forked from vigente/gerardus
-
Notifications
You must be signed in to change notification settings - Fork 0
/
ChangeLog
12279 lines (8061 loc) · 412 KB
/
ChangeLog
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
275
276
277
278
279
280
281
282
283
284
285
286
287
288
289
290
291
292
293
294
295
296
297
298
299
300
301
302
303
304
305
306
307
308
309
310
311
312
313
314
315
316
317
318
319
320
321
322
323
324
325
326
327
328
329
330
331
332
333
334
335
336
337
338
339
340
341
342
343
344
345
346
347
348
349
350
351
352
353
354
355
356
357
358
359
360
361
362
363
364
365
366
367
368
369
370
371
372
373
374
375
376
377
378
379
380
381
382
383
384
385
386
387
388
389
390
391
392
393
394
395
396
397
398
399
400
401
402
403
404
405
406
407
408
409
410
411
412
413
414
415
416
417
418
419
420
421
422
423
424
425
426
427
428
429
430
431
432
433
434
435
436
437
438
439
440
441
442
443
444
445
446
447
448
449
450
451
452
453
454
455
456
457
458
459
460
461
462
463
464
465
466
467
468
469
470
471
472
473
474
475
476
477
478
479
480
481
482
483
484
485
486
487
488
489
490
491
492
493
494
495
496
497
498
499
500
501
502
503
504
505
506
507
508
509
510
511
512
513
514
515
516
517
518
519
520
521
522
523
524
525
526
527
528
529
530
531
532
533
534
535
536
537
538
539
540
541
542
543
544
545
546
547
548
549
550
551
552
553
554
555
556
557
558
559
560
561
562
563
564
565
566
567
568
569
570
571
572
573
574
575
576
577
578
579
580
581
582
583
584
585
586
587
588
589
590
591
592
593
594
595
596
597
598
599
600
601
602
603
604
605
606
607
608
609
610
611
612
613
614
615
616
617
618
619
620
621
622
623
624
625
626
627
628
629
630
631
632
633
634
635
636
637
638
639
640
641
642
643
644
645
646
647
648
649
650
651
652
653
654
655
656
657
658
659
660
661
662
663
664
665
666
667
668
669
670
671
672
673
674
675
676
677
678
679
680
681
682
683
684
685
686
687
688
689
690
691
692
693
694
695
696
697
698
699
700
701
702
703
704
705
706
707
708
709
710
711
712
713
714
715
716
717
718
719
720
721
722
723
724
725
726
727
728
729
730
731
732
733
734
735
736
737
738
739
740
741
742
743
744
745
746
747
748
749
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
780
781
782
783
784
785
786
787
788
789
790
791
792
793
794
795
796
797
798
799
800
801
802
803
804
805
806
807
808
809
810
811
812
813
814
815
816
817
818
819
820
821
822
823
824
825
826
827
828
829
830
831
832
833
834
835
836
837
838
839
840
841
842
843
844
845
846
847
848
849
850
851
852
853
854
855
856
857
858
859
860
861
862
863
864
865
866
867
868
869
870
871
872
873
874
875
876
877
878
879
880
881
882
883
884
885
886
887
888
889
890
891
892
893
894
895
896
897
898
899
900
901
902
903
904
905
906
907
908
909
910
911
912
913
914
915
916
917
918
919
920
921
922
923
924
925
926
927
928
929
930
931
932
933
934
935
936
937
938
939
940
941
942
943
944
945
946
947
948
949
950
951
952
953
954
955
956
957
958
959
960
961
962
963
964
965
966
967
968
969
970
971
972
973
974
975
976
977
978
979
980
981
982
983
984
985
986
987
988
989
990
991
992
993
994
995
996
997
998
999
1000
2017-11-07 Ramon <rcasero@MRC1006>
* release v0.12.0. Fixed some long standing issues in the linux
build. Current version builds successfully in Ubuntu zesty, Matlab
R2016b, g++ 4.9, cmake 3.7.2
- Matlab determined gcc version now used across the project.
- GMP and MPFR are built at cmake .. time
- Suppress warnings from initialised variables that are not used
2017-10-27 Ramon Casero <rcasero@marcel>
* Update build to Matlab2016b and new sourceforge paths for ITK
and Boost.
2017-04-04 Ramon Casero <[email protected]>
* Add matlab/RegistrationToolbox/transfdiff.m
* Add matlab/RegistrationToolbox/transfdiffreg.m: Functions
implementing the Transformation Diffusion Reconstruction from
Casero2017 MIA paper.
2017-03-06 Ramón Casero <rcasero@marcel>
* Remove python/, I've created a new github project called "pysto"
to put python code there. Gerardus already has too much misc code.
* Add python/requirements.txt: pip dependencies of the python
library.
* Add python/imgproc/matchHist.py (1.0.0): Modify image
intensities to match the histogram of a reference image.
* Add python/ for python functions.
2017-03-01 Ramón Casero <[email protected]>
* shell-script/pre-commit-git-diff-docx.sh: (0.3.0) Fix
bug. dtdoering's patch avoids trying to create the .md file with
pandoc if the .docx has been deleted. It also deletes the .md file
if the .docx file has been deleted. But the delete is not
commited. Now we add the deleted .md file to
.commit-amend-markdown so that the post-commit hook commits the
delete. Also, only consider .docx to denote a Word file if it's at
the end of the file's name.
2017-01-09 Darryl McClymont <[email protected]>
new file: matlab/FileFormatToolbox/scimat_tformarray.m
* this function will transform any 3D array in scimat format to another space, defined
by the new rotation matrix, min, etc. Tested with preclinical data.
modified: matlab/FileFormatToolbox/scimat_varian2scimat.m
* Sorry I trampled on your edits to this function Nick, but I think we did the same thing,
and my version works with the non-zero slice gap.
Minor:
modified: matlab/DiffusionMRIToolbox/fit_DT.m
modified: matlab/DiffusionMRIToolbox/quiver_image.m
modified: matlab/DiffusionMRIToolbox/view_tensors.m
modified: matlab/DiffusionMRIToolbox/weighted_linear_fit.m
2016-12-20 Ramon Casero <[email protected]>
* matlab/RegistrationToolbox/regmatchedfilt.m (0.4.0): Fix
bug. The alignment was not correct if IMF, IMM didn't have the
same pixel size and offset. Now the function takes into account
pixel size and offset if the input images are in scimat format.
2016-12-16 Ramon Casero <[email protected]>
* matlab/CardiacToolbox/histology_preprocessing.m (0.5.1): Fix
bug. For histogram reference, the image was not being converted to
grayscale when the user requested it.
* matlab/CardiacToolbox/histology_preprocessing.m (0.5.0): Add
syntax for reference histogram.
2016-12-09 Ramon Casero <[email protected]>
* matlab/FiltersToolbox/scimat_crop.m (0.5.2): When input is list
of files, now it's possible to select several crops at the same
time. This saves time, as every file only needs to be loaded once
for all crops.
2016-12-07 Ramon Casero <[email protected]>
* matlab/FiltersToolbox/scimat_crop.m (0.5.1): Add info to the
help header about input argument DS.
2016-12-06 Ramon Casero <[email protected]>
* matlab/FiltersToolbox/scimat_crop.m (0.5.0): Add new syntax so
that a 3D image volume can be provided as a list of files, each
with a 2D image.
2016-12-05 Ramon Casero <[email protected]>
* matlab/FileFormatToolbox/scimat_load.m (0.5.11):
* matlab/FileFormatToolbox/scimat_save.m (0.6.8): Fix
bug. Save/read XPosition, YPosition fields to/from tiff
files. This way we can save/read the offset info of the image.
2016-11-28 Nicolas Basty <[email protected]>
* matlab/FileFormatToolbox/scimat_varian2scimat.m (0.1.2)
Can now also convert acquisitions where the data is not acquired in stacks of parallel 2D images but rather
in spokes spanning different values of psi, stored in an array. In my case this is for LA views.
*matlab/FileFormatToolbox/scimat_slice_GUI.m
Changing the view and axis
2016-11-23 Ramon Casero <[email protected]>
* matlab/ElastixToolbox/transformix_pts.m (0.1.2): Fix bug. Minus
sign of output x-coordinates was being ignored.
2016-11-17 Darryl McClymont <[email protected]>
* matlab/FileFormatToolbox/scimat_slice_GUI.m (0.1.1)
Fix bug. The GUI uses the matlab function surface, which wants corner
coordinates. It was being given pixel centres, so the whole image was
off by half a pixel.
* matlab/FileFormatToolbox/scimat_varian2scimat.m (0.1.1)
Fix bug when gap between slices is not zero - it is now added to the
slice thickness, which is obviously not the same thing as having thicker
slices, but at least the slice centres are in the right place now.
2016-11-14 Darryl McClymont <[email protected]>
* Minor changes and some new functions for processing diffusion images:
modified: matlab/DiffusionMRIToolbox/weighted_linear_fit.m
modified: matlab/DiffusionMRIToolbox/wild_bootstrapping_DTI.m
modified: matlab/FiltersToolbox/forward_TV.m
modified: matlab/DiffusionMRIToolbox/quiver_image.m
modified: matlab/DiffusionMRIToolbox/fit_DKI_model.m
modified: matlab/DiffusionMRIToolbox/fit_DT.m
modified: matlab/DiffusionMRIToolbox/fit_biexponential_tensor.m
new file: matlab/DiffusionMRIToolbox/fit_triexponential_tensor.m
new file: matlab/DiffusionMRIToolbox/plot_diffusion_profiles.m
new file: matlab/CardiacToolbox/mask2LV_cavity.m
new file: matlab/DiffusionMRIToolbox/dt2params.m
* Added some tools for kurtosis tensor processing:
new file: matlab/DiffusionMRIToolbox/rotate_tensor.m
new file: matlab/DiffusionMRIToolbox/kurtosis_3333_to_66.m
new file: matlab/DiffusionMRIToolbox/kurtosis_66_to_3333.m
new file: matlab/DiffusionMRIToolbox/kurtosis_ijkl_to_rc.m
new file: matlab/DiffusionMRIToolbox/tensor2vector.m
new file: matlab/DiffusionMRIToolbox/vector2tensor.m
2016-11-03 Ramon Casero <[email protected]>
* matlab/ElastixToolbox/elastix_compose_afftransf.m (0.2.7): Fix
bug. Make sure that tfc.NumberOfParameters is correct at the
output.
2016-10-31 Ramon Casero <[email protected]>
* Add matlab/FileFormatToolbox/nuimagesc.m (0.1.0): NUIMAGESC
imagesc() with non-uniform pixel spacing.
2016-10-27 Ramon Casero <[email protected]>
* matlab/ElastixToolbox/elastix_fitgeotrans.m (0.2.0): Add input
argument alpha, to allow partial deformations of the image,
following Alexa 2002.
* Add matlab/ElastixToolbox/elastix_fitgeotrans.m (0.1.0):
Transformix struct for image transformation obtained from matching
two sets of landmarks.
2016-10-26 Ramon Casero <[email protected]>
* matlab/ElastixToolbox/elastix.m (0.5.5): Fix bug. When regParam
was given as a filename, the filename was replaced by a struct
before making a copy of the filename.
2016-10-25 Ramon Casero <[email protected]>
* Add matlab/FileFormatToolbox/im_resize.m (0.1.0): IM_RESIZE
Resize a list of image files (.tif, .png, etc) with ImageMagick
convert, directly file to file.
2016-10-24 Ramon Casero <[email protected]>
* matlab/FileFormatToolbox/scimat_load.m: (0.5.10) Fix bug. When
.tif images have a thumbnail, imfinfo() produces a 2-vector of
structs, one for the image and one for the thumbnail. Now we
discard the thumbnail metadata.
2016-10-21 Nicolas Basty <[email protected]>
* matlab\FileFormatToolbox\scimat_varian2scimat.m: This function
converts data from varian scanners, which follow an odd
convention, into scimat format. Either stacks of 2D images or
single 3D images. For example to visualise 2D data using the
scimat_slice_GUI.
2016-10-11 Nicolas Basty <[email protected]>
* matlab\FileFormatToolbox\scimat_im2scimat.m: Edited to handle 2D
slices in 3D space
2016-10-09 Ramon Casero <[email protected]>
* matlab/PointsToolbox/cons_smacof_pip.m (0.4.6): Simplify code to
generate the objective function terms.
2016-10-08 Ramon Casero <[email protected]>
* matlab/ManifoldToolbox/tri_ccqp_smacof_nofold_sph_pip.m (0.5.1):
Fix bug. Edge length constraints: we can ignore edges where both
vertices are fixed. But if one or two vertices are free, we have
to write the constraint accordingly (for free vertices we use
variable names, and for fixed vertices we use the numerical value
of their coordinates).
2016-10-07 Ramon Casero <[email protected]>
* matlab/ManifoldToolbox/tri_ccqp_smacof_nofold_sph_pip.m (0.5.0):
New input argument "lmax": Maximum length allowed to any edge of
the output parametrization. This can avoid triangles moving to the
opposite side of the sphere to become positive.
2016-10-06 Ramon Casero <[email protected]>
* matlab/ManifoldToolbox/sphtri_foldcc.m (0.3.0): New input
isManuallyGood, to manually label vertices as good, even if they
belong to a bad triangle.
* matlab/ManifoldToolbox/sphtri_foldcc.m (0.2.1): Fix
bug. Function broke if there were no good vertices within any
fold.
2016-10-05 Ramon Casero <[email protected]>
* matlab/ManifoldToolbox/sphtri_foldcc.m (0.2.0): Fix bug. The
function was not producing the right lists of vertices. Now the
code is simpler and seems to work well.
2016-10-04 Ramon Casero <[email protected]>
* Add matlab/ManifoldToolbox/sphtri_foldcc.m (0.1.0):
SPHTRI_FOLDCC Find connected components of groups of vertices
causing a fold on the sphere.
2016-09-27 Ramon Casero <[email protected]>
* Delete matlab/ManifoldToolbox/tri_sphparam.m: Move to
private-gerardus. Paper not published yet, and function needs
substantial rewriting.
* matlab/ManifoldToolbox/tri_ccqp_smacof_nofold_sph_pip.m (0.4.0):
Change the way we compute the box that bounds where the vertices
can move to. Now we compute the convex hull of the component we
are unfolding, and take into account whether it intersects any of
the Cartesian axes. If it does, the box extends to the radius of
the sphere. This is to avoid chopping off part of the sphere where
the vertices could move to.
* Add matlab/ThirdPartyToolbox/TriangleRayIntersectionToolbox:
* matlab/add_gerardus_paths.m (0.3.8):
- Toolbox to compute intersections with triangulations. We use it
in the new box computation in tri_ccqp_smacof_nofold_sph_pip.m. By
Jaroslaw Tuszynski, 29 Sep 2011 (Updated 15 Jun 2016)
http://uk.mathworks.com/matlabcentral/fileexchange/33073-triangle-ray-intersection
2016-09-26 Ramon Casero <[email protected]>
* PointsToolbox/cons_smacof_pip.m (0.4.5): Don't use the same file
for initial and computed solutions. Delete model and solution
files after being used, to avoid cluttering /tmp. Fix bug with the
format string when writing the initial solution to file. Close
file after writing it.
* ManifoldToolbox/tri_ccqp_smacof_nofold_sph_pip.m (0.3.1): Check
that there are no NaN values in input Y. Reduce search space for
solution to box that encloses the points. Correct the index of a
group of constraints (it had no practical effect, but it was
jumping one number).
2016-09-22 Ramon Casero <[email protected]>
* tri_sphparam.m (0.5.1): Fix bug. Bad concatenation of vectors.
2016-09-20 Ramon Casero <[email protected]>
* matlab/ManifoldToolbox/tri_ccqp_smacof_nofold_sph_pip.m (0.3.0):
Improve the constraint that says that the points have to be within
a box that encloses the sphere. Now we form the box enclosing the
fixed vertices of the component.
The reason for this change is that a negative triangle can flip by
sending a vertex to a far away point on the sphere. With a smaller
box, we prevent this from happening. A smaller box of possible
solutions also accelerates the solver.
* matlab/PointsToolbox/cons_smacof_pip.m (0.4.4): Change expected
names for SCIP binary. We remove the version number so that we
don't need to be changing it every time they release a new
version.
2016-09-19 Ramon Casero <[email protected]>
* .gitignore: Add extensions of Windows library and directory for
Boost libraries.
2016-09-14 Ramon Casero <[email protected]>
* .gitignore: Add list of files that are automatically generated
by the CMake build system, so git shouldn't track them.
* matlab/FiltersToolbox/scimat_resize3.m (0.1.1): Specify that the
inputs SZ and SIGMA are in [row, col, slice] order, so that they
agree with the SCIMAT format, and then swap rows and columns
internally to match the resize3D format.
2016-09-13 Ramon Casero <[email protected]>
* Update matlab/ThirdPartyToolbox/Iso2meshToolbox to latest version
* add_gerardus_paths.m: (0.3.7)
- iso2mesh-1.7.9 for linux64 by Qianqian Fang <q.fang at neu.edu>
- https://sourceforge.net/projects/iso2mesh/files/iso2mesh/1.7.9%20%28Deviled%20Egg-beta%29/
* Rename matlab/ThirdPartyToolbox/iso2meshToolbox as
matlab/ThirdPartyToolbox/Iso2meshToolbox.
* .gitignore: Some of the directories needed a "/" before their
name, so that they refer to the directory at the root of gerardus,
instead of every directory or file with the same name.
2016-09-12 Ramon Casero <[email protected]>
* matlab/FiltersToolbox/scimat_lconvhull_smoothing.m (0.8.0)
- No longer remove non-manifold vertices. We leave that to an
external program like meshlab.
* Add matlab/FiltersToolbox/scimat_resize3.m: (0.1.0)
* matlab/FiltersToolbox/scimat_downsample.m: (0.3.2)
* matlab/FileFormatToolbox/scimat_resample.m: (0.1.2)
- SCIMAT_RESIZE3 Resize a 3D scimat image.
2016-09-11 Ramon Casero <[email protected]>
* matlab/FiltersToolbox/scimat_downsample.m: (0.3.1)
* matlab/FileFormatToolbox/scimat_resample.m: (0.1.1)
- Small edits to help header to make them have the format expected
by update_README.sh.
* Delete stlread.m, stlwrite.m, license-stlwrite.txt:
- Redundant with GraphToolbox.
* Add ThirdPartyToolbox/GraphToolbox:
* add_gerardus_paths.m: (0.3.6)
- Add Toolbox Graph, by Gabriel Peyre 26 Jun 2004 (Updated 19 Jul
2009.
A toolbox to perform computations on graph. We are particularly
interested in functions to write/read meshes in .off format to
interact with Meshlab.
http://uk.mathworks.com/matlabcentral/fileexchange/5355-toolbox-graph
2016-09-07 Ramon Casero <[email protected]>
* matlab/FiltersToolbox/scimat_lconvhull_smoothing.m: (0.8.0)
- Simplify code removing the attempts at cleaning non-manifold
vertices. I think the code was buggy, and was producing
non-manifold meshes. Better clean the meshes up manually with
meshlab.
* matlab/FileFormatToolbox/scimat_load.m: (0.5.9)
- Fix bug. When the scimat struct didn't have the field
scimat.property, the function crashed when trying to delete
it. Now it only deletes the field if it exists. I have extended
this check to fields that are removed in scimat.axis too.
2016-09-06 Ramon Casero <[email protected]>
* Add matlab/ThirdPartyToolbox/stlwrite.m:
- Export a variety of inputs (patch, surface) to an STL triangular
mesh. by Sven 30 Jul 2008 (Updated 30 Mar 2015).
https://www.mathworks.com/matlabcentral/fileexchange/20922-stlwrite-filename--varargin-
2016-07-24 Ramon Casero <[email protected]>
* matlab/CardiacToolbox/blockface_correct_frame_shifts.m: (0.2.2)
- Loop to produce output images is now parallel (parfor). It makes
things faster.
2016-07-21 Ramon Casero <[email protected]>
* matlab/CardiacToolbox/blockface_correct_frame_shifts.m: (0.2.2)
- Put transformation of images into a parfor loop, to make use of
multiple cores.
* matlab/CardiacToolbox/blockface_correct_frame_shifts.m: (0.2.1)
- Delete temp output file created by transformix, so that we don't
swamp /tmp.
2016-07-20 Ramon Casero <[email protected]>
* matlab/CardiacToolbox/blockface_correct_frame_shifts.m: (0.2.0)
- Fix bug. Affine transformations are not commutative, so it was
incorrect to first accumulate the transformations that propagate,
and then add on top the transformations that don't propagate. Now,
for non-propagating transformation T at slice I, we add T^-1 at
slice I+1, to cancel it.
* matlab/FileFormatToolbox/scimat_load.m: (0.5.8)
- If the file extension is not one of the special cases (.mat,
.mha.mhd, .lsm, .vmu), try to read the file with imread. Before,
we only attempted this for .png and .tif files, but there's no
reason why we should be restricted that way.
2016-07-18 Ramon Casero <[email protected]>
* matlab/CardiacToolbox/blockface_intraframe_reg.m: (0.5.0)
- Add IDX input argument so that we can select which slices to
register to the previous one, rather than having to register every
I to I-1.
2016-07-11 Ramon Casero <[email protected]>
* Normalize all the line endings in the repository, so that we
don't have a mix of CRLF for Windows and LF for linux.
2016-07-06 Ramon Casero <[email protected]>
* .gitattributes:
- Protect .mha from automatic changes in end of line characters by
telling git that they are always binary.
2016-06-29 Ramon Casero <[email protected]>
* FileFormatToolbox/match_file_lists.m: (0.2.0)
- Sort the lists alphabetically.
- Fix bug so that filenames in a list can have different formats
and lengths as long as they have the same token in the same place.
2016-06-27 Ramon Casero <[email protected]>
* matlab/CardiacToolbox/blockface_intraframe_reg.m: (0.4.3)
- Fix bug. Typo in field name in a struct.
* Add .gitignore:
- To prevent getting lots of clutter in "git status".
2016-05-27 Ramon Casero <[email protected]>
* CMakeLists.txt: (0.9.6)
- Add g++ version for Matlab2015b.
2016-05-25 Hao Xu <[email protected]>
* Delete common.svnprops.
- It was for the old subversion repository.
2016-05-18 Ramon Casero <[email protected]>
* Add shell-script/pre-commit-git-diff-docx: (0.1.0)
- Git hook to create a copy of .docx files in Markdown format
(.md) before the commit. That way, automatic diff emails will show
the differences in the Word document.
2016-05-11 Nicolas Basty <[email protected]>
* add matlab\FileFormatToolbox\scimat_resample.m
- Adding this function that I wrote to resample scimat files. I'm using it to extract slices of volumes or profiles of images.
2016-05-11 Nicolas Basty <[email protected]>
*matlab\FiltersToolbox\im2col3.m: (0.2)
*matlab\FiltersToolbox\im2col3.m: (0.2)
- Fixed a bug where X and Y were the wrong way round. Did not notice at first because I always used the same X & Y.
2016-01-19 Jo Bates <[email protected]>
*matlab/DiffusionMRIToolbox/dt_from_smoldyn_pt1
*matlab/DiffusionMRIToolbox/dt_from_smoldyn_pt2
*matlab/DiffusionMRIToolbox/dt_from_smoldyn_pt3
- added these 3 functions which calculate the diffusion tensor from the smoldyn data
*matlab/FileFormatToolbox/smoldyn2matlab
- amended to include cutting down the data to only those molecules which finish
inside the voxel to be analysed to reduce the data to be saved.
2015-10-23 Ramon Casero <[email protected]>
* Add matlab/ThirdPartyToolbox/ExportFigureToolbox:
* matlab/add_gerardus_paths.m: (0.3.5)
- Add export_fig by by Yair Altman 11 Apr 2009 (Updated 05 Oct
2015). Downloaded from
http://uk.mathworks.com/matlabcentral/fileexchange/23629-export-fig
This function saves a figure or single axes to one or more vector
and/or bitmap file formats, and/or outputs a rasterized version to
the workspace. This function is especially suited to exporting
figures for use in publications and presentations, because of the
high quality and portability of media produced.
?2015-10-19 Jo Bates <[email protected]>
* matlab/DiffusionMRIToolbox/add_Rician_noise_to_simulated_dMRI_data
- changed to allow any dimension of data
2015-10-19 Jo Bates <[email protected]>
* matlab/DiffusionMRIToolbox/add_Rician_noise_to_simulated_dMRI_data
- Allows Rician noise with known SNR to be added to simulated data
2015-10-16 Ramon Casero <[email protected]>
* matlab/ThirdPartyToolbox/dijkstra.m: (0.4.0)
* matlab/ThirdPartyToolbox/dijkstra.cpp: (0.4.0)
* matlab/test/test_dijkstra.m: (0.3.3)
- Fix bug. The adjacency-distance matrix input to dijkstra()
should be transposed, i.e. (j,i) is the distance from i to j,
because of how the corresponding MEX file is implemented. We have
changed the interface rather than transposing internally, because
in that case we would have to make a copy of a potentially large
matrix. It's better to let the user transpose the matrix on the
Matlab side, and that way not have both the matrix and its
transpose in memory.
