+
−/* ----------------------------- MNI Header -----------------------------------
+
−@NAME       : gyro_to_minc.c
+
−@DESCRIPTION: Code to convert a list of gyroscan acr-nema files to minc 
+
−              format.
+
−@METHOD     : 
+
−@GLOBALS    : 
+
−@CALLS      : 
+
−@CREATED    : November 25, 1993 (Peter Neelin)
+
−@MODIFIED   : 
+
− * $Log: gyro_to_minc.c,v $
+
− * Revision 6.2  2001-04-09 23:02:49  neelin
+
− * Modified copyright notice, removing permission statement since copying,
+
− * etc. is probably not permitted by our non-disclosure agreement with
+
− * Philips.
+
− *
+
− * Revision 6.1  1999/10/29 17:52:03  neelin
+
− * Fixed Log keyword
+
− *
+
− * Revision 6.0  1997/09/12 13:23:50  neelin
+
− * Release of minc version 0.6
+
− *
+
− * Revision 5.0  1997/08/21  13:24:50  neelin
+
− * Release of minc version 0.5
+
− *
+
− * Revision 4.0  1997/05/07  20:01:07  neelin
+
− * Release of minc version 0.4
+
− *
+
− * Revision 3.0  1995/05/15  19:31:44  neelin
+
− * Release of minc version 0.3
+
− *
+
− * Revision 2.3  1995/02/14  18:12:26  neelin
+
− * Added project names and defaults files (using volume name).
+
− * Added process id to log file name.
+
− * Moved temporary files to subdirectory.
+
− *
+
− * Revision 2.2  1995/02/08  19:31:47  neelin
+
− * Moved ARGSUSED statements for irix 5 lint.
+
− *
+
− * Revision 2.1  1994/10/20  13:50:12  neelin
+
− * Write out direction cosines to support rotated volumes.
+
− * Store single slices as 1-slice volumes (3D instead of 2D).
+
− * Changed storing of minc history (get args for gyrotominc).
+
− *
+
− * Revision 2.0  94/09/28  10:35:28  neelin
+
− * Release of minc version 0.2
+
− * 
+
− * Revision 1.5  94/09/28  10:35:01  neelin
+
− * Pre-release
+
− * 
+
− * Revision 1.4  94/01/18  13:36:11  neelin
+
− * Added command line options to gyrotominc and fixed error message bug in
+
− * gyro_to_minc.
+
− * 
+
− * Revision 1.3  94/01/14  11:37:21  neelin
+
− * Fixed handling of multiple reconstructions and image types. Add spiinfo variable with extra info (including window min/max). Changed output
+
− * file name to include reconstruction number and image type number.
+
− * 
+
− * Revision 1.2  93/12/08  09:13:27  neelin
+
− * Delete group list.
+
− * 
+
− * Revision 1.1  93/11/30  14:41:20  neelin
+
− * Initial revision
+
− * 
+
−@COPYRIGHT  :
+
−              Copyright 1993 Peter Neelin, McConnell Brain Imaging Centre, 
+
−              Montreal Neurological Institute, McGill University.
+
−---------------------------------------------------------------------------- */
+
−
+
−#include <gcomserver.h>
+
−
+
−extern int Do_logging;
+
−
+
−/* ----------------------------- MNI Header -----------------------------------
+
−@NAME       : gyro_to_minc
+
−@INPUT      : num_files - number of image files
+
−              file_list - list of file names
+
−              minc_file - name of output minc file (NULL means make one
+
−                 up)
+
−              clobber - if TRUE, then open the output with NC_CLOBBER
+
−              file_prefix - string providing any directory or prefix 
+
−                 for internally generated filename (if it is a directory,
+
−                 then it must contain the last "/")
+
−@OUTPUT     : output_file_name - returns a pointer to an internal area
+
−                 containing the file name of the created file if minc_file
+
−                 is NULL, or simply a pointer to minc_file. If NULL, then
+
−                 nothing is returned.
+
−@RETURNS    : EXIT_SUCCESS if no error, EXIT_FAILURE on error.
+
−@DESCRIPTION: Routine to convert a list of gyroscan acr-nema files to minc 
+
−              format.
