CHANGELOG.rst 32.1 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
2.9.0 (Under development)
-------------------------


Added
^^^^^


Paul McCarthy's avatar
Paul McCarthy committed
13
14
* New wrapper functions for the FSL :func:`.prelude` and :func:`applyxfm4D`
  commands.
Paul McCarthy's avatar
Paul McCarthy committed
15
16
17
* New ``firstDot`` option to the :func:`.path.getExt`,
  :func:`.path.removeExt`, and :func:`.path.splitExt`, functions, offering
  rudimentary support for double-barrelled filenames.
Paul McCarthy's avatar
Paul McCarthy committed
18
19
* The :func:`.nonlinear.applyDeformation` function now accepts a ``premat``
  affine, which is applied to the input image before the deformation field.
Paul McCarthy's avatar
Paul McCarthy committed
20

Paul McCarthy's avatar
Paul McCarthy committed
21

Paul McCarthy's avatar
Paul McCarthy committed
22
23
24
25
Changed
^^^^^^^


Paul McCarthy's avatar
Paul McCarthy committed
26
27
* The :func:`.gifti.relatedFiles` function now supports files with
  BIDS-style naming conventions.
Paul McCarthy's avatar
Paul McCarthy committed
28
29
30
31
32
* The :func:`.run.run` and :func:`.run.runfsl` functions now pass through any
  additional keyword arguments to ``subprocess.Popen`` or, if ``submit=True``,
  to :func:`fslsub.submit`.
* The :func:`.fslsub.submit` function now accepts an ``env`` option, allowing
  environment variables to be specified.
Paul McCarthy's avatar
Paul McCarthy committed
33
34
* The :func:`.run.runfsl` function now raises an error on attempts to
  run a command which is not present in ``$FSLDIR/bin/`` (e.g. ``ls``).
Paul McCarthy's avatar
Paul McCarthy committed
35
36
37
* The :mod:`.bids` module has been updated to support files with any
  extension, not just those in the core BIDS specification (``.nii``,
  ``.nii.gz``, ``.json``, ``.tsv``).
Paul McCarthy's avatar
Paul McCarthy committed
38
39
40
41
42
43
44
* The return value of a function decorated with :func:`.fileOrImage`,
  :func:`.fileOrArray`, or :func:`.fileOrText` is now accessed via an attribute
  called ``stdout``, instead of ``output``.
* Output files of functions decorated with :func:`.fileOrImage`,
  :func:`.fileOrArray`, or :func:`.fileOrText`, which have been loaded via the
  :attr:`.LOAD` symbol, can now be accessed as attributes of the returned
  results object, in addition to being accessed as dict items.
Paul McCarthy's avatar
Paul McCarthy committed
45
46
47
48
49
50
* Wrapper functions decorated with the :func:`.fileOrImage`,
 :func:`.fileOrArray`, or :func:`.fileOrText` decorators will now pass all
  arguments and return values through unchanged if an argument called ``submit``
  is passed in, and is set to ``True`` (or any non-``False``
  value). Furthermore, in such a scenario a :exc:`ValueError` will be raised if
  any in-memory objects or ``LOAD`` symbols are passed.
Paul McCarthy's avatar
Paul McCarthy committed
51
52
53
* The :func:`.fileOrText` decorator has been updated to work with input
  values - file paths must be passed in as ``pathlib.Path`` objects, so they
  can be differentiated from input values.
Paul McCarthy's avatar
Paul McCarthy committed
54
55


Paul McCarthy's avatar
Paul McCarthy committed
56
57
58
59
60
61
62
Fixed
^^^^^


* Updated the :func:`.prepareArgs` function to use ``shlex.split`` when
  preparing shell command arguments, instead of performing a naive whitespace
  split.
Paul McCarthy's avatar
Paul McCarthy committed
63
64
* Fixed some bugs in the :func:`.fslsub.info` and :func:`.fslinfo.wait`
  functions.
Paul McCarthy's avatar
Paul McCarthy committed
65
66
* Fixed the :func:`.DeformationField.transform` method so it works with
  a single set of coordinates.
Paul McCarthy's avatar
Paul McCarthy committed
67
68


Paul McCarthy's avatar
Paul McCarthy committed
69
70
71
72
73
74
75
76
77
78
79
80
81
82
2.8.4 (Monday 2nd March 2020)
-----------------------------


Added
^^^^^


* Added a new ``partial_fill`` option to :meth:`.FileTree.read`, which
  effectively eliminates any variables which only have one value. This was
  added to accommodate some behavioural changes that were introduced in 2.8.2.



Paul McCarthy's avatar
Paul McCarthy committed
83
84
85
86
87
88
89
90
91
92
2.8.3 (Friday 28th February 2020)
---------------------------------


Fixed
^^^^^


* Fixed a bug in the :meth:`.Image.save` method.

Paul McCarthy's avatar
Paul McCarthy committed
93
94
95
96
97
98
99
100
101
102
103
104

2.8.2 (Thursday 27th February 2020)
-----------------------------------


Fixed
^^^^^


* Fixed some subtle bugs in the :func:`.filetree.utils.get_all` function.


