mipav.git
4 years agoversion 7.2.0 release-7.2.0
mccreedy@NIH.GOV [Tue, 9 Dec 2014 18:31:30 +0000 (18:31 +0000)]
version 7.2.0

git-svn-id: https://citdcbmipav.cit.nih.gov/repos-pub/mipav/tags/release-7.2.0@13272 ba61647d-9d00-f842-95cd-605cb4296b96

4 years agoversion 7.2.0 release-7.2.0@13271
mccreedy@NIH.GOV [Tue, 9 Dec 2014 18:31:23 +0000 (18:31 +0000)]
version 7.2.0

git-svn-id: https://citdcbmipav.cit.nih.gov/repos-pub/mipav/trunk/mipav@13271 ba61647d-9d00-f842-95cd-605cb4296b96

4 years agoupdated imagej jar: Tue Dec 9 13:22:36 EST 2014
mccreedy@NIH.GOV [Tue, 9 Dec 2014 18:22:39 +0000 (18:22 +0000)]
updated imagej jar: Tue Dec  9 13:22:36 EST 2014

git-svn-id: https://citdcbmipav.cit.nih.gov/repos-pub/mipav/trunk/mipav@13270 ba61647d-9d00-f842-95cd-605cb4296b96

4 years agoAdded some more error handling of FS or DEs in CSV files that aren't in the DDT.
mccreedy@NIH.GOV [Tue, 9 Dec 2014 15:27:55 +0000 (15:27 +0000)]
Added some more error handling of FS or DEs in CSV files that aren't in the DDT.

git-svn-id: https://citdcbmipav.cit.nih.gov/repos-pub/mipav/trunk/mipav@13269 ba61647d-9d00-f842-95cd-605cb4296b96

4 years agoNew brics DDT webservice jars and libs they depend on.
mccreedy@NIH.GOV [Tue, 9 Dec 2014 15:22:41 +0000 (15:22 +0000)]
New brics DDT webservice jars and libs they depend on.

git-svn-id: https://citdcbmipav.cit.nih.gov/repos-pub/mipav/trunk/mipav@13268 ba61647d-9d00-f842-95cd-605cb4296b96

4 years agoPorting continues.
ilb@NIH.GOV [Mon, 8 Dec 2014 23:10:01 +0000 (23:10 +0000)]
Porting continues.

git-svn-id: https://citdcbmipav.cit.nih.gov/repos-pub/mipav/trunk/mipav@13267 ba61647d-9d00-f842-95cd-605cb4296b96

4 years agoPorting started.
ilb@NIH.GOV [Fri, 5 Dec 2014 23:13:18 +0000 (23:13 +0000)]
Porting started.

git-svn-id: https://citdcbmipav.cit.nih.gov/repos-pub/mipav/trunk/mipav@13266 ba61647d-9d00-f842-95cd-605cb4296b96

4 years agoAdded some more cleanup of progress bar on error during dicom read.
mccreedy@NIH.GOV [Thu, 4 Dec 2014 21:08:08 +0000 (21:08 +0000)]
Added some more cleanup of progress bar on error during dicom read.

git-svn-id: https://citdcbmipav.cit.nih.gov/repos-pub/mipav/trunk/mipav@13265 ba61647d-9d00-f842-95cd-605cb4296b96

4 years agoAdding in an image stitching GUI for the Shroff lab. It is very rudimentary and doesn...
wangvg@NIH.GOV [Mon, 1 Dec 2014 21:08:49 +0000 (21:08 +0000)]
Adding in an image stitching GUI for the Shroff lab. It is very rudimentary and doesn't have a fancy UI but does the job for them. Also adding a basic phase correlation registration algorithm as accessory code to the image stitching.

git-svn-id: https://citdcbmipav.cit.nih.gov/repos-pub/mipav/trunk/mipav@13264 ba61647d-9d00-f842-95cd-605cb4296b96

4 years agoLocal variance added to Algorithms Filters (spatial).
ilb@NIH.GOV [Mon, 1 Dec 2014 20:40:47 +0000 (20:40 +0000)]
Local variance added to Algorithms Filters (spatial).

git-svn-id: https://citdcbmipav.cit.nih.gov/repos-pub/mipav/trunk/mipav@13263 ba61647d-9d00-f842-95cd-605cb4296b96

4 years agoCall to JDialogLocalVariance added.
ilb@NIH.GOV [Mon, 1 Dec 2014 20:39:32 +0000 (20:39 +0000)]
Call to JDialogLocalVariance added.

git-svn-id: https://citdcbmipav.cit.nih.gov/repos-pub/mipav/trunk/mipav@13262 ba61647d-9d00-f842-95cd-605cb4296b96

4 years agoDialog completed.
ilb@NIH.GOV [Mon, 1 Dec 2014 20:38:41 +0000 (20:38 +0000)]
Dialog completed.

git-svn-id: https://citdcbmipav.cit.nih.gov/repos-pub/mipav/trunk/mipav@13261 ba61647d-9d00-f842-95cd-605cb4296b96

4 years agoFinished for black and white.
ilb@NIH.GOV [Mon, 1 Dec 2014 20:38:09 +0000 (20:38 +0000)]
Finished for black and white.

git-svn-id: https://citdcbmipav.cit.nih.gov/repos-pub/mipav/trunk/mipav@13260 ba61647d-9d00-f842-95cd-605cb4296b96

4 years agoStarted work on.
ilb@NIH.GOV [Fri, 28 Nov 2014 22:18:46 +0000 (22:18 +0000)]
Started work on.

git-svn-id: https://citdcbmipav.cit.nih.gov/repos-pub/mipav/trunk/mipav@13259 ba61647d-9d00-f842-95cd-605cb4296b96

4 years agoMoved over tumor simulation plugin from non-open source repository at the request...
mccreedy@NIH.GOV [Fri, 28 Nov 2014 16:16:29 +0000 (16:16 +0000)]
Moved over tumor simulation plugin from non-open source repository at the request of Moira Schieke.

git-svn-id: https://citdcbmipav.cit.nih.gov/repos-pub/mipav/trunk/mipav@13258 ba61647d-9d00-f842-95cd-605cb4296b96

4 years agoProgress bar values now appear in run3D.
ilb@NIH.GOV [Wed, 26 Nov 2014 16:01:56 +0000 (16:01 +0000)]
Progress bar values now appear in run3D.

git-svn-id: https://citdcbmipav.cit.nih.gov/repos-pub/mipav/trunk/mipav@13257 ba61647d-9d00-f842-95cd-605cb4296b96

4 years agoChange initial values of pixelsContract and pixelsExpand from 2 to 5.
ilb@NIH.GOV [Tue, 25 Nov 2014 23:24:03 +0000 (23:24 +0000)]
Change initial values of pixelsContract and pixelsExpand from 2 to 5.

git-svn-id: https://citdcbmipav.cit.nih.gov/repos-pub/mipav/trunk/mipav@13256 ba61647d-9d00-f842-95cd-605cb4296b96

4 years agoMultiply pixelsExpand and pixelsContract by costheta[i] and sintheta[i] instead of...
ilb@NIH.GOV [Tue, 25 Nov 2014 23:23:15 +0000 (23:23 +0000)]
Multiply pixelsExpand and pixelsContract by costheta[i] and sintheta[i] instead of delX[i] and delY[i].

git-svn-id: https://citdcbmipav.cit.nih.gov/repos-pub/mipav/trunk/mipav@13255 ba61647d-9d00-f842-95cd-605cb4296b96

4 years agoCorrected labelContract and labelExpand.
ilb@NIH.GOV [Tue, 25 Nov 2014 22:41:31 +0000 (22:41 +0000)]
Corrected labelContract and labelExpand.

git-svn-id: https://citdcbmipav.cit.nih.gov/repos-pub/mipav/trunk/mipav@13254 ba61647d-9d00-f842-95cd-605cb4296b96

4 years agoNo longer disable dual contour for 3D.
ilb@NIH.GOV [Tue, 25 Nov 2014 22:38:20 +0000 (22:38 +0000)]
No longer disable dual contour for 3D.

git-svn-id: https://citdcbmipav.cit.nih.gov/repos-pub/mipav/trunk/mipav@13253 ba61647d-9d00-f842-95cd-605cb4296b96

4 years agoAdd in pixelsContract and pixelsExpand for 3D images.
ilb@NIH.GOV [Tue, 25 Nov 2014 22:36:44 +0000 (22:36 +0000)]
Add in pixelsContract and pixelsExpand for 3D images.

git-svn-id: https://citdcbmipav.cit.nih.gov/repos-pub/mipav/trunk/mipav@13252 ba61647d-9d00-f842-95cd-605cb4296b96

4 years agoAdd in 2.5D capability.
ilb@NIH.GOV [Tue, 25 Nov 2014 22:35:21 +0000 (22:35 +0000)]
Add in 2.5D capability.

git-svn-id: https://citdcbmipav.cit.nih.gov/repos-pub/mipav/trunk/mipav@13251 ba61647d-9d00-f842-95cd-605cb4296b96

4 years agoLinkedComparator corrected.
ilb@NIH.GOV [Tue, 25 Nov 2014 21:21:42 +0000 (21:21 +0000)]
LinkedComparator corrected.

git-svn-id: https://citdcbmipav.cit.nih.gov/repos-pub/mipav/trunk/mipav@13250 ba61647d-9d00-f842-95cd-605cb4296b96

4 years agoTyped in and proofread.
ilb@NIH.GOV [Fri, 21 Nov 2014 18:29:46 +0000 (18:29 +0000)]
Typed in and proofread.

git-svn-id: https://citdcbmipav.cit.nih.gov/repos-pub/mipav/trunk/mipav@13249 ba61647d-9d00-f842-95cd-605cb4296b96

4 years agoStarted porting.
ilb@NIH.GOV [Thu, 20 Nov 2014 23:11:59 +0000 (23:11 +0000)]
Started porting.

git-svn-id: https://citdcbmipav.cit.nih.gov/repos-pub/mipav/trunk/mipav@13248 ba61647d-9d00-f842-95cd-605cb4296b96

4 years agoAdded option in the new viewer to use absolute length to determine the secondary...
wangvg@NIH.GOV [Fri, 14 Nov 2014 20:14:57 +0000 (20:14 +0000)]
Added option in the new viewer to use absolute length to determine the secondary branching order instead of using the Imaris file's order

git-svn-id: https://citdcbmipav.cit.nih.gov/repos-pub/mipav/trunk/mipav@13247 ba61647d-9d00-f842-95cd-605cb4296b96

4 years agoCode cleanup
wangvg@NIH.GOV [Fri, 14 Nov 2014 18:04:23 +0000 (18:04 +0000)]
Code cleanup

git-svn-id: https://citdcbmipav.cit.nih.gov/repos-pub/mipav/trunk/mipav@13246 ba61647d-9d00-f842-95cd-605cb4296b96

