/*=========================================================================

  Program: DICOM for VTK

  Copyright (c) 2012-2024 David Gobbi
  All rights reserved.
  See Copyright.txt or http://dgobbi.github.io/bsd3.txt for details.

     This software is distributed WITHOUT ANY WARRANTY; without even
     the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR
     PURPOSE.  See the above copyright notice for more information.

=========================================================================*/

#include "vtkDICOMConfig.h"
#include "vtkDICOMParser.h"
#include "vtkDICOMDictionary.h"
#include "vtkDICOMDirectory.h"
#include "vtkDICOMMetaData.h"
#include "vtkDICOMItem.h"
#include "vtkDICOMUtilities.h"

// from dicomcli
#include "vtkConsoleOutputWindow.h"
#include "mainmacro.h"
#include "readquery.h"

#include "vtkSortFileNames.h"
#include "vtkStringArray.h"
#include "vtkSmartPointer.h"

#include <stdio.h>
#include <string.h>
#include <stdlib.h>

#define MAX_INDENT 24
#define INDENT_SIZE 2
#define MAX_LENGTH 120

// print the version
void printVersion(FILE *file, const char *cp)
{
  fprintf(file, "%s %s\n", cp, DICOM_VERSION);
  fprintf(file, "\n"
    "Copyright (c) 2012-2024, David Gobbi.\n\n"
    "This software is distributed under an open-source license.  See the\n"
    "Copyright.txt file that comes with the vtk-dicom source distribution.\n");
}

// print the usage
void printUsage(FILE *file, const char *cp)
{
  fprintf(file, "usage:\n"
    "  %s file1.dcm [file2.dcm ...]\n\n", cp);
  fprintf(file, "options:\n"
    "  -k tag          Provide a tag or key to be printed.\n"
    "  -q <query.txt>  Provide a file that lists which elements to print.\n"
    "  --charset <cs>  Charset to use if SpecificCharacterSet is missing.\n"
    "  --help          Print a brief help message.\n"
    "  --version       Print the software version.\n");
}

// print the help
void printHelp(FILE *file, const char *cp)
{
  printUsage(file, cp);
  fprintf(file, "\n"
    "Dump the metadata from a set of DICOM files as text.\n"
    "\n"
    "By default, all the attributes are dumped.  However, If only a few\n"
    "attributes are to be dumped, then their tags can be given with \"-k\"\n"
    "(the \"-k\" option can be repeated as many times as needed).  Tags can\n"
    "be given in hexadecimal GGGG,EEEE format, or in text format as specified\n"
    "in the DICOM dictionary key.  Alternatively, the tags can be listed in\n"
    "a query file given with the \"-q\" option (one tag per line).\n"
    "Attributes nested within sequences can be specified by giving a tag\n"
    "path e.g. \"-k Tag1/Tag2/Tag3\".  Either a forward slash or a backslash\n"
    "can be used to separate the components of the path.\n"
    "\n"
    "For text attribute values, any unprintable bytes will be replaced with\n"
    "the four characters \"\\nnn\", where \"nnn\" is the three digit octal code\n"
    "for the byte.  Unprintable bytes are control characters or bytes that\n"
    "cannot be decoded with the SpecificCharacterSet of the DICOM file.  A\n"
    "backslash itself will be replaced by its byte value \"\\134\" if the VR is\n"
    "ST, LT or UT (that is, any VR where backslash isn't used as a separator\n"
    "for multi-valued attributes).\n\n");
}

// remove path portion of filename
const char *fileBasename(const char *filename)
{
  const char *cp = filename + strlen(filename);
  while (cp != filename && cp[-1] != '\\' && cp[-1] != '/') { --cp; }
  return cp;
}

