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Commit bfd7abd0 authored by Max Breitenfeldt's avatar Max Breitenfeldt
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Add Python communication

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.gitignore
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...@@ -75,4 +75,6 @@ bst_workspace.code-workspace ...@@ -75,4 +75,6 @@ bst_workspace.code-workspace
*.ini *.ini
*.xml *.xml
*.csv *.csv
build build/**
\ No newline at end of file .ccls-cache/**
CMakeLists.txt
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cmake_minimum_required(VERSION 3.15) cmake_minimum_required(VERSION 3.15)
exec_program("git" ${CMAKE_CURRENT_SOURCE_DIR} ARGS "describe --dirty --always --exclude '*'" OUTPUT_VARIABLE SOURCE_VERSION) exec_program("git" ${CMAKE_CURRENT_SOURCE_DIR} ARGS "describe --dirty --always --exclude '*'" OUTPUT_VARIABLE SOURCE_VERSION)
set(CMAKE_MODULE_PATH ${CMAKE_MODULE_PATH} "${CMAKE_SOURCE_DIR}/cmake/")
project(biotracker-background_subtraction_tracker project(biotracker-background_subtraction_tracker
LANGUAGES CXX LANGUAGES CXX
......
Src/CMakeLists.txt
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...@@ -4,7 +4,7 @@ ...@@ -4,7 +4,7 @@
include(biotracker-utility/TrackerPlugin) include(biotracker-utility/TrackerPlugin)
set(target biotracker-backgroundSubtraction.bio_tracker) set(target python.bio_tracker)
add_behavior_plugin(${target} add_behavior_plugin(${target}
"PluginContext.cpp" "PluginContext.cpp"
...@@ -44,4 +44,5 @@ add_behavior_plugin(${target} ...@@ -44,4 +44,5 @@ add_behavior_plugin(${target}
install(TARGETS ${target} OPTIONAL DESTINATION .) install(TARGETS ${target} OPTIONAL DESTINATION .)
find_package(Qt5 REQUIRED COMPONENTS Xml Network) find_package(Qt5 REQUIRED COMPONENTS Xml Network)
target_link_libraries (${target} Qt5::Xml Qt5::Network) find_package( ZeroMQ REQUIRED )
target_link_libraries (${target} Qt5::Xml Qt5::Network rt zmq)
Src/Model/BioTrackerTrackingAlgorithm.cpp
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#include <errno.h>
#include <fcntl.h>
#include <stdio.h>
#include <stdlib.h>
#include <string>
#include <sys/mman.h>
#include <sys/stat.h>
#include <unistd.h>
#include <iostream>
#include "BioTrackerTrackingAlgorithm.h" #include "BioTrackerTrackingAlgorithm.h"
#include <future> #include <future>
#include "TrackedComponents/TrackedComponentFactory.h" #include "TrackedComponents/TrackedComponentFactory.h"
#include <chrono> #include <chrono>
#include <zmq.hpp>
#include "json.hpp"
using json = nlohmann::json;
void* init_shm_mmap(const char *path, int len) {
int fd = shm_open(path, O_RDWR, 0);
if (fd == -1) {
throw "shm_open";
}
void *shm_buf = mmap(NULL, len,
PROT_READ | PROT_WRITE,
MAP_SHARED, fd, 0);
close(fd);
if (shm_buf == MAP_FAILED) {
throw "mmap";
}
return shm_buf;
}
BioTrackerTrackingAlgorithm::BioTrackerTrackingAlgorithm(IController *parent, IModel* parameter, IModel* trajectory) BioTrackerTrackingAlgorithm::BioTrackerTrackingAlgorithm(IController *parent, IModel* parameter, IModel* trajectory)
: IModelTrackingAlgorithm(parent) : IModelTrackingAlgorithm(parent)
...@@ -13,7 +45,6 @@ BioTrackerTrackingAlgorithm::BioTrackerTrackingAlgorithm(IController *parent, IM ...@@ -13,7 +45,6 @@ BioTrackerTrackingAlgorithm::BioTrackerTrackingAlgorithm(IController *parent, IM
