/***************************************************************************** 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 */ 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 ; /*! Clear the MRILIB globals (which are designed to 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; \ } while(0) #include #include #include #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 MAX # define MAX(a,b) (((a)<(b)) ? (b) : (a)) #endif #ifndef MIN # define MIN(a,b) (((a)>(b)) ? (b) : (a)) #endif #undef DONT_USE_MEMCPY /**** 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 */ /*! 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. */ #ifndef TYPEDEF_complex #define TYPEDEF_complex typedef struct complex { float r , i ; } complex ; #endif /*-------*/ /*! Triple to hold RGB bytes. */ #ifndef TYPEDEF_rgbyte #define TYPEDEF_rgbyte typedef struct rgbyte { byte r,g,b ; } rgbyte ; /* 15 Feb 1999 */ #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 *. */ 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 ; /** 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 USE_MRI_DELAY /* 01 Jan 1997 */ #ifdef USE_MRI_DELAY # define INPUT_DELAY 1 # define BSWAP_DELAY 2 #endif /*! 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 #ifdef USE_MRI_DELAY char * fname ; /*< to read actual image data after delay */ int foffset ; /*< offset into fname of image data */ int fondisk ; /*< flag to indicate if is on disk (?) */ #endif 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) ((iq)->im.byte_data) #define MRI_SHORT_PTR(iq) ((iq)->im.short_data) #define MRI_INT_PTR(iq) ((iq)->im.int_data) #define MRI_FLOAT_PTR(iq) ((iq)->im.float_data) #define MRI_DOUBLE_PTR(iq) ((iq)->im.double_data) #define MRI_COMPLEX_PTR(iq) ((iq)->im.complex_data) #define MRI_RGB_PTR(iq) ((iq)->im.rgb_data) #define MRI_RGBA_PTR(iq) ((iq)->im.rgba_data) #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 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 USE_MRI_DELAY 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 * ) ; #endif 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 * ) ; 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( 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_fix_data_pointer( void * , MRI_IMAGE * ) ; extern char * mri_dicom_header( char * ) ; /* 15 Jul 2002 */ extern void mri_dicom_pxlarr( off_t *, unsigned 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 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_7D( char * , MRI_IMAGE * ) ; extern int mri_datum_size( MRI_TYPE typ ) ; extern MRI_IMAGE *mri_read_ascii( char * ) ; 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_1D( char * ) ; /* 16 Nov 1999 */ 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_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[] ) ; /** 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 ) ; long mri_filesize( char * pathname ) ; char * my_strdup( char * str ) ; 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 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 MRI_IMAGE *mri_resize( MRI_IMAGE * , int , int ) ; 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 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 * ) ; #define FILT_FFT_WRAPAROUND 1 extern MRI_IMAGE * mri_filt_fft( MRI_IMAGE * im , float,int,int,int ) ; 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 */ /*---------------------------------------------------------------------*/ /* 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 ); /**********************************************************************/ #include "coxplot.h" #undef min #undef max 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 ) ; extern double gamma ( double ) ; extern double gamma_asympt( 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 ) ; /*----------------- Misc other types -------------------------------------*/ typedef struct { int i,j; } int_pair ; /* 12 Aug 2002 */ typedef struct { int i,j,k; } int_triple ; /*----------------- 30 Oct 1996: incorporation of cdflib ----------------*/ #include "cdflib.h" /*------------------------------------------------------------------------*/ /*----------------- 01 Feb 1998: incoroporation of mcw_glob -------------*/ #include "mcw_glob.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 */ /*------------------------------------------------------------------------*/ 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 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 */ #endif /* _MCW_MRILIB_HEADER_ */