mipav.git
3 years agoversion 7.3.0 release-7.3.0
mccreedy@NIH.GOV [Wed, 23 Dec 2015 21:22:52 +0000 (21:22 +0000)]
version 7.3.0

git-svn-id: https://citdcbmipav.cit.nih.gov/repos-pub/mipav/tags/release-7.3.0@14000 ba61647d-9d00-f842-95cd-605cb4296b96

3 years agoversion 7.3.0 release-7.3.0@13999
mccreedy@NIH.GOV [Wed, 23 Dec 2015 21:22:45 +0000 (21:22 +0000)]
version 7.3.0

git-svn-id: https://citdcbmipav.cit.nih.gov/repos-pub/mipav/trunk/mipav@13999 ba61647d-9d00-f842-95cd-605cb4296b96

3 years agoupdated imagej jar: Wed Dec 23 16:09:49 EST 2015
mccreedy@NIH.GOV [Wed, 23 Dec 2015 21:09:54 +0000 (21:09 +0000)]
updated imagej jar: Wed Dec 23 16:09:49 EST 2015

git-svn-id: https://citdcbmipav.cit.nih.gov/repos-pub/mipav/trunk/mipav@13997 ba61647d-9d00-f842-95cd-605cb4296b96

3 years agoblur.setDoMultiThread(doMultiThread) and blur2.setDoMultiThread(doMultiThread) added...
ilb@NIH.GOV [Thu, 17 Dec 2015 16:18:36 +0000 (16:18 +0000)]
blur.setDoMultiThread(doMultiThread) and blur2.setDoMultiThread(doMultiThread) added so that AlgorithGaussianBlur invocations inherit the AlgorithmRegOAR3D multithread setting instead of the default AlgorithmBase multithread setting.

git-svn-id: https://citdcbmipav.cit.nih.gov/repos-pub/mipav/trunk/mipav@13996 ba61647d-9d00-f842-95cd-605cb4296b96

3 years agoBefore multiThreading would always be decided by AlgorithmBase.isMultiThreadingEnable...
ilb@NIH.GOV [Thu, 17 Dec 2015 16:14:01 +0000 (16:14 +0000)]
Before multiThreading would always be decided by AlgorithmBase.isMultiThreadingEnabled.  A public setDoMultiThread accessor was added to allow the user to overrule the default multithreading setting from AlgorithmBase.

git-svn-id: https://citdcbmipav.cit.nih.gov/repos-pub/mipav/trunk/mipav@13995 ba61647d-9d00-f842-95cd-605cb4296b96

3 years ago3 static methods calculateCenterOfMass3D, subsampleBy2, and subsampleBy2XY were chang...
ilb@NIH.GOV [Tue, 15 Dec 2015 22:44:58 +0000 (22:44 +0000)]
3 static methods calculateCenterOfMass3D, subsampleBy2, and subsampleBy2XY were changed to static synchronized.

git-svn-id: https://citdcbmipav.cit.nih.gov/repos-pub/mipav/trunk/mipav@13994 ba61647d-9d00-f842-95cd-605cb4296b96

3 years agoAdded masking to the lattice straightening. Began prototype for the skin marker segme...
abokinsky [Fri, 11 Dec 2015 03:16:23 +0000 (03:16 +0000)]
Added masking to the lattice straightening. Began prototype for the skin marker segmentation.

git-svn-id: https://citdcbmipav.cit.nih.gov/repos-pub/mipav/trunk/mipav@13993 ba61647d-9d00-f842-95cd-605cb4296b96

3 years agoAdded boolean jpeg2000.
ilb@NIH.GOV [Wed, 9 Dec 2015 16:34:13 +0000 (16:34 +0000)]
Added boolean jpeg2000.

git-svn-id: https://citdcbmipav.cit.nih.gov/repos-pub/mipav/trunk/mipav@13992 ba61647d-9d00-f842-95cd-605cb4296b96

