项目笔记《DeepLung:Deep 3D Dual Path Nets for Automated Pulmonary Nodule Detection and Classification》（三）（下）结果评估

在（上）中讲了如何得到csv文件并调用noduleCADEvaluationLUNA16.py求取froc值，这里就讲一讲froc值是如何求取的。

　　 annotations_filename = './annotations/annotations.csv'
    annotations_excluded_filename = './annotations/annotations_excluded.csv'
    seriesuids_filename = './annotations/seriesuids.csv'
    results_filename = './annotations/3DRes18FasterR-CNN.csv'#3D Faster R-CNN - Res18.csv' #top5.csv'#
    seriesuids_path = '/home/ustc/lclin/code/DeepLung/evaluationScript/series_uid9.csv'
    results_path = "/home/ustc/lclin/code/DeepLung/detector/results/wzy_res18/retrft969/val120/predanno-0.125pbb.csv"
    noduleCADEvaluation(annotations_filename,annotations_excluded_filename,seriesuids_path,results_path,'./')

如上面代码所示，输入标签文件，结果文件，调用noduleCADEvaluation函数即可，任务完成，十分简单。

接下来看一下这个函数。

def noduleCADEvaluation(annotations_filename,annotations_excluded_filename,seriesuids_filename,results_filename,outputDir):
    '''
    function to load annotations and evaluate a CAD algorithm
    @param annotations_filename: list of annotations
    @param annotations_excluded_filename: list of annotations that are excluded from analysis
    @param seriesuids_filename: list of CT images in seriesuids
    @param results_filename: list of CAD marks with probabilities
    @param outputDir: output directory
    '''

    print annotations_filename

    (allNodules, seriesUIDs) = collect(annotations_filename, annotations_excluded_filename, seriesuids_filename) #根据标签和用户id，求出所有结节，所有用户

    evaluateCAD(seriesUIDs, results_filename, outputDir, allNodules, #根据结节，用户，结果文件，输出froc值
                os.path.splitext(os.path.basename(results_filename))[0],
                maxNumberOfCADMarks=100, performBootstrapping=bPerformBootstrapping,
                numberOfBootstrapSamples=bNumberOfBootstrapSamples, confidence=bConfidence)

这个函数调用了两个函数collect和evaluateCAD。先从collect开始看。

def collect(annotations_filename,annotations_excluded_filename,seriesuids_filename):
    annotations          = csvTools.readCSV(annotations_filename)
    annotations_excluded = csvTools.readCSV(annotations_excluded_filename)
    seriesUIDs_csv = csvTools.readCSV(seriesuids_filename)

    seriesUIDs = [] #建立一个用户列表，将用户id添加进去
    for seriesUID in seriesUIDs_csv:
        seriesUIDs.append(seriesUID[0]) #seriesUID也是一个列表，只不过只有一个元素

    allNodules = collectNoduleAnnotations(annotations, annotations_excluded, seriesUIDs) 

    return (allNodules, seriesUIDs)

该函数又调用了另一个函数collectNoduleAnnotations。

def collectNoduleAnnotations(annotations, annotations_excluded, seriesUIDs):
    allNodules = {} #将所有结节存储在字典中
    noduleCount = 0
    noduleCountTotal = 0

    for seriesuid in seriesUIDs:
        # print 'adding nodule annotations: ' + seriesuid

        nodules = []
        numberOfIncludedNodules = 0    #对真正用来检测的结节计数

        # add included findings
        header = annotations[0]
        for annotation in annotations[1:]:
            nodule_seriesuid = annotation[header.index(seriesuid_label)]

            if seriesuid == nodule_seriesuid:  #将结节所属的用户id与要建立字典索引的id比较，若相同，就获取它
                nodule = getNodule(annotation, header, state = "Included")
                nodules.append(nodule)
                numberOfIncludedNodules += 1

