clustering.py 文件源码

def merge(self, anomFlag, thr):
        FlatC = hierarchy.fcluster(self.Tree, thr, criterion='distance')
        Log = open(self.CurrentDir+'/.cc_cluster.log', 'a')
        counter=collections.Counter(FlatC)
        Best = max(counter.iteritems(), key=operator.itemgetter(1))[0]
        Process = True
#change checkboxes to standard variables
        if Process:
            ToProcess = [Best]    
        else:
            ToProcess = set(Clusters)
            for key in ToProcess:
                if counter[key]==1:
                    ToProcess = [x for x in ToProcess if x != key]



#Processing pipeline, 
#Does all the XSCALE run
        for x in ToProcess:
            if [thr,x, anomFlag] not in  self.alreadyDone:
                os.mkdir(self.CurrentDir+'/cc_Cluster_%.2f_%s_%s'%(float(thr),x, anomFlag))
                Xscale=open(self.CurrentDir+'/cc_Cluster_%.2f_%s_%s/XSCALE.INP'%(float(thr),x, anomFlag), 'a')
                Pointless=open(self.CurrentDir+'/cc_Cluster_%.2f_%s_%s/launch_pointless.sh'%(float(thr),x,anomFlag ), 'a')
                print('OUTPUT_FILE=scaled.hkl',file=Xscale)
                print('MERGE= TRUE', file=Xscale)
                print('pointless hklout clustered.mtz << eof', file=Pointless)
                if anomFlag=='ano':
                    print('FRIEDEL\'S_LAW= FALSE', file=Xscale)
                elif anomFlag=='no_ano':
                    print('FRIEDEL\'S_LAW= TRUE', file=Xscale)
                Xscale.close()
                Pointless.close()

        for cluster, filename in zip(FlatC,self.labelList):
            if cluster in ToProcess:
                OUT = open(self.CurrentDir+'/cc_Cluster_%.2f_%s_%s/XSCALE.INP'%(float(thr),cluster,anomFlag), 'a')
                Pointless=open(self.CurrentDir+'/cc_Cluster_%.2f_%s_%s/launch_pointless.sh'%(float(thr),cluster,anomFlag), 'a')
                print ('INPUT_FILE= ../%s'%(filename), file=OUT)
                #print ('INCLUDE_RESOLUTION_RANGE=20, 1.8', file=OUT)
                print ('MINIMUM_I/SIGMA= 0', file=OUT)
                print ('XDSIN ../%s'%(filename), file= Pointless)
                OUT.close()
                Pointless.close()
        #optional run of XSCALE

        newProcesses=[]
        for x in ToProcess:
            if [thr,x, anomFlag] not in  self.alreadyDone:
                plt.savefig(self.CurrentDir+'/cc_Cluster_%.2f_%s_%s/Dendrogram.png'%(float(thr),x,anomFlag))
                P= subprocess.Popen('/opt/pxsoft/xds/vdefault/linux-x86_64/xscale_par',cwd=self.CurrentDir+'/cc_Cluster_%.2f_%s_%s/'%(float(thr), x, anomFlag))     
                P.wait()
                print('Cluster, %s , %s , %s'%(float(thr),x, anomFlag), file=Log)             
                Pointless=open(self.CurrentDir+'/cc_Cluster_%.2f_%s_%s/launch_pointless.sh'%(float(thr),x,anomFlag), 'a')
                print('COPY \n bg\n TOLERANCE 4 \n eof', file= Pointless)
                Pointless.close()
                os.chmod(self.CurrentDir+'/cc_Cluster_%.2f_%s_%s/launch_pointless.sh'%(self.threshold,x,self.anomFlag ), st.st_mode | 0o111)              
                newProcesses.append([thr,x, anomFlag])