Current data structures

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Main data structure

To access the data structure from the command line (debugging etc.)

global data

 data = 
            PanelH: 0.0339
         plotprops: [1x1 struct]
         cellprops: [1x1 struct]
        iterations: 0
       projectname: 'MT_Edinb_20120427'
         parentdir: 'C:\MyDocuments2012\Matlab\Microtubules'
       factorprops: [1x1 struct]
    organelleprops: [1x1 struct]
    useoforganelle: [1x1 struct]
        CustomMode: 1
         oldcolour: [0.7020 0.7020 0.7020]
        view_steps: 1
    FlashCollision: 0
           working: [1x1 struct]
   label2organelle: {[]  'nucleus'  'vacuole'  'plasma_membrane'  'cell_wall'  'microtubules'  'actin'}

Cell organisation

Re-initialised with Initialise

data.cellprops
                  shape: 'Sphere'
             sheetmodel: 0
       maxLengthMicrons: 20
         secondsPerStep: 1
    micronsPerVoxelEdge: 0.8000
   cubicMicronsPerVoxel: 0.5120
               cellsize: [25 25 25]
             colourType: 1
                    Vol: [25x25x25 int8]
                 Smooth: 'None'
                dynamic: {1x8 cell}
         bound_distance: 5
       collide_distance: 10
                vacuole: [1x1 struct]
              cell_wall: [1x1 struct]
        plasma_membrane: [1x1 struct]
              cytoplasm: [1x1 struct]
               Diameter: [1x1 struct]
           microtubules: [1x1 struct]
       sheetPlaneNormal: [0 1 0]

Organelle specification

Re-initialised with Initialise Not all organelles may be in use - the InUse flag

data.organelleprops
         cell_wall: [1x1 struct]
   plasma_membrane: [1x1 struct]
         cytoplasm: [1x1 struct]
           nucleus: [1x1 struct]
      microtubules: [1x1 struct]
             actin: [1x1 struct]
           vacuole: [1x1 struct]

Factor specification

Re-initialised with Initialise Factors represent diffusable, reacting solutes. They occupy the volume (after reshaping) with a value >0. The diffusion constants are also per-voxel.

data.factorprops
       Name2Index: [0x0 struct]
       Index2Name: []
    Concentration: []
   DiffusionConst: []
            Color: []

Working arrays

Re-initialised with Restart

 data.working
                 Vol: [25x25x25 int8]
             CellAge: 9
   nucleationNumbers: [1x1 struct]
     organelle_label: [1x1 struct]
                 dyn: [1x1 struct]
            VideoObj: []

Microtubule details are in the dyn (dynamic organelle) field. Here we show microtubule 1. It contains a local copy of microtubule properties in the field: Props (derived from data.organelles.microtubules)

  data.working.dyn.microtubules.Org(1)
               Type: 0
      PauseDuration: 0
                Age: 5
      TimeNucleated: 0
                 ID: 1
              Alive: 1
            Growing: 1
          Shrinking: 1
        Catastrophe: 0
           BoundPLM: 0
    PLMBindVertNums: []
           BoundMic: 0
     MTBindVertNums: []
           BoundVac: 0
    VacBindVertNums: []
                Hit: [1x1 struct]
              HitMe: [1x1 struct]
              Verts: [6x3 double]
   CurrentDirection: [-0.1172 -0.0224 -0.2197]
        planeNormal: []
              Props: [1x1 struct]
          AgeFormed: 3

GUI and plotted output

plotprops used for GUI and plotting - uihandles probably not used at all in the code. The key handles are

data.PanelH
data.plotprops.AxesH

data.plotprops
               markers: 0
                  FigH: 1
   VolViewerFoldername: 'D:\ab\Matlab stuff\VolViewer\WatchedData'
                 AxesH: 287.0339
                TitleH: 288.0339
               XlabelH: 289.0339
               YlabelH: 290.0339
        cameratoolbarH: 291.0339
             uihandles: [1x1 struct]
            axislabels: [1x1 struct]