forgeryscope 0.0.5

Tools for the competition

Forgeryscope

Forgeryscope is a Python package for scientific image forgery detection. It contains tools for panel detection, embedding, and image/panel matching.

This is a simplified and refactored version of my winning solution for the Kaggle Scientific Image Forgery Detection competition.

For the full competition approach and design notes, see SOLUTION.md.

Features

• Panel detection with YOLO-based extractors
• Image embeddings with PyTorch/timm checkpoints
• Panel matching with LightGlue, SIFT, ALIKED, and geometry helpers
• On-demand model download from GitHub Releases

Installation

Create and activate a virtual environment:

python3 -m venv .venv
source .venv/bin/activate
python -m pip install --upgrade pip

Install Forgeryscope from PyPI:

pip install forgeryscope

To install the latest version directly from GitHub:

pip install git+https://github.com/vlad3996/forgeryscope.git

If you work from a local clone:

git clone https://github.com/vlad3996/forgeryscope.git
cd forgeryscope
pip install -e .

Model Weights

Model weights are not stored in git and are not bundled into the Python package. They are downloaded on first use from the Forgeryscope GitHub Release and cached locally.

Forgeryscope resolves these model names through forgeryscope.model_zoo:

• yolo_panel_extractor.pt
• yolo_lane_extractor.pt
• aliked_wblot.pth
• wblot_duplicate_embedder.ckpt
• wblot_overlap_embedder.ckpt
• wblot_lane_embedder.ckpt
• micro_overlap_embedder.ckpt

To override the default model release location:

export FORGERYSCOPE_MODEL_BASE_URL="https://github.com/vlad3996/forgeryscope/releases/download/models-v1"

The first run downloads each requested file to:

~/.cache/forgeryscope

To use a different cache directory:

export FORGERYSCOPE_CACHE_DIR="/path/to/cache"

Quick Start

from ultralytics import YOLO
import numpy as np
import pandas as pd
from PIL import Image

from forgeryscope import Embedder, PanelExtractor, get_model_path, load_aliked_wblot_weights
from forgeryscope.matcher.lightglue import LightGlueOverlap, create_duplicate_masks, merge_masks_by_max_cliques
from forgeryscope.matcher.geometry import get_intersections
from forgeryscope.matcher.plot import visualize_duplicate_masks
from forgeryscope.matcher.lane import find_lanes_in_blot_panels, create_lane_match_masks

DEVICE = "cuda"
PRINT_MODEL_DEFINITION = False
VERBOSE = False

panel_extractor = PanelExtractor(
    weights_path="yolo_panel_extractor",
    device=DEVICE,
    conf_threshold=0.7,
    iou_threshold=0.4,
    verbose=PRINT_MODEL_DEFINITION,
)
panel_extractor.EXCLUDED_LABELS = {"Graphs", "Flow Cytometry", "Body Imaging"}

lane_extractor = YOLO(get_model_path("yolo_lane_extractor"))

wblot_duplicate_embedder = Embedder("wblot_duplicate_embedder", device=DEVICE, verbose=PRINT_MODEL_DEFINITION)
wblot_overlap_embedder = Embedder("wblot_overlap_embedder", device=DEVICE, verbose=PRINT_MODEL_DEFINITION)
wblot_lane_embedder = Embedder("wblot_lane_embedder", device=DEVICE, verbose=PRINT_MODEL_DEFINITION)
micro_overlap_embedder = Embedder("micro_overlap_embedder", device=DEVICE, verbose=PRINT_MODEL_DEFINITION)

matcher_micro = LightGlueOverlap(
    max_keypoints=4096,
    matcher_features="sift",
    device=DEVICE,
    depth_confidence=0.9,
    width_confidence=0.9,
    verbose=PRINT_MODEL_DEFINITION,
)

matcher_blot = LightGlueOverlap(
    max_keypoints=512,
    matcher_features="aliked",
    device=DEVICE,
    depth_confidence=-1,
    width_confidence=-1,
    estimator_method="MAGSAC",
    reprojThreshold=3.0,
    estimator_confidence=0.9999,
    estimator_maxIters=5000,
    estimator_refineIters=10,
    verbose=PRINT_MODEL_DEFINITION,
)
load_aliked_wblot_weights(matcher_blot)

Optional embedding sanity check:

img1 = np.array(Image.open("/path/to/wblot_sample.png").convert("RGB"))
img2 = np.array(Image.open("/path/to/wblot_sample_sub2.png").convert("RGB"))

print("wblot_duplicate_embedder:", wblot_duplicate_embedder.compare(img1, img2))
print("wblot_overlap_embedder:", wblot_overlap_embedder.compare(img1, img2))
print("micro_overlap_embedder:", micro_overlap_embedder.compare(img1, img2))

Single-image example:

MATCH_SCORE_THRESHOLD = 0.73
INLIER_THRESHOLD = 8
MATCH_FILTER_STR = "mean_match_score"

