NrrdSaver¶

class io.savers.NrrdSaver¶

Bases: io.savers.BaseSaver

NRRDSAVER - Saver for NRRD (Nearly Raw Raster Data) format output.

Handles two format variants: ‘NRRD Data Format (*.nrrd)’ - standard NRRD volume ‘NRRD for 3D Slicer (*.nrrd)’ - NRRD with 3D Slicer-compatible metadata (RAS space, voxel-to-world transform, etc.)

Both image and label/mask volumes can be saved. The layer type is inferred from options.layerType (default ‘image’). For multi-channel or time-series data only the first channel (C=1) and first time point (T=1) are passed to the underlying helper; a warning is issued if C>1.

The saver delegates the actual I/O to the legacy helper bitmap2nrrd(), which is ported from MIB2.

DATA DIMENSIONS Input data : [H, W, D, C, T] (MIB3 native order) bitmap2nrrd() expects [H, W, D] - obtained by squeezing the first channel and time point.

BOUNDING BOX The bounding box is read from metadata.boundingBox as [xmin xmax ymin ymax zmin zmax]. If not present, zeros(1,6) is used as a default.

FILENAME GENERATOR options.FilenameGenerator controls how the output file is named: ‘Use sequential filename’ (default) - numbered naming ‘Use original filename’ - derived from metadata.sliceName

TODO: port bitmap2nrrd from MIB2_RENAMED_FOR_MIB3/ImportExportTools/nrrd/bitmap2nrrd.m to mib/+io/+NRRD/bitmap2nrrd.m

USAGE EXAMPLES

%% 1. Save image volume as standard NRRD
saver = io.SaverFactory.create('NRRD Data Format (``*.nrrd``)');

opts.Format            = 'NRRD Data Format (``*.nrrd``)';
opts.showWaitbar       = false;
opts.silent            = true;
opts.overwrite         = true;
opts.layerType         = 'image';
opts.FilenameGenerator = 'Use sequential filename';

meta.filename    = 'source_stack.tif';
meta.colorType   = 'grayscale';
meta.lutColors   = [1 1 1];
meta.dataClass   = 'uint16';
meta.maxInt      = 65535;
meta.pixSize     = struct('x',0.065,'y',0.065,'z',0.2, ...
                          'units','um','t',1,'tunits','s');
meta.boundingBox = [0 33.3 0 33.3 0 10];

data = uint16(rand(512,512,50,1,1)*65535);  % [H W D C T]
fnOut = saver.save(data, meta, '/output/myStack.nrrd', opts);
fprintf('Saved: %s\n', fnOut);

%% 2. Save labels as NRRD for 3D Slicer
saver = io.SaverFactory.create('NRRD for 3D Slicer (``*.nrrd``)');

opts.Format      = 'NRRD for 3D Slicer (``*.nrrd``)';
opts.showWaitbar = false;
opts.silent      = true;
opts.overwrite   = true;
opts.layerType   = 'labels';

meta.filename    = 'source_stack.tif';
meta.pixSize     = struct('x',0.065,'y',0.065,'z',0.2, ...
                          'units','um','t',1,'tunits','s');
meta.boundingBox = [0 33.3 0 33.3 0 10];

labels = uint8(rand(512,512,50,1,1)*3);  % [H W D C T]
fnOut = saver.save(labels, meta, '/output/Labels_Slicer.nrrd', opts);

SEE ALSO io.SaverFactory, io.savers.BaseSaver, io.savers.TiffSaver, core.MibImage.save, core.MibDataset.save, models.MibModel.save

Constructor Summary

NrrdSaver(options)¶

NRRDSAVER - Constructor for NrrdSaver class.

Syntax:

saver = io.savers.NrrdSaver(options)

Input Arguments:

• options - (optional) struct, saver-level options (usually empty; per-save options are passed to save() instead)

Output Arguments:

• obj - instance of the NrrdSaver class

Method Summary

getSupportedFormats(~)¶

GETSUPPORTEDFORMATS - Return format strings handled by NrrdSaver.

Syntax:

formats = obj.getSupportedFormats()

Input Arguments:

(none)

Output Arguments:

• formats - cell array of format strings for NRRD output

save(data, metadata, filename, options)¶

SAVE - Write data as a NRRD file.

Syntax:

fnOut = obj.save(data, metadata, filename, options)

NRRD supports single-channel data (C=1); a warning is issued and only the first channel is written if C>1. Similarly, only the first time point (T=1) is used for time-series data.

Input Arguments:

• data - [H, W, D, C, T] numeric array

• metadata - struct with fields:

  • colorType - 'grayscale' | 'multichannel' | 'indexed'

  • dataClass - 'uint8' | 'uint16' | …

  • maxInt - maximum intensity value

  • pixSize - struct {.x, .y, .z, .units, .t, .tunits}

  • boundingBox - [xmin xmax ymin ymax zmin zmax]; default: zeros(1,6)

  • sliceName - (optional) per-slice source filenames

• filename - full output path, e.g. '/out/stack.nrrd'

• options - struct with fields:

  • Format - format string ('NRRD Data Format (*.nrrd)' or 'NRRD for 3D Slicer (*.nrrd)')

  • layerType - 'image' | 'mask' | 'labels'; default: 'image'

  • showWaitbar - logical; default: true

  • silent - logical, suppress dialogs; default: false

  • overwrite - logical; default: true

  • FilenameGenerator - 'Use original filename' | 'Use sequential filename'

Output Arguments:

• fnOut - [char] path of saved .nrrd file, [] on failure

Example - see class-level documentation above.