_nn2d = std::make_shared<NN2dMapper>(_TrackedTrajectoryMajor); _nn2d = std::make_shared<NN2dMapper>(_TrackedTrajectoryMajor);
_bd = BlobsDetector(); _bd = BlobsDetector();
_noFish = -1; _noFish = -1;
if (_cfg->DoNetwork) { if (_cfg->DoNetwork) {
...@@ -25,8 +56,23 @@ BioTrackerTrackingAlgorithm::BioTrackerTrackingAlgorithm(IController *parent, IM ...@@ -25,8 +56,23 @@ BioTrackerTrackingAlgorithm::BioTrackerTrackingAlgorithm(IController *parent, IM
_lastImage = nullptr; _lastImage = nullptr;
_lastFramenumber = -1; _lastFramenumber = -1;
_sock = zmq::socket_t(_ctx, zmq::socket_type::req);
_sock.bind("ipc:///tmp/biotracker.python.zmq");
} }
void BioTrackerTrackingAlgorithm::request_shared_memory() {
json j = {
{ "type", "request_shared_memory" },
{ "width", _imageX },
{ "height", _imageY },
};
_sock.send(zmq::buffer(j.dump()));
auto res = _sock.recv(_zmq_msg, zmq::recv_flags::none);
auto msg = json::parse(_zmq_msg.to_string_view());
std::string shm_path = msg["path"];
_shm_img = (float*)init_shm_mmap(shm_path.c_str(), _imageX * _imageY * sizeof(float));
}
void BioTrackerTrackingAlgorithm::receiveAreaDescriptorUpdate(IModelAreaDescriptor *areaDescr) { void BioTrackerTrackingAlgorithm::receiveAreaDescriptorUpdate(IModelAreaDescriptor *areaDescr) {
_AreaInfo = areaDescr; _AreaInfo = areaDescr;
...@@ -37,114 +83,14 @@ BioTrackerTrackingAlgorithm::~BioTrackerTrackingAlgorithm() ...@@ -37,114 +83,14 @@ BioTrackerTrackingAlgorithm::~BioTrackerTrackingAlgorithm()
{ {
} }
std::vector<FishPose> BioTrackerTrackingAlgorithm::getLastPositionsAsPose() {
//TODO: This seems kinda fragile: I just assume that the tree has this very certain structure:
// Trajectory -> M Trajectories -> N TrackedElements
// For every of M Trajectories grab the last (highest index) of TrackedElements.
//TODO: If we are tracking somewhere in the middle, this is bad. Do it by id!
std::vector<FishPose> last;
for (int i = 0; i < _TrackedTrajectoryMajor->size(); i++) {
BST::TrackedTrajectory *t = dynamic_cast<BST::TrackedTrajectory *>(_TrackedTrajectoryMajor->getChild(i));
if (t && t->getValid() && !t->getFixed()) {
BST::TrackedElement *e = (BST::TrackedElement *)t->getLastChild();
last.push_back(e->getFishPose());
}
}
return last;
}
void BioTrackerTrackingAlgorithm::refreshPolygon() {
}
void BioTrackerTrackingAlgorithm::receiveParametersChanged() { void BioTrackerTrackingAlgorithm::receiveParametersChanged() {
if (_lastFramenumber >= 0 && _lastImage && !_lastImage->empty()) { if (_lastFramenumber >= 0 && _lastImage && !_lastImage->empty()) {
doTracking(_lastImage, _lastFramenumber); doTracking(_lastImage, _lastFramenumber);
} }
} }
void BioTrackerTrackingAlgorithm::sendSelectedImage(std::map<std::string, std::shared_ptr<cv::Mat>> *images) {
std::shared_ptr<cv::Mat> sendImage;
//Send forth whatever the user selected
switch (_TrackingParameter->getSendImage()) {
case 0: //Send none
//sendImage = images.find(std::string("Original"))->second;
//Q_EMIT emitCvMatA(sendImage, QString("Original"));
Q_EMIT emitChangeDisplayImage("Original");
break;
case 1:
sendImage = images->find(std::string("Binarized"))->second;
