ENH: self-test to reproduce crash in issue 2512


git-svn-id: http://svn.slicer.org/Slicer4/trunk@21313 3bd1e089-480b-0410-8dfb-8563597acbee
STYLE: fix notification message


git-svn-id: http://svn.slicer.org/Slicer4/trunk@21314 3bd1e089-480b-0410-8dfb-8563597acbee
COMP: find package of Slicer is now sufficient to include OpenIGTLink

git-svn-id: http://svn.slicer.org/Slicer4/trunk@21315 3bd1e089-480b-0410-8dfb-8563597acbee
ENH: Updated OpenIGTLinkIF revision (fixed CMakeLists.txt to biuld outside Slicer directory / fixed timer issue)

git-svn-id: http://svn.slicer.org/Slicer4/trunk@21316 3bd1e089-480b-0410-8dfb-8563597acbee
BUG: make sure view widgets exist for use in layout changes #2512

This patch fixes the crash of the type reported in the but note referenced
below.  Since this avoids the crash, I'm committing it now even though
we may want to revisit the design at a later date.

http://www.na-mic.org/Bug/view.php?id=2512#c6994

git-svn-id: http://svn.slicer.org/Slicer4/trunk@21317 3bd1e089-480b-0410-8dfb-8563597acbee
BUG: ensure that the temp directory is unique

Avoid possible name clashes with other tests.

git-svn-id: http://svn.slicer.org/Slicer4/trunk@21318 3bd1e089-480b-0410-8dfb-8563597acbee
COMP: Complain if git config "insteadof" are not as expected

See http://na-mic.org/Mantis/view.php?id=2731

Fixes #2731

git-svn-id: http://svn.slicer.org/Slicer4/trunk@21319 3bd1e089-480b-0410-8dfb-8563597acbee
COMP: Oops. Reworking jqplot repository on the Slicer Community

Turns out I don't have the admin rights to create the Downloads panel.
The Downloads panel is where we host the tarballs of jqplot for the build.

Since the Nightly builds are about to start, I am modifying the
External_jqPlot.cmake file to point to a copy of the tarballs on
my github.

I'll fix it tomorrow when I can reach the admins.

git-svn-id: http://svn.slicer.org/Slicer4/trunk@21320 3bd1e089-480b-0410-8dfb-8563597acbee
COMP: jqplot on the Slicer Community back online.  Backing out previous checkin

git-svn-id: http://svn.slicer.org/Slicer4/trunk@21321 3bd1e089-480b-0410-8dfb-8563597acbee
BUG: more useful error messages when dicom database cannot be used

Provide diagnostic info about missing or non-readable/non-writable
directories and files.  Also point user to directory selection button
in the dicom browser dialog to indicate where to make the fix.

Fixes issue #2715.

git-svn-id: http://svn.slicer.org/Slicer4/trunk@21322 3bd1e089-480b-0410-8dfb-8563597acbee
BUG: Simplify mechanism to ignore settings (options --testing and --disable-settings)

This commit ensure that the method instantiateSettings is called once after
the argument are parsed.

Doing so allows to avoid the following issues:

1) Settings application name after the method instantiateSettings was called
wasn't affecting the already instantiated object.

2) Side effect of (1) was the deletion of the original "Slicer.ini" settings
file

3) Creating a QSettings using the constructor taking filename as a parameter
is NOT updating the convenience QSettings singleton.


Note also that the method qSlicerCoreApplication::handlePreApplicationCommandLineArguments
is not called anymore by "qSlicerCoreApplicationPrivate::parseArguments"
but is called directly after all core objects have been instantiated.

See http://www.na-mic.org/Bug/view.php?id=2719

Fixes #2719

git-svn-id: http://svn.slicer.org/Slicer4/trunk@21323 3bd1e089-480b-0410-8dfb-8563597acbee
ENH: updated version of jqPlot to 1.0.4

This appears to fix bugs in zooming of bar charts.

git-svn-id: http://svn.slicer.org/Slicer4/trunk@21324 3bd1e089-480b-0410-8dfb-8563597acbee
STYLE: documentation on how dates are specified in plots

git-svn-id: http://svn.slicer.org/Slicer4/trunk@21325 3bd1e089-480b-0410-8dfb-8563597acbee
ENH: added date axis and boxplot

dcommit failed a pre-commit hook and unstaged a series of commits.
recommitting as a single commit

    ENH: support for dates on X-axis

    First attempt at supporting date axes.

    jqPlot date support is designed for continuous dates like in
    tracking stocks.  It allows for "gaps" in the dates, which are
    interpolated across for line plots and remain as gaps in bar plots.
    However, this scheme does not really align with our use case.

