Volume Loader

The volume_loader operator reads 3D volumes from the specified input file.

Supported Formats

The operator supports these medical volume file formats:

• MHD (MetaImage)
  • Detached-header format only (.mhd + .raw)
• NIFTI
• NRRD (Nearly Raw Raster Data)
  • Attached-header format (.nrrd)
  • Detached-header format (.nhdr + .raw)

You must convert your data to one of these formats to load it with VolumeLoaderOp. Some third party open source tools for volume file format conversion include:

• Command Line Tools
  • the Insight Toolkit (ITK) (PyPI, Image IO Examples)
  • SimpleITK (PyPI)
  • Utah NRRD Utilities (unu)
• GUI Applications
  • 3D Slicer
  • ImageJ

API

holoscan::ops::VolumeLoaderOp

Operator class to read a volume.

Parameters

• file_name: Volume data file name
  • type: std::string
• allocator: Allocator used to allocate the volume data
  • type: std::shared_ptr<Allocator>

Outputs

• volume: Output volume data
  • type: nvidia::gxf::Tensor
• spacing: Physical size of each volume element
  • type: std::array<float, 3>
• permute_axis: Volume axis permutation of data space to world space, e.g. if x and y of a volume is swapped this is {1, 0, 2}
  • type: std::array<uint32_t, 3>
• flip_axes: Volume axis flipping from data space to world space, e.g. if x is flipped this is {true, false, false}
  • type: std::array<bool, 3>
• extent: Physical size of the the volume in world space
  • type: std::array<float, 3>