mipav.git
2 years agoversion 7.4.0 release-7.4.0@14775
mccreedy@NIH.GOV [Fri, 9 Dec 2016 20:30:07 +0000 (20:30 +0000)]
version 7.4.0

git-svn-id: https://citdcbmipav.cit.nih.gov/repos-pub/mipav/trunk/mipav@14775 ba61647d-9d00-f842-95cd-605cb4296b96

2 years agoupdated imagej jar: Fri Dec 9 15:21:03 EST 2016
mccreedy@NIH.GOV [Fri, 9 Dec 2016 20:21:08 +0000 (20:21 +0000)]
updated imagej jar: Fri Dec  9 15:21:03 EST 2016

git-svn-id: https://citdcbmipav.cit.nih.gov/repos-pub/mipav/trunk/mipav@14774 ba61647d-9d00-f842-95cd-605cb4296b96

2 years agoImproved seam cell segmentation for worm untwisitng and dual-color untwisting. Added...
abokinsky [Fri, 9 Dec 2016 02:30:19 +0000 (02:30 +0000)]
Improved seam cell segmentation for worm untwisitng and dual-color untwisting. Added batch mode testing for seam cell segmentation.

git-svn-id: https://citdcbmipav.cit.nih.gov/repos-pub/mipav/trunk/mipav@14773 ba61647d-9d00-f842-95cd-605cb4296b96

2 years agoRemoved <String> parameterization of JComboBox, which isn't available in Java 1.7.
mccreedy@NIH.GOV [Thu, 8 Dec 2016 21:34:54 +0000 (21:34 +0000)]
Removed <String> parameterization of JComboBox, which isn't available in Java 1.7.

git-svn-id: https://citdcbmipav.cit.nih.gov/repos-pub/mipav/trunk/mipav@14772 ba61647d-9d00-f842-95cd-605cb4296b96

2 years agoChanged URLS to https.
mccreedy@NIH.GOV [Thu, 8 Dec 2016 21:28:25 +0000 (21:28 +0000)]
Changed URLS to https.

git-svn-id: https://citdcbmipav.cit.nih.gov/repos-pub/mipav/trunk/mipav@14771 ba61647d-9d00-f842-95cd-605cb4296b96

2 years agoIn setVariables() requestFocus() and selectAll() lines add for text entry conditions.
ilb@NIH.GOV [Wed, 7 Dec 2016 21:32:11 +0000 (21:32 +0000)]
In setVariables() requestFocus() and selectAll() lines add for text entry conditions.

git-svn-id: https://citdcbmipav.cit.nih.gov/repos-pub/mipav/trunk/mipav@14770 ba61647d-9d00-f842-95cd-605cb4296b96

2 years agoIn setVariables() requestFocus and selectAll lines added for text entry errors.
ilb@NIH.GOV [Wed, 7 Dec 2016 21:26:51 +0000 (21:26 +0000)]
In setVariables() requestFocus and selectAll lines added for text entry errors.

git-svn-id: https://citdcbmipav.cit.nih.gov/repos-pub/mipav/trunk/mipav@14769 ba61647d-9d00-f842-95cd-605cb4296b96

2 years agoIn setVariables() added requestFocus and selectAll lines for incorrect responses.
ilb@NIH.GOV [Wed, 7 Dec 2016 20:20:34 +0000 (20:20 +0000)]
In setVariables() added requestFocus and selectAll lines for incorrect responses.

git-svn-id: https://citdcbmipav.cit.nih.gov/repos-pub/mipav/trunk/mipav@14768 ba61647d-9d00-f842-95cd-605cb4296b96

2 years agoIn subspaceEstim in 2 places changed itcee[i] to itcee[itceeIndex+i].
ilb@NIH.GOV [Wed, 7 Dec 2016 18:00:00 +0000 (18:00 +0000)]
In subspaceEstim in 2 places changed itcee[i] to itcee[itceeIndex+i].

git-svn-id: https://citdcbmipav.cit.nih.gov/repos-pub/mipav/trunk/mipav@14767 ba61647d-9d00-f842-95cd-605cb4296b96

2 years agoComments added.
ilb@NIH.GOV [Wed, 7 Dec 2016 17:47:44 +0000 (17:47 +0000)]
Comments added.

git-svn-id: https://citdcbmipav.cit.nih.gov/repos-pub/mipav/trunk/mipav@14766 ba61647d-9d00-f842-95cd-605cb4296b96

2 years agoComments added.
ilb@NIH.GOV [Wed, 7 Dec 2016 17:47:15 +0000 (17:47 +0000)]
Comments added.

git-svn-id: https://citdcbmipav.cit.nih.gov/repos-pub/mipav/trunk/mipav@14765 ba61647d-9d00-f842-95cd-605cb4296b96

2 years agoreplaceImage radio button disabled for color images.
ilb@NIH.GOV [Wed, 7 Dec 2016 17:27:09 +0000 (17:27 +0000)]
replaceImage radio button disabled for color images.

git-svn-id: https://citdcbmipav.cit.nih.gov/repos-pub/mipav/trunk/mipav@14764 ba61647d-9d00-f842-95cd-605cb4296b96

2 years agoRemove cf factor from destImage.importData and srcImage.importData since always impor...
ilb@NIH.GOV [Wed, 7 Dec 2016 17:21:46 +0000 (17:21 +0000)]
Remove cf factor from destImage.importData and srcImage.importData since always importing byte edge data and will not replace color image.