Q_EMIT emitCvMatA(sendImage, QString("Binarized"));
Q_EMIT emitChangeDisplayImage(QString("Binarized"));
break;
case 2:
sendImage = images->find(std::string("Eroded"))->second;
Q_EMIT emitCvMatA(sendImage, QString("Eroded"));
Q_EMIT emitChangeDisplayImage(QString("Eroded"));
break;
case 3:
sendImage = images->find(std::string("Dilated"))->second;
Q_EMIT emitCvMatA(sendImage, QString("Dilated"));
Q_EMIT emitChangeDisplayImage(QString("Dilated"));
break;
case 4:
sendImage = images->find(std::string("Difference"))->second;
Q_EMIT emitCvMatA(sendImage, QString("Difference"));
Q_EMIT emitChangeDisplayImage(QString("Difference"));
break;
case 5:
sendImage = images->find(std::string("Background"))->second;
Q_EMIT emitCvMatA(sendImage, QString("Background"));
Q_EMIT emitChangeDisplayImage(QString("Background"));
break;
}
}
std::vector<BlobPose> BioTrackerTrackingAlgorithm::getContourCentroids(cv::Mat& image, int minSize){
std::vector<std::vector<cv::Point> > contours;
std::vector<cv::Vec4i> hierarchy;
std::vector<BlobPose> centroids;
findContours( image, contours, hierarchy, cv::RETR_TREE, cv::CHAIN_APPROX_SIMPLE, cv::Point(0, 0) );
for(auto x: contours){
cv::Point2f c(0,0);
float i=0;
for(auto y: x){
c += cv::Point2f(y);
i++;
}
c.x = c.x / i;
c.y = c.y / i;
//cv::RotatedRect minEllipse;
cv::RotatedRect bb = minAreaRect( x );
//check if blob is in tracking area --> this can be optimized by checking earlier (only search blobs in tracking area)
if(!_AreaInfo->inTrackingArea(c)){
continue;
}
BlobPose bc(_AreaInfo->pxToCm(c), c, bb.angle, bb.size.width, bb.size.height);
centroids.push_back(bc);
}
return centroids;
}
#define EEE duration = std::chrono::duration_cast< std::chrono::milliseconds> (std::chrono::steady_clock::now() - startt); block++; std::cout << "Block " << block << ": " << duration.count() << std::endl;
#define SSS startt = std::chrono::steady_clock::now();
void BioTrackerTrackingAlgorithm::doTracking(std::shared_ptr<cv::Mat> p_image, uint framenumber) void BioTrackerTrackingAlgorithm::doTracking(std::shared_ptr<cv::Mat> p_image, uint framenumber)
{ {
//Q_EMIT emitCvMatA(p_image, QString("Original"));
//Q_EMIT emitChangeDisplayImage("Original");
//Q_EMIT emitTrackingDone(framenumber);
//return;
int block = 0;
_ipp.m_TrackingParameter = _TrackingParameter; _ipp.m_TrackingParameter = _TrackingParameter;
_lastImage = p_image; _lastImage = p_image;
_lastFramenumber = framenumber; _lastFramenumber = framenumber;
...@@ -157,77 +103,33 @@ void BioTrackerTrackingAlgorithm::doTracking(std::shared_ptr<cv::Mat> p_image, u ...@@ -157,77 +103,33 @@ void BioTrackerTrackingAlgorithm::doTracking(std::shared_ptr<cv::Mat> p_image, u
if (_imageX != p_image->size().width || _imageY != p_image->size().height) { if (_imageX != p_image->size().width || _imageY != p_image->size().height) {
_imageX = p_image->size().width; _imageX = p_image->size().width;
_imageY = p_image->size().height; _imageY = p_image->size().height;
request_shared_memory();
Q_EMIT emitDimensionUpdate(_imageX, _imageY); Q_EMIT emitDimensionUpdate(_imageX, _imageY);
} }
std::chrono::system_clock::time_point start = std::chrono::system_clock::now();
//Refuse to run tracking if we have no area info... //Refuse to run tracking if we have no area info...
if (_AreaInfo == nullptr) { if (_AreaInfo == nullptr) {
Q_EMIT emitTrackingDone(framenumber); Q_EMIT emitTrackingDone(framenumber);
return; return;
} }
cv::Mat grayscale, float_img;
//The user changed the # of fish. Reset the history and start over! cv::cvtColor(*p_image, grayscale, cv::COLOR_BGR2GRAY);
if (_noFish != _TrackedTrajectoryMajor->validCount()) { grayscale.convertTo(float_img, CV_32F);
_noFish = _TrackedTrajectoryMajor->validCount(); float *img_data = float_img.ptr<float>(0);
//resetFishHistory(_noFish); int img_data_len = float_img.cols * float_img.rows * sizeof(float);
_nn2d = std::make_shared<NN2dMapper>(_TrackedTrajectoryMajor); memcpy(_shm_img, img_data, img_data_len);
}
json j = {
if (_TrackingParameter->getResetBackground()) { { "type", "predict_frame" },
_TrackingParameter->setResetBackground(false); { "frame_id", framenumber },
_ipp.resetBackgroundImage(); };
} _sock.send(zmq::buffer(j.dump()));
auto res = _sock.recv(_zmq_msg, zmq::recv_flags::none);
//Do the preprocessing auto msg = json::parse(_zmq_msg.to_string_view());
std::map<std::string, std::shared_ptr<cv::Mat>> images = _ipp.preProcess(p_image);
std::shared_ptr<cv::Mat> dilated = images.find(std::string("Dilated"))->second;
std::shared_ptr<cv::Mat> greyMat = images.find(std::string("Greyscale"))->second;
//Find blobs via ellipsefitting
_bd.setMaxBlobSize(_TrackingParameter->getMaxBlobSize());
_bd.setMinBlobSize(_TrackingParameter->getMinBlobSize());
//std::vector<BlobPose> blobs = _bd.getPoses(*dilated, *greyMat);
std::vector<BlobPose> blobs = getContourCentroids(*dilated, 111);
// Never switch the position of the trajectories. The NN2d mapper relies on this!
// If you mess up the order, add or remove some t, then create a new mapper.
std::vector<FishPose> fish = getLastPositionsAsPose();
//Find new positions using 2D nearest neighbor
std::tuple<std::vector<FishPose>, std::vector<float>> poses = _nn2d->getNewPoses(_TrackedTrajectoryMajor, framenumber, blobs);
//Insert new poses into data structure
int trajNumber = 0;
for (int i = 0; i < _TrackedTrajectoryMajor->size(); i++) {
BST::TrackedTrajectory *t = dynamic_cast<BST::TrackedTrajectory *>(_TrackedTrajectoryMajor->getChild(i));
if (t && t->getValid() && !t->getFixed()) {
BST::TrackedElement *e = new BST::TrackedElement(t, "n.a.", t->getId());
e->setFishPose(std::get<0>(poses)[trajNumber]);
e->setTime(start);
t->add(e, framenumber);
trajNumber++;
}
}
//Send forth new positions to the robotracker, if networking is enabled
if (_TrackingParameter->getDoNetwork()){
std::vector<FishPose> ps = std::get<0>(poses);
_listener->sendPositions(framenumber, ps, std::vector<cv::Point2f>(), start);
}
sendSelectedImage(&images);
//First the user still wants to see the original image, right?
