mipav.git
3 years agoCleaned up/refactored/commented code, fixed bug with switching between ModelImages... worm-untwisting-plugin-elife@13931
abokinsky [Fri, 6 Nov 2015 01:24:30 +0000 (01:24 +0000)]
Cleaned up/refactored/commented code, fixed bug with switching between ModelImages with different sizes in the volume renderer.

git-svn-id: https://citdcbmipav.cit.nih.gov/repos-pub/mipav/trunk/mipav@13931 ba61647d-9d00-f842-95cd-605cb4296b96

3 years agoIncreased panel and button widths.
ilb@NIH.GOV [Wed, 4 Nov 2015 15:48:39 +0000 (15:48 +0000)]
Increased panel and button widths.

git-svn-id: https://citdcbmipav.cit.nih.gov/repos-pub/mipav/trunk/mipav@13930 ba61647d-9d00-f842-95cd-605cb4296b96

3 years agoCorrected fireProgressStateChanged message.
ilb@NIH.GOV [Wed, 4 Nov 2015 15:38:34 +0000 (15:38 +0000)]
Corrected fireProgressStateChanged message.

git-svn-id: https://citdcbmipav.cit.nih.gov/repos-pub/mipav/trunk/mipav@13929 ba61647d-9d00-f842-95cd-605cb4296b96

3 years agoAllow scaleX and scaleY to go down to 0.01 instead of 0.5.
ilb@NIH.GOV [Mon, 2 Nov 2015 19:53:11 +0000 (19:53 +0000)]
Allow scaleX and scaleY to go down to 0.01 instead of 0.5.

git-svn-id: https://citdcbmipav.cit.nih.gov/repos-pub/mipav/trunk/mipav@13928 ba61647d-9d00-f842-95cd-605cb4296b96

3 years agoRemoved old versions of the worm straightening plugins.
abokinsky [Mon, 2 Nov 2015 16:41:47 +0000 (16:41 +0000)]
Removed old versions of the worm straightening plugins.

git-svn-id: https://citdcbmipav.cit.nih.gov/repos-pub/mipav/trunk/mipav@13927 ba61647d-9d00-f842-95cd-605cb4296b96

3 years agoCode corrected.
ilb@NIH.GOV [Fri, 30 Oct 2015 20:17:10 +0000 (20:17 +0000)]
Code corrected.

git-svn-id: https://citdcbmipav.cit.nih.gov/repos-pub/mipav/trunk/mipav@13926 ba61647d-9d00-f842-95cd-605cb4296b96

3 years agoDebugging code.
ilb@NIH.GOV [Thu, 29 Oct 2015 20:41:28 +0000 (20:41 +0000)]
Debugging code.

git-svn-id: https://citdcbmipav.cit.nih.gov/repos-pub/mipav/trunk/mipav@13925 ba61647d-9d00-f842-95cd-605cb4296b96

3 years agoCorrected dialog.
ilb@NIH.GOV [Thu, 29 Oct 2015 18:36:14 +0000 (18:36 +0000)]
Corrected dialog.

git-svn-id: https://citdcbmipav.cit.nih.gov/repos-pub/mipav/trunk/mipav@13924 ba61647d-9d00-f842-95cd-605cb4296b96

3 years agoFuzzy Connectedness added to Segmentation menu.
ilb@NIH.GOV [Thu, 29 Oct 2015 18:24:28 +0000 (18:24 +0000)]
Fuzzy Connectedness added to Segmentation menu.

git-svn-id: https://citdcbmipav.cit.nih.gov/repos-pub/mipav/trunk/mipav@13923 ba61647d-9d00-f842-95cd-605cb4296b96

3 years agoCall to JDialogFuzzyConnectednessSegmentation added.
ilb@NIH.GOV [Thu, 29 Oct 2015 18:23:50 +0000 (18:23 +0000)]
Call to JDialogFuzzyConnectednessSegmentation added.

git-svn-id: https://citdcbmipav.cit.nih.gov/repos-pub/mipav/trunk/mipav@13922 ba61647d-9d00-f842-95cd-605cb4296b96

3 years agoDialog connected.
ilb@NIH.GOV [Thu, 29 Oct 2015 18:16:14 +0000 (18:16 +0000)]
Dialog connected.

git-svn-id: https://citdcbmipav.cit.nih.gov/repos-pub/mipav/trunk/mipav@13921 ba61647d-9d00-f842-95cd-605cb4296b96

3 years agoCan now run both afc and irfc.
ilb@NIH.GOV [Thu, 29 Oct 2015 16:11:50 +0000 (16:11 +0000)]
Can now run both afc and irfc.

git-svn-id: https://citdcbmipav.cit.nih.gov/repos-pub/mipav/trunk/mipav@13920 ba61647d-9d00-f842-95cd-605cb4296b96

3 years agoChanged method to algorithm.
ilb@NIH.GOV [Thu, 29 Oct 2015 15:42:32 +0000 (15:42 +0000)]
Changed method to algorithm.

