dicomfind.cxx

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

  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 "vtkDICOMDirectory.h"
#include "vtkDICOMMetaData.h"
#include "vtkDICOMItem.h"
#include "vtkDICOMDataElement.h"
#include "vtkDICOMMetaData.h"

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

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

#ifndef _WIN32
// includes for execvp
#include <unistd.h>
#include <sys/wait.h>
#include <errno.h>
#else
// includes for spawn
#include <windows.h>
#include <process.h>
#include <errno.h>
// include for getcwd
#include <direct.h>
#endif

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

#include <limits>

// print the version
void dicomfind_version(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 dicomfind_usage(FILE *file, const char *cp)
{
  fprintf(file, "usage:\n"
    "  %s [options] <directory> ...\n\n", cp);
  fprintf(file, "options:\n"
    "  -L                Follow symbolic links (default).\n"
    "  -P                Do not follow symbolic links.\n"
    "  -k tag=value      Provide an attribute to be queried and matched.\n"
    "  -q <query.txt>    Provide a file to describe the find query.\n"
    "  -u <uids.txt>     Provide a file that contains a list of UIDs.\n"
    "  -maxdepth n       Set the maximum directory depth.\n"
    "  -name pattern     Set a pattern to match (with \"*\" or \"?\").\n"
    "  -image            Restrict the search to files with PixelData.\n"
    "  -series           Find all files in series if even one file matches.\n"
    "  -print            Print the filenames of all matched files (default).\n"
    "  -print0           Print the filenames with terminating null, for xargs.\n"
    "  -exec ... +       Execute the given command for every series matched.\n"
    "  -exec ... %s      Execute the given command for every file matched.\n"
    "  -execdir ... +    Go to directory and execute command on every series.\n"
    "  -execdir ... %s   Go to directory and execute command on every file.\n"
    "  --directory-only  Do not scan files themselves if DICOMDIR is present.\n"
    "  --ignore-dicomdir Ignore the DICOMDIR file even if it is present.\n"
    "  --charset <cs>    Charset to use if SpecificCharacterSet is missing.\n"
    "  --help            Print a brief help message.\n"
    "  --version         Print the software version.\n",
#ifndef _WIN32
    "\\;", "\\;"
#else
    "; ", "; "
#endif
    );
}

// print the help
void dicomfind_help(FILE *file, const char *cp)
{
  dicomfind_usage(file, cp);
  fprintf(file, "\n"
    "This command is like the UNIX \"find\" command, but for DICOM files.\n"
    "\n"
    "When searching for files with a specific attribute (with \"-k\"), the\n"
    "tag can be in its hexadecimal form GGGG,EEEE or with its keyword form\n"
    "Modality=MR.  Alternatively, the tags can be listed in a query file\n"
    "with the \"-q\" option (one tag per line).  Attributes nested within\n"
    "sequences can be specified by giving a tag path \"-k Tag1/Tag2/Tag3\".\n"
    "Either a forward slash or a backslash can be used to separate the\n"
    "components of the path.  Private tags hould be preceded by the private\n"
    "dictionary name in square brackets.\n"
    "\n"
    "The \"-exec\" and \"-execdir\" arguments cause dicomfind to run the\n"
    "specified program on the found files.  For example, to dump each file\n"
    "one would use \"-exec dicomdump {} \\;\" where each instance of {} will\n"
    "be replaced by a found file, and \";\" indicates the end of the args\n"
    "to dicomdump.  Alternately, if \"+\" is used to end the args, then the\n"
    "program will be run on each DICOM series and {} will be replaced by all\n"
    "files in the series.  The \"-execdir\" argument is similar, except that\n"
    "it runs the program from within the directory of the file (or files),\n"
    "and {} is replaced by just the filenames instead of with the full paths.\n\n");

}

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

// get directory portion of filename
std::string dicomfind_dirname(const char *filename)
{
  const char *cp = filename + strlen(filename);
  while (cp != filename)
  {
    --cp;
    if (cp[0] == '\\' || cp[0] == '/') { break; }
  }
  return std::string(filename, cp - filename);
}

typedef vtkDICOMVR VR;

// Execute a subprocess
#ifndef _WIN32
bool execute_command(const char *command, char *argv[])
{
  // flush the output
  fflush(stdout);
  fflush(stderr);

