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PES and Voja

As implemented by @neworderofjamie

Squashed commit of:

commit 043576232
Author: neworderofjamie <james.knight@manchester.ac.uk>
Date:   Mon May 23 13:52:48 2016 +0100

    Python 3

commit b90e21903
Author: neworderofjamie <james.knight@manchester.ac.uk>
Date:   Mon May 23 13:49:54 2016 +0100

    pepepep

commit b9a818bea
Author: neworderofjamie <james.knight@manchester.ac.uk>
Date:   Mon May 23 13:44:02 2016 +0100

    PEP8 and fixes

commit 2c605437e
Author: neworderofjamie <james.knight@manchester.ac.uk>
Date:   Mon May 23 13:28:13 2016 +0100

    Already bored of build times - made scipy optional and imported it where it's used

commit c0cfe0ece
Author: neworderofjamie <james.knight@manchester.ac.uk>
Date:   Mon May 23 13:17:57 2016 +0100

    Umm, dependency-resolution much!?!

commit 29ccde0cc
Author: neworderofjamie <james.knight@manchester.ac.uk>
Date:   Mon May 23 13:15:43 2016 +0100

    lapack

commit 302985ec1
Author: neworderofjamie <james.knight@manchester.ac.uk>
Date:   Mon May 23 13:12:29 2016 +0100

    Attempt alternative means of installing scipy

commit 1b674cf44
Author: neworderofjamie <james.knight@manchester.ac.uk>
Date:   Mon May 23 13:10:13 2016 +0100

    Attempt to install scipy from apt-get (reverted from commit <a class=hub.com/project-rig/nengo_spinnaker/commit/9db5dfcc386a893d4102a47ae62de575e7d8ff23">9db5dfcc3)

commit 9db5dfcc386a893d4102a47ae62de575e7d8ff23
Author: neworderofjamie <james.knight@manchester.ac.uk>
Date:   Mon May 23 13:08:09 2016 +0100

    Attempt to install scipy from apt-get

commit f4eda4a68
Author: neworderofjamie <james.knight@manchester.ac.uk>
Date:   Mon May 23 12:26:05 2016 +0100

    Actually, for correctness, binned_statistic was present in 0.11 of SciPy

commit d893ee3db
Author: neworderofjamie <james.knight@manchester.ac.uk>
Date:   Mon May 23 12:24:45 2016 +0100

    Scipy dependency

commit c53920731
Author: neworderofjamie <james.knight@manchester.ac.uk>
Date:   Mon May 23 12:19:57 2016 +0100

    Binaries

commit 8a409d3a0
Author: neworderofjamie <james.knight@manchester.ac.uk>
Date:   Mon May 23 12:19:28 2016 +0100

    More tests

commit 4768040ef
Merge: f7ca695 d33c53e
Author: neworderofjamie <james.knight@manchester.ac.uk>
Date:   Mon May 23 12:16:50 2016 +0100

    Merge remote-tracking branch 'origin/master' into new_ensemble-new_learning

    Conflicts:
    	nengo_spinnaker/binaries/nengo_ensemble.aplx
    	nengo_spinnaker/binaries/nengo_ensemble_profiled.aplx
    	nengo_spinnaker/binaries/nengo_filter.aplx
    	nengo_spinnaker/binaries/nengo_mc_player.aplx
    	nengo_spinnaker/binaries/nengo_rx.aplx
    	nengo_spinnaker/binaries/nengo_tx.aplx
    	nengo_spinnaker/binaries/nengo_value_sink.aplx
    	nengo_spinnaker/binaries/nengo_value_source.aplx
    	nengo_spinnaker/operators/lif.py
    	nengo_spinnaker/regions/__init__.py
    	nengo_spinnaker/regions/filters.py
    	nengo_spinnaker/regions/recording.py
    	nengo_spinnaker/simulator.py
    	spinnaker_components/ensemble/Makefile
    	spinnaker_components/ensemble/ensemble.c
    	spinnaker_components/ensemble/ensemble.h
    	spinnaker_components/ensemble/neuron_lif.h
    	spinnaker_components/filter/filter_main.c
    	spinnaker_components/value_sink/value_sink.c
    	tests/operators/test_lif.py
    	tests/regions/test_region_recording.py

commit f7ca6951e
Author: neworderofjamie <james.knight@manchester.ac.uk>
Date:   Wed Apr 6 12:50:28 2016 +0100

    New executables built with spinnaker tools 2.0.0

commit 53965aaa0
Author: neworderofjamie <james.knight@manchester.ac.uk>
Date:   Wed Apr 6 12:39:40 2016 +0100

