CHANGELOG.rst 39.8 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

Paul McCarthy's avatar
Paul McCarthy committed
4

Paul McCarthy's avatar
Paul McCarthy committed
5
6
7
8
9
10
11
12
13
14
15

3.6.0 (Under development)
-------------------------


Changed
^^^^^^^


* The :class:`.TaskThread` now allows an error handler function to be
  specified, which is run on the :mod:`.idle` loop.
Paul McCarthy's avatar
Paul McCarthy committed
16
17
* The :func:`.bids.loadMetadata` function no long resolves sym-links when
  determining whether a file is contained within a BIDS data set.
Paul McCarthy's avatar
Paul McCarthy committed
18
19


Paul McCarthy's avatar
Paul McCarthy committed
20
21
22
23
24
25
26
27
28
Deprecated
^^^^^^^^^^


* Deprecated a number of GUI-specific properties in the
  :mod:`fsl.utils.platform` module, including ``frozen``, ``haveGui``,
  ``canHaveGui``, ``inSSHSession``, ``inVNCSession``, ``wxPlatform``,
  ``wxFlavour``, ``glVersion``, ``glRenderer``, and ``glIsSoftwareRenderer``.
  Equivalent functions are being added to the ``fsleyes-widgets`` library.
Paul McCarthy's avatar
Paul McCarthy committed
29
30
31
* The :mod:`fsl.utils.filetree` package has been deprecated, and will be
  removed in a future version of ``fslpy`` - it is now published as a separate
  library on [PyPI](https://pypi.org/project/file-tree/).
Paul McCarthy's avatar
Paul McCarthy committed
32
33


Paul McCarthy's avatar
Paul McCarthy committed
34
35
36
37
38
39
40
Fixed
^^^^^

* Fixed an edge-case in the :mod:`.gifti` module, where a surface with a
  single triangle was being loaded incorrectly.


Paul McCarthy's avatar
Paul McCarthy committed
41

Paul McCarthy's avatar
Paul McCarthy committed
42
43
44
45
46
47
48
49
50
51
52
3.5.3 (Tuesday 9th February 2021)
---------------------------------


Fixed
^^^^^


* Fixed a bug in :func:`.featanalysis.loadClusterResults` (!281).


Paul McCarthy's avatar
Paul McCarthy committed
53
54
55
56
57
58
59
60
61
62
3.5.2 (Friday 29th January 2021)
---------------------------------


Fixed
^^^^^


* Adjusted the :func:`.dicom.scanDir` function so that it will set a
  default value for ``SeriesDescription`` if it is not present in the
Paul McCarthy's avatar
Paul McCarthy committed
63
64
  ``dcm2niix`` ``json`` output (!279).
* Fixed some issues with API documentation generation (!279).
Paul McCarthy's avatar
Paul McCarthy committed
65
66


Paul McCarthy's avatar
Paul McCarthy committed
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
3.5.1 (Thursday 21st January 2021)
----------------------------------


Added
^^^^^


* New :func:`.featanalysis.loadFsf` function, for loading arbitrary ``.fsf``
  files (!276).


Fixed
^^^^^


* Adjustments to :mod:`.dicom` tests to work with different versions of
  ``dcm2niix`` (!277).


Paul McCarthy's avatar
Paul McCarthy committed
87
88
3.5.0 (Wednesday 20th January 2021)
-----------------------------------
Paul McCarthy's avatar
Paul McCarthy committed
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109


Added
^^^^^


* New ``fsl_anat.tree``, for use with the :mod:`.filetree` package (!264).
* New :func:`.fsl_prepare_fieldmap` wrapper function (!265).
* The :class:`.fslmaths` wrapper now supports the ``fslmaths -s`` option
  via the :meth:`.fslmaths.smooth` method (!271).


Fixed
^^^^^


* Windows/WSL-specific workaround to the :func:`fsl.utils.run.run` function to
  avoid console windows from popping up, when used from a graphical program
  (!272).


Paul McCarthy's avatar
Paul McCarthy committed
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
3.4.0 (Tuesday 20th October 2020)
---------------------------------


Added
^^^^^


* New :mod:`.tbss` wrapper functions for `TBSS
  <https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/TBSS>`_ commands.


Changed
^^^^^^^


* Calls to functions in the :mod:`.assertions` module are disabled when a
  wrapper function is called with ``cmdonly=True``.


Paul McCarthy's avatar
Paul McCarthy committed
130
131
132
133
134
135
136
137
138
139
140
141
142
143
3.3.3 (Wednesday 13th October 2020)
-----------------------------------


Changed
^^^^^^^


* The :func:`.fileOrImage` (and related) decorators will not manipulate the
  return value of a decorated function if an argument ``cmdonly=True`` is
  passed. This is so that wrapper functions will directly return the command
  that would be executed when ``cmdonly=True``.


