/*****************************************************************************
Major portions of this software are copyrighted by the Medical College
of Wisconsin, 1994-2000, and are released under the Gnu General Public
License, Version 2. See the file README.Copyright for details.
******************************************************************************/
#ifndef _MCW_MRILIB_HEADER_
#define _MCW_MRILIB_HEADER_
#define MRILIB_7D
#define COXEMAIL "rwcox@nih.gov" /* or /dev/null, if you prefer */
#ifdef __cplusplus
extern "C" { /* care of Greg Balls 7 Aug 2006 [rickr] */
#endif
extern char MRILIB_orients[] ; /* 12 Mar 2001 */
extern float MRILIB_zoff ; /* global variables from mri_read.c */
extern float MRILIB_tr ; /* 03 Dec 2001 */
extern float MRILIB_xoff ; /* 07 Dec 2001 */
extern float MRILIB_yoff ;
extern int use_MRILIB_zoff ; /* 20 Dec 2001 */
extern int use_MRILIB_xoff ;
extern int use_MRILIB_yoff ;
extern int use_MRILIB_xcos ; /* 22 Jul 2002 */
extern int use_MRILIB_ycos ;
extern int use_MRILIB_zcos ;
extern float MRILIB_xcos[3] ;
extern float MRILIB_ycos[3] ;
extern float MRILIB_zcos[3] ;
extern int use_MRILIB_slicespacing ; /* 10 Jan 2004 */
extern float MRILIB_slicespacing ;
extern int assume_dicom_mosaic ; /* mri_read_dicom.c 13 Mar 2006 [rickr] */
#ifdef __cplusplus
}
#endif
#include "nifti1_io.h"
extern int use_MRILIB_dicom_matrix ; /* 26 Jan 2006 */
extern mat44 MRILIB_dicom_matrix ;
#include "mri_dicom_stuff.h"
extern int MRILIB_dicom_count ; /* 15 Mar 2006 */
extern AFD_dicom_header **MRILIB_dicom_header ;
/*! Clear the MRILIB globals
(which transmit info from image files to to3d.c). */
#define CLEAR_MRILIB_globals \
do{ MRILIB_orients[0]='\0'; \
MRILIB_zoff=MRILIB_xoff=MRILIB_yoff=MRILIB_tr=0.0; \
use_MRILIB_xoff=use_MRILIB_yoff=use_MRILIB_zoff=0; \
use_MRILIB_xcos=use_MRILIB_ycos=use_MRILIB_zcos=0; \
use_MRILIB_slicespacing=0; \
use_MRILIB_dicom_matrix=0; \
MRILIB_dicom_count=0; MRILIB_dicom_header=NULL; \
} while(0)
#include <stdio.h>
#include <stdlib.h>
#include <math.h>
#include "mcw_malloc.h" /* 06 Mar 1999 addition */
#include "debugtrace.h" /* 26 Jan 2001 addition */
#include "Amalloc.h" /* 09 Dec 2003 addition */
#ifndef PI
# define PI 3.14159265358979323846
#endif
#ifndef WAY_BIG
/*! A big number (anything over this is infinity). */
# define WAY_BIG 1.e+10
#endif
#ifndef FLDIF
/*! Are 2 floats significantly different? */
# define FLDIF(x,y) ( fabs(x-y) > 1.e-4 * (fabs(x)+fabs(y)) )
#endif
#ifndef MAX
# define MAX(a,b) (((a)<(b)) ? (b) : (a))
#endif
#ifndef MIN
# define MIN(a,b) (((a)>(b)) ? (b) : (a))
#endif
/**** define types ****/
/*! The MRI_byte data type. */
#ifndef TYPEDEF_byte
#define TYPEDEF_byte
typedef unsigned char byte ;
#endif
/*! RGBA data type; not used anywhere (yet). */
#ifndef TYPEDEF_rgba
#define TYPEDEF_rgba
typedef struct { byte r,g,b,a ; } rgba ; /* 24 Aug 2001 */
#endif
#define LOAD_rgba(s,rr,gg,bb,aa) ((s).r=(rr),(s).g=(gg),(s).b=(bb),(s).a=(bb))
#define UNLOAD_rgba(s,rr,gg,bb,aa) ((rr)=(s).r,(gg)=(s).g,(bb)=(s).b,(aa)=(s).a)
/*! Scale a byte [0..255] to a float in [0..1). */
#define BYTE_TO_ZONE(b) (0.00392157*(b))
/*! Scale a float in [0..1] to a byte in [0..255]. */
#define ZONE_TO_BYTE(z) ((byte)(255.49*(z)))
/*! Integer flags for different image types. Sometimes called the "datum". */
typedef enum MRI_TYPE {
MRI_byte , MRI_short , MRI_int ,
MRI_float , MRI_double , MRI_complex , MRI_rgb , MRI_rgba } MRI_TYPE ;
#define MRI_KIND MRI_TYPE ; /* to alleviate stupidity */
#define MRI_type MRI_TYPE ;
#define MRI_kind MRI_TYPE ;
#define MRI_rgbyte MRI_rgb
/*! The last MRI_TYPE yet defined. */
#define LAST_MRI_TYPE 7
/*! String names for MRI_TYPE. */
static char * MRI_TYPE_name[8] =
{ "byte", "short", "int", "float", "double", "complex", "rgb", "RGBA" } ;
#define MRI_type_name MRI_TYPE_name /* because I forget */
#define MRI_TYPE_NAME(iimm) MRI_TYPE_name[(iimm)->kind] /* 26 Apr 2005 */
/*! Max value of a byte. */
#define MRI_maxbyte 255
/*! Max value of a short. */
#define MRI_maxshort 32767
/*! Max value of an int. */
#define MRI_maxint 2147483647
/*! Max values for various types, if they have them. */
static float MRI_TYPE_maxval[7] =
{ 255.0 , 32767.0 , 2147483647.0 , 0.0,0.0,0.0 , 255.0 } ;
/*! Force a float into a short. */
#define SHORTIZE(xx) ( ((xx) < -32767.0) ? (short)-32767 \
: ((xx) > 32767.0) ? (short) 32767 : (short)rint(xx) )
/*! Force a float into a byte. */
#define BYTEIZE(xx) ( ((xx) < 0.0) ? (byte)0 \
: ((xx) > 255.0) ? (byte)255 : (byte)rint(xx) )
/*! Determine if a MRI_TYPE is an integer type. */
#define MRI_IS_INT_TYPE(typ) ((typ) < 3)
/*! I suppose that the next C makes this pleonastic. */
#if defined(_SUNPERF_COMPLEX) || defined(DONT_DECLARE_COMPLEX)
# define TYPEDEF_complex
#endif
#ifndef TYPEDEF_complex
#define TYPEDEF_complex
typedef struct complex { float r , i ; } complex ;
#endif
#ifndef TYPEDEF_float_pair
#define TYPEDEF_float_pair
typedef struct { float a,b ; } float_pair ;
#endif
/*-------*/
/*! Triple to hold RGB bytes. */
#ifndef TYPEDEF_rgbyte
#define TYPEDEF_rgbyte
typedef struct rgbyte { byte r,g,b ; } rgbyte ; /* 15 Feb 1999 */
#undef RGBZEQ
#undef RGBZAS
#define RGBZEQ(q) ( (q).r==0 && (q).g==0 && (q).b==0 ) /* is == (0,0,0)? */
#define RGBZAS(q) ( (q).r = (q).g = (q).b = 0 ) /* set = (0,0,0). */
#endif
static rgbyte tEMp_rgbyte_aAa ;
/*! Convert one RBG triple (rgbyte) to a single int. */
#define RGBYTE_TO_INT(rgb) ( (rgb).r << 16 | (rgb).g << 8 | (rgb).b )
/*! Convert one int to a RGB triple (rgbyte). */
#define INT_TO_RGB(q) ( tEMp_rgbyte_aAa.r = ((q) >> 16) & 0xff , \
tEMp_rgbyte_aAa.g = ((q) >> 8) & 0xff , \
tEMp_rgbyte_aAa.b = (q) & 0xff , tEMp_rgbyte_aAa )
/*-------*/
/*! A union type to hold all possible MRI_IMAGE types.
This was created before I really understood how to use void *. */
#undef USE_UNION_DATA
#ifdef USE_UNION_DATA
typedef union MRI_DATA {
byte *byte_data ;
short *short_data ;
int *int_data ;
float *float_data ;
double *double_data ;
complex *complex_data ;
byte *rgb_data ; /* Apr 1996: not well supported yet */
rgba *rgba_data ; /* Mar 2002 */
} MRI_DATA ;
#else
# define MRI_DATA void * /* 21 Dec 2006: the big changeover */
#endif
/** Mar 1996: Extended to images up to 7D;
Not all routines work with images > 2D --
check top of file for "7D SAFE" comments **/
#undef USE_MRI_LABELS
#ifdef USE_MRI_LABELS
# define MRI_LABEL_SIZE 4
#endif
#define INPUT_DELAY 1
#define BSWAP_DELAY 2
#define IS_PURGED 4
/*! Stores one image (1D to 7D).
