ImzMLHandlerHelper.h

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// Copyright (c) 2002-present, OpenMS Inc. -- EKU Tuebingen, ETH Zurich, and FU Berlin
// SPDX-License-Identifier: BSD-3-Clause
//
// --------------------------------------------------------------------------
// $Maintainer: Timo Sachsenberg $
// $Authors: Aditya Sarna $
// --------------------------------------------------------------------------
 
#pragma once
 
#include <OpenMS/OpenMSConfig.h>
#include <OpenMS/DATASTRUCTURES/StringUtils.h>
 
#include <cstdint>
#include <cstdio>
#include <optional>
#include <string>
#include <vector>
 
namespace OpenMS
{
  class MSSpectrum;
 
  struct OPENMS_DLLAPI ImzMLMeta
  {
    // -------------------------------------------------------------------------
    // Imaging geometry
    // -------------------------------------------------------------------------
 
    uint32_t max_count_x  {0};  
    uint32_t max_count_y  {0};  
    uint32_t max_count_z  {1};  
    double   pixel_size_x {-1}; 
    double   pixel_size_y {-1}; 
    std::string pixel_size_unit {"unknown"}; 
    double   max_dim_x    {0};  
    double   max_dim_y    {0};  
 
    // -------------------------------------------------------------------------
    // Imaging mode
    // -------------------------------------------------------------------------
 
    std::string imaging_mode;
 
    // -------------------------------------------------------------------------
    // IBD companion file
    // -------------------------------------------------------------------------
 
    std::string ibd_file_path; 
    std::string ibd_sha1;      
    std::string ibd_md5;       
    std::string uuid;          
 
    // -------------------------------------------------------------------------
    // Array data types (first occurrence, dataset-level summary)
    // -------------------------------------------------------------------------
 
    std::string mz_data_type;   
    std::string int_data_type;  
 
    // -------------------------------------------------------------------------
    // Acquisition geometry
    // -------------------------------------------------------------------------
 
    std::string scan_pattern;        
    std::string scan_direction;      
    std::string line_scan_direction; 
    std::string polarity;            
  };
 
  OPENMS_DLLAPI std::optional<int> lengthUnitExponent(const std::string& unit_accession);
 
 
  struct OPENMS_DLLAPI ImzMLSpectrumIndex
  {
    enum class DataType : uint8_t { FLOAT32, FLOAT64, INT32, INT64, UNKNOWN };
 
    struct AuxArray
    {
      std::string name;                 
      std::string accession;            
      std::string unit_accession;       
      uint64_t offset {0};              
      uint64_t length {0};              
      uint64_t encoded_bytes {0};       
      DataType type {DataType::UNKNOWN};
      bool compressed {false};          
    };
 
    int32_t  index      {0};               
    uint32_t x          {0};               
    uint32_t y          {0};               
    uint32_t z          {1};               
    uint64_t mz_offset  {0};              
    uint64_t mz_length  {0};              
    DataType mz_type    {DataType::UNKNOWN};
    bool mz_compressed {false};           
    uint64_t int_offset {0};              
    uint64_t int_length {0};              
    DataType int_type   {DataType::UNKNOWN};
    bool int_compressed {false};          
    std::vector<AuxArray> aux;            
  };
 
  class OPENMS_DLLAPI ImzMLBinaryIO
  {
  public:
    static void readMzArray(FILE* ibd,
                            uint64_t offset,
                            uint64_t count,
                            ImzMLSpectrumIndex::DataType dt,
                            std::vector<double>& out,
                            const std::string& ibd_path);
 
    static void readIntArray(FILE* ibd,
                             uint64_t offset,
                             uint64_t count,
                             ImzMLSpectrumIndex::DataType dt,
                             std::vector<float>& out,
                             const std::string& ibd_path);
 
    static void readAuxArray(FILE* ibd,
                             uint64_t offset,
                             uint64_t count,
                             ImzMLSpectrumIndex::DataType dt,
                             std::vector<float>& out,
                             const std::string& ibd_path,
                             const std::string& array_name);
 
    static void writeFloat32Array(FILE* ibd,
                                  const float* data,
                                  uint64_t count,
                                  const std::string& ibd_path);
 
    static void writeMzAsFloat32(FILE* ibd,
                                 const std::vector<double>& mz,
                                 const std::string& ibd_path);
 
    static void writeFloat64Array(FILE* ibd,
                                  const double* data,
                                  uint64_t count,
                                  const std::string& ibd_path);
 
    static void writeMzAsFloat64(FILE* ibd,
                                 const std::vector<double>& mz,
                                 const std::string& ibd_path);
  };
 
  class OPENMS_DLLAPI ImzMLSpectrumRules
  {
  public:
    static double scanStartTime(const MSSpectrum& s);
 
    static bool isLoadableAuxArray(const std::string& name, uint64_t length,
                                   ImzMLSpectrumIndex::DataType type, uint64_t n_peaks,
                                   bool warn = false, uint32_t x = 0, uint32_t y = 0, uint32_t z = 0);
 
    static void applyIMPeakType(MSSpectrum& s, bool has_im_array);
 
    static void attachAuxArray(MSSpectrum& s, const std::string& name, const std::string& unit_accession,
                               const std::vector<float>& values);
 
    static void pruneEmptyDataArrays(MSSpectrum& s);
  };
 
} // namespace OpenMS