GUI Guide¶

Status¶

autoflow-gui is supported for interactive loading, segmentation review, grouped vessel processing, step execution, and visualization.

Entry files:

pyproject.toml
autoflow/ui/launcher.py
autoflow/ui/app.py
autoflow/ui/remote_plotter.py
autoflow/ui/theme.py

The desktop GUI uses PySide6. The three orthogonal slice views and the manual segmentation editor use pyqtgraph; the selected oblique-plane plot and analysis plots continue to use Matplotlib.

Start The GUI¶

autoflow-gui

On Windows, a packaged release can be started directly with AutoFlow-GUI.exe. The standalone build includes the GUI dependencies, nnUNet inference runtime, dataset.json, plans.json, and fold_all/checkpoint_final.pth; it does not require a Python installation or a separate model directory. The single-file build extracts its runtime to a temporary directory at startup, so its first launch is slower than the installed Python entry point.

Or load defaults from a custom config directory:

autoflow-gui --config-dir ./configs

For a regular forwarded SSH session, connect with trusted X11 forwarding and start the same command:

ssh -Y <host>
autoflow-gui

When DISPLAY has the forwarded localhost:N.0 form, AutoFlow automatically renders VTK through off-screen EGL and transfers the completed 3D image into a normal Qt widget. In the 3-D view, VTK's default trackball-camera mapping is used: left-drag rotates, middle-drag pans, right-drag performs dolly/zoom, and the mouse wheel zooms. When PC-MRA is visible, Shift+left-drag adjusts its window/level. Existing 3D picking and edit controls remain available. A local display such as DISPLAY=:1 continues to use the native embedded VTK widget. SSH rendering affects display latency only; loaded arrays, processing, and saved numerical results are identical.

Main Layout¶

The main window contains:

menu bar
workflow navigation for Input & QC, Segmentation, Phase Unwrapping, Centerline & Planes, Hemodynamics, and Review & Export
left browser
central 3D view
steps area
parameter panels
right ortho viewer
bottom timeline
bottom Selection and Log tabs
right segmentation dock
right analysis dock

The GUI uses a shared light workbench theme across the main window, dialogs, tables, parameter panels, and docks. The timeline uses fixed-size previous, play, pause, and next icons; hover each icon for its action name. Its ms value is the requested delay between frames, not the acquisition time resolution. While playback runs, the timeline reports a rolling scene-and-slice render time plus the effective FPS. When render time exceeds the requested delay, playback runs at the fastest rate the visible scene can sustain. Selection details and the runtime log share a compact bottom tab area so the 3D and ortho views retain more vertical space.

The loaded arrays are already normalized to LR/AP/FH. The 3D orientation axes, ortho sliders, flow-component names, pressure-gradient component names, and slice titles use those physical direction labels instead of generic X/Y/Z. The source file's original SpatialOrder remains visible in the input settings and metadata for auditing, but it is not reused to label arrays after normalization. The top-level Settings > 3D Axis Orientation action can apply a display-only reversal of the X/Y/Z positive directions (for example LR to RL); all rendered 3D objects are mirrored together while internal arrays and analysis coordinates remain unchanged.

The left browser is group-aware and path-aware. When the loaded segmentation produces multiple vessel groups, the browser shows one top-level section per group. Path geometry, generated planes, and their pathlines are organized as Paths -> Path -> Plane -> Pathline; each path row shows its plane count. Manual or unmatched planes appear under Unbound Planes. Group, path, and plane checkboxes control all descendants, while selecting a path or plane updates the corresponding 3D highlight and analysis panel. Use Ctrl/Shift selection with a plane context menu to launch pathlines for that subset; the main Pathlines action runs all planes.