Paul McCarthy's avatar
Paul McCarthy committed
105
106
2.8.1 (Thursday 20th February 2020)
-----------------------------------
Paul McCarthy's avatar
Paul McCarthy committed
107
108
109
110
111
112
113
114
115


Fixed
^^^^^


* Fixed a bug where an error would be raised on attempts to load an image file
  without a BIDS-compatible name from a BIDS-like directory.

Paul McCarthy's avatar
Paul McCarthy committed
116

Paul McCarthy's avatar
Paul McCarthy committed
117
118
2.8.0 (Wednesday 29th January 2020)
-----------------------------------
Paul McCarthy's avatar
Paul McCarthy committed
119
120


Paul McCarthy's avatar
Paul McCarthy committed
121
122
123
124
125
126
127
128
Added
^^^^^


* New :meth:`.Nifti.adjust` method, for creating a copy of a :class:`.Nifti`
  header with adjusted shape, pixdims, and affine. This can be useful for
  creating a resampling reference.
* New :func:`.affine.rescale` function, for adjusting a scaling matrix.
Paul McCarthy's avatar
Paul McCarthy committed
129
130
* New :func:`.mghimage.voxToSurfMat` function, for creating a
  voxel-to-freesurfer affine transform from any image.
Paul McCarthy's avatar
Paul McCarthy committed
131
132


Paul McCarthy's avatar
Paul McCarthy committed
133
134
135
136
137
138
139
140
141
142
Changed
^^^^^^^


* The :class:`.ImageWrapper` now maintains its own image data cache, rather
  than depending on ``nibabel``.
* Internal changes to avoid using the deprecated
  ``nibabel.dataobj_images.DataobjImage.get_data`` method.


Paul McCarthy's avatar
Paul McCarthy committed
143
144
145
146
147
Fixed
^^^^^


* Improved the algorithm used by the :func:`.mesh.needsFixing` function.
Paul McCarthy's avatar
Paul McCarthy committed
148
149
* The :meth:`.fslmaths.run` method now accepts :attr:`.wrappers.LOAD` as an
  output specification.
Paul McCarthy's avatar
Paul McCarthy committed
150
151
* Fixed a bug in the :class:`.Mesh` class to prevent indices from being loaded
  as floating point type.
Paul McCarthy's avatar
Paul McCarthy committed
152
* Fixed a bug in the :func:`.resample` function.
Paul McCarthy's avatar
Paul McCarthy committed
153
154
* Fixed a bug in the :class:`.MGHImage` class, which was causing pixdims to
  be overridden by scales derived from the affine.
Paul McCarthy's avatar
Paul McCarthy committed
155
156


Paul McCarthy's avatar
Paul McCarthy committed
157
158
159
160
161
162
163
164
Deprecated
^^^^^^^^^^


* :func:`.calculateMatrix` - its functionality has been moved to the
  :func:`.affine.rescale` function.


Paul McCarthy's avatar
Paul McCarthy committed
165
166
2.7.0 (Wednesday 6th November 2019)
-----------------------------------
Paul McCarthy's avatar
Paul McCarthy committed
167
168
169
170
171
172
173
174
175


Added
^^^^^


* New ``until`` option to the :func:`.idle.block` function.
* New :meth:`.Idle.neverQueue` setting, which can be used to force all
  tasks passed to :func:`.idle.idle` to be executed synchronously.
Paul McCarthy's avatar
Paul McCarthy committed
176
177
* New :meth:`.IdleLoop.synchronous` context manager, to temporarily change the
  value of :meth:`.IdleLoop.neverQueue`.
Paul McCarthy's avatar
Paul McCarthy committed
178
179
* New :mod:`.bids` module, containing a few simple functions for working with
  `BIDS <https://bids.neuroimaging.io>`_ datasets.
Paul McCarthy's avatar
Paul McCarthy committed
180
181
182
* New :func:`.image.loadMetadata` function, and ``loadMeta`` option to the
  :class:`.Image` class, to automatically find and load any sidecar JSON files
  associated with an image file.
Paul McCarthy's avatar
Paul McCarthy committed
183
184
185
186
187
188


Changed
^^^^^^^


Paul McCarthy's avatar
Paul McCarthy committed
189
* Internal reorganisation in the :mod:`.idle` module.
Paul McCarthy's avatar
Paul McCarthy committed
190
191


Paul McCarthy's avatar
Paul McCarthy committed
192
193
194
195
196
197
198
199
Fixed
^^^^^


* Fixed incorrect usage of ``setuptools.find_packages``, which was causing
  unit tests to be installed.


Paul McCarthy's avatar
Paul McCarthy committed
200
201
202
203
204
205
206
207
208
209
210
Deprecated
^^^^^^^^^^


* :func:`.idle.inIdle` - replaced by :meth:`.IdleLoop.inIdle`.
* :func:`.idle.cancelIdle` - replaced by :meth:`.IdleLoop.cancelIdle`.
* :func:`.idle.idleReser` - replaced by :meth:`.IdleLoop.idleReset`.
* :func:`.idle.getIdleTimeout` - replaced by :meth:`.IdleLoop.callRate`.
* :func:`.idle.setIdleTimeout` - replaced by :meth:`.IdleLoop.callRate`.


