SEGYImport.cpp 94.7 KB
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/****************************************************************************
** Copyright 2019 The Open Group
** Copyright 2019 Bluware, Inc.
**
** Licensed under the Apache License, Version 2.0 (the "License");
** you may not use this file except in compliance with the License.
** You may obtain a copy of the License at
**
**   http://www.apache.org/licenses/LICENSE-2.0
**
** Unless required by applicable law or agreed to in writing, software
** distributed under the License is distributed on an "AS IS" BASIS,
** WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
** See the License for the specific language governing permissions and
** limitations under the License.
****************************************************************************/

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#define _CRT_SECURE_NO_WARNINGS 1
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#include <SEGYUtils/SEGYFileInfo.h>
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#include "IO/File.h"
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#include "VDS/Hash.h"
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#include <SEGYUtils/DataProvider.h>
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#include <SEGYUtils/TraceDataManager.h>
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#include <OpenVDS/OpenVDS.h>
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#include <OpenVDS/MetadataContainer.h>
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#include <OpenVDS/VolumeDataLayoutDescriptor.h>
#include <OpenVDS/VolumeDataAxisDescriptor.h>
#include <OpenVDS/VolumeDataChannelDescriptor.h>
#include <OpenVDS/VolumeDataAccess.h>
#include <OpenVDS/Range.h>
#include <OpenVDS/VolumeDataLayout.h>
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#include <OpenVDS/KnownMetadata.h>
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#include <OpenVDS/GlobalMetadataCommon.h>
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#include "IO/IOManager.h"

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#include <mutex>
#include <cstdlib>
#include <climits>
#include <cassert>
#include <algorithm>

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#include <cxxopts/cxxopts.hpp>
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#include <json/json.h>
#include <fmt/format.h>

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#include "SplitUrl.h"
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#include <PrintHelpers.h>
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#include <HelpConnection.h>
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#include <chrono>
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#include <numeric>
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#if defined(WIN32)
#undef WIN32_LEAN_AND_MEAN // avoid warnings if defined on command line
#define WIN32_LEAN_AND_MEAN 1
#define NOMINMAX 1
#include <io.h>
#include <windows.h>
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int64_t GetTotalSystemMemory()
{
    MEMORYSTATUSEX status;
    status.dwLength = sizeof(status);
    GlobalMemoryStatusEx(&status);
    return int64_t(status.ullTotalPhys);
}

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#else
#include <unistd.h>
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int64_t GetTotalSystemMemory()
{
    long pages = sysconf(_SC_PHYS_PAGES);
    long page_size = sysconf(_SC_PAGE_SIZE);
    return int64_t(pages) * int64_t(page_size);
}
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#endif

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inline char asciitolower(char in) {
  if (in <= 'Z' && in >= 'A')
    return in - ('Z' - 'z');
  return in;
}

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static DataProvider CreateDataProviderFromFile(const std::string &filename, OpenVDS::Error &error)
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{
  std::unique_ptr<OpenVDS::File> file(new OpenVDS::File());
  if (!file->Open(filename, false, false, false, error))
    return DataProvider((OpenVDS::File *)nullptr);
  return DataProvider(file.release());
}

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static DataProvider CreateDataProviderFromOpenOptions(const std::string &url, const std::string &connectionString, OpenVDS::Error &error)
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{
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  std::unique_ptr<OpenVDS::IOManager> ioManager(OpenVDS::IOManager::CreateIOManager(url, connectionString, OpenVDS::IOManager::AccessPattern::ReadOnly, error));
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  if (error.code)
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    return DataProvider("", (OpenVDS::IOManager*)nullptr, error);
  return DataProvider(url, ioManager.release(), error);
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}

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DataProvider CreateDataProvider(const std::string& url, const std::string& connection, OpenVDS::Error& error)
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{
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  if (OpenVDS::IsSupportedProtocol(url))
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  {
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    return CreateDataProviderFromOpenOptions(url, connection, error);
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  }
  else
  {
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    return CreateDataProviderFromFile(url, error);
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  }
  return DataProvider(nullptr);
}

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static std::vector<DataProvider> CreateDataProviders(const std::vector<std::string> &fileNames, const std::string &connection, OpenVDS::Error &error, std::string &errorFileName)
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{
  std::vector<DataProvider>
    dataProviders;

  for (const auto& fileName : fileNames)
  {
    dataProviders.push_back(CreateDataProvider(fileName, connection, error));

    if (error.code != 0)
    {
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      errorFileName = fileName;
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      dataProviders.clear();
      break;
    }
  }
  return dataProviders;
}