Why 7D, you ask? Well, I originally only had 2D images here.
When extending AFNI from 3D to 3D+time and buckets, I thought
that I might use 4D images (x,y,z,t) as the basic element.
Instead, I decided to use an array of 3D images (in a THD_datablock),
but by then I'd extended this typedef to allow (x,y,z,t,u,v,w) dimensioned
arrays. I don't think anyplace ever uses more than 3D images, though.
*/
typedef struct MRI_IMAGE {
int nx ; /*!< 1st dimension of image */
int ny ; /*!< 2nd dimension of image (1 for 1D image) */
int nz ; /*!< 3rd dimension of image (1 for 2D image) */
int nt ; /*!< 4th dimension of image (1 for 3D image) */
int nu ; /*!< 5th dimension of image (1 for 4D image) */
int nv ; /*!< 6th dimension of image (1 for 5D image) */
int nw ; /*!< 7th dimension of image (1 for 6D image) */
int nxy ; /*!< nx*ny */
int nxyz ; /*!< nx*ny*nz */
int nxyzt ; /*!< nx*ny*nz*nt */
int nvox ; /*!< number of voxels total */
int pixel_size ; /*!< bytes per pixel */
MRI_TYPE kind ; /*!< one of the MRI_TYPE codes above */
MRI_DATA im ; /*!< pointer to actual pixel data */
char *name ; /*!< string attached; may be NULL; might be filename */
float dx ; /*!< physical pixel size, if != 0 */
float dy ; /*!< physical pixel size, if != 0 */
float dz ; /*!< physical pixel size, if != 0 */
float dt ; /*!< physical pixel size, if != 0 */
float du ; /*!< physical pixel size, if != 0 */
float dv ; /*!< physical pixel size, if != 0 */
float dw ; /*!< physical pixel size, if != 0 */
float xo ; /*!< spatial origin of axis */
float yo ; /*!< spatial origin of axis */
float zo ; /*!< spatial origin of axis */
float to ; /*!< spatial origin of axis */
float uo ; /*!< spatial origin of axis */
float vo ; /*!< spatial origin of axis */
float wo ; /*!< spatial origin of axis */
#ifdef USE_MRI_LABELS
char xlab[MRI_LABEL_SIZE] ; /*!< labels for each dimension */
ylab[MRI_LABEL_SIZE] ; /*!< labels for each dimension */
zlab[MRI_LABEL_SIZE] ; /*!< labels for each dimension */
tlab[MRI_LABEL_SIZE] ; /*!< labels for each dimension */
ulab[MRI_LABEL_SIZE] ; /*!< labels for each dimension */
vlab[MRI_LABEL_SIZE] ; /*!< labels for each dimension */
wlab[MRI_LABEL_SIZE] ; /*!< labels for each dimension */
#endif
char *fname ; /*!< to read actual image data after delay */
unsigned int foffset ; /*!< offset into fname of image data */
int fondisk ; /*!< flag to indicate if is on disk (?) */
int was_swapped ; /* 07 Mar 2002 */
} MRI_IMAGE ;
#ifdef USE_MRI_LABELS
/*! Copy auxiliary data from one MRI_IMAGE to another. */
# define MRI_COPY_AUX(nn,oo) \
( (nn)->dx = (oo)->dx , (nn)->dy = (oo)->dy , (nn)->dz = (oo)->dz , \
(nn)->dt = (oo)->dt , (nn)->du = (oo)->du , (nn)->dv = (oo)->dv , \
(nn)->dw = (oo)->dw , \
(nn)->xo = (oo)->xo , (nn)->yo = (oo)->yo , (nn)->zo = (oo)->zo , \
(nn)->to = (oo)->to , (nn)->uo = (oo)->uo , (nn)->vo = (oo)->vo , \
(nn)->wo = (oo)->wo , \
strcpy((nn)->xlab,(oo)->xlab) , strcpy((nn)->ylab,(oo)->ylab) , \
strcpy((nn)->zlab,(oo)->zlab) , strcpy((nn)->tlab,(oo)->tlab) , \
strcpy((nn)->ulab,(oo)->ulab) , strcpy((nn)->vlab,(oo)->vlab) , \
strcpy((nn)->wlab,(oo)->wlab) , \
mri_add_name( (oo)->name , (nn) ) )
#else
# define MRI_COPY_AUX(nn,oo) \
( (nn)->dx = (oo)->dx , (nn)->dy = (oo)->dy , (nn)->dz = (oo)->dz , \
(nn)->dt = (oo)->dt , (nn)->du = (oo)->du , (nn)->dv = (oo)->dv , \
(nn)->dw = (oo)->dw , \
(nn)->xo = (oo)->xo , (nn)->yo = (oo)->yo , (nn)->zo = (oo)->zo , \
(nn)->to = (oo)->to , (nn)->uo = (oo)->uo , (nn)->vo = (oo)->vo , \
(nn)->wo = (oo)->wo , \
mri_add_name( (oo)->name , (nn) ) )
#endif
/*! Check if MRI_IMAGE is 1D (ny=1) */
#define MRI_IS_1D(iq) ((iq)->ny == 1)
/*! Check if MRI_IMAGE is 2D (nz=1) */
#define MRI_IS_2D(iq) ((iq)->ny > 1 && (iq)->nz == 1)
/*! Check if MRI_IMAGE is 3D (nt=1) */
#define MRI_IS_3D(iq) ((iq)->nz > 1 && (iq)->nt == 1)
/*! Check if MRI_IMAGE is 4D (nu=1) */
#define MRI_IS_4D(iq) ((iq)->nt > 1 && (iq)->nu == 1)
/*! Return dimensionality of MRI_IMAGE */
#define MRI_DIMENSIONALITY(iq) \
( ((iq)->ny == 1) ? 1 : ((iq)->nz == 1) ? 2 : \
((iq)->nt == 1) ? 3 : ((iq)->nu == 1) ? 4 : \
((iq)->nv == 1) ? 5 : ((iq)->nw == 1) ? 6 : 7 )
#define MRI_BYTE_PTR(iq) ((byte *)mri_data_pointer(iq))
#define MRI_SHORT_PTR(iq) ((short *)mri_data_pointer(iq))
#define MRI_INT_PTR(iq) ((int *)mri_data_pointer(iq))
#define MRI_FLOAT_PTR(iq) ((float *)mri_data_pointer(iq))
#define MRI_DOUBLE_PTR(iq) ((double *)mri_data_pointer(iq))
#define MRI_COMPLEX_PTR(iq) ((complex *)mri_data_pointer(iq))
#define MRI_RGB_PTR(iq) ((byte *)mri_data_pointer(iq))
#define MRI_RGBA_PTR(iq) ((rgba *)mri_data_pointer(iq))
/* only used in afni.c -- don't use these generally! */
#define MRI_BYTE_2D(iq,ix,jy) MRI_BYTE_PTR(iq)[(ix)+(jy)*(iq)->nx]
#define MRI_SHORT_2D(iq,ix,jy) MRI_SHORT_PTR(iq)[(ix)+(jy)*(iq)->nx]
#define MRI_INT_2D(iq,ix,jy) MRI_INT_PTR(iq)[(ix)+(jy)*(iq)->nx]
#define MRI_FLOAT_2D(iq,ix,jy) MRI_FLOAT_PTR(iq)[(ix)+(jy)*(iq)->nx]
#define MRI_DOUBLE_2D(iq,ix,jy) MRI_DOUBLE_PTR(iq)[(ix)+(jy)*(iq)->nx]
#define MRI_COMPLEX_2D(iq,ix,jy) MRI_COMPLEX_PTR(iq)[(ix)+(jy)*(iq)->nx]
#define FLOAT_TO_BYTE(fff) \
( ((fff)<=0.0) ? (0) : ((fff)>=255.5) ? (255) : (byte)((fff)+0.49) )
#define SHORT_TO_BYTE(fff) \
( ((fff)<=0) ? (0) : ((fff)>=255) ? (255) : (byte)(fff) )
#define FLOAT_TO_SHORT(fff) ((short)(fff))
/*********** Type: array of MRI_IMAGE pointers ***********/
/*! Array of MRI_IMAGE pointers. */
typedef struct MRI_IMARR {
int num ; /*!< Number of actual MRI_IMAGE here */
int nall ; /*!< Size of imarr array currently allocated */
MRI_IMAGE ** imarr ; /*!< Array of MRI_IMAGE pointers */
} MRI_IMARR ;
/*! Get the nn-th image from the image array "name". */
#define IMAGE_IN_IMARR(name,nn) ((name)->imarr[(nn)])
#define IMARR_SUBIMAGE IMAGE_IN_IMARR
#define IMARR_SUBIM IMAGE_IN_IMARR
/*! Get the number of images in the image array "name". */
#define IMARR_COUNT(name) ((name)->num)
#define IMARR_LASTIM(name) ((name)->imarr[(name)->num-1])
#define IMARR_FIRSTIM(name) ((name)->imarr[0])
#define INC_IMARR 32
/*! Initialize an MRI_IMARR struct. */
#define INIT_IMARR(name) \
do{ int iq ; (name) = (MRI_IMARR *) malloc(sizeof(MRI_IMARR)) ; \
(name)->num = 0 ; (name)->nall = INC_IMARR ; \
(name)->imarr = (MRI_IMAGE **)malloc(sizeof(MRI_IMAGE *)*INC_IMARR) ; \
for( iq=(name)->num ; iq < (name)->nall ; iq++ ) (name)->imarr[iq] = NULL ; \
