Image Processing in Python for 3D image stacks.
Image Processing in Python for 3D image stacks, or IMPPY3D, is a software repository comprising mostly Python scripts that simplify post-processing and 3D shape characterization of grayscale image stacks, otherwise known as volume-based images, 3D images, or voxel models. IMPPY3D was originally created for post-processing image stacks generated from X-ray computed tomography measurements. However, IMPPY3D also contains a functions to aid in post-processing general 2D/3D images.
Python was chosen for this library because of it is a productive, easy-to-use language. However, for computationally intense calculations, compiled codes and libraries are used for improved performance, such as well known libraries like Numpy and SciKit-Image. Compiled libraries internal to IMPPY3D were created using Cython. IMPPY3D was developed in an Anaconda environment with Windows 10 and Linux in mind, and suitable Anaconda environment files for these operating systems are provided to simplify the process of installing the necessary dependencies although some dependancy resolution may still be required.
Some of the highlighted capabilies of IMPPY3D include: interactive graphical user-interfaces (GUIs) available for many image processing functions, various 2D/3D image filters (e.g., blurring, sharpening, denoising, erosion/dilation), the ability to segment and label continuous 3D objects, precisely rotating an image stack in 3D and re-slicing along the new Z-axis, multiple algorithms available for fitting rotated bounding boxes to continuous voxel objects, image stacks can be converted into 3D voxel models suitable for viewing in ParaView, and voxel models can be represented as smooth surface-based models like STL meshes. Additional information and example scripts can be found in the included ReadMe files.
The development of IMPPY3D uses the Mamba
package manager for handling dependencies, similar to the popular Conda package
manager. We recommend creating a new Python 3.10 environment (in Mamba/Conda)
prior to installing IMPPY3D. The easiest method of installing IMPPY3D is
through pip. Wheel files(.whl) for pip can be found either on PyPi or in
the IMPPY3D repository(for Windows or Linux machines). Alternatively, IMPPY3D
can be compiled using setuptools. The following subsections go into more
details for each of these installation cases.
The simplest method of installing IMPPY3D is through PyPi.
Installing IMPPY3D from PyPi can be achieved using pip via the following,
pip install imppy3d=1.1.3
It is important that you explicitly specify the latest version of IMPPY3D, in this case, version 1.1.3. Moreover, the pip installation process of IMPPY3D is currently restricted to Python 3.10 environments.
The binary .whl files are located in the folder, "./dist/", of the
GitHub repository. The name
of the .whl files will contain information about the Python version, IMPPY3D
version number, and operating system. Currently, precompiled .whl files are
only available for Windows and Linux operating systems using Python 3.10. To
install IMPPY3D using one of these precompiled .whl files, choose the
appropriate .whl for your operating system and use the pip command in your
Python environment,
pip install /path/to/file.whl
IMPPY3D is largely Python-based, but there are also C extensions, via Cython,
that must be compiled in order to use all of the features of IMPPY3D. A
setup.py file is provided in the GitHub repository for easier compilation of IMPPY3D. To
compile IMPPY3D, open a terminal with your Python environment active and type,
python setup.py bdist_wheel sdist
This command will use the setuptools library to compile IMPPY3D into a wheel
(.whl). Upon successful completion, the binary .whl file will be located in the
folder, "./dist/". Additionally, the above command will create source
distribution, which is an alternative installation file to the binary
distribution. With the new .whl file created, simply follow the instructions
above stated about installing IMPPY3D using pip and a local binary file.
It is important to ensure that your Python environment also has the appropriate environment variables set for your C compiler. If setuptools cannot find your compiler, then compilation of IMPPY3D will fail. Furthermore, the same C-compiler as that which was used to compile the specific Python version you are using should also be used to create the IMPPY3D C extensions. For Windows users, see the documentation, https://wiki.python.org/moin/WindowsCompilers.
A number of example Python scripts are provided in the "./examples/" folder to help facilitate rapid development of new projects. As we continue to use IMPPY3D in new applications, we aim to continue to provide new example scripts in this folder.
To confirm that IMPPY3D was successfully installed, we recommend running the example, "./examples/calc_metrics_pores/".
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Convert the comment blocks in function definitions to a common standard for automatic generation of the documentation using Sphinx.
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Incoporate additional libraries like TomoPy for reconstruction of X-ray CT radiographs and removal of ring artifacts.
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Create an optimization routine that stitches multiple X-ray CT fields-of-view together.
If you encounter any bugs or unintended behavior, please create an "Issue" in the IMPPY3D GitHub repository and report a bug. You can also make a request for new features in this way.
For questions on how best to use IMPPY3D for a specific application, feel free to contact Dr. Newell Moser (see below).
- Dr. Newell Moser, NIST ([email protected])
-
Dr. Alexander K. Landauer, NIST
-
Dr. Orion L. Kafka, NIST
- Dr. Edward J. Garboczi
If IMPPY3D has been significant in your research, and you would like to acknowledge the project in your academic publication, we suggest citing the following NIST data repository:
Moser, Newell H., Landauer, Alexander K., Kafka, Orion L. (2023), IMPPY3D: Image processing in python for 3D image stacks, National Institute of Standards and Technology, https://doi.org/10.18434/mds2-2806