    Updates to profile_communication_channel example including fix for #118

commit 7832e7e9e
Author: neworderofjamie <james.knight@manchester.ac.uk>
Date:   Wed Apr 6 12:29:10 2016 +0100

    Update to spinnaker_tools 2.0.0

commit 58ddf1ee5
Author: neworderofjamie <james.knight@manchester.ac.uk>
Date:   Thu Jan 14 12:52:08 2016 +0000

    Mega-optimisation!

commit 0c3ec0c3e
Author: neworderofjamie <james.knight@manchester.ac.uk>
Date:   Fri Jan 8 14:34:37 2016 +0000

    whole status is actually quite a lot more useful

commit 536d29ec1
Author: neworderofjamie <james.knight@manchester.ac.uk>
Date:   Fri Jan 8 14:31:37 2016 +0000

    ahh shared memory, it works great when you read from it as well as writing

commit 4f9f4e9a1
Author: neworderofjamie <james.knight@manchester.ac.uk>
Date:   Fri Jan 8 13:54:19 2016 +0000

    Input filters now get sliced - saves memory and doesn't break Voja implementation

commit e5b040fc4
Author: neworderofjamie <james.knight@manchester.ac.uk>
Date:   Thu Jan 7 15:13:56 2016 +0000

    region-size mismatch

commit 686f21e1f
Author: neworderofjamie <james.knight@manchester.ac.uk>
Date:   Thu Jan 7 15:13:29 2016 +0000

    use correct RTE code

commit 437fc16f6
Author: neworderofjamie <james.knight@manchester.ac.uk>
Date:   Thu Jan 7 14:43:20 2016 +0000

    Python side dma transfer of learnt signals

commit d33e3cb68
Author: neworderofjamie <james.knight@manchester.ac.uk>
Date:   Thu Jan 7 14:42:59 2016 +0000

    actually run learn_associations on SpiNNaker backend...

commit e857616d4
Author: neworderofjamie <james.knight@manchester.ac.uk>
Date:   Thu Jan 7 14:42:39 2016 +0000

    Also show errors if application dies during runtime

commit c56051e20
Author: neworderofjamie <james.knight@manchester.ac.uk>
Date:   Thu Jan 7 14:06:15 2016 +0000

    C-side extended DMA state machine

commit 13385c344
Author: neworderofjamie <james.knight@manchester.ac.uk>
Date:   Thu Jan 7 13:52:03 2016 +0000

    C-side data structures for dma transfer of learnt signals

commit ce9b6fec3
Author: neworderofjamie <james.knight@manchester.ac.uk>
Date:   Thu Jan 7 13:51:38 2016 +0000

    Thanks @mundya - never actually hits exit

commit 31cccacf0
Author: neworderofjamie <james.knight@manchester.ac.uk>
Date:   Thu Jan 7 10:51:12 2016 +0000

    Fix malloc_or_die

    Calls RT_ERROR to kill the core after a malloc fails.

commit 1d2c3a7ba
Author: neworderofjamie <james.knight@manchester.ac.uk>
Date:   Wed Jan 6 15:59:36 2016 +0000

    Full encoder width should be used for top level partitioning

commit 98fc0711b
Author: neworderofjamie <james.knight@manchester.ac.uk>
Date:   Wed Jan 6 12:36:35 2016 +0000

    Added additional constraint to SMULL instruction - otherwise (codesourcery) assigns sasme registers for output and input :(

commit 7b9571d2d
Merge: d9e95f4 e56c246
Author: neworderofjamie <james.knight@manchester.ac.uk>
Date:   Tue Jan 5 18:17:55 2016 +0000

    Merge remote-tracking branch 'origin/recording_buffer_reset' into new_ensemble-new_learning

commit d9e95f466
Author: neworderofjamie <james.knight@manchester.ac.uk>
Date:   Tue Jan 5 18:17:29 2016 +0000

    Improved handling of errors during simulation

commit e56c2464b
Author: neworderofjamie <james.knight@manchester.ac.uk>
Date:   Tue Jan 5 18:12:57 2016 +0000

    Reset recording regions between simulation runs

commit 0f9bb8d72
Author: jamie <neworderofjamie@gmail.com>
Date:   Mon Dec 28 18:46:14 2015 +0000

    Profiling tweaks
    * Re-implemented print-stats in terms of my new favourite function - scipy.stats.binned_statistic
    * Also used this rather than mean for writing CSV rows - generally rather more meaningful

commit 13287c8a8
Author: neworderofjamie <james.knight@manchester.ac.uk>
Date:   Wed Dec 23 12:24:38 2015 +0000

    Spike recording didn't work on clustered ensembles

commit 52cf92e72
Author: neworderofjamie <james.knight@manchester.ac.uk>
Date:   Fri Dec 18 11:06:52 2015 +0000

    Extra PES tests

commit 016aa0709
Author: neworderofjamie <james.knight@manchester.ac.uk>
Date:   Thu Dec 17 17:27:53 2015 +0000

    test learning rule probing

commit 9bcff4e65
Author: neworderofjamie <james.knight@manchester.ac.uk>
Date:   Thu Dec 17 17:16:44 2015 +0000

    Encoder recording test

commit 9dbf316a7
Author: neworderofjamie <james.knight@manchester.ac.uk>
Date:   Thu Dec 17 16:28:44 2015 +0000

    Executables

commit 0cd4d6aea
Author: neworderofjamie <james.knight@manchester.ac.uk>
Date:   Thu Dec 17 16:28:38 2015 +0000

    Voja tests

commit a4c1f419c
Author: jamie <neworderofjamie@gmail.com>
Date:   Thu Dec 17 11:40:02 2015 +0000

    beginning of work on PES test - need advice from JH regarding how best to test slicing logic

commit 9607dadb9
Author: jamie <neworderofjamie@gmail.com>
Date:   Thu Dec 17 11:39:07 2015 +0000

    Caught bug in PESRegion (it's like testing works)

commit 2fa4034ef
Author: jamie <neworderofjamie@gmail.com>
Date:   Thu Dec 17 10:52:17 2015 +0000

    Learning rule connectivity builder tests

commit b34b4bdc6
Author: jamie <neworderofjamie@gmail.com>
Date:   Thu Dec 17 10:25:19 2015 +0000

    fixup existing tests, add some to cover learnt_slices etc

commit 7eea2e2be
Author: jamie <neworderofjamie@gmail.com>
Date:   Thu Dec 17 10:24:56 2015 +0000

    Fix for numpy 1.8

commit 717041e96
Author: jamie <neworderofjamie@gmail.com>
Date:   Wed Dec 16 18:30:51 2015 +0000

    Voja profiling

commit 5e24cd517
Author: jamie <neworderofjamie@gmail.com>
Date:   Wed Dec 16 13:21:50 2015 +0000

    correct SDRAM usage

commit 03918f8a9
Author: jamie <neworderofjamie@gmail.com>
Date:   Mon Dec 14 15:30:17 2015 +0000

    how the crap did that compile

commit be21a6640
Author: jamie <neworderofjamie@gmail.com>
Date:   Mon Dec 14 14:08:32 2015 +0000

    fixed DTCM partitioning

commit 86becf58b
Author: jamie <neworderofjamie@gmail.com>
Date:   Mon Dec 14 13:23:00 2015 +0000

    Profiling
    * Tidied up PES function a bit - just takes ensemble pointer rather than numerous parameters
    * Added profiler tags
    * Renamed skip() nop() as it resulted in some epically confusing errors
    * Added PES profiling tags

commit a9c3e0e79
Author: jamie <neworderofjamie@gmail.com>
Date:   Mon Dec 14 11:23:39 2015 +0000

    write voja-learnt encoder to write location!

commit b25365a8b
Author: jamie <neworderofjamie@gmail.com>
Date:   Mon Dec 14 10:11:07 2015 +0000

    Re-figured out matplotlib animation and made animated encoder plot

commit a79cc3eb4
Author: jamie <neworderofjamie@gmail.com>
Date:   Fri Dec 11 12:32:44 2015 +0000

    Re-added total encoder width parameter - recorded encoders now don't look TOTALLY trashes

commit 101d361a5
Author: neworderofjamie <james.knight@manchester.ac.uk>
Date:   Thu Dec 10 16:58:28 2015 +0000

    Small bug fixes in scaled encoder recording - still doesn't actually work

commit d9a6ed7bb
Author: neworderofjamie <james.knight@manchester.ac.uk>
Date:   Thu Dec 10 16:17:26 2015 +0000

    Examples that can be removed from here before merging, but I want to not lose this time :)

commit 7103e0a12
Author: neworderofjamie <james.knight@manchester.ac.uk>
Date:   Thu Dec 10 15:26:36 2015 +0000

    pep8

commit 82d3cb506
Author: neworderofjamie <james.knight@manchester.ac.uk>
Date:   Thu Dec 10 15:18:36 2015 +0000

    Correct slicing of PES learning

commit 2c0ce8fb4
Author: neworderofjamie <james.knight@manchester.ac.uk>
Date:   Thu Dec 10 12:32:43 2015 +0000