        # add excluded findings
        header = annotations_excluded[0]
        for annotation in annotations_excluded[1:]:
            nodule_seriesuid = annotation[header.index(seriesuid_label)]

            if seriesuid == nodule_seriesuid: #对无关结节也执行上面的操作，不同的是不对include计数
                nodule = getNodule(annotation, header, state = "Excluded")
                nodules.append(nodule)

        allNodules[seriesuid] = nodules
        noduleCount      += numberOfIncludedNodules
        noduleCountTotal += len(nodules)

    print 'Total number of included nodule annotations: ' + str(noduleCount)
    print 'Total number of nodule annotations: ' + str(noduleCountTotal)
    return allNodules

这段代码比较简单，其中有一个获取结节的函数getNodule，需要看一下

def getNodule(annotation, header, state = ""):
    nodule = NoduleFinding()
    nodule.coordX = annotation[header.index(coordX_label)] #依次将x,y,z添加到nodule对象的属性中
    nodule.coordY = annotation[header.index(coordY_label)]
    nodule.coordZ = annotation[header.index(coordZ_label)]

    if diameter_mm_label in header:          #检查有无直径标签，有则添加
        nodule.diameter_mm = annotation[header.index(diameter_mm_label)]

    if CADProbability_label in header:       #检查有无概率标签，有则添加
        nodule.CADprobability = annotation[header.index(CADProbability_label)]

    if not state == "":
        nodule.state = state

    return nodule

这里又又出现一个函数，准确地说是类，NoduleFinding()，这个类存在于nodulefinding.py模块，也是在evaluationScript这个文件夹中。

一起来欣赏下这个类，一目了然，而且这个模块也只有这段代码。

class NoduleFinding(object):
  '''
  Represents a nodule
  '''

  def __init__(self, noduleid=None, coordX=None, coordY=None, coordZ=None, coordType="World",
               CADprobability=None, noduleType=None, diameter=None, state=None, seriesInstanceUID=None):

    # set the variables and convert them to the correct type
    self.id = noduleid
    self.coordX = coordX
    self.coordY = coordY
    self.coordZ = coordZ
    self.coordType = coordType
    self.CADprobability = CADprobability
    self.noduleType = noduleType
    self.diameter_mm = diameter
    self.state = state
    self.candidateID = None
    self.seriesuid = seriesInstanceUID

另外，大家可能会奇怪，xxx_label都是些什么，这些在文件noduleCADEvaluationLUNA16.py中都有定义，如下，看一下标签文件就明白了。

seriesuid_label = 'seriesuid'
coordX_label = 'coordX'
coordY_label = 'coordY'
coordZ_label = 'coordZ'
diameter_mm_label = 'diameter_mm'
CADProbability_label = 'probability'

最后，回到起点，看看froc究竟是如何计算的，有请evaluateCAD函数，这段代码超级长。

def evaluateCAD(seriesUIDs, results_filename, outputDir, allNodules, CADSystemName, maxNumberOfCADMarks=-1,#输入病人id，检测结果，评估结果的输出目录，所有标签结节，
                performBootstrapping=True,numberOfBootstrapSamples=1000,confidence = 0.95):　　　　　　　　　#检测系统的名字，其余参数与自助采样有关，不太懂
    '''
    function to evaluate a CAD algorithm
    @param seriesUIDs: list of the seriesUIDs of the cases to be processed
    @param results_filename: file with results
    @param outputDir: output directory
    @param allNodules: dictionary with all nodule annotations of all cases, keys of the dictionary are the seriesuids
    @param CADSystemName: name of the CAD system, to be used in filenames and on FROC curve
    '''

    nodOutputfile = open(os.path.join(outputDir,'CADAnalysis.txt'),'w') #写入CADAnalysis文件
    nodOutputfile.write("\n")
    nodOutputfile.write((60 * "*") + "\n")
    nodOutputfile.write("CAD Analysis: %s\n" % CADSystemName)
    nodOutputfile.write((60 * "*") + "\n")
    nodOutputfile.write("\n")

    results = csvTools.readCSV(results_filename)#读取检测结果csv格式，seriesuid,coordX,coordY,coordZ,probability

