Metadata-Version: 2.1
Name: itkwidgets
Version: 0.32.3
Summary: Interactive Jupyter widgets to visualize images, point sets, and meshes in 2D and 3D
Home-page: https://github.com/InsightSoftwareConsortium/itkwidgets
Author: Matthew McCormick
Author-email: matt.mccormick@kitware.com
License: UNKNOWN
Description: itkwidgets
        ==========
        
        .. image:: https://img.shields.io/pypi/v/itkwidgets.svg
            :target: https://pypi.python.org/pypi/itkwidgets
            :alt: PyPI version
        
        .. image:: https://img.shields.io/npm/v/itkwidgets/latest
            :target: https://www.npmjs.com/package/itkwidgets
            :alt: npm
        
        .. image:: https://github.com/InsightSoftwareConsortium/itkwidgets/workflows/Build%20and%20test/badge.svg
            :target: https://github.com/InsightSoftwareConsortium/itkwidgets/actions?query=workflow%3A%22Build+and+test%22
            :alt: Build status
        
        .. image:: https://mybinder.org/badge_logo.svg
            :target: https://mybinder.org/v2/gh/InsightSoftwareConsortium/itkwidgets/master?filepath=examples%2F3DImage.ipynb
            :alt: Interactive example on MyBinder
        
        .. image:: https://img.shields.io/badge/License-Apache%202.0-blue.svg
            :target: https://github.com/InsightSoftwareConsortium/itkwidgets/blob/master/LICENSE
            :alt: License
        
        .. image:: https://zenodo.org/badge/121581663.svg
            :target: https://zenodo.org/badge/latestdoi/121581663
            :alt: Software citation DOI
        
        Interactive Jupyter_ widgets to visualize images, point sets, and meshes on the web.
        
        .. image:: https://i.imgur.com/d8aXycW.png
            :width: 800px
            :alt: itkwidgets chest CT in JupyterLab
        
        **Key Features**:
        
        - Visualize 2D and 3D images, point sets, and geometry, e.g. meshes, in Jupyter_
        - Support for
        
          - `NumPy array <https://docs.scipy.org/doc/numpy/reference/generated/numpy.ndarray.html>`_ images
          - `itk.Image <https://itkpythonpackage.readthedocs.io/en/latest/Quick_start_guide.html>`_
          - `Dask array <https://docs.dask.org/en/latest/array.html>`_ images
          - `vtk.vtkImageData <https://vtk.org>`_
          - `pyvista.UniformGrid <https://pyvista.org>`_
          - `vedo.Volume <https://vedo.embl.es/index.html>`_
          - `pyimagej ImageJ / Fiji / ImageJ2 images <https://github.com/imagej/pyimagej>`_
          - Additional NumPy array-like objects
          - `SimpleITK.Image <https://simpleitk-prototype.readthedocs.io/en/latest/user_guide/plot_image.html#sphx-glr-user-guide-plot-image-py>`_
        
          - NumPy array point sets
          - `itk.PointSet <https://itk.org/Doxygen/html/classitk_1_1PointSet.html>`_
          - `itk.PointBasedSpatialObject <https://itk.org/Doxygen/html/classitk_1_1PointBasedSpatialObject.html>`_
          - `vtk.vtkPolyData <https://vtk.org/doc/nightly/html/classvtkPolyData.html>`_ point sets
          - `pyvista.PolyData <https://docs.pyvista.org/core/points.html>`_ point sets
        
