llExtractWithLayerSeparation

Usage

Usage: llExtractWithLayerSeparation
Options:
    [-i[nput]            In                  (NULL      ).as(inFileListNoOpen    ) ] :Essential :InputDataFile(mrcImage:Fourier Space)
    [-I[nput]            InLLNea             (NULL      ).as(inFileListNoOpen    ) 
                         InLLFar             (NULL      ).as(inFileListNoOpen    ) ] :Optional  :InputDataFile(llData:Already separated)
    [-r[ef]              Ref                 (NULL      ).as(inFile              ) ] :Optional  :ReferenceData(llData:Gnl(R) Space)
    [-o[utput]           Out                 (NULL      ).as(outFile             ) ] :Essential :OutputDataFile(llData: Average File)
    [-o2[utput]          Out2                (NULL      ).as(outFileListNoOpen   ) ] :Optional  :OutputDataFileList(llData: Each Filament which has the same orientation as average)
    [-o3[utput]          Out3                (NULL      ).as(outFileListNoOpen   ) ] :Optional  :OutputDataFileList(llData: Difference of each filament)
    [-o4[utput]          Out4                (NULL      ).as(outFileListNoOpen   ) ] :Optional  :OutputDataFileList(llData: Each Filament which has the same orientaion as original filament)
    [-o5[utput]          Out5                (NULL      ).as(outFileListNoOpen   ) ] :Optional  :OutputDataFileList(mrcImage: P-Value)
    [-o6[utput]          Out6                (NULL      ).as(outFileListNoOpen   ) ] :Optional  :OutputDataFileList(mrcImage: Q-Value)
    [-o7[utput]          Out7                (NULL      ).as(outFile             ) ] :Optional  :OutputDataFile(Text: Two subsets for resolution estimation)
    [-o8[utput]          Out8                (NULL      ).as(outFile             ) ] :Optional  :OutputDataFile(Text: For Back Projection)
    [-o9[utput]          Out9                (NULL      ).as(outFileListNoOpen   ) ] :Optional  :OutputDataFileList(Text: x shift, z shift and dY information)
    [-comment            InComment           (NULL      ).as(String              ) ] :Optional  :Comment
    [-symmetry           symmetry            (1.0       ).as(Real                ) ] :Optional  :Symmetry for back projection text file
    [-l[ayerInfo]        llInfo              (NULL      ).as(inFileListNoOpen    ) ] :Essential :LayerLineInformation
    [-l[ayerInfo]final   llInfoFinal         (NULL      ).as(inFile              ) ] :Optional  :LayerLineInformation(Final)
    [-li[ayerInfo]       llInfoImp           (NULL      ).as(inFileListNoOpen    ) ] :Optional  :LayerLineInformationImportant
    [-liw[ayerInfo]      liWeight            (1.0       ).as(Real                ) ] :Optional  :Weight of Important Layer
    [-liwStart[ayerInfo] liWeightStart       (1.0       ).as(Real                ) ] :Optional  :Weight of Important Layer
    [-liwStep[ayerInfo]  liWeightStep        (1.0       ).as(Real                ) ] :Optional  :Weight of Important Layer
    [-la[ayerInfo]       llInfoAxis          (NULL      ).as(inFileListNoOpen    ) ] :Optional  :LayerLineInformationForAxisSearch
    [-law[ayerInfo]      laWeight            (1.0       ).as(Real                ) ] :Optional  :Weight of Important Layer for AS
    [-lawStart[ayerInfo] laWeightStart       (1.0       ).as(Real                ) ] :Optional  :Weight of Important Layer for AS
    [-lawStep[ayerInfo]  laWeightStep        (1.0       ).as(Real                ) ] :Optional  :Weight of Important Layer for AS
    [-truePitch          truePitch           (430.0     ).as(Real                ) ] :Essential :true pitch [A]
    [-rMax               rMax                (100.0     ).as(Real                ) ] :Essential :rMax [A]
    [-rMaxMin            rMaxMin             (100.0     ).as(Real                ) ] :Optional  :rMaxMin [A]
    [-RMax               RMax                (0.1       ).as(Real                ) ] :Optional  :RMax [/A]
    [-RMaxFirst          RMaxFirst           (0.04      ).as(Real                ) ] :Optional  :RMaxFirst [/A]: Def: RMax
    [-RMaxStep           RMaxStep            (0.02      ).as(Real                ) ] :Optional  :RMaxStep [/A]
    [-RRMax              RRMax               (0.1       ).as(Real                ) ] :Optional  :Radial RMax [/A]
