MinimalImpactTEDWriter::MinimalImpactTEDWriter() :
_teDistance(boost::make_shared<TolerantEditDistance>()),
_gsimCreator(boost::make_shared<IdMapCreator>()),
_rimCreator(boost::make_shared<IdMapCreator>()),
_rNeuronExtractor(boost::make_shared<NeuronExtractor>()),
_gsNeuronExtractor(boost::make_shared<NeuronExtractor>()),
_rReconstructor(boost::make_shared<Reconstructor>()),
_linearSolver(boost::make_shared<LinearSolver>()),
_objectiveGenerator(boost::make_shared<ObjectiveGenerator>()),
_hammingCostFunction(boost::make_shared<HammingCostFunction>())
{
registerInput(_goldStandard, "gold standard");
registerInput(_groundTruth, "ground truth");
registerInput(_linearConstraints, "linear constraints");
registerInput(_segments, "segments");
registerInput(_reference, "reference");
registerInput(_problemConfiguration, "problem configuration");
}
Sopnet::Sopnet(const std::string& projectDirectory) :
_projectDirectory(projectDirectory),
_membraneExtractor(boost::make_shared<ImageExtractor>()),
_problemAssembler(boost::make_shared<ProblemAssembler>()),
_segmentFeaturesExtractor(boost::make_shared<SegmentFeaturesExtractor>()),
_randomForestReader(boost::make_shared<RandomForestHdf5Reader>(optionRandomForestFile.as<std::string>())),
_randomForestCostFunction(boost::make_shared<RandomForestCostFunction>()),
_segmentationCostFunction(boost::make_shared<SegmentationCostFunction>()),
_priorCostFunction(boost::make_shared<PriorCostFunction>()),
_objectiveGenerator(boost::make_shared<ObjectiveGenerator>()),
_linearSolver(boost::make_shared<LinearSolver>()),
_reconstructor(boost::make_shared<Reconstructor>()),
_groundTruthExtractor(boost::make_shared<GroundTruthExtractor>()),
_segmentRfTrainer(boost::make_shared<RandomForestTrainer>()) {
// tell the outside world what we need
registerInput(_rawSections, "raw sections");
registerInput(_membranes, "membranes");
registerInput(_groundTruth, "ground truth");
registerInput(_segmentationCostFunctionParameters, "segmentation cost parameters");
registerInput(_priorCostFunctionParameters, "prior cost parameters");
registerInput(_forceExplanation, "force explanation");
_membranes.registerBackwardCallback(&Sopnet::onMembranesSet, this);
_rawSections.registerBackwardCallback(&Sopnet::onRawSectionsSet, this);
_groundTruth.registerBackwardCallback(&Sopnet::onGroundTruthSet, this);
_segmentationCostFunctionParameters.registerBackwardCallback(&Sopnet::onParametersSet, this);
_priorCostFunctionParameters.registerBackwardCallback(&Sopnet::onParametersSet, this);
_forceExplanation.registerBackwardCallback(&Sopnet::onParametersSet, this);
// tell the outside world what we've got
registerOutput(_reconstructor->getOutput(), "solution");
registerOutput(_problemAssembler->getOutput("segments"), "segments");
registerOutput(_groundTruthExtractor->getOutput("ground truth segments"), "ground truth segments");
registerOutput(_segmentRfTrainer->getOutput("gold standard"), "gold standard");
registerOutput(_segmentRfTrainer->getOutput("negative samples"), "negative samples");
registerOutput(_segmentRfTrainer->getOutput("random forest"), "random forest");
}
CostWriter::CostWriter()
{
registerInput(_store, "store");
registerInput(_segments, "segments");
registerInput(_objective, "objective");
}
//---------------------------------------------
void XMLProcessor::registerModuleInputs()
{
registerInput(new XMLDocumentInput, "xml");
}
Sine() : Node(ExecutionMode::Consumer) {
registerInput ("Enabled", "Boolean", type::Boolean(true));
registerInput ("Input", "Double", type::Double(0.0));
registerOutput ("Output", "Double", type::Double(0.0));
}
MeshView::MeshView() {
registerInput(_meshes, "meshes");
registerOutput(_painter, "painter");
}
HammingCostFunction::HammingCostFunction() :
_costFunction(new costs_function_type(boost::bind(&HammingCostFunction::costs, this, _1, _2, _3, _4))) {
registerInput(_goldStandard, "gold standard");
registerOutput(_costFunction, "cost function");
}
int
main(int argc, char **argv)
{
int oldpid, oldumask, fd, parentPid;
char *pt, *errorLogFile, **opts;
/* make sure at least world write access is disabled */
if (((oldumask = umask(022)) & 002) == 002)
(void)umask(oldumask);
/* give /dev/null as stdin */
if ((fd = open("/dev/null", O_RDONLY)) > 0) {
dup2(fd, 0);
close(fd);
}
if (fcntl(1, F_GETFD) < 0)
dup2(0, 1);
if (fcntl(2, F_GETFD) < 0)
dup2(0, 2);
#ifndef nowMonotonic
nowMonotonic = sysconf(_SC_MONOTONIC_CLOCK) >= 200112L;
#endif
#if KDM_LIBEXEC_STRIP == -1
prog = strrchr(argv[0], '/');
progname = prog = prog ? prog + 1 : argv[0];
#else
if (argv[0][0] == '/') {
if (!strDup(&progpath, argv[0]))
panic("Out of memory");
} else
# ifdef __linux__
{
/* note that this will resolve symlinks ... */
int len;
char fullpath[PATH_MAX];
if ((len = readlink("/proc/self/exe", fullpath, sizeof(fullpath))) < 0)
panic("Invoke with full path specification or mount /proc");
if (!strNDup(&progpath, fullpath, len))
panic("Out of memory");
}
# else
# if 0
panic("Must be invoked with full path specification");
# else
{
char directory[PATH_MAX+1];
if (!getcwd(directory, sizeof(directory)))
panic("Can't find myself (getcwd failed)");
if (strchr(argv[0], '/')) {
strApp(&progpath, directory, "/", argv[0], (char *)0);
} else {
int len;
char *path, *pathe, *name, *thenam, nambuf[PATH_MAX+1];
if (!(path = getenv("PATH")))
panic("Can't find myself (no PATH)");
len = strlen(argv[0]);
name = nambuf + PATH_MAX - len;
memcpy(name, argv[0], len + 1);
*--name = '/';
do {
if (!(pathe = strchr(path, ':')))
pathe = path + strlen(path);
len = pathe - path;
if (!len || (len == 1 && *path == '.')) {
len = strlen(directory);
path = directory;
}
thenam = name - len;
if (thenam >= nambuf) {
memcpy(thenam, path, len);
if (!access(thenam, X_OK))
goto found;
}
path = pathe;
} while (*path++ != '\0');
panic("Can't find myself (not in PATH)");
found:
if (!strDup(&progpath, thenam))
panic("Out of memory");
}
}
# endif
# endif
prog = strrchr(progpath, '/') + 1;
# if KDM_LIBEXEC_STRIP
for (progname = pt = prog, fd = 0; fd < KDM_LIBEXEC_STRIP + 1; fd++) {
for (;;) {
pt--;
if (pt == progpath)
panic("Executable is obviously located outside BINDIR");
if (*pt == '/')
break;
}
}
*pt = 0;
# endif
#endif
#if !defined(HAVE_SETPROCTITLE) && !defined(NOXDMTITLE)
title = argv[0];
titleLen = (argv[argc - 1] + strlen(argv[argc - 1])) - title;
#endif
/*
* Parse command line options
*/
parentPid = getppid();
errorLogFile = 0;
if (!(opts = Malloc(2 * sizeof(char *))))
return 1;
opts[0] = (char *)"";
opts[1] = 0;
while (*++argv) {
if (**argv != '-')
break;
pt = *argv + 1;
if (*pt == '-')
pt++;
if (!strcmp(pt, "help") || !strcmp(pt, "h")) {
printf("Usage: %s [options] [tty]\n"
" -daemon\t - Daemonize even when started by init\n"
" -nodaemon\t - Do not daemonize even when started from command line\n"
" -config <file> - Use alternative master configuration file\n"
" -xrm <res>\t - Override frontend-specific resource\n"
" -error <file>\t - Use alternative log file\n"
" -debug <num>\t - Debug option bitfield:\n"
"\t\t\t0x1 - core log\n"
"\t\t\t0x2 - config reader log\n"
"\t\t\t0x4 - greeter log\n"
"\t\t\t0x8 - IPC log\n"
"\t\t\t0x10 - session sub-daemon post-fork delay\n"
"\t\t\t0x20 - config reader post-start delay\n"
"\t\t\t0x40 - greeter post-start delay\n"
"\t\t\t0x80 - do not use syslog\n"
"\t\t\t0x100 - core Xauth log\n"
"\t\t\t0x200 - debug greeter theming\n"
"\t\t\t0x400 - valgrind config reader and greeter\n"
"\t\t\t0x800 - strace config reader and greeter\n"
, prog);
exit(0);
} else if (!strcmp(pt, "daemon")) {
parentPid = 0;
} else if (!strcmp(pt, "nodaemon")) {
parentPid = 1;
} else if (argv[1] && !strcmp(pt, "config")) {
strDup(opts, *++argv);
} else if (argv[1] && !strcmp(pt, "xrm")) {
opts = addStrArr(opts, *++argv, -1);
} else if (argv[1] && !strcmp(pt, "debug")) {
sscanf(*++argv, "%i", &debugLevel);
} else if (argv[1] && (!strcmp(pt, "error") || !strcmp(pt, "logfile"))) {
errorLogFile = *++argv;
} else {
fprintf(stderr, "\"%s\" is an unknown option or is missing a parameter\n", *argv);
exit(1);
}
}
/*
* Only allow root to run in non-debug mode to avoid problems
*/
if (!debugLevel && getuid()) {
fprintf(stderr, "Only root wants to run %s\n", prog);
exit(1);
}
initErrorLog(errorLogFile);
if (parentPid != 1)
becomeDaemon();
/*
* Step 1 - load configuration parameters
*/
if (!initResources(opts) || scanConfigs(False) < 0)
logPanic("Config reader failed. Aborting ...\n");
/* SUPPRESS 560 */
if ((oldpid = storePid())) {
if (oldpid == -1)
logError("Cannot create/lock pid file %s\n", pidFile);
else
logError("Cannot lock pid file %s, another xdm is running (pid %d)\n",
pidFile, oldpid);
exit(1);
}
#ifdef NEED_ENTROPY
addOtherEntropy();
#endif
/*
* We used to clean up old authorization files here. As authDir is
* supposed to be /var/run/xauth or /tmp, we needn't to care for it.
*/
#ifdef XDMCP
initXdmcp();
#else
debug("not compiled for XDMCP\n");
#endif
if (pipe(signalFds))
logPanic("Unable to create signal notification pipe.\n");
registerInput(signalFds[0]);
registerCloseOnFork(signalFds[0]);
registerCloseOnFork(signalFds[1]);
(void)Signal(SIGTERM, sigHandler);
(void)Signal(SIGINT, sigHandler);
(void)Signal(SIGHUP, sigHandler);
(void)Signal(SIGCHLD, sigHandler);
(void)Signal(SIGUSR1, sigHandler);
/*
* Step 2 - run a sub-daemon for each entry
*/
openCtrl(0);
#ifdef XDMCP
updateListenSockets();
#endif
mainLoop();
closeCtrl(0);
if (sdRec.how) {
int pid;
commitBootOption();
if (Fork(&pid) <= 0) {
char *cmd = sdRec.how == SHUT_HALT ? cmdHalt : cmdReboot;
execute(parseArgs((char **)0, cmd), (char **)0);
logError("Failed to execute shutdown command %\"s\n", cmd);
exit(1);
} else {
sigset_t mask;
sigemptyset(&mask);
sigaddset(&mask, SIGCHLD);
sigaddset(&mask, SIGHUP);
sigsuspend(&mask);
}
}
debug("nothing left to do, exiting\n");
return 0;
}
void
openCtrl(struct display *d)
{
CtrlRec *cr;
const char *dname;
char *sockdir;
struct sockaddr_un sa;
if (!*fifoDir)