Paul McCarthy's avatar
Paul McCarthy committed
144
145
146
147
148
149
150
151
152
153
154
155
156
3.3.2 (Tuesday 12th October 2020)
---------------------------------


Changed
^^^^^^^


* Most :func:`.wrapper` functions now accept an argument called ``cmdonly``
  which, if ``True``, will cause the generated command-line call to be
  returned, instead of executed.


Paul McCarthy's avatar
Paul McCarthy committed
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
3.3.1 (Thursday 8th October 2020)
---------------------------------


Changed
^^^^^^^


* The :func:`.affine.decompose` and :func:`.affine.compose` functions now
  have the ability to return/accept shear components.


Fixed
^^^^^


* Fixed a bug in the :func:`.affine.decompose` function which was corrupting
  the scale estimates when given an affine containing shears.

Paul McCarthy's avatar
Paul McCarthy committed
176

Paul McCarthy's avatar
Paul McCarthy committed
177
178
3.3.0 (Tuesday 22nd September 2020)
-----------------------------------
Paul McCarthy's avatar
Paul McCarthy committed
179
180
181
182
183
184
185
186


Added
^^^^^

* New ported versions of various core FSL tools, including ``imrm``, ``imln``,
  ``imtest``, ``fsl_abspath``, ``remove_ext``, ``Text2Vest``, and
  ``Vest2Text``.
Paul McCarthy's avatar
Paul McCarthy committed
187
* New :func:`.gps` function, wrapping the FSL ``gps`` command.
Paul McCarthy's avatar
Paul McCarthy committed
188
* New :func:`.vest.loadVestFile` and :func:`.vest.generateVest` functions.
Paul McCarthy's avatar
Paul McCarthy committed
189
190
191
192
193
194
195


Changed
^^^^^^^


* Updates to the BIDS filetree specification.
Paul McCarthy's avatar
Paul McCarthy committed
196
197


Paul McCarthy's avatar
Paul McCarthy committed
198
199
Fixed
^^^^^
Paul McCarthy's avatar
Paul McCarthy committed
200
201


Paul McCarthy's avatar
Paul McCarthy committed
202
203
204
* The :class:`.CoefficientField` class now works with alternate reference
  images (i.e. a reference image with different dimensions to that which
  was originally used when the non-linear transformation was calculated).
Paul McCarthy's avatar
Paul McCarthy committed
205
206


Paul McCarthy's avatar
Paul McCarthy committed
207
208
209
210
211
212
213
214
215
216
217
3.2.2 (Thursday 9th July 2020)
------------------------------


Changed
^^^^^^^


* The :func:`.fslsub.func_to_cmd` function allows more fine-grained control
  over whether the script file is removed after the job has finished running.

Paul McCarthy's avatar
Paul McCarthy committed
218
219
220
221
222
223
224
225
226
227
228
229

3.2.1 (Tuesday 23rd June 2020)
------------------------------


Changed
^^^^^^^


* Minor updates to documentation.


Paul McCarthy's avatar
Paul McCarthy committed
230
231
232
233
234
235
236
237
238
239
3.2.0 (Thursday 11th June 2020)
-------------------------------


Added
^^^^^


* A new :func:`.fslsub.hold` function to wait on previously submitted jobs, to
  be used in place of the ``wait`` function.
Paul McCarthy's avatar
Paul McCarthy committed
240
241
242
243
244
245
246
247
248
249
250


Removed
^^^^^^^


* The :func:`.fslsub.wait` (and :func:`.run.wait`) function has been removed, as
  repeated calls to ``qstat`` can adversely affect the cluster job submission
  system.


Paul McCarthy's avatar
Paul McCarthy committed
251
252
3.1.0 (Thursday 21st May 2020)
------------------------------
Paul McCarthy's avatar
Paul McCarthy committed
253
254


Paul McCarthy's avatar
Paul McCarthy committed
255
256
257
258
Added
^^^^^


Paul McCarthy's avatar
Paul McCarthy committed
259
* New :mod:`.cifti` module, providing classes and functions for working with
Paul McCarthy's avatar
Paul McCarthy committed
260
  `CIFTI <https://www.nitrc.org/projects/cifti/>`_ data.
Paul McCarthy's avatar
Paul McCarthy committed
261
262
263
264
265
266
* New :func:`.winpath` and :func:`wslpath` functions for working with paths
  when using FSL in a Windows Subsystem for Linux (WSL) environment.
* New :func:`.wslcmd` function for generating a path to a FSL command installed
  in a WSL environment.
* New :meth:`.Platform.fslwsl` attribute for detecting whether FSL is installed
  in a WSL environment.
Paul McCarthy's avatar
Paul McCarthy committed
267
268
269
270
271
272
273
274
275
276
277
278
* New :meth:`.Image.niftiDataType` property.
* The :class:`.FileTree` class has been updated to allow creation of
  deep copies via the new :meth:`.FileTree.copy` method.