git-svn-id: https://citdcbmipav.cit.nih.gov/repos-pub/mipav/trunk/mipav@14763 ba61647d-9d00-f842-95cd-605cb4296b96

2 years agoConvert color to black and white with RED_WEIGHT, GREEN_WEIGHT, and BLUE_WEIGHT....
ilb@NIH.GOV [Wed, 7 Dec 2016 17:14:31 +0000 (17:14 +0000)]
Convert color to black and white with RED_WEIGHT, GREEN_WEIGHT, and BLUE_WEIGHT.  Color edge detection now works.

git-svn-id: https://citdcbmipav.cit.nih.gov/repos-pub/mipav/trunk/mipav@14762 ba61647d-9d00-f842-95cd-605cb4296b96

2 years agoCorrected srcImage.exportData for color images. Edge detection works for black and...
ilb@NIH.GOV [Wed, 7 Dec 2016 16:57:01 +0000 (16:57 +0000)]
Corrected srcImage.exportData for color images.  Edge detection works for black and white but not for color.

git-svn-id: https://citdcbmipav.cit.nih.gov/repos-pub/mipav/trunk/mipav@14761 ba61647d-9d00-f842-95cd-605cb4296b96

2 years agoIn init() changed setSize(600,600) to setSize(600,550).
ilb@NIH.GOV [Wed, 7 Dec 2016 16:33:44 +0000 (16:33 +0000)]
In init() changed setSize(600,600) to setSize(600,550).

git-svn-id: https://citdcbmipav.cit.nih.gov/repos-pub/mipav/trunk/mipav@14760 ba61647d-9d00-f842-95cd-605cb4296b96

2 years agoEmbedded confidence added to Edge detection menu.
ilb@NIH.GOV [Wed, 7 Dec 2016 16:29:28 +0000 (16:29 +0000)]
Embedded confidence added to Edge detection menu.

git-svn-id: https://citdcbmipav.cit.nih.gov/repos-pub/mipav/trunk/mipav@14759 ba61647d-9d00-f842-95cd-605cb4296b96

2 years agoAdded call to JDialogEmbeddedConfidenceEdgeDetection.
ilb@NIH.GOV [Wed, 7 Dec 2016 16:23:30 +0000 (16:23 +0000)]
Added call to JDialogEmbeddedConfidenceEdgeDetection.

git-svn-id: https://citdcbmipav.cit.nih.gov/repos-pub/mipav/trunk/mipav@14758 ba61647d-9d00-f842-95cd-605cb4296b96

2 years agoDialog created.
ilb@NIH.GOV [Tue, 6 Dec 2016 23:09:32 +0000 (23:09 +0000)]
Dialog created.

git-svn-id: https://citdcbmipav.cit.nih.gov/repos-pub/mipav/trunk/mipav@14757 ba61647d-9d00-f842-95cd-605cb4296b96

2 years agoInitialize kernelSize = KERNEL_SIZE.
ilb@NIH.GOV [Tue, 6 Dec 2016 23:09:01 +0000 (23:09 +0000)]
Initialize kernelSize = KERNEL_SIZE.

git-svn-id: https://citdcbmipav.cit.nih.gov/repos-pub/mipav/trunk/mipav@14756 ba61647d-9d00-f842-95cd-605cb4296b96

2 years agoUnneeded imports removed and extraneous line removed from init.
ilb@NIH.GOV [Tue, 6 Dec 2016 21:23:07 +0000 (21:23 +0000)]
Unneeded imports removed and extraneous line removed from init.

git-svn-id: https://citdcbmipav.cit.nih.gov/repos-pub/mipav/trunk/mipav@14755 ba61647d-9d00-f842-95cd-605cb4296b96

2 years agoError message corrected.
ilb@NIH.GOV [Tue, 6 Dec 2016 21:17:24 +0000 (21:17 +0000)]
Error message corrected.

git-svn-id: https://citdcbmipav.cit.nih.gov/repos-pub/mipav/trunk/mipav@14754 ba61647d-9d00-f842-95cd-605cb4296b96

2 years agoFinished typing in.
ilb@NIH.GOV [Tue, 6 Dec 2016 20:38:58 +0000 (20:38 +0000)]
Finished typing in.

git-svn-id: https://citdcbmipav.cit.nih.gov/repos-pub/mipav/trunk/mipav@14753 ba61647d-9d00-f842-95cd-605cb4296b96

2 years agoPorting continues.
ilb@NIH.GOV [Mon, 5 Dec 2016 23:16:36 +0000 (23:16 +0000)]
Porting continues.

git-svn-id: https://citdcbmipav.cit.nih.gov/repos-pub/mipav/trunk/mipav@14752 ba61647d-9d00-f842-95cd-605cb4296b96

2 years agoRemoved <String> parameterization of JComboBox, which isn't available in Java 1.7.
mccreedy@NIH.GOV [Mon, 5 Dec 2016 22:18:59 +0000 (22:18 +0000)]
Removed <String> parameterization of JComboBox, which isn't available in Java 1.7.

git-svn-id: https://citdcbmipav.cit.nih.gov/repos-pub/mipav/trunk/mipav@14751 ba61647d-9d00-f842-95cd-605cb4296b96

2 years agoStarted porting.
ilb@NIH.GOV [Fri, 2 Dec 2016 23:19:21 +0000 (23:19 +0000)]
Started porting.

