CHANGELOG.rst 33.5 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


5

Paul McCarthy's avatar
Paul McCarthy committed
6
7
3.0.0 (Sunday 29th March 2020)
------------------------------
Paul McCarthy's avatar
Paul McCarthy committed
8
9
10
11
12
13


Added
^^^^^


Paul McCarthy's avatar
Paul McCarthy committed
14
15
* New wrapper functions for the FSL :class:`.fslstats`, :func:`.prelude` and
  :func:`applyxfm4D` commands.
Paul McCarthy's avatar
Paul McCarthy committed
16
17
18
* 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
19
20
* 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
21
22
* New :class:`.SubmitParams` class, providing a higer level interface for
  cluster submission.
Paul McCarthy's avatar
Paul McCarthy committed
23
* New :meth:`.FileTree.load_json` and  :meth:`.FileTree.save_json` methods.
Paul McCarthy's avatar
Paul McCarthy committed
24

Paul McCarthy's avatar
Paul McCarthy committed
25

Paul McCarthy's avatar
Paul McCarthy committed
26
27
28
29
Changed
^^^^^^^


Paul McCarthy's avatar
Paul McCarthy committed
30
* ``fslpy`` now requires a minimum Python version of 3.7.
Paul McCarthy's avatar
Paul McCarthy committed
31
* The default value for the ``partial_fill`` option to :meth:`.FileTree.read`
Paul McCarthy's avatar
Paul McCarthy committed
32
33
34
  has been changed to ``False``. Accordingly, the :class:`.FileTreeQuery`
  calls the :meth:`.FileTree.partial_fill` method on the ``FileTree`` it is
  given.
Paul McCarthy's avatar
Paul McCarthy committed
35
36
* The :func:`.gifti.relatedFiles` function now supports files with
  BIDS-style naming conventions.
Paul McCarthy's avatar
Paul McCarthy committed
37
38
39
40
41
* 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
42
43
* 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
44
45
46
* 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
47
48
49
50
51
52
53
* 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
54
55
56
57
58
59
* 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
60
61
62
* 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
63
64
* Loaded :class:`.Image` objects returned by :mod:`fsl.wrappers` functions
  are now named according to the wrapper function argument name.
Paul McCarthy's avatar
Paul McCarthy committed
65
66


Paul McCarthy's avatar
Paul McCarthy committed
67
68
69
70
71
72
73
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
74
75
* Fixed some bugs in the :func:`.fslsub.info` and :func:`.fslinfo.wait`
  functions.
Paul McCarthy's avatar
Paul McCarthy committed
76
77
* Fixed the :func:`.DeformationField.transform` method so it works with
  a single set of coordinates.
Paul McCarthy's avatar
Paul McCarthy committed
78
79
* :class:`.Image` creation does not fail if ``loadMeta`` is set, and a
  sidecar file containing invalid JSON is present.
Paul McCarthy's avatar
Paul McCarthy committed
80

Paul McCarthy's avatar
Paul McCarthy committed
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
Removed
^^^^^^^


* Removed the deprecated ``.StatisticAtlas.proportions``,
  ``.StatisticAtlas.coordProportions``, and
  ``.StatisticAtlas.maskProportions`` methods.
* Removed the deprecated ``indexed`` option to :meth:`.Image.__init__`.
* Removed the deprecated ``.Image.resample`` method.
* Removed the deprecated ``.image.loadIndexedImageFile`` function.
* Removed the deprecatd ``.FileTreeQuery.short_names`` and
  ``.Match.short_name`` properties.
* Removed the deprecated ``.idle.inIdle``, ``.idle.cancelIdle``,
  ``.idle.idleReset``, ``.idle.getIdleTimeout``, and
  ``.idle.setIdleTimeout`` functions.
* Removed the deprecated ``resample.calculateMatrix`` function.