if (framenumber==1) {
Q_EMIT emitChangeDisplayImage("Original");
}
std::string newSel = _TrackingParameter->getNewSelection(); std::string newSel = _TrackingParameter->getNewSelection();
Q_EMIT emitChangeDisplayImage("Original");
Q_EMIT emitTrackingDone(framenumber); Q_EMIT emitTrackingDone(framenumber);
} }
Src/Model/BioTrackerTrackingAlgorithm.h
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...@@ -17,6 +17,7 @@ ...@@ -17,6 +17,7 @@
#include "TrackingAlgorithm/NN2dMapper.h" #include "TrackingAlgorithm/NN2dMapper.h"
#include "Interfaces/IModel/IModelAreaDescriptor.h" #include "Interfaces/IModel/IModelAreaDescriptor.h"
#include <iostream> #include <iostream>
#include <zmq.hpp>
#include "Network/TcpListener.h" #include "Network/TcpListener.h"
#include "../Config.h" #include "../Config.h"
...@@ -40,11 +41,7 @@ public Q_SLOTS: ...@@ -40,11 +41,7 @@ public Q_SLOTS:
void receiveParametersChanged(); void receiveParametersChanged();
private: private:
std::vector<BlobPose> getContourCentroids(cv::Mat& image, int minSize); void request_shared_memory();
void refreshPolygon();
void sendSelectedImage(std::map<std::string, std::shared_ptr<cv::Mat>>* images);
std::vector<FishPose> getLastPositionsAsPose();
BST::TrackedTrajectory* _TrackedTrajectoryMajor; BST::TrackedTrajectory* _TrackedTrajectoryMajor;
TrackerParameter* _TrackingParameter; TrackerParameter* _TrackingParameter;
...@@ -69,6 +66,11 @@ std::vector<BlobPose> getContourCentroids(cv::Mat& image, int minSize); ...@@ -69,6 +66,11 @@ std::vector<BlobPose> getContourCentroids(cv::Mat& image, int minSize);
std::shared_ptr<cv::Mat> _lastImage; std::shared_ptr<cv::Mat> _lastImage;
uint _lastFramenumber; uint _lastFramenumber;
Config *_cfg; Config *_cfg;
zmq::context_t _ctx;
zmq::socket_t _sock;
zmq::message_t _zmq_msg;
float *_shm_img;
}; };
#endif // BIOTRACKERTRACKINGALGORITHM_H #endif // BIOTRACKERTRACKINGALGORITHM_H
Src/Model/json.hpp 0 → 100644
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cmake/FindZeroMQ.cmake 0 → 100644
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set(PKG_CONFIG_USE_CMAKE_PREFIX_PATH ON)
find_package(PkgConfig)
pkg_check_modules(PC_LIBZMQ QUIET libzmq)
set(ZeroMQ_VERSION ${PC_LIBZMQ_VERSION})
find_library(ZeroMQ_LIBRARY NAMES libzmq.so libzmq.dylib libzmq.dll
PATHS ${PC_LIBZMQ_LIBDIR} ${PC_LIBZMQ_LIBRARY_DIRS})
find_library(ZeroMQ_STATIC_LIBRARY NAMES libzmq-static.a libzmq.a libzmq.dll.a
PATHS ${PC_LIBZMQ_LIBDIR} ${PC_LIBZMQ_LIBRARY_DIRS})
if(ZeroMQ_LIBRARY OR ZeroMQ_STATIC_LIBRARY)
set(ZeroMQ_FOUND ON)
endif()
if (TARGET libzmq)
# avoid errors defining targets twice
return()
endif()
add_library(libzmq SHARED IMPORTED)
set_property(TARGET libzmq PROPERTY INTERFACE_INCLUDE_DIRECTORIES ${PC_LIBZMQ_INCLUDE_DIRS})
set_property(TARGET libzmq PROPERTY IMPORTED_LOCATION ${ZeroMQ_LIBRARY})
add_library(libzmq-static STATIC IMPORTED ${PC_LIBZMQ_INCLUDE_DIRS})
set_property(TARGET libzmq-static PROPERTY INTERFACE_INCLUDE_DIRECTORIES ${PC_LIBZMQ_INCLUDE_DIRS})
set_property(TARGET libzmq-static PROPERTY IMPORTED_LOCATION ${ZeroMQ_STATIC_LIBRARY})
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