  // fork a new process
  pid_t command_pid = fork();
  if (command_pid == -1)
  {
    fprintf(stderr, "Unable to create subprocess: %s\n", argv[0]);
  }

  // if fork() returned a pid, then this is the original process
  if (command_pid != 0)
  {
    int command_status;
    while (waitpid(command_pid, &command_status, 0) == static_cast<pid_t>(-1))
    {
      if (errno != EINTR)
      {
        fprintf(stderr, "Unknown error with subprocess: %s\n", argv[0]);
        return false;
      }
    }
    if (WIFEXITED(command_status))
    {
      if (WEXITSTATUS(command_status) != 0)
      {
        fprintf(stderr, "Subprocess returned negative result: %s\n", argv[0]);
      }
      return true;
    }
    else
    {
      fprintf(stderr, "Abnormal subprocess termination: %s\n", argv[0]);
    }
  }
  else if (execvp(command, argv) == -1)
  {
    if (errno == ENOENT)
    {
      fprintf(stderr, "Executable not found: %s\n", argv[0]);
    }
    else if (errno == ENOEXEC)
    {
      fprintf(stderr, "File is not executable: %s\n", argv[0]);
    }
    else if (errno == EACCES)
    {
      fprintf(stderr, "Access (permission) error: %s\n", argv[0]);
    }
    else if (errno == E2BIG)
    {
      fprintf(stderr, "Command line to long for command: %s\n", argv[0]);
    }
    else if (errno == ENOMEM)
    {
      fprintf(stderr, "Out of memory while running command: %s\n", argv[0]);
    }
    else if (errno == EMFILE)
    {
      fprintf(stderr, "No more available file handles: %s\n", argv[0]);
    }
    else
    {
      fprintf(stderr, "Unknown error while running command: %s\n", argv[0]);
    }

    return false;
  }

  return true;
}
#else
bool execute_command(const char *, char *argv[])
{
  bool rval = true;

  // flush the output
  fflush(stdout);
  fflush(stderr);

  int m = 0;
  while (argv[m] != 0)
  {
    m++;
  }

  wchar_t **wargv = new wchar_t *[m + 1];

  for (int i = 0; i < m; i++)
  {
    int n = MultiByteToWideChar(CP_UTF8, 0, argv[i], -1, nullptr, 0);
    wargv[i] = new wchar_t[n];
    MultiByteToWideChar(CP_UTF8, 0, argv[i], -1, wargv[i], n);
  }

  wargv[m] = 0;

  if (_wspawnvp(_P_WAIT, wargv[0], wargv) != 0)
  {
    if (errno == ENOENT)
    {
      fprintf(stderr, "Executable not found: %s\n", argv[0]);
    }
    else if (errno == ENOEXEC)
    {
      fprintf(stderr, "File is not executable: %s\n", argv[0]);
    }
    else if (errno == E2BIG)
    {
      fprintf(stderr, "Command line to long for command: %s\n", argv[0]);
    }
    else if (errno == ENOMEM)
    {
      fprintf(stderr, "Out of memory while running command: %s\n", argv[0]);
    }
    else
    {
      fprintf(stderr, "Unknown error while running command: %s\n", argv[0]);
    }

    rval = false;
  }

  for (int i = 0; i < m; i++)
  {
    delete [] wargv[i];
  }
  delete [] wargv;

  return rval;
}
#endif

#ifndef _WIN32
int dicomfind_chdir(const char *dirname)
{
  return chdir(dirname);
}
#else
int dicomfind_chdir(const char *dirname)
{
  // use _wchdir to allow paths longer than the 260 char limit
  int n = MultiByteToWideChar(CP_UTF8, 0, dirname, -1, nullptr, 0);
  wchar_t *wp = new wchar_t[n];
  MultiByteToWideChar(CP_UTF8, 0, dirname, -1, wp, n);
  int rval = _wchdir(wp);
  delete [] wp;
  return rval;
}
#endif

#ifndef _WIN32
std::string dicomfind_getcwd()
{
  char buffer[2048];
  return getcwd(buffer, sizeof(buffer));
}
#else
std::string dicomfind_getcwd()
{
  wchar_t wbuffer[2048];
  wchar_t *wp = _wgetcwd(wbuffer, sizeof(wbuffer)/sizeof(wchar_t));
  int n = WideCharToMultiByte(
    CP_UTF8, 0, wp, -1, nullptr, 0, nullptr, nullptr);
  char *cp = new char[n];
  WideCharToMultiByte(
    CP_UTF8, 0, wp, -1, cp, n, nullptr, nullptr);
  std::string s = cp;
  delete [] cp;
  return s;
}
#endif

// The type used to store an operation
struct Operation
{
  Operation(const char *type) : Type(type) {}

  std::string Type;
  std::vector<std::string> Args;
};

// Apply the given operations to the given list of files
void dicomfind_operations(
  std::vector<Operation>& operationList, vtkStringArray *sa,
  const std::string& originalDir)
{
  for (std::vector<Operation>::iterator op = operationList.begin();
       op != operationList.end();
       ++op)
  {
    if (op->Type == "-print" || op->Type == "-print0")
    {
      char endchar = (op->Type == "-print0" ? '\0' : '\n');
      for (int kk = 0; kk < sa->GetNumberOfValues(); kk++)
      {
        fprintf(stdout, "%s", sa->GetValue(kk).c_str());
        fputc(endchar, stdout);
      }
      fflush(stdout);
    }
    else if (op->Type == "-exec" || op->Type == "-execdir")
    {
      bool execdir = (op->Type == "-execdir");

      // Count the number of times {} appears in exec args
      size_t subcount = 0;
      for (size_t jj = 0; jj < op->Args.size(); jj++)
      {
        subcount += (op->Args[jj].find("{}") != std::string::npos);
      }

      // remember the current subdirectory
      std::string currentSubdir;

      if (op->Args.back() == ";")
      {
        // call program for each file
        for (int kk = 0; kk < sa->GetNumberOfValues(); kk++)
        {
          size_t sub_argc = op->Args.size() + subcount - 1;
          char **sub_argv = new char *[sub_argc+1];
          std::vector<std::string> temp_args(subcount);
          size_t subc = 0;

          size_t ii = 0;
          size_t nn = op->Args.size()-1;
          for (size_t jj = 0; jj < nn; jj++)
          {
            const std::string& arg = op->Args[jj];
            size_t pos = arg.find("{}");
            if (pos != std::string::npos)
            {
              const char *sub = sa->GetValue(kk).c_str();
              if (execdir)
              {
                sub = dicomfind_basename(sub);
              }

              std::string& temp_arg = temp_args[subc++];
              temp_arg = arg;
              do
              {
                temp_arg.replace(pos, 2, sub);
                pos = temp_arg.find("{}", pos + strlen(sub));
              }
              while (pos != std::string::npos);

              sub_argv[ii++] = const_cast<char *>(temp_arg.c_str());
            }
            else
            {
              sub_argv[ii++] = const_cast<char *>(arg.c_str());
            }
          }
          sub_argv[ii] = nullptr;

          if (execdir)
          {
            std::string dirname =
              dicomfind_dirname(sa->GetValue(kk).c_str());
            if (dirname != currentSubdir)
            {
              dicomfind_chdir(originalDir.c_str());
              dicomfind_chdir(dirname.c_str());
            }
          }

          if (!execute_command(sub_argv[0], sub_argv))
          {
            fprintf(stderr, "failure!");
          }

          delete [] sub_argv;
        }

        if (execdir && currentSubdir != "")
        {
          dicomfind_chdir(originalDir.c_str());
        }
      }
      else
      {
        // call program for each series
        // for execdir, what if series is split across directories?
        // need to call executable once per directory, using only
        // the files in that directory.
        size_t sub_argc = op->Args.size() +
          subcount*sa->GetNumberOfTuples() - 1;
        char **sub_argv = new char *[sub_argc+1];
        std::vector<std::string> temp_args(subcount*sa->GetNumberOfValues());
        size_t subc = 0;