Changed
^^^^^^^


* :func:`.Image` objects created from ``numpy`` arrays will be NIFTI1 or
  NIFTI2, depending on the value of the ``$FSLOUTPUTTYPE`` environment
  variable.
Paul McCarthy's avatar
Paul McCarthy committed
279
280


Paul McCarthy's avatar
Paul McCarthy committed
281
282
283
284
285
286
287
288
Fixed
^^^^^


* Updated the :func:`.fast` wrapper to support some single-character
  command-line flags.


Paul McCarthy's avatar
Paul McCarthy committed
289
290
291
292
293
294
295
296
297
298
3.0.1 (Wednesday 15th April 2020)
---------------------------------


Changed
^^^^^^^


* The :func:`.isMelodicDir` function now accepts directories that do not end
  with ``.ica``, as long as all required files are present.
Paul McCarthy's avatar
Paul McCarthy committed
299
300
* Added the ``dataclasses`` backport, so ``fslpy`` is now compatible with
  Python 3.6 again.
Paul McCarthy's avatar
Paul McCarthy committed
301
302


Paul McCarthy's avatar
Paul McCarthy committed
303
304
3.0.0 (Sunday 29th March 2020)
------------------------------
Paul McCarthy's avatar
Paul McCarthy committed
305
306
307
308
309
310


Added
^^^^^


Paul McCarthy's avatar
Paul McCarthy committed
311
312
* New wrapper functions for the FSL :class:`.fslstats`, :func:`.prelude` and
  :func:`applyxfm4D` commands.
Paul McCarthy's avatar
Paul McCarthy committed
313
314
315
* 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
316
317
* 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
318
319
* New :class:`.SubmitParams` class, providing a higer level interface for
  cluster submission.
Paul McCarthy's avatar
Paul McCarthy committed
320
* New :meth:`.FileTree.load_json` and  :meth:`.FileTree.save_json` methods.
Paul McCarthy's avatar
Paul McCarthy committed
321

Paul McCarthy's avatar
Paul McCarthy committed
322

Paul McCarthy's avatar
Paul McCarthy committed
323
324
325
326
Changed
^^^^^^^


Paul McCarthy's avatar
Paul McCarthy committed
327
* ``fslpy`` now requires a minimum Python version of 3.7.
Paul McCarthy's avatar
Paul McCarthy committed
328
* The default value for the ``partial_fill`` option to :meth:`.FileTree.read`
Paul McCarthy's avatar
Paul McCarthy committed
329
330
331
  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
332
333
* The :func:`.gifti.relatedFiles` function now supports files with
  BIDS-style naming conventions.
Paul McCarthy's avatar
Paul McCarthy committed
334
335
336
337
338
* 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
339
340
* 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
341
342
343
* 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
344
345
346
347
348
349
350
* 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
351
* Wrapper functions decorated with the :func:`.fileOrImage`,
Paul McCarthy's avatar
Paul McCarthy committed
352
  :func:`.fileOrArray`, or :func:`.fileOrText` decorators will now pass all
Paul McCarthy's avatar
Paul McCarthy committed
353
354
355
356
  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
357
358
359
* 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
360
361
* 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
362
363


Paul McCarthy's avatar
Paul McCarthy committed
364
365
366
367
368
369
370
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
371
372
* Fixed some bugs in the :func:`.fslsub.info` and :func:`.fslinfo.wait`
  functions.
Paul McCarthy's avatar
Paul McCarthy committed
373
374
* Fixed the :func:`.DeformationField.transform` method so it works with
  a single set of coordinates.
Paul McCarthy's avatar
Paul McCarthy committed
375
376
* :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
377

Paul McCarthy's avatar
Paul McCarthy committed
378
379
380
381
382
383
384
385
386
387
388
389
390
391
392
393
394
395
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
396
397
398
399
400
401
402
403
404
405
406
407
408
409
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
410
411
412
413
414
415
416
417
418
419
2.8.3 (Friday 28th February 2020)
---------------------------------


Fixed
^^^^^


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

Paul McCarthy's avatar
Paul McCarthy committed
420
421
422
423
424
425
426
427
428
429
430
431

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
432
433
2.8.1 (Thursday 20th February 2020)
-----------------------------------
Paul McCarthy's avatar
Paul McCarthy committed
434
435
436
437
438
439
440
441
442


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
443

Paul McCarthy's avatar
Paul McCarthy committed
444
445
2.8.0 (Wednesday 29th January 2020)
-----------------------------------
Paul McCarthy's avatar
Paul McCarthy committed
446
447


Paul McCarthy's avatar
Paul McCarthy committed
448
449
450
451
452
453
454
455
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
456
457
* New :func:`.mghimage.voxToSurfMat` function, for creating a
  voxel-to-freesurfer affine transform from any image.
Paul McCarthy's avatar
Paul McCarthy committed
458
459


