fiducio 0.1.0__tar.gz

fiducio-0.1.0/.python-version

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+3.12

fiducio-0.1.0/CHANGELOG.md

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+# Changelog
+
+All notable changes to this project are documented in this file.
+
+The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.1.0/),
+and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
+
+## [Unreleased]
+
+## [0.1.0] - 2026-09-21
+
+First public beta release. It accompanies the paper *Rethinking Post-Hoc
+Calibration in Semantic Segmentation* (Transactions on Machine Learning Research).
+
+### Added
+
+- Model-agnostic `Calibrator` API with a consistent
+  `fit` / `transform` / `predict_proba` / `fit_transform` / `decision_function` /
+  `save` interface and a top-level `load_calibrator` loader. `transform` and
+  `decision_function` run under `torch.no_grad()`.
+- Support for 2D `(B, C, H, W)`, 3D `(B, C, D, H, W)` and general
+  `(B, C, *spatial)` inputs, with logits **or** probabilities, masks and
+  `ignore_index`.
+- Calibrators, with the paper's shorthand as aliases:
+  - `TemperatureScaling` (`TS`), `EnsembleTemperatureScaling` (`ETS`),
+    `VectorScaling` (`VS`), `MatrixScaling` (`MS`), `DirichletCalibration` (`DC`);
+  - `TranslationInvariantMatrixScaling` (`MSc`): optimizes `C-1` free columns and
+    a common row sum, reconstructs the last column and regularizes the
+    reconstructed matrix;
+  - `ClassConditionalMatrixScaling` (`CMS`, `CDC`), `ArgmaxPreservingMatrixScaling`
+    (`CMSAP`, `CMSap`) and `OrderPreservingMatrixScaling` (`CMSOP`, `CMSop`):
+    one affine map per uncalibrated top class. All experts are optimized
+    **jointly** by default (one optimizer, one cross-entropy loss over every
+    voxel, regularization averaged across experts in the common logit space, as
+    in the paper); `independent_experts=True` fits each expert in its own loop.
+- Configurable optimizer on every calibrator: `optimizer="adam"` (default) or
+  `optimizer="lbfgs"`, with per-optimizer `lr` / `max_iter` defaults; a
+  non-positive `max_iter` is rejected.
+- Validation-based early stopping (`patience`, `min_delta`, `lr_patience`,
+  `lr_factor`; Adam only) with `fit(..., val_predictions=, val_targets=,
+  val_mask=)`: the iterate with the best validation NLL is kept, and the
+  learning rate can decay on plateaus.
+- Calibration metrics: negative log-likelihood, expected calibration error
+  (ECE), average calibration error (ACE, unweighted over non-empty bins),
+  multiclass Brier score and `reliability_curve` / `ReliabilityCurve`.
+- Optional plotting: `fiducio.plots.reliability_diagram` (matplotlib,
+  lazy-imported, `[plots]` extra; `metric="ece"|"ace"|None`).
+- Helpers: `two_channel_from_binary` (single-channel sigmoid → two channels) and
+  `get_calibrator_class` (build a calibrator from its registered id).
+- Registry-backed persistence (`save` / `load_calibrator`) that loads on CPU by
+  default, accepts `map_location`, avoids importing arbitrary module paths, and
+  warns on a major-version mismatch.
+- Synthetic numerical references for MS, MSc, CDC, CMSap and CMSop against the
+  research implementation, an ensemble-pooling example and a paper
+  implementation guide (`reproducibility/`).
+- Documentation (MkDocs Material), runnable CPU examples, a README with a
+  reliability figure (`examples/readme_figure.py`), locked uv development
+  environments and a CI matrix for Python 3.10, 3.11 and 3.12.
+
+[Unreleased]: https://github.com/fiducio-ai/Fiducio/compare/v0.1.0...HEAD
+[0.1.0]: https://github.com/fiducio-ai/Fiducio/releases/tag/v0.1.0

