Introducing holes or removing a patch of cells from within a tissue

[sniffo]

I was wondering if there is a way to remove cells from the middle of a tissue patch? I tried the remove_face method, but running the update_all method from the geometry classes seems to connect all the loose edges and fill the gap - is there a way to prevent this from happening - not quite sure which update method is causing it to close.

Thanks,
Tasnif

[glyg]

Hi Tasnif,

When you draw the sheet with sheet_view(sheet, face={"visible": True}, edge={'headwidth': 1.0}) does the face appear? The only edges left should be the ones form the adjacent faces. You should also see the arrows from the edges

[sniffo]

This is what it looks like after removing the faces

[sniffo]

After running update_all method:

[sniffo]

I would like to connect the dangling edges. Or remove them and sanitize the inner border if you will.

[sniffo]

Apologies for multiple comments, but here it is with faces visible

[glyg]

IDK why all the edges are not deleted by the remove_faces method. I suspect that what you see is matplotlib replacing Nans by 0s.

What you can try after the remove_face is to apply sheet.sanitize(trim_borders=True) hopefully it should do what you want.
I think there is still something buggy in the remove_face method. Can you loolk if you have NaNs in sheet.edge_df?

[glyg]

Also it is not clear to me if you want to keep the partially deleted cells on you first graph

[sniffo]

No Nans in edge_df, I believe remove_face removes the face by collapsing all edges to a single vertex in the center. However, the method does not run update_all since it does not take geom as an argument, and that may be required to display the correct connections.

# collapse all edges connected to the face vertices sheet.edge_df.replace({"srce": verts, "trgt": verts}, new_vert, inplace=True)

The sheet.sanitize method does not work unfortunately

I do want to keep the partially deleted cells, their indices were not included when using remove_face. The missing edges are the edges shared by the deleted face and their neighbors.

You can find the code in this notebook: https://github.com/sniffo/Tyssue-General-Notebooks/blob/main/Hole%20in%20Tissue.ipynb

[sniffo]

I propose an alternative method for removing a face, which simply removes the face itself, and only the half-edges associated with the face. This should achieve what I am trying to do, please let me know if that is incorrect. I will start working on this asap.

[glyg]

Oh yes you're right! Maybe the method could be caled drop_face or someting!

You can use the remove method that removes the edges (and the associated face)

Please open a PR when you have something if you don't mind (maybe also add a comment in remove_face docstring)

[sniffo]

I came up with the following, however, there seems to be an issue with removing multiple faces. Using sanitize or setting trim_borders = True removes some unwanted edges.

This is what I have:

def drop_face(sheet, face, **kwargs):
    """
    Removes the face indexed by "face" and all associated edges
    """    
    edge = sheet.edge_df.loc[(sheet.edge_df['face'] == face)].index
    
     
    sheet.remove(edge, **kwargs)

Currently only takes one face as an argument, changing it to array-like for multiple faces should be simple. However, there is the following issue. The initial tissue:

After sequentially "dropping" the center face and its 5 neighbors:

After running sanitize with trim_borders = True:

Seems that for the cells that have two border edges on the new "inner" border, the edges are simply removed and a new edge is not created. Currently trying to figure out why this might be.

[sniffo]

Apologies, I have figured out the issue here, it was the order of operations. Running geom.update_all after running sanitize seems to do the trick.

I will update the method to take a list of face indices and create the PR.

[glyg]

Great, thank you Tasnif

[glyg]

hi @sniffo did you have a chance to update your code, are you up to create a PR?
Thanks

Guillaume

[sniffo]

Hi @glyg sincere apologies, have not been working on simulations for a bit so I just saw this. The code has been updated I will put in the PR this weekend,

Best,
Tasnif

[glyg]

Hi Tasnif, I'm on holiday for tow more weeks, will review your PR then with great pleasure!