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Merge pull request #73 from ofgulban/devel
v1.5.0
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# C extensions | ||
*.so | ||
*.c | ||
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# Distribution / packaging | ||
.Python | ||
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Contributing | ||
============ | ||
If you want to contribute to Segmentator and make it better, your help is very welcome. | ||
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## Opening an issue | ||
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- Please post your quesions, bug reports and feature requests [here](https://github.com/ofgulban/segmentator/issues). | ||
- When reporting a bug, please specify your system and a complete copy of the error message that you are getting. | ||
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## Making a pull request | ||
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- Create a personal fork of the project on Github. | ||
- Clone the fork on your local machine. | ||
- Create a new branch to work on. Branch from `devel`. | ||
- Implement/fix your feature, comment your code. | ||
- Follow the code style of the project. | ||
- Add or change the documentation as needed. | ||
- Push your branch to your fork on Github. | ||
- From your fork open a pull request in the correct branch. Target `devel` branch of the original Segmentator repository. | ||
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__Note:__ Please write your commit messages in the present tense. Your commit message should describe what the commit, when applied, does to the code – not what you did to the code. | ||
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___ | ||
This guideline is adapted from [link](https://github.com/MarcDiethelm/contributing/blob/master/README.md) |
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numpy==1.13.1 | ||
scipy==0.19.1 | ||
matplotlib==2.0.2 | ||
nibabel==2.1.0 | ||
numpy==1.14.2 | ||
scipy==1.0.0 | ||
matplotlib==2.2.2 | ||
nibabel==2.2.1 | ||
pytest-cov==2.5.1 | ||
compoda>=0.3 |
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The dataset used for developing Segmentator can be found at: | ||
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[https://doi.org/10.5281/zenodo.1117858](https://doi.org/10.5281/zenodo.1117858) | ||
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"""All this stuff is to get the version from setup.py.""" | ||
"""Make the version number available.""" | ||
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from pkg_resources import get_distribution, DistributionNotFound | ||
import os.path | ||
import pkg_resources # part of setuptools | ||
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try: | ||
_dist = get_distribution('segmentator') | ||
# Normalize case for Windows systems | ||
dist_loc = os.path.normcase(_dist.location) | ||
here = os.path.normcase(__file__) | ||
if not here.startswith(os.path.join(dist_loc, 'segmentator')): | ||
# not installed, but there is another version that *is* | ||
raise DistributionNotFound | ||
except DistributionNotFound: | ||
__version__ = 'Version information not found. Please install this project \ | ||
with setup.py)' | ||
else: | ||
__version__ = _dist.version | ||
__version__ = pkg_resources.require("segmentator")[0].version |
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"""This file contains variables that are used in filters.""" | ||
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filename = 'sample_filename_here' | ||
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# filter defult parameters | ||
smoothing = 'STEDI' | ||
noise_scale = 0.5 | ||
feature_scale = 0.5 | ||
nr_iterations = 20 | ||
save_every = 10 | ||
edge_thr = 0.001 | ||
gamma = 1 | ||
downsampling = 0 |
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"""This file contains GUI related variables.""" | ||
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import matplotlib.pyplot as plt | ||
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# Colormap for mask overlays | ||
palette = plt.cm.Reds | ||
palette.set_over('r', 1.0) | ||
palette.set_under('w', 0) | ||
palette.set_bad('m', 1.0) | ||
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# Slider colors | ||
axcolor = '0.875' | ||
hovcolor = '0.975' |
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