Madagascar Programming Reference Manual
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Madagascar Programming Reference Manual
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Madagascar Programming Reference Manual
Contents
Introduction
An example: Finite-Difference modeling
Introduction
C program
Explanation of the code
Data types
Data types
Complex numbers and FFT
Files
Operators
Geometry
Lists
sys/types.h
Preparing for input
Convenience allocation programs (alloc.c)
sf_alloc
sf_realloc
sf_charalloc
sf_ucharalloc
sf_shortalloc
sf_intalloc
sf_largeintalloc
sf_floatalloc
sf_complexalloc
sf_complexalloc2
sf_complexalloc3
sf_complexalloc4
sf_boolalloc
sf_boolalloc2
sf_boolalloc3
sf_floatalloc2
sf_floatalloc3
sf_floatalloc4
sf_floatalloc5
sf_floatalloc6
sf_intalloc2
sf_intalloc3
sf_intalloc4
sf_charalloc2
sf_uncharalloc2
sf_uncharalloc3
Simbol Table for parameters (simtab.c)
sf_simtab_init
sf_simtab_close
sf_simtab_enter
sf_simtab_get
sf_simtab_getint
sf_simtab_getlargeint
sf_simtab_getfloat
sf_simtab_getdouble
sf_simtab_getfloats
sf_simtab_getstring
sf_simtab_getbool
sf_simtab_getbools
sf_simtab_getints
sf_simtab_getstrings
sf_simtab_put
sf_simtab_input
sf_simtab_output
Parameter handling (getpar.c)
sf_stdin
sf_init
sf_par_close
sf_parout
sf_getprog
sf_getuser
sf_gethost
sf_getcdir
sf_getint
sf_getlargeint
sf_getints
sf_getfloat
sf_getdouble
sf_getfloats
sf_getstring
sf_getstrings
sf_getbool
sf_getbools
sf_getpars
Operations with RSF files
Main operations with RSF files (file.c)
sf_file_error
sf_error
sf_input
sf_output
sf_gettype
sf_getform
sf_esize
sf_settype
sf_setpars
sf_bufsiz
sf_setform
sf_setformat
sf_getfilename
sf_gettmpdatapath
sf_getdatapath
sf_readpathfile
sf_fileclose
sf_histint
sf_histints
sf_histlargeint
sf_histfloat
sf_histdouble
sf_histfloats
sf_histbool
sf_histtbools
sf_histstring
sf_fileflush
sf_putint
sf_putints
sf_putlargeint
sf_putfloat
sf_putstring
sf_putline
sf_setaformat
sf_complexwrite
sf_complexread
sf_charwrite
sf_uncharwrite
sf_charread
sf_uncharread
sf_intwrite
sf_intread
sf_shortread
sf_shortwrite
sf_floatwrite
sf_floatread
sf_bytes
sf_tell
sf_tempfile
sf_seek
sf_unpipe
sf_close
Additional operations with RSF files (files.c)
sf_filedims
sf_largefiledims
sf_memsize
sf_filesize
sf_leftsize
sf_cp
sf_rm
sf_shiftdim
sf_unshiftdim
sf_endian
Complex number operations (komplex.c)
creal
cimag
dcneg
dcadd
dcsub
dcmul
dccmul
dcdmul
dcrmul
dcdiv
cabs
cabs
crealf
cimagf
cprint
cadd
csub
csqrtf
cdiv
cmul
crmul
cneg
conjf
cabsf
cargf
ctanhf
ccosf
ccoshf
ccosf
csinhf
clogf
cexpf
ctanf
casinf
cacosf
catanf
catanhf
casinhf
cacoshf
cpowf
Error handling
Handling warning and error messages (error.c)
sf_error
sf_warning
Linear operators
Introduction
Definition of operators
Products of operators
Adjoint operators
The dot-product test
Implementation of operators
Adjoint zeroing (adjnull.c)
sf_adjnull
sf_cadjnull
Simple identity (copy) operator (copy.c)
sf_copy_lop
Simple identity (copy) operator for complex data (ccopy.c)
sf_ccopy_lop
Simple mask operator (mask.c)
sf_mask_init
sf_mask_lop
sf_cmask_lop
Simple weight operator (weight.c)
sf_weight_init
sf_weight_lop
sf_cweight_lop
sf_weight_apply
