Converted NEST by example to Jupyter notebook and updated for 2.12. #602

hakonsbm · 2016-12-22T12:45:12Z

Converted NEST by example to Jupyter notebook. Also made sure that it works with 2.12, as specified in #558.

It is possible to convert the notebook to pdf. I did not get nbconvert --to pdf to work with references however, so it has to be converted to latex first, then one can use bibtex and pdflatex to make a pdf:

> jupyter nbconvert --to latex --template latex_template.tplx <filename.ipynb>
> pdflatex <filename.tex>
> bibtex <filename>
> pdflatex <filename.tex>
> pdflatex <filename.tex>

When converting to a pdf, authors, abstract, and proper references are inserted. This is specified in the template-file latex_template.tplx.

Silmathoron · 2017-01-04T14:26:29Z

Hi @hakonsbm, I started reviewing your PR but there are a lot more file-changes than what is stated in your description... is this normal? What is the relation between your PR and #580?

…er' into nest_by_example

hakonsbm · 2017-01-04T15:28:18Z

@Silmathoron When updating for 2.12 I had to make sure that the examples didn't raise any deprecation warnings. This meant that the branch had to include changes from #580. But now that #580 is merged into master I have updated the branch, and files changed in #580 no longer show up here.

Silmathoron · 2017-01-05T08:55:19Z

...le/NEST by Example - An Introduction to the Neural Simulation Tool NEST Version 2.12.0.ipynb

+   },
+   "outputs": [],
+   "source": [
+    "nest.PrintNetwork(2)"


Under Python 3, with current master, this returns None

@Silmathoron The PrintNetwork function has no return value. It only outputs the network tree to the terminal you used to start Jupyter notebook.

My bad, should have read what was written below a little more carefully...
Ok! Everything is working under py3, then, I'll start reading the text ASAP ;)

stinebuu

This looks mostly good to me. I have made some rephrasing suggestions, and found some typos.

stinebuu · 2017-01-10T13:33:28Z

...le/NEST by Example - An Introduction to the Neural Simulation Tool NEST Version 2.12.0.ipynb

+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "# Introduction\n",


I think there should be a headline at the beginning of the notebook, "NEST by Example - An Introduction to the Neural Simulation Tool NEST Version 2.12". I know it is written at the top when you open Jupyter notebook, but the notebook starts quite abruptly when it starts right on 'Introduction'.

stinebuu · 2017-01-10T13:38:39Z

...le/NEST by Example - An Introduction to the Neural Simulation Tool NEST Version 2.12.0.ipynb

+    "simulated, how simulations can be run in parallel, using multiple\n",
+    "cores or computer clusters, and how parts of a model can be\n",
+    "randomized.\n",
+    "\n",


This paragraph (lines 20-25) should be removed. You say the same in the paragraph above and the paragraph below.

stinebuu · 2017-01-10T13:41:58Z

...le/NEST by Example - An Introduction to the Neural Simulation Tool NEST Version 2.12.0.ipynb

+    "simulator (for the Blue Brain Project: <cite data-cite=\"Migliore06_119\">Migliore et al., 2006</cite>) and\n",
+    "IBM's C2 simulator <cite data-cite=\"Ananthanarayanan09\">(Ananthanarayanan et al. 2009)</cite>.\n",
+    "\n",
+    "Today, in 2012, there are several simulators for large spiking\n",


stinebuu · 2017-01-10T13:48:44Z

...le/NEST by Example - An Introduction to the Neural Simulation Tool NEST Version 2.12.0.ipynb

+    "  \n",
+    "In the next sections, we will illustrate how to use NEST, using\n",
+    "examples with increasing complexity. Each of the examples is\n",
+    "self-contained. \n",


The PDF has a line that says 'Additionaly, you can find all examples in your NEST distribution.' Maybe keep that line in case people want to run them from the source or something.

stinebuu · 2017-01-10T14:04:28Z

...le/NEST by Example - An Introduction to the Neural Simulation Tool NEST Version 2.12.0.ipynb

+    "A node appears in the source position of `Connect` if it sends events\n",
+    "to the target node. In our example, the sine generator is in the\n",
+    "source position because it injects an alternating current into the\n",
+    "neuron. The voltmeter is in the source position, because it polls the\n",


Remove the comma after source position.

stinebuu · 2017-01-10T15:16:06Z

...le/NEST by Example - An Introduction to the Neural Simulation Tool NEST Version 2.12.0.ipynb

+    "    \\end{equation*}<br></td>\n",
+    "  </tr>\n",
+    "  <tr>\n",
+


Where is this?

