ddsimca 1.0.2__tar.gz → 1.1.0__tar.gz

ddsimca-1.1.0/.gitignore

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+__pycache__
+.venv
+.pytest_cache
+.DS_Store
+
+# Claude Code local working files — never push to GitHub/PyPI
+CLAUDE.md
+.claude/

ddsimca-1.1.0/PKG-INFO

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+Metadata-Version: 2.4
+Name: ddsimca
+Version: 1.1.0
+Summary: Implementation of Data Driven SIMCA one class classification method
+Project-URL: Homepage, https://github.com/svkucheryavski/ddsimca
+Project-URL: Documentation, https://github.com/svkucheryavski/ddsimca
+Project-URL: Repository, https://github.com/svkucheryavski/ddsimca
+Project-URL: Bug Tracker, https://github.com/svkucheryavski/ddsimca/issues
+Author-email: Sergey Kucheryavskiy <svkucheryavski@gmail.com>
+License: MIT
+License-File: LICENSE
+Keywords: anomaly-detection,chemometrics,ddsimca,one-class-classification,simca
+Classifier: Development Status :: 4 - Beta
+Classifier: Intended Audience :: Science/Research
+Classifier: License :: OSI Approved :: MIT License
+Classifier: Operating System :: OS Independent
+Classifier: Programming Language :: Python :: 3
+Classifier: Programming Language :: Python :: 3.10
+Classifier: Programming Language :: Python :: 3.11
+Classifier: Programming Language :: Python :: 3.12
+Classifier: Topic :: Scientific/Engineering :: Artificial Intelligence
+Requires-Python: >=3.10
+Requires-Dist: matplotlib>=3.8.0
+Requires-Dist: numpy>=2.0
+Requires-Dist: pandas>=2.2.0
+Requires-Dist: prcv>1.2.0
+Requires-Dist: scipy>=1.6.0
+Provides-Extra: 3way
+Requires-Dist: tensorly<0.10,>=0.9; extra == '3way'
+Provides-Extra: dev
+Requires-Dist: nbval>=0.11.0; extra == 'dev'
+Requires-Dist: pytest>=7.0.0; extra == 'dev'
+Description-Content-Type: text/markdown
+
+# Data Driven SIMCA
+
+The package *ddsimca* implements *Data Driven SIMCA* — a method for creating one-class classification (OCC) models (also known as *anomaly detectors* or *novelty detectors*). The theoretical background and practical examples for the conventional (PCA/SVD-based) DD-SIMCA method are described in [this paper](https://doi.org/10.1002/cem.3556); please cite it when using this package. The paper is freely available via open access. Other papers describing different theoretical aspects of the method are listed in the *References* section below.
+
+The paper shows all examples using the DD-SIMCA web application ([mda.tools/ddsimca](https://mda.tools/ddsimca)). This package implements the same functionality in Python, so you can obtain the same outcomes and similar plots. The package can be installed from [PyPI](https://pypi.org) using `pip` or any other package manager compatible with PyPI, e.g.:
+
+
+```
+pip install ddsimca
+```
+
+It requires `numpy`, `scipy`, `pandas`, `prcv`, and `matplotlib`, which will be installed automatically as dependencies.
+
+Since v. 1.1.0 the package also provides two methods for **3-way (multi-mode) data** — `ddsimca_parafac` and `ddsimca_tucker`. Their theoretical background is described in [this paper](https://doi.org/10.1021/acs.analchem.3c05096).
+
+These two methods rely on an additional library, `tensorly`, which is **not** installed by the standard `pip install ddsimca` command shown above. If you plan to use the 3-way methods, run this instead:
+
+```
+pip install ddsimca[3way]
+```
+
+This installs everything from the standard `ddsimca` plus `tensorly` in one step. If you already have `ddsimca` installed and only want to add 3-way support, run `pip install tensorly` separately.
+
+
+## Getting started
+
+Use the Jupyter notebook [demo.ipynb](https://github.com/svkucheryavski/ddsimca-py/blob/main/demo/demo.ipynb) to get started with the conventional PCA-based DD-SIMCA. To run the examples in this notebook you need to download a zip file with the datasets (the same dataset is used to illustrate the method in the paper). Here is a [direct link](https://mda.tools/ddsimca/Oregano.zip) to the archive.
+
+Simply download the dataset, unzip it to the same directory as the notebook, and follow the guidelines. The dataset can also be downloaded from GitHub.
+
+
+For 3-way DD-SIMCA, use the Jupyter notebook [demo_3way.ipynb](https://github.com/svkucheryavski/ddsimca-py/blob/main/demo/demo_3way.ipynb). It assumes you already know how conventional DD-SIMCA works. The dataset for this notebook can be downloaded from [here](https://github.com/svkucheryavski/ddsimca-py/blob/main/demo/simdata.mat). It is a MATLAB data file (.mat) with simulated data, kindly prepared and shared by Alejandro Olivieri. The notebook explains how to load the data.
+
+Both notebooks are also available as PDF files with all plots and outputs: [demo.pdf](https://github.com/svkucheryavski/ddsimca-py/blob/main/demo/demo.pdf) and [demo_3way.pdf](https://github.com/svkucheryavski/ddsimca-py/blob/main/demo/demo_3way.pdf)
+
+## Releases
+
+**1.1.0** (12/6/2026)
+* added support for custom colors and markers in `plotAcceptance()` and `plotDistance()`.
+* added support for showing log-transformed values in `plotDistance()`.
+* added `ddsimca_parafac` variant for 3-way (multi-mode) data based on PARAFAC decomposition.
+* added `ddsimca_tucker` variant for 3-way (multi-mode) data based on Tucker decomposition.
+* added `demo_3way.ipynb` Jupyter notebook with a user guide for the 3-way methods.
+
+
+**1.0.3** (6/1/2026)
+* small improvements to code.
+* better documentation text.
+
+**1.0.2** (1/1/2026)
+* initial release
+
+
+
+## References
+
+1. S. Kucheryavskiy, O. Rodionova, A. Pomerantsev. *A comprehensive tutorial on Data-Driven SIMCA: Theory and implementation in web*. Journal of Chemometrics, 38 (7), 2024. DOI: [10.1002/cem.3556](http://dx.doi.org/10.1002/cem.3556).
+
+2. A. Pomerantsev, O. Rodionova. *Selectivity in Nontargeted Qualitative Analysis*. Analytica Chimica Acta, 1332, 2024. DOI: [10.1016/j.aca.2024.343352](https://doi.org/10.1016/j.aca.2024.343352).
+
+3. A. Pomerantsev, O. Rodionova. *Popular decision rules in SIMCA: Critical review*. Journal of Chemometrics, 34 (8), 2020. DOI: [10.1002/cem.3250](https://doi.org/10.1002/cem.3250)
+
+4. A. Pomerantsev, O. Rodionova. *On the type II error in SIMCA method*. Journal of Chemometrics, 28 (6), 2014. DOI: [10.1002/cem.2610](https://doi.org/10.1002/cem.2610).
+
+5. A. P. Pagani, G. Camargo, G. A. Ibañez, A. C. Olivieri, A. L. Pomerantsev, O. Ye. Rodionova. *Data-Driven Version of Multiway Soft Independent Modeling of Class Analogy (N-Way DD-SIMCA): Theory and Application*. Analytical Chemistry, 96 (12), 2024. DOI: [10.1021/acs.analchem.3c05096](https://doi.org/10.1021/acs.analchem.3c05096).

ddsimca-1.1.0/README.md

@@ -0,0 +1,65 @@
+# Data Driven SIMCA
+
+The package *ddsimca* implements *Data Driven SIMCA* — a method for creating one-class classification (OCC) models (also known as *anomaly detectors* or *novelty detectors*). The theoretical background and practical examples for the conventional (PCA/SVD-based) DD-SIMCA method are described in [this paper](https://doi.org/10.1002/cem.3556); please cite it when using this package. The paper is freely available via open access. Other papers describing different theoretical aspects of the method are listed in the *References* section below.
+
+The paper shows all examples using the DD-SIMCA web application ([mda.tools/ddsimca](https://mda.tools/ddsimca)). This package implements the same functionality in Python, so you can obtain the same outcomes and similar plots. The package can be installed from [PyPI](https://pypi.org) using `pip` or any other package manager compatible with PyPI, e.g.:
+
+
+```
+pip install ddsimca
+```
+
+It requires `numpy`, `scipy`, `pandas`, `prcv`, and `matplotlib`, which will be installed automatically as dependencies.
+
+Since v. 1.1.0 the package also provides two methods for **3-way (multi-mode) data** — `ddsimca_parafac` and `ddsimca_tucker`. Their theoretical background is described in [this paper](https://doi.org/10.1021/acs.analchem.3c05096).
+
+These two methods rely on an additional library, `tensorly`, which is **not** installed by the standard `pip install ddsimca` command shown above. If you plan to use the 3-way methods, run this instead:
+
+```
+pip install ddsimca[3way]
+```
+
+This installs everything from the standard `ddsimca` plus `tensorly` in one step. If you already have `ddsimca` installed and only want to add 3-way support, run `pip install tensorly` separately.
+
+
+## Getting started
+
+Use the Jupyter notebook [demo.ipynb](https://github.com/svkucheryavski/ddsimca-py/blob/main/demo/demo.ipynb) to get started with the conventional PCA-based DD-SIMCA. To run the examples in this notebook you need to download a zip file with the datasets (the same dataset is used to illustrate the method in the paper). Here is a [direct link](https://mda.tools/ddsimca/Oregano.zip) to the archive.
+
+Simply download the dataset, unzip it to the same directory as the notebook, and follow the guidelines. The dataset can also be downloaded from GitHub.
+
+
+For 3-way DD-SIMCA, use the Jupyter notebook [demo_3way.ipynb](https://github.com/svkucheryavski/ddsimca-py/blob/main/demo/demo_3way.ipynb). It assumes you already know how conventional DD-SIMCA works. The dataset for this notebook can be downloaded from [here](https://github.com/svkucheryavski/ddsimca-py/blob/main/demo/simdata.mat). It is a MATLAB data file (.mat) with simulated data, kindly prepared and shared by Alejandro Olivieri. The notebook explains how to load the data.
+
+Both notebooks are also available as PDF files with all plots and outputs: [demo.pdf](https://github.com/svkucheryavski/ddsimca-py/blob/main/demo/demo.pdf) and [demo_3way.pdf](https://github.com/svkucheryavski/ddsimca-py/blob/main/demo/demo_3way.pdf)
+
+## Releases
+
+**1.1.0** (12/6/2026)
+* added support for custom colors and markers in `plotAcceptance()` and `plotDistance()`.
+* added support for showing log-transformed values in `plotDistance()`.
+* added `ddsimca_parafac` variant for 3-way (multi-mode) data based on PARAFAC decomposition.
+* added `ddsimca_tucker` variant for 3-way (multi-mode) data based on Tucker decomposition.
+* added `demo_3way.ipynb` Jupyter notebook with a user guide for the 3-way methods.
+
+
+**1.0.3** (6/1/2026)
+* small improvements to code.
+* better documentation text.
+
+**1.0.2** (1/1/2026)
+* initial release
+
+
+
+## References
+
+1. S. Kucheryavskiy, O. Rodionova, A. Pomerantsev. *A comprehensive tutorial on Data-Driven SIMCA: Theory and implementation in web*. Journal of Chemometrics, 38 (7), 2024. DOI: [10.1002/cem.3556](http://dx.doi.org/10.1002/cem.3556).
+
+2. A. Pomerantsev, O. Rodionova. *Selectivity in Nontargeted Qualitative Analysis*. Analytica Chimica Acta, 1332, 2024. DOI: [10.1016/j.aca.2024.343352](https://doi.org/10.1016/j.aca.2024.343352).
+
+3. A. Pomerantsev, O. Rodionova. *Popular decision rules in SIMCA: Critical review*. Journal of Chemometrics, 34 (8), 2020. DOI: [10.1002/cem.3250](https://doi.org/10.1002/cem.3250)
+
+4. A. Pomerantsev, O. Rodionova. *On the type II error in SIMCA method*. Journal of Chemometrics, 28 (6), 2014. DOI: [10.1002/cem.2610](https://doi.org/10.1002/cem.2610).
+
+5. A. P. Pagani, G. Camargo, G. A. Ibañez, A. C. Olivieri, A. L. Pomerantsev, O. Ye. Rodionova. *Data-Driven Version of Multiway Soft Independent Modeling of Class Analogy (N-Way DD-SIMCA): Theory and Application*. Analytical Chemistry, 96 (12), 2024. DOI: [10.1021/acs.analchem.3c05096](https://doi.org/10.1021/acs.analchem.3c05096).

ddsimca-1.1.0/ddsimca/__init__.py

@@ -0,0 +1,37 @@
+"""
+DD-SIMCA: one-class classification method
+"""
+
+__version__ = "1.1.0"
+__author__ = "Sergey Kucheryavskiy"
+__email__ = "svkucheryavski@gmail.com"
+
+from .ddsimca import (
+    DDSIMCA, DDSIMCARes, ddsimca,
+    get_distparams, get_limits, process_members, process_strangers,
+    COLORS_FOMS, COLORS_ROLES, COLORS_DECISIONS,
+    MARKERS_ROLES, MARKERS_DECISIONS,
+)
+
+__all__ = [
+    "DDSIMCA", "DDSIMCARes", "ddsimca",
+    "get_distparams", "get_limits", "process_members", "process_strangers",
+    "COLORS_FOMS", "COLORS_ROLES", "COLORS_DECISIONS",
+    "MARKERS_ROLES", "MARKERS_DECISIONS",
+]
+
+# PARAFAC and Tucker variants — both require tensorly (install with:
+# pip install ddsimca[3way]). The tensorly imports are lazy inside each
+# variant's train(), so this module imports cleanly without tensorly.
+# The guard below is narrow defense-in-depth for the case where someone
+# reintroduces an import-time tensorly dependency in one of the variant
+# modules; arbitrary ImportError still propagates so real bugs are not
+# masked.
+try:
+    from ddsimca.ddsimca_parafac import DDSIMCAParafac, ddsimca_parafac
+    from ddsimca.ddsimca_tucker import DDSIMCATucker, ddsimca_tucker
+    __all__ = list(__all__) + ["DDSIMCAParafac", "ddsimca_parafac",
+                               "DDSIMCATucker", "ddsimca_tucker"]
+except ModuleNotFoundError as _err:
+    if _err.name != "tensorly":
+        raise