sf_cweight_apply
1-D finite difference (igrad1.c)
sf_igrad1_lop
Causal integration (causint.c)
sf_causint_lop
Chaining linear operators (chain.c)
sf_chain
sf_cchain
sf_array
sf_normal
sf_chain3
Dot product test for linear operators (dottest.c)
sf_dot_test
Data analysis
FFT (kiss_fftr.c)
sf_kiss_fftr_alloc
kiss_fftr
kiss_fftri
Cosine window weighting function (tent2.c)
sf_tent2
Anisotropic diffusion, 2-D (impl2.c)
sf_impl2_init
sf_impl2_close
sf_impl2_set
sf_impl2_set
sf_impl2_lop
Filtering
Frequency-domain filtering (freqfilt.c)
sf_freqfilt_init
sf_freqfilt_set
sf_freqfilt_cset
sf_freqfilt_close
sf_freqfilt
sf_freqfilt_lop
Frequency-domain filtering in 2-D (freqfilt.c)
sf_freqfilt2_init
sf_freqfilt2_set
sf_freqfilt2_close
sf_freqfilt2_spec
sf_freqfilt2_lop
Helical convolution (helicon.c)
sf_helicon_init
sf_helicon_lop
Helical filter definition and allocation (helix.c)
sf_allocatehelix
sf_deallocatehelix
sf_displayhelix
Recursive convolution (polynomial division) (recfilt.c)
sf_recfilt_init
sf_recfilt_lop
sf_recfilt_close
Cosine Fourier transform (cosft.c)
sf_cosft
sf_cosft_close
sf_cosft_frw
sf_cosft_inv
Solvers
Banded matrix solver (banded.c)
sf_banded_init
sf_banded_define
sf_banded_const_define
sf_banded_const_define_reflect
sf_banded_solve
sf_banded_close
Claerbout's conjugate-gradient iteration (cgstep.c)
sf_cgstep
sf_cgstep_close
Conjugate-gradient with shaping regularization (conjgrad.c)
sf_conjgrad_init
sf_conjgrad_close
sf_conjgrad
Conjugate-gradient with preconditioning (conjprec.c)
sf_conjprec_init
sf_conjprec_close
sf_conjprec
Claerbout's conjugate-gradient iteration for complex numbers (cgstep.c)
sf_ccgstep
sf_ccgstep_close
dotprod
Conjugate-gradient with shaping regularization for complex numbers (cconjgrad.c)
norm
sf_cconjgrad_init
sf_cconjgrad_close
sf_cconjgrad
Conjugate-direction iteration (cdstep.c)
sf_cdstep_init
sf_cdstep_close
sf_cdstep
sf_cdstep_diag
sf_cdstep_mat
Linked list for use in conjugate-direction-type methods (llist.c)
sf_list_init
sf_llist_rewind
sf_llist_depth
sf_llist_add
sf_llist_down
sf_llist_close
sf_llist_chop
Conjugate-direction iteration for complex numbers (ccdstep.c)
sf_ccdstep_init
sf_ccdstep_close
sf_ccdstep
saxpy
dsdot
Linked list for conjugate-direction-type methods (complex data) (clist.c)
sf_clist_init
sf_clist_rewind
sf_clist_depth
sf_clist_add
sf_llist_down
sf_clist_close
sf_clist_chop
Solving quadratic equations (quadratic.c)
sf_quadratic_solve
Zero finder (fzero.c)
sf_zero
Runge-Kutta ODE solvers (runge.c)
sf_runge_init
sf_ode23
sf_ode23_step
Solver function for iterative least-squares optimization (tinysolver.c)
sf_tinysolver
Solver functions for iterative least-squares optimization (bigsolver.c)
sf_solver_prec
sf_csolver_prec
sf_solver_reg
sf_solver
sf_left_solver
sf_csolver
Weighting for iteratively-reweighted least squares (irls.c)
sf_irls_init
sf_irls_close
sf_l1
sf_cauchy
Tridiagonal matrix solver (tridiagonal.c)
sf_tridiagonal_init
sf_tridiagonal_define
sf_tridiagonal_const_define
sf_tridiagonal_solve
sf_tridiagonal_close
Interpolation
1-D interpolation (int1.c)
sf_int1_init
sf_int1_lop
sf_cint1_lop
sf_int1_close
2-D interpolation (int2.c)
