Welcome to pypet’s documentation!

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

Latest version: 0.1b.4

IMPORTANT!

The program is currently under development, please keep that in mind and use it very carefully.

Before publishing the official 0.1.0 release I will integrate pypet first in my own research project. Thus, I have a more profound testing environment than only using unittests. Accordingly, you still have to deal with the naming 0.1b.X for a little while. However, unless it is really, really, really necessary I do not plan to change the API anymore. So feel free to use this beta version and feel free to give feedback, suggestions, and report bugs. Use github (https://github.com/SmokinCaterpillar/pypet) issues or write to the pypet Google Group :-)

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 >= 0.3.1

To utilize the cap feature for multiprocessing (see Multiprocessing) you need

• psutil >= 2.0.0

If you use Python 2.6 you also need

• ordereddict >= 1.1

ToC

Contents:

• What is pypet all about?
  • Main Features
• Getting Started!
  • Install
  • What to do with pypet?
  • Basic Work Flow
  • Quick Working Example
• Cookbook
  • Naming Convention
  • More about the Environment
  • More on Trajectories and Single Runs
  • Interaction with Trajectories after an Experiment
  • Annotations
  • More on Parameters and Results
  • How to Structure your Simulations
  • Using BRIAN with pypet
• Examples
  • 01 First Steps
  • 02 Natural Naming, Storage and Loading
  • 03 Merging of Trajectories
  • 04 Multiprocessing
  • 05 Custom Parameter (Strange Attractor Inside!)
  • 06 Parameter Presetting
  • 07 Short BRIAN Example
  • 08 Using the f_find_idx Function
  • 09 Storing and Loading Large Results (or just parts of them)
  • 10 Accessing Results from All Runs at Once
  • 11 Large scale BRIAN simulation
• FAQs and Known Issues
• Library Reference
  • The Environment
  • The Trajectory, Single Runs and Group Nodes
  • Parameters and Results
  • Annotations
  • Utils
  • Exceptions
  • Global Constants
  • Storage Services
  • Brian Parameters, Results and Monitors
  • Brian Network Framework

Publications

BBD2013 Poster

There is a poster about pypet that was shown at the Berlin Brain Days 2013.

Download:

• CLICK ME for PDF DOWNLOAD
• CLICK ME for PNG DOWNLOAD

Acknowledgments

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

  You might wanna check out their SpykeViewer tool for visualization of MEA recordings and NEO data

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

• Thanks to the BCCN Berlin, the Research Training Group GRK 1589/1, and the Neural Information Processing Group for support

Tests

Tests can be found in pypet/tests. Note that they involve heavy file IO 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.

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().

If you do not want to browse to your installation folder, you can also download the all_tests.py script.

Running all tests can take up to 15 minutes and might temporarily take up to 8 GB of disk space. The test suite encompasses more than 300 tests (including the BRIAN based tests) and has a code coverage of more than 90%!

Contact

Robert Meyer

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

Marchstr. 23

MAR 5.046

D-10587 Berlin

Indices

• Index

License

Copyright (c) 2013, Robert Meyer
All rights reserved.

Redistribution and use in source and binary forms, with or without modification,
are permitted provided that the following conditions are met:

  Redistributions of source code must retain the above copyright notice, this
  list of conditions and the following disclaimer.

  Redistributions in binary form must reproduce the above copyright notice, this
  list of conditions and the following disclaimer in the documentation and/or
  other materials provided with the distribution.

  Neither the name of the author nor the names of other contributors
  may be used to endorse or promote products
  derived from this software without specific prior written permission.

THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND
ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR
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(INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES;
LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON
ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
(INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.