4 years agoFixed lingering issue where translating the image would cause an irreversible shift.
wangvg@NIH.GOV [Fri, 14 Nov 2014 17:12:57 +0000 (17:12 +0000)]
Fixed lingering issue where translating the image would cause an irreversible shift.

git-svn-id: https://citdcbmipav.cit.nih.gov/repos-pub/mipav/trunk/mipav@13245 ba61647d-9d00-f842-95cd-605cb4296b96

4 years agoIn buildFuzzyPanel changed fuzzyCheckbox.setEnabled(true) to fuzzyCheckbox.setEnabled...
ilb@NIH.GOV [Fri, 14 Nov 2014 16:52:04 +0000 (16:52 +0000)]
In buildFuzzyPanel changed fuzzyCheckbox.setEnabled(true) to fuzzyCheckbox.setEnabled(false);

git-svn-id: https://citdcbmipav.cit.nih.gov/repos-pub/mipav/trunk/mipav@13244 ba61647d-9d00-f842-95cd-605cb4296b96

4 years agoReference to fuzzy connectedness in AlgorithmRegionGrow removed.
ilb@NIH.GOV [Fri, 14 Nov 2014 16:47:24 +0000 (16:47 +0000)]
Reference to fuzzy connectedness in AlgorithmRegionGrow removed.

git-svn-id: https://citdcbmipav.cit.nih.gov/repos-pub/mipav/trunk/mipav@13243 ba61647d-9d00-f842-95cd-605cb4296b96

4 years agoReference to fuzzy connectedness in AlgorithmRegionGrow removed.
ilb@NIH.GOV [Fri, 14 Nov 2014 16:46:48 +0000 (16:46 +0000)]
Reference to fuzzy connectedness in AlgorithmRegionGrow removed.

git-svn-id: https://citdcbmipav.cit.nih.gov/repos-pub/mipav/trunk/mipav@13242 ba61647d-9d00-f842-95cd-605cb4296b96

4 years agoAll code and text related to fuzzy connectedness removed.
ilb@NIH.GOV [Fri, 14 Nov 2014 16:45:45 +0000 (16:45 +0000)]
All code and text related to fuzzy connectedness removed.

git-svn-id: https://citdcbmipav.cit.nih.gov/repos-pub/mipav/trunk/mipav@13241 ba61647d-9d00-f842-95cd-605cb4296b96

4 years agoNow correctly transforms the neuron when dragging on the image.
wangvg@NIH.GOV [Fri, 14 Nov 2014 16:44:47 +0000 (16:44 +0000)]
Now correctly transforms the neuron when dragging on the image.

git-svn-id: https://citdcbmipav.cit.nih.gov/repos-pub/mipav/trunk/mipav@13240 ba61647d-9d00-f842-95cd-605cb4296b96

4 years agoMouse rotation and translation is not working correctly still, so I have disabled...
wangvg@NIH.GOV [Thu, 13 Nov 2014 19:22:39 +0000 (19:22 +0000)]
Mouse rotation and translation is not working correctly still, so I have disabled it until I can find a better way to do it.

git-svn-id: https://citdcbmipav.cit.nih.gov/repos-pub/mipav/trunk/mipav@13239 ba61647d-9d00-f842-95cd-605cb4296b96

4 years agoAdded in ability to rotate and translate the neuron structure using the left and...
wangvg@NIH.GOV [Thu, 13 Nov 2014 18:06:09 +0000 (18:06 +0000)]
Added in ability to rotate and translate the neuron structure using the left and right mouse buttons much like a traditional 3D viewer.

git-svn-id: https://citdcbmipav.cit.nih.gov/repos-pub/mipav/trunk/mipav@13238 ba61647d-9d00-f842-95cd-605cb4296b96

4 years agoAdded translation and zoom sliders for more complete 3D viewing.
wangvg@NIH.GOV [Wed, 12 Nov 2014 17:33:51 +0000 (17:33 +0000)]
Added translation and zoom sliders for more complete 3D viewing.

git-svn-id: https://citdcbmipav.cit.nih.gov/repos-pub/mipav/trunk/mipav@13237 ba61647d-9d00-f842-95cd-605cb4296b96

4 years agoAdded in comments for the things that aren't in the original 3DSWCStats plugin
wangvg@NIH.GOV [Wed, 12 Nov 2014 15:18:38 +0000 (15:18 +0000)]
Added in comments for the things that aren't in the original 3DSWCStats plugin

git-svn-id: https://citdcbmipav.cit.nih.gov/repos-pub/mipav/trunk/mipav@13236 ba61647d-9d00-f842-95cd-605cb4296b96

4 years agoAdd minThreshold, slidingWindow, and call to setMaxProjVariables to setGUIFromParams...
ilb@NIH.GOV [Mon, 10 Nov 2014 23:29:06 +0000 (23:29 +0000)]
Add minThreshold, slidingWindow, and call to setMaxProjVariables to setGUIFromParams and storeParamsFromGUI.

git-svn-id: https://citdcbmipav.cit.nih.gov/repos-pub/mipav/trunk/mipav@13235 ba61647d-9d00-f842-95cd-605cb4296b96

4 years agoAdded resX, resY, and resZ to setGUIFromParams() and storeGUIFromParams().
ilb@NIH.GOV [Mon, 10 Nov 2014 22:31:39 +0000 (22:31 +0000)]
Added resX, resY, and resZ to setGUIFromParams() and storeGUIFromParams().

