I am trying to export all the plots of my NetLogo model after simulation runs in a csv format with the primitive export-all-plots.
I haven't found yet the way to open this csv file with an external reader in order to get more clear plots. I tried with gnuplot but it looks like it's not able to open the csv format created with NetLogo:
"export-plots data (NetLogo 5.0.5)"
^
"C:\results\interface.csv", line 1: invalid command
How can I open csv plots with an external reader?
There are two complicating factors about NetLogo's plot export format. First, there's a three line header at the beginning (plus an empty line after) that just gives information about the model and when the data was generated. Next, there's data about the model settings, the plot state (pen colors and such). Finally, there's the data itself, which itself is somewhat complicated by the fact that you can have multiple pens per plot. So I'm not surprised gnuplot couldn't read it as is.
The table's are quite easy to use in GUI spreadsheet application, like Excel, LibreOffice's Calc, or Gnumeric. You can just select the data you want and generate the plots.
To do this at the command line, I'm afraid you might have to write a script to read it in. This should be pretty easy in something like Python or R. Just skip the metadata lines, and use a CSV parser to read in the rest.
You might also try using BehaviorSpace to generate the data, but make sure to use the table output. It let's you generate the data from many runs at once, and the format is a little more consistent. There are still 6 lines of metadata at the top, but you can just delete that. I believe this is more the standard practice in NetLogo.
Related
How can I edit a large JSON manually?
I have a large JSON file, about 100 MB. I'd like to manually inspect some attributes, and then add more attributes to some of the objects.
I'd start off by looking at a subset of the file. Say, the 1st 100 objects. I'd gradually scale up to looking then at maybe 250, then a thousand, etc.
Can someone suggest a language or software (I'm running Windows) that excels at this task?
Some previous suggestion that aren't working or can't work.
Sublime - Could never load the file. Loading bar forever. Had to kill.
NotePad++ - Could never load. Froze. Had to kill.
Anything online - The data is confidential.
More Python and Jupyter information.
with open(path, 'r') as f:
data = json.load(f)
for i, (k, v) in enumerate(data.items()):
print(i, k, v)
if i == 2:
break
Causes an error. I think it has to do with Jupyter, but I'm not sure.
IOPub data rate exceeded.
The notebook server will temporarily stop sending output
to the client in order to avoid crashing it.
To change this limit, set the config variable
`--NotebookApp.iopub_data_rate_limit`.
Current values:
NotebookApp.iopub_data_rate_limit=1000000.0 (bytes/sec)
NotebookApp.rate_limit_window=3.0 (secs)
That makes me wonder if going about it this way is just dumb.
Possible Solutions
Build a custom app using TKinter
Just don't use a Jupyter Notebook
What you can do is to write a simple GUI program. use TKinter, to create a window and a text area inside it to show the json, a text box where you will input, how many objects you want to see, and a button named Next or something to see next and one more button to save.The following will be the functionalities for each of the items.
First you will be reading complete json in python and making it a dict.
Next Button - This will keep iterating based on the value in the TextBox. you could write a custom generator, where it will be yielding based on the number of values required.
Save Button-: This will keep saving the current json into a new json or if you could, you can try to write a function to update the current json directly.
Text Area - you should take the dictionary and convert to json and show the output from the Next Button's generator.
If you are using linux (or have an opportunity to transfer the file to *nix) you might wish to check out for number of lines within a file via
wc -l myfile.json
Let's say, for the purpose of simplicity, that your file has 2530000 lines and you wish to split it into 100k lines each, you can utilize any of the commands available at your distro to split the file further into desired chunks and then to edit them, one by one.
If you are comfortable with going the "linux way", check out some of the hints given on other topics, i.e.
edit multi-GB file when vi editor doesn't work
I hope it helps!
The only viewer I have used that works on large files (I had up to 250MB size files) is Dadroit. It is fast to view and comes with search.
Now, to edit, I use vi. I search for the location and make local edits. Vim or another simpler editor should work on Windows. Have you tried vscode? 100MB shouldn't be too large for it.
The other awesome terminal tool for viewing and editing data is Visidata. I have had mixed luck with it working on json files.
Not the best answer, but the problem with reading the JSON seems limited to Jupyter Notebooks (or even the limitations of my laptop).
Working in Spyder or running from the command line circumvents the Jupyter error mentioned in the original question.
It'd be great if someone knew how to tweak Jupyter to avoid this problem (sorry, I'm not sure how yet).
for editor,try notepad++
for language, try Python
since you haven't give your data structure, I can't give more answer.
Since Dygraphs apparently does not have any functionality for adding separate series of data to a chart one at a time (but rather only loading all the data series of a chart at once from a CSV file, or an in-memory array of arrays) I'm looking to make some code to do this myself.
