], 'shifty':shiftpeak['shift'][1], 'scale':shiftpeak['scalefactor']} searchimgdata = sibling else: searchimgdata = imgdata shiftdata = {'shiftx':0, 'shifty':0, 'scale':1} partq = appiondata.ApParticleData() partq['image'] = searchimgdata stackpartq = appiondata.ApStackParticleData() stackpartq['stack'] = stackdata stackpartq['particle'] = partq stackpartdatas = stackpartq.query() partdatas = [] partorder = [] for stackpartdata in stackpartdatas: if self.params['partlimit'] and self.params['partlimit'] < stackpartdata['particleNumber']: continue partdata = stackpartdata['particle'] partdatas.append(partdata) partorder.append(stackpartdata['particleNumber']) partdatas.reverse() partorder.reverse() self.writeStackParticleOrderFile(partorder) return partdatas, shiftdata
def getParticlesFromStack(self, stackdata, imgdata, is_defocpair=False): """ For image (or defocal pair), imgdata get particles in corresponding stack """ if is_defocpair is True: sibling, shiftpeak = apDefocalPairs.getShiftFromImage( imgdata, self.params['sessionname']) if shiftpeak is None: return [], {'shiftx': 0, 'shifty': 0, 'scale': 1} shiftdata = { 'shiftx': shiftpeak['shift'][0], 'shifty': shiftpeak['shift'][1], 'scale': shiftpeak['scalefactor'] } searchimgdata = sibling else: searchimgdata = imgdata shiftdata = {'shiftx': 0, 'shifty': 0, 'scale': 1} partq = appiondata.ApParticleData() partq['image'] = searchimgdata stackpartq = appiondata.ApStackParticleData() stackpartq['stack'] = stackdata stackpartq['particle'] = partq stackpartdatas = stackpartq.query() partdatas = [] partorder = [] for stackpartdata in stackpartdatas: if self.params['partlimit'] and self.params[ 'partlimit'] < stackpartdata['particleNumber']: continue partdata = stackpartdata['particle'] partdatas.append(partdata) partorder.append(stackpartdata['particleNumber']) partdatas.reverse() partorder.reverse() self.writeStackParticleOrderFile(partorder) return partdatas, shiftdata
def loopProcessImage(self, imgdata): #creates self.peaktree and filterLoop sets self.filtarray self.peaktree = filterLoop.FilterLoop.loopProcessImage(self, imgdata) if self.params['background'] is False: apDisplay.printMsg("Found "+str(len(self.peaktree))+" particles for " +apDisplay.shortenImageName(imgdata['filename'])) self.stats['lastpeaks'] = len(self.peaktree) if self.params['nojpegs'] is False: if self.threadJpeg is True: threading.Thread(target=apPeaks.createPeakJpeg, args=(imgdata, self.peaktree, self.params, self.filtarray)).start() else: apPeaks.createPeakJpeg(imgdata, self.peaktree, self.params, self.filtarray) elif self.params['background'] is False: apDisplay.printWarning("Skipping JPEG creation") if self.params['defocpair'] is True: self.sibling, self.shiftpeak = apDefocalPairs.getShiftFromImage(imgdata, self.params['sessionname']) return
def processImage(self, imgdata): self.sibling, self.shiftpeak = apDefocalPairs.getShiftFromImage( imgdata, self.params['sessionname'])
def processImage(self, imgdata): self.sibling, self.shiftpeak = apDefocalPairs.getShiftFromImage(imgdata, self.params['sessionname'])