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Video Tracking Framework for the Analysis of Animal Behavior - Core Component

CMake 3.13% C++ 96.11% Python 0.73% C 0.04%

biotracker

biotracker_core's Introduction

README

Using BioTracker

See the wiki.

Running BioTracker from prebuild binaries:

The releases github page provides stable version. Most recent binaries can be grabbed from the pipeline.

BioTracker core application
Some trackers. For example the Background subtraction tracker

Building trackers against prebuild BioTracker

This will enable you to only build your own plugin without having to care about the robotracker toolchaining/dependencies/etc..

Download Interfaces project and add it to your toolchain (e.g. cmake prefix path)
Optional: Do the same for the utility project, if you need it
Download and install the BioTracker core application
It might be helpful to use some basic tracker as a template: https://github.com/BioroboticsLab/biotracker_sampletracker
Make sure to implement the IBehavior interface
Build
Put your artifact in the Plugins section
Run and Enjoy

Build dependencies

Building the BioTracker needs:

opencv (> 3.0)
QT (>= 5.4)
Boost
CMake (>= 3.13)
Buildtools (Tested: MSVC buildtools or g++)
recommendet: ninja

Building BioTracker (Windows x64)

The dockerfile documents the dependency installation: (includes dependencies for all projects, e.g. BioTracker, interfaces, ...)

Install and configure those dependencies. A shorthand to the dockerfile is using vcpkg Get the boost and opencv packages:
vcpkg install boost-property-tree:x64-windows-14.16 boost-bimap:x64-windows-14.16 boost-assign:x64-windows-14.16 boost-system:x64-windows-14.16 boost-filesystem:x64-windows-14.16 boost-chrono:x64-windows-14.16 boost-timer:x64-windows-14.16 boost-program-options:x64-windows-14.16
vcpkg install openblas:x64-windows-14.16 opencv[opengl,ffmpeg,ximea,cuda]:x64-windows-14.16
... and Qt systemwide using Qt5_dir
Now call cmake with some switches to include vcpkg: -DCMAKE_TOOLCHAIN_FILE=C:/vcpkg/scripts/buildsystems/vcpkg.cmake -DVCPKG_TARGET_TRIPLET=x64-windows-14.16
... and build. Proceed withe the build steps as in the linux section.

Building BioTracker (Linux)

The dockerfile documents the dependency installation: (includes dependencies for all projects, e.g. BioTracker, interfaces, ...)
Having set all the library paths you can build it just like any cmake project. It's split into a few repositories for modularization. Clone, build and install them in order: Interfaces, Utility, Behavior loader, the BioTracker itself and any tracking plugin of your liking, eg. the Background subtraction tracker.

Building BioTracker (OSX)

Technically the BioTracker should build using the CMake toolchain and run on OSX. This is not officially supported, though.

biotracker_core's People

Contributors

Stargazers

Watchers

Forkers

walachey anjoer failure-to-thrive kehan777 junxen evermountaintech mxbrt

biotracker_core's Issues

Biotracker / TrackingThread status not in sync

Both the Biotracker facade as well as the TrackingThread keep "track" of the Tracking Threads status which just makes no sense thus we should unify their functionality

ZMQ: kill child processes on crash

Add handler that kills possible child processes when the parent (the biotracker) crashes.

ProtoBuf for zmq

We should consider using ProtoBuf to send messages from server to client with zmq

provide paintOverlay with the tracker view

tbd

Split into Core and GUI repositories

The biotracker repository should be split into two parts for the following reasons:

Multiple applications in the Lab depend on some parts of the BioTracker, but not on the GUI component.
Seperating the two parts would lead to a cleaner codebase and make testing (of the core components) easier
The TrackingAlgorithms should only (explicitly) depend on the core components
Integration with cpm would be easier

Details for splitting a git repository can be found here:

Qt5 static compilation

As we link boost statically now because of issue #25 we might think about linking Qt statically as well. We should consider this for example.. http://stackoverflow.com/questions/17259277/cmake-static-link-qt5

Add numpy to CMakeList

add the moment numpy gets included without the help of cmake. We need to change that asap

zmq: unify track, paint and paintOverlay

The zmq client functions for paint, track and paintOverlay can be unified in one function to simplify the API. The tracking algorithm should "store" the paint results then and paint them when the appropriate events are called.

zmq: message type

Implementation of message types for simple zmq-server-client communication as described in the documentation.

