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Archeo-Cluster processes archaeological imagery through a three-stage pipeline: color-based object detection, K-Means clustering, and spatial analysis. Each stage produces its own output files, and the whole sequence can be run in a single command.

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Pipeline overview

┌─────────────┐    ┌─────────────┐    ┌─────────────┐    ┌─────────────┐
│   Images    │ -> │  Detection  │ -> │  Clustering │ -> │  Analysis   │
│             │    │  (OpenCV)   │    │  (K-Means)  │    │  (Spatial)  │
└─────────────┘    └─────────────┘    └─────────────┘    └─────────────┘
                          │                  │                  │
                          v                  v                  v
                     features.csv      clustered.csv       descriptive_stats.csv
                     contours.png      elbow_method.png    ann_results.csv
All outputs are written to a session directory so nothing is overwritten between runs. See Session Management for details on where sessions are stored.

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Running the full pipeline

The pipeline command chains all three stages and stores everything in one session: 
# Simplest form — session name is derived from the input folder name
uv run archeo-cluster pipeline --input-dir ./dataset

# Specify a session name and a custom target color
uv run archeo-cluster pipeline \
  --input-dir ./dataset \
  --session "site_a_2025" \
  --color "#A98876"

# Open the results folder automatically when done
uv run archeo-cluster pipeline --input-dir ./dataset --open
The --open flag launches the system file manager pointing at the session directory once the pipeline finishes. It is enabled by default.

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Stage-by-stage walkthrough

1

Stage 1: Object Detection

The detect command converts each image to HSV color space, applies a color mask around the target hue, runs morphological operations to clean noise, and extracts contour features.
uv run archeo-cluster detect \
  --input-dir ./dataset \
  --session "site_a_detection" \
  --color "#A98876" \
  --min-area 50 \
  --max-area 5000
What gets saved:
FileDescription
detection/features.csvOne row per detected object: image_filename, contour_index, area, perimeter, centroid_x, centroid_y, circularity, aspect_ratio, solidity, extent
detection/<image>/01_hsv.pngHSV-converted source image
detection/<image>/02_mask_initial.pngRaw color mask before morphology
detection/<image>/03_mask_closed.pngMask after MORPH_CLOSE
detection/<image>/04_mask_morph_final.pngMask after MORPH_OPEN
detection/<image>/05_raw_contours.pngAll contours before area filtering (red)
detection/<image>/06_filtered_contours_final.pngContours that passed the area filter (green)
The session status transitions from DETECTING → DETECTION_DONE on success.
2

Stage 2: K-Means Clustering

The cluster command reads features.csv, normalises the six morphological features with StandardScaler, runs the elbow method to pick the optimal K, and fits a KMeans model.
uv run archeo-cluster cluster \
  --input ./session_dir/detection/features.csv \
  --output-dir ./session_dir/clustering \
  --max-k 10
What gets saved (one sub-directory per image):
FileDescription
clustering/<image>/<image>_clustered.csvfeatures.csv with an added cluster column
clustering/<image>/elbow_method.pngInertia vs K with the selected elbow marked
clustering/<image>/silhouette_analysis.pngSilhouette score vs K (when compute_silhouette=True)
clustering/<image>/cluster_distribution.pngScatter of centroid positions coloured by cluster
clustering/<image>/morphological_scatter.pngArea vs circularity scatter coloured by cluster
clustering/<image>/clusters_visualization.pngCentroid overlays on the filtered contours image
clustering/<image>/cluster_groups.pngRotated bounding rectangles per cluster
Features used for clustering: area, perimeter, circularity, aspect_ratio, solidity, extent. Centroid coordinates are not used as clustering features — they are preserved for spatial analysis only.The session status transitions from CLUSTERING → CLUSTERING_DONE.
3

Stage 3: Spatial Analysis

The analyze command reads each _clustered.csv file and computes descriptive statistics and the Average Nearest Neighbor (ANN) index for each cluster.
uv run archeo-cluster analyze \
  --input ./session_dir/clustering/image_name/image_name_clustered.csv \
  --output-dir ./session_dir/analysis/image_name
What gets saved:
FileDescription
analysis/<image>/descriptive_stats.csvPer-cluster mean/std/min/max for area and perimeter
analysis/<image>/ann_results.csvANN R-index and interpretation (Clustered / Random / Dispersed) per cluster
analysis/<image>/ann_results.pngBar chart of R-index values with the random baseline (R=1) marked
analysis/<image>/spatial_distribution_map.pngScatter map of objects by cluster (Y-axis inverted to match image coordinates)
analysis/<image>/boxplot_area.pngBoxplots of morphological features by cluster
The session status transitions from ANALYZING → COMPLETED.

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Performance metrics

After pipeline finishes it prints a metrics table showing how long each stage took and peak memory usage: 
─────────────── Performance Summary ────────────────
┏━━━━━━━━━━━━━┳━━━━━━━━━━━━━━━┳━━━━━━━━━━━━━━━━━━┓
┃ Stage       ┃ Duration (s)  ┃ Peak Memory (MB) ┃
┡━━━━━━━━━━━━━╇━━━━━━━━━━━━━━━╇━━━━━━━━━━━━━━━━━━┩
│ Detection   │ 1.243         │ 142.3            │
│ Clustering  │ 0.817         │ 98.7             │
│ Analysis    │ 0.391         │ 61.2             │
│ Total       │ 2.451         │ 142.3            │
└─────────────┴───────────────┴──────────────────┘
The same metrics are persisted in the session’s metadata.json so you can retrieve them later.

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Using the Python API

You can drive the full pipeline from code instead of the CLI: 
from archeo_cluster.core.detection import ObjectDetector
from archeo_cluster.core.clustering import KMeansAnalyzer
from archeo_cluster.core.spatial import run_spatial_analysis
from archeo_cluster.models import DetectionConfig, ClusteringConfig
import pandas as pd

# Stage 1 — Detection
detection_config = DetectionConfig(
    target_color="#A98876",
    min_area=50,
    max_area=5000,
)
detector = ObjectDetector(config=detection_config)
batch = detector.process_directory("./dataset", "./output/detection")

# Save features.csv
df = pd.DataFrame(batch.to_feature_rows())
df.to_csv("./output/features.csv", index=False)

# Stage 2 — Clustering
analyzer = KMeansAnalyzer(config=ClusteringConfig(max_k=10))
clustering = analyzer.process_features_csv(
    "./output/features.csv",
    "./output/clustering",
)

# Stage 3 — Spatial analysis (per image)
for result in clustering.results:
    clustered_csv = f"./output/clustering/{result.image_name}/{result.image_name}_clustered.csv"
    run_spatial_analysis(clustered_csv, f"./output/analysis/{result.image_name}")
Set save_intermediate=False on ObjectDetector if you only need features.csv and want to skip writing the step-by-step mask images to disk.

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