mipav.git
10 months agoPorting continues. svn/trunk
ilb@NIH.GOV [Wed, 25 Apr 2018 22:16:51 +0000 (22:16 +0000)]
Porting continues.

git-svn-id: https://citdcbmipav.cit.nih.gov/repos-pub/mipav/trunk@15459 ba61647d-9d00-f842-95cd-605cb4296b96

10 months agoFixed interaction bug with the automatic seam cells generated from the lattice.
abokinsky [Wed, 25 Apr 2018 00:09:52 +0000 (00:09 +0000)]
Fixed interaction bug with the automatic seam cells generated from the lattice.

git-svn-id: https://citdcbmipav.cit.nih.gov/repos-pub/mipav/trunk@15458 ba61647d-9d00-f842-95cd-605cb4296b96

10 months agoPorting continues.
ilb@NIH.GOV [Tue, 24 Apr 2018 20:44:42 +0000 (20:44 +0000)]
Porting continues.

git-svn-id: https://citdcbmipav.cit.nih.gov/repos-pub/mipav/trunk@15457 ba61647d-9d00-f842-95cd-605cb4296b96

10 months agoPorting continues.
ilb@NIH.GOV [Mon, 23 Apr 2018 22:15:34 +0000 (22:15 +0000)]
Porting continues.

git-svn-id: https://citdcbmipav.cit.nih.gov/repos-pub/mipav/trunk@15456 ba61647d-9d00-f842-95cd-605cb4296b96

10 months agoAdded automatic naming of seam cells based on the lattice and the 488 marker.
abokinsky [Mon, 23 Apr 2018 17:52:49 +0000 (17:52 +0000)]
Added automatic naming of seam cells based on the lattice and the 488 marker.

git-svn-id: https://citdcbmipav.cit.nih.gov/repos-pub/mipav/trunk@15455 ba61647d-9d00-f842-95cd-605cb4296b96

11 months agoPorting continues.
ilb@NIH.GOV [Thu, 19 Apr 2018 20:54:10 +0000 (20:54 +0000)]
Porting continues.

git-svn-id: https://citdcbmipav.cit.nih.gov/repos-pub/mipav/trunk@15454 ba61647d-9d00-f842-95cd-605cb4296b96

11 months agoPorting continues.
ilb@NIH.GOV [Wed, 18 Apr 2018 21:29:51 +0000 (21:29 +0000)]
Porting continues.

git-svn-id: https://citdcbmipav.cit.nih.gov/repos-pub/mipav/trunk@15453 ba61647d-9d00-f842-95cd-605cb4296b96

11 months agoStarted work on.
ilb@NIH.GOV [Tue, 17 Apr 2018 22:13:54 +0000 (22:13 +0000)]
Started work on.

git-svn-id: https://citdcbmipav.cit.nih.gov/repos-pub/mipav/trunk@15452 ba61647d-9d00-f842-95cd-605cb4296b96

11 months agoFixed bug in annotation animation with spreadsheets.
abokinsky [Tue, 17 Apr 2018 15:53:56 +0000 (15:53 +0000)]
Fixed bug in annotation animation with spreadsheets.

git-svn-id: https://citdcbmipav.cit.nih.gov/repos-pub/mipav/trunk@15451 ba61647d-9d00-f842-95cd-605cb4296b96

11 months agoSpelling corrected.
ilb@NIH.GOV [Wed, 11 Apr 2018 16:47:45 +0000 (16:47 +0000)]
Spelling corrected.

git-svn-id: https://citdcbmipav.cit.nih.gov/repos-pub/mipav/trunk@15450 ba61647d-9d00-f842-95cd-605cb4296b96

11 months agoSpellihg correction.
ilb@NIH.GOV [Wed, 11 Apr 2018 16:30:25 +0000 (16:30 +0000)]
Spellihg correction.

git-svn-id: https://citdcbmipav.cit.nih.gov/repos-pub/mipav/trunk@15449 ba61647d-9d00-f842-95cd-605cb4296b96

11 months agoCompleted runcvsAdvDiff_FSA_non().
ilb@NIH.GOV [Fri, 6 Apr 2018 21:35:55 +0000 (21:35 +0000)]
Completed runcvsAdvDiff_FSA_non().

git-svn-id: https://citdcbmipav.cit.nih.gov/repos-pub/mipav/trunk@15448 ba61647d-9d00-f842-95cd-605cb4296b96