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Json::Value
SerializeSEGYBinInfo(SEGYBinInfo const& binInfo)
{
  Json::Value
    jsonBinInfo;

  jsonBinInfo["inlineNumber"] = binInfo.m_inlineNumber;
  jsonBinInfo["crosslineNumber"] = binInfo.m_crosslineNumber;

  jsonBinInfo["ensembleXCoordinate"] = binInfo.m_ensembleXCoordinate;
  jsonBinInfo["ensembleYCoordinate"] = binInfo.m_ensembleYCoordinate;

  return jsonBinInfo;
}

Json::Value
SerializeSEGYSegmentInfo(SEGYSegmentInfo const& segmentInfo)
{
  Json::Value
    jsonSegmentInfo;

  jsonSegmentInfo["primaryKey"] = segmentInfo.m_primaryKey;
  jsonSegmentInfo["traceStart"] = segmentInfo.m_traceStart;
  jsonSegmentInfo["traceStop"] = segmentInfo.m_traceStop;

  jsonSegmentInfo["binInfoStart"] = SerializeSEGYBinInfo(segmentInfo.m_binInfoStart);
  jsonSegmentInfo["binInfoStop"] = SerializeSEGYBinInfo(segmentInfo.m_binInfoStop);

  return jsonSegmentInfo;
}

std::string
ToString(SEGY::Endianness endiannness)
{
  switch (endiannness)
  {
  case SEGY::Endianness::BigEndian:  return "BigEndian";
  case SEGY::Endianness::LittleEndian: return "LittleEndian";
  default:
    assert(0); return "";
  }
}

std::string
ToString(SEGY::FieldWidth fieldWidth)
{
  switch (fieldWidth)
  {
  case SEGY::FieldWidth::TwoByte:  return "TwoByte";
  case SEGY::FieldWidth::FourByte: return "FourByte";
  default:
    assert(0); return "";
  }
}

Json::Value
SerializeSEGYHeaderField(SEGY::HeaderField const& headerField)
{
  Json::Value
    jsonHeaderField(Json::ValueType::arrayValue);

  jsonHeaderField.append(headerField.byteLocation);
  jsonHeaderField.append(ToString(headerField.fieldWidth));

  return jsonHeaderField;
}

Json::Value
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SerializeSEGYFileInfo(SEGYFileInfo const& fileInfo, const int fileIndex)
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{
  Json::Value
    jsonFileInfo;

  jsonFileInfo["persistentID"] = fmt::format("{:X}", fileInfo.m_persistentID);
  jsonFileInfo["headerEndianness"] = ToString(fileInfo.m_headerEndianness);
  jsonFileInfo["dataSampleFormatCode"] = (int)fileInfo.m_dataSampleFormatCode;
  jsonFileInfo["sampleCount"] = fileInfo.m_sampleCount;
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  jsonFileInfo["startTime"] = fileInfo.m_startTimeMilliseconds;
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  jsonFileInfo["sampleInterval"] = fileInfo.m_sampleIntervalMilliseconds;
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  jsonFileInfo["traceCount"] = fileInfo.m_traceCounts[fileIndex];
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  jsonFileInfo["primaryKey"] = SerializeSEGYHeaderField(fileInfo.m_primaryKey);
  jsonFileInfo["secondaryKey"] = SerializeSEGYHeaderField(fileInfo.m_secondaryKey);

  Json::Value
    jsonSegmentInfoArray(Json::ValueType::arrayValue);

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  for (auto const& segmentInfo : fileInfo.m_segmentInfoLists[fileIndex])
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  {
    jsonSegmentInfoArray.append(SerializeSEGYSegmentInfo(segmentInfo));
  }

  jsonFileInfo["segmentInfo"] = jsonSegmentInfoArray;

  return jsonFileInfo;
}

std::map<std::string, SEGY::HeaderField>
g_traceHeaderFields =
{
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 { "tracesequencenumber",           SEGY::TraceHeader::TraceSequenceNumberHeaderField },
 { "tracesequencenumberwithinfile", SEGY::TraceHeader::TraceSequenceNumberWithinFileHeaderField },
 { "energysourcepointnumber",       SEGY::TraceHeader::EnergySourcePointNumberHeaderField },
 { "ensemblenumber",                SEGY::TraceHeader::EnsembleNumberHeaderField },
 { "tracenumberwithinensemble",     SEGY::TraceHeader::TraceNumberWithinEnsembleHeaderField },
 { "traceidentificationcode",       SEGY::TraceHeader::TraceIdentificationCodeHeaderField },
 { "coordinatescale",               SEGY::TraceHeader::CoordinateScaleHeaderField },
 { "sourcexcoordinate",             SEGY::TraceHeader::SourceXCoordinateHeaderField },
 { "sourceycoordinate",             SEGY::TraceHeader::SourceYCoordinateHeaderField },
 { "groupxcoordinate",              SEGY::TraceHeader::GroupXCoordinateHeaderField },
 { "groupycoordinate",              SEGY::TraceHeader::GroupYCoordinateHeaderField },
 { "coordinateunits",               SEGY::TraceHeader::CoordinateUnitsHeaderField },
 { "starttime",                     SEGY::TraceHeader::StartTimeHeaderField },
 { "numsamples",                    SEGY::TraceHeader::NumSamplesHeaderField },
 { "sampleinterval",                SEGY::TraceHeader::SampleIntervalHeaderField },
 { "ensemblexcoordinate",           SEGY::TraceHeader::EnsembleXCoordinateHeaderField },
 { "ensembleycoordinate",           SEGY::TraceHeader::EnsembleYCoordinateHeaderField },
 { "inlinenumber",                  SEGY::TraceHeader::InlineNumberHeaderField },
 { "crosslinenumber",               SEGY::TraceHeader::CrosslineNumberHeaderField },
 { "receiver",                      SEGY::TraceHeader::ReceiverHeaderField },
 { "offset",                        SEGY::TraceHeader::OffsetHeaderField }
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};

