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jonnew
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Added Trode, Time, EphysInput. Does not work.
1 parent 6c9b142 commit df31480

6 files changed

Lines changed: 409 additions & 147 deletions

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‎examples/src/DecoderTypes.h‎

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#pragma once
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#include <array>
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#include "react/Event.h"
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namespace decoder {
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namespace types {
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using namespace react;
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// Primatives
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using VoltageT = float;
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using LocationT = float;
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using SampleIndexT = uint64_t;
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using TimeT = double;
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// Voltage
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template <typename D>
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using VoltageSource = EventSource<D, VoltageT>;
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template <typename D, size_t N>
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using VoltateSourceVec = std::array<VoltageSource<D>, N>;
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template <typename D>
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using Voltages = Events<D, VoltageT>;
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//template <typename D, typename... Args>
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//using VoltagePack = std::tuple<Args...>;
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//
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//template <typename D, typename... Args>
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//using VoltagePacks = Events<D, std::tuple<Args...>>;
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// LFP
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template <size_t N>
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using LFP = std::array<VoltageT, N>;
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template <typename D, size_t N>
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using LFPs = Events<D, LFP<N>>;
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// Spikes
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template <size_t L, size_t N>
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using SpikeWaveform = std::array<LFP<N>, L>;
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template <typename D, size_t L, size_t N>
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using Spikes = Events<D, SpikeWaveform<L, N>>;
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// Amplitudes
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template <size_t N>
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using Amplitude = std::array<VoltageT, N>;
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template <typename D, size_t N>
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using Amplitudes = Signal<D, Amplitude<N>>;
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// Position
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using Position = std::tuple<LocationT, LocationT, LocationT>;
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template <typename D>
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using Positions = Events<D, Position>;
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} // namespace types
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} // namespace decoder

‎examples/src/EphysInput.hpp‎

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#pragma once
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#include "DecoderTypes.h"
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#include "react/Domain.h"
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namespace decoder {
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using namespace react;
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using namespace decoder::types;
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namespace detail {
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template <size_t N>
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struct VoltageTuple {
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typedef std::tuple<VoltageT> type;
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};
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template <>
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struct VoltageTuple<1> {
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typedef std::tuple<VoltageT> type;
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};
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template <>
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struct VoltageTuple<2> {
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typedef std::tuple<VoltageT, VoltageT> type;
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};
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template <>
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struct VoltageTuple<4> {
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typedef std::tuple<VoltageT, VoltageT, VoltageT, VoltageT> type;
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};
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template <>
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struct VoltageTuple<8> {
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typedef std::tuple<VoltageT,
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VoltageT,
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VoltageT,
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VoltageT,
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VoltageT,
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VoltageT,
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VoltageT,
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VoltageT> type;
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};
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template <size_t N>
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using VTuple = typename VoltageTuple<N>::type;
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}
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// Voltage Event streams to LFPs
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template <typename D, typename... Vs>
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class EphysInput {
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static constexpr size_t N {sizeof...(Vs)};
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public:
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USING_REACTIVE_DOMAIN(D)
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Events<D, detail::VTuple<N>> voltages; // Input
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LFPs<D,N> lfp = Transform(voltages, [](detail::VTuple<N> v, LFP<N> l) {
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for (size_t i = 0; i < N; i++)
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l[i] = std::get<0>(v);
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return l;
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}); // Output
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EphysInput(Time<D>& t, Vs& ...sources)
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: time(time)
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{
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voltages = Join(sources...);
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}
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private:
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Time<D> &time;
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};
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template <typename D>
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using EphysInput1 = EphysInput<D, VoltageSource<D>>;
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template <typename D>
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using EphysInput2 = EphysInput<D, VoltageSource<D>, VoltageSource<D>>;
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template <typename D>
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using EphysInput4 = EphysInput<D,
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VoltageSource<D>,
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VoltageSource<D>,
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VoltageSource<D>,
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VoltageSource<D>>;
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template <typename D>
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using EphysInput8 = EphysInput<D,
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VoltageSource<D>,
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VoltageSource<D>,
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VoltageSource<D>,
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VoltageSource<D>>;
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} // namespace decoder
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‎examples/src/SpikeDetect.cpp‎

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#include "SpikeDetect.h"
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#include "Time.hpp"
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#include "Trode.hpp"
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#include "EphysInput.hpp"
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#define MakeVoltSource(D)
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using namespace decoder;
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int main()
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{
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REACTIVE_DOMAIN(D, sequential)
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const size_t N = 256;
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REACTIVE_DOMAIN(D, sequential)
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using raw_size_t = std::array<EventSource<D, double>, N>::size_type;
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const size_t M = 8;
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// Time
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Time<D> time(30.0e3);
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std::cout << "Sample period: " << time.Ts << std::endl;
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// 256 electrodes
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//std::vector<Electrode<D>> electrodes {256, time};
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// 256 raw data sources, bandpass filters
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std::array<EventSource<D, double>, N> raw;
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for (raw_size_t i = 0; i < N; i++)
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raw[i] = MakeEventSource<D, double>();
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//BandPassFilter<D> filter(time, raw[0]);
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std::vector<BandPassFilter<D>> filters;
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for (auto &r :raw)
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filters.emplace_back(time, r);
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//std::cout << "Filter N: " << filters.size() << std::endl;
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// Are merged into 1 TT
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using Tetrode = NTrode<D,
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Events<D, double>,
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Events<D, double>,
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Events<D, double>,
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Events<D, double>>;
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//Tetrode tt(time,
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std::vector<VoltageSource<D>> e;
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for (int i = 0; i < M; i++)
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e.emplace_back(MakeEventSource<D, VoltageT>());
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EphysInput4<D> lfp(time, e[0], e[1], e[2], e[3]);
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// //BandPassFilter<D> filter(time, raw[0]);
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// std::vector<BandPassFilter<D>> filters;
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// for (auto &r :raw)
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// filters.emplace_back(time, r);
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//
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// std::cout << "Sample period: " << time.Ts << std::endl;
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// //std::cout << "Filter N: " << filters.size() << std::endl;
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//
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// // Are merged into 1 TT
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// using Tetrode = NTrode<D,
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// Events<D, double>,
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// Events<D, double>,
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// Events<D, double>,
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// Events<D, double>>;
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//
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// Tetrode tt(time,
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// 0.01,
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// filters[0].Out,
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// filters[1].Out,
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// std::cout << "Current value: " << out << std::endl;
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//});
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// /////////////////////
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///////////////////////
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// HARDWARE SIMULATION
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// This is simulating 100 transactions hardware
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for (int i = 0; i < 100; i++) {
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std::random_device rd;
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std::mt19937 gen(rd());
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std::normal_distribution<> d(0, 1);
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// Make a sample block coming from 4 contacts
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for (int j = 0; j < BLOCKSIZE; j++) {
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// Graph update step
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DoTransaction<D>([&] {
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// Increment sample counter
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time.NewSample();
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// Make noise on all electrodes
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for (auto &r : raw)
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r << d(gen);
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});
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}
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//////////////////////
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std::random_device rd;
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std::mt19937 gen(rd());
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std::normal_distribution<> d(0, 1);
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// Make a sample block coming from 4 contacts
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for (int j = 0; j < 1000; j++) {
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// Graph update step
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DoTransaction<D>([&] {
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// Increment sample counter
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time.NewSample();
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// Make noise on all electrodes
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for (auto &electrode : e)
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electrode << d(gen);
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});
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}
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return 0;

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