// Print out one data element
void printElement(
  vtkDICOMMetaData *meta, const vtkDICOMItem *item,
  const vtkDICOMDataElementIterator &iter, int depth,
  unsigned int pixelDataVL)
{
  vtkDICOMTag tag = iter->GetTag();
  int g = tag.GetGroup();
  int e = tag.GetElement();
  vtkDICOMVR vr = iter->GetVR();
  const char *name = "";
  vtkDICOMDictEntry d;
  if (item)
  {
    d = item->FindDictEntry(tag);
  }
  else if (meta)
  {
    d = meta->FindDictEntry(tag);
  }
  if (d.IsValid())
  {
    name = d.GetName();
    if (d.GetVR() != vr &&
        !(d.GetVR() == vtkDICOMVR::XS &&
          (vr == vtkDICOMVR::SS || vr == vtkDICOMVR::US)) &&
        !(d.GetVR() == vtkDICOMVR::OX &&
          (vr == vtkDICOMVR::OB || vr == vtkDICOMVR::OW)))
    {
      printf("VR mismatch! %s != %s %s\n",
             vr.GetText(), d.GetVR().GetText(), name);
    }
  }
  else if ((tag.GetGroup() & 0xFFFE) != 0 && tag.GetElement() == 0)
  {
    // group is even, element is zero
    name = "GroupLength";
  }
  else if ((tag.GetGroup() & 0x0001) != 0 &&
           (tag.GetElement() & 0xFF00) == 0)
  {
    // group is odd, element is a creator element
    name = "PrivateCreator";
  }
  // allow multiple values (i.e. for each image in series)
  vtkDICOMValue v = iter->GetValue();
  size_t vn = v.GetNumberOfValues();
  const vtkDICOMValue *vp = v.GetMultiplexData();
  if (vp == nullptr)
  {
    vp = &v;
    vn = 1;
  }

  // make an indentation string
  if (INDENT_SIZE*depth > MAX_INDENT)
  {
    depth = MAX_INDENT/INDENT_SIZE;
  }
  static const char spaces[MAX_INDENT+1] = "                        ";
  const char *indent = spaces + (MAX_INDENT - INDENT_SIZE*depth);

  for (size_t vi = 0; vi < vn; vi++)
  {
    v = vp[vi];
    unsigned int vl = v.GetVL();
    if (tag == DC::PixelData ||
        tag == DC::FloatPixelData ||
        tag == DC::DoubleFloatPixelData)
    {
      vl = (depth == 0 && vl == 0 ? pixelDataVL : v.GetVL());
    }
    std::string s;
    if (vr == vtkDICOMVR::UN ||
        vr == vtkDICOMVR::SQ)
    {
      // sequences are printed later
      s = (vl > 0 ? "..." : "");
    }
    else if (vr == vtkDICOMVR::LT ||
             vr == vtkDICOMVR::ST ||
             vr == vtkDICOMVR::UT)
    {
      vtkDICOMCharacterSet cs = v.GetCharacterSet();
      const char *cp = v.GetCharData();
      size_t l = vl;
      bool truncated = false;
      while (l > 0 && cp[l-1] == ' ')
      {
        l--;
      }
      if (l > MAX_LENGTH)
      {
        l = MAX_LENGTH;
        truncated = true;
      }
      std::string utf8 = cs.ToSafeUTF8(cp, l);
      cp = utf8.data();
      l = utf8.length();
      if (l > MAX_LENGTH)
      {
        l = MAX_LENGTH-3;
        truncated = true;
        // remove possibly incomplete final character
        while (l > 1 && (cp[l-1] & 0xC0) == 0x80)
        {
          l--;
        }
        l--;
      }
      s.append(cp, l);
      if (truncated)
      {
        s.append("...");
      }
    }
    else if (vr.HasTextValue())
    {
      vtkDICOMCharacterSet cs = v.GetCharacterSet();
      const char *cp = v.GetCharData();
      const char *ep = cp + vl;
      size_t pos = 0;
      while (cp != ep && *cp != '\0')
      {
        size_t n = cs.NextBackslash(cp, ep);
        while (n > 0 && *cp == ' ') { cp++; n--; }
        size_t m = n;
        while (m > 0 && cp[m-1] == ' ') { m--; }
        s.append(cs.ToSafeUTF8(cp, m));
        cp += n;
        if (cp != ep && *cp == '\\')
        {
          s.append(cp, 1);
          cp++;
        }
        if (s.size() > MAX_LENGTH-4)
        {
          s.resize(pos);
          s.append("...");
          break;
        }
        pos = s.size();
      }
    }
    else
    {
      // print any other VR via conversion to string
      size_t n = v.GetNumberOfValues();
      size_t pos = 0;
      for (size_t i = 0; i < n; i++)
      {
        v.AppendValueToString(s, i);
        if (i < n - 1)
        {
          s.append("\\");
        }
        if (s.size() > MAX_LENGTH-4)
        {
          s.resize(pos);
          s.append("...");
          break;
        }
        pos = s.size();
      }
    }

