intanlib.h

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// 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 2
// 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, write to the Free Software
// Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA.

 
/*
Mostly a Python version of read_Intan_CLP_file.m from
http://www.intantech.com/files/Intan_CLAMP_software_compiled_v1_0.zip
as of 2016-11-05
 
Example:
>>> import matplotlib.pyplot as plt
>>> import intan
>>> intan_file = intan.IntanFile('myexperiment_A_160916_142731.clp')
>>> plt.plot(intan_file.data["Time"], intan_file.data["Measured"])
>>> intan_file = intan.IntanFile('myexperiment_AUX_160916_142731.clp')
>>> plt.plot(intan_file.data["Time"], intan_file.data["ADC"][1])
*/
#ifndef INTANLIB_H
#define INTANLIB_H
 
#if __cplusplus > 199711L
#include <cstdint>
#else
#include <boost/cstdint.hpp>
#endif
 
#include "./../stfio.h"
 
#if defined(_MSC_VER) && (_MSC_VER < 1600)
typedef __int8 int8_t;
typedef __int16 int16_t;
typedef __int32 int32_t;
typedef __int64 int64_t;
typedef unsigned __int8 uint8_t;
typedef unsigned __int16 uint16_t;
typedef unsigned __int32 uint32_t;
typedef unsigned __int64 uint64_t;
#endif
 
class Recording;
 
static const int MAX_REGISTERS = 14;
static const uint32_t MAGIC_NUMBER = 0xf3b1a481;
 
struct Segment {
    uint8_t waveformNumber;
    uint32_t tOffset;
    uint32_t startIndex;
    uint32_t endIndex;
    float appliedValue;
};
 
struct VoltageClampSettings {
    float holdingVoltage;
    float nominalResistance;
    float resistance;
    float desiredBandwidth;
    float actualBandwidth;
};
 
struct CurrentClampSettings {
    float holdingCurrent;
    float currentStepSize;
};
 
struct HeaderSettings {
    uint8_t enableCapacitiveCompensation;
    float capCompensationMagnitude;
    float filterCutoff;
    float pipetteOffset;
    float samplingRate;
    float cellRs;
    float cellRm;
    float cellCm;
    uint8_t isVoltageClamp;
    uint8_t vClampX2Mode;
    VoltageClampSettings vcSettings;
    CurrentClampSettings ccSettings;
    std::vector<Segment> waveform;
};
 
struct Calibration {
    uint8_t coarse;
    uint8_t fine;
};
 
struct ChannelHeader {
    uint16_t registers[MAX_REGISTERS];
    uint32_t differenceAmpResidual;
    uint32_t voltageAmpResidual;
    Calibration bestCalibration[2][4];
    float rFeedback[5];
    float desiredBandwidth;
};
 
struct ChipHeader {
    std::vector<ChannelHeader> channels;
    uint16_t chipRegisters[4];
};
 
struct IntanHeader {
    int16_t version_major;
    int16_t version_minor;
    int16_t datatype;
    int16_t date_Year;
    int16_t date_Month;
    int16_t date_Day;
    int16_t date_Hour;
    int16_t date_Minute;
    int16_t date_Second;
    std::vector<ChipHeader> Chips;
    HeaderSettings Settings;
    uint16_t numADCs;
 
};
 
namespace stfio {


    void importIntanFile(const std::string &fName, Recording &ReturnData, ProgressInfo& progDlg);
 
}
#endif