Merge remote-tracking branch 'upstream/master' into enh/cifti2

* upstream/master:
  DOC: change notation, add intermediate logic
  Address more comments.
  Format string {} not allowed in Python 2.6
  Test case and more complete fix for missing variable values.
  Address more comments, add a test case for 4d float64 data.
  Fix overly long line.
  Test some MINC 1 and MINC 2 edge cases.
  Address comments.
  Address comments.
  BF: back out unnecessary change.
  BF: Some NetCDF variables have no data allocated - they end up having a shape with a single element set to zero. Assigning an _empty_ shape triggers an exception in this case. We now harmlessly avoid the assignment in these cases.
  BF: use correct defaults for step in get_zooms().
  BF: use correct defaults for start and step.
  BF: Correctly use data type's inherent range if the valid_range attribute is missing.
  BF: never more dimension names than the variable actually has. It is possible (though incorrect) that the dimorder can be set on a scalar image-min, e.g. This fix avoids triggering an error on these (arguably malformed) files.
  RF+TST: allow dtype specifiers as fileslice input
  DOC: add advice for citing nibabel

Author: satra

README.rst

@@ -77,3 +77,13 @@ License
 Nibabel is licensed under the terms of the MIT license. Some code included
 with nibabel is licensed under the BSD license.  Please see the COPYING file
 in the nibabel distribution.
+
+Citing nibabel
+==============
+
+Please see the `available releases`_ for the release of nibabel that you are
+using.  Recent releases have a Zenodo_ `Digital Object Identifier`_ badge at
+the top of the release notes.  Click on the badge for more information.
+
+.. _zenodo: https://zenodo.org
+.. _Digital Object Identifier: https://en.wikipedia.org/wiki/Digital_object_identifier

doc/source/coordinate_systems.rst

@@ -515,16 +515,16 @@ We could record the parameters necessary for $f$ as the 3 by 3 matrix, $M$
 and the 3 by 1 vector $(a, b, c)$.
 
 In fact, the 4 by 4 image *affine array* does include exactly this
-information. If $m_{ij}$ is the value in row $i$ column $j$ of matrix $M$,
+information. If $m_{i,j}$ is the value in row $i$ column $j$ of matrix $M$,
 then the image affine matrix $A$ is:
 
 .. math::
 
     A =
     \begin{bmatrix}
-    m_{11} & m_{12} & m_{13} & a \\
-    m_{21} & m_{22} & m_{23} & b \\
-    m_{31} & m_{32} & m_{33} & c \\
+    m_{1,1} & m_{1,2} & m_{1,3} & a \\
+    m_{2,1} & m_{2,2} & m_{2,3} & b \\
+    m_{3,1} & m_{3,2} & m_{3,3} & c \\
     0 & 0 & 0 & 1 \\
     \end{bmatrix}
 
@@ -546,9 +546,9 @@ vectors:
     1\\
     \end{bmatrix} =
     \begin{bmatrix}
-    m_{11} & m_{12} & m_{13} & a \\
-    m_{21} & m_{22} & m_{23} & b \\
-    m_{31} & m_{32} & m_{33} & c \\
+    m_{1,1} & m_{1,2} & m_{1,3} & a \\
+    m_{2,1} & m_{2,2} & m_{2,3} & b \\
+    m_{3,1} & m_{3,2} & m_{3,3} & c \\
     0 & 0 & 0 & 1 \\
     \end{bmatrix}
     \begin{bmatrix}
@@ -614,6 +614,19 @@ matrix.  Put another way:
     1\\
     \end{bmatrix}
 
+    A^{-1}\begin{bmatrix}
+    x\\
+    y\\
+    z\\
+    1\\
+    \end{bmatrix} = A^{-1} A
+    \begin{bmatrix}
+    i\\
+    j\\
+    k\\
+    1\\
+    \end{bmatrix}
+
     \begin{bmatrix}
     i\\
     j\\

doc/source/devel/make_release.rst

@@ -292,6 +292,22 @@ Release checklist
     Please take a look at the Makefile rules ``devel-src``, ``devel-dsc`` and
     ``orig-src``.
 
