mipav.git
13 months agoCorrected CVodeSensFree.
ilb@NIH.GOV [Mon, 19 Mar 2018 15:09:19 +0000 (15:09 +0000)]
Corrected CVodeSensFree.

git-svn-id: https://citdcbmipav.cit.nih.gov/repos-pub/mipav/trunk@15419 ba61647d-9d00-f842-95cd-605cb4296b96

13 months agoFor cvsRoberts_FSA_dns, sensi_meth = CV_SIMULTANEOUS, err_con = true, solutions and...
ilb@NIH.GOV [Fri, 16 Mar 2018 22:15:25 +0000 (22:15 +0000)]
For cvsRoberts_FSA_dns, sensi_meth = CV_SIMULTANEOUS, err_con = true, solutions and sensitivities match the examples manual for t = 0.4, 4.0, 40.0, 4.0E2, 4.0E3, 4.0E4, and 4.0E5.  At 4.0E6 the solutions are still correct but the sensitivities blow up to ridiculously large values and we see the error message: In module CVODES in function CVodeAt t = 1.2548638616460832E7 and h = 4.797483802250223E-4, the corrector convergence test failed repeatedly or with |h| = hmin.

git-svn-id: https://citdcbmipav.cit.nih.gov/repos-pub/mipav/trunk@15418 ba61647d-9d00-f842-95cd-605cb4296b96

13 months agoPorting continues.
ilb@NIH.GOV [Thu, 15 Mar 2018 21:13:35 +0000 (21:13 +0000)]
Porting continues.

git-svn-id: https://citdcbmipav.cit.nih.gov/repos-pub/mipav/trunk@15417 ba61647d-9d00-f842-95cd-605cb4296b96

13 months agoWorking on cvsRoberts_FSA_dns.
ilb@NIH.GOV [Wed, 14 Mar 2018 21:52:41 +0000 (21:52 +0000)]
Working on cvsRoberts_FSA_dns.

git-svn-id: https://citdcbmipav.cit.nih.gov/repos-pub/mipav/trunk@15416 ba61647d-9d00-f842-95cd-605cb4296b96

13 months agoExample cvsRoberts_dns_uw works. Added capability for user supplied ewt function...
ilb@NIH.GOV [Wed, 14 Mar 2018 18:59:59 +0000 (18:59 +0000)]
Example cvsRoberts_dns_uw works.  Added capability for user supplied ewt function to compute error weights.

git-svn-id: https://citdcbmipav.cit.nih.gov/repos-pub/mipav/trunk@15415 ba61647d-9d00-f842-95cd-605cb4296b96

13 months agoAdded a registration using thin-plate splines to retwisting so the user can retwist...
abokinsky [Wed, 14 Mar 2018 15:12:06 +0000 (15:12 +0000)]
Added a registration using thin-plate splines to retwisting so the user can retwist one set of annotations into a different worm. The user specifies points for both images in the untwisted space which are used to calculate the registration, then the registered points are retwisted into the original, twisted target.

git-svn-id: https://citdcbmipav.cit.nih.gov/repos-pub/mipav/trunk@15414 ba61647d-9d00-f842-95cd-605cb4296b96

13 months agoDicom reader now calculates and sets z resolution values after sorting the files...
mccreedy@NIH.GOV [Tue, 13 Mar 2018 16:47:23 +0000 (16:47 +0000)]
Dicom reader now calculates and sets z resolution values after sorting the files according to the slice positions.  Before, the z res would be set based on the file name order, causing a problem if the files are out of order.

git-svn-id: https://citdcbmipav.cit.nih.gov/repos-pub/mipav/trunk@15413 ba61647d-9d00-f842-95cd-605cb4296b96

13 months agoNow call cvDlsDenseDQJac if a difference quotient Jacobian is used instead of a user...
ilb@NIH.GOV [Mon, 12 Mar 2018 20:45:20 +0000 (20:45 +0000)]
Now call cvDlsDenseDQJac if a difference quotient Jacobian is used instead of a user supplied Jacobian.  The part of problem 1 from cvsDirectDemo_ls that has been typed in is working.

git-svn-id: https://citdcbmipav.cit.nih.gov/repos-pub/mipav/trunk@15412 ba61647d-9d00-f842-95cd-605cb4296b96

13 months agoPorting continues.
ilb@NIH.GOV [Fri, 9 Mar 2018 23:30:12 +0000 (23:30 +0000)]
Porting continues.

git-svn-id: https://citdcbmipav.cit.nih.gov/repos-pub/mipav/trunk@15411 ba61647d-9d00-f842-95cd-605cb4296b96

13 months agoAdded TRACEW imageType to DWI sorting. Added step to remove the first N slices ...
mccreedy@NIH.GOV [Fri, 9 Mar 2018 20:55:13 +0000 (20:55 +0000)]
Added TRACEW imageType to DWI sorting.  Added step to remove the first N slices (default 7) from the ADC threshold mask, so that the cerebellum areas present fewer false positives.

git-svn-id: https://citdcbmipav.cit.nih.gov/repos-pub/mipav/trunk@15410 ba61647d-9d00-f842-95cd-605cb4296b96

