mrcImage3DPad

mrcImage3DPad is Eos's Command that is padding the mrcImage(3D) of particle or filament.

List of option

Main option

Option	Essential/Optional	Description	Default
-i	Essential	Input: mrcImage	NULL
-o	Essential	Output: mrcImage	NULL
-r	Optional	Threshold radius of signal.(cf: -M)	Nx
-w	Optional	Width of slope. (For m=1.)	1
-v	Optional	Pad value	0
-Nx	Optional	Output's Nx	Input's Nx
-Ny	Optional	Output's Ny	Input's Ny
-Nz	Optional	Output's Nz	Input's Nz
-Floating	Optional	Floating
-c	Optional	ConfigurationFile	NULL
-m	Optional	Mode of calculating pad value	0
-M	Optional	Mode of calculating -r	0
-h	Optional	Help

-m details

Value	Description
0	Out of threshold is avrage of threshold plain.(Default)
1	Mulplying cos function. Default: Out of threshold is avrage of threshold plain.

About pad value, -v is precedence.

-M details

Value	Description
0	For filaments. (R is calculated from its axis.)
1	For particles. (R is calculated from its center.)

Execution example

Input file image

xy-plane

yz-plane

Min Max Mean SD SE

-0.307724 (52, 10, 79) 1.52145 (47, 41, 47) 0.00295664 0.0916201 0.000132783

Input file's image (for M=1)

xy-plane

yz-plane

Min Max Mean SD SE

-2255.49 (1, 42, 21) 4032.8 (49, 53, 30) 12.0338 475.034 0.48225

Example of options only essential

Output

Tailer: 0
Program Start
N: 69 69 100
TailerNum 0
r: 34 

Output file's image

xy-plane

yz-plane

Min Max Mean SD SE

-0.307724 (52, 10, 79) 1.52145 (47, 41, 47) 0.00295664 0.0916201 0.000132783

Image does not change almost by default.

Option -Nx, -Ny, -Nz

Case: Nx=50, Ny=50, Nz=75

Output

Tailer: 0
Program Start
N: 50 50 75
TailerNum 0
r: 34 

Output file's image

xy-plane

yz-plane

Min Max Mean SD SE

-0.295151 (23, 12, 71) 1.52145 (38, 32, 47) 0.00688378 0.1116 0.000257729

Option -r

Case: r=20

Output

Tailer: 0
Program Start
N: 69 69 100
TailerNum 0
r: 20 

Output file's image

xy-plane

yz-plane

Min Max Mean SD SE

-0.295151 (32, 21, 71) 1.52145 (47, 41, 47) 0.00236564 0.0675752 9.79351e-05

In the following, setting at r=20.

Option -v

Case: v=0.1

Output

Tailer: 0
Program Start
N: 69 69 100
TailerNum 0

Output file's image

xy-plane

yz-plane

Min Max Mean SD SE

-0.295151 (32, 21, 71) 1.52145 (47, 41, 47) 0.0766349 0.0778349 0.000112804

Option -Floating

Output

Tailer: 0
Program Start
N: 69 69 100
TailerNum 0
r: 20 
Floating avg:-0.000912

Output file's image

xy-plane

yz-plane

Min Max Mean SD SE

-0.294238 (32, 21, 71) 1.52236 (47, 41, 47) 0.00327779 0.0675752 9.79351e-05

Option -m

Case: m=1

Case: No other settings

Output

Tailer: 0
Program Start
N: 69 69 100
TailerNum 0
r: -0.000245498 
av: -0.000245498 

Output file's image

xy-plane

yz-plane

Min Max Mean SD SE

-0.295151 (32, 21, 71) 1.52145 (47, 41, 47) 0.00286168 0.0672918 9.75243e-05

Case: w=2

Output

Tailer: 0
Program Start
N: 69 69 100
TailerNum 0
r: -0.000162708 
av: -0.000162708 

Output file's image

xy-plane

yz-plane

Min Max Mean SD SE

-0.255166 (37, 36, 69) 1.06472 (47, 41, 47) 0.00197785 0.0497011 7.20306e-05

Option -M

Case: M=1, r=30

Output

Tailer: 0
Program Start
N: 99 99 99
99 99 99

Output file's image

xy-plane

yz-plane

Min Max Mean SD SE

-1991.84 (41, 38, 29) 4032.8 (49, 53, 30) 13.2658 197.192 0.200188