Merge remote branch 'nipy/master'

Author: mih

Makefile

@@ -133,9 +133,12 @@ upload-website: website
 	rsync -rzhvp --delete --chmod=Dg+s,g+rw $(WWW_DIR)/* \
 		web.sourceforge.net:/home/groups/n/ni/niftilib/htdocs/nibabel/
 
-upload-htmldoc: htmldoc
+# This one udates for the specific user named at the top of the makefile
+upload-htmldoc: htmldoc upload-htmldoc-$(SF_USER)
+
+upload-htmldoc-%: htmldoc
 	rsync -rzhvp --delete --chmod=Dg+s,g+rw $(HTML_DIR)/* \
-		$(SF_USER),[email protected]:/home/groups/n/ni/nipy/htdocs/nibabel/
+		$*,[email protected]:/home/groups/n/ni/nipy/htdocs/nibabel/
 
 #
 # Sources

doc/source/conf.py

@@ -32,7 +32,7 @@
 
 # We load the nibabel release info into a dict by explicit execution
 rel = {}
-execfile('../../nibabel/version.py', rel)
+execfile('../../nibabel/info.py', rel)
 
 # Add any Sphinx extension module names here, as strings. They can be extensions
 # coming with Sphinx (named 'sphinx.ext.*') or your custom ones.

doc/source/data_pkg_design.rst

@@ -162,7 +162,7 @@ NIPY-related packages such as ``pbrain``).  The ``data`` subdirectory of
 ``config.ini`` file, that has at least an entry like this::
 
   [DEFAULT]
-  version = 0.1
+  version = 0.2
 
 giving the version of the data package.
 
@@ -189,9 +189,8 @@ For the example above this will result in these subdirectories::
 because ``nipy`` is both the project, and the package to which the data
 relates.
 
-If you install to a particular location, you will need to add that location to
-the output of ``nipy.data.get_data_path()`` using one of the mechanisms above,
-for example, in your system configuration::
+If you install to a particular location, you will need to add that
+location to the output of ``nipy.data.get_data_path()`` using one of the mechanisms above, for example, in your system configuration::
 