My reason? My problem/scenario is that I have a "base file" containing a series of data many million values large. I will then need to show many separate charts that display this large data series TOGETHER with a bunch of other respective smaller data series, and I'd very much rather not duplicate the large dataseries in a new CSV file on disk for each such chart, but rather first load the big "base data series" from the CSV "base file" directly from my Javascript, and then for each such chart integrate one such smaller data series with it before sending it off to rendering by means of a new Dygraph(...) call.
The CSV file loading functionality that already obviously exists somewhere inside the Dygraphs code is very nice, so I'd very much like to use it for this loading of the large "base data series" if possible, from a single separate CSV file.
So, in short, the question is:
How can I use the existing CSV file loading functionality of Dygraphs separately from inside my own code, in order to load arbitrary CSV files into the Dygraphs chart data array format in-memory, so that I can finally merge these multiple data series arrays using my own custom code?
What I'm hoping for is something like this:
loaded_data_series_1 = some_secret_internal_function_or_method_of_dygraphs('file1.csv');
loaded_data_series_2 = some_secret_internal_function_or_method_of_dygraphs('file2.csv');
merged_data_series = my_own_custom_dataseries_merging_code(loaded_data_series_1, loaded_data_series_2);
g = new Dygraph(document.getElementById('my_chart'), merged_data_series,{});
The key here would thus be to know what some_secret_internal_function_or_method_of_dygraphs() should be replaced with for this to work.
Could the Dygraph devs or anyone else possibly point me in the right direction here?
(I tried to look inside the Dygraphs code myself, but unfortunately got lost pretty quickly due to insufficient Javascript coding skills on my side)
The full error is "java.lang.RuntimeException: java.lang.Exception: Inconsistent number of matrix lines compared to the number of labels."
I am trying to pull an adjacency matrix stored in a CSV file into Gephi so that I can use its modularity optimization tool and make a really slick chart of my data. I compiled the data in Excel (yes, it took forever) and saved it as CSV, and then I opened the file in Notepad and used Ctrl + H to replace all commas with semicolons (and saved it as a CSV file again). My dataset is 5,654 x 5,654 cells, not counting the labels. It is an r-neighborhood graph with r = .6299 (80th percentile and above).
I searched Google and StackOverflow and I only found one solution for my error message: to remove all the spaces in the file. I used Ctrl + H again to remove all spaces, but I received the same error message when I tried to upload the "spaceless" CSV file. Just to double-check that saving it as CSV didn't cause an issue, I checked the CSV by opening it up in Excel. The file opened correctly, but I do not have much experience with CSV files so I do not know if anything was off. It seemed as though all the records were separated by semicolons instead of commas and I did not see any spaces.
Is it the size of my file? I am currently struggling through learning some Python and R, and I would be open to creating this adjacency matrix CSV file in either of those environments and then feeding it to Gephi. I just need a dependable solution that works without bogging my computer down in Excel all afternoon and allows me to be the "slick graph superhero" of my office.
Not a direct answer to your problem but there is also the Excel/CSV import spigot to whatever it might be useful. Otherwise you could perhaps try to import the network with NodeXL and then save it in GraphML format which can then be opened by Gephi
Good tip from http://social-dynamics.org/gephi-faq/
A. One thing to try is removing any extra spaces from your csv file.
Sometimes these trip up the import. Open the csv file using a simple
text editor like NotePad or TextEdit, and then use find/replace to
remove any spaces. Save the adjacency matrix and then try importing it
again.
Removing spaces helped me to fix the issue.
I've trained a classifier in Weka, and I'm able to use it on test data. Additionally, I can opt to display the classifier's predictions in the log window for this test data.
However, for my current project, it would be convenient for me to be able to get this data in CSV format. Is this possible in Weka ? Is it only possible when using the command line (something I'll eventually move towards) ?
I could always save the entire buffer result to a text file, but in that case, I would have to parse the file and remove all the "noise" (which isn't really noise, but you get the point).
So, to conclude, is there any way to output Weka's predictions for a test set to a CSV file ?
Edit: as the answer below shows, there is an option to do this. However, it can only be found in Weka 3.7 and above !
I assume you use Weka's Explorer. In the Classify tab click on More options..., then click on Output predictions and select CSV. Now click on the box showing CSV and a window opens where you can fill in the properties of writing to a CSV file. Click on outputFile and select a folder and type a filename (note: you must supply a filename). Running a new test will now save the prediction results to your CSV file.
In Weka 3.6.x you can right-click your model, choose "Visualize classifier errors" and Save the data (including the prediction) from there.
If you use weka knowledge flow to build models (Easier than explorer), there are CSV data sinks you can use to save as CSV file.
I'm using JFreeChart to generate line graphs from a simple array of integers.
However, I'd like to use a csv file for the input of the graph. Are there any applications which do it automatically? Also, my csv file will new entries appended every 3 seconds. How can I generate dynamic graphs? I will have to use these graphs in a swing application. Thanks!
I've had good luck with org.h2.tools.Csv, part of H2 Database. You might also look at org.jfree.data.io.CSV, "A utility class for reading CategoryDataset data from a CSV file."