Merge branch 'master' into removing-fvtk

README.rst

@@ -46,11 +46,11 @@ You can find our sources and single-click downloads:
 Installing DIPY
 ===============
 
-DIPY can be installed using `pip`:
+DIPY can be installed using `pip`::
 
     pip install dipy
 
-or using `conda`:
+or using `conda`::
 
     conda install -c conda-forge dipy vtk
 

doc/devel/gitwash/development_workflow.rst

@@ -4,14 +4,14 @@
 Development workflow
 ####################
 
-You already have your own forked copy of the `dipy`_ repository, by
+You already have your own forked copy of the dipy_ repository, by
 following :ref:`forking`. You have :ref:`set-up-fork`. You have configured
 git by following :ref:`configure-git`.  Now you are ready for some real work.
 
 Workflow summary
 ================
 
-In what follows we'll refer to the upstream dipy ``master`` branch, as
+In what follows we'll refer to the upstream DIPY ``master`` branch, as
 "trunk".
 
 * Don't use your ``master`` branch for anything.  Consider deleting it.
@@ -81,7 +81,7 @@ what the changes in the branch are for.  For example ``add-ability-to-fly``, or
     git checkout my-new-feature
 
 Generally, you will want to keep your feature branches on your public github_
-fork of `dipy`_.  To do this, you `git push`_ this new branch up to your
+fork of dipy_. To do this, you `git push`_ this new branch up to your
 github repo.  Generally (if you followed the instructions in these pages, and by
 default), git will have a link to your github repo, called ``origin``.  You push
 up to your own repo on github with::

doc/devel/gitwash/following_latest.rst

@@ -5,7 +5,7 @@
 =============================
 
 These are the instructions if you just want to follow the latest
-*dipy* source, but you don't need to do any development for now.
+DIPY source, but you don't need to do any development for now.
 
 The steps are:
 

doc/devel/gitwash/forking_hell.rst

@@ -1,12 +1,12 @@
 .. _forking:
 
 ======================================================
-Making your own copy (fork) of dipy
+Making your own copy (fork) of DIPY
 ======================================================
 
-You need to do this only once.  The instructions here are very similar
+You need to do this only once. The instructions here are very similar
 to the instructions at http://help.github.com/forking/ |emdash| please see
-that page for more detail.  We're repeating some of it here just to give the
+that page for more detail. We're repeating some of it here just to give the
 specifics for the `dipy`_ project, and to suggest some default names.
 
 Set up and configure a github account
@@ -17,7 +17,7 @@ If you don't have a github account, go to the github page, and make one.
 You then need to configure your account to allow write access |emdash| see
 the ``Generating SSH keys`` help on `github help`_.
 
-Create your own forked copy of `dipy`_
+Create your own forked copy of dipy_
 ======================================================
 
 #. Log into your github account.

doc/devel/gitwash/git_intro.rst

@@ -2,14 +2,14 @@
  Introduction
 ==============
 
-These pages describe a git_ and github_ workflow for the `dipy`_
+These pages describe a git_ and github_ workflow for the dipy_
 project.
 
 There are several different workflows here, for different ways of
-working with *dipy*.
+working with DIPY.
 
 This is not a comprehensive git reference, it's just a workflow for our
-own project.  It's tailored to the github hosting service. You may well
+own project. It's tailored to the github hosting service. You may well
 find better or quicker ways of getting stuff done with git, but these
 should get you started.
 

doc/devel/gitwash/index.rst

@@ -1,6 +1,6 @@
 .. _using-git:
 
-Working with *dipy* source code
+Working with DIPY source code
 ================================================
 
 Contents:

doc/devel/index.rst

@@ -1,6 +1,6 @@
  .. _development:
 
-DiPy development
+DIPY development
 ================
 
 Contents:

doc/devel/make_release.rst

@@ -1,19 +1,19 @@
 .. _release-guide:
 
 *********************************
-A guide to making a dipy release
+A guide to making a DIPY release
 *********************************
 
-A guide for developers who are doing a dipy release
+A guide for developers who are doing a DIPY release
 
 .. _release-tools:
 
 Release tools
 =============
 
-There are some release utilities that come with nibabel_.  nibabel should
+There are some release utilities that come with nibabel_. nibabel should
 install these as the ``nisext`` package, and the testing stuff is understandably
-in the ``testers`` module of that package.  Dipy has Makefile targets for their
+in the ``testers`` module of that package. DIPY has Makefile targets for their
 use.  The relevant targets are::
 
     make check-version-info
@@ -75,10 +75,10 @@ Release checklist
   ``README`` in the root directory, maybe with ``vim`` ``diffthis`` command.
   Check all the links are still valid.
 
