CHANGELOG.rst 13.9 KB
Newer Older
Paul McCarthy's avatar
Paul McCarthy committed
1
2
This document contains the ``fslpy`` release history in reverse chronological
order.
Paul McCarthy's avatar
Paul McCarthy committed
3
4


Paul McCarthy's avatar
Paul McCarthy committed
5
6
7
8
9
10
11
12
13
14
15
16
1.8.0 (Under development)
-------------------------


Added
^^^^^


* New :mod:`.wrappers` package, containing wrapper functions for a range of
  FSL tools.
* New :mod:`fsl.utils.run` module, to replace the :mod:`fsl.utils.callfsl`
  module.
Paul McCarthy's avatar
Paul McCarthy committed
17
18
* New :mod:`fsl.utils.fslsub` module, containing a :func:`.fslsub.submit`
  function which submits a cluster job via ``fsl_sub`` (by Michiel Cottaar).
Paul McCarthy's avatar
Paul McCarthy committed
19
20
* Assertions (in the :mod:`.assertions` module) can be disabled with the
  new :func:`.assertions.disabled` context manager.
Paul McCarthy's avatar
Paul McCarthy committed
21
22
* New :mod:`fsl.utils.parse_data` module containing various neuroimaging
  data constructors for use with ``argparse``.
Paul McCarthy's avatar
Paul McCarthy committed
23
24
* The :func:`.memoize.skipUnchanged` decorator has an ``invalidate`` function
  which allows its cache to be cleared.
Paul McCarthy's avatar
Paul McCarthy committed
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41


Changed
^^^^^^^


* The :func:`.tempdir` function has an option to not change to the newly
  created directory.


Deprecated
^^^^^^^^^^


* The :mod:`fsl.utils.callfsl` module (replaced with :mod:`fsl.utils.run`).


42
43
1.7.2 (Monday March 19th 2018)
------------------------------
Paul McCarthy's avatar
Paul McCarthy committed
44
45
46
47
48
49


Added
^^^^^


50
51
* Added the :meth:`.MGHImage.voxToSurfMat` and related properties, giving
  access to the voxel-to-surface affine for an MGH image.
Paul McCarthy's avatar
Paul McCarthy committed
52
53


Paul McCarthy's avatar
Paul McCarthy committed
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
1.7.1 (Monday March 12th 2018)
------------------------------



Changed
^^^^^^^


* Adjusted :func:`.parseVersionString` so it accepts ``.dev*`` suffixes.


Fixed
^^^^^


Paul McCarthy's avatar
Paul McCarthy committed
70
* Removed deprecated use of :func:`.imagewrapper.canonicalShape`.
Paul McCarthy's avatar
Paul McCarthy committed
71
72


Paul McCarthy's avatar
Paul McCarthy committed
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
1.7.0 (Tuesday March 6th 2018)
------------------------------


Added
^^^^^


* The :mod:`fsl.utils.assertions` module contains a range of functions
  which can be used to assert that some condition is met.
* The :mod:`fsl.utils.ensure` module contains a range of functions (currently
  just one) which can be used to ensure that some condiution is met.


Changed
^^^^^^^


* The :mod:`.settings` module now saves its files in a format that is
  compatible with Python 2 and 3.
* The :func:`.tempdir` function now accepts a ``root`` argument, which
  specifies the location in which the temporary directory should be created.
* An image's data source can now be set via  :meth:`.Image.__init__`.
* :meth:`.MGHImage` objects now have a :meth:`.MGHImage.save` method.
* Adjustments to the ``conda`` package build and deployment process.
* The :func:`.ImageWrapper.canonicalShape` function has been moved
  to the :mod:`.image` class.
* The :func:`.ImageWrapper.naninfrange` function has been moved
  into its own :mod:`.naninfrange` module.


Fixed
^^^^^


* Fixed a bug in the :class:`.MutexFactory` class.


Deprecated
^^^^^^^^^^


* :func:`.ImageWrapper.canonicalShape` (moved to the :mod:`.image` module)
* :func:`.ImageWrapper.naninfrange` function (moved to the :mod:`.naninfrange`
  module)


Paul McCarthy's avatar
Paul McCarthy committed
120
121
122
123
124
125
126
1.6.8 (Monday February 12th 2018)
---------------------------------


* The `atlasq`, `immv`, `imcp` and `imglob` scripts suppress some warnings.