+* Go to: https://github.com/nipy/nibabel/tags and select the new tag, to fill
+  in the release notes.  Copy the relevant part of the Changelog into the
+  release notes.  Click on "Publish release".  This will cause Zenodo_ to
+  generate a new release "upload", including a DOI.  After a few minutes, go
+  to https://zenodo.org/deposit and click on the new release upload.  Click on
+  the "View" button and click on the DOI badge at the right to display the
+  text for adding a DOI badge in various formats. Copy the DOI Markdown text.
+  The markdown will look something like this::
+
+    [![DOI](https://zenodo.org/badge/doi/10.5281/zenodo.60847.svg)](http://dx.doi.org/10.5281/zenodo.60847)
+
+  Go back to the Github release page for this release, click "Edit release".
+  and copy the DOI into the release notes.  Click "Update release".
+
+  See: https://guides.github.com/activities/citable-code
+
 * Announce to the mailing lists.
 
 .. _setuptools intro: https://pythonhosted.org/an_example_pypi_project/setuptools.html

doc/source/links_names.txt

@@ -42,6 +42,7 @@
 .. _reST: http://docutils.sourceforge.net/rst.html
 .. _docutils: http://docutils.sourceforge.net
 .. _IPython notebook viewer: http://nbviewer.ipython.org
+.. _zenodo: https://zenodo.org
 
 .. Licenses
 .. _GPL: https://www.gnu.org/licenses/gpl.html

nibabel/deprecator.py

@@ -146,7 +146,7 @@ def __call__(self, message, since='', until='',
         if since:
             messages.append('* deprecated from version: ' + since)
         if until:
-            messages.append('* {} {} as of version: {}'.format(
+            messages.append('* {0} {1} as of version: {2}'.format(
                 "Raises" if self.is_bad_version(until) else "Will raise",
                 error_class,
                 until))

nibabel/externals/netcdf.py

@@ -210,6 +210,14 @@ def __init__(self, filename, mode='r', mmap=None, version=1):
             self.fp = open(self.filename, '%sb' % mode)
             if mmap is None:
                 mmap = True
+        try:
+            self.fp.seek(0, 2)
+        except ValueError:
+            self.file_bytes = -1 # Unknown file length (gzip).
+        else:
+            self.file_bytes = self.fp.tell()
+            self.fp.seek(0)
+
         self.use_mmap = mmap
         self.version_byte = version
 
@@ -599,14 +607,22 @@ def _read_var_array(self):
             else:  # not a record variable
                 # Calculate size to avoid problems with vsize (above)
                 a_size = reduce(mul, shape, 1) * size
-                if self.use_mmap:
+                if self.file_bytes >= 0 and begin_ + a_size > self.file_bytes:
+                    data = fromstring(b'\x00'*a_size, dtype=dtype_)
+                elif self.use_mmap:
                     mm = mmap(self.fp.fileno(), begin_+a_size, access=ACCESS_READ)
                     data = ndarray.__new__(ndarray, shape, dtype=dtype_,
                             buffer=mm, offset=begin_, order=0)
                 else:
                     pos = self.fp.tell()
                     self.fp.seek(begin_)
-                    data = fromstring(self.fp.read(a_size), dtype=dtype_)
+                    # Try to read file, which may fail because the data is
+                    # at or past the end of file. In that case, we treat
+                    # this data as zeros.
+                    buf = self.fp.read(a_size)
+                    if len(buf) < a_size:
+                        buf = b'\x00'*a_size
+                    data = fromstring(buf, dtype=dtype_)
                     data.shape = shape
                     self.fp.seek(pos)
 