When magnitude and flow are loaded, Global → PC-MRA (4D) is available as a grayscale VTK volume backdrop. It is phase-resolved (magnitude_t × speed_t) and updates with the timeline/playback, with a low-intensity transfer function to suppress background noise. The default volume color transfer is grayscale with white high intensities, and the default 3-D background is black. Select any Browser object to adjust its individual Opacity with the slider below the tree; the context menu also has Set Opacity… and Reset Opacity (100%). Selecting a group applies the slider to all of its descendants. The right-hand ortho viewer has a separate Overlay slider for the 2-D segmentation overlay; it does not change the underlying scalar window/level.

When PC-MRA (4D) is visible, hold Shift and the central 3-D view's left mouse button, then drag horizontally for window width and vertically for window level. The Browser context menu's Reset PC-MRA Window/Level restores the automatic current-frame range. Without Shift, the default left-drag rotation and middle-drag pan remain unchanged.

The Window/Level control bar below the 3-D view provides Window and Level sliders for the selected scalar scene object. It works for PC-MRA, WSS, TKE, pressure-gradient layers, and streamline objects; Auto restores that object's automatic range. The Overlay opacity slider is independent and controls the 2-D segmentation overlay directly.

On SSH-forwarded X11, autoflow-gui automatically selects the off-screen rendering widget and transfers the rendered image into the Qt window. The terminal remains occupied while the GUI is open; close the AutoFlow window or press Ctrl+C to end the process.

The workflow navigation filters actions and parameters to the active task. Everyday controls remain visible; advanced skeleton, WSS, and pressure parameters are hidden until Advanced is enabled, while vortex controls remain visible in Hemodynamics. In Hemodynamics, plane metrics, derived metrics, live streamlines, and pathlines form a 2x2 action grid; Run All and Compute PWV are full-width rows below it. The segmentation dock appears only in the Segmentation stage, and the Analysis dock appears in Hemodynamics and Review. The status beside the navigation reports Ready, Needs review, Incomplete, or Not ready from current workspace prerequisites.

Input also provides Reload Input with Current Parameters. An unchanged input signature is skipped; changed correction, geometry, VENC, or DICOM override settings reload the source and invalidate downstream artifacts. The default correction method is WRLS + ARTO. Corr content is enabled only after correction is applied or reused; dual-venc cases show separate normalized Corr Low LR/AP/FH and Corr High LR/AP/FH fields.

Menu item	What it does	Main code
`Open H5`	open an H5 or HDF5 case; prompts for a data-group path when one file contains multiple supported cases, then reuses a compatible correction cache when available	`autoflow/ui/app.py`
`Import DICOM Directory`	scan a DICOM directory and choose a case	`autoflow/ui/app.py`, `autoflow/ui/dicom_confirm.py`
`Clear Workspace`	clear loaded data and restore config defaults in the UI	`autoflow/ui/app.py`
`Exit`	close the GUI	`autoflow/ui/app.py`

Menu item	What it does	Main code
`Export Videos...`	choose an output directory and export selected plane, WSS, TKE, pressure-analysis, or streamline videos	`autoflow/ui/app.py`, `autoflow/rendering/videos.py`
`Export Plane Coordinates...`	export selected Browser planes, or all planes when none are selected	`autoflow/ui/app.py`, `autoflow/plane_io.py`
`Export QC Report...`	write the current staged automated quality report	`autoflow/ui/app.py`, `autoflow/quality.py`

Menu item	What it does	Main code
`3D Axis Orientation...`	choose the displayed positive direction for each 3D axis; the scene mirrors around its center while internal data remains unchanged	`autoflow/ui/app.py`, `autoflow/ui/viewer.py`
`3D Background Color...`	choose the 3-D viewport background color; the choice applies to surfaces and PC-MRA volume rendering and starts from the `ui.background_color` config value	`autoflow/config.py`, `autoflow/ui/app.py`, `autoflow/ui/viewer.py`