std::map<std::string, std::string>
g_aliases =
{
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 { "inline",              "inlinenumber" },
 { "crossline",           "crosslinenumber" },
 { "shot",                "energysourcepointnumber" },
 { "sp",                  "energysourcepointnumber" },
 { "cdp",                 "ensemblenumber" },
 { "cmp",                 "ensemblenumber" },
 { "easting",             "ensemblexcoordinate" },
 { "northing",            "ensembleycoordinate" },
 { "cdpxcoordinate",      "ensemblexcoordinate" },
 { "cdpycoordinate",      "ensembleycoordinate" },
 { "cdp-x",               "ensemblexcoordinate" },
 { "cdp-y",               "ensembleycoordinate" },
 { "source-x",            "sourcexcoordinate" },
 { "source-y",            "sourceycoordinate" },
 { "group-x",             "groupxcoordinate" },
 { "group-y",             "groupycoordinate" },
 { "receiverxcoordinate", "groupxcoordinate" },
 { "receiverycoordinate", "groupycoordinate" },
 { "receiver-x",          "groupxcoordinate" },
 { "receiver-y",          "groupycoordinate" },
 { "scalar",              "coordinatescale" }
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};

void
ResolveAlias(std::string& fieldName)
{
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  std::transform(fieldName.begin(), fieldName.end(), fieldName.begin(), asciitolower);
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  if (g_aliases.find(fieldName) != g_aliases.end())
  {
    fieldName = g_aliases[fieldName];
  }
}

SEGY::Endianness
EndiannessFromJson(Json::Value const& jsonEndianness)
{
  std::string
    endiannessString = jsonEndianness.asString();

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  std::transform(endiannessString.begin(), endiannessString.end(), endiannessString.begin(), asciitolower);
  if (endiannessString == "bigendian")
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  {
    return SEGY::Endianness::BigEndian;
  }
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  else if (endiannessString == "littleendian")
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  {
    return SEGY::Endianness::LittleEndian;
  }

  throw Json::Exception("Illegal endianness");
}

SEGY::FieldWidth
FieldWidthFromJson(Json::Value const& jsonFieldWidth)
{
  std::string
    fieldWidthString = jsonFieldWidth.asString();
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  std::transform(fieldWidthString.begin(), fieldWidthString.end(), fieldWidthString.begin(), asciitolower);
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  if (fieldWidthString == "twobyte")
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  {
    return SEGY::FieldWidth::TwoByte;
  }
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  else if (fieldWidthString == "fourbyte")
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  {
    return SEGY::FieldWidth::FourByte;
  }

  throw Json::Exception("Illegal field width");
}

SEGY::HeaderField
HeaderFieldFromJson(Json::Value const& jsonHeaderField)
{
  int
    bytePosition = jsonHeaderField[0].asInt();

  SEGY::FieldWidth
    fieldWidth = FieldWidthFromJson(jsonHeaderField[1]);

  if (bytePosition < 1 || bytePosition > SEGY::TraceHeaderSize - ((fieldWidth == SEGY::FieldWidth::TwoByte) ? 2 : 4))
  {
    throw Json::Exception(std::string("Illegal field definition: ") + jsonHeaderField.toStyledString());
  }

  return SEGY::HeaderField(bytePosition, fieldWidth);
}

bool
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ParseHeaderFormatFile(DataProvider &dataProvider, std::map<std::string, SEGY::HeaderField>& traceHeaderFields, SEGY::Endianness& headerEndianness, OpenVDS::Error &error)
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{
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  int64_t dataSize = dataProvider.Size(error);
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  if (error.code != 0)
  {
    return false;
  }

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  if (dataSize > INT_MAX)
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  {
    return false;
  }

  std::unique_ptr<char[]>
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    buffer(new char[dataSize]);
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  dataProvider.Read(buffer.get(), 0, (int32_t)dataSize, error);
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  if (error.code != 0)
  {
    return false;
  }

  try
  {
    Json::CharReaderBuilder
      rbuilder;

    rbuilder["collectComments"] = false;

    std::string
      errs;

    std::unique_ptr<Json::CharReader>
      reader(rbuilder.newCharReader());

    Json::Value
      root;

    bool
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      success = reader->parse(buffer.get(), buffer.get() + dataSize, &root, &errs);
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    if (!success)
    {
      throw Json::Exception(errs);
    }

    for (std::string const& fieldName : root.getMemberNames())
    {
      std::string canonicalFieldName = fieldName;
      ResolveAlias(canonicalFieldName);

