baderlab / cy3d-impl

3D Graph Renderer for Cytoscape using OpenGL

Cy3D - A 3D Renderer App for Cytoscape.

Download from the Cytoscape App Store

User Guide

cy3d-impl's Issues

Cytoscape is shutdown

I installed Cytoscape and cy3d on ubuntu 20.04. When I try to cread a 3d view, the program shutdown and I get this error.

Inconsistency detected by ld.so: dl-lookup.c: 111: check_match: Assertion `version->filename == NULL || ! _dl_name_match_p (version->filename, map)' failed!

java -version command:

openjdk version "11.0.10" 2021-01-19
OpenJDK Runtime Environment (build 11.0.10+9-Ubuntu-0ubuntu1.20.04)
OpenJDK 64-Bit Server VM (build 11.0.10+9-Ubuntu-0ubuntu1.20.04, mixed mode, sharing)

echo $JAVA_HOME:

/usr/lib/jvm/java-11-openjdk-amd64

"Export as Image..." is not supported?

I tried "Export as Image..." for a Cy3D network in this session file.
https://www.dropbox.com/s/4nx0de5of09apao/akt_insulin.cys?dl=0

The result was all black.

I think Cy3D does not implement this function yet.
Please tell me if there is anything I can help with implementing this function.

Black screen after trying to create Cy3D view

Black screen after trying to create Cy3D view

Windows 7 64 bit
Java 11.0.6
Tried both Cytoscape 3.8.2, 3.8.0 and 3.7.2 both with Cy3D 1.1.3 and 1.1.0 versions.

Also tried on Linux - nothing works. Please help.

Nothing strange in log.

Suggestion: drag and move nodes

Hello. In Cytoscape 2D you can easily hold each node with left mouse button and then move it to any place on a graph. But in Cy3D view, you cannot drag nodes! Is it possible to implement this feature?

[Request] Node Label Size property

Since it is difficult to distinguish which node is which label in Cy3D visualization,
I would like to ask you to add a Node Label Size property to Cy3D style.

I think this is a duplicate of #6 , but I would like to create issue with this title.

Some fonts cause exception in JOGL

Reported here:
https://www.biostars.org/p/456350/

This forum post describes the bug:
http://forum.jogamp.org/FontRenderContext-td4035841.html

Upgrading JOGL is the suggested action. However the 2.3.X line is not backwards compatible with the current version (2.2.4) used by Cy3D. Meaning it would be a big change to upgrade.

Z Location Style is not reflected in Cy3D network view(?)

I tried to layout Z Location with some node attribute.
But it seems those are not reflected to Cy3D network view.

How can I set the 3D node layout with Style in Control Panel tab?

Toolbar buttons are just dots ("...") on Linux

Typical font problem. If the text used for a JButton doesn't fit in the button then Swing displays "...". On linux the 'camera', 'select' and 'labels' toolbar buttons just have dots.

Style panel default buttons are blank.

When using ding the style panel shows icons under the 'def' column. When using Cy3D that column is totally blank.

Graph is mirrored about the x-axis.

Likely due to swing measuring the Y coordinate from the top while OpenGL measures it from the bottom.

Moderately sized network freezes when labels are rendered

Hello. When rendering a moderately sized network (61 nodes and 136 edges), the network will render, rotate, and zoom in and out perfectly, as long as the node labels are not rendered. Clicking the label button in the upper right-hand corner will cause panning, rotating, and zooming to become choppy, and eventually the main view will freeze, although the Birdseye view will not freeze. Turning off the labels will cause the program to unfreeze most of the time, although sometimes cytoscape crashes. I've attempted this on three different Windows machines, with different graphics cards, and watching task manager on two of the machines indicates that it's not overtaxing the graphics card. Also, testing with a tiny network two square nodes with a single edge between them the program never crashes. So it's somehow connected to network size. Your assistance in resolving this freezing issue would be greatly appreciated. Thank you for the excellent work on this 3D visualization tool. I've attached an example session where the bug is repeatable
example file.zip

Images for Wiki

Adding desired centroids for layout

Hi,

I'm attempting to use cy3d to visualize my graphs, and wish to position my nodes based on given (x,y,z) triplets as the node centroids. I am having trouble making this happen as all of the layout options I see determine the clustering based on a clustering algorithm rather than a set of desired points - does this feature exist? If not, would it be something the developer would be interested in adding?

Thanks

Edit Label Text Size?

This is really great, many thanks for sharing.
Is it possible to change the size of the text in the window?
(as I go towards a node, the text stays the same size, and it's too small).
Many thanks.

Assertion failure when trying to create a Cy3D view, Inconsistency detected

I have followed the steps to create a Cy3d view (https://cy3d.readthedocs.io/en/latest/Installing.html)

1. Install Cy3d app.
2. Right click "Create 1 View"
3. Select "Cy3D" as network renderer
4. Click ok
5. Cytoscape is terminated with the following assertion failure:

./Cytoscape
Inconsistency detected by ld.so: dl-lookup.c: 106: check_match: Assertion `version->filename == NULL || ! _dl_name_match_p (version->filename, map)' failed!

I'm not sure if there is a workaround or something I can do to do further troubleshooting.

Configuration:

Version: 3.9.1
Java: 11.0.16 by Ubuntu
Java Home: /usr/lib/jvm/java-11-openjdk-amd64
OS: Linux 5.15.0-50-generic - amd64

Cy3D version 1.1.3