void BitsetSaver::save(
const std::vector<bool> &bits)
{
char byte = 0;
for (size_t i = 0; i < bits.size(); ++ i)
{
const unsigned shift = i % 8;
const char positionHasNeighbors = bits[i];
byte |= positionHasNeighbors << shift;
if (7 == shift)
{
if (!os_.write(&byte, sizeof(byte)))
{
const boost::format message = boost::format("Failed to write bits into %s: %s") % filePath_.string() % strerror(errno);
BOOST_THROW_EXCEPTION(common::IoException(errno, message.str()));
}
byte = 0;
}
}
if (!os_.write(&byte, sizeof(byte)))
{
const boost::format message = boost::format("Failed to write final bits byte into %s: %s") % filePath_.string() % strerror(errno);
BOOST_THROW_EXCEPTION(common::IoException(errno, message.str()));
}
}
void FastaDumperOptions::postProcess(bpo::variables_map &vm)
{
eagle::common::OptionsHelper check(vm);
if (fastaFiles.empty())
{
throw bpo::validation_error(bpo::validation_error::at_least_one_value_required, "", "positional");
}
check.addPathOptions(fastaFiles,"positional");
check.inputPathsExist();
if ( 1 == fastaFiles.size() && bfs::is_directory(fastaFiles[0]) )
{
mode = WHOLE_DIR;
} else {
for (unsigned int i = 0; i < fastaFiles.size(); i++)
{
if (bfs::is_directory(fastaFiles[i]))
{
const boost::format message = boost::format("\n *** FASTA file #%d has an invalid value: ***"
"\n *** It should point to a file, but a directory already exists with name %s ***\n")
% i % fastaFiles[i];
BOOST_THROW_EXCEPTION(eagle::common::InvalidOptionException(message.str()));
}
}
mode = SAFE_MODE;
}
check.inRange<unsigned long>(std::make_pair(size,"size"),1); // 1 <= size < inf
// (size == 0) not allowed, so internally used to represent 'until the end'
}
static std::vector<std::string > expandUseBasesMask (
const std::vector<unsigned int> &readLengths,
const std::string &useBasesMask,
const boost::filesystem::path &baseCallsDirectory)
{
std::vector<std::string > result;
std::string::const_iterator parseIt(useBasesMask.begin());
const std::string::const_iterator parseEnd(useBasesMask.end());
UseBasesMaskGrammar<std::string::const_iterator> parser(readLengths);
if (!boost::spirit::qi::parse(parseIt, parseEnd, parser, result) ||
parseEnd != parseIt)
{
const boost::format message = boost::format("\n *** Could not parse the use-bases-mask '%s' for '%s' at: %s ***\n") %
useBasesMask % baseCallsDirectory.string() % useBasesMask.substr(parseIt - useBasesMask.begin());
BOOST_THROW_EXCEPTION(common::InvalidOptionException(message.str()));
}
ISAAC_THREAD_CERR << "use bases mask: " << boost::algorithm::join(result, ",") << "\n";
ISAAC_THREAD_CERR << "reads parsed: " << parser.currentRead_ << "\n";
if (result.size() != readLengths.size())
{
const boost::format message = boost::format("\n *** use-bases-mask '%s' is incompatible with number of reads (%d) in %s ***\n") %
useBasesMask % readLengths.size() % baseCallsDirectory.string();
BOOST_THROW_EXCEPTION(common::InvalidOptionException(message.str()));
}
return result;
}
BitsetSaver::BitsetSaver(const boost::filesystem::path filePath) :
filePath_(filePath),
os_(filePath.c_str())
{
if (!os_)
{
const boost::format message = boost::format("Failed to open file %s for writing: %s") % filePath_ % strerror(errno);
BOOST_THROW_EXCEPTION(common::IoException(errno, message.str()));
}
}
void vfeSession::AppendStatusMessage (const boost::format& fmt, int RecommendedPause)
{
boost::mutex::scoped_lock lock(m_MessageMutex);
m_StatusQueue.push (StatusMessage (*this, fmt.str(), RecommendedPause));
m_StatusLineMessage = fmt.str();
if (m_MaxStatusMessages != -1)
while (m_StatusQueue.size() > m_MaxStatusMessages)
m_StatusQueue.pop();
NotifyEvent(stStatusMessage);