return;
if (d)
cr = &d->ctrl, dname = displayName(d);
else
cr = &ctrl, dname = 0;
if (cr->fd < 0) {
if (mkdir(fifoDir, 0755)) {
if (errno != EEXIST) {
logError("mkdir %\"s failed: %m; no control sockets will be available\n",
fifoDir);
return;
}
} else {
chmod(fifoDir, 0755); /* override umask */
}
sockdir = 0;
strApp(&sockdir, fifoDir, dname ? "/dmctl-" : "/dmctl",
dname, (char *)0);
if (sockdir) {
strApp(&cr->path, sockdir, "/socket", (char *)0);
if (cr->path) {
if (strlen(cr->path) >= sizeof(sa.sun_path)) {
logError("path %\"s too long; control socket will not be available\n",
cr->path);
#ifdef HONORS_SOCKET_PERMS
} else if (mkdir(sockdir, 0700) && errno != EEXIST) {
logError("mkdir %\"s failed: %m; control socket will not be available\n",
sockdir);
} else if (unlink(cr->path) && errno != ENOENT) {
logError("unlink %\"s failed: %m; control socket will not be available\n",
cr->path);
} else {
#else
} else if (unlink(sockdir) && errno != ENOENT) {
logError("unlink %\"s failed: %m; control socket will not be available\n",
sockdir);
} else if (!strApp(&cr->realdir, sockdir, "-XXXXXX", (char *)0)) {
} else if (!mkTempDir(cr->realdir)) {
logError("mkdir %\"s failed: %m; control socket will not be available\n",
cr->realdir);
free(cr->realdir);
cr->realdir = 0;
} else if (symlink(cr->realdir, sockdir)) {
logError("symlink %\"s => %\"s failed: %m; control socket will not be available\n",
sockdir, cr->realdir);
rmdir(cr->realdir);
free(cr->realdir);
cr->realdir = 0;
} else {
chown(sockdir, 0, d ? 0 : fifoGroup);
chmod(sockdir, 0750);
#endif
if ((cr->fd = socket(PF_UNIX, SOCK_STREAM, 0)) < 0) {
logError("Cannot create control socket: %m\n");
} else {
sa.sun_family = AF_UNIX;
strcpy(sa.sun_path, cr->path);
if (!bind(cr->fd, (struct sockaddr *)&sa, sizeof(sa))) {
if (!listen(cr->fd, 5)) {
#ifdef HONORS_SOCKET_PERMS
chmod(cr->path, 0660);
if (!d)
chown(cr->path, -1, fifoGroup);
chmod(sockdir, 0755);
#else
chmod(cr->path, 0666);
#endif
registerCloseOnFork(cr->fd);
registerInput(cr->fd);
free(sockdir);
return;
}
unlink(cr->path);
logError("Cannot listen on control socket %\"s: %m\n",
cr->path);
} else {
logError("Cannot bind control socket %\"s: %m\n",
cr->path);
}
close(cr->fd);
cr->fd = -1;
}
#ifdef HONORS_SOCKET_PERMS
rmdir(sockdir);
#else
unlink(sockdir);
rmdir(cr->realdir);
free(cr->realdir);
cr->realdir = 0;
#endif
}
free(cr->path);
cr->path = 0;
}
free(sockdir);
}
}
BufferWriterNode::BufferWriterNode(Buffer<float>& _buff){
outBuff = &_buff;
inVar = registerInput(inBuff);
output = NULL;
inVarRemaining = 0;
}
ConvexDecomposition::ConvexDecomposition() {
registerInput(_mesh, "mesh");
registerInput(_compacityWeight, "compacity weight", pipeline::Optional);
registerInput(_volumeWeight, "volume weight", pipeline::Optional);
registerInput(_connectDistance, "connect distance", pipeline::Optional);
registerInput(_minNumClusters, "min num clusters", pipeline::Optional);
registerInput(_maxNumHullVertices, "max num hull vertices", pipeline::Optional);
registerInput(_maxConcavity, "max concavity", pipeline::Optional);
registerInput(_smallClusterThreshold, "small cluster threshold", pipeline::Optional);
registerInput(_numTargetTriangles, "num target triangles", pipeline::Optional);
registerInput(_addExtraDistPoints, "add extra dist points", pipeline::Optional);