Paul McCarthy's avatar
Paul McCarthy committed
99
100
101
102
103
104
105
106
107
108
109
110
111
112
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
113
114
115
116
117
118
119
120
121
122
2.8.3 (Friday 28th February 2020)
---------------------------------


Fixed
^^^^^


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

Paul McCarthy's avatar
Paul McCarthy committed
123
124
125
126
127
128
129
130
131
132
133
134

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
135
136
2.8.1 (Thursday 20th February 2020)
-----------------------------------
Paul McCarthy's avatar
Paul McCarthy committed
137
138
139
140
141
142
143
144
145


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
146

Paul McCarthy's avatar
Paul McCarthy committed
147
148
2.8.0 (Wednesday 29th January 2020)
-----------------------------------
Paul McCarthy's avatar
Paul McCarthy committed
149
150


Paul McCarthy's avatar
Paul McCarthy committed
151
152
153
154
155
156
157
158
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
159
160
* New :func:`.mghimage.voxToSurfMat` function, for creating a
  voxel-to-freesurfer affine transform from any image.
Paul McCarthy's avatar
Paul McCarthy committed
161
162


Paul McCarthy's avatar
Paul McCarthy committed
163
164
165
166
167
168
169
170
171
172
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
173
174
175
176
177
Fixed
^^^^^


* Improved the algorithm used by the :func:`.mesh.needsFixing` function.
Paul McCarthy's avatar
Paul McCarthy committed
178
179
* The :meth:`.fslmaths.run` method now accepts :attr:`.wrappers.LOAD` as an
  output specification.
Paul McCarthy's avatar
Paul McCarthy committed
180
181
* 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
182
* Fixed a bug in the :func:`.resample` function.
Paul McCarthy's avatar
Paul McCarthy committed
183
184
* 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
185
186


Paul McCarthy's avatar
Paul McCarthy committed
187
188
189
190
191
192
193
194
Deprecated
^^^^^^^^^^


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


Paul McCarthy's avatar
Paul McCarthy committed
195
196
2.7.0 (Wednesday 6th November 2019)
-----------------------------------
Paul McCarthy's avatar
Paul McCarthy committed
197
198
199
200
201
202
203
204
205


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
206
207
* New :meth:`.IdleLoop.synchronous` context manager, to temporarily change the
  value of :meth:`.IdleLoop.neverQueue`.
Paul McCarthy's avatar
Paul McCarthy committed
208
209
* 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
210
211
212
* 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
213
214
215
216
217
218


Changed
^^^^^^^


Paul McCarthy's avatar
Paul McCarthy committed
219
* Internal reorganisation in the :mod:`.idle` module.
Paul McCarthy's avatar
Paul McCarthy committed
220
221


Paul McCarthy's avatar
Paul McCarthy committed
222
223
224
225
226
227
228
229
Fixed
^^^^^


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


Paul McCarthy's avatar
Paul McCarthy committed
230
231
232
233
234
235
236
237
238
239
240
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
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
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
256
257
258
259
260
261
262
263
264
265
266
267
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
268
269
2.6.0 (Tuesday 10th September 2019)
-----------------------------------
Paul McCarthy's avatar
Paul McCarthy committed
270
271


Paul McCarthy's avatar
Paul McCarthy committed
272
273
274
275
276
Added
^^^^^


* New :meth:`.Image.iscomplex` attribute.
Paul McCarthy's avatar
Paul McCarthy committed
277
* Support for a new ``Statistic`` atlas type.
Paul McCarthy's avatar
Paul McCarthy committed
278
279


Paul McCarthy's avatar
Paul McCarthy committed
280
281
282
283
284
285
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
286
287
* 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
288
289
290
* 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
291
292
* The :mod:`.dicom` module has been updated to work with the latest version of
  ``dcm2niix``.
Paul McCarthy's avatar
Paul McCarthy committed
293
294
295
296
297
298
299
300
301
302
303


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
304
305


Paul McCarthy's avatar
Paul McCarthy committed
306
307
2.5.0 (Tuesday 6th August 2019)
-------------------------------
Paul McCarthy's avatar
Paul McCarthy committed
308
309