11 months agoCompleted runcvsAdvDiff_FSA_non().
ilb@NIH.GOV [Fri, 6 Apr 2018 21:35:38 +0000 (21:35 +0000)]
Completed runcvsAdvDiff_FSA_non().

git-svn-id: https://citdcbmipav.cit.nih.gov/repos-pub/mipav/trunk@15447 ba61647d-9d00-f842-95cd-605cb4296b96

11 months agoRemoved unused code in fBTestMode.
ilb@NIH.GOV [Fri, 6 Apr 2018 18:08:24 +0000 (18:08 +0000)]
Removed unused code in fBTestMode.

git-svn-id: https://citdcbmipav.cit.nih.gov/repos-pub/mipav/trunk@15446 ba61647d-9d00-f842-95cd-605cb4296b96

11 months agoCompleted runcvsRoberts_ASAi_dns(). In CVodeB added
ilb@NIH.GOV [Fri, 6 Apr 2018 18:03:48 +0000 (18:03 +0000)]
Completed runcvsRoberts_ASAi_dns().  In CVodeB added
CVodeSetMaxNumSteps(tmp_cvB_mem.cv_mem, -1) for unlimited integration steps before call to CVode.  Changed TOUT = 4.0E7 and TB1 = 4.0E7 to TOUT = 4.0E4 and TB1 = 4.0E4 so problem runs in a reasonable amount of time.

git-svn-id: https://citdcbmipav.cit.nih.gov/repos-pub/mipav/trunk@15445 ba61647d-9d00-f842-95cd-605cb4296b96

11 months agoCompleted runcvsRoberts_ASAi_dns().
ilb@NIH.GOV [Fri, 6 Apr 2018 18:00:16 +0000 (18:00 +0000)]
Completed runcvsRoberts_ASAi_dns().

git-svn-id: https://citdcbmipav.cit.nih.gov/repos-pub/mipav/trunk@15444 ba61647d-9d00-f842-95cd-605cb4296b96

11 months agoPorting continues.
ilb@NIH.GOV [Thu, 5 Apr 2018 22:17:48 +0000 (22:17 +0000)]
Porting continues.

git-svn-id: https://citdcbmipav.cit.nih.gov/repos-pub/mipav/trunk@15443 ba61647d-9d00-f842-95cd-605cb4296b96

11 months agoPorting continues.
ilb@NIH.GOV [Wed, 4 Apr 2018 22:10:24 +0000 (22:10 +0000)]
Porting continues.

git-svn-id: https://citdcbmipav.cit.nih.gov/repos-pub/mipav/trunk@15442 ba61647d-9d00-f842-95cd-605cb4296b96

11 months agoPorting continues.
ilb@NIH.GOV [Wed, 4 Apr 2018 22:10:05 +0000 (22:10 +0000)]
Porting continues.

git-svn-id: https://citdcbmipav.cit.nih.gov/repos-pub/mipav/trunk@15441 ba61647d-9d00-f842-95cd-605cb4296b96

11 months agoAdded automatic name matching of the landmark registration points for the thin-plate...
abokinsky [Wed, 4 Apr 2018 16:16:54 +0000 (16:16 +0000)]
Added automatic name matching of the landmark registration points for the thin-plate spline calculation.

git-svn-id: https://citdcbmipav.cit.nih.gov/repos-pub/mipav/trunk@15440 ba61647d-9d00-f842-95cd-605cb4296b96

11 months agoAdded automatic name matching of the landmark registration points for the thin-plate...
abokinsky [Wed, 4 Apr 2018 15:46:50 +0000 (15:46 +0000)]
Added automatic name matching of the landmark registration points for the thin-plate spline calculation.

git-svn-id: https://citdcbmipav.cit.nih.gov/repos-pub/mipav/trunk@15439 ba61647d-9d00-f842-95cd-605cb4296b96

11 months agoPorting continues.
ilb@NIH.GOV [Tue, 3 Apr 2018 22:15:13 +0000 (22:15 +0000)]
Porting continues.

git-svn-id: https://citdcbmipav.cit.nih.gov/repos-pub/mipav/trunk@15438 ba61647d-9d00-f842-95cd-605cb4296b96

11 months agoPorting continues.
ilb@NIH.GOV [Tue, 3 Apr 2018 22:14:57 +0000 (22:14 +0000)]
Porting continues.