git-svn-id: https://citdcbmipav.cit.nih.gov/repos-pub/mipav/trunk/mipav@13234 ba61647d-9d00-f842-95cd-605cb4296b96

4 years agoAdding new functionality to the 3D SWC stats plugin for Akanni. Now includes a very...
wangvg@NIH.GOV [Mon, 10 Nov 2014 21:31:54 +0000 (21:31 +0000)]
Adding new functionality to the 3D SWC stats plugin for Akanni. Now includes a very basic 3D viewer to help choose which branch is considered the axon.

git-svn-id: https://citdcbmipav.cit.nih.gov/repos-pub/mipav/trunk/mipav@13233 ba61647d-9d00-f842-95cd-605cb4296b96

4 years agoIn setGUIFromParams() and storeParamsFromGUI() added ariMeanDirString, geoMeanDirStri...
ilb@NIH.GOV [Mon, 10 Nov 2014 20:30:39 +0000 (20:30 +0000)]
In setGUIFromParams() and storeParamsFromGUI() added ariMeanDirString, geoMeanDirString, prefusionBaseDirString, and prefusionTransformDirString.

git-svn-id: https://citdcbmipav.cit.nih.gov/repos-pub/mipav/trunk/mipav@13232 ba61647d-9d00-f842-95cd-605cb4296b96

4 years agoAdded boolean variables xMaxBoxSelected, yMaxBoxSelected, and zMaxBoxSelected.
ilb@NIH.GOV [Mon, 10 Nov 2014 20:03:15 +0000 (20:03 +0000)]
Added boolean variables xMaxBoxSelected, yMaxBoxSelected, and zMaxBoxSelected.

git-svn-id: https://citdcbmipav.cit.nih.gov/repos-pub/mipav/trunk/mipav@13231 ba61647d-9d00-f842-95cd-605cb4296b96

4 years agoFinished adding variables to setGUIFromParams() and storeParamsFromGUI().
ilb@NIH.GOV [Mon, 10 Nov 2014 19:33:40 +0000 (19:33 +0000)]
Finished adding variables to setGUIFromParams() and storeParamsFromGUI().

git-svn-id: https://citdcbmipav.cit.nih.gov/repos-pub/mipav/trunk/mipav@13230 ba61647d-9d00-f842-95cd-605cb4296b96

4 years agoAdded allowScriptRecording to 5 createBlankImage commands.
ilb@NIH.GOV [Mon, 10 Nov 2014 19:31:59 +0000 (19:31 +0000)]
Added allowScriptRecording to 5 createBlankImage commands.

git-svn-id: https://citdcbmipav.cit.nih.gov/repos-pub/mipav/trunk/mipav@13229 ba61647d-9d00-f842-95cd-605cb4296b96

4 years agoAdded input parameter final boolean allowRecording to public ModelImage createBlankIm...
ilb@NIH.GOV [Mon, 10 Nov 2014 19:30:43 +0000 (19:30 +0000)]
Added input parameter final boolean allowRecording to public ModelImage createBlankImage routine.

git-svn-id: https://citdcbmipav.cit.nih.gov/repos-pub/mipav/trunk/mipav@13228 ba61647d-9d00-f842-95cd-605cb4296b96

4 years agoAdded flexibility in the annotation folder (works if it's annotations or annotation...
abokinsky [Mon, 10 Nov 2014 17:14:38 +0000 (17:14 +0000)]
Added flexibility in the annotation folder (works if it's annotations or annotation) for the lattice straightening plugin.

git-svn-id: https://citdcbmipav.cit.nih.gov/repos-pub/mipav/trunk/mipav@13227 ba61647d-9d00-f842-95cd-605cb4296b96

4 years agoWork continuing on scripting.
ilb@NIH.GOV [Fri, 7 Nov 2014 23:08:20 +0000 (23:08 +0000)]
Work continuing on scripting.

git-svn-id: https://citdcbmipav.cit.nih.gov/repos-pub/mipav/trunk/mipav@13226 ba61647d-9d00-f842-95cd-605cb4296b96

4 years agoScripting now works for the 3 2D file options.
ilb@NIH.GOV [Fri, 7 Nov 2014 20:48:58 +0000 (20:48 +0000)]
Scripting now works for the 3 2D file options.

git-svn-id: https://citdcbmipav.cit.nih.gov/repos-pub/mipav/trunk/mipav@13225 ba61647d-9d00-f842-95cd-605cb4296b96

4 years agoPut part of the original algorithm back in as an option for the user. This will allow...
wangvg@NIH.GOV [Fri, 7 Nov 2014 19:35:00 +0000 (19:35 +0000)]
Put part of the original algorithm back in as an option for the user. This will allow the user to choose two different ways (for right now) of choosing which filaments constitute the axon: using absolute length or inferring from the Imaris file.

git-svn-id: https://citdcbmipav.cit.nih.gov/repos-pub/mipav/trunk/mipav@13224 ba61647d-9d00-f842-95cd-605cb4296b96

4 years agoAdded allowScriptRecording parameter to fileIO.writeImage.
ilb@NIH.GOV [Fri, 7 Nov 2014 18:26:33 +0000 (18:26 +0000)]
Added allowScriptRecording parameter to fileIO.writeImage.

git-svn-id: https://citdcbmipav.cit.nih.gov/repos-pub/mipav/trunk/mipav@13223 ba61647d-9d00-f842-95cd-605cb4296b96

4 years agoAdded allowScriptRecording parameter to imWriter.writeImage.
ilb@NIH.GOV [Fri, 7 Nov 2014 18:24:35 +0000 (18:24 +0000)]
Added allowScriptRecording parameter to imWriter.writeImage.

