Experimental Tools

Scripts and utilities in active development. These tools work but may have bugs or rough edges. Use with caution and report issues.

fast_validate_ids.py

Experimental

Parallel ID validator using ThreadPoolExecutor. Processes 5,000+ root IDs in under 2 minutes by parallelizing supervoxel lookups, then batching root lookups in a single API call. Uses the accurate supervoxel tracking method (not get_latest_roots).

Usage

python fast_validate_ids.py --input ids.txt python fast_validate_ids.py --input ids.txt --output results.txt --workers 20
Repo: tracer-tools-extensions/fast_validate_ids.py Default datastack: brain_and_nerve_cord Default workers: 20

Known Issues

  • No retry logic for transient API failures; a single thread error loses that ID
  • Progress reporting is coarse (every 500 IDs)
  • High worker count may trigger CAVE API rate limits on some networks

fast_validate_ids_updated_auto_detect_path.py

Experimental

Updated version of fast_validate_ids with automatic path detection. Resolves the correct datastack path automatically, removing the need for manual configuration.

Usage

python fast_validate_ids_updated_auto_detect_path.py --input ids.txt --output results.txt
Repo: tracer-tools-extensions/fast_validate_ids_updated_auto_detect_path.py

fast_get_coords.py

Experimental

Parallel coordinate fetcher. Gets viewer-resolution coordinates for thousands of root IDs by parallelizing L2 chunk lookups, then batching L2 coordinate fetches. Output is tab-separated (root_id, x, y, z) ready to paste into Google Sheets.

Usage

python fast_get_coords.py --input ids.txt python fast_get_coords.py --input ids.txt --output coords.tsv --workers 20
Repo: tracer-tools-extensions/fast_get_coords.py Default datastack: brain_and_nerve_cord Default workers: 20

Known Issues

  • No retry logic for transient API failures; a single thread error loses that ID
  • Uses L2 representative coordinates only (not skeleton centroids)
  • L2 cache batches of 100 may still occasionally 504 on slow connections

full_pipeline.py

Experimental

Complete workflow script: update IDs → get coordinates → output to file, clipboard, or Google Sheets. Combines multiple steps into one command.

Usage

python tracer_tools/scripts/full_pipeline.py --input ids.txt --output results.tsv
Location: tracer_tools/scripts/full_pipeline.py

validate_ids_batch.py

Experimental

Batch ID validator for large datasets (1,000+ IDs). Processes in chunks with progress reporting. More robust than fast_validate_ids for very large batches and Windows environments.

Usage

python tracer_tools/scripts/validate_ids_batch.py --input ids.txt --output results.txt
Location: tracer_tools/scripts/validate_ids_batch.py Default datastack: brain_and_nerve_cord

process_file_column.py

Experimental

Adds coordinate columns to CSV/TSV files. Reads root IDs from a specified column, fetches coordinates, and writes them to adjacent columns in-place.

Usage

python tracer_tools/scripts/process_file_column.py --input data.csv
Location: tracer_tools/scripts/process_file_column.py

Google Sheets Integration

sheets_get_coords.py

Experimental

Reads root IDs from a Google Sheet, fetches coordinates via CAVE, and writes the coordinates back to columns in the same sheet. Modifies in-place.

Location: tracer_tools/scripts/sheets_get_coords.py

sheets_get_coords_safe.py

Experimental

Safe mode version: creates a new worksheet with coordinate results rather than modifying the original sheet.

Location: tracer_tools/scripts/sheets_get_coords_safe.py

sheets_coords_oauth.py

Experimental

OAuth-based Google Sheets coordinate updater. Uses browser-based OAuth flow instead of service account credentials. Includes offset/limit support for processing sheets in batches.

Usage

python tracer_tools/scripts/sheets_coords_oauth.py --sheet "SHEET_ID" --offset 0 --limit 1000 --update-ids
Location: tracer_tools/scripts/sheets_coords_oauth.py

sheets_merge.py

Experimental

Merges multiple Google Sheets into one. Useful for combining parallel batch outputs or consolidating results from multiple processing runs.

Location: tracer_tools/scripts/sheets_merge.py

CLI Utilities

get_coords_cli.py

Stable

Interactive CLI for fetching coordinates for root IDs. Sequential processing (for small batches or one-off lookups).

Usage

python tracer_tools/scripts/get_coords_cli.py --datastack brain_and_nerve_cord --ids 720575941471915328
Location: tracer_tools/scripts/get_coords_cli.py

update_ids_cli.py

Stable

Interactive CLI for updating outdated segment IDs. Uses the accurate supervoxel method to track IDs through splits and merges.

Usage

python tracer_tools/scripts/update_ids_cli.py --datastack brain_and_nerve_cord --with-coords
Location: tracer_tools/scripts/update_ids_cli.py

monitor_validation.py

Utility

Monitors real-time progress of running batch ID validation. Useful when processing large datasets with validate_ids_batch.py.

Location: tracer_tools/scripts/monitor_validation.py

save_cave_token.py

Setup

Saves your CAVE authentication token to the standard location. Run this once before using any CAVE-dependent scripts.

Location: tracer_tools/scripts/save_cave_token.py