7 files changed, 556 insertions, 0 deletions

diff --git a/SD-VBS/common/matlab/timingFuncs/cycle.h b/SD-VBS/common/matlab/timingFuncs/cycle.h
new file mode 100644
index 0000000..2652a04
--- /dev/null
+++ b/SD-VBS/common/matlab/timingFuncs/cycle.h
@@ -0,0 +1,514 @@
+/*
+ * Copyright (c) 2003, 2007-8 Matteo Frigo
+ * Copyright (c) 2003, 2007-8 Massachusetts Institute of Technology
+ *
+ * Permission is hereby granted, free of charge, to any person obtaining
+ * a copy of this software and associated documentation files (the
+ * "Software"), to deal in the Software without restriction, including
+ * without limitation the rights to use, copy, modify, merge, publish,
+ * distribute, sublicense, and/or sell copies of the Software, and to
+ * permit persons to whom the Software is furnished to do so, subject to
+ * the following conditions:
+ *
+ * The above copyright notice and this permission notice shall be
+ * included in all copies or substantial portions of the Software.
+ *
+ * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
+ * EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
+ * MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
+ * NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE
+ * LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION
+ * OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION
+ * WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
+ *
+ */
+
+
+/* machine-dependent cycle counters code. Needs to be inlined. */
+
+/***************************************************************************/
+/* To use the cycle counters in your code, simply #include "cycle.h" (this
+   file), and then use the functions/macros:
+
+                 ticks getticks(void);
+
+   ticks is an opaque typedef defined below, representing the current time.
+   You extract the elapsed time between two calls to gettick() via:
+
+                 double elapsed(ticks t1, ticks t0);
+
+   which returns a double-precision variable in arbitrary units.  You
+   are not expected to convert this into human units like seconds; it
+   is intended only for *comparisons* of time intervals.
+
+   (In order to use some of the OS-dependent timer routines like
+   Solaris' gethrtime, you need to paste the autoconf snippet below
+   into your configure.ac file and #include "config.h" before cycle.h,
+   or define the relevant macros manually if you are not using autoconf.)
+*/
+
+/***************************************************************************/
+/* This file uses macros like HAVE_GETHRTIME that are assumed to be
+   defined according to whether the corresponding function/type/header
+   is available on your system.  The necessary macros are most
+   conveniently defined if you are using GNU autoconf, via the tests:
+   
+   dnl ---------------------------------------------------------------------
+
+   AC_C_INLINE
+   AC_HEADER_TIME
+   AC_CHECK_HEADERS([sys/time.h c_asm.h intrinsics.h mach/mach_time.h])
+
+   AC_CHECK_TYPE([hrtime_t],[AC_DEFINE(HAVE_HRTIME_T, 1, [Define to 1 if hrtime_t is defined in <sys/time.h>])],,[#if HAVE_SYS_TIME_H
+#include <sys/time.h>
+#endif])
+
+   AC_CHECK_FUNCS([gethrtime read_real_time time_base_to_time clock_gettime mach_absolute_time])
+
+   dnl Cray UNICOS _rtc() (real-time clock) intrinsic
+   AC_MSG_CHECKING([for _rtc intrinsic])
+   rtc_ok=yes
+   AC_TRY_LINK([#ifdef HAVE_INTRINSICS_H
+#include <intrinsics.h>
+#endif], [_rtc()], [AC_DEFINE(HAVE__RTC,1,[Define if you have the UNICOS _rtc() intrinsic.])], [rtc_ok=no])
+   AC_MSG_RESULT($rtc_ok)
+
+   dnl ---------------------------------------------------------------------
+*/
+
+/***************************************************************************/
+
+#if TIME_WITH_SYS_TIME
+# include <sys/time.h>
+# include <time.h>
+#else
+# if HAVE_SYS_TIME_H
+#  include <sys/time.h>
+# else
+#  include <time.h>
+# endif
+#endif
+
+#define INLINE_ELAPSED(INL) static INL double elapsed(ticks t1, ticks t0) \
+{                                                                         \
+     return (double)t1 - (double)t0;                                      \
+}
+
+/*----------------------------------------------------------------*/
+/* Solaris */
+#if defined(HAVE_GETHRTIME) && defined(HAVE_HRTIME_T) && !defined(HAVE_TICK_COUNTER)
+typedef hrtime_t ticks;
+
+#define getticks gethrtime
+
+INLINE_ELAPSED(inline)
+
+#define HAVE_TICK_COUNTER
+#endif
+
+/*----------------------------------------------------------------*/
+/* AIX v. 4+ routines to read the real-time clock or time-base register */
+#if defined(HAVE_READ_REAL_TIME) && defined(HAVE_TIME_BASE_TO_TIME) && !defined(HAVE_TICK_COUNTER)
+typedef timebasestruct_t ticks;
+
+static __inline ticks getticks(void)
+{
+     ticks t;
+     read_real_time(&t, TIMEBASE_SZ);
+     return t;
+}
+
+static __inline double elapsed(ticks t1, ticks t0) /* time in nanoseconds */
+{
+     time_base_to_time(&t1, TIMEBASE_SZ);
+     time_base_to_time(&t0, TIMEBASE_SZ);
+     return (((double)t1.tb_high - (double)t0.tb_high) * 1.0e9 + 
+             ((double)t1.tb_low - (double)t0.tb_low));
+}
+
+#define HAVE_TICK_COUNTER
+#endif
+
+/*----------------------------------------------------------------*/
+/*
+ * PowerPC ``cycle'' counter using the time base register.