break ; } while(0)
/*! Add one MRI_IMAGE to the MRI_IMARR struct. */
#define ADDTO_IMARR(name,imm) \
do{ int nn , iq ; \
if( (name)->num == (name)->nall ){ \
nn = (name)->nall = 1.1*(name)->nall + INC_IMARR ; \
(name)->imarr = (MRI_IMAGE **)realloc( (name)->imarr,sizeof(MRI_IMAGE *)*nn );\
for( iq=(name)->num ; iq < (name)->nall ; iq++ ) (name)->imarr[iq] = NULL ; } \
nn = (name)->num ; ((name)->num)++ ; \
(name)->imarr[nn] = (imm) ; break ; } while(0)
/*! Free the MRI_IMARR struct (but not the images within). */
#define FREE_IMARR(name) \
do{ if( (name) != NULL ){ \
free((name)->imarr); free((name)); (name) = NULL; } break; } while(0)
/*! Free the MRI_IMARR struct, including the images within. */
#define DESTROY_IMARR(name) \
do{ int nn ; \
if( (name) != NULL ){ \
for( nn=0 ; nn < (name)->num ; nn++ ) mri_free((name)->imarr[nn]) ; \
free((name)->imarr); free((name)); (name) = NULL; } break; } while(0)
/*! Free all images at-and-after [qq] in the MRI_IMARR struct. */
#define TRUNCATE_IMARR(name,qq) \
do{ int nn ; \
if( (name) != NULL && qq < (name)->num ){ \
for( nn=qq ; nn < (name)->num ; nn++ ) mri_free((name)->imarr[nn]); \
(name)->num = qq ; \
} } while(0)
/******* macros for complex arithmetic, using comma operator *******/
static float MRI_fla ; /* float temporaries */
static complex MRI_cxa , MRI_cxb , MRI_cxc ; /* complex temporaries */
/*! Return a complex from two floats. */
#define CMPLX(x,y) ( MRI_cxa.r = (x) , MRI_cxa.i = (y) , MRI_cxa )
/*! Return complex u+v */
#define CADD(u,v) ( MRI_cxa.r = u.r + v.r , \
MRI_cxa.i = u.i + v.r , MRI_cxa )
/*! complex u += v */
#define CADDTO(u,v) ( u.r += v.r , u.i += v.i )
/*! Return complex u-v */
#define CSUB(u,v) ( MRI_cxa.r = u.r - v.r , \
MRI_cxa.i = u.i - v.i , MRI_cxa )
/*! complex u -= v */
#define CSUBFROM(u,v) ( u.r -= v.r , u.i -= v.i )
/*! Return complex u*v */
#define CMULT(u,v) ( MRI_cxb.r = u.r * v.r - u.i * v.i , \
MRI_cxb.i = u.r * v.i + u.i * v.r , MRI_cxb )
/*! complex u *= v */
#define CMULTBY(u,v) ( MRI_fla = u.r * v.r - u.i * v.i , \
u.i = u.r * v.i + u.i * v.r , u.r = MRI_fla )
/*! Return complex u * conjg(v) */
#define CJMULT(u,v) ( MRI_cxb.r = u.r * v.r + u.i * v.i , \
MRI_cxb.i = u.i * v.r - u.r * v.i , MRI_cxb )
/*! complex u *= conjg(v) */
#define CJMULTBY(u,v) ( MRI_fla = u.r * v.r + u.i * v.i , \
u.i = u.i * v.r - u.r * v.i , u.r = MRI_fla )
/*! complex w += u*v */
#define CMADD(u,v,w) ( w.r += u.r * v.r - u.i * v.i , \
w.i += u.r * v.i + u.i * v.r )
/*! Return complex exp(I*t) */
#define CEXPIT(t) ( MRI_cxc.r = cos(t) , MRI_cxc.i = sin(t) , MRI_cxc )
/**** macros ****/
static int MRI_mm ;
/*! Median of 3. */
#define MEDIAN(a,b,c) ( MRI_mm = 4*((a)<(b)) + 2*((a)<(c)) + ((b)<(c)) , \
(MRI_mm==3||MRI_mm==4) ? (a) : \
(MRI_mm==7||MRI_mm==0) ? (b) : (c) )
/*! Order-statistic filter of 3. */
#define OSFSUM(p,q,r) (0.70*(p)+0.15*((q)+(r)))
/*! Order-statistic filter of 3. */
#define OSFILT(a,b,c) ( MRI_mm = 4*((a)<(b)) + 2*((a)<(c)) + ((b)<(c)) , \
(MRI_mm==3||MRI_mm==4) ? OSFSUM(a,b,c) : \
(MRI_mm==7||MRI_mm==0) ? OSFSUM(b,a,c) : OSFSUM(c,a,b) )
#ifndef TRUE
# define TRUE (1)
#endif
#ifndef FALSE
# define FALSE (0)
#endif
#define MRI_BILINEAR (1) /* for the warping function */
#define MRI_LINEAR (1)
#define MRI_BICUBIC (2)
#define MRI_CUBIC (2)
#define MRI_FOURIER (3)
#define MRI_NN (0)
#define MRI_QUINTIC (4) /* Nov 1998 */
#define MRI_HEPTIC (5)
#define MRI_TSSHIFT (6) /* Dec 1999 */
#define MRI_FOURIER_NOPAD (66) /* 13 May 2003 */
#define MRI_HIGHORDER(x) ((x) != MRI_NN && (x) != MRI_LINEAR)
#define SQR(x) ((x)*(x))
#define CSQR(z) (SQR(z.r)+SQR(z.i))
#define CABS(z) sqrt(CSQR(z))
#define CARG(z) ( ((z).r!=0.0 || (z).i!=0.0) ? atan2((z).i,(z).r) : 0.0 )
/*! complex z /= abs(z) */
#define CUNITIZE(z) ( MRI_fla=CABS(z) , z.r=z.r/MRI_fla , z.i=z.i/MRI_fla )
#ifdef MRI_DEBUG
# define WHOAMI fprintf(stderr,"in file: %s at line %d\n",__FILE__,__LINE__);
#else
# define WHOAMI
#endif
#ifdef MRI_DEBUG
# define IMHEADER(f) \
fprintf(stderr,"%s: nx=%d ny=%d kind=%d\n",#f,f->nx,f->ny,f->kind);
#else
# define IMHEADER(f)
#endif
#define MRI_FATAL_ERROR \
{fprintf(stderr,"in file: %s at line %d\n",__FILE__,__LINE__);EXIT(1);}
/**** prototypes ****/
#ifdef __cplusplus
extern "C" { /* care of Greg Balls 7 Aug 2006 [rickr] */
#endif
extern void mri_input_delay( MRI_IMAGE * ) ;
extern void mri_purge_delay( MRI_IMAGE * ) ;
extern void mri_add_fname_delay( char * , MRI_IMAGE * ) ;
extern MRI_IMARR * mri_read_file_delay( char * ) ;
extern MRI_IMARR * mri_read_3D_delay( char * ) ;
extern void mri_purge ( MRI_IMAGE * ) ; /* 20 Dec 2006 */
extern void mri_unpurge ( MRI_IMAGE * ) ;
extern void mri_killpurge( MRI_IMAGE * ) ;
extern char * mri_purge_get_tmpdir(void) ; /* 21 Dec 2006 */
#define MRI_IS_PURGED(iq) \
( (iq)!=NULL && (iq)->fondisk==IS_PURGED && (iq)->fname!=NULL )
#define MRI_HAS_DATA(iq) \
( (iq)!= NULL && \
( ( (iq)->fondisk==IS_PURGED && (iq)->fname!=NULL ) || \
mri_data_pointer_unvarnished(iq) != NULL ) )
extern int mri_equal( MRI_IMAGE *, MRI_IMAGE * ) ; /* 30 Jun 2003 */
extern MRI_IMARR * mri_read_analyze75( char * ) ; /* 05 Feb 2001 */
extern MRI_IMARR * mri_read_siemens( char * ) ; /* 12 Mar 2001 */
extern MRI_IMARR * mri_read3D_analyze75( char * ); /* 26 Aug 2002 */
extern MRI_IMAGE * mri_read_stuff( char * ) ; /* 22 Nov 2002 */
extern void mri_inflate_pbm( MRI_IMAGE * ); /* 02 Jan 2002 */
extern void mri_add_name( char * , MRI_IMAGE * ) ;
extern MRI_IMAGE ** mri_stat_seq( MRI_IMAGE * ) ;
#define NSTAT_MEAN 0
#define NSTAT_SIGMA 2
#define NSTAT_CVAR 3
#define NSTAT_MEDIAN 4
#define NSTAT_MAD 5
#define NSTAT_MAX 6
#define NSTAT_MIN 7
#define NSTAT_ABSMAX 13
#define NSTAT_VAR 17
#define NSTAT_NUM 18
#define NSTAT_FWHMx 63
#define NSTAT_FWHMy 64
#define NSTAT_FWHMz 65
#define NBISTAT_BASE 66601
#define NBISTAT_SPEARMAN_CORR 66601
#define NBISTAT_QUADRANT_CORR 66602
#define NBISTAT_PEARSON_CORR 66603
#define NBISTAT_MUTUAL_INFO 66604
#define NBISTAT_NORMUT_INFO 66605
#define NBISTAT_JOINT_ENTROPY 66606
#define NBISTAT_HELLINGER 66607
#define NBISTAT_CORR_RATIO_M 66608
#define NBISTAT_CORR_RATIO_A 66609
#define NBISTAT_CORR_RATIO_U 66610
#define NBISTAT_NUM 66611
extern float mri_nstat ( int , MRI_IMAGE * ) ; /* 19 Aug 2005 */
extern float mri_nbistat( int , MRI_IMAGE *, MRI_IMAGE * ) ; /* 26 Oct 2006 */
