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mrcImageCorrelation
mrcImageCorrelation
Usage
Usage: mrcImageCorrelation
Options:
[-i[nput] In (NULL ).as(inFile ) ] :Essential :InputDataFile
[-o[utput] Out (NULL ).as(outFile ) ] :Optional :OutputDataFile: Correlation Map
[-O[utput] Out2 (NULL ).as(outFile ) ] :Optional :OutputDataFile: Correlation Map for Refinement
[-r[eference] Ref (NULL ).as(inFile ) ] :Essential :ReferenceDataFile
[-cor[relation]Info OutCor (stdout ).as(outFile ) ] :Optional :Output: Correlation Info
[-a[verage] Avg (NULL ).as(outFile ) ] :Optional :OutputDataFile: Averaged File
[-s[hit] Shift (NULL ).as(outFile ) ] :Optional :OutputDataFile: Shifted InputFile
[-refine RefineStep (0.25 ).as(Real )
RefineRange (3.0 ).as(Real )
RefineMode (2 ).as(Integer ) ] :Optional :Refinemnet: Step Range[pixelUnit]
[-c[onfig] configFile (NULL ).as(inFile ) ] :Optional :ConfigurationFile
[-m[ode] mode (0 ).as(Integer ) ] :Optional :Mode
[-M[ode2] mode2 (0 ).as(Integer ) ] :Optional :Mode2
----- Mode: -m -----
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| )
----- Mode2: -M -----
mode 0: Correlation by FFT. Output is a mrcImage to file.
-a : Averaged image after Shift Transform [pixel unit] and Averaging
-s : Shifted image after Shift Transform [pixel unit]
-o : Correation Map
mode 1: Correlation by multiplying in normal space. Output is a real value
Normalized correlation value
No shift transform
No Correlation Map
----- Refinement: -refine -----
refineStep[PixelUnit] : refinement step size
refineRange[PixelUnit] : refinement range
refineMode : refinement mode
--- search area -----
the position of max correlation +- refineRange / refineStep
Attention: If this option is set, the meaning of -o option is changed to a residual map