# NeuTomPy toolbox
<img src="https://github.com/dmici/NeuTomPy-toolbox/blob/master/img/logo_neutompy.png" width="850">
**NeuTomPy toolbox** is a Python package for tomographic data processing and reconstruction.
Such toolbox includes pre-processing algorithms, artifacts removal and a wide range of iterative
reconstruction methods as well as the Filtered Back Projection algorithm.
The NeuTomPy toolbox was conceived primarily for Neutron Tomography and developed to support
the need of users and researchers to compare state-of-the-art reconstruction methods and choose the optimal data-processing workflow for their data.
# Features
* Readers and writers for TIFF and FITS files and stack of images
* Data normalization with dose correction, correction of the rotation axis tilt, ring-filters, outlier removals, beam-hardening correction
* A wide range of reconstruction algorithms powered by [ASTRA toolbox](https://www.astra-toolbox.com/): FBP, SIRT, SART, ART, CGLS, NN-FBP, MR-FBP
* Image quality assessment with several metrics
# Installation
NeuTomPy toolbox supports **Linux**, **Windows** and **Mac OS** 64-bit operating systems.
First of all, install a [conda](https://www.anaconda.com/download/) python environment with **Python 3.6** and then activate it:
```
conda create -n ntp_env python=3.6
conda activate ntp_env
```
Install some dependencies:
```
conda install -c simpleitk simpleitk
conda install scikit-image
conda install ipython numexpr astropy tifffile mkl_fft tqdm
conda install -c astra-toolbox astra-toolbox
pip install opencv-python read-roi
pip install -U numpy
```
Finally, install NeuTomPy toolbox via `pip`:
```
pip install neutompy
```
NB: If a segmentation fault occurs when importing NeuTomPy, install PyQt5 via `pip`:
```
pip install PyQt5
```
# Update
To update a NeuTomPy installation to the latest version run:
```
pip install neutompy --upgrade
```
# Documentation
Complete documentation can be found on Read the Docs: <https://neutompy-toolbox.readthedocs.io>.
Tutorials and code examples of typical usage can be found in the folder [examples](https://github.com/dmici/NeuTomPy-toolbox/blob/master/examples).
A sample dataset for testing purpose can be found [here](https://mega.nz/#F!k0g32QiC!zbGZMuTES4WOzrxJEfPaSA). This dataset includes neutron radiographs of a phantom sample acquired at the IMAT beamline, ISIS neutron spallation source, UK.
# Reference
If you use the NeuTomPy toolbox for your research, please cite the following paper:
D. Micieli, T. Minniti, G. Gorini, “NeuTomPy toolbox, a Python package for tomographic data processing and reconstruction”, SoftwareX, Volume 9 (2019), pp. 260-264, https://doi.org/10.1016/j.softx.2019.01.005.
# License
The project is licensed under the [GPLv3](https://github.com/dmici/NeuTomPy-toolbox/blob/master/LICENSE) license.
# Contact
If you want to contact us for any reasons, please send an email to: [email protected]
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NeuTomPy-toolbox 断层重建python工具包
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NeuTomPy-toolbox是一个用于断层数据处理和重建的python包。 这种工具箱包括预处理算法、伪影去除和广泛应用的迭代重建方法以及滤波反投影算法。 Neutompy工具箱最初是为中子断层成像设计的,它的开发是为了支持有需要的用户和研究人员对比不同的重建方法,以选择最优的处理方式。
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NeuTomPy-toolbox-master.zip (64个子文件)
NeuTomPy-toolbox-master
docs
make.bat 823B
requirements.txt 129B
Makefile 616B
source
api.rst 375B
conf.py 6KB
neutompy.recon.mrfbp.astra_plugin.rst 184B
neutompy.recon.optomo.rst 144B
neutompy.metrics.metrics.rst 153B
neutompy.recon.nnfbp.astra_plugin.rst 184B
installation.rst 1018B
neutompy.recon.recon.rst 141B
modules.rst 77B
neutompy.image.rebin.rst 141B
neutompy.image.image.rst 141B
neutompy.recon.nnfbp.TrainingData.rst 182B
neutompy.misc.uitools.rst 144B
examples
nnfbp.rst 172B
compare.rst 211B
fbp_gpu.rst 192B
sirt_gpu.rst 194B
fbp_cpu.rst 192B
examples.rst 426B
neutompy.postproc.convert.rst 156B
neutompy.rst 150B
neutompy.preproc.preproc.rst 153B
index.rst 2KB
neutompy.postproc.crop.rst 147B
img
logo_neutompy.png 27KB
logo_neutompy_trasparente.png 24KB
LICENSE 34KB
neutompy
misc
uitools.py 4KB
__init__.py 1B
metrics
metrics.py 13KB
__init__.py 1B
image
rebin.py 3KB
__init__.py 1B
image.py 23KB
postproc
crop.py 2KB
__init__.py 0B
convert.py 2KB
__init__.py 604B
preproc
__init__.py 1B
preproc.py 39KB
recon
mrfbp
__init__.py 998B
astra_plugin.py 7KB
optomo.py 9KB
__init__.py 1B
recon.py 14KB
nnfbp
TrainingData.py 8KB
__init__.py 1KB
astra_plugin.py 19KB
version.py 23B
examples
scripts
fbp_gpu_reconstruction.py 2KB
compare_reconstructions.py 3KB
nnfbp_reconstruction.py 3KB
data
signal.roi 128B
sinogram.tiff 3.97MB
background.roi 128B
fbp_cpu_reconstruction.py 2KB
sirt_gpu_reconstruction.py 2KB
setup.py 950B
.gitignore 1KB
README.md 3KB
安装说明.doc 21KB
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