Standard Workflow¶

start the GUI
load a case through Open H5 or Import DICOM Directory
for H5, the GUI uses an existing correction cache and embedded segmentation directly; when correction is missing, it first asks whether correction is needed and then shows a method dropdown with MSAC and WRLS + ARTO
for DICOM, confirm or edit resolution, venc, spatial order, venc order, and RR
check loader parameters in Input / Background Correction, including dual-venc ratios for legacy Nv=7 H5 when needed
in the Segmentation workflow stage, configure nnUNet if needed and click Run Automatic Segmentation explicitly
optionally open Phase Unwrapping, choose gc3D, lap4D, or nprs, and click Unwrap Phase; method-specific parameters appear for the selected method and dual-VENC inputs are skipped automatically
if phase unwrapping ran, inspect Estimated Wrap Locations, Phase Wrap Count, and the Unwrapped − Wrapped views to see where wraps were detected
if the segmentation is a label mask, AutoFlow will reduce 4D labels to 3D by time majority vote, remove small connected components per label, merge labels by configured groups, filter grouped components with the configured skeleton cleanup rule, and then run grouped skeleton, graph, and plane generation
move through the workflow stages and run the actions shown for the current stage; Run All is limited to the active stage
inspect group sections in the browser, 3D view, ortho viewer, and selection panel
click Pathlines to generate all planes by default, or use a plane context menu to choose This Plane or Selected Planes; generated planes accumulate, and requesting an existing single-plane pathline selects it instead of integrating it again
open Review & Export, refresh QC, inspect warnings and suggested actions, then export the report when needed
open the top-level Settings > 3D Axis Orientation action to reverse any displayed positive axis direction (LR/RL, AP/PA, or FH/HF) when the case's viewing convention requires it
use Export > Export Videos... when you want selected offline MP4 exports
save the active segmentation if you want to reuse it later

Step Buttons¶

Step	Purpose	Notes
`Generate Skeleton`	skeletonize the active segmentation	binary masks run as one group; label masks run per configured group
`Generate Graph`	build graph, branches, and paths	depends on skeleton and preserves group names
`Generate Planes`	create uniform or fixed-step planes with anchor, direction, and distance/fraction spacing	defaults to center/both/3/25%; segmentation filter is enabled and QC records actual counts
`Calculate && Save Metrics`	compute and save basic plane flow, area, and velocity metrics; reuse derived fields only when they already exist	requires segmentation and flow; it does not implicitly start WSS/TKE/pressure computation
`WSS / TKE / Pressure / Vortex`	compute missing derived families, add supported derived summaries to existing plane metrics, and refresh scene objects	TKE stays optional; vortex fields are whole-volume only; cached families are not recomputed
`Generate Streamlines`	enable live streamlines from the combined segmentation	requires segmentation
`Pathlines`	launch time-resolved pathlines for all planes by default	runs in the same Qt background-worker/progress-dialog pattern as automatic segmentation; use the plane context menu for This Plane or Selected Planes. Existing plane pathlines are preserved and skipped; a repeated single-plane request selects its existing Browser object. Particles are released once at `t=0`; playback reveals their cached trajectory prefix at each later phase without re-running VTK. `Fixed Count` seeds default to `250`; use `Ratio` for area-dependent density. Pathline-only controls, including seed settings, tube radius, colors, and temporal cache, load from `configs/pathlines.json`; live streamline settings remain in `configs/streamlines.json`.
`Import Plane Coordinates...`	import v2 or legacy plane JSON beside `Generate Planes` using world, local, or relative-centerline mapping	available in Centerline & Planes
`Edit Skeleton`	enter a dedicated skeleton edit mode	select a group object in the browser to edit that vessel directly; otherwise choose a vessel group in the dialog. The scene hides unrelated layers; select and drag points, use Delete/Backspace to remove, then use `Save Changes`, `Cancel`, or Esc
`Edit Graph`	enter a dedicated graph edit mode	select a group object in the browser to edit that vessel directly; otherwise choose a vessel group in the dialog. The scene hides unrelated layers; select/drag nodes, select/delete edges, press E or use Edge Mode to add/remove edges, then save or cancel
`Run All`	in `Centerline & Planes`, run skeleton, graph, and planes; in `Hemodynamics`, run plane metrics, derived metrics, live streamlines, and all-plane pathlines	does not create segmentation automatically; `Compute PWV` remains explicit