          - `itk.Mesh <https://itk.org/Doxygen/html/classitk_1_1Mesh.html>`_
          - `itk.PolyLineParametricPath <https://itk.org/Doxygen/html/classitk_1_1PolyLineParametricPath.html>`_
          - `vtk.vtkPolyData <https://vtk.org/doc/nightly/html/classvtkPolyData.html>`_
          - `vtk.vtkStructuredGrid <https://vtk.org/doc/nightly/html/classvtkStructuredGrid.html>`_
          - `vtk.vtkUnstructuredGrid <https://vtk.org/doc/nightly/html/classvtkUnstructuredGrid.html>`_
          - `vtk.vtkActor <https://vtk.org/doc/nightly/html/classvtkActor.html>`_
          - `vtk.vtkVolume <https://vtk.org/doc/nightly/html/classvtkVolume.html>`_
          - `vtk.vtkAssembly <https://vtk.org/doc/nightly/html/classvtkAssembly.html>`_
          - `pyvista.PolyData <https://docs.pyvista.org/core/points.html>`_
          - `pyvista.StructuredGrid <https://docs.pyvista.org/core/point-grids.html#structured-grid-creation>`_
          - `pyvista.UnstructuredGrid <https://docs.pyvista.org/core/point-grids.html#unstructured-grid-creation>`_
          - `vedo.Actor <https://vedo.embl.es/index.html>`_
          - `vedo.Assembly <https://vedo.embl.es/index.html>`_
          - `skan.csr.Skeleton <https://jni.github.io/skan/api/skan.csr.html#module-skan.csr>`_
        
        - 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
        
        .. image:: https://thumbs.gfycat.com/ShyFelineBeetle-size_restricted.gif
            :width: 640px
            :alt: itkwidgets demo
            :align: center
        
        These widgets are designed to support spatial analysis with the `Insight Toolkit
        (ITK) <https://itk.org/>`_, but they work equally well with other spatial analysis tools
        in the scientific Python ecosystem.
        
        These widgets are built on
        `itk.js <https://github.com/InsightSoftwareConsortium/itk-js>`_ and
        `vtk.js <https://github.com/Kitware/vtk-js>`_.
        
        Examples on Binder
        ------------------
        
        Data types:
        
        - `Binder: 2D ITK Images <https://mybinder.org/v2/gh/InsightSoftwareConsortium/itkwidgets/master?filepath=examples%2F2DImage.ipynb>`_
        - `Binder: 3D ITK Images <https://mybinder.org/v2/gh/InsightSoftwareConsortium/itkwidgets/master?filepath=examples%2F3DImage.ipynb>`_
        - `Binder: 3D Label Images <https://mybinder.org/v2/gh/InsightSoftwareConsortium/itkwidgets/master?filepath=examples%2FLabelImages.ipynb>`_
        - `Binder: Dask Array images <https://mybinder.org/v2/gh/InsightSoftwareConsortium/itkwidgets/master?filepath=examples/DaskArray.ipynb>`_
        - `Binder: Large volumes <https://mybinder.org/v2/gh/InsightSoftwareConsortium/itkwidgets/master?filepath=examples/LargeVolumes.ipynb>`_
        - `Binder: NumPy array images (processed with SciPy) <https://mybinder.org/v2/gh/InsightSoftwareConsortium/itkwidgets/master?filepath=examples/NumPyArrayImage.ipynb>`_
        - `Binder: NumPy array images (processed with scikit-image) <https://mybinder.org/v2/gh/InsightSoftwareConsortium/itkwidgets/master?filepath=examples/scikit-image.ipynb>`_
        - `Binder: NumPy array for image with anisotropic spacing <https://mybinder.org/v2/gh/InsightSoftwareConsortium/itkwidgets/master?filepath=examples/ImageWithAnisotropicPixelSpacing.ipynb>`_
        - `Binder: NumPy array point sets <https://mybinder.org/v2/gh/InsightSoftwareConsortium/itkwidgets/master?filepath=examples/NumPyArrayPointSet.ipynb>`_
        - `Binder: ITK Mesh <https://mybinder.org/v2/gh/InsightSoftwareConsortium/itkwidgets/master?filepath=examples/Mesh.ipynb>`_
        - `Binder: ITK PointBasedSpatialObject <https://mybinder.org/v2/gh/InsightSoftwareConsortium/itkwidgets/master?filepath=examples/PointBasedSpatialObject.ipynb>`_
        - `Binder: skan segmentation skeleton <https://mybinder.org/v2/gh/InsightSoftwareConsortium/itkwidgets/master?filepath=examples/SegmentationSkeleton.ipynb>`_
        - `Binder: skan segmentation skeleton <https://mybinder.org/v2/gh/InsightSoftwareConsortium/itkwidgets/master?filepath=examples/SegmentationSkeleton.ipynb>`_
        
        Recipes:
        
