/*
//
//  Copyright 2014, 2019 Google LLC
//
//  Copyright 1997-2012 Torsten Rohlfing
//
//  Copyright 2004-2014 SRI International
//
//  This file is part of the Computational Morphometry Toolkit.
//
//  http://www.nitrc.org/projects/cmtk/
//
//  The Computational Morphometry Toolkit 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.
//
//  The Computational Morphometry Toolkit 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 the Computational Morphometry Toolkit.  If not, see
//  <http://www.gnu.org/licenses/>.
//
//  $Revision: 5441 $
//
//  $LastChangedDate: 2019-01-24 20:23:24 -0800 (Thu, 24 Jan 2019) $
//
//  $LastChangedBy: torstenrohlfing $
//
*/

#include <cmtkconfig.h>

#include <System/cmtkConsole.h>
#include <System/cmtkDebugOutput.h>
#include <System/cmtkCommandLine.h>
#include <System/cmtkStrUtility.h>
#include <System/cmtkExitException.h>

#include <Base/cmtkMetaInformationObject.h>

#include <IO/cmtkImageFileDICOM.h>
#include <IO/cmtkImageStackDICOM.h>

#ifndef CMTK_USE_DCMTK
#error Build system is broken: this application should not be build if CMTK_USE_DCMTK is not set.
#endif

#ifdef _MSC_VER
#  include <windows.h>
#else
#  include <dirent.h>
#  include <fnmatch.h>
#  include <unistd.h>
#endif

#include <ctype.h>

#include <sys/types.h>
#include <sys/stat.h>

#include <vector>
#include <map>
#include <algorithm>
#include <string>
#include <sstream>

#include <iostream>
#include <fstream>

#include <dcmtk/dcmdata/dctk.h>

void
AddPatternToMap( std::map<DcmTagKey,std::string>& map, const char* pattern )
{
  const char* equals = strchr( pattern, '=' );
  if ( equals )
    {
    const std::string tagName( pattern, static_cast<size_t>( equals-pattern ) );

    const DcmDictEntry* dictEntry = dcmDataDict.rdlock().findEntry( tagName.c_str() );
#if PACKAGE_VERSION_NUMBER < 364
    dcmDataDict.unlock();
#else
    dcmDataDict.rdunlock();
#endif

    if ( dictEntry )
      {
      map.insert( std::pair<DcmTagKey,std::string>( dictEntry->getKey(), equals+1 ) );      
      }
    else
      {
      cmtk::StdErr << "WARNING: DCMTK data dictionary does not have a tag entry named '" << tagName << "' - ignoring this\n";
      }
    }
}

// Map of file includion patterns
std::map<DcmTagKey,std::string> IncludePatterns;

void
CallbackAddInclude( const char* pattern )
{
  AddPatternToMap( IncludePatterns, pattern );
}

// Map of file exclusion patterns
std::map<DcmTagKey,std::string> ExcludePatterns;

void
CallbackAddExclude( const char* pattern )
{
  AddPatternToMap( ExcludePatterns, pattern );
}

const char* OutPathPattern = "image%n.nii";
std::vector<std::string> SearchRootDirVector;

std::ofstream cnull( "/dev/null" );

bool Progress = true;
bool Recursive = false;

/// Enum type to select sort order key.
typedef enum
{
  /// No sorting - take files in order stored in file system.
  SORT_NONE = 0,
  /// Sort by file name.
  SORT_FILENAME = 1,
  /// Sort by instance number.
  SORT_INSTANCE_NUMBER = 2
} SortKeyEnum;

SortKeyEnum SortFiles = SORT_INSTANCE_NUMBER;

bool WriteXML = false;
bool IncludeIdentifiers = false;

bool WriteSingleSlices = false;

bool DisableOrientationCheck = false;
double Tolerance = 1e-5;

bool IgnoreAcquisitionNumber = false;

using cmtk::ImageFileDICOM;
using cmtk::ImageStackDICOM;

/// Selector for embedded image information.
ImageStackDICOM::EmbedInfoEnum EmbedInfo = ImageStackDICOM::EMBED_NONE;

/// Class handling a list of image stacks, i.e., volumes.
class VolumeList : 
  public std::vector<ImageStackDICOM::SmartPtr> 
{
public:
  /// This class.
  typedef VolumeList Self;

  /// Constructor.
  VolumeList( const cmtk::Types::Coordinate tolerance = 0 /*!< Tolerance for floating point comparisons, e.g., when testing for uniform pixel/slice spacings.*/ ) : m_Tolerance( tolerance ) {}