git-svn-id: https://citdcbmipav.cit.nih.gov/repos-pub/mipav/trunk/mipav@13222 ba61647d-9d00-f842-95cd-605cb4296b96

4 years agoTo fileIO.writeImage commands added allowScriptRecording parameter.
ilb@NIH.GOV [Fri, 7 Nov 2014 18:22:13 +0000 (18:22 +0000)]
To fileIO.writeImage commands added allowScriptRecording parameter.

git-svn-id: https://citdcbmipav.cit.nih.gov/repos-pub/mipav/trunk/mipav@13221 ba61647d-9d00-f842-95cd-605cb4296b96

4 years agoAdded boolean allowScriptRecording = false;
ilb@NIH.GOV [Fri, 7 Nov 2014 18:18:52 +0000 (18:18 +0000)]
Added boolean allowScriptRecording = false;
Added allowScriptRecording to all io.writeImage commands.

git-svn-id: https://citdcbmipav.cit.nih.gov/repos-pub/mipav/trunk/mipav@13220 ba61647d-9d00-f842-95cd-605cb4296b96

4 years agoTo public void writeImage added inputParameter final boolean allowScriptRecording...
ilb@NIH.GOV [Fri, 7 Nov 2014 18:17:14 +0000 (18:17 +0000)]
To public void writeImage added inputParameter final boolean allowScriptRecording to allow script recording to be prevented for image save and image save as.

git-svn-id: https://citdcbmipav.cit.nih.gov/repos-pub/mipav/trunk/mipav@13219 ba61647d-9d00-f842-95cd-605cb4296b96

4 years agoIn storeParamsFromGUI replaced baseImageText with baseImage.
ilb@NIH.GOV [Fri, 7 Nov 2014 17:08:15 +0000 (17:08 +0000)]
In storeParamsFromGUI replaced baseImageText with baseImage.

git-svn-id: https://citdcbmipav.cit.nih.gov/repos-pub/mipav/trunk/mipav@13218 ba61647d-9d00-f842-95cd-605cb4296b96

4 years agoRemoved the method that was being replaced, as well as unused imports resulting from...
wangvg@NIH.GOV [Fri, 7 Nov 2014 15:27:33 +0000 (15:27 +0000)]
Removed the method that was being replaced, as well as unused imports resulting from the removal.

git-svn-id: https://citdcbmipav.cit.nih.gov/repos-pub/mipav/trunk/mipav@13217 ba61647d-9d00-f842-95cd-605cb4296b96

4 years agoImaris filament files are patterned in a way that branch organization can be inferred...
wangvg@NIH.GOV [Fri, 7 Nov 2014 14:53:18 +0000 (14:53 +0000)]
Imaris filament files are patterned in a way that branch organization can be inferred from it. Simplified the algorithm to determine the axon/branch number so that it is based on the pattern seen in the files.

git-svn-id: https://citdcbmipav.cit.nih.gov/repos-pub/mipav/trunk/mipav@13216 ba61647d-9d00-f842-95cd-605cb4296b96

4 years agoCorrected enabling and disabling of masks.
ilb@NIH.GOV [Thu, 6 Nov 2014 22:33:24 +0000 (22:33 +0000)]
Corrected enabling and disabling of masks.

git-svn-id: https://citdcbmipav.cit.nih.gov/repos-pub/mipav/trunk/mipav@13215 ba61647d-9d00-f842-95cd-605cb4296b96

4 years agoAllow holes type mask to be used in all methods.
ilb@NIH.GOV [Thu, 6 Nov 2014 22:32:52 +0000 (22:32 +0000)]
Allow holes type mask to be used in all methods.

git-svn-id: https://citdcbmipav.cit.nih.gov/repos-pub/mipav/trunk/mipav@13214 ba61647d-9d00-f842-95cd-605cb4296b96

4 years agoIn equations for phi changed FGDist[i] - BGDist[i] to BGDist[i] - FGDist[i].
ilb@NIH.GOV [Thu, 6 Nov 2014 21:54:44 +0000 (21:54 +0000)]
In equations for phi changed FGDist[i] - BGDist[i] to BGDist[i] - FGDist[i].
Changed VOIs.VOIAt(i).setActive to VOIs.VOIAt(i).setAllActive.

git-svn-id: https://citdcbmipav.cit.nih.gov/repos-pub/mipav/trunk/mipav@13213 ba61647d-9d00-f842-95cd-605cb4296b96

4 years agoAdded more debugging information for the user in case of errors. Also fixed some...
wangvg@NIH.GOV [Thu, 6 Nov 2014 18:16:27 +0000 (18:16 +0000)]
Added more debugging information for the user in case of errors. Also fixed some lingering issues with trying to run the plugin on a directory.

git-svn-id: https://citdcbmipav.cit.nih.gov/repos-pub/mipav/trunk/mipav@13212 ba61647d-9d00-f842-95cd-605cb4296b96

4 years agoChanged to allow for slightly disconnected filaments because the file Akanni gave...
wangvg@NIH.GOV [Thu, 6 Nov 2014 17:24:15 +0000 (17:24 +0000)]
Changed to allow for slightly disconnected filaments because the file Akanni gave me was not overlapping like the ones that Chun-Yuan had given me.

git-svn-id: https://citdcbmipav.cit.nih.gov/repos-pub/mipav/trunk/mipav@13211 ba61647d-9d00-f842-95cd-605cb4296b96