}
boost::format CustomFormat(const char* s)
{
using namespace boost::io;
boost::format format(s);
format.exceptions(all_error_bits ^ (too_many_args_bit | too_few_args_bit));
return format;
}
int main(int argc, char** argv)
{
ros::init(argc, argv, "image_saver", ros::init_options::AnonymousName);
ros::NodeHandle nh;
image_transport::ImageTransport it(nh);
//std::string topic = nh.resolveName("image");
// std::string topic = "/ardrone/image_raw";
std::string topic = "/ardrone/kinect/image_raw";
std::string topic_depth = "/ardrone/kinect/depth/image_raw";
Callbacks callbacks;
//callbacks.control ="10000000";
//callbacks.path = "/home/jay/data/";
//obtain saving location
std::string saving_location = nh.resolveName("generated_set");
//if(saving_location.compare("generated_set")) saving_location = "remote_images/set_online";
callbacks.path = "/home/jay/data/"+saving_location;
boost::filesystem::path dir(callbacks.path);
boost::filesystem::remove_all(dir);
if(boost::filesystem::create_directory(dir)) {
callbacks.path_depth = callbacks.path+"/depth";
boost::filesystem::path dir_depth(callbacks.path_depth);
if(boost::filesystem::create_directory(dir_depth)) {
std::cout << "Success in creating: "<<callbacks.path_depth << "\n";
}
callbacks.path = callbacks.path+"/RGB";
boost::filesystem::path dir_rgb(callbacks.path);
if(boost::filesystem::create_directory(dir_rgb)) {
std::cout << "Success in creating: "<<callbacks.path << "\n";
}
}else{
std::cout <<"Failed to make saving direction "<<callbacks.path <<"\n";
}
// Useful when CameraInfo is being published
/*image_transport::CameraSubscriber sub_image_and_camera = it.subscribeCamera(topic, 1,
&Callbacks::callbackWithCameraInfo,
&callbacks);*/
// Useful when CameraInfo is not being published
image_transport::Subscriber sub_image = it.subscribe(
topic, 1, boost::bind(&Callbacks::callbackWithoutCameraInfo, &callbacks, _1));
//depth
image_transport::Subscriber sub_image_depth = it.subscribe(
topic_depth, 1, boost::bind(&Callbacks::callbackWithoutCameraInfoWithDepth, &callbacks, _1));
// Make subscriber to cmd_vel in order to set the name.
ros::Subscriber takeOff = nh.subscribe("/ardrone/takeoff",1,&Callbacks::callbackTakeoff, &callbacks);
ros::Subscriber subControl = nh.subscribe("/dagger_vel",1,&Callbacks::callbackCmd, &callbacks);
// [hover, back, forward, turn right, turn left, down, up, clockwise, ccw]
// Adapt name instead of left0000.jpg it should be 00000-gt1.jpg when receiving control 1 ~ straight
ros::NodeHandle local_nh("~");
std::string format_string;
local_nh.param("filename_format", format_string, std::string("%s/%010i-gt%s.%s"));
local_nh.param("encoding", encoding, std::string("bgr8"));
local_nh.param("save_all_image", save_all_image, true);
g_format.parse(format_string);
ros::ServiceServer save = local_nh.advertiseService ("save", service);
ros::spin();
}
hpgl_exception::hpgl_exception(
const std::string & a_where,
const boost::format & what)
:m_where(a_where), m_what(what.str())
{
m_message = m_where + ": " + m_what;
//std::cerr << m_message << std::endl;
}
error::error(
bool _status,
long long _code,
boost::format _msg,
std::string _file,
int _line,
std::string _fcn ) :
error::error( _status, _code, _msg.str(), _file, _line, _fcn ) {}
void Logger::log(
const Level& level,
const boost::format& message,
const std::string& filename,
const int& lineNumber
)
{
log( level, message.str(), filename, lineNumber );
}
bs_exception::bs_exception (const std::string &who, const boost::format &message)
: who_ (who),
what_ (who_ + ": " + message.str ()),
m_err_ (user_defined)
{
#ifdef BS_EXCEPTION_COLLECT_BACKTRACE
what_ += detail::collect_backtrace ();
#endif
}
void Trace::send(const boost::format& str, TraceLevelOptions level)
{
if (not Trace::Pimpl::mTrace) {
Trace::init();
}
boost::mutex::scoped_lock lock(Trace::Pimpl::mTrace->getMutex());
Pimpl::mTrace->send(str.str(), level);
}
void chronometer_t::event_dumb(boost::format const& params) {
if (is_dumb) {
if (!log_ptr) {
log_ptr = logger::instance();
}
if (log_ptr) {
log_ptr->debug("raw/begin/" + name, params.str());
}
}
}
void Log::Critical( boost::format &fmt )
{
int ConsoleLogLevel = sConfig.GetIntDefault("Log.ConsoleLogLevel",LOGLEVEL_INFO);
int FileLogLevel = sConfig.GetIntDefault("Log.FileLogLevel",LOGLEVEL_WARNING);
if (ConsoleLogLevel >= LOGLEVEL_CRITICAL || FileLogLevel >= LOGLEVEL_CRITICAL)
{
Critical(fmt.str());
}
}
void Log::Debug( boost::format &fmt )
{
int ConsoleLogLevel = sConfig.GetIntDefault("Log.ConsoleLogLevel",LOGLEVEL_INFO);
int FileLogLevel = sConfig.GetIntDefault("Log.FileLogLevel",LOGLEVEL_WARNING);
if (ConsoleLogLevel >= LOGLEVEL_DEBUG || FileLogLevel >= LOGLEVEL_DEBUG)
{
Debug(fmt.str());
}
}
void Log::Error( boost::format &fmt )
{
int ConsoleLogLevel = sConfig.GetIntDefault("Log.ConsoleLogLevel",LOGLEVEL_INFO);
int FileLogLevel = sConfig.GetIntDefault("Log.FileLogLevel",LOGLEVEL_WARNING);
if (ConsoleLogLevel >= LOGLEVEL_ERROR || FileLogLevel >= LOGLEVEL_ERROR)
{
Error(fmt.str());
}
}
int main(int argc, char** argv)
{
ros::init(argc, argv, "image_saver", ros::init_options::AnonymousName);
ros::NodeHandle nh;
g_format.parse("left%04i.%s");
image_transport::ImageTransport it(nh);
std::string topic = nh.resolveName("image");
image_transport::CameraSubscriber sub = it.subscribeCamera(topic, 1, &callback);
ros::spin();
}
bool saveImage(cv::Mat image, std::string &filename, bool depth = false) {
if (!image.empty()) {
try {
filename = (g_format).str();
} catch (...) { g_format.clear(); }
try {
filename = (g_format % path).str();
} catch (...) { g_format.clear(); }
try {
filename = (g_format % path % count_).str();
} catch (...) { g_format.clear(); }
try {
filename = (g_format % path % count_ % "jpg").str();
} catch (...) { g_format.clear(); }
try {
if(!depth){
filename = (g_format % path % count_ % control % "jpg").str();
}else{
filename = (g_format % path_depth % count_ % control % "jpg").str();
}
} catch (...) { g_format.clear(); }
if ( save_all_image || save_image_service ) {
try{
cv::imwrite(filename, image);
ROS_INFO("Saved image %s", filename.c_str());
save_image_service = false;
}catch(runtime_error& ex){
fprintf(stderr, "Exception converting image to PNG format: %s\n", ex.what());
return false;
}
} else {
return false;
}
} else {
ROS_WARN("Couldn't save image, no data!");
return false;
}
return true;
}
void ImageNodelet::onInit()
{
ros::NodeHandle nh = getNodeHandle();
ros::NodeHandle local_nh = getPrivateNodeHandle();
// Command line argument parsing
const std::vector<std::string>& argv = getMyArgv();
// First positional argument is the transport type
std::string transport;
local_nh.param("image_transport", transport, std::string("raw"));
for (int i = 0; i < (int)argv.size(); ++i)
{
if (argv[i][0] != '-')
{
transport = argv[i];
break;
}
}
NODELET_INFO_STREAM("Using transport \"" << transport << "\"");
// Internal option, should be used only by the image_view node
bool shutdown_on_close = std::find(argv.begin(), argv.end(),
"--shutdown-on-close") != argv.end();
// Default window name is the resolved topic name
std::string topic = nh.resolveName("image");
local_nh.param("window_name", window_name_, topic);
bool autosize;
local_nh.param("autosize", autosize, false);
std::string format_string;
local_nh.param("filename_format", format_string, std::string("frame%04i.jpg"));
