/usr/include/volume_io/volume.h is in libminc-dev 2.2.00-3.
This file is owned by root:root, with mode 0o644.
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#define DEF_VOLUME
/* ----------------------------------------------------------------------------
@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.
@VERSION : $Header: /private-cvsroot/minc/volume_io/Include/volume_io/volume.h,v 1.57 2006-04-07 14:47:15 rotor Exp $
---------------------------------------------------------------------------- */
/* ----------------------------- MNI Header -----------------------------------
@NAME : volume.h
@INPUT :
@OUTPUT :
@RETURNS :
@DESCRIPTION: Types for use in dealing with volumes.
@METHOD :
@GLOBALS :
@CALLS :
@CREATED : 1993 David MacDonald
@MODIFIED :
---------------------------------------------------------------------------- */
#include <minc.h>
#include <volume_io/transforms.h>
#include <volume_io/multidim.h>
typedef struct
{
VIO_Real global_image_range[2];
VIO_STR dimension_names[VIO_MAX_DIMENSIONS];
VIO_BOOL use_starts_set;
VIO_BOOL use_volume_starts_and_steps;
} minc_output_options;
#include <volume_io/volume_cache.h>
extern VIO_STR XYZ_dimension_names[];
extern VIO_STR File_order_dimension_names[];
/* -------------------------- volume struct --------------------- */
#define ANY_SPATIAL_DIMENSION "any_spatial_dimension"
#define MI_UNKNOWN_SPACE "unknown___"
typedef struct
{
VIO_BOOL is_cached_volume;
VIO_volume_cache_struct cache;
VIO_multidim_array array;
VIO_STR dimension_names[VIO_MAX_DIMENSIONS];
int spatial_axes[VIO_N_DIMENSIONS];
nc_type nc_data_type;
VIO_BOOL signed_flag;
VIO_BOOL is_rgba_data;
VIO_Real voxel_min;
VIO_Real voxel_max;
VIO_BOOL real_range_set;
VIO_Real real_value_scale;
VIO_Real real_value_translation;
VIO_Real separations[VIO_MAX_DIMENSIONS];
VIO_Real starts[VIO_MAX_DIMENSIONS];
VIO_Real direction_cosines[VIO_MAX_DIMENSIONS][VIO_N_DIMENSIONS];
VIO_BOOL voxel_to_world_transform_uptodate;
VIO_General_transform voxel_to_world_transform;
VIO_STR coordinate_system_name;
VIO_Real *irregular_starts[VIO_MAX_DIMENSIONS];
VIO_Real *irregular_widths[VIO_MAX_DIMENSIONS];
} volume_struct;
typedef volume_struct *VIO_Volume;
#if !VIO_PREFIX_NAMES
typedef VIO_Volume Volume;
#endif /* !VIO_PREFIX_NAMES */
/* ---- macro for stepping through entire volume */
#define BEGIN_ALL_VOXELS( volume, v0, v1, v2, v3, v4 ) \
{ \
int _i_, _sizes_[VIO_MAX_DIMENSIONS]; \
int _size0_, _size1_, _size2_, _size3_, _size4_; \
\
get_volume_sizes( volume, _sizes_ ); \
for_less( _i_, get_volume_n_dimensions(volume), VIO_MAX_DIMENSIONS ) \
_sizes_[_i_] = 1; \
_size0_ = _sizes_[0]; \
_size1_ = _sizes_[1]; \
_size2_ = _sizes_[2]; \
_size3_ = _sizes_[3]; \
_size4_ = _sizes_[4]; \
\
for_less( v0, 0, _size0_ ) \
for_less( v1, 0, _size1_ ) \
for_less( v2, 0, _size2_ ) \
for_less( v3, 0, _size3_ ) \
for_less( v4, 0, _size4_ ) \
{
#define END_ALL_VOXELS \
} \
}
/* ------------------------- set voxel value ------------------------ */
/* --- public macros to set the [x][y]... voxel of 'volume' to 'value' */
#define SET_VOXEL_1D( volume, x, value ) \
if( (volume)->is_cached_volume ) \
set_cached_volume_voxel( volume, x, 0, 0, 0, 0, (VIO_Real) value ); \
else \
SET_MULTIDIM_1D( (volume)->array, x, value )