Ship Python

We need to agree upon what is the best way to portably ship BioTracker with Python.

http://stackoverflow.com/questions/11275407/embed-python-numpy-matplotlib-in-a-c-qt-application

My current suggestion would be: We ship the Interpreter + std lib + numpy + opencv ourselfs, so we are independent of clients Python installations. I guess this would also imply that we will need some sort of installer to put all files in the right place..

connect the tracker "update" event to the frontend

tbd

zmq: shutdown function

Implement the shutdown function for the zmq tracker system. This is related to Bug #21

Replace boost fs with native fs

To remove dependencies

Implement Camera Capture

tbd

QPainter and TextureLoading

There is an order problem with loading the texture (aka a cv::Mat) and drawing to QPainter: When we draw to the QPainter first it is not possible to load a texture anymore, so we have to load the matrix prior to use QPainter. This creates a problem when we want to both change the matrix (e.g. change color space) AND want to use the QPainter. I see 3 possible solutions:

(i) We only allow the tracker to use EITHER the QPainter or set a new matrix
(ii) We create a new object that buffers the QPainter calls without executing them and then the tracking thread executes the actual QPainter calls AFTER the texture is loaded
(iii) We revert the changes made #17 , provide two functions for PAINT and PAINT_OVERLAY and make sure that PAINT_OVERLAY always gets called after PAINT.

My favorite so far is (iii)...

Unify namespaces

Some classes (like Settings) do not use proper namespaces while others do. We should make sure all classes use proper namespacing.

zmq: Implement zmq paint function

implement the full paint-roundtrip between biotracker and zmq client

Segfault when closing application

Here's the stack trace. Seems to be caused by the QOpenGLDebugLogger dtor. Most likely, QOpenGLDebugLogger is destroyed after the QOpenGLContext:

==21697==ERROR: AddressSanitizer: SEGV on unknown address 0x000000000008 (pc 0x7fbae6b92634 bp 0x7fffa0da5390 sp 0x7fffa0da5230 T0)
#0 0x7fbae6b92633 in QOpenGLContext::functions() const (/usr/lib/libQt5Gui.so.5+0x143633)
#1 0x7fbae6e9e519 in QOpenGLDebugLogger::stopLogging() (/usr/lib/libQt5Gui.so.5+0x44f519)
#2 0x7fbae6e9eaec (/usr/lib/libQt5Gui.so.5+0x44faec)
#3 0x7fbae662bfe9 in QMetaObject::activate(QObject_, int, int, void__) (/usr/lib/libQt5Core.so.5+0x2c9fe9)
#4 0x7fbae6b959a7 in QOpenGLContext::destroy() (/usr/lib/libQt5Gui.so.5+0x1469a7)
#5 0x7fbae6b95e86 in QOpenGLContext::~QOpenGLContext() (/usr/lib/libQt5Gui.so.5+0x146e86)
#6 0x7fbae6b95e98 in QOpenGLContext::~QOpenGLContext() (/usr/lib/libQt5Gui.so.5+0x146e98)
#7 0x7fbae739981b (/usr/lib/libQt5Widgets.so.5+0x1de81b)
#8 0x7fbae739a0b2 (/usr/lib/libQt5Widgets.so.5+0x1df0b2)
#9 0x7fbae66342c7 in QObject::~QObject() (/usr/lib/libQt5Core.so.5+0x2d22c7)
#10 0x7fbae737581e in QWidget::~QWidget() (/usr/lib/libQt5Widgets.so.5+0x1ba81e)
#11 0x626089 in BioTracker::Gui::VideoView::~VideoView() /home/ben/tmp/biorobotics-dev-environment/build/Debug/biotracker_gui/biotracker/../../../../source/biotracker_gui/biotracker/VideoView.h:23
#12 0x6260f1 in BioTracker::Gui::VideoView::~VideoView() /home/ben/tmp/biorobotics-dev-environment/build/Debug/biotracker_gui/biotracker/../../../../source/biotracker_gui/biotracker/VideoView.h:23
#13 0x58884b in std::default_deleteBioTracker::Gui::VideoView::operator()(BioTracker::Gui::VideoView_) const /usr/include/c++/5.2.0/bits/unique_ptr.h:76
#14 0x588166 in std::unique_ptr<BioTracker::Gui::VideoView, std::default_deleteBioTracker::Gui::VideoView >::~unique_ptr() /usr/include/c++/5.2.0/bits/unique_ptr.h:236
#15 0x58778d in BioTracker::Gui::MainWindow::~MainWindow() /home/ben/tmp/biorobotics-dev-environment/build/Debug/biotracker_gui/biotracker/../../../../source/biotracker_gui/biotracker/MainWindow.h:18
#16 0x587c51 in BioTracker::Gui::Gui::~Gui() /home/ben/tmp/biorobotics-dev-environment/build/Debug/biotracker_gui/biotracker/../../../../source/biotracker_gui/biotracker/Gui.h:14
#17 0x57f3a9 in main /home/ben/tmp/biorobotics-dev-environment/source/biotracker_gui/biotracker/src/main.cpp:31
#18 0x7fbae105660f in __libc_start_main (/usr/lib/libc.so.6+0x2060f)
#19 0x57f008 in _start (/home/ben/tmp/biorobotics-dev-environment/build/Debug/biotracker_gui/biotracker/BioTracker+0x57f008)

std::string to std::__cxx11::string

some auto-generated functions add 'wrong' data type

Render bugs when drawing text with QPainter

Cmake: set qt5.4 as dependencies

Currently the build "works" with all versions of qt but we need qt54>=

Fix zmq entry for CMake to work on all operation systems

I did not confirm but I got a hunch that the current zmq-add functionality in cmake will only work on linux due to the hint-folders. We should make this platform-independent as soon as needed.

c6e42a2

using zmq for interop with scripting languages

To simplify the hassle with embedded scripting environments we might take a look on zmq and make our tool interop with scripts on this way.

I wrote a naive performance test for a stream of images of size 1024x768 and so far I get 4 - 6 ms for a full roundtrip (sender -> receiver -> sender) including encoding the numpy array and decoding it on the other end. We should see if we can improve this (use different socket type etc) or if it is a lost case from the beginning

Remove QWidget parent from TrackingThread

as we use TrackingThreads only as shared pointers we do not need the QWidget parent and thus we can make the Tracker much simpler and easier to use

compilation fails with clang 3.7.0

[23:26]-leon@tpad:bioroboticslab/biotracker_core/build-clang $ cmake -DCMAKE_CXX_COMPILER=/usr/bin/clang++ -DCMAKE_BUILD_TYPE=Release ..                                  
-- Found Git: /usr/bin/git (found version "2.6.2") 
-- Cloning repo (https://github.com/iauns/cpm)
-- Cloning git repo (https://github.com/BioroboticsLab/cpm_cereal @ 874092ae503eec016192ddd6ff17ae23839085be)
-- Failed to fetch repository 'https://github.com/BioroboticsLab/cpm_cereal'. Skipping fetch.
-- Cloning git repo (https://github.com/USCiLab/cereal.git @ v1.1.2)
-- Cloning git repo (https://github.com/BioroboticsLab/cmakeconfig @ master)
CMake Warning (dev) at build-clang/cpm-packages/CPM.cmake:667 (set):
  Cannot set "CPM_EXPORTED_MODULES": current scope has no parent.
Call Stack (most recent call first):
  CMakeLists.txt:54 (CPM_InitModule)
This warning is for project developers.  Use -Wno-dev to suppress it.

CMake Warning (dev) at build-clang/cpm-packages/CPM.cmake:673 (set):
  Cannot set "CPM_ADDITIONAL_DEFINITIONS": current scope has no parent.
Call Stack (most recent call first):
  CMakeLists.txt:54 (CPM_InitModule)
This warning is for project developers.  Use -Wno-dev to suppress it.

-- Found OpenGL: /usr/lib64/libGL.so  
-- Looking for pthread.h
-- Looking for pthread.h - found
-- Looking for pthread_create
-- Looking for pthread_create - not found
-- Looking for pthread_create in pthreads
-- Looking for pthread_create in pthreads - not found
-- Looking for pthread_create in pthread
-- Looking for pthread_create in pthread - found
-- Found Threads: TRUE  
-- Boost version: 1.59.0
-- Found the following Boost libraries:
--   filesystem
--   serialization
--   system
-- Found PythonLibs: /usr/lib64/libpython3.5m.so (found version "3.5.0") 
CMake Warning (dev) at build-clang/cpm-packages/CPM.cmake:770 (set):
  Cannot set "CPM_ADDITIONAL_DEFINITIONS": current scope has no parent.
Call Stack (most recent call first):
  CMakeLists.txt:82 (CPM_ExportAdditionalDefinition)
This warning is for project developers.  Use -Wno-dev to suppress it.

