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IDProjectCategoryView StatusLast Update
0004399Slicer4Core: Segmentationpublic2018-03-31 00:37
ReporterpinterAssigned Topinter 
PrioritynormalSeverityminorReproducibilityN/A
Status assignedResolutionopen 
Product VersionSlicer 4.7.0 
Target VersionSlicer 4.11.0Fixed in Version 
Summary0004399: Save segmentations into vtm also when master is labelmap
Description

Currently vtm (multiblock dataset format) is written for poly data master representations, but a 4D NRRD is written for labelmaps. The problem with 4D nrrd is that it may have huge memory usage especially in case of many segments, because the union of the extents are used.
It would be better in this sense to use vtm file (which is an XML pointing to files in a directory with the same name) for labelmaps too, because the segments can be saved one by one. Other advantages:

  • The resulting NRRD files can be loaded as labelmaps individually if needed
  • vtm can be the file extension for segmentations in Slicer, and we could get rid of the extension problems too (0000758)

Implementation: vtkXMLMultiBlockDataWriter::WriteComposite writes the individual blocks into files, but for images it probably uses vti. It will need to be subclassed to use the NRRD writer. It can be done by also subclassing vtkXMLCompositeDataWriter and reimplement CreateWriters so that it creates NRRD writer instead of vtkXMLImageDataWriter

Additional Information

Moved here from SlicerRT because Segmentations is now in Slicer core
https://app.assembla.com/spaces/slicerrt/tickets/826-save-segmentations-into-vtm-with-labelmap-master-too/details

TagsNo tags attached.

Relationships

related to 0004329 closedlassoan Slicer crashes when attempting to load large segmentations from nrrd files in 4.7 nightlies 

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Issue History

Date Modified Username Field Change
2017-07-25 14:23 pinter New Issue
2017-07-25 14:23 pinter Status new => assigned
2017-07-25 14:23 pinter Assigned To => pinter
2017-07-25 14:25 pinter Relationship added related to 0004329
2018-03-31 00:37 jcfr Target Version Slicer 4.9.0 => Slicer 4.11.0