Paul McCarthy's avatar
Paul McCarthy committed
127
128
129
130
131
1.6.7 (Friday February 9th 2018)
--------------------------------


* More further adjustments to the ``conda`` package build.
Paul McCarthy's avatar
Paul McCarthy committed
132
* Adjustments to pypi source distribution - the ``requirements-extra.txt`` file
Paul McCarthy's avatar
Paul McCarthy committed
133
134
135
  was not being included.


Paul McCarthy's avatar
Paul McCarthy committed
136
137
138
139
140
141
142
1.6.6 (Thursday February 8th 2018)
----------------------------------


* Further adjustments to the ``conda`` package build.


Paul McCarthy's avatar
Paul McCarthy committed
143
144
145
146
147
148
149
1.6.5 (Tuesday February 6th 2018)
---------------------------------


* Adjustments to the ``conda`` package build.


Paul McCarthy's avatar
Paul McCarthy committed
150
151
152
153
154
155
156
1.6.4 (Monday February 5th 2018)
--------------------------------


* The :mod:`.platform` module emits a warning if it cannot import ``wx``.


Paul McCarthy's avatar
Paul McCarthy committed
157
158
1.6.3 (Friday February 2nd 2018)
--------------------------------
Paul McCarthy's avatar
Paul McCarthy committed
159
160
161


* Minor enhancements to the :class:`.WeakFunctionRef` class.
Paul McCarthy's avatar
Paul McCarthy committed
162
163
164
* Some bugfixes to the :mod:`fsl.utils.imcp` module, with respect to handling
  relative path names, moving file groups (e.g. `.img`/`.hdr` pairs), and
  non-existent directories.
Paul McCarthy's avatar
Paul McCarthy committed
165
166


Paul McCarthy's avatar
Paul McCarthy committed
167
168
169
170
171
172
173
174
175
1.6.2 (Tuesday January 30th 2018)
---------------------------------


* Updates to the ``conda`` installation process.
* A new script is installed when ``fslpy`` is installed via ``pip`` or
  ``conda`` - ``atlasquery``, which emulates the FSL ``atlasquery`` tool.


Paul McCarthy's avatar
Paul McCarthy committed
176
177
178
179
180
181
182
183
1.6.1 (Monday January 29th 2018)
--------------------------------


* Removed ``lxml`` as a dependency - this was necessary in older versions of
  ``trimesh``.


Paul McCarthy's avatar
Paul McCarthy committed
184
185
1.6.0 (Friday January 26th 2018)
--------------------------------
Paul McCarthy's avatar
Paul McCarthy committed
186
187


Paul McCarthy's avatar
Paul McCarthy committed
188
189
190
191
192
193
194
195
196
197
198
199
200
* The new :class:`.Mesh` class is now the base class for all mesh types. It
  has been written to allow multiple sets of vertices to be associated with a
  mesh object (to support e.g. white matter, inflated, spherical models for a
  GIFTI/freeusrfer mesh).
* The new :class:`.VTKMesh` class must now be used for loading VTK model files,
  instead of the old :class:`.TriangleMesh` class.
* The new :class:`.Mesh` class uses the ``trimesh`` library
  (https://github.com/mikedh/trimesh) to perform various geometrical
  operations, accessible via new :meth:`.Mesh.rayIntersection`,
  :meth:`.Mesh.planeIntersection`, :meth:`.Mesh.nearestVertex` methods.
* The :class:`.Nifti` and :class:`.Mesh` classes have new methods allowing
  arbitrary metadata to be stored with the image, as key-value
  pairs. These are provided by a new mixin class, :class:`.Meta`.
Paul McCarthy's avatar
Paul McCarthy committed
201
202
* Freesurer surface files and vertex data can now be loaded via the
  :class:`.FreesurferMesh` class, in the new :mod:`.freesurfer` module.
Paul McCarthy's avatar
Paul McCarthy committed
203
204
205
* Freesurfer ``mgz`` / ``mgh`` image files can now be loaded via the new
  :mod:`.mghimage` module. Internally, these image files are converted to NIFTI
  - the :class:`.MGHImage` class derives from the :class:`.Image` class.
Paul McCarthy's avatar
Paul McCarthy committed
206
207
208
209
210
* Meta-data access methods on the :class:`.DicomImage` class have been
  deprecated, as their functionality is provided by the new :class:`.Meta`
  mixin.
* The :class:`.TriangleMesh` class has been deprecated in favour of the new
  :class:`.Mesh` class.
Paul McCarthy's avatar
Paul McCarthy committed
211
* Optional dependencies ``wxpython``, ``indexed_gzip``, ``trimesh``, and
Paul McCarthy's avatar
Paul McCarthy committed
212
213
  ``rtree`` are now listed separately, so ``fslpy`` can be used without them
  (although relevant functionality will be disabled if they are not present).
Paul McCarthy's avatar
Paul McCarthy committed
214
215


