cat_creator.cpp

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/*
 * cat_creator.cpp
 * Copyright 2013 University of Massachusetts Lowell
 * Author: Jonathan Hasenzahl
 */

#include "burst_calc/cat_creator.h"
#include <cstdio>

CatCreator::~CatCreator()
{
    if (cat_file_.is_open())
        cat_file_.close();
}


void CatCreator::init()
{
    is_init_ = false;
    save_to_file_ = true;

    getParams();

    // Initialize publisher
    cat_pub_ = n_.advertise<burst_calc::cat>("cats", 1000);
    ca_pub_ = n_.advertise<burst_calc::ca>("cas", 1000);

    // Wait for subscribers
    ROS_INFO("Waiting for subscribers...");
    while (cat_pub_.getNumSubscribers() < 1 && ca_pub_.getNumSubscribers() &&
           ros::ok());

    // Initialize subscribers
    burst_sub_ = n_.subscribe("bursts_to_cat_creator", 1000, &CatCreator::callback, this);
    ranges_sub_ = n_.subscribe("ranges_to_cat_creator", 1, &CatCreator::rangesCallback,
                               this);

    if (save_to_file_)
        initFile(file_name_.c_str());

    ros::spin();
}

void CatCreator::getParams()
{
    // Get cat log path parameter
    if (!n_.getParam("cat_log_path", file_name_))
    {
        ROS_WARN("Could not load burst_log_path parameter, logging will be disabled");
        save_to_file_ = false;
    }
}

void CatCreator::updateOffsets(const neuro_recv::dish_state& d)
{
    for (int i = 0; i < 60; i++)
    {
        if (d.samples[i] < offsets_[i])
        {
            offsets_[i] = d.samples[i];
            //printf("Offset correction: channel %d set to %f\n", i, d.samples[i]);
        }
    }
}

void CatCreator::callback(const burst_calc::burst::ConstPtr& b)
{
    if (is_init_)
    {
        // Write burst header to file
        if (save_to_file_)
            headerToFile(*b);

        // Create a new CAT
        burst_calc::cat cat;
        cat.header.stamp = b->header.stamp;
        cat.end = b->end;
        cat.channels = b->channels;

        for (unsigned int i = 0; i < b->dishes.size(); i++)
        {
            // Update offsets in case a new min voltage is encountered
            updateOffsets(b->dishes[i]);

            if (caExists(b->dishes[i]))
            {
                // A center of activity exists for this dish state:
                // Add CA to CAT, publish CA, and write CAT & burst to file
                burst_calc::ca ca = getCa(b->dishes[i]);
                cat.cas.push_back(ca);
                ca_pub_.publish(ca);
                if (save_to_file_)
                    toFile(i, b->dishes[i], ca);
            }
            else
            {
                // No center of activity for this dish state:
                // Just write burst to file
                if (save_to_file_)
                    toFile(i, b->dishes[i]);
            }
        }

        // Publish CAT
        cat_pub_.publish(cat);
        ROS_INFO("CAT of size %d created from burst of size %d",
                 static_cast<int>(cat.cas.size()), static_cast<int>(b->dishes.size()));
    }
    else
        ROS_ERROR("Minimum voltages not initialized, skipping CAT creation");
}

void CatCreator::rangesCallback(const burst_calc::ranges::ConstPtr& r)
{
    ROS_INFO("CAT Creator initialized");

    for (int i = 0; i < 60; i++)
    {
        offsets_[i] = r->min_volts[i];
        thresholds_[i] = r->thresholds[i];
    }

    if (save_to_file_)
    {
        cat_file_ << "threshold_volts,,,,";
        for (int i = 0; i < 60; i++)
            cat_file_ << r->thresholds[i] << ',';
        cat_file_ << "\n\n";
    }

    is_init_ = true;
}

bool CatCreator::caExists(const neuro_recv::dish_state& d)
{
    // Only dish states with at least 1 spike will have a CA calculated
    for (int i = 0; i < 60; i ++)
    {
        if (d.samples[i] > thresholds_[i])
            return true;
    }

    // No spikes in this dish state
    return false;
}

const burst_calc::ca CatCreator::getCa(const neuro_recv::dish_state& d)
{
    // Center of activity = summation(position*activity) / total activity
    double x_sum = 0.0;
    double y_sum = 0.0;
    double activity = 0.0;

    for (int i = 0; i < 60; i++)
    {
        // Only spikes are used for CA calculation
        if (d.samples[i] > thresholds_[i])
        {
            double this_activity = d.samples[i] - offsets_[i];
            if (this_activity < 0.0)
            {
                ROS_ERROR("Activity is lower than recorded minimum, CA will not be accurate");
                ROS_ERROR("%d: %f = %f - %f\n", i, this_activity, d.samples[i],
                          offsets_[i]);
                this_activity = -this_activity;
            }

            x_sum += this_activity * X_COORD_[i];
            y_sum += this_activity * Y_COORD_[i];
            activity += this_activity;
        }
    }

    burst_calc::ca ca;
    ca.header.stamp = d.header.stamp;
    if (activity > 0.0)
    {
        ca.x = x_sum / activity;
        ca.y = y_sum / activity;
    }
    else
        ROS_ERROR("No activity recorded for this CA");

    //printf("ca.x = %f / %f = %f\n", x_sum, activity, ca.x);
    //printf("ca.y = %f / %f = %f\n\n", y_sum, activity, ca.y);

    return ca;
}

void CatCreator::initFile(const char* cat_file)
{
    cat_file_.open(cat_file, std::ios_base::trunc | std::ios_base::out);
    if (!cat_file_.is_open())
    {
        ROS_ERROR("Cannot open %s. CSV logging will be disabled.", cat_file);
        save_to_file_ = false;
        return;
    }

    cat_file_ << "index,seconds,ca_x,ca_y,";
    for (int i = 0; i < 60; i++)
    {
        cat_file_ << "channel_" << i << ',';
    }
    cat_file_ << '\n';
}

void CatCreator::headerToFile(const burst_calc::burst& b)
{
    cat_file_ << "begin_time," << b.header.stamp.toSec() << ",\n";
    cat_file_ << "end_time," << b.end.toSec() << ",\n";
    cat_file_ << "duration," << (b.end - b.header.stamp).toSec() << ",\n";
    cat_file_ << "bursting_channels,\n";
    for (unsigned int i = 0; i < b.channels.size(); i++)
        cat_file_ << static_cast<int>(b.channels[i]) << ",\n";
}

void CatCreator::toFile(int i, const neuro_recv::dish_state& d,
                        const burst_calc::ca& c)
{
    cat_file_ << i << ',' << d.header.stamp.toSec() << ',' << c.x << ','
              << c.y << ',';
    for (int j = 0; j < 60; j++)
        cat_file_ << d.samples[j] << ',';
    cat_file_ << '\n';
}

void CatCreator::toFile(int i, const neuro_recv::dish_state& d)
{
    cat_file_ << i << ',' << d.header.stamp.toSec() << ",,,";
    for (int j = 0; j < 60; j++)
        cat_file_ << d.samples[j] << ',';
    cat_file_ << '\n';
}

int main(int argc, char** argv)
{
    ros::init(argc, argv, "cat_creator");
    CatCreator cat_creator;
    return 0;
}