13 months agoAdded public abstract f, fQ, g, and Jac for external calls. Use fTestMode, fQTestMod...
ilb@NIH.GOV [Fri, 9 Mar 2018 17:19:04 +0000 (17:19 +0000)]
Added public abstract f, fQ, g, and Jac for external calls.  Use fTestMode, fQTestMode, gTestMode, and JacTestMode when internal testMode is true.

git-svn-id: https://citdcbmipav.cit.nih.gov/repos-pub/mipav/trunk@15409 ba61647d-9d00-f842-95cd-605cb4296b96

13 months agoBy reducing tolerances cvsRoberts_dns now agrees with manual for every decade from...
ilb@NIH.GOV [Thu, 8 Mar 2018 22:55:07 +0000 (22:55 +0000)]
By reducing tolerances cvsRoberts_dns now agrees with manual for every decade from t = 0.4 to t = 4.0E8.  At t = 4.0E9 disagreement with manual appears.  This successfully solves a stiff problem using BDF method and Newton iteration.

git-svn-id: https://citdcbmipav.cit.nih.gov/repos-pub/mipav/trunk@15408 ba61647d-9d00-f842-95cd-605cb4296b96

13 months agoTry converting any MM/DD/YYYY values in date fields to ISO standard before writing...
mccreedy@NIH.GOV [Thu, 8 Mar 2018 21:40:49 +0000 (21:40 +0000)]
Try converting any MM/DD/YYYY values in date fields to ISO standard before writing to CSV.

git-svn-id: https://citdcbmipav.cit.nih.gov/repos-pub/mipav/trunk@15407 ba61647d-9d00-f842-95cd-605cb4296b96

13 months agoAdded clipping to annotating volumes for worm untwisting.
abokinsky [Thu, 8 Mar 2018 21:30:17 +0000 (21:30 +0000)]
Added clipping to annotating volumes for worm untwisting.

git-svn-id: https://citdcbmipav.cit.nih.gov/repos-pub/mipav/trunk@15406 ba61647d-9d00-f842-95cd-605cb4296b96

13 months agoDisabled remembering of previous run's dir/files at Marie's request. Directory selec...
mccreedy@NIH.GOV [Thu, 8 Mar 2018 18:27:12 +0000 (18:27 +0000)]
Disabled remembering of previous run's dir/files at Marie's request.  Directory selection will now recursively search for DICOM files and sort them as DWI and ADC based on the values in tag 0008,0008 - Image type.

git-svn-id: https://citdcbmipav.cit.nih.gov/repos-pub/mipav/trunk@15405 ba61647d-9d00-f842-95cd-605cb4296b96

13 months agoAuto-add extension to files without them when not zipping them up for upload. Added...
mccreedy@NIH.GOV [Wed, 7 Mar 2018 21:57:14 +0000 (21:57 +0000)]
Auto-add extension to files without them when not zipping them up for upload.  Added more modalities to auto-modality determination based on form.  Changed default image browser file filter to show all files, not Medical/preferred filter.

git-svn-id: https://citdcbmipav.cit.nih.gov/repos-pub/mipav/trunk@15404 ba61647d-9d00-f842-95cd-605cb4296b96

13 months agoNo longer remove characters after end of digits.
ilb@NIH.GOV [Wed, 7 Mar 2018 21:42:46 +0000 (21:42 +0000)]
No longer remove characters after end of digits.

git-svn-id: https://citdcbmipav.cit.nih.gov/repos-pub/mipav/trunk@15403 ba61647d-9d00-f842-95cd-605cb4296b96

13 months agoAdded bounds checking.
abokinsky [Wed, 7 Mar 2018 21:39:18 +0000 (21:39 +0000)]
Added bounds checking.

git-svn-id: https://citdcbmipav.cit.nih.gov/repos-pub/mipav/trunk@15402 ba61647d-9d00-f842-95cd-605cb4296b96

13 months agoNeed to debug so cvsRoberts_dns example gives the correct answer.
ilb@NIH.GOV [Tue, 6 Mar 2018 22:49:43 +0000 (22:49 +0000)]
Need to debug so cvsRoberts_dns example gives the correct answer.

git-svn-id: https://citdcbmipav.cit.nih.gov/repos-pub/mipav/trunk@15401 ba61647d-9d00-f842-95cd-605cb4296b96

13 months agoPrototype straight->twisted takes a file of annotations in the straightened space...
abokinsky [Tue, 6 Mar 2018 21:23:18 +0000 (21:23 +0000)]
Prototype straight->twisted takes a file of annotations in the straightened space (.csv) and retwists the annotations into the target space.

git-svn-id: https://citdcbmipav.cit.nih.gov/repos-pub/mipav/trunk@15400 ba61647d-9d00-f842-95cd-605cb4296b96

13 months agoAdded clipping outer layers to the interface for selecting points in the volume so...
abokinsky [Tue, 6 Mar 2018 14:53:08 +0000 (14:53 +0000)]
Added clipping outer layers to the interface for selecting points in the volume so when the volume is clipped the user can only select point inside the visible area.

git-svn-id: https://citdcbmipav.cit.nih.gov/repos-pub/mipav/trunk@15399 ba61647d-9d00-f842-95cd-605cb4296b96

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