sigima 0.0.1.dev0__tar.gz → 1.0.4__tar.gz

{sigima-0.0.1.dev0 → sigima-1.0.4}/LICENSE

@@ -1,29 +1,29 @@
-BSD 3-Clause License
-
-Copyright (c) 2023, DataLab Platform Developers.
-All rights reserved.
-
-Redistribution and use in source and binary forms, with or without
-modification, are permitted provided that the following conditions are met:
-
-1. Redistributions of source code must retain the above copyright notice, this
-   list of conditions and the following disclaimer.
-
-2. Redistributions in binary form must reproduce the above copyright notice,
-   this list of conditions and the following disclaimer in the documentation
-   and/or other materials provided with the distribution.
-
-3. Neither the name of the copyright holder nor the names of its
-   contributors may be used to endorse or promote products derived from
-   this software without specific prior written permission.
-
-THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
-AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
-IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
-DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE
-FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
-DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
-SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
-CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
-OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
-OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+BSD 3-Clause License
+
+Copyright (c) 2023, DataLab Platform Developers.
+All rights reserved.
+
+Redistribution and use in source and binary forms, with or without
+modification, are permitted provided that the following conditions are met:
+
+1. Redistributions of source code must retain the above copyright notice, this
+   list of conditions and the following disclaimer.
+
+2. Redistributions in binary form must reproduce the above copyright notice,
+   this list of conditions and the following disclaimer in the documentation
+   and/or other materials provided with the distribution.
+
+3. Neither the name of the copyright holder nor the names of its
+   contributors may be used to endorse or promote products derived from
+   this software without specific prior written permission.
+
+THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE
+FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
+SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
+OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
+OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.

sigima-1.0.4/MANIFEST.in

@@ -0,0 +1,3 @@
+graft doc
+include CONTRIBUTING.md
+include requirements.txt

sigima-1.0.4/PKG-INFO

@@ -0,0 +1,261 @@
+Metadata-Version: 2.4
+Name: sigima
+Version: 1.0.4
+Summary: Scientific computing engine for 1D signals and 2D images, part of the DataLab open-source platform.
+Author-email: Pierre Raybaut <p.raybaut@codra.fr>
+Maintainer-email: DataLab Platform Developers <p.raybaut@codra.fr>
+License: BSD 3-Clause License
+        
+        Copyright (c) 2023, DataLab Platform Developers.
+        All rights reserved.
+        
+        Redistribution and use in source and binary forms, with or without
+        modification, are permitted provided that the following conditions are met:
+        
+        1. Redistributions of source code must retain the above copyright notice, this
+           list of conditions and the following disclaimer.
+        
+        2. Redistributions in binary form must reproduce the above copyright notice,
+           this list of conditions and the following disclaimer in the documentation
+           and/or other materials provided with the distribution.
+        
+        3. Neither the name of the copyright holder nor the names of its
+           contributors may be used to endorse or promote products derived from
+           this software without specific prior written permission.