4 years agoSimplified checkstop routine for twophase method.
ilb@NIH.GOV [Wed, 5 Nov 2014 22:00:18 +0000 (22:00 +0000)]
Simplified checkstop routine for twophase method.

git-svn-id: https://citdcbmipav.cit.nih.gov/repos-pub/mipav/trunk/mipav@13210 ba61647d-9d00-f842-95cd-605cb4296b96

4 years agoIn reinitialization corrected padValue from 1 to 0.
ilb@NIH.GOV [Wed, 5 Nov 2014 21:49:37 +0000 (21:49 +0000)]
In reinitialization corrected padValue from 1 to 0.

git-svn-id: https://citdcbmipav.cit.nih.gov/repos-pub/mipav/trunk/mipav@13209 ba61647d-9d00-f842-95cd-605cb4296b96

4 years agoChanged textField to textPane to allow for errors in the debugging input to be shown...
wangvg@NIH.GOV [Wed, 5 Nov 2014 21:08:56 +0000 (21:08 +0000)]
Changed textField to textPane to allow for errors in the debugging input to be shown in red for easier visiblity

git-svn-id: https://citdcbmipav.cit.nih.gov/repos-pub/mipav/trunk/mipav@13208 ba61647d-9d00-f842-95cd-605cb4296b96

4 years agoAdded No 2D registration radio button.
ilb@NIH.GOV [Wed, 5 Nov 2014 18:11:31 +0000 (18:11 +0000)]
Added No 2D registration radio button.

git-svn-id: https://citdcbmipav.cit.nih.gov/repos-pub/mipav/trunk/mipav@13207 ba61647d-9d00-f842-95cd-605cb4296b96

4 years agoAdded input boolean noRegister2D to transform 2D files using existing transformation...
ilb@NIH.GOV [Wed, 5 Nov 2014 18:11:02 +0000 (18:11 +0000)]
Added input boolean noRegister2D to transform 2D files using existing transformation file.

git-svn-id: https://citdcbmipav.cit.nih.gov/repos-pub/mipav/trunk/mipav@13206 ba61647d-9d00-f842-95cd-605cb4296b96

4 years agoAdded a text area to display run information as well as errors in lieu of the console...
wangvg@NIH.GOV [Wed, 5 Nov 2014 18:00:59 +0000 (18:00 +0000)]
Added a text area to display run information as well as errors in lieu of the console as this is expected to be run from the webstart.

git-svn-id: https://citdcbmipav.cit.nih.gov/repos-pub/mipav/trunk/mipav@13205 ba61647d-9d00-f842-95cd-605cb4296b96

4 years agoAdded a little bit of information that was in the 2D version of the plugins.
wangvg@NIH.GOV [Wed, 5 Nov 2014 17:15:11 +0000 (17:15 +0000)]
Added a little bit of information that was in the 2D version of the plugins.

git-svn-id: https://citdcbmipav.cit.nih.gov/repos-pub/mipav/trunk/mipav@13204 ba61647d-9d00-f842-95cd-605cb4296b96

4 years agoRemoved unnecessary imports from previous work.
wangvg@NIH.GOV [Wed, 5 Nov 2014 16:41:03 +0000 (16:41 +0000)]
Removed unnecessary imports from previous work.

git-svn-id: https://citdcbmipav.cit.nih.gov/repos-pub/mipav/trunk/mipav@13203 ba61647d-9d00-f842-95cd-605cb4296b96

4 years agoRemoved radius searching. Chun-Yuan wanted a constant radius output so it makes no...
wangvg@NIH.GOV [Wed, 5 Nov 2014 16:37:05 +0000 (16:37 +0000)]
Removed radius searching. Chun-Yuan wanted a constant radius output so it makes no sense to actually search for it anymore.

git-svn-id: https://citdcbmipav.cit.nih.gov/repos-pub/mipav/trunk/mipav@13202 ba61647d-9d00-f842-95cd-605cb4296b96

4 years agoFixed bug that caused program to say that filaments were not properly connected....
wangvg@NIH.GOV [Wed, 5 Nov 2014 16:36:16 +0000 (16:36 +0000)]
Fixed bug that caused program to say that filaments were not properly connected. Also added CSV output for branching stats.

git-svn-id: https://citdcbmipav.cit.nih.gov/repos-pub/mipav/trunk/mipav@13201 ba61647d-9d00-f842-95cd-605cb4296b96

4 years agoCorrected expression for fim2 and put in missing export of eroded image into seg11.
ilb@NIH.GOV [Tue, 4 Nov 2014 22:51:43 +0000 (22:51 +0000)]
Corrected expression for fim2 and put in missing export of eroded image into seg11.

git-svn-id: https://citdcbmipav.cit.nih.gov/repos-pub/mipav/trunk/mipav@13200 ba61647d-9d00-f842-95cd-605cb4296b96

4 years agoAdded debugging output for user in case anything went wrong.
wangvg@NIH.GOV [Tue, 4 Nov 2014 21:44:02 +0000 (21:44 +0000)]
Added debugging output for user in case anything went wrong.

git-svn-id: https://citdcbmipav.cit.nih.gov/repos-pub/mipav/trunk/mipav@13199 ba61647d-9d00-f842-95cd-605cb4296b96

4 years agoAdded some information about what these plugins are supposed to do.
wangvg@NIH.GOV [Tue, 4 Nov 2014 21:25:31 +0000 (21:25 +0000)]
Added some information about what these plugins are supposed to do.

git-svn-id: https://citdcbmipav.cit.nih.gov/repos-pub/mipav/trunk/mipav@13198 ba61647d-9d00-f842-95cd-605cb4296b96