-- Found Doxygen: /usr/bin/doxygen (found version "1.8.10") 
-- Configuring done
-- Generating done
-- Build files have been written to: /home/leon/uni/bioroboticslab/biotracker_core/build-clang
[23:27]-leon@tpad:bioroboticslab/biotracker_core/build-clang % mj                                                              [0]
Scanning dependencies of target BioTrackerLib_automoc
[  5%] Automatic moc for target BioTrackerLib
Generating moc_BioTrackerApp.cpp
Generating moc_Registry.cpp
Generating moc_TrackingAlgorithm.cpp
Generating moc_TrackingThread.cpp
[  5%] Built target BioTrackerLib_automoc
Scanning dependencies of target BioTrackerLib
[ 11%] Building CXX object biotracker/CMakeFiles/BioTrackerLib.dir/src/settings/StringTranslator.cpp.o
[ 17%] Building CXX object biotracker/CMakeFiles/BioTrackerLib.dir/src/settings/SystemCompatibilityCheck.cpp.o
[ 23%] Building CXX object biotracker/CMakeFiles/BioTrackerLib.dir/src/settings/Settings.cpp.o
[ 29%] Building CXX object biotracker/CMakeFiles/BioTrackerLib.dir/src/Registry.cpp.o
[ 35%] Building CXX object biotracker/CMakeFiles/BioTrackerLib.dir/src/serialization/ObjectModel.cpp.o
[ 41%] Building CXX object biotracker/CMakeFiles/BioTrackerLib.dir/src/serialization/TrackedObject.cpp.o
[ 47%] Building CXX object biotracker/CMakeFiles/BioTrackerLib.dir/src/util/CvHelper.cpp.o
[ 52%] Building CXX object biotracker/CMakeFiles/BioTrackerLib.dir/src/util/imagePreProcessor/ImagePreProcessor.cpp.o
[ 58%] Building CXX object biotracker/CMakeFiles/BioTrackerLib.dir/src/util/stringTools.cpp.o
[ 64%] Building CXX object biotracker/CMakeFiles/BioTrackerLib.dir/src/TrackingAlgorithm.cpp.o
[ 70%] Building CXX object biotracker/CMakeFiles/BioTrackerLib.dir/src/BioTrackerApp.cpp.o
[ 76%] Building CXX object biotracker/CMakeFiles/BioTrackerLib.dir/src/ImageStream.cpp.o
/home/leon/uni/bioroboticslab/biotracker_core/biotracker/src/ImageStream.cpp:274:45: warning: unused parameter 'frame_number'
      [-Wunused-parameter]
    virtual bool setFrameNumber_impl(size_t frame_number) override {
                                            ^
[ 82%] Building CXX object biotracker/CMakeFiles/BioTrackerLib.dir/src/TextureObject.cpp.o
1 warning generated.
[ 88%] Building CXX object biotracker/CMakeFiles/BioTrackerLib.dir/src/TrackingThread.cpp.o
[ 94%] Building CXX object biotracker/CMakeFiles/BioTrackerLib.dir/BioTrackerLib_automoc.cpp.o
In file included from /home/leon/uni/bioroboticslab/biotracker_core/biotracker/src/BioTrackerApp.cpp:1:
In file included from /home/leon/uni/bioroboticslab/biotracker_core/biotracker/BioTrackerApp.h:12:
/home/leon/uni/bioroboticslab/biotracker_core/biotracker/TrackingThread.h:72:20: error: empty paragraph passed to '@param' command
      [-Werror,-Wdocumentation]
     * @param device
       ~~~~~~~~~~~~^
/home/leon/uni/bioroboticslab/biotracker_core/biotracker/TrackingThread.h:73:21: error: empty paragraph passed to '@param' command
      [-Werror,-Wdocumentation]
     * @param painter
       ~~~~~~~~~~~~~^
/home/leon/uni/bioroboticslab/biotracker_core/biotracker/TrackingThread.h:79:15: error: empty paragraph passed to '@return' command
      [-Werror,-Wdocumentation]
     * @return
       ~~~~~~~^
In file included from /home/leon/uni/bioroboticslab/biotracker_core/biotracker/src/BioTrackerApp.cpp:1:
/home/leon/uni/bioroboticslab/biotracker_core/biotracker/BioTrackerApp.h:79:20: error: empty paragraph passed to '@param' command
      [-Werror,-Wdocumentation]
     * @param device
       ~~~~~~~~~~~~^
/home/leon/uni/bioroboticslab/biotracker_core/biotracker/BioTrackerApp.h:80:21: error: empty paragraph passed to '@param' command
      [-Werror,-Wdocumentation]
     * @param painter
       ~~~~~~~~~~~~~^
/home/leon/uni/bioroboticslab/biotracker_core/biotracker/BioTrackerApp.h:116:21: error: empty paragraph passed to '@param' command
      [-Werror,-Wdocumentation]
     * @param enabled
       ~~~~~~~~~~~~~^
/home/leon/uni/bioroboticslab/biotracker_core/biotracker/BioTrackerApp.h:174:18: error: empty paragraph passed to '@param' command
      [-Werror,-Wdocumentation]
     * @param path
       ~~~~~~~~~~^
7 errors generated.
biotracker/CMakeFiles/BioTrackerLib.dir/build.make:302: recipe for target 'biotracker/CMakeFiles/BioTrackerLib.dir/src/BioTrackerApp.cpp.o' failed
make[2]: *** [biotracker/CMakeFiles/BioTrackerLib.dir/src/BioTrackerApp.cpp.o] Error 1
make[2]: *** Waiting for unfinished jobs....
In file included from /home/leon/uni/bioroboticslab/biotracker_core/biotracker/src/TrackingThread.cpp:1:
/home/leon/uni/bioroboticslab/biotracker_core/biotracker/TrackingThread.h:72:20: error: empty paragraph passed to '@param' command
      [-Werror,-Wdocumentation]
     * @param device
       ~~~~~~~~~~~~^
/home/leon/uni/bioroboticslab/biotracker_core/biotracker/TrackingThread.h:73:21: error: empty paragraph passed to '@param' command
      [-Werror,-Wdocumentation]
     * @param painter
       ~~~~~~~~~~~~~^
/home/leon/uni/bioroboticslab/biotracker_core/biotracker/TrackingThread.h:79:15: error: empty paragraph passed to '@return' command
      [-Werror,-Wdocumentation]
