The current convention on loading mrml scenes is that data files
overwrite information in the mrml scene file.

I noticed that in particular vector field transform is stored in the
mrml file that may create huge mrml files. This should be addressed.

svn 20977 reduces the size of the mrml scene a bit by not writing out non named colors. Still have to test if this leads to fixing the problems I saw with not writing out colors in mrml at all and just relying on storage node files.

vtkMRMLGridTransformNode stores the displacement values in the MRML. I can remove them, but it may cause compatibility issues if somebody relies on the data being present in MRML

Just write an email to the developer and user mailing list that you plan to remove the storage from the Scene file. If nobody objects for one week then you can go on and remove.

Removed grid transform displacement field output to MRML file.
Also grid transform can be written as NRRD file now. Reassigning to Jim to verify that it works correctly and can be passed between slicer and CLI's

From Nicole:

Hi Tiziano,

Yes, the numcolors tag needs to come before the colors tag, due to the
way the color look up table is currently being built. When reading from
file, I parse the file twice to get the hightest index, but the MRML
file is assumed to provide this information. numcolors should be set to
the highest index + 1.

There's a Mantis issue open that will track work to remove the color
information from the MRML file and only read from the separate color
table file, which will be implemented in version 4.3 and hopefully
remove confusion.
http://www.na-mic.org/Bug/view.php?id=2486

A safer way to incorporate your custom color file is to load the ctbl
file via File -> Add Data, then save a scene to see how it looks in
MRML. The order is sometimes important for MRML nodes, check for the
order in which attributes are output in the WriteXML methods of the
nodes in question (or link to the MRML library and use the code directly).

The warnings are from the order of reading the volume nodes, display
nodes and color table nodes from a MRML file or when restoring a scene,
I'm working on detecting the "safe" time to not print out a warning.

Nicole

Revisiting this, here's Alex's check in to remove grid transform displacement fields:
http://viewvc.slicer.org/viewvc.cgi/Slicer4?view=revision&revision=21024
For passing to CLI's BSplineDeformableRegistration and TestGridTransformRegistration have them as parameters. Running the latter with fixed.nrrd and moving.nrrd, moving apperas in the Data module under Output Transform. In the Save dialog, I picked Deformation field .nrrd to save the Output Transform. In the resulting mrml file, no extra entries. Tryign to load the Output transform.nrrd file in Add Data, I can only pick a volume file format (or Scalar Overlay or Fibre Bundle). If I load the .mrml scene file, everything loads okay and looks fine.
Doesn't look like there's a CLI that takes a grid transform as input.

Closing the scene, adding a new color file to the scene, and making a copy so there's a new one, then saving... didn't save the mrml file. Checking it to save it, the non empty color entries are saved to both mrml and the ctbl file.

Exit and restart, added 5 fiducials, 2 rulers, 1 ROI, then saved:
Markups fiducial points only saved to disk in one .fcsv file
Annotation Ruler node saved to mrml file and to disk in 2 .acsv files
Annotation ROI node save to mrml file and to disk in 1 .acsv file.
Looading the csv files from disk worked for all of the types.
Loading the scene file worked as well (though the Markups fiducial list didn't get set active on the Markups module node selector).

So: nodes that got moved out of mrml: fiducials, grid transform.
Nodes that did not: rulers, rois, color tables.

Did some testing and leaving in the number of colors in the color table in mrml but not writing out the colors seems to be working (aka no crashes like I had last time I tried to fix this). Checked that in as svn 22344[1].

Looking again at the Annotation nodes, I would advise against modifying the Ruler and ROI to not write their control points into MRML.
The Ruler will get moved to the Markups module and will be just written to file via the storage node, not included in MRML.
Alex, if you want to look at the ROI node to take the points out of MRML, please be sure to test scene close, save, load, scene view restore.

[1]http://viewvc.slicer.org/viewvc.cgi/Slicer4?view=revision&revision=22344

@Alex: Could you update both Nighly / 4.3 module documentation ?

Not clear when there will be time to work on this.

Retargeting stale issues to backlog.