API Reference

This page provides a concise reference for the public API of each class. Full Doxygen documentation is available in the header files under include/.

itk::TrxStreamlineData

Central data container for TRX tractography data. Inherits itk::DataObject. Holds lazy-loaded streamline positions (float16, float32, or float64) and per-streamline offsets. Supports AABB spatial queries, lazy and eager subsetting, named group access, DPS/DPV field retrieval, and group connectivity computation.

Streamline access

Method

Description

GetNumberOfStreamlines()

Total number of streamlines

GetNumberOfVertices()

Total number of vertices across all streamlines

GetStreamline(i)

Streamline i as std::vector<PointType> in LPS+

GetStreamlineRange(i)

Forward-iterable range over LPS+ points of streamline i

GetStreamlineView(i, view)

Zero-copy raw pointer view; returns false if positions are not yet loaded

ForEachStreamlineChunked(fn)

Iterate all streamlines with on-the-fly coordinate conversion

Subsetting and queries

Method

Description

QueryAabb(min, max)

Streamlines whose bounding boxes intersect the LPS+ box

QueryAabb(min, max, cache, maxN, seed)

As above, capped at maxN streamlines (random sample when over limit)

SubsetStreamlines(ids)

Eager subset by index list

SubsetStreamlinesLazy(ids)

Lazy subset; delegates to TRX handle when available

Groups

Method

Description

HasGroups()

True if the file contains at least one named group

GetGroupNames()

Names of all groups in file order

GetGroup(name)

TrxGroup::Pointer for the named group; cached after first call

GetGroupStreamlineCount(name)

Streamline count for a group without loading indices

DPS / DPV fields

Method

Description

GetDpsFieldNames()

Names of all per-streamline scalar fields

GetDpvFieldNames()

Names of all per-vertex scalar fields

GetDpsField(name)

Per-streamline values widened to float; flat row-major for multi-column fields

GetDpvField(name)

Per-vertex values widened to float

Transforms

Method

Description

TransformInPlace(transform)

Apply ITK transform to all positions in memory

TransformToWriterChunked(transform, writer)

Stream transformed positions to a TrxStreamWriter in chunks

TransformToWriterChunkedReuseVnlBuffer(transform, writer, buf)

As above, reusing a caller-supplied vnl_matrix<double> buffer

Connectivity

Method

Description

ComputeGroupConnectivity(dpsField="")

N×N symmetric matrix of shared streamline counts (or weighted sums)

Metadata

Method

Description

GetVoxelToRasMatrix()

4×4 voxel-to-RAS affine from the TRX header

GetVoxelToLpsMatrix()

4×4 voxel-to-LPS affine

GetDimensions()

Grid dimensions from the TRX header

Save(filename, useCompression)

Write the data to a new TRX file

itk::TrxStreamWriter

Incremental streaming writer for TRX files. Inherits itk::Object. DPS and DPV fields must be registered before the first PushStreamline() call. Every push must supply values for all registered fields with consistent lengths.

Method

Description

SetFileName(path)

Output file path

UseCompressionOn() / UseCompressionOff()

Enable or disable ZIP compression (default: off)

RegisterDpsField(name, dtype)

Declare a per-streamline field; dtype is "float32", "float64", etc.

RegisterDpvField(name, dtype)

Declare a per-vertex field

PushStreamline(pts, dps, dpv)

Push one streamline as std::vector<itk::Point<double,3>>

PushStreamline(mat, dps, dpv)

Push one streamline as an N×3 vnl_matrix<double>

Finalize()

Seal the ZIP archive; required before the file is usable

SetPositionsBufferMaxBytes(n)

Buffer positions in memory before flushing (useful on slow disks)

itk::TrxFileReader

ProcessObject wrapper for reading TRX files into a TrxStreamlineData. Follows the itk::ImageFileReader interface pattern.

Method

Description

SetFileName(path)

Input file path

Update()

Open the file and populate the output object (positions remain lazy)

GetOutput()

TrxStreamlineData::Pointer

itk::TrxFileWriter

ProcessObject wrapper for writing a TrxStreamlineData to a TRX file.

Method

Description

SetFileName(path)

Output file path

SetInput(data)

TrxStreamlineData to write

Update()

Write the file

itk::TrxGroup

Represents a named bundle of streamlines. Inherits itk::Object. Created by TrxStreamlineData::GetGroup(); do not construct directly. Streamline indices are loaded lazily on first access.

Method

Description

GetName()

Group name as stored in the TRX file

GetStreamlineIndices()

Indices into the parent TrxStreamlineData

GetStreamlines(parent)

Lazy TrxStreamlineData subset; no position data is copied

GetDpgFieldNames()

Names of per-group scalar metadata fields

HasDpgField(name)

True if the named DPG field exists

GetDpgField(name)

Per-group scalar values as std::vector<float>

SetVisible(bool)

Observer-pattern visibility toggle (for GUI integration)

SetColor(r, g, b)

Observer-pattern color assignment (for GUI integration)

itk::TrxParcellationLabeler

Assigns streamlines to named TRX groups based on one or more NIfTI-1 parcellation images. Inherits itk::Object. Each label image contributes groups whose names follow the pattern <prefix>_<label_name>.

Method

Description

SetInput(data)

TrxStreamlineData to parcellate

AddAtlas(niftiPath, labelTxtPath, prefix)

Register a parcellation atlas; may be called multiple times

SetDilationRadius(n)

Expand each parcel by n voxels before intersection testing

Update()

Run parcellation and populate output groups

GetOutput()

TrxStreamlineData::Pointer with groups appended

itk::TrxGroupTdiMapper

Maps streamlines from selected groups onto a reference NIfTI grid to produce a track density image. Inherits itk::Object.

Method

Description

SetInput(data)

TrxStreamlineData to map

SetReferenceImage(img)

NIfTI reference image defining the output grid

SetGroupPredicate(predicate)

Select streamlines by group membership (all-of, any-of, none-of)

SetWeightField(name)

DPS field to use as per-streamline weight (empty = unweighted count)

Update()

Compute the density image

GetOutput()

itk::Image<float, 3>::Pointer track density image