nwbio_utils.hpp

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#pragma once
 
#include <memory>
#include <string>
#include <vector>
 
#include "Channel.hpp"
#include "Types.hpp"
#include "io/RecordingObjects.hpp"
#include "nwb/base/TimeSeries.hpp"
#include "nwb/ecephys/ElectricalSeries.hpp"
#include "nwb/ecephys/SpikeEventSeries.hpp"
#include "nwb/misc/AnnotationSeries.hpp"

namespace AQNWB::IO
{

static inline AQNWB::Types::Status writeTimeseriesData(
    std::shared_ptr<RecordingObjects> recording_objects,
    const AQNWB::Types::SizeType& containerInd,
    const AQNWB::Channel& channel,
    const std::vector<AQNWB::Types::SizeType>& dataShape,
    const std::vector<AQNWB::Types::SizeType>& positionOffset,
    const void* data,
    const void* timestamps,
    const void* controlInput = nullptr)
{
  auto registeredObject = recording_objects->getRecordingObject(containerInd);
  // Cast to TimeSeries
  // This assumes that the object at containerInd is a TimeSeries
  auto ts = std::dynamic_pointer_cast<AQNWB::NWB::TimeSeries>(registeredObject);
  if (ts == nullptr) {
    return AQNWB::Types::Status::Failure;
  }
 
  // write data and timestamps to datasets
  if (channel.getLocalIndex() == 0) {
    // write with timestamps if it's the first channel
    return ts->writeData(
        dataShape, positionOffset, data, timestamps, controlInput);
  } else {
    // write without timestamps and controlInput if its another channel in the
    // same timeseries
    return ts->writeData(dataShape, positionOffset, data);
  }
}

static inline AQNWB::Types::Status writeElectricalSeriesData(
    std::shared_ptr<RecordingObjects> recording_objects,
    const AQNWB::Types::SizeType& containerInd,
    const AQNWB::Channel& channel,
    const AQNWB::Types::SizeType& numSamples,
    const void* data,
    const void* timestamps,
    const void* controlInput = nullptr)
{
  auto registeredObject = recording_objects->getRecordingObject(containerInd);
  auto es =
      std::dynamic_pointer_cast<AQNWB::NWB::ElectricalSeries>(registeredObject);
 
  if (es == nullptr)
    return AQNWB::Types::Status::Failure;
 
  return es->writeChannel(
      channel.getLocalIndex(), numSamples, data, timestamps, controlInput);
}

static inline AQNWB::Types::Status writeElectricalSeriesData(
    std::shared_ptr<RecordingObjects> recording_objects,
    const AQNWB::Types::SizeType& containerInd,
    const AQNWB::Types::SizeType& numSamples,
    const void* data,
    const void* timestamps = nullptr,
    const void* controlInput = nullptr)
{
  auto registeredObject = recording_objects->getRecordingObject(containerInd);
  auto es =
      std::dynamic_pointer_cast<AQNWB::NWB::ElectricalSeries>(registeredObject);
 
  if (es == nullptr)
    return AQNWB::Types::Status::Failure;
 
  return es->writeAllChannels(numSamples, data, timestamps, controlInput);
}

static inline AQNWB::Types::Status writeSpikeEventData(
    std::shared_ptr<RecordingObjects> recording_objects,
    const AQNWB::Types::SizeType& containerInd,
    const AQNWB::Types::SizeType& numSamples,
    const AQNWB::Types::SizeType& numChannels,
    const void* data,
    const void* timestamps,
    const void* controlInput = nullptr)
{
  auto registeredObject = recording_objects->getRecordingObject(containerInd);
  auto ses =
      std::dynamic_pointer_cast<AQNWB::NWB::SpikeEventSeries>(registeredObject);
 
  if (ses == nullptr)
    return AQNWB::Types::Status::Failure;
 
  return ses->writeSpike(
      numSamples, numChannels, data, timestamps, controlInput);
}

static inline AQNWB::Types::Status writeAnnotationSeriesData(
    std::shared_ptr<RecordingObjects> recording_objects,
    const AQNWB::Types::SizeType& containerInd,
    const AQNWB::Types::SizeType& numSamples,
    const std::vector<std::string>& data,
    const void* timestamps,
    const void* controlInput = nullptr)
{
  auto registeredObject = recording_objects->getRecordingObject(containerInd);
  auto as =
      std::dynamic_pointer_cast<AQNWB::NWB::AnnotationSeries>(registeredObject);
 
  if (as == nullptr)
    return AQNWB::Types::Status::Failure;
 
  return as->writeAnnotation(numSamples, data, timestamps, controlInput);
}
 
}  // namespace AQNWB::IO