    allCandsCAD = {}

    for seriesuid in seriesUIDs: #对每个病例读取相应的候选结节

        # collect candidates from result file
        nodules = {}  #从检测结果文件中获取与病例对应的候选结节，添加进字典
        header = results[0]

        i = 0
        for result in results[1:]:
            nodule_seriesuid = result[header.index(seriesuid_label)]

            if seriesuid == nodule_seriesuid:
                nodule = getNodule(result, header)
                nodule.candidateID = i
                nodules[nodule.candidateID] = nodule
                i += 1

        if (maxNumberOfCADMarks > 0):
            # number of CAD marks, only keep must suspicous marks

            if len(nodules.keys()) > maxNumberOfCADMarks:
                # make a list of all probabilities
                probs = []
                for keytemp, noduletemp in nodules.iteritems():
                    probs.append(float(noduletemp.CADprobability))
                probs.sort(reverse=True) # sort from large to small
                probThreshold = probs[maxNumberOfCADMarks]
                nodules2 = {}
                nrNodules2 = 0
                for keytemp, noduletemp in nodules.iteritems():
                    if nrNodules2 >= maxNumberOfCADMarks:
                        break
                    if float(noduletemp.CADprobability) > probThreshold:
                        nodules2[keytemp] = noduletemp
                        nrNodules2 += 1

                nodules = nodules2

        # print 'adding candidates: ' + seriesuid
        allCandsCAD[seriesuid] = nodules #将病例与对应候选结节存入字典

    # open output files
    nodNoCandFile = open(os.path.join(outputDir, "nodulesWithoutCandidate_%s.txt" % CADSystemName), 'w')

    # --- iterate over all cases (seriesUIDs) and determine how
    # often a nodule annotation is not covered by a candidate

    # initialize some variables to be used in the loop
    candTPs = 0    #这里是一堆定义，让人头大
    candFPs = 0
    candFNs = 0
    candTNs = 0
    totalNumberOfCands = 0 #总候选结节数，也就是你的检测结果文件中的所有结节数量
    totalNumberOfNodules = 0 #总标签结节数
    doubleCandidatesIgnored = 0
    irrelevantCandidates = 0
    minProbValue = -1000000000.0 # minimum value of a float
    FROCGTList = []
    FROCProbList = []
    FPDivisorList = []
    excludeList = []
    FROCtoNoduleMap = []
    ignoredCADMarksList = []

    # -- loop over the cases
    for seriesuid in seriesUIDs:
        # get the candidates for this case
        try:
            candidates = allCandsCAD[seriesuid]
        except KeyError:
            candidates = {}

        # add to the total number of candidates
        totalNumberOfCands += len(candidates.keys())

        # make a copy in which items will be deleted
        candidates2 = candidates.copy() #对候选结节复制一个副本

        # get the nodule annotations on this case
        try:
            noduleAnnots = allNodules[seriesuid] #获取所有结节中属于该病例的结节（既包括真的结节，也包括无关的结节）
        except KeyError:
            noduleAnnots = []

        # - loop over the nodule annotations
        for noduleAnnot in noduleAnnots: #对标签结节循环处理
            # increment the number of nodules
            if noduleAnnot.state == "Included": #如果是用来评测的真结节，则
                totalNumberOfNodules += 1

            x = float(noduleAnnot.coordX) #获取结节坐标
            y = float(noduleAnnot.coordY)
            z = float(noduleAnnot.coordZ)