WBLOT_DUP_SCORE_THRESH = 0.84
MICROSCOPY_EMB_THRESH = 0.58
MICRO_DUP_SCORE_THRESH = 0.85
WBLOT_OVERLAP_THRESHOLD = 0.85
SEG_SIM_THRESH = 0.65

def find_similar_panel_pairs(panel_ids, crops, embedder, threshold, label):
    embeddings = embedder.get_embedding_batch(crops).cpu()
    return [
        (label, score, panel_ids[i], panel_ids[j])
        for i, j, score in Embedder.find_similar_pairs(embeddings, threshold=threshold)
    ]


image_path = "/path/to/image.png"
img = PanelExtractor._load_image(image_path)
panels = panel_extractor.extract_panels(img)
crops_list = PanelExtractor.crop_panels(img, panels)
intersections = get_intersections(panels, margin=10)

blot_ids = [i for i, panel in enumerate(panels) if panel[0] == "Blots"]
micro_ids = [i for i, panel in enumerate(panels) if panel[0] == "Microscopy"]

similar_pairs = []
similar_pairs_blot = []
if blot_ids:
    blot_crops = PanelExtractor.crop_panels(img, [panels[i] for i in blot_ids])
    blot_overlap_pairs = find_similar_panel_pairs(
        blot_ids,
        blot_crops,
        wblot_overlap_embedder,
        WBLOT_OVERLAP_THRESHOLD,
        "Blots",
    )
    blot_duplicate_pairs = find_similar_panel_pairs(
        blot_ids,
        blot_crops,
        wblot_duplicate_embedder,
        WBLOT_DUP_SCORE_THRESH,
        "Blots",
    )

    best_blot_scores = {}
    for label, score, i, j in blot_overlap_pairs + blot_duplicate_pairs:
        key = tuple(sorted((i, j)))
        if key not in best_blot_scores or score > best_blot_scores[key]:
            best_blot_scores[key] = score

    similar_pairs_blot = [
        ("Blots", score, i, j)
        for (i, j), score in best_blot_scores.items()
    ]
    similar_pairs.extend(similar_pairs_blot)

if micro_ids:
    micro_crops = PanelExtractor.crop_panels(img, [panels[i] for i in micro_ids])
    similar_pairs.extend(
        find_similar_panel_pairs(
            micro_ids,
            micro_crops,
            micro_overlap_embedder,
            MICROSCOPY_EMB_THRESH,
            "Microscopy",
        )
    )

similar_pairs = [
    (label, score, i, j)
    for label, score, i, j in similar_pairs
    if (i, j) not in intersections and (j, i) not in intersections
]

clf_predicts = pd.DataFrame(similar_pairs, columns=["label", "score", "idx1", "idx2"])
match_results = create_duplicate_masks(
    img,
    panels,
    crops_list,
    clf_predicts,
    matcher_micro,
    matcher_blot,
    to_bbox_micro=False,
    to_bbox_blot=True,
    fallback_for_wblot=True,
    test_transforms_blot=False,
    test_transforms_micro=True,
)

pred_masks, duplicate_info = [], []
for info in match_results:
    label = info["panel_label"]
    match_result = info["match_result"]
    inliers = match_result["inliers"]
    matcher_score = match_result[MATCH_FILTER_STR]

    if label != "Blots":
        if inliers < INLIER_THRESHOLD or matcher_score < MATCH_SCORE_THRESHOLD:
            continue

    pred_masks.append((info["mask0"] | info["mask1"]).astype(np.uint8))
    duplicate_info.append(info)

mask_matcher, merged_info = merge_masks_by_max_cliques(
    pred_masks,
    duplicate_info,
    verbose=VERBOSE,
)

if blot_ids and not similar_pairs_blot:
    lane_match_result = find_lanes_in_blot_panels(
        panels=panels,
        blot_panels_ids=blot_ids,
        crops_list=crops_list,
        segmentator=lane_extractor,
        blot_duplicate_detector=wblot_lane_embedder,
        similarity_threshold=SEG_SIM_THRESH,
        overlap_threshold=5,
    )
    if lane_match_result:
        mask_lanes = create_lane_match_masks(
            img.shape,
            lane_match_result["best_matches"],
            lanes=lane_match_result["lanes"],
        )
        mask_matcher += mask_lanes

annotation = "authentic" if not mask_matcher else mask_matcher
visualize_duplicate_masks(img, mask_matcher, merged_info, show_fallbacks=False)

You can also pass a local checkpoint path instead of a model name:

embedder = Embedder("/path/to/wblot_duplicate_embedder.ckpt", device="cuda", verbose=False)

Available Model Names

• yolo_panel_extractor
• yolo_lane_extractor
• aliked_wblot
• wblot_duplicate_embedder
• wblot_overlap_embedder
• wblot_lane_embedder
• micro_overlap_embedder

Maintainer Notes

Keep checkpoints/ ignored by git. Large .pt, .pth, and .ckpt files should live in GitHub Releases, not in normal repository history.

When a checkpoint changes:

1. Upload the new file to a new GitHub Release tag.
2. Update FORGERYSCOPE_MODEL_BASE_URL to the new release URL.
3. Update the SHA256 value in forgeryscope/model_zoo.py.

Requirements

• Python >= 3.9
• PyTorch >= 1.9.0
• torchvision >= 0.10.0
• OpenCV >= 4.5.0
• Dependencies listed in pyproject.toml

License

This project is licensed under the MIT License. See LICENSE.

Author

Uladzislau Leketush ([e-mail])