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      if (canonicalFieldName == "endianness")
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      {
        headerEndianness = EndiannessFromJson(root[fieldName]);
      }
      else
      {
        traceHeaderFields[canonicalFieldName] = HeaderFieldFromJson(root[fieldName]);
      }
    }
  }
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  catch (Json::Exception &e)
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  {
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    error.code = -1;
    error.string = e.what();
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    return false;
  }

  return true;
}

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bool OnlyDigits(const std::string& str)
{
  for (auto a : str)
  {
    if (a < '0' || a > '9')
      return false;
  }
  return true;
}

bool
ParseHeaderFieldArgs(const std::vector<std::string> &header_fields_args, std::map<std::string, SEGY::HeaderField>& traceHeaderFields, SEGY::Endianness& headerEndianness, OpenVDS::Error& error)
{
  for (auto& header_field : header_fields_args)
  {
    if (header_field.empty())
    {
      error.code = -1;
      error.string = "Cannot parse empty header-field";
      return false;
    }
    auto it = std::find(header_field.begin(), header_field.end(), '=');
    if (it == header_field.end())
    {
      error.code = -1;
      error.string = fmt::format("Failed to parse header-field {}.", header_field);
      return false;
    }
    std::string header_name(header_field.begin(), it);
    if (it + 1 == header_field.end())
    {
      error.code = -1;
      error.string = fmt::format("Can not find value for header-field {}.", header_name);
      return false;
    }
    std::string header_value(it + 1, header_field.end());
    auto min_delimiter = std::find(header_value.begin(), header_value.end(), '-');
    int field_width = -1;
    int offset = -1;
    if (min_delimiter != header_value.end())
    {
      if (min_delimiter + 1 == header_value.end())
      {
        error.code = -1;
        error.string = fmt::format("unable to parse value for header-field {} with value {}.", header_name, header_value);
        return false;
      }
      std::string value_start(header_value.begin(), min_delimiter);
      std::string value_end(min_delimiter + 1, header_value.end());
      if (!OnlyDigits(value_start) || !OnlyDigits(value_end))
      {
        error.code = -1;
        error.string = fmt::format("unable to parse header-field {} value range {}.", header_name, header_value);
        return false;
      }
      int value_start_value = atoi(value_start.c_str());
      int value_end_value = atoi(value_end.c_str());
      offset = value_start_value;
      field_width = value_end_value - value_start_value;
    }
    else
    {
      auto colon_delimiter = std::find(header_value.begin(), header_value.end(), ':');
      std::string offset_str(header_value.begin(), colon_delimiter);
      if (!OnlyDigits(offset_str))
      {
        error.code = -1;
        error.string = fmt::format("unable to parse offset for header-field {}: {}.", header_name, header_value);
        return false;
      }
      offset = atoi(offset_str.c_str());
      if (colon_delimiter < header_value.end() && colon_delimiter + 1 < header_value.end())
      {
        std::string width_str(colon_delimiter + 1, header_value.end());
        if (!OnlyDigits(width_str))
        {
          error.code = -1;
          error.string = fmt::format("unable to parse width specifier for header-field {}: {}.", header_name, width_str);
          return false;
        }
        field_width = atoi(width_str.c_str());
      }
    }
    if (offset < 0)
    {
      error.code = -1;
      error.string = fmt::format("unable to find offset for header-field {}: {}.", header_name, header_value);
      return false;
    }
    ResolveAlias(header_name);
    auto& traceHeaderField = traceHeaderFields[header_name];
    traceHeaderField.byteLocation = offset;
    if (field_width != -1)
    {
      if (field_width == 2)
      {
        traceHeaderField.fieldWidth = SEGY::FieldWidth::TwoByte;
      }
      else if (field_width == 4)
      {
        traceHeaderField.fieldWidth = SEGY::FieldWidth::FourByte;
      }
      else
      {
        error.code = -1;
        error.string = fmt::format("header-field {} has illegal field width of {}. Only widths of 2 or 4 are accepted.", header_name, field_width);
        return false;
      }
    }
  }
  return true;
}

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SEGYBinInfo
binInfoFromJson(Json::Value const& jsonBinInfo)
{
  int inlineNumber = jsonBinInfo["inlineNumber"].asInt();
  int crosslineNumber = jsonBinInfo["crosslineNumber"].asInt();
  double ensembleXCoordinate = jsonBinInfo["ensembleXCoordinate"].asDouble();
  double ensembleYCoordinate = jsonBinInfo["ensembleYCoordinate"].asDouble();

  return SEGYBinInfo(inlineNumber, crosslineNumber, ensembleXCoordinate, ensembleYCoordinate);
}

SEGYSegmentInfo
segmentInfoFromJson(Json::Value const& jsonSegmentInfo)
{
  int primaryKey = jsonSegmentInfo["primaryKey"].asInt();
  int traceStart = jsonSegmentInfo["traceStart"].asInt();
  int traceStop = jsonSegmentInfo["traceStop"].asInt();
  SEGYBinInfo binInfoStart = binInfoFromJson(jsonSegmentInfo["binInfoStart"]);
  SEGYBinInfo binInfoStop = binInfoFromJson(jsonSegmentInfo["binInfoStop"]);

  return SEGYSegmentInfo(primaryKey, traceStart, traceStop, binInfoStart, binInfoStop);
}

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std::vector<int>
getOrderedSegmentListIndices(SEGYFileInfo const& fileInfo, size_t& globalTotalSegments)
{
  // Generate a list of indices that will traverse m_segyFileInfo.m_segmentInfoLists in primary key order, which
  // may be different from the order that the files were given.