Paul McCarthy's avatar
Paul McCarthy committed
216
217
218
219
220
221
222
1.5.4 (Wednesday January 10th 2018)
-----------------------------------


* Actually included the fix that was supposed to be in version 1.5.3.


Paul McCarthy's avatar
Paul McCarthy committed
223
1.5.3 (Tuesday January 9th 2018)
224
225
226
227
228
229
230
--------------------------------


* Bug fix to :meth:`.ImageWrapper.__expandCoverage` - was not correctly handling
  large images with lots of ``nan`` values.


Paul McCarthy's avatar
Paul McCarthy committed
231
232
233
234
235
236
237
1.5.2 (Tuesday January 2nd 2018)
--------------------------------


* Fixed issue with ``MANIFEST.in`` file.


Paul McCarthy's avatar
Paul McCarthy committed
238
239
240
241
242
243
244
1.5.1 (Thursday December 14th 2017)
-----------------------------------


* Fixed bug in :func:`.dicom.scanDir` function related to data series ordering.


Paul McCarthy's avatar
Paul McCarthy committed
245
246
1.5.0 (Wednesday December 13th 2017)
------------------------------------
Paul McCarthy's avatar
Paul McCarthy committed
247
248
249
250
251
252


* New module :mod:`.dicom`, which provides a thin wrapper on top of Chris
  Rorden's `dcm2niix <https://github.com/rordenlab/dcm2niix>`_.
* New module :mod:`.tempdir`, which has a convenience function for creating
  temporary directories.
Paul McCarthy's avatar
Paul McCarthy committed
253
254
255
* Fixed small issue in :meth:`.Image.dtype` - making sure that it access
  image data via the :class:`.ImageWrapper`, rather than via the `Nifti1Image`
  object.
Paul McCarthy's avatar
Paul McCarthy committed
256
257


Paul McCarthy's avatar
Paul McCarthy committed
258
259
1.4.2 (Tuesday December 5th 2017)
---------------------------------
Paul McCarthy's avatar
Paul McCarthy committed
260
261
262
263
264


* New function :func:`.transform.rmsdev` function, which implements the RMS
  deviation equation for comparing two affine transformations (FMRIB Technical
  Report TR99MJ1, available at https://www.fmrib.ox.ac.uk/datasets/techrep/).
Paul McCarthy's avatar
Paul McCarthy committed
265
* Some small bugfixes to the :mod:`.atlasq` and :mod:`.atlases` moduless.
Paul McCarthy's avatar
Paul McCarthy committed
266
267
268


1.4.1 (Thursday November 9th 2017)
Paul McCarthy's avatar
Paul McCarthy committed
269
270
271
272
273
274
----------------------------------


* Fixed bug in ``setup.py``.


Paul McCarthy's avatar
Paul McCarthy committed
275
1.4.0 (Thursday November 9th 2017)
Paul McCarthy's avatar
Paul McCarthy committed
276
----------------------------------
Paul McCarthy's avatar
Paul McCarthy committed
277

