mrcImageAutoRotationCorrelation
Usage
Usage: mrcImageAutoRotationCorrelation
Options:
[-i[nput] In (NULL ).as(inFile ) ] :Essential :Input: testImage [mrcImage]
[-r[eference] Ref (NULL ).as(inFile ) ] :Essential :Input: refImage [mrcImage]
[-nRot1 nRot1 (1 ).as(Integer ) ] :Optional :Rotation number of Ref for Rot1: Def 1
[-nRot2 nRot2 (1 ).as(Integer ) ] :Optional :Rotation number of Ref for Rot2: Def 1
[-nRot3 nRot3 (1 ).as(Integer ) ] :Optional :Rotation number of Ref for Rot3: Def 1
[-dRot1 dRot1 (1.0 ).as(Real ) ] :Optional :Delta Angle [Degree] of Ref for Rot1; Def.: 360/nRot1
[-dRot2 dRot2 (1.0 ).as(Real ) ] :Optional :Delta Angle [Degree] of Ref for Rot2; Def.: 360/nRot2
[-dRot3 dRot3 (1.0 ).as(Real ) ] :Optional :Delta Angle [Degree] of Ref for Rot3; Def.: 360/nRot3
[-startRot1 startRot1 (0.0 ).as(Real ) ] :Optional :Start Angle [Degree] of Ref for Rot1; Def.: 0
[-startRot2 startRot2 (0.0 ).as(Real ) ] :Optional :Start Angle [Degree] of Ref for Rot2; Def.: 0
[-startRot3 startRot3 (0.0 ).as(Real ) ] :Optional :Start Angle [Degree] of Ref for Rot3; Def.: 0
[-StackOrder StackOrder (0 ).as(Integer ) ] :Optional :Stack Order for Stacked 2D of references, refer to attention
[-o[utput] Out (NULL ).as(outFile ) ] :Optional :Output: Parameter [mrcImage-format]
[-O[utput] OutASC (stdout ).as(outFile ) ] :Optional :Output: Parameter [ASCII]
[-cor[relation] corFile (NULL ).as(outFile ) ] :Optional :Correation Map at Maximum (Linear) [mrcImage-format]
[-cor[relation]2 corFile2 (NULL ).as(outFile ) ] :Optional :Correation Map2 at Maximum (Set Mode Correlation)[mrcImage-format]
[-cor[relation]All corAllFile (NULL ).as(outFile ) ] :Optional :Correation Map with All Rotation [mrcImage-format]
[-fit[tedToRef] fitFile (NULL ).as(outFile ) ] :Optional :Output: rotatedImage at Maximum(Linear Correlation) [mrcImage]
[-fit[tedToRef]2 fitFile2 (NULL ).as(outFile ) ] :Optional :Output: rotatedImage at Maximum(Set Correlation mode) [mrcImage]
[-RefineMode RefineMode (0 ).as(Integer ) ] :Optional :RefinementStep: Linear:0 or SetMode:1
[-n[umber] Rot (36 ).as(Real ) ] :Optional :Input: Rotation around the vertical axis against image plane: dRot = 360/n [degree]
[-range minAngle (-5.0 ).as(Real )
maxAngle (5.0 ).as(Real ) ] :Optional :Input: SearchRange: Rotation around the vertical axis against image plane
[-refStep1 refStep1 (1 ).as(Integer ) ] :Optional :SearchStep for Ref: Each Image along Rot1
[-refStep2 refStep2 (1 ).as(Integer ) ] :Optional :SearchStep for Ref: Each Image along Rot2
[-refStep3 refStep3 (1 ).as(Integer ) ] :Optional :SearchStep for Ref: Each Image along Rot3
[-nRot1Area nRot1AreaMin (-360 ).as(Real )
nRot1AreaMax (360 ).as(Real )
nRot1AreaStep (25 ).as(Real ) ] :Optional :number of Ref for Rot1
[-nRot2Area nRot2AreaMin (-360 ).as(Real )
nRot2AreaMax (360 ).as(Real )
nRot2AreaStep (25 ).as(Real ) ] :Optional :number of Ref for Rot2
[-nRot3Area nRot3AreaMin (-360 ).as(Real )
nRot3AreaMax (360 ).as(Real )
nRot3AreaStep (25 ).as(Real ) ] :Optional :number of Ref for Rot3
[-MagRange MagRangeMin (1.0 ).as(Real )
MagRangeMax (1.0 ).as(Real )
MagRangeStep (0.1 ).as(Real ) ] :Optional :Magnification Range
[-Iter[ation] Iter (1 ).as(Integer ) ] :Optional :Iteration for Rotation around the vertical axis against image plane
[-Method Method (0 ).as(Integer ) ] :Optional :0: Correlation, 1: SSDA
[-s[earchRegion] sminx (0 ).as(Real )
sminy (0 ).as(Real )
smaxx (0/*N.x-1*/).as(Real )
smaxy (0/*N.y-1*/).as(Real ) ] :Optional :SearchRegion [pixel]: used in lmrcImageAutoRotationCorrelation
[-Shift ] :Optional :Image Shift, when in > ref
[-RepeatX RepeatX (27.3 ).as(Real ) ] :Optional :RepeatX[A]
[-RepeatXDelta RepeatXDelta (5 ).as(Real ) ] :Optional :RepeatXDelta[A]
[-RepeatY RepeatY (27.3 ).as(Real ) ] :Optional :RepeatY[A]
[-RepeatYDelta RepeatYDelta (5 ).as(Real ) ] :Optional :RepeatYDelta[A]
[-Xshift ] :Optional :X-Shift Only
[-NoShift ] :Optional :No-Shift
[-Log Log (stdout ).as(outFile ) ] :Optional :Output: LogFile
[-pvm pvm (1 ).as(Integer ) ] :Optional :Task Number
[-pvmList pvmList (NULL ).as(inFile ) ] :Optional :ConfigurationFile
[-c[onfig] configFile (NULL ).as(inFile ) ] :Optional :ConfigurationFile
[-m[ode] mode (0 ).as(Integer ) ] :Optional :Mode
----- Mode -----
When, -Method 0(Default:Correlation)
0: Normal Correlation FxG*
1: Phase Correlation FxG*/ |FxG*|
2: Phase Correlation FxG*/sqrt(|FxG*|)
3: Normalized Normal Correlation FxG*/|F||G|)
16: (0,0) = 0
Refinement Correlation Map
0: sqrt(Sum |Fi-Gi|^2 / Sum |Gi|^2)
1: Sum |Gi||phaseFi - phaseGi| / Sum |Gi|
2: sqrt(Sum |Gi||phaseFi - phaseGi|^2 / Sum |Gi| )
----- Attention -----
You must not set bit 16: bit 16 is set in this program as default.
When, -Method 1 (SSDA:Sequential Similarity Detection Algorithm)
When, -Method 2 (Rotational Cross-Correlation Function)
-m NotSupported
>>>>>>>> Attention 1 -----
You should set -n or -range. These parameters are used for reference image rotation
>>>>>>>> Attention 2 -----
You must set -nRot1/2/3.
-nRot[1|2|3] Number of Reference Images:
You should set -dRot1/2/3.
-dRot[1|2|3] Delta Angle [degree] of Reference Images:
You should set -startRot1/2/3.
-startRot[1|2|3] Start Angle [degree] of Reference Images:
e.g.) If mrc3Dto2D -Rot1 89 91 1 -Rot2 0 359 2 -Rot3 3 12 3,
-nRot1 3 -dRot1 1 -startRot1 89
-nRot2 180 -dRot2 2 -startRot2 0
-nRot3 4 -dRot1 3 -startRot1 3
>>>>>>>> Attention 3 : the relation between dRot1 and nRotArea ----
-nRot[1|2|3]Area Min[degree] Max[degree] Step[degree]
If not -dRot[1|2|3], we cannot estimate nStep, which is the number of skip step using referencefiles .
>>>>>>>> Attention 4 : Stack order of ref-image -----
-StackOrder
0: for pdb2mrc2d : default
1: for mrc3Dto2D
If not -dRot[1|2|3], we cannot estimate nStep, which is the number of skip step using referencefiles .
>>>>>>>> Attention 5 : Refinement Mode -----
-RefineMode
0: for LinearCorrelation; default
1: for SetModeCorrelation
>>>>>>>> Attention 6 : Search Area -----
-refStep[1|2|3]
Skip image number: Just skip ref-images
or
-nRot[1|2|3]Area
Set the search area. You finally can refine parameters by each ref-image following -RefineMode.