A library of supporting code for numerical modelling (JSON config, HDF5 data, Modern OpenGL visualization)
Home Page: https://abrg-models.github.io/morphologica/
License: Apache License 2.0
make[2]:` Entering directory '/home/seb/src/morphologica/build'
[ 21%] Linking CXX executable testboundary
cd /home/seb/src/morphologica/build/src && /usr/local/bin/cmake -E cmake_link_script CMakeFiles/testboundary.dir/link.txt --verbose=ON
/usr/bin/g++-7 -D__GLN__ -Wall -g -std=c++11 -DGL3_PROTOTYPES -DGL_GLEXT_PROTOTYPES -rdynamic CMakeFiles/testboundary.dir/testboundary.cpp.o -o testboundary -Wl,-rpath,/home/seb/src/morphologica/build/src:/usr/local/lib: libmorphologica.so /usr/local/lib/libarmadillo.so /usr/lib/x86_64-linux-gnu/libopencv_videostab.so.2.4.9 /usr/lib/x86_64-linux-gnu/libopencv_ts.so.2.4.9 /usr/lib/x86_64-linux-gnu/libopencv_superres.so.2.4.9 /usr/lib/x86_64-linux-gnu/libopencv_stitching.so.2.4.9 /usr/lib/x86_64-linux-gnu/libopencv_ocl.so.2.4.9 /usr/lib/x86_64-linux-gnu/libopencv_gpu.so.2.4.9 /usr/lib/x86_64-linux-gnu/libopencv_photo.so.2.4.9 /usr/lib/x86_64-linux-gnu/libopencv_legacy.so.2.4.9 /usr/lib/x86_64-linux-gnu/libopencv_contrib.so.2.4.9 /usr/lib/x86_64-linux-gnu/libopencv_video.so.2.4.9 /usr/lib/x86_64-linux-gnu/libopencv_objdetect.so.2.4.9 /usr/lib/x86_64-linux-gnu/libopencv_ml.so.2.4.9 /usr/lib/x86_64-linux-gnu/libopencv_calib3d.so.2.4.9 /usr/lib/x86_64-linux-gnu/libopencv_features2d.so.2.4.9 /usr/lib/x86_64-linux-gnu/libopencv_highgui.so.2.4.9 /usr/lib/x86_64-linux-gnu/libopencv_imgproc.so.2.4.9 /usr/lib/x86_64-linux-gnu/libopencv_flann.so.2.4.9 /usr/lib/x86_64-linux-gnu/libopencv_core.so.2.4.9 -lGL -lGLU -lglut -lXmu -lXi -lX11 /usr/local/lib/libhdf5.so.103.2.0 -ldl -lopenblas -L/usr/local/lib -ljsoncpp -lglfw3
libmorphologica.so: undefined reference to `glCreateVertexArrays'
libmorphologica.so: undefined reference to `glCreateBuffers'
collect2: error: ld returned 1 exit status
src/CMakeFiles/testboundary.dir/build.make:111: recipe for target 'src/testboundary' failed
make[2]: *** [src/testboundary] Error 1
make[2]: Leaving directory '/home/seb/src/morphologica/build'
CMakeFiles/Makefile2:348: recipe for target 'src/CMakeFiles/testboundary.dir/all' failed
make[1]: *** [src/CMakeFiles/testboundary.dir/all] Error 2
make[1]: Leaving directory '/home/seb/src/morphologica/build'
Makefile:140: recipe for target 'all' failed
make: *** [all] Error 2
seb@ubu16:~/src/morphologica/build$
Looks like there's a null vertex that shows up when the schnakenberg example runs on a Mac.
I suspect a bug in the setting of vertices or normals in HexGridVisual.
Perhaps @stuartwilson would like to buy that Macbook for me to debug it ;)
The issue lies with the inclusion of Visual.h.
@stuartwilson found that he had to include the line
#include <OpenGL/gl3.h>BEFORE
#include <morph/Visual.h>even though morph/Visual.h has the line
#include <GL3/gl3.h>which is the include of the morph-installed gl3.h header; which it is my understanding is the right way to refer to the gl3.h header.
It's possible that the correct include paths have not been set up for Mac in the schnakenberg CMakeLists.txt.
E.g.
Monitor xscale: 1, monitor yscale: 1
Shader compiler present
Using compiled-in vertex shader
Successfully compiled vertex shader!
