View source for Slicer3:3.6 Final Issues

'''Notes: 
* Include the [http://www.na-mic.org/Bug/ mantis] bug number in your svn commit messages
* Test your fixes in the slicer3 trunk - when you are sure they work, (1) move them to the Slicer-3-6 branch (2) move them from the TODO to the DONE category on this page
* The Slicer3 repository is in maintenance mode - please do not add new features.  New modules should be added only as [http://www.slicer.org/slicerWiki/index.php/Slicer3:Extensions extensions].
'''

==TODO: Issues to fix for the 3.6.4 patch release==


* Integrate SPECTRE plugin as an extension once MIPAV is open sourced (Nicole)
* Resample widget does not work properly in linked mode. In that situation, the slices should maintain the relative positions as the widget reorients them. (Steve, Jim, Michal)
* Adjust the appearance of slices in 3D view [http://www.na-mic.org/Bug/view.php?id=1061 1061] Steve)
* Interface settings in Application settings are not saved http://na-mic.org/Mantis/view.php?id=1076 (Steve?)
* http://na-mic.org/Mantis/view.php?id=1028 Request to compute checksum or md5sum and save as part of any storable node has registered as a feature request in Mantis. Plan right now is to create a method on MRMLScene->DataIOManager that will check for any data transfer with a status vtkDataTransfer::Failed. This status is set inside Base/Logic/vtkDataIOManagerLogic before data is loaded into slicer. Debugging this now... (Wendy)
* Move vtkEMSegmentLogic::AddDataIOFromScene to base code and replace in Slicer3.cxx corresponding code with function call
** commandlines currently cannot execute links to files with http address   (Wendy, Dominique)
* Generate Robust MRI brain registration for EMSegmenter (Kilian, Dominik)


* BRAINSResample is not available as a shared library (C++ symbol name in .so) [http://www.na-mic.org/Bug/view.php?id=941 941] (Jim)
* CompareView slice spacing issue [http://na-mic.org/Mantis/view.php?id=936 936] (Jim) 
* CompareView + side-by-sideLightbox + Widescreen CompareView problems [http://www.na-mic.org/Bug/view.php?id=995 995] (Jim)
* Compareviewer and crosshairs in Navigator mode: 4 compare viewers in wide screen mode (e.g. use [http://www.na-mic.org/Wiki/index.php/File:RSNA2010_fMRICase040Dataset.zip case 40] for data). text is not suppressed, display is slow. (Jim)
* Migrate latest version of GrowCut into release branch (Harini and Jim)

* Migrate the fix for --evalpython (Daniel)

* [[Slicer3:ChangingVersionsCheckList | update to version]] 3.6.4 (Steve)
* Create distribution binaries and extensions (Steve)
* Fix numpy builds on some windows systems by migrating to clapack (Steve, Dave)

==TODO: Issues to fix for the 3.6.3 patch release==
''Fixes for these issues should be checked in to the Slicer-3-6 release branch by 3pm Eastern time on Monday, Feb 14, 2011''


* Issue with slice not displaying in atlas scene [http://www.na-mic.org/Bug/view.php?id=1106] (Alex)

* Create distribution binaries and extensions (Steve)