I think it might be line 929, and that I wanted you to change 'having' to 'have'. But I can't be sure now, so I think it might be okay to leave it be.

stinebuu · 2017-01-10T15:38:33Z

...le/NEST by Example - An Introduction to the Neural Simulation Tool NEST Version 2.12.0.ipynb

+    "    \\end{equation*}<br></td>\n",
+    "  </tr>\n",
+    "  <tr>\n",
+


Why three lines ---?

stinebuu · 2017-01-10T15:47:45Z

...le/NEST by Example - An Introduction to the Neural Simulation Tool NEST Version 2.12.0.ipynb

+    "    \\end{equation*}<br></td>\n",
+    "  </tr>\n",
+    "  <tr>\n",
+


I would remove 'the' before 'Example 1'.

stinebuu · 2017-01-10T15:59:24Z

...le/NEST by Example - An Introduction to the Neural Simulation Tool NEST Version 2.12.0.ipynb

+    "    \\end{equation*}<br></td>\n",
+    "  </tr>\n",
+    "  <tr>\n",
+


The first function from the code above is also the first one...

Where is this?

Line 1995.
I realize my comment isn't the best one, sorry about that. I think you should switch 'above' and 'code' from the original sentence, and remove 'we look at', so that the sentence becomes 'The first function from the code above is also the first one that is called for every class object.'. But this is just a suggestion :)

stinebuu · 2017-01-10T16:06:38Z

...le/NEST by Example - An Introduction to the Neural Simulation Tool NEST Version 2.12.0.ipynb

+    "    \\end{equation*}<br></td>\n",
+    "  </tr>\n",
+    "  <tr>\n",
+


I would write an alternative version.

heplesser

@hakonsbm This looks generally very fine. But you should shorten the file name to "NEST_by_Example.ipynb". Also, it seems that even though you have defined the template file with abstract, authors, etc, this is not included in exported PDF, and the "Nordlie tables" are not rendered properly in PDF, at least when exporting to PDF via "Download as PDF via LaTeX". Is there any way to fix this?

heplesser · 2017-01-10T20:06:41Z

doc/nest_by_example/latex_template.tplx

+  \cite{Gewa:2012(533)} and has been updated for NEST 2.12.
+
+\begin{description}
+\item[Updated to 2.12.0] Håkon\ Mørk, December 2016


You could add here "Converted to Jupyter Notebook and updated ..."

heplesser · 2017-01-10T20:19:02Z

...le/NEST by Example - An Introduction to the Neural Simulation Tool NEST Version 2.12.0.ipynb

+    "\n",
+    "<table class=\"image\">\n",
+    "<caption align=\"bottom\">The network consists of three populations: $N_E$ excitatory neurons (circle labeled E), $N_I$ inhibitory neurons (circle labeled I), and a population of identical, independent Poisson processes (PGs) representing activity from outside the network. Arrows represent connections between the network nodes. Triangular arrow-heads represent excitatory and round arrow-heads represent inhibitory connections. The numbers at the start and end of each arrow indicate the multiplicity of the connection.</caption>\n",
+    "<tr><td><img src=\"figures/brunel_detailed_external_single2.jpg\" alt=\"Brunel detailed network\" style=\"width: 500px;\"/></td></tr>\n",


I would maybe remove the "width" specification. Or is there a way to specify that you want a width of at most 500px?

It is indeed a way to limit the size of the figure. But there is maybe no need for that here, so I can remove it.

heplesser · 2017-01-10T20:25:07Z

...le/NEST by Example - An Introduction to the Neural Simulation Tool NEST Version 2.12.0.ipynb

+    "    \\end{equation*}<br></td>\n",
+    "  </tr>\n",
+    "  <tr>\n",
+


I would update this to "refer to NEST documentation at [www.nest-simulator.org](http://www.nest-simulator.org/documentation/)"

heplesser · 2017-01-10T20:43:17Z

...le/NEST by Example - An Introduction to the Neural Simulation Tool NEST Version 2.12.0.ipynb

+    "    \\end{equation*}<br></td>\n",
+    "  </tr>\n",
+    "  <tr>\n",
+


Are these real rates??? They seem too "perfect"!

Where do you refer to here?