  /// Build a volume list by traversing a directory.
  void AppendFromDirectory( const std::string& path, const char *wildcard );
  
  /** Write all volumes in this list.
   *\return Return code - 0, no problems; 3, at least one volume was not written correctly (e.g., due to non-uniform slice spacing).
   */
  int WriteVolumes();

private:
  /// Stored floating point tolerance.
  cmtk::Types::Coordinate m_Tolerance;
  
  /// Add a new image file to the correct stack or create a new stack.
  void AddImageFile( ImageFileDICOM::SmartConstPtr& newImage );
};

std::string
PutNumberAndSanitize( const std::string& path, const std::string& numberString )
{
  if ( numberString.empty() )
    return cmtk::StrReplace( cmtk::StrReplace( path, "%n", "" ), "%N", "" );
  else
    return cmtk::StrReplace( cmtk::StrReplace( path, "%n", numberString ), "%N", "-" + numberString );
}

int
VolumeList::WriteVolumes() 
{
  int returnCode = 0;
  
  size_t cntSingleImages = 0;

  std::map<std::string,Self> pathToVolumeMap;
  for ( const_iterator it = this->begin(); it != this->end(); ++it ) 
    {
    if ( ((*it)->size() > 1) || (*(*it)->begin())->m_IsMultislice || WriteSingleSlices )
      {
      // replace place holders
      std::string path( OutPathPattern );
      path = cmtk::StrReplace( path, "%D", cmtk::StrMakeLegalInPath( (*it)[0][0]->GetTagValue( DCM_SeriesDescription ) ) );
      path = cmtk::StrReplace( path, "%R", cmtk::StrMakeLegalInPath( (*it)[0][0]->GetTagValue( DCM_RepetitionTime ) ) );
      path = cmtk::StrReplace( path, "%E", cmtk::StrMakeLegalInPath( (*it)[0][0]->GetTagValue( DCM_EchoTime ) ) );
      path = cmtk::StrReplace( path, "%T", (*it)[0][0]->m_RawDataType );

      // replace %0 with file name
      path = cmtk::StrReplace( path, "%0", (*it)[0][0]->m_FileName );

      // and replace %1 through %9 with directory components of decreasing depth
      char replaceThis[3] = { '%', '0', 0 }; // this will be modified to be the current replacement
      std::string directory = (*it)[0][0]->m_FileDir; // start with full directory
      for ( size_t dirIdx = 1; (dirIdx < 10) && !directory.empty(); ++dirIdx )
	{
	replaceThis[1] = '0' + dirIdx;
	const size_t lastSlash = directory.rfind( CMTK_PATH_SEPARATOR );
	if ( lastSlash == std::string::npos )
	  {
	  path = cmtk::StrReplace( path, replaceThis, directory );
	  directory.clear();
	  }
	else
	  {
	  path = cmtk::StrReplace( path, replaceThis, directory.substr( lastSlash+1 ) );
	  directory = directory.substr( 0, lastSlash );

	  // trim trailing slashes, both forward and back
	  const size_t lastNotSlash = directory.find_last_not_of( "/\\" );
	  if ( lastNotSlash != std::string::npos )
	    {
	    directory.erase( lastNotSlash+1 );
	    }
	  else
	    {
	    directory.clear();
	    }
	  }
	}
      
      if ( path.length() > PATH_MAX )
	cmtk::StdErr << "ERROR: output path exceeds maximum path length";
      else
	pathToVolumeMap[path].push_back( *it );
      }
    else
      {
      ++cntSingleImages;
      }
    }

  if ( cntSingleImages )
    {
    cmtk::DebugOutput( 1 ) << "\n====================================================\n";
    cmtk::DebugOutput( 1 ) << "WARNING: " << cntSingleImages << " single image(s) could not be assigned to multi-image stacks:\n\n";
    for ( const_iterator it = begin(); it != end(); ++it ) 
      {
      if ( ((*it)->size() == 1) && !(*(*it)->begin())->m_IsMultislice )
	{
	(*(*it))[0]->Print();
	cmtk::DebugOutput( 1 ) << "\n";
	}
      }
    cmtk::DebugOutput( 1 ) << "\n====================================================\n";
    }
  
  for ( std::map<std::string,Self>::const_iterator it = pathToVolumeMap.begin(); it != pathToVolumeMap.end(); ++it )
    {						
    const size_t nVolumes = it->second.size();

    // if there is only one volume with the given output path, just write it
    if ( nVolumes == 1 )
      {					       
      // if there's a "number" tag, get rid of it.
      std::string uniquePath = PutNumberAndSanitize( it->first, "" );

      cmtk::UniformVolume::SmartConstPtr volume = it->second[0]->WriteImage( uniquePath.c_str(), EmbedInfo );

      if ( volume )
	{
	if ( WriteXML )
	  {
	  it->second[0]->WriteXML( (uniquePath+".xml").c_str(), *volume, IncludeIdentifiers );
	  }
	}
      else
	{
	returnCode = 3;
	}
      }
    else
      {			
      // otherwise, make unique paths for each of them
      for ( size_t i = 0; i < nVolumes; ++i )
	{
	std::ostringstream numberString;
	numberString.width( 1 + static_cast<int>( log( (double)nVolumes ) / M_LN10 ) );
	numberString.fill( '0' );
	numberString << std::right << 1+i;

	std::string uniquePath = PutNumberAndSanitize( it->first, numberString.str() );

	cmtk::UniformVolume::SmartConstPtr volume = it->second[i]->WriteImage( uniquePath.c_str(), EmbedInfo );

	if ( volume) 
	  {
	  if ( WriteXML )
	    {
	    it->second[i]->WriteXML( (uniquePath + ".xml").c_str(), *volume, IncludeIdentifiers );
	    }
	  }
	else
	  {
	  returnCode = 3;
	  }
	}
      }
    }

  return returnCode;
}


void
VolumeList::AddImageFile( ImageFileDICOM::SmartConstPtr& newImage )
{
  if ( !empty() ) 
    {
    const_iterator it = this->begin();
    while ( it != this->end() ) 
      {
      ImageStackDICOM::SmartPtr study = *it;
      if ( study->Match( *newImage, this->m_Tolerance, DisableOrientationCheck, IgnoreAcquisitionNumber) ) 
	{
	study->AddImageFile( newImage );
	return;
	} 
      else 
	{
	++it;
	}
      }
    }    

  ImageStackDICOM::SmartPtr newImageStack( new ImageStackDICOM( this->m_Tolerance ) );
  newImageStack->AddImageFile( newImage );
  push_back( newImageStack );    
}
  
void
VolumeList::AppendFromDirectory( const std::string& path, const char *wildcard )
{
  std::vector<ImageFileDICOM::SmartConstPtr> fileList;

#ifdef _MSC_VER
  static int progress = 0;
  const char progress_chars[] = "-\\|/";

  WIN32_FIND_DATA fData;
  const std::string pattern = path + "\\" + wildcard;
  HANDLE hFind = FindFirstFile( pattern.c_str(), &fData);
  do
    {
    const std::string fullname = path + "\\" + fData.cFileName;
    if ( fData.dwFileAttributes & FILE_ATTRIBUTE_DIRECTORY )
      {
      if ( Recursive && (fData.cFileName[0] != '.') )
	{
	this->AppendFromDirectory( fullname, wildcard );
	}
      }
    else
      {
      try
	{
	ImageFileDICOM::SmartPtr newFile( new ImageFileDICOM( fullname ) );

	if ( newFile->MatchAllPatterns( IncludePatterns ) && !newFile->MatchAnyPattern( ExcludePatterns ) )
	  {
	  newFile->ReleaseDocument();
	  fileList.push_back( newFile );
	  }

	if ( Progress )
	  {
	  (cmtk::StdErr << "\r" << progress_chars[ ++progress % 4 ]).flush();
	  }
	}
      catch ( ... )
	{
	// not a valid DICOM file
	}
      }
    }
  while (FindNextFile(hFind, &fData) != 0);
#else    
  DIR *dir_pointer = opendir ( path.c_str() );
  if ( dir_pointer != NULL ) 
    {
    static int progress = 0;
    const char progress_chars[] = "-\\|/";
    struct dirent *entry_pointer;

    while ( (entry_pointer = readdir(dir_pointer)) ) 
      {
      const std::string fullname = path + "/" + entry_pointer->d_name;

      struct stat entry_status;
      if ( !stat(fullname.c_str(), &entry_status) ) 
	{
	if ( S_ISDIR( entry_status.st_mode ) && Recursive && (entry_pointer->d_name[0] != '.') ) 
	  {
	  this->AppendFromDirectory( fullname + "/" , wildcard );
	  } 
	else
	  {
	  if ( !fnmatch(wildcard,entry_pointer->d_name,FNM_PERIOD) ) 
	    {
	    try
	      {
	      ImageFileDICOM::SmartPtr newFile( new ImageFileDICOM( fullname ) );
	      
