segfix

A GUI tool to fix the instance segmentation of tree point clouds. Load a segmented LiDAR cloud, see each tree in its own colour, and correct mistakes by lassoing points and reassigning, splitting off, or dismissing them — then save back to a corrected version of the input, retaining all fields.

Built on napari for fast 3D rendering and point selection.

Contributing

Feedback, issues, and PRs all welcome. For issues please use GitHub issues (not a personal message) so the community can benefit.

Install

Requires Python 3.10–3.12 (napari/Qt do not yet ship wheels for 3.13+).

git clone https://github.com/tim-devereux/segfix.git
cd segfix
conda create -n segfix python=3.11
conda activate segfix
pip install -e .

Run

segfix
# or generate a practice cloud with built-in segmentation errors first:
python scripts/make_sample.py sample.ply
python scripts/make_sample.py --format las sample.las   # arbor-shaped LAS

segfix will open a startup dialog. Double-click a recent project to reopen it, or click New Project… to import a point cloud file. Importing copies the file into a new project folder (created inside the directory you pick, named after the source file) and opens that copy — edits are always saved to the copy, never the original source file.

Every project opened this way is recorded in ~/.config/segfix/registry.json (a plain JSON file) so it shows up in the "Recent projects" list next time — most-recently-opened at the top and preselected, each row showing how long ago it was last opened.

The per-point tree ID field is auto-detected (treeID, PredInstance, label, …); override with --label-field NAME if needed.

Accepted formats

Binary PLY — RGB-segmented (raycloudtools) or with a label field — and LAS. Both store their points as fixed-size records at a known offset, which is what lets treecatalog.py memory-map a whole plot, read back just the points of one tree, and on save patch only the label bytes that changed.

raycloudtools output

raycloudtools' rayextract trees writes <plot>_segmented.ply — a binary PLY with no label column, each point instead coloured by tree (x y z time nx ny nz red green blue alpha, double xyz). segfix detects the RGB encoding, maps each distinct colour to a tree, and treats pure black (0, 0, 0) as unsegmented. Import the .ply directly; Save patches the colour bytes of points whose tree changed, in place, so the file stays in exactly the format rayextract produced.

One caveat: noise (X) and unassigned points are both written back as black, so once such a file is reloaded the two are indistinguishable (segfix's .segfix.json sidecar still remembers which were noise for the current project). New trees created during editing (N, splits) get a deterministic colour derived from their id.

arbor output

arbor's pipeline (arbor segment …) writes <plot>_output/<plot>_segmented.laz — a point cloud with a per-point treeID Extra-Bytes column (0 = unassigned). Import that .laz directly: segfix decompresses it to a .las working copy in the project folder (the original .laz is never touched), you fix the treeIDs with the workflow below, and Save patches the .las in place and re-compresses a fresh .laz beside it for arbor to re-read.

One caveat: if a cloud's treeID column is an unsigned type, points you dismiss as noise (X) are written back as 0 (unassigned) — segfix's own .segfix.json sidecar still remembers they were noise, but a reader of the LAS alone cannot tell noise from unassigned. (arbor writes a signed treeID, so this does not apply to its output.)

Editing workflow

Navigation matches CloudCompare: clouds open Z-up, left-drag rotates, right-drag pans, wheel zooms.

Two tables stack in the right-hand panel. All Trees (top) lists every tree in the file, with a ✓ once it has been reviewed — double-click a row to load that tree plus its spatial neighbours into the 3D view. Selected Tree + Neighbours (below) is the review queue for what's currently loaded: a Done checkbox per tree, a 👁 column to hide one from the view, a Fade column to ghost one (still shown, still selectable), and the Prev / Done buttons. Both read the same <cloud>.segfix.json sidecar, written next to the working copy, so a half-finished plot resumes where you left off.

1. Double-click a tree in All Trees. The camera flies to it and a wireframe box marks it. To declutter a crowded view, use the 👁 (hide) or Fade column in the lower table on specific trees — or Hide others / Fade others in the top-bar View group to do it to every loaded tree except the one under review. Fading keeps a tree visible as faint context and still lets the lasso grab its points; hiding removes it from both.

2. Inspect it. If it's correct, press Space — the tree is marked done, progress is saved, and the next unfinished tree in the loaded set becomes current. That's the loop.

3. If it needs fixing, select points with the lasso: press L, drag a freehand loop (Shift adds), Esc to go back to navigating. The tree under review is always the implicit target.

   Key	Operation
   Space	Mark current tree done, jump to next unfinished
   ← / →	Previous / next tree (without marking done)
   L	Lasso select
   Ctrl+L	Lasso, but only points already in the current tree — grabs a clean patch out of an overlapping crown
   Esc	Back to camera / navigation
   A	Add selection to the current tree (missing branches, unassigned canopy)
   N	Split selection off as a new tree (it joins the queue unreviewed)
   U	Unassign selection — or the whole current tree if nothing is selected
   X	Mark selection as noise — or the whole current tree if nothing is selected (dismiss a bush/wall in one key)
   Delete / Backspace	Same as X (mark noise)
   H	Show/hide the unassigned + noise points
   C	Cross section on/off
   Shift+L	Draw a lasso-section outline
   Shift+C	Lasso section on/off
   Ctrl+Z / Ctrl+Shift+Z	Undo / Redo
   Ctrl+S	Save Project

   To move stray points to a neighbour instead, lasso them and click one of the → id buttons in the Current tree panel — one per tree within "reach" metres of this one. Clicking that neighbour's table row to make it current and pressing A does the same thing.

   To merge an over-segmented fragment back in, lasso the whole fragment and press A; there is no separate merge key.

4. For a crowded canopy, two tools in the top bar cut the view down. Both fold into the same visibility as the 👁 column, so hidden points are also unselectable and the lasso can't grab through them:

   • Cross section (C) — a slab along X, Y or Z, set with two sliders.
   • Lasso section (Shift+C) — same idea, but the kept region is an outline you draw (Shift+L, then drag). It's frozen into a point mask as you release, so the camera moves freely afterwards.

   Both reset when a new tree is loaded.

5. Leftover unassigned points may hide missed trees: they're loaded alongside every tree you open, so lasso one and press N to promote it to a tree of its own (it joins the queue unreviewed).

6. Save (Ctrl+S) writes to the project copy, never the original import. It patches only the points whose label changed, in place, so the header and every other column are untouched byte for byte.

Layout

Tests

pytest        # core model, operations, and IO round-trip (no GUI needed)