MO 3 - Model volume creation

PURPOSE

Creates a 3-D model density distribution.

SEE ALSO

MO	[Model image creation]
BL	[Create Blank image]

USAGE

.OPERATION: MO 3

.OUTPUT FILE: MOD001
[Enter the name of the file where the 3-D density distribution is to be kept.]

.ENTER DIMENSIONS (NSAM,NROW,NSLICE): 32,32,16

[Following menu appears.]

.MENU:

(B)LANK -- CONSTANT DENSITY
(C)YLINDER -- SET OF CYLINDERS
(H)ELIX -- HELIX OF SPHERES
(HA) -- HELIX OF SPHERES, ADD DENSITITY
(G) -- GAUSSIAN DENSITITY DISTRIBUTION
(NUM)BERS -- LINE NUMBERS
(R)ANDOM -- RANDOM STATISTICS
(S)INE -- SET OF SINE WAVES
(SP)HERE -- SET OF SPHERES
(SPA) -- SET OF SPHERES, ADD DENSITIES
(SPV) -- SET OF SPHERES, VARIABLE DENSITIES
(T)EST -- 3D SINE WAVE
(W)EDGE -- DENSITY WEDGE

.B/C/H/HA/NUM/Q/R/S/SP/SPA/SPV/T/W: SPA
[Enter the desired menu option.]

For option "B" - Blank.

A blank volume of constant background is created.

.CONSTANT BACKGROUND: 7.0
[Enter intensity value for the image.]

For Option "C" - Cylinder

A cylinder with uniform density is created. Cylinder axis lies along the Y-coordinate.

.VALUE OF VOLUME BACKGROUND: 0
[Enter value the volume outside of the cylinder(s) will be filled with]

.CHOOSE X, Y, Z (OR Q TO END CYLINDER ENTRY): Y
[Give axis direction of cylinder]

.RADIUS, HEIGHT: 4.5,6.2
[Give radius and height of cylinder.]

.X & Y COORDINATES OF CENTER: 12.,4.3
[Enter X, Y coordinates of center.]

.Z COORDINATE, DENSITY: 7.8,2
[Enter Z coordinate of center, and density value.]

.CHOOSE X, Y, Z (OR Q TO END CYLINDER ENTRY) Y
[You may specify another cylinder now or enter 'Q' to terminate.]

For Options "H/HA" - Helix

A helical arrangement of spheres running in the Y-direction is created.

.ENTER MASS VALUE PER VOXEL (DEFAULT = 2.0):

.SPHERE RADIUS, HELIX RADIUS: 4.2, 8.5
[Enter the radiI for spheres and helix.]

.NO. OF SPHERES, NO. OF TURNS: 12,2
[Enter the total number of sphereS and the total number of turns in NROW.]

For Option "G" - Gaussian distribution

A 3D Gaussian density distribution is created. The normalization is such that the sum of all the voxel deinsities is equal one.

.COORDINATES OF THE CENTER X,Y,Z: 12,23.12,10

.STD. DEVIATIONS X,Y,Z 4.2, 8.5, 12.3
[Enter the standard deviations for Gaussian function.]

For Option "NUM"- NUMBERS

A test volume containing numbers is created. The line number in the 3D file is put into each line at a specified position.

.POSITION IN LINE: 5
[Enter the position where the line number should be put in each line]

.SCALING FACTOR: 3
[Enter scaling factor]

.NUMBER PIXELS IN LINE? (Y/N): Y
[If answer is "Y" following two questions appear.]

.SLICE NUMBER, LINE NUMBER: 3,4
[Enter slice number and line number]

.SCALING FACTOR: 2
[Enter scaling number]

For Option "R" - Random

A volume containing random densities is created.

.GAUSSIAN DISTRIBUTION? (Y/N): N
[For 'N' a random image with the values uniformly distributed between 0 and 1 is generated. If 'Y' was specified, SPIDER will ask]

.MEAN AND STANDARD DEVIATION OF GAUSSIAN DIST.: 0.0,0.35
[Enter the mean value and standard deviation of the gaussian distribution for random numbers to be generated.]

For Option "S" - Sine.

A volume containing a 3-D distribution from an arbitrary number of 3-d sine waves with arbitrary spatial frequency vector is created.

.NUMBER OF SINE WAVES: 3
[Enter number of sine waves, with a maximum of 20.]

.I=1 REL.AMPL.,SPATIAL FREQUENCY(KX,KY,KZ): .5,1,2,4

.I=2 REL.AMPL.,SPATIAL FREQUENCY(KX,KY,KZ): 1.,2,2,2

.I=3 REL.AMPL.,SPATIAL FREQUENCY(KX,KY,KZ): 1.,1,2,1
[Enter relative amplitude and spatial frequency for each sine wave.]

[The actual amplitudes used "AMPL" are calculated from the input amplitudes according to the formula:
AMPL = 2. * AMPLIN / AMPSUM
where "AMPSUM" is the sum of all input amplitudes. A list of the actual amplitudes is printed out.]

For Options "SP/SPA/SPV"

Spheres of given outer and inner radius with a given density are created, with centers located at specified points. The default inner radius is zero and the default density value is 2.0. After modelling a sphere of a given radius the program should ask for the radii (but does not) and location of the next sphere. If the any spheres outer radius exceeds the boundary of the 3-D file, the program warns that part of the sphere will be truncated.

.GET COORDINATES FROM DOCUMENT FILE (Y/N): N
[Otherwise the user will input sphere coordinates from the command line.]

If the answer is 'Y' SPIDER asks:]

.DOCUMENT FILE: DOC001
[Enter name of document file with center coordinates of spheres, in order: X,Y,Z ( ,Radius2, Radius1 - optional) (,Mass value - optional) starting in any column]

.NUMBER OF SPHERES, STARTING COL. FOR X,Y,Z: 50,1
[Enter number of spheres and column of X-coordinate in document file]

.X,Y, & Z OFFSET: 20.,-10.,51.
[Enter offset for X,Y,Z]

.OUTER AND INNER RADII OF SPHERES: 4.5, 1.7
[Enter radius of sphere as a floating point number. If a negative value is entered for one or both of the radii, they are taken from the document file. If the inner radius is taken from the document file, the outer radius also must be in this file. But, the outer radius can be taken from the document file while the inner one can be fixed for all spheres and entered explicitly.]

For Option "SP/SPA":

.ENTER MASS VALUE PER VOXEL (DEFAULT = 2.0): 3.0
[Enter the density value to placed inside sphere.]

For Options "SP/SPA/SPV" without input from a doc file:

.OUTER AND INNER RADII OF SPHERES: 4.5, 1.7
[Enter radii of spheres as a floating point number. To exit: enter '0,0,0' as coordinates.]

.X,Y,Z: 10,10,15
[Enter the coordinates for center the sphere. To exit: enter '0, 0, 0' as coordinates.]

For Option "T" - Test

A three-dimensional (circularly continuous) sine wave is created in the given volume. It has the spatial frequency (1,1,1).]

For Option "W" - Wedge

A three-dimensional, linearly increasing density distribution is created. The values increase linearly with increasing X, Y, and Z.

SUBROUTINES

MODEL3, RANN

CALLER

UTIL1