git-svn-id: https://citdcbmipav.cit.nih.gov/repos-pub/mipav/trunk/mipav@14750 ba61647d-9d00-f842-95cd-605cb4296b96

2 years agoAdded check box to create segmentation boundaries image.
ilb@NIH.GOV [Fri, 2 Dec 2016 19:27:08 +0000 (19:27 +0000)]
Added check box to create segmentation boundaries image.

git-svn-id: https://citdcbmipav.cit.nih.gov/repos-pub/mipav/trunk/mipav@14749 ba61647d-9d00-f842-95cd-605cb4296b96

2 years agoPass boundariesImage input parameter and if not null create segmentation boundaries...
ilb@NIH.GOV [Fri, 2 Dec 2016 19:26:22 +0000 (19:26 +0000)]
Pass boundariesImage input parameter and if not null create segmentation boundaries image.

git-svn-id: https://citdcbmipav.cit.nih.gov/repos-pub/mipav/trunk/mipav@14748 ba61647d-9d00-f842-95cd-605cb4296b96

2 years agoCheck box to create filtered image added.
ilb@NIH.GOV [Fri, 2 Dec 2016 17:31:08 +0000 (17:31 +0000)]
Check box to create filtered image added.

git-svn-id: https://citdcbmipav.cit.nih.gov/repos-pub/mipav/trunk/mipav@14747 ba61647d-9d00-f842-95cd-605cb4296b96

2 years agofilteredImage input parameter added and if not null filteredImage is created.
ilb@NIH.GOV [Fri, 2 Dec 2016 17:30:07 +0000 (17:30 +0000)]
filteredImage input parameter added and if not null filteredImage is created.

git-svn-id: https://citdcbmipav.cit.nih.gov/repos-pub/mipav/trunk/mipav@14746 ba61647d-9d00-f842-95cd-605cb4296b96

2 years agowidth*height and height*width replaced with L.
ilb@NIH.GOV [Thu, 1 Dec 2016 17:48:54 +0000 (17:48 +0000)]
width*height and height*width replaced with L.

git-svn-id: https://citdcbmipav.cit.nih.gov/repos-pub/mipav/trunk/mipav@14745 ba61647d-9d00-f842-95cd-605cb4296b96

2 years agoRemoved class_state.INPUT_DEFINED and class_state.LATTICE_DEFINED.
ilb@NIH.GOV [Thu, 1 Dec 2016 17:09:10 +0000 (17:09 +0000)]
Removed class_state.INPUT_DEFINED and class_state.LATTICE_DEFINED.

git-svn-id: https://citdcbmipav.cit.nih.gov/repos-pub/mipav/trunk/mipav@14744 ba61647d-9d00-f842-95cd-605cb4296b96

2 years agoRemoved unused byte [] visitTable.
ilb@NIH.GOV [Thu, 1 Dec 2016 16:34:49 +0000 (16:34 +0000)]
Removed unused byte [] visitTable.

git-svn-id: https://citdcbmipav.cit.nih.gov/repos-pub/mipav/trunk/mipav@14743 ba61647d-9d00-f842-95cd-605cb4296b96

2 years agoRemoved unused ErrorLevel and ErrorStatus code.
ilb@NIH.GOV [Thu, 1 Dec 2016 16:28:29 +0000 (16:28 +0000)]
Removed unused ErrorLevel and ErrorStatus code.

git-svn-id: https://citdcbmipav.cit.nih.gov/repos-pub/mipav/trunk/mipav@14742 ba61647d-9d00-f842-95cd-605cb4296b96

2 years agoin newNonOptimizedFilter for N other than 1 or 3 fixed error in original source code...
ilb@NIH.GOV [Wed, 30 Nov 2016 21:45:21 +0000 (21:45 +0000)]
in newNonOptimizedFilter for N other than 1 or 3 fixed error in original source code.  Replaced second sdata[idxs++] = (i%width)/sigmaS; with sdata[idxs++] = (i/width)/sigmaS;

git-svn-id: https://citdcbmipav.cit.nih.gov/repos-pub/mipav/trunk/mipav@14741 ba61647d-9d00-f842-95cd-605cb4296b96

2 years agoIn RGBtoLUV corrected offsets of rgb array.
ilb@NIH.GOV [Wed, 30 Nov 2016 19:59:02 +0000 (19:59 +0000)]
In RGBtoLUV corrected offsets of rgb array.

git-svn-id: https://citdcbmipav.cit.nih.gov/repos-pub/mipav/trunk/mipav@14740 ba61647d-9d00-f842-95cd-605cb4296b96

2 years agoIn segment() corrected pxValue = (byte)(msRawData[i] + 0.5) to pxValue = (int)(msRawD...
ilb@NIH.GOV [Wed, 30 Nov 2016 18:21:42 +0000 (18:21 +0000)]
In segment() corrected pxValue = (byte)(msRawData[i] + 0.5) to pxValue = (int)(msRawData[i]+ 0.5).

git-svn-id: https://citdcbmipav.cit.nih.gov/repos-pub/mipav/trunk/mipav@14739 ba61647d-9d00-f842-95cd-605cb4296b96