        // for execdir, keep a list of directories that are done
        std::vector<std::string> done_dirs;
        std::string doing_dir;

        bool notdone = true;

        while (notdone)
        {
          notdone = false;
          if (execdir)
          {
            bool foundDirToProcess = false;
            for (vtkIdType kk = 0; kk < sa->GetNumberOfValues(); kk++)
            {
              std::string dirname =
                dicomfind_dirname(sa->GetValue(kk).c_str());
              if (!foundDirToProcess)
              {
                bool dirIsDone = false;
                for (size_t ll = 0; ll < done_dirs.size(); ll++)
                {
                  if (dirname == done_dirs[ll])
                  {
                    dirIsDone = true;
                    break;
                  }
                }
                if (!dirIsDone)
                {
                  foundDirToProcess = true;
                  doing_dir = dirname;
                  done_dirs.push_back(dirname);
                  break;
                }
              }
            }
            if (foundDirToProcess)
            {
              notdone = true;
            }
            else
            {
              break;
            }
          }

          size_t ii = 0;
          size_t nn = op->Args.size()-1;
          for (size_t jj = 0; jj < nn; jj++)
          {
            const std::string& arg = op->Args[jj];
            size_t pos = arg.find("{}");
            if (pos != std::string::npos)
            {
              for (vtkIdType kk = 0; kk < sa->GetNumberOfValues(); kk++)
              {
                const char *sub = sa->GetValue(kk).c_str();

                if (execdir)
                {
                  std::string dirname = dicomfind_dirname(sub);
                  if (dirname != doing_dir)
                  {
                    continue;
                  }
                  sub = dicomfind_basename(sub);
                }

                std::string& temp_arg = temp_args[subc++];
                temp_arg = arg;
                pos = temp_arg.find("{}");
                do
                {
                  temp_arg.replace(pos, 2, sub);
                  pos = temp_arg.find("{}", pos + strlen(sub));
                }
                while (pos != std::string::npos);

                sub_argv[ii++] = const_cast<char *>(temp_arg.c_str());
              }
            }
            else
            {
              sub_argv[ii++] = const_cast<char *>(arg.c_str());
            }
          }
          sub_argv[ii] = nullptr;

          if (execdir)
          {
            if (doing_dir != currentSubdir)
            {
              dicomfind_chdir(originalDir.c_str());
              dicomfind_chdir(doing_dir.c_str());
            }
          }

          if (!execute_command(sub_argv[0], sub_argv))
          {
            fprintf(stderr, "failure!");
          }
        }

        if (execdir && currentSubdir != "")
        {
          dicomfind_chdir(originalDir.c_str());
        }

        delete [] sub_argv;
      }
    }
  }
}

// Delay wildcard expansion for -name option
MAINMACRO_PASSTHROUGH(-name);

// 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();

  std::vector<Operation> operationList;

  int rval = 0;
  int scandepth = std::numeric_limits<int>::max();
  const char *pattern = "";
  QueryTagList qtlist;
  vtkDICOMItem query;
  bool followSymlinks = true;
  bool onlyDicomdir = false;
  bool ignoreDicomdir = false;
  bool requirePixelData = false;
  bool findSeries = false;
  vtkDICOMCharacterSet charset;

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

  // always query SpecificCharacterSet
  query.Set(DC::SpecificCharacterSet, vtkDICOMValue(VR::CS));

  // always query the functional sequences for advanced files
  query.Set(DC::SharedFunctionalGroupsSequence, vtkDICOMValue(VR::SQ));
  query.Set(DC::PerFrameFunctionalGroupsSequence, vtkDICOMValue(VR::SQ));

  if (argc < 2)
  {
    dicomfind_usage(stdout, dicomfind_basename(argv[0]));
    return rval;
  }
  else if (argc == 2 && strcmp(argv[1], "--help") == 0)
  {
    dicomfind_help(stdout, dicomfind_basename(argv[0]));
    return rval;
  }
  else if (argc == 2 && strcmp(argv[1], "--version") == 0)
  {
    dicomfind_version(stdout, dicomfind_basename(argv[0]));
    return rval;
  }