git-svn-id: https://citdcbmipav.cit.nih.gov/repos-pub/mipav/trunk@15437 ba61647d-9d00-f842-95cd-605cb4296b96

11 months agoCreated for running runcvsRoberts_ASAi_dns().
ilb@NIH.GOV [Tue, 3 Apr 2018 18:25:16 +0000 (18:25 +0000)]
Created for running runcvsRoberts_ASAi_dns().

git-svn-id: https://citdcbmipav.cit.nih.gov/repos-pub/mipav/trunk@15436 ba61647d-9d00-f842-95cd-605cb4296b96

11 months agoCVODES split int CVODES and CVODES_ASA for running runcvsRoberts_ASAi_dns().
ilb@NIH.GOV [Tue, 3 Apr 2018 18:24:33 +0000 (18:24 +0000)]
CVODES split int CVODES and CVODES_ASA for running runcvsRoberts_ASAi_dns().

git-svn-id: https://citdcbmipav.cit.nih.gov/repos-pub/mipav/trunk@15435 ba61647d-9d00-f842-95cd-605cb4296b96

11 months agoFile becoming too large. Must put runCVSRoberts_ASAi_dns() in a second file if work...
ilb@NIH.GOV [Mon, 2 Apr 2018 21:27:26 +0000 (21:27 +0000)]
File becoming too large.  Must put runCVSRoberts_ASAi_dns() in a second file if work is to continue.

git-svn-id: https://citdcbmipav.cit.nih.gov/repos-pub/mipav/trunk@15434 ba61647d-9d00-f842-95cd-605cb4296b96

11 months agoStarted work on cvsRoberts_ASAi_dns.
ilb@NIH.GOV [Fri, 30 Mar 2018 22:16:06 +0000 (22:16 +0000)]
Started work on cvsRoberts_ASAi_dns.

git-svn-id: https://citdcbmipav.cit.nih.gov/repos-pub/mipav/trunk@15433 ba61647d-9d00-f842-95cd-605cb4296b96

11 months agocvsRoberts_dnsL example added which uses LAPACK dgetrf and dgetrs instead of denseGET...
ilb@NIH.GOV [Wed, 28 Mar 2018 18:54:25 +0000 (18:54 +0000)]
cvsRoberts_dnsL example added which uses LAPACK dgetrf and dgetrs instead of denseGETRF and denseGETRS.  The version using LAPACK calls is far slower.

git-svn-id: https://citdcbmipav.cit.nih.gov/repos-pub/mipav/trunk@15432 ba61647d-9d00-f842-95cd-605cb4296b96

11 months agoAdded thin-plate spline registration for an input image to the worm retwisting so...
abokinsky [Mon, 26 Mar 2018 21:02:19 +0000 (21:02 +0000)]
Added thin-plate spline registration for an input image to the worm retwisting so the user can view the registered image.

git-svn-id: https://citdcbmipav.cit.nih.gov/repos-pub/mipav/trunk@15431 ba61647d-9d00-f842-95cd-605cb4296b96

11 months agoChanged core seg lightbox to be on the ADC image. Tweaks to report based on Marie...
mccreedy@NIH.GOV [Fri, 23 Mar 2018 16:19:50 +0000 (16:19 +0000)]
Changed core seg lightbox to be on the ADC image.  Tweaks to report based on Marie's feedback.  Added additional error checking on config load.

git-svn-id: https://citdcbmipav.cit.nih.gov/repos-pub/mipav/trunk@15430 ba61647d-9d00-f842-95cd-605cb4296b96

11 months agoFixed report file generation on disk. Changed seg dialog to be a frame so that it...
mccreedy@NIH.GOV [Thu, 22 Mar 2018 20:59:41 +0000 (20:59 +0000)]
Fixed report file generation on disk.  Changed seg dialog to be a frame so that it shows up in the toolbar when run standalone.  Moved scripting param config to properties file (with same defaults).

git-svn-id: https://citdcbmipav.cit.nih.gov/repos-pub/mipav/trunk@15429 ba61647d-9d00-f842-95cd-605cb4296b96

11 months agoMoved email configuration for stroke listener plugin to separate prop file. Added...
mccreedy@NIH.GOV [Thu, 22 Mar 2018 19:53:08 +0000 (19:53 +0000)]
Moved email configuration for stroke listener plugin to separate prop file.  Added email checkbox to dialog.  Improved report formatting.