2 years agoIn buildRAM initialize raList and raPool arrays with new RAList() at every array...
ilb@NIH.GOV [Wed, 30 Nov 2016 17:50:11 +0000 (17:50 +0000)]
In buildRAM initialize raList and raPool arrays with new RAList() at every array position.  Set raPool[i].next = new RAList[1] before setting raPool[i].next[0] = raPool[i+1].

git-svn-id: https://citdcbmipav.cit.nih.gov/repos-pub/mipav/trunk/mipav@14738 ba61647d-9d00-f842-95cd-605cb4296b96

2 years agoAdded in JRadioButton newImage and JRadioButton replaceImage.
ilb@NIH.GOV [Wed, 30 Nov 2016 17:46:07 +0000 (17:46 +0000)]
Added in JRadioButton newImage and JRadioButton replaceImage.

git-svn-id: https://citdcbmipav.cit.nih.gov/repos-pub/mipav/trunk/mipav@14737 ba61647d-9d00-f842-95cd-605cb4296b96

2 years agoIn setVariables create weightMap.
ilb@NIH.GOV [Wed, 30 Nov 2016 16:50:55 +0000 (16:50 +0000)]
In setVariables create weightMap.

git-svn-id: https://citdcbmipav.cit.nih.gov/repos-pub/mipav/trunk/mipav@14736 ba61647d-9d00-f842-95cd-605cb4296b96

2 years agoAdded Mean shift to Segmentation menu.
ilb@NIH.GOV [Wed, 30 Nov 2016 16:43:28 +0000 (16:43 +0000)]
Added Mean shift to Segmentation menu.

git-svn-id: https://citdcbmipav.cit.nih.gov/repos-pub/mipav/trunk/mipav@14735 ba61647d-9d00-f842-95cd-605cb4296b96

2 years agoAdded call to JDialogMeanShiftSegmentation.
ilb@NIH.GOV [Wed, 30 Nov 2016 16:41:52 +0000 (16:41 +0000)]
Added call to JDialogMeanShiftSegmentation.

git-svn-id: https://citdcbmipav.cit.nih.gov/repos-pub/mipav/trunk/mipav@14734 ba61647d-9d00-f842-95cd-605cb4296b96

2 years agoDialog completed.
ilb@NIH.GOV [Wed, 30 Nov 2016 16:41:07 +0000 (16:41 +0000)]
Dialog completed.

git-svn-id: https://citdcbmipav.cit.nih.gov/repos-pub/mipav/trunk/mipav@14733 ba61647d-9d00-f842-95cd-605cb4296b96

2 years agoImproved worm segmentation post-untwisting for embryos with both the skin and seam...
abokinsky [Wed, 30 Nov 2016 04:17:28 +0000 (04:17 +0000)]
Improved worm segmentation post-untwisting for embryos with both the skin and seam cell markers.

git-svn-id: https://citdcbmipav.cit.nih.gov/repos-pub/mipav/trunk/mipav@14732 ba61647d-9d00-f842-95cd-605cb4296b96

2 years agoDialog started.
ilb@NIH.GOV [Mon, 28 Nov 2016 23:16:15 +0000 (23:16 +0000)]
Dialog started.

git-svn-id: https://citdcbmipav.cit.nih.gov/repos-pub/mipav/trunk/mipav@14731 ba61647d-9d00-f842-95cd-605cb4296b96

2 years agoComment corrected.
ilb@NIH.GOV [Mon, 28 Nov 2016 23:15:33 +0000 (23:15 +0000)]
Comment corrected.

git-svn-id: https://citdcbmipav.cit.nih.gov/repos-pub/mipav/trunk/mipav@14730 ba61647d-9d00-f842-95cd-605cb4296b96

2 years agoChanged private enum SpeedUpLevel to public enum SpeedUpLevel and changed private...
ilb@NIH.GOV [Mon, 28 Nov 2016 22:09:34 +0000 (22:09 +0000)]
Changed private enum SpeedUpLevel to public enum SpeedUpLevel and changed private enum kernelType to public enum kernelType.

git-svn-id: https://citdcbmipav.cit.nih.gov/repos-pub/mipav/trunk/mipav@14729 ba61647d-9d00-f842-95cd-605cb4296b96

2 years agoFinished port. No proofing or running yet.
ilb@NIH.GOV [Mon, 28 Nov 2016 20:43:22 +0000 (20:43 +0000)]
Finished port.  No proofing or running yet.

git-svn-id: https://citdcbmipav.cit.nih.gov/repos-pub/mipav/trunk/mipav@14728 ba61647d-9d00-f842-95cd-605cb4296b96

2 years agoPorting continues.
ilb@NIH.GOV [Fri, 25 Nov 2016 23:14:51 +0000 (23:14 +0000)]
Porting continues.

git-svn-id: https://citdcbmipav.cit.nih.gov/repos-pub/mipav/trunk/mipav@14727 ba61647d-9d00-f842-95cd-605cb4296b96

2 years agoStarted porting.
ilb@NIH.GOV [Wed, 23 Nov 2016 23:12:50 +0000 (23:12 +0000)]
Started porting.

git-svn-id: https://citdcbmipav.cit.nih.gov/repos-pub/mipav/trunk/mipav@14726 ba61647d-9d00-f842-95cd-605cb4296b96

2 years agoAdded permission to port from Ilan Shimshoni.
ilb@NIH.GOV [Wed, 23 Nov 2016 21:23:45 +0000 (21:23 +0000)]
Added permission to port from Ilan Shimshoni.