Paul McCarthy's avatar
Paul McCarthy committed
310
311
312
313
Added
^^^^^


Paul McCarthy's avatar
Paul McCarthy committed
314
315
316
317
318
319
320
321
322
323
324
325
* 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
326
327


Paul McCarthy's avatar
Paul McCarthy committed
328
329
330
331
Changed
^^^^^^^


Paul McCarthy's avatar
Paul McCarthy committed
332
333
* The :mod:`.vest.looksLikeVestLutFile` function has been made slightly more
  lenient.
Paul McCarthy's avatar
Paul McCarthy committed
334
335
336
337
338
339
340
* `h5py <https://www.h5py.org/>`_ has been added to the ``fslpy`` dependencies.


Deprecated
^^^^^^^^^^


Paul McCarthy's avatar
Paul McCarthy committed
341
* The :mod:`fsl.utils.transform` module has been deprecated; its functions can
Paul McCarthy's avatar
Paul McCarthy committed
342
343
  now be found in the :mod:`fsl.transforms.affine` and
  :mod:`fsl.transform.flirt` modules.
Paul McCarthy's avatar
Paul McCarthy committed
344
345


Paul McCarthy's avatar
Paul McCarthy committed
346
347
348
349
350
351
352
353
354
355
356
357
358
359
360
361
362
363
364
365
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
366
367
368
369
370
371
372
373
374
375
376
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
377
378
2.3.0 (Tuesday June 25th 2019)
------------------------------
Paul McCarthy's avatar
Paul McCarthy committed
379
380
381
382
383
384


Added
^^^^^


Paul McCarthy's avatar
Paul McCarthy committed
385
386
387
388
389
* 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
390
391
* New :attr:`.Image.nvals` property, for use with ``RGB24``/``RGBA32``
  images.
Paul McCarthy's avatar
Paul McCarthy committed
392
393
394
395
396
397
398
399
400
401
402
403
404
405
* 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
406
* Fixed a bug in the :meth:`.GitfitMesh.loadVertices` method.
Paul McCarthy's avatar
Paul McCarthy committed
407
408
* 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
409
410


Paul McCarthy's avatar
Paul McCarthy committed
411
412
2.2.0 (Wednesday May 8th 2019)
------------------------------
Paul McCarthy's avatar
Paul McCarthy committed
413
414


Paul McCarthy's avatar
Paul McCarthy committed
415
416
417
418
419
420
421
422
423
424
425
426
427
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
428
429
430
431
Changed
^^^^^^^


Paul McCarthy's avatar
Paul McCarthy committed
432
433
434
435
436
437
438
* 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
439
440
441
442
Fixed
^^^^^


Paul McCarthy's avatar
Paul McCarthy committed
443
* Minor fixes to some :mod:`.filetree.filetree` tree definitions.
Paul McCarthy's avatar
Paul McCarthy committed
444
445


Paul McCarthy's avatar
Paul McCarthy committed
446
447
448
449
450
451
Deprecated
^^^^^^^^^^


* The :meth:`.Image.resample` method has been deprecated in favour of the
  :func:`.resample.resample` function.
Paul McCarthy's avatar
Paul McCarthy committed
452
453


Paul McCarthy's avatar
Paul McCarthy committed
454
455
2.1.0 (Saturday April 13th 2019)
--------------------------------
Paul McCarthy's avatar
Paul McCarthy committed
456
457
458
459
460
461
462
463


Added
^^^^^


* New tensor conversion routines in the :mod:`.dtifit` module (Michiel
  Cottaar).
Paul McCarthy's avatar
Paul McCarthy committed
464
465
* 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
466
467


Paul McCarthy's avatar
Paul McCarthy committed
468
469
470
471
472
Changed
^^^^^^^


* The :class:`.GiftiMesh` class no longer creates copies of the mesh
Paul McCarthy's avatar
Paul McCarthy committed
473
474
  vertex/index arrays. This means that, these arrays will be flagged as
  read-only.
Paul McCarthy's avatar
Paul McCarthy committed
475
476
477
* 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
478
479