Paul McCarthy's avatar
Paul McCarthy committed
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
2.6.2 (Monday 7th October 2019)
-------------------------------


Changed
^^^^^^^


* Added a debugging hook in the :mod:`.idle` module.
* The :func:`.fslsub.submit` function is now more flexible in the way it
  accepts the command and input arguments.
* The :func:`.run.prepareArgs` function has been renamed (from
  ``_prepareArgs``).


Paul McCarthy's avatar
Paul McCarthy committed
226
227
228
229
230
231
232
233
234
235
236
237
2.6.1 (Thursday 19th September 2019)
------------------------------------


Changed
^^^^^^^


* ``fslpy`` is no longer tested against Python 3.5, and is now tested against
  Python 3.6, 3.7, and 3.8.


Paul McCarthy's avatar
Paul McCarthy committed
238
239
2.6.0 (Tuesday 10th September 2019)
-----------------------------------
Paul McCarthy's avatar
Paul McCarthy committed
240
241


Paul McCarthy's avatar
Paul McCarthy committed
242
243
244
245
246
Added
^^^^^


* New :meth:`.Image.iscomplex` attribute.
Paul McCarthy's avatar
Paul McCarthy committed
247
* Support for a new ``Statistic`` atlas type.
Paul McCarthy's avatar
Paul McCarthy committed
248
249


Paul McCarthy's avatar
Paul McCarthy committed
250
251
252
253
254
255
Changed
^^^^^^^


* The :class:`.Cache` class has a new ``lru`` option, allowing it to be used
  as a least-recently-used cache.
Paul McCarthy's avatar
Paul McCarthy committed
256
257
* The :mod:`fsl.utils.filetree` module has been refactored to make it easier
  for the :mod:`.query` module to work with file tree hierarchies.
Paul McCarthy's avatar
Paul McCarthy committed
258
259
260
* The :meth:`.LabelAtlas.get` method has a new ``binary`` flag, allowing
  either a binary mask, or a mask with the original label value, to be
  returned.
Paul McCarthy's avatar
Paul McCarthy committed
261
262
* The :mod:`.dicom` module has been updated to work with the latest version of
  ``dcm2niix``.
Paul McCarthy's avatar
Paul McCarthy committed
263
264
265
266
267
268
269
270
271
272
273


Deprecated
^^^^^^^^^^


* :meth:`.ProbabilisticAtlas.proportions`,
  :meth:`.ProbabilisticAtlas.maskProportions`, and
  :meth:`.ProbabilisticAtlas.labelProportions` have been deprecated in favour
  of :meth:`.StatisticAtlas.values`, :meth:`.StatisticAtlas.maskValues`, and
  :meth:`.StatisticAtlas.labelValues`
Paul McCarthy's avatar
Paul McCarthy committed
274
275


Paul McCarthy's avatar
Paul McCarthy committed
276
277
2.5.0 (Tuesday 6th August 2019)
-------------------------------
Paul McCarthy's avatar
Paul McCarthy committed
278
279


Paul McCarthy's avatar
Paul McCarthy committed
280
281
282
283
Added
^^^^^


Paul McCarthy's avatar
Paul McCarthy committed
284
285
286
287
288
289
290
291
292
293
294
295
* 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*).

Paul McCarthy's avatar
Paul McCarthy committed
296
297


Paul McCarthy's avatar
Paul McCarthy committed
298
299
300
301
Changed
^^^^^^^


Paul McCarthy's avatar
Paul McCarthy committed
302
303
* The :mod:`.vest.looksLikeVestLutFile` function has been made slightly more
  lenient.
Paul McCarthy's avatar
Paul McCarthy committed
304
305
306
307
308
309
310
* `h5py <https://www.h5py.org/>`_ has been added to the ``fslpy`` dependencies.


Deprecated
^^^^^^^^^^


Paul McCarthy's avatar
Paul McCarthy committed
311
* The :mod:`fsl.utils.transform` module has been deprecated; its functions can
Paul McCarthy's avatar
Paul McCarthy committed
312
313
  now be found in the :mod:`fsl.transforms.affine` and
  :mod:`fsl.transform.flirt` modules.
Paul McCarthy's avatar
Paul McCarthy committed
314
315


Paul McCarthy's avatar
Paul McCarthy committed
316
317
318
319
320
321
322
323
324
325
326
327
328
329
330
331
332
333
334
335
2.4.0 (Wednesday July 24th 2019)
--------------------------------


Added
^^^^^


* New :mod:`.image.roi` module, for extracting an ROI of an image, or expanding
  its field-of-view.


Changed
^^^^^^^


* The :mod:`.resample_image` script has been updated to support resampling of
  images with more than 3 dimensions.


Paul McCarthy's avatar
Paul McCarthy committed
336
337
338
339
340
341
342
343
344
345
346
2.3.1 (Friday July 5th 2019)
----------------------------


Fixed
^^^^^


* The :class:`.Bitmap` class now supports greyscale images and palette images.