git-svn-id: https://citdcbmipav.cit.nih.gov/repos-pub/mipav/trunk/mipav@13919 ba61647d-9d00-f842-95cd-605cb4296b96

3 years agoFinished typing in.
ilb@NIH.GOV [Thu, 29 Oct 2015 15:26:24 +0000 (15:26 +0000)]
Finished typing in.

git-svn-id: https://citdcbmipav.cit.nih.gov/repos-pub/mipav/trunk/mipav@13918 ba61647d-9d00-f842-95cd-605cb4296b96

3 years agoPorting continues.
ilb@NIH.GOV [Wed, 28 Oct 2015 22:13:11 +0000 (22:13 +0000)]
Porting continues.

git-svn-id: https://citdcbmipav.cit.nih.gov/repos-pub/mipav/trunk/mipav@13917 ba61647d-9d00-f842-95cd-605cb4296b96

3 years agoAdd Esc key listener to the frame. User can press the Esc key to exit the full...
ruida@NIH.GOV [Wed, 28 Oct 2015 15:32:51 +0000 (15:32 +0000)]
Add Esc key listener to the frame.   User can press the Esc key to exit the full screen mode.    Current left mouse button click exit with system.exit(0) call.   Comment it out.

git-svn-id: https://citdcbmipav.cit.nih.gov/repos-pub/mipav/trunk/mipav@13916 ba61647d-9d00-f842-95cd-605cb4296b96

3 years agoMinor bug fixes.
abokinsky [Tue, 27 Oct 2015 21:48:51 +0000 (21:48 +0000)]
Minor bug fixes.

git-svn-id: https://citdcbmipav.cit.nih.gov/repos-pub/mipav/trunk/mipav@13915 ba61647d-9d00-f842-95cd-605cb4296b96

3 years agoStarted work on.
ilb@NIH.GOV [Tue, 27 Oct 2015 21:38:05 +0000 (21:38 +0000)]
Started work on.

git-svn-id: https://citdcbmipav.cit.nih.gov/repos-pub/mipav/trunk/mipav@13914 ba61647d-9d00-f842-95cd-605cb4296b96

3 years agoIn zunik calling argument int init changed to int init[].
ilb@NIH.GOV [Tue, 27 Oct 2015 16:42:27 +0000 (16:42 +0000)]
In zunik calling argument int init changed to int init[].

git-svn-id: https://citdcbmipav.cit.nih.gov/repos-pub/mipav/trunk/mipav@13913 ba61647d-9d00-f842-95cd-605cb4296b96

3 years agoaddScannerLabels no longer gives array index error for 2D image.
ilb@NIH.GOV [Tue, 27 Oct 2015 15:51:04 +0000 (15:51 +0000)]
addScannerLabels no longer gives array index error for 2D image.

git-svn-id: https://citdcbmipav.cit.nih.gov/repos-pub/mipav/trunk/mipav@13912 ba61647d-9d00-f842-95cd-605cb4296b96

3 years agoRemoved JComboBox String parameterization.
mccreedy@NIH.GOV [Mon, 26 Oct 2015 20:10:36 +0000 (20:10 +0000)]
Removed JComboBox String parameterization.

git-svn-id: https://citdcbmipav.cit.nih.gov/repos-pub/mipav/trunk/mipav@13911 ba61647d-9d00-f842-95cd-605cb4296b96

3 years agoWeb page source of downloaded code cited.
ilb@NIH.GOV [Mon, 26 Oct 2015 17:06:15 +0000 (17:06 +0000)]
Web page source of downloaded code cited.

git-svn-id: https://citdcbmipav.cit.nih.gov/repos-pub/mipav/trunk/mipav@13910 ba61647d-9d00-f842-95cd-605cb4296b96

3 years agogaussianAlgo.setRed(true), gaussianAlgo.setGreen(true), and gaussianAlgo(true) added...
ilb@NIH.GOV [Mon, 26 Oct 2015 16:55:21 +0000 (16:55 +0000)]
gaussianAlgo.setRed(true), gaussianAlgo.setGreen(true), and gaussianAlgo(true) added.  Now works.

git-svn-id: https://citdcbmipav.cit.nih.gov/repos-pub/mipav/trunk/mipav@13909 ba61647d-9d00-f842-95cd-605cb4296b96

3 years agoCorrected sigmas from new float[32] to new float[2].
ilb@NIH.GOV [Mon, 26 Oct 2015 15:06:28 +0000 (15:06 +0000)]
Corrected sigmas from new float[32] to new float[2].

git-svn-id: https://citdcbmipav.cit.nih.gov/repos-pub/mipav/trunk/mipav@13908 ba61647d-9d00-f842-95cd-605cb4296b96

3 years agoIn runAlgorithm corrected blue[index] to blue[comp].
ilb@NIH.GOV [Fri, 23 Oct 2015 20:33:22 +0000 (20:33 +0000)]
In runAlgorithm corrected blue[index] to blue[comp].

git-svn-id: https://citdcbmipav.cit.nih.gov/repos-pub/mipav/trunk/mipav@13907 ba61647d-9d00-f842-95cd-605cb4296b96

3 years agoGraph Based added to segmentation menu.
ilb@NIH.GOV [Fri, 23 Oct 2015 20:10:22 +0000 (20:10 +0000)]
Graph Based added to segmentation menu.

git-svn-id: https://citdcbmipav.cit.nih.gov/repos-pub/mipav/trunk/mipav@13906 ba61647d-9d00-f842-95cd-605cb4296b96

3 years agoFinished typing in.
ilb@NIH.GOV [Fri, 23 Oct 2015 20:09:36 +0000 (20:09 +0000)]
Finished typing in.

git-svn-id: https://citdcbmipav.cit.nih.gov/repos-pub/mipav/trunk/mipav@13905 ba61647d-9d00-f842-95cd-605cb4296b96

3 years agoCall to JDialogGraphBasedSegmentation added.
ilb@NIH.GOV [Fri, 23 Oct 2015 19:54:37 +0000 (19:54 +0000)]
Call to JDialogGraphBasedSegmentation added.

git-svn-id: https://citdcbmipav.cit.nih.gov/repos-pub/mipav/trunk/mipav@13904 ba61647d-9d00-f842-95cd-605cb4296b96

3 years agoIntegrated display for the worm straightening semi-automatic plugin.
abokinsky [Fri, 23 Oct 2015 19:53:02 +0000 (19:53 +0000)]
Integrated display for the worm straightening semi-automatic plugin.
Plugin is done - next minor code cleanup.

git-svn-id: https://citdcbmipav.cit.nih.gov/repos-pub/mipav/trunk/mipav@13903 ba61647d-9d00-f842-95cd-605cb4296b96

3 years agoDialog created.
ilb@NIH.GOV [Fri, 23 Oct 2015 19:51:39 +0000 (19:51 +0000)]
Dialog created.

git-svn-id: https://citdcbmipav.cit.nih.gov/repos-pub/mipav/trunk/mipav@13902 ba61647d-9d00-f842-95cd-605cb4296b96

3 years agoDispose of any created grayImage and colorImage.
ilb@NIH.GOV [Fri, 23 Oct 2015 15:05:07 +0000 (15:05 +0000)]
Dispose of any created grayImage and colorImage.

git-svn-id: https://citdcbmipav.cit.nih.gov/repos-pub/mipav/trunk/mipav@13901 ba61647d-9d00-f842-95cd-605cb4296b96

3 years agoStarted work on.
ilb@NIH.GOV [Thu, 22 Oct 2015 21:46:28 +0000 (21:46 +0000)]
Started work on.

git-svn-id: https://citdcbmipav.cit.nih.gov/repos-pub/mipav/trunk/mipav@13900 ba61647d-9d00-f842-95cd-605cb4296b96

3 years agoCleaned up comments.
ilb@NIH.GOV [Thu, 22 Oct 2015 20:43:51 +0000 (20:43 +0000)]
Cleaned up comments.

git-svn-id: https://citdcbmipav.cit.nih.gov/repos-pub/mipav/trunk/mipav@13899 ba61647d-9d00-f842-95cd-605cb4296b96

3 years agoIn RandomWalker corrected return false at end of if (fill_A to return true.
ilb@NIH.GOV [Thu, 22 Oct 2015 17:11:32 +0000 (17:11 +0000)]
In RandomWalker corrected return false at end of if (fill_A to return true.

git-svn-id: https://citdcbmipav.cit.nih.gov/repos-pub/mipav/trunk/mipav@13898 ba61647d-9d00-f842-95cd-605cb4296b96

3 years agoRestored Power watershed, q = 2 button.
ilb@NIH.GOV [Wed, 21 Oct 2015 21:11:06 +0000 (21:11 +0000)]
Restored Power watershed, q = 2 button.

git-svn-id: https://citdcbmipav.cit.nih.gov/repos-pub/mipav/trunk/mipav@13897 ba61647d-9d00-f842-95cd-605cb4296b96

3 years agoPower watershed segmentation looks okay for 2 levels, not so good for multilevels.
ilb@NIH.GOV [Wed, 21 Oct 2015 21:08:59 +0000 (21:08 +0000)]
Power watershed segmentation looks okay for 2 levels, not so good for multilevels.

git-svn-id: https://citdcbmipav.cit.nih.gov/repos-pub/mipav/trunk/mipav@13896 ba61647d-9d00-f842-95cd-605cb4296b96

3 years agoUse only one global invocation of new RandomGen(), because otherwise if calls of...
ilb@NIH.GOV [Wed, 21 Oct 2015 17:40:38 +0000 (17:40 +0000)]
Use only one global invocation of new RandomGen(), because otherwise if calls of RandomGen() get made close together on the same system clock setting, the same random numbers will be generated.

git-svn-id: https://citdcbmipav.cit.nih.gov/repos-pub/mipav/trunk/mipav@13895 ba61647d-9d00-f842-95cd-605cb4296b96