3 years agoCan read CMU-1-Small-Region.SVS.
ilb@NIH.GOV [Mon, 7 Dec 2015 17:36:21 +0000 (17:36 +0000)]
Can read CMU-1-Small-Region.SVS.

git-svn-id: https://citdcbmipav.cit.nih.gov/repos-pub/mipav/trunk/mipav@13991 ba61647d-9d00-f842-95cd-605cb4296b96

3 years agoWhen lzwCompression = true, set jpegCompression = false and when jpegCompression...
ilb@NIH.GOV [Thu, 3 Dec 2015 23:14:04 +0000 (23:14 +0000)]
When lzwCompression = true, set jpegCompression = false and when jpegCompression = true, set lzwCompression = false.

git-svn-id: https://citdcbmipav.cit.nih.gov/repos-pub/mipav/trunk/mipav@13990 ba61647d-9d00-f842-95cd-605cb4296b96

3 years agoStarted work on.
ilb@NIH.GOV [Thu, 3 Dec 2015 22:36:18 +0000 (22:36 +0000)]
Started work on.

git-svn-id: https://citdcbmipav.cit.nih.gov/repos-pub/mipav/trunk/mipav@13989 ba61647d-9d00-f842-95cd-605cb4296b96

3 years agoStarted work on.
ilb@NIH.GOV [Thu, 3 Dec 2015 22:35:52 +0000 (22:35 +0000)]
Started work on.

git-svn-id: https://citdcbmipav.cit.nih.gov/repos-pub/mipav/trunk/mipav@13988 ba61647d-9d00-f842-95cd-605cb4296b96

3 years agoAdded readSVS.
ilb@NIH.GOV [Thu, 3 Dec 2015 22:35:28 +0000 (22:35 +0000)]
Added readSVS.

git-svn-id: https://citdcbmipav.cit.nih.gov/repos-pub/mipav/trunk/mipav@13987 ba61647d-9d00-f842-95cd-605cb4296b96

3 years agoAdded FileUtility.SVS.
ilb@NIH.GOV [Thu, 3 Dec 2015 22:15:57 +0000 (22:15 +0000)]
Added FileUtility.SVS.

git-svn-id: https://citdcbmipav.cit.nih.gov/repos-pub/mipav/trunk/mipav@13986 ba61647d-9d00-f842-95cd-605cb4296b96

3 years agoAdded SVS file format.
ilb@NIH.GOV [Thu, 3 Dec 2015 22:12:12 +0000 (22:12 +0000)]
Added SVS file format.

git-svn-id: https://citdcbmipav.cit.nih.gov/repos-pub/mipav/trunk/mipav@13985 ba61647d-9d00-f842-95cd-605cb4296b96

3 years agoexp() fixed. Multiplications on integer part of positive exponent and divisions...
ilb@NIH.GOV [Mon, 30 Nov 2015 18:15:45 +0000 (18:15 +0000)]
exp() fixed.  Multiplications on integer part of positive exponent and divisions on integer part of negative exponent.

git-svn-id: https://citdcbmipav.cit.nih.gov/repos-pub/mipav/trunk/mipav@13984 ba61647d-9d00-f842-95cd-605cb4296b96

3 years agoComments corrected. All 6 self tests pass with fix in DoubleDouble exp().
ilb@NIH.GOV [Mon, 30 Nov 2015 18:05:48 +0000 (18:05 +0000)]
Comments corrected.  All 6 self tests pass with fix in DoubleDouble exp().

git-svn-id: https://citdcbmipav.cit.nih.gov/repos-pub/mipav/trunk/mipav@13983 ba61647d-9d00-f842-95cd-605cb4296b96

3 years agoSped up exp() for large magnitude numbers.
ilb@NIH.GOV [Fri, 27 Nov 2015 22:35:25 +0000 (22:35 +0000)]
Sped up exp() for large magnitude numbers.

git-svn-id: https://citdcbmipav.cit.nih.gov/repos-pub/mipav/trunk/mipav@13982 ba61647d-9d00-f842-95cd-605cb4296b96