+ */
+#if ((((defined(__GNUC__) && (defined(__powerpc__) || defined(__ppc__))) || (defined(__MWERKS__) && defined(macintosh)))) || (defined(__IBM_GCC_ASM) && (defined(__powerpc__) || defined(__ppc__))))  && !defined(HAVE_TICK_COUNTER)
+typedef unsigned long long ticks;
+
+static __inline__ ticks getticks(void)
+{
+     unsigned int tbl, tbu0, tbu1;
+
+     do {
+          __asm__ __volatile__ ("mftbu %0" : "=r"(tbu0));
+          __asm__ __volatile__ ("mftb %0" : "=r"(tbl));
+          __asm__ __volatile__ ("mftbu %0" : "=r"(tbu1));
+     } while (tbu0 != tbu1);
+
+     return (((unsigned long long)tbu0) << 32) | tbl;
+}
+
+INLINE_ELAPSED(__inline__)
+
+#define HAVE_TICK_COUNTER
+#endif
+
+/* MacOS/Mach (Darwin) time-base register interface (unlike UpTime,
+   from Carbon, requires no additional libraries to be linked). */
+#if defined(HAVE_MACH_ABSOLUTE_TIME) && defined(HAVE_MACH_MACH_TIME_H) && !defined(HAVE_TICK_COUNTER)
+#include <mach/mach_time.h>
+typedef uint64_t ticks;
+#define getticks mach_absolute_time
+INLINE_ELAPSED(__inline__)
+#define HAVE_TICK_COUNTER
+#endif
+
+/*----------------------------------------------------------------*/
+/*
+ * Pentium cycle counter 
+ */
+#if (defined(__GNUC__) || defined(__ICC)) && defined(__i386__)  && !defined(HAVE_TICK_COUNTER)
+typedef unsigned long long ticks;
+
+static __inline__ ticks getticks(void)
+{
+     ticks ret;
+
+     __asm__ __volatile__("rdtsc": "=A" (ret));
+     /* no input, nothing else clobbered */
+     return ret;
+}
+
+INLINE_ELAPSED(__inline__)
+
+#define HAVE_TICK_COUNTER
+#define TIME_MIN 5000.0   /* unreliable pentium IV cycle counter */
+#endif
+
+/* Visual C++ -- thanks to Morten Nissov for his help with this */
+#if _MSC_VER >= 1200 && _M_IX86 >= 500 && !defined(HAVE_TICK_COUNTER)
+#include <windows.h>
+typedef LARGE_INTEGER ticks;
+#define RDTSC __asm __emit 0fh __asm __emit 031h /* hack for VC++ 5.0 */
+
+static __inline ticks getticks(void)
+{
+     ticks retval;
+
+     __asm {
+          RDTSC
+          mov retval.HighPart, edx
+          mov retval.LowPart, eax
+     }
+     return retval;
+}
+
+static __inline double elapsed(ticks t1, ticks t0)
+{  
+     return (double)t1.QuadPart - (double)t0.QuadPart;
+}  
+
+#define HAVE_TICK_COUNTER
+#define TIME_MIN 5000.0   /* unreliable pentium IV cycle counter */
+#endif
+
+/*----------------------------------------------------------------*/
+/*
+ * X86-64 cycle counter
+ */
+#if (defined(__GNUC__) || defined(__ICC) || defined(__SUNPRO_C)) && defined(__x86_64__)  && !defined(HAVE_TICK_COUNTER)
+typedef unsigned long long ticks;
+
+static __inline__ ticks getticks(void)
+{
+     unsigned a, d; 
+     asm volatile("rdtsc" : "=a" (a), "=d" (d)); 
+     return ((ticks)a) | (((ticks)d) << 32); 
+}
+
+INLINE_ELAPSED(__inline__)
+
+#define HAVE_TICK_COUNTER
+#endif
+
+/* PGI compiler, courtesy Cristiano Calonaci, Andrea Tarsi, & Roberto Gori.