Paul McCarthy's avatar
Paul McCarthy committed
480
481
482
483
484
485
486
487
488
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
489
490
491
492
493
494
495
496
497
498
499
500
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
501
502
2.0.0 (Friday March 20th 2019)
------------------------------
503
504


505
506
507
Added
^^^^^

Paul McCarthy's avatar
Paul McCarthy committed
508
* New :mod:`fsl.utils.filetree` package for defining and working with
Paul McCarthy's avatar
Paul McCarthy committed
509
  file/directory templates (Michiel Cottaar).
Paul McCarthy's avatar
Paul McCarthy committed
510
* Simple built-in :mod:`.deprecated` decorator.
Paul McCarthy's avatar
Paul McCarthy committed
511
* New :mod:`fsl.data.utils` module, which currently contains one function
512
  :func:`.guessType`, which guesses the data type of a file/directory path.
513
* New :func:`.commonBase` function for finding the common prefix of a set of
Paul McCarthy's avatar
Paul McCarthy committed
514
  file/directory paths.
515
516


517
518
519
Changed
^^^^^^^

Paul McCarthy's avatar
Paul McCarthy committed
520

521
* Removed support for Python 2.7 and 3.4.
522
523
524
* 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
525
* The :class:`.GiftiMesh` class can now load surface files which contain
Paul McCarthy's avatar
Paul McCarthy committed
526
527
528
  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
529
530


Paul McCarthy's avatar
Paul McCarthy committed
531
532
533
534
535
536
Removed
^^^^^^^

* Many deprecated items removed.


Paul McCarthy's avatar
Paul McCarthy committed
537
538
539
540
541
542
543
544
Deprecated
^^^^^^^^^^


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


Paul McCarthy's avatar
Paul McCarthy committed
545
546
547
548
1.13.3 (Friday February 8th 2019)
---------------------------------


Paul McCarthy's avatar
Paul McCarthy committed
549
550
551
Fixed
^^^^^

Paul McCarthy's avatar
Paul McCarthy committed
552

553
* Fixed an issue with the :func:`.dicom.loadSeries` using memory-mapping for
Paul McCarthy's avatar
Paul McCarthy committed
554
  image files that would subsequently be deleted.
Paul McCarthy's avatar
Paul McCarthy committed
555
* Fixed an issue in the :class:`.GiftiMesh` class, where
Paul McCarthy's avatar
Paul McCarthy committed
556
557
558
  ``numpy``/``nibabel`` was returning read-only index arrays.


Paul McCarthy's avatar
Paul McCarthy committed
559
560
561
562
563
564
565
566
1.13.2 (Friday November 30th 2018)
----------------------------------


Changed
^^^^^^^


Paul McCarthy's avatar
Paul McCarthy committed
567
568
* The :meth:`.Image.resample` method now supports images with more than three
  dimensions.
Michiel Cottaar's avatar
Michiel Cottaar committed
569
570
571
572
* 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.
573
574


Paul McCarthy's avatar
Paul McCarthy committed
575
576
Fixed
^^^^^
Paul McCarthy's avatar
Paul McCarthy committed
577

Paul McCarthy's avatar
Paul McCarthy committed
578
579
580
581
582
583

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


1.13.1 (Friday November 23rd 2018)
----------------------------------
Paul McCarthy's avatar
Paul McCarthy committed
584
585


Paul McCarthy's avatar
Paul McCarthy committed
586
587
588
589
Fixed
^^^^^


Paul McCarthy's avatar
Paul McCarthy committed
590
* Added a missing ``image`` attribute in the :class:`.VoxelwiseConfoundEV`
Paul McCarthy's avatar
Paul McCarthy committed
591
  class.
Paul McCarthy's avatar
Paul McCarthy committed
592
593
594
* 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
595
596


Paul McCarthy's avatar
Paul McCarthy committed
597
598
1.13.0 (Thursday 22nd November 2018)
------------------------------------
Paul McCarthy's avatar
Paul McCarthy committed
599

Paul McCarthy's avatar
Paul McCarthy committed
600
601
602
603

Added
^^^^^

Paul McCarthy's avatar
Paul McCarthy committed
604
* New wrapper functions for :func:`.fsl_anat`, :func:`.applytopup` (Martin
Paul McCarthy's avatar
Paul McCarthy committed
605
  Craig).
Paul McCarthy's avatar
Paul McCarthy committed
606
* New :func:`.fileOrText` decorator for use in wrapper functions (Martin
Paul McCarthy's avatar
Paul McCarthy committed
607
608
609
610
  Craig).