    export NIPY_DATA_PATH=/my/prefix/share/nipy
 
@@ -215,8 +214,8 @@ contents::
 Current implementation
 ``````````````````````
 
-This section describes how we (the nibabel package) implement data packages
-at the moment.
+This section describes how we (the nipy community) implement data packages at
+the moment.
 
 The data in the data packages will not usually be under source control.  This is
 because images don't compress very well, and any change in the data will result
@@ -226,7 +225,7 @@ the data files aren't going to change, then a repository could work OK.
 The data packages will be available at a central release location.  For
 now this will be: http://nipy.sourceforge.net/data-packages/ .
 
-A package, such as ``nipy-templates-0.1.tar.gz`` will have the following
+A package, such as ``nipy-templates-0.2.tar.gz`` will have the following
 sort of structure::
 
 
@@ -236,6 +235,8 @@ sort of structure::
     |-- MANIFEST.in
     `-- templates
         |-- ICBM152
+        |   |-- 1mm
+        |   |   `-- T1_brain.nii.gz
         |   `-- 2mm
         |       `-- T1.nii.gz
         |-- colin27
@@ -246,14 +247,14 @@ sort of structure::
 
 There should be only one ``nipy/packagename`` directory delivered by a
 particular package.  For example, this package installs
-``nipy/templates``, but does not contain ``nipy/data``.  
+``nipy/templates``, but does not contain ``nipy/data``.
 
 Making a new package tarball is simply:
 
 #. Downloading and unpacking e.g ``nipy-templates-0.1.tar.gz`` to form
    the directory structure above.
 #. Making any changes to the directory
-#. Running ``setup.py sdist`` to recreate the package.  
+#. Running ``setup.py sdist`` to recreate the package.
 
 The process of making a release should be:
 
@@ -264,8 +265,7 @@ The process of making a release should be:
 There is an example nipy data package ``nipy-examplepkg`` in the
 ``examples`` directory of the NIPY repository.
 
-The machinery for creating and maintaining data packages is available with::
-   
-   svn co https://nipy.svn.sourceforge.net/svnroot/nipy/data-packaging/trunk
+The machinery for creating and maintaining data packages is available at
+http://github.com/nipy/data-packaging
 
 See the ``README.txt`` file there for more information.

doc/source/devdiscuss.rst

@@ -0,0 +1,24 @@
+.. -*- mode: rst; fill-column: 79 -*-
+.. ex: set sts=4 ts=4 sw=4 et tw=79:
+  ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ###
+  #
+  #   See COPYING file distributed along with the NiBabel package for the
+  #   copyright and license terms.
+  #
+  ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ###
+
+.. _chap_devdiscuss:
+
+*********************
+Developer discussions
+*********************
+
+Some discussions of usecases and other design issues.  Most of these don't apply
+to the current codebase, and are only for discussion of future directions.
+
+.. toctree::
+    :maxdepth: 2
+
+    usecases/index
+    refactoring/index
+    data_pkg_design

doc/source/devguide.rst

@@ -13,11 +13,13 @@
 NiBabel Developer Guidelines
 ****************************
 
+NiBabel source code
+===================
+
 .. toctree::
     :maxdepth: 2
 
     gitwash/index
-    refactoring/index
 
 Documentation
 =============
@@ -86,10 +88,11 @@ Merges
 ------
 
 For easy tracking of what changes were absorbed during merge, we
-advice to enable merge summary within git:
+advise that you enable merge summaries within git:
 
   git-config merge.summary true
 
+See :ref:`configure-git` for more detail.
 
 Changelog
 =========

doc/source/index.rst

@@ -15,6 +15,8 @@ Documentation
 * :ref:`User Documentation <manual>` (manual)
 * :ref:`API Documentation <api>` (comprehensive reference)
 * :ref:`Developer Guidelines <chap_devguide>` (for those who want to contribute)
+* :ref:`Developer discussions <chap_devdiscuss>` (arcane discussions about code
+  design)
 * :ref:`Development Changelog <changelog>` (see what has changed)
 * :ref:`genindex` (access by keywords)
 * :ref:`search` (online and offline full-text search)

doc/source/manual.rst

@@ -8,7 +8,6 @@ NiBabel Manual
 
   installation
   gettingstarted
-  usecases/index
   dicom/dicom
   legal
   changelog

nibabel/nicom/__init__.py

@@ -19,3 +19,10 @@
    dwiparams
    structreader
 """
+import warnings
+
+warnings.warn('The DICOM readers are highly experimental, unstable,'
+              ' and only work for Siemens time-series at the moment\n'
+              'Please use with caution.  We would be grateful for your '
+              'help in improving them',
+              UserWarning, stacklevel=2)

nibabel/nicom/dicomreaders.py

@@ -40,7 +40,7 @@ def read_mosaic_dwi_dir(dicom_path, globber='*.dcm'):
 
 
 def read_mosaic_dir(dicom_path, globber='*.dcm', check_is_dwi=False):
-    ''' Read all Siemens DICOMs in directory, return arrays, params
+    ''' Read all Siemens mosaic DICOMs in directory, return arrays, params
 
     Parameters
     ----------
@@ -77,6 +77,11 @@ def read_mosaic_dir(dicom_path, globber='*.dcm', check_is_dwi=False):
         raise IOError('Found no files with "%s"' % full_globber)
     for fname in filenames:
         dcm_w = wrapper_from_file(fname)
+        # Because the routine sorts by filename, it only makes sense to use this
+        # order for mosaic images.  Slice by slice dicoms need more sensible
+        # sorting
+        if not dcm_w.is_mosaic:
+            raise DicomReadError('data does not appear to be in mosaic format')
         arrays.append(dcm_w.get_data()[...,None])
         q = dcm_w.q_vector
         if q is None:  # probably not diffusion

nibabel/spatialimages.py

@@ -381,12 +381,12 @@ def from_filename(klass, filename):
         return klass.from_file_map(file_map)
 
     @classmethod
-    def from_filespec(klass, img, filespec):
+    def from_filespec(klass, filespec):
         warnings.warn('``from_filespec`` class method is deprecated\n'
                       'Please use the ``from_filename`` class method '
                       'instead',
-                      DeprecationWarning)
-        klass.from_filespec(filespec)
+                      DeprecationWarning, stacklevel=2)
+        klass.from_filename(filespec)
 
     @classmethod
     def from_file_map(klass, file_map):
@@ -397,7 +397,7 @@ def from_files(klass, file_map):
         warnings.warn('``from_files`` class method is deprecated\n'
                       'Please use the ``from_file_map`` class method '
                       'instead',
-                      DeprecationWarning)
+                      DeprecationWarning, stacklevel=2)
         return klass.from_file_map(file_map)
 
     @classmethod
@@ -419,7 +419,7 @@ def filespec_to_files(klass, filespec):
         warnings.warn('``filespec_to_files`` class method is deprecated\n'
                       'Please use the ``filespec_to_file_map`` class method '
                       'instead',
-                      DeprecationWarning)
+                      DeprecationWarning, stacklevel=2)
         return klass.filespec_to_file_map(filespec)
 
     def to_filename(self, filename):
@@ -442,7 +442,7 @@ def to_filename(self, filename):
     def to_filespec(self, filename):
         warnings.warn('``to_filespec`` is deprecated, please '
                       'use ``to_filename`` instead',
-                      DeprecationWarning)
+                      DeprecationWarning, stacklevel=2)
         self.to_filename(filename)
 
     def to_file_map(self, file_map=None):
@@ -452,7 +452,7 @@ def to_files(self, file_map=None):
         warnings.warn('``to_files`` method is deprecated\n'
                       'Please use the ``to_file_map`` method '
                       'instead',
-                      DeprecationWarning)
+                      DeprecationWarning, stacklevel=2)
         self.to_file_map(file_map)
 
     @classmethod
@@ -495,7 +495,7 @@ def save(klass, img, filename):
         warnings.warn('``save`` class method is deprecated\n'
                       'You probably want the ``to_filename`` instance '
                       'method, or the module-level ``save`` function',
-                      DeprecationWarning)
+                      DeprecationWarning, stacklevel=2)
         klass.instance_to_filename(img, filename)
 
     @classmethod