landmark_file.c

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/* ----------------------------------------------------------------------------
@COPYRIGHT  :
              Copyright 1993,1994,1995 David MacDonald,
              McConnell Brain Imaging Centre,
              Montreal Neurological Institute, McGill University.
              Permission to use, copy, modify, and distribute this
              software and its documentation for any purpose and without
              fee is hereby granted, provided that the above copyright
              notice appear in all copies.  The author and McGill University
              make no representations about the suitability of this
              software for any purpose.  It is provided "as is" without
              express or implied warranty.
---------------------------------------------------------------------------- */

#include  <volume_io/internal_volume_io.h>
#include  <bicpl/objects.h>
#include  <bicpl/vols.h>

#ifndef lint
static char rcsid[] = "$Header: /software/source//libraries/bicpl/Objects/landmark_file.c,v 1.9 2000/02/06 15:30:43 stever Exp $";
#endif

/* ----------------------------- MNI Header -----------------------------------
@NAME       : get_default_landmark_file_suffix
@INPUT      : 
@OUTPUT     : 
@RETURNS    : "lmk"
@DESCRIPTION: Returns the default suffix for landmark files.
@METHOD     : 
@GLOBALS    : 
@CALLS      : 
@CREATED    : 1993            David MacDonald
@MODIFIED   : 
---------------------------------------------------------------------------- */

public  STRING  get_default_landmark_file_suffix( void )
{
    return( "lmk" );
}

/* ----------------------------- MNI Header -----------------------------------
@NAME       : input_landmark_file
@INPUT      : volume
              filename
              colour
              size
              type
@OUTPUT     : 
@RETURNS    : OK or ERROR
@DESCRIPTION: Reads a landmark.lmk file and creates an object list consisting
              of markers, with the given colour, size, and type.
@METHOD     : 
@GLOBALS    : 
@CALLS      : 
@CREATED    : 1993            David MacDonald
@MODIFIED   : 
---------------------------------------------------------------------------- */

public  Status   input_landmark_file(
    Volume         volume,
    STRING         filename,
    Colour         colour,
    Real           size,
    Marker_types   type,
    int            *n_objects,
    object_struct  **object_list[] )
{
    Status                  status;
    object_struct           *object;
    marker_struct           marker;
    FILE                    *file;

    status = open_file_with_default_suffix( filename,
                                            get_default_landmark_file_suffix(),
                                            READ_FILE,
                                            ASCII_FORMAT, &file );

    *n_objects = 0;

    if( status == OK )
    {
        while( io_tag_point( file, READ_FILE, volume, size, &marker ) == OK )
        {
            marker.colour = colour;
            marker.type = type;
            object = create_object( MARKER );
            *(get_marker_ptr(object)) = marker;

            add_object_to_list( n_objects, object_list, object );
        }

        status = close_file( file );
    }

    return( status );
}

/* ----------------------------- MNI Header -----------------------------------
@NAME       : io_tag_point
@INPUT      : file
              io_direction
              volume
              size
@OUTPUT     : marker
@RETURNS    : OK or ERROR
@DESCRIPTION: Inputs one marker in landmark format from the file.
@METHOD     : 
@GLOBALS    : 
@CALLS      : 
@CREATED    : 1993            David MacDonald
@MODIFIED   : 
---------------------------------------------------------------------------- */

public  Status  io_tag_point(
    FILE            *file,
    IO_types        io_direction,
    Volume          volume,
    Real            size,
    marker_struct   *marker )
{
    Status   status;
    STRING   line, stripped;
    Point    position;
    int      sizes[MAX_DIMENSIONS];
    int      len, offset;
    Real     voxel[MAX_DIMENSIONS];
    Real     x, y, z;
    Real     x_w, y_w, z_w;

    status = OK;

    if( volume != (Volume) NULL && get_volume_n_dimensions(volume) != 3 )
    {
        print_error( "Error:  volume must be 3d to use for input landmarks.\n");
        volume = (Volume) NULL;
    }

    if( io_direction == WRITE_FILE )
    {
        if( volume == (Volume) NULL )
        {
            position = marker->position;
        }
        else
        {
            convert_world_to_voxel( volume,
                                    (Real) Point_x(marker->position),
                                    (Real) Point_y(marker->position),
                                    (Real) Point_z(marker->position),
                                    voxel );

            get_volume_sizes( volume, sizes );

            convert_voxel_to_talairach( voxel[X], voxel[Y], voxel[Z],
                                        sizes[X], sizes[Y], sizes[Z],
                                        &x, &y, &z );

            fill_Point( position, x, y, z );
        }
    }

    if( status == OK )
        status = io_point( file, io_direction, ASCII_FORMAT, &position );

    if( io_direction == READ_FILE )
    {
        marker->colour = WHITE;
        marker->type = BOX_MARKER;

        if( volume == (Volume) NULL )
        {
            marker->position = position;
        }
        else
        {
            get_volume_sizes( volume, sizes );

            convert_talairach_to_voxel( (Real) Point_x(position),
                                        (Real) Point_y(position),
                                        (Real) Point_z(position),
                                        sizes[X], sizes[Y], sizes[Z],
                                        &voxel[X], &voxel[Y], &voxel[Z] );

            convert_voxel_to_world( volume, voxel, &x_w, &y_w, &z_w );
            fill_Point( marker->position, x_w, y_w, z_w );
        }
    }

#define USE_X_POSITION_FOR_WEIGHT
#ifdef  USE_X_POSITION_FOR_WEIGHT
    if( status == OK )
    {
        if( io_direction == WRITE_FILE )
            status = io_float( file, io_direction, ASCII_FORMAT,
                               &Point_x(position));
        else
        {
            status = io_real( file, io_direction, ASCII_FORMAT, &marker->size );
            marker->size = size;
        }
    }
#else
    if( status == OK )
        status = io_real( file, io_direction, ASCII_FORMAT, &marker->size );
#endif

    if( status == OK )
        status = io_int( file, io_direction, ASCII_FORMAT,
                         &marker->structure_id );

    if( status == OK )
        status = io_int( file, io_direction, ASCII_FORMAT,
                         &marker->patient_id );

    if( io_direction == WRITE_FILE )
    {
        if( status == OK && string_length(marker->label) > 0 )
            status = io_quoted_string( file, io_direction, ASCII_FORMAT,
                                       &marker->label );
    }
    else
    {
        if( status == OK )
            status = input_line( file, &line );

        if( status == OK )
        {
            stripped = strip_outer_blanks( line );
            delete_string( line );

            if( stripped[0] == '"' )
                offset = 1;
            else
                offset = 0;

            marker->label = create_string( &stripped[offset] );

            len = string_length( marker->label );

            if( len > 0 && marker->label[len-1] == '"' )
                 marker->label[len-1] = END_OF_STRING;

            delete_string( stripped );
        }
    }

    if( status == OK )
        status = io_newline( file, io_direction, ASCII_FORMAT );

    return( status );
}

---