+   NOTE: this code will fail to link unless you use the -Masmkeyword compiler
+   option (grrr). */
+#if defined(__PGI) && defined(__x86_64__) && !defined(HAVE_TICK_COUNTER) 
+typedef unsigned long long ticks;
+static ticks getticks(void)
+{
+    asm(" rdtsc; shl    $0x20,%rdx; mov    %eax,%eax; or     %rdx,%rax;    ");
+}
+INLINE_ELAPSED(__inline__)
+#define HAVE_TICK_COUNTER
+#endif
+
+/* Visual C++, courtesy of Dirk Michaelis */
+#if _MSC_VER >= 1400 && (defined(_M_AMD64) || defined(_M_X64)) && !defined(HAVE_TICK_COUNTER)
+
+#include <intrin.h>
+#pragma intrinsic(__rdtsc)
+typedef unsigned __int64 ticks;
+#define getticks __rdtsc
+INLINE_ELAPSED(__inline)
+
+#define HAVE_TICK_COUNTER
+#endif
+
+/*----------------------------------------------------------------*/
+/*
+ * IA64 cycle counter
+ */
+
+/* intel's icc/ecc compiler */
+#if (defined(__EDG_VERSION) || defined(__ECC)) && defined(__ia64__) && !defined(HAVE_TICK_COUNTER)
+typedef unsigned long ticks;
+#include <ia64intrin.h>
+
+static __inline__ ticks getticks(void)
+{
+     return __getReg(_IA64_REG_AR_ITC);
+}
+ 
+INLINE_ELAPSED(__inline__)
+ 
+#define HAVE_TICK_COUNTER
+#endif
+
+/* gcc */
+#if defined(__GNUC__) && defined(__ia64__) && !defined(HAVE_TICK_COUNTER)
+typedef unsigned long ticks;
+
+static __inline__ ticks getticks(void)
+{
+     ticks ret;
+
+     __asm__ __volatile__ ("mov %0=ar.itc" : "=r"(ret));
+     return ret;
+}
+
+INLINE_ELAPSED(__inline__)
+
+#define HAVE_TICK_COUNTER
+#endif
+
+/* HP/UX IA64 compiler, courtesy Teresa L. Johnson: */
+#if defined(__hpux) && defined(__ia64) && !defined(HAVE_TICK_COUNTER)
+#include <machine/sys/inline.h>
+typedef unsigned long ticks;
+
+static inline ticks getticks(void)
+{
+     ticks ret;
+
+     ret = _Asm_mov_from_ar (_AREG_ITC);
+     return ret;
+}
+
+INLINE_ELAPSED(inline)
+
+#define HAVE_TICK_COUNTER
+#endif
+
+/* Microsoft Visual C++ */
+#if defined(_MSC_VER) && defined(_M_IA64) && !defined(HAVE_TICK_COUNTER)
+typedef unsigned __int64 ticks;
+
+#  ifdef __cplusplus
+extern "C"
+#  endif
+ticks __getReg(int whichReg);
+#pragma intrinsic(__getReg)
+
+static __inline ticks getticks(void)
+{
+     volatile ticks temp;
+     temp = __getReg(3116);
+     return temp;
+}
+
+INLINE_ELAPSED(inline)
+
+#define HAVE_TICK_COUNTER
+#endif
+
+/*----------------------------------------------------------------*/
+/*
+ * PA-RISC cycle counter 
+ */
+#if defined(__hppa__) || defined(__hppa) && !defined(HAVE_TICK_COUNTER)
+typedef unsigned long ticks;
+
+#  ifdef __GNUC__
+static __inline__ ticks getticks(void)
+{
+     ticks ret;
+
+     __asm__ __volatile__("mfctl 16, %0": "=r" (ret));
+     /* no input, nothing else clobbered */
+     return ret;
+}
+#  else
+#  include <machine/inline.h>
+static inline unsigned long getticks(void)
+{
+     register ticks ret;
+     _MFCTL(16, ret);
+     return ret;
+}
+#  endif
+
+INLINE_ELAPSED(inline)
+
+#define HAVE_TICK_COUNTER
+#endif
+
+/*----------------------------------------------------------------*/
+/* S390, courtesy of James Treacy */
+#if defined(__GNUC__) && defined(__s390__) && !defined(HAVE_TICK_COUNTER)
+typedef unsigned long long ticks;
+
+static __inline__ ticks getticks(void)
+{
+     ticks cycles;
+     __asm__("stck 0(%0)" : : "a" (&(cycles)) : "memory", "cc");
+     return cycles;
+}
+
+INLINE_ELAPSED(__inline__)
+
+#define HAVE_TICK_COUNTER
+#endif
+/*----------------------------------------------------------------*/
+#if defined(__GNUC__) && defined(__alpha__) && !defined(HAVE_TICK_COUNTER)
+/*
+ * The 32-bit cycle counter on alpha overflows pretty quickly, 
+ * unfortunately.  A 1GHz machine overflows in 4 seconds.
