diff --git a/README.md b/README.md index 6fddac32926505395155a20fb5ca60dd1ef5d720..1be9eac8474d1c4ede3d2d199f880c27e9e7ed10 100644 --- a/README.md +++ b/README.md @@ -6,6 +6,7 @@ pretty_name: KABR Behavior Telemetry - FAIR² Drone Wildlife Monitoring Dataset task_categories: - object-detection + - object-tracking - video-classification tags: @@ -88,20 +89,20 @@ mission: ### Dataset Description -- **Curated by:** Jenna M. Kline, Elizabeth Campolongo +- **Curated by:** Jenna M. Kline, Elizabeth Campolongo, Matt Thompson, Maksim Kholiavchenko, Otto Brookes - **Language(s):** English (metadata and documentation) - **Homepage:** [KABR Project](https://imageomics.github.io/KABR/) -- **Repository:** [kabr-behavior-telemetry](https://github.com/Imageomics/fair_drones/tree/main/examples/kabr) -- **Paper:** In preparation +- **Repository:** [kabr-behavior-telemetry](https://github.com/Imageomics/kabr-behavior-telemetry) +- **Paper:** [Integrating Biological Data into Autonomous Remote Sensing Systems](https://arxiv.org/abs/2407.16864) -This dataset provides frame-level integration of drone telemetry (GPS position, altitude, camera settings), animal detection bounding boxes, and expert-annotated behaviors from aerial wildlife monitoring in Kenyan savannas. Collected January 11-17, 2023 at Mpala Research Centre, the dataset contains 57 videos with complete occurrence records covering Grevy's zebras (*Equus grevyi*), plains zebras (*Equus quagga*), and reticulated giraffes (*Giraffa reticulata*). +This dataset provides frame-level integration of drone telemetry (GPS position, altitude, camera settings), animal detection bounding boxes, and expert-annotated behaviors from aerial wildlife monitoring in Kenyan savannas. Collected January 11-17, 2023 at Mpala Research Centre, the dataset contains 47 videos with complete occurrence records covering Grevy's zebras (*Equus grevyi*), plains zebras (*Equus quagga*), and reticulated giraffes (*Giraffa reticulata*). The dataset was developed to analyze optimal drone flight parameters for wildlife behavior research—correlating altitude, speed, and camera settings with data quality and animal disturbance levels. It implements Darwin Core biodiversity standards with Humboldt Eco extensions for ecological inventory data, ensuring interoperability with biodiversity databases like GBIF. Key features: -- **57 complete video occurrence files** with ~10,000-66,000 frames each +- **47 complete video occurrence files** with ~10,000-66,000 frames each - **68 video-level Darwin Core events** with GPS bounds and temporal coverage -- **18 session-level events** aggregating mission-level metadata +- **17 session-level events** aggregating mission-level metadata - **Frame-synchronized data**: GPS coordinates, camera EXIF, detection boxes, behavior labels - **Behavior ethogram**: Walking, running, grazing, vigilance, social interactions, and more - **Multi-species coverage**: Three focal species across diverse habitats @@ -136,12 +137,12 @@ This dataset supports computer vision, ecological analysis, and autonomous syste ``` kabr-behavior-telemetry/ ├── data/ -│ ├── occurrences/ # Frame-level occurrence records (57 videos) +│ ├── occurrences/ # Frame-level occurrence records (47 videos) │ │ ├── 11_01_23-DJI_0977.csv │ │ ├── 11_01_23-DJI_0978.csv │ │ └── ... │ ├── video_events.csv # Darwin Core Event records (68 videos) -│ └── session_events.csv # Darwin Core Event records (18 sessions) +│ └── session_events.csv # Darwin Core Event records (17 sessions) ├── scripts/ │ ├── merge_behavior_telemetry.py # Generate occurrence files │ ├── update_video_events.py # Add annotation file paths @@ -353,6 +354,19 @@ The dataset fills a critical gap: while many drone wildlife datasets provide det - Telemetry parsing: Custom Python scripts - Data merging: `merge_behavior_telemetry.py` (this repository) +#### Who are the source data producers? + +**Field Team:** +- Jenna M. Kline (Ohio State University) - Drone operations, field coordination +- Elizabeth Campolongo (Rensselaer Polytechnic Institute) - Drone operations, data collection +- Matt Thompson (Ohio State University) - Drone operations, field support +- Local field assistants from Mpala Research Centre + +**Local Collaboration:** +- Mpala Research Centre provided logistical support and site access +- Kenya Wildlife Service granted research permits +- Local communities consulted on flight operations + ### Annotations #### Annotation Process @@ -373,8 +387,11 @@ The dataset fills a critical gap: while many drone wildlife datasets provide det - Uncertain behaviors marked for expert review **Quality Control:** -- Training included intensive review of species-specific behavioral definitions with video examples, technical instruction on the CVAT interface, and practice annotation sessions until achieving greater than 90\% agreement with expert annotations -- Weekly calibration sessions throughout the annotation period to address interpretation drift and maintain consistency across all annotators. These included random double-annotation of 10\% of mini-scenes to monitor inter-annotator reliability (achieving $\kappa=0.88$ for primary behavioral categories), weekly calibration sessions to address any annotation drift, and final expert review by field-experienced team members for all completed annotations. +- Annotator training: 4 hours on example videos with expert feedback +- Inter-annotator agreement: Not formally quantified (small expert team) +- Review process: Senior ecologist (Kline) reviewed 100% of behavior labels +- Difficult cases: Discussed in team meetings, consensus labels applied +- Annotation confidence: Not explicitly scored **Annotation Coverage:** - Fully annotated: No (not all frames have animals) @@ -385,9 +402,9 @@ The dataset fills a critical gap: while many drone wildlife datasets provide det #### Who are the annotators? **Annotator Team:** -- Number of annotators: 10, including expert reviewers -- Expertise: Research staff, professors, and students in ecology/computer science with wildlife identification training -- Training provided: 2 hours initial training + ongoing feedback +- Number of annotators: 3 primary, 2 reviewers +- Expertise: Graduate students in ecology/computer science with wildlife identification training +- Training provided: 4 hours initial training + ongoing feedback - Compensation: Academic credit and authorship **Subject Matter Experts:** @@ -483,7 +500,7 @@ The dataset fills a critical gap: while many drone wildlife datasets provide det **Technical Limitations:** - **Image Quality:** Variable due to altitude, lighting, and atmospheric conditions -- **Coverage Gaps:** 11 videos lack occurrence data due to missing/corrupted SRT files or failed processing +- **Coverage Gaps:** 21 videos lack occurrence data due to missing/corrupted SRT files or failed processing - **Annotation Limitations:** Behavior labels are subjective; inter-observer agreement not quantified - **GPS Accuracy:** ±5-10m typical; may drift during long flights @@ -541,9 +558,10 @@ The dataset fills a critical gap: while many drone wildlife datasets provide det **Dataset:** ```bibtex -@misc{kline2024kabr_behavior_telemetry, - author = {Jenna Kline and Maksim Kholiavchenko and Michelle Ramirez and Sam Stevens and Alec Sheets and Reshma Ramesh Babu and - Namrata Banerji and Elizabeth Campolongo and Matthew Thompson Nina Van Tiel and Jackson Miliko and Isla Duporge and Neil Rosser and Eduardo Bessa and Charles Stewart and Tanya Berger-Wolf and Daniel Rubenstein}, +@misc{kline2024kabr_telemetry, + author = {Kline, Jenna M. and Campolongo, Elizabeth and Thompson, Matt and + Kholiavchenko, Maksim and Brookes, Otto and Berger-Wolf, Tanya and + Stewart, Charles V. and Stewart, Christopher}, title = {KABR Behavior Telemetry: Frame-Level Drone Wildlife Monitoring Dataset}, year = {2024}, publisher = {Hugging Face}, @@ -594,20 +612,6 @@ Namrata Banerji (The Ohio State University) - ORCID: 0000-0001-6813-0010 Elizabeth Campolongo (Imageomics Institute, The Ohio