Reported by Matthew Morena, issue 89
https://github.com/rcasero/gerardus/issues/89
2015-10-09 Ramon Casero <[email protected]>
* matlab/CardiacToolbox/histology_preprocessing.m: (0.4.2)
- Now the reference image is output in the same format as at the
input. Internally, now it's always processed as an array.
2015-10-07 Ramon Casero <[email protected]>
* Add matlab/ThirdPartyToolbox/rotateXLabels.m:
- Rotate x-tick labels to any angle, preserving font settings and
coping with resize, zoom, pan etc.
- Note that as of R2014b this functionality is built into MATLAB
axes using the 'XTickLabelRotation' property.
- By Ben Tordoff, 01 Jun 2010 (Updated 08 Oct 2014), downloaded
from
http://www.mathworks.com/matlabcentral/fileexchange/27812-rotatexlabels--ax--angle--varargin--
2015-09-30 Ramon Casero <[email protected]>
* Add matlab/FileFormatToolbox/scimat_scimat2imref.m: (0.1.0)
- SCIMAT_SCIMAT2IMREF Matlab's image reference frame from SCIMAT
metadata.
2015-09-29 Ramon Casero <[email protected]>
* matlab/FileFormatToolbox/scimat_load.m: (0.5.7)
- Allow to load metadata only for .tif/.png files, without the
actual image. (This speeds things up a lot when you don't need the
image).
2015-09-26 Ramon Casero <[email protected]>
* Add matlab/FileFormatToolbox/scimat_imagesc.m: (0.1.0)
- Display 2D image in real world coordinate axes.
2015-09-25 Ramon Casero <[email protected]>
* matlab/ElastixToolbox/transformix_pts.m: (0.1.1)
- Fix bug. The delimiter in the points files has to be ' ' instead
of ',', otherwise transformix fails to read the points (without
giving an error message). Also, increase the precision of the
numbers we write to 15 digits. This has limited value, because
transformix output coordinates only have 6 digits, anyway.
* matlab/ElastixToolbox/transformix.m: (0.3.1)
- Minor, some comments and the way opts is initialized.
* Add matlab/ElastixToolbox/transformix_pts.m: (0.1.0)
- Matlab interface to the image warping program "transformix", but
for point transformation.
2015-09-23 Darryl McClymont <[email protected]>
* Add matlab/DiffusionMRIToolbox/quiver_image.m (0.0.1)
- Displays a 2D slice of a 3D image with a quiver plot
overlaid on top.
* Add matlab/FiltersToolbox/forward_TGV.m (0.0.1)
- Second order total generalised variation of an image (up to 3D)
* Add matlab/FiltersToolbox/inverse_TGV.m (0.0.1)
- Returns the residuals of 2nd order total generalised variation
2015-09-03 Ramon Casero <[email protected]>
* matlab/FileFormatToolbox/scimat_load.m: (0.5.5)
- Fix bug. For.mha/.mhd files, if the first byte of the raw data
was ASCII 13 (CR = carriage return), then fgetl combined it with
the last \n (ASCII 10, LF new line feed) after "ElementDataFile =
LOCAL", so it read one byte too few.
2015-09-02 Ramon Casero <[email protected]>
* matlab/FileFormatToolbox/writemetaimagefile.m: (0.2.2)
- If output file cannot be open, give an error instead of just a
message.
* matlab/ElastixToolbox/elastix.m: (0.5.4)
- If input images are filenames, don't first load them to memory
to write them as temp files again. Use the original files
directly. This speeds things up.
- Internally, we want to keep both a struct with the registration
parameters to do some checks and a file to pass to elastix.
- Fix bug. When filenames contained whitespaces, the call to
elastix on the command line would fail. Now filename passed to
command line in "".
2015-08-28 Darryl McClymont <[email protected]>
* Delete matlab/ThirdPartyToolbox/waveletcdf97
- Toolbox has no licence, so we cannot redistribute it.
* Add matlab/ThirdPartyToolbox/waveletcdf97/
- This tool computes the CohenDaubechiesFeauveau 9/7 (CDF 9/7)
wavelet transform. It was downloaded from
http://www.getreuer.info/home/waveletcdf97
on 2015-03-26.
* Add matlab/ThirdPartyToolbox/waveletcdf97/waveletcdf97_3D.m
- An extension of Pascal Getreuers CohenDaubechiesFeauveau 9/7
wavelet code to handle 3D images.
2015-08-26 Darryl McClymont <[email protected]>
* matlab/DiffusionMRIToolbox/weighted_linear_fit.m (0.1.1)
- Parameters now passed through a struct rather than individual
arguments.
- Now can use a unique weighting vector for each signal (but this
is slower)
- Now gives the option of weighting by Y^2, which may be used for
signals with noise following a Rician distribution.
* matlab/DiffusionMRIToolbox/fit_DT.m (0.1.10)
- Modified to work with the new version of weighted_linear_fit.
2015-08-21 Ramon Casero <[email protected]>
* matlab/CardiacToolbox/histology_preprocessing.m: (0.4.0)
- Now we can process a stack of images, and the inputs can be
filenames as well as scimats or arrays. Converting to grayscale is
optional. Some general rewriting of the function.
2015-08-15 Ramon Casero <[email protected]>
* matlab/FileFormatToolbox/scimat_load.m: (0.5.4)
- For .png/.tif files, scimat.rotmat gets created last, so that
the fields are in the same order as with other functions. Matlab
gives an error if you try to do scimat(I) = scimat_other and the
fields are not in the same order. A proper solution to this would
be to reorder the fields automatically, but this is a quick fix
that works for the moment.
* matlab/CardiacToolbox/histology_preprocessing.m: (0.3.1)
- Accept inputs given in scimat format.
2015-08-11 Ramon Casero <[email protected]>
* matlab/RegistrationToolbox/regmatchedfilt.m: (0.3.0)
- Input images now can be in scimat format, so we can work with
physical units.
- Fix bug. CenterOfRotation is in (x,y) format, but we were using
(row,col) format.
2015-08-06 Ramon Casero <[email protected]>
* matlab/FileFormatToolbox/scimat_load.m: (0.5.3)
- Fix bug. When the file header doesn't provide ResolutionUnit,
XResolution or YResolution, the function now gives a warning, and
chooses defaults, instead of failing.
* matlab/ElastixToolbox/transformix.m: (0.3.0)
- Now input image can be in scimat format, so transforms can be in
physical coordinates. Better support for .png/.tif/.mha files.
* matlab/ElastixToolbox/elastix.m: (0.5.3)
- Fix bug. When the input image was in array form, we kept the
channels in dimension 3 instead of 5 in the conversion to scimat.
2015-08-05 Ramon Casero <[email protected]>
* matlab/ElastixToolbox/elastix.m: (0.5.2)
- If .png/.tif files doesn't provide SamplesPerPixel tag, compute
number of channels from BitDepth.
* matlab/FileFormatToolbox/scimat_load.m: (0.5.2)
- Add 'meter' as a valid resolution unit for .tif/.png files.
2015-08-04 Ramon Casero <[email protected]>
* matlab/FileFormatToolbox/scimat_save.m: (0.6.7)
- Fix bug. For PNG and TIFF output formats. scimat.data channels
are now 5th instead of 3rd dimension.
* matlab/ElastixToolbox/elastix.m: (0.5.1)
- Fix bug. When deleting temp files, we no longer store the names
in a cell array, but as a matrix, with one filename per row.
* matlab/ElastixToolbox/elastix_read_reg_output.m: (0.3.0)
- Change output from IM to SCIMAT. This way, the output is not
only the image, but also contains the metadata.
* matlab/FileFormatToolbox/scimat_load.m: (0.5.1)
- Support reading compressed .mha/.mhd files. Thanks to function
provided in mha_read_volume() by Dirk-Jan Kroon, 10 Nov 2010
(Updated 23 Feb 2011)
http://uk.mathworks.com/matlabcentral/fileexchange/29344-read-medical-data-3d/content/mha/mha_read_volume.m
- In .mha/.mhd code, write labels as 'ObjectType' instead of
'objecttype' to improve readability of code.
- In .mha/.mhd code, recognise and process a couple more labels.
* matlab/ElastixToolbox/elastix.m: (0.5.0)
- Accept SCIMAT structs as inputs. This allows to provide images
in physical coordinates (i.e. with spacing and offset values).
2015-08-03 Ramon Casero <[email protected]>
* matlab/FileFormatToolbox/scimat_im2scimat.m: (0.3.1)
- Extend to SCIMAT images with 2D or 3D, and with frames and
channels.
* matlab/FiltersToolbox/scimat.m: (0.2.3)
- Explain better the difference between number of spatial
dimensions and number of axes.
2015-07-31 Ramon Casero <[email protected]>
* matlab/ElastixToolbox/elastix.m: (0.4.6)
- Accept input .mha/.mhd images.
- Deal with colour images better. Now images can have any number
of channels, and they are split into the corresponding number of
temporal files. The temporal files are no longer PNG, but the same
format as the input images.
- Fix bug. If the images format is .tif, elastix produces both a
.tif and .dcm file. To avoid this kind of problems, now we are
more specific when looking for the output image file.
* matlab/FileFormatToolbox/scimat_save.m: (0.6.6)
- Fix bug. When input image was 2D, the function threw an error
because it assumed that all images were 3D.
* matlab/FileFormatToolbox/writemetaimagefile.m: (0.2.1)
- Fix bug. When input image is 2D and in colour, the dimension has
to be 2 (not 3) with 3 channels.
* matlab/FileFormatToolbox/scimat_load.m: (0.5.0)
- Add input optional parameter 'HeaderOnly'.
* matlab/FileFormatToolbox/scimat_load.m: (0.4.7)
- Fix bug. When reading colour TIFF, PNG files, channels need to
go in the 5th dimension of scimat.data.
2015-07-30 Ramon Casero <[email protected]>
* matlab/ElastixToolbox/elastix_read_reg_output.m: (0.2.4)
- Fix bug. If the images format is .tif, elastix produces both a
.tif and .dcm file. To avoid this kind of problems, now we are
more specific when looking for the output image file.
* matlab/FiltersToolbox/scimat.m: (0.2.2)
- Add multi-channel images to the scimat standard (e.g. RGB
images).
* matlab/FileFormatToolbox/scimat_save.m: (0.6.5)
- Now we can write rotation matrices to MetaImage files.
* matlab/FileFormatToolbox/writemetaimagefile.m: (0.2.0)
- Add input argument for rotation matrix, and deal with images
with more than one channel.
- Deal with cases for resolution, offset when image has 2 to 4
dimensions (before, we always assumed 3 dimensions).
- Replace separate blocks of code for 2D, 3D and 4D images with a
single block of code for any number of dimensions. This makes the
code much shorter.
- Update to new syntax of narginchk, nargoutchk.
* matlab/FileFormatToolbox/scimat_load.m: (0.4.6)
- Read PNG, TIFF files.
- Now we can have scimat with number of channels
('ElementNumberOfChannels') and rotation matrix ('Orientation',
'TransformMatrix', 'Rotation').
- Deal with synomyms for MetaImage tag 'Offset'.
- Deal with minor MetaImage tags: 'ObjectType', 'HeaderSize'.
- Explicitly check that 'CenterOfRotation' is 0. We cannot deal
with other centers of rotation yet.
- If file reports ElementSpacing(:) == 0, replace by
ElementSpacing(:) == 1.0 to potentially avoid problems with
ITK/Elastix registration.
2015-07-29 Ben Villard <[email protected]>
* CMakelists.txt
* matlab/FindMatlab.cmake
- Added the compiler information for the latest MATLAB version (2015Ra)
- Changed the tarball url for ITK, as the source forge one was obsolete.
- created a dummy project in FindMatlab.cmake
2015-07-28 Darryl McClymont <[email protected]>
* matlab/FiltersToolbox/forward_TV.m (0.1.3)
* matlab/FiltersToolbox/inverse_TV.m (0.1.1)
- Now works in 1 dimension.
2015-07-28 Ramon Casero <[email protected]>
* Add shell-script/imresize-meta.sh: (0.1.0)
- Script to resize image files, changing the pixel spacing
accordingly so that the real world print size remains the same.
2015-07-23 Nicolas Basty <[email protected]>
* Add matlab\FiltersToolbox\im2col3.m: (0.1.0)
- IM2COL3 rearranges 3D image blocks into columns
* Add matlab\FiltersToolbox\col2im3.m: (0.1.0)
- COL2IM3 rearranges matrix columns into a 3D image
2015-07-20 Darryl McClymont <[email protected]>
* Add matlab/DiffusionMRIToolbox/view_tensors.m (0.1.1)
- VIEW_TENSORS Renders diffusion tensors in 3D, colour coded by HA
* matlab/DiffusionMRIToolbox/wild_bootstrapping_DTI.m (0.1.2)
* matlab/DiffusionMRIToolbox/fit_DKI_model.m (0.1.0)
- Minor bug fixes
2015-07-03 Ramon Casero <[email protected]>
* matlab/ElastixToolbox/elastix_colon.m: (0.1.2)
- Fix bug. If not all the levels were the same transform, the
function gave an error when trying to remove the top level.
* matlab/ElastixToolbox/elastix_colon.m: (0.1.1)
- Fix bug. If you wanted to extract more than one level, the
second level repeated the same transform for every image, instead
of the real ones.
2015-07-02 Ramon Casero <[email protected]>
* matlab/ElastixToolbox/elastix_cat.m: (0.3.2)
- Fix bug. Function broke when one of the input transforms was
empty or a cell vector of empties.
2015-07-01 Ramon Casero <[email protected]>
* matlab/FindMatlab.cmake: (0.2.10)
- Find Matlab version without having to run matlab (solves
Gerardus issue #50).
2015-06-25 Ramon Casero <[email protected]>
* Add matlab/ElastixToolbox/elastix_length.m: (0.1.0)
- ELASTIX_LENGTH Number of transform levels in an elastix series.
2015-06-24 Ramon Casero <[email protected]>
* Add matlab/ElastixToolbox/elastix_colon.m: (0.1.0)
- ELASTIX_COLON Colon operator for elastix transforms.
2015-06-16 Ramon Casero <[email protected]>
* matlab/FiltersToolbox/CMakeLists.txt: (0.2.8)
- Fix bug. forward_TV_mex was renamed by Darryl to forward_TV_aux
some time ago, but this file still had the old name.
2015-06-14 Ramon Casero <[email protected]>
* matlab/FileFormatToolbox/vmu2png.m: (0.2.2)
- Fix bug. We were not setting ResolutionUnit to "meter", so it
was an undefined value in the file metadata, and conversion to