3 years agoChanged lu6sol from private to public.
ilb@NIH.GOV [Wed, 21 Oct 2015 14:48:45 +0000 (14:48 +0000)]
Changed lu6sol from private to public.

git-svn-id: https://citdcbmipav.cit.nih.gov/repos-pub/mipav/trunk/mipav@13894 ba61647d-9d00-f842-95cd-605cb4296b96

3 years agoUpdated the semi-automatic worm straightening pipeline plugin. Added review straighte...
abokinsky [Wed, 21 Oct 2015 00:47:05 +0000 (00:47 +0000)]
Updated the semi-automatic worm straightening pipeline plugin. Added review straightened option.

git-svn-id: https://citdcbmipav.cit.nih.gov/repos-pub/mipav/trunk/mipav@13893 ba61647d-9d00-f842-95cd-605cb4296b96

3 years agoWorking on RandomWalker routine.
ilb@NIH.GOV [Tue, 20 Oct 2015 21:47:51 +0000 (21:47 +0000)]
Working on RandomWalker routine.

git-svn-id: https://citdcbmipav.cit.nih.gov/repos-pub/mipav/trunk/mipav@13892 ba61647d-9d00-f842-95cd-605cb4296b96

3 years agoindex_seeds and index_labels are now put into ascending index order.
ilb@NIH.GOV [Tue, 20 Oct 2015 17:13:33 +0000 (17:13 +0000)]
index_seeds and index_labels are now put into ascending index order.

git-svn-id: https://citdcbmipav.cit.nih.gov/repos-pub/mipav/trunk/mipav@13891 ba61647d-9d00-f842-95cd-605cb4296b96

3 years agoPrim is working now that index_seeds and index_labels are in ascending index order...
ilb@NIH.GOV [Tue, 20 Oct 2015 17:12:21 +0000 (17:12 +0000)]
Prim is working now that index_seeds and index_labels are in ascending index order.  nblabels is now calculated from the maximum value in index_labels.

git-svn-id: https://citdcbmipav.cit.nih.gov/repos-pub/mipav/trunk/mipav@13890 ba61647d-9d00-f842-95cd-605cb4296b96

3 years agoUpdated the semi-automatic worm straightening pipeline plugin.
abokinsky [Tue, 20 Oct 2015 00:58:41 +0000 (00:58 +0000)]
Updated the semi-automatic worm straightening pipeline plugin.

git-svn-id: https://citdcbmipav.cit.nih.gov/repos-pub/mipav/trunk/mipav@13889 ba61647d-9d00-f842-95cd-605cb4296b96

3 years agolifoTest added.
ilb@NIH.GOV [Sun, 18 Oct 2015 18:46:13 +0000 (18:46 +0000)]
lifoTest added.

git-svn-id: https://citdcbmipav.cit.nih.gov/repos-pub/mipav/trunk/mipav@13888 ba61647d-9d00-f842-95cd-605cb4296b96

3 years agoAdded indicTest.
ilb@NIH.GOV [Sun, 18 Oct 2015 18:01:21 +0000 (18:01 +0000)]
Added indicTest.

git-svn-id: https://citdcbmipav.cit.nih.gov/repos-pub/mipav/trunk/mipav@13887 ba61647d-9d00-f842-95cd-605cb4296b96

3 years agoError message generated if maskButton pressed when no maskImage is present.
ilb@NIH.GOV [Sun, 18 Oct 2015 17:57:42 +0000 (17:57 +0000)]
Error message generated if maskButton pressed when no maskImage is present.

git-svn-id: https://citdcbmipav.cit.nih.gov/repos-pub/mipav/trunk/mipav@13886 ba61647d-9d00-f842-95cd-605cb4296b96

3 years agoRemoved 2 incorrect breaks from RbtInteractiveTest.
ilb@NIH.GOV [Sun, 18 Oct 2015 15:36:45 +0000 (15:36 +0000)]
Removed 2 incorrect breaks from RbtInteractiveTest.

git-svn-id: https://citdcbmipav.cit.nih.gov/repos-pub/mipav/trunk/mipav@13885 ba61647d-9d00-f842-95cd-605cb4296b96

3 years agoDebugging algorithm Prim.
ilb@NIH.GOV [Fri, 16 Oct 2015 22:13:08 +0000 (22:13 +0000)]
Debugging algorithm Prim.

git-svn-id: https://citdcbmipav.cit.nih.gov/repos-pub/mipav/trunk/mipav@13884 ba61647d-9d00-f842-95cd-605cb4296b96

3 years agoChanged setTagBuffer() to set a flag to enable skipping the image data when reading...
mccreedy@NIH.GOV [Fri, 16 Oct 2015 15:52:20 +0000 (15:52 +0000)]
Changed setTagBuffer() to set a flag to enable skipping the image data when reading the image headers (which caused problems because the raFile was not set) from the dicom receiver.

git-svn-id: https://citdcbmipav.cit.nih.gov/repos-pub/mipav/trunk/mipav@13883 ba61647d-9d00-f842-95cd-605cb4296b96

