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chore: updated just recipes
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@danellecline
danellecline committed Feb 20, 2025
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Expand Up @@ -70,53 +70,59 @@ Recipes are available to run the pipelines. To see the available recipes, run t
just list
```
# Available Recipes

| **Recipe** | **Description** |
|-------------------------------------|----------------------------------------------------------------------------------------------------------|
| `list` | List recipes. |
| `install` | Setup the environment. |
| `cp-env` | Copy the default `.env` file to the project. |
| `update_trackers` | Update the environment. Run this command after checking out any code changes. |
| `update-env` | Update environment. |
| `cp-core` | Copy core dev code to the project on Doris. |
| `cp-dev-uav` | Copy UAV dev code to the project on Doris. |
| `cp-dev-bio` | Copy bio dev code to the project on Doris. |
| `cp-dev-i2map` | Copy i2map dev code to the project on Doris. |
| `plot-tsne-vss project='uav'` | Generate a t-SNE plot of the VSS database. |
| `optimize-vss project='uav'` | Optimize the VSS database. |
| `calc-acc-vss project='uav'` | Calculate the accuracy of the VSS database; run after download, then optimize. |
| `reset-vss-all` | Reset the VSS database, removing all data. Proceed with caution! |
| `reset-vss project='uav'` | Reset the VSS database for the specified project (e.g., `uav`). |
| `remove-vss project='uav'` | Remove an entry from the VSS database (e.g., `remove-vss i2map --doc 'doc:marine organism:*'`). |
| `init-vss project='uav'` | Initialize the VSS database for a project. |
| `load-vss project='uav'` | Load precomputed exemplars into the VSS database. |
| `load-cfe-isiis-videos` | Load CFE ISII mission videos listed in `missions-to-process.txt`. |
| `cluster-uav` | Cluster missions listed in `missions-to-process.txt`. |
| `detect-uav` | Detect missions listed in `missions-to-process.txt`. |
| `detect-uav-test` | Detect mission data for testing purposes. |
| `load-uav-images` | Load UAV mission images listed in `missions-to-process.txt`. |
| `load-uav type="cluster"` | Load UAV detections or clusters from `missions-to-process.txt`. |
| `fix-uav-metadata` | Fix UAV metadata for latitude, longitude, and altitude. |
| `compute-saliency project='uav'` | Compute saliency for downloaded VOC data and update the Tator database. |
| `crop project='uav'` | Crop detections from VOC-formatted downloads. |
| `download-crop project='uav'` | Download and crop images. |
| `download project='uav'` | Download only. |
| `predict-vss project='uav'` | Predict images using the VSS database. |
| `run-ctenoA-test` | Run strided inference on a single video. |
| `run-ctenoA-prod` | Run strided inference on a collection of videos listed in a TSV file. |
| `run-mega-inference` | Run mega strided inference on a single video. |
| `run-mega-track-bio-video` | Run mega strided tracking for a single video in the bio project. |
| `run-mega-track-bio-dive` | Run mega strided tracking for an entire dive in the bio project. |
| `run-mega-track-i2map-video` | Run mega strided tracking for a single video in the i2map project. |
| `run-mega-track-test-1min` | Run mega strided tracking on a single video to test the pipeline. |
| `run-mega-track-test-fastapiyv5` | Run mega strided tracking on a single video with FastAPI. |
| `cluster-i2mapbulk` | Run inference and clustering on i2map bulk data. |
| `load-i2mapbulk` | Load i2map bulk data using a `cluster_detections.csv` file. |
| `gen-cfe-data` | Generate training data for the CFE project. |
| `gen-i2map-data` | Generate training data for the i2map project. |
| `gen-i2mapbulk-data` | Generate training data for i2map from bulk server data. |
| `gen-uav-data` | Generate training data for the UAV project. |
| `gen-stats-csv project='UAV'` | Generate training data statistics. |
| Recipe | Description |
|---------------------------------|-------------|
| list | List recipes |
| install | Setup the environment |
| cp-env | Copy the default .env file to the project |
| update_trackers | Update the environment. Run after checking out code changes |
| update-env | Update environment |
| cp-core | Copy core dev code to the project on doris |
| cp-dev-ptvr | Copy planktivore dev code to the project on doris |
| cp-dev-uav | Copy UAV dev code to the project on doris |
| cp-dev-bio | Copy bio dev code to the project on doris |
| cp-dev-i2map | Copy i2map dev code to the project on doris |
| plot-tsne-vss project='uav' | Generate a t-SNE plot of the VSS database |
| optimize-vss project='uav' | Optimize the VSS database |
| calc-acc-vss project='uav' | Calculate the accuracy of the VSS database |
| reset-vss-all | Reset the VSS database, removing all data (caution!) |
| reset-vss project='uav' | Reset the VSS database before initializing or creating it |
| remove-vss project='uav' | Remove an entry from the VSS database |
| init-vss project='uav' | Initialize the VSS database for a project |
| load-vss project='uav' | Load computed exemplars into the VSS database |
| load-cfe-isiis-videos | Load CFE ISIIS mission videos |
| load-ptvr-images images='tmp/roi' | Load planktivore ROI images |
| cluster-ptvr-images images='tmp/roi' | Cluster planktivore ROI images |
| load-ptvr-clusters clusters='tmp/roi/cluster.csv' | Load planktivore ROI clusters |
| cluster-uav | Cluster UAV mission data |
| detect-uav | Detect UAV mission data |
| detect-uav-test | Detect UAV mission data (test mode) |
| load-uav-images | Load UAV mission images |
| load-uav type="cluster" | Load UAV detections/clusters |
| fix-uav-metadata | Fix UAV metadata (lat/lon/alt) |
| compute-saliency project='uav' | Compute saliency for VOC data and update Trackers in Tator |
| crop project='uav' | Crop detections from VOC formatted downloads |
| download-crop project='uav' | Download and crop with defaults for a project |
| download project='uav' | Download only |
| predict-vss project='uav' | Predict images using the VSS database |
| run-ctenoA-test | Run strided inference on a single video |
| run-ctenoA-prod | Run strided inference on a collection of videos in a TSV file |
| run-mega-inference | Run mega strided inference on a single video |
| run-mega-track-bio-video | Run mega tracking on a single bio project video |
| run-m | Run mega tracking on a single bio project video |
| run-mega-track-bio-dive | Run mega tracking on an entire dive for the bio project |
| run-mega-track-i2map-video | Run mega tracking on an i2MAP video |
| run-mega-track-test-1min | Test mega tracking on a single video (1 min) |
| run-mega-track-test-fastapiyv5 | Test mega tracking with FastAPI |
| cluster-i2mapbulk | Run inference and cluster on i2MAP bulk data |
| init-i2map-vss | Initialize VSS with combined i2MAP training data |
| load-i2mapbulk data='data' | Load i2MAP bulk data |
| download-i2mapbulk-unlabeled | Download unlabeled i2MAP bulk data |
| gen-cfe-data | Generate training data for the CFE project |
| gen-i2map-data | Generate training data for the i2MAP project |
| gen-i2mapbulk-data | Generate training data for the i2MAP bulk server |
| gen-uav-data | Generate training data for the UAV project |
| gen-stats-csv project='UAV' | Generate training data stats |

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