itkwidgets

v0.32.6

Interactive Jupyter widgets to visualize images, point sets, and meshes in 2D and 3D For more information about how to use this package see README

Latest version published 1 year ago

License: Apache-2.0

PyPI

GitHub

Package Health Score

59 / 100

security
Security review needed
popularity
Recognized
maintenance
Inactive
community
Sustainable

Popularity

Recognized

GitHub Stars: 572
Forks: 84
Contributors: 7

Direct Usage Popularity

Based on project statistics from the GitHub repository for the PyPI package itkwidgets, we found that it has been starred 572 times.

Security

Security review needed

Security and license risk for latest version

Release Date: Mar 2, 2023
Direct Vulnerabilities: 0
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0
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0
M
0
L
Indirect Vulnerabilities: 0
C
0
H
0
M
0
L
License Risk: 0
H
0
M
0
L

All security vulnerabilities belong to production dependencies of direct and indirect packages.

License

Apache-2.0

Security Policy

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Maintenance

Inactive

Commit Frequency

Open Issues: 111
Open PR: 4
Last Release: 1 year ago
Last Commit: 15 days ago

Further analysis of the maintenance status of itkwidgets based on released PyPI versions cadence, the repository activity, and other data points determined that its maintenance is Inactive.

An important project maintenance signal to consider for itkwidgets is that it hasn't seen any new versions released to PyPI in the past 12 months, and could be considered as a discontinued project, or that which receives low attention from its maintainers.

As a healthy sign for on-going project maintenance, we found that the GitHub repository had at least 1 pull request or issue interacted with by the community.

Community

Sustainable

Readme: Yes
Contributing.md: No
Code of Conduct: Yes
Contributors: 7
Funding: No

This project has seen only 10 or less contributors.

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Package

Python Versions Compatibility: ==3.10.*, ==3.11.*, ==3.7.*, ==3.8.*, ==3.9.*

Age: 6 years
Latest Release: 15 days ago
Dependencies: 14 Direct / 78 Total
Versions: 121
Maintainers: 3
Wheels: OS Independent

Not sure how to use itkwidgets?

To help you get started, we've collected the most common ways that itkwidgets is being used within popular public projects.

InsightSoftwareConsortium / itkwidgets / tests / test_trait_types.py View on Github

def test_polydata_list_from_json():
    number_of_points = 10
    point_set_array_1 = np.random.multivariate_normal(gaussian_1_mean, gaussian_1_cov,
                                                      number_of_points)
    point_set_array_2 = np.random.multivariate_normal(gaussian_2_mean, gaussian_2_cov,
                                                      number_of_points)

    point_set_1 = to_point_set(point_set_array_1)
    point_set_2 = to_point_set(point_set_array_2)
    polydata_list = [point_set_1, point_set_2]

    asjson = trait_types.polydata_list_to_json(polydata_list)
    polydata_list_from_json = trait_types.polydata_list_from_json(asjson)
    assert(len(polydata_list_from_json) == 2)
    polydata_1 = polydata_list_from_json[0]
    assert(polydata_1['vtkClass'] == 'vtkPolyData')
    assert(polydata_1['points']['vtkClass'] == 'vtkPoints')
    assert(polydata_1['points']['numberOfComponents'] == 3)
    assert(polydata_1['points']['dataType'] == 'Float32Array')
    assert(np.array_equal(polydata_1['points']['values'],
                          point_set_array_1.astype(np.float32)))

View more ways to use itkwidgets

itkwidgets

Interactive Jupyter widgets to visualize images, point sets, and meshes on the web.