Paul McCarthy's avatar
Paul McCarthy committed
460
461
462
463
464
465
466
467
468
469
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
470
471
472
473
474
Fixed
^^^^^


* Improved the algorithm used by the :func:`.mesh.needsFixing` function.
Paul McCarthy's avatar
Paul McCarthy committed
475
476
* The :meth:`.fslmaths.run` method now accepts :attr:`.wrappers.LOAD` as an
  output specification.
Paul McCarthy's avatar
Paul McCarthy committed
477
478
* 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
479
* Fixed a bug in the :func:`.resample` function.
Paul McCarthy's avatar
Paul McCarthy committed
480
481
* 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
482
483


Paul McCarthy's avatar
Paul McCarthy committed
484
485
486
487
488
489
490
491
Deprecated
^^^^^^^^^^


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


Paul McCarthy's avatar
Paul McCarthy committed
492
493
2.7.0 (Wednesday 6th November 2019)
-----------------------------------
Paul McCarthy's avatar
Paul McCarthy committed
494
495
496
497
498
499
500
501
502


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
503
504
* New :meth:`.IdleLoop.synchronous` context manager, to temporarily change the
  value of :meth:`.IdleLoop.neverQueue`.
Paul McCarthy's avatar
Paul McCarthy committed
505
506
* 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
507
508
509
* 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
510
511
512
513
514
515


Changed
^^^^^^^


Paul McCarthy's avatar
Paul McCarthy committed
516
* Internal reorganisation in the :mod:`.idle` module.
Paul McCarthy's avatar
Paul McCarthy committed
517
518


Paul McCarthy's avatar
Paul McCarthy committed
519
520
521
522
523
524
525
526
Fixed
^^^^^


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


Paul McCarthy's avatar
Paul McCarthy committed
527
528
529
530
531
532
533
534
535
536
537
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
538
539
540
541
542
543
544
545
546
547
548
549
550
551
552
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
553
554
555
556
557
558
559
560
561
562
563
564
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
565
566
2.6.0 (Tuesday 10th September 2019)
-----------------------------------
Paul McCarthy's avatar
Paul McCarthy committed
567
568


Paul McCarthy's avatar
Paul McCarthy committed
569
570
571
572
573
Added
^^^^^


* New :meth:`.Image.iscomplex` attribute.
Paul McCarthy's avatar
Paul McCarthy committed
574
* Support for a new ``Statistic`` atlas type.
Paul McCarthy's avatar
Paul McCarthy committed
575
576


Paul McCarthy's avatar
Paul McCarthy committed
577
578
579
580
581
582
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
583
584
* 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
585
586
587
* 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
588
589
* The :mod:`.dicom` module has been updated to work with the latest version of
  ``dcm2niix``.
Paul McCarthy's avatar
Paul McCarthy committed
590
591
592
593
594
595
596
597
598
599
600


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
601
602


Paul McCarthy's avatar
Paul McCarthy committed
603
604
2.5.0 (Tuesday 6th August 2019)
-------------------------------
Paul McCarthy's avatar
Paul McCarthy committed
605
606


Paul McCarthy's avatar
Paul McCarthy committed
607
608
609
610
Added
^^^^^


Paul McCarthy's avatar
Paul McCarthy committed
611
612
613
614
615
616
617
618
619
620
621
622
* 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
623
624


Paul McCarthy's avatar
Paul McCarthy committed
625
626
627
628
Changed
^^^^^^^


Paul McCarthy's avatar
Paul McCarthy committed
629
630
* The :mod:`.vest.looksLikeVestLutFile` function has been made slightly more
  lenient.
Paul McCarthy's avatar
Paul McCarthy committed
631
632
633
634
635
636
637
* `h5py <https://www.h5py.org/>`_ has been added to the ``fslpy`` dependencies.


Deprecated
^^^^^^^^^^


Paul McCarthy's avatar
Paul McCarthy committed
638
* The :mod:`fsl.utils.transform` module has been deprecated; its functions can
Paul McCarthy's avatar
Paul McCarthy committed
639
640
  now be found in the :mod:`fsl.transforms.affine` and
  :mod:`fsl.transform.flirt` modules.
Paul McCarthy's avatar
Paul McCarthy committed
641
642


Paul McCarthy's avatar
Paul McCarthy committed
643
644
645
646
647
648
649
650
651
652
653
654
655
656
657
658
659
660
661
662
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
663
664
665
666
667
668
669
670
671
672
673
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
674
675
2.3.0 (Tuesday June 25th 2019)
------------------------------
Paul McCarthy's avatar
Paul McCarthy committed
676
677
678
679
680
681


Added
^^^^^


Paul McCarthy's avatar
Paul McCarthy committed
682
683
684
685
686
* 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
687
688
* New :attr:`.Image.nvals` property, for use with ``RGB24``/``RGBA32``
  images.
Paul McCarthy's avatar
Paul McCarthy committed
689
690
691
692
693
694
695
696
697
698
699
700
701
702
* 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
703
* Fixed a bug in the :meth:`.GitfitMesh.loadVertices` method.
Paul McCarthy's avatar
Paul McCarthy committed
704
705
* 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
706
707


Paul McCarthy's avatar
Paul McCarthy committed
708
709
2.2.0 (Wednesday May 8th 2019)
------------------------------
Paul McCarthy's avatar
Paul McCarthy committed
710
711


Paul McCarthy's avatar
Paul McCarthy committed
712
713
714
715
716
717
718
719
720
721
722
723
724
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
725
726
727
728
Changed
^^^^^^^


Paul McCarthy's avatar
Paul McCarthy committed
729
730
731
732
733
734
735
* 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
736
737
738
739
Fixed
^^^^^


Paul McCarthy's avatar
Paul McCarthy committed
740
* Minor fixes to some :mod:`.filetree.filetree` tree definitions.
Paul McCarthy's avatar
Paul McCarthy committed
741
742


Paul McCarthy's avatar
Paul McCarthy committed
743
744
745
746
747
748
Deprecated
^^^^^^^^^^


* The :meth:`.Image.resample` method has been deprecated in favour of the
  :func:`.resample.resample` function.
Paul McCarthy's avatar
Paul McCarthy committed
749
750


Paul McCarthy's avatar
Paul McCarthy committed
751
752
2.1.0 (Saturday April 13th 2019)
--------------------------------
Paul McCarthy's avatar
Paul McCarthy committed
753
754
755
756
757
758
759
760


Added
^^^^^


* New tensor conversion routines in the :mod:`.dtifit` module (Michiel
  Cottaar).
Paul McCarthy's avatar
Paul McCarthy committed
761
762
* 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
763
764


Paul McCarthy's avatar
Paul McCarthy committed
765
766
767
768
769
Changed
^^^^^^^


* The :class:`.GiftiMesh` class no longer creates copies of the mesh
Paul McCarthy's avatar
Paul McCarthy committed
770
771
  vertex/index arrays. This means that, these arrays will be flagged as
  read-only.
Paul McCarthy's avatar
Paul McCarthy committed
772
773
774
* 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
775
776


Paul McCarthy's avatar
Paul McCarthy committed
777
778
779
780
781
782
783
784
785
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
786
787
788
789
790
791
792
793
794
795
796
797
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
798
799
2.0.0 (Friday March 20th 2019)
------------------------------
800
801


802
803
804
Added
^^^^^

Paul McCarthy's avatar
Paul McCarthy committed
805
* New :mod:`fsl.utils.filetree` package for defining and working with
Paul McCarthy's avatar
Paul McCarthy committed
806
  file/directory templates (Michiel Cottaar).
Paul McCarthy's avatar
Paul McCarthy committed
807
* Simple built-in :mod:`.deprecated` decorator.
Paul McCarthy's avatar
Paul McCarthy committed
808
* New :mod:`fsl.data.utils` module, which currently contains one function
809
  :func:`.guessType`, which guesses the data type of a file/directory path.
810
* New :func:`.commonBase` function for finding the common prefix of a set of
Paul McCarthy's avatar
Paul McCarthy committed
811
  file/directory paths.
812
813


814
815
816
Changed
^^^^^^^

Paul McCarthy's avatar
Paul McCarthy committed
817

818
* Removed support for Python 2.7 and 3.4.
819
820
821
* 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
822
* The :class:`.GiftiMesh` class can now load surface files which contain
Paul McCarthy's avatar
Paul McCarthy committed
823
824
825
  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
826
827


Paul McCarthy's avatar
Paul McCarthy committed
828
829
830
831
832
833
Removed
^^^^^^^

* Many deprecated items removed.


Paul McCarthy's avatar
Paul McCarthy committed
834
835
836
837
838
839
840
841
Deprecated
^^^^^^^^^^


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


Paul McCarthy's avatar
Paul McCarthy committed
842
843
844
845
1.13.3 (Friday February 8th 2019)
---------------------------------


Paul McCarthy's avatar
Paul McCarthy committed
846
847
848
Fixed
^^^^^

Paul McCarthy's avatar
Paul McCarthy committed
849

850
* Fixed an issue with the :func:`.dicom.loadSeries` using memory-mapping for
Paul McCarthy's avatar
Paul McCarthy committed
851
  image files that would subsequently be deleted.
Paul McCarthy's avatar
Paul McCarthy committed
852
* Fixed an issue in the :class:`.GiftiMesh` class, where
Paul McCarthy's avatar
Paul McCarthy committed
853
854
855
  ``numpy``/``nibabel`` was returning read-only index arrays.


Paul McCarthy's avatar
Paul McCarthy committed
856
857
858
859
860
861
862
863
1.13.2 (Friday November 30th 2018)
----------------------------------


Changed
^^^^^^^


Paul McCarthy's avatar
Paul McCarthy committed
864
865
* The :meth:`.Image.resample` method now supports images with more than three
  dimensions.
Michiel Cottaar's avatar
Michiel Cottaar committed
866
867
868
869
* 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.
870
871


Paul McCarthy's avatar
Paul McCarthy committed
872
873
Fixed
^^^^^
Paul McCarthy's avatar
Paul McCarthy committed
874

Paul McCarthy's avatar
Paul McCarthy committed
875
876
877
878
879
880

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


1.13.1 (Friday November 23rd 2018)
----------------------------------
Paul McCarthy's avatar
Paul McCarthy committed
881
882


Paul McCarthy's avatar
Paul McCarthy committed
883
884
885
886
Fixed
^^^^^


Paul McCarthy's avatar
Paul McCarthy committed
887
* Added a missing ``image`` attribute in the :class:`.VoxelwiseConfoundEV`
Paul McCarthy's avatar
Paul McCarthy committed
888
  class.
Paul McCarthy's avatar
Paul McCarthy committed
889
890
891
* 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
892
893


Paul McCarthy's avatar
Paul McCarthy committed
894
895
1.13.0 (Thursday 22nd November 2018)
------------------------------------
Paul McCarthy's avatar
Paul McCarthy committed
896

Paul McCarthy's avatar
Paul McCarthy committed
897
898
899
900

Added
^^^^^

Paul McCarthy's avatar
Paul McCarthy committed
901
* New wrapper functions for :func:`.fsl_anat`, :func:`.applytopup` (Martin
Paul McCarthy's avatar
Paul McCarthy committed
902
  Craig).
Paul McCarthy's avatar
Paul McCarthy committed
903
* New :func:`.fileOrText` decorator for use in wrapper functions (Martin
Paul McCarthy's avatar
Paul McCarthy committed
904
905
906
907
  Craig).


Changed
Paul McCarthy's avatar
Paul McCarthy committed
908
909
^^^^^^^

Paul McCarthy's avatar
Paul McCarthy committed
910
911
* Various minor changes and enhancements to the FSL function :mod:`.wrappers`
  interfaces (Martin Craig).
Paul McCarthy's avatar
Paul McCarthy committed
912
913
914
915
916
917
918


Fixed
^^^^^

* The ``immv`` and ``imcp`` scripts now accept incorrect file extensions on
  input arguments.
Paul McCarthy's avatar
Paul McCarthy committed
919
920


Paul McCarthy's avatar
Paul McCarthy committed
921
922
1.12.0 (Sunday October 21st 2018)
---------------------------------
Paul McCarthy's avatar
Paul McCarthy committed
923
924
925
926
927
928
929
930
931
932
933
934
935
936
937
938
939
940


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
941
942
943
944
945
946
947
948
949
950
951
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
952
953
954
955
956
957
958
959
960
961
962
963
964
965
966
967
968
969
970
971
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
972
973
974
975
976
977
978
979
980
981
982
983
984
985
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
986
987
988
989
990
991
992
993
994
995
996
997
1.10.2 (Friday September 7th 2018)
----------------------------------


Fixed
^^^^^


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


998
999
1000
1001
1002
1003
1004
1005
1006
1007
1008
1009
1010
1011
1.10.1 (Friday August 3rd 2018)
-------------------------------


Changed
^^^^^^^


* Minor adjustmenets to improve Windows compatibility.


Fixed
^^^^^

Paul McCarthy's avatar
Paul McCarthy committed
1012
* The :mod:`.FEATImage.getCOPE` method was returning PE images.
1013
1014


1015
1016
1.10.0 (Wednesday July 18th 2018)
---------------------------------
Paul McCarthy's avatar
Paul McCarthy committed
1017
1018
1019
1020
1021
1022
1023
1024
1025
1026


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.
1027
* The :func:`.fileOrImage` and :func:`.fileOrArray` decorators now support
Paul McCarthy's avatar
Paul McCarthy committed
1028
  loading of files which are specified with an output basename.
1029
* New :mod:`.fast` wrapper function for the FSL FAST tool.
Paul McCarthy's avatar
Paul McCarthy committed
1030
1031
1032
1033
1034
1035
1036
1037
1038
1039
1040


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
1041
1042
1.9.0 (Monday June 4th 2018)
----------------------------
Paul McCarthy's avatar
Paul McCarthy committed
1043
1044
1045
1046
1047
1048
1049
1050
1051
1052
1053
1054
1055
1056
1057
1058
1059
1060
1061
1062
1063
1064
1065
1066
1067
1068
1069
1070
1071
1072
1073
1074
1075
1076


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
1077
1078
1079
1080
1081
1082
1083
1084
1085
1086
1087
1088
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
1089
1090
1.8.0 (Thursday May 3rd 2018)
-----------------------------
Paul McCarthy's avatar
Paul McCarthy committed
1091
1092
1093
1094
1095
1096
1097
1098
1099
1100


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
1101
* New :mod:`fsl.utils.fslsub` module, containing a :func:`.fslsub.submit`
Paul McCarthy's avatar
Paul McCarthy committed
1102
  function which submits a cluster job via ``fsl_sub``.
Paul McCarthy's avatar
Paul McCarthy committed
1103
1104
* Assertions (in the :mod:`.assertions` module) can be disabled with the
  new :func:`.assertions.disabled` context manager.
Paul McCarthy's avatar
Paul McCarthy committed
1105
1106
* New :mod:`fsl.utils.parse_data` module containing various neuroimaging
  data constructors for use with ``argparse``.
Paul McCarthy's avatar
Paul McCarthy committed
1107
1108
* The :func:`.memoize.skipUnchanged` decorator has an ``invalidate`` function
  which allows its cache to be cleared.
Paul McCarthy's avatar
Paul McCarthy committed
1109
1110
1111
1112
1113
1114
1115
1116
1117
1118
1119
1120
1121
1122
1123
1124
1125


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`).


1126
1127
1.7.2 (Monday March 19th 2018)
------------------------------
Paul McCarthy's avatar
Paul McCarthy committed
1128
1129
1130
1131
1132
1133


Added
^^^^^


1134
1135
* 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
1136
1137


Paul McCarthy's avatar
Paul McCarthy committed
1138
1139
1140
1141
1142
1143
1144
1145
1146
1147
1148
1149
1150
1151
1152
1153
1.7.1 (Monday March 12th 2018)
------------------------------



Changed
^^^^^^^


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


Fixed
^^^^^


Paul McCarthy's avatar
Paul McCarthy committed
1154
* Removed deprecated use of :func:`.imagewrapper.canonicalShape`.
Paul McCarthy's avatar
Paul McCarthy committed
1155
1156


Paul McCarthy's avatar
Paul McCarthy committed
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
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
1183
  to the :mod:`.data.image` class.
Paul McCarthy's avatar
Paul McCarthy committed
1184
1185
1186
1187
1188
1189
1190
1191
1192
1193
1194
1195
1196
1197
1198
* 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
1199
* :func:`.ImageWrapper.canonicalShape` (moved to the :mod:`.data.image` module)
Paul McCarthy's avatar
Paul McCarthy committed
1200
1201
1202
1203
* :func:`.ImageWrapper.naninfrange` function (moved to the :mod:`.naninfrange`
  module)


Paul McCarthy's avatar
Paul McCarthy committed
1204
1205
1206
1207
1208
1209
1210
1.6.8 (Monday February 12th 2018)
---------------------------------


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


Paul McCarthy's avatar
Paul McCarthy committed
1211
1212
1213
1214
1215
1.6.7 (Friday February 9th 2018)
--------------------------------


* More further adjustments to the ``conda`` package build.
Paul McCarthy's avatar
Paul McCarthy committed
1216
* Adjustments to pypi source distribution - the ``requirements-extra.txt`` file
Paul McCarthy's avatar
Paul McCarthy committed
1217
1218
1219
  was not being included.


Paul McCarthy's avatar
Paul McCarthy committed
1220
1221
1222
1223
1224
1225
1226
1.6.6 (Thursday February 8th 2018)
----------------------------------


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


Paul McCarthy's avatar
Paul McCarthy committed
1227
1228
1229
1230
1231
1232
1233
1.6.5 (Tuesday February 6th 2018)
---------------------------------


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


Paul McCarthy's avatar
Paul McCarthy committed
1234
1235
1236
1237
1238
1239
1240
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
1241
1242
1.6.3 (Friday February 2nd 2018)
--------------------------------
Paul McCarthy's avatar
Paul McCarthy committed
1243
1244
1245


* Minor enhancements to the :class:`.WeakFunctionRef` class.
Paul McCarthy's avatar
Paul McCarthy committed
1246
1247
1248
* 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
1249
1250


Paul McCarthy's avatar
Paul McCarthy committed
1251
1252
1253
1254
1255
1256
1257
1258
1259
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
1260
1261
1262
1263
1264
1265
1266
1267
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
1268
1269
1.6.0 (Friday January 26th 2018)
--------------------------------
Paul McCarthy's avatar
Paul McCarthy committed
1270
1271


Paul McCarthy's avatar
Paul McCarthy committed
1272
1273
1274
1275
1276
1277
1278
1279
1280
1281
1282
1283
1284
* 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
1285
1286
* 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
1287
1288
1289
* 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
1290
1291
1292
1293
1294
* 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
1295
* Optional dependencies ``wxpython``, ``indexed_gzip``, ``trimesh``, and
Paul McCarthy's avatar
Paul McCarthy committed
1296
1297
  ``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
1298
1299


Paul McCarthy's avatar
Paul McCarthy committed
1300
1301
1302
1303
1304
1305
1306
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
1307
1.5.3 (Tuesday January 9th 2018)
1308
1309
1310
1311
1312
1313
1314
--------------------------------


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


Paul McCarthy's avatar
Paul McCarthy committed
1315
1316
1317
1318
1319
1320
1321
1.5.2 (Tuesday January 2nd 2018)
--------------------------------


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


Paul McCarthy's avatar
Paul McCarthy committed
1322
1323
1324
1325
1326
1327
1328
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
1329
1330
1.5.0 (Wednesday December 13th 2017)
------------------------------------
Paul McCarthy's avatar
Paul McCarthy committed
1331
1332
1333
1334
1335
1336


* 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
1337
1338
1339
* 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
1340
1341


Paul McCarthy's avatar
Paul McCarthy committed
1342
1343
1.4.2 (Tuesday December 5th 2017)
---------------------------------
Paul McCarthy's avatar
Paul McCarthy committed
1344
1345
1346
1347
1348


* 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
1349
* Some small bugfixes to the :mod:`.atlasq` and :mod:`.atlases` moduless.
Paul McCarthy's avatar
Paul McCarthy committed
1350
1351
1352


1.4.1 (Thursday November 9th 2017)
Paul McCarthy's avatar
Paul McCarthy committed
1353
1354
1355
1356
1357
1358
----------------------------------


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


Paul McCarthy's avatar
Paul McCarthy committed
1359
1.4.0 (Thursday November 9th 2017)
Paul McCarthy's avatar
Paul McCarthy committed
1360
----------------------------------
Paul McCarthy's avatar
Paul McCarthy committed
1361

Paul McCarthy's avatar
Paul McCarthy committed
1362

Paul McCarthy's avatar
Paul McCarthy committed
1363
1364
* 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
1365
1366
1367
* 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
1368
1369
1370
1371
1372
1373
1374
1375
1376
1377
1378
1379
1380
1381
* 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
1382
1.3.1 (Wednesday October 25th 2017)
Paul McCarthy's avatar
Paul McCarthy committed
1383
1384
1385
1386
1387
1388
1389
-----------------------------------


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


Paul McCarthy's avatar
Paul McCarthy committed
1390
1.3.0 (Wednesday October 25th 2017)
Paul McCarthy's avatar
Paul McCarthy committed
1391
-----------------------------------
Paul McCarthy's avatar
Paul McCarthy committed
1392
1393
1394
1395


* :class:`.Atlas` classes can now pass ``kwargs`` through to the
  :class:`.Image` constructor.
Paul McCarthy's avatar
Paul McCarthy committed
1396
1397
1398
* :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
1399
* :class:`.Cache` now implements ``__getitem__`` and ``__setitem__``
Paul McCarthy's avatar
Paul McCarthy committed
1400
1401
* 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
1402
1403
* :func:`.platform.isWidgetAlive` is deprecated in favour of an equivalent
  function in the ``fsleyes-widgets`` library.
Paul McCarthy's avatar
Paul McCarthy committed
1404
1405
* ``scipy`` is now explicitly listed as a requirement (this should have been
  done in 1.2.1).
Paul McCarthy's avatar
Paul McCarthy committed
1406
1407
1408
1409
1410
1411
1412



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


Paul McCarthy's avatar
Paul McCarthy committed
1413
1414
* 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
1415
1416
1417
1418
1419


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

Paul McCarthy's avatar
Paul McCarthy committed
1420

Paul McCarthy's avatar
Paul McCarthy committed
1421
1422
1423
1424
1425
1426
1427
1428
1429
1430
1431
1432
1433
1434
1435
1436
* 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
1437
  favour of new :meth:`.Nifti.voxToScaledVoxMat` and
Paul McCarthy's avatar
Paul McCarthy committed
1438
1439
1440
1441
1442
1443
1444
1445
1446
1447
1448
1449
1450
1451
1452
1453
1454
1455
1456
1457
1458
  :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
1459
1460
1461
1462
1463
1464
1465
1466
1467
1468
1469
1470

 - :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
1471
1472
1473
1474
1475
1476
1477
1478
1479
1480
1481
1482
1483
1484
1485
1486
1487
1488
1489
1490
1491
1492
1493
1494
1495
1496
1497
1498
1499
1500
1501
1502
1503
1504
1505
1506
1507
1508
1509
1510
1511
1512
1513
1514
1515
1516
1517
1518
1519
1520
1521
1522
1523
1524
1525
1526
1527
1528
1529
1530
1531
1532
1533
1534
1535
1536
1537
1538
1539
1540
1541
1542
1543
1544
1545
* 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