[IPython-dev] Building an integrated measurement system with IPython

Ronen Abravanel ronena@gmail....
Mon Feb 17 16:18:56 CST 2014


This is awesome.   I would very much like to see something like that
working (at least as a proof of concept. And also in order to help and try
to 'cell' python \ IPython to the experimentalists in my department.

Regarding your first question, try looking at IPython 2.0 and the new
widget mechanism,
For some examples, see
http://nbviewer.ipython.org/github/ipython/ipython/tree/master/examples/widgets/




On Mon, Feb 17, 2014 at 8:27 PM, Zahari Dim <zaharid@gmail.com> wrote:

> Hi,
>
> My name is Zahari Dimitrov, and I am a last year Physics Student. My final
> year project consists on developing a system on top of IPython which is
> able to integrate the configuration of laboratory measurements with the
> analysis of the data of those measurements (which could be made in remote
> clusters). I would appreciate it very much if you could tell me what do you
> think on the overall design, and answer some (I'm afraid too many) specific
> questions I have. Apologies for this long message.
>
> Some information on this project can be found on zigzah.com (but it's not
> really up to date...)
>
> I have already done the part dedicated to talking with instruments (more
> or less), and now I would like to do the following:
>
> - I'd like to represent the computation process as a polytree (
> http://en.wikipedia.org/wiki/Polytree ) where the nodes (which I call
> IObjects) would be functions that run on some ipengine. These functions
> have some parameters (inputs) and return a dict of outputs. The outputs of
> one node can be connected to the inputs of the next, and to execute a child
> node, all the parents must be executed and have some results.
>
> -This structures are saved on a MongoDb Database (seems really easy to use
> for now) and managed with the mongoengine ORM,
>
> -I'd like to be able to transform the inputs of the graph that are not
> connected to an output (or have a constant value set) in an html form (the
> inputs declare some types like str, int or range which are mapped to
> different JS input widgets where possible). The free outputs are turned
> into some display widgets as well.
>
> -When you type ipython notebook --iograph=mygraph, the form appears on the
> top of your ipython notebook, and you can set the parameters and execute
> different parts of the graph. The results are accessible as variables in
> the notebook.
>
> -Things like the instrument commands (ie, ask for the frequency in an
> oscilloscope) are just things that extend the IObject class and run on a
> dedicated engine with id __instruments in the computer where the instrument
> is connected (could be different for different instruments).
>
> -Other more complicated classes like RangedExperiment (measure something
> over a given range which is an input) are also IObjects. This classes would
> have the capability of reporting the measurements as they are produced and
> fill sequentially a plot with that.
>
> -Other IObjects can take the results from the experiment and process them
> in a remote cluster.
>
> -For a given IObject, all results (outputs) it produces are logged by
> default in the mongo database. You can always set the value of the outputs
> to a previous result and execute its children with this input.
>
> -There will be a decorator that converts any function in a IObject (and
> possibly use python 3 annotations for that)
>
>
>
> As said, I'd be very happy if I could complete this. But here are the
> questions:
>
> -At what level do I hack the IPython notebook to add  the forms? I haven't
> found an extension mechanism capable of doing what I need, so I thing I
> have to fork the project. Is there any place that explains the conventions
> used for the templates and the JavaScript code in the notebook?
>
> -I believe the Ipython controller has some log system. Could it be
> integrated with the one I want for the IObjects?
>
> -I am thinking about using mongodb to deploy a shared filesystem in the
> computers where Ipython is running, so it's possible load data from
> anywhere. Is this a good solution, particularly to save things like
> text-pickled python objects?
>
> -How do I avoid moving around large amounts of data when the output and
> input IObjects are in the same computer, different from the controller.
>
> -Which is the best way to obtain partial results from the engines, like
> the ones needed for the RangedExperiment example (ie, display the
> measurement after it is produced and then do the next)?
>
> -Which is the current best way to display interactive plots in IPython?
> Thinking again about the Ranged Experiment.
>
> -I understand each Ipengine will see the hardware of the computer it runs
> in. Is this right?
>
> -Is there any problem for a node to itself run a paralell algorithm on
> other engines?
>
> Thank you again for your patience,
>
> Best regards,
>
> Zahari.
>
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