git-svn-id: https://citdcbmipav.cit.nih.gov/repos-pub/mipav/trunk/mipav@14725 ba61647d-9d00-f842-95cd-605cb4296b96

2 years agoWorks on 2D image with 2000 points. percent and width now properly initialized.
ilb@NIH.GOV [Tue, 22 Nov 2016 19:22:54 +0000 (19:22 +0000)]
Works on 2D image with 2000 points.  percent and width now properly initialized.

git-svn-id: https://citdcbmipav.cit.nih.gov/repos-pub/mipav/trunk/mipav@14724 ba61647d-9d00-f842-95cd-605cb4296b96

2 years agoWorks on 2D image with 2000 points.
ilb@NIH.GOV [Tue, 22 Nov 2016 19:21:44 +0000 (19:21 +0000)]
Works on 2D image with 2000 points.

git-svn-id: https://citdcbmipav.cit.nih.gov/repos-pub/mipav/trunk/mipav@14723 ba61647d-9d00-f842-95cd-605cb4296b96

2 years agoCreate prunedModesImage to pass to algorithm call.
ilb@NIH.GOV [Mon, 21 Nov 2016 23:14:12 +0000 (23:14 +0000)]
Create prunedModesImage to pass to algorithm call.

git-svn-id: https://citdcbmipav.cit.nih.gov/repos-pub/mipav/trunk/mipav@14722 ba61647d-9d00-f842-95cd-605cb4296b96

2 years agoAdded input parameter ModelImage prunedModesImage. Debugging so now runs without...
ilb@NIH.GOV [Mon, 21 Nov 2016 23:12:20 +0000 (23:12 +0000)]
Added input parameter ModelImage prunedModesImage.  Debugging so now runs without crashing.

git-svn-id: https://citdcbmipav.cit.nih.gov/repos-pub/mipav/trunk/mipav@14721 ba61647d-9d00-f842-95cd-605cb4296b96

2 years agoFixed init().
ilb@NIH.GOV [Fri, 18 Nov 2016 22:55:07 +0000 (22:55 +0000)]
Fixed init().

git-svn-id: https://citdcbmipav.cit.nih.gov/repos-pub/mipav/trunk/mipav@14720 ba61647d-9d00-f842-95cd-605cb4296b96

2 years agoIn actionPerformed added call to JDialogMeanShiftClustering.
ilb@NIH.GOV [Fri, 18 Nov 2016 22:32:36 +0000 (22:32 +0000)]
In actionPerformed added call to JDialogMeanShiftClustering.

git-svn-id: https://citdcbmipav.cit.nih.gov/repos-pub/mipav/trunk/mipav@14719 ba61647d-9d00-f842-95cd-605cb4296b96

2 years agoAdded Mean shift clustering to Systems analysis menu.
ilb@NIH.GOV [Fri, 18 Nov 2016 22:10:50 +0000 (22:10 +0000)]
Added Mean shift clustering to Systems analysis menu.

git-svn-id: https://citdcbmipav.cit.nih.gov/repos-pub/mipav/trunk/mipav@14718 ba61647d-9d00-f842-95cd-605cb4296b96

2 years agoAdded call to JDialogMeanShiftClustering.
ilb@NIH.GOV [Fri, 18 Nov 2016 22:07:26 +0000 (22:07 +0000)]
Added call to JDialogMeanShiftClustering.

git-svn-id: https://citdcbmipav.cit.nih.gov/repos-pub/mipav/trunk/mipav@14717 ba61647d-9d00-f842-95cd-605cb4296b96

2 years agoDialog created.
ilb@NIH.GOV [Fri, 18 Nov 2016 21:58:23 +0000 (21:58 +0000)]
Dialog created.

git-svn-id: https://citdcbmipav.cit.nih.gov/repos-pub/mipav/trunk/mipav@14716 ba61647d-9d00-f842-95cd-605cb4296b96

2 years agoInput data file read moved from algorithm to dialog.
ilb@NIH.GOV [Fri, 18 Nov 2016 21:56:43 +0000 (21:56 +0000)]
Input data file read moved from algorithm to dialog.

git-svn-id: https://citdcbmipav.cit.nih.gov/repos-pub/mipav/trunk/mipav@14715 ba61647d-9d00-f842-95cd-605cb4296b96

2 years agoSpelling corrected.
ilb@NIH.GOV [Fri, 18 Nov 2016 21:49:47 +0000 (21:49 +0000)]
Spelling corrected.

git-svn-id: https://citdcbmipav.cit.nih.gov/repos-pub/mipav/trunk/mipav@14714 ba61647d-9d00-f842-95cd-605cb4296b96

2 years agoIn init() deleted buttonImage.setActionCommand("AddImageBrowse");
ilb@NIH.GOV [Fri, 18 Nov 2016 17:41:22 +0000 (17:41 +0000)]
In init() deleted buttonImage.setActionCommand("AddImageBrowse");

git-svn-id: https://citdcbmipav.cit.nih.gov/repos-pub/mipav/trunk/mipav@14713 ba61647d-9d00-f842-95cd-605cb4296b96

2 years agoCode typed in but not proofed or run.
ilb@NIH.GOV [Thu, 17 Nov 2016 23:12:43 +0000 (23:12 +0000)]
Code typed in but not proofed or run.

git-svn-id: https://citdcbmipav.cit.nih.gov/repos-pub/mipav/trunk/mipav@14712 ba61647d-9d00-f842-95cd-605cb4296b96

