/*
* Do a remote procedure call (RPC) and wait for its reply.
* If from_p is non-null, then we are doing broadcast, and
* the address from whence the response came is saved there.
* data: input/output
* from_p: output
*/
int
krpc_call(struct sockaddr_in *sa, u_int prog, u_int vers, u_int func,
struct mbuf **data, struct mbuf **from_p, int retries)
{
struct socket *so;
struct sockaddr_in *sin;
struct mbuf *m, *nam, *mhead, *from, *mopt;
struct rpc_call *call;
struct rpc_reply *reply;
struct uio auio;
int error, rcvflg, timo, secs, len;
static u_int32_t xid = 0;
char addr[INET_ADDRSTRLEN];
int *ip;
struct timeval tv;
/*
* Validate address family.
* Sorry, this is INET specific...
*/
if (sa->sin_family != AF_INET)
return (EAFNOSUPPORT);
/* Free at end if not null. */
nam = mhead = NULL;
from = NULL;
/*
* Create socket and set its receive timeout.
*/
if ((error = socreate(AF_INET, &so, SOCK_DGRAM, 0)))
goto out;
m = m_get(M_WAIT, MT_SOOPTS);
tv.tv_sec = 1;
tv.tv_usec = 0;
memcpy(mtod(m, struct timeval *), &tv, sizeof tv);
m->m_len = sizeof(tv);
if ((error = sosetopt(so, SOL_SOCKET, SO_RCVTIMEO, m)))
goto out;
/*
* Enable broadcast if necessary.
*/
if (from_p) {
int32_t *on;
m = m_get(M_WAIT, MT_SOOPTS);
on = mtod(m, int32_t *);
m->m_len = sizeof(*on);
*on = 1;
if ((error = sosetopt(so, SOL_SOCKET, SO_BROADCAST, m)))
goto out;
}
/*
* Bind the local endpoint to a reserved port,
* because some NFS servers refuse requests from
* non-reserved (non-privileged) ports.
*/
MGET(mopt, M_WAIT, MT_SOOPTS);
mopt->m_len = sizeof(int);
ip = mtod(mopt, int *);
*ip = IP_PORTRANGE_LOW;
error = sosetopt(so, IPPROTO_IP, IP_PORTRANGE, mopt);
if (error)
goto out;
MGET(m, M_WAIT, MT_SONAME);
sin = mtod(m, struct sockaddr_in *);
sin->sin_len = m->m_len = sizeof (struct sockaddr_in);
sin->sin_family = AF_INET;
sin->sin_addr.s_addr = INADDR_ANY;
sin->sin_port = htons(0);
error = sobind(so, m, &proc0);
m_freem(m);
if (error) {
printf("bind failed\n");
goto out;
}
MGET(mopt, M_WAIT, MT_SOOPTS);
mopt->m_len = sizeof(int);
ip = mtod(mopt, int *);
*ip = IP_PORTRANGE_DEFAULT;
error = sosetopt(so, IPPROTO_IP, IP_PORTRANGE, mopt);
if (error)
goto out;
/*
* Setup socket address for the server.
*/
nam = m_get(M_WAIT, MT_SONAME);
sin = mtod(nam, struct sockaddr_in *);
bcopy((caddr_t)sa, (caddr_t)sin, (nam->m_len = sa->sin_len));
/*
* Prepend RPC message header.
*/
mhead = m_gethdr(M_WAIT, MT_DATA);
mhead->m_next = *data;
call = mtod(mhead, struct rpc_call *);
mhead->m_len = sizeof(*call);
bzero((caddr_t)call, sizeof(*call));
/* rpc_call part */
xid = krpc_get_xid();
call->rp_xid = txdr_unsigned(xid);
/* call->rp_direction = 0; */
call->rp_rpcvers = txdr_unsigned(2);
call->rp_prog = txdr_unsigned(prog);
call->rp_vers = txdr_unsigned(vers);
call->rp_proc = txdr_unsigned(func);
/* rpc_auth part (auth_unix as root) */
call->rpc_auth.authtype = txdr_unsigned(RPCAUTH_UNIX);
call->rpc_auth.authlen = txdr_unsigned(sizeof(struct auth_unix));
/* rpc_verf part (auth_null) */
call->rpc_verf.authtype = 0;
call->rpc_verf.authlen = 0;
/*
* Setup packet header
*/
len = 0;
m = mhead;
while (m) {
len += m->m_len;
m = m->m_next;
}
mhead->m_pkthdr.len = len;
mhead->m_pkthdr.rcvif = NULL;
/*
* Send it, repeatedly, until a reply is received,
* but delay each re-send by an increasing amount.
* If the delay hits the maximum, start complaining.
*/
for (timo = 0; retries; retries--) {
/* Send RPC request (or re-send). */
m = m_copym(mhead, 0, M_COPYALL, M_WAIT);
if (m == NULL) {
error = ENOBUFS;
goto out;
}
error = sosend(so, nam, NULL, m, NULL, 0);
if (error) {
printf("krpc_call: sosend: %d\n", error);
goto out;
}
m = NULL;
/* Determine new timeout. */
if (timo < MAX_RESEND_DELAY)
timo++;
else
printf("RPC timeout for server %s (0x%x) prog %u\n",
inet_ntop(AF_INET, &sin->sin_addr,
addr, sizeof(addr)),
ntohl(sin->sin_addr.s_addr), prog);
/*
* Wait for up to timo seconds for a reply.
* The socket receive timeout was set to 1 second.
*/
secs = timo;
while (secs > 0) {
if (from) {
m_freem(from);
from = NULL;
}
if (m) {
m_freem(m);
m = NULL;
}
auio.uio_resid = len = 1<<16;
auio.uio_procp = NULL;
rcvflg = 0;
error = soreceive(so, &from, &auio, &m, NULL, &rcvflg,
0);
if (error == EWOULDBLOCK) {
secs--;
continue;
}
if (error)
goto out;
len -= auio.uio_resid;
/* Does the reply contain at least a header? */
if (len < MIN_REPLY_HDR)
continue;
if (m->m_len < MIN_REPLY_HDR)
continue;
reply = mtod(m, struct rpc_reply *);
/* Is it the right reply? */
if (reply->rp_direction != txdr_unsigned(RPC_REPLY))
continue;
if (reply->rp_xid != txdr_unsigned(xid))
continue;
/* Was RPC accepted? (authorization OK) */
if (reply->rp_astatus != 0) {
error = fxdr_unsigned(u_int32_t, reply->rp_errno);
printf("rpc denied, error=%d\n", error);
continue;
}
/* Did the call succeed? */
if (reply->rp_status != 0) {
error = fxdr_unsigned(u_int32_t, reply->rp_status);
printf("rpc denied, status=%d\n", error);
continue;
}
goto gotreply; /* break two levels */
} /* while secs */
} /* forever send/receive */
error = ETIMEDOUT;
goto out;
gotreply:
/*
* Get RPC reply header into first mbuf,
* get its length, then strip it off.
*/
len = sizeof(*reply);
if (m->m_len < len) {
m = m_pullup(m, len);
if (m == NULL) {
error = ENOBUFS;
goto out;
}
}
reply = mtod(m, struct rpc_reply *);
if (reply->rp_auth.authtype != 0) {
len += fxdr_unsigned(u_int32_t, reply->rp_auth.authlen);
len = (len + 3) & ~3; /* XXX? */
}
m_adj(m, len);
/* result */
*data = m;
if (from_p && error == 0) {
*from_p = from;
from = NULL;
}
out:
if (nam) m_freem(nam);
if (mhead) m_freem(mhead);
if (from) m_freem(from);
soclose(so);
return error;
}
static void bootp_reply(struct bootp_t *bp)
{
BOOTPClient *bc;
struct mbuf *m;
struct bootp_t *rbp;
struct sockaddr_in saddr, daddr;
struct in_addr dns_addr;
int dhcp_msg_type, val;
uint8_t *q;
int freply_nack = 0;
/* extract exact DHCP msg type */
dhcp_decode(bp->bp_vend, DHCP_OPT_LEN, &dhcp_msg_type);
dprintf("bootp packet op=%d msgtype=%d\n", bp->bp_op, dhcp_msg_type);
if (dhcp_msg_type == 0)
dhcp_msg_type = DHCPREQUEST; /* Force reply for old BOOTP clients */
if (dhcp_msg_type == DHCPRELEASE) {
release_addr(&bp->bp_ciaddr);
dprintf("released addr=%08lx\n", ntohl(bp->bp_ciaddr.s_addr));
/* This message is not to be answered in any way. */
return;
}
if (dhcp_msg_type != DHCPDISCOVER &&
dhcp_msg_type != DHCPREQUEST)
return;
/* XXX: this is a hack to get the client mac address */
memcpy(client_ethaddr, bp->bp_hwaddr, 6);
if ((m = m_get()) == NULL)
return;
m->m_data += if_maxlinkhdr;
rbp = (struct bootp_t *)m->m_data;
m->m_data += sizeof(struct udpiphdr);
memset(rbp, 0, sizeof(struct bootp_t));
if (dhcp_msg_type == DHCPDISCOVER) {
bc = get_new_addr(&daddr.sin_addr);
if (!bc) {
dprintf("no address left\n");
return;
}
memcpy(bc->macaddr, client_ethaddr, 6);
} else {
bc = find_addr(&daddr.sin_addr, bp->bp_hwaddr);
if (!bc) {
/* if never assigned, reply DHCPNACK to BROADCAST.
(windows fix because it remembers its address). */
daddr.sin_addr.s_addr = htonl(0xffffffff);
freply_nack = 1;
dprintf("reply NACK\n");
}
}
dprintf("offered addr=%08lx\n", ntohl(daddr.sin_addr.s_addr));
saddr.sin_addr.s_addr = htonl(ntohl(special_addr.s_addr) | CTL_ALIAS);
saddr.sin_port = htons(BOOTP_SERVER);
daddr.sin_port = htons(BOOTP_CLIENT);
rbp->bp_op = BOOTP_REPLY;
rbp->bp_xid = bp->bp_xid;
rbp->bp_htype = 1;
rbp->bp_hlen = 6;
memcpy(rbp->bp_hwaddr, bp->bp_hwaddr, 6);
if (freply_nack)
rbp->bp_yiaddr.s_addr = htonl(0); /* When NACK, IP address is 0. */
else
rbp->bp_yiaddr = daddr.sin_addr; /* Client IP address */
rbp->bp_siaddr = saddr.sin_addr; /* Server IP address */
q = rbp->bp_vend;
memcpy(q, rfc1533_cookie, 4);
q += 4;
if (dhcp_msg_type == DHCPDISCOVER) {
*q++ = RFC2132_MSG_TYPE;
*q++ = 1;
*q++ = DHCPOFFER;
} else if (dhcp_msg_type == DHCPREQUEST) {
*q++ = RFC2132_MSG_TYPE;
*q++ = 1;
if (freply_nack)
*q++ = DHCPNACK;
else
*q++ = DHCPACK;
}
if (dhcp_msg_type == DHCPDISCOVER ||
((dhcp_msg_type == DHCPREQUEST) && !freply_nack)) {
*q++ = RFC2132_SRV_ID;
*q++ = 4;
memcpy(q, &saddr.sin_addr, 4);
q += 4;
*q++ = RFC1533_NETMASK;
*q++ = 4;
*q++ = 0xff;
*q++ = 0xff;
*q++ = 0xff;
*q++ = 0x00;
*q++ = RFC1533_GATEWAY;
*q++ = 4;
memcpy(q, &saddr.sin_addr, 4);
q += 4;
*q++ = RFC1533_DNS;
*q++ = 4;
dns_addr.s_addr = htonl(ntohl(special_addr.s_addr) | CTL_DNS);
memcpy(q, &dns_addr, 4);
q += 4;
*q++ = RFC2132_LEASE_TIME;
*q++ = 4;
val = htonl(LEASE_TIME);
memcpy(q, &val, 4);
q += 4;
if (*slirp_hostname) {
val = strlen(slirp_hostname);
*q++ = RFC1533_HOSTNAME;
*q++ = val;
memcpy(q, slirp_hostname, val);
q += val;
}
}
*q++ = RFC1533_END;
m->m_len = sizeof(struct bootp_t) -
sizeof(struct ip) - sizeof(struct udphdr);
udp_output2(NULL, m, &saddr, &daddr, IPTOS_LOWDELAY);
}
void icmp6_send_error(struct mbuf *m, uint8_t type, uint8_t code)
{
Slirp *slirp = m->slirp;
struct mbuf *t;
struct ip6 *ip = mtod(m, struct ip6 *);
DEBUG_CALL("icmp6_send_error");
DEBUG_ARGS((dfd, " type = %d, code = %d\n", type, code));
if (IN6_IS_ADDR_MULTICAST(&ip->ip_src) ||
IN6_IS_ADDR_UNSPECIFIED(&ip->ip_src)) {
/* TODO icmp error? */
return;
}
t = m_get(slirp);
/* IPv6 packet */
struct ip6 *rip = mtod(t, struct ip6 *);
rip->ip_src = (struct in6_addr)LINKLOCAL_ADDR;
rip->ip_dst = ip->ip_src;
#if !defined(_WIN32) || (_WIN32_WINNT >= 0x0600)
char addrstr[INET6_ADDRSTRLEN];
inet_ntop(AF_INET6, &rip->ip_dst, addrstr, INET6_ADDRSTRLEN);
DEBUG_ARG("target = %s", addrstr);
#endif
rip->ip_nh = IPPROTO_ICMPV6;
const int error_data_len = min(m->m_len,
IF_MTU - (sizeof(struct ip6) + ICMP6_ERROR_MINLEN));
rip->ip_pl = htons(ICMP6_ERROR_MINLEN + error_data_len);
t->m_len = sizeof(struct ip6) + ntohs(rip->ip_pl);
/* ICMPv6 packet */
t->m_data += sizeof(struct ip6);
struct icmp6 *ricmp = mtod(t, struct icmp6 *);
ricmp->icmp6_type = type;
ricmp->icmp6_code = code;
ricmp->icmp6_cksum = 0;
switch (type) {
case ICMP6_UNREACH:
case ICMP6_TIMXCEED:
ricmp->icmp6_err.unused = 0;
break;
case ICMP6_TOOBIG:
ricmp->icmp6_err.mtu = htonl(IF_MTU);
break;
case ICMP6_PARAMPROB:
/* TODO: Handle this case */
break;
default:
g_assert_not_reached();
break;
}
t->m_data += ICMP6_ERROR_MINLEN;
memcpy(t->m_data, m->m_data, error_data_len);
/* Checksum */
t->m_data -= ICMP6_ERROR_MINLEN;
t->m_data -= sizeof(struct ip6);
ricmp->icmp6_cksum = ip6_cksum(t);
ip6_output(NULL, t, 0);
}
void ellipseevolve(MAT *f, double *xc0, double *yc0, double *r0, double *t, int Np, double Er, double Ey) {
/*
% ELLIPSEEVOLVE evolves a parametric snake according
% to some energy constraints.