3 years agoCan now load maskImage.
ilb@NIH.GOV [Thu, 15 Oct 2015 22:12:34 +0000 (22:12 +0000)]
Can now load maskImage.

git-svn-id: https://citdcbmipav.cit.nih.gov/repos-pub/mipav/trunk/mipav@13882 ba61647d-9d00-f842-95cd-605cb4296b96

3 years agoDebugging algorithm Prim.
ilb@NIH.GOV [Thu, 15 Oct 2015 22:12:10 +0000 (22:12 +0000)]
Debugging algorithm Prim.

git-svn-id: https://citdcbmipav.cit.nih.gov/repos-pub/mipav/trunk/mipav@13881 ba61647d-9d00-f842-95cd-605cb4296b96

3 years agoChanged some error messages and added manual workaround for .METADATA file that NICoE...
mccreedy@NIH.GOV [Thu, 15 Oct 2015 17:41:10 +0000 (17:41 +0000)]
Changed some error messages and added manual workaround for .METADATA file that NICoE was including in their .tar.gz files.

git-svn-id: https://citdcbmipav.cit.nih.gov/repos-pub/mipav/trunk/mipav@13880 ba61647d-9d00-f842-95cd-605cb4296b96

3 years agoUnused code removed.
ilb@NIH.GOV [Thu, 15 Oct 2015 17:35:14 +0000 (17:35 +0000)]
Unused code removed.

git-svn-id: https://citdcbmipav.cit.nih.gov/repos-pub/mipav/trunk/mipav@13879 ba61647d-9d00-f842-95cd-605cb4296b96

3 years agoCan now read color files with .PPM extensions.
ilb@NIH.GOV [Thu, 15 Oct 2015 17:33:40 +0000 (17:33 +0000)]
Can now read color files with .PPM extensions.

git-svn-id: https://citdcbmipav.cit.nih.gov/repos-pub/mipav/trunk/mipav@13878 ba61647d-9d00-f842-95cd-605cb4296b96

3 years agoFile created.
ilb@NIH.GOV [Thu, 15 Oct 2015 17:33:08 +0000 (17:33 +0000)]
File created.

git-svn-id: https://citdcbmipav.cit.nih.gov/repos-pub/mipav/trunk/mipav@13877 ba61647d-9d00-f842-95cd-605cb4296b96

3 years agoComment added.
ilb@NIH.GOV [Thu, 15 Oct 2015 16:53:35 +0000 (16:53 +0000)]
Comment added.

git-svn-id: https://citdcbmipav.cit.nih.gov/repos-pub/mipav/trunk/mipav@13876 ba61647d-9d00-f842-95cd-605cb4296b96

3 years agoComment corrected.
ilb@NIH.GOV [Thu, 15 Oct 2015 16:32:16 +0000 (16:32 +0000)]
Comment corrected.

git-svn-id: https://citdcbmipav.cit.nih.gov/repos-pub/mipav/trunk/mipav@13875 ba61647d-9d00-f842-95cd-605cb4296b96

3 years agoComment corrected.
ilb@NIH.GOV [Thu, 15 Oct 2015 16:29:57 +0000 (16:29 +0000)]
Comment corrected.

git-svn-id: https://citdcbmipav.cit.nih.gov/repos-pub/mipav/trunk/mipav@13874 ba61647d-9d00-f842-95cd-605cb4296b96

3 years agoFile created.
ilb@NIH.GOV [Thu, 15 Oct 2015 16:27:46 +0000 (16:27 +0000)]
File created.

git-svn-id: https://citdcbmipav.cit.nih.gov/repos-pub/mipav/trunk/mipav@13873 ba61647d-9d00-f842-95cd-605cb4296b96

3 years agoAdded extension .ppm.
ilb@NIH.GOV [Thu, 15 Oct 2015 16:03:25 +0000 (16:03 +0000)]
Added extension .ppm.

git-svn-id: https://citdcbmipav.cit.nih.gov/repos-pub/mipav/trunk/mipav@13872 ba61647d-9d00-f842-95cd-605cb4296b96

3 years agoPortable Pixmap Utilities (.PPM) added.
ilb@NIH.GOV [Thu, 15 Oct 2015 16:00:35 +0000 (16:00 +0000)]
Portable Pixmap Utilities (.PPM) added.

git-svn-id: https://citdcbmipav.cit.nih.gov/repos-pub/mipav/trunk/mipav@13871 ba61647d-9d00-f842-95cd-605cb4296b96

3 years agoRewrote so xDim, yDim, and zDim values must be on the same line.
ilb@NIH.GOV [Wed, 14 Oct 2015 22:08:53 +0000 (22:08 +0000)]
Rewrote so xDim, yDim, and zDim values must be on the same line.

git-svn-id: https://citdcbmipav.cit.nih.gov/repos-pub/mipav/trunk/mipav@13870 ba61647d-9d00-f842-95cd-605cb4296b96

3 years ago3D read capability added.
ilb@NIH.GOV [Wed, 14 Oct 2015 22:01:10 +0000 (22:01 +0000)]
3D read capability added.