Using compiled-in fragment shader
Successfully compiled fragment shader!
Successfully linked shader!
Success configuring the morph::Visual object!
One of the tests stopped working on my laptop. Not sure why. The program runs fine, but the number of hexes in the hex grid has changed by 1 compared to the old test value.
It shouldn't fail, should just gracefully refrain from compiling anything with OpenMP.
Building under windows vf_dvsansData etc. is undeclared for some reason.
1>C:\src\thirdparty\vcpkg\installed\x64-windows-static\include\morph/VisualFace.h(198,76): error C2065: 'vf_dvsansData': undeclared identifier
1>C:\src\thirdparty\vcpkg\installed\x64-windows-static\include\morph/VisualFace.h(198,91): error C2065: 'vf_dvsansEnd': undeclared identifier
1>C:\src\thirdparty\vcpkg\installed\x64-windows-static\include\morph/VisualFace.h(204,76): error C2065: 'vf_dvsansitData': undeclared identifier
1>C:\src\thirdparty\vcpkg\installed\x64-windows-static\include\morph/VisualFace.h(204,93): error C2065: 'vf_dvsansitEnd': undeclared identifier
1>C:\src\thirdparty\vcpkg\installed\x64-windows-static\include\morph/VisualFace.h(210,76): error C2065: 'vf_dvsansbdData': undeclared identifier
1>C:\src\thirdparty\vcpkg\installed\x64-windows-static\include\morph/VisualFace.h(210,93): error C2065: 'vf_dvsansbdEnd': undeclared identifier
1>C:\src\thirdparty\vcpkg\installed\x64-windows-static\include\morph/VisualFace.h(216,76): error C2065: 'vf_dvsansbiData': undeclared identifier
1>C:\src\thirdparty\vcpkg\installed\x64-windows-static\include\morph/VisualFace.h(216,93): error C2065: 'vf_dvsansbiEnd': undeclared identifier
Should probably be HDF_ACC_RDONLY, BUT probably also want a true 'read-write' mode for HdfData so that an H5 file can be appended to.
So that morph::RandomUniformFloat becomes morph::RandomUniform and RandomUniformInt becomes a specialization of morph::RandomUniform for std::is_integral types
-Is there a way to plot different radiuses for the points in a scatter visual (instead of in different colors) ?
@stuartwilson you noticed this. Can you describe?
does not exist. Can the occurrences be replaced by i.e;
#ifndef USE_GLEW
#ifdef __OSX__
# include <OpenGL/gl3.h>
#elif _WIN32
# include <glad/glad.h>
# include <GLFW/glfw3.h>
#else
# include <GL3/gl3.h>
#endif
#endif
It's hanging at the end of my BarrelEmerge simulations.
With the latest commit, I am getting the following output under Arch Linux:
$ make
make[1]: Entering directory '/home/tim/edu/morphologica/build'
make[2]: Entering directory '/home/tim/edu/morphologica/build'
Scanning dependencies of target morphstatic
make[2]: Leaving directory '/home/tim/edu/morphologica/build'
make[2]: Entering directory '/home/tim/edu/morphologica/build'
[ 1%] Building CXX object src/CMakeFiles/morphstatic.dir/display.cpp.o
[ 2%] Building CXX object src/CMakeFiles/morphstatic.dir/sockserve.cpp.o
[ 3%] Building CXX object src/CMakeFiles/morphstatic.dir/tools.cpp.o
[ 4%] Building CXX object src/CMakeFiles/morphstatic.dir/world.cpp.o
[ 5%] Building CXX object src/CMakeFiles/morphstatic.dir/ReadCurves.cpp.o
[ 6%] Building CXX object src/CMakeFiles/morphstatic.dir/HexGrid.cpp.o
[ 7%] Building CXX object src/CMakeFiles/morphstatic.dir/HdfData.cpp.o
[ 8%] Building CXX object src/CMakeFiles/morphstatic.dir/Process.cpp.o
[ 9%] Building CXX object src/CMakeFiles/morphstatic.dir/Visual.cpp.o
[ 10%] Linking CXX static library libmorphologica.a
make[2]: Leaving directory '/home/tim/edu/morphologica/build'
[ 10%] Built target morphstatic
make[2]: Entering directory '/home/tim/edu/morphologica/build'
Scanning dependencies of target morphologica
make[2]: Leaving directory '/home/tim/edu/morphologica/build'
make[2]: Entering directory '/home/tim/edu/morphologica/build'
