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first set of changes from Brent Fulgham, a bunch more coming in the C…

… code.
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1 parent 981c085 commit 317cb33d7c567bfb296d4dd2c1b8c1b4acf02493 @blindglobe committed Sep 17, 2008
Showing with 78 additions and 38 deletions.
  1. +3 −7 lib/betabase.c
  2. +27 −0 src/lisptests.lisp
  3. +19 −13 src/numerics/ladata.lsp
  4. +20 −15 src/numerics/linalg.lsp
  5. +9 −3 src/numerics/optimize.lisp
@@ -27,17 +27,15 @@ double ppbeta(double p, double a, double b, int *ifault)
Static routines
-static double logbeta(p, q)
- double p, q;
+static double logbeta(double p, double q)
return(gamma(p) + gamma(q) - gamma(p + q));
#define Min(x,y) (((x) < (y)) ? (x) : (y))
#define Max(x,y) (((x) > (y)) ? (x) : (y))
-static double betai(x, pin, qin)
- double x, pin, qin;
+static double betai(double x, double pin, double qin)
/* Translated from FORTRAN
july 1977 edition. w. fullerton, c3, los alamos scientific lab.
@@ -154,9 +152,7 @@ static double betai(x, pin, qin)
cause an underflow; a value of -308 or thereabouts will often be
-static double xinbta(p, q, beta, alpha, ifault)
- double *p, *q, *beta, *alpha;
- int *ifault;
+static double xinbta(double *p, double *q, double *beta, double *alpha, int *ifault)
/* Initialized data */
static double sae = -30.0; /* this should be sufficient */
@@ -0,0 +1,27 @@
+(asdf:oos 'asdf:load-op 'lispstat)
+(in-package :ls-user)
+(trace lisp-stat-linalg-data::la-allocate)
+(trace lisp-stat-linalg-data::la-put-double)
+(trace lisp-stat-linalg-data::la-data-to-matrix)
+(trace lisp-stat-linalg-data::la-matrix)
+(trace lisp-stat-linalg::lu-solve)
+ (lu-decomp #2A((2 3 4) (1 2 4) (2 4 5)))
+ #(2 3 4))
+;; #(-2.333333333333333 1.3333333333333335 0.6666666666666666)
+(dotimes (i 3)
+ (declare (fixnum i))
+ (let ((vec (lisp-stat-linalg-data::la-get-pointer mat i)))
+ (format t "vec => ~A~%" vec)
+ (dotimes (j 3)
+ (format t "LA-PUT-DOUBLE ~A <- (~A ~A)~%" vec j (aref data i j))
+ (lisp-stat-linalg-data::la-put-double vec j (aref data i j)))))
@@ -36,7 +36,13 @@
(in-package :lisp-stat-linalg-data)
+(defctype size-t :unsigned-long)
+(defctype size-t :unsigned-int)
+;; Should we do the same with int's and long's? There is some
+;; evidence that it might be useful?
@@ -95,7 +101,7 @@
(defun ptr-eq (p q) (cffi:pointer-eq p q))
(cffi:defcfun ("la_base_allocate" ccl-la-base-allocate)
- :pointer (n :int) (m :int))
+ :pointer (n size-t) (m size-t))
(defun la-base-allocate (n m)
(ccl-la-base-allocate n m))
@@ -105,7 +111,7 @@
(ccl-la-base-free-alloc p))
(cffi:defcfun ("la_mode_size" ccl-la-mode-size)
- :int (x :int))
+ size-t (x size-t))
(defun la-mode-size (mode)
(ccl-la-mode-size mode))
@@ -114,13 +120,13 @@
;;; Callbacks for Internal Storage
-(cffi:defcallback lisp-la-allocate :void ((n :long) (m :long))
+(cffi:defcallback lisp-la-allocate :void ((n size-t) (m size-t))
(ccl-store-ptr (la-allocate n m)))
(cffi:defcfun ("register_la_allocate" register-la-allocate)
:void (p :pointer))
(register-la-allocate (cffi:callback lisp-la-allocate))
(cffi:defcfun ("la_allocate" la)
- :pointer (x :int) (y :int))
+ :pointer (x size-t) (y size-t))
(cffi:defcallback lisp-la-free-alloc
:void ((p :pointer))
@@ -138,53 +144,53 @@
(cffi:defcfun ("la_get_integer" ccl-la-get-integer)
- :int (p :pointer) (i :int))
+ :long (p :pointer) (i size-t)) ;; was int, not long, for first
(defun la-get-integer (p i)
(ccl-la-get-integer p i))
(cffi:defcfun ("la_get_double" ccl-la-get-double)
- :double (p :pointer) (i :int))
+ :double (p :pointer) (i size-t))
(defun la-get-double (p i)
(ccl-la-get-double p i))
(cffi:defcfun ("la_get_complex_real" ccl-la-get-complex-real)
- :double (p :pointer) (i :int))
+ :double (p :pointer) (i size-t))
(defun la-get-complex-real (p i)
(ccl-la-get-complex-real p i))
(cffi:defcfun ("la_get_complex_imag" ccl-la-get-complex-imag)
- :double (p :pointer) (i :int))
+ :double (p :pointer) (i size-t))
(defun la-get-complex-imag (p i)
(ccl-la-get-complex-imag p i))
(defun la-get-complex (p i)
(complex (la-get-complex-real p i) (la-get-complex-imag p i)))
(cffi:defcfun ("la_get_pointer" ccl-la-get-pointer)
- :pointer (p :pointer) (i :int))
+ :pointer (p :pointer) (i size-t))
(defun la-get-pointer (p i)
(ccl-la-get-pointer p i))
;;; CFFI glue for Storage Mutation Functions
(cffi:defcfun ("la_put_integer" ccl-la-put-integer)
- :void (p :pointer) (i :int) (x :int))
+ :void (p :pointer) (i size-t) (x :long)) ;; last was :int ?
