SpikeDetector.h

/*
    ------------------------------------------------------------------

    This file is part of the Open Ephys GUI
    Copyright (C) 2013 Open Ephys

    ------------------------------------------------------------------

    This program is free software: you can redistribute it and/or modify
    it under the terms of the GNU General Public License as published by
    the Free Software Foundation, either version 3 of the License, or
    (at your option) any later version.

    This program is distributed in the hope that it will be useful,
    but WITHOUT ANY WARRANTY; without even the implied warranty of
    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
    GNU General Public License for more details.

    You should have received a copy of the GNU General Public License
    along with this program.  If not, see <http://www.gnu.org/licenses/>.

*/

#ifndef __SPIKEDETECTOR_H_3F920F95__
#define __SPIKEDETECTOR_H_3F920F95__

#include "../../JuceLibraryCode/JuceHeader.h"

#include "GenericProcessor.h"
#include "Editors/SpikeDetectorEditor.h"

#include "Visualization/SpikeObject.h"

struct Electrode
{

    String name;

    int numChannels;
    int prePeakSamples, postPeakSamples;
    int lastBufferIndex;
    bool isMonitored;

    int* channels;
    double* thresholds;
    bool* isActive;

};

class SpikeDetectorEditor;

/**

  Detects spikes in a continuous signal and outputs events containing the spike data.

  @see GenericProcessor, SpikeDetectorEditor

*/

class SpikeDetector : public GenericProcessor

{
public:

    // CONSTRUCTOR AND DESTRUCTOR //

    /** constructor */
    SpikeDetector();

    /** destructor */
    ~SpikeDetector();


    // PROCESSOR METHODS //

    /** Processes an incoming continuous buffer and places new
        spikes into the event buffer. */
    void process(AudioSampleBuffer& buffer, MidiBuffer& events, int& nSamples);

    /** Used to alter parameters of data acquisition. */
    void setParameter(int parameterIndex, float newValue);

    /** Called whenever the signal chain is altered. */
    void updateSettings();

    /** Called prior to start of acquisition. */
    bool enable();

    /** Called after acquisition is finished. */
    bool disable();

    /** Creates the SpikeDetectorEditor. */
    AudioProcessorEditor* createEditor();


    // INTERNAL BUFFERS //

    /** Extra samples are placed in this buffer to allow seamless
        transitions between callbacks. */
    AudioSampleBuffer overflowBuffer;


    // CREATE AND DELETE ELECTRODES //

    /** Adds an electrode with n channels to be processed. */
    bool addElectrode(int nChans);

    /** Removes an electrode with a given index. */
    bool removeElectrode(int index);


    // EDIT AND QUERY ELECTRODE SETTINGS //

    /** Returns the number of channels for a given electrode. */
    int getNumChannels(int index);

    /** Edits the mapping between input channels and electrode channels. */
    void setChannel(int electrodeIndex, int channelNum, int newChannel);

    /** Returns the continuous channel that maps to a given
    	electrode channel. */
    int getChannel(int index, int chan);

    /** Sets the name of a given electrode. */
    void setElectrodeName(int index, String newName);

    /** */
    void setChannelActive(int electrodeIndex, int channelNum, bool active);

    /** */
    bool isChannelActive(int electrodeIndex, int channelNum);

    // RETURN STRING ARRAYS //

    /** Returns a StringArray containing the names of all electrodes */
    StringArray getElectrodeNames();

    /** Returns array of electrodes. */
    Array<Electrode*> getElectrodes();

    /** Returns array of electrodes. */
    Electrode* getActiveElectrode();

    /** Sets the current electrode index */
    Electrode* setCurrentElectrodeIndex(int);

    /** Returns a list of possible electrode types (e.g., stereotrode, tetrode). */
    StringArray electrodeTypes;

    void setChannelThreshold(int electrodeNum, int channelNum, float threshold);

    double getChannelThreshold(int electrodeNum, int channelNum);

    void saveCustomParametersToXml(XmlElement* parentElement);
    void loadCustomParametersFromXml();

private:
    /** Pointer to a continuous buffer. */
    AudioSampleBuffer* dataBuffer;

    float getDefaultThreshold();

    int overflowBufferSize;

    int sampleIndex;

    Array<int> electrodeCounter;

    float getNextSample(int& chan);
    float getCurrentSample(int& chan);
    bool samplesAvailable(int& nSamples);

    bool useOverflowBuffer;

    int currentElectrode;
    int currentChannelIndex;
    int currentIndex;

    uint8_t* spikeBuffer;///[256];
    int64 timestamp;

    Array<Electrode*> electrodes;

    // void createSpikeEvent(int& peakIndex,
    // 					  int& electrodeNumber,
    // 					  int& currentChannel,
    // 					  MidiBuffer& eventBuffer);

    void handleEvent(int eventType, MidiMessage& event, int sampleNum);

    void addSpikeEvent(SpikeObject* s, MidiBuffer& eventBuffer, int peakIndex);
    void addWaveformToSpikeObject(SpikeObject* s,
                                  int& peakIndex,
                                  int& electrodeNumber,
                                  int& currentChannel);

    void resetElectrode(Electrode*);

    JUCE_DECLARE_NON_COPYABLE_WITH_LEAK_DETECTOR(SpikeDetector);

};



#endif  // __SPIKEDETECTOR_H_3F920F95__