[ 11%] Building CXX object src/CMakeFiles/morphologica.dir/display.cpp.o
[ 12%] Building CXX object src/CMakeFiles/morphologica.dir/sockserve.cpp.o
[ 13%] Building CXX object src/CMakeFiles/morphologica.dir/tools.cpp.o
[ 14%] Building CXX object src/CMakeFiles/morphologica.dir/world.cpp.o
[ 15%] Building CXX object src/CMakeFiles/morphologica.dir/ReadCurves.cpp.o
[ 16%] Building CXX object src/CMakeFiles/morphologica.dir/HexGrid.cpp.o
[ 17%] Building CXX object src/CMakeFiles/morphologica.dir/HdfData.cpp.o
[ 18%] Building CXX object src/CMakeFiles/morphologica.dir/Process.cpp.o
[ 19%] Building CXX object src/CMakeFiles/morphologica.dir/Visual.cpp.o
[ 20%] Linking CXX shared library libmorphologica.so
make[2]: Leaving directory '/home/tim/edu/morphologica/build'
[ 20%] Built target morphologica
make[2]: Entering directory '/home/tim/edu/morphologica/build'
Scanning dependencies of target testboundary
make[2]: Leaving directory '/home/tim/edu/morphologica/build'
make[2]: Entering directory '/home/tim/edu/morphologica/build'
[ 21%] Building CXX object src/CMakeFiles/testboundary.dir/testboundary.cpp.o
[ 22%] Linking CXX executable testboundary
/usr/bin/ld: libmorphologica.so: undefined reference to `wrapper2_dgemv_'
/usr/bin/ld: libmorphologica.so: undefined reference to `wrapper2_sgemv_'
/usr/bin/ld: libmorphologica.so: undefined reference to `wrapper2_sgemm_'
/usr/bin/ld: libmorphologica.so: undefined reference to `wrapper2_dgemm_'
collect2: error: ld returned 1 exit status
make[2]: *** [src/CMakeFiles/testboundary.dir/build.make:141: src/testboundary] Error 1
make[2]: Leaving directory '/home/tim/edu/morphologica/build'
make[1]: *** [CMakeFiles/Makefile2:322: src/CMakeFiles/testboundary.dir/all] Error 2
make[1]: Leaving directory '/home/tim/edu/morphologica/build'
make: *** [Makefile:141: all] Error 2I could not find the place where these functions are referenced. Presumably, they are wrappers around LAPACK functions.
Here are the changes I have made to the build files such that CMake could find all libraries: master...tindzk:feat/arch-linux
conformant implementations won't allow ostream << char32_t
template< class Traits >
basic_ostream<char,Traits>& operator<<( basic_ostream<char,Traits>& os,
char32_t ch ) = delete;
C:\src\thirdparty\vcpkg\installed\x64-windows-static\include\morph/VisualFace.h(399,80): error C2280: 'std::basic_ostream<char,std::char_traits> &std::operator <<<std::char_traits>(std::basic_ostream<char,std::char_traits> &,char32_t)': attempting to reference a deleted function
1>C:\Program Files\Microsoft Visual Studio\2022\Preview\VC\Tools\MSVC\14.32.31114\include\ostream(967): message : see declaration of 'std::operator <<'
1>C:\src\thirdparty\vcpkg\installed\x64-windows-static\include\morph/VisualFace.h(399,80): error C2088: '<<': illegal for class
Add a bgcolour attribute to morph::Visual and make it possible for user to construct with a bg colour or set the bg colour prior to rendering.
As it stands, keepOpen() runs until the user presses 'x' to exit. It would be nice to have a keepOpen() call that can be used to show a simulation at a certain point, the user can examine, rotate, etc, take a screenshot, then press a key to 'continue' on.
The code which trips up both the Intel compiler (version 19.0.5.281) and gcc 7 is in Random.h.
This bug looks like this:
To date, I have about 20 or 30 lines of boilerplate code that has to be incorporated into the start of each model code file. This should all be incorporated into morph::Config
So that they reflect the fact that most of the morphologica code is now header-only
The code base is incompatible with OpenGL 4 which is shipped with most recent distributions. Therefore, I have created a minimal Docker image based on Alpine Linux (Dockerfile).