     * @return
       ~~~~~~~^
In file included from /home/leon/uni/bioroboticslab/biotracker_core/build-clang/biotracker/BioTrackerLib_automoc.cpp:2:
In file included from /home/leon/uni/bioroboticslab/biotracker_core/build-clang/biotracker/moc_BioTrackerApp.cpp:9:
In file included from /home/leon/uni/bioroboticslab/biotracker_core/build-clang/biotracker/../../biotracker/BioTrackerApp.h:12:
/home/leon/uni/bioroboticslab/biotracker_core/biotracker/TrackingThread.h:72:20: error: empty paragraph passed to '@param' command
      [-Werror,-Wdocumentation]
     * @param device
       ~~~~~~~~~~~~^
/home/leon/uni/bioroboticslab/biotracker_core/biotracker/TrackingThread.h:73:21: error: empty paragraph passed to '@param' command
      [-Werror,-Wdocumentation]
     * @param painter
       ~~~~~~~~~~~~~^
/home/leon/uni/bioroboticslab/biotracker_core/biotracker/TrackingThread.h:79:15: error: empty paragraph passed to '@return' command
      [-Werror,-Wdocumentation]
     * @return
       ~~~~~~~^
/home/leon/uni/bioroboticslab/biotracker_core/biotracker/src/TrackingThread.cpp:43:55: warning: unused parameter 'context'
      [-Wunused-parameter]
void TrackingThread::initializeOpenGL(QOpenGLContext *context,
                                                      ^
/home/leon/uni/bioroboticslab/biotracker_core/biotracker/src/TrackingThread.cpp:204:13: error: reading variable 'm_tracker'
      requires holding mutex 'm_trackerMutex' [-Werror,-Wthread-safety-analysis]
        if (m_tracker) {
            ^
/home/leon/uni/bioroboticslab/biotracker_core/biotracker/src/TrackingThread.cpp:205:13: error: reading variable 'm_tracker'
      requires holding mutex 'm_trackerMutex' [-Werror,-Wthread-safety-analysis]
            m_tracker->setCurrentFrameNumber(frameNumber);
            ^
/home/leon/uni/bioroboticslab/biotracker_core/biotracker/src/TrackingThread.cpp:213:13: error: reading variable 'm_tracker'
      requires holding mutex 'm_trackerMutex' [-Werror,-Wthread-safety-analysis]
        if (m_tracker) {
            ^
/home/leon/uni/bioroboticslab/biotracker_core/biotracker/src/TrackingThread.cpp:214:13: error: reading variable 'm_tracker'
      requires holding mutex 'm_trackerMutex' [-Werror,-Wthread-safety-analysis]
            m_tracker->setCurrentFrameNumber(m_imageStream->currentFrameNumber());
            ^
/home/leon/uni/bioroboticslab/biotracker_core/biotracker/src/TrackingThread.cpp:337:13: error: reading variable 'm_tracker'
      requires holding mutex 'm_trackerMutex' [-Werror,-Wthread-safety-analysis]
        if (m_tracker) {
            ^
/home/leon/uni/bioroboticslab/biotracker_core/biotracker/src/TrackingThread.cpp:338:13: error: reading variable 'm_tracker'
      requires holding mutex 'm_trackerMutex' [-Werror,-Wthread-safety-analysis]
            m_tracker.get()->paint(proxy, &painter);
            ^
In file included from /home/leon/uni/bioroboticslab/biotracker_core/build-clang/biotracker/BioTrackerLib_automoc.cpp:2:
In file included from /home/leon/uni/bioroboticslab/biotracker_core/build-clang/biotracker/moc_BioTrackerApp.cpp:9:
/home/leon/uni/bioroboticslab/biotracker_core/build-clang/biotracker/../../biotracker/BioTrackerApp.h:79:20: error: empty paragraph
      passed to '@param' command [-Werror,-Wdocumentation]
     * @param device
       ~~~~~~~~~~~~^
/home/leon/uni/bioroboticslab/biotracker_core/build-clang/biotracker/../../biotracker/BioTrackerApp.h:80:21: error: empty paragraph
      passed to '@param' command [-Werror,-Wdocumentation]
     * @param painter
       ~~~~~~~~~~~~~^
/home/leon/uni/bioroboticslab/biotracker_core/build-clang/biotracker/../../biotracker/BioTrackerApp.h:116:21: error: empty
      paragraph passed to '@param' command [-Werror,-Wdocumentation]
     * @param enabled
       ~~~~~~~~~~~~~^
/home/leon/uni/bioroboticslab/biotracker_core/build-clang/biotracker/../../biotracker/BioTrackerApp.h:174:18: error: empty
      paragraph passed to '@param' command [-Werror,-Wdocumentation]
     * @param path
       ~~~~~~~~~~^
1 warning and 9 errors generated.
biotracker/CMakeFiles/BioTrackerLib.dir/build.make:374: recipe for target 'biotracker/CMakeFiles/BioTrackerLib.dir/src/TrackingThread.cpp.o' failed
make[2]: *** [biotracker/CMakeFiles/BioTrackerLib.dir/src/TrackingThread.cpp.o] Error 1
7 errors generated.
biotracker/CMakeFiles/BioTrackerLib.dir/build.make:398: recipe for target 'biotracker/CMakeFiles/BioTrackerLib.dir/BioTrackerLib_automoc.cpp.o' failed
make[2]: *** [biotracker/CMakeFiles/BioTrackerLib.dir/BioTrackerLib_automoc.cpp.o] Error 1
CMakeFiles/Makefile2:186: recipe for target 'biotracker/CMakeFiles/BioTrackerLib.dir/all' failed
make[1]: *** [biotracker/CMakeFiles/BioTrackerLib.dir/all] Error 2
Makefile:127: recipe for target 'all' failed
make: *** [all] Error 2
[23:28]-leon@tpad:bioroboticslab/biotracker_core/build-clang % clang --version                                                 [2]
clang version 3.7.0 (tags/RELEASE_370/final)
Target: x86_64-unknown-linux-gnu
Thread model: posix
[23:29]-leon@tpad:bioroboticslab/biotracker_core/build-clang %

