MA Y - Mask - image/volume in Y direction

(3/27/14)

PURPOSE

Masks a specified image/volume in a band in the Y 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 Z [Mask - volume in Z direction]
MM [Mask Multiplication]

USAGE

.OPERATION: MA Y

.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, 0.0
[Enter the radii of the outer and inner mask circles, in pixels. Pixels in areas outside the outer radius and inside the inner radius are set to background. Enter zero inner radius for no inner radius masking. Enter zero outer radius for inner masking only.]

.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.]

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