I have been trying to load some gis data from a postgis database into Cytoscape 3.6. I am trying to get some inDegree and outDegree values I have used the sif file format.
As long as the data is written out in the follow format
source_point\tinteracts with\ttarget_point
Cytoscape is happy to read it.
I am just wondering if there is anyway of including my own metric for the cost of getting between source_point and target_point
Sure! There are several ways to read in text files into Cytoscape -- SIF is just one of them. I would create a file that looks like SIF, but is actually a more complete text file:
Source\tTarget\tScore
source_point\ttarget_point\t1.1
...
And then use the "File->Import Network->File", choose your source and target and leave score as an edge attribute. You can have as many attributes on each line as you want, and can even mix edge attributes, source node attributes, and target node attributes.
-- scooter
Related
Dear Anylogic Community,
I am struggling with finding the right approach for storing my simulation results. I have datasets created that keep track of every value I am interested in. They live in Main (see below)
My aim is to do a parameter variation experiment. In every run, I change the value for p_nDrones (see below)
After the experiment, I would like to store all the datasets in one excel sheet.
However, when I do the parameter variation experiment and afterwards check the log of the dataset (datasets_log), the changed values do not even show up (2 is the value I did set up in the normal simulation).
Now my question. Do I need to create another type of dataset if I want to track the values that are produced in the experiments? Why are they not stored after executing the experiment?
I really would appreciate if someone could share the best way to set up this export of experiment results. I would like to store the whole time series for every dataset.
Thank you!
Best option would be to write the outputs to some external file at the end of each model run.
If you want to use Excel, which I personally would not advise, even though it has a nice excelFile.writeDataSet() function, you can.
I would rather write the data to a text file as you will have much for control over the writing, the file itself, it is thread-safe, and useable in many many more platforms than Microsoft Excel.
See my example below:
Setup parameters in your model that you will write the data to at the end of the model of type TextFile. Here I used the model on destroy code to write out the data from the data sets.
Here you can immediately see the benefit of using the text file! You can add the number of drones we are simulating (or scenario name or any other parameter) in a column, whereas with Excel this would be a pain...
Now you can pass your specific text file to the model to use by adding it to the parameter variation page, providing it to the model through the parameters.
You will see that I also set up some headers for the text file in the Initial Experiment setup part, and then at the very end of the experiment, I close the text files in the After experiment section so that the text files can be used.
Here is the result if you simply right-click on the text files and open them in Excel. (Excel will always have a purpose, even if it is just to open text files ;-) )
I am a beginner on Talend, I have a problem processing a json file via talend. I have a json file with several levels and containing tables on different levels (or depths) of json. I just want to add an attribute in a json area located at a given depth via thmap. So in input I have the json file and in output the same json file with the new attribute. I have no idea how to configure the thmap although it is dedicated to simplify complex mappings.
difficult to answer without more information can you create a screen grab of your TMAP usually it's quite simple in the output field to on the left cell you add it there
I'm download osm-file with some city. In QGIS this map looks good, all streets is connected. Next, i execute osm2pgrouting and in QGIS (when i connect to postgres db) i watch map without some segments in street. Therefore, find path not worked (i think so). Because of what the problem is and how to solve it?
And more, after i executed osm2pgrouting in QGIS i watch many lines from what that point (like sun, extensively). I'm define coordinates of point and delete all ways with this coordinates.
UPDATE. I'm download two maps. First map is contain town (Russia, Krasnoyarsk) and i got it from openstreetmap.org, chosen area and export it. Second map contain region. I got it from some gis-site, but i forgot the address. Unfortunately I can not post a picture for an example. In map in postgress missing half segments of all. Some hightways segments is missing, but some is not.
UPDATE2. I have osm2pgrouting log:
Trying to load data
Trying to parse data
Reference nd=1162932299 has no corresponding Node Entry (Maybe Node entry after Reference?)
Reference nd=1162931037 has no corresponding Node Entry (Maybe Node entry after Reference?)
...
Split ways
Dropping tables...
Creating tables...
Nodes table created
2create ways failed:
Types table created
Way_tag table created
Relations table created
Relation_ways table created
Classes table created
Adding tag types and classes to database...
Adding relations to database...
Adding nodes to database...
Adding ways to database...
Creating topology...
size of streets: 62931
size of splitted ways : 97921
finished
And i use with osm2pgrouting standart mapconfig.xml.
I noticed that line from the some point and the other end is at the beginning of the missing segment. I think, means that this line is missing segments. But osm file open in QGIS and is correct.
I have created some links between agents (turtles) in NetLogo. This links will change at each time step. My aim is to export this data (i.e., turtles and links b/w them) to graph with vertices (turtles) edges (links), which can be given as input to Gephi. Is it possible to see the changes which occurs in netlogo in the graph when it is linked with Gephi. Can someone help me out. Thanks.
To export your network data in a format usable by Gephi, I would suggest using the nw:save-graphml primitive from NetLogo's NW Extension. This will give produce a file in the GraphML file format, which Gephi can read.
I guess you could re-save your network at each time step and overwrite your file, but I'm not sure if Gephi can display your changes dynamically. And depending on the size of your network, it might be slow.
Are you trying to use Gephi to see how the network changes over time, in a changing network that is generated by NetLogo? That's what #NicolasPayette's answer suggests, so I'll make the same assumption.
Gephi can display "dynamic graphs", i.e. networks that change over time. My understanding is that are two file formats that allow Gephi to import dynamic graphs: GEXF, and a special CSV (comma-separated) format that Gephi calls "Spreadsheet". Nicolas mentioned GraphML, which is a very nice network data format, but it doesn't handle dynamic graphs. And as far as I know, NetLogo doesn't generate GEXF or Gephi's "Spreadsheet" format.
However, the Gephi Spreadsheet format is very simple, and it would not be difficult to write a NetLogo procedure that would write a file in that format. This procedure would write new rows to the "Spreadsheet" CSV file on each NetLogo tick. Then Gephi could read in the file, and you'd be able to move back and forth in time, seeing how the graph changes. (You might need to use a bit of trial and error to figure out how to write Spreadsheet files based on the description on the Gephi site.)
Another option would be to display the evolving graph online using the graphstream protocol. Plugins for NetLogo as well as for gephi provide support for this.
Is there anyway to filter the results returned using xapi so that I don't have a ton of results to work through? I thought something like [filter=tag] might only show tags but I can't seem to find any documentation saying this is possible.
Thanks
(1) The standard way of using XAPI lets you filter to retrieve only objects tagged with a certain tag, for example just to get pubs you'd use:
http://jxapi.osm.rambler.ru/xapi/api/0.6/*[amenity=pub]
(2) If you want to filter an OSM file after you've downloaded it (e.g. to remove certain tags), Osmosis is a command-line tool that can do various types of filtering.
(3) If you want to filter an OSM file into some other format (i.e. you're not interested in having an OSM-format XML file at the end) you could use XSLT. Here is an XSLT I made which extracts a small number of pub parameters from an OSM file to CSV.