Display settings

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These settings in the cometparams.ini affect the way data is displayed. There are two display outputs, bitmaps (2D) and VTK (3D). Bitmaps are automatically created during the initial calculation run, but usually start only after the symmetry breaking direction is determined (since this determines the observer position). Bitmaps can also be produced after the initial calculation run is complete with comet post, and VTK output is produced only after the initial calculation run with comet view or comet vtk:

Producing Bitmaps

You can call the bitmap processing with

comet post 0:0

where 0:0 processes all frames, or a range of frames if specified.

Producing VTK output

You can call the VTK processing either interactively with

comet view 300:300  

Note only a single frame can be specified for the interactive view.

or in batch mode with

comet vtk 0:0

VTK can also produce vrml files to import the 3D models into other software (e.g. Acrobat 3D) by calling with one frame only

comet vtk 300:300

Bitmap display settings

Basic settings

X_BMP                   true          # whether to write a bitmap for x axis (default for symmetry breaking plane)  
Y_BMP                   true          # whether to write a bitmap for y axis
Z_BMP                   true          # whether to write a bitmap for z axis
WRITE_BMPS_PRE_SYMBREAK false         # whether to write images before symmetry breaks.  (mainly useful to see what is going on for conditions when symmetry doesn't break!)
BMP_WIDTH               800           # width of bitmap in pixels
BMP_HEIGHT              800           # height of bitmap in pixels
VIEW_HEIGHT             30            # bitmap scale (height of image in um)
BMP_OUTPUT_FILETYPE     jpeg          # graphic type for bitmap save (must be recognized ImageMagick type)
BMP_COMPRESSION         100           # bitmap quality setting (ImageMagick)
DRAW_CAGE               false         # whether to draw the nucleator on the bitmaps (as a 2D projection of cage of points)
CAGE_ON_SIDE            false         # whether to draw the cage on the side of the image   
GAUSSFWHM               0.70          # width of the gaussian used to blur the node points to make the pseudo microscope image
INIT_R_GAIN             80            # initial gain for red bitmap channel (rescaled at symmetry breaking)
INIT_G_GAIN             30            # initial gain for green bitmap channel (rescaled at symmetry breaking)
INIT_B_GAIN             200           # initial gain for blue bitmap channel (rescaled at symmetry breaking)
BMP_AA_FACTOR           1             # antialiasing factor (produces bigger image and resizes)

Plotting forces on bead

SEGMENT_BINS            false         # whether to plot radial segments
RADIAL_SEGMENTS         12            # number of radial segments
PLOTFORCES              false         # whether to plot forces
PLOTFORCES_INCLUDEIMPACTS true        # whether to include surface impacts in force display vectors
PLOTFORCES_INCLUDELINKFORCES true     # whether to include link tension in force display vectors
FORCE_BAR_SCALE         10            # scale factor for force plotting

Plotting speckle in shell and tail

SPECKLE                 true          # whether to color actin with speckles
SPECKLEGRID             true          # specles as grid?
SPECKLEGRIDPERIOD       1000          # grid period (time)
SPECKLEGRIDTIMEWIDTH    0             # grid stripe pulse width (time)
SPECKLEGRIDSTRIPEWIDTH  0.3           # grid bar width (distance)
SPECKLE_FACTOR          0.3           # density of speckles if no grid

VTK settings (3D)

Basic Settings

VTK_WIDTH               800           # VTK image width
VTK_HEIGHT              800           # VTK image height
VIS_PROJECTION          z             # position of camera: x,y,z or rip ; x,y,z correspond to the bitmap images, rip puts the camera ahead of and slightly above bead to view the rip
VTK_AA_FACTOR           2             # antialias factor
COLOUR_GAMMA            1.6           # color scale gamma

What to display

VIS_NUCLEATOR           true          # whether to display nucleator
VTK_NUC_WIREFRAME       true          # whether to display wireframe nucleator in addition (helps show rotation)
VIS_NODES               false         # whether to display individual nodes as balls
VIS_LINKS               false         # whether to display links as lines
VIS_SHADELINKS          true          # whether to color links by strain
VIS_ISONODES            false         # whether to display isosurfaces of node density
VIS_NUCOPACITY          1.0           # opacity of nucleator
VIS_TRACKS              true          # whether to display node tracks
VIS_USENUCTEXMAP        false         # whether to put texture on nucleator

3D view settings

VTK_MOVE_WITH_BEAD      false         # whether to keep bead in center of screen
VIS_LINETHICKNESS       1.2           # line thickness for links
VIS_PSCALE              55            # scaling factor
VTK_VIEWANGLE           50            # camera zoom
VIS_PARALLELPROJECTION  true          # turns off perspective
VIS_CAMERADISTMULT      5             # how far to put camera (multiple of radius)
VIS_NORMALISEFRAMES     false         # whether to normalize intensity of node density isosurface


VIS_VTK_HIGHQUAL        false         # VTK antialiasing
VIS_FILEPREFIX          vtk           # output file prefix

Settings that apply to both bitmaps and VTK

SYM_BREAK_TO_RIGHT true               # rotate camera to orient symmetry break direction to the right (else just rotate to be in the y-z plane)
FOCALDEPTH 2.5                        # restrict plotting of nodes etc. to slab twice this distance thick centered on bead
BMP_FIX_BEAD_MOVEMENT false           # move camera with bead so bead stays in center of screen
BMP_FIX_BEAD_ROTATION false           # rotate the camera with the bead