(defun la-put-integer (p i x)
(ccl-la-put-integer p i x))
(cffi:defcfun ("la_put_double" ccl-la-put-double)
- :void (p :pointer) (i :int) (x :double))
+ :void (p :pointer) (i size-t) (x :double))
(defun la-put-double (p i x)
(ccl-la-put-double p i (float x 1d0)))
(cffi:defcfun ("la_put_complex" ccl-la-put-complex)
- :void (p :pointer) (i :int) (x :double) (y :double))
+ :void (p :pointer) (i size-t) (x :double) (y :double))
(defun la-put-complex (p i x y)
(ccl-la-put-complex p i (float x 1d0) (float y 1d0)))
(cffi:defcfun ("la_put_pointer" ccl-la-put-pointer)
- :void (p :pointer) (i :int) (q :pointer))
+ :void (p :pointer) (i size-t) (q :pointer))
(defun la-put-pointer (p i q)
(ccl-la-put-pointer p i q))
@@ -57,6 +57,11 @@
(in-package #:lisp-stat-linalg)
+(defctype size-t :unsigned-long)
+(defctype size-t :unsigned-int)
;;; CFFI Support
@@ -70,7 +75,7 @@
(cffi:defcfun ("ccl_chol_decomp_front" ccl-chol-decomp-front)
- :int (x :pointer) (y :int) (z :pointer))
+ :int (x :pointer) (y size-t) (z :pointer))
(defun chol-decomp-front (x y z)
(ccl-chol-decomp-front x y z))
@@ -79,17 +84,17 @@
(cffi:defcfun ("ccl_lu_decomp_front" ccl-lu-decomp-front)
- :int (x :pointer) (y :int) (z :pointer) (u :int) (v :pointer))
+ :int (x :pointer) (y size-t) (z :pointer) (u :int) (v :pointer))
(defun lu-decomp-front (x y z u v)
(ccl-lu-decomp-front x y z u v))
(cffi:defcfun ("ccl_lu_solve_front" ccl-lu-solve-front)
- :int (x :pointer) (y :int) (z :pointer) (u :pointer) (v :int))
+ :int (x :pointer) (y size-t) (z :pointer) (u :pointer) (v :int))
(defun lu-solve-front (x y z u v)
(ccl-lu-solve-front x y z u v))
(cffi:defcfun ("ccl_lu_inverse_front" ccl-lu-inverse-front)
- :int (x :pointer) (y :int) (z :pointer) (u :pointer) (v :int) (w :pointer))
+ :int (x :pointer) (y size-t) (z :pointer) (u :pointer) (v :int) (w :pointer))
(defun lu-inverse-front (x y z u v w)
(ccl-lu-inverse-front x y z u v w))
@@ -98,7 +103,7 @@
(cffi:defcfun ("ccl_sv_decomp_front" ccl-sv-decomp-front)
- :int (x :pointer) (y :int) (z :int) (u :pointer) (v :pointer))
+ :int (x :pointer) (y size-t) (z size-t) (u :pointer) (v :pointer))
(defun sv-decomp-front (x y z u v)
(ccl-sv-decomp-front x y z u v))
@@ -107,7 +112,7 @@
(cffi:defcfun ("ccl_qr_decomp_front" ccl-qr-decomp-front)
- :int (x :pointer) (y :int) (z :int) (u :pointer) (v :pointer) (w :int))
+ :int (x :pointer) (y size-t) (z size-t) (u :pointer) (v :pointer) (w :int))
(defun qr-decomp-front (x y z u v w)
(ccl-qr-decomp-front x y z u v w))
@@ -116,7 +121,7 @@
(cffi:defcfun ("ccl_rcondest_front" ccl-rcondest-front)
- :double (x :pointer) (y :int))
+ :double (x :pointer) (y size-t))
(defun rcondest-front (x y)
(ccl-rcondest-front x y))
@@ -176,7 +181,7 @@
(cffi:defcfun ("ccl_make_rotation_front" ccl-make-rotation-front)
- :int (x :int) (y :pointer) (z :pointer) (u :pointer) (v :int) (w :double))
+ :int (x size-t) (y :pointer) (z :pointer) (u :pointer) (v :int) (w :double))
(defun make-rotation-front (x y z u v w)
(ccl-make-rotation-front x y z u v (float w 1d0)))
@@ -185,7 +190,7 @@
(cffi:defcfun ("ccl_eigen_front" ccl-eigen-front)
- :int (x :pointer) (y :int) (z :pointer) (u :pointer) (v :pointer))
+ :int (x :pointer) (y size-t) (z :pointer) (u :pointer) (v :pointer))
(defun eigen-front (x y z u v)
(ccl-eigen-front x y z u v))