git-svn-id: https://citdcbmipav.cit.nih.gov/repos-pub/mipav/trunk@15428 ba61647d-9d00-f842-95cd-605cb4296b96

11 months agoExample report email prototype.
mccreedy@NIH.GOV [Wed, 21 Mar 2018 20:09:02 +0000 (20:09 +0000)]
Example report email prototype.

git-svn-id: https://citdcbmipav.cit.nih.gov/repos-pub/mipav/trunk@15427 ba61647d-9d00-f842-95cd-605cb4296b96

11 months agoChanged all usages of variables just named '_' to something else to be compatible...
mccreedy@NIH.GOV [Wed, 21 Mar 2018 18:30:07 +0000 (18:30 +0000)]
Changed all usages of variables just named '_' to something else to be compatible with Java 9.

git-svn-id: https://citdcbmipav.cit.nih.gov/repos-pub/mipav/trunk@15426 ba61647d-9d00-f842-95cd-605cb4296b96

11 months agoRemoved JAI jar, which was causing problems if loaded before our jj2k lib.
mccreedy@NIH.GOV [Wed, 21 Mar 2018 18:20:35 +0000 (18:20 +0000)]
Removed JAI jar, which was causing problems if loaded before our jj2k lib.

git-svn-id: https://citdcbmipav.cit.nih.gov/repos-pub/mipav/trunk@15425 ba61647d-9d00-f842-95cd-605cb4296b96

11 months agoCreated new plugin that listens for dicoms pushed to it, sorts them as adc/dwi, runs...
mccreedy@NIH.GOV [Wed, 21 Mar 2018 15:46:48 +0000 (15:46 +0000)]
Created new plugin that listens for dicoms pushed to it, sorts them as adc/dwi, runs the stroke segmentation plugin, and then generates a report on the segmentation.

git-svn-id: https://citdcbmipav.cit.nih.gov/repos-pub/mipav/trunk@15424 ba61647d-9d00-f842-95cd-605cb4296b96

11 months agoAdded dcm4che library for dicom communication in the stroke segmentation listener...
mccreedy@NIH.GOV [Wed, 21 Mar 2018 15:45:11 +0000 (15:45 +0000)]
Added dcm4che library for dicom communication in the stroke segmentation listener plugin.

git-svn-id: https://citdcbmipav.cit.nih.gov/repos-pub/mipav/trunk@15423 ba61647d-9d00-f842-95cd-605cb4296b96

11 months agoChanged a number of places that used indexOf(".") to extract the file extension inste...
mccreedy@NIH.GOV [Wed, 21 Mar 2018 15:38:21 +0000 (15:38 +0000)]
Changed a number of places that used indexOf(".") to extract the file extension instead of lastIndexOf(), which caused problems with files including multiple periods.  Added better Jimi/ImageIO writing support for single 2D images (instead of writing out to just the selected file name, the writer would add a "slice number" before the extension).

git-svn-id: https://citdcbmipav.cit.nih.gov/repos-pub/mipav/trunk@15422 ba61647d-9d00-f842-95cd-605cb4296b96

12 months agoIn CVodeCreate set cv_mem.cv_user_data = null.
ilb@NIH.GOV [Tue, 20 Mar 2018 22:14:19 +0000 (22:14 +0000)]
In CVodeCreate set cv_mem.cv_user_data = null.

git-svn-id: https://citdcbmipav.cit.nih.gov/repos-pub/mipav/trunk@15421 ba61647d-9d00-f842-95cd-605cb4296b96

12 months agoFixed threshold image for single images.
abokinsky [Mon, 19 Mar 2018 15:52:28 +0000 (15:52 +0000)]
Fixed threshold image for single images.

git-svn-id: https://citdcbmipav.cit.nih.gov/repos-pub/mipav/trunk@15420 ba61647d-9d00-f842-95cd-605cb4296b96

12 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

12 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

12 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

12 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

12 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

12 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

12 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

12 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

12 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

12 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

12 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

12 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

12 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

12 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

12 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

12 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

12 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

12 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

12 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

12 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

12 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

12 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

12 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

12 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

12 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

12 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

12 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

12 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

12 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

12 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

12 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

12 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

12 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

12 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

12 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

12 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

13 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

13 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

13 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

13 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

13 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

13 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

13 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

13 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

13 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

13 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

13 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

13 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

13 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

13 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

13 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

13 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

13 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

13 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

13 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

13 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

13 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

13 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

13 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

13 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