filename_format_.parse(format_string);
cv::namedWindow(window_name_, autosize ? cv::WND_PROP_AUTOSIZE : 0);
cv::setMouseCallback(window_name_, &ImageNodelet::mouseCb, this);
#ifdef HAVE_GTK
// Register appropriate handler for when user closes the display window
GtkWidget *widget = GTK_WIDGET( cvGetWindowHandle(window_name_.c_str()) );
if (shutdown_on_close)
g_signal_connect(widget, "destroy", G_CALLBACK(destroyNode), NULL);
else
g_signal_connect(widget, "destroy", G_CALLBACK(destroyNodelet), &sub_);
#endif
// Start the OpenCV window thread so we don't have to waitKey() somewhere
startWindowThread();
image_transport::ImageTransport it(nh);
image_transport::TransportHints hints(transport, ros::TransportHints(), getPrivateNodeHandle());
sub_ = it.subscribe(topic, 1, &ImageNodelet::imageCb, this, hints);
}
formatter()
{
try{
fmt_ = boost::format(getenv("IPI_LOG_FORMAT") ? getenv("IPI_LOG_FORMAT") : "[%1%] ");
}catch(const std::exception& e){
std::cerr << "Could not used IPI_LOG_FORMAT!\n" << fmt_ << "\n" << e.what() << std::endl;
abort();
}
fmt_.exceptions( boost::io::all_error_bits ^ ( boost::io::too_many_args_bit
| boost::io::too_few_args_bit ) );
}
int main(int argc, char **argv)
{
ros::init(argc, argv, "image_view", ros::init_options::AnonymousName);
if (ros::names::remap("image") == "image") {
ROS_WARN("Topic 'image' has not been remapped! Typical command-line usage:\n"
"\t$ rosrun image_view image_view image:=<image topic> [transport]");
}
ros::NodeHandle nh;
ros::NodeHandle local_nh("~");
// Default window name is the resolved topic name
std::string topic = nh.resolveName("image");
local_nh.param("window_name", g_window_name, topic);
std::string format_string;
local_nh.param("filename_format", format_string, std::string("frame%04i.jpg"));
g_filename_format.parse(format_string);
// Handle window size
bool autosize;
local_nh.param("autosize", autosize, false);
cv::namedWindow(g_window_name, autosize ? (CV_WINDOW_AUTOSIZE | CV_WINDOW_KEEPRATIO | CV_GUI_EXPANDED) : 0);
cv::setMouseCallback(g_window_name, &mouseCb);
// Start the OpenCV window thread so we don't have to waitKey() somewhere
cv::startWindowThread();
// Handle transport
// priority:
// 1. command line argument
// 2. rosparam '~image_transport'
std::string transport;
local_nh.param("image_transport", transport, std::string("raw"));
ros::V_string myargv;
ros::removeROSArgs(argc, argv, myargv);
for (size_t i = 1; i < myargv.size(); ++i) {
if (myargv[i][0] != '-') {
transport = myargv[i];
break;
}
}
ROS_INFO_STREAM("Using transport \"" << transport << "\"");
image_transport::ImageTransport it(nh);
image_transport::TransportHints hints(transport, ros::TransportHints(), local_nh);
image_transport::Subscriber sub = it.subscribe(topic, 1, imageCb, hints);
ros::spin();
cv::destroyWindow(g_window_name);
return 0;
}
bool saveImage(const sensor_msgs::ImageConstPtr& image_msg, std::string &filename) {
cv::Mat image;
try
{
image = cv_bridge::toCvShare(image_msg, encoding)->image;
} catch(cv_bridge::Exception)
{
ROS_ERROR("Unable to convert %s image to bgr8", image_msg->encoding.c_str());
return false;
}
if (!image.empty()) {
try {
filename = (g_format).str();
} catch (...) { g_format.clear(); }
try {
filename = (g_format % count_).str();
} catch (...) { g_format.clear(); }
try {
filename = (g_format % count_ % "jpg").str();
} catch (...) { g_format.clear(); }
if ( save_all_image || save_image_service ) {
cv::imwrite(filename, image);
ROS_INFO("Saved image %s", filename.c_str());
save_image_service = false;
} else {
return false;
}
} else {
ROS_WARN("Couldn't save image, no data!");
return false;
