Supported raw and label formats

[hanslovsky]

We need to specify a source structure that is supported in the Paintera main class entry point.

First Draft

Note that this is relevant only for sources that are added through the open dialog or via command line arguments. Any source that is specified in the project's attributes.json can be loaded as long as the appropriate de-serializer is on the classpath.

Raw

Accept any of these:

1. any regular (i.e. default mode) three-dimensional N5 dataset that is integer or float. Optional attributes are "resolution": [x,y,z] and "offset": [x,y,z].
2. any multiscale N5 group that has "multiScale" : true attribute and contains three-dimensional multi-scale datasets s0 ... sN. Optional attributes are "resolution": [x,y,z] and "offset: [x,y,z]". In addition to the requirements from (1), all s1 ... sN datasets must contain "downsamplingFactors": [x,y,z] entry (s0 is exempt, will default to [1.0, 1.0, 1.0]). All datasets must have same type. Optional attributes from (1) will be ignored.
3. (preferred) any N5 group with attribute "painteraData : {"type" : "raw"} and a dataset/group data that conforms with (1) or (2).

Labels

Accept any of these:

1. any regular (i.e. default mode) integer or varlength LabelMultisetType ("isLabelMultiset": true) three-dimensional N5 dataset. Optional attributes are "resolution": [x,y,z], "offset": [x,y,z], "maxId": <id>. If "maxId" is not specified, it is determined at start-up and added.
2. any multiscale N5 group that has "multiScale" : true attribute and contains three-dimensional multi-scale datasets s0 ... sN. Optional attributes are "resolution": [x,y,z], "offset": [x,y,z], "maxId": <id>. If "maxId" is not specified, it is determined at start-up and added (this can be expensive). In addition to the requirements from (1), all s1 ... sN datasets must contain "downsamplingFactors": [x,y,z] entry (s0 is exempt, will default to [1.0, 1.0, 1.0]). All datasets must have same type. Optional attributes from (1) will be ignored.
3. (preferred) any N5 group with attribute "painteraData : {"type" : "label"} and a dataset/group data that conforms with (1) or (2). Optional sub-groups are:

• fragment-segment-assignment -- Dataset to store fragment-segment lookup table. Can be empty or will be initialized empty if it does not exist.
• unique-label-lists -- Multiscale varlength dataset with same 'dimensions'/'blockSize' and as dataset(s) in data. Holds unique block lists from which relevant blocks for specific ids are retrieved.

Things to consider for labels:

• make "maxId" attribute mandatory because IdService needs it and would require to scan whole dataset (can be huge)
• Efficient mesh generation
• only possible if
  • option (3) and unique-label-lists exists, or
  • LabelMultisetType dataset (currently, VolatileLabelMultisetArray holds a set of contained labels).
• If none of these are true, ask user if
  • unique label lists should be generated from highest resolution to lowest resolution (slow, would need to be generated once and cached or saved as unique-label-lists if option (3), probably useful for looking at small datasets), or
  • generate unique label lists on the fly from lowest resolution to highest resolution (fast, only do the work that's currently necessary, but potentially incomplete), or
  • 3D support should be disabled for that source.
• If (1) or (2), fragment-segment-assignment cannot be committed back to source (only stored as actions in project's attributes.json). There should be an option to export fragment-segment-assignment as N5 dataset. That way, users can choose to update their source in order to conform with (3) and not lose their work on fragment-segment assignments
• (3) leaves room for adding related data in the future, e.g. annotations

[hanslovsky]

Addressed in https://github.com/saalfeldlab/paintera/tree/paintera-datasets
Will need to use it for a while before making a merge decision

[hanslovsky]

Option (3) does not work for HDF5 (without further thinking/hacking of the HDF5 bindings, which is an OK restriction)