Installation¶
morphMan (morphological manipulation) is a collection of scripts to objectively manipulate morphological features of patient-specific vascular geometries. The project is accessible through GitHub, Anaconda, and conda-forge .
Compatibility and Dependencies¶
The general dependencies of morphMan are
- VMTK 1.5.0
- VTK 9.1.0
- Numpy 1.23
- SciPy 1.8.1
- Python >=3.8
Basic Installation¶
We recommend that you can install morphMan through conda-forge. First, install Anaconda or Miniconda. Then execute the following command in a terminal window to add the conda-forge channel:
$ conda config --add channels conda-forge
$ conda config --set channel_priority strict
Once the conda-forge channel has been added, you can create a conda environment with morphman installed with:
$ conda create -n your_environment morphman
Note
Replace your_environment
with the environment name.
You can then activate your environment by running conda activate your_environment
or source activate your_environment
.
Now you are all set, and can start using morphMan. morphMan can be accessed by opening a Python console
and typing:
>>> import morphman
which will give you access to every method within the framework. Alternatively you can use one of the six main methods of manipulation directly through the terminal, by typing:
$ morphman-[METHOD]
followed by the command line arguments for the selected method. A detailed explanation for usage of morphMan is described in Using morphMan.
Warning
Windows users may experience import errors from VMTK such as:
ImportError: DLL load failed while importing vtkvmtkSegmentationPython: The specified module could not be found.
A temporary fix is to comment out the following lines in the script vtkvmtk.py
, commonly located in
C:\Miniconda-x64\envs\your_environment\lib\site-packages\vmtk\vtkvmtk.py
:
from .vtkvmtkSegmentationPython import *
from .vtkvmtkITKPython import *
or to use Dependency Walker to locate missing DLL files as suggested here.
Development version¶
Downloading¶
The latest development version of morphMan can be found on the official morphMan git repository on GitHub. Make sure Git is installed, which is needed to clone the repository. To clone the morphMan repository, navigate to the directory where you wish morphMan to be stored, type the following command, and press Enter:
$ git clone https://github.com/KVSlab/morphMan
If it not already present, this will install Python for you.
After the source distribution has been downloaded, all the files required will be located
in the newly created morphMan
folder.
Building¶
In order to build and install morphMan, navigate into the morphMan
folder, where a setup.py
file will be located. First, make sure that all dependencies are installed. Then, building and installation of morphMan
can be performed with pip
by running the following command:
$ python -m pip install --editable .
The --editable
flag installs the project in editable mode meaning that any changes to the original package will be reflected directly in your environment.
Alternatively, morphMan can be installed using Python directly (deprecated):
$ python setup.py install