}
return true;
}
void ExtractNeighborsWorkflow::scanMaskFile(
const reference::SortedReferenceMetadata::MaskFile &maskFile,
const std::vector<uint64_t> &contigOffsets,
const std::vector<unsigned> &karyotypes,
std::vector<bool> &neighbors,
std::vector<bool> &highRepeats)
{
if (!exists(maskFile.path))
{
const boost::format message = boost::format("Mask file %s does not exist: %s") % maskFile.path;
BOOST_THROW_EXCEPTION(common::IoException(ENOENT, message.str()));
}
std::ifstream maskInput(maskFile.path.c_str());
if (!maskInput)
{
const boost::format message = boost::format("Failed to open mask file %s for reading: %s") % maskFile.path % strerror(errno);
BOOST_THROW_EXCEPTION(common::IoException(errno, message.str()));
}
std::size_t scannedKmers = 0, maskNeighbors = 0, maskNonHighRepeats = 0;
while(maskInput)
{
reference::ReferenceKmer<KmerT> referenceKmer;
if (maskInput.read(reinterpret_cast<char *>(&referenceKmer), sizeof(referenceKmer)))
{
++scannedKmers;
const reference::ReferencePosition pos = referenceKmer.getReferencePosition();
if (!pos.isTooManyMatch())
{
const reference::ReferencePosition translatedPos = pos.translateContig(karyotypes);
if (translatedPos.hasNeighbors())
{
neighbors.at(contigOffsets.at(translatedPos.getContigId()) + translatedPos.getPosition()) = true;
++maskNeighbors;
}
if (!highRepeats.empty())
{
highRepeats.at(contigOffsets.at(translatedPos.getContigId()) + translatedPos.getPosition()) = false;
}
++maskNonHighRepeats;
}
}
}
if (!maskInput.eof())
{
const boost::format message = boost::format("Failed to scan %s to the end") % maskFile.path % strerror(errno);
BOOST_THROW_EXCEPTION(common::IoException(errno, message.str()));
}
else
{
ISAAC_THREAD_CERR << "Scanning " << maskFile.path << " found " << scannedKmers << " kmers of which " <<
maskNeighbors << " neighbors and " << (scannedKmers - maskNonHighRepeats) << " high repeats" << std::endl;
}
}
ExtractImages(const ros::NodeHandle& nh, const std::string& transport)
: filename_format_(""), count_(0), _time(ros::Time::now().toSec())
{
std::string topic = nh.resolveName("image");
ros::NodeHandle local_nh("~");
std::string format_string;
local_nh.param("filename_format", format_string, std::string("frame%05i.png"));
filename_format_.parse(format_string);
local_nh.param("sec_per_frame", sec_per_frame_, 0.1);
image_transport::ImageTransport it(nh);
sub_ = it.subscribe(topic, 1, &ExtractImages::image_cb, this, transport);
#if defined(_VIDEO)
video_writer = 0;
#endif
ROS_INFO("Initialized sec per frame to %f", sec_per_frame_);
}
int main(int argc, char** argv)
{
ros::init(argc, argv, "image_saver", ros::init_options::AnonymousName);
ros::NodeHandle nh;
image_transport::ImageTransport it(nh);
std::string topic = nh.resolveName("image");
Callbacks callbacks;
// Useful when CameraInfo is being published
image_transport::CameraSubscriber sub_image_and_camera = it.subscribeCamera(topic, 1,
&Callbacks::callbackWithCameraInfo,
&callbacks);
// Useful when CameraInfo is not being published
image_transport::Subscriber sub_image = it.subscribe(
topic, 1, boost::bind(&Callbacks::callbackWithoutCameraInfo, &callbacks, _1));
ros::NodeHandle local_nh("~");
std::string format_string;
local_nh.param("filename_format", format_string, std::string("left%04i.%s"));
local_nh.param("encoding", encoding, std::string("bgr8"));
local_nh.param("save_all_image", save_all_image, true);
local_nh.param("request_start_end", request_start_end, false);
g_format.parse(format_string);
ros::ServiceServer save = local_nh.advertiseService ("save", service);
if (request_start_end && !save_all_image)
ROS_WARN("'request_start_end' is true, so overwriting 'save_all_image' as true");
