doc/SmallTools/llExtractWithLayerSeparation.html

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   3 <TITLE>llExtractWithLayerSeparation</TITLE>
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   5 <BODY>
   6 <H1>llExtractWithLayerSeparation</H1>
   7 <H2>Usage</H2>
   8 <PRE>
   9 Usage: llExtractWithLayerSeparation
  10 Options:
  11     [-i[nput]            In                  (NULL      ).as(inFileListNoOpen    ) ] :Essential :InputDataFile(mrcImage:Fourier Space)
  12     [-I[nput]            InLLNea             (NULL      ).as(inFileListNoOpen    )
  13                          InLLFar             (NULL      ).as(inFileListNoOpen    ) ] :Optional  :InputDataFile(llData:Already separated)
  14     [-r[ef]              Ref                 (NULL      ).as(inFile              ) ] :Optional  :ReferenceData(llData:Gnl(R) Space)
  15     [-o[utput]           Out                 (NULL      ).as(outFile             ) ] :Essential :OutputDataFile(llData: Average File)
  16     [-o2[utput]          Out2                (NULL      ).as(outFileListNoOpen   ) ] :Optional  :OutputDataFileList(llData: Each Filament which has the same orientation as average)
  17     [-o3[utput]          Out3                (NULL      ).as(outFileListNoOpen   ) ] :Optional  :OutputDataFileList(llData: Difference of each filament)
  18     [-o4[utput]          Out4                (NULL      ).as(outFileListNoOpen   ) ] :Optional  :OutputDataFileList(llData: Each Filament which has the same orientaion as original filament)
  19     [-o5[utput]          Out5                (NULL      ).as(outFileListNoOpen   ) ] :Optional  :OutputDataFileList(mrcImage: P-Value)
  20     [-o6[utput]          Out6                (NULL      ).as(outFileListNoOpen   ) ] :Optional  :OutputDataFileList(mrcImage: Q-Value)
  21     [-o7[utput]          Out7                (NULL      ).as(outFile             ) ] :Optional  :OutputDataFile(Text: Two subsets for resolution estimation)
  22     [-o8[utput]          Out8                (NULL      ).as(outFile             ) ] :Optional  :OutputDataFile(Text: For Back Projection)
  23     [-o9[utput]          Out9                (NULL      ).as(outFileListNoOpen   ) ] :Optional  :OutputDataFileList(Text: x shift, z shift and dY information)
  24     [-comment            InComment           (NULL      ).as(String              ) ] :Optional  :Comment
  25     [-symmetry           symmetry            (1.0       ).as(Real                ) ] :Optional  :Symmetry for back projection text file
  26     [-l[ayerInfo]        llInfo              (NULL      ).as(inFileListNoOpen    ) ] :Essential :LayerLineInformation
  27     [-l[ayerInfo]final   llInfoFinal         (NULL      ).as(inFile              ) ] :Optional  :LayerLineInformation(Final)
  28     [-li[ayerInfo]       llInfoImp           (NULL      ).as(inFileListNoOpen    ) ] :Optional  :LayerLineInformationImportant
  29     [-liw[ayerInfo]      liWeight            (1.0       ).as(Real                ) ] :Optional  :Weight of Important Layer
  30     [-liwStart[ayerInfo] liWeightStart       (1.0       ).as(Real                ) ] :Optional  :Weight of Important Layer
  31     [-liwStep[ayerInfo]  liWeightStep        (1.0       ).as(Real                ) ] :Optional  :Weight of Important Layer
  32     [-la[ayerInfo]       llInfoAxis          (NULL      ).as(inFileListNoOpen    ) ] :Optional  :LayerLineInformationForAxisSearch
  33     [-law[ayerInfo]      laWeight            (1.0       ).as(Real                ) ] :Optional  :Weight of Important Layer for AS
  34     [-lawStart[ayerInfo] laWeightStart       (1.0       ).as(Real                ) ] :Optional  :Weight of Important Layer for AS
  35     [-lawStep[ayerInfo]  laWeightStep        (1.0       ).as(Real                ) ] :Optional  :Weight of Important Layer for AS
  36     [-truePitch          truePitch           (430.0     ).as(Real                ) ] :Essential :true pitch [A]
  37     [-rMax               rMax                (100.0     ).as(Real                ) ] :Essential :rMax [A]
  38     [-rMaxMin            rMaxMin             (100.0     ).as(Real                ) ] :Optional  :rMaxMin [A]
  39     [-RMax               RMax                (0.1       ).as(Real                ) ] :Optional  :RMax [/A]
  40     [-RMaxFirst          RMaxFirst           (0.04      ).as(Real                ) ] :Optional  :RMaxFirst [/A]: Def: RMax
  41     [-RMaxStep           RMaxStep            (0.02      ).as(Real                ) ] :Optional  :RMaxStep [/A]
  42     [-RRMax              RRMax               (0.1       ).as(Real                ) ] :Optional  :Radial RMax [/A]