  for (int argi = 1; argi < argc; argi++)
  {
    const char *arg = argv[argi];
    if (strcmp(arg, "-P") == 0)
    {
      followSymlinks = false;
    }
    else if (strcmp(arg, "-L") == 0)
    {
      followSymlinks = true;
    }
    else if (strcmp(arg, "-q") == 0)
    {
      if (argi + 1 == argc || argv[argi+1][0] == '-')
      {
        fprintf(stderr, "%s must be followed by a file.\n\n", arg);
        dicomfind_usage(stderr, dicomfind_basename(argv[0]));
        return 1;
      }
      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 (strcmp(arg, "-u") == 0)
    {
      if (argi + 1 == argc || argv[argi+1][0] == '-')
      {
        fprintf(stderr, "Error: %s must be followed by a file.\n\n", arg);
        dicomfind_usage(stderr, dicomfind_basename(argv[0]));
        return 1;
      }
      const char *qfile = argv[++argi];
      if (!dicomcli_readuids(qfile, &query, &qtlist))
      {
        fprintf(stderr, "Error: Can't read uid file %s\n\n", qfile);
        return 1;
      }
    }
    else if (strcmp(arg, "-k") == 0)
    {
      vtkDICOMTag tag;
      ++argi;
      if (argi == argc)
      {
        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, "-maxdepth") == 0)
    {
      ++argi;
      if (argi == argc)
      {
        fprintf(stderr, "%s must be followed by an argument.\n\n", arg);
        return 1;
      }
      scandepth = static_cast<int>(atol(argv[argi]));
    }
    else if (strcmp(arg, "-name") == 0)
    {
      ++argi;
      if (argi == argc)
      {
        fprintf(stderr, "%s must be followed by an argument.\n\n", arg);
        return 1;
      }
      pattern = argv[argi];
    }
    else if (strcmp(arg, "-image") == 0)
    {
      requirePixelData = true;
    }
    else if (strcmp(arg, "-series") == 0)
    {
      findSeries = true;
    }
    else if (strcmp(arg, "-print") == 0 ||
             strcmp(arg, "-print0") == 0)
    {
      operationList.push_back(arg);
    }
    else if (strcmp(arg, "-exec") == 0 ||
             strcmp(arg, "-execdir") == 0)
    {
      operationList.push_back(arg);
      int argj = ++argi;
      for (; argj < argc; argj++)
      {
        if (strcmp(argv[argj], ";") == 0 ||
            strcmp(argv[argj], "+") == 0)
        {
          break;
        }
      }
      if (argj == argc)
      {
        fprintf(stderr, "%s must be terminated with + or \\; "
                "(plus or semicolon).\n\n",
                arg);
        return 1;
      }
      for (; argi <= argj; argi++)
      {
        operationList.back().Args.push_back(argv[argi]);
      }
      argi = argj;
    }
    else if (strcmp(arg, "--directory-only") == 0)
    {
      onlyDicomdir = true;
    }
    else if (strcmp(arg, "--ignore-dicomdir") == 0)
    {
      ignoreDicomdir = true;
    }
    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);
      dicomfind_usage(stderr, dicomfind_basename(argv[0]));
      return 1;
    }
    else
    {
      a->InsertNextValue(arg);
    }
  }

  // if no operations were specified, default to "print"
  if (operationList.empty())
  {
    operationList.push_back("-print");
  }

  // Remember the current directory
  std::string originalDir = dicomfind_getcwd();

  // Write data for every input directory
  if (a->GetNumberOfTuples() > 0)
  {
    vtkSmartPointer<vtkDICOMDirectory> finder =
      vtkSmartPointer<vtkDICOMDirectory>::New();
    finder->SetDefaultCharacterSet(charset);
    finder->SetInputFileNames(a);
    finder->SetFilePattern(pattern);
    finder->SetScanDepth(scandepth);
    finder->SetFindQuery(query);
    finder->SetIgnoreDicomdir(ignoreDicomdir);
    if (onlyDicomdir)
    {
      finder->SetQueryFilesToNever();
    }
    finder->SetFollowSymlinks(followSymlinks);
    finder->SetRequirePixelData(requirePixelData);
    finder->SetFindLevel(
      findSeries ? vtkDICOMDirectory::SERIES : vtkDICOMDirectory::IMAGE);
    finder->Update();

    for (int j = 0; j < finder->GetNumberOfStudies(); j++)
    {
      int k0 = finder->GetFirstSeriesForStudy(j);
      int k1 = finder->GetLastSeriesForStudy(j);

      for (int k = k0; k <= k1; k++)
      {
        vtkStringArray *sa = finder->GetFileNamesForSeries(k);
        dicomfind_operations(operationList, sa, originalDir);
      }
    }
  }

  return rval;
}