+ */
+typedef unsigned int ticks;
+
+static __inline__ ticks getticks(void)
+{
+     unsigned long cc;
+     __asm__ __volatile__ ("rpcc %0" : "=r"(cc));
+     return (cc & 0xFFFFFFFF);
+}
+
+INLINE_ELAPSED(__inline__)
+
+#define HAVE_TICK_COUNTER
+#endif
+
+/*----------------------------------------------------------------*/
+#if defined(__GNUC__) && defined(__sparc_v9__) && !defined(HAVE_TICK_COUNTER)
+typedef unsigned long ticks;
+
+static __inline__ ticks getticks(void)
+{
+     ticks ret;
+     __asm__ __volatile__("rd %%tick, %0" : "=r" (ret));
+     return ret;
+}
+
+INLINE_ELAPSED(__inline__)
+
+#define HAVE_TICK_COUNTER
+#endif
+
+/*----------------------------------------------------------------*/
+#if (defined(__DECC) || defined(__DECCXX)) && defined(__alpha) && defined(HAVE_C_ASM_H) && !defined(HAVE_TICK_COUNTER)
+#  include <c_asm.h>
+typedef unsigned int ticks;
+
+static __inline ticks getticks(void)
+{
+     unsigned long cc;
+     cc = asm("rpcc %v0");
+     return (cc & 0xFFFFFFFF);
+}
+
+INLINE_ELAPSED(__inline)
+
+#define HAVE_TICK_COUNTER
+#endif
+/*----------------------------------------------------------------*/
+/* SGI/Irix */
+#if defined(HAVE_CLOCK_GETTIME) && defined(CLOCK_SGI_CYCLE) && !defined(HAVE_TICK_COUNTER)
+typedef struct timespec ticks;
+
+static inline ticks getticks(void)
+{
+     struct timespec t;
+     clock_gettime(CLOCK_SGI_CYCLE, &t);
+     return t;
+}
+
+static inline double elapsed(ticks t1, ticks t0)
+{
+     return ((double)t1.tv_sec - (double)t0.tv_sec) * 1.0E9 +
+          ((double)t1.tv_nsec - (double)t0.tv_nsec);
+}
+#define HAVE_TICK_COUNTER
+#endif
+
+/*----------------------------------------------------------------*/
+/* Cray UNICOS _rtc() intrinsic function */
+#if defined(HAVE__RTC) && !defined(HAVE_TICK_COUNTER)
+#ifdef HAVE_INTRINSICS_H
+#  include <intrinsics.h>
+#endif
+
+typedef long long ticks;
+
+#define getticks _rtc
+
+INLINE_ELAPSED(inline)
+
+#define HAVE_TICK_COUNTER
+#endif
+
+/*----------------------------------------------------------------*/
+/* MIPS ZBus */
+#if HAVE_MIPS_ZBUS_TIMER
+#if defined(__mips__) && !defined(HAVE_TICK_COUNTER)
+#include <sys/mman.h>
+#include <unistd.h>
+#include <fcntl.h>
+
+typedef uint64_t ticks;
+
+static inline ticks getticks(void)
+{
+  static uint64_t* addr = 0;
+
+  if (addr == 0)
+  {
+    uint32_t rq_addr = 0x10030000;
+    int fd;
+    int pgsize;
+
+    pgsize = getpagesize();
+    fd = open ("/dev/mem", O_RDONLY | O_SYNC, 0);
+    if (fd < 0) {
+      perror("open");
+      return NULL;
+    }
+    addr = mmap(0, pgsize, PROT_READ, MAP_SHARED, fd, rq_addr);
+    close(fd);
+    if (addr == (uint64_t *)-1) {
+      perror("mmap");
+      return NULL;
+    }
+  }
+
+  return *addr;
+}
+
+INLINE_ELAPSED(inline)
+