Paul McCarthy's avatar
Paul McCarthy committed
278

Paul McCarthy's avatar
Paul McCarthy committed
279
280
* The :func:`.uniquePrefix` function now raises a :exc:`~.path.PathError`
  instead of a :exc:`.ValueError`, when an invalid path is provided.
Paul McCarthy's avatar
Paul McCarthy committed
281
282
283
* The :mod:`fsl.utils.async` module is now deprecated, as ``async`` will
  become a reserved word in Python 3.7. It has been renamed to
  ``fsl.utils.idle``, with no other API changes.
Paul McCarthy's avatar
Paul McCarthy committed
284
285
286
287
288
289
290
291
292
293
294
295
296
297
* For image file pairs, the ``hdr`` extension now takes precedence over the
  ``img`` extension, when using the :func:`fsl.data.image.addExt` (and
  related) functions.
* The :func:`fsl.utils.path.addExt` function accepts a new parameter,
  ``unambiguous`` which causes it to allow an ambiguous prefix, and return
  all matching paths.
* New :mod:`~fsl.scripts.atlasq` application, intended to replace the FSL
  ``atlasquery`` tool.
* New :mod:`~fsl.scripts.imglob` application, intended to replace the FSL
  ``imglob`` tool.
* The :meth:`.Image.resample` method explicitly raises a ``ValueError``
  if incompatible shapes are provided.


Paul McCarthy's avatar
Paul McCarthy committed
298
1.3.1 (Wednesday October 25th 2017)
Paul McCarthy's avatar
Paul McCarthy committed
299
300
301
302
303
304
305
-----------------------------------


* Fixed bug in :meth:`.Platform.wxPlatform` causing it to always return
  ``WX_UNKNOWN``.


Paul McCarthy's avatar
Paul McCarthy committed
306
1.3.0 (Wednesday October 25th 2017)
Paul McCarthy's avatar
Paul McCarthy committed
307
-----------------------------------
Paul McCarthy's avatar
Paul McCarthy committed
308
309
310
311


* :class:`.Atlas` classes can now pass ``kwargs`` through to the
  :class:`.Image` constructor.
Paul McCarthy's avatar
Paul McCarthy committed
312
313
314
* :class:`.LabelAtlas` image values no longer need to match the index of the
  label into the :class:`.AtlasDescription` ``labels`` list. This means that
  label atlas XML files may contain non-sequential label values.
Paul McCarthy's avatar
Paul McCarthy committed
315
* :class:`.Cache` now implements ``__getitem__`` and ``__setitem__``
Paul McCarthy's avatar
Paul McCarthy committed
316
317
* The :func:`.image.read_segments` function (monkey-patched into ``nibabel``)
  is deprecated, as it is no longer necessary as of ``nibabel`` 2.2.0.
Paul McCarthy's avatar
Paul McCarthy committed
318
319
* :func:`.platform.isWidgetAlive` is deprecated in favour of an equivalent
  function in the ``fsleyes-widgets`` library.
Paul McCarthy's avatar
Paul McCarthy committed
320
321
* ``scipy`` is now explicitly listed as a requirement (this should have been
  done in 1.2.1).
Paul McCarthy's avatar
Paul McCarthy committed
322
323
324
325
326
327
328



1.2.2 (Saturday October 21st 2017)
----------------------------------


Paul McCarthy's avatar
Paul McCarthy committed
329
330
* The :func:`.image.read_segments` function is only monkey-patched into
  ``nibabel`` 2.1.0, as it breaks when used with 2.2.0.
Paul McCarthy's avatar
Paul McCarthy committed
331
332
333
334
335


1.2.1 (Saturday October 7th 2017)
---------------------------------

Paul McCarthy's avatar
Paul McCarthy committed
336

Paul McCarthy's avatar
Paul McCarthy committed
337
338
339
340
341
342
343
344
345
346
347
348
349
350
351
352
* If an :class:`.Image` is passed an existing ``nibabel`` header object,
  it creates a copy, rather than using the original.
* New :meth:`.Image.resample` method, which resamples the image data to a
  different resolution.
* New :meth:`.LabelAtlas.coordLabel`, :meth:`.LabelAtlas.maskLabel`,
  :meth:`.ProbabilisticAtlas.coordProportions` and
  :meth:`.ProbabilisticAtlas.maskProportions` methods. The ``coord``
  methods perform coordinate queries in voxel or world coordinates,
  and the ``mask`` methods perform mask-based queries.


1.2.0 (Thursday September 21st 2017)
------------------------------------


* :meth:`fsl.data.image.Nifti.voxelsToScaledVoxels` method deprecated in
Paul McCarthy's avatar
Paul McCarthy committed
353
  favour of new :meth:`.Nifti.voxToScaledVoxMat` and
Paul McCarthy's avatar
Paul McCarthy committed
354
355
356
357
358
359
360
361
362
363
364
365
366
367
368
369
370
371
372
373
374
  :meth:`Nifti.scaledVoxToVoxMat` properties.