All of the custom libraries compiled successfully and were installed to /usr/local/lib. However, when I try to use Morphologica in a downstream project, some of its dependencies cannot be found by cmake. This is reproducible as follows:
git clone https://github.com/stuartwilson/SelfOrganisingMaps.git
cd SelfOrganisingMaps
docker run -v $(pwd):/code -i tindzk/morphologica:2019-02-07 sh
cd /code
mkdir build
cd build
cmake ..The output is:
-- Install prefix: /usr/local
-- (This can be changed with `cmake -DCMAKE_INSTALL_PREFIX=/some/place`
-- Operating system: Linux-5.5.3-arch1-1
-- Have pkg_config, searching for libmorphologica...
-- Checking for module 'libmorphologica'
-- Package 'hdf5', required by 'libmorphologica', not found
Package 'lapack', required by 'libmorphologica', not found
CMake Error at /usr/share/cmake/Modules/FindPkgConfig.cmake:419 (message):
A required package was not found
Call Stack (most recent call first):
/usr/share/cmake/Modules/FindPkgConfig.cmake:586 (_pkg_check_modules_internal)
CMakeLists.txt:82 (pkg_check_modules)
-- Configuring incomplete, errors occurred!
See also "/code/build/CMakeFiles/CMakeOutput.log".
The following files exist in /usr/local/lib:
/usr/local/lib
/usr/local/lib/pkgconfig
/usr/local/lib/pkgconfig/opencv.pc
/usr/local/lib/pkgconfig/libmorphologica.pc
/usr/local/lib/pkgconfig/jsoncpp.pc
/usr/local/lib/pkgconfig/armadillo.pc
/usr/local/lib/pkgconfig/hdf5_cpp-1.10.6.pc
/usr/local/lib/pkgconfig/hdf5_hl_cpp-1.10.6.pc
/usr/local/lib/pkgconfig/hdf5_hl-1.10.6.pc
/usr/local/lib/pkgconfig/hdf5-1.10.6.pc
/usr/local/lib/morph
/usr/local/lib/morph/libmorphologica.a
/usr/local/lib/libmorphologica.so
/usr/local/lib/libarmadillo.so
/usr/local/lib/libjsoncpp.a
/usr/local/lib/cmake
/usr/local/lib/cmake/jsoncpp
/usr/local/lib/cmake/jsoncpp/jsoncppConfig.cmake
/usr/local/lib/cmake/jsoncpp/jsoncppConfig-release.cmake
/usr/local/lib/cmake/jsoncpp/jsoncppConfigVersion.cmake
/usr/local/lib/libarmadillo.so.9
/usr/local/lib/libarmadillo.so.9.850.1
/usr/local/lib/libhdf5.so.103.2.0
/usr/local/lib/libhdf5_hl.so
/usr/local/lib/libhdf5_hl_cpp.a
/usr/local/lib/libhdf5_hl_cpp.so
/usr/local/lib/libhdf5_cpp.so.103.2.0
/usr/local/lib/libhdf5_tools.so.100
/usr/local/lib/libhdf5.so.103
/usr/local/lib/libhdf5.settings
/usr/local/lib/libhdf5_hl.a
/usr/local/lib/libhdf5_tools.so
/usr/local/lib/libhdf5.so
/usr/local/lib/libhdf5.a
/usr/local/lib/libhdf5_hl.so.100
/usr/local/lib/libhdf5_tools.a
/usr/local/lib/libhdf5_cpp.a
/usr/local/lib/libhdf5_cpp.so
/usr/local/lib/libhdf5_hl.so.100.1.3
/usr/local/lib/libhdf5_hl_cpp.so.100.1.4
/usr/local/lib/libhdf5_hl_cpp.so.100
/usr/local/lib/libhdf5_cpp.so.103
/usr/local/lib/libhdf5_tools.so.100.1.3
/usr/local/lib/libopencv_objdetect.so
/usr/local/lib/libopencv_shape.so
/usr/local/lib/libopencv_stitching.so.3.2
/usr/local/lib/libopencv_photo.so.3.2
/usr/local/lib/libopencv_flann.so.3.2
/usr/local/lib/libopencv_videostab.so
/usr/local/lib/libopencv_videostab.so.3.2
/usr/local/lib/libopencv_features2d.so
/usr/local/lib/libopencv_superres.so.3.2
/usr/local/lib/libopencv_ml.so.3.2
/usr/local/lib/libopencv_photo.so
/usr/local/lib/libopencv_highgui.so.3.2.0
/usr/local/lib/libopencv_imgproc.so.3.2
/usr/local/lib/libopencv_objdetect.so.3.2.0
/usr/local/lib/libopencv_videoio.so.3.2.0
/usr/local/lib/libopencv_video.so.3.2.0
/usr/local/lib/libopencv_superres.so
/usr/local/lib/libopencv_imgcodecs.so.3.2
/usr/local/lib/libopencv_objdetect.so.3.2
/usr/local/lib/libopencv_imgcodecs.so.3.2.0
