ChameleonIQ 1.0.0__tar.gz

chameleoniq-1.0.0/PKG-INFO

@@ -0,0 +1,110 @@
+Metadata-Version: 2.4
+Name: ChameleonIQ
+Version: 1.0.0
+Summary: A tool for NEMA NU 2-2018 Image Quality analysis.
+Author: Edwing Ulin-Briseno
+Author-email: EdAlita <eyulibri@i3m.upv.es>
+Platform: unix
+Platform: linux
+Platform: osx
+Platform: cygwin
+Platform: win32
+Classifier: Programming Language :: Python :: 3
+Classifier: License :: OSI Approved :: MIT License
+Classifier: Operating System :: OS Independent
+Classifier: Topic :: Scientific/Engineering :: Medical Science Apps.
+Requires-Python: >=3.8
+Description-Content-Type: text/markdown
+Requires-Dist: numpy==2.2.6
+Requires-Dist: scipy==1.16.0
+Requires-Dist: scipy-stubs==1.16.0.2
+Requires-Dist: nibabel==5.3.2
+Requires-Dist: matplotlib==3.10.3
+Requires-Dist: seaborn==0.13.2
+Requires-Dist: pandas==2.3.1
+Requires-Dist: yacs==0.1.8
+Requires-Dist: opencv-python==4.12.0.88
+Requires-Dist: pillow==11.3.0
+Requires-Dist: reportlab==4.4.2
+Requires-Dist: types-reportlab==4.4.1.20250602
+Requires-Dist: SimpleITK==2.5.2
+Requires-Dist: scikit-image==0.25.2
+Requires-Dist: rich==14.2.0
+Provides-Extra: dev
+Requires-Dist: pytest==8.4.1; extra == "dev"
+Requires-Dist: pytest-cov==6.2.1; extra == "dev"
+Requires-Dist: mypy==1.16.1; extra == "dev"
+Requires-Dist: mypy_extensions==1.1.0; extra == "dev"
+Requires-Dist: flake8==7.3.0; extra == "dev"
+
+<p align="center">
+  <img alt="Logo Banner" src="data/banner.png">
+</p>
+
+<p align="center">
+  <a href="https://github.com/EdAlita/nema_analysis_tool/actions/workflows/tests.yml">
+    <img alt="Tests" src="https://github.com/EdAlita/nema_analysis_tool/actions/workflows/tests.yml/badge.svg?branch=main">
+  </a>
+  <a href="https://github.com/psf/black">
+    <img alt="Code style: black" src="https://img.shields.io/badge/code%20style-black-000000.svg">
+  </a>
+  <a href="https://github.com/EdAlita/nema_analysis_tool/blob/main/LICENSE">
+    <img alt="License: Apache-2.0" src="https://img.shields.io/badge/License-Apache_2.0-blue.svg">
+  </a>
+  <a>
+    <img alt="Python" src="https://img.shields.io/badge/language-Python-blue?logo=python">
+  </a>
+  <a>
+    <img alt="Git Download" src="https://img.shields.io/github/downloads/EdAlita/nema_analysis_tool/total">
+  </a>
+  <a>
+    <img alt="Git Release" src="https://img.shields.io/github/v/release/EdAlita/ChameleonIQ">
+  </a>
+</p>
+
+
+# ChameleonIQ: Nema-aware Image Quality Tool for Python
+
+This project is a Python-based tool for the automated analysis of PET image quality based on the NEMA NU 2-2018 standard, specifically focusing on Section 7.4.1.
+
+## Features
+
+*   Calculates Percent Contrast (Q_H,j), Percent Background Variability (N_j), and Accuracy of Corrections (ΔC_lung,i).
+*   Utilizes 3D Regions of Interest (ROIs) based on the NEMA Body Phantom.
+*   Loads nii image data with user-defined dimensions and voxel spacing.
+*   Automatic postions of ROIs on given centers
+
+## Project Structure
+
+```bash
+nema-analysis-tool
+├── data
+├── documentation
+├── src
+│  ├── config
+│  ├── nema_merge
+│  ├── nema_quant
+│  └── nema_quant_iter
+└── tests
+```
+
+- [**Config**](src/config): configuration files to run the tool
+- [**Data**](src/data): Data for testing and logos used for PDF reports
+- [**Documentation**](src/nema_quant_iter): Documentation, wikis and how to install the tool
+- [**nema_merge**](src/nema_merge): scripts for creating fusing of individuals runs
+- [**nema_quant**](src/nema_quant): scripts for individuals test runs
+- [**nema_quant_iter**](src/nema_quant_iter): scripts for a iteration based analysis
+
+## How to get Started?
+Read these:
+- [**Installation instructions**](documentation/INSTALLATION.md)
+- [**Usage instructions**](documentation/USAGE.md)
+- [**How it works?**](documentation/HOW_IT_WORKS.md)
+
+Additional information:
+- [**What will change?**](documentation/CHANGELOG.md)
+
+## License
+This project is licensed under the Apache Lincese 2.0 - see the [LICENSE.md](LICENSE) file for details.
+
+[//]: # (- [Ignore label]&#40;documentation/ignore_label.md&#41;)