4 years agoCreated new plugin for Akanni of the Giniger lab. Similar in nature to the Drosophila...
wangvg@NIH.GOV [Tue, 4 Nov 2014 21:19:13 +0000 (21:19 +0000)]
Created new plugin for Akanni of the Giniger lab. Similar in nature to the DrosophilaCreateSWC plugin for Chun-Yuan Ting. Also includes stat tracking along with the conversion of .iv to .swc.

git-svn-id: https://citdcbmipav.cit.nih.gov/repos-pub/mipav/trunk/mipav@13197 ba61647d-9d00-f842-95cd-605cb4296b96

4 years agoFor making mask corrected if (T[index] > thre) to if (Math.abs(T[index] > thre).
ilb@NIH.GOV [Tue, 4 Nov 2014 20:46:52 +0000 (20:46 +0000)]
For making mask corrected if (T[index] > thre) to if (Math.abs(T[index] > thre).

git-svn-id: https://citdcbmipav.cit.nih.gov/repos-pub/mipav/trunk/mipav@13196 ba61647d-9d00-f842-95cd-605cb4296b96

4 years agoReplaced image with srcImage where possible.
ilb@NIH.GOV [Mon, 3 Nov 2014 23:33:19 +0000 (23:33 +0000)]
Replaced image with srcImage where possible.

git-svn-id: https://citdcbmipav.cit.nih.gov/repos-pub/mipav/trunk/mipav@13195 ba61647d-9d00-f842-95cd-605cb4296b96

4 years agoIn equations for phi1[i] and phi2[i] changed + BGDist[i] to - BGDist[i].
ilb@NIH.GOV [Mon, 3 Nov 2014 17:33:44 +0000 (17:33 +0000)]
In equations for phi1[i] and phi2[i] changed + BGDist[i] to - BGDist[i].

git-svn-id: https://citdcbmipav.cit.nih.gov/repos-pub/mipav/trunk/mipav@13194 ba61647d-9d00-f842-95cd-605cb4296b96

4 years agoCreate resultImage for all methods.
ilb@NIH.GOV [Mon, 3 Nov 2014 17:21:31 +0000 (17:21 +0000)]
Create resultImage for all methods.

git-svn-id: https://citdcbmipav.cit.nih.gov/repos-pub/mipav/trunk/mipav@13193 ba61647d-9d00-f842-95cd-605cb4296b96

4 years agoCreate destImage for chan and vector methods. Remove original VOI from source image.
ilb@NIH.GOV [Mon, 3 Nov 2014 17:20:58 +0000 (17:20 +0000)]
Create destImage for chan and vector methods.  Remove original VOI from source image.

git-svn-id: https://citdcbmipav.cit.nih.gov/repos-pub/mipav/trunk/mipav@13192 ba61647d-9d00-f842-95cd-605cb4296b96

4 years agoIn equation for phi0[i] corrected + BGDist[i] to - BGDist[i].
ilb@NIH.GOV [Mon, 3 Nov 2014 17:10:34 +0000 (17:10 +0000)]
In equation for phi0[i] corrected + BGDist[i] to - BGDist[i].

git-svn-id: https://citdcbmipav.cit.nih.gov/repos-pub/mipav/trunk/mipav@13191 ba61647d-9d00-f842-95cd-605cb4296b96

4 years agoActive contours without edges added to Segmentation menu.
ilb@NIH.GOV [Fri, 31 Oct 2014 22:14:10 +0000 (22:14 +0000)]
Active contours without edges added to Segmentation menu.

git-svn-id: https://citdcbmipav.cit.nih.gov/repos-pub/mipav/trunk/mipav@13190 ba61647d-9d00-f842-95cd-605cb4296b96

4 years agoCall to JDialogActiveContoursWithoutEdges added.
ilb@NIH.GOV [Fri, 31 Oct 2014 22:12:54 +0000 (22:12 +0000)]
Call to JDialogActiveContoursWithoutEdges added.

git-svn-id: https://citdcbmipav.cit.nih.gov/repos-pub/mipav/trunk/mipav@13189 ba61647d-9d00-f842-95cd-605cb4296b96

4 years agoDialog created.
ilb@NIH.GOV [Fri, 31 Oct 2014 22:12:10 +0000 (22:12 +0000)]
Dialog created.

git-svn-id: https://citdcbmipav.cit.nih.gov/repos-pub/mipav/trunk/mipav@13188 ba61647d-9d00-f842-95cd-605cb4296b96

4 years agoAdd resultImage for method == twophase. Needs debugging.
ilb@NIH.GOV [Fri, 31 Oct 2014 22:11:38 +0000 (22:11 +0000)]
Add resultImage for method == twophase.  Needs debugging.

git-svn-id: https://citdcbmipav.cit.nih.gov/repos-pub/mipav/trunk/mipav@13187 ba61647d-9d00-f842-95cd-605cb4296b96

4 years agoChanged whole to holes and multiphase to twophase.
ilb@NIH.GOV [Fri, 31 Oct 2014 19:44:27 +0000 (19:44 +0000)]
Changed whole to holes and multiphase to twophase.

git-svn-id: https://citdcbmipav.cit.nih.gov/repos-pub/mipav/trunk/mipav@13186 ba61647d-9d00-f842-95cd-605cb4296b96

4 years agoChanged variable name from mask to maskType.
ilb@NIH.GOV [Fri, 31 Oct 2014 19:11:52 +0000 (19:11 +0000)]
Changed variable name from mask to maskType.