1.1.0 (Monday September 11th 2017)
----------------------------------


* The :mod:`fsl` package is now a ``pkgutil``-style `namespace package
  <https://packaging.python.org/guides/packaging-namespace-packages/>`_, so it
  can be used for different projects.
* Updates to :class:`fsl.data.image.Nifti` and :class:`fsl.data.image.Image`
  to add support for images with more than 4 dimensions:
  - New ``ndims`` property
  - ``is4DImage`` method deprecated


1.0.5 (Thursday August 10th 2017)
---------------------------------


* New functions and further adjustments in :mod:`fsl.utils.transform` module:
Paul McCarthy's avatar
Paul McCarthy committed
375
376
377
378
379
380
381
382
383
384
385
386

 - :func:`.transform.rotMatToAffine` converts a ``(3, 3)`` rotation matrix
   into a ``(4, 4)`` affine.
 - :func:`.transform.transformNormal` applies an affine transform to one or
   more vectors.
 - :func:`.transform.veclength` calculates the length of a vector
 - :func:`.transform.normalise` normalises a vector
 - :func:`.transform.scaleOffsetXform` adjusted to have more flexibility with
   respect to inputs.
 - :func:`.transform.decompose` can return rotations either as three
   axis-angles, or as a rotation matrix

Paul McCarthy's avatar
Paul McCarthy committed
387
388
389
390
391
392
393
394
395
396
397
398
399
400
401
402
403
404
405
406
407
408
409
410
411
412
413
414
415
416
417
418
419
420
421
422
423
424
425
426
427
428
429
430
431
432
433
434
435
436
437
438
439
440
441
442
443
444
445
446
447
448
449
450
451
452
453
454
455
456
457
458
459
460
461
* Updates to :class:`fsl.data.mesh.TriangleMesh` - ``vertices`` and ``indices``
  are now ``property`` attributes. New lazily generated ``normals`` and
  ``vnormals`` properties (face and vertex normals respectively). Option
  to ``__init__`` to fix the face winding order of a mesh.
* :func:`fsl.utils.memoize.memoize` decorator made into a class rather than a
  function. The new :class:`.Memoize` class has an ``invalidate`` method, which
  clears the cache.


1.0.4 (Friday July 14th 2017)
-----------------------------


* Python 2/3 compatibility fix to :mod:`fsl.utils.callfsl`.
* Fix to :func:`fsl.utils.transform.scaleOffsetXform` - accepts inputs
  that are not lists.
* :func:`fsl.utils.transform.compose` accepts either a sequence of three
  axis angles, or a ``(3, 3)`` rotation matrix.


1.0.3 (Sunday June 11th 2017)
-----------------------------


* Fix to :mod:`fsl.utils.async` which was breaking environments where multiple
  ``wx.App`` instances were being created.


1.0.2 (Thursday June 8th 2017)
------------------------------


* Python 2/3 compatibility fixes
* New :func:`fsl.version.patchVersion` function.


1.0.1 (Sunday 4th June 2017)
----------------------------


* New version number parsing functions in :mod:`fsl.version`.


1.0.0 (Saturday May 27th 2017)
------------------------------


* Removed many GUI-related modules - they have been moved to the
  ``fsleyes-widgets`` project. The following modules have been removed:
  - :mod:`fsl.utils.colourbarbitmap`
  - :mod:`fsl.utils.dialog`
  - :mod:`fsl.utils.imagepanel`
  - :mod:`fsl.utils.layout`
  - :mod:`fsl.utils.platform`
  - :mod:`fsl.utils.runwindow`
  - :mod:`fsl.utils.status`
  - :mod:`fsl.utils.textbitmap`
  - :mod:`fsl.utils.typedict`
  - :mod:`fsl.utils.webpage`
* :mod:`fsl.utils.settings` module rewritten. It no longer uses ``wx``,
  but instead stores plain-text and ``pickle`` files in the user's home
  directory.
* Software GL renderer test in :mod:`fsl.utils.platform` is more lenient
* New :class:`.AtlasLabel` class
* :meth:`.Image.__init__` allows arguments to be passed through to
  ``nibabel.load``.
* New :meth:`.Nifti.strval` method to handle escaped strings in NIFTI headers.
* Python 2/3 compatibility fixes


0.11.0 (Thursday April 20th 2017)
---------------------------------


* First public release as part of FSL 5.0.10