Metadata-Version: 2.4
Name: segfix
Version: 1.0.6
Summary: GUI tool to fix instance segmentation of tree point clouds
Author-email: Tim Devereux <devereux.tj@gmail.com>
License-Expression: MIT
Project-URL: Homepage, https://github.com/tim-devereux/segfix
Project-URL: Issues, https://github.com/tim-devereux/segfix/issues
Project-URL: PyPI, https://pypi.org/project/segfix/
Keywords: lidar,point-cloud,segmentation,forestry,vispy
Classifier: Development Status :: 5 - Production/Stable
Classifier: Environment :: X11 Applications :: Qt
Classifier: Intended Audience :: Science/Research
Classifier: Programming Language :: Python :: 3.10
Classifier: Programming Language :: Python :: 3.11
Classifier: Programming Language :: Python :: 3.12
Classifier: Topic :: Scientific/Engineering :: Visualization
Requires-Python: <3.13,>=3.10
Description-Content-Type: text/markdown
License-File: LICENSE
Requires-Dist: vispy>=0.14
Requires-Dist: PyQt6>=6.5
Requires-Dist: qtpy>=2.4
Requires-Dist: numpy>=1.24
Requires-Dist: plyfile>=1.0
Requires-Dist: scipy>=1.10
Requires-Dist: laspy[lazrs]>=2.5
Provides-Extra: dev
Requires-Dist: pytest>=7.0; extra == "dev"
Dynamic: license-file

# segfix

[![PyPI](https://img.shields.io/pypi/v/segfix)](https://pypi.org/project/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.

<img alt="Segfix Screenshot" src="https://github.com/user-attachments/assets/03a63367-6350-4198-99ad-c29a593d971d" />

## Walkthrough video

A 12-minute captioned tour of every tool, fixing every tree in the example
cloud from `scripts/make_sample.py`, including large coordinates and dense
clouds. Click to watch:

[![Watch the segfix walkthrough](https://raw.githubusercontent.com/tim-devereux/segfix/main/docs/walkthrough.jpg)](https://github.com/tim-devereux/segfix/releases/download/v1.0.0/segfix_walkthrough.mp4)

Testing is done on Fedora Linux 44 and Windows 11. macOS should work but has not been tested.

## Contributing

Feedback, issues, and PRs all welcome. For issues please use [GitHub issues](https://github.com/tim-devereux/segfix/issues) (not a personal message) so the community can benefit.

## Install

Requires Python 3.10–3.12. The package is on PyPI:
[pypi.org/project/segfix](https://pypi.org/project/segfix/).

```bash
pip install segfix
```

The startup dialog tells you when a newer release is on PyPI, and its
**Update…** button runs `pip install --upgrade` for you (restart segfix
afterwards). On Windows, which can't replace a program while it runs, segfix
closes first and the update installs in its own window; start segfix again
when that window says it's done. Running from a clone instead, it tracks new commits on the branch
you're on and updates with `git pull` + `pip install -e .`, so a development
checkout stays a checkout.

Using a dedicated environment:

```bash
conda create -n segfix python=3.11
conda activate segfix
pip install segfix
```

### From source

For development, or to get `scripts/make_sample.py`:

```bash
git clone https://github.com/tim-devereux/segfix.git
cd segfix
pip install -e .
```

### On Windows

Two ready-made builds on the
[releases page](https://github.com/tim-devereux/segfix/releases), neither
needing admin and neither needing Python:

**The installer** — `segfix-<version>-setup.exe`. Installs per-user by
default (all-users only if you have the rights), adds a Start Menu entry and
an uninstaller. Being unsigned, Windows shows a SmartScreen warning the
first time: **More info** → **Run anyway**.

**The portable zip** — `segfix-<version>-portable.zip`. Unzip anywhere and
run `segfix.exe` from the folder. Nothing is written outside it.

Both bundle their own Python, Qt, numpy and scipy, including Qt's software
OpenGL fallback for machines without a usable graphics driver. If a managed
machine refuses to run either — some block unsigned executables outright —
`pip install segfix` into an existing Python still works, as above.