=== DONE: Issues fixed for inclusion in Slicer 3.6.3 ===
* Migrate BRAINS test fixes to the Slicer-3-6 release branch (Hans, Mark)
* File extension saving issues [http://na-mic.org/Mantis/view.php?id=1056 1056] [http://na-mic.org/Mantis/view.php?id=1064 1064] (Alex)
* Warning and block when file type is changed using filename field in the Save dialog [http://www.na-mic.org/Bug/view.php?id=1064 1064] (Alex)
* Display a warning message during installation on Windows if VC redistributable package is not installed (fix committed to the trunk by partyd on October 29, 2010)
* Model Hierarchy issues [http://www.na-mic.org/Bug/view.php?id=961 961] (Alex)
* Warning on unsaved data on scene close and exit (Alex)
* Status of fade slider is not captured by scenesnapshot (Alexy).
* Models Display UI cleanup (Alex)
* models under transforms do not move after save/load scene [http://www.na-mic.org/Bug/view.php?id=1058 1058] (Alex)
* multiple fiber tubes rendering performance (Alex)
* Slicer crash related to fiducials/MRML [http://www.na-mic.org/Bug/view.php?id=1042 1042] (Alex)
* Fixes to Camera/View handling (Alex & Wendy)
* Resolve bugs concerning vtkMRMLScene::GetReferencedSubScene [[http://na-mic.org/Mantis/view.php?id=1036 1036], etc. (Alex)
* Modify ProstateNav so that it does not get recompiled all the time. Fixed in rev [http://viewvc.slicer.org/viewcvs.cgi?rev=15446&sortby=rev&sortdir=down&view=rev 15446], now only one file is recompiled. (Andras)
* Fixed BSplineDeformableRegistration (Fast non-rigid registration) CLI module to work correctly with rotated images (with direction cosines different from identity matrix) (Andras)
* Fix for vtkITKBSpline transform save with scene snapshot [http://www.na-mic.org/Bug/view.php?id=1050] (Steve)
* Fix for passing parameters to command line modules from Luca
* Fix to CropVolume module to correctly propagate the name for the output volume (Andrey)
* FastMarching crashes when applied two two different volumes one after another [http://www.na-mic.org/Bug/view.php?id=1057 1057] (Andrey)
* ChangeTracker deformable metric did not work because demons binary was not properly installed (Andrey)
* Setup node selector in LabelStatistics to allow label maps only (Andrey)
* CropVolume would not work anymore after scene is closed (Andrey)
* While in the volume rendering module, the render speed is slow while looking at a composited cross section. [http://www.na-mic.org/Bug/view.php?id=1052 1052]
* http://na-mic.org/Mantis/view.php?id=983 (fixed)
* Migrate DicomToNrrd fixes to the Slicer-3-6 release branch (Xiaodong)
* Migrate MRML Node test fixes to the Slicer-3-6 release branch (Nicole)
* Fix cygwin compile issue http://www.na-mic.org/Bug/view.php?id=1078  (Andras)
* Model Maker naming bug [http://www.na-mic.org/Bug/view.php?id=1043 1043] (Nicole)
* Loading *.mask files via 'Add Data' doesn't work [http://na-mic.org/Mantis/view.php?id=1067 1067] (Vince, Hans, Dominique)
* Expose step size parameter for Endoscopy (Steve)
* Label Grid should be off by default and should not come on automatically (Steve)
* Slice volume selectors are reset after executing CLI http://na-mic.org/Mantis/view.php?id=1077 (Steve)
* 4D Image: origin is not consistent with "Add volume" loaded data [http://www.na-mic.org/Bug/view.php?id=1000 1000] (Steve, Andrey, Junichi, Isaiah)
* Switch to tclkit for running genlib to work around [http://viewvc.slicer.org/viewcvs.cgi?rev=15824&view=rev cygwin tclsh PATH] issue (Steve and Andras)
* fix 3 view layout with endoscopy, external, and volume rendering view in distinct viewers to support Jay's programmaticly defined use-case (Steve) (not all functionality will be exposed in the GUI).
** switching layouts loses observers on scene
** no way to filter display of models or volume rendering in different viewers
* Migrate fixes for oblique volume editing and threshold paint optimization after testing in trunk (Steve, Andrey)
* Integrate Endoscopic layout. (Wendy)
* Move Cache and DataIO manager setup out of Slicer3.cxx and into SlicerApplicationLogic (not MRML). Not done for 3.6.3 but workaround is being used. (Wendy) [http://na-mic.org/Mantis/view.php?id=1033 1033]
* Debug leaks in FetchMI http://na-mic.org/Mantis/view.php?id=1029
* Error messages in FetchMI: http://na-mic.org/Mantis/view.php?id=1027 (related to 1028)
* Model maker pad fix http://na-mic.org/Mantis/view.php?id=813 (Nicole)
* Remove bugs and simplify user interface of Extension manager: (Steve) - committed to trunk for testing
** uninstall does not work 
** "Download /install" and "Uninstall" button should be removed and be executed via next button to keep philosophy of workflow wizard
* Fix for level tracing http://na-mic.org/Mantis/view.php?id=1084
* Extensions (Steve / Daniel)
** Download problems http://na-mic.org/Mantis/view.php?id=1080
* Migrate latest version of GrowCut into release branch (Harini)
* Include Atlas Creator (Kilian, Daniel)
* Migrate EMSegment test fixes to the Slicer-3-6 release branch (Dominique, Kilian, Daniel)
* Data loading and FetchMI (Wendy -- fixes have been checked into trunk, and propagated to branch.)
* Slice view toggles [http://www.na-mic.org/Bug/view.php?id=1003 1003] (Nicole)