+#define HAVE_TICK_COUNTER
+#endif
+#endif /* HAVE_MIPS_ZBUS_TIMER */
+
diff --git a/SD-VBS/common/matlab/timingFuncs/photonEndTiming.c b/SD-VBS/common/matlab/timingFuncs/photonEndTiming.c
new file mode 100644
index 0000000..bbf5231
--- /dev/null
+++ b/SD-VBS/common/matlab/timingFuncs/photonEndTiming.c
@@ -0,0 +1,15 @@
+#include"mex.h"
+#include <stdio.h>
+#include <stdlib.h>
+#include <stdint.h>
+#include <math.h>
+
+void mexFunction(int nlhs, mxArray* plhs[], int nrhs, const mxArray* prhs[])
+{
+    uint32_t* cycles;
+    plhs[0] = mxCreateNumericMatrix(1, 2, mxUINT32_CLASS, mxREAL);
+    cycles = (uint32_t*)mxGetPr(plhs[0]);
+    __asm__ __volatile__( "rdtsc": "=a" (cycles[0]), "=d" (cycles[1]));    
+ 
+    return;
+}
diff --git a/SD-VBS/common/matlab/timingFuncs/photonEndTiming.mexglx b/SD-VBS/common/matlab/timingFuncs/photonEndTiming.mexglx
new file mode 100755
index 0000000..fa9d4b6
--- /dev/null
+++ b/SD-VBS/common/matlab/timingFuncs/photonEndTiming.mexglx
diff --git a/SD-VBS/common/matlab/timingFuncs/photonPrintTiming.m b/SD-VBS/common/matlab/timingFuncs/photonPrintTiming.m
new file mode 100644
index 0000000..b9c7b22
--- /dev/null
+++ b/SD-VBS/common/matlab/timingFuncs/photonPrintTiming.m
@@ -0,0 +1,5 @@
+%! _photonPrintTiming_NA_i2
+
+function photonPrintTiming(elapsed)
+    disp(elapsed);
+end
\ No newline at end of file
diff --git a/SD-VBS/common/matlab/timingFuncs/photonReportTiming.m b/SD-VBS/common/matlab/timingFuncs/photonReportTiming.m
new file mode 100644
index 0000000..e991175
--- /dev/null
+++ b/SD-VBS/common/matlab/timingFuncs/photonReportTiming.m
@@ -0,0 +1,7 @@
+%! _photonReportTiming_i2_i2i2
+
+function elapsed = photonReportTiming(startCycles, endCycles)
+    elapsed = zeros(1,2);
+    elapsed(1) = endCycles(1) - startCycles(1);
+    elapsed(2) = endCycles(2) - startCycles(2);
+end
\ No newline at end of file
diff --git a/SD-VBS/common/matlab/timingFuncs/photonStartTiming.c b/SD-VBS/common/matlab/timingFuncs/photonStartTiming.c
new file mode 100644
index 0000000..bbf5231
--- /dev/null
+++ b/SD-VBS/common/matlab/timingFuncs/photonStartTiming.c
@@ -0,0 +1,15 @@
+#include"mex.h"
+#include <stdio.h>
+#include <stdlib.h>
+#include <stdint.h>
+#include <math.h>
+
+void mexFunction(int nlhs, mxArray* plhs[], int nrhs, const mxArray* prhs[])
+{
+    uint32_t* cycles;
+    plhs[0] = mxCreateNumericMatrix(1, 2, mxUINT32_CLASS, mxREAL);
+    cycles = (uint32_t*)mxGetPr(plhs[0]);
+    __asm__ __volatile__( "rdtsc": "=a" (cycles[0]), "=d" (cycles[1]));    
+ 
+    return;
+}
diff --git a/SD-VBS/common/matlab/timingFuncs/photonStartTiming.mexglx b/SD-VBS/common/matlab/timingFuncs/photonStartTiming.mexglx
new file mode 100755
index 0000000..8b55b98
--- /dev/null
+++ b/SD-VBS/common/matlab/timingFuncs/photonStartTiming.mexglx