MA Z - Mask - volume in Z direction

(3/27/14)

PURPOSE

Masks a volume in Z direction. Pixels in the area inside the inner extent and the area outside the outer extent are set to a specified background.   Example.

SEE ALSO

MA [Mask - image/volume with a circular mask]
MA L [Mask - line across image/volume]
MA X [Mask - image/volume in X direction]
MA Y [Mask - image/volume in Y direction]
MM [Mask Multiplication]

USAGE

.OPERATION: MA Z

.INPUT FILE: PIC001
[Enter the name of the file to be masked.]

.OUTPUT FILE: IMG032
[Enter the name of the output file.]

.OUTER & INNER HALFWIDTH EXTENTS: 12.0
[Enter the radius of the mask circle, in pixels.]

.SHARP, COSINE, GAUSSIAN EDGE, OR TRUE GAUSSIAN (S/C/G/T): S
[Type of mask edge:
['S' for sharp profile cutoff.
'C' for no modification inside the mask extent and cosine-shaped falloff from this extent outwards.
'G' for no modification inside the mask extent and Gaussian-shaped falloff from this extent outwards).
'T' for true Gaussian mask.]

.AVG, PREV AVG, CIRCUMFERANCE, OR EXTERNAL BACKGROUND? (A/P/C/E): P
[Value to be used for background:
'A' is average of the image after masking.
'P' is the average of the image before masking.
'C' is the average along the border of the mask.
'E' is specified externally.
].

If 'E' was entered, SPIDER asks:

.BACKGROUND: 3.0
[Enter the desired background for masked area.]

.Z CENTER OF MASK OR <CR> FOR IMAGE CENTER: 50
[Enter the Z coordinate of the mask center. Note that you have to specify an X coordinate equal to NZ/2+1 or <CR> if you want the mask center to coincide with the nominal volume center.]

If a 'C' was specified in response to the 'DISK, COSINE, GAUSSIAN EDGE, OR TRUE GAUSSIAN:' prompt, SPIDER asks:

.WIDTH: 3.5
[Enter width of the cosine falloff function.]

If a 'G' was specified in response to the 'DISK, COSINE, GAUSSIAN EDGE, OR TRUE GAUSSIAN:' prompt, SPIDER asks:

.HALFWIDTH: 3.5
[Enter halfwidth of the Gaussian falloff function.]

SUBROUTINES

MASK

CALLER

UTIL2

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