2 years agoPorting continues.
ilb@NIH.GOV [Wed, 16 Nov 2016 23:09:05 +0000 (23:09 +0000)]
Porting continues.

git-svn-id: https://citdcbmipav.cit.nih.gov/repos-pub/mipav/trunk/mipav@14711 ba61647d-9d00-f842-95cd-605cb4296b96

2 years agoPorting continues.
ilb@NIH.GOV [Tue, 15 Nov 2016 22:55:19 +0000 (22:55 +0000)]
Porting continues.

git-svn-id: https://citdcbmipav.cit.nih.gov/repos-pub/mipav/trunk/mipav@14710 ba61647d-9d00-f842-95cd-605cb4296b96

2 years agoPorting continues.
ilb@NIH.GOV [Mon, 14 Nov 2016 23:12:16 +0000 (23:12 +0000)]
Porting continues.

git-svn-id: https://citdcbmipav.cit.nih.gov/repos-pub/mipav/trunk/mipav@14709 ba61647d-9d00-f842-95cd-605cb4296b96

2 years agoStarted work on.
ilb@NIH.GOV [Thu, 10 Nov 2016 23:09:37 +0000 (23:09 +0000)]
Started work on.

git-svn-id: https://citdcbmipav.cit.nih.gov/repos-pub/mipav/trunk/mipav@14708 ba61647d-9d00-f842-95cd-605cb4296b96

2 years agoAdded a user input for the margin around the skin segmentation for testing.
abokinsky [Thu, 10 Nov 2016 19:05:35 +0000 (19:05 +0000)]
Added a user input for the margin around the skin segmentation for testing.

git-svn-id: https://citdcbmipav.cit.nih.gov/repos-pub/mipav/trunk/mipav@14707 ba61647d-9d00-f842-95cd-605cb4296b96

2 years agoAdded a 1.5micron margin around the skin segmentation for testing.
abokinsky [Tue, 8 Nov 2016 19:13:41 +0000 (19:13 +0000)]
Added a 1.5micron margin around the skin segmentation for testing.

git-svn-id: https://citdcbmipav.cit.nih.gov/repos-pub/mipav/trunk/mipav@14706 ba61647d-9d00-f842-95cd-605cb4296b96

2 years agoSymmetric Nearest Neighbor added to Filters (spatial) menu.
ilb@NIH.GOV [Fri, 4 Nov 2016 21:12:48 +0000 (21:12 +0000)]
Symmetric Nearest Neighbor added to Filters (spatial) menu.

git-svn-id: https://citdcbmipav.cit.nih.gov/repos-pub/mipav/trunk/mipav@14705 ba61647d-9d00-f842-95cd-605cb4296b96

2 years agoAdded call to JDialogSymmetricNearestNeighbor.
ilb@NIH.GOV [Fri, 4 Nov 2016 21:11:28 +0000 (21:11 +0000)]
Added call to JDialogSymmetricNearestNeighbor.

git-svn-id: https://citdcbmipav.cit.nih.gov/repos-pub/mipav/trunk/mipav@14704 ba61647d-9d00-f842-95cd-605cb4296b96

2 years agoDialog created.
ilb@NIH.GOV [Fri, 4 Nov 2016 21:10:37 +0000 (21:10 +0000)]
Dialog created.

git-svn-id: https://citdcbmipav.cit.nih.gov/repos-pub/mipav/trunk/mipav@14703 ba61647d-9d00-f842-95cd-605cb4296b96

2 years agoAlgorithm created for black and white images.
ilb@NIH.GOV [Fri, 4 Nov 2016 21:10:00 +0000 (21:10 +0000)]
Algorithm created for black and white images.

git-svn-id: https://citdcbmipav.cit.nih.gov/repos-pub/mipav/trunk/mipav@14702 ba61647d-9d00-f842-95cd-605cb4296b96

2 years agoCorrected comment.
ilb@NIH.GOV [Fri, 4 Nov 2016 20:49:45 +0000 (20:49 +0000)]
Corrected comment.

git-svn-id: https://citdcbmipav.cit.nih.gov/repos-pub/mipav/trunk/mipav@14701 ba61647d-9d00-f842-95cd-605cb4296b96

2 years agoIn init() removed textIterations.addActionListener(this).
ilb@NIH.GOV [Fri, 4 Nov 2016 20:35:59 +0000 (20:35 +0000)]
In init() removed textIterations.addActionListener(this).

git-svn-id: https://citdcbmipav.cit.nih.gov/repos-pub/mipav/trunk/mipav@14700 ba61647d-9d00-f842-95cd-605cb4296b96

2 years agoChange if (iter > 1) to if (iter >= 1).
ilb@NIH.GOV [Fri, 4 Nov 2016 19:31:18 +0000 (19:31 +0000)]
Change if (iter > 1) to if (iter >= 1).

git-svn-id: https://citdcbmipav.cit.nih.gov/repos-pub/mipav/trunk/mipav@14699 ba61647d-9d00-f842-95cd-605cb4296b96

