@@ -652,8 +652,8 @@ Enhancements
652652
653653Bug fixes
654654---------
655- * Preserve first point of ` LazyTractogram ` (pr/588) (MC, reviewed by Nil
656- Goyette, CM, MB)
655+ * Preserve first point of :py:class: ` ~nibabel.streamlines. LazyTractogram `
656+ (pr/588) (MC, reviewed by Nil Goyette, CM, MB)
657657* Stop adding extraneous metadata padding (pr/593) (Jon Stutters, reviewed by
658658 CM, MB)
659659* Accept lower-case orientation codes in TRK files (pr/600) (Kesshi Jordan,
@@ -727,7 +727,7 @@ Enhancements
727727* Support for alternative header field name variants in .PAR files
728728 (pr/507) (Gregory R. Lee)
729729* Various enhancements to streamlines API by MC: support for reading TRK
730- version 1 (pr/512); concatenation of tractograms using `+ `/` += ` operators
730+ version 1 (pr/512); concatenation of tractograms using `` + ``/`` += ` ` operators
731731 (pr/495); function to concatenate multiple ArraySequence objects (pr/494)
732732* Support for numpy 1.12 (pr/500, pr/502) (MC, MB)
733733* Allow dtype specifiers as fileslice input (pr/485) (MB)
@@ -807,7 +807,7 @@ Enhancements
807807 (Brendan Moloney);
808808* More explicit error when trying to read image from non-existent file
809809 (pr/455) (Ariel Rokem);
810- * Extension to `nib-ls ` command to show image statistics (pr/437) and other
810+ * Extension to `` nib-ls ` ` command to show image statistics (pr/437) and other
811811 header files (pr/348) (Yarik Halchenko).
812812
813813Bug fixes
@@ -1100,7 +1100,7 @@ Special thanks to Chris Burns, Jarrod Millman and Yaroslav Halchenko.
11001100* ``parrec2nii `` script to convert PAR/REC images to NIfTI format (MH)
11011101* Very preliminary, limited and highly experimental DICOM reading support (MB,
11021102 Ian Nimmo Smith).
1103- * Some functions (`nibabel.funcs `) for basic image shape changes, including
1103+ * Some functions (:py:mod: `nibabel.funcs `) for basic image shape changes, including
11041104 the ability to transform to the image with data closest to the cononical
11051105 image orientation (first axis left-to-right, second back-to-front, third
11061106 down-to-up) (MB, Jonathan Taylor)
@@ -1143,7 +1143,7 @@ visiting the URL::
11431143* Bugfix: Removed left-over print statement in extension code.
11441144* Bugfix: Prevent saving of bogus 'None.nii' images when the filename
11451145 was previously assign, before calling NiftiImage.save() (Closes: #517920).
1146- * Bugfix: Extension length was to short for all `edata ` whose length matches
1146+ * Bugfix: Extension length was to short for all `` edata ` ` whose length matches
11471147 n*16-8, for all integer n.
11481148
114911490.20090205.1 (Thu, 5 Feb 2009)
@@ -1152,13 +1152,13 @@ visiting the URL::
11521152* This release is the first in a series that aims stabilize the API and
11531153 finally result in PyNIfTI 1.0 with full support of the NIfTI1 standard.
11541154* The whole package was restructured. The included renaming
1155- `nifti.nifti(image,format,clibs) ` to `nifti.(image,format,clibs) `. Redirect
1155+ `` nifti.nifti(image,format,clibs) `` to `` nifti.(image,format,clibs) ` `. Redirect
11561156 modules make sure that existing user code will not break, but they will
11571157 issue a DeprecationWarning and will be removed with the release of PyNIfTI
11581158 1.0.
11591159* Added a special extension that can embed any serializable Python object
11601160 into the NIfTI file header. The contents of this extension is
1161- automatically expanded upon request into the `.meta ` attribute of each
1161+ automatically expanded upon request into the `` .meta ` ` attribute of each
11621162 NiftiImage. When saving files to disk the content of the dictionary is also
11631163 automatically dumped into this extension.
11641164 Embedded meta data is not loaded automatically, since this has security
@@ -1173,11 +1173,11 @@ visiting the URL::
11731173* Added methods :meth: `~nifti.format.NiftiFormat.vx2q ` and
11741174 :meth: `~nifti.format.NiftiFormat.vx2s ` to convert voxel indices into
11751175 coordinates defined by qform or sform respectively.
1176- * Updating the `cal_min ` and `cal_max ` values in the NIfTI header when
1176+ * Updating the `` cal_min `` and `` cal_max ` ` values in the NIfTI header when
11771177 saving a file is now conditional, but remains enabled by default.
11781178* Full set of methods to query and modify axis units. This includes
1179- expanding the previous `xyzt_units ` field in the header dictionary into
1180- editable `xyz_unit ` and `time_unit ` fields. The former `xyzt_units ` field
1179+ expanding the previous `` xyzt_units ` ` field in the header dictionary into
1180+ editable `` xyz_unit `` and `` time_unit `` fields. The former `` xyzt_units ` ` field
11811181 is no longer available. See:
11821182 :meth: `~nifti.format.NiftiFormat.getXYZUnit `,
11831183 :meth: `~nifti.format.NiftiFormat.setXYZUnit `,
@@ -1193,19 +1193,19 @@ visiting the URL::
11931193 :attr: `~nifti.format.NiftiFormat.qform_code `,
11941194 :attr: `~nifti.format.NiftiFormat.sform_code `
11951195* Each image instance is now able to generate a human-readable dump of its
1196- most important header information via `__str__() `.
1196+ most important header information via `` __str__() ` `.
11971197* :class: `~nifti.image.NiftiImage ` objects can now be pickled.
11981198* Switched to NumPy's distutils for building the package. Cleaned and
11991199 simplified the build procedure. Added optimization flags to SWIG call.
12001200* :attr: `nifti.image.NiftiImage.filename ` can now also be used to assign a
12011201 filename.
12021202* Introduced :data: `nifti.__version__ ` as canonical version string.
1203- * Removed `updateQFormFromQuarternion() ` from the list of public methods of
1203+ * Removed `` updateQFormFromQuarternion() ` ` from the list of public methods of
12041204 :class: `~nifti.format.NiftiFormat `. This is an internal method that
12051205 should not be used in user code. However, a redirect to the new method
12061206 will remain in-place until PyNIfTI 1.0.
12071207* Bugfix: :meth: `~nifti.image.NiftiImage.getScaledData ` returns a
1208- unmodified data array if `slope ` is set to zero (as required by the NIfTI
1208+ unmodified data array if `` slope ` ` is set to zero (as required by the NIfTI
12091209 standard). Thanks to Thomas Ross for reporting.
12101210* Bugfix: Unicode filenames are now handled properly, as long as they do not
12111211 contain pure-unicode characters (since the NIfTI library does not support
@@ -1259,9 +1259,9 @@ visiting the URL::
12591259 Thyreau for reporting.
12601260* Bugfix: setPixDims() stored meaningless values.
12611261* Use new NumPy API and replace deprecated function calls
1262- (`PyArray_FromDimsAndData `).
1262+ (`` PyArray_FromDimsAndData ` `).
12631263* Initial support for memory mapped access to uncompressed NIfTI files
1264- (`MemMappedNiftiImage `).
1264+ (`` MemMappedNiftiImage ` `).
12651265* Add a proper Makefile and setup.cfg for compiling PyNIfTI under Windows
12661266 with MinGW.
12671267* Include a minimal copy of the most recent nifticlibs (just libniftiio and
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