	      if ( newFile->MatchAllPatterns( IncludePatterns ) && !newFile->MatchAnyPattern( ExcludePatterns ) )
		{
		newFile->ReleaseDocument();
		fileList.push_back( newFile );
		}
	      
	      if ( Progress )
		{
		(cmtk::StdErr << "\r" << progress_chars[ ++progress % 4 ]).flush();
		}
	      }
	    catch ( ... )
	      {
	      // not a valid DICOM file
	      }
	    }
	  }
	}
      }
    (void) closedir(dir_pointer);
    }
#endif

  switch ( SortFiles )
    {
    case SORT_NONE:
    default:
      break;
    case SORT_FILENAME:
      std::sort( fileList.begin(), fileList.end(), ImageFileDICOM::lessFileName );
      break;
    case SORT_INSTANCE_NUMBER:
      std::sort( fileList.begin(), fileList.end(), ImageFileDICOM::lessInstanceNumber );
      break;
    }
  
  for ( std::vector<ImageFileDICOM::SmartConstPtr>::iterator it = fileList.begin(); it != fileList.end(); ++it )
    {
    try 
      {
      this->AddImageFile( *it );
      }
    catch (int)
      {
      }
    }

  if ( Progress )
    {
    cmtk::StdErr << "\r";
    }
}


int
doMain ( const int argc, const char *argv[] )
{
  if (! dcmDataDict.isDictionaryLoaded() ) 
    {
#ifdef CMTK_DCMDICTPATH
    if ( dcmDataDict.wrlock().loadDictionary( CMTK_DCMDICTPATH ) )
      {
#if PACKAGE_VERSION_NUMBER < 364
      dcmDataDict.unlock();
#else
      dcmDataDict.wrunlock();
#endif
      }
    else
#endif
#ifdef CMTK_DCMDICTPATH_INSTALL
    if ( dcmDataDict.wrlock().loadDictionary( CMTK_DCMDICTPATH_INSTALL ) )
      {
#if PACKAGE_VERSION_NUMBER < 364
      dcmDataDict.unlock();
#else
      dcmDataDict.wrunlock();
#endif
      }
    else
#endif
      {
      cmtk::StdErr << "Data dictionary not avaliable. Please set DCMDICTPATH variable as path to dicom.dic file.\n";
      throw cmtk::ExitException( 1 );
      }
    }

  try
    {
    cmtk::CommandLine cl;
    cl.SetProgramInfo( cmtk::CommandLine::PRG_TITLE, "DICOM to Image" );
    cl.SetProgramInfo( cmtk::CommandLine::PRG_DESCR, "Combine sets of DICOM slices to 3D image stacks" );

    typedef cmtk::CommandLine::Key Key;
    cl.AddSwitch( Key( "no-progress" ), &Progress, false, "Disable progress reporting." );

    cl.BeginGroup( "Input", "Input Options");
    cl.AddSwitch( Key( 'r', "recurse" ), &Recursive, true, "Recurse into directories" );
    cl.EndGroup();

    cl.BeginGroup( "Output", "Output Options");
    cl.AddOption( Key( 'O', "out-pattern" ), &OutPathPattern, "Output image path pattern. Use the following substitutions: "
		  "printf-style %d variante (image number); "
		  "%n (image number with automatic number of digits); "
		  "%N (like %n, but with a hyphen '-' before number if there is more than one image); "
		  "%D (DICOM SeriesDescription); "
		  "%R (DICOM RepetitionTime - MRI only); "
		  "%E (DICOM EchoTime - MRI only); "
		  "%T (RawDataType - vendor-specific, currently GE MRI only)" );

    cl.AddSwitch( Key( 'x', "xml" ), &WriteXML, true, "Write XML sidecar file for each created image." );
    cl.AddSwitch( Key( "include-identifiers" ), &IncludeIdentifiers, true, "Include potentially protected identifying information (e.g., UIDs, device serial numbers, dates) in the created XML sidecar files." );

    cmtk::CommandLine::EnumGroup<cmtk::ImageStackDICOM::EmbedInfoEnum>::SmartPtr embedGroup = cl.AddEnum( "embed", &EmbedInfo, "Embed DICOM information into output images as 'description' (if supported by output file format)." );
    embedGroup->AddSwitch( Key( "StudyID_StudyDate" ), cmtk::ImageStackDICOM::EMBED_STUDYID_STUDYDATE, "StudyID, tag (0020,0010), then underscore, followed by StudyDate, tag (0008,0020). "
			   "Date is appended because StudyID is four digits only and will repeat sooner or later." );
    embedGroup->AddSwitch( Key( "PatientName" ), cmtk::ImageStackDICOM::EMBED_PATIENTNAME, "Patient name, tag (0010,0010)" );
    embedGroup->AddSwitch( Key( "SeriesDescription" ), cmtk::ImageStackDICOM::EMBED_SERIESDESCR, "Series description, tag (0008,103e)" );
    embedGroup->AddSwitch( Key( "None" ), cmtk::ImageStackDICOM::EMBED_NONE, "Embed no information - leave 'description' field empty." );
    cl.EndGroup();