==TODO: Issues to fix for the 3.6.2 patch release Oct 22/10==



=== DONE: Issues fixed for inclusion in Slicer 3.6.2 ===
* Merge "reference" volume attribute feature into CommandLineModule (Andrey)
* 3D Viewer does not update when slice model is visible and dragging the Fg/Bg slider [http://www.na-mic.org/Bug/view.php?id=1019 1019] (Alex)
* N4 module bug in histogram sharpening parameter passing (Andrey)
* Updated versions of BRAINS tools (Hans)
* Detection of some BRAINS modules (e.g. BRAINSResample) (Steve)
* Resolve bugs concerning vtkMRMLScene::GetReferencedSubScene [http://na-mic.org/Mantis/view.php?id=1032 1032]
* Import does not correctly update reference [http://www.na-mic.org/Bug/view.php?id=1010 1010] (Alex)
* Changing names of volume nodes is not propagated to GUI [http://www.na-mic.org/Bug/view.php?id=1012 1012] (Steve)
* Editor tweaks:
** add search to the color selector box - color list dynamically filtered when typing in search box
** pick a new default size for the color selector box (or perhaps have it remember the last size/location picked by the user)  - color box remembers size selected by user
** give the color box a 'recently used' section - most recently used colors are now added at top of list for easy access
** rename 'check points' to 'undo/redo'
** implement compression (to vtk stencils) for label maps in the undo/redo stack (update: vtk stencils only represent a single value so they won't work for a multi-value labelmap - looking for alternatives).  Done: implemented using new vtkImageStash class that uses ZLib to compress scalar image data.  Also allows for compression in background thread so it does not get in the way of interactive use.
* Failed memory allocation dialog box (Steve) - in slicer3 trunk
* 3D Viewer disappears [http://www.na-mic.org/Bug/view.php?id=1004 1004] (Alex)
* in the editor module compress saved label maps into stencils (Steve)
* Side-by-side and Widescreen compare view linking problems appear fixed.
* Ron requests default for crosshair to be navigator OFF 
* Import of XNAT xcat files not working [http://www.na-mic.org/Bug/view.php?id=996 996] (Works for nrrd, not dicom. Release note added.)
* FetchMi does not store path names correctly [http://www.na-mic.org/Bug/view.php?id=993 (was listed as 998, but refers to duplicate bug 993] which appears to be fixed now. 
* FetchMI problems mentioned here [http://www.na-mic.org/Bug/view.php?id=998 998] and here [http://na-mic.org/Mantis/view.php?id=955 955] are due to (1) no or loss of network connection or (2) a full cache. (Wendy) added tests for network and server availability in fetchmi and for a full cache before attempting to transact with services. 
* FetchMI segfaults when uploading  mrml file [http://www.na-mic.org/Bug/view.php?id=1011 1011] (Wendy: this problem is due to having no cache space. Clear the cache and make sure your filesystem has enough free space to play with, then the upload works.)
* CompareView issue [http://na-mic.org/Mantis/view.php?id=929 929] (Jim)
* Display tab in the volumes module should be open by default [http://www.na-mic.org/Bug/view.php?id=1001 1001]
* in the editor module replace the words "Check Points" with the word "Undo" (Steve)
* CompareView + Crosshairs issue [http://na-mic.org/Mantis/view.php?id=928 928] (Jim)
* Cannot change the window/level on color-by-orientation dti volumes (Alex [http://na-mic.org/Mantis/view.php?id=988]).
* Ron's requested changes to the volume rendering transfer function (email from 8/20) (Alex->Steve: implemented and checked in trunk for testing): 
**add thumbnails to show effect of the transfer functions, 
**remove unneeded ones, correct a typo. 
**Materials are in drop box in Ronsexamples in a zipped folder called Transferfunctions. 
* [http://na-mic.org/Mantis/view.php?id=971 971] Scene import does not work correctly (Alex: fixed on the trunk, Slicer3.6, SLicer4)
* Fiber bundle display GUI issue (Alex) [http://www.na-mic.org/Bug/view.php?id=994] '''NOTE: there is a MRML scene compatibility issue, see comments in [http://www.na-mic.org/Bug/view.php?id=994] '''
* Color-orientation display for DTI volumes crashes Slicer when trying to save scene [http://na-mic.org/Mantis/view.php?id=976 976] (Alex)
* Diffusion Tensor Glyphs not showing (Demian)
* Diffusion Tensor Tractography having a strange no-tracking through high FA areas case  (Demian)
* Make shift-leftbutton-drag be shift for slice viewers (Steve) (Committed to trunk -sending a binary to Ron for testing)
* volume rendering: sampling rate and a few other tweaks (Yanling)
* CompareView issues [http://na-mic.org/Mantis/view.php?id=927 927]
* Bug when volume rendering volumes with smooth gradients [http://viewvc.slicer.org/viewcvs.cgi?rev=14752&view=rev][http://viewvc.slicer.org/viewcvs.cgi?rev=14751&view=rev] (Steve)
* Import scene does not update 3D viewer (Nicole, Wendy) http://na-mic.org/Mantis/view.php?id=840
* Loading a scene that contains a fiducial seeding node breaks fiducial seeding if the node points to an invalid fiducial node (Nicole)
* missing quick timeout if connection to web resource is blocked [http://na-mic.org/Mantis/view.php?id=969 969]
* [http://na-mic.org/Mantis/view.php?id=954 954] EMSegmentCommandLine throws errors if started from a current working directory different than ./Slicer3-build
* [http://na-mic.org/Mantis/view.php?id=948 948] + [http://na-mic.org/Mantis/view.php?id=958 958] Segfault during segmentation when saving intermediate results
* [http://na-mic.org/Mantis/view.php?id=970 970] EMSegmentMRMMLanager cannot handle two taks
* [http://na-mic.org/Mantis/view.php?id=973 973] MRML file does not read nrrd files correctly when the files are located in different directory
* Ordering of the series by number in DICOM browser [http://na-mic.org/Mantis/view.php?id=965 965] (Steve)
* Create robust pipeline for 3D MRI brain images [http://na-mic.org/Mantis/view.php?id=972 972] (Kilian)
* It seems that the camera does not transform correctly under transform node (Steve). [http://na-mic.org/Mantis/view.php?id=957 957] fixed and checked in.
* Reading fiducial lists with .txt extensions. [http://www.na-mic.org/Bug/view.php?id=991 991] (Nicole)
* add the --tmpdir option to the start up allowing one to specify slicers temporary directory (Dominique)
* Fix the leaks in the nightly tests [http://www.cdash.org/CDash/viewTest.php?onlyfailed&buildid=731096] (Dominique)
* Issue [http://na-mic.org/Mantis/view.php?id=968 968]: LD_LIBRARY_PATH screwewd up when no network connection (Steve with Kilian)
* Relative paths in volume storage nodes [http://www.na-mic.org/Bug/view.php?id=993 993] (Nicole)
* [https://slicer.spl.harvard.edu/slicerWiki/index.php/Slicer3:GPURayCaster#Open_Issues VTK GPU Ray Cast issues] (Julien)
** Flickering has not been improved since 3.6.1.
** Crash on MAC: the 2 Apple bug reports from Francois Bertel and James Barabas are still open (rank #1). Apple didn't contact them.
* Change names of the grow cut gesture volume nodes to be consistent with the naming conventions of label map (Harini)
* Grow Cut: Change the gesture volume node to be displayed on the foreground and the segmented label volume node to be displayed on the label layer of the slice views (Harini)
* Grow Cut: Modify the opacities of the label layer and the foreground layer to overlay the user input gestures, the resulting segmentation on the image background (Harini)
* Grow Cut: Modify user interface for setting inputs to the Grow Cut algorithm (Harini)
* [[Slicer3:ChangingVersionsCheckList | update to version]] 3.6.2 (Steve)
* [[Slicer3:Editor_Tuning_3.6.2|Several tweaks to the Editor Module]] (Steve)
* Resolve EMSegmenter related bug in connection with BRAINSFit [http://na-mic.org/Mantis/view.php?id=1025 1025] (Dominique)
* Resolved GetReferenceSubScene bugs: [http://na-mic.org/Mantis/view.php?id=1023 1023], [http://na-mic.org/Mantis/view.php?id=1031 1031], [http://na-mic.org/Mantis/view.php?id=1031 1034], [http://na-mic.org/Mantis/view.php?id=1035 1035]
* Create extensions for all versions of Slicer for the release (Steve)