extern void mri_nbistat_setclip( float, float , float, float ) ;
extern MRI_IMAGE * mri_edit_image( float pthr, float power, MRI_IMAGE * im ) ;
extern MRI_IMARR * mri_read_mpeg( char * ) ; /* 03 Dec 2003 */
extern int mri_isgray( MRI_IMAGE * ) ;
extern int mri_imcount_mpeg( char * ) ;
extern void cfft( int , int , float * , float * ) ;
extern void cfft2d_cox( int , int , int , float * , float * ) ;
extern void csfft_cox( int,int , complex * ) ;
extern void csfft_many( int,int,int , complex * ) ;
extern int csfft_nextup(int) ;
extern int csfft_nextup_one35(int) ;
extern int csfft_nextup_even(int) ;
extern void csfft_scale_inverse(int) ;
extern void csfft_use_fftw( int ) ; /* 20 Oct 2000 */
extern void mri_fftshift( MRI_IMAGE *, float,float,float, int ) ; /* 13 May 2003 */
extern void * mri_data_pointer( MRI_IMAGE * ) ;
extern void mri_free( MRI_IMAGE * ) ;
extern void mri_clear( MRI_IMAGE * ) ; /* 31 Jan 2007 */
extern void mri_fix_data_pointer( void * , MRI_IMAGE * ) ;
#define mri_set_data_pointer(iq,pt) mri_fix_data_pointer((pt),(iq))
#define MRI_FREE(iq) do{ mri_free(iq); (iq)=NULL; } while(0)
#ifdef USE_UNION_DATA
extern void * mri_data_pointer_unvarnished( MRI_IMAGE *im ) ;
#else
# define mri_data_pointer_unvarnished(iq) ((iq)->im)
#endif
extern char * mri_dicom_header( char * ) ; /* 15 Jul 2002 */
extern void mri_dicom_pxlarr( off_t *, int * ) ;
extern void mri_dicom_noname( int ) ;
extern void mri_dicom_nohex ( int ) ;
extern void mri_dicom_setvm ( int ) ; /* 28 Oct 2002 */
extern void mri_dicom_seterr( int ) ; /* 05 Nov 2002 */
extern MRI_IMARR * mri_read_dicom( char * ) ;
extern int mri_imcount_dicom( char * ) ;
extern char * mri_dicom_sexinfo( void ) ; /* 23 Dec 2002 */
extern char * mri_dicom_sex1010( void ) ;
extern int mri_possibly_dicom( char * ) ; /* 07 May 2003 */
/*! Set the data pointer in an MRI_IMAGE to NULL. */
#define mri_clear_data_pointer(iq) mri_fix_data_pointer(NULL,(iq))
/*! Set all pixels in MRI_IMAGE to zero. */
#define mri_zero_image(iq) \
memset(mri_data_pointer(iq),0,(iq)->nvox*(iq)->pixel_size)
extern MRI_IMAGE * mri_zeropad_3D( int,int,int,int,int,int , MRI_IMAGE * ) ;
extern MRI_IMAGE * mri_zeropad_2D( int,int,int,int, MRI_IMAGE * ) ;
extern double mri_max( MRI_IMAGE * ) ;
extern double mri_min( MRI_IMAGE * ) ;
extern double mri_maxabs( MRI_IMAGE * ) ;
extern MRI_IMAGE * mri_cut_2D( MRI_IMAGE * , int,int,int,int ) ;
extern MRI_IMAGE * mri_cut_3D( MRI_IMAGE * , int,int,int,int,int,int ) ;
/** 15 Apr 1999 **/
extern void upsample_7( int , int , float * , float * ) ;
extern void upsample_1( int , int , float * , float * ) ; /* 12 Mar 2002 */
extern MRI_IMAGE * mri_dup2D( int , MRI_IMAGE * ) ;
extern void mri_dup2D_mode( int ) ; /* 12 Mar 2002 */
extern void mri_move_guts( MRI_IMAGE *, MRI_IMAGE * ) ; /* 28 Mar 2002 */
extern MRI_IMAGE * mri_copy( MRI_IMAGE * ) ; /* 17 Apr 2000 */
extern MRI_IMAGE * mri_expand_2D( int , MRI_IMAGE * ) ; /* 22 Feb 2004 */
extern MRI_IMAGE *mri_new( int , int , MRI_TYPE ) ;
extern MRI_IMAGE *mri_read( char * ) ;
extern MRI_IMAGE *mri_read_ge4( char * ) ; /* 03 Jun 2003 */
extern int mri_write( char * , MRI_IMAGE * ) ;
extern int mri_write_pnm( char * , MRI_IMAGE * ) ;
extern int mri_write_jpg( char * , MRI_IMAGE * ) ; /* 15 Apr 2005 */
extern int mri_write_png( char * , MRI_IMAGE * ) ; /* 11 Dec 2006 */
extern int mri_write_filtered( char * , MRI_IMAGE * ) ; /* 15 Dec 2006 */
extern int mri_write_7D( char * , MRI_IMAGE * ) ;
extern int mri_datum_size( MRI_TYPE typ ) ;
extern MRI_IMAGE *mri_read_ascii( char * ) ;
extern MRI_IMAGE *mri_read_double_ascii( char * ) ;
extern MRI_IMAGE *mri_read_complex_ascii( char * ) ;
extern MRI_IMAGE *mri_read_ascii_ragged(char *, float) ; /* 28 Jul 2004 */
extern int mri_write_ascii( char * , MRI_IMAGE * ) ;
extern int mri_write_raw( char * , MRI_IMAGE * ) ; /* 05 Jan 2000 */
extern void mri_write_analyze( char * , MRI_IMAGE * ) ; /* 29 Nov 2001 */
extern MRI_IMAGE * mri_read_ascii_ragged_complex(char *,float); /* 08 Mar 2007 */
extern MRI_IMAGE * mri_read_ragged_fromstring( char *, float); /* 05 Jan 2007 */
extern MRI_IMAGE * mri_read_1D( char * ) ; /* 16 Nov 1999 */
extern MRI_IMAGE * mri_read_double_1D( char * ) ;
extern MRI_IMAGE * mri_read_complex_1D( char * ) ;
extern int mri_write_1D( char * , MRI_IMAGE * ) ; /* 16 Nov 1999 */
extern MRI_IMAGE * mri_1D_fromstring( char * ) ; /* 28 Apr 2003 */
extern int setup_mri_write_angif( void ) ; /* 28 Jun 2001 */
extern int mri_write_angif( char *, MRI_IMARR * ) ;
extern MRI_IMAGE * mri_colorsetup( int,int,int,int ) ; /* 05 Oct 2004 */
extern MRI_IMAGE *mri_new_vol ( int,int,int , MRI_TYPE ) ;
extern MRI_IMAGE *mri_new_vol_empty( int,int,int , MRI_TYPE ) ;
MRI_IMAGE *mri_new_7D_generic( int nx, int ny, int nz, int nt,
int nu, int nv, int nw,
MRI_TYPE kind , int make_space ) ;
/*! Create new MRI_IMAGE of type kk, with same dimensions as iq. */
#define mri_new_conforming(iq,kk) \
mri_new_7D_generic( (iq)->nx, (iq)->ny, (iq)->nz , (iq)->nt , \
(iq)->nu, (iq)->nv, (iq)->nw , (kk) , TRUE )
/*! Create new MRI_IMAGE of type kk, with same dimensions as iq,
and with no data space allocated. */
#define mri_empty_conforming(iq,kk) \
mri_new_7D_generic( (iq)->nx, (iq)->ny, (iq)->nz , (iq)->nt , \
(iq)->nu, (iq)->nv, (iq)->nw , (kk) , FALSE )
extern MRI_IMARR * mri_read_3D( char * ) ;
extern MRI_IMARR * mri_read_3A( char * ) ;
extern MRI_IMARR * mri_read_file( char * ) ;
extern int mri_imcount( char * ) ;
extern MRI_IMARR * mri_read_many_files( int nf , char * fn[] ) ;
extern MRI_IMARR * mri_read_resamp_many_files( int nf, char * fn[] , int nxnew, int nynew);
/** returns array of byte images: red, green, blue **/
extern MRI_IMARR * mri_read_ppm3( char * fname ) ;
extern MRI_IMAGE * mri_read_ppm( char * fname ) ;
extern void mri_read_ppm_header( char *, int *, int *) ; /* 17 Sep 2001 */
MRI_IMAGE *mri_read_just_one( char * fname ) ;
MRI_IMAGE *mri_read_nsize( char * fname ) ;
MRI_IMARR *mri_read_many_nsize( int nf , char * fn[] ) ;
void init_MCW_sizes(void) ;
char * imsized_fname( char * fname ) ;
char * my_strdup( char * str ) ;
#define mri_filesize THD_filesize /* 22 Mar 2007 */
extern void mri_overlay_2D( MRI_IMAGE *, MRI_IMAGE *, int,int ) ;
extern void mri_swapbytes( MRI_IMAGE * ) ;
extern void swap_twobytes ( int n , void * ar ) ; /* 14 Sep 1998 */