Changed
Paul McCarthy's avatar
Paul McCarthy committed
611
612
^^^^^^^

Paul McCarthy's avatar
Paul McCarthy committed
613
614
* Various minor changes and enhancements to the FSL function :mod:`.wrappers`
  interfaces (Martin Craig).
Paul McCarthy's avatar
Paul McCarthy committed
615
616
617
618
619
620
621


Fixed
^^^^^

* The ``immv`` and ``imcp`` scripts now accept incorrect file extensions on
  input arguments.
Paul McCarthy's avatar
Paul McCarthy committed
622
623


Paul McCarthy's avatar
Paul McCarthy committed
624
625
1.12.0 (Sunday October 21st 2018)
---------------------------------
Paul McCarthy's avatar
Paul McCarthy committed
626
627
628
629
630
631
632
633
634
635
636
637
638
639
640
641
642
643


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
644
645
646
647
648
649
650
651
652
653
654
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
655
656
657
658
659
660
661
662
663
664
665
666
667
668
669
670
671
672
673
674
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
675
676
677
678
679
680
681
682
683
684
685
686
687
688
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
689
690
691
692
693
694
695
696
697
698
699
700
1.10.2 (Friday September 7th 2018)
----------------------------------


Fixed
^^^^^


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


701
702
703
704
705
706
707
708
709
710
711
712
713
714
1.10.1 (Friday August 3rd 2018)
-------------------------------


Changed
^^^^^^^


* Minor adjustmenets to improve Windows compatibility.


Fixed
^^^^^

Paul McCarthy's avatar
Paul McCarthy committed
715
* The :mod:`.FEATImage.getCOPE` method was returning PE images.
716
717


718
719
1.10.0 (Wednesday July 18th 2018)
---------------------------------
Paul McCarthy's avatar
Paul McCarthy committed
720
721
722
723
724
725
726
727
728
729


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.
730
* The :func:`.fileOrImage` and :func:`.fileOrArray` decorators now support
Paul McCarthy's avatar
Paul McCarthy committed
731
  loading of files which are specified with an output basename.
732
* New :mod:`.fast` wrapper function for the FSL FAST tool.
Paul McCarthy's avatar
Paul McCarthy committed
733
734
735
736
737
738
739
740
741
742
743


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
744
745
1.9.0 (Monday June 4th 2018)
----------------------------
Paul McCarthy's avatar
Paul McCarthy committed
746
747
748
749
750
751
752
753
754
755
756
757
758
759
760
761
762
763
764
765
766
767
768
769
770
771
772
773
774
775
776
777
778
779


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
780
781
782
783
784
785
786
787
788
789
790
791
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
792
793
1.8.0 (Thursday May 3rd 2018)
-----------------------------
Paul McCarthy's avatar
Paul McCarthy committed
794
795
796
797
798
799
800
801
802
803


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
804
* New :mod:`fsl.utils.fslsub` module, containing a :func:`.fslsub.submit`
Paul McCarthy's avatar
Paul McCarthy committed
805
  function which submits a cluster job via ``fsl_sub``.
Paul McCarthy's avatar
Paul McCarthy committed
806
807
* Assertions (in the :mod:`.assertions` module) can be disabled with the
  new :func:`.assertions.disabled` context manager.
Paul McCarthy's avatar
Paul McCarthy committed
808
809
* New :mod:`fsl.utils.parse_data` module containing various neuroimaging
  data constructors for use with ``argparse``.
Paul McCarthy's avatar
Paul McCarthy committed
810
811
* The :func:`.memoize.skipUnchanged` decorator has an ``invalidate`` function
  which allows its cache to be cleared.
Paul McCarthy's avatar
Paul McCarthy committed
812
813
814
815
816
817
818
819
820
821
822
823
824
825
826
827
828


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`).