Key Features:

Visualize 2D and 3D images, point sets, and geometry, e.g. meshes, in Jupyter
Support for
- NumPy array images
- itk.Image
- Dask array images
- vtk.vtkImageData
- pyvista.UniformGrid
- vedo.Volume
- pyimagej ImageJ / Fiji / ImageJ2 images
- Additional NumPy array-like objects
- SimpleITK.Image
- NumPy array point sets
- itk.PointSet
- itk.PointBasedSpatialObject
- vtk.vtkPolyData point sets
- pyvista.PolyData point sets
- itk.Mesh
- itk.PolyLineParametricPath
- vtk.vtkPolyData
- vtk.vtkStructuredGrid
- vtk.vtkUnstructuredGrid
- vtk.vtkActor
- vtk.vtkVolume
- vtk.vtkAssembly
- pyvista.PolyData
- pyvista.StructuredGrid
- pyvista.UnstructuredGrid
- vedo.Actor
- vedo.Assembly
- skan.csr.Skeleton
Exquisite volume rendering
Tri-plane volume slicing
Innovative, powerful opacity transfer function / window / level widget
Label image segmentation 2D and 3D rendering
Anisotropic voxel spacing supported
Image line profile widget
Image statistics widget
Compare images widget
Widgets to select solid colors for geometry or colormaps when point data or cell data is available
Visualize point sets as points or spheres and interactively adjust the point size
Combine with other ipywidgets to quickly create graphical interfaces that interactively provide insights into data algorithms

These widgets are designed to support spatial analysis with the Insight Toolkit (ITK), but they work equally well with other spatial analysis tools in the scientific Python ecosystem.

These widgets are built on itk.js and vtk.js.

Examples on Binder

Data types:

Recipes:

Installation

To install the widgets for the Jupyter Notebook with pip:

pip install itkwidgets

For Jupyter Lab, additionally, run:

jupyter labextension install @jupyter-widgets/jupyterlab-manager jupyter-matplotlib jupyterlab-datawidgets itkwidgets

Note

JupyterLab 3 support is not yet available. JupyterLab 2 or the Jupyter Notebook are possible alternatives.

Usage

In Jupyter, import the view function:

from itkwidgets import view

Then, call the view function at the end of a cell, passing in the image to examine:

view(image)

For information on additional options, see the view function docstring:

view?

Other available widgets:

itkwidgets.line_profile: Plot an intensity line profile.
itkwidgets.checkerboard: Compare two images in a checkerboard pattern.
itkwidgets.compare: Compare two images side-by-side.

Using within a Docker Container

You can use itkwidgets from within a docker container with jupyterlab. To create a local docker image:

Install docker and build the docker image with:

git clone https://github.com/InsightSoftwareConsortium/itkwidgets
cd itkwidgets/docker
IMAGE=itkwidgets:0.1.0
docker build -t $IMAGE .

Then run the docker container with:

EXAMPLESDIR=`pwd`/../examples
docker run -it --rm -v $EXAMPLESDIR:/home/jovyan -p 8888:8888 itkwidgets:0.1.0

Finally, connect to your notebook at

Advanced Usage

The itkwidgets are based on ipywidgets. As a consequence, widgets traits can be queried, assigned, or observed with the viewer object returned by the view function. itkwidgets can be combined with other ipywidgets to quickly explore algorithm parameters, create graphical interfaces, or create data visualization dashboards.

Mouse Controls

Left click + drag
Rotate

Right click + drag or shift + left click + drag
Pan

Mouse wheel or control + left click + drag or pinch
Zoom

Alt + left click + drag left-right
Change color transfer function window

Shift + left click + drag top-bottom
Change color transfer function level

Shift + alt + left click + drag top-bottom
Change primary Gaussian volume opacity transfer function magnitude

Keyboard Shortcuts

Keyboard shortcuts take effect when the mouse is positioned inside the viewer. All shortcuts are prefixed with Alt+. Corresponding keys for the Dvorak keyboard layout have the same effect.

Alt + 1
X-plane mode

Alt + 2
Y-plane mode

Alt + 3
Z-plane mode

Alt + 4
Volume rendering mode

Alt + q
Toggle user interface

Alt + w
Toggle region of interest (ROI) selection widget

Alt + e
Reset ROI

Alt + r
Reset camera

Alt + s
Toggle slicing planes in volume rendering mode

Alt + f
Toggle fullscreen

Examples

After installation, try the following examples that demonstrate how to visualize:

or how to:

Troubleshooting

IOPub data rate exceeded.

If you experience the notebook warning:

IOPub data rate exceeded.
The notebook server will temporarily stop sending output
to the client in order to avoid crashing it.
To change this limit, set the config variable
`--NotebookApp.iopub_data_rate_limit`.

