Cytosim PI Cytoskeleton Simulator

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Variables
Display parameters: Fibers
Display Parameters

## Variables
int | visible
| visibility flag : 0=hidden, 1=opaque (-1 is used in 3D for transparent objects)
gle_color | color
| color of fiber
int | coloring
| if true, use different colors to display some property of the fibers More...
real | line_width
| width of lines (also known as `line`[0])
int | line_style
| style for lines (also known as `line`[1]) More...
real | point_size
| size of points (also known as `point`[0]) More...
int | point_style
| style for display of points (also known as `point`[1]) More...
int | end_style [2]
| style of fiber tips for { PLUS_END, MINUS_END } More...
real | end_size [2]
| size of fiber tips for { PLUS_END, MINUS_END } More...
real | end_section [2]
| length of a section displayed near the fiber tips More...
gle_color | end_color [5]
| colors of the different FiberTip states More...
int | speckle_style
| style for speckle display (also know as speckles) More...
real | interval
| distance between speckles (also known as `speckles`[1])
int | exclude
| a bit-field to hide certain categories of fibers More...
Vector | right
| the reference direction used for hiding left- or right-pointing fibers, etc. (also known as `exclude`[1])
unsigned int | mask
| period used to attribute colors with the coloring option
int | phase
| phase used to attribute colors with the coloring option (also known as `mask`[1])
real | rainbow
| conversion coefficient from tension to color, for line_style==2 More...
real | forces
| ( if > 0 ) display the net forces FP acting on model points More...
int | explode
| the 'explosion' effect shift the fibers in space More...
real | explode_range
| amount of lateral shift to separate fibers when display is exploded (known as `explode`[1])
int | show_average
| if true, display the average fiber More...

## Detailed Description

## Variable Documentation

int coloring

Values for coloring:

- 0 : no coloring,
- 1 : color fibers according to ID-number,
- 2 : color fibers depending on direction,
- 3 : color fibers depending on the mark,
- 4 : color fibers by connectivity.

gle_color end_color[5]

This determines the set of color that are used to display the fiber tips, according to their assembly state (Fiber::dynamicState):

- static ends (dynamic-state 0) use end_color[0],
- growing end (dynamic-state 1), use end_color[1],
- shrinking end (dynamic-state 4), use end_color[4]

real end_section[2]

if end_section[0] > 0, a section near the PLUS_ENDD is displayed with the color of the PLUS_END. if end_section[1] > 0, a section near the MINUS_END is displayed with the color of the MINUS_END.

real end_size[2]

You can also specify:

plus_end = SIZE, STYLE
minus_end = SIZE, STYLE

int end_style[2]

end_style[0] determines the style of the PLUS_END, and end_style[1] the style of the MINUS_END.

Possible end_style:

- 0 : hide,
- 1 : display a disc/sphere,
- 2 : display a cone,
- 3 : display a disc,
- 4 : draw arrowhead,
- 5 : draw arrowhead in the inverted direction (for actin)

int exclude

Possible values for exclude:

- 0 : all fibers are displayed,
- 1 : show only right-pointing fibers,
- 2 : show only left-pointing fibers,
- 4 : show only counter-clockwise fibers,
- 8 : show only clockwise fibers.

You may also address each bit directly, knowning that:

- bit 1 on: hide left-pointing fibers
- bit 2 on: hide right-pointing fibers
- bit 3 on: hide clockwise fibers
- bit 4 on: hide counter-clockwise fibers

int explode

This can be useful to visualize dense regions, but is only implemented for style=2

real forces

The force is displayed as segments of length forces*PF. A color can be specified as forces[1]

int line_style

Possible line_style:

- 0 : hide,
- 1 : plain lines,
- 2 : rainbow coloring based on compressive forces,
- 3 : color set by the angle of the fiber in XY plane,
- 4 : local color gradient that indicates polarity.

real point_size

point_size and line_width are normally set in pixels, but if display:point_value is set, their value is understood in multiples of point_value, which itself is a distance.

For example, if you set line_width=2.5 and point_value=0.01, the fibers will be displayed with a diameter of 0.025.

int point_style

Possible point_style:

- 0 : hide,
- 1 : show model points,
- 2 : show arrow-heads along fiber, separated by `interval`,
- 3 : indicate abscissa.

real rainbow

Possible values for rainbow:

- 0 : disabled,
- rainbow > 0 : compressive forces are highlighted in red,
- rainbow < 0 : traction/elongation forces are highlighted.

int show_average

The 'average fiber' is calculated from the centroid of the fiber tips, and the centroid of the polymer mass. It is useful to evaluate the amount of order in the network.

int speckle_style

Possible speckle_style:

- 0 : hide,
- 1 : random speckles, separated on average by `interval`,
- 2 : regular speckes, separated by `interval`.