git-svn-id: https://citdcbmipav.cit.nih.gov/repos-pub/mipav/trunk/mipav@13869 ba61647d-9d00-f842-95cd-605cb4296b96

3 years agoNo longer pass parameter multi to algorithm.
ilb@NIH.GOV [Wed, 14 Oct 2015 21:38:21 +0000 (21:38 +0000)]
No longer pass parameter multi to algorithm.

git-svn-id: https://citdcbmipav.cit.nih.gov/repos-pub/mipav/trunk/mipav@13868 ba61647d-9d00-f842-95cd-605cb4296b96

3 years agoCannot port RandomWalker routine because it uses CSparse which requires a LGPL license.
ilb@NIH.GOV [Wed, 14 Oct 2015 21:37:38 +0000 (21:37 +0000)]
Cannot port RandomWalker routine because it uses CSparse which requires a LGPL license.

git-svn-id: https://citdcbmipav.cit.nih.gov/repos-pub/mipav/trunk/mipav@13867 ba61647d-9d00-f842-95cd-605cb4296b96

3 years agoPorting continues.
ilb@NIH.GOV [Tue, 13 Oct 2015 20:49:11 +0000 (20:49 +0000)]
Porting continues.

git-svn-id: https://citdcbmipav.cit.nih.gov/repos-pub/mipav/trunk/mipav@13866 ba61647d-9d00-f842-95cd-605cb4296b96

3 years agoAdded multiple 'nose' annotations for the worm straightening.
abokinsky [Mon, 12 Oct 2015 02:09:14 +0000 (02:09 +0000)]
Added multiple 'nose' annotations for the worm straightening.

git-svn-id: https://citdcbmipav.cit.nih.gov/repos-pub/mipav/trunk/mipav@13865 ba61647d-9d00-f842-95cd-605cb4296b96

3 years agoPorting continues.
ilb@NIH.GOV [Fri, 9 Oct 2015 22:07:46 +0000 (22:07 +0000)]
Porting continues.

git-svn-id: https://citdcbmipav.cit.nih.gov/repos-pub/mipav/trunk/mipav@13864 ba61647d-9d00-f842-95cd-605cb4296b96

3 years agoChanged resultImage from USHORT to UBYTE.
ilb@NIH.GOV [Fri, 9 Oct 2015 19:07:18 +0000 (19:07 +0000)]
Changed resultImage from USHORT to UBYTE.

git-svn-id: https://citdcbmipav.cit.nih.gov/repos-pub/mipav/trunk/mipav@13863 ba61647d-9d00-f842-95cd-605cb4296b96

3 years agoOnly display grayImage if srcImage.isColorImage().
ilb@NIH.GOV [Fri, 9 Oct 2015 17:40:23 +0000 (17:40 +0000)]
Only display grayImage if srcImage.isColorImage().

git-svn-id: https://citdcbmipav.cit.nih.gov/repos-pub/mipav/trunk/mipav@13862 ba61647d-9d00-f842-95cd-605cb4296b96

3 years agoPorting continues.
ilb@NIH.GOV [Thu, 8 Oct 2015 21:56:39 +0000 (21:56 +0000)]
Porting continues.

git-svn-id: https://citdcbmipav.cit.nih.gov/repos-pub/mipav/trunk/mipav@13861 ba61647d-9d00-f842-95cd-605cb4296b96

3 years agoAdded Power Watershed to Segmentation menu.
ilb@NIH.GOV [Thu, 8 Oct 2015 20:43:22 +0000 (20:43 +0000)]
Added Power Watershed to Segmentation menu.

git-svn-id: https://citdcbmipav.cit.nih.gov/repos-pub/mipav/trunk/mipav@13860 ba61647d-9d00-f842-95cd-605cb4296b96

3 years agoDebugged dialog.
ilb@NIH.GOV [Thu, 8 Oct 2015 20:40:23 +0000 (20:40 +0000)]
Debugged dialog.

git-svn-id: https://citdcbmipav.cit.nih.gov/repos-pub/mipav/trunk/mipav@13859 ba61647d-9d00-f842-95cd-605cb4296b96

3 years agoAdded call to JDialogPowerWatershed.
ilb@NIH.GOV [Thu, 8 Oct 2015 20:10:17 +0000 (20:10 +0000)]
Added call to JDialogPowerWatershed.

git-svn-id: https://citdcbmipav.cit.nih.gov/repos-pub/mipav/trunk/mipav@13858 ba61647d-9d00-f842-95cd-605cb4296b96

3 years agoDialog created.
ilb@NIH.GOV [Thu, 8 Oct 2015 19:57:29 +0000 (19:57 +0000)]
Dialog created.

git-svn-id: https://citdcbmipav.cit.nih.gov/repos-pub/mipav/trunk/mipav@13857 ba61647d-9d00-f842-95cd-605cb4296b96

3 years agoStarted work on.
ilb@NIH.GOV [Wed, 7 Oct 2015 17:40:09 +0000 (17:40 +0000)]
Started work on.

