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/* 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()));
}
}
}
}
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