/usr/local/lib/libopencv_calib3d.so.3.2.0
/usr/local/lib/libopencv_ml.so.3.2.0
/usr/local/lib/libopencv_core.so.3.2
/usr/local/lib/libopencv_flann.so.3.2.0
/usr/local/lib/libopencv_calib3d.so.3.2
/usr/local/lib/libopencv_flann.so
/usr/local/lib/libopencv_shape.so.3.2.0
/usr/local/lib/libopencv_videoio.so.3.2
/usr/local/lib/libopencv_calib3d.so
/usr/local/lib/libopencv_video.so.3.2
/usr/local/lib/libopencv_video.so
/usr/local/lib/libopencv_highgui.so
/usr/local/lib/libopencv_shape.so.3.2
/usr/local/lib/libopencv_core.so
/usr/local/lib/libopencv_imgproc.so.3.2.0
/usr/local/lib/libopencv_stitching.so
/usr/local/lib/libopencv_photo.so.3.2.0
/usr/local/lib/libopencv_features2d.so.3.2.0
/usr/local/lib/libopencv_stitching.so.3.2.0
/usr/local/lib/libopencv_ml.so
/usr/local/lib/libopencv_features2d.so.3.2
/usr/local/lib/libopencv_superres.so.3.2.0
/usr/local/lib/libopencv_videoio.so
/usr/local/lib/libopencv_highgui.so.3.2
/usr/local/lib/libopencv_videostab.so.3.2.0
/usr/local/lib/libopencv_core.so.3.2.0
/usr/local/lib/libopencv_imgproc.so
/usr/local/lib/libopencv_imgcodecs.so
Also, the ctest command returns with a non-zero exit code because some of the test cases fail. Is this expected?
spwilson 3:04 PM
Hi Seb - I'm finding that updating the data in a graph visual on each step of a sim leads to a massive slow down (up to a minute after about 1000 updates) at the end of a simulation. Should I be calling some kind of clear function after each update?
sebjames 3:24 PM
How are you doing the update? are you using GraphView::append?
3:25
Like the example in morphologica/examples/graph4.cpp?
spwilson 3:26 PM
no i'm not doing append, I'm overwriting the entire vector -- bad?!
sebjames 3:26 PM
So you're calling gv->update()?
spwilson 3:26 PM
yep
sebjames 3:26 PM
Ok, that's slower
spwilson 3:27 PM
seems like a cumulative thing, so longer I run it the slower the shutdown time (doesn't effect runtime speed)
3:27
I'll try append though
sebjames 3:27 PM
gv->append only appends the primitive objects required to add on to your preexisting graph. See graph4.cpp
3:28
What you're describing sounds a bit like the terrible slowdown problem updating HexGridVisuals, so there may be a bug (edited)
spwilson 3:28 PM
yes thats what i thought
sebjames 3:28 PM
in the update() method, which makes it slower than it should be
3:29
I'll check - I can remember what that problem was - it was a failure to clear out the OpenGL indices and vertices
3:29
Yes! Same bug
spwilson 3:29 PM
but that would slow at runtime, and get progressively worse. I don't notice runtime slowdown (printout of current time seems to increment about as long), just massive at the end, i.e., when cleqring the data
sebjames 3:30 PM
It's a one line fix
3:30
I'll do it now and push
spwilson 3:30 PM
ah yes, cool!
3:30
thanks
sebjames 3:36 PM
Hmm, I was mistaken. When you call GraphVisual::update, it updates the data and the scalings and then it calls VisualDataModel::reinit which DOES clear out vertexPositions, vertexNormals, vertexColors and indices. So I don't know why you're getting a slow down.
Currently, the repository does not specify a licence. The authors' copyright is therefore not protected. I suggest to choose an open source licence and add the corresponding LICENSE file.
Further reading:
Review again why I have Hex::di as well as Hex::vi. Make sure to understand when they might contain the same value and when they might contain different values.