Compute-oriented pipeline buttons execute in Qt workers. Pathline integration also runs in its own worker before the GUI creates its VTK scene actors, so slow integration does not block the application window. The progress dialog remains responsive while algorithms run. After completion, the GUI invalidates and rebuilds only scene objects affected by those steps instead of recreating every VTK actor. Closing the window is blocked while a task is active so the workspace cannot be destroyed during a calculation.

Run All scope:

Centerline & Planes: Generate Skeleton -> Generate Graph -> Generate Planes
Hemodynamics: Calculate && Save Metrics -> WSS / TKE / Pressure / Vortex -> Generate Streamlines -> Pathlines for every plane. The metric stages run in a background worker; streamlines are then added to the live scene and pathline integration runs in its own worker.

Parameter Panels¶

Panel	Main purpose	Main code
`Input / Background Correction`	loader and DICOM settings, including the active `MSAC` or `WRLS + ARTO` correction method	`autoflow/ui/app.py`, `autoflow/config.py`
`Generate Skeleton Parameters`	cleanup and morphology controls, including the `Separate Special Label Contacts` switch for `RBCT`/`CCA`/`LBCT` contacts	`autoflow/ui/app.py`, `autoflow/config.py`
`Generate Planes Parameters`	uniform/fixed-step layout, segmentation filter, and advanced trim controls	`autoflow/ui/app.py`
`PWV Parameters`	edit groups, waveform selection, spacing, and plot styling	`autoflow/ui/app.py`
`Streamline Parameters`	seed density, steps, terminal speed, colors	`autoflow/ui/app.py`
`WSS Parameters`	WSS-specific controls plus runtime render and shared colorbar controls for live scalar layers, including width, height, position, and font sizes	`autoflow/ui/app.py`
`Flow / TKE / Pressure Parameters`	WSS, TKE, and pressure controls; shown with `Advanced`	`autoflow/ui/app.py`
`Vortex Kinematics Parameters`	Gaussian smoothing and support-erosion controls; visible in Hemodynamics by default	`autoflow/ui/app.py`

After WSS / TKE / Pressure / Vortex completes, the ortho viewer Content menu provides Vorticity Magnitude (s⁻¹), Q-Criterion (s⁻²), and Swirling Strength λci (s⁻¹). Vortex Support Erosion (vox) defaults to 1; it only limits the valid derivative region and does not alter the segmentation.

The correction-method dropdown defaults to WRLS + ARTO. Choosing MSAC enables the MSAC-only threshold control; WRLS tuning values continue to come from configs/loader.json. CUDA use inside WRLS+ARTO is automatic and has no GUI device selector.

Segmentation Workflow¶

The GUI segmentation system supports:

original segmentation
imported segmentation
threshold segmentation
automatic segmentation through nnUNet
external segmentation editing through the optional SpatioTemporal Labeler

Important behavior:

Run All does not auto-start segmentation
segmentation must already exist when segmentation-dependent steps run
opening H5 checks the selected case group before loading: a reusable corr cache selects the cached correction method; embedded segmask, segmentation, or seg becomes the initial active source
when correction is absent, the GUI asks whether it should run; answering Yes opens a second dropdown for MSAC or WRLS + ARTO, while cancelling either dialog cancels the load
input loading never starts or asks to start automatic segmentation
the top menu bar has no separate Segmentation menu; source switching and segmentation commands are kept in the right-side Segmentation dock
use Source -> Configure... to save automatic-segmentation settings, then click Run Automatic Segmentation in the Segmentation dock; Import... and Save... are beside the source settings
an input case's embedded segmentation is activated during loading; click Run Automatic Segmentation only when you want to replace it with a new model result
Open in SpatioTemporal Labeler is available when the optional labeler extra is installed; it exports mag, three flow components, pcmra, and the active segmentation as NIfTI files through a separate editor process
the shipped automatic-segmentation settings default to the Dataset7020 nnUNet4D script; enter a static model folder and select nnUNet when a 3D model is required
GUI auto segmentation uses the same window-modal progress dialog as other long-running GUI tasks; closing it hides progress permanently for that run and does not cancel the background worker, while completion still applies the result and failure opens an explicit error dialog
automatic and threshold segmentations save sidecar H5 files after a successful run
automatic segmentation also saves the predicted segmentation NIfTI plus the feature-channel NIfTI inputs used for that run
the Labeler export dialog advances once for mag, flow_x, flow_y, flow_z, pcmra, and segmentation; files are uncompressed .nii for faster exchange
save the original segmentation.nii in Labeler with Ctrl+S; after Labeler exits, AutoFlow detects the changed file and offers to apply it as the imported source, preserving the embedded original
optional 4D connected-component cleanup removes components below a physical volume or keeps the largest component per label and frame

Grouped label-mask behavior:

binary masks and single-label masks are treated as one group
4D label masks are reduced to 3D labels by majority vote along time before vessel steps run
connected-component cleanup runs per label value before labels are merged into groups
grouped vessel masks use the skeleton connected-component filter mode; the default hybrid rule keeps every component above max(min_cc_volume_mm3, cc_rel_min_ratio * largest_component_volume_mm3)
label grouping, browser colors, and per-group preprocessing come from configs/labels.json
each group can apply its own Gaussian smoothing and morphology overrides before skeletonization

PWV behavior:

the PWV Parameters panel exposes groups, waveform key, spacing, transit-time method, foot definition, cross-correlation window, cross-correlation interpolation factor, cycle-wrap correction, smoothing, minimum valid planes, and plot colors. The GUI always runs PWV when Compute PWV is clicked; there is no enable checkbox. The default foot-to-foot waveform is flowrate_mL_s
when Allow Cycle Wrap is enabled, foot detection can follow an upstroke that starts at the end of the cardiac cycle and peaks in the first frames instead of pinning those planes to 0 ms
group labels can be entered as symbolic names from configs/labels.json such as AAO, ARCH, DAO or as integer ids
step buttons use the current GUI PWV values immediately after Load, Clear Workspace, or manual edits; the values do not write back to configs/pwv.json automatically
the GUI shows one Analysis dock with a Display selector. PWV keeps the group selector and two-panel PWV plot. Plane Curve shows the selected plane's chosen metric across cardiac phase, including pressure-gradient and relative-pressure series when available. Centerline Pressure shows the selected path's current relative-pressure profile plus its per-phase pressure drop. Internal Consistency shows the selected path or plane's path-level and branch-level internal consistency
PWV planes appear in the browser as one grouped item named PWV planes; the GUI does not list every PWV plane separately

Video Export¶

Use Export > Export Videos... for interactive offline export.

choose an output directory
select any combination of plane, wss, tke, pg, and streamlines
plane is checked by default
WSS, TKE, pressure-gradient, and relative-pressure exports compute missing derived data before rendering
GUI video export reads shared camera and sizing defaults from configs/video_exporting.json
GUI live planes read configs/planes.json -> render for GUI plane styling
GUI live WSS, TKE, pressure-gradient, relative-pressure, streamline, vorticity, Q-criterion, and swirling-strength objects read the corresponding render settings; the single live colorbar always uses the compact geometry and fonts from configs/colorbar.json, while per-metric bar_cfg remains the offline-video default
streamline clim defaults to auto, which uses 0 to the P99 finite velocity inside the segmentation across all phases so isolated dual-VENC outliers do not flatten the useful range; enter two numeric limits for a fixed range, or enter auto in both fields to restore automatic scaling
pressure-gradient and relative-pressure 3D layers are rendered on a smoothed pressure support surface
the GUI keeps one shared scene colorbar for segmentation labels, WSS, TKE, pressure-gradient, relative-pressure, streamlines, vorticity, Q-criterion, and swirling strength; when you show or hide one of these layers, the colorbar is rebuilt for the active visible scalar layer instead of stacking multiple bars
segmentation uses a categorical colorbar containing only label values present in the rendered surface, with label names instead of interpolated decimal ticks
after loading into an empty 3D scene, the camera resets once to the first visible actor bounds; later time changes and scene-property edits preserve the current camera
if summary.json already exists in the output directory, the GUI updates videos, video_times_sec, and adds gui_video_export

