Feature/curvature compartments fpp tutorial #30

maciekswat · 2024-08-31T21:51:57Z

I added a full tutorial that walks users from a simulation involving a single cell to a simulation containing multiple elongated cells. Each cell is a compartmentalized cell and we used FPP and Curvature plugins to control cell shape

tjsego

This looks great. I only recommend fixing various typos throughout.

fyffep

I like the overall style of this tutorial, and it all seems technically sound. I just have a lot of nitpick comments. I hope I can convince you to try the Grammarly plugin for VSCode.🙂 It's easy to set up, and it saved me a lot of time for doc writing.
I think the scope is well-chosen so that a person could follow this tutorial without much background knowledge.

docs/example_compartmental_elongated_cells_tutorial.rst

fyffep · 2024-09-14T12:20:29Z

docs/index.rst

+    :caption: Complete Tutorials
+    :hidden:
+
+    example_compartmental_elongated_cells_tutorial


This could go inside section_real_world_examples, which holds our list of complete tutorials, instead of index.rst

Does the "Real-World Examples" display for you when you open documentation? It does not for me.

https://compucell3dreferencemanual.readthedocs.io/en/latest/

We might need to do some upgrades to the index but I agree we should group it

It's hidden for me too. Could you please adjust this part of index.rst

.. toctree:: :maxdepth: 1 :hidden: :caption: Real-world Examples section_real_world_examples

so that either maxdepth is 2 or hidden is removed?

Done - it worked, thanks!

docs/example_compartmental_elongated_cells_tutorial.rst

fyffep · 2024-09-14T12:23:39Z

docs/example_compartmental_elongated_cells_tutorial.rst

+Building Simulation of Elongated Cells. Case Study in using Compartments, FPP Links, Curvature energy terms.
+------------------------------------------------------------------------------------------------------------
+
+The goal of this tutorial is to build a simulation of multiple elongated cells where each sell is composed of compartments.


sell -> cell

fyffep · 2024-09-14T12:26:17Z

docs/example_compartmental_elongated_cells_tutorial.rst

+.. note::
+
+    Our intention is to teach you how you can start building complex simulation from grounds up
+    by starting with a single ce,, understand the behavior of the single cell under different set of parameters


ce,, -> cell
firs -> first

fyffep · 2024-09-14T13:12:17Z

docs/example_compartmental_elongated_cells_tutorial.rst

+
+Let us now put everything together an implement elongated compartmentalized cell. The solution that will prevent two
+``Center`` cells (the ones that initially were touching ``Top`` cell), from forming an extra FPP link,
+is to use Curvature Plugin. The way Curvature plugin works is by constraining the angle that two adjacent links can form


Change sentence to: "The Curvature plugin constrains the angle at which two adjacent links can form."

fyffep · 2024-09-14T13:13:03Z

docs/example_compartmental_elongated_cells_tutorial.rst

+By using high value of Curvature lambda you may constrain two adjacent links to form a straight line
+and by adiabatically lowering the lambda you can control how much elongated cell can bend.
+The code for this section is in ``Demos/CompuCellPythonTutorial/ElongatedCellsTutorial/Tutorial_08``
+


Add a link to curvature.rst

fyffep · 2024-09-14T13:16:37Z

docs/example_compartmental_elongated_cells_tutorial.rst

+to the cell that is created first in each cluster. We will store a list of "first" cells inside member variable
+``self.list_of_leading_cells = []`` which is a list. . we have to be careful to ensure that cells stored in that list do
+not disappear because if the do disappear and we try to reference them we will get Segmentation Fault Error.
+We will show later how we could avoid this issue in the code , just to show you how to handle situation of that type.


To help break up this long paragraph, move

"we have to be careful to ensure that cells stored in that list do
not disappear because if the do disappear and we try to reference them we will get Segmentation Fault Error.
We will show later how we could avoid this issue in the code , just to show you how to handle situation of that type."

a little ways down so that it is closer to the code that addresses this pitfall.

fyffep · 2024-09-14T13:17:05Z

docs/example_compartmental_elongated_cells_tutorial.rst

+The simulation code can be found in ``Demos/CompuCellPythonTutorial/ElongatedCellsTutorial/Tutorial_09``
+
+
+In terms of XML modification, we only need to add a one-liner that enavbles ExternalPotential plugin that simulates


fyffep · 2024-09-14T13:19:13Z

docs/example_compartmental_elongated_cells_tutorial.rst

+            self.maxAbsLambdaX = 10
+
+        def start(self):
+            self.create_arranged_cells(x_s=25, y_s=25, size=5, cell_type_ids=[1, 2, 2, 2, 2, 1])


You could have a comment to explain why the cells are being created in this particular pattern.

I added it in different place

…lNumberOfLinks CellType="Center">2</InternalMaxTotalNumberOfLinks> to control a total number of links a given cell type can form

maciekswat · 2024-09-15T17:24:45Z

@fyffep Thank you for your diligent reading of the tutorial and for the comments. I addressed most of them. NOw, there is this issue of index.rst I do not see your REal-world examples displayed in the side panel so how about I move the content of the

fyffep · 2024-09-18T00:05:03Z

docs/example_compartmental_elongated_cells_tutorial.rst

+                <MaxNumberOfJunctions>2</MaxNumberOfJunctions>
+            </InternalParameters>
+
+            <InternalMaxTotalNumberOfLinks CellType="Center">2</InternalMaxTotalNumberOfLinks>


Nice! Although it's hard to say how much traffic our docs get, it might be worthwhile to say that InternalMaxTotalNumberOfLinks will be supported as of version 4.4.0.
Also, would this new feature work if a user omits <MaxNumberOfJunctions>2</MaxNumberOfJunctions>? To me, it seems like the override is meant to replace the old syntax since that produced less desirable results.

Yes, the simulation would work without it. While this may look like a workaround inspired by this tutorial it is not. This is an additional constraint on the number of links that a given cell type can have. We should have added it at the beginning to FPP

fyffep · 2024-09-18T00:10:23Z

docs/focal_point_plasticity.rst

+The total number of links a given cell can form is computed as a sum of ``<MaxNumberOfJunctions>`` values coming from ``<Parameters>``
+or ``<InternalParameters>`` sections where a given cell type appears. In the example above ``Center`` can form maximum of 2 internal links (between compartments)
+
+CompuCell3D gives you ability to override this default algorithm by adding additional tag that control the total number of links:


nitpick: This could say, ". . . the total number of links of a given cell type." It took me a moment to realize that it's not possible to control the global, simulation-wide number of links. Instead, "total" just pertains to each cell.

maciekswat · 2024-10-12T22:53:40Z

@fyffep how about I merge this PR and then you can fix the details - I think it will be more efficient to do it like this rather than having an elaborate conversation here. You would just commit directly to the branch without PR. What do you think about it?

fyffep · 2024-10-13T22:12:46Z

how about I merge this PR

@maciekswat Go for it! Nitpicking is just one of my hobbies. (It's a real hobby, I swear.)
As I mentioned in my last email, you have already addressed almost all of the feedback.

maciekswat added 4 commits August 24, 2024 17:53

added elongated cell tutorial - w.i.p

0797174

added elongated cell tutorial - w.i.p

7e74d86

added new content

12930d7

finished case study of how to build elongated cells

3c1c774

maciekswat requested review from tjsego and fyffep August 31, 2024 21:51

maciekswat mentioned this pull request Aug 31, 2024

Feature/elongated cells tutorial CompuCell3D/CompuCell3D#756

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tjsego approved these changes Sep 13, 2024

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fyffep requested changes Sep 14, 2024

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maciekswat added 2 commits September 14, 2024 12:00

Addressed most PR comments

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fixing index for real-world examples

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maciekswat requested a review from fyffep September 14, 2024 18:42

maciekswat added 2 commits September 15, 2024 11:11

Updated the tutorial to highlight the ability to use <InternalMaxTota…

557e0d9

…lNumberOfLinks CellType="Center">2</InternalMaxTotalNumberOfLinks> to control a total number of links a given cell type can form

updated FPP plugin manual to include :

b1492f2

<MaxTotalNumberOfLinks CellType="Center">1</MaxTotalNumberOfLinks> <InternalMaxTotalNumberOfLinks CellType="Center">1</InternalMaxTotalNumberOfLinks>

fyffep reviewed Sep 18, 2024

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maciekswat added 3 commits September 28, 2024 11:32

fixing the "Real World Examples" section

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Implementing PR changes

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addressing PR comments

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maciekswat requested a review from fyffep September 28, 2024 18:52

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Feature/curvature compartments fpp tutorial #30

Feature/curvature compartments fpp tutorial #30

maciekswat commented Aug 31, 2024

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maciekswat commented Oct 12, 2024

fyffep commented Oct 13, 2024 •

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		The simulation code can be found in ``Demos/CompuCellPythonTutorial/ElongatedCellsTutorial/Tutorial_09``


		In terms of XML modification, we only need to add a one-liner that enavbles ExternalPotential plugin that simulates

Feature/curvature compartments fpp tutorial #30

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Feature/curvature compartments fpp tutorial #30

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maciekswat commented Aug 31, 2024

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maciekswat commented Sep 15, 2024

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