Paul McCarthy's avatar
Paul McCarthy committed
347
348
2.3.0 (Tuesday June 25th 2019)
------------------------------
Paul McCarthy's avatar
Paul McCarthy committed
349
350
351
352
353
354


Added
^^^^^


Paul McCarthy's avatar
Paul McCarthy committed
355
356
357
358
359
* New :class:`.Bitmap` class, for loading bitmap images. The
  :meth:`.Bitmap.asImage` method can be used to convert a ``Bitmap`` into
  an :class:`.Image`.
* The :class:`.Image` class now has support for the ``RGB24`` and ``RGBA32``
  NIfTI data types.
Paul McCarthy's avatar
Paul McCarthy committed
360
361
* New :attr:`.Image.nvals` property, for use with ``RGB24``/``RGBA32``
  images.
Paul McCarthy's avatar
Paul McCarthy committed
362
363
364
365
366
367
368
369
370
371
372
373
374
375
* New :meth:`.LabelAtlas.get` and :meth:`ProbabilisticAtlas.get` methods,
  which return an :class:`.Image` for a specific region.
* The :meth:`.AtlasDescription.find` method also now a ``name`` parameter,
  allowing labels to be looked up by name.
* New :meth:`.FileTree.defines` and :meth:`.FileTree.on_disk` methods, to
  replace the :func:`.FileTree.exists` method.


Fixed
^^^^^


* The :func:`.makeWriteable` function will always create a copy of an
  ``array`` if its base is a ``bytes`` object.
Paul McCarthy's avatar
Paul McCarthy committed
376
* Fixed a bug in the :meth:`.GitfitMesh.loadVertices` method.
Paul McCarthy's avatar
Paul McCarthy committed
377
378
* Fixed a bug in the :meth:`.Mesh.addVertices` method where the wrong face
  normals could be used for newly added vertex sets.
Paul McCarthy's avatar
Paul McCarthy committed
379
380


Paul McCarthy's avatar
Paul McCarthy committed
381
382
2.2.0 (Wednesday May 8th 2019)
------------------------------
Paul McCarthy's avatar
Paul McCarthy committed
383
384


Paul McCarthy's avatar
Paul McCarthy committed
385
386
387
388
389
390
391
392
393
394
395
396
397
Added
^^^^^


* New :mod:`.resample_image` script.
* New :mod:`.resample` module (replacing the :func:`.Image.resample` method),
  containing functions to resample an :class:`.Image`.
* New :func:`.resample.resampleToPixdim` and
  :func:`.resample.resampleToReference` functions, convenience wrappers around
  :func:`.resample.resample`.
* New :func:`.idle.block` function.


Paul McCarthy's avatar
Paul McCarthy committed
398
399
400
401
Changed
^^^^^^^


Paul McCarthy's avatar
Paul McCarthy committed
402
403
404
405
406
407
408
* The :func:`.resample` function (formerly :meth:`.Image.resample`) now
  accepts ``origin`` and ``matrix`` parameters, which can be used to adjust
  the alignment of the voxel grids of the input and output images.
* The :func:`.transform.decompose` function now accepts both ``(3, 3)``
  and ``(4, 4)`` matrices.


Paul McCarthy's avatar
Paul McCarthy committed
409
410
411
412
Fixed
^^^^^


Paul McCarthy's avatar
Paul McCarthy committed
413
* Minor fixes to some :mod:`.filetree.filetree` tree definitions.
Paul McCarthy's avatar
Paul McCarthy committed
414
415


Paul McCarthy's avatar
Paul McCarthy committed
416
417
418
419
420
421
Deprecated
^^^^^^^^^^


* The :meth:`.Image.resample` method has been deprecated in favour of the
  :func:`.resample.resample` function.
Paul McCarthy's avatar
Paul McCarthy committed
422
423


Paul McCarthy's avatar
Paul McCarthy committed
424
425
2.1.0 (Saturday April 13th 2019)
--------------------------------
Paul McCarthy's avatar
Paul McCarthy committed
426
427
428
429
430
431
432
433


Added
^^^^^


* New tensor conversion routines in the :mod:`.dtifit` module (Michiel
  Cottaar).
Paul McCarthy's avatar
Paul McCarthy committed
434
435
* New :func:`.makeWriteable` function which ensures that a ``numpy.array`` is
  writeable, and creates a copy if necessary
Paul McCarthy's avatar
Paul McCarthy committed
436
437


Paul McCarthy's avatar
Paul McCarthy committed
438
439
440
441
442
Changed
^^^^^^^


* The :class:`.GiftiMesh` class no longer creates copies of the mesh
Paul McCarthy's avatar
Paul McCarthy committed
443
444
  vertex/index arrays. This means that, these arrays will be flagged as
  read-only.
Paul McCarthy's avatar
Paul McCarthy committed
445
446
447
* The :class:`.Mesh` class handles vertex data sets requiring different
  triangle unwinding orders, at the cost of potentially having to store
  two copies of the mesh indices.
Paul McCarthy's avatar
Paul McCarthy committed
448
449


Paul McCarthy's avatar
Paul McCarthy committed
450
451
452
453
454
455
456
457
458
Fixed
^^^^^


* The :class:`.FeatDesign` class now handles "compressed" voxelwise EV files,
  such as those generated by `PNM
  <https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/PNM>`_.


Paul McCarthy's avatar
Paul McCarthy committed
459
460
461
462
463
464
465
466
467
468
469
470
2.0.1 (Monday April 1st 2019)
-----------------------------


Fixed
^^^^^


* Fixed a bug with the :func:`.gifti.relatedFiles` function returning
  duplicate files.