Implement Geometry config

tbd

Multiple copies of the Grid3D class

The Grid3D Class needs the biotracker and the pipeline.
As the biotracker and the pipeline are two independent modules, it cannot belong to either of them.
This has lead to the strange situation, that every package that needs the Grid3D class, has its own
copy.

A list of all Grid3D class copies:

https://github.com/berleon/pybeesgrid/blob/master/src/Grid3D.h
https://github.com/BioroboticsLab/parameteroptimization/blob/master/parameteroptimization/Grid3D.h
https://github.com/BioroboticsLab/groundtruthConvert/blob/master/groundtruthConvert/Grid3D.h
There should also be a copy in the ground truth creation module.

There are twp possible fixes:

create a new repository for the Grid3D class and use it in all above listed projects.
as the Grid3D class is only legacy code, try to remove it and only use the PipelineGrid class.
This would change the GT file format and therefore all existing GT files must be converted. It is
not clear to me, if the PipelineGrid could replace the Grid3D to 100 percent.

Port exisiting functionality from old codebase

There are a couple of things that have not been ported from the old codebase yet. When we started the refactoring, the old main GUI class BioTracker was replaced by a couple of smaller GUI components. There's still a couple of things from the old BioTracker class that should be ported to the new codebase.

see: https://github.com/BioroboticsLab/biotracker_core/blob/982f00430dfa70f838ebf6356f76c2198b79eea7/source/gui/BioTracker.cpp

Examples:

Automatically restoring Tracker state when switching from one Tracker to another: BioTracker::trackingAlgChanged(Algorithms::Type trackingAlg)
Serialization and file hash calculation: BioTracker::storeTrackingData(const std::string &filename)
Saving of window geometry and state when closing the application: BioTracker::closeEvent(QCloseEvent* event)
Forwarding of keyboard/mouse events to TrackingAlgorithm: BioTracker::event(QEvent *event)

zmq: Serialization

We must provide an API for the zmq client to serialize/deserialize data from previous calculations. Suggestion would be JSON as it is widely available and easy to use.