    Python side of working Voja
    * Seperate decoders and keys regions for learnt and static decoders
    * Static and learnt output space partitioned seperately
    * 'Properly' disabled filtered activity mode

commit 3fea6988f
Author: neworderofjamie <james.knight@manchester.ac.uk>
Date:   Thu Dec 10 12:30:54 2015 +0000

    c-side of functioning PES
    * ensemble.parameters hampers anything approximating 80 character lines - assigned to params in a bunch of places
    * Seperate learnt and static decoder and keys regions concatenated when loaded so existing static processing can be employed

commit cdebc3832
Author: neworderofjamie <james.knight@manchester.ac.uk>
Date:   Wed Dec 9 16:25:52 2015 +0000

    New C implementation of non-filtered PES

commit 6b43f698f
Author: neworderofjamie <james.knight@manchester.ac.uk>
Date:   Wed Dec 9 13:43:28 2015 +0000

    Small bits of python learning which failed to merge

commit 5b29214b0
Author: neworderofjamie <james.knight@manchester.ac.uk>
Date:   Wed Dec 9 13:43:03 2015 +0000

    * decode_spike_train doesn't belong in the header - Discuss!
    * looping on n suggests neurons which made me more confused than seemed necessary
    * PES can't be updated in simulate_neurons

commit 6448dcaba
Author: neworderofjamie <james.knight@manchester.ac.uk>
Date:   Fri Dec 4 11:14:57 2015 +0000

    Most of c-code integrated - still needs more thought in places
    * Filtered activity basically disabled

commit 302d31a12
Author: neworderofjamie <james.knight@manchester.ac.uk>
Date:   Thu Dec 3 11:33:25 2015 +0000

    flake8

commit e9c2db7c3
Author: neworderofjamie <james.knight@manchester.ac.uk>
Date:   Thu Dec 3 11:23:25 2015 +0000

    Tidying of include guards #includes to match new names post-rename

commit c9bd1b095
Author: neworderofjamie <james.knight@manchester.ac.uk>
Date:   Thu Dec 3 11:18:05 2015 +0000

    Renames of c files

commit 3801cad8e
Author: neworderofjamie <james.knight@manchester.ac.uk>
Date:   Thu Dec 3 11:13:40 2015 +0000

    Renamed EnsembleRegions to Regions for terseness - discuss!

commit 67edf4da8
Author: neworderofjamie <james.knight@manchester.ac.uk>
Date:   Thu Dec 3 11:02:06 2015 +0000

    Python side of encoder learning

commit 800a3b3b6
Author: neworderofjamie <james.knight@manchester.ac.uk>
Date:   Thu Dec 3 10:34:38 2015 +0000

    Python side of learning rule re-integration
    * ConnectionMap.get_signals_from_object builds a DEFAULTdict of lists
    * ReceptionParams and TransmissionParams contain reference to learning rule

commit 0e05a33fa
Author: neworderofjamie <james.knight@manchester.ac.uk>
Date:   Tue Dec 1 17:07:30 2015 +0000

    Updated ensemble builder to use new semantics

commit 4a34ddc0e
Author: Andrew Mundy <andrew.mundy@ieee.org>
Date:   Mon Oct 12 15:52:43 2015 +0100

    Shared memory ensembles

    Use SDRAM to reduce the communication load presented by Ensembles.  Each
    Ensemble in a `cluster` writes its spike vector into SDRAM and is then
    responsible for decoding a subspace of the entire output space.

commit 497fe489e
Author: Andrew Mundy <andrew.mundy@ieee.org>
Date:   Mon Oct 12 15:52:43 2015 +0100

    Shared memory ensembles

    Use SDRAM to reduce the communication load presented by Ensembles.  Each
    Ensemble in a `cluster` writes its spike vector into SDRAM and is then
    responsible for decoding a subspace of the entire output space.

    Includes suggestions by @neworderofjamie

commit 67bc0af45
Author: Andrew Mundy <andrew.mundy@ieee.org>
Date:   Thu Oct 15 20:32:26 2015 +0100

    Make Region.sizeof_padded use args, kwargs

    This makes the API more flexible.

commit 7ef8a1139
Author: Andrew Mundy <andrew.mundy@ieee.org>
Date:   Sat Dec 5 10:55:34 2015 +0000

    Expand partitioning to deal with multiple slices

    Creates a new `partition_multiple` tool for partitioning multiple slices
    simultaneously; the original `partition` function is rewritten as a
    wrapper for this new function.

6590 of 8216 relevant lines covered (80.21%)

1.16 hits per line