#define SET_VOXEL_2D( volume, x, y, value ) \
if( (volume)->is_cached_volume ) \
set_cached_volume_voxel( volume, x, y, 0, 0, 0, (VIO_Real) value ); \
else \
SET_MULTIDIM_2D( (volume)->array, x, y, value )
#define SET_VOXEL_3D( volume, x, y, z, value ) \
if( (volume)->is_cached_volume ) \
set_cached_volume_voxel( volume, x, y, z, 0, 0, (VIO_Real) value ); \
else \
SET_MULTIDIM_3D( (volume)->array, x, y, z, value )
#define SET_VOXEL_4D( volume, x, y, z, t, value ) \
if( (volume)->is_cached_volume ) \
set_cached_volume_voxel( volume, x, y, z, t, 0, (VIO_Real) value ); \
else \
SET_MULTIDIM_4D( (volume)->array, x, y, z, t, value )
#define SET_VOXEL_5D( volume, x, y, z, t, v, value ) \
if( (volume)->is_cached_volume ) \
set_cached_volume_voxel( volume, x, y, z, t, v, (VIO_Real) value ); \
else \
SET_MULTIDIM_5D( (volume)->array, x, y, z, t, v, value )
/* --- same as previous, but don't have to know dimensions of volume */
#define SET_VOXEL( volume, x, y, z, t, v, value ) \
if( (volume)->is_cached_volume ) \
set_cached_volume_voxel( volume, x, y, z, t, v, (VIO_Real) value ); \
else \
SET_MULTIDIM( (volume)->array, x, y, z, t, v, value )
/* --- public macros to place the [x][y]...'th voxel of 'volume' in 'value' */
#define GET_VOXEL_1D_TYPED( value, vtype, volume, x ) \
if( (volume)->is_cached_volume ) \
(value) = vtype get_cached_volume_voxel( volume, x, 0, 0, 0, 0 ); \
else \
GET_MULTIDIM_1D( value, vtype, (volume)->array, x )
#define GET_VOXEL_2D_TYPED( value, vtype, volume, x, y ) \
if( (volume)->is_cached_volume ) \
(value) = vtype get_cached_volume_voxel( volume, x, y, 0, 0, 0 ); \
else \
GET_MULTIDIM_2D( value, vtype, (volume)->array, x, y )
#define GET_VOXEL_3D_TYPED( value, vtype, volume, x, y, z ) \
if( (volume)->is_cached_volume ) \
(value) = vtype get_cached_volume_voxel( volume, x, y, z, 0, 0 ); \
else \
GET_MULTIDIM_3D( value, vtype, (volume)->array, x, y, z )
#define GET_VOXEL_4D_TYPED( value, vtype, volume, x, y, z, t ) \
if( (volume)->is_cached_volume ) \
(value) = vtype get_cached_volume_voxel( volume, x, y, z, t, 0 ); \
else \
GET_MULTIDIM_4D( value, vtype, (volume)->array, x, y, z, t )
#define GET_VOXEL_5D_TYPED( value, vtype, volume, x, y, z, t, v ) \
if( (volume)->is_cached_volume ) \
(value) = vtype get_cached_volume_voxel( volume, x, y, z, t, v ); \
else \
GET_MULTIDIM_5D( value, vtype, (volume)->array, x, y, z, t, v )
/* --- same as previous, but no need to know volume dimensions */
#define GET_VOXEL_TYPED( value, vtype, volume, x, y, z, t, v ) \
if( (volume)->is_cached_volume ) \
(value) = vtype get_cached_volume_voxel( volume, x, y, z, t, v ); \
else \
GET_MULTIDIM( value, vtype, (volume)->array, x, y, z, t, v )
/* --- public macros to place the [x][y]...'th voxel of 'volume' in 'value' */
#define GET_VOXEL_1D( value, volume, x ) \
GET_VOXEL_1D_TYPED( value, , volume, x )
#define GET_VOXEL_2D( value, volume, x, y ) \
GET_VOXEL_2D_TYPED( value, , volume, x, y )
#define GET_VOXEL_3D( value, volume, x, y, z ) \
GET_VOXEL_3D_TYPED( value, , volume, x, y, z )
#define GET_VOXEL_4D( value, volume, x, y, z, t ) \
GET_VOXEL_4D_TYPED( value, , volume, x, y, z, t )
#define GET_VOXEL_5D( value, volume, x, y, z, t, v ) \
GET_VOXEL_5D_TYPED( value, , volume, x, y, z, t, v )
/* --- same as previous, but no need to know volume dimensions */
#define GET_VOXEL( value, volume, x, y, z, t, v ) \
GET_VOXEL_TYPED( value, , volume, x, y, z, t, v )
/* ------------------------- get voxel ptr ------------------------ */
/* --- public macros to return a pointer to the [x][y]'th voxel of the
'volume', and place it in 'ptr' */
#define GET_VOXEL_PTR_1D( ptr, volume, x ) \
if( (volume)->is_cached_volume ) \
/* handle_internal_error( "Cannot get pointer to cached Volume.\n");\
else */ \
GET_MULTIDIM_PTR_1D( ptr, (volume)->array, x )
#define GET_VOXEL_PTR_2D( ptr, volume, x, y ) \
if( (volume)->is_cached_volume ) \
handle_internal_error( "Cannot get pointer to cached Volume.\n");\
else \
GET_MULTIDIM_PTR_2D( ptr, (volume)->array, x, y )
#define GET_VOXEL_PTR_3D( ptr, volume, x, y, z ) \
if( (volume)->is_cached_volume ) \
handle_internal_error( "Cannot get pointer to cached Volume.\n");\
else \
GET_MULTIDIM_PTR_3D( ptr, (volume)->array, x, y, z )
#define GET_VOXEL_PTR_4D( ptr, volume, x, y, z, t ) \
if( (volume)->is_cached_volume ) \
handle_internal_error( "Cannot get pointer to cached Volume.\n");\
else \
GET_MULTIDIM_PTR_4D( ptr, (volume)->array, x, y, z, t )
#define GET_VOXEL_PTR_5D( ptr, volume, x, y, z, t, v ) \
if( (volume)->is_cached_volume ) \
handle_internal_error( "Cannot get pointer to cached Volume.\n");\
else \
GET_MULTIDIM_PTR_5D( ptr, (volume)->array, x, y, z, t, v )
/* --- same as previous, but no need to know voxel dimensions */
#define GET_VOXEL_PTR( ptr, volume, x, y, z, t, v ) \
if( (volume)->is_cached_volume ) \
handle_internal_error( "Cannot get pointer to cached Volume.\n");\
else \
GET_MULTIDIM_PTR( ptr, (volume)->array, x, y, z, t, v )
/* --- returns the conversion of the 'voxel' value to a real value */
#define CONVERT_VOXEL_TO_VALUE( volume, voxel ) \
convert_voxel_to_value( volume, voxel )
/* --- returns the conversion of the 'real' value to a voxel value */
#define CONVERT_VALUE_TO_VOXEL( volume, value ) \
convert_value_to_voxel( volume, value )
/* --- assigns 'value' the value of the [x][y]...'th voxel of 'volume' */
#define GET_VALUE_1D_TYPED( value, vtype, volume, x ) \
{ \
GET_VOXEL_1D_TYPED( value, vtype, volume, x ); \
value = CONVERT_VOXEL_TO_VALUE( volume, value ); \
}
#define GET_VALUE_2D_TYPED( value, vtype, volume, x, y ) \
{ \
GET_VOXEL_2D_TYPED( value, vtype, volume, x, y ); \
value = CONVERT_VOXEL_TO_VALUE( volume, value ); \
}
#define GET_VALUE_3D_TYPED( value, vtype, volume, x, y, z ) \
{ \
GET_VOXEL_3D_TYPED( value, vtype, volume, x, y, z ); \
value = CONVERT_VOXEL_TO_VALUE( volume, value ); \
}
#define GET_VALUE_4D_TYPED( value, vtype, volume, x, y, z, t ) \
{ \
GET_VOXEL_4D_TYPED( value, vtype, volume, x, y, z, t ); \
value = CONVERT_VOXEL_TO_VALUE( volume, value ); \
}
#define GET_VALUE_5D_TYPED( value, vtype, volume, x, y, z, t, v ) \
{ \
GET_VOXEL_5D_TYPED( value, vtype, volume, x, y, z, t, v ); \
value = CONVERT_VOXEL_TO_VALUE( volume, value ); \
}
/* --- same as previous, without knowing number of dimensions of volume */
#define GET_VALUE_TYPED( value, vtype, volume, x, y, z, t, v ) \
switch( (volume)->n_dimensions ) \
{ \
case 1: GET_VALUE_1D_TYPED( value, vtype, volume, x ); break; \
case 2: GET_VALUE_2D_TYPED( value, vtype, volume, x, y ); break; \