2 years agoIn setSelectedKeys removed if (k.getGroup().toLowerCase().indexOf("xx) == 2) {
ilb@NIH.GOV [Fri, 4 Nov 2016 15:20:49 +0000 (15:20 +0000)]
In setSelectedKeys removed if (k.getGroup().toLowerCase().indexOf("xx) == 2) {
    continue;
}
In compare replaced
int gdiff = k.getGroupNumber() - q.getGroupNumber();
int ediff = k.getElementNumber() - q.getElementNumber();
with
int gdiff = k.getGroup().compareTo(q.getGroup());
int ediff = k.getElement().compareTo(q.getElement());

git-svn-id: https://citdcbmipav.cit.nih.gov/repos-pub/mipav/trunk/mipav@14698 ba61647d-9d00-f842-95cd-605cb4296b96

2 years agoIn loadProfile in last for loop now have
ilb@NIH.GOV [Fri, 4 Nov 2016 15:14:16 +0000 (15:14 +0000)]
In loadProfile in last for loop now have
if (group.toLowerCase().indexOf("xx') == 2) {
  publicKeys.add(new FileDicomKey(key));
}

git-svn-id: https://citdcbmipav.cit.nih.gov/repos-pub/mipav/trunk/mipav@14697 ba61647d-9d00-f842-95cd-605cb4296b96

2 years agoIn setSelectedKeys check for "xx" after offset is adjusted in first for loop instead...
ilb@NIH.GOV [Thu, 3 Nov 2016 22:33:36 +0000 (22:33 +0000)]
In setSelectedKeys check for "xx" after offset is adjusted in first for loop instead of before offset is adjusted.

git-svn-id: https://citdcbmipav.cit.nih.gov/repos-pub/mipav/trunk/mipav@14696 ba61647d-9d00-f842-95cd-605cb4296b96

2 years agoIn loadProfile in last for loop added if (group.toLowerCase().indexOf("xx") == 2) {
ilb@NIH.GOV [Thu, 3 Nov 2016 22:19:06 +0000 (22:19 +0000)]
In loadProfile in last for loop added if (group.toLowerCase().indexOf("xx") == 2) {
    continue
}
so 50xx and 60xx won't cause a failure on int groupNum = Integer.valueOf(group, 0x10).

git-svn-id: https://citdcbmipav.cit.nih.gov/repos-pub/mipav/trunk/mipav@14695 ba61647d-9d00-f842-95cd-605cb4296b96

2 years agoIn setSelectedKeys() in first for loop added
ilb@NIH.GOV [Thu, 3 Nov 2016 22:16:16 +0000 (22:16 +0000)]
In setSelectedKeys() in first for loop added
if (k.getGroup.toLowerCase.indexOf("xx") == 2) {
    continue;
}
so that 50xx and 60xx won't fail when compare function does getGroupNum().

git-svn-id: https://citdcbmipav.cit.nih.gov/repos-pub/mipav/trunk/mipav@14694 ba61647d-9d00-f842-95cd-605cb4296b96

2 years agoIn compare changed int gdiff = k.getGroupNumber() - k.getGroupNumber() to
ilb@NIH.GOV [Thu, 3 Nov 2016 20:17:38 +0000 (20:17 +0000)]
In compare changed int gdiff = k.getGroupNumber() - k.getGroupNumber() to
int gdiff = k.getGroupNumber() - q.getGroupNumber().

git-svn-id: https://citdcbmipav.cit.nih.gov/repos-pub/mipav/trunk/mipav@14693 ba61647d-9d00-f842-95cd-605cb4296b96

2 years agoRadio buttons allow choosing type of maximum homogeneity neighbor filter, standard...
ilb@NIH.GOV [Thu, 3 Nov 2016 19:09:45 +0000 (19:09 +0000)]
Radio buttons allow choosing type of maximum homogeneity neighbor filter, standard from Nagao or extended from Wang.

git-svn-id: https://citdcbmipav.cit.nih.gov/repos-pub/mipav/trunk/mipav@14692 ba61647d-9d00-f842-95cd-605cb4296b96

2 years agoCan now also do extended maximum homogeneity neighbor filter from Wang.
ilb@NIH.GOV [Thu, 3 Nov 2016 19:07:44 +0000 (19:07 +0000)]
Can now also do extended maximum homogeneity neighbor filter from Wang.

git-svn-id: https://citdcbmipav.cit.nih.gov/repos-pub/mipav/trunk/mipav@14691 ba61647d-9d00-f842-95cd-605cb4296b96

2 years agoCorrected comment.
ilb@NIH.GOV [Wed, 2 Nov 2016 19:32:01 +0000 (19:32 +0000)]
Corrected comment.

git-svn-id: https://citdcbmipav.cit.nih.gov/repos-pub/mipav/trunk/mipav@14690 ba61647d-9d00-f842-95cd-605cb4296b96

2 years agoFor valid bounds of masks change x > 1, y > 1, x > 2, y > 2 to x >= 1, y >= 1,
ilb@NIH.GOV [Wed, 2 Nov 2016 14:40:07 +0000 (14:40 +0000)]
For valid bounds of masks change x > 1, y > 1, x > 2, y > 2 to x >= 1, y >= 1,
x >= 2, y >= 2.

git-svn-id: https://citdcbmipav.cit.nih.gov/repos-pub/mipav/trunk/mipav@14689 ba61647d-9d00-f842-95cd-605cb4296b96

2 years agoEdge Preserving Smoothing added to Filters (spatial) menu.
ilb@NIH.GOV [Tue, 1 Nov 2016 21:34:01 +0000 (21:34 +0000)]
Edge Preserving Smoothing added to Filters (spatial) menu.