%
% INPUTS:
% f............potential surface
% xc0,yc0......initial center position
% r0,t.........initial radii & angle vectors (with Np elements each)
% Np...........number of snaxel points per snake
% Er...........expected radius
% Ey...........expected y position
%
% OUTPUTS
% xc0,yc0.......final center position
% r0...........final radii
%
% Matlab code written by: DREW GILLIAM (based on work by GANG DONG /
% NILANJAN RAY)
% Ported to C by: MICHAEL BOYER
*/
// Constants
double deltax = 0.2;
double deltay = 0.2;
double deltar = 0.2;
double converge = 0.1;
double lambdaedge = 1;
double lambdasize = 0.2;
double lambdapath = 0.05;
int iterations = 1000; // maximum number of iterations
int i, j;
// Initialize variables
double xc = *xc0;
double yc = *yc0;
double *r = (double *) malloc(sizeof(double) * Np);
for (i = 0; i < Np; i++) r[i] = r0[i];
// Compute the x- and y-gradients of the MGVF matrix
MAT *fx = gradient_x(f);
MAT *fy = gradient_y(f);
// Normalize the gradients
int fh = f->m, fw = f->n;
for (i = 0; i < fh; i++) {
for (j = 0; j < fw; j++) {
double temp_x = m_get_val(fx, i, j);
double temp_y = m_get_val(fy, i, j);
double fmag = sqrt((temp_x * temp_x) + (temp_y * temp_y));
m_set_val(fx, i, j, temp_x / fmag);
m_set_val(fy, i, j, temp_y / fmag);
}
}
double *r_old = (double *) malloc(sizeof(double) * Np);
VEC *x = v_get(Np);
VEC *y = v_get(Np);
// Evolve the snake
int iter = 0;
double snakediff = 1.0;
while (iter < iterations && snakediff > converge) {
// Save the values from the previous iteration
double xc_old = xc, yc_old = yc;
for (i = 0; i < Np; i++) {
r_old[i] = r[i];
}
// Compute the locations of the snaxels
for (i = 0; i < Np; i++) {
v_set_val(x, i, xc + r[i] * cos(t[i]));
v_set_val(y, i, yc + r[i] * sin(t[i]));
}
// See if any of the points in the snake are off the edge of the image
double min_x = v_get_val(x, 0), max_x = v_get_val(x, 0);
double min_y = v_get_val(y, 0), max_y = v_get_val(y, 0);
for (i = 1; i < Np; i++) {
double x_i = v_get_val(x, i);
if (x_i < min_x) min_x = x_i;
else if (x_i > max_x) max_x = x_i;
double y_i = v_get_val(y, i);
if (y_i < min_y) min_y = y_i;
else if (y_i > max_y) max_y = y_i;
}
if (min_x < 0.0 || max_x > (double) fw - 1.0 || min_y < 0 || max_y > (double) fh - 1.0) break;
// Compute the length of the snake
double L = 0.0;
for (i = 0; i < Np - 1; i++) {
double diff_x = v_get_val(x, i + 1) - v_get_val(x, i);
double diff_y = v_get_val(y, i + 1) - v_get_val(y, i);
L += sqrt((diff_x * diff_x) + (diff_y * diff_y));
}
double diff_x = v_get_val(x, 0) - v_get_val(x, Np - 1);
double diff_y = v_get_val(y, 0) - v_get_val(y, Np - 1);
L += sqrt((diff_x * diff_x) + (diff_y * diff_y));
// Compute the potential surface at each snaxel
MAT *vf = linear_interp2(f, x, y);
MAT *vfx = linear_interp2(fx, x, y);
MAT *vfy = linear_interp2(fy, x, y);
// Compute the average potential surface around the snake
double vfmean = sum_m(vf ) / L;
double vfxmean = sum_m(vfx) / L;
double vfymean = sum_m(vfy) / L;
// Compute the radial potential surface
int m = vf->m, n = vf->n;
MAT *vfr = m_get(m, n);
for (i = 0; i < n; i++) {
double vf_val = m_get_val(vf, 0, i);
double vfx_val = m_get_val(vfx, 0, i);
double vfy_val = m_get_val(vfy, 0, i);
double x_val = v_get_val(x, i);
double y_val = v_get_val(y, i);
double new_val = (vf_val + vfx_val * (x_val - xc) + vfy_val * (y_val - yc) - vfmean) / L;
m_set_val(vfr, 0, i, new_val);
}
// Update the snake center and snaxels
xc = xc + (deltax * lambdaedge * vfxmean);
yc = (yc + (deltay * lambdaedge * vfymean) + (deltay * lambdapath * Ey)) / (1.0 + deltay * lambdapath);
double r_diff = 0.0;
for (i = 0; i < Np; i++) {
r[i] = (r[i] + (deltar * lambdaedge * m_get_val(vfr, 0, i)) + (deltar * lambdasize * Er)) /
(1.0 + deltar * lambdasize);
r_diff += fabs(r[i] - r_old[i]);
}
// Test for convergence
snakediff = fabs(xc - xc_old) + fabs(yc - yc_old) + r_diff;
// Free temporary matrices
m_free(vf);
m_free(vfx);
m_free(vfy);
m_free(vfr);
iter++;
}
// Set the return values
*xc0 = xc;
*yc0 = yc;
for (i = 0; i < Np; i++)
r0[i] = r[i];
// Free memory
free(r); free(r_old);
v_free( x); v_free( y);
m_free(fx); m_free(fy);
}
static int
kttcp_soreceive(struct socket *so, unsigned long long slen,
unsigned long long *done, struct lwp *l, int *flagsp)
{
struct mbuf *m, **mp;
int flags, len, error, offset, moff, type;
long long orig_resid, resid;
const struct protosw *pr;
struct mbuf *nextrecord;
pr = so->so_proto;
mp = NULL;
type = 0;
resid = orig_resid = slen;
if (flagsp)
flags = *flagsp &~ MSG_EOR;
else
flags = 0;
if (flags & MSG_OOB) {
m = m_get(M_WAIT, MT_DATA);
solock(so);
error = (*pr->pr_usrreqs->pr_recvoob)(so, m, flags & MSG_PEEK);
sounlock(so);
if (error)
goto bad;
do {
resid -= min(resid, m->m_len);
m = m_free(m);
} while (resid && error == 0 && m);
bad:
if (m)
m_freem(m);
return (error);
}
if (mp)
*mp = NULL;
solock(so);
restart:
if ((error = sblock(&so->so_rcv, SBLOCKWAIT(flags))) != 0)
return (error);
m = so->so_rcv.sb_mb;
/*
* If we have less data than requested, block awaiting more
* (subject to any timeout) if:
* 1. the current count is less than the low water mark,
* 2. MSG_WAITALL is set, and it is possible to do the entire
* receive operation at once if we block (resid <= hiwat), or
* 3. MSG_DONTWAIT is not set.
* If MSG_WAITALL is set but resid is larger than the receive buffer,
* we have to do the receive in sections, and thus risk returning
* a short count if a timeout or signal occurs after we start.
*/
if (m == NULL || (((flags & MSG_DONTWAIT) == 0 &&
so->so_rcv.sb_cc < resid) &&
(so->so_rcv.sb_cc < so->so_rcv.sb_lowat ||
((flags & MSG_WAITALL) && resid <= so->so_rcv.sb_hiwat)) &&
m->m_nextpkt == NULL && (pr->pr_flags & PR_ATOMIC) == 0)) {
#ifdef DIAGNOSTIC
if (m == NULL && so->so_rcv.sb_cc)
panic("receive 1");
#endif
if (so->so_error) {
if (m)
goto dontblock;
error = so->so_error;
if ((flags & MSG_PEEK) == 0)
so->so_error = 0;
goto release;
}
if (so->so_state & SS_CANTRCVMORE) {
if (m)
goto dontblock;
else
goto release;
}
for (; m; m = m->m_next)
if (m->m_type == MT_OOBDATA || (m->m_flags & M_EOR)) {
m = so->so_rcv.sb_mb;
goto dontblock;
}
if ((so->so_state & (SS_ISCONNECTED|SS_ISCONNECTING)) == 0 &&
(so->so_proto->pr_flags & PR_CONNREQUIRED)) {
error = ENOTCONN;
goto release;
}
if (resid == 0)
goto release;
if ((so->so_state & SS_NBIO) ||
(flags & (MSG_DONTWAIT|MSG_NBIO))) {
error = EWOULDBLOCK;
goto release;
}
sbunlock(&so->so_rcv);
error = sbwait(&so->so_rcv);
if (error) {
sounlock(so);
return (error);
}
goto restart;
}
dontblock:
/*
* On entry here, m points to the first record of the socket buffer.
* While we process the initial mbufs containing address and control
* info, we save a copy of m->m_nextpkt into nextrecord.
*/
#ifdef notyet /* XXXX */
if (uio->uio_lwp)
uio->uio_lwp->l_ru.ru_msgrcv++;
#endif
KASSERT(m == so->so_rcv.sb_mb);
SBLASTRECORDCHK(&so->so_rcv, "kttcp_soreceive 1");
SBLASTMBUFCHK(&so->so_rcv, "kttcp_soreceive 1");
nextrecord = m->m_nextpkt;
if (pr->pr_flags & PR_ADDR) {
#ifdef DIAGNOSTIC
if (m->m_type != MT_SONAME)
panic("receive 1a");
#endif
orig_resid = 0;
if (flags & MSG_PEEK) {
m = m->m_next;
} else {
sbfree(&so->so_rcv, m);
MFREE(m, so->so_rcv.sb_mb);
m = so->so_rcv.sb_mb;
}
}
while (m && m->m_type == MT_CONTROL && error == 0) {
if (flags & MSG_PEEK) {
m = m->m_next;
} else {
sbfree(&so->so_rcv, m);
MFREE(m, so->so_rcv.sb_mb);
m = so->so_rcv.sb_mb;
}
}
/*
* If m is non-NULL, we have some data to read. From now on,
* make sure to keep sb_lastrecord consistent when working on
* the last packet on the chain (nextrecord == NULL) and we
* change m->m_nextpkt.
*/
if (m) {
if ((flags & MSG_PEEK) == 0) {
m->m_nextpkt = nextrecord;
/*
* If nextrecord == NULL (this is a single chain),
* then sb_lastrecord may not be valid here if m
* was changed earlier.
*/
if (nextrecord == NULL) {
KASSERT(so->so_rcv.sb_mb == m);
so->so_rcv.sb_lastrecord = m;
}
}
type = m->m_type;
if (type == MT_OOBDATA)
flags |= MSG_OOB;
} else {
if ((flags & MSG_PEEK) == 0) {
KASSERT(so->so_rcv.sb_mb == m);
so->so_rcv.sb_mb = nextrecord;
SB_EMPTY_FIXUP(&so->so_rcv);
}
}
SBLASTRECORDCHK(&so->so_rcv, "kttcp_soreceive 2");
SBLASTMBUFCHK(&so->so_rcv, "kttcp_soreceive 2");
moff = 0;
offset = 0;
while (m && resid > 0 && error == 0) {
if (m->m_type == MT_OOBDATA) {
if (type != MT_OOBDATA)
break;
} else if (type == MT_OOBDATA)
break;
#ifdef DIAGNOSTIC
else if (m->m_type != MT_DATA && m->m_type != MT_HEADER)
panic("receive 3");
#endif
so->so_state &= ~SS_RCVATMARK;
len = resid;
if (so->so_oobmark && len > so->so_oobmark - offset)
len = so->so_oobmark - offset;
if (len > m->m_len - moff)
len = m->m_len - moff;
/*
* If mp is set, just pass back the mbufs.
* Otherwise copy them out via the uio, then free.
* Sockbuf must be consistent here (points to current mbuf,
* it points to next record) when we drop priority;
* we must note any additions to the sockbuf when we
* block interrupts again.
*/
resid -= len;
if (len == m->m_len - moff) {
if (m->m_flags & M_EOR)
flags |= MSG_EOR;
if (flags & MSG_PEEK) {
m = m->m_next;
moff = 0;
} else {
nextrecord = m->m_nextpkt;
sbfree(&so->so_rcv, m);
if (mp) {
*mp = m;
mp = &m->m_next;
so->so_rcv.sb_mb = m = m->m_next;
*mp = NULL;
} else {
MFREE(m, so->so_rcv.sb_mb);
m = so->so_rcv.sb_mb;
}
/*
* If m != NULL, we also know that
* so->so_rcv.sb_mb != NULL.
*/
KASSERT(so->so_rcv.sb_mb == m);
if (m) {
m->m_nextpkt = nextrecord;
if (nextrecord == NULL)
so->so_rcv.sb_lastrecord = m;
} else {
so->so_rcv.sb_mb = nextrecord;
SB_EMPTY_FIXUP(&so->so_rcv);
}
SBLASTRECORDCHK(&so->so_rcv,
"kttcp_soreceive 3");
SBLASTMBUFCHK(&so->so_rcv,
"kttcp_soreceive 3");
}
} else {
if (flags & MSG_PEEK)
moff += len;
else {
if (mp) {
sounlock(so);
*mp = m_copym(m, 0, len, M_WAIT);
solock(so);
}
m->m_data += len;
m->m_len -= len;
so->so_rcv.sb_cc -= len;
}
}
if (so->so_oobmark) {
if ((flags & MSG_PEEK) == 0) {
so->so_oobmark -= len;
if (so->so_oobmark == 0) {
so->so_state |= SS_RCVATMARK;
break;
}
} else {
offset += len;
if (offset == so->so_oobmark)
break;
}
}
if (flags & MSG_EOR)
break;
/*
* If the MSG_WAITALL flag is set (for non-atomic socket),
* we must not quit until "uio->uio_resid == 0" or an error
* termination. If a signal/timeout occurs, return
* with a short count but without error.
* Keep sockbuf locked against other readers.
*/
while (flags & MSG_WAITALL && m == NULL && resid > 0 &&
!sosendallatonce(so) && !nextrecord) {
if (so->so_error || so->so_state & SS_CANTRCVMORE)
break;
/*
* If we are peeking and the socket receive buffer is
* full, stop since we can't get more data to peek at.
*/
if ((flags & MSG_PEEK) && sbspace(&so->so_rcv) <= 0)
break;
/*
* If we've drained the socket buffer, tell the
* protocol in case it needs to do something to
* get it filled again.
*/
if ((pr->pr_flags & PR_WANTRCVD) && so->so_pcb) {
(*pr->pr_usrreqs->pr_rcvd)(so, flags, l);
}
SBLASTRECORDCHK(&so->so_rcv,
"kttcp_soreceive sbwait 2");
SBLASTMBUFCHK(&so->so_rcv,
"kttcp_soreceive sbwait 2");
error = sbwait(&so->so_rcv);
if (error) {
sbunlock(&so->so_rcv);
sounlock(so);
return (0);
}
if ((m = so->so_rcv.sb_mb) != NULL)
nextrecord = m->m_nextpkt;
}
}
if (m && pr->pr_flags & PR_ATOMIC) {
flags |= MSG_TRUNC;
if ((flags & MSG_PEEK) == 0)
(void) sbdroprecord(&so->so_rcv);
}
if ((flags & MSG_PEEK) == 0) {
if (m == NULL) {
/*
* First part is an SB_EMPTY_FIXUP(). Second part
* makes sure sb_lastrecord is up-to-date if
* there is still data in the socket buffer.
*/
so->so_rcv.sb_mb = nextrecord;
if (so->so_rcv.sb_mb == NULL) {
so->so_rcv.sb_mbtail = NULL;
so->so_rcv.sb_lastrecord = NULL;
} else if (nextrecord->m_nextpkt == NULL)
so->so_rcv.sb_lastrecord = nextrecord;
}
SBLASTRECORDCHK(&so->so_rcv, "kttcp_soreceive 4");
SBLASTMBUFCHK(&so->so_rcv, "kttcp_soreceive 4");
if (pr->pr_flags & PR_WANTRCVD && so->so_pcb) {
(*pr->pr_usrreqs->pr_rcvd)(so, flags, l);
}
}
if (orig_resid == resid && orig_resid &&
(flags & MSG_EOR) == 0 && (so->so_state & SS_CANTRCVMORE) == 0) {
sbunlock(&so->so_rcv);
goto restart;
}
if (flagsp)
*flagsp |= flags;
release:
sbunlock(&so->so_rcv);
sounlock(so);
*done = slen - resid;
#if 0
printf("soreceive: error %d slen %llu resid %lld\n", error, slen, resid);
#endif
return (error);
}
static void bootp_reply(Slirp *slirp, const struct bootp_t *bp)
{
BOOTPClient *bc = NULL;
struct mbuf *m;
struct bootp_t *rbp;
struct sockaddr_in saddr, daddr;
struct in_addr preq_addr;
int dhcp_msg_type, val;
uint8_t *q;
uint8_t *end;
uint8_t client_ethaddr[ETH_ALEN];
/* extract exact DHCP msg type */
dhcp_decode(bp, &dhcp_msg_type, &preq_addr);
DPRINTF("bootp packet op=%d msgtype=%d", bp->bp_op, dhcp_msg_type);
if (preq_addr.s_addr != htonl(0L))
DPRINTF(" req_addr=%08" PRIx32 "\n", ntohl(preq_addr.s_addr));
else {
DPRINTF("\n");
}
if (dhcp_msg_type == 0)
dhcp_msg_type = DHCPREQUEST; /* Force reply for old BOOTP clients */
if (dhcp_msg_type != DHCPDISCOVER &&
dhcp_msg_type != DHCPREQUEST)
return;
/* Get client's hardware address from bootp request */
memcpy(client_ethaddr, bp->bp_hwaddr, ETH_ALEN);
m = m_get(slirp);
if (!m) {
return;
}
m->m_data += IF_MAXLINKHDR;
rbp = (struct bootp_t *)m->m_data;
m->m_data += sizeof(struct udpiphdr);
memset(rbp, 0, sizeof(struct bootp_t));
if (dhcp_msg_type == DHCPDISCOVER) {
if (preq_addr.s_addr != htonl(0L)) {
bc = request_addr(slirp, &preq_addr, client_ethaddr);
if (bc) {
daddr.sin_addr = preq_addr;
}
}
if (!bc) {
new_addr:
bc = get_new_addr(slirp, &daddr.sin_addr, client_ethaddr);
if (!bc) {
DPRINTF("no address left\n");
return;
}
}
memcpy(bc->macaddr, client_ethaddr, ETH_ALEN);
} else if (preq_addr.s_addr != htonl(0L)) {
bc = request_addr(slirp, &preq_addr, client_ethaddr);
if (bc) {
daddr.sin_addr = preq_addr;
memcpy(bc->macaddr, client_ethaddr, ETH_ALEN);
} else {
/* DHCPNAKs should be sent to broadcast */
daddr.sin_addr.s_addr = 0xffffffff;
}
} else {
bc = find_addr(slirp, &daddr.sin_addr, bp->bp_hwaddr);
if (!bc) {
/* if never assigned, behaves as if it was already
assigned (windows fix because it remembers its address) */
goto new_addr;
}
}
/* Update ARP table for this IP address */
arp_table_add(slirp, daddr.sin_addr.s_addr, client_ethaddr);
saddr.sin_addr = slirp->vhost_addr;
saddr.sin_port = htons(BOOTP_SERVER);
daddr.sin_port = htons(BOOTP_CLIENT);
rbp->bp_op = BOOTP_REPLY;
rbp->bp_xid = bp->bp_xid;
rbp->bp_htype = 1;
rbp->bp_hlen = 6;
memcpy(rbp->bp_hwaddr, bp->bp_hwaddr, ETH_ALEN);
rbp->bp_yiaddr = daddr.sin_addr; /* Client IP address */
rbp->bp_siaddr = saddr.sin_addr; /* Server IP address */
q = rbp->bp_vend;
end = (uint8_t *)&rbp[1];
memcpy(q, rfc1533_cookie, 4);
q += 4;
if (bc) {
DPRINTF("%s addr=%08" PRIx32 "\n",
(dhcp_msg_type == DHCPDISCOVER) ? "offered" : "ack'ed",
ntohl(daddr.sin_addr.s_addr));
if (dhcp_msg_type == DHCPDISCOVER) {
*q++ = RFC2132_MSG_TYPE;
*q++ = 1;
*q++ = DHCPOFFER;
} else /* DHCPREQUEST */ {
*q++ = RFC2132_MSG_TYPE;
*q++ = 1;
*q++ = DHCPACK;
}
if (slirp->bootp_filename)
snprintf((char *)rbp->bp_file, sizeof(rbp->bp_file), "%s",
slirp->bootp_filename);
*q++ = RFC2132_SRV_ID;
*q++ = 4;
memcpy(q, &saddr.sin_addr, 4);
q += 4;
*q++ = RFC1533_NETMASK;
*q++ = 4;
memcpy(q, &slirp->vnetwork_mask, 4);
q += 4;
if (!slirp->restricted) {
*q++ = RFC1533_GATEWAY;
*q++ = 4;
memcpy(q, &saddr.sin_addr, 4);
q += 4;
*q++ = RFC1533_DNS;
*q++ = 4;
memcpy(q, &slirp->vnameserver_addr, 4);
q += 4;
}
*q++ = RFC2132_LEASE_TIME;
*q++ = 4;
val = htonl(LEASE_TIME);
memcpy(q, &val, 4);
q += 4;
if (*slirp->client_hostname) {
val = strlen(slirp->client_hostname);
if (q + val + 2 >= end) {
g_warning("DHCP packet size exceeded, "
"omitting host name option.");
} else {
*q++ = RFC1533_HOSTNAME;
*q++ = val;
memcpy(q, slirp->client_hostname, val);
q += val;
}
}
if (slirp->vdomainname) {
val = strlen(slirp->vdomainname);
if (q + val + 2 >= end) {
g_warning("DHCP packet size exceeded, "
"omitting domain name option.");
} else {
*q++ = RFC1533_DOMAINNAME;
*q++ = val;
memcpy(q, slirp->vdomainname, val);
q += val;
}
}
if (slirp->tftp_server_name) {
val = strlen(slirp->tftp_server_name);
if (q + val + 2 >= end) {
g_warning("DHCP packet size exceeded, "
"omitting tftp-server-name option.");
} else {
*q++ = RFC2132_TFTP_SERVER_NAME;
*q++ = val;
memcpy(q, slirp->tftp_server_name, val);
q += val;
}
}
if (slirp->vdnssearch) {
val = slirp->vdnssearch_len;
if (q + val >= end) {
g_warning("DHCP packet size exceeded, "
"omitting domain-search option.");
} else {
memcpy(q, slirp->vdnssearch, val);
q += val;
}
}
} else {
static const char nak_msg[] = "requested address not available";
DPRINTF("nak'ed addr=%08" PRIx32 "\n", ntohl(preq_addr.s_addr));
*q++ = RFC2132_MSG_TYPE;
*q++ = 1;
*q++ = DHCPNAK;
*q++ = RFC2132_MESSAGE;
*q++ = sizeof(nak_msg) - 1;
memcpy(q, nak_msg, sizeof(nak_msg) - 1);
q += sizeof(nak_msg) - 1;
}
assert(q < end);
*q = RFC1533_END;
daddr.sin_addr.s_addr = 0xffffffffu;
m->m_len = sizeof(struct bootp_t) -
sizeof(struct ip) - sizeof(struct udphdr);
udp_output(NULL, m, &saddr, &daddr, IPTOS_LOWDELAY);
}
MAT *MGVF(MAT *I, double vx, double vy) {
/*
% MGVF calculate the motion gradient vector flow (MGVF)
% for the image 'I'
%
% Based on the algorithm in:
% Motion gradient vector flow: an external force for tracking rolling
% leukocytes with shape and size constrained active contours
% Ray, N. and Acton, S.T.