==DONE: Issues included in 3.6.1 patch release - in Slicer-3-6 branch by 2010-08-03 6pm==

* make sure all BRAINS and Registration fixes are in the 3.6 branch (Hans and Jim with help from Dominik)
* check for duplicate filepaths when saving data (Alex) http://www.na-mic.org/Bug/view.php?id=925
* tractography seeding issue (Alexy) http://www.na-mic.org/Bug/view.php?id=885: Changed Tracttography/LabelMapSeeding module: 1. added UseIndexSpace option for seeding placement. 2. Also found that IJK indexes used for traversing the label volume were floats. Changed them to doubles that may crate slightly different tracts, but it is less prone to error accumulation (Alex). 
* Added multi-label selection to Tractography/ROISelect module (PNL request for Slicer2 compatibility, Alex)
* Added more scalar options to Diffusion Tensor Scalar Measurement module (PNL request for Slicer2 compatibility, Alex)
* [http://www.na-mic.org/Bug/view.php?id=871 fix] for Python programming tutorial (Steve, Luca)
* Fixes for color table preview icons showing up in node selectors (Wendy and Nicole)
** [http://viewvc.slicer.org/viewcvs.cgi?rev=13771&view=rev svn 1377]
* DicomToNrrd issues reported by AlexZ and Sylvain (Xiaodong)
* Crosshair traking modes (Jim); also see [http://na-mic.org/Mantis/view.php?id=861 bug #861]
* Wizard page transition error in ProstateNav. The issue was fixed by Haiying.
* OpenIGTLink reslice performance (Junichi) (fixed by Steve)
* Updated meshing module (Curt) - checked in trunk for [http://www.na-mic.org/Wiki/index.php/Slicer3:IAFEMesh_TutorialContestSummer2010|tutorial contest]; needs merge to branch if all is well.
* "Change island" effect of Editor is not functioning when the Scope is set to "all"
* Scene save/restore crash for dti tutorial (Steve/Alex). [http://viewvc.slicer.org/viewcvs.cgi?rev=14416&view=rev] and [http://viewvc.slicer.org/viewcvs.cgi?rev=14415&view=rev]
* brackets in filenames (Steve - fixed in trunk, migrate to branch if tests well) http://www.na-mic.org/Bug/view.php?id=851
* changes to avoid error messages when using single-slice volumes (Steve) - in trunk, need to move to branch
* Editor rounding issue [http://www.na-mic.org/Bug/view.php?id=932] (Steve) - in trunk, need to move to branch
* KWWidgets issue with "%" in file names produced by DICOM browser -- fixed in trunk, need to make sure propagated to 3.6 [http://na-mic.org/Mantis/view.php?id=886 bug 886] (Steve)
* Tractography display modes issue with Data module (FiberBundles have 3 display nodes but the Data tree has only one eye icon). (Alex) (Steve disabled the eye icon for in the Data tree for any displayable with more than one display node)
* Fix for crash after Save Island operation on windows (Steve) [http://viewvc.slicer.org/viewcvs.cgi?rev=14505&view=rev]
* EMSegment command line works now  with BRAINS (Kilian)
* Removed KWWidgets that do not work under Windows (Kilian)
* fixed warning for some bad image spacing geometries http://www.na-mic.org/Bug/view.php?id=951 (Steve)
* fixed editor error dialog when editing on rotated volumes with some geometries (Steve [http://viewvc.slicer.org/viewcvs.cgi?rev=14668&view=rev], [http://viewvc.slicer.org/viewcvs.cgi?rev=14667&view=rev])
* Snapshot issue [http://na-mic.org/Mantis/view.php?id=933] (Alex)