829
830
1.7.2 (Monday March 19th 2018)
------------------------------
Paul McCarthy's avatar
Paul McCarthy committed
831
832
833
834
835
836


Added
^^^^^


837
838
* 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
839
840


Paul McCarthy's avatar
Paul McCarthy committed
841
842
843
844
845
846
847
848
849
850
851
852
853
854
855
856
1.7.1 (Monday March 12th 2018)
------------------------------



Changed
^^^^^^^


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


Fixed
^^^^^


Paul McCarthy's avatar
Paul McCarthy committed
857
* Removed deprecated use of :func:`.imagewrapper.canonicalShape`.
Paul McCarthy's avatar
Paul McCarthy committed
858
859


Paul McCarthy's avatar
Paul McCarthy committed
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
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
886
  to the :mod:`.data.image` class.
Paul McCarthy's avatar
Paul McCarthy committed
887
888
889
890
891
892
893
894
895
896
897
898
899
900
901
* 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
902
* :func:`.ImageWrapper.canonicalShape` (moved to the :mod:`.data.image` module)
Paul McCarthy's avatar
Paul McCarthy committed
903
904
905
906
* :func:`.ImageWrapper.naninfrange` function (moved to the :mod:`.naninfrange`
  module)


Paul McCarthy's avatar
Paul McCarthy committed
907
908
909
910
911
912
913
1.6.8 (Monday February 12th 2018)
---------------------------------


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


Paul McCarthy's avatar
Paul McCarthy committed
914
915
916
917
918
1.6.7 (Friday February 9th 2018)
--------------------------------


* More further adjustments to the ``conda`` package build.
Paul McCarthy's avatar
Paul McCarthy committed
919
* Adjustments to pypi source distribution - the ``requirements-extra.txt`` file
Paul McCarthy's avatar
Paul McCarthy committed
920
921
922
  was not being included.


Paul McCarthy's avatar
Paul McCarthy committed
923
924
925
926
927
928
929
1.6.6 (Thursday February 8th 2018)
----------------------------------


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


Paul McCarthy's avatar
Paul McCarthy committed
930
931
932
933
934
935
936
1.6.5 (Tuesday February 6th 2018)
---------------------------------


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


Paul McCarthy's avatar
Paul McCarthy committed
937
938
939
940
941
942
943
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
944
945
1.6.3 (Friday February 2nd 2018)
--------------------------------
Paul McCarthy's avatar
Paul McCarthy committed
946
947
948


* Minor enhancements to the :class:`.WeakFunctionRef` class.
Paul McCarthy's avatar
Paul McCarthy committed
949
950
951
* 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
952
953


Paul McCarthy's avatar
Paul McCarthy committed
954
955
956
957
958
959
960
961
962
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
963
964
965
966
967
968
969
970
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
971
972
1.6.0 (Friday January 26th 2018)
--------------------------------
Paul McCarthy's avatar
Paul McCarthy committed
973
974


Paul McCarthy's avatar
Paul McCarthy committed
975
976
977
978
979
980
981
982
983
984
985
986
987
* 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
988
989
* 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
990
991
992
* 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
993
994
995
996
997
* 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
998
* Optional dependencies ``wxpython``, ``indexed_gzip``, ``trimesh``, and
Paul McCarthy's avatar
Paul McCarthy committed
999
1000
  ``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
1001
1002


Paul McCarthy's avatar
Paul McCarthy committed
1003
1004
1005
1006
1007
1008
1009
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
1010
1.5.3 (Tuesday January 9th 2018)
1011
1012
1013
1014
1015
1016
1017
--------------------------------


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


Paul McCarthy's avatar
Paul McCarthy committed
1018
1019
1020
1021
1022
1023
1024
1.5.2 (Tuesday January 2nd 2018)
--------------------------------


