Difference between revisions of "Display settings"
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| − | + | These settings in the <code>cometparams.ini</code> 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 <code>comet post</code>, and VTK output is produced only after the initial calculation run with <code>comet view</code> or <code>comet vtk</code>: | |
| + | |||
| + | ===Producing Bitmaps=== | ||
| + | You can call the bitmap processing with | ||
| + | comet post 0:0 | ||
| + | |||
| + | where <code>0:0</code> 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== | ==Bitmap display settings== | ||
===Basic settings=== | ===Basic settings=== | ||
| − | X_BMP true | + | X_BMP true # whether to write a bitmap for x axis (default for symmetry breaking plane) |
| − | Y_BMP true | + | Y_BMP true # whether to write a bitmap for y axis |
| − | Z_BMP true | + | Z_BMP true # whether to write a bitmap for z axis |
| − | BMP_OUTPUT_FILETYPE jpeg | + | 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_COMPRESSION 100 | + | BMP_WIDTH 800 # width of bitmap in pixels |
| − | DRAW_CAGE false | + | BMP_HEIGHT 800 # height of bitmap in pixels |
| − | CAGE_ON_SIDE false | + | VIEW_HEIGHT 30 # bitmap scale (height of image in um) |
| − | GAUSSFWHM 0.70 | + | 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) | |
| − | INIT_R_GAIN 80 | + | CAGE_ON_SIDE false # whether to draw the cage on the side of the image |
| − | INIT_G_GAIN 30 | + | GAUSSFWHM 0.70 # width of the gaussian used to blur the node points to make the pseudo microscope image |
| − | INIT_B_GAIN 200 | + | 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=== | ===Plotting forces on bead=== | ||
| − | SEGMENT_BINS false | + | SEGMENT_BINS false # whether to plot radial segments |
| − | RADIAL_SEGMENTS 12 | + | RADIAL_SEGMENTS 12 # number of radial segments |
| − | PLOTFORCES false | + | 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=== | ===Plotting speckle in shell and tail=== | ||
| − | SPECKLE true | + | SPECKLE true # whether to color actin with speckles |
| − | SPECKLEGRID true | + | SPECKLEGRID true # specles as grid? |
| − | SPECKLEGRIDPERIOD 1000 | + | SPECKLEGRIDPERIOD 1000 # grid period (time) |
| − | SPECKLEGRIDTIMEWIDTH 0 # | + | SPECKLEGRIDTIMEWIDTH 0 # grid stripe pulse width (time) |
| − | SPECKLEGRIDSTRIPEWIDTH 0.3 # | + | SPECKLEGRIDSTRIPEWIDTH 0.3 # grid bar width (distance) |
| − | SPECKLE_FACTOR 0.3 | + | SPECKLE_FACTOR 0.3 # density of speckles if no grid |
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===Basic Settings=== | ===Basic Settings=== | ||
| − | VTK_WIDTH 800 | + | VTK_WIDTH 800 # VTK image width |
| − | VTK_HEIGHT 800 | + | VTK_HEIGHT 800 # VTK image height |
| − | VIS_PROJECTION z | + | 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 | + | VTK_AA_FACTOR 2 # antialias factor |
| − | COLOUR_GAMMA 1.6 | + | COLOUR_GAMMA 1.6 # color scale gamma |
===What to display=== | ===What to display=== | ||
| − | VIS_NUCLEATOR true | + | VIS_NUCLEATOR true # whether to display nucleator |
| − | VIS_NODES false | + | VTK_NUC_WIREFRAME true # whether to display wireframe nucleator in addition (helps show rotation) |
| − | VIS_LINKS false | + | VIS_NODES false # whether to display individual nodes as balls |
| − | VIS_SHADELINKS true | + | VIS_LINKS false # whether to display links as lines |
| − | + | VIS_SHADELINKS true # whether to color links by strain | |
| − | VIS_ISONODES false | + | VIS_ISONODES false # whether to display isosurfaces of node density |
| − | VIS_NUCOPACITY 1.0 | + | VIS_NUCOPACITY 1.0 # opacity of nucleator |
| − | VIS_TRACKS true | + | VIS_TRACKS true # whether to display node tracks |
| − | + | VIS_USENUCTEXMAP false # whether to put texture on nucleator | |
| − | VIS_USENUCTEXMAP false | + | |
===3D view settings=== | ===3D view settings=== | ||
| − | VTK_MOVE_WITH_BEAD false | + | VTK_MOVE_WITH_BEAD false # whether to keep bead in center of screen |
| − | VIS_LINETHICKNESS 1.2 | + | VIS_LINETHICKNESS 1.2 # line thickness for links |
| − | + | VIS_PSCALE 55 # scaling factor | |
| − | + | VTK_VIEWANGLE 50 # camera zoom | |
| − | VIS_PSCALE 55 | + | VIS_PARALLELPROJECTION true # turns off perspective |
| − | VTK_VIEWANGLE 50 | + | VIS_CAMERADISTMULT 5 # how far to put camera (multiple of radius) |
| − | VIS_PARALLELPROJECTION true | + | VIS_NORMALISEFRAMES false # whether to normalize intensity of node density isosurface |
| − | VIS_CAMERADISTMULT 5 | + | |
==Misc== | ==Misc== | ||
| − | VIS_VTK_HIGHQUAL false | + | VIS_VTK_HIGHQUAL false # VTK antialiasing |
| − | + | VIS_FILEPREFIX vtk # output file prefix | |
| − | VIS_FILEPREFIX vtk | + | |
==Settings that apply to both bitmaps and VTK== | ==Settings that apply to both bitmaps and VTK== | ||
| − | FOCALDEPTH 2.5 | + | 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) |
| − | BMP_FIX_BEAD_MOVEMENT false | + | FOCALDEPTH 2.5 # restrict plotting of nodes etc. to slab twice this distance thick centered on bead |
| − | BMP_FIX_BEAD_ROTATION false | + | 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 | ||
Latest revision as of 16:43, 16 April 2009
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:
Contents
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
Misc
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
