Geometry Repair Toolkit

The Geometry Repair Toolkit is a standalone dialog-based tool for validating, inspecting, and repairing polygon geometries. It provides a comprehensive interface for detecting and fixing common topology and geometry issues across polygon layers directly within QGIS.

Access

• Menu: Gemma → Others → Geometry Repair Toolkit
• Component Algorithm IDs: gmd_pipeline:scangeometryerrors, gmd_pipeline:repairpolygongeometries
• This tool opens as a separate dialog window (not through the Processing Toolbox).

When to Use

Use this tool when:

• You suspect polygon layers contain invalid, self-intersecting, or corrupted geometries.
• QGIS reports geometry errors during processing or spatial operations.
• You need to clean up and validate polygon layers before running other GMD tools (such as MBI Checker or Fill Polygon Gaps).
• You want to identify and fix duplicate vertices, null geometries, empty shapes, wrong geometry types, ring/structure errors, or duplicate features.

Features & Tab Structure

The toolkit features a tabbed interface:

1. Geometry Fixer (Tab 1) — Scan layers, inspect detected issues in an interactive table, highlight error geometries on the map canvas, and run automated repairs.
2. Help and Information (Tab 2) — View reference tables for error types, repair mechanisms, layer edit behavior, and limitations.

Error Types Reference

The toolkit scans polygon layers for the following topology and geometry issues:

Error Type	Description	Repair Mechanism
Null Geometry	The feature record exists, but there is no geometry object.	Auto-fixable (Recovery from surrounding polygons)
Empty/Missing Geometry	The feature exists, but its geometry has no usable shape or coordinates.	Auto-fixable (Recovery from surrounding polygons)
Invalid Geometry	The polygon has geometry errors such as ring errors, spikes, or folded edges.	Auto-fixable (Polygon reconstruction)
Self Intersection	The polygon boundary crosses itself (e.g. bowtie rings).	Auto-fixable (Polygon reconstruction)
Invalid Geometry + Self Intersection	Combined report when a feature exhibits both general invalidity and self-intersection.	Auto-fixable (Polygon reconstruction)
Duplicate Vertex	The ring contains a duplicate or near-duplicate vertex (or a zero-length segment). Reported only when QGIS's validator specifically detects duplicate nodes (e.g. accidental self-snaps during manual digitization).	Auto-fixable (Direct duplicate vertex removal via progressive tolerance sweep)
Wrong-type Geometry	The feature's geometry type does not match the layer's declared geometry type (e.g. a line or GeometryCollection stored in a polygon layer).	Auto-fixable (Polygon reconstruction)
Ring/Structure Error	GEOS accepts the geometry, but QGIS's internal validator objects to how rings or parts are arranged (e.g. interior hole ring not fully inside outer ring, or a part nested inside another part).	Requires manual review (No automatic repair; correct rings using the Vertex Tool)
Duplicate Geometry	Two or more features share the exact same geometry.	Requires manual review / deduplication
Dangle (Loose End)	A line endpoint doesn't connect to any other line.	Requires manual review

How to Use

1. Open the tool from Gemma → Others → Geometry Repair Toolkit.
2. Under Input Layers, select one or more polygon layers to check.
3. Click Scan Layers to initiate the background geometry scan.
4. Review the detected errors in the results table:
   • White rows: Auto-fixable issues with selectable checkboxes.
   • Grey rows: Issues requiring manual review (e.g. Ring/Structure Error, Duplicate Geometry, Dangles). Their checkboxes are disabled because they cannot be resolved automatically.
5. Double-click any row to zoom to the affected feature on the map. The toolkit places rubber-band outlines and vertex markers over problematic geometry locations.
6. Check the rows to repair (or click the checkbox in the first column header to select or clear all auto-fixable rows at once).
7. Click Repair Selected Features. The toolkit routes each checked row to its specific repair mechanism and applies changes directly in-place:
   • If checked rows have no automatic fix, a warning dialog alerts the operator and logs individual reasons.
   • Features that cannot be resolved automatically are logged with their specific diagnostic reason (such as collapsing to a line or missing geometry) and flagged for manual review with the Vertex Tool.
8. Review the summary log:
   • The execution summary reports Finished. Fixed: <count> Needs manual repair: <count>.
   • Repaired features are kept in active edit mode on the source layer.
9. Re-run Scan Layers on the layer while still in edit mode to verify all errors are resolved before saving.
10. Use QGIS's Save Edits to persist changes to disk, or Cancel Edits to discard all repairs and revert to the original state.

