Installation problems

[dagonzalezfo]

Hi @etasnadi,

I am trying to compile your release 0.2-alpha on a CentOS 7 machine but I am having some problems.

For instance, to compile SelectiveSegmentation gives:

3DCellAnnotator-0.2-alpha/SelectiveSegmentation/src/imagetools.cu(152): error: identifier "CV_LOAD_IMAGE_ANYDEPTH" is undefined. Some post suggests that this error is related to the absence of TIFF support. However, our version has it.

Therefore, I want to know if it is possible to get a list of build required dependencies and their respective versions.

Best,

Danilo

[etasnadi]

Hi,

Thanks for your feedback.

OpenCV 4.2.0 and Boost 1.71.0 should be compatible with the SelectiveSegmentation project.

However, a slight modification is needed to be able to compile with recent versions of opencv: the CV_LOAD_IMAGE_ANYDEPTH constant in the mentioned line should be replaced to cv::IMREAD_ANYDEPTH. I could built the project from scratch, but not tested if it surely works at runtime. I will update the source later.

[etasnadi]

Hi,

I rebuilt the project from scratch on Ubuntu 20.04 with the fix above and the software seems to work properly, now you can build directly from the master branch. See commit.

I recorded every step.

1. Install 3D Cell Annotator dependencies

• OpenCV: sudo apt install libopencv-dev (I have 4.2.0)
• Boost: sudo apt install libboost-all-dev (I have 1.71.0)

2. Install the MITK depdendencies:

• Install Qt (with the installer). Use 5.14.2. (The 5.15 may cause the superbuild to fail when building VTK: https://gitlab.kitware.com/vtk/vtk/-/issues/18005)

3. Build 3D Cel Annotator:

• Build the SelectiveSegmentation subproject using cmake.
• The next step is to build the MITK. Checkout the version ac93ed9baf (2018.04 version) from the official github repo: https://github.com/MITK/MITK , create the superbuild folder and make sure it builds successfully:
  • Use GCC 7: set the environment variables CC=gcc-7 and CXX=g++-7 (gcc/g++ version: 7.5.0 worked for me, see)
  • Set cmake -D CMAKE_CXX_FLAGS="-Wno-error=deprecated-declarations" to suppress build errors caused by using deprecated functionality in the MITK source (or set the variable using cmake-gui).
  • Set CMAKE_BUILD_TYPE to Release to build a release version of MITK (more compact, does not contain debug info).
  • Go to the MITK-build directory under the superbuild and enable the following plugins (essential for the 3DCellAnnotator):
    • MITK_BUILD_org.mitk.gui.qt.multilabelsegmentation
    • MITK_BUILD_org.mitk.gui.qt.segmentation
  • Now you can execute the build
• Build and execute the MITKIntegration subproject.
  • First set the variables:
    • The MITK_PATH should point to the MITK source directory
    • The PATCH_DIR should point to the mitk-patch subdirectory of the MITKIntegration source directory.
  • Then, build the project using make
  • Go to the build folder and then execute python3 patch.py apply (This will patch the MITK source with the integration code).
• Go to the MITK-build directory under the superbuild again, run cmake and set the Selective_DIR in cmake to point to the previously built SelectiveSegmentation project.
• Then, build MITK again with make. You will see the built app in the bin folder. To build the final version, run make install.
  Copy the settings_3DCA.conf configuration file into the bin directory from the SelectiveSegmentation project

Result: