mipav.git
13 months agoPorting continues.
ilb@NIH.GOV [Mon, 5 Mar 2018 23:12:02 +0000 (23:12 +0000)]
Porting continues.

git-svn-id: https://citdcbmipav.cit.nih.gov/repos-pub/mipav/trunk@15398 ba61647d-9d00-f842-95cd-605cb4296b96

13 months agoPorting continues.
ilb@NIH.GOV [Fri, 2 Mar 2018 23:10:08 +0000 (23:10 +0000)]
Porting continues.

git-svn-id: https://citdcbmipav.cit.nih.gov/repos-pub/mipav/trunk@15397 ba61647d-9d00-f842-95cd-605cb4296b96

13 months agoAdded a quick prototype for visually clipping the volume so the user can annotate...
abokinsky [Fri, 2 Mar 2018 20:21:08 +0000 (20:21 +0000)]
Added a quick prototype for visually clipping the volume so the user can annotate areas where the nuclei are densely packed.

git-svn-id: https://citdcbmipav.cit.nih.gov/repos-pub/mipav/trunk@15396 ba61647d-9d00-f842-95cd-605cb4296b96

13 months agoPorting continues.
ilb@NIH.GOV [Thu, 1 Mar 2018 23:09:33 +0000 (23:09 +0000)]
Porting continues.

git-svn-id: https://citdcbmipav.cit.nih.gov/repos-pub/mipav/trunk@15395 ba61647d-9d00-f842-95cd-605cb4296b96

13 months agoAdded removal of symmetric areas from the ADC thresholded mask up to slice 10 to...
mccreedy@NIH.GOV [Thu, 1 Mar 2018 18:35:02 +0000 (18:35 +0000)]
Added removal of symmetric areas from the ADC thresholded mask up to slice 10 to reduce selection of cerebellum regions as the largest single object.

git-svn-id: https://citdcbmipav.cit.nih.gov/repos-pub/mipav/trunk@15394 ba61647d-9d00-f842-95cd-605cb4296b96

13 months agoPorting continues.
ilb@NIH.GOV [Wed, 28 Feb 2018 23:20:05 +0000 (23:20 +0000)]
Porting continues.

git-svn-id: https://citdcbmipav.cit.nih.gov/repos-pub/mipav/trunk@15393 ba61647d-9d00-f842-95cd-605cb4296b96

13 months agoPorting continues.
ilb@NIH.GOV [Tue, 27 Feb 2018 23:14:17 +0000 (23:14 +0000)]
Porting continues.

git-svn-id: https://citdcbmipav.cit.nih.gov/repos-pub/mipav/trunk@15392 ba61647d-9d00-f842-95cd-605cb4296b96

13 months agoPorting continues.
ilb@NIH.GOV [Mon, 26 Feb 2018 23:16:37 +0000 (23:16 +0000)]
Porting continues.

git-svn-id: https://citdcbmipav.cit.nih.gov/repos-pub/mipav/trunk@15391 ba61647d-9d00-f842-95cd-605cb4296b96

13 months agoPorting continues.
ilb@NIH.GOV [Fri, 23 Feb 2018 23:08:26 +0000 (23:08 +0000)]
Porting continues.

git-svn-id: https://citdcbmipav.cit.nih.gov/repos-pub/mipav/trunk@15390 ba61647d-9d00-f842-95cd-605cb4296b96

13 months agoFixed bugFixed bug in the reslice image option for the track annotations plugin.
abokinsky [Thu, 22 Feb 2018 22:50:22 +0000 (22:50 +0000)]
Fixed bugFixed bug in the reslice image option for the track annotations plugin.

git-svn-id: https://citdcbmipav.cit.nih.gov/repos-pub/mipav/trunk@15389 ba61647d-9d00-f842-95cd-605cb4296b96

13 months agoStarted work on.
ilb@NIH.GOV [Thu, 22 Feb 2018 22:28:57 +0000 (22:28 +0000)]
Started work on.

git-svn-id: https://citdcbmipav.cit.nih.gov/repos-pub/mipav/trunk@15388 ba61647d-9d00-f842-95cd-605cb4296b96

13 months agoFixed bug in the reslice image option. Was producing the mirror-image instead of...
abokinsky [Wed, 21 Feb 2018 22:21:50 +0000 (22:21 +0000)]
Fixed bug in the reslice image option. Was producing the mirror-image instead of the correctly rotated image.

git-svn-id: https://citdcbmipav.cit.nih.gov/repos-pub/mipav/trunk@15387 ba61647d-9d00-f842-95cd-605cb4296b96

13 months agoCorrected c1 expressions.
ilb@NIH.GOV [Wed, 21 Feb 2018 22:04:03 +0000 (22:04 +0000)]
Corrected c1 expressions.

git-svn-id: https://citdcbmipav.cit.nih.gov/repos-pub/mipav/trunk@15386 ba61647d-9d00-f842-95cd-605cb4296b96

13 months agoCorrected expressions for c1 in run2D,run2DC,run3D, and run3DC.
ilb@NIH.GOV [Wed, 21 Feb 2018 21:55:41 +0000 (21:55 +0000)]
Corrected expressions for c1 in run2D,run2DC,run3D, and run3DC.

git-svn-id: https://citdcbmipav.cit.nih.gov/repos-pub/mipav/trunk@15385 ba61647d-9d00-f842-95cd-605cb4296b96

14 months agoBoth FORTRAN and JAVA still have abnormal JAPHYC exits if machine precision is reduce...
ilb@NIH.GOV [Tue, 20 Feb 2018 17:52:38 +0000 (17:52 +0000)]
Both FORTRAN and JAVA still have abnormal JAPHYC exits if machine precision is reduced from 2.22E-16 to 1.0E-8.

git-svn-id: https://citdcbmipav.cit.nih.gov/repos-pub/mipav/trunk@15384 ba61647d-9d00-f842-95cd-605cb4296b96

14 months agoComments about ABNORMAL JAPHYC exit in both FORTRAN AND Java due to parameter bounds...
ilb@NIH.GOV [Fri, 16 Feb 2018 23:15:09 +0000 (23:15 +0000)]
Comments about ABNORMAL JAPHYC exit in both FORTRAN AND Java due to parameter bounds being exceeded.

git-svn-id: https://citdcbmipav.cit.nih.gov/repos-pub/mipav/trunk@15383 ba61647d-9d00-f842-95cd-605cb4296b96

14 months agoPrevent infinite looping in DELEG7 and DEJAC7. Get JAPHYC abnormal exit Number of...
ilb@NIH.GOV [Fri, 16 Feb 2018 19:26:52 +0000 (19:26 +0000)]
Prevent infinite looping in DELEG7 and DEJAC7.  Get JAPHYC abnormal exit Number of quadrature panels exceeds IBNDS[2] DURING REFINEMENT.

git-svn-id: https://citdcbmipav.cit.nih.gov/repos-pub/mipav/trunk@15382 ba61647d-9d00-f842-95cd-605cb4296b96

14 months agoSaves any annotations in the resliced coordinates when the user selects 'reslice...
abokinsky [Fri, 16 Feb 2018 02:30:30 +0000 (02:30 +0000)]
Saves any annotations in the resliced coordinates when the user selects 'reslice' for the straightened image output.

git-svn-id: https://citdcbmipav.cit.nih.gov/repos-pub/mipav/trunk@15381 ba61647d-9d00-f842-95cd-605cb4296b96

14 months agoIn SUBIN7, DEJAC7, and DELEG7 changed double TOL to double TOL[] = new double[1]...
ilb@NIH.GOV [Thu, 15 Feb 2018 22:22:56 +0000 (22:22 +0000)]
In SUBIN7, DEJAC7, and DELEG7 changed double TOL to double TOL[] = new double[1], but still wind up with infinite looping in DELEG7.

git-svn-id: https://citdcbmipav.cit.nih.gov/repos-pub/mipav/trunk@15380 ba61647d-9d00-f842-95cd-605cb4296b96

14 months agoin DELEG7 corrected zmlt of XI * XI and setting of REMND[K - 1][1], but still getting...
ilb@NIH.GOV [Thu, 15 Feb 2018 22:09:24 +0000 (22:09 +0000)]
in DELEG7 corrected zmlt of XI * XI and setting of REMND[K - 1][1], but still getting into an infinite loop in DELEG7.

git-svn-id: https://citdcbmipav.cit.nih.gov/repos-pub/mipav/trunk@15379 ba61647d-9d00-f842-95cd-605cb4296b96

14 months agoIn visuallization GUI, fix the surface saving issues with .ply and .stl
ruida@NIH.GOV [Thu, 15 Feb 2018 22:01:39 +0000 (22:01 +0000)]
In visuallization GUI, fix the surface saving issues with .ply and .stl

git-svn-id: https://citdcbmipav.cit.nih.gov/repos-pub/mipav/trunk@15378 ba61647d-9d00-f842-95cd-605cb4296b96

14 months agoIn DELEG7 corrected expressions for GG[I - 1][0] and GG{I - 1][1].
ilb@NIH.GOV [Thu, 15 Feb 2018 20:39:58 +0000 (20:39 +0000)]
In DELEG7 corrected expressions for GG[I - 1][0] and GG{I - 1][1].

git-svn-id: https://citdcbmipav.cit.nih.gov/repos-pub/mipav/trunk@15377 ba61647d-9d00-f842-95cd-605cb4296b96

14 months agoChanged stats file output to be pre-java8 compliant.
mccreedy@NIH.GOV [Thu, 15 Feb 2018 19:59:26 +0000 (19:59 +0000)]
Changed stats file output to be pre-java8 compliant.

git-svn-id: https://citdcbmipav.cit.nih.gov/repos-pub/mipav/trunk@15376 ba61647d-9d00-f842-95cd-605cb4296b96

14 months agoEPS now set in public SymmsIntegralMapping(). In CSCAL3 changed double PP[] = new...
ilb@NIH.GOV [Thu, 15 Feb 2018 19:17:07 +0000 (19:17 +0000)]
EPS now set in public SymmsIntegralMapping().  In CSCAL3 changed double PP[] = new double[NQPTS-1] to double PP[] = new double[NQPTS].  In JAPHYC changed MNEQN,MNEQN to NROWS,NROWS in ge.dlange and le2.dgetrf.

git-svn-id: https://citdcbmipav.cit.nih.gov/repos-pub/mipav/trunk@15375 ba61647d-9d00-f842-95cd-605cb4296b96

14 months agoversion 8.0.2
mccreedy@NIH.GOV [Tue, 13 Feb 2018 19:45:27 +0000 (19:45 +0000)]
version 8.0.2

git-svn-id: https://citdcbmipav.cit.nih.gov/repos-pub/mipav/trunk@15373 ba61647d-9d00-f842-95cd-605cb4296b96

14 months agoAdded flipping right/left for the lattices as part of the building process.
abokinsky [Mon, 12 Feb 2018 19:17:24 +0000 (19:17 +0000)]
Added flipping right/left for the lattices as part of the building process.

git-svn-id: https://citdcbmipav.cit.nih.gov/repos-pub/mipav/trunk@15372 ba61647d-9d00-f842-95cd-605cb4296b96

14 months agoRunning JAPHYC produces a failure to converge in EIGSYS error.
ilb@NIH.GOV [Fri, 9 Feb 2018 22:55:35 +0000 (22:55 +0000)]
Running JAPHYC produces a failure to converge in EIGSYS error.

git-svn-id: https://citdcbmipav.cit.nih.gov/repos-pub/mipav/trunk@15371 ba61647d-9d00-f842-95cd-605cb4296b96

14 months agoAdded debugging printouts for saving annotations. Fixed bug in loading creating the...
abokinsky [Fri, 9 Feb 2018 22:10:41 +0000 (22:10 +0000)]
Added debugging printouts for saving annotations. Fixed bug in loading creating the annotation animations.

git-svn-id: https://citdcbmipav.cit.nih.gov/repos-pub/mipav/trunk@15370 ba61647d-9d00-f842-95cd-605cb4296b96

14 months agoversion 8.0.1
mccreedy@NIH.GOV [Fri, 9 Feb 2018 21:56:21 +0000 (21:56 +0000)]
version 8.0.1

git-svn-id: https://citdcbmipav.cit.nih.gov/repos-pub/mipav/trunk@15368 ba61647d-9d00-f842-95cd-605cb4296b96

14 months agoupdated imagej jar: Fri Feb 9 16:48:16 EST 2018
mccreedy@NIH.GOV [Fri, 9 Feb 2018 21:48:19 +0000 (21:48 +0000)]
updated imagej jar: Fri Feb  9 16:48:16 EST 2018

git-svn-id: https://citdcbmipav.cit.nih.gov/repos-pub/mipav/trunk@15367 ba61647d-9d00-f842-95cd-605cb4296b96

14 months agoIn DRIVE0() TSTPLT works with all 4 examples. Maximum misfit value of 9.86E-16.
ilb@NIH.GOV [Thu, 8 Feb 2018 21:35:21 +0000 (21:35 +0000)]
In DRIVE0() TSTPLT works with all 4 examples.  Maximum misfit value of 9.86E-16.

git-svn-id: https://citdcbmipav.cit.nih.gov/repos-pub/mipav/trunk@15366 ba61647d-9d00-f842-95cd-605cb4296b96

14 months agoExamples 2 and 4 added to PARFUN and DPARFN.
ilb@NIH.GOV [Thu, 8 Feb 2018 19:01:00 +0000 (19:01 +0000)]
Examples 2 and 4 added to PARFUN and DPARFN.

git-svn-id: https://citdcbmipav.cit.nih.gov/repos-pub/mipav/trunk@15365 ba61647d-9d00-f842-95cd-605cb4296b96

14 months agoAdded PARFUN and DPARFN for examples 1 and 3. Corrected PTFUN2.
ilb@NIH.GOV [Wed, 7 Feb 2018 23:14:07 +0000 (23:14 +0000)]
Added PARFUN and DPARFN for examples 1 and 3.  Corrected PTFUN2.

git-svn-id: https://citdcbmipav.cit.nih.gov/repos-pub/mipav/trunk@15364 ba61647d-9d00-f842-95cd-605cb4296b96

14 months agoPARGEN and supporting routines corrected so that ex01.f and ex03.f are correctly...
ilb@NIH.GOV [Wed, 7 Feb 2018 20:06:11 +0000 (20:06 +0000)]
PARGEN and supporting routines corrected so that ex01.f and ex03.f are correctly reproduced as ex01.java and ex03.java.

git-svn-id: https://citdcbmipav.cit.nih.gov/repos-pub/mipav/trunk@15363 ba61647d-9d00-f842-95cd-605cb4296b96

14 months agoPARGEN, PTFUN1, and PTFUN2 corrected so that ex01.f can be successfully created.
ilb@NIH.GOV [Tue, 6 Feb 2018 21:48:38 +0000 (21:48 +0000)]
PARGEN, PTFUN1, and PTFUN2 corrected so that ex01.f can be successfully created.

git-svn-id: https://citdcbmipav.cit.nih.gov/repos-pub/mipav/trunk@15362 ba61647d-9d00-f842-95cd-605cb4296b96

14 months agoCorrections put in PTFUN1 and PTFUN2.
ilb@NIH.GOV [Mon, 5 Feb 2018 23:10:37 +0000 (23:10 +0000)]
Corrections put in PTFUN1 and PTFUN2.

git-svn-id: https://citdcbmipav.cit.nih.gov/repos-pub/mipav/trunk@15361 ba61647d-9d00-f842-95cd-605cb4296b96

14 months agoInitial version of stroke core segmentation plugin.
mccreedy@NIH.GOV [Mon, 5 Feb 2018 16:39:50 +0000 (16:39 +0000)]
Initial version of stroke core segmentation plugin.

git-svn-id: https://citdcbmipav.cit.nih.gov/repos-pub/mipav/trunk@15360 ba61647d-9d00-f842-95cd-605cb4296b96

14 months agoAdded method for generating default centroids for an image.
mccreedy@NIH.GOV [Mon, 5 Feb 2018 16:39:23 +0000 (16:39 +0000)]
Added method for generating default centroids for an image.

git-svn-id: https://citdcbmipav.cit.nih.gov/repos-pub/mipav/trunk@15359 ba61647d-9d00-f842-95cd-605cb4296b96

14 months agoAdded method for retrieving the extracted VOI.
mccreedy@NIH.GOV [Mon, 5 Feb 2018 16:38:48 +0000 (16:38 +0000)]
Added method for retrieving the extracted VOI.

git-svn-id: https://citdcbmipav.cit.nih.gov/repos-pub/mipav/trunk@15358 ba61647d-9d00-f842-95cd-605cb4296b96

14 months agoDebugging PARGEN and supporting routines.
ilb@NIH.GOV [Fri, 2 Feb 2018 23:10:18 +0000 (23:10 +0000)]
Debugging PARGEN and supporting routines.

git-svn-id: https://citdcbmipav.cit.nih.gov/repos-pub/mipav/trunk@15357 ba61647d-9d00-f842-95cd-605cb4296b96

14 months agoStarted debugging PARGEN.
ilb@NIH.GOV [Wed, 31 Jan 2018 23:08:32 +0000 (23:08 +0000)]
Started debugging PARGEN.

git-svn-id: https://citdcbmipav.cit.nih.gov/repos-pub/mipav/trunk@15356 ba61647d-9d00-f842-95cd-605cb4296b96

14 months agoPorting continues.
ilb@NIH.GOV [Tue, 30 Jan 2018 23:14:38 +0000 (23:14 +0000)]
Porting continues.

git-svn-id: https://citdcbmipav.cit.nih.gov/repos-pub/mipav/trunk@15355 ba61647d-9d00-f842-95cd-605cb4296b96

14 months agoPorting continues.
ilb@NIH.GOV [Mon, 29 Jan 2018 23:12:36 +0000 (23:12 +0000)]
Porting continues.

git-svn-id: https://citdcbmipav.cit.nih.gov/repos-pub/mipav/trunk@15354 ba61647d-9d00-f842-95cd-605cb4296b96

14 months agoTracking plugin now automatically re-twists the annotations back to the original...
abokinsky [Sat, 27 Jan 2018 01:57:40 +0000 (01:57 +0000)]
Tracking plugin now automatically re-twists the annotations back to the original worm volume when the user presses 'done'.

git-svn-id: https://citdcbmipav.cit.nih.gov/repos-pub/mipav/trunk@15353 ba61647d-9d00-f842-95cd-605cb4296b96

14 months agoPorting continues.
ilb@NIH.GOV [Fri, 26 Jan 2018 23:13:40 +0000 (23:13 +0000)]
Porting continues.

git-svn-id: https://citdcbmipav.cit.nih.gov/repos-pub/mipav/trunk@15352 ba61647d-9d00-f842-95cd-605cb4296b96

14 months agoPorting continues.
ilb@NIH.GOV [Thu, 25 Jan 2018 23:12:28 +0000 (23:12 +0000)]
Porting continues.

git-svn-id: https://citdcbmipav.cit.nih.gov/repos-pub/mipav/trunk@15351 ba61647d-9d00-f842-95cd-605cb4296b96

14 months agoPorting continues.
ilb@NIH.GOV [Wed, 24 Jan 2018 23:22:45 +0000 (23:22 +0000)]
Porting continues.

git-svn-id: https://citdcbmipav.cit.nih.gov/repos-pub/mipav/trunk@15350 ba61647d-9d00-f842-95cd-605cb4296b96