Paul McCarthy's avatar
Paul McCarthy committed
471
472
2.0.0 (Friday March 20th 2019)
------------------------------
473
474


475
476
477
Added
^^^^^

Paul McCarthy's avatar
Paul McCarthy committed
478
* New :mod:`fsl.utils.filetree` package for defining and working with
Paul McCarthy's avatar
Paul McCarthy committed
479
  file/directory templates (Michiel Cottaar).
Paul McCarthy's avatar
Paul McCarthy committed
480
* Simple built-in :mod:`.deprecated` decorator.
Paul McCarthy's avatar
Paul McCarthy committed
481
* New :mod:`fsl.data.utils` module, which currently contains one function
482
  :func:`.guessType`, which guesses the data type of a file/directory path.
483
* New :func:`.commonBase` function for finding the common prefix of a set of
Paul McCarthy's avatar
Paul McCarthy committed
484
  file/directory paths.
485
486


487
488
489
Changed
^^^^^^^

Paul McCarthy's avatar
Paul McCarthy committed
490

491
* Removed support for Python 2.7 and 3.4.
492
493
494
* Minimum required version of ``nibabel`` is now 2.3.
* The :class:`.Image` class now fully delegates to ``nibabel`` for managing
  file handles.
Paul McCarthy's avatar
Paul McCarthy committed
495
* The :class:`.GiftiMesh` class can now load surface files which contain
Paul McCarthy's avatar
Paul McCarthy committed
496
497
498
  vertex data, and will accept surface files which end in ``.gii``, rather
  than requiring files which end in ``.surf.gii``.
* The ``name`` property of :class:`.Mesh` instances can now be updated.
Paul McCarthy's avatar
Paul McCarthy committed
499
500


Paul McCarthy's avatar
Paul McCarthy committed
501
502
503
504
505
506
Removed
^^^^^^^

* Many deprecated items removed.


Paul McCarthy's avatar
Paul McCarthy committed
507
508
509
510
511
512
513
514
Deprecated
^^^^^^^^^^


* Deprecated the :func:`.loadIndexedImageFile`  function, and the ``indexed``
  flag to the :class:`.Image` constructor.


Paul McCarthy's avatar
Paul McCarthy committed
515
516
517
518
1.13.3 (Friday February 8th 2019)
---------------------------------


Paul McCarthy's avatar
Paul McCarthy committed
519
520
521
Fixed
^^^^^

Paul McCarthy's avatar
Paul McCarthy committed
522

523
* Fixed an issue with the :func:`.dicom.loadSeries` using memory-mapping for
Paul McCarthy's avatar
Paul McCarthy committed
524
  image files that would subsequently be deleted.
Paul McCarthy's avatar
Paul McCarthy committed
525
* Fixed an issue in the :class:`.GiftiMesh` class, where
Paul McCarthy's avatar
Paul McCarthy committed
526
527
528
  ``numpy``/``nibabel`` was returning read-only index arrays.


Paul McCarthy's avatar
Paul McCarthy committed
529
530
531
532
533
534
535
536
1.13.2 (Friday November 30th 2018)
----------------------------------


Changed
^^^^^^^


Paul McCarthy's avatar
Paul McCarthy committed
537
538
* The :meth:`.Image.resample` method now supports images with more than three
  dimensions.
Michiel Cottaar's avatar
Michiel Cottaar committed
539
540
541
542
* The :func:`fsl.utils.fslsub.submit` now returns the job-id as a string
  rather than a one-element tuple. It now also accepts a nested sequence
  of job ids rather than just a flat sequence. This will also changes the
  output from the function wrappers in :mod:`fsl.wrappers` if submitted.
543
544


Paul McCarthy's avatar
Paul McCarthy committed
545
546
Fixed
^^^^^
Paul McCarthy's avatar
Paul McCarthy committed
547

Paul McCarthy's avatar
Paul McCarthy committed
548
549
550
551
552
553

* Fix to the :class:`.ImageWrapper` regarding complex data types.


1.13.1 (Friday November 23rd 2018)
----------------------------------
Paul McCarthy's avatar
Paul McCarthy committed
554
555


Paul McCarthy's avatar
Paul McCarthy committed
556
557
558
559
Fixed
^^^^^


Paul McCarthy's avatar
Paul McCarthy committed
560
* Added a missing ``image`` attribute in the :class:`.VoxelwiseConfoundEV`
Paul McCarthy's avatar
Paul McCarthy committed
561
  class.
Paul McCarthy's avatar
Paul McCarthy committed
562
563
564
* Make sure that FEAT ``Cluster`` objects (created by the
  :func:`.loadClusterResults` function) contain ``p`` and ``logp`` attributes,
  even when cluster thresholding was not used.
Paul McCarthy's avatar
Paul McCarthy committed
565
566


Paul McCarthy's avatar
Paul McCarthy committed
567
568
1.13.0 (Thursday 22nd November 2018)
------------------------------------
Paul McCarthy's avatar
Paul McCarthy committed
569

Paul McCarthy's avatar
Paul McCarthy committed
570
571
572
573

Added
^^^^^

Paul McCarthy's avatar
Paul McCarthy committed
574
* New wrapper functions for :func:`.fsl_anat`, :func:`.applytopup` (Martin
Paul McCarthy's avatar
Paul McCarthy committed
575
  Craig).
Paul McCarthy's avatar
Paul McCarthy committed
576
* New :func:`.fileOrText` decorator for use in wrapper functions (Martin
Paul McCarthy's avatar
Paul McCarthy committed
577
578
579
580
  Craig).


