# llExtractWithLayerSeparation

## Usage

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