extern void swap_fourbytes ( int n , void * ar ) ;
extern void swap_eightbytes( int n , void * ar ) ; /* 06 Feb 2003 */
extern MRI_IMAGE *mri_to_float( MRI_IMAGE * ) ;
extern MRI_IMAGE *mri_to_short( double , MRI_IMAGE * ) ;
extern MRI_IMAGE *mri_to_short_scl( double,double , MRI_IMAGE * ) ;
extern MRI_IMAGE *mri_to_short_sclip( double,double , int,int , MRI_IMAGE * ) ;
extern MRI_IMAGE *mri_to_complex( MRI_IMAGE * ) ;
extern MRI_IMAGE *mri_to_byte( MRI_IMAGE * ) ;
extern MRI_IMAGE *mri_to_byte_scl( double , double , MRI_IMAGE * ) ;
extern MRI_IMAGE * mri_to_rgb( MRI_IMAGE * ) ;
extern MRI_IMAGE * mri_3to_rgb( MRI_IMAGE * , MRI_IMAGE * , MRI_IMAGE * ) ;
extern MRI_IMARR * mri_rgb_to_3float( MRI_IMAGE * ) ;
extern MRI_IMARR * mri_rgb_to_3byte( MRI_IMAGE * ) ;
extern MRI_IMAGE * mri_sharpen_rgb( float , MRI_IMAGE * ) ;
extern MRI_IMAGE * mri_flatten_rgb( MRI_IMAGE * ) ;
extern void mri_invert_inplace( MRI_IMAGE *) ; /* 07 Apr 2003 */
extern void mri_gamma_rgb_inplace( float gam , MRI_IMAGE *im ) ;
extern MRI_IMAGE * mri_to_rgba( MRI_IMAGE * ) ; /* 20 Mar 2002 */
extern MRI_IMAGE *mri_pair_to_complex( MRI_IMAGE * , MRI_IMAGE * ) ;
extern MRI_IMARR *mri_complex_to_pair( MRI_IMAGE * ) ;
extern MRI_IMAGE *mri_to_complex_ext( MRI_IMAGE * , int , int , int ) ;
extern MRI_IMAGE *mri_scale_to_float( float , MRI_IMAGE * ) ;
extern void mri_threshold( double , double , MRI_IMAGE * , MRI_IMAGE * ) ;
extern MRI_IMAGE * mri_mult_to_float( float * , MRI_IMAGE * ) ;
extern MRI_IMAGE * mri_scalize( MRI_IMAGE *, int, float * ) ; /* 20 Oct 2003 */
extern MRI_IMAGE *mri_multiply_complex( int , MRI_IMAGE * , MRI_IMAGE * ) ;
extern MRI_IMAGE *mri_complex_phase( MRI_IMAGE * ) ;
extern MRI_IMAGE *mri_to_mri( int , MRI_IMAGE * ) ;
extern MRI_IMAGE *mri_to_mri_scl( int , double , MRI_IMAGE * ) ;
extern MRI_IMAGE *mri_complex_abs( MRI_IMAGE * ) ;
extern void mri_fft_complex( int , float , MRI_IMAGE * ) ;
extern float *mri_setup_taper( int , float ) ;
extern MRI_IMAGE *mri_warp( MRI_IMAGE * , int , int , int ,
void func(float,float,float *,float *) ) ;
extern MRI_IMAGE *mri_warp_bicubic( MRI_IMAGE * , int , int ,
void func(float,float,float *,float *) ) ;
extern MRI_IMAGE *mri_warp_bilinear( MRI_IMAGE * , int , int ,
void func(float,float,float *,float *) ) ;
#undef WARP_POINT_ROUTINES
#ifdef WARP_POINT_ROUTINES
extern float mri_warp_bicubic_point( MRI_IMAGE * , int , int ,
void func( float,float,float *,float *) ) ;
extern float mri_rotate_point( MRI_IMAGE *im, float,float,float,float, int,int ) ;
#endif /* WARP_POINT_ROUTINES */
extern void mri_warp_setpow( float gg ) ; /* 15 Jan 2007 */
extern MRI_IMAGE *mri_resize( MRI_IMAGE * , int , int ) ;
extern MRI_IMAGE *mri_resize_NN( MRI_IMAGE *, int , int ) ; /* 08 Jun 2004 */
extern MRI_IMAGE *mri_squareaspect( MRI_IMAGE * ) ;
extern MRI_IMAGE *mri_rotate ( MRI_IMAGE * , float,float,float,float ) ;
extern MRI_IMAGE *mri_rotate_bilinear( MRI_IMAGE * , float,float,float,float ) ;
extern MRI_IMAGE *mri_rota ( MRI_IMAGE * , float,float,float ) ;
extern MRI_IMAGE *mri_rota_bilinear( MRI_IMAGE * , float,float,float ) ;
extern MRI_IMAGE *mri_rota_shear ( MRI_IMAGE * , float,float,float ) ;
extern MRI_IMAGE *mri_rota_variable( int, MRI_IMAGE * , float,float,float ) ;
extern MRI_IMAGE *mri_aff2d_byte( MRI_IMAGE *,int,float,float,float,float) ;
extern MRI_IMAGE *mri_aff2d_rgb ( MRI_IMAGE *,int,float,float,float,float) ;
/** 27 Nov 2001: mri_scale.c **/
extern void mri_scale_inplace( float , MRI_IMAGE * ) ;
extern void ft_shift2( int, int, float, float *, float, float * ) ;
extern MRI_IMAGE *mri_float_func( int,int,
float , float , float , float ,
float (*func)(float,float) ) ;
extern void mri_histogram( MRI_IMAGE * , float,float ,
int,int, int h[] ) ;
extern void mri_histobyte ( MRI_IMAGE * , int * ) ;
extern void mri_histoshort_all ( MRI_IMAGE * , int * ) ; /* 25 Jul 2001 */
extern void mri_histoshort_nonneg( MRI_IMAGE * , int * ) ;
extern void mri_percents( MRI_IMAGE * , int nper , float per[] ) ;
extern MRI_IMAGE * mri_flatten( MRI_IMAGE * ) ;
extern float mri_quantile( MRI_IMAGE * im , float alpha ) ;
extern float_pair mri_twoquantiles( MRI_IMAGE * im, float alpha, float beta ) ;
extern void qsort_short( int , short * ) ;
extern void qsort_float( int , float * ) ;
extern void qsort_pair( int , float * , int * ) ;
extern void qsort_int( int , int * ) ;
extern void isort_short( int , short * ) ;
extern void isort_float( int , float * ) ;
extern void isort_pair ( int , float * , int * ) ;
extern MRI_IMAGE * mri_nsize( MRI_IMAGE * ) ;
extern float * mri_lsqfit( MRI_IMAGE * fitim , MRI_IMARR * refim , MRI_IMAGE * ) ;
extern double * mri_startup_lsqfit( MRI_IMARR * , MRI_IMAGE * ) ;
extern float * mri_delayed_lsqfit( MRI_IMAGE * , MRI_IMARR * , double * ) ;
extern float * lsqfit( int , float * , float * , int , float *ref[] ) ;
extern double * startup_lsqfit( int , float * , int , float *ref[] ) ;
extern float * delayed_lsqfit( int , float * , int , float *ref[] , double * ) ;
extern MRI_IMAGE * mri_sobel( int , int , MRI_IMAGE * ) ;
extern MRI_IMAGE * mri_sharpen( float , int , MRI_IMAGE * ) ;
extern MRI_IMAGE * mri_transpose( MRI_IMAGE * ) ;
extern MRI_IMAGE * mri_clusterize( float,float, MRI_IMAGE *, float, MRI_IMAGE * );
extern char * mri_clusterize_report(void) ;
#define FILT_FFT_WRAPAROUND 1
extern MRI_IMAGE * mri_filt_fft( MRI_IMAGE * im , float,int,int,int ) ;
extern MRI_IMAGE *mri_medianfilter( MRI_IMAGE *, float, byte *, int ); /* 22 Feb 2005 */
extern void mri_medianfilter_usedxyz( int i ) ; /* 08 Aug 2006 */
void mri_Set_KO_catwrap(void);
void mri_Set_OK_catwrap(void);
extern MRI_IMAGE * mri_cat2D( int,int,int,void *,MRI_IMARR *) ;
extern MRI_IMARR * mri_uncat2D( int , int , MRI_IMAGE * im ) ; /* 09 May 2000 */
extern MRI_IMAGE * mri_shift_1D( MRI_IMAGE * im , float shift ) ;
/*** image alignment procedures and constants ***/
#define ALIGN_DFSPACE_TYPE 1
#define ALIGN_DFTIME_TYPE 2
#define ALIGN_VERBOSE_CODE 1 /* verbose output during routine */
#define ALIGN_NOITER_CODE 2 /* don't iterate alignment algorithm */
#define ALIGN_REGISTER_CODE 4 /* return MRI_IMARR * of registered images */
#define ALIGN_DETREND_CODE 8 /* remove trend from registered images (DFTIME only) */
#define ALIGN_DOBOTH_CODE 16 /* do dfspace before dftime (DFTIME only) */
#define ALIGN_DEBUG_CODE 32 /* print out debugging info */
#define ALIGN_FREEUP_CODE 64 /* free input images when no longer needed */
#define ALIGN_BILINEAR_CODE 128 /* use bilinear interpolation in mri_align */
#define ALIGN_FOURIER_CODE 256 /* use Fourier interpolation in mri_align */
extern MRI_IMARR * mri_align_dfspace( MRI_IMAGE *, MRI_IMAGE * , MRI_IMARR *,
int, float *, float *, float * ) ;
extern MRI_IMARR * mri_align_dftime( MRI_IMAGE *, MRI_IMAGE * , MRI_IMARR *,
int, float *, float *, float * ) ;
extern void mri_align_params( int,float,float,float,float,float,float ) ;
extern void mri_align_method( int,int,int ) ; /* 01 Oct 1998 */
extern void mri_get_cmass_2D( MRI_IMAGE *, float *, float * ); /* 12 Nov 2001 */
extern void mri_get_cmass_3D( MRI_IMAGE *, float *, float * , float *);
extern float mri_spearman_corr( MRI_IMAGE *, MRI_IMAGE * ) ; /* 08 Mar 2006 */
/*---------------------------------------------------------------------*/
/* 07 April 1998: routines for one-at-a-time alignment (mri_2dalign.c) */
/*! Struct used in 2D image registration. */
typedef struct {
MRI_IMARR * fitim , * fine_fitim ;
double * chol_fitim , * chol_fine_fitim ;
} MRI_2dalign_basis ;
extern void mri_2dalign_params( int,float,float,float,float,float,float ) ;
extern void mri_2dalign_method( int,int,int ) ;
extern MRI_2dalign_basis * mri_2dalign_setup( MRI_IMAGE * , MRI_IMAGE * ) ;
extern MRI_IMAGE * mri_2dalign_one( MRI_2dalign_basis * , MRI_IMAGE * ,
float * , float * , float * ) ;
extern MRI_IMARR * mri_2dalign_many( MRI_IMAGE *, MRI_IMAGE * , MRI_IMARR *,
float * , float * , float * ) ;
extern void mri_2dalign_cleanup( MRI_2dalign_basis * ) ;
/*---------------------------------------------------------------------*/
/*** routine to flip 2D images around ***/
#define MRI_ROT_0 1 /* codes for various rotations */
#define MRI_ROT_90 2 /* [do not change these unless */
#define MRI_ROT_180 4 /* imseq.h is changed also!] */
#define MRI_ROT_270 8
#define MRI_FLMADD 128
extern MRI_IMAGE * mri_flippo( int rot , int mirror , MRI_IMAGE * im ) ;
extern MRI_IMAGE * mri_flip3D( int,int,int , MRI_IMAGE *inim ) ; /* 19 Mar 2003 */
/*---------------------------------------------------------------------*/
/*--------- 22 April 1998: byte order routines (mri_order.c) ----------*/
#define LSB_FIRST 1
#define MSB_FIRST 2
#define NATIVE_ORDER -1
#define REVERSE_ORDER(bord) (3-(bord)) /* 21 Jun 2002 */
#define ORDER_LEN 9
#define LSB_FIRST_STRING "LSB_FIRST"
#define MSB_FIRST_STRING "MSB_FIRST"
#define NATIVE_STRING "NATIVE_ORDER"
#define BYTE_ORDER_STRING(qq) ( ((qq)==LSB_FIRST) ? LSB_FIRST_STRING \
: ((qq)==MSB_FIRST) ? MSB_FIRST_STRING \
: "Illegal Value" )
extern int mri_short_order(void) ;
extern int mri_int_order(void) ;
extern void mri_swap2( int , short * ) ;
extern void mri_swap4( int , int * ) ;
/*---------------------------------------------------------------------*/
/*------------------ 18 Sep 2001: drawing stuff -----------------------*/
extern void mri_drawline( MRI_IMAGE *im, int x0,int y0, int x1,int y1,
byte r,byte g,byte b );
extern void mri_drawfilledrectangle( MRI_IMAGE *im ,
int x, int y, int width, int height ,
byte r,byte g,byte b );
extern void mri_drawemptyrectangle( MRI_IMAGE *im ,
int x, int y, int width, int height ,
byte r,byte g,byte b );
extern void mri_drawtext( MRI_IMAGE *im ,
int x, int y, int height, int angle, char *s,
byte r,byte g,byte b );
extern void mri_draw_opacity( float ) ;
/**********************************************************************/
#ifdef __cplusplus
}
#endif
#include "coxplot.h"
#undef min
#undef max
#ifdef __cplusplus
extern "C" { /* care of Greg Balls 7 Aug 2006 [rickr] */
#endif
extern void set_memplot_RGB_box( int xbot, int ybot, int xtop, int ytop ) ;
extern void memplot_to_RGB_sef( MRI_IMAGE *im , MEM_plotdata * mp ,
int start , int end , int freee ) ;
/************************ Statistics routines *************************/
/**
if the math library doesn't have the log(gamma(x))
function (as on Linux, for example)
**/
#ifdef NO_GAMMA
/* extern double gamma_12 ( double ) ; these are static functions */
/* extern double gamma_asympt( double ) ; 7 Aug 2006 [rickr] */
extern double gamma ( double ) ;
#endif
extern double lnbeta ( double , double ) ;
extern double incbeta ( double , double , double , double ) ;
extern double incbeta_inverse( double , double , double , double ) ;
extern double qginv ( double ) ;
extern double qg ( double ) ; /* 21 Mar 2001 */
extern double log10qg ( double ) ;
#define QG(x) (0.5*erfc(x/1.414213562373095))
#define erfcinv(y) (0.70710678*qginv(0.5*y)) /* 07 Oct 1999 */
extern double student_t2p( double , double ) ;
extern double student_p2t( double , double ) ;
extern double student_t2z( double , double ) ;
extern double correl_t2p ( double , double , double , double ) ;
extern double correl_t2z ( double , double , double , double ) ;
extern double correl_p2t ( double , double , double , double ) ;
extern double studave_t2p( double , double , double ) ; /* not implemented */
extern double studave_t2z( double , double , double ) ; /* not implemented */
extern double studave_p2t( double , double , double ) ;
extern double fstat_p2t( double , double , double ) ;
extern double fstat_t2p( double , double , double ) ;
extern double fstat_t2z( double , double , double ) ;
extern double normal_t2p ( double zz ) ;
extern double normal_p2t ( double qq ) ;
#define normal_t2z(x) (x) /* no function needed here! */
extern double chisq_t2p ( double xx , double dof ) ;
extern double chisq_t2z ( double xx , double dof ) ;
extern double chisq_p2t ( double qq , double dof ) ;
extern double beta_t2p ( double xx , double aa , double bb ) ;
extern double beta_t2z ( double xx , double aa , double bb ) ;
extern double beta_p2t ( double qq , double aa , double bb ) ;
extern double binomial_t2p( double ss , double ntrial , double ptrial ) ;
extern double binomial_t2z( double ss , double ntrial , double ptrial ) ;
extern double binomial_p2t( double qq , double ntrial , double ptrial ) ;
extern double gamma_t2p ( double xx , double sh , double sc ) ;
extern double gamma_t2z ( double xx , double sh , double sc ) ;
extern double gamma_p2t ( double qq , double sh , double sc ) ;
extern double poisson_t2p ( double xx , double lambda ) ;
extern double poisson_t2z ( double xx , double lambda ) ;
extern double poisson_p2t ( double qq , double lambda ) ;
#ifdef __cplusplus
}
#endif
/*----------------- Misc other types -------------------------------------*/
typedef struct { int i,j; } int_pair ; /* 12 Aug 2002 */
typedef struct { int i,j,k; } int_triple ;
typedef struct { int nar ; float *ar ; } floatvec ;
typedef struct { int nar ; double *ar ; } doublevec ;
#define KILL_floatvec(fv) \
do{ if( (fv) != NULL ){ \
if( (fv)->ar != NULL ) free((fv)->ar); \
free(fv); (fv) = NULL; \
}} while(0)
#define KILL_doublevec KILL_floatvec
#define MAKE_floatvec(fv,n) \
do{ (fv) = (floatvec *)malloc(sizeof(floatvec)) ; \
(fv)->nar = (n) ; \
(fv)->ar = (float *)calloc(sizeof(float),(n)) ; \
} while(0)
#define MAKE_doublevec(dv,n) \
do{ (dv) = (doublevec *)malloc(sizeof(doublevec)) ; \
(dv)->nar = (n) ; \
(dv)->ar = (double *)calloc(sizeof(double),(n)) ; \
} while(0)
typedef struct { int nvec ; floatvec *fvar ; } floatvecvec ;
typedef struct { int nar ; int *ar ; } intvec ;
#define KILL_intvec(iv) \
do{ if( (iv) != NULL ){ \
if( (iv)->ar != NULL ) free((iv)->ar); \
free(iv); (iv) = NULL; \
} } while(0)
#define MAKE_intvec(iv,n) \
do{ (iv) = (intvec *)malloc(sizeof(intvec)) ; \
(iv)->nar = (n) ; \
(iv)->ar = (int *)calloc(sizeof(int),(n)) ; \
} while(0)
typedef struct {
int nbot, ntop , gbot ;
char name[64] ;
} SYM_irange ;
extern floatvecvec * SYM_expand_ranges( int, int, SYM_irange *, char * );
extern int SYM_expand_errcount(void) ; /* 03 May 2007 */
/*----------------- 30 Oct 1996: incorporation of cdflib ----------------*/
/*----------------- 09 May 2007: get them from nifticdf ----------------*/
#ifndef __COMPILE_UNUSED_FUNCTIONS__
#define __COMPILE_UNUSED_FUNCTIONS__
#endif
#include "nifticdf.h" /* was cdflib.h */
/*------------------------------------------------------------------------*/
/*----------------- 01 Feb 1998: incoroporation of mcw_glob -------------*/
#include "mcw_glob.h"
/*------------------------------------------------------------------------*/
/*----------------- 06 Dec 2004: incorporation of list_struct ----------*/
#include "list_struct.h"
/*----------------- 02 Feb 1998:
incoroporation of 3ddata, 3dmaker, iochan -----------*/
#include "thd_iochan.h"
#include "3ddata.h"
#include "thd_maker.h"
#include "editvol.h"
#include "cs.h" /* 17 Aug 1998 addition */
#include "multivector.h" /* 18 May 1999 addition */
#include "afni_environ.h" /* 07 Jun 1999 addition */
/*------------------------------------------------------------------------*/
/*--- Functions in mri_matrix.c (matrix operations, stored as images) ----*/
#ifdef __cplusplus
extern "C" { /* care of Greg Balls 7 Aug 2006 [rickr] */
#endif
extern MRI_IMAGE * mri_matrix_mult ( MRI_IMAGE *, MRI_IMAGE *);
extern MRI_IMAGE * mri_matrix_multranA ( MRI_IMAGE *, MRI_IMAGE *);
extern MRI_IMAGE * mri_matrix_multranB ( MRI_IMAGE *, MRI_IMAGE *);
extern MRI_IMAGE * mri_matrix_psinv ( MRI_IMAGE *, float * , float );
extern void mri_matrix_psinv_svd( int ) ;
extern MRI_IMAGE * mri_matrix_ortproj ( MRI_IMAGE * , int ) ;
extern MRI_IMAGE * mri_matrix_sadd ( float, MRI_IMAGE *, float, MRI_IMAGE * ) ;
extern MRI_IMAGE * mri_matrix_scale ( float, MRI_IMAGE * ) ;
extern MRI_IMAGE * mri_matrix_evalrpn ( char * ) ;
extern char * mri_matrix_evalrpn_help(void) ;
extern void mri_matrix_evalrpn_verb(int) ;
#define mri_matrix_transpose(x) mri_transpose(x)
extern double Plegendre( double x , int m ) ;
/*------------------------------------------------------------------------*/
extern MRI_IMAGE * THD_average_timeseries( MCW_cluster_array *, THD_3dim_dataset *) ;
extern MRI_IMAGE * THD_average_one_timeseries( MCW_cluster *, THD_3dim_dataset *) ;
/** mri_warp3D.c functions: 14 Apr 2003 */
extern MRI_IMAGE *mri_warp3D_cubic ( MRI_IMAGE *, int,int,int ,
void func( float,float,float,
float *,float *,float *) ) ;
extern MRI_IMAGE *mri_warp3D_linear( MRI_IMAGE *, int,int,int ,
void func( float,float,float,
float *,float *,float *) ) ;
extern MRI_IMAGE *mri_warp3D_NN ( MRI_IMAGE *, int,int,int ,
void func( float,float,float,
float *,float *,float *) ) ;
extern MRI_IMAGE *mri_warp3D ( MRI_IMAGE *, int,int,int ,
void func( float,float,float,
float *,float *,float *) ) ;
extern void mri_warp3D_method( int ) ;
extern void mri_warp3D_zerout( int ) ;
extern void mri_warp3D_set_womask( MRI_IMAGE * ) ; /* 19 Nov 2004 */
extern MRI_IMAGE *mri_warp3D_quintic( MRI_IMAGE *, int,int,int , /* 06 Aug 2003 */
void func( float,float,float,
float *,float *,float *) ) ;
extern MRI_IMAGE * mri_warp3D_affine( MRI_IMAGE * , THD_vecmat ) ;
extern MRI_IMAGE * mri_warp3D_resize( MRI_IMAGE *, int,int,int ) ;
extern double mri_entropy16( MRI_IMAGE * ) ; /* 09 Jan 2004 */
extern double mri_entropy8 ( MRI_IMAGE * ) ; /* 09 Jan 2004 */
extern float mri_scaled_diff( MRI_IMAGE *bim, MRI_IMAGE *nim, MRI_IMAGE *msk ) ;
/*------------------------------------------------------------------*/
#undef INLINE
#ifdef __GNUC__
# define INLINE __inline__
#else
# define INLINE /*nada*/
#endif
#undef RESTRICT
#ifdef __GNUC__
# define RESTRICT __restrict__
#else
# define RESTRICT /*nada*/
#endif
#ifdef __cplusplus
}
#endif
/*------------------------------------------------------------------*/
#include "AFNI_label.h"
#undef PRINT_VERSION
#define PRINT_VERSION(pp) \
INFO_message("%s: AFNI version=%s (" __DATE__ ") [%d-bit]", \
(pp),AFNI_VERSION_LABEL,(int)(sizeof(void *)*8))
#undef AUTHOR
#define AUTHOR(aa) INFO_message("Authored by: %s",aa)
#undef WROTE_DSET_MSG
#define WROTE_DSET_MSG(dd,ss) \
INFO_message("Output dataset %s {%s}",DSET_BRIKNAME(dd),(ss))
#undef WROTE_DSET
#define WROTE_DSET(dd) \
INFO_message("Output dataset %s",DSET_BRIKNAME(dd))
#undef CHECK_OPEN_ERROR
#define CHECK_OPEN_ERROR(dd,nn) \
do{ if( !ISVALID_DSET(dd) ) ERROR_exit("Can't open dataset '%s'",nn); }while(0)
#undef CHECK_LOAD_ERROR
#define CHECK_LOAD_ERROR(dd) \
do{ if( ISVALID_DSET(dd) && !DSET_LOADED(dd) ) \
ERROR_exit("Can't load dataset '%s': is it complete?",DSET_BRIKNAME(dd));\
} while(0)
/*------------------------------------------------------------------*/
#define METRIC_KULL 0
#define METRIC_HELL 1
#define METRIC_TRIA 2
#define METRIC_JDIV 3
#define METRIC_JSDV 4
#define METRIC_XISQ 5
#define METRIC_XXSQ 6
#define METRIC_AGDV 7
extern void mri_metrics( MRI_IMAGE *, MRI_IMAGE *, float * ) ;
/*--------------------------------------------------------------------*/
