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