arbor js - save and load graph

Question

I'm using arbor js to create diagrams using its force-based alorithm.

I would like to be able to save the x,y system coordinates of the nodes after the total energy has got below a certain point, so that I can load them back in when accessing the graph, to avoid having to re-process all the energy from scratch.

I have had two problems doing this:

1. sys.energy().sum always returns NaN

   • as an alternative I decided to use setTimeout to save the graph node positions after a given period of time has elapsed

2. While I have been able to save the nodes x,y system coordinates to DB, when I try to load the data into the graph (using sys.merge or sys.addNode) with saved x y coordinates, the graph fails to display, and an 'out of memory' message appears in the console log.

Here is an example of data with node x,y system coordinates that were saved, and which causes arbor js to crash which loading:

{"nodes":{"0":{"edgeCount":0,"x":13.11901,"y":14.89151,"id":0,"name":"Global"},"23":

{"edgeCount":1,"x":18.08981,"y":-0.8355745,"id":23,"name":"Aristotle"},"26":  
{"edgeCount":1,"x":5.688836,"y":14.86863,"id":26,"name":"Socrates"},"27":
{"edgeCount":1,"x":14.84461,"y":-1.687457,"id":27,"name":"Christianity"},"34":
{"edgeCount":1,"x":-2.265221,"y":13.59168,"id":34,"name":"Maths"},"91":
{"edgeCount":11,"x":5.868572,"y":-1.315289,"id":91,"name":"Plato"},"92":
{"edgeCount":4,"x":-3.14131,"y":8.81194,"id":92,"name":"Virtue"},"127": 
{"edgeCount":1,"x":-3.308347,"y":8.463552,"id":127,"name":"Poetry"},"131":
{"edgeCount":1,"x":7.605158,"y":-3.951363,"id":131,"name":"Wisdom"},"147":
{"edgeCount":1,"x":6.195698,"y":-4.572639,"id":147,"name":"Person"},"149":
{"edgeCount":1,"x":2.10395,"y":-2.390886,"id":149,"name":"Republic"},"171":
{"edgeCount":1,"x":3.359434,"y":-3.996424,"id":171,"name":"Justice"},"172":
{"edgeCount":1,"x":-0.2544371,"y":-4.218832,"id":172,"name":"Temperance"},"173":
{"edgeCount":1,"x":-8.773163,"y":2.587845,"id":173,"name":"Courage"},"178":
{"edgeCount":1,"x":-2.380451,"y":-5.787674,"id":178,"name":"Schopenhauer"},"194":
{"edgeCount":2,"x":-7.747643,"y":-1.653015,"id":194,"name":"Beauty"},"195":
{"edgeCount":1,"x":-10.45985,"y":-2.670299,"id":195,"name":"Objective"},"196":
{"edgeCount":1,"x":-10.64573,"y":-6.874766,"id":196,"name":"Truth"},"219":
{"edgeCount":1,"x":-6.22574,"y":-7.565969,"id":219,"name":"Theory of forms"},"221":
{"edgeCount":1,"x":-8.314561,"y":-7.570002,"id":221,"name":"Platinus"},"245":
{"edgeCount":0,"x":-13.20351,"y":-8.421284,"id":245,"name":"Diagram"},"254":
{"edgeCount":1,"x":-13.54734,"y":-7.7437,"id":254,"name":"Green"}},
    "edges":{"23":{"91":{"context":{"id":0,"name":"Global"},"source":
{"id":23,"name":"Aristotle"},"predicate":{"id":21,"name":"studied with"},"target":
{"id":91,"name":"Plato"}}},"26":{"91":{"context":{"id":0,"name":"Global"},"source":
{"id":26,"name":"Socrates"},"predicate":{"id":2,"name":"inspires"},"target":
{"id":91,"name":"Plato"}}},"91":{"149":{"context":{"id":0,"name":"Global"},"source":
{"id":91,"name":"Plato"},"predicate":{"id":1,"name":"writes"},"target":
{"id":149,"name":"Republic"}},"219":{"context":{"id":0,"name":"Global"},"source":
{"id":91,"name":"Plato"},"predicate":{"id":1,"name":"writes"},"target":{"id":219,"name":"Theory of forms"}},"27":{"context":{"id":0,"name":"Global"},"source":{"id":91,"name":"Plato"},"predicate":
{"id":3,"name":"influences"},"target":{"id":27,"name":"Christianity"}},"178":{"context":
{"id":0,"name":"Global"},"source":{"id":91,"name":"Plato"},"predicate":
{"id":3,"name":"influences"},"target":{"id":178,"name":"Schopenhauer"}},"221":{"context":
{"id":0,"name":"Global"},"source":{"id":91,"name":"Plato"},"predicate":
{"id":3,"name":"influences"},"target":{"id":221,"name":"Platinus"}},"254":{"context":
{"id":245,"name":"Diagram"},"source":{"id":91,"name":"Plato"},"predicate":
{"id":28,"name":"is"},"target":{"id":254,"name":"Green"}},"34":{"context":
{"id":0,"name":"Global"},"source":{"id":91,"name":"Plato"},"predicate":{"id":33,"name":"is associated with"},"target":{"id":34,"name":"Maths"}},"127":{"context":
{"id":0,"name":"Global"},"source":{"id":91,"name":"Plato"},"predicate":{"id":47,"name":"is obsessed with"},"target":{"id":127,"name":"Poetry"}},"147":{"context":
{"id":0,"name":"Global"},"source":{"id":91,"name":"Plato"},"predicate":{"id":56,"name":"is type of"},"target":{"id":147,"name":"Person"}}},"92":{"131":{"context":{"id":91,"name":"Plato"},"source":
{"id":92,"name":"Virtue"},"predicate":{"id":28,"name":"is"},"target":
{"id":131,"name":"Wisdom"}},"171":{"context":{"id":91,"name":"Plato"},"source":
{"id":92,"name":"Virtue"},"predicate":{"id":28,"name":"is"},"target":
{"id":171,"name":"Justice"}},"172":{"context":{"id":91,"name":"Plato"},"source":
{"id":92,"name":"Virtue"},"predicate":{"id":28,"name":"is"},"target":
{"id":172,"name":"Temperance"}},"173":{"context":{"id":91,"name":"Plato"},"source":
{"id":92,"name":"Virtue"},"predicate":{"id":28,"name":"is"},"target":
{"id":173,"name":"Courage"}}},"194":{"195":{"context":{"id":91,"name":"Plato"},"source":
{"id":194,"name":"Beauty"},"predicate":{"id":28,"name":"is"},"target":
{"id":195,"name":"Objective"}},"196":{"context":{"id":91,"name":"Plato"},"source":
{"id":194,"name":"Beauty"},"predicate":{"id":33,"name":"is associated with"},"target":
{"id":196,"name":"Truth"}}}}} 

I can find no examples of graphs where the node x,y coordinates are in the input data.

Answer 1

Looking at https://github.com/samizdatco/arbor/blob/master/src/physics/system.js#L83 it seems that it should be alright to include x and y value in the data dictionary. I'm not really sure from your example how you pass the data to the methods. Maybe try just adding a few of the nodes and see where they are placed. I have the same problem with the energy being NaN. Probably using a debugger will help.