fiducio-0.1.0/CITATION.cff

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+cff-version: 1.2.0
+message: "If you use Fiducio in your research, please cite the paper below."
+title: "Fiducio: Model-agnostic post-hoc calibration for 2D and 3D semantic segmentation"
+version: "0.1.0"
+date-released: "2026-09-21"
+authors:
+  - name: "Fiducio maintainers (fiducio-ai)"
+repository-code: "https://github.com/fiducio-ai/Fiducio"
+url: "https://fiducio-ai.github.io/Fiducio/"
+license: "Apache-2.0"
+type: software
+keywords:
+  - calibration
+  - semantic segmentation
+  - uncertainty
+  - pytorch
+abstract: >
+  Fiducio is a model-agnostic Python library for post-hoc calibration of 2D and
+  3D semantic segmentation models. It provides a consistent fit / transform API
+  for temperature, vector, matrix, Dirichlet and class-conditional matrix scaling
+  calibrators that operate on logits or probabilities produced by any segmentation
+  model.
+preferred-citation:
+  type: article
+  title: "Rethinking Post-Hoc Calibration in Semantic Segmentation"
+  authors:
+    - given-names: "Tristan"
+      family-names: "Kirscher"
+    - given-names: "Kim-Celine"
+      family-names: "Kahl"
+    - given-names: "Balint"
+      family-names: "Kovacs"
+    - given-names: "Maximilian R."
+      family-names: "Rokuss"
+    - given-names: "Klaus"
+      family-names: "Maier-Hein"
+    - given-names: "Xavier"
+      family-names: "Coubez"
+    - given-names: "Philippe"
+      family-names: "Meyer"
+    - given-names: "Sylvain"
+      family-names: "Faisan"
+  journal: "Transactions on Machine Learning Research"
+  issn: "2835-8856"
+  year: 2026
+  month: 9
+  url: "https://openreview.net/forum?id=xwNoSNxgxV"
+  identifiers:
+    - type: url
+      value: "https://arxiv.org/abs/2607.01902"
+      description: "arXiv preprint (arXiv:2607.01902)"

fiducio-0.1.0/LICENSE

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fiducio-0.1.0/MANIFEST.in

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+include CITATION.cff CHANGELOG.md mkdocs.yml
+include uv.lock .python-version
+recursive-include tests *.py *.json
+recursive-include reproducibility *.py *.md
+recursive-include docs *.md
+recursive-include examples *.py

fiducio-0.1.0/PKG-INFO

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+Metadata-Version: 2.4
+Name: fiducio
+Version: 0.1.0
+Summary: Model-agnostic post-hoc calibration for 2D and 3D semantic segmentation
+Author: Fiducio maintainers (fiducio-ai)
+Maintainer: fiducio-ai
+License-Expression: Apache-2.0
+Project-URL: Homepage, https://github.com/fiducio-ai/Fiducio
+Project-URL: Documentation, https://fiducio-ai.github.io/Fiducio/
+Project-URL: Repository, https://github.com/fiducio-ai/Fiducio
+Project-URL: Issues, https://github.com/fiducio-ai/Fiducio/issues
+Project-URL: Changelog, https://github.com/fiducio-ai/Fiducio/blob/main/CHANGELOG.md
+Keywords: calibration,post-hoc calibration,semantic segmentation,uncertainty,temperature scaling,matrix scaling,dirichlet calibration,pytorch
+Classifier: Development Status :: 4 - Beta
+Classifier: Intended Audience :: Science/Research
+Classifier: Programming Language :: Python :: 3
+Classifier: Programming Language :: Python :: 3.10
+Classifier: Programming Language :: Python :: 3.11
+Classifier: Programming Language :: Python :: 3.12
+Classifier: Operating System :: OS Independent
+Classifier: Topic :: Scientific/Engineering :: Artificial Intelligence
+Classifier: Typing :: Typed
+Requires-Python: >=3.10
+Description-Content-Type: text/markdown
+License-File: LICENSE
+Requires-Dist: numpy>=1.22
+Requires-Dist: torch>=2.0
+Provides-Extra: plots
+Requires-Dist: matplotlib>=3.5; extra == "plots"
+Provides-Extra: docs
+Requires-Dist: mkdocs>=1.6; extra == "docs"
+Requires-Dist: mkdocs-material>=9.5; extra == "docs"
+Requires-Dist: mkdocstrings[python]>=0.30; extra == "docs"
+Provides-Extra: dev
+Requires-Dist: fiducio[plots]; extra == "dev"
+Requires-Dist: pytest>=8.0; extra == "dev"
+Requires-Dist: pytest-cov>=4.0; extra == "dev"
+Requires-Dist: ruff>=0.4.0; extra == "dev"
+Requires-Dist: mypy>=1.11; extra == "dev"
+Requires-Dist: build>=1.0; extra == "dev"
+Provides-Extra: all
+Requires-Dist: fiducio[plots]; extra == "all"
+Requires-Dist: fiducio[docs]; extra == "all"
+Requires-Dist: fiducio[dev]; extra == "all"
+Dynamic: license-file
+
+# Fiducio
+
+[![Tests](https://github.com/fiducio-ai/Fiducio/actions/workflows/tests.yml/badge.svg)](https://github.com/fiducio-ai/Fiducio/actions/workflows/tests.yml)
+[![Docs](https://github.com/fiducio-ai/Fiducio/actions/workflows/docs.yml/badge.svg)](https://fiducio-ai.github.io/Fiducio/)
+[![Python](https://img.shields.io/badge/python-3.10%20%7C%203.11%20%7C%203.12-blue)](https://www.python.org/)
+[![License](https://img.shields.io/badge/license-Apache--2.0-green)](https://github.com/fiducio-ai/Fiducio/blob/main/LICENSE)
+
+**Fiducio** is a model-agnostic Python library of **post-hoc calibrators for 2D
+and 3D semantic segmentation**. Give it the logits or probabilities of any
+segmentation model and a labelled calibration set, and a calibrator returns
+better-calibrated probabilities without retraining the segmentation model.
+It implements temperature, vector, matrix and Dirichlet scaling, their
+translation-invariant variants, and the class-conditional (CDC, CMSap, CMSop)
+calibrators introduced in our paper
+[*Rethinking Post-Hoc Calibration in Semantic Segmentation*](https://arxiv.org/abs/2607.01902),
+accepted at TMLR. Whether the segmentation is preserved depends on the
+calibrator; see the guarantees below.
+
+It works with PyTorch U-Net, nnU-Net, SegFormer or any model that produces
+logits: Fiducio only ever sees `(B, C, *spatial)` tensors and never needs to know
+the architecture.
+
+![Reliability diagrams of an over-confident model before and after calibration with TemperatureScaling and CMSop](https://raw.githubusercontent.com/fiducio-ai/Fiducio/main/docs/assets/reliability_before_after.png)
+
+*Top-1 reliability diagrams on held-out synthetic data (regenerate with
+[`examples/readme_figure.py`](https://github.com/fiducio-ai/Fiducio/blob/main/examples/readme_figure.py)).*
+
+## Install
