Merge pull request #73 from SlicerRt/update-SlicerRT

ENH: Updated SlicerRT (0.4.0): Isodose module added. See more info at https://www.assembla.com/code/slicerrt/subversion/changesets/compare/289..299
ENH: Reset icon to Steve Jordan's version
Merge pull request #74 from chrismullins/master

ENH: Reset icon
Merge pull request #1 from Slicer/master

Pull the latest Slicer/ExtensionsIndex
ENH: Update URLs for icon and screenshot images.
Merge pull request #75 from tokjun/update-VolumeResliceDriver

Update VolumeResliceDriver extension file
Fixed configuration errors.
Merge pull request #76 from ungi/update-PerkNav

Update PerkNav extension please
ENH: Updated SlicerRT: Version 0.5.0, new Contours module added to convert contour representations, fixes in Isodose and Dose Accumulation modules. See more info at https://www.assembla.com/code/slicerrt/subversion/changesets/compare/299..344
Merge pull request #78 from SlicerRt/update-SlicerRT

ENH: Updated SlicerRT: Version 0.5.0, new Contours module added to conve...
ENH: update version to integrate various fixes; see #77
Merge branch '77-Reporting-fixes'; closes #77

* 77-Reporting-fixes:
  ENH: update version to integrate various fixes as described below; see #77

Release note: there is a known problem with adding markups to multiple reports; see Reporting issue 16

commit 684cfd1e74215c8c2077d39ac0c25e5269c75029
Author: Andrey Fedorov <fedorov@bwh.harvard.edu>
Date:   Wed Oct 10 11:55:18 2012 -0400

    ENH: script to convert a segmentation saved as an RGB stack into a volume format and a DICOM SEG

commit d0f9271f035f3708625b774e8f9d5fa8aae37e43
Author: Andrey Fedorov <fedorov@bwh.harvard.edu>
Date:   Wed Oct 10 11:28:43 2012 -0400

    ENH: do not export the referenced DICOMs by default

    TODO: add option to the GUI

commit 278750aa693afcf1c70206cbc8ab1b2f11b394d2
Author: Andrey Fedorov <fedorov@bwh.harvard.edu>
Date:   Wed Oct 10 10:57:32 2012 -0400

    ENH: more error checks

commit f91d57f69982b5c6ef38d956460c27000830e68f
Author: Andrey Fedorov <fedorov@bwh.harvard.edu>
Date:   Wed Oct 10 10:30:18 2012 -0400

    ENH: optimize image buffer access

    Direct access to the buffer speeds up DICOM SEG read/write tremendously
    (thanks Steve for the hint!); closes #35

commit fd01954f87407067dffc1c20bed4e342c336b5b8
Author: Andrey Fedorov <fedorov@bwh.harvard.edu>
Date:   Mon Oct 8 13:04:26 2012 -0400

    BUG: correct the attribute name

commit 0b3a48bdc0349d9a627e7b4184c5dcb069c31f9e
Merge: 6e6bbb4 560f097
Author: Andrey Fedorov <fedorov@bwh.harvard.edu>
Date:   Mon Oct 8 12:53:02 2012 -0400

    Merge branch 'master' of https://github.com/fedorov/Reporting

commit 6e6bbb4be5f7b12a521ad1ee1b6d1a4046ad4080
Author: Andrey Fedorov <fedorov@bwh.harvard.edu>
Date:   Mon Oct 8 12:49:19 2012 -0400

    BUG: fix XML issues related XSD validation

    * date/time format fixed
    * order of the elements is fixed

    ENH: re-enable insertion of DICOM SEG, since related Slicer issue with DB lockup has been resolved

commit 560f0972f6bc4c60c554745c0abd05b3528b9840
Author: Andrey Fedorov <fedorov@bwh.harvard.edu>
Date:   Mon Oct 8 12:49:19 2012 -0400

    BUG: fix XML issues related XSD validation

    * date/time format fixed
    * order of the elements is fixed

commit db18d393376404fb0c2bbcab8d654d513e734a06
Author: Andrey Fedorov <fedorov@bwh.harvard.edu>
Date:   Sun Oct 7 22:19:47 2012 -0400

    BUG: use more unique tag for the report node
    BUG: fixing XML errors that break schema validation (validation is still unsuccessful)

commit 037390fb3a8e8ba822d9f96e0eaacb6a940b9868
Author: Nicole Aucoin <nicole@bwh.harvard.edu>
Date:   Thu Oct 4 18:36:48 2012 -0400

