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napari-nibabel's Introduction

NIPY

Neuroimaging tools for Python.

The aim of NIPY is to produce a platform-independent Python environment for the analysis of functional brain imaging data using an open development model.

In NIPY we aim to:

  1. Provide an open source, mixed language scientific programming environment suitable for rapid development.
  2. Create software components in this environment to make it easy to develop tools for MRI, EEG, PET and other modalities.
  3. Create and maintain a wide base of developers to contribute to this platform.
  4. To maintain and develop this framework as a single, easily installable bundle.

NIPY is the work of many people. We list the main authors in the file AUTHOR in the NIPY distribution, and other contributions in THANKS.

Website

Current information can always be found at the NIPY project website.

Mailing Lists

For questions on how to use nipy or on making code contributions, please see the neuroimaging mailing list:

https://mail.python.org/mailman/listinfo/neuroimaging

Please report bugs at github issues:

https://github.com/nipy/nipy/issues

You can see the list of current proposed changes at:

https://github.com/nipy/nipy/pulls

Code

You can find our sources and single-click downloads:

Tests

To run nipy's tests, you will need to install the pytest Python testing package:

pip install pytest

Then:

pytest nipy

You can run the doctests along with the other tests with:

pip install pytest-doctestplus

Then:

pytest --doctest-plus nipy

Installation

See the latest installation instructions.

License

We use the 3-clause BSD license; the full license is in the file LICENSE in the nipy distribution.

napari-nibabel's People

Contributors

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Stargazers

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Forkers

grlee77 effigies chris-n-k cstakcjahvoidhexloenterprise

napari-nibabel's Issues

Writer functions

I would like to create a branch with the _writer.py script. At the moment my solution only supports the nifti format.

The functions works by creating a nibabel.Nifti1Image from the selected layer (image or labels) data and metadata. Do have an idea for a more elegant way to support the different formats in nibabel other than writing a specific writer for each?

Pip install command doesn't work

When using the pip command located in the README file in Python (I'm using Python 3.7.1), I receive an error saying the following:

ERROR: Could not find a version that satisfies the requirement napari-nibabel (from versions: none)
ERROR: No matching distribution found for napari-nibabel

Cooperation proposal

Hi,

I wrote a nifti format oriented IO plugin for napari based on nibabel at the end of last year. It worked fine for me and was quite similar to your solution but lacked the scale and translate support. Recently I included writers for image and label layers. During this task I discovered your solution.

Might it be interesting to combine our solutions?

Best regards,
Christopher N.-K.

Package structure

Hi,

I would like to discuss the structure of the package. Wouldn't it be good to split the scripts into a _reader.py and _writer.py file in the future? Possily a _widget.py or _header_info.py as well? I used this structure in my approach and I think it might be beneficial.

Best regards,
Christopher

Reader update

Hi,

I have a question regarding the dimension order the reader uses. Wouldn't it be convenient if we change the axis order to the order napari uses (reader at the moment: t,x,y,z vs napari: t,z,y,x). This way the image gets displayed in a more natural way.

I use to flip the y axis to display the patients back at the bottom, as the reading direction of this dimension differ between my files and napari. Is this a general problem or just specific for my files?

Best Regards
Christopher

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