% IEEE Transactions on Medical Imaging
% Volume: 23, Issue: 12, December 2004
% Pages: 1466 - 1478
%
% INPUTS
% I...........image
% vx,vy.......velocity vector
%
% OUTPUT
% IMGVF.......MGVF vector field as image
%
% Matlab code written by: DREW GILLIAM (based on work by GANG DONG /
% NILANJAN RAY)
% Ported to C by: MICHAEL BOYER
*/
// Constants
double converge = 0.00001;
double mu = 0.5;
double epsilon = 0.0000000001;
double lambda = 8.0 * mu + 1.0;
// Smallest positive value expressable in double-precision
double eps = pow(2.0, -52.0);
// Maximum number of iterations to compute the MGVF matrix
int iterations = 500;
// Find the maximum and minimum values in I
int m = I->m, n = I->n, i, j;
double Imax = m_get_val(I, 0, 0);
double Imin = m_get_val(I, 0, 0);
for (i = 0; i < m; i++) {
for (j = 0; j < n; j++) {
double temp = m_get_val(I, i, j);
if (temp > Imax) Imax = temp;
else if (temp < Imin) Imin = temp;
}
}
// Normalize the image I
double scale = 1.0 / (Imax - Imin + eps);
for (i = 0; i < m; i++) {
for (j = 0; j < n; j++) {
double old_val = m_get_val(I, i, j);
m_set_val(I, i, j, (old_val - Imin) * scale);
}
}
// Initialize the output matrix IMGVF with values from I
MAT *IMGVF = m_get(m, n);
for (i = 0; i < m; i++) {
for (j = 0; j < n; j++) {
m_set_val(IMGVF, i, j, m_get_val(I, i, j));
}
}
// Precompute row and column indices for the
// neighbor difference computation below
int *rowU = (int *) malloc(sizeof(int) * m);
int *rowD = (int *) malloc(sizeof(int) * m);
int *colL = (int *) malloc(sizeof(int) * n);
int *colR = (int *) malloc(sizeof(int) * n);
rowU[0] = 0;
rowD[m - 1] = m - 1;
for (i = 1; i < m; i++) {
rowU[i] = i - 1;
rowD[i - 1] = i;
}
colL[0] = 0;
colR[n - 1] = n - 1;
for (j = 1; j < n; j++) {
colL[j] = j - 1;
colR[j - 1] = j;
}
// Allocate matrices used in the while loop below
MAT *U = m_get(m, n), *D = m_get(m, n), *L = m_get(m, n), *R = m_get(m, n);
MAT *UR = m_get(m, n), *DR = m_get(m, n), *UL = m_get(m, n), *DL = m_get(m, n);
MAT *UHe = m_get(m, n), *DHe = m_get(m, n), *LHe = m_get(m, n), *RHe = m_get(m, n);
MAT *URHe = m_get(m, n), *DRHe = m_get(m, n), *ULHe = m_get(m, n), *DLHe = m_get(m, n);
// Precompute constants to avoid division in the for loops below
double mu_over_lambda = mu / lambda;
double one_over_lambda = 1.0 / lambda;
// Compute the MGVF
int iter = 0;
double mean_diff = 1.0;
while ((iter < iterations) && (mean_diff > converge)) {
// Compute the difference between each pixel and its eight neighbors
for (i = 0; i < m; i++) {
for (j = 0; j < n; j++) {
double subtrahend = m_get_val(IMGVF, i, j);
m_set_val(U, i, j, m_get_val(IMGVF, rowU[i], j) - subtrahend);
m_set_val(D, i, j, m_get_val(IMGVF, rowD[i], j) - subtrahend);
m_set_val(L, i, j, m_get_val(IMGVF, i, colL[j]) - subtrahend);
m_set_val(R, i, j, m_get_val(IMGVF, i, colR[j]) - subtrahend);
m_set_val(UR, i, j, m_get_val(IMGVF, rowU[i], colR[j]) - subtrahend);
m_set_val(DR, i, j, m_get_val(IMGVF, rowD[i], colR[j]) - subtrahend);
m_set_val(UL, i, j, m_get_val(IMGVF, rowU[i], colL[j]) - subtrahend);
m_set_val(DL, i, j, m_get_val(IMGVF, rowD[i], colL[j]) - subtrahend);
}
}
// Compute the regularized heaviside version of the matrices above
heaviside( UHe, U, -vy, epsilon);
heaviside( DHe, D, vy, epsilon);
heaviside( LHe, L, -vx, epsilon);
heaviside( RHe, R, vx, epsilon);
heaviside(URHe, UR, vx - vy, epsilon);
heaviside(DRHe, DR, vx + vy, epsilon);
heaviside(ULHe, UL, -vx - vy, epsilon);
heaviside(DLHe, DL, vy - vx, epsilon);
// Update the IMGVF matrix
double total_diff = 0.0;
for (i = 0; i < m; i++) {
for (j = 0; j < n; j++) {
// Store the old value so we can compute the difference later
double old_val = m_get_val(IMGVF, i, j);
// Compute IMGVF += (mu / lambda)(UHe .*U + DHe .*D + LHe .*L + RHe .*R +
// URHe.*UR + DRHe.*DR + ULHe.*UL + DLHe.*DL);
double vU = m_get_val(UHe, i, j) * m_get_val(U, i, j);
double vD = m_get_val(DHe, i, j) * m_get_val(D, i, j);
double vL = m_get_val(LHe, i, j) * m_get_val(L, i, j);
double vR = m_get_val(RHe, i, j) * m_get_val(R, i, j);
double vUR = m_get_val(URHe, i, j) * m_get_val(UR, i, j);
double vDR = m_get_val(DRHe, i, j) * m_get_val(DR, i, j);
double vUL = m_get_val(ULHe, i, j) * m_get_val(UL, i, j);
double vDL = m_get_val(DLHe, i, j) * m_get_val(DL, i, j);
double vHe = old_val + mu_over_lambda * (vU + vD + vL + vR + vUR + vDR + vUL + vDL);
// Compute IMGVF -= (1 / lambda)(I .* (IMGVF - I))
double vI = m_get_val(I, i, j);
double new_val = vHe - (one_over_lambda * vI * (vHe - vI));
m_set_val(IMGVF, i, j, new_val);
// Keep track of the absolute value of the differences
// between this iteration and the previous one
total_diff += fabs(new_val - old_val);
}
}
// Compute the mean absolute difference between this iteration
// and the previous one to check for convergence
mean_diff = total_diff / (double) (m * n);
iter++;
}
// Free memory
free(rowU); free(rowD); free(colL); free(colR);
m_free(U); m_free(D); m_free(L); m_free(R);
m_free(UR); m_free(DR); m_free(UL); m_free(DL);
m_free(UHe); m_free(DHe); m_free(LHe); m_free(RHe);
m_free(URHe); m_free(DRHe); m_free(ULHe); m_free(DLHe);
return IMGVF;
}
/*
* Send NDP Router Advertisement
*/
void ndp_send_ra(Slirp *slirp)
{
DEBUG_CALL("ndp_send_ra");
/* Build IPv6 packet */
struct mbuf *t = m_get(slirp);
struct ip6 *rip = mtod(t, struct ip6 *);
size_t pl_size = 0;
struct in6_addr addr;
uint32_t scope_id;
rip->ip_src = (struct in6_addr)LINKLOCAL_ADDR;
rip->ip_dst = (struct in6_addr)ALLNODES_MULTICAST;
rip->ip_nh = IPPROTO_ICMPV6;
/* Build ICMPv6 packet */
t->m_data += sizeof(struct ip6);
struct icmp6 *ricmp = mtod(t, struct icmp6 *);
ricmp->icmp6_type = ICMP6_NDP_RA;
ricmp->icmp6_code = 0;
ricmp->icmp6_cksum = 0;
/* NDP */
ricmp->icmp6_nra.chl = NDP_AdvCurHopLimit;
ricmp->icmp6_nra.M = NDP_AdvManagedFlag;
ricmp->icmp6_nra.O = NDP_AdvOtherConfigFlag;
ricmp->icmp6_nra.reserved = 0;
ricmp->icmp6_nra.lifetime = htons(NDP_AdvDefaultLifetime);
ricmp->icmp6_nra.reach_time = htonl(NDP_AdvReachableTime);
ricmp->icmp6_nra.retrans_time = htonl(NDP_AdvRetransTime);
t->m_data += ICMP6_NDP_RA_MINLEN;
pl_size += ICMP6_NDP_RA_MINLEN;
/* Source link-layer address (NDP option) */
struct ndpopt *opt = mtod(t, struct ndpopt *);
opt->ndpopt_type = NDPOPT_LINKLAYER_SOURCE;
opt->ndpopt_len = NDPOPT_LINKLAYER_LEN / 8;
in6_compute_ethaddr(rip->ip_src, opt->ndpopt_linklayer);
t->m_data += NDPOPT_LINKLAYER_LEN;
pl_size += NDPOPT_LINKLAYER_LEN;
/* Prefix information (NDP option) */
struct ndpopt *opt2 = mtod(t, struct ndpopt *);
opt2->ndpopt_type = NDPOPT_PREFIX_INFO;
opt2->ndpopt_len = NDPOPT_PREFIXINFO_LEN / 8;
opt2->ndpopt_prefixinfo.prefix_length = slirp->vprefix_len;
opt2->ndpopt_prefixinfo.L = 1;
opt2->ndpopt_prefixinfo.A = 1;
opt2->ndpopt_prefixinfo.reserved1 = 0;
opt2->ndpopt_prefixinfo.valid_lt = htonl(NDP_AdvValidLifetime);
opt2->ndpopt_prefixinfo.pref_lt = htonl(NDP_AdvPrefLifetime);
opt2->ndpopt_prefixinfo.reserved2 = 0;
opt2->ndpopt_prefixinfo.prefix = slirp->vprefix_addr6;
t->m_data += NDPOPT_PREFIXINFO_LEN;
pl_size += NDPOPT_PREFIXINFO_LEN;
/* Prefix information (NDP option) */
if (get_dns6_addr(&addr, &scope_id) >= 0) {
/* Host system does have an IPv6 DNS server, announce our proxy. */
struct ndpopt *opt3 = mtod(t, struct ndpopt *);
opt3->ndpopt_type = NDPOPT_RDNSS;
opt3->ndpopt_len = NDPOPT_RDNSS_LEN / 8;
opt3->ndpopt_rdnss.reserved = 0;
opt3->ndpopt_rdnss.lifetime = htonl(2 * NDP_MaxRtrAdvInterval);
opt3->ndpopt_rdnss.addr = slirp->vnameserver_addr6;
t->m_data += NDPOPT_RDNSS_LEN;
pl_size += NDPOPT_RDNSS_LEN;
}
rip->ip_pl = htons(pl_size);
t->m_data -= sizeof(struct ip6) + pl_size;
t->m_len = sizeof(struct ip6) + pl_size;
/* ICMPv6 Checksum */
ricmp->icmp6_cksum = ip6_cksum(t);
ip6_output(NULL, t, 0);
}
/*
* Initialize the aurp pipe -
* -Create, initialize, and start the aurpd kernel process; we need
* a process to permit queueing between the socket and the stream,
* which is necessary for orderly access to the socket structure.
* -The user process (aurpd) is there to 'build' the AURP
* stream, act as a 'logging agent' (:-}), and hold open the stream
* during its use.
* -Data and AURP packets from the DDP stream will be fed into the
* UDP tunnel (AURPsend())
* -Data and AURP packets from the UDP tunnel will be fed into the
* DDP stream (ip_to_atalk(), via the kernel process).
*/
int
aurpd_start()
{
register int error;
register struct socket *so;
struct mbuf *m;
int maxbuf;
struct sockopt sopt;
if (suser(current_proc()->p_ucred, ¤t_proc()->p_acflag) != 0 )
return(EPERM);
/*
* Set up state prior to starting kernel process so we can back out
* (error return) if something goes wrong.
*/
bzero((char *)&aurp_global.tunnel, sizeof(aurp_global.tunnel));
/*lock_alloc(&aurp_global.glock, LOCK_ALLOC_PIN, AURP_EVNT_LOCK, -1);*/
ATLOCKINIT(aurp_global.glock);
ATEVENTINIT(aurp_global.event_anchor);
/* open udp socket */
if (aurp_global.udp_port == 0)
aurp_global.udp_port = AURP_SOCKNUM;
error = socreate(AF_INET, &aurp_global.tunnel, SOCK_DGRAM,
IPPROTO_UDP);
if (error)
{ dPrintf(D_M_AURP, D_L_FATAL, ("AURP: Can't get socket (%d)\n",
error));
return(error);
}
so = aurp_global.tunnel;
if ((error = aurp_bindrp(so)) != 0)
{ dPrintf(D_M_AURP, D_L_FATAL,
("AURP: Can't bind to port %d (error %d)\n",
aurp_global.udp_port, error));
soclose(so);
return(error);
}
sblock(&so->so_rcv, M_WAIT);
sblock(&so->so_snd, M_WAIT);
/*
* Set socket Receive buffer size
*/
m = m_get(M_WAIT, MT_SOOPTS);
if (m == NULL) {
error = ENOBUFS;
goto out;
} else {
maxbuf = M_RCVBUF;
sopt.sopt_val = &maxbuf;
sopt.sopt_valsize = sizeof(maxbuf);
sopt.sopt_level = SOL_SOCKET;
sopt.sopt_name = SO_RCVBUF;
sopt.sopt_dir = SOPT_SET;
sopt.sopt_p = NULL;
if ((error = sosetopt(so, &sopt)) != 0)
goto out;
}
/*
* Set socket Send buffer size
*/
m = m_get(M_WAIT, MT_SOOPTS);
if (m == NULL) {
error = ENOBUFS;
goto out;
} else {
maxbuf = M_SNDBUF;
sopt.sopt_val = &maxbuf;
sopt.sopt_valsize = sizeof(maxbuf);
sopt.sopt_level = SOL_SOCKET;
sopt.sopt_name = SO_SNDBUF;
sopt.sopt_dir = SOPT_SET;
sopt.sopt_p = NULL;
if ((error = sosetopt(so, &sopt)) != 0)
goto out;
}
so->so_upcall = aurp_wakeup;
so->so_upcallarg = (caddr_t)AE_UDPIP; /* Yuck */
so->so_state |= SS_NBIO;
so->so_rcv.sb_flags |=(SB_SEL|SB_NOINTR);
so->so_snd.sb_flags |=(SB_SEL|SB_NOINTR);
out:
sbunlock(&so->so_snd);
sbunlock(&so->so_rcv);
return(error);
}
void check_variography(const VARIOGRAM **v, int n_vars)
/*
* check for intrinsic correlation, linear model of coregionalisation
* or else (with warning) Cauchy Swartz
*/
{
int i, j, k, ic = 0, lmc, posdef = 1;
MAT **a = NULL;
double b;
char *reason = NULL;
if (n_vars <= 1)
return;
/*
* find out if lmc (linear model of coregionalization) hold:
* all models must have equal base models (sequence and range)
*/
for (i = 1, lmc = 1; lmc && i < get_n_vgms(); i++) {
if (v[0]->n_models != v[i]->n_models) {
reason = "number of models differ";
lmc = 0;
}
for (k = 0; lmc && k < v[0]->n_models; k++) {
if (v[0]->part[k].model != v[i]->part[k].model) {
reason = "model types differ";
lmc = 0;
}
if (v[0]->part[k].range[0] != v[i]->part[k].range[0]) {
reason = "ranges differ";
lmc = 0;
}
}
for (k = 0; lmc && k < v[0]->n_models; k++)
if (v[0]->part[k].tm_range != NULL) {
if (v[i]->part[k].tm_range == NULL) {
reason = "anisotropy for part of models";
lmc = 0;
} else if (
v[0]->part[k].tm_range->ratio[0] != v[i]->part[k].tm_range->ratio[0] ||
v[0]->part[k].tm_range->ratio[1] != v[i]->part[k].tm_range->ratio[1] ||
v[0]->part[k].tm_range->angle[0] != v[i]->part[k].tm_range->angle[0] ||
v[0]->part[k].tm_range->angle[1] != v[i]->part[k].tm_range->angle[1] ||
v[0]->part[k].tm_range->angle[2] != v[i]->part[k].tm_range->angle[2]
) {
reason = "anisotropy parameters are not equal";
lmc = 0;
}
} else if (v[i]->part[k].tm_range != NULL) {
reason = "anisotropy for part of models";
lmc = 0;
}
}
if (lmc) {
/*
* check for ic:
*/
a = (MAT **) emalloc(v[0]->n_models * sizeof(MAT *));
for (k = 0; k < v[0]->n_models; k++)
a[k] = m_get(n_vars, n_vars);
for (i = 0; i < n_vars; i++) {
for (j = 0; j < n_vars; j++) { /* for all variogram triplets: */
for (k = 0; k < v[0]->n_models; k++)
ME(a[k], i, j) = v[LTI(i,j)]->part[k].sill;
}
}
/* for ic: a's must be scaled versions of each other: */
ic = 1;
for (k = 1, ic = 1; ic && k < v[0]->n_models; k++) {
b = ME(a[0], 0, 0)/ME(a[k], 0, 0);
for (i = 0; ic && i < n_vars; i++)
for (j = 0; ic && j < n_vars; j++)
if (fabs(ME(a[0], i, j) / ME(a[k], i, j) - b) > EPSILON)
ic = 0;
}
/* check posdef matrices */
for (i = 0, lmc = 1, posdef = 1; i < v[0]->n_models; i++) {
posdef = is_posdef(a[i]);
if (posdef == 0) {
reason = "coefficient matrix not positive definite";
if (DEBUG_COV) {
printlog("non-positive definite coefficient matrix %d:\n",
i);
m_logoutput(a[i]);
}
ic = lmc = 0;
}
if (! posdef)
printlog(
"non-positive definite coefficient matrix in structure %d",
i+1);
}
for (k = 0; k < v[0]->n_models; k++)
m_free(a[k]);
efree(a);
if (ic) {
printlog("Intrinsic Correlation found. Good.\n");
return;
} else if (lmc) {
printlog("Linear Model of Coregionalization found. Good.\n");
return;
}
}
/*
* lmc does not hold: check on Cauchy Swartz
*/
pr_warning("No Intrinsic Correlation or Linear Model of Coregionalization found\nReason: %s", reason ? reason : "unknown");
if (gl_nocheck == 0) {
pr_warning("[add `set = list(nocheck = 1)' to the gstat() or krige() to ignore the following error]\n");
ErrMsg(ER_IMPOSVAL, "variograms do not satisfy a legal model");
}
printlog("Now checking for Cauchy-Schwartz inequalities:\n");
for (i = 0; i < n_vars; i++)
for (j = 0; j < i; j++)
if (is_valid_cs(v[LTI(i,i)], v[LTI(j,j)], v[LTI(i,j)])) {
printlog("variogram(%s,%s) passed Cauchy-Schwartz\n",
name_identifier(j), name_identifier(i));
} else
pr_warning("Cauchy-Schwartz inequality found for variogram(%s,%s)",
name_identifier(j), name_identifier(i) );
return;
}
/*
* Take incoming datagram fragment and try to
* reassemble it into whole datagram. If a chain for
* reassembly of this datagram already exists, then it
* is given as fp; otherwise have to make a chain.