Changed
Paul McCarthy's avatar
Paul McCarthy committed
581
582
^^^^^^^

Paul McCarthy's avatar
Paul McCarthy committed
583
584
* Various minor changes and enhancements to the FSL function :mod:`.wrappers`
  interfaces (Martin Craig).
Paul McCarthy's avatar
Paul McCarthy committed
585
586
587
588
589
590
591


Fixed
^^^^^

* The ``immv`` and ``imcp`` scripts now accept incorrect file extensions on
  input arguments.
Paul McCarthy's avatar
Paul McCarthy committed
592
593


Paul McCarthy's avatar
Paul McCarthy committed
594
595
1.12.0 (Sunday October 21st 2018)
---------------------------------
Paul McCarthy's avatar
Paul McCarthy committed
596
597
598
599
600
601
602
603
604
605
606
607
608
609
610
611
612
613


Changed
^^^^^^^


* The ``extract_noise`` script has been renamed to :mod:`.fsl_ents`.
* Increased the minimum required version of ``dcm2niix`` in the
  :mod:`fsl.data.dicom` module.


Deprecated
^^^^^^^^^^


* The ``extract_noise`` script.


Paul McCarthy's avatar
Paul McCarthy committed
614
615
616
617
618
619
620
621
622
623
624
1.11.1 (Friday September 14th 2018
----------------------------------


Fixed
^^^^^


* Fixed a Python 2 incompatibility in the :mod:`.settings` module.


Paul McCarthy's avatar
Paul McCarthy committed
625
626
627
628
629
630
631
632
633
634
635
636
637
638
639
640
641
642
643
644
1.11.0 (Thursday September 13th 2018)
-------------------------------------


Added
^^^^^


* A couple of new convenience functions to the :mod:`.settings` module.


Changed
^^^^^^^


* Development (test and documentation dependencies) are no longer listed
  in ``setup.py`` - they now need to be installed manually.
* Removed conda build infrastructure.


Paul McCarthy's avatar
Paul McCarthy committed
645
646
647
648
649
650
651
652
653
654
655
656
657
658
1.10.3 (Sunday September 9th 2018)
----------------------------------


Added
^^^^^


* The :func:`.parseVersionString` function accepts (and ignores) `local
  version identifer
  <https://www.python.org/dev/peps/pep-0440/#local-version-identifiers>`_
  strings.


Paul McCarthy's avatar
Paul McCarthy committed
659
660
661
662
663
664
665
666
667
668
669
670
1.10.2 (Friday September 7th 2018)
----------------------------------


Fixed
^^^^^


* The :meth:`.Image.save` method was not handling memory-mapped images
  correctly.


671
672
673
674
675
676
677
678
679
680
681
682
683
684
1.10.1 (Friday August 3rd 2018)
-------------------------------


Changed
^^^^^^^


* Minor adjustmenets to improve Windows compatibility.


Fixed
^^^^^

Paul McCarthy's avatar
Paul McCarthy committed
685
* The :mod:`.FEATImage.getCOPE` method was returning PE images.
686
687


688
689
1.10.0 (Wednesday July 18th 2018)
---------------------------------
Paul McCarthy's avatar
Paul McCarthy committed
690
691
692
693
694
695
696
697
698
699


Added
^^^^^


* A new script, :mod:`.extract_noise`, which can be used to extract ICA
  component time courses from a MELODIC ICA analysis.
* New :func:`.path.allFiles` function which returns all files underneath a
  directory.
700
* The :func:`.fileOrImage` and :func:`.fileOrArray` decorators now support
Paul McCarthy's avatar
Paul McCarthy committed
701
  loading of files which are specified with an output basename.
702
* New :mod:`.fast` wrapper function for the FSL FAST tool.
Paul McCarthy's avatar
Paul McCarthy committed
703
704
705
706
707
708
709
710
711
712
713


Changed
^^^^^^^


* When using the :func:`.run.run` function, the command output/error streams
  are now forwarded immediately.
* Removed dependency on ``pytest-runner``.


Paul McCarthy's avatar
Paul McCarthy committed
714
715
1.9.0 (Monday June 4th 2018)
----------------------------
Paul McCarthy's avatar
Paul McCarthy committed
716
717
718
719
720
721
722
723
724
725
726
727
728
729
730
731
732
733
734
735
736
737
738
739
740
741
742
743
744
745
746
747
748
749


Added
^^^^^


* New :meth:`.Image.data` property method, for easy access to image data
  as a ``numpy`` array.
* New ``log`` option to the :func:`.run.run` function, allowing more
  fine-grained control over sub-process output streams.
* New :meth:`.Platform.fsldevdir` property, allowing the ``$FSLDEVDIR``
  environment variable to be queried/changed.