14 months agoAdded the resliced/rotated image option to the annotation tracking plugin and to...
abokinsky [Wed, 24 Jan 2018 00:13:56 +0000 (00:13 +0000)]
Added the resliced/rotated image option to the annotation tracking plugin and to the untwisted->twisted conversion plugin.

git-svn-id: https://citdcbmipav.cit.nih.gov/repos-pub/mipav/trunk@15349 ba61647d-9d00-f842-95cd-605cb4296b96

14 months agoPorting continues.
ilb@NIH.GOV [Tue, 23 Jan 2018 21:06:53 +0000 (21:06 +0000)]
Porting continues.

git-svn-id: https://citdcbmipav.cit.nih.gov/repos-pub/mipav/trunk@15348 ba61647d-9d00-f842-95cd-605cb4296b96

15 months agoPorting continues.
ilb@NIH.GOV [Fri, 19 Jan 2018 23:14:05 +0000 (23:14 +0000)]
Porting continues.

git-svn-id: https://citdcbmipav.cit.nih.gov/repos-pub/mipav/trunk@15347 ba61647d-9d00-f842-95cd-605cb4296b96

15 months agoPorting continues.
ilb@NIH.GOV [Thu, 18 Jan 2018 22:57:20 +0000 (22:57 +0000)]
Porting continues.

git-svn-id: https://citdcbmipav.cit.nih.gov/repos-pub/mipav/trunk@15346 ba61647d-9d00-f842-95cd-605cb4296b96

15 months agoPorting continues.
ilb@NIH.GOV [Wed, 17 Jan 2018 23:08:19 +0000 (23:08 +0000)]
Porting continues.

git-svn-id: https://citdcbmipav.cit.nih.gov/repos-pub/mipav/trunk@15345 ba61647d-9d00-f842-95cd-605cb4296b96

15 months agoPorting continues.
ilb@NIH.GOV [Tue, 16 Jan 2018 22:02:08 +0000 (22:02 +0000)]
Porting continues.

git-svn-id: https://citdcbmipav.cit.nih.gov/repos-pub/mipav/trunk@15344 ba61647d-9d00-f842-95cd-605cb4296b96

15 months agoPorting continues.
ilb@NIH.GOV [Fri, 12 Jan 2018 23:11:52 +0000 (23:11 +0000)]
Porting continues.

git-svn-id: https://citdcbmipav.cit.nih.gov/repos-pub/mipav/trunk@15343 ba61647d-9d00-f842-95cd-605cb4296b96

15 months agoAdded an image reslice and rotation option after straightening.
abokinsky [Fri, 12 Jan 2018 00:50:47 +0000 (00:50 +0000)]
Added an image reslice and rotation option after straightening.

git-svn-id: https://citdcbmipav.cit.nih.gov/repos-pub/mipav/trunk@15342 ba61647d-9d00-f842-95cd-605cb4296b96

15 months agoPorting continues.
ilb@NIH.GOV [Thu, 11 Jan 2018 23:09:40 +0000 (23:09 +0000)]
Porting continues.

git-svn-id: https://citdcbmipav.cit.nih.gov/repos-pub/mipav/trunk@15341 ba61647d-9d00-f842-95cd-605cb4296b96

15 months agoContinued updates
mcmatt@NIH.GOV [Thu, 11 Jan 2018 15:04:56 +0000 (15:04 +0000)]
Continued updates

git-svn-id: https://citdcbmipav.cit.nih.gov/repos-pub/mipav/trunk@15340 ba61647d-9d00-f842-95cd-605cb4296b96

15 months agoPorting continues.
ilb@NIH.GOV [Wed, 10 Jan 2018 20:30:25 +0000 (20:30 +0000)]
Porting continues.

git-svn-id: https://citdcbmipav.cit.nih.gov/repos-pub/mipav/trunk@15339 ba61647d-9d00-f842-95cd-605cb4296b96

15 months agoPorting continues.
ilb@NIH.GOV [Tue, 9 Jan 2018 22:50:43 +0000 (22:50 +0000)]
Porting continues.

git-svn-id: https://citdcbmipav.cit.nih.gov/repos-pub/mipav/trunk@15338 ba61647d-9d00-f842-95cd-605cb4296b96

15 months agoConvert NIH prostate data to nii format
ruida@NIH.GOV [Tue, 9 Jan 2018 17:40:17 +0000 (17:40 +0000)]
Convert NIH prostate data to nii format

git-svn-id: https://citdcbmipav.cit.nih.gov/repos-pub/mipav/trunk@15337 ba61647d-9d00-f842-95cd-605cb4296b96

15 months agoPorting continues.
ilb@NIH.GOV [Mon, 8 Jan 2018 23:15:06 +0000 (23:15 +0000)]
Porting continues.

git-svn-id: https://citdcbmipav.cit.nih.gov/repos-pub/mipav/trunk@15336 ba61647d-9d00-f842-95cd-605cb4296b96