        - `Binder: Compare images with a checkerboard pattern <https://mybinder.org/v2/gh/InsightSoftwareConsortium/itkwidgets/master?filepath=examples/Checkerboard.ipynb>`_
        - `Binder: Compare images side by side <https://mybinder.org/v2/gh/InsightSoftwareConsortium/itkwidgets/master?filepath=examples/CompareImages.ipynb>`_
        - `Binder: Examine a line profile <https://mybinder.org/v2/gh/InsightSoftwareConsortium/itkwidgets/master?filepath=examples/LineProfile.ipynb>`_
        - `Binder: Inspect image label statistics <https://mybinder.org/v2/gh/InsightSoftwareConsortium/itkwidgets/master?filepath=examples/ImageLabelStatistics.ipynb>`_
        - `Binder: Interactively explore algorithm parameters <https://mybinder.org/v2/gh/InsightSoftwareConsortium/itkwidgets/master?filepath=examples/InteractiveParameterExploration.ipynb>`_
        - `Binder: Record a video <https://mybinder.org/v2/gh/InsightSoftwareConsortium/itkwidgets/master?filepath=examples/RecordAVideo.ipynb>`_
        - `Binder: Restore a volume opacity transfer function <https://mybinder.org/v2/gh/InsightSoftwareConsortium/itkwidgets/master?filepath=examples/VolumeOpacityTransferFunction.ipynb>`_
        - `Binder: Select a region of interest <https://mybinder.org/v2/gh/InsightSoftwareConsortium/itkwidgets/master?filepath=examples/SelectRegionOfInterest.ipynb>`_
        - `Binder: Specify camera parameters <https://mybinder.org/v2/gh/InsightSoftwareConsortium/itkwidgets/master?filepath=examples/CameraParameters.ipynb>`_
        - `Binder: Specify a colormap <https://mybinder.org/v2/gh/InsightSoftwareConsortium/itkwidgets/master?filepath=examples/SpecifyAColormap.ipynb>`_
        
        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 http://127.0.0.1:8888/lab
        
        Advanced Usage
        ^^^^^^^^^^^^^^
        
        The *itkwidgets* are based on `ipywidgets
        <https://ipywidgets.readthedocs.io/en/latest/examples/Widget%20Basics.html>`_.
        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:
        
        - `2D ITK Images <https://github.com/InsightSoftwareConsortium/itkwidgets/blob/master/examples/2DImage.ipynb>`_
        - `3D ITK Images <https://github.com/InsightSoftwareConsortium/itkwidgets/blob/master/examples/3DImage.ipynb>`_
        - `3D Label maps <https://github.com/InsightSoftwareConsortium/itkwidgets/blob/master/examples/LabelImages.ipynb>`_
        - `Dask Array images <https://github.com/InsightSoftwareConsortium/itkwidgets/blob/master/examples/DaskArray.ipynb>`_
        - `Large volumes <https://github.com/InsightSoftwareConsortium/itkwidgets/blob/master/examples/LargeVolumes.ipynb>`_
        - `ImageJ ImgLib2 images <https://github.com/InsightSoftwareConsortium/itkwidgets/blob/master/examples/ImageJImgLib2.ipynb>`_ (requires `conda <https://conda.io/>`_ and a local `Fiji <https://fiji.sc/>`_ installation)
        - `NumPy array images (processed with SciPy) <https://github.com/InsightSoftwareConsortium/itkwidgets/blob/master/examples/NumPyArrayImage.ipynb>`_
        - `NumPy array images (processed with scikit-image) <https://github.com/InsightSoftwareConsortium/itkwidgets/blob/master/examples/scikit-image.ipynb>`_
        - `NumPy array for image with anisotropic spacing <https://github.com/InsightSoftwareConsortium/itkwidgets/blob/master/examples/ImageWithAnisotropicPixelSpacing.ipynb>`_
        - `VTK vtkImageData <https://github.com/InsightSoftwareConsortium/itkwidgets/blob/master/examples/vtkImageData.ipynb>`_
        - `pyvista UniformGrid <https://github.com/InsightSoftwareConsortium/itkwidgets/blob/master/examples/pyvista.UniformGrid.ipynb>`_
        - `NumPy array point sets <https://github.com/InsightSoftwareConsortium/itkwidgets/blob/master/examples/NumPyArrayPointSet.ipynb>`_
        - `ITK Mesh <https://github.com/InsightSoftwareConsortium/itkwidgets/blob/master/examples/Mesh.ipynb>`_
        - `ITK PointBasedSpatialObject <https://github.com/InsightSoftwareConsortium/itkwidgets/blob/master/examples/PointBasedSpatialObject.ipynb>`_
        - `VTK vtkPolyData <https://github.com/InsightSoftwareConsortium/itkwidgets/blob/master/examples/vtkPolyData.ipynb>`_
        - `VTK vtkUnstructuredGrid <https://github.com/InsightSoftwareConsortium/itkwidgets/blob/master/examples/vtkUnstructuredGrid.ipynb>`_
        - `pyvista PolyData <https://github.com/InsightSoftwareConsortium/itkwidgets/blob/master/examples/pyvista.PolyData.ipynb>`_
        - `pyvista StructuredGrid <https://github.com/InsightSoftwareConsortium/itkwidgets/blob/master/examples/pyvista.StructuredGrid.ipynb>`_
        - `pyvista UnstructuredGrid <https://github.com/InsightSoftwareConsortium/itkwidgets/blob/master/examples/pyvista.UnstructuredGrid.ipynb>`_
        - `pyvista LiDAR <https://github.com/InsightSoftwareConsortium/itkwidgets/blob/master/examples/pyvistaLiDAR.ipynb>`_
        - `vedo actors and volumes <https://github.com/InsightSoftwareConsortium/itkwidgets/blob/master/examples/vedo.ipynb>`_
        - `skan segmentation skeleton <https://github.com/InsightSoftwareConsortium/itkwidgets/blob/master/examples/SegmentationSkeleton.ipynb>`_
        