Changed
^^^^^^^


* :meth:`.Image.ndims` has been renamed to :meth:`.Image.ndim`, to align
  more closely with ``numpy`` naming conventions.
* The ``err`` and ``ret`` parameters to the :func:`.run.run` function have
  been renamed to ``stderr`` and ``exitcode`` respectively.
* The :func:`.runfsl` function will give priority to the ``$FSLDEVDIR``
  environment variable if it is set.


Deprecated
^^^^^^^^^^


* :meth:`.Image.ndims`.
* The ``err`` and ``ret`` parameters to :func:`.run.run`.


Paul McCarthy's avatar
Paul McCarthy committed
750
751
752
753
754
755
756
757
758
759
760
761
1.8.1 (Friday May 11th 2018)
----------------------------


Changed
^^^^^^^


* The :func:`.fileOrImage` decorator function now accepts :class:`.Image`
  objects as well as ``nibabel`` image objects.


Paul McCarthy's avatar
Paul McCarthy committed
762
763
1.8.0 (Thursday May 3rd 2018)
-----------------------------
Paul McCarthy's avatar
Paul McCarthy committed
764
765
766
767
768
769
770
771
772
773


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
774
* New :mod:`fsl.utils.fslsub` module, containing a :func:`.fslsub.submit`
Paul McCarthy's avatar
Paul McCarthy committed
775
  function which submits a cluster job via ``fsl_sub``.
Paul McCarthy's avatar
Paul McCarthy committed
776
777
* Assertions (in the :mod:`.assertions` module) can be disabled with the
  new :func:`.assertions.disabled` context manager.
Paul McCarthy's avatar
Paul McCarthy committed
778
779
* New :mod:`fsl.utils.parse_data` module containing various neuroimaging
  data constructors for use with ``argparse``.
Paul McCarthy's avatar
Paul McCarthy committed
780
781
* The :func:`.memoize.skipUnchanged` decorator has an ``invalidate`` function
  which allows its cache to be cleared.
Paul McCarthy's avatar
Paul McCarthy committed
782
783
784
785
786
787
788
789
790
791
792
793
794
795
796
797
798


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`).


799
800
1.7.2 (Monday March 19th 2018)
------------------------------
Paul McCarthy's avatar
Paul McCarthy committed
801
802
803
804
805
806


Added
^^^^^


807
808
* 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
809
810


Paul McCarthy's avatar
Paul McCarthy committed
811
812
813
814
815
816
817
818
819
820
821
822
823
824
825
826
1.7.1 (Monday March 12th 2018)
------------------------------



Changed
^^^^^^^


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


Fixed
^^^^^


Paul McCarthy's avatar
Paul McCarthy committed
827
* Removed deprecated use of :func:`.imagewrapper.canonicalShape`.
Paul McCarthy's avatar
Paul McCarthy committed
828
829


Paul McCarthy's avatar
Paul McCarthy committed
830
831
832
833
834
835
836
837
838
839
840
841
842
843
844
845
846
847
848
849
850
851
852
853
854
855
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
Paul McCarthy's avatar
Paul McCarthy committed
856
  to the :mod:`.data.image` class.
Paul McCarthy's avatar
Paul McCarthy committed
857
858
859
860
861
862
863
864
865
866
867
868
869
870
871
* The :func:`.ImageWrapper.naninfrange` function has been moved
  into its own :mod:`.naninfrange` module.


Fixed
^^^^^


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


Deprecated
^^^^^^^^^^


Paul McCarthy's avatar
Paul McCarthy committed
872
* :func:`.ImageWrapper.canonicalShape` (moved to the :mod:`.data.image` module)
Paul McCarthy's avatar
Paul McCarthy committed
873
874
875
876
* :func:`.ImageWrapper.naninfrange` function (moved to the :mod:`.naninfrange`
  module)


Paul McCarthy's avatar
Paul McCarthy committed
877
878
879
880
881
882
883
1.6.8 (Monday February 12th 2018)
---------------------------------


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


Paul McCarthy's avatar
Paul McCarthy committed
884
885
886
887
888
1.6.7 (Friday February 9th 2018)
--------------------------------


* More further adjustments to the ``conda`` package build.
Paul McCarthy's avatar
Paul McCarthy committed
889
* Adjustments to pypi source distribution - the ``requirements-extra.txt`` file
Paul McCarthy's avatar
Paul McCarthy committed
890
891
892
  was not being included.


Paul McCarthy's avatar
Paul McCarthy committed
893
894
895
896
897
898
899
1.6.6 (Thursday February 8th 2018)
----------------------------------


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


Paul McCarthy's avatar
Paul McCarthy committed
900
901
902
903
904
905
906
1.6.5 (Tuesday February 6th 2018)
---------------------------------


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


Paul McCarthy's avatar
Paul McCarthy committed
907
908
909
910
911
912
913
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
914
915
1.6.3 (Friday February 2nd 2018)
--------------------------------
Paul McCarthy's avatar
Paul McCarthy committed
916
917
918


* Minor enhancements to the :class:`.WeakFunctionRef` class.
Paul McCarthy's avatar
Paul McCarthy committed
919
920
921
* 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
922
923


