Merge branch 'enh/transforms' into 'master'

enh/transforms

See merge request fsl/fslpy!113

CHANGELOG.rst

@@ -12,6 +12,18 @@ Added
 
 * New :mod:`.image.roi` module, for exracting an ROI of an image, or expanding
   its field-of-view.
+* New :meth:`.Image.getAffine` method, for retrieving an affine between any of
+  the voxel, FSL, or world coordinate systems.
+* New :mod:`fsl.transforms` package, which contains classes and functions for
+  working with linear and non-linear FLIRT and FNIRT transformations.
+* New static methods :meth:`.Nifti.determineShape`,
+  :meth:`.Nifti.determineAffine`, :meth:`.Nifti.generateAffines`, and
+  :meth:`.Nifti.identifyAffine`.
+* New prototype :mod:`fsl.transforms.x5`  module, for reading/writing linear
+  and non-linear X5 files (*preliminary release, subject to change*).
+* New prototype :mod:`.fsl_convert_x5` :mod:`.fsl_apply_x5` programs, for
+  working with X5 transformations (*preliminary release, subject to change*).
+
 
 
 Changed
@@ -20,6 +32,16 @@ Changed
 
 * The :mod:`.resample_image` script has been updated to support resampling of
   images with more than 3 dimensions.
+* `h5py <https://www.h5py.org/>`_ has been added to the ``fslpy`` dependencies.
+
+
+Deprecated
+^^^^^^^^^^
+
+
+* The :mod:`fsl.utils.transform` module has been deprecated its functions can
+  now be found in the :mod:`fsl.transforms.affine` and
+  :mod:`fsl.transform.flirt` modules.
 
 
 2.3.1 (Friday July 5th 2019)
@@ -169,7 +191,7 @@ Added
 * Simple built-in :mod:`.deprecated` decorator.
 * New :mod:`fsl.data.utils` module, which currently contains one function
   :func:`.guessType`, which guesses the data type of a file/directory path.
-* New `.commonBase` function for finding the common prefix of a set of
+* New :func:`.commonBase` function for finding the common prefix of a set of
   file/directory paths.
 
 
@@ -209,7 +231,7 @@ Fixed
 ^^^^^
 
 
-* Fixed an issue with the `.dicom.loadSeries` using memory-mapping for
+* Fixed an issue with the :func:`.dicom.loadSeries` using memory-mapping for
   image files that would subsequently be deleted.
 * Fixed an issue in the :class:`.GiftiMesh` class, where
   ``numpy``/``nibabel`` was returning read-only index arrays.

README.rst

@@ -91,6 +91,10 @@ The ``rtree`` library assumes that ``libspatialindex`` is installed on
 your system.
 
 
+The :mod:`fsl.transform.x5` module uses `h5py <https://www.h5py.org/>`_,
+which requires ``libhdf5``.
+
+
 Documentation
 -------------
 

doc/_static/theme_overrides.css

+/* override table width restrictions */
+.wy-table-responsive table td, .wy-table-responsive table th {
+    white-space: normal;
+}
+
+.wy-table-responsive {
+    margin-bottom: 24px;
+    max-width: 100%;
+    overflow: visible;
+}

doc/conf.py

@@ -33,7 +33,8 @@ date = datetime.date.today()
 # ones.
 extensions = [
     'sphinx.ext.autodoc',
-    'sphinx.ext.autosummary', 
+    'sphinx.ext.viewcode',
+    'sphinx.ext.autosummary',
     'sphinx.ext.mathjax',
     'sphinx.ext.graphviz',
     'sphinx.ext.todo',
@@ -121,6 +122,7 @@ pygments_style = 'sphinx'
 # a list of builtin themes.
 html_theme = 'sphinx_rtd_theme'
 
+
 # Theme options are theme-specific and customize the look and feel of a theme
 # further.  For a list of options available for each theme, see the
 # documentation.
@@ -148,7 +150,13 @@ html_theme = 'sphinx_rtd_theme'
 # Add any paths that contain custom static files (such as style sheets) here,
 # relative to this directory. They are copied after the builtin static files,
 # so a file named "default.css" will overwrite the builtin "default.css".
-html_static_path = []
+html_static_path = ['_static']
+
+html_context = {
+    'css_files': [
+        '_static/theme_overrides.css',  # overrides for wide tables in RTD theme
+        ],
+    }
 
