update structure

1.8.0/_downloads/38ac926e4e838ee7e9e6bb179c1a9375/tissue_classification.ipynb

@@ -130,7 +130,7 @@
       "cell_type": "markdown",
       "metadata": {},
       "source": [
-        ".. figure:: probabilities.png\n   :align: center\n   :scale: 120\n\n   These are the probability maps of each of the three tissue classes.\n\n.. [Zhang2001] Zhang, Y., Brady, M. and Smith, S. Segmentation of Brain MR\n   Images Through a Hidden Markov Random Field Model and the\n   Expectation-Maximization Algorithm IEEE Transactions on Medical Imaging,\n   20(1): 45-56, 2001\n\n.. [Avants2011] Avants, B. B., Tustison, N. J., Wu, J., Cook, P. A. and Gee,\n   J. C. An open source multivariate framework for n-tissue segmentation with\n   evaluation on public data. Neuroinformatics, 9(4): 381-400, 2011.\n\n\n"
+        "These are the probability maps of each of the three tissue classes.\n\n.. [Zhang2001] Zhang, Y., Brady, M. and Smith, S. Segmentation of Brain MR\n   Images Through a Hidden Markov Random Field Model and the\n   Expectation-Maximization Algorithm IEEE Transactions on Medical Imaging,\n   20(1): 45-56, 2001\n\n.. [Avants2011] Avants, B. B., Tustison, N. J., Wu, J., Cook, P. A. and Gee,\n   J. C. An open source multivariate framework for n-tissue segmentation with\n   evaluation on public data. Neuroinformatics, 9(4): 381-400, 2011.\n\n\n"
       ]
     },
     {

1.8.0/_downloads/c7cc6c76bfc8d13ae10567b16c93ee19/tissue_classification.py

@@ -132,10 +132,6 @@
 plt.show()
 
 ###############################################################################
-# .. figure:: probabilities.png
-#    :align: center
-#    :scale: 120
-# 
 #    These are the probability maps of each of the three tissue classes.
 # 
 # .. [Zhang2001] Zhang, Y., Brady, M. and Smith, S. Segmentation of Brain MR

1.8.0/_sources/devel/index.rst.txt

@@ -1,7 +1,7 @@
  .. _development:
 
-DIPY development
-================
+DIPY Developer Guide
+====================
 
 .. toctree::
    :maxdepth: 2

1.8.0/_sources/documentation.rst.txt

@@ -1,11 +1,151 @@
 .. _documentation:
 
-Documentation
-===============
+Diffusion Imaging In Python - Documentation
+===========================================
+
+.. container:: index-paragraph
+
+   DIPY_ is the paragon 3D/4D+ imaging library in Python. Contains generic methods for
+   spatial normalization, signal processing, machine learning, statistical analysis
+   and visualization of medical images. Additionally, it contains
+   specialized methods for computational anatomy including diffusion,
+   perfusion and structural imaging.
+
+   DIPY is part of the `NiPy ecosystem <https://nipy.org/>`__.
+
+
+***********
+Quick links
+***********
+
+.. grid:: 2
+    :gutter: 3
+
+    .. grid-item-card:: :octicon:`rocket` Get started
+        :link: user_guide/install
+        :link-type: any
+
+        New to DIPY_? Start with our installation guide and DIPY key
+        concepts.
+
+    .. grid-item-card:: :octicon:`image` Tutorials
+        :link: examples_built/index
+        :link-type: any
+
+        Browse our tutorials gallery.
+
+    .. grid-item-card:: :octicon:`image` Recipes
+        :link: recipes/index
+        :link-type: any
+
+        How to X ?  This is a section to provides you quick answer.
+
+    .. grid-item-card:: :octicon:`zap` Workflows
+        :link: interfaces/index
+        :link-type: any
+
+        Not confortable with coding? we have command line interfaces for you.
+        An easy way to use DIPY_ via a terminal.
+
+    .. grid-item-card:: :octicon:`rocket` Theory
+        :link: theory/index
+        :link-type: any
+
+        Back to the basics. Learn the theory behind the methods implemented in DIPY_.
+
+    .. grid-item-card:: :octicon:`tools` Developer Guide
+        :link: development
+        :link-type: any
+
+        Saw a typo? Found a bug? Want to improve a function? Learn how to
+        contribute to DIPY_!
+
+    .. grid-item-card:: :octicon:`repo` API reference
+        :link: reference/index
+        :link-type: any
+
+        A detailed description of DIPY public Python API.
+
+    .. grid-item-card:: :octicon:`repo` Workflows API reference
+        :link: reference/index
+        :link-type: any
+
+        A detailed description of all the DIPY workflows command line.
+
+    .. grid-item-card:: :octicon:`history` Release notes
+        :link: stateoftheart
+        :link-type: any
+
+        Upgrading from a previous version? See what's new and changed between
+        each release of DIPY_.
+
+    .. grid-item-card:: :octicon:`comment-discussion` Get help :octicon:`link-external`
+        :link: https://github.com/dipy/dipy/discussions
+
+        Need help with your processing? Ask us and a large
+        neuroimaging community.
+
+
+**********
+Highlights
+**********
+
+**DIPY 1.7.0** is now available. New features include:
+
+- NF: BundleWarp - Streamline-based nonlinear registration method for bundles added.
+- NF: DKI+ - Diffusion Kurtosis modeling with advanced constraints added.
+- NF: Synb0 - Synthetic b0 creation added using deep learning added.
+- NF: New Parallel Transport Tractography (PTT) added.
+- NF: Fast Streamline Search algorithm added.
+- NF: New denoising methods based on 1D CNN added.
+- Handle Asymmetric Spherical Functions.
+- Large update of DIPY Horizon features.
+- Multiple Workflows updated
+- Large codebase cleaning.
+- Large documentation update. Integration of Sphinx-Gallery.
+- Closed 53 issues and merged 34 pull requests.
+
+See :ref:`Older Highlights <old_highlights>`.
+
+*************
+Announcements
+*************
+- :doc:`DIPY 1.7.0 <release_notes/release1.7>` released April 23, 2023.
+- :doc:`DIPY 1.6.0 <release_notes/release1.6>` released January 16, 2023.
+- :doc:`DIPY 1.5.0 <release_notes/release1.5>` released March 11, 2022.
+
+
+
+
+See some of our :ref:`Past Announcements <old_news>`
+
+*******
+Support
+*******
+
+We acknowledge support from the following organizations:
+
+- The department of Intelligent Systems Engineering of Indiana University.
+
+- The National Institute of Biomedical Imaging and Bioengineering, NIH.
+
+- The Gordon and Betty Moore Foundation and the Alfred P. Sloan Foundation, through the
+  University of Washington eScience Institute Data Science Environment.
+
+- Google supported DIPY through the Google Summer of Code Program during
+  Summer 2015, 2016 and 2018.
+
+- The International Neuroinformatics Coordination Facility.
+
+
+
+
+.. include:: links_names.inc
 
 .. This tree is helping populate the side navigation panel
 .. toctree::
    :maxdepth: 2
+   :hidden:
 
    introduction
    mission
@@ -24,12 +164,3 @@ Documentation
 
 .. Main content will be displayed using the jinja template
 
-
-..
-   Indices and tables
-   ==================
-
-   * :ref:`genindex`
-   * :ref:`modindex`
-   * :ref:`search`
-

1.8.0/_sources/examples_built/index.rst.txt

@@ -1,14 +1,26 @@
 :orphan:
 
+:html_theme.sidebar_secondary.remove:
+
 .. _examples:
 
+
 Examples
 ========
 
-.. toctree::
-   :maxdepth: 1
+.. note::
+    The examples here are some uses of the analysis and visualization functionality
+    of DIPY, with example data from actual neuroscience experiments, or with
+    synthetic data, which is generated as part of the example.
+
+    All the examples presented in the documentation are generated from
+    *fully functioning* python scripts, which are available as part of the
+    source distribution in the `doc/examples` folder.
+
+    If you want to replicate a particular analysis or visualization, simply copy
+    or download the relevant `.py` script from the source distribution, edit out
+    the body of the text of the example and alter it to your purpose.
 
-   ../note_about_examples
 
 .. contents::
    :depth: 2
@@ -298,7 +310,8 @@ Reconstruction
 
 Below, an overview of all reconstruction models available on DIPY.
 
-Note: Some reconstruction models do not have a tutorial yet
+.. note::
+    Some reconstruction models do not have a tutorial yet
 
 .. include:: ../reconstruction_models_list.rst
 

1.8.0/_sources/examples_built/reconstruction/index.rst.txt

@@ -7,7 +7,8 @@ Reconstruction
 
 Below, an overview of all reconstruction models available on DIPY.
 
-Note: Some reconstruction models do not have a tutorial yet
+.. note::
+    Some reconstruction models do not have a tutorial yet
 
 .. include:: ../reconstruction_models_list.rst