Set the notebook configuration value:

jupyter notebook --NotebookApp.iopub_data_rate_limit=1e12

Scrolling in JupyterLab

Cell output scrolls by default in JupyterLab. To disable scrolling, right click in the region to the left of the output and select Disable Scrolling for Outputs.

'Permission denied' during installation

If Permission denied errors occur during installation, install the Python package with user permission via:

> pip install --user itkwidgets

For JupyterLab extension installation, configure JupyterLab to use your user application directory by setting the environmental variable, `JUPYTERLAB_DIR`:

export JUPYTERLAB_DIR=$HOME/.local/share/jupyter/lab

Check that this is picked up in the value of the Application directory reported by:

jupyter lab path

Then, install the extension as usual:

jupyter labextension install @jupyter-widgets/jupyterlab-manager jupyter-matplotlib jupyterlab-datawidgets itkwidgets

Hacking

Participation is welcome! For a development installation (requires Node.js):

git clone https://github.com/InsightSoftwareConsortium/itkwidgets.git
cd itkwidgets
python -m pip install -r requirements-dev.txt -r requirements.txt
python -m pip install -e .
jupyter nbextension install --py --symlink --sys-prefix itkwidgets
jupyter nbextension enable --py --sys-prefix itkwidgets
jupyter nbextension enable --py --sys-prefix widgetsnbextension
python -m pytest
python -m pytest --nbmake examples/*.ipynb

The above commands will setup your system for development with the Jupyter Notebook. In one terminal, start Jupyter:

cd itkwidgets
jupyter notebook

In another terminal, put Webpack in watch mode to rebuild any Javascript changes when you save a Javascript file:

cd itkwidgets
npm run watch

If Python code is changed, restart the kernel to see the changes. If Javascript code is changed, reload the page after to Webpack has finished building.

To develop for Jupyter Lab, additionally run:

jupyter labextension install @jupyter-widgets/jupyterlab-manager jupyter-matplotlib jupyterlab-datawidgets jupyter-webrtc
jupyter labextension install ./js
jupyter lab --watch

Note

Historical note: this project was previously named itk-jupyter-widgets, but it was renamed to itkwidgets to be consistent with the package name.

Warning

This project is under active development. Its API and behavior may change at any time. We mean it.

itkwidgets dependencies

colorcet ipydatawidgets ipympl ipywidgets itk-core itk-filtering itk-meshtopolydata itk-numerics matplotlib notebook numpy six traitlets zstandard

FAQs

What is itkwidgets?

Interactive Jupyter widgets to visualize images, point sets, and meshes in 2D and 3D. Visit Snyk Advisor to see a full health score report for itkwidgets, including popularity, security, maintenance & community analysis.

Is itkwidgets popular?

The python package itkwidgets receives a total of 5,545 weekly downloads. As such, itkwidgets popularity was classified as a recognized. Visit the popularity section on Snyk Advisor to see the full health analysis.

Is itkwidgets well maintained?

We found indications that itkwidgets is an Inactive project. See the full package health analysis to learn more about the package maintenance status.

Is itkwidgets safe to use?

While scanning the latest version of itkwidgets, we found that a security review is needed. A total of 0 vulnerabilities or license issues were detected. See the full security scan results.

Last updated on 4 May-2024, at 16:49 (UTC).

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Snyk Vulnerability Scanner

Not sure how to use itkwidgets?

itkwidgets

Examples on Binder

Installation

Usage

Using within a Docker Container

Advanced Usage

Mouse Controls

Keyboard Shortcuts

Examples

Troubleshooting

IOPub data rate exceeded.

Scrolling in JupyterLab

'Permission denied' during installation

Hacking

itkwidgets dependencies

FAQs

What is itkwidgets?

Is itkwidgets popular?

Is itkwidgets well maintained?

Is itkwidgets safe to use?

Build a secure application checklist

Select a recommended open source package

Scan your app for vulnerabilities

Source Code

Open Source

Container

Config

Fix identified vulnerabilities

Monitor for new issues