+        
+        THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+        AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+        IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+        DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE
+        FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+        DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
+        SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+        CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
+        OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
+        OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+        
+Project-URL: Homepage, https://github.com/DataLab-Platform/Sigima
+Project-URL: Documentation, https://sigima.readthedocs.io/
+Classifier: Development Status :: 4 - Beta
+Classifier: Intended Audience :: Developers
+Classifier: Intended Audience :: Education
+Classifier: Intended Audience :: Science/Research
+Classifier: Intended Audience :: End Users/Desktop
+Classifier: Operating System :: MacOS :: MacOS X
+Classifier: Operating System :: Microsoft :: Windows :: Windows 7
+Classifier: Operating System :: Microsoft :: Windows :: Windows 8
+Classifier: Operating System :: Microsoft :: Windows :: Windows 10
+Classifier: Operating System :: Microsoft :: Windows :: Windows 11
+Classifier: Operating System :: POSIX :: Linux
+Classifier: Programming Language :: Python :: 3.9
+Classifier: Programming Language :: Python :: 3.10
+Classifier: Programming Language :: Python :: 3.11
+Classifier: Programming Language :: Python :: 3.12
+Classifier: Programming Language :: Python :: 3.13
+Classifier: Topic :: Scientific/Engineering
+Classifier: Topic :: Scientific/Engineering :: Image Processing
+Classifier: Topic :: Software Development :: Libraries :: Python Modules
+Requires-Python: <4,>=3.9
+Description-Content-Type: text/markdown
+License-File: LICENSE
+Requires-Dist: guidata>=3.13
+Requires-Dist: NumPy>=1.22
+Requires-Dist: SciPy>=1.10.1
+Requires-Dist: scikit-image>=0.19.2
+Requires-Dist: pandas>=1.4
+Requires-Dist: PyWavelets>=1.2
+Requires-Dist: packaging>=21.3
+Requires-Dist: typing-extensions>=4.0
+Requires-Dist: makefun>=1.13.1
+Provides-Extra: opencv
+Requires-Dist: opencv-python-headless>=4.8.1.78; extra == "opencv"
+Provides-Extra: dev
+Requires-Dist: build; extra == "dev"
+Requires-Dist: babel; extra == "dev"
+Requires-Dist: ruff; extra == "dev"
+Requires-Dist: pylint; extra == "dev"
+Requires-Dist: Coverage; extra == "dev"
+Requires-Dist: pre-commit; extra == "dev"
+Provides-Extra: doc
+Requires-Dist: sphinx; extra == "doc"
+Requires-Dist: sphinx-gallery; extra == "doc"
+Requires-Dist: sphinx_intl; extra == "doc"
+Requires-Dist: myst_parser; extra == "doc"
+Requires-Dist: sphinx_design; extra == "doc"
+Requires-Dist: sphinx-copybutton; extra == "doc"
+Requires-Dist: pydata-sphinx-theme; extra == "doc"
+Requires-Dist: qtpy; extra == "doc"
+Requires-Dist: PyQt5; extra == "doc"
+Requires-Dist: plotpy; extra == "doc"
+Requires-Dist: opencv-python-headless>=4.8.1.78; extra == "doc"
+Provides-Extra: test
+Requires-Dist: pytest; extra == "test"
+Requires-Dist: pytest-xvfb; extra == "test"
+Provides-Extra: qt
+Requires-Dist: qtpy; extra == "qt"
+Requires-Dist: PyQt5; extra == "qt"
+Requires-Dist: plotpy; extra == "qt"
+Dynamic: license-file
+
+# Sigima - Scientific Image and Signal Processing Library
+
+![Sigima](https://raw.githubusercontent.com/DataLab-Platform/Sigima/main/doc/images/Sigima-Banner.svg)
+
+[![license](https://img.shields.io/pypi/l/sigima.svg)](./LICENSE)
+[![pypi version](https://img.shields.io/pypi/v/sigima.svg)](https://pypi.org/project/sigima/)
+[![PyPI status](https://img.shields.io/pypi/status/sigima.svg)](https://github.com/DataLab-Platform/Sigima)
+[![PyPI pyversions](https://img.shields.io/pypi/pyversions/sigima.svg)](https://pypi.org/project/sigima/)
+
+**Sigima** is an **open-source Python library for scientific image and signal processing**,
+designed as a modular and testable foundation for building advanced analysis pipelines.
+
+🔬 Developed by the [DataLab Platform Developers](https://github.com/DataLab-Platform), Sigima powers the computation backend of [DataLab](https://datalab-platform.com/).
+
+## 🌟 Project & Sponsors
+
+| Project/Sponsor     | Description |
+|---------------------|-------------|
+| <a href="https://datalab-platform.com/"><img src="https://raw.githubusercontent.com/DataLab-Platform/DataLab/main/resources/DataLab-Banner.svg" alt="DataLab logo" style="height:80px;"/></a> | Open-source platform for scientific signal and image processing, powered by Sigima. |
+| <a href="https://nlnet.nl/"><img src="https://nlnet.nl/logo/banner.svg" alt="NLnet logo" style="height:80px;width:209px;"/></a> | European non-profit supporting open-source and internet projects. Sigima has received funding from NLnet for its development, through the DataLab project. |
+
+---
+
+## ✨ Highlights
+
+- Unified processing model for **1D signals** and **2D images**
+- Works with **object-oriented wrappers** (`SignalObj`, `ImageObj`) extending NumPy arrays
+- Includes common processing tasks: filtering, smoothing, binning, thresholding, labeling, etc.