@@ -194,12 +199,12 @@
(cffi:defcfun ("ccl_range_to_rseq" ccl-range-to-rseq)
- :int (x :int) (y :pointer) (z :int) (u :pointer))
+ :int (x size-t) (y :pointer) (z size-t) (u :pointer))
(defun la-range-to-rseq (x y z u)
(ccl-range-to-rseq x y z u))
(cffi:defcfun ("ccl_spline_front" ccl-spline-front)
- :int (x :int) (y :pointer) (z :pointer) (u :int) (v :pointer) (w :pointer) (a :pointer))
+ :int (x size-t) (y :pointer) (z :pointer) (u size-t) (v :pointer) (w :pointer) (a :pointer))
(defun spline-front (x y z u v w a)
(ccl-spline-front x y z u v w a))
@@ -208,12 +213,12 @@
(cffi:defcfun ("ccl_kernel_dens_front" ccl-kernel-dens-front)
- :int (x :pointer) (y :int) (z :double) (u :pointer) (v :pointer) (w :int) (a :int))
+ :int (x :pointer) (y size-t) (z :double) (u :pointer) (v :pointer) (w size-t) (a :int))
(defun kernel-dens-front (x y z u v w a)
(ccl-kernel-dens-front x y (float z 1d0) u v w a))
(cffi:defcfun ("ccl_kernel_smooth_front" ccl-kernel-smooth-front)
- :int (x :pointer) (y :pointer) (z :int) (u :double) (v :pointer) (w :pointer) (a :int) (b :int))
+ :int (x :pointer) (y :pointer) (z size-t) (u :double) (v :pointer) (w :pointer) (a size-t) (b :int))
(defun kernel-smooth-front (x y z u v w a b)
(ccl-kernel-smooth-front x y z (float u 1d0) v w a b))
@@ -222,7 +227,7 @@
(cffi:defcfun ("ccl_base_lowess_front" ccl-base-lowess-front)
- :int (x :pointer) (y :pointer) (z :int) (u :double) (v :int) (w :double) (a :pointer) (b :pointer) (c :pointer))
+ :int (x :pointer) (y :pointer) (z size-t) (u :double) (v size-t) (w :double) (a :pointer) (b :pointer) (c :pointer))
(defun base-lowess-front (x y z u v w a b c)
(ccl-base-lowess-front x y z (float u 1d0) v (float w 1d0) a b c))
@@ -231,7 +236,7 @@
(cffi:defcfun ("ccl_fft_front" ccl-fft-front)
- :int (x :int) (y :pointer) (z :pointer) (u :int))
+ :int (x size-t) (y :pointer) (z :pointer) (u :int))
(defun fft-front (x y z u)
(ccl-fft-front x y z u))
@@ -7,6 +7,7 @@
(defpackage :lisp-stat-optimize
(:use :common-lisp
+ :cffi
@@ -41,6 +42,11 @@
(in-package :lisp-stat-optimize)
+(defctype size-t :unsigned-long)
+(defctype size-t :unsigned-int)
(defvar *maximize-callback-function* nil
"Used in generic optimization to determine function name -- symbol or string?")
@@ -68,17 +74,17 @@
(register-maximize-callback (cffi:callback ccl-maximize-callback))
(cffi:defcfun ("ccl_numgrad_front" ccl-numgrad-front)
- :int (x :int) (y :pointer) (z :pointer) (u :double) (v :pointer))
+ :void (x size-t) (y :pointer) (z :pointer) (u :double) (v :pointer))
(defun numgrad-front (x y z u v)
(ccl-numgrad-front x y z (float u 1d0) v))
(cffi:defcfun ("ccl_numhess_front" ccl-numhess-front)
- :int (x :int) (y :pointer) (z :pointer) (u :pointer) (v :pointer) (w :double) (a :pointer))
+ :void (x size-t) (y :pointer) (z :pointer) (u :pointer) (v :pointer) (w :double) (a :pointer))
(defun numhess-front (x y z u v w a)
(ccl-numhess-front x y z u v (float w 1d0) a))
(cffi:defcfun ("ccl_minfo_maximize" ccl-minfo-maximize)
- :int (x :pointer) (y :pointer) (z :pointer) (u :pointer) (v :pointer) (w :int))
+ :void (x :pointer) (y :pointer) (z :pointer) (u :pointer) (v :pointer) (w :int))
(defun base-minfo-maximize (x y z u v w)
(ccl-minfo-maximize x y z u v w))

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