-* Check all the dipy builds are green on the `nipy buildbot`_
+* Check all the DIPY builds are green on the `nipy buildbot`_
 
 * If you have travis-ci_ building set up you might want to push the code in its
-  current state to a branch that will build, e.g::
+current state to a branch that will build, e.g.::
 
     git branch -D pre-release-test # in case branch already exists
     git co -b pre-release-test
@@ -128,7 +128,7 @@ Release checklist
     git clean -fxd
     python setup.py build_ext --inplace
 
-* Make sure all tests pass on your local machine (from the dipy root directory)::
+* Make sure all tests pass on your local machine (from the ``<dipy root>`` directory)::
 
     cd ..
     nosetests --with-doctest dipy
@@ -144,14 +144,16 @@ Release checklist
   running the doctests in the code, where the doctests pass when run in nose -
   we should find out why this is at some point, but leave it for now.
 
-* Trigger builds of all the binary build testers for dipy, using the web
-  interface.  You may need permissions set to do this - contact Matthew or
+* Trigger builds of all the binary build testers for DIPY, using the web
+  interface. You may need permissions set to do this - contact Matthew or
   Eleftherios if you do.
 
-  At the moment, the useful dipy binary build testers are:
+  At the moment, the useful DIPY binary build testers are:
 
-      * http://nipy.bic.berkeley.edu/builders/dipy-bdist32-26
+      * http://nipy.bic.berkeley.edu/builders/dipy-bdist32-35
       * http://nipy.bic.berkeley.edu/builders/dipy-bdist32-27
+      * http://nipy.bic.berkeley.edu/builders/dipy-bdist64-27
+      * http://nipy.bic.berkeley.edu/builders/dipy-bdist64-35
       * http://nipy.bic.berkeley.edu/builders/dipy-bdist-mpkg-2.6
       * http://nipy.bic.berkeley.edu/builders/dipy-bdist-mpkg-2.7
 
@@ -263,9 +265,9 @@ tag to github, so the buildbots can find the released code and build it.
 
   Download the builds and upload to pypi.
 
-  You can upload the exe files with the *files* interface for the new dipy release.
+  You can upload the exe files with the *files* interface for the new DIPY release.
   Obviously you'll need to log in to do this, and you'll need to be an admin for
-  the dipy pypi project.
+  the DIPY pypi project.
 
   For reference, if you need to do binary exe builds by hand, use something
   like::

doc/examples/affine_registration_3d.py

@@ -66,7 +66,7 @@
 .. figure:: resampled_2.png
    :align: center
 
-   **Input images before alignment**.
+   Input images before alignment.
 """
 
 """
@@ -99,7 +99,7 @@
 .. figure:: transformed_com_2.png
    :align: center
 
-   **Registration result by aligning the centers of mass of the images**.
+   Registration result by aligning the centers of mass of the images.
 """
 
 """
@@ -203,7 +203,7 @@
 .. figure:: transformed_trans_2.png
    :align: center
 
-   **Registration result by translating the moving image, using MI**.
+   Registration result by translating the moving image, using Mutual Information.
 """
 
 """
@@ -238,7 +238,7 @@
 .. figure:: transformed_rigid_2.png
    :align: center
 
-   **Registration result with a rigid transform, using Mutual Information**.
+   Registration result with a rigid transform, using Mutual Information.
 """
 
 """
@@ -274,7 +274,7 @@
 .. figure:: transformed_affine_2.png
    :align: center
 
-   **Registration result with an affine transform, using Mutual Information**.
+   Registration result with an affine transform, using Mutual Information.
 
