llExtract

llExtract is Eos's Command that extracts llData from FFT data. llDataPrint can display output file as graph.

List of option

Main option

Option	Essential/Optional	Description	Default
-t	Optional	Tiltle: ASCII[80]	NULL
-s	Optional	Step[A]: (xStep, yStep)	(1.0, 1.0)
-M	Optional	Max[GridUnit]: (MaxX, MaxY)	(1.0, 1.0)
-i	Optional	Input: mrcImage(FFT)	NULL
-1	Optional	Output: NearSide: [llData]	NULL
-2	Optional	Output: FarSide: [llData]	NULL
-R	Optional	RotationAngle: [Degree]	0.0
-O	Optional	Omega: [Degree]	0.0
-S	Optional	Shear: [Degree]	0.0
-I	Optional	ievery	0
-axl	Optional	axl	0.0
-ayl	Optional	ayl	0.0
-x	Optional	xShift: [GridUnit]	0.0
-l	Optional	llMax	0
-d	Optional	delRInv: [A]	0.0
-f	Optional	flagOutputInfo
-L	Optional	Variable: LayerLineInfo: (n, l, Y, leftMin, leftMax, rightMin, rightMax, weight) ...	(0, 0, 0.0, 0.0, 0.0, 0.0, 0.0, 1.0)
-c	Optional	ConfigurationFile: ASCII	NULL
-m	Optional	Mode	0
-h	Optional	Help

-s: must set (Lengthx, Lengthy).

-d: must set Nx * Lengthx

-m details

Value	Description
0

ConfigurationFile format

Title
xStep  yStep
MaxX  MaxY
InputFileName
OutputFileName(NearSide)
OutputFileName(FarSide)
RotationAngle
Omega
Share
ievery
axl
ayl
xShift
llMax
delRInv
flagOutputInfo
n0  l0  Y0  leftMin0  leftMax0  rightMin0  rightMax0  weight0
n1  l1  Y1  leftMin1  leftMax1  rightMin1  rightMax1  weight1
.
.

llExtractCtrlFileCreate can create it.

The data that is set by option is not read, but these lines must not be omitted.

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

Option -c

ConfigurationFile1

Setting the following data.

llData
2 2
255 572
In
Nea
Far
0.0
0.0
0.0
0
0.0
0.0
256
12
1024
0
     0      0      0 0 255 0 255 0.5
     2      2     72 0 255 0 255 1.0
     4      4    144 0 255 0 255 1.0
    -3     11    -66 0 255 0 255 1.0
    -1     13      6 0 255 0 255 1.0
     1     15     78 0 255 0 255 1.0
     3     17    150 0 255 0 255 1.0
    -4     24    -60 0 255 0 255 1.0
    -2     26     12 0 255 0 255 1.0
     0     28     84 0 255 0 255 1.0
     2     30    156 0 255 0 255 1.0
     4     32    228 0 255 0 255 1.0

-1 's data

LAYERLINE   0 NEAR................................................................................ 5.00000e-01    0    0
 0.00000e+00 1.09661e-01 1.00179e-05
 9.76562e-04 1.07064e-01 1.66569e-07
 1.95312e-03 9.94539e-02 1.79314e-06
 2.92969e-03 8.73620e-02 1.63306e-06
 3.90625e-03 7.16275e-02 9.95900e-07

...

 2.48047e-01 2.45430e-02 1.00179e-05
 2.49023e-01 2.57134e-02 1.00179e-05
 0.00000e+00 0.00000e+00 0.00000e+00
LAYERLINE   1 NEAR................................................................................ 1.00000e+00    2    2
 0.00000e+00 2.36747e-04 3.27016e+02
 9.76562e-04 2.19473e-05 3.21478e+02
 1.95312e-03 9.17815e-05 1.00204e+02
 2.92969e-03 2.42726e-04 4.08337e+01
 3.90625e-03 7.48780e-04 1.25217e+01

...

 2.48047e-01 5.52613e-03 7.64794e+01
 2.49023e-01 6.03607e-03 8.58422e+01
 0.00000e+00 0.00000e+00 0.00000e+00
LAYERLINE   2 NEAR................................................................................ 1.00000e+00    4    4
 0.00000e+00 1.56065e-03 2.94032e+02
 9.76562e-04 1.02912e-03 2.90051e+02
 1.95312e-03 7.23528e-04 2.77422e+02
 2.92969e-03 6.94803e-04 2.59534e+02
 3.90625e-03 8.97704e-04 2.50892e+02

...

LAYERLINE   3 NEAR................................................................................ 1.00000e+00   -3   11

...

LAYERLINE  11 NEAR................................................................................ 1.00000e+00    4   32

...

 2.45117e-01 2.10039e-02 3.42847e+02
 2.46094e-01 2.36644e-02 3.43764e+02
 2.47070e-01 2.59560e-02 3.44583e+02
 2.48047e-01 2.78412e-02 3.45314e+02
 2.49023e-01 2.92789e-02 3.45958e+02
 0.00000e+00 0.00000e+00 0.00000e+00

-2 's data

LAYERLINE   0 FAR ................................................................................ 5.00000e-01    0    0
 0.00000e+00 1.09661e-01 1.00179e-05
 9.76562e-04 1.07064e-01 1.00179e-05
 1.95312e-03 9.94539e-02 1.00179e-05
 2.92969e-03 8.73620e-02 1.00179e-05
 3.90625e-03 7.16275e-02 1.00179e-05

...

 2.48047e-01 2.45430e-02 5.44967e-07
 2.49023e-01 2.57134e-02 8.66931e-07
 0.00000e+00 0.00000e+00 0.00000e+00
LAYERLINE   1 FAR ................................................................................ 1.00000e+00    2    2
 0.00000e+00 2.36747e-04 3.27016e+02
 9.76562e-04 5.38817e-04 3.33733e+02
 1.95312e-03 9.34154e-04 3.39000e+02
 2.92969e-03 1.47219e-03 3.43420e+02
 3.90625e-03 2.23950e-03 3.46949e+02

...

 2.48047e-01 6.32650e-03 7.40293e+01
 2.49023e-01 6.41878e-03 8.40146e+01
 0.00000e+00 0.00000e+00 0.00000e+00
LAYERLINE   2 FAR ................................................................................ 1.00000e+00    4    4
 0.00000e+00 1.56065e-03 2.94032e+02
 9.76562e-04 2.26294e-03 2.94056e+02
 1.95312e-03 3.08391e-03 2.92763e+02
 2.92969e-03 3.96259e-03 2.91127e+02
 3.90625e-03 4.82953e-03 2.89482e+02

...

LAYERLINE   3 FAR ................................................................................ 1.00000e+00   -3   11

...

LAYERLINE  11 FAR ................................................................................ 1.00000e+00    4   32

...

 2.45117e-01 2.58909e-02 3.47760e+02
 2.46094e-01 2.80857e-02 3.47725e+02
 2.47070e-01 2.95940e-02 3.47578e+02
 2.48047e-01 3.04287e-02 3.47325e+02
 2.49023e-01 3.06231e-02 3.46968e+02
 0.00000e+00 0.00000e+00 0.00000e+00