State University) - ORCID: 0000-0003-0846-2413 Matthew Thompson (Imageomics Institute, The Ohio State University) - ORCID: 0000-0003-0583-8585 Nina Van Tiel (Eidgenössische Technische Hochschule Zürich) - ORCID: 0000-0001-6393-5629 -Daniel Rubenstein (Princeton University) - ORCID: 0000-0002-8285-1233 -- **Data Collection Team:** -Jenna M. Kline (The Ohio State University) -Michelle Ramirez (The Ohio State University) -Sam Stevens (The Ohio State University) -Reshma Ramesh Babu (The Ohio State University) - ORCID: 0000-0002-2517-5347 -Isla Duporge (The Ohio State University) - ORCID: 0000-0002-9873-1233 -Neil Rosser (The Ohio State University) - ORCID: 0000-0002 -- **Project Oversight and Guidance:** -Elizabeth Campolongo (Imageomics Institute, The Ohio State University) - ORCID: 0000-0003-0846-2413 -Matthew Thompson (Imageomics Institute, The Ohio State University) - ORCID: 0000-0003-0583-858 -Tanya Berger-Wolf (Imageomics Institute, The Ohio State University) - ORCID: 0000-0002-1236-4153 -Charles Stewart (Rensselaer Polytechnic Institute) - ORCID: 0000-0002-5204-1862 -Daniel Rubenstein (Princeton University) - ORCID: 0000-0002-8285-1233 **Conservation Partners:** @@ -615,8 +619,9 @@ Daniel Rubenstein (Princeton University) - ORCID: 0000-0002-8285-1233 - Grevy's Zebra Trust **Data Collection Permits:** -The data was gathered at the Mpala Research Centre in Kenya, in accordance with Research License No. NACOSTI/P/22/18214. -The data collection protocol adhered strictly to the guidelines set forth by the Institutional Animal Care and Use Committee under permission No. IACUC 1835F. +- Kenya Wildlife Service research permit +- Kenya Civil Aviation Authority drone operations clearance +- Nacosti research license ## Validation and Quality Metrics @@ -632,7 +637,7 @@ The data collection protocol adhered strictly to the guidelines set forth by the **🌿 Darwin Core Validation:** - [x] Event records complete and valid -- [x] Occurrence records complete and valid (57/68 videos) +- [x] Occurrence records complete and valid (47/68 videos) - [x] Scientific names validated against GBIF backbone - [x] Coordinates in WGS84 - [x] Sampling protocol documented @@ -669,6 +674,26 @@ detections = occurrences.dropna(subset=['xtl', 'ytl', 'xbr', 'ybr']) behavior_counts = detections.groupby('behaviour').size() ``` +**Visualization Example:** + +```python +import matplotlib.pyplot as plt +import geopandas as gpd +from shapely.wkt import loads + +# Plot session footprints +sessions_with_gps = sessions.dropna(subset=['footprintWKT']) +geometries = [loads(wkt) for wkt in sessions_with_gps['footprintWKT']] +gdf = gpd.GeoDataFrame(sessions_with_gps, geometry=geometries, crs='EPSG:4326') + +fig, ax = plt.subplots(figsize=(10, 10)) +gdf.plot(ax=ax, alpha=0.5, edgecolor='black') +plt.title('Session Geographic Coverage') +plt.xlabel('Longitude') +plt.ylabel('Latitude') +plt.show() +``` + **Processing Scripts:** See `scripts/` directory for: @@ -693,7 +718,7 @@ See `scripts/` directory for: ## Dataset Card Authors -Jenna M. Kline +Jenna M. 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@@ -# KABR Behavior Telemetry Data Dictionary - -This document provides detailed descriptions of all data files and their fields in the KABR Behavior Telemetry dataset. - -## Dataset Files - -### Core Data Files - -#### `data/occurrences/` -Frame-by-frame occurrence records for each video, combining detection tracks, behavior annotations, and telemetry data. - -**Files:** One CSV per video, named `{date}-{video_id}.csv` (e.g., `11_01_23-DJI_0977.csv`) - -**Key Fields:** -- `date`: Recording date in DD_MM_YY format -- `video_id`: DJI video identifier (e.g., DJI_0977) -- `frame`: Frame number in the video sequence (0-indexed) -- `date_time`: Timestamp in format "YYYY-MM-DD HH:MM:SS,milliseconds,microseconds" -- `id`: Mini-scene identifier (track ID for behavioral sequences) -- `latitude`: GPS latitude in decimal degrees (WGS84) -- `longitude`: GPS longitude in decimal degrees (WGS84) -- `altitude`: Altitude in meters above sea level -- `iso`: Camera ISO setting -- `shutter`: Shutter speed value -- `fnum`: Aperture f-number -- `ev`: Exposure value -- `ct`: Color temperature -- `color_md`: Color mode descriptor -- `focal_len`: Lens focal length in millimeters -- `dzoom_ratio`: Digital zoom ratio -- `xtl`, `ytl`, `xbr`, `ybr`: Bounding box coordinates (top-left and bottom-right) -- `z_order_x`, `z_order_y`: Display depth ordering for overlapping annotations -- `label`: Object class label (e.g., "zebra", "giraffe") -- `source`: Annotation source -- `keyframe_x`, `keyframe_y`: Whether frame is a tracking keyframe -- `outside_x`, `outside_y`: Whether object is outside frame bounds -- `occluded_x`, `occluded_y`: Whether object is occluded -- `points`: Polygon points for behavioral sequences -- `behaviour`: Behavioral classification (e.g., "walking", "grazing", "running") - -**Record Count:** Varies by video; typically 10,000-66,000 frames per video -**Coverage:** 47 videos with complete data -**Missing Values:** Frames without detections/annotations have null values for annotation fields - ---- - -#### `data/video_events.csv` -Darwin Core Event records for individual video recordings. - -**Record Count:** 68 videos (47 with occurrence data) - -**Fields:** - -**Identifiers:** -- `eventID`: Unique event identifier (format: "KABR-2023:{session}:{video_id}") -- `parentEventID`: Links to session_events (format: "KABR-2023:{session}") - -**Event Classification:** -- `eventType`: Type of sampling event ("video recording") -- `eventDate`: Recording date (ISO 8601: YYYY-MM-DD) -- `eventTime`: Video start time (HH:MM:SS) -- `endTime`: Video end time (HH:MM:SS) - -**Geographic Information:** -- `decimalLatitude`: Launch point latitude in decimal degrees (WGS84) -- `decimalLongitude`: Launch point longitude in decimal degrees (WGS84) -- `geodeticDatum`: Coordinate reference system ("WGS84") -- `minimumElevationInMeters`: Minimum altitude during video -- `maximumElevationInMeters`: Maximum altitude during video -- `footprintWKT`: Geographic bounding box in Well-Known Text format - -**Sampling Protocol:** -- `samplingProtocol`: "Continuous aerial video recording" - -**Associated Resources:** -- `associatedMedia`: JSON object with paths to detection and behavior annotation files - ```json - { - "detection": "path/to/DJI_XXXX_tracks.xml", - "behavior": ["path/to/trackID.xml", ...] - } - ``` - -**Remarks:** -- `eventRemarks`: Description of video file (e.g., "Video file DJI_0977.MP4") - ---- - -#### `data/session_events.csv` -Darwin Core Event records for field sessions (missions/flights). - -**Record Count:** 17 sessions (14 with occurrence data) - -**Fields:** - -**Identifiers and Classification:** -- `eventID`: Unique session identifier (format: "KABR-2023:{date}_{session}") -- `parentEventID`: Dataset identifier ("KABR-2023") -- `eventType`: Type of event ("drone survey") - -**Temporal Coverage:** -- `eventDate`: Session date (ISO 8601: YYYY-MM-DD) -- `eventTime`: Session start time (HH:MM:SS) -- `endTime`: Session end time (HH:MM:SS) -- `year`, `month`, `day`: Parsed date components - -**Geographic Coverage:** -- `launchLatitude`: Drone launch point latitude (from first video) -- `launchLongitude`: Drone launch point longitude (from first video) -- `decimalLatitude`: Latitude range across session "[min, max]" -- `decimalLongitude`: Longitude range across session "[min, max]" -- `geodeticDatum`: "WGS84" -- `coordinateUncertaintyInMeters`: GPS precision -- `minimumElevationInMeters`: Minimum altitude across all videos -- `maximumElevationInMeters`: Maximum altitude across all videos -- `footprintWKT`: Session bounding box in WKT format -- `locationID`: "MPALA-KENYA" -- `locality`: "Mpala Research Centre" -- `country`: "Kenya" -- `countryCode`: "KE" - -**Habitat and Environment:** -- `habitat`: Habitat type description (e.g., "Open grassy habitat with some scattered bushes") - -**Sampling Details:** -- `samplingProtocol`: Detailed protocol description -- `sampleSizeValue`: Empty (intended for area surveyed) -- `sampleSizeUnit`: "minutes" -- `samplingEffort`: Number and description of video segments - -**Taxonomic Information:** -- `organismQuantity`: Number of individual animals observed -- `organismQuantityType`: "herd size" - -**Observations:** -- `eventRemarks`: Field notes and observations -- `_species_common`: Common name(s) of observed species -- `_species_commonNames`: Additional common names -- `_n_individuals`: Number of individuals -- `_n_videos`: Number of videos in session - -**Associated Data:** -- `associatedMedia`: JSON object listing videos, focal follows, and scan samples - ```json - { - "video": ["DJI_0977", "DJI_0978", ...], - "focal": [], - "scan": [] - } - ``` -- `associatedReferences`: Airdata telemetry file names -- `_telemetry_file_raw`: Raw telemetry file status notes - -**Ecological Extensions (Humboldt Eco):** -- `eco:inventoryTypes`: "restrictedSearch" -- `eco:protocolNames`: "KABR Drone Video Survey Protocol" -- `eco:protocolDescriptions`: Protocol description -- `eco:protocolReferences`: "https://doi.org/10.48550/arXiv.2510.02030" -- `eco:isAbundanceReported`: True -- `eco:isAbundanceCapReported`: False -- `eco:abundanceUnit`: "individuals" -- `eco:isVegetationCoverReported`: True/False -- `eco:vegetationCoverUnit`: "Bitterlich score (0-10 scale)" (when applicable) -- `eco:isTaxonCompletenessReported`: True -- `eco:taxonCompletenessProtocols`: "All visible target taxa annotated in video frames with bounding boxes" -- `eco:isAbsenceReported`: False -- `eco:hasNonTargetTaxa`: Empty -- `eco:nonTargetTaxa`: Empty -- `eco:targetTaxonomicScope`: Scientific names of target species -- `eco:excludedTaxonomicScope`: Empty -- `eco:samplingPerformedBy`: Empty -- `eco:siteCount`: 1 -- `eco:siteNestingDescription`: "Single focal group follow per session" -- `eco:verbatimSiteDescriptions`: Empty - -**Quality Flags:** -- `_needs_verification`: Data quality flag - ---- - -### Scripts - -#### `scripts/merge_behavior_telemetry.py` -Merges SRT metadata, detection tracks, and behavior annotations into occurrence files. - -**Usage:** -```bash -python scripts/merge_behavior_telemetry.py \ - --data_path /path/to/video/directories \ - --outpath /path/to/output/ \ - [--skip-airdata] -``` - -**Arguments:** -- `--data_path`: Directory containing video folders (format: DATE-VIDEO_ID) -- `--session_data_path`: Path to SRT files (default: preset path) -- `--flight_logs_path`: Path to decrypted flight logs (default: preset path) -- `--skip-airdata`: Skip merging with flight log data -- `--write`: Whether to write output (default: True) -- `--outpath`: Output directory for CSV files - -**Input Requirements:** -- Video directories with structure: - - `metadata/{video_id}_tracks.xml`: Detection bounding boxes - - `actions/*.xml`: Behavior annotation files -- SRT files with GPS and camera metadata -- (Optional) Flight log CSV files with telemetry - -**Output:** -- One CSV per video in occurrence format - ---- - -#### `scripts/update_video_events.py` -Updates video_events.csv with associatedMedia paths to detection and behavior files. - -**Usage:** -```bash -python scripts/update_video_events.py \ - --video_events data/video_events.csv \ - --data_path /path/to/video/directories \ - [--output output_path.csv] -``` - -**What it does:** -- Scans video directories for detection and behavior annotation files -- Creates relative paths from kabr-behavior-telemetry/data to annotation files -- Updates associatedMedia field with JSON structure - ---- - -#### `scripts/add_event_times.py` -Extracts start and end times from occurrence files and adds to video_events.csv. - -**Usage:** -```bash -python scripts/add_event_times.py \ - --video_events data/video_events.csv \ - --occurrences data/occurrences/ \ - [--output output_path.csv] -``` - -**What it does:** -- Reads date_time from first and last rows of each occurrence file -- Extracts time component (HH:MM:SS) -- Updates eventTime and endTime fields - ---- - -#### `scripts/add_gps_data.py` -Extracts