pypet 0.2.0

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 of any numerical simulation in python, thereby storing your data into HDF5 files for you. Moreover, pypet offers a new data container which lets you access all your parameters and results from a single source. Data I/O of your simulations and analyses becomes a piece of cake!

Requirements

Python 2.6, 2.7, 3.3, 3.4, or 3.5, and

• tables >= 2.3.1

• pandas >= 0.14.1

• numpy >= 1.6.1

• scipy >= 0.9.0

• HDF5 >= 1.8.9

If you use Python 2.6 you also need

• ordereddict >= 1.1

• importlib >= 1.0.1

• logutils >= 0.3.3

• unittest2

There are also some optional packages that you can but do not have to install.

If you want to combine pypet with SCOOP you need

• scoop >= 0.7.1

For git integration you additionally need

• GitPython >= 0.3.1

To utilize the cap feature for multiprocessing you need

• psutil >= 2.0.0

To utilize the continuing of crashed trajectories you need

• dill >= 0.2.1

Automatic Sumatra records are supported for

• Sumatra >= 0.7.1

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 I/O 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 formatting your data than doing science.

Indeed, this was a situation I was confronted with pretty soon at the beginning of my PhD. So this project was born. I wanted to tackle the I/O 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. The storage format of choice is HDF5 (http://www.hdfgroup.org/HDF5/) via PyTables (http://www.pytables.org/).

Package Organization

This project encompasses these core modules:

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

• 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.parameters module including containers for parameters and results

• The pypet.storageservice for saving your data to disk

Install

If you don’t have all prerequisites (numpy, scipy, tables, pandas) install them first. These are standard python packages, so chances are high that they are already installed. By the way, in case you use the python package manager pip you can list all installed packages with pip freeze.

Next, simply install pypet via pip install --pre pypet (--pre since the current version is still beta)

Or

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

Or

In case you use Windows, you have to download the tar file from https://pypi.python.org/pypi/pypet and unzip it. 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.

Documentation and Support

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

There is a Google Groups mailing list for support: https://groups.google.com/forum/?hl=de#!forum/pypet

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

Main Features

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

• Group your parameters and results into meaningful categories

• Access data via natural naming, e.g. traj.parameters.traffic.ncars

• Automatic storage of simulation data into HDF5 files via PyTables

• 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 and monitors (http://briansimulator.org/)

• Easily extendable to other data formats!

• Exploration of the parameter space of your simulations

• Merging of trajectories residing in the same space

• Support for multiprocessing, pypet can run your simulations in parallel

• Analyse your data on-the-fly during multiprocessing

• Adaptively explore tha parameter space combining pypet with optimization tools like the evolutionary algorithms framework DEAP (http://deap.readthedocs.org/en/)

• Dynamic Loading, load only the parts of your data you currently need

• Resume a crashed or halted simulation

• Annotate your parameters, results and groups

• Git Integration, let pypet make automatic commits of your codebase

• Sumatra Integration, let pypet add your simulations to the electronic lab notebook tool Sumatra (http://neuralensemble.org/sumatra/)

• pypet can be used on computing clusters or multiple servers at once if it is combined with SCOOP (http://scoop.readthedocs.org/)

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 import Environment, cartesian_product

def multiply(traj):
    """Example of a sophisticated simulation that involves multiplying two values.

    :param traj:

        Trajectory containing the parameters in a particular combination,
        it also serves as a container for results.

    """
    z=traj.x * traj.y
    traj.f_add_result('z',z, comment='I am the product of two values!')

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

# Get the trajectory from the environment
traj = env.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 with all parameter combinations
env.run(multiply)

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

def multiply(traj):
    """Example of a sophisticated simulation that involves multiplying two values.

    :param traj:

        Trajectory containing the parameters in a particular combination,
        it also serves as a container for results.

    """
    z=traj.x * traj.y
    traj.f_add_result('z',z, comment='I am the product of two values!')

This is our simulation 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 value of z is simply added as a result 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 our simulation
env = Environment(trajectory='Multiplication',filename='./HDF/example_01.hdf5',
                  file_title='Example_01',
                  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, 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.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 with all parameter combinations.

# Run the simulation with all parameter combinations
env.run(multiply)

And that’s it. The environment will evoke the function multiply now 12 times with all parameter combinations. Every time it will pass a traj container with another one of these 12 combinations of different x and y values to calculate the value of z. Moreover, the environment and the storage service will have taken care about the storage of our trajectory - including the results we have computed - into an HDF5 file.

So have fun using this tool!

Cheers,

Robert

Miscellaneous

Acknowledgements

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

  You might want to 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

Tests

Tests can be found in pypet/tests. Note that they involve heavy file I/O and you need privileges to write files to a temporary folder. The tests suite will make use of the tempfile.gettempdir() function to create such a temporary folder.

Each test module can be run individually, for instance $ python trajectory_test.py.

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 and log 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().

Running all tests can take up to 20 minutes. The test suite encompasses more than 900 tests and has a code coverage of about 90%!

Moreover, pypet is constantly tested with Python 2.6, 2.7, 3.3 and 3.4 for Linux using Travis-CI. Testing for Windows platforms is performed via Appveyor. The source code is available at https://github.com/SmokinCaterpillar/pypet/.

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