sf_int2_init
sf_int2_lop
sf_int2_close
3-D interpolation (int3.c)
sf_int3_init
sf_int3_lop
sf_int3_close
Basic interpolation functions (interp.c)
sf_bin_int
sf_lin_int
sf_lg_int
sf_taylor_int
Convert data to B-spline coefficients by fast B-spline transform (prefilter.c)
sf_prefilter_init
sf_prefilter_apply
sf_prefilter
sf_prefilter_close
B-spline interpolation (spline.c)
sf_spline_init
sf_spline4_init
sf_spline4_post
sf_spline_post
sf_spline2
Inverse linear interpolation (stretch.c)
sf_stretch_init
sf_stretch_define
sf_stretch_apply
sf_stretch_invert
sf_stretch_close
1-D ENO interpolation (eno.c)
sf_eno_init
sf_eno_close
sf_eno_set
sf_eno_apply
ENO interpolation in 2-D (eno2.c)
sf_eno2_init
sf_eno2_set
sf_eno2_set1
sf_eno2_close
sf_eno2_apply
1-D ENO power-p interpolation (pweno.c)
sf_pweno_init
sf_pweno_close
powerpeno
sf_pweno_set
sf_pweno_apply
Smoothing
1-D triangle smoothing as a linear operator (triangle1.c)
sf_triangle1_init
sf_triangle1_lop
sf_triangle1_close
2-D triangle smoothing as a linear operator (triangle2.c)
sf_triangle2_init
sf_triangle2_lop
sf_triangle2_close
Triangle smoothing (triangle.c)
sf_triangle_init
fold
fold2
doubint
doubint2
triple
triple2
sf_smooth
sf_smooth2
sf_triangle_close
Smooth gradient operations (edge.c)
sf_grad2
sf_sobel
sf_sobel2
sf_sobel32
Ray tracing
Cell ray tracing (celltrace.c)
sf_celltrace_init
sf_celltrace_close
sf_cell_trace
Cell ray tracing (cell.c)
sf_cell1_intersect
sf_cell1_update1
sf_cell1_update2
sf_cell11_intersect2
sf_cell11_update1
sf_cell11_update2
sf_cell_intersect
sf_cell_snap
sf_cell_update1
sf_cell_update2
sf_cell_p2a
General tools
First derivative FIR filter (deriv.c)
sf_deriv_init
sf_deriv_free
sf_deriv
Computing quantiles by Hoare's algorithm (quantile.c)
sf_quantile
Pseudo-random numbers: uniform and normally distributed (randn.c)
sf_randn1
sf_randn
sf_random
Evaluating mathematical expressions (math1.c)
myabs
myconj
myarg
sf_math_evaluate
sf_complex_math_evaluate
sf_math_parse
sf_math_parse
Geometry
Construction of points (point.c)
printpt2d
printpt3d
pt2dwrite1
pt2dwrite2
pt3dwrite1
pt3dwrite2
pt2dread1
pt2dread2
pt3dread1
pt3dread2
pt2dalloc1
pt2dalloc2
pt2dalloc3
pt3dalloc1
pt3dalloc2
pt3dalloc3
Construction of vectors (vector.c)
det3
det2
jac3d
vec3d
axa3d
scp3d
vcp3d
len3d
nor3d
ang3d
tip3d
scl3d
Conversion between line and Cartesian coordinates of a vector (decart.c)
sf_line2cart
sf_cart2line
sf_first_index
sf_large_line2cart
sf_large_cart2line
sf_large_first_index
Axes (axa.c)
sf_maxa
sf_iaxa
sf_oaxa
sf_raxa
sf_n
sf_o
sf_d
sf_nod
sf_setn
sf_seto
sf_setd
sf_setlabel
sf_setunit
Miscellaneous
sharpening (sharpen.c)
sf_sharpen_init
sf_sharpen_close
sf_sharpen
sf_csharpen
Sharpening inversion added Bregman iteration (sharpinv.c)
sf_csharpinv
sf_sharpinv
System
Priority queue (heap sorting) (pqueue.c)
sf_pqueue_init
sf_pqueue_start
sf_pqueue_close
sf_pqueue_insert
sf_pqueue_insert2
sf_pqueue_extract
sf_pqueue_extract2
sf_pqueue_update
Simplified system command (system.c)
sf_system
Generic stack (FILO) structure operations (stack.c)
sf_stack_init
sf_stack_print
sf_stack_get
sf_stack_set
sf_push
sf_pop
sf_full
sf_top
sf_stack_close
Index
2011-07-02