/** July 2006: stuff for generic alignment functions: mri_genalign.c **/
/* methods for matching scalar-valued images */
#define GA_MATCH_PEARSON_SCALAR 1 /* least squares, more-or-less */
#define GA_MATCH_SPEARMAN_SCALAR 2 /* rank-order correlation */
#define GA_MATCH_KULLBACK_SCALAR 3 /* Mutual Info */
#define GA_MATCH_MUTINFO_SCALAR 3
#define GA_MATCH_CORRATIO_SCALAR 4 /* Correlation Ratio: Sym Mul */
#define GA_MATCH_NORMUTIN_SCALAR 5 /* Normalized Mutual Info */
#define GA_MATCH_JOINTENT_SCALAR 6 /* Joint Entropy */
#define GA_MATCH_HELLINGER_SCALAR 7 /* Hellinger metric */
#define GA_MATCH_CRAT_SADD_SCALAR 8 /* Correlation Ratio: Sym Add */
#define GA_MATCH_CRAT_USYM_SCALAR 9 /* Correlation Ratio: Unsym */
#define GA_MATCH_METHNUM_SCALAR 9 /* Largest value in sequence above */
/* methods for smoothing images */
#define GA_SMOOTH_GAUSSIAN 1
#define GA_SMOOTH_MEDIAN 2
/* kernels for histogram estimation */
#define GA_KERNEL_GAUSSIAN 1
#define GA_KERNEL_QUADRATIC 2
#define GA_KERNEL_QUARTIC 3
/* prototype/typedef for a spatial warping function */
typedef void GA_warpfunc( int, float *,
int, float *,float *,float *,
float *,float *,float * );
typedef MRI_warp3D_param_def GA_param ; /* cf. 3ddata.h */
#define GA_HIST_EQWIDE 1
#define GA_HIST_EQHIGH 2
#define GA_HIST_CLEQWD 3
/* struct to control mri_genalign.c optimization */
typedef struct {
int match_code ; /* set by user */
int smooth_code ; /* set by user */
float smooth_radius_base ; /* set by user */
float smooth_radius_targ ; /* set by user */
int interp_code ; /* set by user */
mat44 base_cmat , targ_cmat ; /* set by user */
mat44 base_imat , targ_imat ;
int usetemp ; /* set by user */
int old_sc ; float old_sr_base , old_sr_targ ;
MRI_IMAGE *bsim , *bsims ;
float bsbot,bstop , bsclip ;
int dim_bvec ;
int nmask ;
int nvox_mask ;
byte *bmask ;
MRI_IMAGE *bwght ;
MRI_IMAGE *ajim , *ajims ;
float ajbot,ajtop , ajclip ;
int dim_avec , abdim ;
int npt_match ; /* set by user */
floatvec *im, *jm, *km , *bvm , *wvm ;
float bvstat ;
int hist_mode ; /* set by user */
float hist_param ; /* set by user */
int need_hist_setup ;
/*** NOT USED YET ***/
int kernel_code ; /* set by user */
float kernel_radius ; /* set by user */
int npt_sum ; /* set by user */
intvec *is, *js, *ks ;
floatvec *bvs ; /********************/
int wfunc_numpar ; /* set by user */
GA_param *wfunc_param ; /* set by user */
GA_warpfunc *wfunc ; /* set by user */
int wfunc_numfree ;
int *wfunc_pma ;
int wfunc_ntrial ;
int setup ;
float vbest ;
} GA_setup ;
#undef IFREE
#define IFREE(x) do{ if((x)!=NULL)free(x); }while(0)
#undef FREE_GA_setup
#define FREE_GA_setup(st) \
do{ if( (st) != NULL ){ \
mri_free((st)->bsim); mri_free((st)->ajim); IFREE((st)->bmask); \
mri_free((st)->bsims);mri_free((st)->ajims);mri_free((st)->bwght); \
KILL_floatvec((st)->im); KILL_floatvec((st)->jm); \
KILL_floatvec((st)->km); KILL_floatvec((st)->bvm); \
KILL_floatvec((st)->wvm); IFREE((st)->wfunc_param) ; \
} \
} while(0)
extern void mri_genalign_scalar_setup( MRI_IMAGE *, MRI_IMAGE *,
MRI_IMAGE *, GA_setup * ) ;
extern int mri_genalign_scalar_optim( GA_setup *, double, double, int) ;
extern void mri_genalign_scalar_ransetup( GA_setup *, int ) ;
extern void mri_genalign_affine( int, float *,
int, float *, float *, float *,
float *, float *, float * ) ;
extern MRI_IMAGE * mri_genalign_scalar_warpim( GA_setup * ) ;
extern void mri_genalign_verbose(int) ;
extern void GA_reset_fit_callback( void (*fc)(int,double*) ) ;
extern void GA_do_dots(int) ;
extern void GA_do_cost(int, byte) ;
extern float mri_genalign_scalar_cost( GA_setup * ) ;
extern void GA_set_outval( float ) ; /* 28 Feb 2007 */
#define MATORDER_SDU 1 /* matrix multiplication order: */
#define MATORDER_SUD 2 /* S = shear matrix */
#define MATORDER_DSU 3 /* D = diagonal scaling matrix */
#define MATORDER_DUS 4 /* U = rotation matrix */
#define MATORDER_USD 5
#define MATORDER_UDS 6
#define SMAT_UPPER 1 /* shear matrix is upper */
#define SMAT_LOWER 2 /* or lower triangular */
#define SMAT_XXX 3 /* x-axis only shears */
#define SMAT_YYY 4 /* y-axis only shears */
#define SMAT_ZZZ 5 /* z-axis only shears */
extern void mri_genalign_affine_setup( int,int,int ) ;
extern void mri_genalign_affine_set_befafter( mat44 *, mat44 * ) ;
extern void mri_genalign_affine_get_befafter( mat44 *, mat44 * ) ;
extern void mri_genalign_affine_get_gammaijk( mat44 * ) ; /* 04 Apr 2007 */
extern void mri_genalign_affine_get_gammaxyz( mat44 * ) ;
extern MRI_IMAGE * mri_genalign_scalar_warpone( /* 26 Sep 2006 */
int npar, float *wpar, GA_warpfunc *wfunc,
MRI_IMAGE *imtarg ,
int nnx , int nny , int nnz , int icode ) ;
extern void mri_genalign_scalar_clrwght( GA_setup * ) ; /* 18 Oct 2006 */
/*--------------------------------------------------------------------------*/
/* Prototypes for functions in nifti_stats.c */
extern int nifti_intent_code ( char * ) ;
extern double nifti_stat2cdf ( double, int, double,double,double ) ;
extern double nifti_stat2rcdf ( double, int, double,double,double ) ;
extern double nifti_cdf2stat ( double, int, double,double,double ) ;
extern double nifti_rcdf2stat ( double, int, double,double,double ) ;
extern double nifti_stat2zscore ( double, int, double,double,double ) ;
extern double nifti_stat2hzscore( double, int, double,double,double ) ;
/*------------------------------------------------------------------*/
extern THD_fvec3 mri_estimate_FWHM_1dif( MRI_IMAGE * , byte * ) ;
extern MRI_IMAGE * THD_estimate_FWHM_all( THD_3dim_dataset *, byte *, int,int ) ;
extern void FHWM_1dif_dontcheckplus( int ) ;
extern THD_fvec3 mriarr_estimate_FWHM_1dif( MRI_IMARR *, byte * , int ) ;
extern THD_fvec3 mri_estimate_FWHM_12dif( MRI_IMAGE * , byte * ) ;
void mri_fwhm_setfester( THD_fvec3 (*func)(MRI_IMAGE *, byte *) ) ;
extern THD_fvec3 mri_nstat_fwhmxyz( int,int,int ,
MRI_IMAGE *, byte *, MCW_cluster * );
extern void mri_blur3D_variable( MRI_IMAGE * , byte * ,
MRI_IMAGE * , MRI_IMAGE * , MRI_IMAGE * ) ;
extern MRI_IMAGE * mri_rgb_blur2D ( float sig , MRI_IMAGE *im ) ;
extern MRI_IMAGE * mri_byte_blur2D( float sig , MRI_IMAGE *im );
extern MRI_IMAGE * mri_float_blur2D( float sig , MRI_IMAGE *im ) ;
extern MRI_IMAGE * mri_float_blur3D( float sig , MRI_IMAGE *im ) ;
#endif /* _MCW_MRILIB_HEADER_ */
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