llExtractWithLayerSeparationFilamentInfo

llExtractWithLayerSeparationFilamentInfo is Eos's Command.

List of option

Main option

Option	Essential/Optional	Description	Default
-i	Essential	Input: mrcImage(FFT)	NULL
-o	Essential	Output: ASCII	NULL
-oF	Optional	Output	NULL
-oI	Optional	Output: ASCII	NULL
-truePitch	Optional	True Pitch	430
-PixelSize	Optional	PixelSize: [A]	5
-deltadY	Optional	A range of deltaY to determine dY.	0.5
-kV	Optional	AccVol: [kV]	200
-Cs	Optional	Cs: [mm]	2.1
-df	Optional	Defocus: [A]: under(+)	27000
-A	Optional	AmplitudeContrast / PhaseContrast	0.1
-c	Optional	ConfigurationFile	NULL
-m	Optional	Mode	0
-h	Optional	Help

-oF 's file name is used by -o .

-m details

Value	Description
0

Output file format

-o format

-oF'sFileName  turn  defocus  Cs  kV  AmplitudeContrast  Mag

-oI format

defocus  Cs  kV  AmplitudeContrast

It can be used by mrcImageCTFCompensation

Execution example

Input file image

by mrcFFTExpression(m=1)

Whole area

Around center

Size Mode Length Min Max Mean SD SE

( 512, 1146, 1) mrcComplexFloatFT ( 2.000, 2.000, 0.000) 4.08519e-10 (257, 572, 0) 0.109661 (0, 0, 0) 0.00909953 0.00776913 1.01425e-05

Case: Options only essential

Output

LengthY 5730.000000 [A] = LengthY 1146 [Pixel] x PixelSize 5.000000 [A/Pixel] x Mag 1.000000
Final CalculatedY        13.325582
      CalculatedY        13.000000
      deltadY             0.325582

-o 's data

oF-Outdata 13 27000.000000 2.100000 200.000000 0.100000 1.0

-oI 's data

27000.000000 2.100000 200.000000 0.100000

Option -truePitch

Case: truePitch=364

Output

LengthY 5730.000000 [A] = LengthY 1146 [Pixel] x PixelSize 5.000000 [A/Pixel] x Mag 1.000000
Final CalculatedY        15.741758
      CalculatedY        16.000000
      deltadY             0.258242

-o 's data

oF-Outdata 16 27000.000000 2.100000 200.000000 0.100000 1.0

Option -PixelSize

Case: PixelSize=2

Output

LengthY 2292.000000 [A] = LengthY 1146 [Pixel] x PixelSize 2.000000 [A/Pixel] x Mag 1.000000
Final CalculatedY         5.330233
      CalculatedY         5.000000
      deltadY             0.330233

-o 's data

oF-Outdata 5 27000.000000 2.100000 200.000000 0.100000 1.0

Option -deltadY

Case: deltadY=0.1

Output

LengthY 5730.000000 [A] = LengthY 1146 [Pixel] x PixelSize 5.000000 [A/Pixel] x Mag 1.000000
Final CalculatedY        13.325582
      CalculatedY        13.000000
      deltadY             0.325582
The deltadY value 0.325582 is larger than permitted deltadY range 0.100000
dY could not be determined

Option -kV

Case: kV=100

-o 's data

oF-Outdata 13 27000.000000 2.100000 100.000000 0.100000 1.0

-oI 's data

27000.000000 2.100000 100.000000 0.100000

Option -Cs

Case: Cs=1.7

-o 's data

oF-Outdata 13 27000.000000 1.700000 200.000000 0.100000 1.0

-oI 's data

27000.000000 1.700000 200.000000 0.100000

Option -df

Case: df=20000

-o 's data

oF-Outdata 13 20000.000000 2.100000 200.000000 0.100000 1.0

-oI 's data

20000.000000 2.100000 200.000000 0.100000

Option -A

Case: A=0.2

-o 's data

oF-Outdata 13 27000.000000 2.100000 200.000000 0.200000 1.0

-oI 's data

27000.000000 2.100000 200.000000 0.200000