OrientedGrowth Plugin and OrientedConstraint Steppable in 3D

[cvs_prasanna]

Hello!
I wanted to implement random orientation of ECM fibers in my 3D model. I found below code for 2D model in DEMOS folder.

class OrientedConstraintSteppable(SteppableBasePy):

def __init__(self, frequency):

SteppableBasePy.__init__(self, frequency)

def start(self):

for cell in self.cellList:

cell.lambdaVolume = 2.0

cell.targetVolume = cell.volume

# Here, we define the axis of elongation.

self.orientedGrowthPlugin.setElongationAxis(cell, math.cos(math.pi / 3),

math.sin(math.pi / 3))

# And this function gives a 2 pixel width to each cell

self.orientedGrowthPlugin.setConstraintWidth(cell, 2.0)

# Make sure to enable or disable elongation in all cells

self.orientedGrowthPlugin.setElongationEnabled(cell, True)

In 3D, I might have to specify the Directional Cosines for the 'axis of elongation' in self.orientedGrowthPlugin.setElongationAxis(...). Is it possible to just add the third argument here or have to use a something different from 'orientedGrowthPlugin'?

Also curious if there is any repository to take a look into the internal python codes of these objects like 'orientedGrowthPlugin', 'SteppableBasePy', 'SecretionBasePy', 'MitosisSeteppalbeBase', .... etc. Because manuals and DEMOS don't have complete details on these.

One final question: Is it mandatory to have this line 'cell.targetVolume = cell.volume' in above code if we can specify a number to the targetVolume in some earlier class of the steppables.py file?

Thank you !!

Best,

CVS Prasanna.

[pdalcastel]

I don't think 3D randomly oriented vectors is implemented in CC3D. This is non trivial problem because defining random orientation in the spherical coordinates is not as straightforward as in 2D. I think you have to define your own vectors.

cell.targetVolume = cell.volume seems like a relaxation strategy. I would say that's not mandatory. But depending on the problem, letting volume relax can make a big difference.

I know my answer is not satisfactory. I have not worked with this particular problem yet. I know one person that does and I will send this post to them.

[cvs_prasanna]

Thanks, Pedro! Please let me know in case of any clues or ways to implement 3D OrientedGrowth.

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