nibabel/fileslice.py

@@ -719,17 +719,19 @@ def fileslice(fileobj, sliceobj, shape, dtype, offset=0, order='C',
     Parameters
     ----------
     fileobj : file-like object
-        binary file-like object. Implements ``read`` and ``seek``
+        file-like object, opened for reading in binary mode. Implements
+        ``read`` and ``seek``.
     sliceobj : object
-        something that can be used to slice an array as in ``arr[sliceobj]``
+        something that can be used to slice an array as in ``arr[sliceobj]``.
     shape : sequence
-        shape of full array inside `fileobj`
-    dtype : dtype object
-        dtype of array inside `fileobj`
+        shape of full array inside `fileobj`.
+    dtype : dtype specifier
+        dtype of array inside `fileobj`, or input to ``numpy.dtype`` to specify
+        array dtype.
     offset : int, optional
         offset of array data within `fileobj`
     order : {'C', 'F'}, optional
-        memory layout of array in `fileobj`
+        memory layout of array in `fileobj`.
     heuristic : callable, optional
         function taking slice object, axis length, stride length as arguments,
         returning one of 'full', 'contiguous', None.  See
@@ -743,7 +745,8 @@ def fileslice(fileobj, sliceobj, shape, dtype, offset=0, order='C',
     """
     if is_fancy(sliceobj):
         raise ValueError("Cannot handle fancy indexing")
-    itemsize = dtype.itemsize
+    dtype = np.dtype(dtype)
+    itemsize = int(dtype.itemsize)
     segments, sliced_shape, post_slicers = calc_slicedefs(
         sliceobj, shape, itemsize, offset, order)
     n_bytes = reduce(operator.mul, sliced_shape, 1) * itemsize

nibabel/info.py

@@ -170,6 +170,16 @@ def cmp_pkg_version(version_str, pkg_version_str=__version__):
 Nibabel is licensed under the terms of the MIT license. Some code included
 with nibabel is licensed under the BSD license.  Please see the COPYING file
 in the nibabel distribution.
+
+Citing nibabel
+==============
+
+Please see the `available releases`_ for the release of nibabel that you are
+using.  Recent releases have a Zenodo_ `Digital Object Identifier`_ badge at
+the top of the release notes.  Click on the badge for more information.
+
+.. _zenodo: https://zenodo.org
+.. _Digital Object Identifier: https://en.wikipedia.org/wiki/Digital_object_identifier
 """
 
 # versions for dependencies. Check these against:

nibabel/minc1.py

@@ -95,8 +95,8 @@ def get_data_shape(self):
     def get_zooms(self):
         """ Get real-world sizes of voxels """
         # zooms must be positive; but steps in MINC can be negative
-        return tuple(
-            [abs(float(dim.step)) for dim in self._dims])
+        return tuple([abs(float(dim.step)) if hasattr(dim, 'step') else 1.0
+                      for dim in self._dims])
 
     def get_affine(self):
         nspatial = len(self._spatial_dims)
@@ -106,13 +106,11 @@ def get_affine(self):
         dim_names = list(self._dim_names)  # for indexing in loop
         for i, name in enumerate(self._spatial_dims):
             dim = self._dims[dim_names.index(name)]
-            try:
-                dir_cos = dim.direction_cosines
-            except AttributeError:
-                dir_cos = _default_dir_cos[name]
-            rot_mat[:, i] = dir_cos
-            steps[i] = dim.step
-            starts[i] = dim.start
+            rot_mat[:, i] = (dim.direction_cosines
+                             if hasattr(dim, 'direction_cosines')
+                             else _default_dir_cos[name])
+            steps[i] = dim.step if hasattr(dim, 'step') else 1.0
+            starts[i] = dim.start if hasattr(dim, 'start') else 0.0
         origin = np.dot(rot_mat, starts)
         aff = np.eye(nspatial + 1)
         aff[:nspatial, :nspatial] = rot_mat * steps

nibabel/minc2.py

@@ -77,7 +77,10 @@ def _get_dimensions(self, var):
             dimorder = var.attrs['dimorder'].decode()
         except KeyError:  # No specified dimensions
             return []
-        return dimorder.split(',')
+        # The dimension name list must contain only as many entries
+        # as the variable has dimensions. This reduces errors when an
+        # unnecessary dimorder attribute is left behind.
+        return dimorder.split(',')[:len(var.shape)]
 
     def get_data_dtype(self):
         return self._image.dtype
@@ -95,7 +98,7 @@ def _get_valid_range(self):
         info = np.iinfo(ddt.type)
         try:
             valid_range = self._image.attrs['valid_range']
-        except AttributeError:
+        except (AttributeError, KeyError):
             valid_range = [info.min, info.max]
         else:
             if valid_range[0] < info.min or valid_range[1] > info.max: