Display settings - Revision history

Markdayel at 00:43, 17 April 2009

2009-04-17T00:43:09Z

Markdayel: /* Plotting forces on bead */

2009-04-17T00:18:50Z

‎Plotting forces on bead

Markdayel at 19:49, 15 April 2009

2009-04-15T19:49:51Z

Markdayel: Created page with 'Many settings in the `cometparams.ini` affect the way data is displayed. ==Bitmap display settings== ===Basic settings=== X_BMP true Y_BMP ...'

2009-04-15T19:37:00Z

Created page with 'Many settings in the <code>cometparams.ini</code> affect the way data is displayed. ==Bitmap display settings== ===Basic settings=== X_BMP true Y_BMP ...'

New page

Many settings in the <code>cometparams.ini</code> affect the way data is displayed.

==Bitmap display settings==

===Basic settings===
X_BMP true
Y_BMP true
Z_BMP true
BMP_OUTPUT_FILETYPE jpeg
BMP_COMPRESSION 100
DRAW_CAGE false
CAGE_ON_SIDE false
GAUSSFWHM 0.70
FORCE_BAR_SCALE 10
VIEW_HEIGHT 30
INIT_R_GAIN 80
INIT_G_GAIN 30
INIT_B_GAIN 200

===Plotting forces on bead===
SEGMENT_BINS false
RADIAL_SEGMENTS 12
PLOTFORCES false

===Plotting speckle in shell and tail===
SPECKLE true
SPECKLEGRID true
SPECKLEGRIDPERIOD 1000
SPECKLEGRIDTIMEWIDTH 0 #250
SPECKLEGRIDSTRIPEWIDTH 0.3 # 0.2
SPECKLE_FACTOR 0.3

==VTK settings (3D)==

===Basic Settings===
VTK_WIDTH 800
VTK_HEIGHT 800
VIS_PROJECTION z
VTK_AA_FACTOR 2
COLOUR_GAMMA 1.6

===What to display===
VIS_NUCLEATOR true
VIS_NODES false
VIS_LINKS false
VIS_SHADELINKS true
VIS_VOLUMENODES false
VIS_ISONODES false
VIS_NUCOPACITY 1.0
VIS_TRACKS true
VIS_TEXT false
VIS_USENUCTEXMAP false

===3D view settings===
VTK_MOVE_WITH_BEAD false
VIS_LINETHICKNESS 1.2
VIS_VXISCALE 20
VIS_NORMALISEFRAMES false
VIS_PSCALE 55
VTK_VIEWANGLE 50
VIS_PARALLELPROJECTION true
VIS_CAMERADISTMULT 5

==Misc==
VIS_VTK_HIGHQUAL false
VIS_INTERACTIVE false
VIS_FILEPREFIX vtk

==Settings that apply to both bitmaps and VTK==

FOCALDEPTH 2.5
BMP_FIX_BEAD_MOVEMENT false
BMP_FIX_BEAD_ROTATION false

@@ Line 24: / Line 24: @@
 ===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_WIDTH               800
+ 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_HEIGHT              800
+  BMP_WIDTH               800           # width of bitmap in pixels
-  BMP_OUTPUT_FILETYPE     jpeg
+  BMP_HEIGHT              800           # height of bitmap in pixels
-  BMP_COMPRESSION         100
+ VIEW_HEIGHT             30            # bitmap scale (height of image in um)
-  DRAW_CAGE               false
+  BMP_OUTPUT_FILETYPE     jpeg          # graphic type for bitmap save (must be recognized ImageMagick type)
-  CAGE_ON_SIDE            false
+  BMP_COMPRESSION         100           # bitmap quality setting (ImageMagick)
-  GAUSSFWHM               0.70
+  DRAW_CAGE               false         # whether to draw the nucleator on the bitmaps (as a 2D projection of cage of points)
- FORCE_BAR_SCALE         10
+  CAGE_ON_SIDE            false         # whether to draw the cage on the side of the image
- VIEW_HEIGHT             30
+  GAUSSFWHM               0.70          # width of the gaussian used to blur the node points to make the pseudo microscope image
-  INIT_R_GAIN             80
+  INIT_R_GAIN             80            # initial gain for red bitmap channel (rescaled at symmetry breaking)
-  INIT_G_GAIN             30
+  INIT_G_GAIN             30            # initial gain for green bitmap channel (rescaled at symmetry breaking)
-  INIT_B_GAIN             200
+  INIT_B_GAIN             200           # initial gain for blue bitmap channel (rescaled at symmetry breaking)
-  BMP_AA_FACTOR           1
+  BMP_AA_FACTOR           1             # antialiasing factor (produces bigger image and resizes)
- WRITE_BMPS_PRE_SYMBREAK false
 ===Plotting forces on bead===
@@ Line 48: / Line 47: @@
   PLOTFORCES_INCLUDEIMPACTS true        # whether to include surface impacts in force display vectors
   PLOTFORCES_INCLUDELINKFORCES true     # whether to include link tension in force display vectors
 ===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 #250
+  SPECKLEGRIDTIMEWIDTH    0             # grid stripe pulse width (time)
-  SPECKLEGRIDSTRIPEWIDTH  0.3 # 0.2
+  SPECKLEGRIDSTRIPEWIDTH  0.3           # grid bar width (distance)
-  SPECKLE_FACTOR          0.3
+  SPECKLE_FACTOR          0.3           # density of speckles if no grid
@@ Line 61: / Line 61: @@
 ===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===
-  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_VOLUMENODES         false
+  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_TEXT                false
+  VIS_USENUCTEXMAP        false         # whether to put texture on nucleator
   VIS_USENUCTEXMAP        false
 ===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_VXISCALE            20
+  VIS_PSCALE              55            # scaling factor
- VIS_NORMALISEFRAMES     false
+  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==
-  VIS_VTK_HIGHQUAL        false
+  VIS_VTK_HIGHQUAL        false         # VTK antialiasing
- VIS_INTERACTIVE         false
+  VIS_FILEPREFIX          vtk           # output file prefix
   VIS_FILEPREFIX          vtk
 ==Settings that apply to both bitmaps and VTK==
-  SYM_BREAK_TO_RIGHT true
+  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
+  FOCALDEPTH 2.5                        # restrict plotting of nodes etc. to slab twice this distance thick centered on bead
-  BMP_FIX_BEAD_MOVEMENT false
+  BMP_FIX_BEAD_MOVEMENT false           # move camera with bead so bead stays in center of screen
-  BMP_FIX_BEAD_ROTATION false
+  BMP_FIX_BEAD_ROTATION false           # rotate the camera with the bead

@@ Line 43: / Line 43: @@
 ===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
 ===Plotting speckle in shell and tail===

Display settings - Revision history

Markdayel at 00:43, 17 April 2009

Markdayel: /* Plotting forces on bead */

Markdayel at 19:49, 15 April 2009

Markdayel: Created page with 'Many settings in the cometparams.ini affect the way data is displayed. ==Bitmap display settings== ===Basic settings=== X_BMP true Y_BMP ...'

Markdayel: Created page with 'Many settings in the `cometparams.ini` affect the way data is displayed. ==Bitmap display settings== ===Basic settings=== X_BMP true Y_BMP ...'