*/
struct ip *ip_reass(struct ipasfrag *ip, struct ipq *fp)
{
struct mbuf *m = dtom(ip);
struct ipasfrag *q;
int hlen = ip->ip_hl << 2;
int i, next;
DEBUG_CALL("ip_reass");
DEBUG_ARG("ip = %lx", (long)ip);
DEBUG_ARG("fp = %lx", (long)fp);
DEBUG_ARG("m = %lx", (long)m);
/*
* Presence of header sizes in mbufs
* would confuse code below.
* Fragment m_data is concatenated.
*/
m->m_data += hlen;
m->m_len -= hlen;
/*
* If first fragment to arrive, create a reassembly queue.
*/
if (fp == 0) {
struct mbuf *t;
if ((t = m_get()) == NULL) goto dropfrag;
fp = mtod(t, struct ipq *);
insque_32(fp, &ipq);
fp->ipq_ttl = IPFRAGTTL;
fp->ipq_p = ip->ip_p;
fp->ipq_id = ip->ip_id;
fp->ipq_next = fp->ipq_prev = (ipasfragp_32)fp;
fp->ipq_src = ((struct ip *)ip)->ip_src;
fp->ipq_dst = ((struct ip *)ip)->ip_dst;
q = (struct ipasfrag *)fp;
goto insert;
}
/*
* Find a segment which begins after this one does.
*/
for (q = (struct ipasfrag *)fp->ipq_next; q != (struct ipasfrag *)fp;
q = (struct ipasfrag *)q->ipf_next)
if (q->ip_off > ip->ip_off)
break;
/*
* If there is a preceding segment, it may provide some of
* our data already. If so, drop the data from the incoming
* segment. If it provides all of our data, drop us.
*/
if (q->ipf_prev != (ipasfragp_32)fp) {
i = ((struct ipasfrag *)(q->ipf_prev))->ip_off +
((struct ipasfrag *)(q->ipf_prev))->ip_len - ip->ip_off;
if (i > 0) {
if (i >= ip->ip_len)
goto dropfrag;
m_adj(dtom(ip), i);
ip->ip_off += i;
ip->ip_len -= i;
}
}
/*
* While we overlap succeeding segments trim them or,
* if they are completely covered, dequeue them.
*/
while (q != (struct ipasfrag *)fp && ip->ip_off + ip->ip_len > q->ip_off) {
i = (ip->ip_off + ip->ip_len) - q->ip_off;
if (i < q->ip_len) {
q->ip_len -= i;
q->ip_off += i;
m_adj(dtom(q), i);
break;
}
q = (struct ipasfrag *) q->ipf_next;
m_freem(dtom((struct ipasfrag *) q->ipf_prev));
ip_deq((struct ipasfrag *) q->ipf_prev);
}
insert:
/*
* Stick new segment in its place;
* check for complete reassembly.
*/
ip_enq(ip, (struct ipasfrag *) q->ipf_prev);
next = 0;
for (q = (struct ipasfrag *) fp->ipq_next; q != (struct ipasfrag *)fp;
q = (struct ipasfrag *) q->ipf_next) {
if (q->ip_off != next)
return (0);
next += q->ip_len;
}
if (((struct ipasfrag *)(q->ipf_prev))->ipf_mff & 1)
return (0);
/*
* Reassembly is complete; concatenate fragments.
*/
q = (struct ipasfrag *) fp->ipq_next;
m = dtom(q);
q = (struct ipasfrag *) q->ipf_next;
while (q != (struct ipasfrag *)fp) {
struct mbuf *t;
t = dtom(q);
q = (struct ipasfrag *) q->ipf_next;
m_cat(m, t);
}
/*
* Create header for new ip packet by
* modifying header of first packet;
* dequeue and discard fragment reassembly header.
* Make header visible.
*/
ip = (struct ipasfrag *) fp->ipq_next;
/*
* If the fragments concatenated to an mbuf that's
* bigger than the total size of the fragment, then and
* m_ext buffer was alloced. But fp->ipq_next points to
* the old buffer (in the mbuf), so we must point ip
* into the new buffer.
*/
if (m->m_flags & M_EXT) {
int delta;
delta = (char *)ip - m->m_dat;
ip = (struct ipasfrag *)(m->m_ext + delta);
}
/* DEBUG_ARG("ip = %lx", (long)ip);
* ip=(struct ipasfrag *)m->m_data; */
ip->ip_len = next;
ip->ipf_mff &= ~1;
((struct ip *)ip)->ip_src = fp->ipq_src;
((struct ip *)ip)->ip_dst = fp->ipq_dst;
remque_32(fp);
(void) m_free(dtom(fp));
m = dtom(ip);
m->m_len += (ip->ip_hl << 2);
m->m_data -= (ip->ip_hl << 2);
return ((struct ip *)ip);
dropfrag:
ipstat.ips_fragdropped++;
m_freem(m);
return (0);
}
bool VecSliderMenuItem::OnKey(int key, int mod)
{
float inc = m_scale * kInc;
if(mod & KMOD_SHIFT) inc = m_scale * kLargeInc;
else if(mod & KMOD_CTRL) inc = m_scale * kSmallInc;
float incAmt = 0.f;
switch(key)
{
case SDLK_UP:
m_pos = Max(0, m_pos - 1);
break;
case SDLK_DOWN:
m_pos = Min(VECSLIDE_NUM-1, m_pos + 1);
break;
case SDLK_LEFT:
incAmt = -inc;
break;
case SDLK_RIGHT:
incAmt = inc;
break;
case SDLK_BACKSPACE:
menu_DeactivateMenuItem();
break;
default:
break;
}
vec3 val = m_get();
vec3 old = val;
float radAmt = (M_PI / 180.f) * incAmt;
mat4 rotmat;
static const vec3 kXAxis = {1,0,0};
static const vec3 kYAxis = {0,1,0};
static const vec3 kZAxis = {0,0,1};
switch(m_pos)
{
case VECSLIDE_RotateX:
rotmat = RotateAround(kXAxis, radAmt);
val = TransformVec(rotmat, val);
break;
case VECSLIDE_RotateY:
rotmat = RotateAround(kYAxis, radAmt);
val = TransformVec(rotmat, val);
break;
case VECSLIDE_RotateZ:
rotmat = RotateAround(kZAxis, radAmt);
val = TransformVec(rotmat, val);
break;
case VECSLIDE_X:
val.x += incAmt;
break;
case VECSLIDE_Y:
val.y += incAmt;
break;
case VECSLIDE_Z:
val.z += incAmt;
break;
case VECSLIDE_Length:
{
float len = Length(val);
val = val * (len+incAmt) / len;
}
break;
default:break;
}
vec3 newVal = m_limits(val);
if(newVal != old)
{
m_set(newVal);
UpdateData();
}
return true;
}
/*
* IP output. The packet in mbuf chain m contains a skeletal IP
* header (with len, off, ttl, proto, tos, src, dst).
* The mbuf chain containing the packet will be freed.
* The mbuf opt, if present, will not be freed.
*/
int
ip_output(struct socket *so, struct mbuf *m0)
{
register struct ip *ip;
register struct mbuf *m = m0;
register int hlen = sizeof(struct ip );
int len, off, error = 0;
DEBUG_CALL("ip_output");
DEBUG_ARG("so = %lx", (long)so);
DEBUG_ARG("m0 = %lx", (long)m0);
/* We do no options */
/* if (opt) {
* m = ip_insertoptions(m, opt, &len);
* hlen = len;
* }
*/
ip = mtod(m, struct ip *);
/*
* Fill in IP header.
*/
ip->ip_v = IPVERSION;
ip->ip_off &= IP_DF;
ip->ip_id = htons(ip_id++);
ip->ip_hl = hlen >> 2;
STAT(ipstat.ips_localout++);
/*
* Verify that we have any chance at all of being able to queue
* the packet or packet fragments
*/
/* XXX Hmmm... */
/* if (if_queued > IF_THRESH && towrite <= 0) {
* error = ENOBUFS;
* goto bad;
* }
*/
/*
* If small enough for interface, can just send directly.
*/
if ((u_int16_t)ip->ip_len <= IF_MTU) {
ip->ip_len = htons((u_int16_t)ip->ip_len);
ip->ip_off = htons((u_int16_t)ip->ip_off);
ip->ip_sum = 0;
ip->ip_sum = cksum(m, hlen);
if_output(so, m);
goto done;
}
/*
* Too large for interface; fragment if possible.
* Must be able to put at least 8 bytes per fragment.
*/
if (ip->ip_off & IP_DF) {
error = -1;
STAT(ipstat.ips_cantfrag++);
goto bad;
}
len = (IF_MTU - hlen) &~ 7; /* ip databytes per packet */
if (len < 8) {
error = -1;
goto bad;
}
{
int mhlen, firstlen = len;
struct mbuf **mnext = &m->m_nextpkt;
/*
* Loop through length of segment after first fragment,
* make new header and copy data of each part and link onto chain.
*/
m0 = m;
mhlen = sizeof (struct ip);
for (off = hlen + len; off < (u_int16_t)ip->ip_len; off += len) {
register struct ip *mhip;
m = m_get();
if (m == NULL) {
error = -1;
STAT(ipstat.ips_odropped++);
goto sendorfree;
}
m->m_data += IF_MAXLINKHDR;
mhip = mtod(m, struct ip *);
*mhip = *ip;
/* No options */
/* if (hlen > sizeof (struct ip)) {
* mhlen = ip_optcopy(ip, mhip) + sizeof (struct ip);
* mhip->ip_hl = mhlen >> 2;
* }
*/
m->m_len = mhlen;
mhip->ip_off = ((off - hlen) >> 3) + (ip->ip_off & ~IP_MF);
if (ip->ip_off & IP_MF)
mhip->ip_off |= IP_MF;
if (off + len >= (u_int16_t)ip->ip_len)
len = (u_int16_t)ip->ip_len - off;
else
mhip->ip_off |= IP_MF;
mhip->ip_len = htons((u_int16_t)(len + mhlen));
if (m_copy(m, m0, off, len) < 0) {
error = -1;
goto sendorfree;
}
mhip->ip_off = htons((u_int16_t)mhip->ip_off);
mhip->ip_sum = 0;
mhip->ip_sum = cksum(m, mhlen);
*mnext = m;
mnext = &m->m_nextpkt;
STAT(ipstat.ips_ofragments++);
}
/*
* Update first fragment by trimming what's been copied out
* and updating header, then send each fragment (in order).
*/
m = m0;
m_adj(m, hlen + firstlen - (u_int16_t)ip->ip_len);
ip->ip_len = htons((u_int16_t)m->m_len);
ip->ip_off = htons((u_int16_t)(ip->ip_off | IP_MF));
ip->ip_sum = 0;
ip->ip_sum = cksum(m, hlen);
sendorfree:
for (m = m0; m; m = m0) {
m0 = m->m_nextpkt;
m->m_nextpkt = NULL;
if (error == 0)
if_output(so, m);
else
m_freem(m);
}
if (error == 0)
STAT(ipstat.ips_fragmented++);
}
done:
return (error);
bad:
m_freem(m0);
goto done;
}
static struct mbuf *
DeflateOutput(void *v, struct ccp *ccp, struct link *l __unused,
int pri __unused, u_short *proto, struct mbuf *mp)
{
struct deflate_state *state = (struct deflate_state *)v;
u_char *wp, *rp;
int olen, ilen, len, res, flush;
struct mbuf *mo_head, *mo, *mi_head, *mi;
ilen = m_length(mp);
log_Printf(LogDEBUG, "DeflateOutput: Proto %02x (%d bytes)\n", *proto, ilen);
log_DumpBp(LogDEBUG, "DeflateOutput: Compress packet:", mp);
/* Stuff the protocol in front of the input */
mi_head = mi = m_get(2, MB_CCPOUT);
mi->m_next = mp;
rp = MBUF_CTOP(mi);
if (*proto < 0x100) { /* Compress the protocol */
rp[0] = *proto & 0377;
mi->m_len = 1;
} else { /* Don't compress the protocol */
rp[0] = *proto >> 8;
rp[1] = *proto & 0377;
mi->m_len = 2;
}
/* Allocate the initial output mbuf */
mo_head = mo = m_get(DEFLATE_CHUNK_LEN, MB_CCPOUT);
mo->m_len = 2;
wp = MBUF_CTOP(mo);
/*{{{ main*/
int main(int argc, char *argv[])
{
/*{{{ variables*/
enum { NOTHING, OTHER_FS, SAME_FS } in=NOTHING;
int c;
int mouse_x,mouse_y;
int image_width,image_height;
int image_xoffset=0,image_yoffset=0;
int my_width,my_height;
int image_depth,image_size;
int err=0,usage=0;
FILE *input=(FILE*)0;
static struct menu_entry menu[] =
{
{ "Normal","|n\n" },
{ "Reverse","|r\n" },
{ "-------", "" },
{ "Quit","|q\n" }
};
char file[_POSIX_PATH_MAX];
char event[20];
/*}}} */
/*{{{ parse arguments*/
while ((c=getopt(argc,argv,"ro:s:"))!=EOF)
{
switch (c)
{
/*{{{ r*/
case 'r': display_op=BIT_NOT(BIT_SRC); break;
/*}}} */
/*{{{ o file*/
case 'o':
{
if ((input=fopen(optarg,"r"))==(FILE*)0)
{
fprintf(stderr,"%s: Can't open %s\r\n",argv[0],optarg);
err=1;
}
else in=OTHER_FS;
break;
}
/*}}} */
/*{{{ s file*/
case 's':
{
char *cwd;
in=SAME_FS;
if (*optarg!='/' && *optarg!='.')
{
if ((cwd=getcwd((char*)0,(size_t)0))!=(char*)0) { strcpy(file,cwd); strcat(file,"/"); strcat(file,optarg); }
else { fprintf(stderr,"%s: Can't get current directory\r\n",argv[0]); err=1; }
}
else strcpy(file,optarg);
break;
}
/*}}} */
/*{{{ default*/
default:
{
usage=1;
break;
}
/*}}} */
}
}
if (err) exit(err);
if (usage || optind!=argc)
{
fprintf(stderr,"Usage: mgrview [-o file | -s file]\n");
exit(1);
}
if (in==NOTHING) { in=OTHER_FS; input=stdin; }
/*}}} */
/*{{{ setup*/
ckmgrterm(argv[0]);
m_setup(M_MODEOK);
signal(SIGINT,clean);
signal(SIGTERM,clean);
signal(SIGPIPE,clean);
m_ttyset();
m_push(P_ALL);
m_setmode(M_ABS);
m_setcursor(CS_INVIS);
menu_load(1,4,menu);
m_setevent(REDRAW, "|R\n");
m_setevent(RESHAPE, "|R\n");
m_setevent(BUTTON_1,"|!%p!\n");
m_setevent(BUTTON_2,"|m\n");
m_flush();
/*}}} */
if (in==OTHER_FS)
{
/*{{{ variables*/
struct b_header bh;
void *bp;
/*}}} */
/*{{{ load bitmap to client space*/
if (fread(&bh,sizeof(struct b_header),1,input)!=1)
{
fprintf(stderr,"%s: Can't read header of bitmap.\r\n",argv[0]);
clean(1);
}
if (!B_ISHDR8(&bh))
{
fprintf(stderr,"%s: No MGR bitmap or old format.\r\n",argv[0]);
clean(1);
}
B_GETHDR8(&bh,image_width,image_height,image_depth);
image_size=B_SIZE8(image_width,image_height,image_depth);
/*}}} */
/*{{{ transfer bitmap to server space*/
m_func(BIT_SRC);
m_bitcreate(IMAGE_BITMAP,image_width,image_height);
m_bitldto(image_width,image_height,0,0,IMAGE_BITMAP,image_size);
bp=malloc(image_size);
fread(bp,image_size,1,input);
fwrite(bp,image_size,1,m_termout);
free(bp);
/*}}} */
}
else if (in==SAME_FS)
/*{{{ transfer bitmap from server fs to server space*/
{
m_bitfromfile(IMAGE_BITMAP,file);
m_get();
if (sscanf(m_linebuf,"%d %d",&image_width,&image_height)<2)
{
fprintf(stderr,"%s: MGR server can't load MGR bitmap.\r\n",argv[0]);
clean(1);
}
}
/*}}} */
/*{{{ user interaction*/
m_getwindowsize(&my_width,&my_height);
display(image_xoffset,image_yoffset,my_width,my_height,image_width,image_height);
m_flush();
do
{
if (m_getevent(10000,&c,event,sizeof(event))==EV_EVENTSTR) switch (event[0])
{
/*{{{ n,r*/
case 'n':
case 'r':
{
display_op=(c=='n' ? BIT_SRC : BIT_NOT(BIT_SRC));
m_func(display_op);
m_bitcopyto(image_xoffset,image_yoffset,image_width,image_height,0,0,WINDOW_BITMAP,IMAGE_BITMAP);
m_flush();
break;
}
/*}}} */
/*{{{ m -- left button displays menu*/
case 'm':
{
m_selectmenu(1);
m_flush();
break;
}
/*}}} */
/*{{{ !%d %d! -- right button*/
case '!':
{
sscanf(event,"!%d %d!",&mouse_x,&mouse_y);
/*{{{ compute new x start*/
if (my_width>image_width) image_xoffset=0;
else if (mouse_x<=0) image_xoffset=0;
else if (mouse_x>=my_width) image_xoffset=my_width-image_width;
else
{
/*{{{ move x start by difference from mouse and middle*/
image_xoffset=image_xoffset-(mouse_x-my_width/2);
/*}}} */
/*{{{ check and corrent range of x start*/
if (image_xoffset<my_width-image_width) image_xoffset=my_width-image_width;
else if (image_xoffset>0) image_xoffset=0;
/*}}} */
}
/*}}} */
/*{{{ compute new y start*/
if (my_height>image_height) image_yoffset=0;
else if (mouse_y<=0) image_yoffset=0;
else if (mouse_y>=my_height) image_yoffset=my_height-image_height;
else
{
/*{{{ move y start by difference from mouse and middle*/
image_yoffset=image_yoffset-(mouse_y-my_height/2);
/*}}} */
/*{{{ check and corrent range of y start*/
if (image_yoffset<my_height-image_height) image_yoffset=my_height-image_height;
else if (image_yoffset>0) image_yoffset=0;
/*}}} */
}
/*}}} */
display(image_xoffset,image_yoffset,my_width,my_height,image_width,image_height);
m_flush();
break;
}
/*}}} */
/*{{{ R -- redraw*/
case 'R':
{
m_getwindowsize(&my_width,&my_height);
/*{{{ compute new x offset*/
if (my_width<image_width)
{
if (image_xoffset<my_width-image_width) image_xoffset=my_width-image_width;
}
else image_xoffset=0;
/*}}} */
/*{{{ compute new y offset*/
if (my_height<image_height)
{
if (image_yoffset<my_height-image_height) image_yoffset=my_height-image_height;
}
else image_yoffset=0;
/*}}} */
m_func(BIT_CLR);
m_bitwrite(0,0,my_width,my_height);
m_func(display_op);
m_bitcopyto(image_xoffset,image_yoffset,image_width,image_height,0,0,WINDOW_BITMAP,IMAGE_BITMAP);
m_flush();
break;
}
/*}}} */
}
} while (event[0]!='q');
/*}}} */
/*{{{ exit*/
m_bitdestroy(IMAGE_BITMAP);
clean(0);
/*}}} */
return 255;
}
/* Routine to take the matrix given and calculate the log-
* determinant, by calling LU decomposition routine and
* then multiplying down diagonals. Returns the
* log-determinant calculated.*/
double * determinant(void){
int a,max,c;
extern int branches;
double *det;
extern int mode;
extern int nodecount;
extern double **expect;
extern double **rootedexpect;
extern int individual;
extern int interesting_branches[];
extern int is_kappa;
double **matrix;
MAT * matrix2;
is_kappa=0;
if(ISMODE(HKY) && NOTMODE(NOKAPPA))
is_kappa=1;
matrix=expect;
max=branches;
if(ISMODE(ROOTED)){ /* If want rooted tree then create new*/
planttree(expect,rootedexpect); /* matrix*/
matrix=rootedexpect;
max=nodecount+2;
if(ISMODE(NODEASROOT))
max=nodecount+1;
}
if(ISMODE(MATRICES)){ /* If want intermediate matrices dumped*/
dump(matrix,max+is_kappa,"Full matrix");
}
if(ISMODE(INDIVIDUAL)){ /* We want information about some, but
* not all of the elements*/
if(NOTMODE(DETINDIV)){
det=calloc(individual+is_kappa,sizeof(double));
for(a=0;a<individual;a++)
det[a]=matrix[interesting_branches[a]][interesting_branches[a]];
if(is_kappa==1)
det[individual]=matrix[max][max];
is_kappa=0;
return det;
}
/* Case - we want the determinate of the sub-matrix formed
* by several parameters*/
/* Get memory for new matrix*/
matrix2 = m_get(individual+is_kappa,individual+is_kappa);
if(NULL==matrix2){
nomemory();
}
m_zero(matrix2);
/* Creates the sub-matrix from the original expected information
* matrix*/
for(a=0;a<individual;a++)
for(c=0;c<individual;c++)
matrix2->me[a][c]=matrix[interesting_branches[a]][interesting_branches[c]];
if(is_kappa==1){
matrix2->me[individual][individual]=matrix[max][max];
}
max=individual;
if(ISMODE(MATRICES))
dump(matrix2->me,max,"Sub-matrix to be calculated");
} else {
matrix2 = m_get(max,max);
if(NULL==matrix2){
nomemory();
}
m_zero(matrix2);
for ( a=0 ; a<max ; a++){
for ( c=0 ; c<max ; c++){
matrix2->me[a][c] = matrix[a][c];
}
}
}
/* Perform LU decomposition on whichever matrix we've been handed*/
det=calloc(1+is_kappa,sizeof(double));
matrix2=CHfactor(matrix2);
/* The determinant of the matrix is the product of
* the diagonal elements of the decomposed form*/
for(a=0;a<max;a++){
det[0] += 2.0 * log(matrix2->me[a][a]);
}
if(is_kappa==1){
det[1] = 2.0 * log(matrix2->me[max][max]);
}
M_FREE(matrix2);
return det;
}
/*
* mbuf_copyback differs from m_copyback in a few ways:
* 1) mbuf_copyback will allocate clusters for new mbufs we append
* 2) mbuf_copyback will grow the last mbuf in the chain if possible
* 3) mbuf_copyback reports whether or not the operation succeeded
* 4) mbuf_copyback allows the caller to specify M_WAITOK or M_NOWAIT
*/
errno_t
mbuf_copyback(
mbuf_t m,
size_t off,
size_t len,
const void *data,
mbuf_how_t how)
{
size_t mlen;
mbuf_t m_start = m;
mbuf_t n;
int totlen = 0;
errno_t result = 0;
const char *cp = data;
if (m == NULL || len == 0 || data == NULL)
return (EINVAL);
while (off > (mlen = m->m_len)) {
off -= mlen;
totlen += mlen;
if (m->m_next == 0) {
n = m_getclr(how, m->m_type);
if (n == 0) {
result = ENOBUFS;
goto out;
}
n->m_len = MIN(MLEN, len + off);
m->m_next = n;
}
m = m->m_next;
}
while (len > 0) {
mlen = MIN(m->m_len - off, len);
if (mlen < len && m->m_next == NULL &&
mbuf_trailingspace(m) > 0) {
size_t grow = MIN(mbuf_trailingspace(m), len - mlen);
mlen += grow;
m->m_len += grow;
}
bcopy(cp, off + (char *)mbuf_data(m), (unsigned)mlen);
cp += mlen;
len -= mlen;
mlen += off;
off = 0;
totlen += mlen;
if (len == 0)
break;
if (m->m_next == 0) {
n = m_get(how, m->m_type);
if (n == NULL) {
result = ENOBUFS;
goto out;
}
if (len > MINCLSIZE) {
/*
* cluster allocation failure is okay,
* we can grow chain
*/
mbuf_mclget(how, m->m_type, &n);
}
n->m_len = MIN(mbuf_maxlen(n), len);
m->m_next = n;
}
m = m->m_next;
}
out:
if ((m_start->m_flags & M_PKTHDR) && (m_start->m_pkthdr.len < totlen))
m_start->m_pkthdr.len = totlen;
return (result);
}
/*
* IP output. The packet in mbuf chain m contains a skeletal IP
* header (with len, off, ttl, proto, tos, src, dst).
* The mbuf chain containing the packet will be freed.
* The mbuf opt, if present, will not be freed.
*/
int
ip_output(struct socket *so, struct mbuf *m0)
{
Slirp *slirp = m0->slirp;
struct ip *ip;
struct mbuf *m = m0;
int hlen = sizeof(struct ip );
int len, off, error = 0;
DEBUG_CALL("ip_output");
DEBUG_ARG("so = %lx", (long)so);
DEBUG_ARG("m0 = %lx", (long)m0);
ip = mtod(m, struct ip *);
/*
* Fill in IP header.
*/
ip->ip_v = IPVERSION;
ip->ip_off &= IP_DF;
ip->ip_id = htons(slirp->ip_id++);
ip->ip_hl = hlen >> 2;
/*
* If small enough for interface, can just send directly.
*/
if ((u_int16_t)ip->ip_len <= IF_MTU) {
ip->ip_len = htons((u_int16_t)ip->ip_len);
ip->ip_off = htons((u_int16_t)ip->ip_off);
ip->ip_sum = 0;
ip->ip_sum = cksum(m, hlen);
if_output(so, m);
goto done;
}
/*
* Too large for interface; fragment if possible.
* Must be able to put at least 8 bytes per fragment.
*/
if (ip->ip_off & IP_DF) {
error = -1;
goto bad;
}
len = (IF_MTU - hlen) &~ 7; /* ip databytes per packet */
if (len < 8) {
error = -1;
goto bad;
}
{
int mhlen, firstlen = len;
struct mbuf **mnext = &m->m_nextpkt;
/*
* Loop through length of segment after first fragment,
* make new header and copy data of each part and link onto chain.
*/
m0 = m;
mhlen = sizeof (struct ip);
for (off = hlen + len; off < (u_int16_t)ip->ip_len; off += len) {
struct ip *mhip;
m = m_get(slirp);
if (m == NULL) {
error = -1;
goto sendorfree;
}
m->m_data += IF_MAXLINKHDR;
mhip = mtod(m, struct ip *);
*mhip = *ip;
m->m_len = mhlen;
mhip->ip_off = ((off - hlen) >> 3) + (ip->ip_off & ~IP_MF);
if (ip->ip_off & IP_MF)
mhip->ip_off |= IP_MF;
if (off + len >= (u_int16_t)ip->ip_len)
len = (u_int16_t)ip->ip_len - off;
else
mhip->ip_off |= IP_MF;
mhip->ip_len = htons((u_int16_t)(len + mhlen));
if (m_copy(m, m0, off, len) < 0) {
error = -1;
goto sendorfree;
}
mhip->ip_off = htons((u_int16_t)mhip->ip_off);
mhip->ip_sum = 0;
mhip->ip_sum = cksum(m, mhlen);
*mnext = m;
mnext = &m->m_nextpkt;
}
/*
* Update first fragment by trimming what's been copied out
* and updating header, then send each fragment (in order).
*/
m = m0;
m_adj(m, hlen + firstlen - (u_int16_t)ip->ip_len);
ip->ip_len = htons((u_int16_t)m->m_len);
ip->ip_off = htons((u_int16_t)(ip->ip_off | IP_MF));
ip->ip_sum = 0;
ip->ip_sum = cksum(m, hlen);
sendorfree:
for (m = m0; m; m = m0) {
m0 = m->m_nextpkt;
m->m_nextpkt = NULL;
if (error == 0)
if_output(so, m);
else
m_freem(m);
}
}
done:
return (error);
bad:
m_freem(m0);
goto done;
}
static void bootp_reply(const struct bootp_t *bp)
{
BOOTPClient *bc = NULL;
struct mbuf *m;
struct bootp_t *rbp;
struct sockaddr_in saddr, daddr;
struct in_addr dns_addr;
const struct in_addr *preq_addr;
int dhcp_msg_type, val;
uint8_t *q;
/* extract exact DHCP msg type */
dhcp_decode(bp, &dhcp_msg_type, &preq_addr);
dprintf("bootp packet op=%d msgtype=%d", bp->bp_op, dhcp_msg_type);
if (preq_addr)
dprintf(" req_addr=%08x\n", ntohl(preq_addr->s_addr));
else
dprintf("\n");
if (dhcp_msg_type == 0)
dhcp_msg_type = DHCPREQUEST; /* Force reply for old BOOTP clients */
if (dhcp_msg_type != DHCPDISCOVER &&
dhcp_msg_type != DHCPREQUEST)
return;
/* XXX: this is a hack to get the client mac address */
memcpy(client_ethaddr, bp->bp_hwaddr, 6);
if ((m = m_get()) == NULL)
return;
m->m_data += IF_MAXLINKHDR;
rbp = (struct bootp_t *)m->m_data;
m->m_data += sizeof(struct udpiphdr);
memset(rbp, 0, sizeof(struct bootp_t));
if (dhcp_msg_type == DHCPDISCOVER) {
if (preq_addr) {
bc = request_addr(preq_addr, client_ethaddr);
if (bc) {
daddr.sin_addr = *preq_addr;
}
}
if (!bc) {
new_addr:
bc = get_new_addr(&daddr.sin_addr, client_ethaddr);
if (!bc) {
dprintf("no address left\n");
return;
}
}
memcpy(bc->macaddr, client_ethaddr, 6);
} else if (preq_addr) {
bc = request_addr(preq_addr, client_ethaddr);
if (bc) {
daddr.sin_addr = *preq_addr;
memcpy(bc->macaddr, client_ethaddr, 6);
} else {
daddr.sin_addr.s_addr = 0;
}
} else {
bc = find_addr(&daddr.sin_addr, bp->bp_hwaddr);
if (!bc) {
/* if never assigned, behaves as if it was already
assigned (windows fix because it remembers its address) */
goto new_addr;
}
}
saddr.sin_addr.s_addr = htonl(ntohl(special_addr.s_addr) | CTL_ALIAS);
saddr.sin_port = htons(BOOTP_SERVER);
daddr.sin_port = htons(BOOTP_CLIENT);
rbp->bp_op = BOOTP_REPLY;
rbp->bp_xid = bp->bp_xid;
rbp->bp_htype = 1;
rbp->bp_hlen = 6;
memcpy(rbp->bp_hwaddr, bp->bp_hwaddr, 6);
rbp->bp_yiaddr = daddr.sin_addr; /* Client IP address */
rbp->bp_siaddr = saddr.sin_addr; /* Server IP address */
q = rbp->bp_vend;
memcpy(q, rfc1533_cookie, 4);
q += 4;
if (bc) {
dprintf("%s addr=%08x\n",
(dhcp_msg_type == DHCPDISCOVER) ? "offered" : "ack'ed",
ntohl(daddr.sin_addr.s_addr));
if (dhcp_msg_type == DHCPDISCOVER) {
*q++ = RFC2132_MSG_TYPE;
*q++ = 1;
*q++ = DHCPOFFER;
} else /* DHCPREQUEST */ {
*q++ = RFC2132_MSG_TYPE;
*q++ = 1;
*q++ = DHCPACK;
}
if (bootp_filename)
snprintf((char *)rbp->bp_file, sizeof(rbp->bp_file), "%s",
bootp_filename);
*q++ = RFC2132_SRV_ID;
*q++ = 4;
memcpy(q, &saddr.sin_addr, 4);
q += 4;
*q++ = RFC1533_NETMASK;
*q++ = 4;
*q++ = 0xff;
*q++ = 0xff;
*q++ = 0xff;
*q++ = 0x00;
if (!slirp_restrict) {
*q++ = RFC1533_GATEWAY;
*q++ = 4;
memcpy(q, &saddr.sin_addr, 4);
q += 4;
*q++ = RFC1533_DNS;
*q++ = 4;
dns_addr.s_addr = htonl(ntohl(special_addr.s_addr) | CTL_DNS);
memcpy(q, &dns_addr, 4);
q += 4;
}
*q++ = RFC2132_LEASE_TIME;
*q++ = 4;
val = htonl(LEASE_TIME);
memcpy(q, &val, 4);
q += 4;
if (*slirp_hostname) {
val = strlen(slirp_hostname);
*q++ = RFC1533_HOSTNAME;
*q++ = val;
memcpy(q, slirp_hostname, val);
q += val;
}
} else {
static const char nak_msg[] = "requested address not available";
dprintf("nak'ed addr=%08x\n", ntohl(preq_addr->s_addr));
*q++ = RFC2132_MSG_TYPE;
*q++ = 1;
*q++ = DHCPNAK;
*q++ = RFC2132_MESSAGE;
*q++ = sizeof(nak_msg) - 1;
memcpy(q, nak_msg, sizeof(nak_msg) - 1);
q += sizeof(nak_msg) - 1;
}
*q++ = RFC1533_END;
daddr.sin_addr.s_addr = 0xffffffffu;
m->m_len = sizeof(struct bootp_t) -
sizeof(struct ip) - sizeof(struct udphdr);
udp_output2(NULL, m, &saddr, &daddr, IPTOS_LOWDELAY);
}
int main(int argc, char *argv[])
{
int opt;
struct pmf *c;
struct pmf *u;
struct pmf *c1;
uint64_t time_start, time_end;
int n, i, j;
Real prob = 0.0;
MAT *matrix;
opt = opts_parse(argc, argv);
if (strcmp(ofile, "") == 0) {
fprintf(stderr, "You must specify an output file.mat\n");
exit(0);
}
c = load(argv[opt], Nc);
c1 = pmf2cdf(c);
//print(c1,"c1");
time_start = get_time();
switch (model) {
case ETFAMODEL:{
if (z == 0)
u = load(argv[opt + 1], Nc);
else {
u = pmf_create(Nc, 0);
pmf_set(u, z, 1.0);
}
n = 100;
matrix = m_get(n, n);
for (i = 0; i < n; i++) {
for (j = 0; j < n; j++) {
prob = prob_efta(i, j, Q, c, u);
m_set_val(matrix, i, j, prob);
}
}
break;
}
case LASTMODEL:{
if (d == 0)
d = Q;
n = pmf_max(c) / d * 3;
matrix = m_get(n, n);
for (i = 0; i < n; i++) {
for (j = 0; j < n; j++) {
prob = prob_last(i, j, Q, z, d, c1);
m_set_val(matrix, i, j, prob);
}
}
break;
}
case RTSSMODEL:{
n = 10;
matrix = m_get(n, n);
for (i = 0; i < n; i++) {
for (j = 0; j < n; j++) {
prob = prob_rtss(i, j, Q, z, c);
m_set_val(matrix, i, j, prob);
}
}
break;
}
default:
fprintf(stderr, "Choose a model please\n");
exit(0);
}
time_end = get_time();
/*for (i=0; i<n; i++){
for (j=0; j<n; j++){
printf("%f ",m_get_val(matrix,i,j));
}
printf("\n");
}*/
//print(matrix);
FILE *fm = fopen(ofile, "w");
m_save(fm, matrix, "matrix");
fclose(fm);
return (0);
}
void ellipsetrack(avi_t *video, double *xc0, double *yc0, int Nc, int R, int Np, int Nf) {
/*
% ELLIPSETRACK tracks cells in the movie specified by 'video', at
% locations 'xc0'/'yc0' with radii R using an ellipse with Np discrete
% points, starting at frame number one and stopping at frame number 'Nf'.