+
−@METHOD     : 
+
−@GLOBALS    : Do_logging
+
−@CALLS      : 
+
−@CREATED    : November 25, 1993 (Peter Neelin)
+
−@MODIFIED   : 
+
−---------------------------------------------------------------------------- */
+
−public int gyro_to_minc(int num_files, char *file_list[], 
+
−                        char *minc_file, int clobber,
+
−                        char *file_prefix, char **output_file_name)
+
−{
+
−   Acr_Group group_list;
+
−   int max_group;
+
−   File_Info *file_info;
+
−   General_Info general_info;
+
−   Image_Data image;
+
−   int icvid;
+
−   int ifile;
+
−   Mri_Index imri;
+
−   char *out_file_name;
+
−
+
−   /* Allocate space for the file information */
+
−   file_info = MALLOC(num_files * sizeof(*file_info));
+
−
+
−   /* Last group needed for first pass */
+
−   max_group = SPI_ACTUAL_IMAGE_GID - 1;
+
−
+
−   /* Initialize some values for general info */
+
−   general_info.initialized = FALSE;
+
−   general_info.group_list = NULL;
+
−   for (imri=0; imri < MRI_NDIMS; imri++) 
+
−      general_info.position[imri] = NULL;
+
−
+
−   /* Loop through file list getting information */
+
−   for (ifile=0; ifile < num_files; ifile++) {
+
−
+
−      /* Read the file */
+
−      group_list = read_gyro(file_list[ifile], max_group);
+
−
+
−      /* Get file-specific information */
+
−      get_file_info(group_list, &file_info[ifile], &general_info);
+
−
+
−      /* Delete the group list */
+
−      acr_delete_group_list(group_list);
+
−
+
−      /* Print log message if not using file */
+
−      if (!file_info[ifile].valid) {
+
−         if (Do_logging >= LOW_LOGGING) {
+
−            (void) fprintf(stderr, "Not using file %s\n",
+
−                           file_list[ifile]);
+
−         }
+
−
+
−      }
+
−
+
−   }
+
−
+
−   /* Create the output file */
+
−   if (general_info.initialized) {
+
−      icvid = create_minc_file(minc_file, clobber, &general_info,
+
−                               file_prefix, &out_file_name);
+
−   }
+
−   if (output_file_name != NULL)
+
−      *output_file_name = out_file_name;
+
−
+
−   /* Check that we found the general info and that the minc file was
+
−      created okay */
+
−   if ((!general_info.initialized) || (icvid == MI_ERROR)) {
+
−      if (general_info.initialized) {
+
−         (void) fprintf(stderr, "Error creating minc file %s.\n",
+
−                        out_file_name);
+
−      }
+
−      free_info(&general_info, file_info, num_files);
+
−      FREE(file_info);
+
−      return EXIT_FAILURE;
+
−   }
+
−
+
−   /* We now read all groups */
+
−   max_group = 0;
+
−
+
−   /* Loop through the files again and put images into the minc file */
+
−   for (ifile=0; ifile < num_files; ifile++) {
+
−
+
−      /* Check that we have a valid file */
+
−      if (!file_info[ifile].valid) {
+
−         continue;
+
−      }
+
−
+
−      /* Read the file */
+
−      group_list = read_gyro(file_list[ifile], max_group);
+
−
+
−      /* Get image */
+
−      get_gyro_image(group_list, &image);
+
−
+
−      /* Save the image and any other information */
+
−      save_minc_image(icvid, &general_info, &file_info[ifile], &image);
+
−
+
−      /* Delete the group list */
+
−      acr_delete_group_list(group_list);
+
−
+
−      /* Free the image data */
+
−      if ((image.data != NULL) && (image.free)) FREE(image.data);
+
−
+
−   }
+
−
+
−   /* Close the output file */
+
−   close_minc_file(icvid);
+
−
+
−   /* Free the general_info and file_info stuff */
+
−   free_info(&general_info, file_info, num_files);
+
−   FREE(file_info);
+
−
+
−   return EXIT_SUCCESS;
+
−}
+
−
+
−/* ----------------------------- MNI Header -----------------------------------
+
−@NAME       : free_info
+
−@INPUT      : general_info
+
−              file_info
+
−              num_files
+
−@OUTPUT     : (none)
+
−@RETURNS    : (nothing)
+
−@DESCRIPTION: Routine to free contents of general and file info structures.
+
−@METHOD     : 
+
−@GLOBALS    : 
+
−@CALLS      : 
+
−@CREATED    : November 26, 1993 (Peter Neelin)
+
−@MODIFIED   : 
+
−---------------------------------------------------------------------------- */
+
−/* ARGSUSED */
+
−public void free_info(General_Info *general_info, File_Info *file_info, 
+
−                      int num_files)
+
−{
+
−   Mri_Index imri;
+
−
+
−   /* Free the general info pointers */
+
−   for (imri=0; imri < MRI_NDIMS; imri++) {
+
−      if (general_info->position[imri] != NULL) {
+
−         FREE(general_info->position[imri]);
+
−      }
+
−   }
+
−
+
−   /* Free the group list */
+
−   if (general_info->group_list != NULL) {
+
−      acr_delete_group_list(general_info->group_list);
+
−   }
+
−
+
−   return;
+
−
+
−}