Paul McCarthy's avatar
Paul McCarthy committed
924
925
926
927
928
929
930
931
932
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
933
934
935
936
937
938
939
940
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
941
942
1.6.0 (Friday January 26th 2018)
--------------------------------
Paul McCarthy's avatar
Paul McCarthy committed
943
944


Paul McCarthy's avatar
Paul McCarthy committed
945
946
947
948
949
950
951
952
953
954
955
956
957
* 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
958
959
* 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
960
961
962
* 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
963
964
965
966
967
* 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
968
* Optional dependencies ``wxpython``, ``indexed_gzip``, ``trimesh``, and
Paul McCarthy's avatar
Paul McCarthy committed
969
970
  ``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
971
972


Paul McCarthy's avatar
Paul McCarthy committed
973
974
975
976
977
978
979
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
980
1.5.3 (Tuesday January 9th 2018)
981
982
983
984
985
986
987
--------------------------------


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


Paul McCarthy's avatar
Paul McCarthy committed
988
989
990
991
992
993
994
1.5.2 (Tuesday January 2nd 2018)
--------------------------------


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


Paul McCarthy's avatar
Paul McCarthy committed
995
996
997
998
999
1000
1001
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
1002
1003
1.5.0 (Wednesday December 13th 2017)
------------------------------------
Paul McCarthy's avatar
Paul McCarthy committed
1004
1005
1006
1007
1008
1009


* 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
1010
1011
1012
* 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
1013
1014


Paul McCarthy's avatar
Paul McCarthy committed
1015
1016
1.4.2 (Tuesday December 5th 2017)
---------------------------------
Paul McCarthy's avatar
Paul McCarthy committed
1017
1018
1019
1020
1021


* 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
1022
* Some small bugfixes to the :mod:`.atlasq` and :mod:`.atlases` moduless.
Paul McCarthy's avatar
Paul McCarthy committed
1023
1024
1025


1.4.1 (Thursday November 9th 2017)
Paul McCarthy's avatar
Paul McCarthy committed
1026
1027
1028
1029
1030
1031
----------------------------------


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


Paul McCarthy's avatar
Paul McCarthy committed
1032
1.4.0 (Thursday November 9th 2017)
Paul McCarthy's avatar
Paul McCarthy committed
1033
----------------------------------
Paul McCarthy's avatar
Paul McCarthy committed
1034

Paul McCarthy's avatar
Paul McCarthy committed
1035

Paul McCarthy's avatar
Paul McCarthy committed
1036
1037
* 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
1038
1039
1040
* 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
1041
1042
1043
1044
1045
1046
1047
1048
1049
1050
1051
1052
1053
1054
* 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
1055
1.3.1 (Wednesday October 25th 2017)
Paul McCarthy's avatar
Paul McCarthy committed
1056
1057
1058
1059
1060
1061
1062
-----------------------------------


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


Paul McCarthy's avatar
Paul McCarthy committed
1063
1.3.0 (Wednesday October 25th 2017)
Paul McCarthy's avatar
Paul McCarthy committed
1064
-----------------------------------
Paul McCarthy's avatar
Paul McCarthy committed
1065
1066
1067
1068


* :class:`.Atlas` classes can now pass ``kwargs`` through to the
  :class:`.Image` constructor.
Paul McCarthy's avatar
Paul McCarthy committed
1069
1070
1071
* :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
1072
* :class:`.Cache` now implements ``__getitem__`` and ``__setitem__``
Paul McCarthy's avatar
Paul McCarthy committed
1073
1074
* 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
1075
1076
* :func:`.platform.isWidgetAlive` is deprecated in favour of an equivalent
  function in the ``fsleyes-widgets`` library.
Paul McCarthy's avatar
Paul McCarthy committed
1077
1078
* ``scipy`` is now explicitly listed as a requirement (this should have been
  done in 1.2.1).
Paul McCarthy's avatar
Paul McCarthy committed
1079
1080
1081
1082
1083
1084
1085



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


Paul McCarthy's avatar
Paul McCarthy committed
1086
1087
* 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
1088
1089
1090
1091
1092


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

Paul McCarthy's avatar
Paul McCarthy committed
1093

Paul McCarthy's avatar
Paul McCarthy committed
1094
1095
1096
1097
1098
1099
1100
1101
1102
1103
1104
1105
1106
1107
1108
1109
* 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
1110
  favour of new :meth:`.Nifti.voxToScaledVoxMat` and
Paul McCarthy's avatar
Paul McCarthy committed
1111
1112
1113
1114
1115
1116
1117
1118
1119
1120
1121
1122
1123
1124
1125
1126
1127
1128
1129
1130
1131
  :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
1132
1133
1134
1135
1136
1137
1138
1139
1140
1141
1142
1143

 - :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
1144
1145
1146
1147
1148
1149
1150
1151
1152
1153
1154
1155
1156
1157
1158
1159
1160
1161
1162
1163
1164
1165
1166
1167
1168
1169
1170
1171
1172
1173
1174
1175
1176
1177
1178
1179
1180
1181
1182
1183
1184
1185
1186
1187
1188
1189
1190
1191
1192
1193
1194
1195
1196
1197
1198
1199
1200
1201
1202
1203
1204
1205
1206
1207
1208
1209
1210
1211
1212
1213
1214
1215
1216
1217
1218
* 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