        or how to:
        
        - `Compares images with a checkerboard pattern <https://github.com/InsightSoftwareConsortium/itkwidgets/blob/master/examples/Checkerboard.ipynb>`_
        - `Compares images side by side <https://github.com/InsightSoftwareConsortium/itkwidgets/blob/master/examples/CompareImages.ipynb>`_
        - `Examine a line profile <https://github.com/InsightSoftwareConsortium/itkwidgets/blob/master/examples/LineProfile.ipynb>`_
        - `Inspect image label statistics <https://github.com/InsightSoftwareConsortium/itkwidgets/blob/master/examples/ImageLabelStatistics.ipynb>`_
        - `Interactively explore algorithm parameters <https://github.com/InsightSoftwareConsortium/itkwidgets/blob/master/examples/InteractiveParameterExploration.ipynb>`_
        - `Record a video <https://github.com/InsightSoftwareConsortium/itkwidgets/blob/master/examples/RecordAVideo.ipynb>`_
        - `Restore a volume opacity transfer function <https://github.com/InsightSoftwareConsortium/itkwidgets/blob/master/examples/VolumeOpacityTransferFunction.ipynb>`_
        - `Select a region of interest <https://github.com/InsightSoftwareConsortium/itkwidgets/blob/master/examples/SelectRegionOfInterest.ipynb>`_
        - `Specify camera parameters <https://github.com/InsightSoftwareConsortium/itkwidgets/blob/master/examples/CameraParameters.ipynb>`_
        - `Specify a colormap <https://github.com/InsightSoftwareConsortium/itkwidgets/blob/master/examples/SpecifyAColormap.ipynb>`_
        
        
        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 <https://nodejs.org/en/download/>`_)::
        
          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.
        
        .. _Jupyter: https://jupyter.org/
        
Keywords: ipython,jupyter,jupyterlab-extension,widgets,itk,imaging,visualization,webgl
Platform: UNKNOWN
Classifier: License :: OSI Approved :: Apache Software License
Classifier: Programming Language :: Python
Classifier: Development Status :: 4 - Beta
Classifier: Framework :: IPython
Classifier: Intended Audience :: Developers
Classifier: Intended Audience :: Science/Research
Classifier: Topic :: Multimedia :: Graphics
Classifier: Programming Language :: Python :: 3
Classifier: Programming Language :: Python :: 3.6
Classifier: Programming Language :: Python :: 3.7
Classifier: Programming Language :: Python :: 3.8
Classifier: Programming Language :: Python :: 3.9
Description-Content-Type: text/x-rst