            # 2. Check if the nodule annotation is covered by a candidate
            # A nodule is marked as detected when the center of mass of the candidate is within a distance R of
            # the center of the nodule. In order to ensure that the CAD mark is displayed within the nodule on the
            # CT scan, we set R to be the radius of the nodule size.
            diameter = float(noduleAnnot.diameter_mm)
            if diameter < 0.0:
              diameter = 10.0
            radiusSquared = pow((diameter / 2.0), 2.0)

            found = False
            noduleMatches = []
            for key, candidate in candidates.iteritems(): #对每一个候选结节，判断是否与真实结节相交
                x2 = float(candidate.coordX)
                y2 = float(candidate.coordY)
                z2 = float(candidate.coordZ)
                dist = math.pow(x - x2, 2.) + math.pow(y - y2, 2.) + math.pow(z - z2, 2.)
                if dist < radiusSquared: #判断是否在半径距离内
                    if (noduleAnnot.state == "Included"): #若是用来检测的结节，添加进noduleMatches，并删除该候选结节
                        found = True
                        noduleMatches.append(candidate)
                        if key not in candidates2.keys():#这里不复杂，就是说把每个与标签结节相交的候选结节提取出来后，要删除副本中的id，这样是检测会否有其它标签结节也与该结节所属的候选结节相交
                            print "This is strange: CAD mark %s detected two nodules! Check for overlapping nodule annotations, SeriesUID: %s, nodule Annot ID: %s" % (str(candidate.id), seriesuid, str(noduleAnnot.id))
                        else:
                            del candidates2[key]
                    elif (noduleAnnot.state == "Excluded"): # an excluded nodule #若是无关结节，则添加进ignoredCADMarksList
                        if bOtherNodulesAsIrrelevant: #    delete marks on excluded nodules so they don't count as false positives
                            if key in candidates2.keys():
                                irrelevantCandidates += 1
                                ignoredCADMarksList.append("%s,%s,%s,%s,%s,%s,%.9f" % (seriesuid, -1, candidate.coordX, candidate.coordY, candidate.coordZ, str(candidate.id), float(candidate.CADprobability)))
                                del candidates2[key]
            if len(noduleMatches) > 1: # double detection #如果一个标签结节对应多个候选结节，记录下数目
                doubleCandidatesIgnored += (len(noduleMatches) - 1)
            if noduleAnnot.state == "Included": #若该结节是include结节
                # only include it for FROC analysis if it is included
                # otherwise, the candidate will not be counted as FP, but ignored in the
                # analysis since it has been deleted from the nodules2 vector of candidates
                if found == True: #若找到与之匹配的候选结节
                    # append the sample with the highest probability for the FROC analysis
                    maxProb = None
                    for idx in range(len(noduleMatches)):
                        candidate = noduleMatches[idx]
                        if (maxProb is None) or (float(candidate.CADprobability) > maxProb):
                            maxProb = float(candidate.CADprobability) #记录匹配的候选结节的概率，将最大概率存入maxProb

                    FROCGTList.append(1.0) #添加 1
                    FROCProbList.append(float(maxProb)) #添加刚刚的最大概率
                    FPDivisorList.append(seriesuid) #添加病例id
                    excludeList.append(False) #添加False
                    FROCtoNoduleMap.append("%s,%s,%s,%s,%s,%.9f,%s,%.9f" % (seriesuid, noduleAnnot.id, noduleAnnot.coordX, noduleAnnot.coordY, noduleAnnot.coordZ, float(noduleAnnot.diameter_mm), str(candidate.id), float(candidate.CADprobability)))
                    candTPs += 1 #添加1
                else: #若未找到与之匹配的结节
                    candFNs += 1
                    # append a positive sample with the lowest probability, such that this is added in the FROC analysis
                    FROCGTList.append(1.0)
                    FROCProbList.append(minProbValue)
                    FPDivisorList.append(seriesuid)
                    excludeList.append(True)
                    FROCtoNoduleMap.append("%s,%s,%s,%s,%s,%.9f,%s,%s" % (seriesuid, noduleAnnot.id, noduleAnnot.coordX, noduleAnnot.coordY, noduleAnnot.coordZ, float(noduleAnnot.diameter_mm), int(-1), "NA"))
                    nodNoCandFile.write("%s,%s,%s,%s,%s,%.9f,%s\n" % (seriesuid, noduleAnnot.id, noduleAnnot.coordX, noduleAnnot.coordY, noduleAnnot.coordZ, float(noduleAnnot.diameter_mm), str(-1)))

        # add all false positives to the vectors
        for key, candidate3 in candidates2.iteritems(): #此时candidata2中都是无人领取的结节，都是FP
            candFPs += 1
            FROCGTList.append(0.0)
            FROCProbList.append(float(candidate3.CADprobability))
            FPDivisorList.append(seriesuid)
            excludeList.append(False)
            FROCtoNoduleMap.append("%s,%s,%s,%s,%s,%s,%.9f" % (seriesuid, -1, candidate3.coordX, candidate3.coordY, candidate3.coordZ, str(candidate3.id), float(candidate3.CADprobability)))

    if not (len(FROCGTList) == len(FROCProbList) and len(FROCGTList) == len(FPDivisorList) and len(FROCGTList) == len(FROCtoNoduleMap) and len(FROCGTList) == len(excludeList)):
        nodOutputfile.write("Length of FROC vectors not the same, this should never happen! Aborting..\n")

    nodOutputfile.write("Candidate detection results:\n")
    nodOutputfile.write("    True positives: %d\n" % candTPs)
    nodOutputfile.write("    False positives: %d\n" % candFPs)
    nodOutputfile.write("    False negatives: %d\n" % candFNs)
    nodOutputfile.write("    True negatives: %d\n" % candTNs)
    nodOutputfile.write("    Total number of candidates: %d\n" % totalNumberOfCands)
    nodOutputfile.write("    Total number of nodules: %d\n" % totalNumberOfNodules)

    nodOutputfile.write("    Ignored candidates on excluded nodules: %d\n" % irrelevantCandidates)
    nodOutputfile.write("    Ignored candidates which were double detections on a nodule: %d\n" % doubleCandidatesIgnored)
    if int(totalNumberOfNodules) == 0:
        nodOutputfile.write("    Sensitivity: 0.0\n")
    else:
        nodOutputfile.write("    Sensitivity: %.9f\n" % (float(candTPs) / float(totalNumberOfNodules)))
    nodOutputfile.write("    Average number of candidates per scan: %.9f\n" % (float(totalNumberOfCands) / float(len(seriesUIDs))))

    # compute FROC
    print FROCGTList
    print FROCProbList
    print len(FROCGTList)
    fps, sens, thresholds = computeFROC(FROCGTList,FROCProbList,len(seriesUIDs),excludeList) #这一步最为关键，计算FROC值，其实返回的是召回率与假阳性率的列表

    if performBootstrapping: #是否使用自助采样，不太懂
        fps_bs_itp,sens_bs_mean,sens_bs_lb,sens_bs_up = computeFROC_bootstrap(FROCGTList,FROCProbList,FPDivisorList,seriesUIDs,excludeList,
                                                                  numberOfBootstrapSamples=numberOfBootstrapSamples, confidence = confidence)

    # Write FROC curve #计算到上面就结束了，后面是一些画图
    with open(os.path.join(outputDir, "froc_%s.txt" % CADSystemName), 'w') as f:
        for i in range(len(sens)):
            f.write("%.9f,%.9f,%.9f\n" % (fps[i], sens[i], thresholds[i]))

    # Write FROC vectors to disk as well
    with open(os.path.join(outputDir, "froc_gt_prob_vectors_%s.csv" % CADSystemName), 'w') as f:
        for i in range(len(FROCGTList)):
            f.write("%d,%.9f\n" % (FROCGTList[i], FROCProbList[i]))

    fps_itp = np.linspace(FROC_minX, FROC_maxX, num=10001)

    sens_itp = np.interp(fps_itp, fps, sens)
    frvvlu = 0
    nxth = 0.125
    for fp, ss in zip(fps_itp, sens_itp):
        if abs(fp - nxth) < 3e-4:
            frvvlu += ss
            nxth *= 2
        if abs(nxth - 16) < 1e-5: break
    print(frvvlu/7, nxth)
    print(sens_itp[fps_itp==0.125]+sens_itp[fps_itp==0.25]+sens_itp[fps_itp==0.5]+sens_itp[fps_itp==1]+sens_itp[fps_itp==2]\
        +sens_itp[fps_itp==4]+sens_itp[fps_itp==8])
    if performBootstrapping:
        # Write mean, lower, and upper bound curves to disk
        with open(os.path.join(outputDir, "froc_%s_bootstrapping.csv" % CADSystemName), 'w') as f:
            f.write("FPrate,Sensivity[Mean],Sensivity[Lower bound],Sensivity[Upper bound]\n")
            for i in range(len(fps_bs_itp)):
                f.write("%.9f,%.9f,%.9f,%.9f\n" % (fps_bs_itp[i], sens_bs_mean[i], sens_bs_lb[i], sens_bs_up[i]))
    else:
        fps_bs_itp = None
        sens_bs_mean = None
        sens_bs_lb = None
        sens_bs_up = None

    # create FROC graphs
    if int(totalNumberOfNodules) > 0:
        graphTitle = str("")
        fig1 = plt.figure()
        ax = plt.gca()
        clr = 'b'
        plt.plot(fps_itp, sens_itp, color=clr, label="%s" % CADSystemName, lw=2)
        if performBootstrapping:
            plt.plot(fps_bs_itp, sens_bs_mean, color=clr, ls='--')
            plt.plot(fps_bs_itp, sens_bs_lb, color=clr, ls=':') # , label = "lb")
            plt.plot(fps_bs_itp, sens_bs_up, color=clr, ls=':') # , label = "ub")
            ax.fill_between(fps_bs_itp, sens_bs_lb, sens_bs_up, facecolor=clr, alpha=0.05)
        xmin = FROC_minX
        xmax = FROC_maxX
        plt.xlim(xmin, xmax)
        plt.ylim(0.5, 1)
        plt.xlabel('Average number of false positives per scan')
        plt.ylabel('Sensitivity')
        plt.legend(loc='lower right')
        plt.title('FROC performance - %s' % (CADSystemName))

        if bLogPlot:
            plt.xscale('log', basex=2)
            ax.xaxis.set_major_formatter(FixedFormatter([0.125,0.25,0.5,1,2,4,8]))

        # set your ticks manually
        ax.xaxis.set_ticks([0.125,0.25,0.5,1,2,4,8])
        ax.yaxis.set_ticks(np.arange(0.5, 1, 0.1))
        # ax.yaxis.set_ticks(np.arange(0, 1.1, 0.1))
        plt.grid(b=True, which='both')
        plt.tight_layout()

        plt.savefig(os.path.join(outputDir, "froc_%s.png" % CADSystemName), bbox_inches=0, dpi=300)

    return (fps, sens, thresholds, fps_bs_itp, sens_bs_mean, sens_bs_lb, sens_bs_up)

这里会计算FROC，调用的是computeFROC函数。

def computeFROC(FROCGTList, FROCProbList, totalNumberOfImages, excludeList):
    # Remove excluded candidates
    FROCGTList_local = []
    FROCProbList_local = []
    for i in range(len(excludeList)):
        if excludeList[i] == False:
            FROCGTList_local.append(FROCGTList[i])
            FROCProbList_local.append(FROCProbList[i])

    numberOfDetectedLesions = sum(FROCGTList_local)
    totalNumberOfLesions = sum(FROCGTList)
    totalNumberOfCandidates = len(FROCProbList_local)
    fpr, tpr, thresholds = skl_metrics.roc_curve(FROCGTList_local, FROCProbList_local, pos_label=1)
    if sum(FROCGTList) == len(FROCGTList): # Handle border case when there are no false positives and ROC analysis give nan values.
      print "WARNING, this system has no false positives.."
      fps = np.zeros(len(fpr))
    else:
      fps = fpr * (totalNumberOfCandidates - numberOfDetectedLesions) / totalNumberOfImages
    sens = (tpr * numberOfDetectedLesions) / totalNumberOfLesions
    return fps, sens, thresholds

到此，结束。