case 3: GET_VALUE_3D_TYPED( value, vtype, volume, x, y, z ); break; \
case 4: GET_VALUE_4D_TYPED( value, vtype, volume, x, y, z, t ); break; \
case 5: GET_VALUE_5D_TYPED( value, vtype, volume, x, y, z, t, v ); break; \
}
/* --- assigns 'value' the value of the [x][y]...'th voxel of 'volume' */
#define GET_VALUE_1D( value, volume, x ) \
GET_VALUE_1D_TYPED( value, , volume, x )
#define GET_VALUE_2D( value, volume, x, y ) \
GET_VALUE_2D_TYPED( value, , volume, x, y )
#define GET_VALUE_3D( value, volume, x, y, z ) \
GET_VALUE_3D_TYPED( value, , volume, x, y, z )
#define GET_VALUE_4D( value, volume, x, y, z, t ) \
GET_VALUE_4D_TYPED( value, , volume, x, y, z, t )
#define GET_VALUE_5D( value, volume, x, y, z, t, v ) \
GET_VALUE_5D_TYPED( value, , volume, x, y, z, t, v )
/* --- same as previous, without knowing number of dimensions of volume */
#define GET_VALUE( value, volume, x, y, z, t, v ) \
GET_VALUE_TYPED( value, , volume, x, y, z, t, v )
/* -------------------- minc file struct -------------------- */
typedef struct
{
int arent_any_yet;
} volume_creation_options;
typedef struct
{
VIO_BOOL promote_invalid_to_zero_flag;
VIO_BOOL convert_vector_to_scalar_flag;
VIO_BOOL convert_vector_to_colour_flag;
int dimension_size_for_colour_data;
int max_dimension_size_for_colour_data;
int rgba_indices[4];
double user_real_range[2];
} minc_input_options;
typedef struct
{
VIO_BOOL file_is_being_read;
/* input and output */
int cdfid;
int img_var;
int n_file_dimensions;
long sizes_in_file[MAX_VAR_DIMS];
long indices[MAX_VAR_DIMS];
VIO_STR dim_names[MAX_VAR_DIMS];
VIO_Volume volume;
int to_volume_index[MAX_VAR_DIMS];
int to_file_index[VIO_MAX_DIMENSIONS];
int minc_icv;
VIO_STR filename;
/* input only */
VIO_BOOL end_volume_flag;
VIO_BOOL converting_to_colour;
int rgba_indices[4];
int n_volumes_in_file;
int valid_file_axes[VIO_MAX_DIMENSIONS];
int n_slab_dims;
int spatial_axes[VIO_N_DIMENSIONS];
VIO_General_transform voxel_to_world_transform;
minc_input_options original_input_options;
/* output only */
int img_var_id;
int min_id;
int max_id;
double image_range[2];
VIO_BOOL end_def_done;
VIO_BOOL ignoring_because_cached;
VIO_BOOL variables_written;
int dim_ids[MAX_VAR_DIMS];
VIO_BOOL outputting_in_order;
VIO_BOOL entire_file_written;
nc_type nc_data_type;
VIO_BOOL signed_flag;
double valid_range[2];
int image_dims[MAX_VAR_DIMS];
int src_cdfid;
int src_img_var;
} minc_file_struct;
typedef minc_file_struct *Minc_file;
#define MNC_ENDING "mnc"
/* --- recognized file formats */
typedef enum { MNC_FORMAT, FREE_FORMAT } Volume_file_formats;
typedef struct
{
Volume_file_formats file_format;
Minc_file minc_file;
/* for free format files only */
FILE *volume_file;
int slice_index;
long sizes_in_file[VIO_MAX_DIMENSIONS];
int axis_index_from_file[VIO_MAX_DIMENSIONS];
VIO_Data_types file_data_type;
VIO_BOOL one_file_per_slice;
VIO_STR directory;
VIO_STR *slice_filenames;
int *slice_byte_offsets;
unsigned char *byte_slice_buffer;
unsigned short *short_slice_buffer;
} volume_input_struct;
/* --------------------- filter types -------------------------------- */
typedef enum {
NEAREST_NEIGHBOUR,
LINEAR_INTERPOLATION,
BOX_FILTER,
TRIANGLE_FILTER,
GAUSSIAN_FILTER } Filter_types;
#endif
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