    cl.BeginGroup( "Filtering", "Filtering Options")->SetProperties( cmtk::CommandLine::PROPS_ADVANCED );
    cl.AddCallback( Key( "filter" ), &CallbackAddInclude, "Filter DICOM files and include only those matching the given pattern of the form 'TagName=text', such that the value of the DICOM tag with the given name contains the given "
		    "text. If multiple filter patterns are provided via repeated use of this option, only files that match ALL patterns are included." );
    cl.AddCallback( Key( "exclude" ), &CallbackAddExclude, "Exclude all DICOM files matching the given pattern of the form 'TagName=text', such that the value of the DICOM tag with the given name contains the given text. "
      "If multiple exclusion patterns are provided, all files are excluded that match ANY of the patterns." );
    cl.EndGroup();

    cl.BeginGroup( "Sorting", "Sorting Options")->SetProperties( cmtk::CommandLine::PROPS_ADVANCED );
    cl.AddSwitch( Key( "no-sort" ), &SortFiles, SORT_NONE, "Do NOT sort files by file name (sorting determines image stack order when resolving spatial collisions)" );
    cl.AddSwitch( Key( "sort-by-name" ), &SortFiles, SORT_FILENAME, "Sort files lexicographically by file name. Use this when instance numbers are non-unique." );
    cl.AddSwitch( Key( "sort-by-instance" ), &SortFiles, SORT_INSTANCE_NUMBER, "Sort files by image instance number. Use this when file names are different lengths, etc." );
    cl.EndGroup();

    cl.BeginGroup( "Stacking", "Stacking Options")->SetProperties( cmtk::CommandLine::PROPS_ADVANCED );
    cl.AddSwitch( Key( "write-single-slices" ), &WriteSingleSlices, true, "Also write output images for single-slice DICOM files that could not be assigned to any 3D stacks. By default, these are skipped." );
    cl.AddSwitch( Key( "ignore-acq-number" ), &IgnoreAcquisitionNumber, true, "Ignore 'AcquisitionNumber' tag for image grouping, i.e., do not separate stacks based on this tag." );
    cl.AddSwitch( Key( "no-orientation-check" ), &DisableOrientationCheck, true, "Disable checking of image orientations (to avoid rounding issues)" );
    cl.AddOption( Key( "tolerance" ), &Tolerance, "Tolerance for floating-point comparisons (must be >= 0; 0 = exact matches only; default: 1e-5). "
		  "If one or more volumes cannot be stacked because of non-uniform slice spacing that exceeds this threshold, dcm2image will return an exit code of 3." );
    cl.EndGroup();

    cl.AddParameterVector( &SearchRootDirVector, "SearchDirList", "List of directories to search for DICOM files. Subdirectories are also search if '--recurse' option is used." );
    
    cl.Parse( argc, const_cast<const char**>( argv ) );
    }
  catch ( const cmtk::CommandLine::Exception& ex )
    {
    cmtk::StdErr << ex << "\n";
    throw cmtk::ExitException( 1 );
    }
  
  if ( !dcmDataDict.rdlock().findEntry( "RawDataType_ImageType" ) )
    {
#if PACKAGE_VERSION_NUMBER < 364
    dcmDataDict.unlock();
#else
    dcmDataDict.rdunlock();
#endif
    dcmDataDict.wrlock().addEntry( new DcmDictEntry( 0x0043, 0x102f, EVR_SS, "RawDataType_ImageType", 1, 1, NULL, OFFalse, "GE" ) );
#if PACKAGE_VERSION_NUMBER < 364
    dcmDataDict.unlock();
#else
    dcmDataDict.wrunlock();
#endif
    }
  
  VolumeList volumeList( Tolerance );
  for ( std::vector<std::string>::const_iterator it = SearchRootDirVector.begin(); it != SearchRootDirVector.end(); ++it )
    {
    volumeList.AppendFromDirectory( *it, "*" );
    }
  
  return volumeList.WriteVolumes();
}

#include "cmtkSafeMain"