    [-RRMaxFirst         RRMaxFirst          (0.04      ).as(Real                ) ] :Optional  :Radial RMaxFirst [/A]: Def: RMax
    [-RRMaxStep          RRMaxStep           (0.02      ).as(Real                ) ] :Optional  :Radial RMaxStep [/A]
    [-delBR              delBR               (0.0002    ).as(Real                ) ] :Optional  :delBR [/A]
    [-rms                rms                 (1e-6      ).as(Real                ) ] :Optional  :rms:
    [-narrowSearch       narrowSearch        (1.0       ).as(Real                ) ] :Optional  :narrowSearch[Degree]: P-Value and Q-Value
    [-nextTimes          nextTimes           (1e-4      ).as(Real                ) ] :Optional  :nextTimes: rms
    [-maxIter[ation]     MaxIteration        (10        ).as(Integer             ) ] :Optional  :max iteration:
    [-maxIter2[ation]    MaxIter2            (1         ).as(Integer             ) ] :Optional  :max iteration on the same RMax and RRMax:
    [-maxIter3[ation]    MaxIter3            (1         ).as(Integer             ) ] :Optional  :max iteration on the same RMax, RRMax, and Weight:
    [-lambda             lambda              (1.0       ).as(Real                ) ] :Optional  :labda:
    [-ctf                CTF                 (0         ).as(Integer             ) ] :Optional  :CTF Compensation
    [-WhiteNoise         WhiteNoise          (0.0       ).as(Real                ) ] :Optional  :White Noise
    [-below              below               (90.0      ).as(Real                ) ] :Optional  :below
    [-noantipole                                                                   ] :Optional  :No Antipole
    [-magLimit                                                                     ] :Optional  :magLimit
    [-eachTime                                                                     ] :Optional  :each time
    [-continue           Continue            (NULL      ).as(inFile              ) ] :Optional  :continue
    [-forContinue        ForContinue         (NULL      ).as(outFile             ) ] :Optional  :For continue
    [-phi                phimin              (0.0       ).as(Real                ) 
                         phimax              (360.0     ).as(Real                ) 
                         delphi              (10.0      ).as(Real                ) ] :Optional  :phi:[degree]
    [-z                  zmin                (0.0       ).as(Real                ) 
                         zmax                (30.0      ).as(Real                ) 
                         delz                (5.0       ).as(Real                ) ] :Optional  :z:[A]
    [-shift              shiftmin            (-10.0     ).as(Real                ) 
                         shiftmax            (10.0      ).as(Real                ) 
                         delshift            (1.0       ).as(Real                ) ] :Optional  :shift:[A]
    [-log                Log                 (stdout    ).as(outFile             ) ] :Optional  :LogFile
    [-Normalization                                                                ] :Optional  :Normalization
    [-pvm                pvm                 (0         ).as(Integer             ) ] :Optional  :pvmNumber
    [-pvmList            pvmList             (NULL      ).as(inFile              ) ] :Optional  :pvmList
    [-pvmServer                                                                    ] :Optional  :Work as a server !!
    [-pvmClient                                                                    ] :Optional  :Work as a client !!
    [-wd                 WorkingDir          (./        ).as(String              ) ] :Optional  :Working Directory !!
    [-c[onfig]           configFile          (NULL      ).as(inFile              ) ] :Optional  :ConfigurationFile
    [-m[ode]             mode                (0         ).as(Integer             ) ] :Optional  :Mode
----- Additional Usage -----
-m 0: The 1st version algorism(Sharing)
-m 1: The 2nd version algorism(Least Square)
>> -ctf option <<
----- Mode -----
    0: |CTFi|/Sigma(SQR(CTFi))
    1:  CTFi /Sigma(SQR(CTFi))
>> If -ctf, the file list indicated by -i must include the below information
filename weight  defocus[A] Cs[mm] AccV[kV] ratioOfAmpToPhase mode
>> llDataSepartionControlFile <<
llMax(different)
nl Z numberOfN n0 n1 n2...