Run All does not export videos automatically. Video export is a separate top-level menu action.

Selection, Browser, And Timeline¶

the browser creates one top-level row per segmentation group and one Global row for non-grouped scene objects
generated planes are grouped by their path_index under Paths; each path contains its path geometry, planes sorted by path distance, and any generated pathline below its plane
manually added planes (path_index=-1) and planes whose path cannot be resolved stay under Unbound Planes
after vortex metrics are computed, the Global row includes Vorticity Magnitude, Q-Criterion, and Swirling Strength metric objects; each can be toggled independently
the default layout gives the browser more width and reserves most of it for Name; Kind is a fixed narrow column with the complete type available as a tooltip, and visibility is controlled by the checkbox beside each name rather than a separate empty column
checking or unchecking a group row shows or hides every object in that group; Paths, an individual Path, or a Plane row applies the same operation to its descendants
right-clicking a Path offers show/hide for its contents and Generate Pathlines for This Path; right-clicking a Plane retains the single-plane and selected-plane pathline actions
group title colors use label_groups.<group>.browser_color from configs/labels.json, with fallback colors for unmatched or single-label cases
grouped objects keep stable internal data keys such as smooth_path_aorta_systemic_branches_3, plane_aorta_systemic_branches_5, and pathline_aorta_systemic_branches_5; the Browser uses (group_name, path_index) to present their relationship without changing those keys
browser-visible names are intentionally shorter, for example path 3, plane 5, and pathline 5
right-clicking an individual grouped pathline in the browser opens Set Pathline Color, which changes only that pathline
selecting a plane updates selection info, the ortho viewer, and the Analysis plane/path views
selecting a path shows its segmentation owner in the lower-right Path panel (for example, label=LBCT (id=7)); this is the label selected by the segmentation filter and does not rename or edit the graph path
the right-side dock initially shows Segmentation; its first Source section provides active-source switching, visibility, opacity, provenance, configuration, import, and save controls
Analysis initially uses Plane Curve, so selecting a plane immediately exposes its available time-resolved metric series
Add Plane creates a free plane at the current ortho cursor; it can be moved anywhere and is saved with placement_mode=manual, so reuse does not project it onto a path
Edit Plane enables a cyan center handle plus orange and yellow in-plane-axis handles; generated plane centers remain constrained to their path, while manual plane centers are unrestricted
dragging either colored axis endpoint rotates the plane directly in the 3D view; there are no numeric Rotate U or Rotate V fields
plane actors update during the drag, while ortho refresh, pathline regeneration, metric computation, and file writes wait until the interaction finishes
releasing a plane handle recomputes only that plane and never starts missing WSS/TKE/pressure work; it updates the metric and plane JSON/H5 records, while the full pixelwise H5 is regenerated by Calculate && Save Metrics
selecting a path shows path-level information and updates Analysis -> Internal Consistency
the timeline controls time-resolved scene objects and ortho slices
the timeline redraws 3D and ortho data while dragging, coalescing rapid changes to one update about every 30 ms; the final position is applied immediately on release
playback uses a single-shot schedule, so slow VTK frames do not queue up; hidden dynamic layers are not rebuilt until they are shown again, which keeps WSS, TKE, pressure, streamlines, pathlines, and segmentation surfaces from reducing playback FPS unnecessarily
the timeline shows rolling render time and effective FPS during playback; reduce the requested ms delay to test the current visible scene's maximum rate
playback updates persistent pyqtgraph slice images, overlays, cursors, and the interactive colorbar without rebuilding three Matplotlib axes; the oblique plane, segmentation table, and analysis plot receive a full refresh once playback is paused
dynamic actors and the shared scalar bar remain attached while cardiac phase changes; only mapper input data is replaced