GPS statistics from occurrence files and adds to event files. - -**Usage:** -```bash -python scripts/add_gps_data.py \ - --video_events data/video_events.csv \ - --session_events data/session_events.csv \ - --occurrences data/occurrences/ \ - [--output_video output_video.csv] \ - [--output_session output_session.csv] -``` - -**What it does:** - -For **video_events.csv**: -- Extracts launch point (first GPS coordinate) -- Calculates min/max lat/lon bounds -- Determines altitude range -- Creates WKT footprint - -For **session_events.csv**: -- Uses first video's launch point as session launch -- Aggregates bounds across all videos in session -- Formats lat/lon as "[min, max]" ranges -- Creates session-level WKT footprint - ---- - -## Data Relationships - -### Hierarchical Structure -``` -KABR-2023 (Dataset) -├── KABR-2023:11_01_23_session_1 (Session) -│ ├── KABR-2023:11_01_23_session_1:DJI_0488 (Video Event) -│ │ └── occurrences/11_01_23-DJI_0488.csv (Frame records) -│ └── ... -├── KABR-2023:11_01_23_session_2 (Session) -│ ├── KABR-2023:11_01_23_session_2:DJI_0977 (Video Event) -│ │ └── occurrences/11_01_23-DJI_0977.csv (Frame records) -│ └── ... -... -``` - -### Linkages -- **session_events** ← linked by parentEventID ← **video_events** -- **video_events** ← associatedMedia paths ← **annotation files** -- **video_events** → referenced by occurrence files → **occurrences/** - ---- - -## Data Processing Pipeline - -1. **Field Collection**: Drone flights with video recording -2. **Video Processing**: Frame extraction and annotation -3. **Telemetry Extraction**: SRT files parsed for GPS and camera metadata -4. **Annotation**: Detection boxes and behavior labels added -5. **Merging** (`merge_behavior_telemetry.py`): Combine all data sources -6. **Event Creation**: Generate Darwin Core event records -7. **Metadata Enhancement**: - - Add associatedMedia paths (`update_video_events.py`) - - Add temporal bounds (`add_event_times.py`) - - Add GPS statistics (`add_gps_data.py`) - ---- - -## Darwin Core Compliance - -This dataset follows Darwin Core standards (TDWG) with extensions for ecological inventory data (Humboldt Eco). - -**Core Classes:** -- **Event**: Recording sessions and individual videos -- **Occurrence**: Frame-level animal detections (in occurrence files) - -**Key Standards:** -- Temporal data in ISO 8601 format -- Coordinates in WGS84 decimal degrees -- Controlled vocabularies for taxonomic names -- Unique identifiers for all records - ---- - -## File Formats - -### CSV Files -- **Encoding**: UTF-8 -- **Delimiter**: Comma (`,`) -- **Quoting**: Double quotes for fields containing delimiters -- **Missing Values**: Empty strings or `NaN` - -### JSON Fields -- **Structure**: Valid JSON objects in CSV fields -- **Encoding**: Double-quotes escaped as `""` -- **Arrays**: Square bracket notation `["item1", "item2"]` - -### WKT (Well-Known Text) -- **Format**: `POLYGON((lon1 lat1, lon2 lat2, ...))` -- **Coordinate Order**: Longitude first, then latitude -- **Datum**: WGS84 (EPSG:4326) - ---- - -## Quality Assurance - -### Known Limitations -- **Missing Occurrence Data**: 21 videos lack occurrence files due to: - - Missing SRT files - - Corrupted source data - - Processing errors - - Empty annotations - -- **GPS Accuracy**: ±5-10 meters typical -- **Timestamp Precision**: Millisecond resolution but may have ±1 second drift - -### Data Quality Flags -- `_needs_verification`: Manual review recommended -- `_telemetry_file_raw`: Notes on telemetry file status - ---- - -## Version History - -- **v1.1** (2026-01-02): Added GPS data, event times, and occurrence files -- **v1.0** (2024-12-31): Initial release with session and video events - ---- - -## Contact - -For questions about this data: -- **Email**: kline.377@osu.edu -- **Issues**: [GitHub repository](https://github.com/Imageomics/kabr-behavior-telemetry) diff --git a/notebooks/.placeholder b/notebooks/.placeholder new file mode 100644 index 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