3 years agoArray initializations put in zunk1 and zqcai. 5 of 6 self tests for BESSEL_H, BESSEL...
ilb@NIH.GOV [Fri, 27 Nov 2015 21:18:47 +0000 (21:18 +0000)]
Array initializations put in zunk1 and zqcai.  5 of 6 self tests for BESSEL_H, BESSEL_I, BESSEL_J, BESSEL_K, and BESSEL_Y pass both without overflow and with overflow.  1 of the 6 self tests AIRY_AI does not complete in a reasonable amount of time when run without overflow.  Must find the cause of slowdown for AIRY_AI self test.

git-svn-id: https://citdcbmipav.cit.nih.gov/repos-pub/mipav/trunk/mipav@13981 ba61647d-9d00-f842-95cd-605cb4296b96

3 years agoPut in precalculated values of epsilon, r1m5, and tiny.
ilb@NIH.GOV [Fri, 27 Nov 2015 20:16:28 +0000 (20:16 +0000)]
Put in precalculated values of epsilon, r1m5, and tiny.

git-svn-id: https://citdcbmipav.cit.nih.gov/repos-pub/mipav/trunk/mipav@13980 ba61647d-9d00-f842-95cd-605cb4296b96

3 years agoChanged Bessel to BesselEP in run.
ilb@NIH.GOV [Fri, 27 Nov 2015 17:56:13 +0000 (17:56 +0000)]
Changed Bessel to BesselEP in run.

git-svn-id: https://citdcbmipav.cit.nih.gov/repos-pub/mipav/trunk/mipav@13979 ba61647d-9d00-f842-95cd-605cb4296b96

3 years agoIn runTest changed Bessel to BesselEP.
ilb@NIH.GOV [Fri, 27 Nov 2015 17:43:07 +0000 (17:43 +0000)]
In runTest changed Bessel to BesselEP.

git-svn-id: https://citdcbmipav.cit.nih.gov/repos-pub/mipav/trunk/mipav@13978 ba61647d-9d00-f842-95cd-605cb4296b96

3 years agoTyped in but not proofed or tested.
ilb@NIH.GOV [Wed, 25 Nov 2015 23:07:29 +0000 (23:07 +0000)]
Typed in but not proofed or tested.

git-svn-id: https://citdcbmipav.cit.nih.gov/repos-pub/mipav/trunk/mipav@13977 ba61647d-9d00-f842-95cd-605cb4296b96

3 years agoCorrected comment.
ilb@NIH.GOV [Fri, 20 Nov 2015 17:43:54 +0000 (17:43 +0000)]
Corrected comment.

git-svn-id: https://citdcbmipav.cit.nih.gov/repos-pub/mipav/trunk/mipav@13976 ba61647d-9d00-f842-95cd-605cb4296b96

3 years agodeprecated getScannerCoordLPS function in ModelImage.java -- should use MipavCoordina...
abokinsky [Fri, 20 Nov 2015 16:56:31 +0000 (16:56 +0000)]
deprecated getScannerCoordLPS function in ModelImage.java -- should use MipavCoordinateSystems.fileToScanner instead.

git-svn-id: https://citdcbmipav.cit.nih.gov/repos-pub/mipav/trunk/mipav@13975 ba61647d-9d00-f842-95cd-605cb4296b96

3 years agoModified gradient magnitude calculation to use Java (not OpenCL). Cleaned up the... worm-untwisting-plugin-elife@13973
abokinsky [Thu, 19 Nov 2015 17:48:42 +0000 (17:48 +0000)]
Modified gradient magnitude calculation to use Java (not OpenCL). Cleaned up the segmentation code.

git-svn-id: https://citdcbmipav.cit.nih.gov/repos-pub/mipav/trunk/mipav@13972 ba61647d-9d00-f842-95cd-605cb4296b96