// FIXME(unkown): This does not make services appear
// if (request_start_end) {
ros::ServiceServer srv_start = local_nh.advertiseService(
"start", &Callbacks::callbackStartSave, &callbacks);
ros::ServiceServer srv_end = local_nh.advertiseService(
"end", &Callbacks::callbackEndSave, &callbacks);
// }
ros::spin();
}
bs_system_exception::bs_system_exception (const std::string &who, error_code ec, const boost::format &message)
: bs_exception (who, message.str () + ". System error: " + system_message (ec))
{
m_err_ = ec;
}
bs_kernel_exception::bs_kernel_exception (const std::string &who, error_code ec, const boost::format &message)
: bs_exception (who, message.str () + ". BlueSky error: " + bs_error_message (ec))
{
m_err_ = ec;
}
bs_dynamic_lib_exception::bs_dynamic_lib_exception (const boost::format &who)
: bs_exception (who.str (), "System error: " + dynamic_lib_error_message ())
{
m_err_ = user_defined;
}
flowcell::Layout FastqFlowcell::createFilteredFlowcell(
const std::string &tilesFilter,
const boost::filesystem::path &baseCallsDirectory,
const bool compressed,
const unsigned laneNumberMax,
const unsigned readNameLength,
std::string useBasesMask,
const bool allowVariableFastqLength,
const char fastqQ0,
const std::string &seedDescriptor,
const unsigned seedLength,
const reference::ReferenceMetadataList &referenceMetadataList,
unsigned &firstPassSeeds)
{
FastqPathPairList flowcellFilePaths = findFastqPathPairs(compressed, laneNumberMax, baseCallsDirectory);
if (flowcellFilePaths.empty())
{
const boost::format message = boost::format("\n *** Could not find any fastq lanes in: %s ***\n") %
baseCallsDirectory;
BOOST_THROW_EXCEPTION(common::InvalidOptionException(message.str()));
}
FastqFlowcellInfo flowcellInfo = parseFastqFlowcellInfo(flowcellFilePaths, allowVariableFastqLength, fastqQ0, readNameLength);
std::vector<unsigned int> readLengths;
if (flowcellInfo.readLengths_.first)
{
readLengths.push_back(flowcellInfo.readLengths_.first);
}
if (flowcellInfo.readLengths_.second)
{
readLengths.push_back(flowcellInfo.readLengths_.second);
}
if ("default" == useBasesMask)
{
if (readLengths.size() == 1)
{
useBasesMask = "y*n";
}
else if (readLengths.size() == 2)
{
useBasesMask = "y*n,y*n";
}
else
{
const boost::format message =
boost::format("\n *** Could not guess the use-bases-mask for '%s', please supply the explicit value ***\n") %
baseCallsDirectory.string();
BOOST_THROW_EXCEPTION(common::InvalidOptionException(message.str()));
}
}
std::vector<unsigned int> readFirstCycles;
ParsedUseBasesMask parsedUseBasesMask;
alignment::SeedMetadataList seedMetadataList;
if (!readLengths.empty())
{
parsedUseBasesMask = parseUseBasesMask(readFirstCycles, readLengths, seedLength, useBasesMask, baseCallsDirectory);
seedMetadataList = parseSeedDescriptor(parsedUseBasesMask.dataReads_, seedDescriptor, seedLength, firstPassSeeds);
}
flowcell::Layout fc(baseCallsDirectory,
flowcell::Layout::Fastq,
flowcell::FastqFlowcellData(compressed, fastqQ0),
laneNumberMax,
flowcellInfo.readNameLength_,
std::vector<unsigned>(),
parsedUseBasesMask.dataReads_,
seedMetadataList, flowcellInfo.flowcellId_);
std::string regexString(tilesFilter);
std::replace(regexString.begin(), regexString.end(), ',', '|');
boost::regex re(regexString);
BOOST_FOREACH(const unsigned int lane, flowcellInfo.getLanes())
{
std::string laneString((boost::format("s_%d") % lane).str());
if (boost::regex_search(laneString, re))
{
fc.addTile(lane, 1);
}
}
return fc;
}
code_generation_error(std::string const& generator_name, boost::format const& format) noexcept
: code_generation_error(generator_name, format.str())
{}