 .. [Mattes03] Mattes, D., Haynor, D. R., Vesselle, H., Lewellen, T. K.,
               Eubank, W. (2003). PET-CT image registration in the chest using

doc/examples/brain_extraction_dwi.py

@@ -3,8 +3,8 @@
 Brain segmentation with median_otsu
 ===================================
 
-We show how to extract brain information and mask from a b0 image using dipy's
-segment.mask module.
+We show how to extract brain information and mask from a b0 image using dipy_'s
+``segment.mask`` module.
 
 First import the necessary modules:
 """
@@ -15,8 +15,8 @@
 """
 Download and read the data for this tutorial.
 
-The scil_b0 dataset contains different data from different companies and
-models. For this example, the data comes from a 1.5 tesla Siemens MRI.
+The ``scil_b0`` dataset contains different data from different companies and
+models. For this example, the data comes from a 1.5 Tesla Siemens MRI.
 """
 
 from dipy.data.fetcher import fetch_scil_b0, read_siemens_scil_b0
@@ -28,7 +28,7 @@
 ``img`` contains a nibabel Nifti1Image object. Data is the actual brain data as
 a numpy ndarray.
 
-Segment the brain using dipy's mask module.
+Segment the brain using DIPY's ``mask`` module.
 
 ``median_otsu`` returns the segmented brain data and a binary mask of the brain.
 It is possible to fine tune the parameters of ``median_otsu`` (``median_radius``
@@ -41,10 +41,10 @@
 b0_mask, mask = median_otsu(data, 2, 1)
 
 """
-Saving the segmentation results is very easy using nibabel. We need the b0_mask,
-and the binary mask volumes. The affine matrix which transform the image's
-coordinates to the world coordinates is also needed. Here, we choose to save
-both images in float32.
+Saving the segmentation results is very easy using nibabel. We need the
+``b0_mask``, and the binary mask volumes. The affine matrix which transform the
+image's coordinates to the world coordinates is also needed. Here, we choose to
+save both images in ``float32``.
 """
 
 mask_img = nib.Nifti1Image(mask.astype(np.float32), img.affine)
@@ -55,7 +55,7 @@
 nib.save(b0_img, fname + '_mask.nii.gz')
 
 """
-Quick view of the results middle slice using matplotlib.
+Quick view of the results middle slice using ``matplotlib``.
 """
 
 import matplotlib.pyplot as plt
@@ -77,12 +77,12 @@
 .. figure:: median_otsu.png
    :align: center
 
-   **An application of median_otsu for brain segmentation**.
+   An application of median_otsu for brain segmentation.
 
 ``median_otsu`` can also automatically crop the outputs to remove the largest
 possible number of background voxels. This makes outputted data significantly
-smaller.  auto cropping in ``median_otsu`` is activated by setting the
-``autocrop`` parameter to True.
+smaller. Auto-cropping in ``median_otsu`` is activated by setting the
+``autocrop`` parameter to ``True``.
 """
 
 b0_mask_crop, mask_crop = median_otsu(data, 4, 4, autocrop=True)
@@ -96,3 +96,9 @@
     b0_mask_crop.astype(np.float32), img.affine)
 nib.save(mask_img_crop, fname + '_binary_mask_crop.nii.gz')
 nib.save(b0_img_crop, fname + '_mask_crop.nii.gz')
+
+"""
+
+.. include:: ../links_names.inc
+
+"""

doc/examples/bundle_registration.py

@@ -73,7 +73,7 @@ def show_both_bundles(bundles, colors=None, show=True, fname=None):
 .. figure:: before_registration.png
    :align: center
 
-   **Before bundle registration**.
+   Before bundle registration.
 """
 
 show_both_bundles([cb_subj1, cb_subj2_aligned],
@@ -84,7 +84,7 @@ def show_both_bundles(bundles, colors=None, show=True, fname=None):
 .. figure:: after_registration.png
    :align: center
 
-   **After bundle registration**.
+   After bundle registration.
 
 As you can see the two cingulum bundles are well aligned although they contain
 many streamlines of different length and shape.