Update installation instructions for PCT #69
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@@ -21,6 +21,15 @@ If no error appears, then PCT was successfully installed. | |
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| If you need to edit the source code of PCT, or tune the compilation process, then you need to manually compile PCT. PCT depends on [ITK](https://itk.org) and [RTK](https://openrtk.org), the first step is therefore to download and compile them. | ||
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| ### Create a python virtual environment | ||
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| If you want to use PCT as a python module, it's preferable to create a new virtual environement. Numpy is also mandatory to compile ITK python wrapping: | ||
| ```bash | ||
| python -m venv venv_pct | ||
| source venv_pct/bin/activate | ||
| pip install numpy | ||
| ``` | ||
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| ### Compiling ITK and RTK | ||
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| RTK comes bundled as an ITK module, so it is enough to download ITK and compile it with an option that indicates that RTK is also required. First, clone ITK from GitHub: | ||
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@@ -30,22 +39,27 @@ git clone git@github.com:InsightSoftwareConsortium/ITK.git | |
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| Then, create a compilation folder for ITK: | ||
| ``` | ||
| mkdir itk-build itk-install | ||
| cd itk-build | ||
| ``` | ||
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| ITK uses [CMake](https://cmake.org) as its building tool. Below is an example of how to configure ITK, but feel free to edit the options as needed (works with ITK v6.0a1). | ||
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Collaborator
There was a problem hiding this comment. I would remove this added reference to ITK v6.0a1 which will soon be outdated.
Contributor
Author
There was a problem hiding this comment. I did not succeed to compile RTK with ITK v6.0a2
Collaborator
There was a problem hiding this comment. I don't want to support ITK alpha versions and even less indicate versions numbers in the documentation. So it's either |
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| ```bash | ||
| cmake \ | ||
| -DITK_WRAP_PYTHON=ON \ | ||
| -DModule_RTK=ON \ | ||
| -DModule_RTK_GIT_TAG=main \ | ||
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Collaborator
There was a problem hiding this comment. I don't think main is necessary, I would remove.
Contributor
Author
There was a problem hiding this comment. I did not succeed to compile ITK v6.0a1 with the tagged version of RTK and CudaCommon |
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| -DModule_CudaCommon=ON \ | ||
| -DModule_CudaCommon_GIT_TAG=ON \ | ||
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Collaborator
There was a problem hiding this comment. I would remove the Cuda options in this documentation. |
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| -DCMAKE_INSTALL_PREFIX=<path-to>/itk-install \ | ||
| ../ITK | ||
| ``` | ||
| `ITK_WRAP_PYTHON` mean that ITK will generate and compile Python wrapping for the C++ code, which is also supported by PCT. This option massively increases compilation time, so if Python wrappings are not needed, this option can be disabled. `Module_RTK` enables the compilation of RTK, which is required for PCT. And CudaCommon is necesary if you want to use your GPU. | ||
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Collaborator
There was a problem hiding this comment. Remove, there is no GPU code in PCT |
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| Once configuration finishes, the compilation is started using. The installation allows you to have access in your python virtual environment if it was activated before. | ||
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Collaborator
There was a problem hiding this comment. This sentence was added in the middle of an unfinished one and I don't really understand what it means... |
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| ``` | ||
| cmake --build . | ||
| make install | ||
| ``` | ||
| Depending on your machine and whether `ITK_WRAP_PYTHON` is on, compiling ITK can take from few minutes up to several hours. | ||
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@@ -58,20 +72,22 @@ git clone https://github.com/RTKConsortium/PCT.git | |
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| Then, create a build directory for PCT: | ||
| ```bash | ||
| mkdir pct-build pct-install | ||
| cd pct-build | ||
| ``` | ||
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| Similar to ITK, configuration and compilation is handled via [CMake](https://cmake.org/). Configuration can be achieved using | ||
| ```bash | ||
| cmake \ | ||
| -DITK_DIR=<path to ITK build folder> \ | ||
| -DCMAKE_INSTALL_PREFIX=<path-to>/pct-install | ||
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Collaborator
There was a problem hiding this comment. Does this actually work? I think you cannot install Python compilation of a remote module if it is compiled independently of ITK. See
Contributor
Author
There was a problem hiding this comment. it works for me with PCT |
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| -DPCT_BUILD_APPLICATIONS=ON \ | ||
| ../PCT | ||
| ``` | ||
| Once configuration completes, the compilation can be achieved using | ||
| ```bash | ||
| cmake --build . | ||
| make install | ||
| ``` | ||
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| Optionally, PCT can be added to the user's `$PATH` variable using for instance | ||
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Replace "compile" with "use" I guess?
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I used "compile" because numpy is necessary during cmake configuration of ITK in order to have the wrappings