  std::vector<int>
    orderedListIndices;
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  size_t
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    longestList = 0;
  globalTotalSegments = 0;
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  for (size_t i = 0; i < fileInfo.m_segmentInfoLists.size(); ++i)
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  {
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    orderedListIndices.push_back(static_cast<int>(i));
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    globalTotalSegments += fileInfo.m_segmentInfoLists[i].size();
    if (fileInfo.m_segmentInfoLists[i].size() > fileInfo.m_segmentInfoLists[longestList].size())
    {
      longestList = i;
    }
  }
  const bool
    isAscending = fileInfo.m_segmentInfoLists[longestList].front().m_binInfoStart.m_inlineNumber <= fileInfo.m_segmentInfoLists[longestList].back().m_binInfoStart.m_inlineNumber;
  auto
    comparator = [&](int i1, int i2)
  {
    const auto
      & v1 = fileInfo.m_segmentInfoLists[i1],
      & v2 = fileInfo.m_segmentInfoLists[i2];
    return isAscending ? v1.front().m_binInfoStart.m_inlineNumber < v2.front().m_binInfoStart.m_inlineNumber : v2.front().m_binInfoStart.m_inlineNumber < v1.front().m_binInfoStart.m_inlineNumber;
  };
  std::sort(orderedListIndices.begin(), orderedListIndices.end(), comparator);

  return orderedListIndices;
}

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SEGYSegmentInfo const&
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findRepresentativeSegment(SEGYFileInfo const& fileInfo, int& primaryStep, int& bestListIndex)
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{
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  // Since we give more weight to segments near the center of the data we need a sorted index of segment lists so that we can
  // traverse the lists in data order, instead of the arbitrary order given by the filename ordering.
  size_t
    globalTotalSegments = 0;
  auto
    orderedListIndices = getOrderedSegmentListIndices(fileInfo, globalTotalSegments);

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  primaryStep = 0;
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  bestListIndex = 0;
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  float bestScore = 0.0f;
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  size_t bestIndex = 0;
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  int segmentPrimaryStep = 0;
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  size_t
    globalOffset = 0;

  for (const auto listIndex : orderedListIndices)
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  {
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    const auto&
      segmentInfoList = fileInfo.m_segmentInfoLists[listIndex];
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    for (size_t i = 0; i < segmentInfoList.size(); i++)
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    {
      int64_t
        numTraces = (segmentInfoList[i].m_traceStop - segmentInfoList[i].m_traceStart + 1);
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      // index of this segment within the entirety of segments from all input files
      const auto
        globalIndex = globalOffset + i;
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      float
        multiplier = 1.5f - abs(globalIndex - (float)globalTotalSegments / 2) / (float)globalTotalSegments; // give 50% more importance to a segment in the middle of the dataset
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      float
        score = float(numTraces) * multiplier;
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      if (score > bestScore)
      {
        bestScore = score;
        bestListIndex = listIndex;
        bestIndex = i;
      }

      // Updating the primary step with the step for the previous segment intentionally ignores the step of the last segment since it can be anomalous
      if (segmentPrimaryStep && (!primaryStep || std::abs(segmentPrimaryStep) < std::abs(primaryStep)))
      {
        primaryStep = segmentPrimaryStep;
      }

      if (i > 0)
      {
        segmentPrimaryStep = segmentInfoList[i].m_primaryKey - segmentInfoList[i - 1].m_primaryKey;
      }
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    }
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    globalOffset += segmentInfoList.size();
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  }

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  // If the primary step couldn't be determined, set it to the last step or 1
  primaryStep = primaryStep ? primaryStep : std::max(segmentPrimaryStep, 1);

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  return fileInfo.m_segmentInfoLists[bestListIndex][bestIndex];
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}

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void
copySamples(const void* data, SEGY::BinaryHeader::DataSampleFormatCode dataSampleFormatCode, SEGY::Endianness endianness, float* target, int sampleStart, int sampleCount)
{
  if (dataSampleFormatCode == SEGY::BinaryHeader::DataSampleFormatCode::IBMFloat)
  {
    if(endianness == SEGY::Endianness::LittleEndian)
    {
      // Reverse endianness since Ibm2ieee expects big endian data
      const char * source = reinterpret_cast<const char*>((intptr_t)data + (size_t)sampleStart * 4);
      std::unique_ptr<char[]> temp(new char[sampleCount * 4]);
      for(int sample = 0; sample < sampleCount; sample++)
      {
        temp[sample * 4 + 0] = source[sample * 4 + 3];
        temp[sample * 4 + 1] = source[sample * 4 + 2];
        temp[sample * 4 + 2] = source[sample * 4 + 1];
        temp[sample * 4 + 3] = source[sample * 4 + 0];
      }
      SEGY::Ibm2ieee(target, temp.get(), sampleCount);
    }
    else
    {
      assert(endianness == SEGY::Endianness::BigEndian);
      SEGY::Ibm2ieee(target, reinterpret_cast<const uint32_t*>((intptr_t)data + (size_t)sampleStart * 4), sampleCount);
    }
  }
  else
  {
    assert(dataSampleFormatCode == SEGY::BinaryHeader::DataSampleFormatCode::IEEEFloat);
    if(endianness == SEGY::Endianness::LittleEndian)
    {
      SEGY::ConvertFromEndianness<SEGY::Endianness::LittleEndian>(target, reinterpret_cast<const char*>((intptr_t)data + (size_t)sampleStart * 4), sampleCount);
    }
    else
    {
      assert(endianness == SEGY::Endianness::BigEndian);
      SEGY::ConvertFromEndianness<SEGY::Endianness::BigEndian>(target, reinterpret_cast<const char*>((intptr_t)data + (size_t)sampleStart * 4), sampleCount);
    }
  }
}