3 years agoChanges to gc_stats Microsoft Excel file completed.
ilb@NIH.GOV [Thu, 19 Nov 2015 17:22:14 +0000 (17:22 +0000)]
Changes to gc_stats Microsoft Excel file completed.

git-svn-id: https://citdcbmipav.cit.nih.gov/repos-pub/mipav/trunk/mipav@13971 ba61647d-9d00-f842-95cd-605cb4296b96

3 years agoBegan changes on right side of Microsoft Excel file.
ilb@NIH.GOV [Wed, 18 Nov 2015 21:27:58 +0000 (21:27 +0000)]
Began changes on right side of Microsoft Excel file.

git-svn-id: https://citdcbmipav.cit.nih.gov/repos-pub/mipav/trunk/mipav@13970 ba61647d-9d00-f842-95cd-605cb4296b96

3 years agoAddition of branches outside of growth cone added to left side of gc_stats Microsoft...
ilb@NIH.GOV [Wed, 18 Nov 2015 19:37:05 +0000 (19:37 +0000)]
Addition of branches outside of growth cone added to left side of gc_stats Microsoft Excel file for Choose filament.

git-svn-id: https://citdcbmipav.cit.nih.gov/repos-pub/mipav/trunk/mipav@13969 ba61647d-9d00-f842-95cd-605cb4296b96

3 years agoRemoved progress bar creation from readTiff() because it was causing reads of a multi...
mccreedy@NIH.GOV [Wed, 18 Nov 2015 18:17:05 +0000 (18:17 +0000)]
Removed progress bar creation from readTiff() because it was causing reads of a multi-slice tiff file to go from ~20s to dozens of minutes.  May be a swing threading issue.

git-svn-id: https://citdcbmipav.cit.nih.gov/repos-pub/mipav/trunk/mipav@13968 ba61647d-9d00-f842-95cd-605cb4296b96

3 years agoAdded memory checks and error dialogs for the volume renderer. Disabled the gradient... worm-untwisting-plugin-elife@13966
abokinsky [Wed, 18 Nov 2015 01:45:16 +0000 (01:45 +0000)]
Added memory checks and error dialogs for the volume renderer. Disabled the gradient magnitude calculation for the plugin.

git-svn-id: https://citdcbmipav.cit.nih.gov/repos-pub/mipav/trunk/mipav@13965 ba61647d-9d00-f842-95cd-605cb4296b96

3 years ago1)Integrate CSV recording into full screen viewer
ruida@NIH.GOV [Tue, 17 Nov 2015 22:20:06 +0000 (22:20 +0000)]
1)Integrate CSV recording into full screen viewer
2)End recording on exit of full screen viewer
3)In CSV make sure that slice number matches instance number (1-based, not 0-based number)
4) Move the landmark icon to half between scaled image and screen.
5) Use upper left icon center as the Min Reference point, right lower icon center as the Max Referece point.
6) Recording now only winlevel and sliding events.  Recording mouse location according to min referece point.

git-svn-id: https://citdcbmipav.cit.nih.gov/repos-pub/mipav/trunk/mipav@13964 ba61647d-9d00-f842-95cd-605cb4296b96

3 years agoOutput position of lower right icon center to console.
ilb@NIH.GOV [Tue, 17 Nov 2015 21:58:49 +0000 (21:58 +0000)]
Output position of lower right icon center to console.

git-svn-id: https://citdcbmipav.cit.nih.gov/repos-pub/mipav/trunk/mipav@13963 ba61647d-9d00-f842-95cd-605cb4296b96

3 years agoIcons moved for widthRatio > heightRatio. Center of upper left icon output to console.
ilb@NIH.GOV [Tue, 17 Nov 2015 21:19:17 +0000 (21:19 +0000)]
Icons moved for widthRatio > heightRatio.  Center of upper left icon output to console.

git-svn-id: https://citdcbmipav.cit.nih.gov/repos-pub/mipav/trunk/mipav@13962 ba61647d-9d00-f842-95cd-605cb4296b96