-Would you consider replacing the "WIN" define with the standard "WIN32" instead ?
However, this is useful code, so really want an extended HdfData with the extra OpenCV-savvy bits.
@niclar writes: "The underlying data structure of the Vector class is a std::array which if misaligned is subject to write tearing.
(Further the atomic read/write assumption (guaranteed on x86/x64 for the fundamental datatypes, int, double..) should probably be asserted if the Vector was to be used in a multi threaded context)"
The OpenCV dylib will require libjpeg, so a Mac developer may need to download and install libjpeg before they can compile sfview/stalefish.
This is the rng.h in AttractorScaffolding, BUT, it needs to be modified so that it can generate 64 bit random numbers; at present it is a 32 bit implementation.
If you edit vVector.h, then a call to make in your build directory will not trigger a re-build of tests/testvVector.h; first you have to make install, THEN the re-build will be triggered.
This is to make it possible to build models such as Lissom which require computations for sets of elements at a given distance from a target element.
Take opencv dependency away from morph::Visual by integrating the code from https://github.com/lvandeve/lodepng to save pngs.
Tying to build an example. -The cmake installation target for morph seem to miss e.g. Visual.h, ScatterVisual.h
When I run ctest, a few test cases are failing:
Test project /opt/morphologica/build
Start 1: testbez
1/34 Test #1: testbez .......................... Passed 0.02 sec
Start 2: testbez2
2/34 Test #2: testbez2 ......................... Passed 0.16 sec
Start 3: testbezcurves
3/34 Test #3: testbezcurves .................... Passed 0.12 sec
Start 4: testbezmatrix
4/34 Test #4: testbezmatrix .................... Passed 0.48 sec
Start 5: testbezfit
5/34 Test #5: testbezfit ....................... Passed 0.01 sec
Start 6: testbezsplit
6/34 Test #6: testbezsplit ..................... Passed 0.01 sec
Start 7: testbezderiv
7/34 Test #7: testbezderiv .....................***Exception: Child aborted 0.65 sec
Start 8: twocurves
8/34 Test #8: twocurves ........................ Passed 0.02 sec
Start 9: testreadcurves
9/34 Test #9: testreadcurves ................... Passed 0.07 sec
Start 10: testreadcurves_circles
10/34 Test #10: testreadcurves_circles ........... Passed 0.04 sec
Start 11: testdisplay
11/34 Test #11: testdisplay ......................***Failed 0.04 sec
Start 12: testhexgrid
12/34 Test #12: testhexgrid ...................... Passed 2.03 sec
Start 13: testhexgrid2
13/34 Test #13: testhexgrid2 ..................... Passed 0.19 sec
Start 14: testhexgrid3
14/34 Test #14: testhexgrid3 .....................***Failed 0.19 sec
Start 15: testhexgridsave
15/34 Test #15: testhexgridsave ..................***Failed 21.67 sec
Start 16: testdom_pgram
16/34 Test #16: testdom_pgram ....................***Failed 3.49 sec
Start 17: testdom_rect
17/34 Test #17: testdom_rect .....................***Failed 3.54 sec
Start 18: testdom_hex
18/34 Test #18: testdom_hex ......................***Failed 2.40 sec
Start 19: testdom_bound
19/34 Test #19: testdom_bound ....................***Failed 0.17 sec
Start 20: testhexbounddist
20/34 Test #20: testhexbounddist ................. Passed 0.45 sec
Start 21: testhdfdata1
21/34 Test #21: testhdfdata1 ..................... Passed 0.03 sec
Start 22: testhdfdata2
22/34 Test #22: testhdfdata2 ..................... Passed 0.04 sec
Start 23: testProcess
23/34 Test #23: testProcess ...................... Passed 0.09 sec
Start 24: testQuaternion
24/34 Test #24: testQuaternion ................... Passed 0.00 sec
Start 25: testVector3
25/34 Test #25: testVector3 ...................... Passed 0.00 sec
Start 26: testTransformMatrix
26/34 Test #26: testTransformMatrix .............. Passed 0.00 sec
Start 27: testHexVertexPos
27/34 Test #27: testHexVertexPos ................. Passed 0.01 sec
Start 28: testHexUserFlags
28/34 Test #28: testHexUserFlags ................. Passed 0.01 sec
Start 29: testDirichlet
29/34 Test #29: testDirichlet ....................***Failed 0.03 sec
Start 30: testDirichlet2
30/34 Test #30: testDirichlet2 ...................***Failed 0.03 sec
Start 31: testDirichlet4
31/34 Test #31: testDirichlet4 ...................***Failed 0.05 sec
Start 32: testDirichlet5
32/34 Test #32: testDirichlet5 ...................***Failed 0.04 sec
Start 33: testMathAlgo
33/34 Test #33: testMathAlgo ..................... Passed 0.00 sec
Start 34: testNMSimplex
34/34 Test #34: testNMSimplex .................... Passed 0.00 sec
65% tests passed, 12 tests failed out of 34
Total Test time (real) = 36.17 sec
The following tests FAILED:
7 - testbezderiv (Child aborted)
11 - testdisplay (Failed)
14 - testhexgrid3 (Failed)
15 - testhexgridsave (Failed)
16 - testdom_pgram (Failed)
17 - testdom_rect (Failed)
18 - testdom_hex (Failed)
19 - testdom_bound (Failed)
29 - testDirichlet (Failed)
30 - testDirichlet2 (Failed)
31 - testDirichlet4 (Failed)
32 - testDirichlet5 (Failed)
Errors while running CTest
This is reproducible as follows:
docker run -i tindzk/morphologica:2020-02-18 sh
cd /opt && \
git clone https://github.com/ABRG-Models/morphologica.git && \
cd morphologica && \
mkdir build && \
cd build && \
cmake .. -DCMAKE_INSTALL_PREFIX=/usr/local && \
make -j$(nproc) && ctestHow would one update e.g the ScatterVisual with real time data points from another thread ?
I see that the Vector class is not thread safe ...
I suspect it's to be handled by the user right ? Like pulling a thread safe queue from the render loop updating the ScatterVisual
Vector (pop_back and push_front)..
As reported by @tindzk there are some OpenCV function calls made in morphologica which have been deprecated in OpenCV 4+. Fix this.
As subject.
@jmartinbrooke found this. Sometimes, t exceeds 1, triggering the runtime error in BezCurve::checkt. I think better runtime checking is required in computePointBySearch. Perhaps somethign like:
diff --git a/morph/BezCurve.h b/morph/BezCurve.h
index d5e246d..b8c79a7 100644
--- a/morph/BezCurve.h
+++ b/morph/BezCurve.h
@@ -1086,6 +1086,14 @@ namespace morph
*/
BezCoord<Flt> computePointBySearch (Flt t, Flt l) const
{
+ // This may be necessary, to fix the intermittent bug discovered by John
+ if (t >= Flt{1}) {
+ BezCoord<Flt> rtn (true);
+ rtn.setRemaining (0);
+ rtn.setParam (t);
+ return rtn;
+ }
+
// Min and max of possible range for dt to make a step of length l in posn space
Flt dtmin = Flt{0};
Flt dtmax = Flt{1} - t;
Also, why is this a != rather than <? (Also BezCurve.h):
// This searches forward to try to find a point which is 'l' further on. If
// at any point t exceeds 1.0, we have to break out.
while (t != Flt{1} && lastnull == false) {
So that libmorphologica.pc pulls in glfw3 if morph was compiled against glfw3
Do so by replacing jsoncpp with nlohmann/json
Commit b2c9fac shows the correct code to get the current framebuffer size.
BUT also as part of this ticket, make sure all the calls where I've set window_w and window_h work the right way - perhaps these should be framebuffer based as well. There may be differences in the way the mouse "feels" right now between Linux and Mac as a result of this...
In using config.getBool("logicalVar",0) the default value is always selected regardless of the value in the .json file, e.g. "logicalVal" : 1 . Other variable types getInt, getDouble, getString are working as expected, i.e. the value in the .json file is selected if it exists.
Pressing the window close button (testing in windows) I'd expect the morph::Visual to close/terminate (as when pressed the 'x' key)
To see: run ./build/examples/visual
Now rotate the surface around until it is edge on. Some of the edge hexes become distorted.
It's linux specific, the ScatterVisual seem to depend on it. -Will there be a windows port of Process.h ?
The current scheme, with several members, each of which is a vector of pointers to the different specializations of VisualModel, is really clunky. Needs sorting. Probably just a question of having a pointer to a vector of VisualModel*s and make sure VisualModel behaves as a good interface class.
the header dependency is missing when installing morph standalone
There's quite a lot of code duplication in functions which could be templatized.
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