==3.6 Release issues==
Final punch list for [[Slicer3:3.6Release|slicer 3.6 release]]:

'''Finalized June 10 for 3.6 binaries and [[Announcements:Slicer3.6]]''' 

*VTK GPU ray-cast clipping issue
**bug fix:[[http://na-mic.org/Mantis/view.php?id=800 Non axis aligned volumes]]
**bug fix:[[http://na-mic.org/Mantis/view.php?id=798#c1780 ROI on Non axis aligned volumes]]
**90% of the flickering when the camera is inside the volume is removed
*compare view + crosshair issue when loading a scene, the crosshair does not appear in all viewers until the slice location is changed, (Jim)

*Picking NCI GPU Raycasting on machine that doesn't support it causes lockup. Not able to reproduce the problem (Yanling).

Done:
* Remove unused color and glyph options from fiber bundle display (Alex)
* fiducial behavior
* fiducial behavior/3D viewer behavior: (Steve, Nicole, Wendy met Jun 7)
** saw one example of persistent place mode being stolen by pick mode. I think this has to do with inappropriate initialization of modes. It is possible for pick mode to take over until transient-pick mode is explicitly chosen. (FIXED)
** tractography updates not happening during drag - fixes checked into SlicerVTK and Slicer3 branch
** tractography updates slow when drag stops (Steve confirmed this was due to update only happening when mouse was moved after button released - made it seem extra slow)
**widget issues (Nicole putting fixes in [http://github.com/pieper/CTK SlicerVTK])
*making sure mouse-modes work same in 3D/2D (Wendy and Nicole) Let's call it DONE!
** done for 2d, Andras has tested it and says it's fine
*editor volume merge feature clarification (Steve meeting Sonia June 2, fixes committed June 3)
*getting BRAINS tests to pass (Hans is working on it)
*tracking down what is making that crash on Mac OsX when several PET volumes are loaded into Slicer (Wendy).
* are there extra pick operations going on?  There seems to be a delay after clicking mouse before camera begins to rotate when large models are present in scene. ''could not replicate - tried 2.5 million triangle model on slicer and paraview and performance is the same''
* should picking of fiducials in 3D be disabled unless user explicitly chooses 'pick mode'? ''Not a good idea to change behavior at this point''
** should parallel behavior be implemented in 2D for consistency? Stevie votes no, Wendy votes yes. ''Not a good idea to change behavior at this point''
* roundtrip to xnat desktop --OK: confirmed that Ron was using dirty files in cache; checking 'always re-download' in the Cache and DataI/O Manager GUI caused fresh download and successful load into slicer. Sometimes, even when you delete cached files thru the GUI, some applicaiton is holding on to files still there and they don't get cleared out. I'm adding a little code to check for remaining files after a ClearCache() is called; if so, we'll warn user that not all files were removed, and to select 'always re-download' to ensure proper data loading.(Wendy)
* view control gui: (Wendy) this guy isn't always updating anymore. He may be a casualty of multiple view nodes in the scene. He was a casualty but is fixed now! 
*The diffusion tensor estimation module is using defaults that are not good and partially incorrect. Can the defaults be as follows:
**for Output DTI volume: DTI Volume
**for Output Baseline Volume: Baseline DTI Volume
**for Otsu Threshold Mask: Otsu Threshold Label Volume
*new default color table (Nicole and Mike)
** Mike working on creating a LUT from <strike>[[CCA:Atlases:Florins_2010_Hierarchy|this hierarchy]]</strike> [[CCA:Atlases:Florins_2010_Hierarchy_Short|this subset]], by Jun 7
** Steve and Nicole to meet June 9 to integrate default editor color table
** Jun 10: checked in new color files, one from [[Slicer3:2010_GenericAnatomyColors|GenericAnatomyColors]], and one based on that but with names set to integer values and the color for 255 changed to blue. Wendy making new drop down menu icons.
*finishing up the DICOM file copy on remote upload, also close (Wendy) (DONE)


Issues that cannot be fixed (or aren't crucial to fix) should be listed in [[Release-notes-3.6| the slicer 3.6 release notes]].