    if (meta && vi == 0)
    {
      printf("%s(%04X,%04X) %s \"%s\" :", indent, g, e, vr.GetText(), name);
    }
    if (meta && vn > 1)
    {
      printf("%s%s  %4.4u",
        (vi == 0 ? " (multiple values)\n" : ""), indent,
        static_cast<unsigned int>(vi + 1));
    }
    if (vr == vtkDICOMVR::SQ)
    {
      size_t m = v.GetNumberOfValues();
      const vtkDICOMItem *items = v.GetSequenceData();
      printf(" (%u %s%s)\n",
        static_cast<unsigned int>(m), (m == 1 ? "item" : "items"),
        (vl == 0xffffffffu ? ", delimited" : ""));
      for (size_t j = 0; j < m; j++)
      {
        printf("%s%s---- SQ Item %04u at offset %u ----\n",
          indent, spaces+(MAX_INDENT - INDENT_SIZE),
          static_cast<unsigned int>(j+1),
          items[j].GetByteOffset());
        vtkDICOMDataElementIterator siter = items[j].Begin();
        vtkDICOMDataElementIterator siterEnd = items[j].End();

        for (; siter != siterEnd; ++siter)
        {
          printElement(meta, &items[j], siter, depth+1, pixelDataVL);
        }
      }
    }
    else if (vl == 0xffffffffu)
    {
      if (tag == DC::PixelData ||
          tag == DC::FloatPixelData ||
          tag == DC::DoubleFloatPixelData)
      {
        printf(" [...] (compressed)\n");
      }
      else
      {
        printf(" [...] (delimited)\n");
      }
    }
    else
    {
      const char *uidName = "";
      if (vr == vtkDICOMVR::UI)
      {
        uidName = vtkDICOMUtilities::GetUIDName(s.c_str());
      }
      if (uidName[0] != '\0')
      {
        printf(" [%s] {%s} (%u bytes)\n", s.c_str(), uidName, vl);
      }
      else if (vr == vtkDICOMVR::OB ||
               vr == vtkDICOMVR::OW ||
               vr == vtkDICOMVR::OF ||
               vr == vtkDICOMVR::OD)
      {
        printf(" [%s] (%u bytes)\n", (vl == 0 ? "" : "..."), vl);
      }
      else
      {
        printf(" [%s] (%u bytes)\n", s.c_str(), vl);
      }
    }
  }
}

void printElementFromTagPathRecurse(
  const vtkDICOMItem *item, const vtkDICOMTagPath& tagPath,
  const vtkDICOMTagPath& fullPath, int *count)
{
  vtkDICOMTag tag = tagPath.GetHead();

  vtkDICOMDataElementIterator iter = item->Begin();
  while (iter != item->End() && iter->GetTag() != tag)
  {
    ++iter;
  }

  if (iter != item->End())
  {
    if (tagPath.HasTail())
    {
      const vtkDICOMItem *items = iter->GetValue().GetSequenceData();
      if (items)
      {
        size_t n = iter->GetValue().GetNumberOfValues();
        for (size_t i = 0; i < n; i++)
        {
          printElementFromTagPathRecurse(
            &items[i], tagPath.GetTail(), fullPath, count);
        }
      }
    }
    else
    {
      ++(*count);
      fprintf(stdout, "  %04d", *count);
      printElement(nullptr, item, iter, 0, 0);
    }
  }
}

void printElementFromTagPath(
  vtkDICOMMetaData *data, const vtkDICOMTagPath& tagPath,
  unsigned int pixelDataVL)
{
  int count = 0;
  vtkDICOMTag tag = tagPath.GetHead();
  vtkDICOMDataElementIterator iter = data->Find(tag);
  if (iter != data->End())
  {
    if (tagPath.HasTail())
    {
      for (vtkDICOMTagPath p = tagPath; ; p = p.GetTail())
      {
        int g = p.GetHead().GetGroup();
        int e = p.GetHead().GetElement();
        if (p.HasTail())
        {
          printf("(%04X,%04X)\\", g, e);
        }
        else
        {
          vtkDICOMDictEntry entry =
            vtkDICOMDictionary::FindDictEntry(p.GetHead());
          vtkDICOMVR vr = entry.GetVR();
          const char *name = entry.GetName();
          name = ((name && name[0]) ? name : "Unknown");
          printf("(%04X,%04X) %s \"%s\" : (nested)\n",
            g, e, vr.GetText(), name);
          break;
        }
      }
      if (iter->IsPerInstance())
      {
        for (int j = 0; j < iter->GetNumberOfInstances(); j++)
        {
          const vtkDICOMItem *items = iter->GetValue(j).GetSequenceData();
          if (items)
          {
            size_t n = iter->GetValue(j).GetNumberOfValues();
            for (size_t i = 0; i < n; i++)
            {
              printElementFromTagPathRecurse(
                &items[i], tagPath.GetTail(), tagPath, &count);
            }
          }
        }
      }
      else
      {
        const vtkDICOMItem *items = iter->GetValue().GetSequenceData();
        if (items)
        {
          size_t n = iter->GetValue().GetNumberOfValues();
          for (size_t i = 0; i < n; i++)
          {
            printElementFromTagPathRecurse(
              &items[i], tagPath.GetTail(), tagPath, &count);
          }
        }
      }
    }
    else
    {
      printElement(data, nullptr, iter, 0, pixelDataVL);
    }
  }
}

// This program will dump all the metadata in the given file
int MAINMACRO(int argc, char *argv[])
{
  // redirect all VTK errors to stderr
  vtkConsoleOutputWindow::Install();

  int rval = 0;

  // for the optional query file
  QueryTagList qtlist;
  vtkDICOMItem query;

  // for the default character set
  vtkDICOMCharacterSet charset;

  if (argc < 2)
  {
    printUsage(stdout, fileBasename(argv[0]));
    return rval;
  }
  else if (argc == 2 && strcmp(argv[1], "--help") == 0)
  {
    printHelp(stdout, fileBasename(argv[0]));
    return rval;
  }
  else if (argc == 2 && strcmp(argv[1], "--version") == 0)
  {
    printVersion(stdout, fileBasename(argv[0]));
    return rval;
  }

  vtkSmartPointer<vtkStringArray> files =
    vtkSmartPointer<vtkStringArray>::New();

  for (int argi = 1; argi < argc; argi++)
  {
    const char *arg = argv[argi];
    if (strcmp(arg, "-q") == 0 || strcmp(arg, "-o") == 0)
    {
      if (argi + 1 == argc || argv[argi+1][0] == '-')
      {
        fprintf(stderr, "%s must be followed by a file.\n\n", arg);
        printUsage(stderr, fileBasename(argv[0]));
        return 1;
      }