git-svn-id: https://citdcbmipav.cit.nih.gov/repos-pub/mipav/trunk/mipav@14688 ba61647d-9d00-f842-95cd-605cb4296b96

2 years agoAdded call to JDialogEdgePreservingSmoothing.
ilb@NIH.GOV [Tue, 1 Nov 2016 21:21:10 +0000 (21:21 +0000)]
Added call to JDialogEdgePreservingSmoothing.

git-svn-id: https://citdcbmipav.cit.nih.gov/repos-pub/mipav/trunk/mipav@14687 ba61647d-9d00-f842-95cd-605cb4296b96

2 years agoDialog created.
ilb@NIH.GOV [Tue, 1 Nov 2016 21:11:31 +0000 (21:11 +0000)]
Dialog created.

git-svn-id: https://citdcbmipav.cit.nih.gov/repos-pub/mipav/trunk/mipav@14686 ba61647d-9d00-f842-95cd-605cb4296b96

2 years agoAlgorithm typed in.
ilb@NIH.GOV [Tue, 1 Nov 2016 20:29:18 +0000 (20:29 +0000)]
Algorithm typed in.

git-svn-id: https://citdcbmipav.cit.nih.gov/repos-pub/mipav/trunk/mipav@14685 ba61647d-9d00-f842-95cd-605cb4296b96

2 years agoAll 8 saveImage calls now pass quiet parameter set equal to true.
ilb@NIH.GOV [Tue, 1 Nov 2016 19:48:34 +0000 (19:48 +0000)]
All 8 saveImage calls now pass quiet parameter set equal to true.

git-svn-id: https://citdcbmipav.cit.nih.gov/repos-pub/mipav/trunk/mipav@14684 ba61647d-9d00-f842-95cd-605cb4296b96

2 years agoModified batch mode so the use can specify the lattice/annotations more efficiently...
abokinsky [Tue, 1 Nov 2016 19:46:19 +0000 (19:46 +0000)]
Modified batch mode so the use can specify the lattice/annotations more efficiently for two color channel images.

git-svn-id: https://citdcbmipav.cit.nih.gov/repos-pub/mipav/trunk/mipav@14683 ba61647d-9d00-f842-95cd-605cb4296b96

2 years agosaveImage now receives quiet input parameter.
ilb@NIH.GOV [Tue, 1 Nov 2016 19:42:36 +0000 (19:42 +0000)]
saveImage now receives quiet input parameter.

git-svn-id: https://citdcbmipav.cit.nih.gov/repos-pub/mipav/trunk/mipav@14682 ba61647d-9d00-f842-95cd-605cb4296b96

2 years agoAdded a batch mode to the fluorescent untwisting. Added two color channel processing...
abokinsky [Tue, 1 Nov 2016 18:08:05 +0000 (18:08 +0000)]
Added a batch mode to the fluorescent untwisting. Added two color channel processing to the fluorescent batch untwisting.

git-svn-id: https://citdcbmipav.cit.nih.gov/repos-pub/mipav/trunk/mipav@14681 ba61647d-9d00-f842-95cd-605cb4296b96

2 years agoChanged VOI XML readers to allow for VOI thickness to be 0. Thickness could be set...
mccreedy@NIH.GOV [Fri, 28 Oct 2016 20:44:20 +0000 (20:44 +0000)]
Changed VOI XML readers to allow for VOI thickness to be 0.  Thickness could be set to 0 in the VOI Props and written out to disk that way.  Thicknesses less than 0 are set to 1.

git-svn-id: https://citdcbmipav.cit.nih.gov/repos-pub/mipav/trunk/mipav@14680 ba61647d-9d00-f842-95cd-605cb4296b96

2 years agoIn setVariables CSVFileName = CSVFileTextField.getText(); moved before a check on...
ilb@NIH.GOV [Thu, 27 Oct 2016 16:59:50 +0000 (16:59 +0000)]
In setVariables CSVFileName = CSVFileTextField.getText(); moved before a check on CSVFileName.

git-svn-id: https://citdcbmipav.cit.nih.gov/repos-pub/mipav/trunk/mipav@14679 ba61647d-9d00-f842-95cd-605cb4296b96

2 years agoCSVFileName = CSVFileTextField.getText() moved from actionPerformed to setVariables.
ilb@NIH.GOV [Thu, 27 Oct 2016 16:57:27 +0000 (16:57 +0000)]
CSVFileName = CSVFileTextField.getText() moved from actionPerformed to setVariables.

git-svn-id: https://citdcbmipav.cit.nih.gov/repos-pub/mipav/trunk/mipav@14678 ba61647d-9d00-f842-95cd-605cb4296b96

2 years agoPlugin created.
ilb@NIH.GOV [Wed, 26 Oct 2016 21:39:35 +0000 (21:39 +0000)]
Plugin created.

git-svn-id: https://citdcbmipav.cit.nih.gov/repos-pub/mipav/trunk/mipav@14677 ba61647d-9d00-f842-95cd-605cb4296b96

2 years agoRemoved unneeded import.
ilb@NIH.GOV [Wed, 26 Oct 2016 21:37:54 +0000 (21:37 +0000)]
Removed unneeded import.

git-svn-id: https://citdcbmipav.cit.nih.gov/repos-pub/mipav/trunk/mipav@14676 ba61647d-9d00-f842-95cd-605cb4296b96