The qim3d
(kɪm θriː diː ) library is designed for Quantitative Imaging in 3D using Python. It offers a range of features, including data loading and manipulation, image processing and filtering, data visualization, and analysis of imaging results.
You can easily load and process 3D image data from various file formats, apply filters and transformations to the data, visualize the results using interactive plots and 3D volumetric rendering.
Whether you are working with medical imaging data, materials science data, or any other type of 3D imaging data, qim3d
provides a convenient and powerful set of tools to help you analyze and understand your data.
Synthetic data generation
Structure tensor
Installation
Create environment
Creating a conda
environment is not required but recommended.
Miniconda installation and setup
Miniconda is a free minimal installer for conda.
Here are some quick instructions to help you set up the latest Miniconda installer for your system:
The easiest way to install Miniconda on Windows is through the graphical interface installer. Follow these steps:
- Download the installer here.
- Run the installer and follow the on-screen instructions.
- When the installation finishes, open
Anaconda Prompt (miniconda3)
from the Start menu.
The easiest way to install Miniconda on macOS is through the graphical interface installer. Follow these steps:
These four commands quickly and quietly install the latest 64-bit version of the installer and then clean up after themselves. To install a different version or architecture of Miniconda for Linux, change the name of the .sh
installer in the wget
command.
mkdir -p ~/miniconda3
wget https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh -O ~/miniconda3/miniconda.sh
bash ~/miniconda3/miniconda.sh -b -u -p ~/miniconda3
rm -rf ~/miniconda3/miniconda.sh
After installing, initialize your newly-installed Miniconda. The following commands initialize for bash and zsh shells:
Once you have conda
installed, open your terminal and create a new enviroment:
conda create -n qim3d python=3.11
After the environment is created, activate it by running:
conda activate qim3d
Remember, if you chose to create an environment to install qim3d
, it needs to be activated each time before using the library.
Install using pip
The latest stable version can be simply installed using pip
. Open your terminal and run:
pip install qim3d
Note
The base installation of qim3d
does not include deep-learning dependencies, keeping the library lighter for scenarios where they are unnecessary. If you need to use deep-learning features, you can install the additional dependencies by running: pip install qim3d['deep-learning']
Troubleshooting
Here are some solutions for commonly found issues during installation and usage of qim3d
.
Failed building
Some Windows users could face an build error during installation.
ERROR: Failed building wheel for noise
Building wheels for collected packages: noise, outputformat, asciitree, ffmpy
Building wheel for noise (setup.py) ... error
error: subprocess-exited-with-error
× python setup.py bdist_wheel did not run successfully.
│ exit code: 1
╰─> [14 lines of output]
running bdist_wheel
running build
running build_py
creating build
creating build\lib.win-amd64-cpython-311
creating build\lib.win-amd64-cpython-311\noise
copying perlin.py -> build\lib.win-amd64-cpython-311\noise
copying shader.py -> build\lib.win-amd64-cpython-311\noise
copying shader_noise.py -> build\lib.win-amd64-cpython-311\noise
copying test.py -> build\lib.win-amd64-cpython-311\noise
copying __init__.py -> build\lib.win-amd64-cpython-311\noise
running build_ext
building 'noise._simplex' extension
error: Microsoft Visual C++ 14.0 or greater is required. Get it with "Microsoft C++ Build Tools": https://visualstudio.microsoft.com/visual-cpp-build-tools/
[end of output]
note: This error originates from a subprocess, and is likely not a problem with pip.
ERROR: Failed building wheel for noise
This issue occurs because the system lacks the necessary tools to compile the library requirements. To resolve this, follow these steps:
- Go to the Visual C++ Build Tools page and click on "Download build tools."
- Run the installer and ensure that
Desktop development with C++
is checked. - Restart your computer
- Activate your conda enviroment and run
pip install qim3d
again
Get the latest version
The library is under constant development, so make sure to keep your installation updated:
pip install --upgrade qim3d
Collaboration
Contributions to qim3d
are welcome!
If you find a bug, have a feature request, or would like to contribute code, please open an issue or submit a pull request.
You can find us at Gitlab: https://lab.compute.dtu.dk/QIM/tools/qim3d
This project is licensed under the MIT License.
Contributors
Below is a list of contributors to the project, arranged in chronological order of their first commit to the repository:
Author | Commits | First commit |
---|---|---|
Felipe Delestro | 195 | 2023-05-12 |
Stefan Engelmann Jensen | 29 | 2023-06-29 |
Oskar Kristoffersen | 15 | 2023-07-05 |
Christian Kento Rasmussen | 22 | 2024-02-01 |
Alessia Saccardo | 7 | 2024-02-19 |
David Grundfest | 8 | 2024-04-12 |
Anna Bøgevang Ekner | 5 | 2024-04-18 |
Support
The development of qim3d
is supported by: