CHANGELOG.rst 23.3 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
2.4.0 (Under development)
-------------------------


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
17
18
19
20
21
22
23
24
25
26
27
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
28
29
2.3.0 (Tuesday June 25th 2019)
------------------------------
Paul McCarthy's avatar
Paul McCarthy committed
30
31
32
33
34
35


Added
^^^^^


Paul McCarthy's avatar
Paul McCarthy committed
36
37
38
39
40
* 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
41
42
* New :attr:`.Image.nvals` property, for use with ``RGB24``/``RGBA32``
  images.
Paul McCarthy's avatar
Paul McCarthy committed
43
44
45
46
47
48
49
50
51
52
53
54
55
56
* 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
57
* Fixed a bug in the :meth:`.GitfitMesh.loadVertices` method.
Paul McCarthy's avatar
Paul McCarthy committed
58
59
* 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
60
61


Paul McCarthy's avatar
Paul McCarthy committed
62
63
2.2.0 (Wednesday May 8th 2019)
------------------------------
Paul McCarthy's avatar
Paul McCarthy committed
64
65


Paul McCarthy's avatar
Paul McCarthy committed
66
67
68
69
70
71
72
73
74
75
76
77
78
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
79
80
81
82
Changed
^^^^^^^


Paul McCarthy's avatar
Paul McCarthy committed
83
84
85
86
87
88
89
* 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
90
91
92
93
Fixed
^^^^^


Paul McCarthy's avatar
Paul McCarthy committed
94
* Minor fixes to some :mod:`.filetree.filetree` tree definitions.
Paul McCarthy's avatar
Paul McCarthy committed
95
96


Paul McCarthy's avatar
Paul McCarthy committed
97
98
99
100
101
102
Deprecated
^^^^^^^^^^


* The :meth:`.Image.resample` method has been deprecated in favour of the
  :func:`.resample.resample` function.
Paul McCarthy's avatar
Paul McCarthy committed
103
104


Paul McCarthy's avatar
Paul McCarthy committed
105
106
2.1.0 (Saturday April 13th 2019)
--------------------------------
Paul McCarthy's avatar
Paul McCarthy committed
107
108
109
110
111
112
113
114


Added
^^^^^


* New tensor conversion routines in the :mod:`.dtifit` module (Michiel
  Cottaar).
Paul McCarthy's avatar
Paul McCarthy committed
115
116
* 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
117
118


Paul McCarthy's avatar
Paul McCarthy committed
119
120
121
122
123
Changed
^^^^^^^


* The :class:`.GiftiMesh` class no longer creates copies of the mesh
Paul McCarthy's avatar
Paul McCarthy committed
124
125
  vertex/index arrays. This means that, these arrays will be flagged as
  read-only.
Paul McCarthy's avatar
Paul McCarthy committed
126
127
128
* 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
129
130


Paul McCarthy's avatar
Paul McCarthy committed
131
132
133
134
135
136
137
138
139
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
140
141
142
143
144
145
146
147
148
149
150
151
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
152
153
2.0.0 (Friday March 20th 2019)
------------------------------
154
155


156
157
158
Added
^^^^^

Paul McCarthy's avatar
Paul McCarthy committed
159
* New :mod:`fsl.utils.filetree` package for defining and working with
Paul McCarthy's avatar
Paul McCarthy committed
160
  file/directory templates (Michiel Cottaar).
Paul McCarthy's avatar
Paul McCarthy committed
161
* Simple built-in :mod:`.deprecated` decorator.
Paul McCarthy's avatar
Paul McCarthy committed
162
* New :mod:`fsl.data.utils` module, which currently contains one function
163
  :func:`.guessType`, which guesses the data type of a file/directory path.
Paul McCarthy's avatar
Paul McCarthy committed
164
165
* New `.commonBase` function for finding the common prefix of a set of
  file/directory paths.
166
167


168
169
170
Changed
^^^^^^^

Paul McCarthy's avatar
Paul McCarthy committed
171

172
* Removed support for Python 2.7 and 3.4.
173
174
175
* 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
176
* The :class:`.GiftiMesh` class can now load surface files which contain
Paul McCarthy's avatar
Paul McCarthy committed
177
178
179
  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
180
181


Paul McCarthy's avatar
Paul McCarthy committed
182
183
184
185
186
187
Removed
^^^^^^^

* Many deprecated items removed.


Paul McCarthy's avatar
Paul McCarthy committed
188
189
190
191
192
193
194
195
Deprecated
^^^^^^^^^^


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


Paul McCarthy's avatar
Paul McCarthy committed
196
197
198
199
1.13.3 (Friday February 8th 2019)
---------------------------------


Paul McCarthy's avatar
Paul McCarthy committed
200
201
202
Fixed
^^^^^

Paul McCarthy's avatar
Paul McCarthy committed
203
204
205

* Fixed an issue with the `.dicom.loadSeries` using memory-mapping for
  image files that would subsequently be deleted.
Paul McCarthy's avatar
Paul McCarthy committed
206
* Fixed an issue in the :class:`.GiftiMesh` class, where
Paul McCarthy's avatar
Paul McCarthy committed
207
208
209
  ``numpy``/``nibabel`` was returning read-only index arrays.


Paul McCarthy's avatar
Paul McCarthy committed
210
211
212
213
214
215
216
217
1.13.2 (Friday November 30th 2018)
----------------------------------


Changed
^^^^^^^


Paul McCarthy's avatar
Paul McCarthy committed
218
219
* The :meth:`.Image.resample` method now supports images with more than three
  dimensions.
Michiel Cottaar's avatar
Michiel Cottaar committed
220
221
222
223
* 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.
224
225


Paul McCarthy's avatar
Paul McCarthy committed
226
227
Fixed
^^^^^
Paul McCarthy's avatar
Paul McCarthy committed
228

Paul McCarthy's avatar
Paul McCarthy committed
229
230
231
232
233
234

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


1.13.1 (Friday November 23rd 2018)
----------------------------------
Paul McCarthy's avatar
Paul McCarthy committed
235
236


Paul McCarthy's avatar
Paul McCarthy committed
237
238
239
240
Fixed
^^^^^


Paul McCarthy's avatar
Paul McCarthy committed
241
* Added a missing ``image`` attribute in the :class:`.VoxelwiseConfoundEV`
Paul McCarthy's avatar
Paul McCarthy committed
242
  class.
Paul McCarthy's avatar
Paul McCarthy committed
243
244
245
* 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
246
247


Paul McCarthy's avatar
Paul McCarthy committed
248
249
1.13.0 (Thursday 22nd November 2018)
------------------------------------
Paul McCarthy's avatar
Paul McCarthy committed
250

Paul McCarthy's avatar
Paul McCarthy committed
251
252
253
254

Added
^^^^^

Paul McCarthy's avatar
Paul McCarthy committed
255
* New wrapper functions for :func:`.fsl_anat`, :func:`.applytopup` (Martin
Paul McCarthy's avatar
Paul McCarthy committed
256
  Craig).
Paul McCarthy's avatar
Paul McCarthy committed
257
* New :func:`.fileOrText` decorator for use in wrapper functions (Martin
Paul McCarthy's avatar
Paul McCarthy committed
258
259
260
261
  Craig).


Changed
Paul McCarthy's avatar
Paul McCarthy committed
262
263
^^^^^^^

Paul McCarthy's avatar
Paul McCarthy committed
264
265
* Various minor changes and enhancements to the FSL function :mod:`.wrappers`
  interfaces (Martin Craig).
Paul McCarthy's avatar
Paul McCarthy committed
266
267
268
269
270
271
272


Fixed
^^^^^

* The ``immv`` and ``imcp`` scripts now accept incorrect file extensions on
  input arguments.
Paul McCarthy's avatar
Paul McCarthy committed
273
274


Paul McCarthy's avatar
Paul McCarthy committed
275
276
1.12.0 (Sunday October 21st 2018)
---------------------------------
Paul McCarthy's avatar
Paul McCarthy committed
277
278
279
280
281
282
283
284
285
286
287
288
289
290
291
292
293
294


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
295
296
297
298
299
300
301
302
303
304
305
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
306
307
308
309
310
311
312
313
314
315
316
317
318
319
320
321
322
323
324
325
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
326
327
328
329
330
331
332
333
334
335
336
337
338
339
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
340
341
342
343
344
345
346
347
348
349
350
351
1.10.2 (Friday September 7th 2018)
----------------------------------


Fixed
^^^^^


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


352
353
354
355
356
357
358
359
360
361
362
363
364
365
1.10.1 (Friday August 3rd 2018)
-------------------------------


Changed
^^^^^^^


* Minor adjustmenets to improve Windows compatibility.


Fixed
^^^^^

Paul McCarthy's avatar
Paul McCarthy committed
366
* The :mod:`.FEATImage.getCOPE` method was returning PE images.
367
368


369
370
1.10.0 (Wednesday July 18th 2018)
---------------------------------
Paul McCarthy's avatar
Paul McCarthy committed
371
372
373
374
375
376
377
378
379
380


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.
381
* The :func:`.fileOrImage` and :func:`.fileOrArray` decorators now support
Paul McCarthy's avatar
Paul McCarthy committed
382
  loading of files which are specified with an output basename.
383
* New :mod:`.fast` wrapper function for the FSL FAST tool.
Paul McCarthy's avatar
Paul McCarthy committed
384
385
386
387
388
389
390
391
392
393
394


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
395
396
1.9.0 (Monday June 4th 2018)
----------------------------
Paul McCarthy's avatar
Paul McCarthy committed
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


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
431
432
433
434
435
436
437
438
439
440
441
442
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
443
444
1.8.0 (Thursday May 3rd 2018)
-----------------------------
Paul McCarthy's avatar
Paul McCarthy committed
445
446
447
448
449
450
451
452
453
454


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
455
* New :mod:`fsl.utils.fslsub` module, containing a :func:`.fslsub.submit`
Paul McCarthy's avatar
Paul McCarthy committed
456
  function which submits a cluster job via ``fsl_sub``.
Paul McCarthy's avatar
Paul McCarthy committed
457
458
* Assertions (in the :mod:`.assertions` module) can be disabled with the
  new :func:`.assertions.disabled` context manager.
Paul McCarthy's avatar
Paul McCarthy committed
459
460
* New :mod:`fsl.utils.parse_data` module containing various neuroimaging
  data constructors for use with ``argparse``.
Paul McCarthy's avatar
Paul McCarthy committed
461
462
* The :func:`.memoize.skipUnchanged` decorator has an ``invalidate`` function
  which allows its cache to be cleared.
Paul McCarthy's avatar
Paul McCarthy committed
463
464
465
466
467
468
469
470
471
472
473
474
475
476
477
478
479


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`).


480
481
1.7.2 (Monday March 19th 2018)
------------------------------
Paul McCarthy's avatar
Paul McCarthy committed
482
483
484
485
486
487


Added
^^^^^


488
489
* 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
490
491


Paul McCarthy's avatar
Paul McCarthy committed
492
493
494
495
496
497
498
499
500
501
502
503
504
505
506
507
1.7.1 (Monday March 12th 2018)
------------------------------



Changed
^^^^^^^


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


Fixed
^^^^^


Paul McCarthy's avatar
Paul McCarthy committed
508
* Removed deprecated use of :func:`.imagewrapper.canonicalShape`.
Paul McCarthy's avatar
Paul McCarthy committed
509
510


Paul McCarthy's avatar
Paul McCarthy committed
511
512
513
514
515
516
517
518
519
520
521
522
523
524
525
526
527
528
529
530
531
532
533
534
535
536
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
537
  to the :mod:`.data.image` class.
Paul McCarthy's avatar
Paul McCarthy committed
538
539
540
541
542
543
544
545
546
547
548
549
550
551
552
* 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
553
* :func:`.ImageWrapper.canonicalShape` (moved to the :mod:`.data.image` module)
Paul McCarthy's avatar
Paul McCarthy committed
554
555
556
557
* :func:`.ImageWrapper.naninfrange` function (moved to the :mod:`.naninfrange`
  module)


Paul McCarthy's avatar
Paul McCarthy committed
558
559
560
561
562
563
564
1.6.8 (Monday February 12th 2018)
---------------------------------


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


Paul McCarthy's avatar
Paul McCarthy committed
565
566
567
568
569
1.6.7 (Friday February 9th 2018)
--------------------------------


* More further adjustments to the ``conda`` package build.
Paul McCarthy's avatar
Paul McCarthy committed
570
* Adjustments to pypi source distribution - the ``requirements-extra.txt`` file
Paul McCarthy's avatar
Paul McCarthy committed
571
572
573
  was not being included.


Paul McCarthy's avatar
Paul McCarthy committed
574
575
576
577
578
579
580
1.6.6 (Thursday February 8th 2018)
----------------------------------


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


Paul McCarthy's avatar
Paul McCarthy committed
581
582
583
584
585
586
587
1.6.5 (Tuesday February 6th 2018)
---------------------------------


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


Paul McCarthy's avatar
Paul McCarthy committed
588
589
590
591
592
593
594
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
595
596
1.6.3 (Friday February 2nd 2018)
--------------------------------
Paul McCarthy's avatar
Paul McCarthy committed
597
598
599


* Minor enhancements to the :class:`.WeakFunctionRef` class.
Paul McCarthy's avatar
Paul McCarthy committed
600
601
602
* 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
603
604


Paul McCarthy's avatar
Paul McCarthy committed
605
606
607
608
609
610
611
612
613
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
614
615
616
617
618
619
620
621
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
622
623
1.6.0 (Friday January 26th 2018)
--------------------------------
Paul McCarthy's avatar
Paul McCarthy committed
624
625


Paul McCarthy's avatar
Paul McCarthy committed
626
627
628
629
630
631
632
633
634
635
636
637
638
* 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
639
640
* 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
641
642
643
* 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
644
645
646
647
648
* 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
649
* Optional dependencies ``wxpython``, ``indexed_gzip``, ``trimesh``, and
Paul McCarthy's avatar
Paul McCarthy committed
650
651
  ``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
652
653


Paul McCarthy's avatar
Paul McCarthy committed
654
655
656
657
658
659
660
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
661
1.5.3 (Tuesday January 9th 2018)
662
663
664
665
666
667
668
--------------------------------


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


Paul McCarthy's avatar
Paul McCarthy committed
669
670
671
672
673
674
675
1.5.2 (Tuesday January 2nd 2018)
--------------------------------


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


Paul McCarthy's avatar
Paul McCarthy committed
676
677
678
679
680
681
682
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
683
684
1.5.0 (Wednesday December 13th 2017)
------------------------------------
Paul McCarthy's avatar
Paul McCarthy committed
685
686
687
688
689
690


* 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
691
692
693
* 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
694
695


Paul McCarthy's avatar
Paul McCarthy committed
696
697
1.4.2 (Tuesday December 5th 2017)
---------------------------------
Paul McCarthy's avatar
Paul McCarthy committed
698
699
700
701
702


* 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
703
* Some small bugfixes to the :mod:`.atlasq` and :mod:`.atlases` moduless.
Paul McCarthy's avatar
Paul McCarthy committed
704
705
706


1.4.1 (Thursday November 9th 2017)
Paul McCarthy's avatar
Paul McCarthy committed
707
708
709
710
711
712
----------------------------------


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


Paul McCarthy's avatar
Paul McCarthy committed
713
1.4.0 (Thursday November 9th 2017)
Paul McCarthy's avatar
Paul McCarthy committed
714
----------------------------------
Paul McCarthy's avatar
Paul McCarthy committed
715

Paul McCarthy's avatar
Paul McCarthy committed
716

Paul McCarthy's avatar
Paul McCarthy committed
717
718
* 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
719
720
721
* 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
722
723
724
725
726
727
728
729
730
731
732
733
734
735
* 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
736
1.3.1 (Wednesday October 25th 2017)
Paul McCarthy's avatar
Paul McCarthy committed
737
738
739
740
741
742
743
-----------------------------------


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


Paul McCarthy's avatar
Paul McCarthy committed
744
1.3.0 (Wednesday October 25th 2017)
Paul McCarthy's avatar
Paul McCarthy committed
745
-----------------------------------
Paul McCarthy's avatar
Paul McCarthy committed
746
747
748
749


* :class:`.Atlas` classes can now pass ``kwargs`` through to the
  :class:`.Image` constructor.
Paul McCarthy's avatar
Paul McCarthy committed
750
751
752
* :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
753
* :class:`.Cache` now implements ``__getitem__`` and ``__setitem__``
Paul McCarthy's avatar
Paul McCarthy committed
754
755
* 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
756
757
* :func:`.platform.isWidgetAlive` is deprecated in favour of an equivalent
  function in the ``fsleyes-widgets`` library.
Paul McCarthy's avatar
Paul McCarthy committed
758
759
* ``scipy`` is now explicitly listed as a requirement (this should have been
  done in 1.2.1).
Paul McCarthy's avatar
Paul McCarthy committed
760
761
762
763
764
765
766



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


Paul McCarthy's avatar
Paul McCarthy committed
767
768
* 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
769
770
771
772
773


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

Paul McCarthy's avatar
Paul McCarthy committed
774

Paul McCarthy's avatar
Paul McCarthy committed
775
776
777
778
779
780
781
782
783
784
785
786
787
788
789
790
* 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
791
  favour of new :meth:`.Nifti.voxToScaledVoxMat` and
Paul McCarthy's avatar
Paul McCarthy committed
792
793
794
795
796
797
798
799
800
801
802
803
804
805
806
807
808
809
810
811
812
  :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
813
814
815
816
817
818
819
820
821
822
823
824

 - :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
825
826
827
828
829
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
856
857
858
859
860
861
862
863
864
865
866
867
868
869
870
871
872
873
874
875
876
877
878
879
880
881
882
883
884
885
886
887
888
889
890
891
892
893
894
895
896
897
898
899
* 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