3 years agoAdded mod function.
ilb@NIH.GOV [Fri, 13 Nov 2015 17:18:08 +0000 (17:18 +0000)]
Added mod function.

git-svn-id: https://citdcbmipav.cit.nih.gov/repos-pub/mipav/trunk/mipav@13961 ba61647d-9d00-f842-95cd-605cb4296b96

3 years agoIn transform2DVOI, transform3DVOI, and transform3DVOIByte curves belonging to the...
ilb@NIH.GOV [Thu, 12 Nov 2015 19:25:39 +0000 (19:25 +0000)]
In transform2DVOI, transform3DVOI, and transform3DVOIByte curves belonging to the original VOI stay grouped in the same VOI after transformation with the same color and names.

git-svn-id: https://citdcbmipav.cit.nih.gov/repos-pub/mipav/trunk/mipav@13960 ba61647d-9d00-f842-95cd-605cb4296b96

3 years agoCode cleanup. Added system.exit when closing the plugin when it's standalone. Cleane... worm-untwisting-plugin-elife@13958
abokinsky [Thu, 12 Nov 2015 14:01:49 +0000 (14:01 +0000)]
Code cleanup. Added system.exit when closing the plugin when it's standalone.  Cleaned up the segmentation code.

git-svn-id: https://citdcbmipav.cit.nih.gov/repos-pub/mipav/trunk/mipav@13957 ba61647d-9d00-f842-95cd-605cb4296b96

3 years agoRemoved System.out.println statements.
ilb@NIH.GOV [Tue, 10 Nov 2015 17:01:04 +0000 (17:01 +0000)]
Removed System.out.println statements.

git-svn-id: https://citdcbmipav.cit.nih.gov/repos-pub/mipav/trunk/mipav@13956 ba61647d-9d00-f842-95cd-605cb4296b96

3 years agoIn transform2DVOI curves belonging to the original VOI stay grouped in the same VOI...
ilb@NIH.GOV [Tue, 10 Nov 2015 16:57:43 +0000 (16:57 +0000)]
In transform2DVOI curves belonging to the original VOI stay grouped in the same VOI after transformation and have the same name and color.

git-svn-id: https://citdcbmipav.cit.nih.gov/repos-pub/mipav/trunk/mipav@13955 ba61647d-9d00-f842-95cd-605cb4296b96

3 years agotransform3DVOI now produces VOIs with the same names and colors as the original VOIs.
ilb@NIH.GOV [Tue, 10 Nov 2015 16:52:06 +0000 (16:52 +0000)]
transform3DVOI now produces VOIs with the same names and colors as the original VOIs.

git-svn-id: https://citdcbmipav.cit.nih.gov/repos-pub/mipav/trunk/mipav@13954 ba61647d-9d00-f842-95cd-605cb4296b96

3 years agoIn transform3DVOI curves belonging to the original VOI stay grouped in the same VOI...
ilb@NIH.GOV [Mon, 9 Nov 2015 22:42:32 +0000 (22:42 +0000)]
In transform3DVOI curves belonging to the original VOI stay grouped in the same VOI after transformation.

git-svn-id: https://citdcbmipav.cit.nih.gov/repos-pub/mipav/trunk/mipav@13953 ba61647d-9d00-f842-95cd-605cb4296b96

3 years agoPrevent out of bounds errors.
ilb@NIH.GOV [Mon, 9 Nov 2015 21:50:47 +0000 (21:50 +0000)]
Prevent out of bounds errors.

git-svn-id: https://citdcbmipav.cit.nih.gov/repos-pub/mipav/trunk/mipav@13952 ba61647d-9d00-f842-95cd-605cb4296b96

3 years agoPrevent out of bounds error in secondOrderAttributes.
ilb@NIH.GOV [Mon, 9 Nov 2015 21:36:29 +0000 (21:36 +0000)]
Prevent out of bounds error in secondOrderAttributes.