  43     [-RRMaxFirst         RRMaxFirst          (0.04      ).as(Real                ) ] :Optional  :Radial RMaxFirst [/A]: Def: RMax
  44     [-RRMaxStep          RRMaxStep           (0.02      ).as(Real                ) ] :Optional  :Radial RMaxStep [/A]
  45     [-delBR              delBR               (0.0002    ).as(Real                ) ] :Optional  :delBR [/A]
  46     [-rms                rms                 (1e-6      ).as(Real                ) ] :Optional  :rms:
  47     [-narrowSearch       narrowSearch        (1.0       ).as(Real                ) ] :Optional  :narrowSearch[Degree]: P-Value and Q-Value
  48     [-nextTimes          nextTimes           (1e-4      ).as(Real                ) ] :Optional  :nextTimes: rms
  49     [-maxIter[ation]     MaxIteration        (10        ).as(Integer             ) ] :Optional  :max iteration:
  50     [-maxIter2[ation]    MaxIter2            (1         ).as(Integer             ) ] :Optional  :max iteration on the same RMax and RRMax:
  51     [-maxIter3[ation]    MaxIter3            (1         ).as(Integer             ) ] :Optional  :max iteration on the same RMax, RRMax, and Weight:
  52     [-lambda             lambda              (1.0       ).as(Real                ) ] :Optional  :labda:
  53     [-ctf                CTF                 (0         ).as(Integer             ) ] :Optional  :CTF Compensation
  54     [-WhiteNoise         WhiteNoise          (0.0       ).as(Real                ) ] :Optional  :White Noise
  55     [-below              below               (90.0      ).as(Real                ) ] :Optional  :below
  56     [-noantipole                                                                   ] :Optional  :No Antipole
  57     [-magLimit                                                                     ] :Optional  :magLimit
  58     [-eachTime                                                                     ] :Optional  :each time
  59     [-continue           Continue            (NULL      ).as(inFile              ) ] :Optional  :continue
  60     [-forContinue        ForContinue         (NULL      ).as(outFile             ) ] :Optional  :For continue
  61     [-phi                phimin              (0.0       ).as(Real                )
  62                          phimax              (360.0     ).as(Real                )
  63                          delphi              (10.0      ).as(Real                ) ] :Optional  :phi:[degree]
  64     [-z                  zmin                (0.0       ).as(Real                )
  65                          zmax                (30.0      ).as(Real                )
  66                          delz                (5.0       ).as(Real                ) ] :Optional  :z:[A]
  67     [-shift              shiftmin            (-10.0     ).as(Real                )
  68                          shiftmax            (10.0      ).as(Real                )
  69                          delshift            (1.0       ).as(Real                ) ] :Optional  :shift:[A]
  70     [-log                Log                 (stdout    ).as(outFile             ) ] :Optional  :LogFile
  71     [-Normalization                                                                ] :Optional  :Normalization
  72     [-pvm                pvm                 (0         ).as(Integer             ) ] :Optional  :pvmNumber
  73     [-pvmList            pvmList             (NULL      ).as(inFile              ) ] :Optional  :pvmList
  74     [-pvmServer                                                                    ] :Optional  :Work as a server !!
  75     [-pvmClient                                                                    ] :Optional  :Work as a client !!
  76     [-wd                 WorkingDir          (./        ).as(String              ) ] :Optional  :Working Directory !!
  77     [-c[onfig]           configFile          (NULL      ).as(inFile              ) ] :Optional  :ConfigurationFile
  78     [-m[ode]             mode                (0         ).as(Integer             ) ] :Optional  :Mode
  79 ----- Additional Usage -----
  80 -m 0: The 1st version algorism(Sharing)
  81 -m 1: The 2nd version algorism(Least Square)
  82 >> -ctf option <<
  83 ----- Mode -----
  84     0: |CTFi|/Sigma(SQR(CTFi))
  85     1:  CTFi /Sigma(SQR(CTFi))
  86 >> If -ctf, the file list indicated by -i must include the below information
  87 filename weight  defocus[A] Cs[mm] AccV[kV] ratioOfAmpToPhase mode
  88 >> llDataSepartionControlFile <<
  89 llMax(different)
  90 nl Z numberOfN n0 n1 n2...
  91 </PRE>
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