15 months agoPorting continues.
ilb@NIH.GOV [Fri, 5 Jan 2018 23:13:24 +0000 (23:13 +0000)]
Porting continues.

git-svn-id: https://citdcbmipav.cit.nih.gov/repos-pub/mipav/trunk@15335 ba61647d-9d00-f842-95cd-605cb4296b96

15 months agoSignificant updates to the transform GUI
mcmatt@NIH.GOV [Fri, 5 Jan 2018 13:31:54 +0000 (13:31 +0000)]
Significant updates to the transform GUI

git-svn-id: https://citdcbmipav.cit.nih.gov/repos-pub/mipav/trunk@15334 ba61647d-9d00-f842-95cd-605cb4296b96

15 months agoPorting continues.
ilb@NIH.GOV [Thu, 4 Jan 2018 23:12:55 +0000 (23:12 +0000)]
Porting continues.

git-svn-id: https://citdcbmipav.cit.nih.gov/repos-pub/mipav/trunk@15333 ba61647d-9d00-f842-95cd-605cb4296b96

15 months agoPorting continues.
ilb@NIH.GOV [Wed, 3 Jan 2018 23:20:22 +0000 (23:20 +0000)]
Porting continues.

git-svn-id: https://citdcbmipav.cit.nih.gov/repos-pub/mipav/trunk@15332 ba61647d-9d00-f842-95cd-605cb4296b96

15 months agoPorting continues.
ilb@NIH.GOV [Tue, 2 Jan 2018 23:12:29 +0000 (23:12 +0000)]
Porting continues.

git-svn-id: https://citdcbmipav.cit.nih.gov/repos-pub/mipav/trunk@15331 ba61647d-9d00-f842-95cd-605cb4296b96

15 months agoFinished saving mapping file to CSV
mcmatt@NIH.GOV [Sun, 31 Dec 2017 14:14:00 +0000 (14:14 +0000)]
Finished saving mapping file to CSV

git-svn-id: https://citdcbmipav.cit.nih.gov/repos-pub/mipav/trunk@15330 ba61647d-9d00-f842-95cd-605cb4296b96

15 months agoPorting continues.
ilb@NIH.GOV [Fri, 29 Dec 2017 23:27:08 +0000 (23:27 +0000)]
Porting continues.

git-svn-id: https://citdcbmipav.cit.nih.gov/repos-pub/mipav/trunk@15329 ba61647d-9d00-f842-95cd-605cb4296b96

15 months agopreparing to saving mapping file
mcmatt@NIH.GOV [Fri, 29 Dec 2017 14:17:56 +0000 (14:17 +0000)]
preparing to saving mapping file

git-svn-id: https://citdcbmipav.cit.nih.gov/repos-pub/mipav/trunk@15328 ba61647d-9d00-f842-95cd-605cb4296b96

15 months agoPorting continues.
ilb@NIH.GOV [Thu, 28 Dec 2017 23:23:11 +0000 (23:23 +0000)]
Porting continues.

git-svn-id: https://citdcbmipav.cit.nih.gov/repos-pub/mipav/trunk@15327 ba61647d-9d00-f842-95cd-605cb4296b96

15 months agoPorting continues.
ilb@NIH.GOV [Wed, 27 Dec 2017 22:22:25 +0000 (22:22 +0000)]
Porting continues.

git-svn-id: https://citdcbmipav.cit.nih.gov/repos-pub/mipav/trunk@15326 ba61647d-9d00-f842-95cd-605cb4296b96

15 months agoComments through 1926
mcmatt@NIH.GOV [Wed, 27 Dec 2017 14:28:01 +0000 (14:28 +0000)]
Comments through 1926

git-svn-id: https://citdcbmipav.cit.nih.gov/repos-pub/mipav/trunk@15325 ba61647d-9d00-f842-95cd-605cb4296b96

15 months agoPorting continues.
ilb@NIH.GOV [Tue, 26 Dec 2017 22:21:23 +0000 (22:21 +0000)]
Porting continues.

git-svn-id: https://citdcbmipav.cit.nih.gov/repos-pub/mipav/trunk@15324 ba61647d-9d00-f842-95cd-605cb4296b96

15 months agoCommented through line 1230
mcmatt@NIH.GOV [Tue, 26 Dec 2017 15:27:24 +0000 (15:27 +0000)]
Commented through line 1230

git-svn-id: https://citdcbmipav.cit.nih.gov/repos-pub/mipav/trunk@15323 ba61647d-9d00-f842-95cd-605cb4296b96

15 months agoUpdated row widths
mcmatt@NIH.GOV [Sun, 24 Dec 2017 16:58:48 +0000 (16:58 +0000)]
Updated row widths

git-svn-id: https://citdcbmipav.cit.nih.gov/repos-pub/mipav/trunk@15322 ba61647d-9d00-f842-95cd-605cb4296b96