registerInput(_addExtraFacesPoints, "add extra faces points", pipeline::Optional);
registerOutput(_convexified, "convex meshes");
}
MulNode::MulNode(){
inVar1 = registerInput(in1);
inVar2 = registerInput(in2);
outVar = registerOutput(outBuffer);
output = makeConstSignal(outBuffer);
}
Sopnet::Sopnet(
const std::string& projectDirectory,
boost::shared_ptr<ProcessNode> problemWriter) :
_problemAssembler(boost::make_shared<ProblemAssembler>()),
_segmentFeaturesExtractor(boost::make_shared<SegmentFeaturesExtractor>()),
_randomForestReader(boost::make_shared<RandomForestHdf5Reader>(optionRandomForestFile.as<std::string>())),
_priorCostFunction(boost::make_shared<PriorCostFunction>()),
_objectiveGenerator(boost::make_shared<ObjectiveGenerator>()),
_linearSolver(boost::make_shared<LinearSolver>()),
_reconstructor(boost::make_shared<Reconstructor>()),
_groundTruthExtractor(boost::make_shared<GroundTruthExtractor>()),
_segmentRfTrainer(boost::make_shared<RandomForestTrainer>()),
_projectDirectory(projectDirectory),
_problemWriter(problemWriter),
_pipelineCreated(false) {
// tell the outside world what we need
registerInput(_rawSections, "raw sections");
registerInput(_membranes, "membranes");
registerInput(_neuronSlices, "neuron slices", pipeline::Optional);
registerInput(_neuronSliceStackDirectories, "neuron slice stack directories", pipeline::Optional);
registerInput(_mitochondriaSlices, "mitochondria slices", pipeline::Optional);
registerInput(_mitochondriaSliceStackDirectories, "mitochondria slice stack directories", pipeline::Optional);
registerInput(_synapseSlices, "synapse slices", pipeline::Optional);
registerInput(_synapseSliceStackDirectories, "synapse slice stack directories", pipeline::Optional);
registerInput(_groundTruth, "ground truth", pipeline::Optional);
registerInput(_segmentationCostFunctionParameters, "segmentation cost parameters");
registerInput(_priorCostFunctionParameters, "prior cost parameters");
registerInput(_forceExplanation, "force explanation");
// tell the outside world what we've got
registerOutput(_reconstructor->getOutput(), "solution");
registerOutput(_problemAssembler->getOutput("segments"), "segments");
registerOutput(_problemAssembler->getOutput("problem configuration"), "problem configuration");
registerOutput(_objectiveGenerator->getOutput("objective"), "objective");
registerOutput(_groundTruthExtractor->getOutput("ground truth segments"), "ground truth segments");
registerOutput(_segmentRfTrainer->getOutput("gold standard"), "gold standard");
registerOutput(_segmentRfTrainer->getOutput("negative samples"), "negative samples");
registerOutput(_segmentRfTrainer->getOutput("random forest"), "random forest");
registerOutput(_segmentRfTrainer->getOutput("ground truth score"), "ground truth score");
registerOutput(_segmentFeaturesExtractor->getOutput("all features"), "all features");
}
ProblemsSolver::ProblemsSolver() :
_solutions(new Solutions()) {
registerInput(_problems, "problems");
registerOutput(_solutions, "solutions");
}
TypeFeatureExtractor::TypeFeatureExtractor() :
_features(new Features()) {
registerInput(_segments, "segments");
registerOutput(_features, "features");
}
ImageExtractor::ImageExtractor() {
registerInput(_stack, "stack");
_stack.registerCallback(&ImageExtractor::onInputSet, this);
}