      if (arg[1] == 'q')
      {
        const char *qfile = argv[++argi];
        if (!dicomcli_readquery(qfile, &query, &qtlist))
        {
          fprintf(stderr, "Can't read query file %s\n\n", qfile);
          return 1;
        }
      }
      else if (arg[1] == 'o')
      {
        fprintf(stderr, "unrecognized option %s.\n\n", arg);
        return 1;
      }
    }
    else if (strcmp(arg, "-k") == 0)
    {
      ++argi;
      if (argi == argc || argv[argi][0] == '-')
      {
        fprintf(stderr, "%s must be followed by gggg,eeee=value "
                        "where gggg,eeee is a DICOM tag.\n\n", arg);
        return 1;
      }
      if (!dicomcli_readkey(argv[argi], &query, &qtlist))
      {
        return 1;
      }
    }
    else if (strcmp(arg, "--charset") == 0)
    {
      ++argi;
      if (argi == argc || argv[argi][0] == '-')
      {
        fprintf(stderr, "%s must be followed by a valid character set\n\n",
                arg);
        return 1;
      }
      charset = vtkDICOMCharacterSet(argv[argi]);
      if (charset.GetKey() == vtkDICOMCharacterSet::Unknown)
      {
        fprintf(stderr, "%s %s is not a known character set\n\n",
                arg, argv[argi]);
        return 1;
      }
    }
    else if (arg[0] == '-')
    {
      fprintf(stderr, "unrecognized option %s.\n\n", arg);
      printUsage(stderr, fileBasename(argv[0]));
      return 1;
    }
    else
    {
      files->InsertNextValue(arg);
    }
  }

  // sort the files by study and series
  vtkSmartPointer<vtkDICOMDirectory> sorter =
    vtkSmartPointer<vtkDICOMDirectory>::New();
  sorter->RequirePixelDataOff();
  sorter->SetScanDepth(0);
  sorter->IgnoreDicomdirOn();
  sorter->SetFindQuery(query);
  sorter->SetInputFileNames(files);
  sorter->Update();

  vtkSmartPointer<vtkDICOMParser> parser =
    vtkSmartPointer<vtkDICOMParser>::New();
  parser->SetDefaultCharacterSet(charset);
  parser->SetQueryItem(query);

  vtkSmartPointer<vtkDICOMMetaData> data =
    vtkSmartPointer<vtkDICOMMetaData>::New();
  parser->SetMetaData(data);

  int m = sorter->GetNumberOfStudies();
  for (int j = 0; j < m; j++)
  {
    int k = sorter->GetFirstSeriesForStudy(j);
    int kl = sorter->GetLastSeriesForStudy(j);
    for (; k <= kl; k++)
    {
      vtkStringArray *a = sorter->GetFileNamesForSeries(k);
      vtkIdType l = a->GetNumberOfValues();
      std::string fname = a->GetValue(0);
      if (l == 1)
      {
        printf("==== %s ====\n", fname.c_str());
      }
      else
      {
        // print the first and last filenames (sorted)
        vtkSmartPointer<vtkSortFileNames> fsort =
          vtkSmartPointer<vtkSortFileNames>::New();
        fsort->NumericSortOn();
        fsort->IgnoreCaseOn();
        fsort->GroupingOff();
        fsort->SetInputFileNames(a);
        fsort->Update();
        printf("==== %s .. %s (%d files) ====\n",
          fsort->GetFileNames()->GetValue(0).c_str(),
          fileBasename(fsort->GetFileNames()->GetValue(l-1).c_str()),
          static_cast<int>(l));
      }

      data->Clear();
      data->SetNumberOfInstances(static_cast<int>(l));

      unsigned int pixelDataVL = 0;
      for (vtkIdType i = 0; i < l; i++)
      {
        fname = a->GetValue(i);
        parser->SetIndex(i);
        parser->SetFileName(fname.c_str());
        parser->Update();
        pixelDataVL = parser->GetPixelDataVL();
      }

      if (query.GetNumberOfDataElements() > 0)
      {
        for (size_t i = 0; i < qtlist.size(); i++)
        {
          printElementFromTagPath(data, qtlist[i], pixelDataVL);
        }
      }
      else
      {
        vtkDICOMDataElementIterator iter = data->Begin();
        vtkDICOMDataElementIterator iterEnd = data->End();

        for (; iter != iterEnd; ++iter)
        {
          printElement(data, nullptr, iter, 0, pixelDataVL);
        }
      }
    }
  }

  return rval;
}