%
% INPUTS:
% video.......pointer to avi video object
% xc0,yc0.....initial center location (Nc entries)
% Nc..........number of cells
% R...........initial radius
% Np..........nbr of snaxels points per snake
% Nf..........nbr of frames in which to track
%
% Matlab code written by: DREW GILLIAM (based on code by GANG DONG /
% NILANJAN RAY)
% Ported to C by: MICHAEL BOYER
*/
int i, j;
// Compute angle parameter
double *t = (double *) malloc(sizeof(double) * Np);
double increment = (2.0 * PI) / (double) Np;
for (i = 0; i < Np; i++) {
t[i] = increment * (double) i ;
}
// Allocate space for a snake for each cell in each frame
double **xc = alloc_2d_double(Nc, Nf + 1);
double **yc = alloc_2d_double(Nc, Nf + 1);
double ***r = alloc_3d_double(Nc, Np, Nf + 1);
double ***x = alloc_3d_double(Nc, Np, Nf + 1);
double ***y = alloc_3d_double(Nc, Np, Nf + 1);
// Save the first snake for each cell
for (i = 0; i < Nc; i++) {
xc[i][0] = xc0[i];
yc[i][0] = yc0[i];
for (j = 0; j < Np; j++) {
r[i][j][0] = (double) R;
}
}
// Generate ellipse points for each cell
for (i = 0; i < Nc; i++) {
for (j = 0; j < Np; j++) {
x[i][j][0] = xc[i][0] + (r[i][j][0] * cos(t[j]));
y[i][j][0] = yc[i][0] + (r[i][j][0] * sin(t[j]));
}
}
// Keep track of the total time spent on computing
// the MGVF matrix and evolving the snakes
long long MGVF_time = 0;
long long snake_time = 0;
// Process each frame
int frame_num, cell_num;
for (frame_num = 1; frame_num <= Nf; frame_num++) {
printf("\rProcessing frame %d / %d", frame_num, Nf);
fflush(stdout);
// Get the current video frame and its dimensions
MAT *I = get_frame(video, frame_num, 0, 1);
int Ih = I->m;
int Iw = I->n;
// Set the current positions equal to the previous positions
for (i = 0; i < Nc; i++) {
xc[i][frame_num] = xc[i][frame_num - 1];
yc[i][frame_num] = yc[i][frame_num - 1];
for (j = 0; j < Np; j++) {
r[i][j][frame_num] = r[i][j][frame_num - 1];
}
}
// Split the work among multiple threads, if OPEN is defined
#ifdef OPEN
#pragma omp parallel for num_threads(omp_num_threads) private(i, j)
#endif
// Track each cell
for (cell_num = 0; cell_num < Nc; cell_num++) {
// Make copies of the current cell's location
double xci = xc[cell_num][frame_num];
double yci = yc[cell_num][frame_num];
double *ri = (double *) malloc(sizeof(double) * Np);
for (j = 0; j < Np; j++) {
ri[j] = r[cell_num][j][frame_num];
}
// Add up the last ten y-values for this cell
// (or fewer if there are not yet ten previous frames)
double ycavg = 0.0;
for (i = (frame_num > 10 ? frame_num - 10 : 0); i < frame_num; i++) {
ycavg += yc[cell_num][i];
}
// Compute the average of the last ten y-values
// (this represents the expected y-location of the cell)
ycavg = ycavg / (double) (frame_num > 10 ? 10 : frame_num);
// Determine the range of the subimage surrounding the current position
int u1 = max(xci - 4.0 * R + 0.5, 0 );
int u2 = min(xci + 4.0 * R + 0.5, Iw - 1);
int v1 = max(yci - 2.0 * R + 1.5, 0 );
int v2 = min(yci + 2.0 * R + 1.5, Ih - 1);
// Extract the subimage
MAT *Isub = m_get(v2 - v1 + 1, u2 - u1 + 1);
for (i = v1; i <= v2; i++) {
for (j = u1; j <= u2; j++) {
m_set_val(Isub, i - v1, j - u1, m_get_val(I, i, j));
}
}
// Compute the subimage gradient magnitude
MAT *Ix = gradient_x(Isub);
MAT *Iy = gradient_y(Isub);
MAT *IE = m_get(Isub->m, Isub->n);
for (i = 0; i < Isub->m; i++) {
for (j = 0; j < Isub->n; j++) {
double temp_x = m_get_val(Ix, i, j);
double temp_y = m_get_val(Iy, i, j);
m_set_val(IE, i, j, sqrt((temp_x * temp_x) + (temp_y * temp_y)));
}
}
// Compute the motion gradient vector flow (MGVF) edgemaps
long long MGVF_start_time = get_time();
MAT *IMGVF = MGVF(IE, 1, 1);
MGVF_time += get_time() - MGVF_start_time;
// Determine the position of the cell in the subimage
xci = xci - (double) u1;
yci = yci - (double) (v1 - 1);
ycavg = ycavg - (double) (v1 - 1);
// Evolve the snake
long long snake_start_time = get_time();
ellipseevolve(IMGVF, &xci, &yci, ri, t, Np, (double) R, ycavg);
snake_time += get_time() - snake_start_time;
// Compute the cell's new position in the full image
xci = xci + u1;
yci = yci + (v1 - 1);
// Store the new location of the cell and the snake
xc[cell_num][frame_num] = xci;
yc[cell_num][frame_num] = yci;
for (j = 0; j < Np; j++) {
r[cell_num][j][frame_num] = ri[j];
x[cell_num][j][frame_num] = xc[cell_num][frame_num] + (ri[j] * cos(t[j]));
y[cell_num][j][frame_num] = yc[cell_num][frame_num] + (ri[j] * sin(t[j]));
}
// Output the updated center of each cell
//printf("%d,%f,%f\n", cell_num, xci[cell_num], yci[cell_num]);
// Free temporary memory
m_free(IMGVF);
free(ri);
}
#ifdef OUTPUT
if (frame_num == Nf)
{
FILE * pFile;
pFile = fopen ("result.txt","w+");
for (cell_num = 0; cell_num < Nc; cell_num++)
fprintf(pFile,"\n%d,%f,%f", cell_num, xc[cell_num][Nf], yc[cell_num][Nf]);
fclose (pFile);
}
#endif
// Output a new line to visually distinguish the output from different frames
//printf("\n");
}
// Free temporary memory
free(t);
free_2d_double(xc);
free_2d_double(yc);
free_3d_double(r);
free_3d_double(x);
free_3d_double(y);
// Report average processing time per frame
printf("\n\nTracking runtime (average per frame):\n");
printf("------------------------------------\n");
printf("MGVF computation: %.5f seconds\n", ((float) (MGVF_time)) / (float) (1000*1000*Nf));
printf(" Snake evolution: %.5f seconds\n", ((float) (snake_time)) / (float) (1000*1000*Nf));
}
/*
* recvfrom() a UDP socket
*/
void
sorecvfrom(struct socket *so)
{
struct sockaddr_in addr;
socklen_t addrlen = sizeof(struct sockaddr_in);
DEBUG_CALL("sorecvfrom");
DEBUG_ARG("so = %p", so);
if (so->so_type == IPPROTO_ICMP) { /* This is a "ping" reply */
char buff[256];
int len;
len = recvfrom(so->s, buff, 256, 0,
(struct sockaddr *)&addr, &addrlen);
/* XXX Check if reply is "correct"? */
if(len == -1 || len == 0) {
u_char code=ICMP_UNREACH_PORT;
if(errno == EHOSTUNREACH) code=ICMP_UNREACH_HOST;
else if(errno == ENETUNREACH) code=ICMP_UNREACH_NET;
DEBUG_MISC((dfd," udp icmp rx errno = %d-%s\n",
errno,strerror(errno)));
icmp_error(so->so_m, ICMP_UNREACH,code, 0,strerror(errno));
} else {
icmp_reflect(so->so_m);
so->so_m = NULL; /* Don't m_free() it again! */
}
/* No need for this socket anymore, udp_detach it */
udp_detach(so);
} else { /* A "normal" UDP packet */
struct mbuf *m;
int len;
#ifdef _WIN32
unsigned long n;
#else
int n;
#endif
m = m_get(so->slirp);
if (!m) {
return;
}
m->m_data += IF_MAXLINKHDR;
/*
* XXX Shouldn't FIONREAD packets destined for port 53,
* but I don't know the max packet size for DNS lookups
*/
len = M_FREEROOM(m);
/* if (so->so_fport != htons(53)) { */
ioctlsocket(so->s, FIONREAD, &n);
if (n > len) {
n = (m->m_data - m->m_dat) + m->m_len + n + 1;
m_inc(m, n);
len = M_FREEROOM(m);
}
/* } */
m->m_len = recvfrom(so->s, m->m_data, len, 0,
(struct sockaddr *)&addr, &addrlen);
DEBUG_MISC((dfd, " did recvfrom %d, errno = %d-%s\n",
m->m_len, errno,strerror(errno)));
if(m->m_len<0) {
u_char code=ICMP_UNREACH_PORT;
if(errno == EHOSTUNREACH) code=ICMP_UNREACH_HOST;
else if(errno == ENETUNREACH) code=ICMP_UNREACH_NET;
DEBUG_MISC((dfd," rx error, tx icmp ICMP_UNREACH:%i\n", code));
icmp_error(so->so_m, ICMP_UNREACH,code, 0,strerror(errno));
m_free(m);
} else {
/*
* Hack: domain name lookup will be used the most for UDP,
* and since they'll only be used once there's no need
* for the 4 minute (or whatever) timeout... So we time them
* out much quicker (10 seconds for now...)
*/
if (so->so_expire) {
if (so->so_fport == htons(53))
so->so_expire = curtime + SO_EXPIREFAST;
else
so->so_expire = curtime + SO_EXPIRE;
}
/*
* If this packet was destined for CTL_ADDR,
* make it look like that's where it came from, done by udp_output
*/
udp_output(so, m, &addr);
} /* rx error */
} /* if ping packet */
}
/*
* Slightly changed version of sosend()
*/
static int
kttcp_sosend(struct socket *so, unsigned long long slen,
unsigned long long *done, struct lwp *l, int flags)
{
struct mbuf **mp, *m, *top;
long space, len, mlen;
int error, dontroute, atomic;
long long resid;
atomic = sosendallatonce(so);
resid = slen;
top = NULL;
/*
* In theory resid should be unsigned.
* However, space must be signed, as it might be less than 0
* if we over-committed, and we must use a signed comparison
* of space and resid. On the other hand, a negative resid
* causes us to loop sending 0-length segments to the protocol.
*/
if (resid < 0) {
error = EINVAL;
goto out;
}
dontroute =
(flags & MSG_DONTROUTE) && (so->so_options & SO_DONTROUTE) == 0 &&
(so->so_proto->pr_flags & PR_ATOMIC);
l->l_ru.ru_msgsnd++;
#define snderr(errno) { error = errno; goto release; }
solock(so);
restart:
if ((error = sblock(&so->so_snd, SBLOCKWAIT(flags))) != 0)
goto out;
do {
if (so->so_state & SS_CANTSENDMORE)
snderr(EPIPE);
if (so->so_error) {
error = so->so_error;
so->so_error = 0;
goto release;
}
if ((so->so_state & SS_ISCONNECTED) == 0) {
if (so->so_proto->pr_flags & PR_CONNREQUIRED) {
snderr(ENOTCONN);
} else {
snderr(EDESTADDRREQ);
}
}
space = sbspace(&so->so_snd);
if (flags & MSG_OOB)
space += 1024;
if ((atomic && resid > so->so_snd.sb_hiwat))
snderr(EMSGSIZE);
if (space < resid && (atomic || space < so->so_snd.sb_lowat)) {
if (so->so_state & SS_NBIO)
snderr(EWOULDBLOCK);
SBLASTRECORDCHK(&so->so_rcv,
"kttcp_soreceive sbwait 1");
SBLASTMBUFCHK(&so->so_rcv,
"kttcp_soreceive sbwait 1");
sbunlock(&so->so_snd);
error = sbwait(&so->so_snd);
if (error)
goto out;
goto restart;
}
mp = ⊤
do {
sounlock(so);
do {
if (top == 0) {
m = m_gethdr(M_WAIT, MT_DATA);
mlen = MHLEN;
m->m_pkthdr.len = 0;
m->m_pkthdr.rcvif = NULL;
} else {
m = m_get(M_WAIT, MT_DATA);
mlen = MLEN;
}
if (resid >= MINCLSIZE && space >= MCLBYTES) {
m_clget(m, M_WAIT);
if ((m->m_flags & M_EXT) == 0)
goto nopages;
mlen = MCLBYTES;
#ifdef MAPPED_MBUFS
len = lmin(MCLBYTES, resid);
#else
if (atomic && top == 0) {
len = lmin(MCLBYTES - max_hdr,
resid);
m->m_data += max_hdr;
} else
len = lmin(MCLBYTES, resid);
#endif
space -= len;
} else {
nopages:
len = lmin(lmin(mlen, resid), space);
space -= len;
/*
* For datagram protocols, leave room
* for protocol headers in first mbuf.
*/
if (atomic && top == 0 && len < mlen)
MH_ALIGN(m, len);
}
resid -= len;
m->m_len = len;
*mp = m;
top->m_pkthdr.len += len;
if (error)
goto release;
mp = &m->m_next;
if (resid <= 0) {
if (flags & MSG_EOR)
top->m_flags |= M_EOR;
break;
}
} while (space > 0 && atomic);
solock(so);
if (so->so_state & SS_CANTSENDMORE)
snderr(EPIPE);
if (dontroute)
so->so_options |= SO_DONTROUTE;
if (resid > 0)
so->so_state |= SS_MORETOCOME;
if (flags & MSG_OOB)
error = (*so->so_proto->pr_usrreqs->pr_sendoob)(so,
top, NULL);
else
error = (*so->so_proto->pr_usrreqs->pr_send)(so,
top, NULL, NULL, l);
if (dontroute)
so->so_options &= ~SO_DONTROUTE;
if (resid > 0)
so->so_state &= ~SS_MORETOCOME;
top = 0;
mp = ⊤
if (error)
goto release;
} while (resid && space > 0);
} while (resid);
release:
sbunlock(&so->so_snd);
out:
sounlock(so);
if (top)
m_freem(top);
*done = slen - resid;
#if 0
printf("sosend: error %d slen %llu resid %lld\n", error, slen, resid);
#endif
return (error);
}
/*
* Implement receive operations on a socket.
*
* We depend on the way that records are added to the signalsockbuf
* by sbappend*. In particular, each record (mbufs linked through m_next)
* must begin with an address if the protocol so specifies,
* followed by an optional mbuf or mbufs containing ancillary data,
* and then zero or more mbufs of data.
*
* Although the signalsockbuf is locked, new data may still be appended.
* A token inside the ssb_lock deals with MP issues and still allows
* the network to access the socket if we block in a uio.
*
* The caller may receive the data as a single mbuf chain by supplying
* an mbuf **mp0 for use in returning the chain. The uio is then used
* only for the count in uio_resid.
*/
int
soreceive(struct socket *so, struct sockaddr **psa, struct uio *uio,
struct sockbuf *sio, struct mbuf **controlp, int *flagsp)
{
struct mbuf *m, *n;
struct mbuf *free_chain = NULL;
int flags, len, error, offset;
struct protosw *pr = so->so_proto;
int moff, type = 0;
size_t resid, orig_resid;
if (uio)
resid = uio->uio_resid;
else
resid = (size_t)(sio->sb_climit - sio->sb_cc);
orig_resid = resid;
if (psa)
*psa = NULL;
if (controlp)
*controlp = NULL;
if (flagsp)
flags = *flagsp &~ MSG_EOR;
else
flags = 0;
if (flags & MSG_OOB) {
m = m_get(MB_WAIT, MT_DATA);
if (m == NULL)
return (ENOBUFS);
error = so_pru_rcvoob(so, m, flags & MSG_PEEK);
if (error)
goto bad;
if (sio) {
do {
sbappend(sio, m);
KKASSERT(resid >= (size_t)m->m_len);
resid -= (size_t)m->m_len;
} while (resid > 0 && m);
} else {
do {
uio->uio_resid = resid;
error = uiomove(mtod(m, caddr_t),
(int)szmin(resid, m->m_len),
uio);
resid = uio->uio_resid;
m = m_free(m);
} while (uio->uio_resid && error == 0 && m);
}
bad:
if (m)
m_freem(m);
return (error);
}
if ((so->so_state & SS_ISCONFIRMING) && resid)
so_pru_rcvd(so, 0);
/*
* The token interlocks against the protocol thread while
* ssb_lock is a blocking lock against other userland entities.
*/
lwkt_gettoken(&so->so_rcv.ssb_token);
restart:
error = ssb_lock(&so->so_rcv, SBLOCKWAIT(flags));
if (error)
goto done;
m = so->so_rcv.ssb_mb;
/*
* If we have less data than requested, block awaiting more
* (subject to any timeout) if:
* 1. the current count is less than the low water mark, or
* 2. MSG_WAITALL is set, and it is possible to do the entire
* receive operation at once if we block (resid <= hiwat).
* 3. MSG_DONTWAIT is not set
* If MSG_WAITALL is set but resid is larger than the receive buffer,
* we have to do the receive in sections, and thus risk returning
* a short count if a timeout or signal occurs after we start.
*/
if (m == NULL || (((flags & MSG_DONTWAIT) == 0 &&
(size_t)so->so_rcv.ssb_cc < resid) &&
(so->so_rcv.ssb_cc < so->so_rcv.ssb_lowat ||
((flags & MSG_WAITALL) && resid <= (size_t)so->so_rcv.ssb_hiwat)) &&
m->m_nextpkt == 0 && (pr->pr_flags & PR_ATOMIC) == 0)) {
KASSERT(m != NULL || !so->so_rcv.ssb_cc, ("receive 1"));
if (so->so_error) {
if (m)
goto dontblock;
error = so->so_error;
if ((flags & MSG_PEEK) == 0)
so->so_error = 0;
goto release;
}
if (so->so_state & SS_CANTRCVMORE) {
if (m)
goto dontblock;
else
goto release;
}
for (; m; m = m->m_next) {
if (m->m_type == MT_OOBDATA || (m->m_flags & M_EOR)) {
m = so->so_rcv.ssb_mb;
goto dontblock;
}
}
if ((so->so_state & (SS_ISCONNECTED|SS_ISCONNECTING)) == 0 &&
(pr->pr_flags & PR_CONNREQUIRED)) {
error = ENOTCONN;
goto release;
}
if (resid == 0)
goto release;
if (flags & (MSG_FNONBLOCKING|MSG_DONTWAIT)) {
error = EWOULDBLOCK;
goto release;
}
ssb_unlock(&so->so_rcv);
error = ssb_wait(&so->so_rcv);
if (error)
goto done;
goto restart;
}
dontblock:
if (uio && uio->uio_td && uio->uio_td->td_proc)
uio->uio_td->td_lwp->lwp_ru.ru_msgrcv++;
/*
* note: m should be == sb_mb here. Cache the next record while
* cleaning up. Note that calling m_free*() will break out critical
* section.
*/
KKASSERT(m == so->so_rcv.ssb_mb);
/*
* Skip any address mbufs prepending the record.
*/
if (pr->pr_flags & PR_ADDR) {
KASSERT(m->m_type == MT_SONAME, ("receive 1a"));
orig_resid = 0;
if (psa)
*psa = dup_sockaddr(mtod(m, struct sockaddr *));
if (flags & MSG_PEEK)
m = m->m_next;
else
m = sbunlinkmbuf(&so->so_rcv.sb, m, &free_chain);
}
int
bootpc_call(
struct bootp_packet *call,
struct bootp_packet *reply, /* output */
struct proc *procp)
{
struct socket *so;
struct sockaddr_in *sin;
struct mbuf *m, *nam;
struct uio auio;
struct iovec aio;
int error, rcvflg, timo, secs, len;
/* Free at end if not null. */
nam = NULL;
/*
* Create socket and set its recieve timeout.
*/
if ((error = socreate(AF_INET, &so, SOCK_DGRAM, 0,procp)))
goto out;
m = m_get(M_WAIT, MT_SOOPTS);
if (m == NULL) {
error = ENOBUFS;
goto out;
} else {
struct timeval *tv;
tv = mtod(m, struct timeval *);
m->m_len = sizeof(*tv);
tv->tv_sec = 1;
tv->tv_usec = 0;
if ((error = sosetopt(so, SOL_SOCKET, SO_RCVTIMEO, m)))
goto out;
}
/*
* Enable broadcast.
*/
{
int *on;
m = m_get(M_WAIT, MT_SOOPTS);
if (m == NULL) {
error = ENOBUFS;
goto out;
}
on = mtod(m, int *);
m->m_len = sizeof(*on);
*on = 1;
if ((error = sosetopt(so, SOL_SOCKET, SO_BROADCAST, m)))
goto out;
}
/*
* Bind the local endpoint to a bootp client port.
*/
m = m_getclr(M_WAIT, MT_SONAME);
sin = mtod(m, struct sockaddr_in *);
sin->sin_len = m->m_len = sizeof(*sin);
sin->sin_family = AF_INET;
sin->sin_addr.s_addr = INADDR_ANY;
sin->sin_port = htons(IPPORT_BOOTPC);
error = sobind(so, m);
m_freem(m);
if (error) {
printf("bind failed\n");
goto out;
}
/*
* Setup socket address for the server.
*/
nam = m_get(M_WAIT, MT_SONAME);
if (nam == NULL) {
error = ENOBUFS;
goto out;
}
sin = mtod(nam, struct sockaddr_in *);
sin-> sin_len = sizeof(*sin);
sin-> sin_family = AF_INET;
sin->sin_addr.s_addr = INADDR_BROADCAST;
sin->sin_port = htons(IPPORT_BOOTPS);
nam->m_len = sizeof(*sin);
/*
* Send it, repeatedly, until a reply is received,
* but delay each re-send by an increasing amount.
* If the delay hits the maximum, start complaining.
*/
for (timo=1; timo <= MAX_RESEND_DELAY; timo++) {
/* Send BOOTP request (or re-send). */
aio.iov_base = (caddr_t) call;
aio.iov_len = sizeof(*call);
auio.uio_iov = &aio;
auio.uio_iovcnt = 1;
auio.uio_segflg = UIO_SYSSPACE;
auio.uio_rw = UIO_WRITE;
auio.uio_offset = 0;
auio.uio_resid = sizeof(*call);
auio.uio_procp = procp;
error = sosend(so, nam, &auio, NULL, NULL, 0);
if (error) {
printf("bootpc_call: sosend: %d\n", error);
switch (error) {
case ENOBUFS: /* No buffer space available */
case ENETUNREACH: /* Network is unreachable */
case ENETDOWN: /* Network interface is not configured */
case EHOSTDOWN: /* Host is down */
case EHOSTUNREACH: /* Host is unreachable */
case EMSGSIZE: /* Message too long */
/* This is a possibly transient error.
We can still receive replies from previous attempts. */
break;
default:
goto out;
}
}
/*
* Wait for up to timo seconds for a reply.
* The socket receive timeout was set to 1 second.
*/
secs = timo;
while (secs > 0) {
aio.iov_base = (caddr_t) reply;
aio.iov_len = sizeof(*reply);
auio.uio_iov = &aio;
auio.uio_iovcnt = 1;
auio.uio_segflg = UIO_SYSSPACE;
auio.uio_rw = UIO_READ;
auio.uio_offset = 0;
auio.uio_resid = sizeof(*reply);
auio.uio_procp = procp;
rcvflg = 0;
error = soreceive(so, NULL, &auio, NULL, NULL, &rcvflg);
if (error == EWOULDBLOCK) {
secs--;
call->secs=htons(ntohs(call->secs)+1);
continue;
}
if (error)
goto out;
len = sizeof(*reply) - auio.uio_resid;
/* Do we have the required number of bytes ? */
if (len < BOOTP_MIN_LEN)
continue;
/* Is it the right reply? */
if (reply->op != 2)
continue;
if (reply->xid != call->xid)
continue;
if (reply->hlen != call->hlen)
continue;
if (bcmp(reply->chaddr,call->chaddr,call->hlen))
continue;
goto gotreply; /* break two levels */
} /* while secs */
} /* send/receive a number of times then return an error */
{
uint32_t addr = ntohl(sin->sin_addr.s_addr);
printf("BOOTP timeout for server %"PRIu32".%"PRIu32".%"PRIu32".%"PRIu32"\n",
(addr >> 24) & 0xff, (addr >> 16) & 0xff,
(addr >> 8) & 0xff, addr & 0xff);
}
error = ETIMEDOUT;
goto out;
gotreply:
out:
if (nam) m_freem(nam);
soclose(so);
return error;
}
int main(int argc, char ** argv) {
// Keep track of the start time of the program
long long program_start_time = get_time();
// Let the user specify the number of frames to process
int num_frames = 1;
if (argc !=5){
fprintf(stderr, "usage: %s <num of frames> <num of threads><input file>", argv[0]);
exit(1);
}
if (argc > 1){
num_frames = atoi(argv[1]);
omp_num_threads = atoi(argv[2]);
omp_num_threads2 = atoi(argv[3]);
}
printf("Num of threads: %d\n", omp_num_threads);
printf("Num of threads: %d\n", omp_num_threads2);
omp_set_nested(1);
// Open video file
char *video_file_name;
video_file_name = argv[4];
avi_t *cell_file = AVI_open_input_file(video_file_name, 1);
if (cell_file == NULL) {
AVI_print_error("Error with AVI_open_input_file");
return -1;
}
int i, j, *crow, *ccol, pair_counter = 0, x_result_len = 0, Iter = 20, ns = 4, k_count = 0, n;
MAT *cellx, *celly, *A;
double *GICOV_spots, *t, *G, *x_result, *y_result, *V, *QAX_CENTERS, *QAY_CENTERS;
double threshold = 1.8, radius = 10.0, delta = 3.0, dt = 0.01, b = 5.0;
// Extract a cropped version of the first frame from the video file
MAT *image_chopped = get_frame(cell_file, 0, 1, 0);
printf("Detecting cells in frame 0\n");
// Get gradient matrices in x and y directions
MAT *grad_x = gradient_x(image_chopped);
MAT *grad_y = gradient_y(image_chopped);
m_free(image_chopped);
// Get GICOV matrix corresponding to image gradients
long long GICOV_start_time = get_time();
MAT *gicov = ellipsematching(grad_x, grad_y);
// Square GICOV values
MAT *max_gicov = m_get(gicov->m, gicov->n);
for (i = 0; i < gicov->m; i++) {
for (j = 0; j < gicov->n; j++) {
double val = m_get_val(gicov, i, j);
m_set_val(max_gicov, i, j, val * val);
}
}
long long GICOV_end_time = get_time();
// Dilate the GICOV matrix
long long dilate_start_time = get_time();
MAT *strel = structuring_element(12);
MAT *img_dilated = dilate_f(max_gicov, strel);
long long dilate_end_time = get_time();
// Find possible matches for cell centers based on GICOV and record the rows/columns in which they are found
pair_counter = 0;
crow = (int *) malloc(max_gicov->m * max_gicov->n * sizeof(int));
ccol = (int *) malloc(max_gicov->m * max_gicov->n * sizeof(int));
for (i = 0; i < max_gicov->m; i++) {
for (j = 0; j < max_gicov->n; j++) {
if (!(m_get_val(max_gicov,i,j) == 0.0) && (m_get_val(img_dilated,i,j) == m_get_val(max_gicov,i,j))) {
crow[pair_counter] = i;
ccol[pair_counter] = j;
pair_counter++;
}
}
}
GICOV_spots = (double *) malloc(sizeof(double)*pair_counter);
for (i = 0; i < pair_counter; i++)
GICOV_spots[i] = m_get_val(gicov, crow[i], ccol[i]);
G = (double *) calloc(pair_counter, sizeof(double));
x_result = (double *) calloc(pair_counter, sizeof(double));
y_result = (double *) calloc(pair_counter, sizeof(double));
x_result_len = 0;
for (i = 0; i < pair_counter; i++) {
if ((crow[i] > 29) && (crow[i] < BOTTOM - TOP + 39)) {
x_result[x_result_len] = ccol[i];
y_result[x_result_len] = crow[i] - 40;
G[x_result_len] = GICOV_spots[i];
x_result_len++;
}
}
// Make an array t which holds each "time step" for the possible cells
t = (double *) malloc(sizeof(double) * 36);
for (i = 0; i < 36; i++) {
t[i] = (double)i * 2.0 * PI / 36.0;
}
// Store cell boundaries (as simple circles) for all cells
cellx = m_get(x_result_len, 36);
celly = m_get(x_result_len, 36);
for(i = 0; i < x_result_len; i++) {
for(j = 0; j < 36; j++) {
m_set_val(cellx, i, j, x_result[i] + radius * cos(t[j]));
m_set_val(celly, i, j, y_result[i] + radius * sin(t[j]));
}
}
A = TMatrix(9,4);
V = (double *) malloc(sizeof(double) * pair_counter);
QAX_CENTERS = (double * )malloc(sizeof(double) * pair_counter);
QAY_CENTERS = (double *) malloc(sizeof(double) * pair_counter);
memset(V, 0, sizeof(double) * pair_counter);
memset(QAX_CENTERS, 0, sizeof(double) * pair_counter);
memset(QAY_CENTERS, 0, sizeof(double) * pair_counter);
// For all possible results, find the ones that are feasibly leukocytes and store their centers
k_count = 0;
for (n = 0; n < x_result_len; n++) {
if ((G[n] < -1 * threshold) || G[n] > threshold) {
MAT * x, *y;
VEC * x_row, * y_row;
x = m_get(1, 36);
y = m_get(1, 36);
x_row = v_get(36);
y_row = v_get(36);
// Get current values of possible cells from cellx/celly matrices
x_row = get_row(cellx, n, x_row);
y_row = get_row(celly, n, y_row);
uniformseg(x_row, y_row, x, y);
// Make sure that the possible leukocytes are not too close to the edge of the frame
if ((m_min(x) > b) && (m_min(y) > b) && (m_max(x) < cell_file->width - b) && (m_max(y) < cell_file->height - b)) {
MAT * Cx, * Cy, *Cy_temp, * Ix1, * Iy1;
VEC *Xs, *Ys, *W, *Nx, *Ny, *X, *Y;
Cx = m_get(1, 36);
Cy = m_get(1, 36);
Cx = mmtr_mlt(A, x, Cx);
Cy = mmtr_mlt(A, y, Cy);
Cy_temp = m_get(Cy->m, Cy->n);
for (i = 0; i < 9; i++)
m_set_val(Cy, i, 0, m_get_val(Cy, i, 0) + 40.0);
// Iteratively refine the snake/spline
for (i = 0; i < Iter; i++) {
int typeofcell;
if(G[n] > 0.0) typeofcell = 0;
else typeofcell = 1;
splineenergyform01(Cx, Cy, grad_x, grad_y, ns, delta, 2.0 * dt, typeofcell);
}
X = getsampling(Cx, ns);
for (i = 0; i < Cy->m; i++)
m_set_val(Cy_temp, i, 0, m_get_val(Cy, i, 0) - 40.0);
Y = getsampling(Cy_temp, ns);
Ix1 = linear_interp2(grad_x, X, Y);
Iy1 = linear_interp2(grad_x, X, Y);
Xs = getfdriv(Cx, ns);
Ys = getfdriv(Cy, ns);
Nx = v_get(Ys->dim);
for (i = 0; i < Ys->dim; i++)
v_set_val(Nx, i, v_get_val(Ys, i) / sqrt(v_get_val(Xs, i)*v_get_val(Xs, i) + v_get_val(Ys, i)*v_get_val(Ys, i)));
Ny = v_get(Xs->dim);
for (i = 0; i < Xs->dim; i++)
v_set_val(Ny, i, -1.0 * v_get_val(Xs, i) / sqrt(v_get_val(Xs, i)*v_get_val(Xs, i) + v_get_val(Ys, i)*v_get_val(Ys, i)));
W = v_get(Nx->dim);
for (i = 0; i < Nx->dim; i++)
v_set_val(W, i, m_get_val(Ix1, 0, i) * v_get_val(Nx, i) + m_get_val(Iy1, 0, i) * v_get_val(Ny, i));
V[n] = mean(W) / std_dev(W);
//get means of X and Y values for all "snaxels" of the spline contour, thus finding the cell centers
QAX_CENTERS[k_count] = mean(X);
QAY_CENTERS[k_count] = mean(Y) + TOP;
k_count++;
// Free memory
v_free(W);
v_free(Ny);
v_free(Nx);
v_free(Ys);
v_free(Xs);
m_free(Iy1);
m_free(Ix1);
v_free(Y);
v_free(X);
m_free(Cy_temp);
m_free(Cy);
m_free(Cx);
}
// Free memory
v_free(y_row);
v_free(x_row);
m_free(y);
m_free(x);
}
}
// Free memory
free(V);
free(ccol);
free(crow);
free(GICOV_spots);
free(t);
free(G);
free(x_result);
free(y_result);
m_free(A);
m_free(celly);
m_free(cellx);
m_free(img_dilated);
m_free(max_gicov);
m_free(gicov);
m_free(grad_y);
m_free(grad_x);
// Report the total number of cells detected
printf("Cells detected: %d\n\n", k_count);
// Report the breakdown of the detection runtime
printf("Detection runtime\n");
printf("-----------------\n");
printf("GICOV computation: %.5f seconds\n", ((float) (GICOV_end_time - GICOV_start_time)) / (1000*1000));
printf(" GICOV dilation: %.5f seconds\n", ((float) (dilate_end_time - dilate_start_time)) / (1000*1000));
printf(" Total: %.5f seconds\n", ((float) (get_time() - program_start_time)) / (1000*1000));
// Now that the cells have been detected in the first frame,
// track the ellipses through subsequent frames
if (num_frames > 1) printf("\nTracking cells across %d frames\n", num_frames);
else printf("\nTracking cells across 1 frame\n");
long long tracking_start_time = get_time();
int num_snaxels = 20;
ellipsetrack(cell_file, QAX_CENTERS, QAY_CENTERS, k_count, radius, num_snaxels, num_frames);
printf(" Total cambine: %.5f seconds\n", ((float) (get_time() - tracking_start_time)) / (float) (1000*1000*num_frames));
// Report total program execution time
printf("\nTotal application run time: %.5f seconds\n", ((float) (get_time() - program_start_time)) / (1000*1000));
return 0;
}
/*
* Peer has sent us a FIN.