Ortho Viewer¶

The ortho viewer supports:

flow components
magnitude
PC-MRA
speed
WSS
TKE
pressure gradient
relative pressure
a persistent interactive colorbar for every scalar source
jump-to-plane-center behavior

The three slice views are labeled Axial (LR-AP), Coronal (LR-FH), and Sagittal (AP-FH). Their slider and voxel-coordinate labels use LR, AP, and FH in the same order as the normalized arrays.

Slice interactions:

Input	Action
left click or drag	move the linked LR/AP/FH cursor
wheel	step the slice orthogonal to the hovered view
`Ctrl` + wheel	zoom around the pointer
`Shift` + left drag	pan one view
middle drag	adjust window width and level
double-click	expand one slice across the complete 2x2 view area or restore the four-panel layout
`R`	reset slice zoom and display range
Left / Right	step through cardiac phases while focus is in the ortho viewer

The Overlay slider changes the segmentation color overlay opacity immediately without changing the scalar image window/level.

External Segmentation Editor¶

The optional SpatioTemporal Labeler is launched from the Segmentation dock. It receives mag, flow_x, flow_y, flow_z, pcmra, and the active label sequence as matching 4D NIfTI files. The case-specific exchange directory is reused on later opens, so Labeler can continue from its saved segmentation.nii instead of overwriting it. AutoFlow keeps the exchange process separate, blocks closing AutoFlow until Labeler exits, and imports the saved label only after its file timestamp changes.

When To Use The GUI¶

Use the GUI when you need:

interactive segmentation review or correction
grouped visibility control for multi-label vessel workflows
skeleton or graph editing in single-group cases
path-constrained generated-plane movement, unrestricted manual-plane placement, two-axis 3D rotation, and automatic metric recomputation
time navigation through 3D and ortho views
interactive selection of which offline videos to export

Use the CLI when you need:

unattended batch processing
repeated runs over many cases
unattended or repeated offline video export pipelines

Status: Experimental

The repository also includes a standalone comparison popup for paired GT and VAA H5 cases:

entry file: ztemp/cmrrecon_popup.py
main code: ztemp/cmrrecon_viewer.py

Current popup behavior:

case switching uses a drop-down selector plus Prev and Next
changing case loads data in a background thread instead of blocking the window
a progress bar and status text show load progress while GT and VAA volumes are prepared
display-only transforms include Rotate 90 deg, Flip H, and Flip V
the transform controls only affect the rendered preview and do not modify source data on disk

GUI Guide¶

Status¶

Start The GUI¶

Main Layout¶

File Menu¶

Export Menu¶

Settings Menu¶

Standard Workflow¶

Step Buttons¶

Parameter Panels¶

Segmentation Workflow¶

Video Export¶

Selection, Browser, And Timeline¶

Ortho Viewer¶

External Segmentation Editor¶

When To Use The GUI¶

GUI Guide¶

Status¶

Start The GUI¶

Main Layout¶

File Menu¶

Export Menu¶

Settings Menu¶

Standard Workflow¶

Step Buttons¶

Parameter Panels¶

Segmentation Workflow¶

Video Export¶

Selection, Browser, And Timeline¶

Ortho Viewer¶

External Segmentation Editor¶

When To Use The GUI¶

CMRRecon Comparison Popup¶