@hakonsbm Commeting ipynb in Github is not straightforward ;). The lines I meant are rather 957-958 in the cell with execution count 9:

"Excitatory rate : 20.00 1/s\n", "Inhibitory rate : 20.00 1/s\n"

I just find it surprising that the simulation here should have resulted in rates of exactly 20.00 for both excitatory and inhibitory neurons.

hakonsbm · 2017-01-13T10:09:22Z

@stinebuu @heplesser Comments made on lines after line 493 are apparently not placed correctly, so I'm unsure about what you refer to in some of them.

hakonsbm · 2017-01-13T13:07:59Z

@heplesser When exporting to PDF via "Download as PDF via LaTeX" it skips the template file completely. Therefore authors, abstract, and tables are missing when creating a PDF this way (the template substitutes the HTML tables with their LaTeX counterparts). For this reason exporting has to be done using the command line: first exporting to LaTeX using the template, then using pdflatex and bibtex to create the PDF.

I can include a small shell script that does the conversion and the clean up, if you want?

Also added the network model figure to the LaTeX conversion.

heplesser · 2017-01-15T12:42:41Z

@hakonsbm A shell-script for the conversion would be useful, and the PDF created by it should also be committed. Then, all the old stuff (bib and latex files, scripts) should be removed, so that only the ipynb, the PDF generated from it, and the files required by the ipynb and for turning it into a nice PDF should remain.

stinebuu

Good job @hakonsbm ! I have nothing more I want changed. 👍

Fixed formatting of references.

heplesser · 2017-01-17T12:13:54Z

@hakonsbm Thanks! I tidied up a little more, see the PR I created against your branch. Once you have merged that, this one will be ready to merge.

Some more tidying

hakonsbm · 2017-01-17T12:27:47Z

@heplesser Thank you! It is merged now.

Conflicts: doc/nest_by_example/scripts/one_neuron_with_sine_wave.py

heplesser · 2017-01-17T13:26:02Z

@hakonsbm Why did you remove the one_neuron_with_sine example? This seems entirely unrelated to this PR.

hakonsbm · 2017-01-17T13:38:39Z

@heplesser It was removed with your PR against my branch, but it had been changed in master, causing conflicts here. So I had to merge master into this branch and remove it again.

But if it shouldn't have been removed I can restore it.

heplesser · 2017-01-17T13:45:17Z

@hakonsbm Sorry, I got confused. You were right to remove the file.

hakonsbm added 5 commits December 8, 2016 15:07

Added IPython Notebook version of NEST by example.

ec7249c

Merge branch 'fix552' into nest_by_example

33953ed

Added table summarizing the network model.

e75454e

Made adjustments for conversion to pdf.

877fc90

Fixed typo.

7978721

heplesser requested review from heplesser and stinebuu January 2, 2017 14:43

heplesser assigned hakonsbm Jan 2, 2017

heplesser added this to the NEST 2.12 milestone Jan 2, 2017

Merge remote-tracking branch 'github.com/nest/nest-simulator.git/mast…

acf51e5

…er' into nest_by_example

Silmathoron reviewed Jan 5, 2017

View reviewed changes

stinebuu suggested changes Jan 10, 2017

View reviewed changes

heplesser requested changes Jan 10, 2017

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heplesser reviewed Jan 10, 2017

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Shortened the file name.

550f10c

Did some rephrasings and fixed some typos.

de2d095

Also added the network model figure to the LaTeX conversion.

hakonsbm added 2 commits January 16, 2017 11:21

Cleaned up folder, fixed examples, added conversion script.

091f47c

Fixed some small typos.

4ac324e

stinebuu approved these changes Jan 17, 2017

View reviewed changes

Removed further files no longer needed after conversion to notebook

d9e5917

Fixed formatting of references.

hakonsbm added 2 commits January 17, 2017 13:16

Merge pull request #15 from heplesser/hakon_nest_by_example

320e692

Some more tidying

Removed a reference to removed example scripts.

7b7e9de

hakonsbm added 2 commits January 17, 2017 14:01

Merge branch 'master' into nest_by_example

f18d721

Conflicts: doc/nest_by_example/scripts/one_neuron_with_sine_wave.py

Removed example script changed in master.

477435c

heplesser approved these changes Jan 17, 2017

View reviewed changes

heplesser merged commit f2e9b51 into nest:master Jan 17, 2017

hakonsbm deleted the nest_by_example branch January 17, 2017 13:48

Converted NEST by example to Jupyter notebook and updated for 2.12. #602

Converted NEST by example to Jupyter notebook and updated for 2.12. #602

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hakonsbm commented Dec 22, 2016

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hakonsbm commented Jan 13, 2017

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