    Therefore, Slicer internally uses categorical axes when told
    to display dates.

    The logic for varyBarColor was modified so the default is off
    and it is only turned on when a lookup table is assigned to a series.

    A few method names in the private implementation were modified
    to make them consistent with new methods added.

    Slicer passes dates in the DoubleArrayNode, which stores things as
    floats.  Thus, dates must be represented as seconds since
    January 1, 1970. Fractional seconds are allowed.  Internally, these
    timestamps are converted to javascript timestamps which are in
    milliseconds.

    Date formating is currently fixed and limited to YYYY-MM-DD style.

    ENH: added boxplot

    Adapted a boxplot renderer from Joshua Bronson. https://bitbucket.org/jab/jqplot/changeset/f0f8eaa7e09e

    Added support for outliers and caching the y-axis bounds

    First version of jqplot that we are tarballing ourselves with modifications/additions from the
    main jqplot repository. Currently using a repository on github (millerjv)
    and will move to Slicer Community.  Slicer Community repository is being used for tarballs.

    Major rewrite of the qMRMLChartWidget to refactor the chart generation into separate
    routines for each chart type.

git-svn-id: http://svn.slicer.org/Slicer4/trunk@21326 3bd1e089-480b-0410-8dfb-8563597acbee
COMP: Remove unused *.tcl files from Base/Tcl

Also verified that non of these tcl modules were used in EMSegment using the
following one-liner:

cd /home/jchris/Projects/Slicer4-Superbuild-Debug/EMSegment
$ for i in `ls -1 ~/Projects/Slicer4/Base/GUI/Tcl/*.tcl`; do bn=`basename $i`; ack --no-mrml  "[^A-Za-z0-9]${bn%.tcl}"; done

See http://na-mic.org/Bug/view.php?id=2735

Fixes #2735

git-svn-id: http://svn.slicer.org/Slicer4/trunk@21327 3bd1e089-480b-0410-8dfb-8563597acbee
COMP: Remove unused *.png files from Base/GUI/ImageData and Base/GUI/Tcl/ImageData

Also verified that non of these png module were used using the
following one-liner:

cd /home/jchris/Projects/Slicer4
for i in `ls -1 ~/Projects/Slicer4/Base/GUI/ImageData/*.png`; do bn=`basename $i`; echo "Checking for ${bn%.png}"; ack --no-mrml  "^[A-Za-z0-9]${bn%.png}"; done
for i in `ls -1 ~/Projects/Slicer4/Base/GUI/Tcl/ImageData/*.png`; do bn=`basename $i`; echo "Checking for ${bn%.png}"; ack --no-mrml  "^[A-Za-z0-9]${bn%.png}"; done

Using the one-liner ack --py "png", I found that the editor module was using the editor effect images from the
Tcl/ImageData folder. Only the effect used by the module have been kept
in the folder.

git-svn-id: http://svn.slicer.org/Slicer4/trunk@21328 3bd1e089-480b-0410-8dfb-8563597acbee
COMP: Remove unused VolumeDisplaySWidget.tcl - W/L implemented in vtkSliceViewInteractorStyle

See http://na-mic.org/Bug/view.php?id=2735

Fixes #2735

git-svn-id: http://svn.slicer.org/Slicer4/trunk@21329 3bd1e089-480b-0410-8dfb-8563597acbee
BUG: Fix generic test ensuring qSlicerApplication instantiate ctkSettings

Fix is a follow up of commit r21323

git-svn-id: http://svn.slicer.org/Slicer4/trunk@21330 3bd1e089-480b-0410-8dfb-8563597acbee
BUG: Add support for installation of distribute and pip

Connect the signal "systemExitExceptionRaised" and so that the
application can be cleanup and terminate nicely. This will allow
the installation of distribute to terminate nicely. Indeed "sys.exit"
is called within the "distribute_setup.py" script.

Also add the "isatty" method to PythonQtRedirectStdOut so that logging
framework can check if the output is a tty-like device. Log mechanism
associated with pip install will now be happy since the call "sys.stdout.isatty"
will be valid.

See http://na-mic.org/Mantis/view.php?id=2694

Fixes #2694

git-svn-id: http://svn.slicer.org/Slicer4/trunk@21331 3bd1e089-480b-0410-8dfb-8563597acbee
BUG 2725. Fixed setting transform node reference. Added test Testing/vtkMRMLTransformableNodeReferenceSaveImportTest.cxx


git-svn-id: http://svn.slicer.org/Slicer4/trunk@21332 3bd1e089-480b-0410-8dfb-8563597acbee