PC-MRA Volume Rendering
Status
| Entry point |
Status |
Notes |
| GUI |
Supported |
A dynamic PC-MRA (4D) layer is added to the Browser after a flow + magnitude case is loaded. |
| CLI |
Not implemented |
Batch outputs remain numerical; the interactive VTK layer is GUI-only. |
| Python API |
Not implemented |
Use the GUI for the interactive volume actor. |
What it does
The GUI computes a phase-resolved phase-contrast MR angiography (PC-MRA) volume
for every cardiac frame: magnitude_t × ||velocity_t||. It renders the current
frame with VTK's grayscale composite volume mapper. The automatic display range
uses the positive finite foreground values from that frame: L=P5 and H=P99,
then WL=(L+H)/2 and WW=H-L. The timeline and playback update the 3-D volume
actor.
When to use it
Use it as a 3-D anatomical backdrop while reviewing segmentation, planes,
streamlines, and pathlines. It is especially useful when a surface-only
segmentation view hides nearby vessels.
Quick use
- Load an H5 or DICOM case with magnitude and flow.
- In the left Browser, select the
PC-MRA (4D) item under Global → PC-MRA and check or uncheck it.
- Adjust
Opacity below the Browser (or use the item's right-click Set Opacity…).
- In the central 3-D view, hold
Shift and the left mouse button and drag
horizontally to change window width and vertically to change window level.
All other camera gestures use VTK's default trackball-camera mapping.
- Use the
Window/Level sliders below the 3-D view to adjust the range, or
use Auto / Reset PC-MRA Window/Level to restore the automatic range.
Without Shift, all three mouse buttons retain VTK's default camera
behavior regardless of PC-MRA visibility.
| Input |
Required |
Meaning |
mag_raw |
yes |
magnitude volume, 3-D or 4-D |
flow_raw |
yes |
normalized XYZT3 velocity in cm/s |
resolution, origin |
yes |
physical spacing and world origin for the VTK image |
Parameters
| Parameter |
Type |
Default |
Where configured |
Effect |
Code owner |
Browser Opacity |
0–100% slider |
85% |
GUI, per SceneObject |
scales the PC-MRA scalar-opacity transfer function |
autoflow/ui/app.py, autoflow/ui/viewer.py |
| automatic range |
current frame positive finite values |
P5 to P99 |
GUI |
derives WL=(L+H)/2 and WW=H-L |
autoflow/ui/viewer.py |
Window slider |
normalized slider |
automatic current-frame width |
GUI |
changes PC-MRA window width |
autoflow/ui/app.py, autoflow/ui/viewer.py |
Level slider |
normalized slider |
automatic current-frame center |
GUI |
changes PC-MRA window level |
autoflow/ui/app.py, autoflow/ui/viewer.py |
| volume blend/shading |
mapper options |
composite, no shading |
code |
displays the raw grayscale volume without added surface lighting |
autoflow/ui/viewer.py |
| 3-D background color |
color string |
#000000 |
Settings → 3D Background Color |
controls the backdrop independently of PC-MRA transfer functions |
autoflow/config.py, autoflow/ui/app.py, autoflow/ui/viewer.py |
Outputs
No file is created automatically. The Browser stores a SceneObject with
data_key="pcmra_volume"; workspace save/restore preserves its visibility and
opacity. The 3-D actor is a VTK volume actor, not a polygon surface.
Limitations
- The volume is phase-resolved, but it uses the loaded temporal frames directly; no temporal interpolation is performed.
- PC-MRA has no scalar bar by default because it is used as an anatomical backdrop.
- GPU volume rendering support depends on the local VTK/OpenGL environment.
Where to change code
| Change you want |
Edit here |
Also check |
Tests |
| PC-MRA calculation and VTK image |
autoflow/ui/viewer.py (_build_dataset) |
autoflow/core/pipeline.py registration |
smoke test and GUI manual check |
| Browser visibility/opacity controls |
autoflow/ui/app.py |
autoflow/core/models.py persistence |
GUI manual check |
| 2-D segmentation overlay opacity |
autoflow/ui/ortho_viewer.py |
autoflow/ui/app.py segmentation dock |
GUI manual check |
Tests
~/miniconda3/envs/ryy/bin/python -m pytest tests/test_smoke_phantoms.py -q~/miniconda3/envs/ryy/bin/python -m pytest tests/test_pressure_gradient_phantom.py -q
Common problems
| Symptom |
Likely cause |
Fix |
PC-MRA is absent |
magnitude or flow was not loaded |
check the input case and loader metadata |
| the backdrop is too faint or too strong |
opacity is low or background intensity is high |
select the Browser item and adjust Opacity |
| volume rendering fails on a remote display |
VTK/OpenGL volume support is unavailable |
use the existing SSH off-screen renderer or hide PC-MRA and review surfaces |