git-svn-id: https://citdcbmipav.cit.nih.gov/repos-pub/mipav/trunk/mipav@13856 ba61647d-9d00-f842-95cd-605cb4296b96

3 years agoAdded multiple 'nose' annotations for the worm straightening.
abokinsky [Tue, 6 Oct 2015 15:44:05 +0000 (15:44 +0000)]
Added multiple 'nose' annotations for the worm straightening.

git-svn-id: https://citdcbmipav.cit.nih.gov/repos-pub/mipav/trunk/mipav@13855 ba61647d-9d00-f842-95cd-605cb4296b96

3 years agoAdded the annotation animation to the straightening plugin pipeline.
abokinsky [Tue, 6 Oct 2015 01:40:24 +0000 (01:40 +0000)]
Added the annotation animation to the straightening plugin pipeline.

git-svn-id: https://citdcbmipav.cit.nih.gov/repos-pub/mipav/trunk/mipav@13854 ba61647d-9d00-f842-95cd-605cb4296b96

3 years agoAdded maximum distance text field.
ilb@NIH.GOV [Mon, 5 Oct 2015 19:43:42 +0000 (19:43 +0000)]
Added maximum distance text field.

git-svn-id: https://citdcbmipav.cit.nih.gov/repos-pub/mipav/trunk/mipav@13853 ba61647d-9d00-f842-95cd-605cb4296b96

3 years agoChanged if (similarity > 0.8) to if (similarity <= maxDistance) and added maxDistance...
ilb@NIH.GOV [Mon, 5 Oct 2015 19:43:06 +0000 (19:43 +0000)]
Changed if (similarity > 0.8) to if (similarity <= maxDistance) and added maxDistance input parameter.

git-svn-id: https://citdcbmipav.cit.nih.gov/repos-pub/mipav/trunk/mipav@13852 ba61647d-9d00-f842-95cd-605cb4296b96

3 years agoCorrected mergeSegments.
ilb@NIH.GOV [Mon, 5 Oct 2015 17:24:28 +0000 (17:24 +0000)]
Corrected mergeSegments.

git-svn-id: https://citdcbmipav.cit.nih.gov/repos-pub/mipav/trunk/mipav@13851 ba61647d-9d00-f842-95cd-605cb4296b96

3 years agoUpdates to the worm straightening plugin. Added 'nose' heuristic for the automatic...
abokinsky [Mon, 5 Oct 2015 02:08:35 +0000 (02:08 +0000)]
Updates to the worm straightening plugin. Added 'nose' heuristic for the automatic lattice building.

git-svn-id: https://citdcbmipav.cit.nih.gov/repos-pub/mipav/trunk/mipav@13850 ba61647d-9d00-f842-95cd-605cb4296b96

3 years agoCheck box for merging color image segments added.
ilb@NIH.GOV [Fri, 2 Oct 2015 21:54:21 +0000 (21:54 +0000)]
Check box for merging color image segments added.

git-svn-id: https://citdcbmipav.cit.nih.gov/repos-pub/mipav/trunk/mipav@13849 ba61647d-9d00-f842-95cd-605cb4296b96

3 years agoFinished mergedSegments for color images.
ilb@NIH.GOV [Fri, 2 Oct 2015 21:53:26 +0000 (21:53 +0000)]
Finished mergedSegments for color images.

git-svn-id: https://citdcbmipav.cit.nih.gov/repos-pub/mipav/trunk/mipav@13848 ba61647d-9d00-f842-95cd-605cb4296b96

3 years agoPorting continues.
ilb@NIH.GOV [Thu, 1 Oct 2015 22:11:25 +0000 (22:11 +0000)]
Porting continues.

git-svn-id: https://citdcbmipav.cit.nih.gov/repos-pub/mipav/trunk/mipav@13847 ba61647d-9d00-f842-95cd-605cb4296b96

3 years agoRemoved field for segment number.
ilb@NIH.GOV [Tue, 29 Sep 2015 22:15:00 +0000 (22:15 +0000)]
Removed field for segment number.

git-svn-id: https://citdcbmipav.cit.nih.gov/repos-pub/mipav/trunk/mipav@13846 ba61647d-9d00-f842-95cd-605cb4296b96

3 years agoPorting continues.
ilb@NIH.GOV [Tue, 29 Sep 2015 22:14:31 +0000 (22:14 +0000)]
Porting continues.

git-svn-id: https://citdcbmipav.cit.nih.gov/repos-pub/mipav/trunk/mipav@13845 ba61647d-9d00-f842-95cd-605cb4296b96

3 years agoAt the end of calc2D() set any remaining INITIAL = -2 values to 0. This stops 65534...
ilb@NIH.GOV [Tue, 29 Sep 2015 17:28:25 +0000 (17:28 +0000)]
At the end of calc2D() set any remaining INITIAL = -2 values to 0. This stops 65534 values from appearing in the final USHORT resultImage.

git-svn-id: https://citdcbmipav.cit.nih.gov/repos-pub/mipav/trunk/mipav@13844 ba61647d-9d00-f842-95cd-605cb4296b96

