pypet 0.1b.1

A toolkit for numerical simulations to allow easy parameter exploration and storage of results.

pypet

The new python parameter exploration toolkit. pypet manages exploration of the parameter space and data storage into HDF5 files for you.

IMPORTANT!

The current program is currently still under development, please treat it as such and use very carefully.

Note that there still might be changes to the API, yet i will try to keep it as stable as possible.

I decided to integrate pypet first in my own research project before publishing the official 0.1.0 release. Thus, I have a more profound testing environment than only using unittests. The official 0.1.0 release is postponed to beginning of next year or end of this year. However, feel free to use this beta version and feel free to give feedback, suggestions, and report bugs. Either write my an email (robert.meyer (at) ni.tu-berlin.de) or use github (https://github.com/SmokinCaterpillar/pypet) issues :-)

Thanks!

Requirements

Python 2.6 or 2.7

• tables >= 2.3.1

• pandas >= 0.12.0

• numpy >= 1.6.1

• scipy >= 0.9.0

For git integration you additionally need

• GitPython

What is pypet all about?

Whenever you do numerical simulations in science, you come across two major challenges. First, you need some way to save your data. Secondly, you extensively explore the parameter space. In order to accomplish both you write some hacky IO functionality to get it done the quick and dirty way. This means storing stuff into text files, as MATLAB m-files, or whatever comes in handy.

After a while and many simulations later, you want to look back at some of your very first results. But because of unforeseen circumstances, you changed a lot of your code. As a consequence, you can no longer use your old data, but you need to write a hacky converter to format your previous results to your new needs. The more complexity you add to your simulations, the worse it gets, and you spend way too much time handling your data and results than doing science.

Indeed, this was a situation I was confronted with pretty soon during my PhD. So this project was born. I wanted to tackle the IO problems more generally and produce code that was not specific to my current simulations, but I could also use for future scientific projects right out of the box.

The python parameter exploration toolkit (pypet) provides a framework to define parameters that you need to run your simulations. You can actively explore these by following a trajectory through the space spanned by the parameters. And finally, you can get your results together and store everything appropriately to disk. Currently the storage method of choice is HDF5 (http://www.hdfgroup.org/HDF5/).

Package Organization

This project encompasses these core modules:

• The pypet.parameters module including containers for parameters and results.

• The pypet.trajectory module for managing the parameters and results, and providing a way to explore your parameter space. Somewhat related is also the pypet.naturalnaming module, that provides functionality to access and put data into the trajectory.

• The pypet.environment module for handling the running of simulations.

• The pypet.storageservice for saving your data to disk.

Install

Simply install via pip install –pre pypet

Or

Package release can also be found on https://pypi.python.org/pypi/pypet. Download, unpack and python setup.py install it.

pypet has been tested for python 2.6 and python 2.7 for Linux using Travis-CI (https://www.travis-ci.org/). However, so far there was only limited testing under Windows.

In principle, pypet should work for Windows out of the box if you have installed all prerequisites (pytables, pandas, scipy, numpy). Yet, installing with pip is not possible. You have to download the tar file from https://pypi.python.org/pypi/pypet and unzip it (using WinRaR, 7zip, etc. You might need to unpack it twice, first the tar.gz file and then the remaining tar file in the subfolder). Next, open a windows terminal and navigate to your unpacked pypet files to the folder containing the setup.py file. As above run from the terminal python setup.py install.

By the way, the source code is available at https://github.com/SmokinCaterpillar/pypet.

Documentation

Documentation can be found on http://pypet.readthedocs.org/.

If you have questions feel free to contact me at robert.meyer (at) ni.tu-berlin.de

Acknowledgements

• Thanks to Robert Pröpper and Philipp Meier for answering all my Python questions.

  You might wanna check out their SpykeViewer (https://github.com/rproepp/spykeviewer) tool for visualization of MEA recordings and NEO (http://pythonhosted.org/neo) data

• Thanks to Owen Mackwood for his SNEP toolbox which provided the initial ideas for this project.

• Thanks to the BCCN Berlin (http://www.bccn-berlin.de), the Research Training Group GRK 1589/1, and the Neural Information Processing Group ( http://www.ni.tu-berlin.de) for support.

Main Features

• Novel tree container Trajectory, for handling and managing of parameters and results of numerical simulations

• Grouping of parameters and results

• Accessing handled items via natural naming, e.g. traj.parameters.traffic.ncars

• Support for many different data formats

  • python native data types: bool, int, long, float, str, complex

  • list, tuple, dict

  • Numpy arrays and matrices

  • Scipy sparse matrices

  • pandas DataFrames (http://pandas.pydata.org/)

  • BRIAN Quantities (http://briansimulator.org/)

  • BRIAN Monitors

• Easily extendible to other data formats!

• Exploration of the parameter space of your simulations

• Merging of trajectories residing in the same space

• Support for multiprocessing, distribute your individual simulation runs to several processes.

• Storage of simulation data, i.e. the trajectory, parameters, and results into HDF5 files

• Dynamic Loading, load only the data you need at the moment and free it afterwards

• Resuming a crashed simulation (maybe due to power shut down) after the latest completed run

• Annotations of parameters, results and groups, these annotations are stored as HDF5 node attributes

• Git Integration, make automatic commits of your source code every time you run an experiment

Quick Working Example

The best way to show how stuff works is by giving examples. I will start right away with a very simple code snippet.

Well, what we have in mind is some sort of numerical simulation. For now we will keep it simple, let’s say we need to simulate the multiplication of 2 values, i.e. z=x*y. We have two objectives, a) we want to store results of this simulation z and b) we want to explore the parameter space and try different values of x and y.

Let’s take a look at the snippet at once:

from pypet.environment import Environment
from pypet.utils.explore import cartesian_product

def multiply(traj):
    z=traj.x*traj.y
    traj.f_add_result('z',z=z, comment='I am the product of two reals!')

# Create an environment that handles running
env = Environment(trajectory='Example1_No1',filename='./HDF/example_01.hdf5',
                  file_title='ExampleNo1', log_folder='./LOGS/')

# Get the trajectory from the environment
traj = env.v_trajectory

# Add both parameters
traj.f_add_parameter('x', 1.0, comment='Im the first dimension!')
traj.f_add_parameter('y', 1.0, comment='Im the second dimension!')

# Explore the parameters with a cartesian product:
traj.f_explore(cartesian_product({'x':[1.0,2.0,3.0,4.0], 'y':[6.0,7.0,8.0]}))

# Run the simulation
env.f_run(multiply)

And now let’s go through it one by one. At first we have a job to do, that is multiplying two real values:

def multiply(traj):
    z=traj.x * traj.y
    traj.f_add_result('z',z)

This is our function multiply. The function uses a so called Trajectory container which manages our parameters. We can access the parameters simply by natural naming, as seen above via traj.x and traj.y. The result z is simply added as a result with name ‘z’ to the traj object.

After the definition of the job that we want to simulate, we create an environment which will run the simulation.

# Create an environment that handles running
env = Environment(trajectory='Example1_01',filename='./HDF/example_01.hdf5',
                  file_title='Example_01', log_folder='./LOGS/',
                  comment = 'I am the first example!')

The environment uses some parameters here, that is the name of the new trajectory, a filename to store the trajectory into, the title of the file, a folder for the log files, and a comment that is added to the trajectory. There are more options available like the number of processors for multiprocessing or how verbose the final hdf5 file is supposed to be. Check out the documentation (http://pypet.readthedocs.org/) if you want to know more. The environment will automatically generate a trajectory for us which we can access via:

# Get the trajectory from the environment
traj = env.v_trajectory

Now we need to populate our trajectory with our parameters. They are added with the default values of x=y=1.0:

# Add both parameters
traj.f_add_parameter('x', 1.0, comment='Im the first dimension!')
traj.f_add_parameter('y', 1.0, comment='Im the second dimension!')

Well, calculating 1.0*1.0 is quite boring, we want to figure out more products, that is the results of the cartesian product set {1.0,2.0,3.0,4.0} x {6.0,7.0,8.0}. Therefore, we use f_explore in combination with the builder function cartesian_product:

# Explore the parameters with a cartesian product:
traj.f_explore(cartesian_product({'x':[1.0,2.0,3.0,4.0], 'y':[6.0,7.0,8.0]}))

Finally, we need to tell the environment to run our job multiply:

# Run the simulation
env.f_run(multiply)

And that’s it. The environment and the storage service will have taken care about the storage of our trajectory and the results we have computed.

So have fun using this tool!

Cheers,

Robert

Miscellaneous

Tests

Tests can be found in pypet/tests. Note that they involve heavy file IO and it might not be the case that you have privileges on your system to write files to a temporary folder. The tests suite will make use of the tempfile.gettempdir() function to access a temporary folder.

You can run all tests with $ python all_tests.py which can also be found under pypet/tests. You can pass additional arguments as $ python all_tests.py -k –folder=myfolder/ with -k to keep the hdf5 files created by the tests (if you want to inspect them, otherwise they will be deleted after the completed tests) and –folder= to specify a folder where to store the hdf5 files instead of the temporary one. If the folder cannot be created the program defaults to tempfile.gettempdir().

License

BSD, please read LICENSE file.

Legal Notice

pypet was created by Robert Meyer at the Neural Information Processing Group (TU Berlin), supported by the Research Training Group GRK 1589/1.

Contact

robert.meyer (at) ni.tu-berlin.de

Marchstr. 23

MAR 5.046

D-10587 Berlin