15 months agoMore updates to the PV Mappings editor
mcmatt@NIH.GOV [Sun, 24 Dec 2017 16:52:01 +0000 (16:52 +0000)]
More updates to the PV Mappings editor

git-svn-id: https://citdcbmipav.cit.nih.gov/repos-pub/mipav/trunk@15321 ba61647d-9d00-f842-95cd-605cb4296b96

15 months agoPorting continues.
ilb@NIH.GOV [Fri, 22 Dec 2017 23:12:14 +0000 (23:12 +0000)]
Porting continues.

git-svn-id: https://citdcbmipav.cit.nih.gov/repos-pub/mipav/trunk@15320 ba61647d-9d00-f842-95cd-605cb4296b96

16 months agoUpdates to the Mapping PVs column
mcmatt@NIH.GOV [Thu, 21 Dec 2017 22:13:16 +0000 (22:13 +0000)]
Updates to the Mapping PVs column

git-svn-id: https://citdcbmipav.cit.nih.gov/repos-pub/mipav/trunk@15319 ba61647d-9d00-f842-95cd-605cb4296b96

16 months agoPorting continues.
ilb@NIH.GOV [Thu, 21 Dec 2017 21:58:34 +0000 (21:58 +0000)]
Porting continues.

git-svn-id: https://citdcbmipav.cit.nih.gov/repos-pub/mipav/trunk@15318 ba61647d-9d00-f842-95cd-605cb4296b96

16 months agoSignificant updates to the mapping tool.
mcmatt@NIH.GOV [Wed, 20 Dec 2017 23:33:01 +0000 (23:33 +0000)]
Significant updates to the mapping tool.

git-svn-id: https://citdcbmipav.cit.nih.gov/repos-pub/mipav/trunk@15317 ba61647d-9d00-f842-95cd-605cb4296b96

16 months agoPorting continues.
ilb@NIH.GOV [Wed, 20 Dec 2017 23:21:28 +0000 (23:21 +0000)]
Porting continues.

git-svn-id: https://citdcbmipav.cit.nih.gov/repos-pub/mipav/trunk@15316 ba61647d-9d00-f842-95cd-605cb4296b96

16 months agoconvert miccai promise 12 data from mgh to nii.gz
ruida@NIH.GOV [Wed, 20 Dec 2017 22:38:41 +0000 (22:38 +0000)]
convert miccai promise 12 data from mgh to nii.gz

git-svn-id: https://citdcbmipav.cit.nih.gov/repos-pub/mipav/trunk@15315 ba61647d-9d00-f842-95cd-605cb4296b96

16 months agoPorting continues.
ilb@NIH.GOV [Tue, 19 Dec 2017 23:12:00 +0000 (23:12 +0000)]
Porting continues.

git-svn-id: https://citdcbmipav.cit.nih.gov/repos-pub/mipav/trunk@15314 ba61647d-9d00-f842-95cd-605cb4296b96

16 months agoPorting continues.
ilb@NIH.GOV [Mon, 18 Dec 2017 23:16:36 +0000 (23:16 +0000)]
Porting continues.

git-svn-id: https://citdcbmipav.cit.nih.gov/repos-pub/mipav/trunk@15313 ba61647d-9d00-f842-95cd-605cb4296b96

16 months agoPorting continues.
ilb@NIH.GOV [Fri, 15 Dec 2017 23:17:23 +0000 (23:17 +0000)]
Porting continues.

git-svn-id: https://citdcbmipav.cit.nih.gov/repos-pub/mipav/trunk@15312 ba61647d-9d00-f842-95cd-605cb4296b96

16 months agoWork started.
ilb@NIH.GOV [Thu, 14 Dec 2017 23:17:44 +0000 (23:17 +0000)]
Work started.

git-svn-id: https://citdcbmipav.cit.nih.gov/repos-pub/mipav/trunk@15311 ba61647d-9d00-f842-95cd-605cb4296b96

16 months agofix a typo for imageOrientation calling
ruida@NIH.GOV [Tue, 12 Dec 2017 22:08:53 +0000 (22:08 +0000)]
fix a typo for imageOrientation calling

git-svn-id: https://citdcbmipav.cit.nih.gov/repos-pub/mipav/trunk@15310 ba61647d-9d00-f842-95cd-605cb4296b96

16 months agoComments corrected.
ilb@NIH.GOV [Tue, 12 Dec 2017 21:30:56 +0000 (21:30 +0000)]
Comments corrected.

git-svn-id: https://citdcbmipav.cit.nih.gov/repos-pub/mipav/trunk@15309 ba61647d-9d00-f842-95cd-605cb4296b96

16 months agoplot routine added.
ilb@NIH.GOV [Tue, 12 Dec 2017 19:44:22 +0000 (19:44 +0000)]
plot routine added.

git-svn-id: https://citdcbmipav.cit.nih.gov/repos-pub/mipav/trunk@15308 ba61647d-9d00-f842-95cd-605cb4296b96

16 months agoCorrected placement of tolLabel and tolText and modified requireLabel2.
ilb@NIH.GOV [Mon, 11 Dec 2017 22:07:10 +0000 (22:07 +0000)]
Corrected placement of tolLabel and tolText and modified requireLabel2.