+
+For development from a checkout, use the committed uv lockfile:
+
+```bash
+uv sync --locked
+uv run --no-sync pytest
+```
+
+This uses CPU PyTorch for development. See [CONTRIBUTING.md](https://github.com/fiducio-ai/Fiducio/blob/main/CONTRIBUTING.md)
+for the pinned uv version, documentation and build commands.
+
+For an existing uv application before the first PyPI release:
+
+```bash
+uv add "fiducio @ git+https://github.com/fiducio-ai/Fiducio.git"
+```
+
+Once a PyPI release is available, the standard installation is:
+
+```bash
+pip install fiducio
+```
+
+With pip, before the first PyPI release, install from GitHub:
+
+```bash
+pip install "git+https://github.com/fiducio-ai/Fiducio.git"
+```
+
+The core install depends only on `numpy` and `torch`. Optional extras:
+`fiducio[plots]` (matplotlib reliability diagrams), `fiducio[docs]`,
+`fiducio[dev]`, `fiducio[all]`.
+
+## Quick start
+
+```python
+import torch
+from fiducio import TemperatureScaling, load_calibrator
+
+# From a held-out, labelled calibration set:
+logits = torch.randn(8, 4, 64, 64)          # (B, C, H, W) model logits
+labels = torch.randint(0, 4, (8, 64, 64))   # (B, H, W) labels
+
+calibrator = TemperatureScaling(input_type="logits").fit(logits, labels)
+
+# Apply to new predictions (returns calibrated probabilities):
+probs = calibrator.transform(torch.randn(2, 4, 64, 64))
+
+# Save and reload (loads on CPU by default):
+calibrator.save("calibrator.pt")
+calibrator = load_calibrator("calibrator.pt")
+```
+
+Every calibrator exposes the same API:
+`fit(predictions, targets, mask=None)`, `transform`, `predict_proba`,
+`fit_transform`, `save`, and the top-level `load_calibrator`.
+
+## Accepted tensor shapes
+
+The class axis is **always** dimension 1.
+
+| Use case | `predictions` | `targets` |
+|----------|---------------|-----------|
+| 2D segmentation | `(B, C, H, W)` | `(B, H, W)` |
+| 3D segmentation | `(B, C, D, H, W)` | `(B, D, H, W)` |
+| general n-D | `(B, C, *spatial)` | `(B, *spatial)` |
+| per-pixel table | `(N, C)` | `(N,)` |
+
+Inputs may be `logits` or `probs` (set `input_type`). Binary segmentation is two
+channels (`C = 2`). `mask` and `ignore_index` exclude voxels from fitting.
+
+## Calibrators
+
+| Class | Alias | Translation-invariant | Decision preservation |
+|-------|-------|:---------------------:|-----------------------|
+| `TemperatureScaling` | `TS` | yes | argmax and full order |
+| `EnsembleTemperatureScaling` | `ETS` | yes | argmax and full order |
+| `VectorScaling` | `VS` | no | — |
+| `MatrixScaling` | `MS` | no | — |
+| `TranslationInvariantMatrixScaling` | `MSc` | yes | — |
+| `DirichletCalibration` | `DC` | yes | — |
+| `ClassConditionalMatrixScaling` | `CMS` / `CDC` | yes | — |
+| `ArgmaxPreservingMatrixScaling` | `CMSAP` / `CMSap` | yes | argmax |
+| `OrderPreservingMatrixScaling` | `CMSOP` / `CMSop` | yes | argmax and full order |
+
+Translation-invariant means the output is unchanged when the same constant is
+added to every input logit of a voxel.
+
+Every calibrator also exposes `decision_function` (calibrated logits) and a
+configurable `optimizer` (`"adam"` default, or `"lbfgs"`).
+
+### Early stopping
+
+Adam-fitted calibrators support the paper's recipe of early stopping on a
+validation set (with an optional learning-rate decay on plateaus):
+
+```python
+from fiducio import OrderPreservingMatrixScaling
+
+calibrator = OrderPreservingMatrixScaling(max_iter=2000, patience=20, lr_patience=10)
+calibrator.fit(
+    logits, labels,
+    val_predictions=val_logits, val_targets=val_labels,  # held out from both
+)
+```
+
+The iterate with the best validation NLL is kept. The default fixed budget
+(`max_iter`) is short, so it can underfit expressive calibrators; prefer a larger
+`max_iter` together with `patience` for CDC, CMSap and CMSop.
+
+### Paper method mapping
+
+| Paper method | Class |
+|--------------|-------|
+| TS | `TemperatureScaling` |
+| MS | `MatrixScaling` |