 # Add any extra paths that contain custom files (such as robots.txt or
 # .htaccess) here, relative to this directory. These files are copied
@@ -354,7 +362,7 @@ epub_exclude_files = ['search.html']
 autoclass_content = 'class'
 
 # Document private members and special members (e.g. __init__)
-autodocsourc_default_flags = ['private-members', 'special-members']
+autodoc_default_flags = ['private-members', 'special-members']
 
 # Documentation for python modules is in the same order
 # as the source code.
@@ -368,7 +376,7 @@ def autodoc_skip_member(app, what, name, obj, skip, options):
     if what == 'class':
         attName = name.split('.')[-1]
         return skip or attName.startswith('_sync_')
-    
+
     return skip or False
 
 

doc/contributing.rst

@@ -34,7 +34,7 @@ the following labels (this convention has been inherited from `nibabel
 
   * *BF*  : bug fix
   * *RF*  : refactoring
-  * *NF*  : new feature
+  * *ENH*:  enhancement/new feature
   * *BW*  : addresses backward-compatibility
   * *OPT* : optimization
   * *BK*  : breaks something and/or tests fail
@@ -102,7 +102,7 @@ Unit and integration tests are currently run with ``py.test`` and
 ``coverage``.
 
 - Aim for 100% code coverage.
-- Tests must pass on python 2.7, 3.4, 3.5, and 3.6
+- Tests must pass on python 3.5, 3.6, and 3.7.
 
 
 Coding conventions

doc/fsl.rst

@@ -7,6 +7,7 @@
    fsl.data
    fsl.scripts
    fsl.utils
+   fsl.transform
    fsl.version
    fsl.wrappers
 

doc/fsl.scripts.fsl_convert_x5.rst

+``fsl.scripts.fsl_convert_x5``
+==============================
+
+.. automodule:: fsl.scripts.fsl_convert_x5
+    :members:
+    :undoc-members:
+    :show-inheritance:

doc/fsl.scripts.rst

@@ -5,6 +5,7 @@
    :hidden:
 
    fsl.scripts.atlasq
+   fsl.scripts.fsl_convert_x5
    fsl.scripts.fsl_ents
    fsl.scripts.imcp
    fsl.scripts.imglob

doc/fsl.transform.affine.rst

+``fsl.transform.affine``
+========================
+
+.. automodule:: fsl.transform.affine
+    :members:
+    :undoc-members:
+    :show-inheritance:

doc/fsl.utils.transform.rst → doc/fsl.transform.flirt.rst

-``fsl.utils.transform``
+``fsl.transform.flirt``
 =======================
 
-.. automodule:: fsl.utils.transform
+.. automodule:: fsl.transform.flirt
     :members:
     :undoc-members:
     :show-inheritance:

doc/fsl.transform.fnirt.rst

+``fsl.transform.fnirt``
+=======================
+
+.. automodule:: fsl.transform.fnirt
+    :members:
+    :undoc-members:
+    :show-inheritance:

doc/fsl.transform.nonlinear.rst

+``fsl.transform.nonlinear``
+===========================
+
+.. automodule:: fsl.transform.nonlinear
+    :members:
+    :undoc-members:
+    :show-inheritance:

doc/fsl.transform.rst

+``fsl.transform``
+=================
+
+.. toctree::
+   :hidden:
+
+   fsl.transform.affine
+   fsl.transform.flirt
+   fsl.transform.fnirt
+   fsl.transform.nonlinear
+   fsl.transform.x5
+
+.. automodule:: fsl.transform
+    :members:
+    :undoc-members:
+    :show-inheritance:

doc/fsl.transform.x5.rst

+``fsl.transform.x5``
+====================
+
+.. automodule:: fsl.transform.x5
+    :members:
+    :undoc-members:
+    :show-inheritance:

doc/fsl.utils.rst

@@ -23,7 +23,6 @@
    fsl.utils.run
    fsl.utils.settings
    fsl.utils.tempdir
-   fsl.utils.transform
    fsl.utils.weakfuncref
 
 .. automodule:: fsl.utils