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/** \internal
* \file minc2_private.h
* \brief MINC 2.0 private constants, types, and functions.
*/
/** The root of all MINC 2.0 objects in the HDF5 hierarchy.
*/
#define MI_ROOT_PATH "/minc-2.0"
#define MI_ROOT_COMMENT "Root of the MINC 2.0 data hierarchy"
#define MI_DIMAGE_PATH "image"
#define MI_INFO_NAME "info"
#define MI_INFO_COMMENT "Group holding directly accessible attributes"
#define MI_DIMENSIONS_PATH "dimensions"
#define MI_DIMS_COMMENT "Group holding dimension variables"
/** The fixed path to the full-resolution image data.
*/
#define MI_IMAGE_PATH MI_ROOT_PATH "/" MI_DIMAGE_PATH
/** The fixed path to the full-resolution image data.
*/
#define MI_FULLIMAGE_PATH MI_IMAGE_PATH "/0"
/** The fixed path to the dimension
*/
#define MI_FULLDIMENSIONS_PATH MI_ROOT_PATH "/dimensions"
/** Size of a linear transform */
#define MI2_LIN_XFM_SIZE 4
/** Standard linear transform, a 4x4 matrix.
*/
typedef double mi_lin_xfm_t[MI2_LIN_XFM_SIZE][MI2_LIN_XFM_SIZE];
#ifdef _WIN32
typedef __int64 mi_i64_t;
#else //_WIN32
typedef long long mi_i64_t;
#endif //_WIN32
/** The fixed path to the dimension
*/
#define MI_FULLDIMENSIONS_PATH MI_ROOT_PATH "/dimensions"
/** \internal
* Volume properties
*/
struct mivolprops {
miboolean_t enable_flag; /* enable multi-res */
int depth; /* multi-res depth */
micompression_t compression_type;
int zlib_level;
int edge_count; /* how many chunks */
int *edge_lengths; /* size of each chunk */
int max_lengths;
long record_length;
char *record_name;
int template_flag;
};
/** \internal
* Dimension handle
*/
struct midimension {
midimattr_t attr; /* Dimension attributes */
midimclass_t class; /* Dimension class */
double direction_cosines[3]; /* Direction cosines */
miflipping_t flipping_order;
char *name; /* Dimension name */
double *offsets; /* Offsets (if irregular) */
double step; /* Step size */
unsigned int length; /* Length */
double start; /* Start value */
char *units; /* Units string */
double width; /* Sample width (if regular) */
double *widths; /* Widths (if irregular) */
char *comments; /* Comment string */
mihandle_t volume_handle; /* Handle of associated volume */
short world_index; /* -1, MI2_X, MI2_Y, or MI2_Z */
};
/** \internal
* Volume handle
*/
struct mivolume {
hid_t hdf_id;
miboolean_t has_slice_scaling;
int number_of_dims;
midimhandle_t *dim_handles; /* file order of dimensions */
int *dim_indices; /* apparent order of dimensions */
mitype_t volume_type;
miclass_t volume_class;
mivolumeprops_t create_props;
double valid_min; /* Volume-wide valid min */
double valid_max; /* Volume-wide valid max */
mi_lin_xfm_t v2w_transform; /* Voxel-to-world transform */
mi_lin_xfm_t w2v_transform; /* World-to-voxel transform (inverse) */
int selected_resolution; /* The current resolution (0-N) */
int mode; /* Open mode */
hid_t ftype_id; /* File type ID of image. */
hid_t mtype_id; /* Memory type ID of image. */
hid_t plist_id; /* Image property list */
hid_t image_id; /* Dataset for image */
hid_t imax_id; /* Dataset for image-max */
hid_t imin_id; /* Dataset for image-min */
double scale_min; /* Global minimum */
double scale_max; /* Global maximum */
miboolean_t is_dirty; /* TRUE if data has been modified. */
};
/**
* \internal
* "semi-private" functions.
****************************************************************************/
/* From m2util.c */
extern hid_t midescend_path(hid_t file_id, const char *path);
extern hid_t mitype_to_hdftype(mitype_t, int);
extern int mitype_to_nctype(mitype_t, int *is_signed);
extern int miget_attribute(mihandle_t volume, const char *varpath,
const char *attname, mitype_t data_type,
int maxvals, void *values);
extern int miset_attr_at_loc(hid_t hdf_loc, const char *attname,
mitype_t data_type,
int maxvals, const void *values);
extern int miset_attribute(mihandle_t volume, const char *varpath,
const char *attname, mitype_t data_type,
int maxvals, const void *values);
extern void mifind_spatial_dims(int mincid, int space_to_dim[], int dim_to_space[]);
extern void miget_voxel_to_world(mihandle_t volume, mi_lin_xfm_t voxel_to_world);
extern void minormalize_vector(double vector[]);
extern void mitransform_coord(double out_coord[],
mi_lin_xfm_t transform,
const double in_coord[]);
extern int miinvert_transform(mi_lin_xfm_t transform, mi_lin_xfm_t inverse);
extern void miinit(void);
extern void miinit_enum(hid_t);
extern int miget_scalar(hid_t loc_id, hid_t type_id, const char *path,
void *data);
extern int minc_create_thumbnail(mihandle_t volume, int grp);
extern int minc_update_thumbnail(mihandle_t volume, hid_t loc_id, int igrp, int ogrp);
extern int minc_update_thumbnails(mihandle_t volume);
extern int scaled_maximal_pivoting_gaussian_elimination(int n,
int row[],
double **a,
int n_values,
double **solution );
extern int scaled_maximal_pivoting_gaussian_elimination_real(int n,
double **coefs,
int n_values,
double **values );
extern double *alloc1d(int);
extern double **alloc2d(int, int);
extern void free2d(int, double **);
extern int create_standard_dataset(hid_t hdf_file, const char *path);
/* From hyper.c */
extern int mitranslate_hyperslab_origin(mihandle_t volume,
const unsigned long start[],
const unsigned long count[],
hssize_t hdf_start[],
hsize_t hdf_count[],
int dir[]);
/* From volume.c */
extern void misave_valid_range(mihandle_t volume);
/* External */
#include "../libsrc/minc_private.h"
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