Repair Mechanisms & In-Place Editing

Repair Selected Features

When you click Repair Selected Features, the tool inspects each checked error row and automatically applies the appropriate repair mechanism directly to the original layer:

• Duplicate Vertex: Eliminates duplicate or near-duplicate vertices through a progressive tolerance sweep (scaled by bounding box diagonal from ${10}^{-12}$ to ${10}^{-6}$) verified against QGIS's internal validator, with a makeValid() fallback to resolve node-clustering defects without requiring full polygon reconstruction.
• Invalid / Wrong-type / Self Intersection: Reconstructs the polygon shape (ring decomposition, unary union planarization, face matching, and hole restoration) to resolve geometry errors and self-intersections.
• Null / Empty / Missing Geometry: Recovers missing shapes using spatial boundary context from surrounding polygons.

Ring/Structure Errors & Manual Intervention

Certain topological defects cannot be resolved by automatic reconstruction or node deduplication:

• Arrangement Defects: When QGIS reports ring arrangement issues (such as an interior hole ring outside the exterior boundary or a polygon part nested inside another), GEOS already evaluates the underlying geometry as valid. Consequently, automated tools like makeValid() leave the geometry completely unchanged, and no duplicate vertex exists to delete.
• Diagnostic Logging: The repair engine evaluates each unfixable feature and logs a specific diagnostic explanation (e.g. FID X could NOT be repaired automatically. Reason: it encloses no area — the outline collapses to a line...) along with guidance to inspect and edit the feature manually using the QGIS Vertex Tool.
• Clear Status Distinction: Unfixable features are tracked as Needs manual repair in the summary log, preventing silent skips and giving operators immediate visibility into which features require manual redigitizing or cleanup.

Multipart Resolution & Artifact Cleanup

Polygon reconstruction can occasionally leave a feature multipart even if it started as a single part (such as resolving a self-intersecting bowtie ring). When this occurs:

• Negligible fragment slivers resulting from reconstruction artifacts (< 0.1% area ratio) are automatically dropped.
• Genuine multi-part survivors sharing original feature attributes remain merged as a single multipart feature.
• Pre-existing legitimate multipart features (such as a barangay with offshore islands) that were not repaired remain completely untouched.

In-Place Editing & Unsaved Changes Guard

• Direct Layer Editing: Repaired features are edited directly on the source layer in QGIS edit mode (indicated by a pencil icon and modified marker).
• Safe Discard: Changes remain unsaved in memory until you choose Save Edits or Cancel Edits from the QGIS Layer menu or editing toolbar.
• Schema Preservation: Attribute fields and schemas are preserved without adding unnecessary tracking columns. Recovery details, repair methods, and notes are logged in the execution console.

Limitations & Review Best Practices

Recommended Workflow

Run the Geometry Repair Toolkit on your layers before using other processing tools like the MBI Checker or Fill Polygon Gaps. Invalid geometries can cause unexpected results in topological analysis.

In-Place Editing

The toolkit applies repairs directly to the layer in edit mode. Always use Save Edits to persist changes to disk or Cancel Edits to revert unwanted modifications.

Limitations & Manual Review

• Visual Inspection: Always visually inspect repaired features before saving edits.
• Re-Scan Verification: Re-scan the layer with Scan Layers while still in edit mode to confirm no secondary errors remain.
• Ring/Structure Errors: Geometry ring placement defects (e.g. holes outside outer rings, nested parts) must be corrected manually using the QGIS Vertex Tool.
• Zero-Area Geometries: Features whose boundary collapses to a line enclose zero area and cannot be reconstructed into polygons; they must be redigitized or deleted manually.
• Deleted Feature Records: Completely deleted attribute records cannot be recovered by this tool.
• Edge Polygons: Edge polygons cannot be safely reconstructed when their outer boundary is unknown. If an edge polygon is missing, return it to the LGU for corrected boundary geometry.
• CRS Sensitivity: Validity is evaluated in the layer's native CRS. Because coordinate reprojection can shift vertices and alter geometry validity, re-run Scan Layers whenever a layer is reprojected.
• Manual Review: Complex topology issues such as Duplicate Geometry and Dangles require manual review and editing.