git-svn-id: https://citdcbmipav.cit.nih.gov/repos-pub/mipav/trunk/mipav@13951 ba61647d-9d00-f842-95cd-605cb4296b96

3 years agoPrevent out of bounds error in distance(Vector3f, Vector3f, float[][]).
ilb@NIH.GOV [Mon, 9 Nov 2015 21:23:02 +0000 (21:23 +0000)]
Prevent out of bounds error in distance(Vector3f, Vector3f, float[][]).

git-svn-id: https://citdcbmipav.cit.nih.gov/repos-pub/mipav/trunk/mipav@13950 ba61647d-9d00-f842-95cd-605cb4296b96

3 years agoPrevent z from going out of bounds in draw3DVOIs.
ilb@NIH.GOV [Mon, 9 Nov 2015 21:15:46 +0000 (21:15 +0000)]
Prevent z from going out of bounds in draw3DVOIs.

git-svn-id: https://citdcbmipav.cit.nih.gov/repos-pub/mipav/trunk/mipav@13949 ba61647d-9d00-f842-95cd-605cb4296b96

3 years agoPrevent slice number for resolutions from going out of bounds.
ilb@NIH.GOV [Mon, 9 Nov 2015 21:07:00 +0000 (21:07 +0000)]
Prevent slice number for resolutions from going out of bounds.

git-svn-id: https://citdcbmipav.cit.nih.gov/repos-pub/mipav/trunk/mipav@13948 ba61647d-9d00-f842-95cd-605cb4296b96

3 years agoIn draw3DVOIs add int z = (int)Math.round(kVOI3D.elementAt(0).z) and change getResolu... worm-untwisting-plugin-elife@13946
ilb@NIH.GOV [Mon, 9 Nov 2015 18:33:24 +0000 (18:33 +0000)]
In draw3DVOIs add int z = (int)Math.round(kVOI3D.elementAt(0).z) and change getResolutions(0) to getResolutions(z).

git-svn-id: https://citdcbmipav.cit.nih.gov/repos-pub/mipav/trunk/mipav@13945 ba61647d-9d00-f842-95cd-605cb4296b96

3 years agoSwitched from use of getLengthPtToPt(float[] resolutions) to getLengthPtToPt(float...
ilb@NIH.GOV [Mon, 9 Nov 2015 17:11:58 +0000 (17:11 +0000)]
Switched from use of getLengthPtToPt(float[] resolutions) to getLengthPtToPt(float[][] resolutions).

git-svn-id: https://citdcbmipav.cit.nih.gov/repos-pub/mipav/trunk/mipav@13944 ba61647d-9d00-f842-95cd-605cb4296b96

3 years agoIn showIntensityInfo use float resolutions[][] = new float[zDim][];
ilb@NIH.GOV [Mon, 9 Nov 2015 16:44:46 +0000 (16:44 +0000)]
In showIntensityInfo use float resolutions[][] = new float[zDim][];

git-svn-id: https://citdcbmipav.cit.nih.gov/repos-pub/mipav/trunk/mipav@13943 ba61647d-9d00-f842-95cd-605cb4296b96

3 years agoCreated double getLengthPtToPt(float[][] resolutions).
ilb@NIH.GOV [Mon, 9 Nov 2015 16:42:17 +0000 (16:42 +0000)]
Created double getLengthPtToPt(float[][] resolutions).

git-svn-id: https://citdcbmipav.cit.nih.gov/repos-pub/mipav/trunk/mipav@13942 ba61647d-9d00-f842-95cd-605cb4296b96

3 years agoCreated double distance(final Vector3f pt1, final Vector3f pt2, final float[][] res).
ilb@NIH.GOV [Mon, 9 Nov 2015 16:40:14 +0000 (16:40 +0000)]
Created double distance(final Vector3f pt1, final Vector3f pt2, final float[][] res).

git-svn-id: https://citdcbmipav.cit.nih.gov/repos-pub/mipav/trunk/mipav@13941 ba61647d-9d00-f842-95cd-605cb4296b96

