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CLI Commands

Cardiotensor provides powerful features for analyzing 3D cardiac imaging data, from processing imaging volumes and calculating orientation to managing large-scale projects with support for multiple configurations and platforms.

Orientation Computation

Compute myocyte orientation from a 3D volume using a configuration file.

  • cardio-tensor Computes structure tensor, helical/intrusion angle, FA, and eigenvectors.

  • cardio-tensor-slurm Submits chunked cardio-tensor runs as SLURM array jobs. See SLURM Launcher.

See the example to get started.

Transmural Analysis

Plot angle profiles across the heart wall using an interactive GUI.

  • cardio-analysis Define transmural lines, adjust sampling, and export results.

See the example for details.

3D Visualization

Visualize results in 3D using vector fields and streamlines.

Note

To use these modules, you must first compute and save the eigenvector field by setting WRITE_VECTORS=True in the configuration file before running the structure tensor calculation.

  • cardio-visualize-vector Render vector fields using Fury. Optionally export to ParaView (VTK format).

  • cardio-generate-streamlines Generate streamlines from the vector field. Outputs .trk files compatible with Amira.

  • cardio-visualize-streamlines Visualize streamlines in 3D using Fury. Can also export to ParaView.

The FURY backend uses FURY 2 (PyGfx/WebGPU). In the streamline viewer:

  • O enables the clipping plane; H shows its transform handles; I flips it and R resets it.
  • C enables the crop box; G shows its transform handles; X resets it.
  • Drag gizmo arrows to translate, spheres to rotate, and cubes to scale along an axis. Click the center to change the gizmo coordinate system.
  • L opens material controls, +/- changes thickness, and 1–4 selects camera views. 5 switches projection.
  • Ctrl+S saves the session; P saves a PNG, Shift+P saves at twice the pixel resolution, and V records an orbit.
  • B changes the background and S toggles a ruler in dataset coordinate units.

Existing VTK-era sessions are read and converted when saved. New sessions use format version 2 and are intended for the FURY 2 viewer. Overlays and gizmos have changed appearance. FURY smoothing now uses a natural cubic spline; set --spline-subdiv 1 to preserve the original points. The PyVista backend retains its VTK smoothing.

See the example for usage.

Next Steps

Read the example for an introduction to each feature.