dataFiles.h

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/* 
 * dataFiles.h : atom probe data file loading header
 * Copyright (C) 2014  Daniel Haley
 * 
 * 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 ATOMPROBE_FILES_H
#define ATOMPROBE_FILES_H
#include <vector>
#include <atomic>
//Include for C99 fixed-width data types
#include <inttypes.h>

#include "atomprobe/primitives/ionHit.h"

namespace AtomProbe {

using std::vector;

//Enum for error codes for epos reader
//Error strings can be extracted using RECORDREAD_ERR_STRINGS[enum value]
enum
{
    RECORDREAD_ERR_GET_FILESIZE=1,
    RECORDREAD_ERR_FILESIZE_MODULO,
    RECORDREAD_ERR_FILE_OPEN,
    RECORDREAD_ERR_NOMEM,
    RECORDREAD_BAD_FILEREAD,
    RECORDREAD_ERR_CHUNKOFFSET,
    RECORDREAD_BAD_RECORD
};
extern const char *RECORDREAD_ERR_STRINGS[];

inline const char *getRecordReadErrString(unsigned int errCode) { return RECORDREAD_ERR_STRINGS[errCode];};


enum
{
    ATO_OPEN_FAIL=1,
    ATO_EMPTY_FAIL,
    ATO_SIZE_ERR,
    ATO_VERSIONCHECK_ERR,
    ATO_MEM_ERR,
    ATO_BAD_ENDIAN_DETECT,
    ATO_ENUM_END
};

enum
{
    TEXT_ERR_FILE_OPEN=1,
    TEXT_ERR_FILE_NUM_FIELDS,   
    TEXT_ERR_FILE_FORMAT,
};

typedef struct ATO_ENTRY
{
    float x,y,z;//Nominally in Angstrom
    float mass; //Nominally in Da/e
    //Ignore cluster-id as redundant, can be re-computed quickly
    float approxPulse;
    float voltage; //standing voltage, in V
    float tof; //Time of flight in us. May or may not be corrected from raw
    float detectorX,detectorY; //In cm
    float pulseVoltage;
} ATO_ENTRY;

extern const char *ATO_ERR_STRINGS[];

inline const char *getAtoErrString(unsigned int errCode) { return ATO_ERR_STRINGS[errCode];};


unsigned int loadPosFile(std::vector<IonHit> &posIons, const char *posFile);



unsigned int loadPosFile(std::vector<IonHit> &posIons, 
    const char *posFile, unsigned int nSamplesMax);


//Convert the error code returned from loadPosFile into a human-readable message 
const char *getPosFileErrString(unsigned int errMesg);


unsigned int savePosFile(const std::vector<Point3D> &points, float mass, const char *name,bool append=false);

unsigned int savePosFile(const std::vector<IonHit> &data, const char *name,bool append=false);


unsigned int saveTapsimBin(const std::vector<IonHit> &posIons,std::ostream &f);

unsigned int saveTapsimBin(const std::vector<IonHit> &posIons, const char *filename);


size_t loadEposFile(std::vector<EPOS_ENTRY> &outData,const char *filename );


size_t chunkLoadEposFile(std::vector<EPOS_ENTRY> &outData, const char *filename, 
    unsigned int chunkSize, unsigned int chunkOffset, unsigned int &nEntriesLeft);



unsigned int loadTextData(const char *cpFilename,
    std::vector<std::vector<float> > &dataVec,std::vector<std::string> &headerVec,
    const char *delim="\t,", bool allowNan=true,bool allowConvFails=false,unsigned int headerCount=-1);

enum
{
    OPSREADER_FORMAT_CLINE_ERR=1,
    OPSREADER_FORMAT_DETECTORLINE_ERR,
    OPSREADER_FORMAT_LINE_DASH_ERR,
    OPSREADER_FORMAT_LINE_VOLTAGE_ERR,
    OPSREADER_FORMAT_LINE_VOLTAGE_NOBETA,
    OPSREADER_FORMAT_LINE_VOLTAGE_DATA_ERR,
    OPSREADER_FORMAT_LINE_VOLTAGE_DATACOUNT_ERR,
    OPSREADER_FORMAT_LINETYPE_ERR,
    OPSREADER_FORMAT_CHANNELS_ERR,
    OPSREADER_CHANNELS_DATA_ERR,
    OPSREADER_FORMAT_SLINE_EVENTCOUNT_ERR,
    OPSREADER_FORMAT_SLINE_EVENTDATA_ERR,
    OPSREADER_FORMAT_SLINE_FORMAT_ERR,
    OPSREADER_FORMAT_SLINE_PREFIX_ERR,
    OPSREADER_FORMAT_DUPLICATE_SYSDATA,
    OPSREADER_FORMAT_DUPLICATE_DETECTORSIZE,
    OPSREADER_FORMAT_TRAILING_DASH_ERR,
    OPSREADER_FORMAT_DOUBLEDASH,
    OPSREADER_OPEN_ERR,
    OPSREADER_READ_ERR,
    OPSREADER_ABORT_ERR,
    OPSREADER_ENUM_END
};

extern const char *OPS_ENUM_ERRSTRINGS[]; 

struct SINGLE_HIT
{
    float x,y;
    float tof;
};

struct VOLTAGE_DATA
{
    size_t nextHitGroupOffset;
    float voltage;
    float pulseVolt;
    //For some reason, OPS files seem to have duplicate beta data
    float beta; 
};

/* See  10.1063/1.2709758 for the details of the correction paramters.
*/
struct THREEDAP_DATA
{
    float flightPath; 
    float alpha; 
    float beta; 
    float tZero;
    float detectorRadius;
    unsigned int detectorChannels;
};

struct THREEDAP_EXPERIMENT
{
    THREEDAP_DATA params;   
    std::vector<::std::vector<SINGLE_HIT> > eventData;
    std::vector<VOLTAGE_DATA> voltageData;
    std::vector<unsigned long long> eventPulseNumber;
};


unsigned int readPosapOps(const char *file, 
        THREEDAP_EXPERIMENT &data, 
            unsigned int &badLine, unsigned int &progress, 
            std::atomic<bool> &wantAbort, 
            unsigned int nDelayLines=2,bool strictMode=false);


unsigned int loadATOFile(const char *fileName, 
    std::vector<ATO_ENTRY> &ions, unsigned int forceEndian=0);
}


#endif