3 years agoAdded fields for sigmaX And sigmaY.
ilb@NIH.GOV [Mon, 28 Sep 2015 22:10:27 +0000 (22:10 +0000)]
Added fields for sigmaX And sigmaY.

git-svn-id: https://citdcbmipav.cit.nih.gov/repos-pub/mipav/trunk/mipav@13843 ba61647d-9d00-f842-95cd-605cb4296b96

3 years agoPorting continues.
ilb@NIH.GOV [Mon, 28 Sep 2015 22:09:48 +0000 (22:09 +0000)]
Porting continues.

git-svn-id: https://citdcbmipav.cit.nih.gov/repos-pub/mipav/trunk/mipav@13842 ba61647d-9d00-f842-95cd-605cb4296b96

3 years agoIn calc2D() prevent array index out of bounds errors.
ilb@NIH.GOV [Mon, 28 Sep 2015 22:09:04 +0000 (22:09 +0000)]
In calc2D() prevent array index out of bounds errors.

git-svn-id: https://citdcbmipav.cit.nih.gov/repos-pub/mipav/trunk/mipav@13841 ba61647d-9d00-f842-95cd-605cb4296b96

3 years agoChanged resultImage from BYTE to USHORT.
ilb@NIH.GOV [Mon, 28 Sep 2015 21:03:22 +0000 (21:03 +0000)]
Changed resultImage from BYTE to USHORT.

git-svn-id: https://citdcbmipav.cit.nih.gov/repos-pub/mipav/trunk/mipav@13840 ba61647d-9d00-f842-95cd-605cb4296b96

3 years agoIn setGUIFromParams corrected factor = dif /histogram.getNDims() to factor = dif...
ilb@NIH.GOV [Mon, 28 Sep 2015 19:49:34 +0000 (19:49 +0000)]
In setGUIFromParams corrected factor = dif /histogram.getNDims() to factor = dif/histogram.getExtents()[0].

git-svn-id: https://citdcbmipav.cit.nih.gov/repos-pub/mipav/trunk/mipav@13839 ba61647d-9d00-f842-95cd-605cb4296b96

3 years agoCorrected factor = dif/histogram.getNDims() to factor = dif/histogram.getExtents...
ilb@NIH.GOV [Mon, 28 Sep 2015 19:44:35 +0000 (19:44 +0000)]
Corrected factor = dif/histogram.getNDims() to factor = dif/histogram.getExtents()[0].

git-svn-id: https://citdcbmipav.cit.nih.gov/repos-pub/mipav/trunk/mipav@13838 ba61647d-9d00-f842-95cd-605cb4296b96

3 years agoIn Segmentation menu added call to Auto Seed Watershed.
ilb@NIH.GOV [Mon, 28 Sep 2015 19:08:18 +0000 (19:08 +0000)]
In Segmentation menu added call to Auto Seed Watershed.

git-svn-id: https://citdcbmipav.cit.nih.gov/repos-pub/mipav/trunk/mipav@13837 ba61647d-9d00-f842-95cd-605cb4296b96

3 years agoAdded call to JDialogAutoSeedWatershed.
ilb@NIH.GOV [Mon, 28 Sep 2015 19:02:39 +0000 (19:02 +0000)]
Added call to JDialogAutoSeedWatershed.

git-svn-id: https://citdcbmipav.cit.nih.gov/repos-pub/mipav/trunk/mipav@13836 ba61647d-9d00-f842-95cd-605cb4296b96

3 years agoCorrected comment.
ilb@NIH.GOV [Mon, 28 Sep 2015 18:59:06 +0000 (18:59 +0000)]
Corrected comment.

git-svn-id: https://citdcbmipav.cit.nih.gov/repos-pub/mipav/trunk/mipav@13835 ba61647d-9d00-f842-95cd-605cb4296b96

3 years agoDialog created.
ilb@NIH.GOV [Mon, 28 Sep 2015 18:57:54 +0000 (18:57 +0000)]
Dialog created.

git-svn-id: https://citdcbmipav.cit.nih.gov/repos-pub/mipav/trunk/mipav@13834 ba61647d-9d00-f842-95cd-605cb4296b96

3 years agoAdded automatic registration/MIP generation. Fixed user-interface for editing annotat...
abokinsky [Mon, 28 Sep 2015 01:11:26 +0000 (01:11 +0000)]
Added automatic registration/MIP generation. Fixed user-interface for editing annotations in the stand-along plugin. Now if the user did not run the automatic segmentation it's still possible to mark the seam cells and other annotations from scratch.

git-svn-id: https://citdcbmipav.cit.nih.gov/repos-pub/mipav/trunk/mipav@13833 ba61647d-9d00-f842-95cd-605cb4296b96

3 years agoPorting continues.
ilb@NIH.GOV [Fri, 25 Sep 2015 22:16:49 +0000 (22:16 +0000)]
Porting continues.

git-svn-id: https://citdcbmipav.cit.nih.gov/repos-pub/mipav/trunk/mipav@13832 ba61647d-9d00-f842-95cd-605cb4296b96