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bool
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analyzeSegment(DataProvider &dataProvider, SEGYFileInfo const& fileInfo, SEGYSegmentInfo const& segmentInfo, float valueRangePercentile, OpenVDS::FloatRange& valueRange, int& fold, int& secondaryStep, const SEGY::SEGYType segyType, int& offsetStart, int& offsetEnd, int& offsetStep, bool jsonOutput, OpenVDS::Error& error)
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{
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  assert(segmentInfo.m_traceStop >= segmentInfo.m_traceStart && "A valid segment info should always have a stop trace greater or equal to the start trace");
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  bool success = true;
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  valueRange = OpenVDS::FloatRange(0.0f, 1.0f);
  secondaryStep = 0;
  fold = 1;
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  offsetStart = 0;
  offsetEnd = 0;
  offsetStep = 0;
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  const int traceByteSize = fileInfo.TraceByteSize();
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  int64_t traceBufferStart = 0;
  int traceBufferSize = 0;
  std::unique_ptr<char[]> buffer;
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  // Create min/max heaps for determining value range
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  int heapSizeMax = int(((100.0f - valueRangePercentile) / 100.0f) * (segmentInfo.m_traceStop - segmentInfo.m_traceStart + 1) * fileInfo.m_sampleCount / 2) + 1;
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  std::vector<float> minHeap, maxHeap;

  minHeap.reserve(heapSizeMax);
  maxHeap.reserve(heapSizeMax);

  // Allocate sample buffer for converting samples to float
  std::unique_ptr<float[]> sampleBuffer(new float[fileInfo.m_sampleCount]);
  float* samples = sampleBuffer.get();

  // Determine fold and secondary step
  int gatherSecondaryKey = 0, gatherFold = 0, gatherSecondaryStep = 0;

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  bool
    hasPreviousGatherOffset = false;
  int
    previousGatherOffset = 0;

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  for (int64_t trace = segmentInfo.m_traceStart; trace <= segmentInfo.m_traceStop; trace++)
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  {
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    if(trace - traceBufferStart >= traceBufferSize)
    {
      traceBufferStart = trace;
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      traceBufferSize = (segmentInfo.m_traceStop - trace + 1) < 1000 ? int(segmentInfo.m_traceStop - trace + 1) : 1000;
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      buffer.reset(new char[traceByteSize * traceBufferSize]);
      int64_t offset = SEGY::TextualFileHeaderSize + SEGY::BinaryFileHeaderSize + traceByteSize * traceBufferStart;
      success = dataProvider.Read(buffer.get(), offset, traceByteSize * traceBufferSize, error);
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      if (!success)
      {
        break;
      }
    }
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    const void *header = buffer.get() + traceByteSize * (trace - traceBufferStart);
    const void *data   = buffer.get() + traceByteSize * (trace - traceBufferStart) + SEGY::TraceHeaderSize;
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    int tracePrimaryKey = SEGY::ReadFieldFromHeader(header, fileInfo.m_primaryKey, fileInfo.m_headerEndianness);
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    int traceSecondaryKey = fileInfo.IsUnbinned() ? static_cast<int>(trace - segmentInfo.m_traceStart + 1) : SEGY::ReadFieldFromHeader(header, fileInfo.m_secondaryKey, fileInfo.m_headerEndianness);
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    if(tracePrimaryKey != segmentInfo.m_primaryKey)
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    {
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      OpenVDS::printWarning(jsonOutput, "SEGY", fmt::format("trace {} has a primary key that doesn't match with the segment. This trace will be ignored.", segmentInfo.m_traceStart + trace));
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      continue;
    }

    if(gatherFold > 0 && traceSecondaryKey == gatherSecondaryKey)
    {
      gatherFold++;
      fold = std::max(fold, gatherFold);
    }
    else
    {
      // Updating the secondary step with the step for the previous gather intentionally ignores the step of the last gather since it can be anomalous
      if(gatherSecondaryStep && (!secondaryStep || std::abs(gatherSecondaryStep) < std::abs(secondaryStep)))
      {
        secondaryStep = gatherSecondaryStep;
      }
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      if(gatherFold > 0)
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      {
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        gatherSecondaryStep = traceSecondaryKey - gatherSecondaryKey;
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      }
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      gatherSecondaryKey = traceSecondaryKey;
      gatherFold = 1;
    }

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    if (fileInfo.HasGatherOffset())
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    {
      auto
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        thisOffset = SEGY::ReadFieldFromHeader(header, g_traceHeaderFields["offset"], fileInfo.m_headerEndianness);
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      if (hasPreviousGatherOffset)
      {
        offsetStart = std::min(offsetStart, thisOffset);
        offsetEnd = std::max(offsetEnd, thisOffset);
        if (thisOffset != previousGatherOffset)
        {
          offsetStep = std::min(offsetStep, std::abs(thisOffset - previousGatherOffset));
        }
      }
      else
      {
        offsetStart = thisOffset;
        offsetEnd = thisOffset;
        offsetStep = INT32_MAX;
        hasPreviousGatherOffset = true;
      }
      previousGatherOffset = thisOffset;
    }

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    // Update value range
    if (fileInfo.m_dataSampleFormatCode == SEGY::BinaryHeader::DataSampleFormatCode::IBMFloat || fileInfo.m_dataSampleFormatCode == SEGY::BinaryHeader::DataSampleFormatCode::IEEEFloat)
    {
      copySamples(data, fileInfo.m_dataSampleFormatCode, fileInfo.m_headerEndianness, samples, 0, fileInfo.m_sampleCount);
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      for (int sample = 0; sample < fileInfo.m_sampleCount; sample++)
      {
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        if (int(minHeap.size()) < heapSizeMax)
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        {
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          minHeap.push_back(samples[sample]);
          std::push_heap(minHeap.begin(), minHeap.end(), std::less<float>());
        }
        else if (samples[sample] < minHeap[0])
        {
          std::pop_heap(minHeap.begin(), minHeap.end(), std::less<float>());
          minHeap.back() = samples[sample];
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          std::push_heap(minHeap.begin(), minHeap.end(), std::less<float>());
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        }

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        if (int(maxHeap.size()) < heapSizeMax)
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        {
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          maxHeap.push_back(samples[sample]);
          std::push_heap(maxHeap.begin(), maxHeap.end(), std::greater<float>());
        }
        else if (samples[sample] > maxHeap[0])
        {
          std::pop_heap(maxHeap.begin(), maxHeap.end(), std::greater<float>());
          maxHeap.back() = samples[sample];
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          std::push_heap(maxHeap.begin(), maxHeap.end(), std::greater<float>());
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        }
      }
    }
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  }

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  if (fileInfo.HasGatherOffset() && !fileInfo.IsUnbinned())
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  {
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    // check that offset start/end/step is consistent
    if (offsetStart + (fold - 1) * offsetStep != offsetEnd)
    {
      const auto
        msgFormat = "The detected gather offset start/end/step of '{0}/{1}/{2}' is not consistent with the detected fold of '{3}'. This usually indicates using the wrong header format for the input dataset.\n.";
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      error.string = fmt::format(msgFormat, offsetStart, offsetEnd, offsetStep, fold);
      error.code = -1;
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      return false;
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    }
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  }

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  // If the secondary step couldn't be determined, set it to the last step or 1
  secondaryStep = secondaryStep ? secondaryStep : std::max(gatherSecondaryStep, 1);

  // Set value range
  if (!minHeap.empty())
  {
    assert(!maxHeap.empty());
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    if (minHeap[0] != maxHeap[0])
    {
      valueRange = OpenVDS::FloatRange(minHeap[0], maxHeap[0]);
    }
    else
    {
      valueRange = OpenVDS::FloatRange(minHeap[0], minHeap[0] + 1.0f);
    }
  }

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  return success;
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}

bool
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createSEGYMetadata(DataProvider &dataProvider, SEGYFileInfo const &fileInfo, OpenVDS::MetadataContainer& metadataContainer, SEGY::BinaryHeader::MeasurementSystem &measurementSystem, OpenVDS::Error& error)
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{
  std::vector<uint8_t> textHeader(SEGY::TextualFileHeaderSize);
  std::vector<uint8_t> binaryHeader(SEGY::BinaryFileHeaderSize);

  // Read headers
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  bool success = dataProvider.Read(textHeader.data(), 0, SEGY::TextualFileHeaderSize, error) &&
    dataProvider.Read(binaryHeader.data(), SEGY::TextualFileHeaderSize, SEGY::BinaryFileHeaderSize, error);
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  if (!success) return false;

  // Create metadata
  metadataContainer.SetMetadataBLOB("SEGY", "TextHeader", textHeader);

  metadataContainer.SetMetadataBLOB("SEGY", "BinaryHeader", binaryHeader);

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  metadataContainer.SetMetadataInt("SEGY", "Endianness", int(fileInfo.m_headerEndianness));
  metadataContainer.SetMetadataInt("SEGY", "DataSampleFormatCode", int(fileInfo.m_dataSampleFormatCode));
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  measurementSystem = SEGY::BinaryHeader::MeasurementSystem(SEGY::ReadFieldFromHeader(binaryHeader.data(), SEGY::BinaryHeader::MeasurementSystemHeaderField, fileInfo.m_headerEndianness));
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  return success;
}

void
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createSurveyCoordinateSystemMetadata(SEGYFileInfo const& fileInfo, SEGY::BinaryHeader::MeasurementSystem measurementSystem, std::string const &crsWkt, OpenVDS::MetadataContainer& metadataContainer)
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{
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  if (fileInfo.m_segmentInfoLists.empty()) return;
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  double inlineSpacing[2] = { 0, 0 };
  double crosslineSpacing[2] = { 0, 0 };