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


Paul McCarthy's avatar
Paul McCarthy committed
1025
1026
1027
1028
1029
1030
1031
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
1032
1033
1.5.0 (Wednesday December 13th 2017)
------------------------------------
Paul McCarthy's avatar
Paul McCarthy committed
1034
1035
1036
1037
1038
1039


* 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
1040
1041
1042
* 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
1043
1044


Paul McCarthy's avatar
Paul McCarthy committed
1045
1046
1.4.2 (Tuesday December 5th 2017)
---------------------------------
Paul McCarthy's avatar
Paul McCarthy committed
1047
1048
1049
1050
1051


* 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
1052
* Some small bugfixes to the :mod:`.atlasq` and :mod:`.atlases` moduless.
Paul McCarthy's avatar
Paul McCarthy committed
1053
1054
1055


1.4.1 (Thursday November 9th 2017)
Paul McCarthy's avatar
Paul McCarthy committed
1056
1057
1058
1059
1060
1061
----------------------------------


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


Paul McCarthy's avatar
Paul McCarthy committed
1062
1.4.0 (Thursday November 9th 2017)
Paul McCarthy's avatar
Paul McCarthy committed
1063
----------------------------------
Paul McCarthy's avatar
Paul McCarthy committed
1064

Paul McCarthy's avatar
Paul McCarthy committed
1065

Paul McCarthy's avatar
Paul McCarthy committed
1066
1067
* 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
1068
1069
1070
* 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
1071
1072
1073
1074
1075
1076
1077
1078
1079
1080
1081
1082
1083
1084
* 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
1085
1.3.1 (Wednesday October 25th 2017)
Paul McCarthy's avatar
Paul McCarthy committed
1086
1087
1088
1089
1090
1091
1092
-----------------------------------


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


Paul McCarthy's avatar
Paul McCarthy committed
1093
1.3.0 (Wednesday October 25th 2017)
Paul McCarthy's avatar
Paul McCarthy committed
1094
-----------------------------------
Paul McCarthy's avatar
Paul McCarthy committed
1095
1096
1097
1098


* :class:`.Atlas` classes can now pass ``kwargs`` through to the
  :class:`.Image` constructor.
Paul McCarthy's avatar
Paul McCarthy committed
1099
1100
1101
* :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
1102
* :class:`.Cache` now implements ``__getitem__`` and ``__setitem__``
Paul McCarthy's avatar
Paul McCarthy committed
1103
1104
* 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
1105
1106
* :func:`.platform.isWidgetAlive` is deprecated in favour of an equivalent
  function in the ``fsleyes-widgets`` library.
Paul McCarthy's avatar
Paul McCarthy committed
1107
1108
* ``scipy`` is now explicitly listed as a requirement (this should have been
  done in 1.2.1).
Paul McCarthy's avatar
Paul McCarthy committed
1109
1110
1111
1112
1113
1114
1115



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


Paul McCarthy's avatar
Paul McCarthy committed
1116
1117
* 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
1118
1119
1120
1121
1122


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

Paul McCarthy's avatar
Paul McCarthy committed
1123

Paul McCarthy's avatar
Paul McCarthy committed
1124
1125
1126
1127
1128
1129
1130
1131
1132
1133
1134
1135
1136
1137
1138
1139
* 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
1140
  favour of new :meth:`.Nifti.voxToScaledVoxMat` and
Paul McCarthy's avatar
Paul McCarthy committed
1141
1142
1143
1144
1145
1146
1147
1148
1149
1150
1151
1152
1153
1154
1155
1156
1157
1158
1159
1160
1161
  :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
1162
1163
1164
1165
1166
1167
1168
1169
1170
1171
1172
1173

 - :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
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
1219
1220
1221
1222
1223
1224
1225
1226
1227
1228
1229
1230
1231
1232
1233
1234
1235
1236
1237
1238
1239
1240
1241
1242
1243
1244
1245
1246
1247
1248
* 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