+| MSc | `TranslationInvariantMatrixScaling` |
+| CDC | `ClassConditionalMatrixScaling` |
+| CMSap | `ArgmaxPreservingMatrixScaling` |
+| CMSop | `OrderPreservingMatrixScaling` |
+
+CDC, CMSap and CMSop are class-conditional: they fit one affine map per
+uncalibrated top class, all experts optimized **jointly** by a single
+optimizer minimizing one cross-entropy loss over every voxel at once, with L2
+regularization (`lambda_reg` / `mu_reg`) applied to the affine map induced in
+the common *logit* space rather than to the raw per-expert parameters — this
+keeps the regularization meaningful for CMSap/CMSop, whose parameters are
+non-negative margins/gaps rather than raw matrix entries. Pass
+`independent_experts=True` to instead fit each expert in its own optimization
+loop on only the voxels routed to it.
+
+Calibration metrics are included: `negative_log_likelihood`,
+`expected_calibration_error` (ECE, population-weighted), `average_calibration_error`
+(ACE, unweighted over the same bins — doesn't let a sparsely populated bin get
+drowned out by a large one), `brier_score`, `reliability_curve`, plus an
+optional reliability-diagram plot (`fiducio.plots.reliability_diagram`, needs
+`fiducio[plots]`).
+
+## Documentation
+
+The [paper implementation guide](https://github.com/fiducio-ai/Fiducio/blob/main/reproducibility/README.md) records method
+mapping, numerical-reference coverage, fitting limits and the remaining steps
+needed to reproduce the paper's experiments. For ensemble inputs, see
+[`examples/ensemble_pooling.py`](https://github.com/fiducio-ai/Fiducio/blob/main/examples/ensemble_pooling.py).
+
+### Results in the paper
+
+The paper compares these calibrators on real segmentation benchmarks. The
+reliability diagrams below (paper appendix) show the uncalibrated ensemble
+pooling (`p0`, `p̄`) against the best calibrator per dataset; the exact
+protocol, datasets and metrics are in the paper. This repository ships the
+calibrators, not the fitted models or benchmark pipelines, so it does not
+regenerate these figures (see the
+[implementation guide](https://github.com/fiducio-ai/Fiducio/blob/main/reproducibility/README.md)).
+
+![Reliability diagrams from the paper on three datasets](https://raw.githubusercontent.com/fiducio-ai/Fiducio/main/docs/assets/paper_reliability.png)
+
+Full guide and API reference: **https://fiducio-ai.github.io/Fiducio/**
+
+- [Installation](https://fiducio-ai.github.io/Fiducio/installation/)
+- [Quickstart](https://fiducio-ai.github.io/Fiducio/quickstart/)
+- [Concepts](https://fiducio-ai.github.io/Fiducio/concepts/)
+- [Calibrators](https://fiducio-ai.github.io/Fiducio/calibrators/)
+- [Examples](https://fiducio-ai.github.io/Fiducio/examples/)
+
+## Citation
+
+Fiducio accompanies the paper *Rethinking Post-Hoc Calibration in Semantic
+Segmentation* (Kirscher et al., Transactions on Machine Learning Research, 2026;
+[OpenReview](https://openreview.net/forum?id=xwNoSNxgxV), preprint: [arXiv:2607.01902](https://arxiv.org/abs/2607.01902)).
+If you use Fiducio in your research, please cite it using the metadata in
+[`CITATION.cff`](https://github.com/fiducio-ai/Fiducio/blob/main/CITATION.cff), or:
+
+```bibtex
+@article{kirscher2026rethinking,
+  title   = {Rethinking Post-Hoc Calibration in Semantic Segmentation},
+  author  = {Kirscher, Tristan and Kahl, Kim-Celine and Kovacs, Balint and
+             Rokuss, Maximilian and Maier-Hein, Klaus and Coubez, Xavier and
+             Meyer, Philippe and Faisan, Sylvain},
+  journal = {Transactions on Machine Learning Research},
+  issn    = {2835-8856},
+  year    = {2026},
+  url     = {https://openreview.net/forum?id=xwNoSNxgxV}
+}
+```
+
+## Status
+
+Fiducio is **beta** (`0.x`): usable and tested, with an API that may still change
+before `1.0`. It is not certified for safety-critical or clinical use.
+
+## License
+
+[Apache-2.0](https://github.com/fiducio-ai/Fiducio/blob/main/LICENSE).