    BUG: reenable adding the segmentatin volume to the database so that the round trip test will pass

commit 7b4c20acee0fd2bc69f595d6bc4490642c4fb95e
Author: Nicole Aucoin <nicole@bwh.harvard.edu>
Date:   Thu Oct 4 18:14:39 2012 -0400

    BUG: need to save the aim file to the report node so can reload it, fixed some syntax errors, added checking. The segmentation label map

commit 67ace02ea26271fda9cb63763bd3a953215e53ed
Author: Nicole Aucoin <nicole@bwh.harvard.edu>
Date:   Thu Oct 4 17:34:43 2012 -0400

    ENH: when reporting nodes are removed, also remove the hierarchy node that points to them

commit a985918bdf6133c15584c53a02559254e9ecf888
Merge: 466bede afd8c56
Author: Nicole Aucoin <nicole@bwh.harvard.edu>
Date:   Fri Sep 28 14:37:48 2012 -0400

    Merge branch 'ReportHierarchy'

commit afd8c5666c61bb2b416fcdfe3281d1fa66541ce7
Author: Nicole Aucoin <nicole@bwh.harvard.edu>
Date:   Fri Sep 28 14:37:14 2012 -0400

    BUG: rearrange the code a bit to avoid the hierarchy display problems

commit 466bede19379888e6a4bac7cc02cf3024aa94374
Author: Andrey Fedorov <fedorov@bwh.harvard.edu>
Date:   Thu Sep 27 08:58:29 2012 -0400

    BUG: testing fix from @jcfr

    Using arguments "--additional-module-paths" was preventing the argument
    "--python-code" from being considered. Using ""--additional-module-path"
    allows the unittest to be properly executed.
    See http://viewvc.slicer.org/viewvc.cgi/Slicer4?view=revision&revision=20710

    See #12

commit 819e3a7ff1668355c479f05d6fc1963c4d927302
Author: Jean-Christophe Fillion-Robin <jchris.fillionr@kitware.com>
Date:   Tue Sep 25 18:18:16 2012 -0400

    BUG: Reference layoutmanager only if it is available

    This will the following error happening when running cxx generic test:

    2: Traceback (most recent call last):
    2:   File "/home/jchris/Projects/Reporting-build/lib/Slicer-4.1/qt-loadable-modules/Python/qSlicerReportingModuleWidget.py", line 249, i
    2:     lm.setLayout(26) # two over two
    2: AttributeError: 'NoneType' object has no attribute 'setLayout'

    See #12

commit 1898d7972d015b6ed01f23d6c3a821f2b704a607
Author: Jean-Christophe Fillion-Robin <jchris.fillionr@kitware.com>
Date:   Tue Sep 25 18:15:15 2012 -0400

    BUG: qMRMLNodeComboBox::onMRMLSceneChanged signal does not exist

    This commit will fix the following error:

      PythonQt: QObject::connect() signal 'onMRMLSceneChanged()' does not exist on qMRMLNodeComboBox

    See #12

commit f875e21ca922761de835c6a64632419fb242bb26
Author: Nicole Aucoin <nicole@bwh.harvard.edu>
Date:   Thu Sep 20 14:29:53 2012 -0400

    BUG: when loading a reporting .xml file make sure that the Reporting module is up, and that the new report is active so that the fiducia

commit 76c0518f99da16e63061829c7b7739d85faef768
Author: Nicole Aucoin <nicole@bwh.harvard.edu>
Date:   Wed Sep 19 18:55:41 2012 -0400

    ENH: add in ability to load AIM XML files from the Load Data panel. Todo: write a report node storage node so can save from the applicat

commit ac16d50bf927f2a975142289f2693ca0743951bd
Author: Nicole Aucoin <nicole@bwh.harvard.edu>
Date:   Wed Sep 19 18:55:17 2012 -0400

    ENH: add in ability to load AIM XML files from the Load Data panel. Todo: write a report node storage node so can save from the applicat
ENH: Updated SlicerRT: Critical fix due to Slicer core changes (build failed); Small fixes and enhancements. See more info at https://www.assembla.com/code/slicerrt/subversion/changesets/compare/344..352
Merge pull request #79 from SlicerRt/update-SlicerRT

ENH: Updated SlicerRT: Critical fix due to Slicer core changes (build fa...
Fixed PerkNav extension compilation error.
Merge pull request #80 from ungi/update-PerkNav

Fixed PerkNav extension compilation error.
Add ABC extension

See issue #4
Merge branch '4-add-ABC'

* 4-add-ABC:
  Add ABC extension
ABC - Add svnusername and svnpassword
ENH: remove references to deprecated annotation visibility API; see #81

TODO: need to find how visibility can be controlled with the new API