/* Copyright (c) 2008-2025 the MRtrix3 contributors.
 *
 * This Source Code Form is subject to the terms of the Mozilla Public
 * License, v. 2.0. If a copy of the MPL was not distributed with this
 * file, You can obtain one at http://mozilla.org/MPL/2.0/.
 *
 * Covered Software is provided under this License on an "as is"
 * basis, without warranty of any kind, either expressed, implied, or
 * statutory, including, without limitation, warranties that the
 * Covered Software is free of defects, merchantable, fit for a
 * particular purpose or non-infringing.
 * See the Mozilla Public License v. 2.0 for more details.
 *
 * For more details, see http://www.mrtrix.org/.
 */

#include "command.h"
#include "debug.h"
#include "file/path.h"
#include "file/dicom/element.h"
#include "file/dicom/quick_scan.h"
#include "file/dicom/definitions.h"


using namespace MR;
using namespace App;

void usage ()
{
  AUTHOR = "J-Donald Tournier (jdtournier@gmail.com)";

  SYNOPSIS = "Edit DICOM file in-place";

  DESCRIPTION
  + "Note that this command simply replaces the existing "
    "values without modifying the DICOM structure in any way. Replacement text "
    "will be truncated if it is too long to fit inside the existing tag."

  + "WARNING: this command will modify existing data! It is recommended to run "
    "this command on a copy of the original data set to avoid loss of data.";


  ARGUMENTS
  + Argument ("file", "the DICOM file to be edited.").type_file_in();

  OPTIONS
  + Option ("anonymise", "remove any identifiable information, by replacing the following tags:\n"
      "- any tag with Value Representation PN will be replaced with 'anonymous'\n"
      "- tag (0010,0030) PatientBirthDate will be replaced with an empty string\n"
      "WARNING: there is no guarantee that this command will remove all identiable "
      "information, since such information may be contained in any number "
      "of private vendor-specific tags. You will need to double-check the "
      "results independently if you " "need to ensure anonymity.")

  + Option ("id", "replace all ID tags with string supplied. This consists of tags "
      "(0010, 0020) PatientID and (0010, 1000) OtherPatientIDs")
  +   Argument ("text").type_text()

  + Option ("tag", "replace specific tag.").allow_multiple()
  +   Argument ("group")
  +   Argument ("element")
  +   Argument ("newvalue");
}


class Tag { NOMEMALIGN
  public:
    Tag (uint16_t group, uint16_t element, const std::string& newvalue) :
      group (group), element (element), newvalue (newvalue) { }
    uint16_t group, element;
    std::string newvalue;
};




inline std::string hex (uint16_t value)
{
  std::ostringstream hex;
  hex << std::hex << value;
  return hex.str();
}

inline uint16_t read_hex (const std::string& m)
{
  uint16_t value;
  std::istringstream hex (m);
  hex >> std::hex >> value;
  return value;
}




void run ()
{
  vector<Tag> tags;
  vector<uint16_t> VRs;

  auto opt = get_options ("anonymise");
  if (opt.size()) {
    tags.push_back (Tag (0x0010U, 0x0030U, "")); // PatientBirthDate
    VRs.push_back (VR_PN);
  }


  opt = get_options ("tag");
  if (opt.size())
    for (size_t n = 0; n < opt.size(); ++n)
      tags.push_back (Tag (read_hex (opt[n][0]), read_hex (opt[n][1]), opt[n][2]));

  opt = get_options ("id");
  if (opt.size()) {
    std::string newid = opt[0][0];
    tags.push_back (Tag (0x0010U, 0x0020U, newid)); // PatientID
    tags.push_back (Tag (0x0010U, 0x1000U, newid)); // OtherPatientIDs
  }

  for (size_t n = 0; n < VRs.size(); ++n) {
    union __VR { uint16_t i; char c[2]; } VR;
    VR.i = VRs[n];
    INFO (std::string ("clearing entries with VR \"") + VR.c[1] + VR.c[0] + "\"");
  }
  for (size_t n = 0; n < tags.size(); ++n)
    INFO ("replacing tag (" + hex(tags[n].group) + "," + hex(tags[n].element) + ") with value \"" + tags[n].newvalue + "\"");

  File::Dicom::Element item;
  item.set (argument[0], true, true);
  while (item.read()) {
    for (size_t n = 0; n < VRs.size(); ++n) {
      if (item.VR == VRs[n]) {
        memset (item.data, 32, item.size);
        memcpy (item.data, "anonymous", std::min<int> (item.size, 9));
      }
    }
    for (size_t n = 0; n < tags.size(); ++n) {
      if (item.is (tags[n].group, tags[n].element)) {
        memset (item.data, 32, item.size);
        memcpy (item.data, tags[n].newvalue.c_str(), std::min<int> (item.size, tags[n].newvalue.size()));
      }
    }
  }
}