## Run

```bash
segfix
```

`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. Labels that can't
be a real tree ID, negatives (other than the noise marker) and values that
overflow a signed 32-bit int, both of which some pipelines use as a "no tree"
sentinel, are folded into *unassigned* on load, so they don't show up as
spurious trees.

### 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](https://github.com/csiro-robotics/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](https://github.com/r-lidar/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 `treeID`s 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.)

### Large coordinates

Georeferenced clouds (UTM, State Plane, …) have coordinates in the millions,
while the detail that matters for fixing a segmentation is sub-metre. segfix
stores coordinates as 32-bit floats, as the GPU does, and a float32 carries only
about 7 significant digits: a northing around 7,000,000 m is kept to the nearest
half metre.

So when any coordinate is more than 10 km from the origin, segfix offers a
**global shift** on load, the way CloudCompare does: a round offset, added to
every coordinate, that brings the cloud near the origin. The suggested shift
puts the cloud's minimum corner within a metre of the origin; you can edit X, Y
and Z before choosing **Apply Shift**, or choose **Keep Original Coordinates**.

The shift applies to this session only. Nothing is written back: **Save**
patches only the label (or, for RGB-segmented PLY, colour) bytes, so the file
keeps its real, georeferenced coordinates byte for byte.

If you keep the original coordinates, the cloud loads with that lost precision,
and segfix skips the dense-cloud check below: a spacing measured on coordinates
rounded to half a metre would be meaningless, so it won't offer to downsample.

### Dense clouds

On load segfix measures the cloud's typical point spacing. If points are closer
than **2 cm** it offers to downsample for the session, one point per voxel (2 cm
by default, editable in the prompt), which is plenty to see and re-label a tree
but a fraction of the points to draw and lasso. Choose **Keep Full Resolution**
and nothing changes.

Downsampling is a working-set choice, not a destructive one. Nothing is written
until you save, and on **Save** the labels you edited are interpolated back onto
every original point: each full-resolution point follows the nearest kept point
*that was the same tree as it*, and only where that kept point is one you
actually re-labelled, so untouched parts of the cloud keep their original
labels byte for byte. The saved file has all of its points and all of its
fields, in the format it came in.

The one thing to know is that a voxel is the resolution limit while you work:
where two trees' points share a voxel, one label represents it, and unassigned
points that fall inside a tree's voxels aren't separately selectable until you
reload at full resolution. Pick a voxel smaller than the detail you need to
separate. Edits that move a whole tree (X or U on the current tree, a complete
merge) still reach every one of its original points, including any in voxels
where another tree's or the ground's point was the one kept.

## Editing workflow

The menu bar carries the session-level actions: **File ▸ Open Project…**
(`Ctrl+O`, reopens the startup dialog and switches project without a manual
restart), **Save Project** (`Ctrl+S`) and **Export Trees…**; **Edit ▸ Undo / Redo** (`Ctrl+Z` /
`Ctrl+Shift+Z`); **Preferences ▸ Theme ▸ Light / Dark**, applied immediately
and remembered (via `QSettings`) for next launch; and **Help ▸ About segfix**
for the version, links, and full MIT licence.

Navigation matches CloudCompare: clouds open **Z-up**, **left-drag rotates,
right-drag pans, wheel zooms**. **Double-click a point** while navigating to
recentre the orbit on it. A metric scale bar and an X/Y/Z orientation tripod
sit in the bottom-left of the view; the **point size** spinner floats in the
top-left, with CloudCompare's standard view buttons below it: **Top**,
**Front**, **Back**, **Left**, **Right** and **Bottom** turn the camera to look
at that side (Top looks straight down, Front along +Y), and **3D** goes back to
the tilted view. They only turn the camera, so whatever you're centred on
stays in view at the same zoom.

The right-hand panel holds two tables. **All Trees** (top) lists every tree in the
file, a Done column (`✓` when reviewed), tree ID and point count, with a
running `N/M trees (X %) done` line above it, **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. Finished rows in either
table get a green tint. The **Current tree** actions (Add selection,
send-to-neighbour, Split / Unassign / Noise) float as a fixed column pinned
to the right edge of the 3D view, next to the points they act on.

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 |
   | `K` | Cluster select: click a point to take the connected patch of its tree; click the same spot again to loosen the gap and grow it |
   | `[` / `]` | Tighten / loosen the cluster gap one step |
   | `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 (also on the **Edit** menu) |
   | `Ctrl+S` | Save Project (also on the **File** menu) |
   | `Ctrl+O` | Open another project |

   **Cluster (`K`)** is the other way to select: click a point and it takes the
   patch of that point's tree that is physically connected to it. How wide a
   hole still counts as connected is the *gap*, in multiples of the cloud's
   point spacing. It starts at 1×, deliberately tight, so a first click is a
   small seed; click the same spot again to loosen it a step and grow the
   patch (1× → 1.5× → 2× … up to 16×), or use `[` / `]`, or the **▾** beside
   the Cluster button for a slider. Changing the gap re-runs your last click,
   so the patch grows or shrinks on screen as you go. The gap goes back to 1×
   when you switch Cluster off, or when the selection is cleared (after
   `A`/`N`/`U`/`X`, a click on empty space, or moving to another tree).

   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.
7. **File ▸ Export Trees…** writes every tree in the cloud to a folder you
   pick, one file per tree, named after the cloud (`plot_a.las` →
   `plot_a_tree_7.las`) and in its format. Each file carries all of that
   tree's points at full resolution — whole trees even from a downsampled
   session — with every column and the file's own coordinates, so an exported
   tree still lands in the right place in any other tool. Unassigned points
   and anything dismissed as noise aren't trees and aren't written. Trees are
   exported as the saved file has them, so segfix offers to save first.

## Layout

| File | Responsibility |
|------|----------------|
| `model.py` | `PointCloud` data + undo/redo (diff-based) |
| `io.py` | whole-cloud load/save (binary PLY, LAS/LAZ), label-field and RGB-segmentation detection |
| `operations.py` | pure, UI-agnostic label edits (reassign/split/unassign/noise) |
| `analysis.py` | which trees touch which, by sampled point distance (KD-tree) |
| `export.py` | File ▸ Export Trees…: one file per tree, full resolution, in the cloud's own format |
| `density.py` | point-spacing measurement, voxel decimation, and the save-time interpolation back to full resolution |
| `lasso.py` | 3D screen-space lasso (camera projection + polygon test) and the click-to-grow cluster tool |
| `cloudview.py` | the vispy 3D canvas: camera, points, selection halo, tree box |
| `viewer.py` | label→colour mapping and visibility masks |
| `overlays.py` | scale bar + orientation axes painted over the canvas |
| `theme.py` | light/dark palette, remembered in `QSettings` |
| `widgets.py` | Qt dock panel wiring selection → operations |
| `icons.py` | inline SVG icons for the panel buttons and window |
| `treecatalog.py` | default mode: memory-mapped tree-label grouping, neighbour load + write-back (`TreeCatalog` = PLY, `LasCatalog` = LAS, `open_catalog` picks) |
| `scene_ui.py` | tree table + scene controller for the default mode |
| `shift_ui.py` | load-time "large coordinates" (global shift) prompt |
| `density_ui.py` | load-time "dense cloud" (downsample) prompt |
| `progress_ui.py` | progress window for the two slow operations, opening and saving |
| `registry.py` | on-disk list of recently opened files/projects |
| `workspace.py` | project folders: copy (or decompress `.laz`→`.las`) an imported file, never touch the source |
| `startup_ui.py` | startup dialog: pick a recent entry or start a new project |
| `update.py` | update check: a newer PyPI release for an installed copy, new commits for a git checkout |
| `app.py` | `segfix` CLI entry point |

## Tests

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