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  size_t
    globalTotalSegments;
  auto
    orderedListIndices = getOrderedSegmentListIndices(fileInfo, globalTotalSegments);

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  // Determine crossline spacing
  int countedCrosslineSpacings = 0;

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  for (size_t listIndex : orderedListIndices)
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  {
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    const auto
      & segmentInfoList = fileInfo.m_segmentInfoLists[listIndex];
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    for (auto const& segmentInfo : segmentInfoList)
    {
      int crosslineCount = segmentInfo.m_binInfoStop.m_crosslineNumber - segmentInfo.m_binInfoStart.m_crosslineNumber;

      if (crosslineCount == 0 || segmentInfo.m_binInfoStart.m_inlineNumber != segmentInfo.m_binInfoStop.m_inlineNumber) continue;
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      segmentCrosslineSpacing[0] = (segmentInfo.m_binInfoStop.m_ensembleXCoordinate - segmentInfo.m_binInfoStart.m_ensembleXCoordinate) / crosslineCount;
      segmentCrosslineSpacing[1] = (segmentInfo.m_binInfoStop.m_ensembleYCoordinate - segmentInfo.m_binInfoStart.m_ensembleYCoordinate) / crosslineCount;
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      crosslineSpacing[0] += segmentCrosslineSpacing[0];
      crosslineSpacing[1] += segmentCrosslineSpacing[1];
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      countedCrosslineSpacings++;
    }
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  }

  if (countedCrosslineSpacings > 0)
  {
    crosslineSpacing[0] /= countedCrosslineSpacings;
    crosslineSpacing[1] /= countedCrosslineSpacings;
  }
  else
  {
    crosslineSpacing[0] = 0;
    crosslineSpacing[1] = 1;
  }

  // Determine inline spacing
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  SEGYSegmentInfo const& firstSegmentInfo = fileInfo.m_segmentInfoLists[orderedListIndices.front()].front();
  SEGYSegmentInfo const& lastSegmentInfo = fileInfo.m_segmentInfoLists[orderedListIndices.back()].back();
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  if (firstSegmentInfo.m_binInfoStart.m_inlineNumber != lastSegmentInfo.m_binInfoStart.m_inlineNumber)
  {
    int inlineNunberDelta = lastSegmentInfo.m_binInfoStart.m_inlineNumber - firstSegmentInfo.m_binInfoStart.m_inlineNumber;
    int crosslineNunberDelta = lastSegmentInfo.m_binInfoStart.m_crosslineNumber - firstSegmentInfo.m_binInfoStart.m_crosslineNumber;

    double offset[2] = { crosslineSpacing[0] * crosslineNunberDelta,
               crosslineSpacing[1] * crosslineNunberDelta };

    inlineSpacing[0] = (lastSegmentInfo.m_binInfoStart.m_ensembleXCoordinate - firstSegmentInfo.m_binInfoStart.m_ensembleXCoordinate - offset[0]) / inlineNunberDelta;
    inlineSpacing[1] = (lastSegmentInfo.m_binInfoStart.m_ensembleYCoordinate - firstSegmentInfo.m_binInfoStart.m_ensembleYCoordinate - offset[1]) / inlineNunberDelta;
  }
  else
  {
    // make square voxels
    inlineSpacing[0] = crosslineSpacing[1];
    inlineSpacing[1] = -crosslineSpacing[0];
  }

  // Determine origin
  double origin[2];

  origin[0] = firstSegmentInfo.m_binInfoStart.m_ensembleXCoordinate;
  origin[1] = firstSegmentInfo.m_binInfoStart.m_ensembleYCoordinate;

  origin[0] -= inlineSpacing[0] * firstSegmentInfo.m_binInfoStart.m_inlineNumber;
  origin[1] -= inlineSpacing[1] * firstSegmentInfo.m_binInfoStart.m_inlineNumber;

  origin[0] -= crosslineSpacing[0] * firstSegmentInfo.m_binInfoStart.m_crosslineNumber;
  origin[1] -= crosslineSpacing[1] * firstSegmentInfo.m_binInfoStart.m_crosslineNumber;

  // Set coordinate system
  metadataContainer.SetMetadataDoubleVector2(LATTICE_CATEGORY, LATTICE_ORIGIN, OpenVDS::DoubleVector2(origin[0], origin[1]));
  metadataContainer.SetMetadataDoubleVector2(LATTICE_CATEGORY, LATTICE_INLINE_SPACING, OpenVDS::DoubleVector2(inlineSpacing[0], inlineSpacing[1]));
  metadataContainer.SetMetadataDoubleVector2(LATTICE_CATEGORY, LATTICE_CROSSLINE_SPACING, OpenVDS::DoubleVector2(crosslineSpacing[0], crosslineSpacing[1]));
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  if(!crsWkt.empty())
  {
    metadataContainer.SetMetadataString(LATTICE_CATEGORY, CRS_WKT, crsWkt);