git-svn-id: https://citdcbmipav.cit.nih.gov/repos-pub/mipav/trunk/mipav@13185 ba61647d-9d00-f842-95cd-605cb4296b96

4 years agoChanged batch registration to use multithreading.
abokinsky [Thu, 30 Oct 2014 23:54:20 +0000 (23:54 +0000)]
Changed batch registration to use multithreading.

git-svn-id: https://citdcbmipav.cit.nih.gov/repos-pub/mipav/trunk/mipav@13184 ba61647d-9d00-f842-95cd-605cb4296b96

4 years agoNow have One time 2D registration and All times 2D registration buttons.
ilb@NIH.GOV [Thu, 30 Oct 2014 20:14:49 +0000 (20:14 +0000)]
Now have One time 2D registration and All times 2D registration buttons.

git-svn-id: https://citdcbmipav.cit.nih.gov/repos-pub/mipav/trunk/mipav@13183 ba61647d-9d00-f842-95cd-605cb4296b96

4 years agoAdded one time 2D registration.
ilb@NIH.GOV [Thu, 30 Oct 2014 20:14:15 +0000 (20:14 +0000)]
Added one time 2D registration.

git-svn-id: https://citdcbmipav.cit.nih.gov/repos-pub/mipav/trunk/mipav@13182 ba61647d-9d00-f842-95cd-605cb4296b96

4 years agoPorting typed in without proofing.
ilb@NIH.GOV [Thu, 30 Oct 2014 18:34:16 +0000 (18:34 +0000)]
Porting typed in without proofing.

git-svn-id: https://citdcbmipav.cit.nih.gov/repos-pub/mipav/trunk/mipav@13181 ba61647d-9d00-f842-95cd-605cb4296b96

4 years agoAdded logic for a probably impossible case where you can't find a major axis.
wangvg@NIH.GOV [Thu, 30 Oct 2014 14:25:55 +0000 (14:25 +0000)]
Added logic for a probably impossible case where you can't find a major axis.

git-svn-id: https://citdcbmipav.cit.nih.gov/repos-pub/mipav/trunk/mipav@13180 ba61647d-9d00-f842-95cd-605cb4296b96

4 years agoPorting continues.
ilb@NIH.GOV [Wed, 29 Oct 2014 22:13:06 +0000 (22:13 +0000)]
Porting continues.

git-svn-id: https://citdcbmipav.cit.nih.gov/repos-pub/mipav/trunk/mipav@13179 ba61647d-9d00-f842-95cd-605cb4296b96

4 years agosetRefWgtImage now sets xStart, xEnd, yStart, and yEnd used to restrict the range...
ilb@NIH.GOV [Wed, 29 Oct 2014 17:39:15 +0000 (17:39 +0000)]
setRefWgtImage now sets xStart, xEnd, yStart, and yEnd used to restrict the range of x and y traversed in the weighted cost functions.

git-svn-id: https://citdcbmipav.cit.nih.gov/repos-pub/mipav/trunk/mipav@13178 ba61647d-9d00-f842-95cd-605cb4296b96

4 years agoCorrected y * T10 to x * T10 and z * T20 to x * T20 in weighted functions.
ilb@NIH.GOV [Wed, 29 Oct 2014 17:12:15 +0000 (17:12 +0000)]
Corrected y * T10 to x * T10 and z * T20 to x * T20 in weighted functions.

git-svn-id: https://citdcbmipav.cit.nih.gov/repos-pub/mipav/trunk/mipav@13177 ba61647d-9d00-f842-95cd-605cb4296b96

4 years agoAdded functionality to adjust the polygonal area VOI as you add/move branches to...
wangvg@NIH.GOV [Wed, 29 Oct 2014 15:45:45 +0000 (15:45 +0000)]
Added functionality to adjust the polygonal area VOI as you add/move branches to the current trace. Should make updating the VOI easier for the user.

git-svn-id: https://citdcbmipav.cit.nih.gov/repos-pub/mipav/trunk/mipav@13176 ba61647d-9d00-f842-95cd-605cb4296b96

4 years agoSimplified setRefWgtImage.
ilb@NIH.GOV [Wed, 29 Oct 2014 14:53:26 +0000 (14:53 +0000)]
Simplified setRefWgtImage.

git-svn-id: https://citdcbmipav.cit.nih.gov/repos-pub/mipav/trunk/mipav@13175 ba61647d-9d00-f842-95cd-605cb4296b96

4 years agosetRefWgtImage now creates a limited x range for weighted functions. The weighted...
ilb@NIH.GOV [Tue, 28 Oct 2014 20:52:22 +0000 (20:52 +0000)]
setRefWgtImage now creates a limited x range for weighted functions.  The weighted functions have been rewritten removing findRangeX and putting in the limited x range.

git-svn-id: https://citdcbmipav.cit.nih.gov/repos-pub/mipav/trunk/mipav@13174 ba61647d-9d00-f842-95cd-605cb4296b96

4 years agoAdded logic for adding free nodes to the primary point. Haven't really used the prima...
wangvg@NIH.GOV [Tue, 28 Oct 2014 20:19:05 +0000 (20:19 +0000)]
Added logic for adding free nodes to the primary point. Haven't really used the primary point as it seemed like Akanni wasn't too keen on using it anymore, but adding it just in case it becomes a thing again.

git-svn-id: https://citdcbmipav.cit.nih.gov/repos-pub/mipav/trunk/mipav@13173 ba61647d-9d00-f842-95cd-605cb4296b96