*/
static int
do_peer_close(struct sge_iq *iq, const struct rss_header *rss, struct mbuf *m)
{
struct adapter *sc = iq->adapter;
const struct cpl_peer_close *cpl = (const void *)(rss + 1);
unsigned int tid = GET_TID(cpl);
struct toepcb *toep = lookup_tid(sc, tid);
struct inpcb *inp = toep->inp;
struct tcpcb *tp = NULL;
struct socket *so;
struct sockbuf *sb;
#ifdef INVARIANTS
unsigned int opcode = G_CPL_OPCODE(be32toh(OPCODE_TID(cpl)));
#endif
KASSERT(opcode == CPL_PEER_CLOSE,
("%s: unexpected opcode 0x%x", __func__, opcode));
KASSERT(m == NULL, ("%s: wasn't expecting payload", __func__));
if (__predict_false(toep->flags & TPF_SYNQE)) {
#ifdef INVARIANTS
struct synq_entry *synqe = (void *)toep;
INP_WLOCK(synqe->lctx->inp);
if (synqe->flags & TPF_SYNQE_HAS_L2TE) {
KASSERT(synqe->flags & TPF_ABORT_SHUTDOWN,
("%s: listen socket closed but tid %u not aborted.",
__func__, tid));
} else {
/*
* do_pass_accept_req is still running and will
* eventually take care of this tid.
*/
}
INP_WUNLOCK(synqe->lctx->inp);
#endif
CTR4(KTR_CXGBE, "%s: tid %u, synqe %p (0x%x)", __func__, tid,
toep, toep->flags);
return (0);
}
KASSERT(toep->tid == tid, ("%s: toep tid mismatch", __func__));
INP_INFO_WLOCK(&V_tcbinfo);
INP_WLOCK(inp);
tp = intotcpcb(inp);
CTR5(KTR_CXGBE, "%s: tid %u (%s), toep_flags 0x%x, inp %p", __func__,
tid, tp ? tcpstates[tp->t_state] : "no tp", toep->flags, inp);
if (toep->flags & TPF_ABORT_SHUTDOWN)
goto done;
tp->rcv_nxt++; /* FIN */
so = inp->inp_socket;
sb = &so->so_rcv;
SOCKBUF_LOCK(sb);
if (__predict_false(toep->ddp_flags & (DDP_BUF0_ACTIVE | DDP_BUF1_ACTIVE))) {
m = m_get(M_NOWAIT, MT_DATA);
if (m == NULL)
CXGBE_UNIMPLEMENTED("mbuf alloc failure");
m->m_len = be32toh(cpl->rcv_nxt) - tp->rcv_nxt;
m->m_flags |= M_DDP; /* Data is already where it should be */
m->m_data = "nothing to see here";
tp->rcv_nxt = be32toh(cpl->rcv_nxt);
toep->ddp_flags &= ~(DDP_BUF0_ACTIVE | DDP_BUF1_ACTIVE);
KASSERT(toep->sb_cc >= sb->sb_cc,
("%s: sb %p has more data (%d) than last time (%d).",
__func__, sb, sb->sb_cc, toep->sb_cc));
toep->rx_credits += toep->sb_cc - sb->sb_cc;
#ifdef USE_DDP_RX_FLOW_CONTROL
toep->rx_credits -= m->m_len; /* adjust for F_RX_FC_DDP */
#endif
sbappendstream_locked(sb, m);
toep->sb_cc = sb->sb_cc;
}
socantrcvmore_locked(so); /* unlocks the sockbuf */
KASSERT(tp->rcv_nxt == be32toh(cpl->rcv_nxt),
("%s: rcv_nxt mismatch: %u %u", __func__, tp->rcv_nxt,
be32toh(cpl->rcv_nxt)));
switch (tp->t_state) {
case TCPS_SYN_RECEIVED:
tp->t_starttime = ticks;
/* FALLTHROUGH */
case TCPS_ESTABLISHED:
tp->t_state = TCPS_CLOSE_WAIT;
break;
case TCPS_FIN_WAIT_1:
tp->t_state = TCPS_CLOSING;
break;
case TCPS_FIN_WAIT_2:
tcp_twstart(tp);
INP_UNLOCK_ASSERT(inp); /* safe, we have a ref on the inp */
INP_INFO_WUNLOCK(&V_tcbinfo);
INP_WLOCK(inp);
final_cpl_received(toep);
return (0);
default:
log(LOG_ERR, "%s: TID %u received CPL_PEER_CLOSE in state %d\n",
__func__, tid, tp->t_state);
}
done:
INP_WUNLOCK(inp);
INP_INFO_WUNLOCK(&V_tcbinfo);
return (0);
}
void
icmp_send_error(struct mbuf *msrc, u_char type, u_char code, int minsize,
const char *message)
{
unsigned hlen, shlen, s_ip_len;
register struct ip *ip;
register struct icmp *icp;
register struct mbuf *m;
DEBUG_CALL("icmp_send_error");
DEBUG_ARG("msrc = %p", msrc);
DEBUG_ARG("msrc_len = %d", msrc->m_len);
if(type!=ICMP_UNREACH && type!=ICMP_TIMXCEED) goto end_error;
/* check msrc */
if(!msrc) goto end_error;
ip = mtod(msrc, struct ip *);
#ifdef DEBUG
{ char bufa[20], bufb[20];
strcpy(bufa, inet_ntoa(ip->ip_src));
strcpy(bufb, inet_ntoa(ip->ip_dst));
DEBUG_MISC((dfd, " %.16s to %.16s\n", bufa, bufb));
}
#endif
if(ip->ip_off & IP_OFFMASK) goto end_error; /* Only reply to fragment 0 */
/* Do not reply to source-only IPs */
if ((ip->ip_src.s_addr & htonl(~(0xf << 28))) == 0) {
goto end_error;
}
shlen=ip->ip_hl << 2;
s_ip_len=ip->ip_len;
if(ip->ip_p == IPPROTO_ICMP) {
icp = (struct icmp *)((char *)ip + shlen);
/*
* Assume any unknown ICMP type is an error. This isn't
* specified by the RFC, but think about it..
*/
if(icp->icmp_type>18 || icmp_flush[icp->icmp_type]) goto end_error;
}
/* make a copy */
m = m_get(msrc->slirp);
if (!m) {
goto end_error;
}
{ int new_m_size;
new_m_size=sizeof(struct ip )+ICMP_MINLEN+msrc->m_len+ICMP_MAXDATALEN;
if(new_m_size>m->m_size) m_inc(m, new_m_size);
}
memcpy(m->m_data, msrc->m_data, msrc->m_len);
m->m_len = msrc->m_len; /* copy msrc to m */
/* make the header of the reply packet */
ip = mtod(m, struct ip *);
hlen= sizeof(struct ip ); /* no options in reply */
/* fill in icmp */
m->m_data += hlen;
m->m_len -= hlen;
icp = mtod(m, struct icmp *);
if(minsize) s_ip_len=shlen+ICMP_MINLEN; /* return header+8b only */
else if(s_ip_len>ICMP_MAXDATALEN) /* maximum size */
s_ip_len=ICMP_MAXDATALEN;
m->m_len=ICMP_MINLEN+s_ip_len; /* 8 bytes ICMP header */
/* min. size = 8+sizeof(struct ip)+8 */
icp->icmp_type = type;
icp->icmp_code = code;
icp->icmp_id = 0;
icp->icmp_seq = 0;
memcpy(&icp->icmp_ip, msrc->m_data, s_ip_len); /* report the ip packet */
HTONS(icp->icmp_ip.ip_len);
HTONS(icp->icmp_ip.ip_id);
HTONS(icp->icmp_ip.ip_off);
#ifdef DEBUG
if(message) { /* DEBUG : append message to ICMP packet */
int message_len;
char *cpnt;
message_len=strlen(message);
if(message_len>ICMP_MAXDATALEN) message_len=ICMP_MAXDATALEN;
cpnt=(char *)m->m_data+m->m_len;
memcpy(cpnt, message, message_len);
m->m_len+=message_len;
}
#endif
icp->icmp_cksum = 0;
icp->icmp_cksum = cksum(m, m->m_len);
m->m_data -= hlen;
m->m_len += hlen;
/* fill in ip */
ip->ip_hl = hlen >> 2;
ip->ip_len = m->m_len;
ip->ip_tos=((ip->ip_tos & 0x1E) | 0xC0); /* high priority for errors */
ip->ip_ttl = MAXTTL;
ip->ip_p = IPPROTO_ICMP;
ip->ip_dst = ip->ip_src; /* ip addresses */
ip->ip_src = m->slirp->vhost_addr;
(void ) ip_output((struct socket *)NULL, m);
end_error:
return;
}
/*
* Make space for a new header of length hlen at skip bytes
* into the packet. When doing this we allocate new mbufs only
* when absolutely necessary. The mbuf where the new header
* is to go is returned together with an offset into the mbuf.
* If NULL is returned then the mbuf chain may have been modified;
* the caller is assumed to always free the chain.
*/
struct mbuf *
m_makespace(struct mbuf *m0, int skip, int hlen, int *off)
{
struct mbuf *m;
unsigned remain;
IPSEC_ASSERT(m0 != NULL, ("null mbuf"));
IPSEC_ASSERT(hlen < MHLEN, ("hlen too big: %u", hlen));
for (m = m0; m && skip > m->m_len; m = m->m_next)
skip -= m->m_len;
if (m == NULL)
return (NULL);
/*
* At this point skip is the offset into the mbuf m
* where the new header should be placed. Figure out
* if there's space to insert the new header. If so,
* and copying the remainder makes sense then do so.
* Otherwise insert a new mbuf in the chain, splitting
* the contents of m as needed.
*/
remain = m->m_len - skip; /* data to move */
if (hlen > M_TRAILINGSPACE(m)) {
struct mbuf *n0, *n, **np;
int todo, len, done, alloc;
n0 = NULL;
np = &n0;
alloc = 0;
done = 0;
todo = remain;
while (todo > 0) {
if (todo > MHLEN) {
n = m_getcl(M_NOWAIT, m->m_type, 0);
len = MCLBYTES;
}
else {
n = m_get(M_NOWAIT, m->m_type);
len = MHLEN;
}
if (n == NULL) {
m_freem(n0);
return NULL;
}
*np = n;
np = &n->m_next;
alloc++;
len = min(todo, len);
memcpy(n->m_data, mtod(m, char *) + skip + done, len);
n->m_len = len;
done += len;
todo -= len;
}
if (hlen <= M_TRAILINGSPACE(m) + remain) {
m->m_len = skip + hlen;
*off = skip;
if (n0 != NULL) {
*np = m->m_next;
m->m_next = n0;
}
}
else {
n = m_get(M_NOWAIT, m->m_type);
if (n == NULL) {
m_freem(n0);
return NULL;
}
alloc++;
if ((n->m_next = n0) == NULL)
np = &n->m_next;
n0 = n;
*np = m->m_next;
m->m_next = n0;
n->m_len = hlen;
m->m_len = skip;
m = n; /* header is at front ... */
*off = 0; /* ... of new mbuf */
}
IPSECSTAT_INC(ips_mbinserted);
} else {
mitkIpInt4_t mitkIpFuncInertia ( mitkIpPicDescriptor *pic_old,
mitkIpFloat8_t **eigen_vekt,
mitkIpFloat8_t **eigen_val )
{
mitkIpUInt4_t index_vect[_mitkIpPicNDIM]; /* loopindex-vector */
mitkIpInt4_t n[_mitkIpPicNDIM]; /* number of pixels in each */
/* dimension */
mitkIpUInt4_t i, j; /* loop index */
mitkIpFloat8_t *gravity; /* center of gravity */
mitkIpFloat8_t *help_vekt; /* pointer to eigen_vekt */
mitkIpFloat8_t *help_val; /* pointer to eigen_val */
MAT *ev; /* eigenvector */
MAT *tt; /* tensor of inertia */
VEC *ew; /* eigenvalue */
mitkIpFloat8_t *s, *s_diag, *dist; /* used to calculate tt */
/* check data */
if ( _mitkIpFuncError ( pic_old ) != mitkIpFuncOK ) return ( mitkIpFuncERROR );
/* initialisation of vectors */
for ( i = 0; i < pic_old->dim; i++ )
n[i] = pic_old->n[i];
for ( i = pic_old->dim; i < _mitkIpPicNDIM; i++ )
n[i] = 1;
for ( i = 0; i < _mitkIpPicNDIM; i++ )
index_vect[i] = 0;
/* memory allocation */
gravity = ( mitkIpFloat8_t * ) malloc ( pic_old->dim * sizeof ( mitkIpFloat8_t ) );
if ( gravity == NULL )
{
_mitkIpFuncSetErrno ( mitkIpFuncMALLOC_ERROR );
return ( mitkIpFuncERROR );
}
dist = ( mitkIpFloat8_t * ) malloc ( pic_old->dim * sizeof ( mitkIpFloat8_t ) );
if ( dist == NULL )
{
_mitkIpFuncSetErrno ( mitkIpFuncMALLOC_ERROR );
free ( gravity );
return ( mitkIpFuncERROR );
}
s_diag = ( mitkIpFloat8_t * ) malloc ( pic_old->dim * sizeof ( mitkIpFloat8_t ) );
if ( s_diag == NULL )
{
_mitkIpFuncSetErrno ( mitkIpFuncMALLOC_ERROR );
free ( gravity );
free ( dist );
return ( mitkIpFuncERROR );
}
s = ( mitkIpFloat8_t * ) malloc ( pic_old->dim * pic_old->dim * sizeof ( mitkIpFloat8_t ) );
if ( s == NULL )
{
_mitkIpFuncSetErrno ( mitkIpFuncMALLOC_ERROR );
free ( gravity );
free ( dist );
free ( s_diag );
return ( mitkIpFuncERROR );
}
tt = m_get ( pic_old->dim, pic_old->dim );
if ( tt == NULL )
{
_mitkIpFuncSetErrno ( mitkIpFuncMALLOC_ERROR );
free ( gravity );
free ( dist );
free ( s_diag );
free ( s );
return ( mitkIpFuncERROR );
}
ev = m_get ( pic_old->dim, pic_old->dim );
if ( ev == NULL )
{
_mitkIpFuncSetErrno ( mitkIpFuncMALLOC_ERROR );
free ( gravity );
free ( dist );
free ( s_diag );
free ( s );
M_FREE ( tt );
return ( mitkIpFuncERROR );
}
ew = v_get ( pic_old->dim-1 );
if ( ew == NULL )
{
_mitkIpFuncSetErrno ( mitkIpFuncMALLOC_ERROR );
free ( gravity );
free ( dist );
free ( s_diag );
free ( s );
M_FREE ( tt );
M_FREE ( ev );
return ( mitkIpFuncERROR );
}
/* calculate center of gravity */
gravity = mitkIpFuncGrav ( pic_old );
/* Initialization of vectors */
for ( i = 0; i < pic_old->dim; i++ )
{
s_diag[i] = 0.;
dist[i] = 0.;
for ( j = 0; j < pic_old->dim; j++ )
s[i*pic_old->dim+j] = 0.;
}
/* preparation for calculating the tensor of inertia */
mitkIpPicFORALL_4 ( GRAV, pic_old, index_vect, s, s_diag, dist )
/* calculate tensor of inertia */
for ( i = 0; i < pic_old->dim; i++ )
{
tt->me[i][i] = 0.;
for ( j = 0; j < pic_old->dim; j++ )
{
if ( i < j )
tt->me[i][j] = s[i*pic_old->dim+j];
else if ( j < i )
tt->me[i][j] = s[j*pic_old->dim+i];
if ( i != j )
tt->me[i][i] = tt->me[i][i] + s_diag[j];
}
}
/* calculate eigenvectors and eigenvalues of the tensor of inertia */
ew = symmeig ( tt, ev, ew );
*eigen_vekt = ( mitkIpFloat8_t * ) malloc ( pic_old->dim * pic_old->dim * sizeof ( mitkIpFloat8_t ) );
help_vekt = *eigen_vekt;
*eigen_val = ( mitkIpFloat8_t * ) malloc ( pic_old->dim * sizeof ( mitkIpFloat8_t ) );
help_val = *eigen_val;
for ( i = 0; i < pic_old->dim; i++ )
{
help_val[i] = ew->ve[i];
for ( j = 0; j < pic_old->dim; j++ )
help_vekt[i*pic_old->dim+j] = ev->me[i][j];
}
M_FREE ( tt );
M_FREE ( ev );
V_FREE ( ew );
free ( s );
free ( dist );
free ( s_diag );
free ( gravity );
return mitkIpFuncOK;
}