3 years agoChanged float[] afResolutions = kImage.getResolutions(0); to
ilb@NIH.GOV [Fri, 6 Nov 2015 22:39:27 +0000 (22:39 +0000)]
Changed float[] afResolutions = kImage.getResolutions(0); to
float[] afResolutions = kImage.getResolutions((int)Math.round(kInput.Z));

git-svn-id: https://citdcbmipav.cit.nih.gov/repos-pub/mipav/trunk/mipav@13940 ba61647d-9d00-f842-95cd-605cb4296b96

3 years agoIn calcStatsPerContour, calcStatsPerContourRGB, calcStatsTotal, and calcStatsTotalRGB...
ilb@NIH.GOV [Fri, 6 Nov 2015 22:05:23 +0000 (22:05 +0000)]
In calcStatsPerContour, calcStatsPerContourRGB, calcStatsTotal, and calcStatsTotalRGB use specific srcImage.getFileInfo()[z] in calcLargestDistance, geometricCenter, and getLengthPtToPt.

git-svn-id: https://citdcbmipav.cit.nih.gov/repos-pub/mipav/trunk/mipav@13939 ba61647d-9d00-f842-95cd-605cb4296b96

3 years agoIn run() before always used fileInfo = srcImage.getFileInfo()[zDim/2]. Now if orient...
ilb@NIH.GOV [Fri, 6 Nov 2015 20:18:36 +0000 (20:18 +0000)]
In run() before always used fileInfo = srcImage.getFileInfo()[zDim/2].  Now if orientation == VOIBase.ZPLANE, use fileInfo = srcImage.getFileInfo()[sortedZ] and z = (int)Math.round(contours.get(q).elementAt(0).Z) and fileInfo = srcImage.getFileInfo()[z].

git-svn-id: https://citdcbmipav.cit.nih.gov/repos-pub/mipav/trunk/mipav@13938 ba61647d-9d00-f842-95cd-605cb4296b96

3 years agoIn secondOrderAttributes changed xRes, yRes, and zRes to xRes[], yRes[], and zRes...
ilb@NIH.GOV [Fri, 6 Nov 2015 19:02:12 +0000 (19:02 +0000)]
In secondOrderAttributes changed xRes, yRes, and zRes to xRes[], yRes[], and zRes[] to contain values for each slice.

git-svn-id: https://citdcbmipav.cit.nih.gov/repos-pub/mipav/trunk/mipav@13936 ba61647d-9d00-f842-95cd-605cb4296b96

3 years agoIn algorithmPerformed introduced specificRedName, specificGreenName, and specificBlue...
ilb@NIH.GOV [Fri, 6 Nov 2015 19:00:28 +0000 (19:00 +0000)]
In algorithmPerformed introduced specificRedName, specificGreenName, and specificBlueName so that properties.getVOIStatistic would not give null pointer errors for color images.

git-svn-id: https://citdcbmipav.cit.nih.gov/repos-pub/mipav/trunk/mipav@13935 ba61647d-9d00-f842-95cd-605cb4296b96

3 years agoUpdated plugin pipeline for two-channel images.
abokinsky [Fri, 6 Nov 2015 18:35:22 +0000 (18:35 +0000)]
Updated plugin pipeline for two-channel images.

git-svn-id: https://citdcbmipav.cit.nih.gov/repos-pub/mipav/trunk/mipav@13934 ba61647d-9d00-f842-95cd-605cb4296b96

3 years agoIn findPositionAndIntensity changed kImage.getResolutions(0) to kImage.getResolutions...
ilb@NIH.GOV [Fri, 6 Nov 2015 17:48:14 +0000 (17:48 +0000)]
In findPositionAndIntensity changed kImage.getResolutions(0) to kImage.getResolutions(indexZ).

git-svn-id: https://citdcbmipav.cit.nih.gov/repos-pub/mipav/trunk/mipav@13933 ba61647d-9d00-f842-95cd-605cb4296b96

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