Dynamic loading of python modules

Enable the core module to load python modules as tracker. I would suggest to extend the Registry functionality to detect weather a py module or a C++ module is loaded and to behave acordingly

Python QPainter

It would be awesome if we could find a nice way to transport the QPainter object to python without creating a wrapper class

zmq: Widgets

We need to provide a basic API for the zmq client to render some Widgets into the BioTracker.
Example widgets could be:
NumberInput
Slider
Button

Documentation: Explain how to install BioTracker

We should write an explanation of how to build/install the BioTracker. I already started with the wiki page:

https://github.com/BioroboticsLab/biotracker_core/wiki/dev_build

Return useful error messages when loading broken

When loading broken videos (e.g. empty file) we should gracefully fail and show a error message

Remove predef

stay compatible with ubuntu linux boost libs

Comply to boost 1.55

Boost 1.55 is the latest boost version found in the newest ubuntu repositories, so we should comply to those standards. Currently we are not!

Use FPS for TrackingAlgorithm

i need to get the fps of the video file

Conflict on gtest cpm module

Error message:

CMake Error at /usr/share/cmake-2.8/Modules/ExternalProject.cmake:1760 (add_custom_target):
  add_custom_target cannot create target "gtest" because another target with
  the same name already exists.  The existing target is a static library
  created in source directory
  "/mnt/ImageCompressBuild/cpm-bin/github_bioroboticslab_cpm_caffe_master/bin/3rdParty/caffe/src/gtest".
  See documentation for policy CMP0002 for more details.
Call Stack (most recent call first):
  /mnt/ImageCompressBuild/cpm-packages/modules/github_bioroboticslab_biotracker_core_master/src/test/CMakeLists.txt:7 (ExternalProject_Add)

Possible cause: (GroundTruthconverter also loads the pipeline)

    # ++ MODULE: Pipeline
  CPM_AddModule("Pipeline"
        GIT_REPOSITORY "https://github.com/BioroboticsLab/pipeline.git"
                GIT_TAG "cpm")

    # ++ MODULE: gtconv
  CPM_AddModule("groundtruthConvert"
        GIT_REPOSITORY "https://github.com/hmoenck/groundtruthConvert.git"
                GIT_TAG "master")

Uncommenting the following fixes the issue: (File cpm-packages/modules/github_bioroboticslab_biotracker_core_master/src/test/CMakeLists.txt)

# Download and install GoogleTest
ExternalProject_Add(
    gtest
    URL https://googletest.googlecode.com/files/gtest-1.7.0.zip
    PREFIX ${CMAKE_CURRENT_BINARY_DIR}/gtest
    # Disable install step
    INSTALL_COMMAND ""
)
[...]

# Set gtest properties
#ExternalProject_Get_Property(gtest source_dir binary_dir)
set_target_properties(libgtest PROPERTIES
    "IMPORTED_LOCATION" "${binary_dir}/libgtest.a"
    "IMPORTED_LINK_INTERFACE_LIBRARIES" "${CMAKE_THREAD_LIBS_INIT}"
#    "INTERFACE_INCLUDE_DIRECTORIES" "${source_dir}/include"
)

Zmq: send error/status messages through the message system rather than to std::out

We should use our own message system rather than std::out for zmq module debugging

move SpinBoxWidthSlider to core

.. so that it is available for the trackers

Dynamic loading of c++ modules

We need to implement a dynamic loading of c++ widgets

Screenshot function

to be implemented

Cmake: static link zmq

static link zmq into the core binary

remove Boost headers download

Biotracker only builds with the boost 1.57 headers. This is due to a regression in the boost serialization introduced in version 1.58 [ticket][stackoverflow]. To build on systems with a boost version higher then 1.57 we download the 1.57 boost headers, compile against them and then link against the possible different boost system library.
It would be better to simple fix our code so it works also with the newer boost versions and remove the cpm_boost module.

bioroboticslab / biotracker_core Goto Github PK

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Running BioTracker from prebuild binaries:

Building trackers against prebuild BioTracker

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Building BioTracker (Windows x64)

Building BioTracker (Linux)

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