git-svn-id: https://citdcbmipav.cit.nih.gov/repos-pub/mipav/trunk@15307 ba61647d-9d00-f842-95cd-605cb4296b96

16 months agoAdded else if (command.equals("PolygonsToAnnulus")) {
ilb@NIH.GOV [Mon, 11 Dec 2017 21:35:42 +0000 (21:35 +0000)]
Added else if (command.equals("PolygonsToAnnulus")) {
    new JDialogDoublyConnectedSC(this, getActiveImage());

git-svn-id: https://citdcbmipav.cit.nih.gov/repos-pub/mipav/trunk@15306 ba61647d-9d00-f842-95cd-605cb4296b96

16 months agoAdded Between 2 polygons to annulus to Transformations tools menu.
ilb@NIH.GOV [Mon, 11 Dec 2017 21:32:42 +0000 (21:32 +0000)]
Added Between 2 polygons to annulus to Transformations tools menu.

git-svn-id: https://citdcbmipav.cit.nih.gov/repos-pub/mipav/trunk@15305 ba61647d-9d00-f842-95cd-605cb4296b96

16 months agoDialog created.
ilb@NIH.GOV [Mon, 11 Dec 2017 21:25:42 +0000 (21:25 +0000)]
Dialog created.

git-svn-id: https://citdcbmipav.cit.nih.gov/repos-pub/mipav/trunk@15304 ba61647d-9d00-f842-95cd-605cb4296b96

16 months agoEntered interface of mapping to MIPAV image in runAlgorithm.
ilb@NIH.GOV [Fri, 8 Dec 2017 22:58:17 +0000 (22:58 +0000)]
Entered interface of mapping to MIPAV image in runAlgorithm.

git-svn-id: https://citdcbmipav.cit.nih.gov/repos-pub/mipav/trunk@15303 ba61647d-9d00-f842-95cd-605cb4296b96

16 months agoIn runPolygonToCircle reduced size of zp put into dmap, in runCrossRatioPolygonToCirc...
ilb@NIH.GOV [Fri, 8 Dec 2017 22:43:06 +0000 (22:43 +0000)]
In runPolygonToCircle reduced size of zp put into dmap, in runCrossRatioPolygonToCircle reduced size of zp put into crmap, and in runPolygonExteriorToCircle reduced size of zp put into demap.

git-svn-id: https://citdcbmipav.cit.nih.gov/repos-pub/mipav/trunk@15302 ba61647d-9d00-f842-95cd-605cb4296b96

16 months agoSuccessful run on ninth test example.
ilb@NIH.GOV [Fri, 8 Dec 2017 20:11:53 +0000 (20:11 +0000)]
Successful run on ninth test example.

git-svn-id: https://citdcbmipav.cit.nih.gov/repos-pub/mipav/trunk@15301 ba61647d-9d00-f842-95cd-605cb4296b96

16 months agoSpelling correction.
ilb@NIH.GOV [Fri, 8 Dec 2017 19:31:10 +0000 (19:31 +0000)]
Spelling correction.

git-svn-id: https://citdcbmipav.cit.nih.gov/repos-pub/mipav/trunk@15300 ba61647d-9d00-f842-95cd-605cb4296b96

16 months agoEighth added test example works.
ilb@NIH.GOV [Fri, 8 Dec 2017 19:27:43 +0000 (19:27 +0000)]
Eighth added test example works.

git-svn-id: https://citdcbmipav.cit.nih.gov/repos-pub/mipav/trunk@15299 ba61647d-9d00-f842-95cd-605cb4296b96

16 months agoIn DSCDATA for IPOLY == 3 changed Z1[5][0] = 2.0 to Z1[5][1] = 2.0. All 7 examples...
ilb@NIH.GOV [Thu, 7 Dec 2017 22:49:29 +0000 (22:49 +0000)]
In DSCDATA for IPOLY == 3 changed Z1[5][0] = 2.0 to Z1[5][1] = 2.0.  All 7 examples now work.  For example 3 listed results agree with MIPAV results, maximum error = 8.06E-7, minimum error = 1.405E-8 even though INFO[0] = 5, unsuccessful exit.

git-svn-id: https://citdcbmipav.cit.nih.gov/repos-pub/mipav/trunk@15298 ba61647d-9d00-f842-95cd-605cb4296b96

16 months agoCorrected looping in IMTQL2. 6 of the 7 examples give good results. Example
ilb@NIH.GOV [Thu, 7 Dec 2017 22:13:56 +0000 (22:13 +0000)]
Corrected looping in IMTQL2.  6 of the 7 examples give good results.  Example
#3, A Heavily Crowded Region gives INFO[0] = 4, unsuccessful exit.

git-svn-id: https://citdcbmipav.cit.nih.gov/repos-pub/mipav/trunk@15297 ba61647d-9d00-f842-95cd-605cb4296b96