+- Structured for **testability**, **modularity**, and **headless usage**
+- 100% **independent of GUI frameworks** (no Qt/PlotPyStack dependencies)
+
+---
+
+## 💡 Use cases
+
+Sigima is meant to be:
+
+- A **processing backend** for scientific/industrial tools
+- A library to **build reproducible analysis pipelines**
+- A component for **headless automation or remote execution**
+- A testbed for **developing and validating new signal/image operations**
+
+---
+
+## 📖 Design Philosophy
+
+The main goal of **Sigima** is to provide a unified, high-level API for handling and processing **1D signals** and **2D images**, through dedicated Python objects: `SignalObj` and `ImageObj`.
+
+The library is organized to separate concerns clearly:
+
+- `sigima.objects`: defines the object model for signals and images.
+- `sigima.params`: contains parameter classes for configuring processing functions.
+- `sigima.proc`: provides high-level processing functions that operate directly on `SignalObj` and `ImageObj` instances.
+- `sigima.io`: handles input/output operations (CSV files, image formats, etc.) for signals and images.
+- `sigima.tools`: contains **low-level, NumPy-based functions** that implement the core logic behind many processing routines.
+
+This structure supports a **layered programming model**:
+
+- Developers can use `computation` to process full signal/image objects in an object-oriented manner.
+- Or they can directly use `tools` to process raw NumPy arrays — for instance, in custom tools or when integrating Sigima into other projects.
+
+> ⚠️ `sigima.tools` is not intended as a general-purpose NumPy extension. Its purpose is to **fill in the gaps** of common scientific libraries (NumPy, SciPy, scikit-image, etc.), offering consistent tools for signal/image processing in the context of Sigima and similar projects.
+
+---
+
+## Usage Outside Sigima
+
+Although Sigima is designed primarily for object-based processing, some of its core functions are useful on their own.
+
+For instance, the [DataLab](https://datalab-platform.com) project — an open-source platform for signal/image processing — uses many functions from `sigima.tools` independently of the object model. This demonstrates how `sigima.tools` can serve as a **lightweight utility layer** in scientific and industrial Python applications, even when the object model is not used directly.
+
+To maintain this flexibility and avoid confusion, the distinction between `tools` (array-based) and `computation` (object-based) is intentional and explicit.
+
+---
+
+## 📦 Installation
+
+```bash
+pip install sigima
+```
+
+Or in a development environment:
+
+```bash
+git clone https://github.com/DataLab-Platform/Sigima.git
+cd Sigima
+pip install -e .
+```
+
+---
+
+## 📚 Documentation
+
+📖 Full documentation (in progress) is available at:
+👉 <https://sigima.readthedocs.io/>
+
+> Want to use Sigima inside DataLab with GUI tools?
+> Check out the full platform: [DataLab](https://datalab-platform.com/)
+
+---
+
+## ⚙️ Architecture
+
+Sigima is organized by data type:
+
+```text
+sigima/
+├── tools/      # Low-level NumPy-based algorithms supporting some computation functions
+├── proc/       # High-level processing functions operating on SignalObj/ImageObj
+│   ├── base/   # Common processing functions
+│   ├── signal/ # 1D signal processing
+│   └── image/  # 2D image processing
+```
+
+Each domain provides:
+
+- Low-level functions operating on NumPy arrays
+- High-level functions operating on `SignalObj` or `ImageObj`
+
+---
+
+## 🧪 Testing
+
+Sigima comes with unit tests based on `pytest`.
+
+To run all tests:
+
+```bash
+pytest
+```
+
+To run GUI-assisted validation tests (optional):
+
+```bash
+pytest --gui
+```
+
+---
+
+## 🧠 License
+
+Sigima is distributed under the terms of the BSD 3-Clause license.
+See [LICENSE](./LICENSE) for details.
+
+---
+
+## 🤝 Contributing
+
+Bug reports, feature requests and pull requests are welcome!
+See the [CONTRIBUTING](https://datalab-platform.com/en/contributing) guide to get started.
+
+---
+
+![Python](https://raw.githubusercontent.com/DataLab-Platform/DataLab/main/doc/images/logos/Python.png)
+![NumPy](https://raw.githubusercontent.com/DataLab-Platform/DataLab/main/doc/images/logos/NumPy.png)
+![SciPy](https://raw.githubusercontent.com/DataLab-Platform/DataLab/main/doc/images/logos/SciPy.png)
+![scikit-image](https://raw.githubusercontent.com/DataLab-Platform/DataLab/main/doc/images/logos/scikit-image.png)
+![OpenCV](https://raw.githubusercontent.com/DataLab-Platform/DataLab/main/doc/images/logos/OpenCV.png)
+
+---
+
+© DataLab Platform Developers

sigima-1.0.4/README.md

@@ -0,0 +1,162 @@
+# Sigima - Scientific Image and Signal Processing Library
+
+![Sigima](https://raw.githubusercontent.com/DataLab-Platform/Sigima/main/doc/images/Sigima-Banner.svg)
+
+[![license](https://img.shields.io/pypi/l/sigima.svg)](./LICENSE)
+[![pypi version](https://img.shields.io/pypi/v/sigima.svg)](https://pypi.org/project/sigima/)
+[![PyPI status](https://img.shields.io/pypi/status/sigima.svg)](https://github.com/DataLab-Platform/Sigima)
+[![PyPI pyversions](https://img.shields.io/pypi/pyversions/sigima.svg)](https://pypi.org/project/sigima/)
+
+**Sigima** is an **open-source Python library for scientific image and signal processing**,
+designed as a modular and testable foundation for building advanced analysis pipelines.
+
+🔬 Developed by the [DataLab Platform Developers](https://github.com/DataLab-Platform), Sigima powers the computation backend of [DataLab](https://datalab-platform.com/).
+
+## 🌟 Project & Sponsors
+
+| Project/Sponsor     | Description |
+|---------------------|-------------|
+| <a href="https://datalab-platform.com/"><img src="https://raw.githubusercontent.com/DataLab-Platform/DataLab/main/resources/DataLab-Banner.svg" alt="DataLab logo" style="height:80px;"/></a> | Open-source platform for scientific signal and image processing, powered by Sigima. |
+| <a href="https://nlnet.nl/"><img src="https://nlnet.nl/logo/banner.svg" alt="NLnet logo" style="height:80px;width:209px;"/></a> | European non-profit supporting open-source and internet projects. Sigima has received funding from NLnet for its development, through the DataLab project. |
+
+---
+
+## ✨ Highlights
+
+- Unified processing model for **1D signals** and **2D images**
+- Works with **object-oriented wrappers** (`SignalObj`, `ImageObj`) extending NumPy arrays
+- Includes common processing tasks: filtering, smoothing, binning, thresholding, labeling, etc.
+- Structured for **testability**, **modularity**, and **headless usage**
+- 100% **independent of GUI frameworks** (no Qt/PlotPyStack dependencies)
+
+---
+
+## 💡 Use cases
+
+Sigima is meant to be:
+
+- A **processing backend** for scientific/industrial tools
+- A library to **build reproducible analysis pipelines**
+- A component for **headless automation or remote execution**
+- A testbed for **developing and validating new signal/image operations**
+
+---
+
+## 📖 Design Philosophy
+
+The main goal of **Sigima** is to provide a unified, high-level API for handling and processing **1D signals** and **2D images**, through dedicated Python objects: `SignalObj` and `ImageObj`.
+
+The library is organized to separate concerns clearly:
+
+- `sigima.objects`: defines the object model for signals and images.
+- `sigima.params`: contains parameter classes for configuring processing functions.
+- `sigima.proc`: provides high-level processing functions that operate directly on `SignalObj` and `ImageObj` instances.
+- `sigima.io`: handles input/output operations (CSV files, image formats, etc.) for signals and images.
+- `sigima.tools`: contains **low-level, NumPy-based functions** that implement the core logic behind many processing routines.
+
+This structure supports a **layered programming model**:
+
+- Developers can use `computation` to process full signal/image objects in an object-oriented manner.
+- Or they can directly use `tools` to process raw NumPy arrays — for instance, in custom tools or when integrating Sigima into other projects.
+
+> ⚠️ `sigima.tools` is not intended as a general-purpose NumPy extension. Its purpose is to **fill in the gaps** of common scientific libraries (NumPy, SciPy, scikit-image, etc.), offering consistent tools for signal/image processing in the context of Sigima and similar projects.
+
+---
+
+## Usage Outside Sigima
+
+Although Sigima is designed primarily for object-based processing, some of its core functions are useful on their own.
+
+For instance, the [DataLab](https://datalab-platform.com) project — an open-source platform for signal/image processing — uses many functions from `sigima.tools` independently of the object model. This demonstrates how `sigima.tools` can serve as a **lightweight utility layer** in scientific and industrial Python applications, even when the object model is not used directly.
+
+To maintain this flexibility and avoid confusion, the distinction between `tools` (array-based) and `computation` (object-based) is intentional and explicit.
+
+---
+
+## 📦 Installation
+
+```bash
+pip install sigima
+```
+
+Or in a development environment:
+
+```bash
+git clone https://github.com/DataLab-Platform/Sigima.git
+cd Sigima
+pip install -e .
+```
+
+---
+
+## 📚 Documentation
+
+📖 Full documentation (in progress) is available at:
+👉 <https://sigima.readthedocs.io/>
+
+> Want to use Sigima inside DataLab with GUI tools?
+> Check out the full platform: [DataLab](https://datalab-platform.com/)
+
+---
+
+## ⚙️ Architecture
+
+Sigima is organized by data type:
+
+```text
+sigima/
+├── tools/      # Low-level NumPy-based algorithms supporting some computation functions
+├── proc/       # High-level processing functions operating on SignalObj/ImageObj
+│   ├── base/   # Common processing functions
+│   ├── signal/ # 1D signal processing
+│   └── image/  # 2D image processing
+```
+
+Each domain provides:
+
+- Low-level functions operating on NumPy arrays
+- High-level functions operating on `SignalObj` or `ImageObj`
+
+---
+
+## 🧪 Testing
+
+Sigima comes with unit tests based on `pytest`.
+
+To run all tests:
+
+```bash
+pytest
+```
+
+To run GUI-assisted validation tests (optional):
+
+```bash
+pytest --gui
+```
+
+---
+
+## 🧠 License
+
+Sigima is distributed under the terms of the BSD 3-Clause license.
+See [LICENSE](./LICENSE) for details.
+
+---
+
+## 🤝 Contributing
+
+Bug reports, feature requests and pull requests are welcome!
+See the [CONTRIBUTING](https://datalab-platform.com/en/contributing) guide to get started.
+
+---
+
+![Python](https://raw.githubusercontent.com/DataLab-Platform/DataLab/main/doc/images/logos/Python.png)
+![NumPy](https://raw.githubusercontent.com/DataLab-Platform/DataLab/main/doc/images/logos/NumPy.png)
+![SciPy](https://raw.githubusercontent.com/DataLab-Platform/DataLab/main/doc/images/logos/SciPy.png)
+![scikit-image](https://raw.githubusercontent.com/DataLab-Platform/DataLab/main/doc/images/logos/scikit-image.png)
+![OpenCV](https://raw.githubusercontent.com/DataLab-Platform/DataLab/main/doc/images/logos/OpenCV.png)
+
+---
+
+© DataLab Platform Developers