chameleoniq-1.0.0/README.md

@@ -0,0 +1,71 @@
+<p align="center">
+  <img alt="Logo Banner" src="data/banner.png">
+</p>
+
+<p align="center">
+  <a href="https://github.com/EdAlita/nema_analysis_tool/actions/workflows/tests.yml">
+    <img alt="Tests" src="https://github.com/EdAlita/nema_analysis_tool/actions/workflows/tests.yml/badge.svg?branch=main">
+  </a>
+  <a href="https://github.com/psf/black">
+    <img alt="Code style: black" src="https://img.shields.io/badge/code%20style-black-000000.svg">
+  </a>
+  <a href="https://github.com/EdAlita/nema_analysis_tool/blob/main/LICENSE">
+    <img alt="License: Apache-2.0" src="https://img.shields.io/badge/License-Apache_2.0-blue.svg">
+  </a>
+  <a>
+    <img alt="Python" src="https://img.shields.io/badge/language-Python-blue?logo=python">
+  </a>
+  <a>
+    <img alt="Git Download" src="https://img.shields.io/github/downloads/EdAlita/nema_analysis_tool/total">
+  </a>
+  <a>
+    <img alt="Git Release" src="https://img.shields.io/github/v/release/EdAlita/ChameleonIQ">
+  </a>
+</p>
+
+
+# ChameleonIQ: Nema-aware Image Quality Tool for Python
+
+This project is a Python-based tool for the automated analysis of PET image quality based on the NEMA NU 2-2018 standard, specifically focusing on Section 7.4.1.
+
+## Features
+
+*   Calculates Percent Contrast (Q_H,j), Percent Background Variability (N_j), and Accuracy of Corrections (ΔC_lung,i).
+*   Utilizes 3D Regions of Interest (ROIs) based on the NEMA Body Phantom.
+*   Loads nii image data with user-defined dimensions and voxel spacing.
+*   Automatic postions of ROIs on given centers
+
+## Project Structure
+
+```bash
+nema-analysis-tool
+├── data
+├── documentation
+├── src
+│  ├── config
+│  ├── nema_merge
+│  ├── nema_quant
+│  └── nema_quant_iter
+└── tests
+```
+
+- [**Config**](src/config): configuration files to run the tool
+- [**Data**](src/data): Data for testing and logos used for PDF reports
+- [**Documentation**](src/nema_quant_iter): Documentation, wikis and how to install the tool
+- [**nema_merge**](src/nema_merge): scripts for creating fusing of individuals runs
+- [**nema_quant**](src/nema_quant): scripts for individuals test runs
+- [**nema_quant_iter**](src/nema_quant_iter): scripts for a iteration based analysis
+
+## How to get Started?
+Read these:
+- [**Installation instructions**](documentation/INSTALLATION.md)
+- [**Usage instructions**](documentation/USAGE.md)
+- [**How it works?**](documentation/HOW_IT_WORKS.md)
+
+Additional information:
+- [**What will change?**](documentation/CHANGELOG.md)
+
+## License
+This project is licensed under the Apache Lincese 2.0 - see the [LICENSE.md](LICENSE) file for details.
+
+[//]: # (- [Ignore label]&#40;documentation/ignore_label.md&#41;)

chameleoniq-1.0.0/pyproject.toml

@@ -0,0 +1,98 @@
+[build-system]
+requires = ["setuptools>=61.0"]
+build-backend = "setuptools.build_meta"
+
+[project]
+name = "ChameleonIQ"
+version = "1.0.0"
+authors = [
+  { name="EdAlita", email="eyulibri@i3m.upv.es" },
+]
+description = "A tool for NEMA NU 2-2018 Image Quality analysis."
+readme = "README.md"
+requires-python = ">=3.8"
+classifiers = [
+    "Programming Language :: Python :: 3",
+    "License :: OSI Approved :: MIT License",
+    "Operating System :: OS Independent",
+    "Topic :: Scientific/Engineering :: Medical Science Apps.",
+]
+dependencies = [
+    "numpy==2.2.6",
+    "scipy==1.16.0",
+    "scipy-stubs==1.16.0.2",
+    "nibabel==5.3.2",
+    "matplotlib==3.10.3",
+    "seaborn==0.13.2",
+    "pandas==2.3.1",
+    "yacs==0.1.8",
+    "opencv-python==4.12.0.88",
+    "pillow==11.3.0",
+    "reportlab==4.4.2",
+    "types-reportlab==4.4.1.20250602",
+    "SimpleITK==2.5.2",
+    "scikit-image==0.25.2",
+    "rich==14.2.0"
+]
+
+[project.scripts]
+nema_quant = "nema_quant.__main__:main"
+nema_quant_iter = "nema_quant_iter.__main__:main"
+nema_merge = "nema_merge.__main__:main"
+nema_coord = "nema_quant.utils:main"
+chameleoniq_quant = "nema_quant.__main__:main"
+chameleoniq_quant_iter = "nema_quant_iter.__main__:main"
+chameleoniq_merge = "nema_merge.__main__:main"
+chameleoniq_coord = "nema_quant.utils:main"
+
+[tool.setuptools]
+package-dir = {"" = "src"}
+
+[tool.setuptools.packages.find]
+where = ["src"]
+
+[project.optional-dependencies]
+dev = [
+    "pytest==8.4.1",
+    "pytest-cov==6.2.1",
+    "mypy==1.16.1",
+    "mypy_extensions==1.1.0",
+    "flake8==7.3.0"
+]
+
+[tool.pytest.ini_options]
+addopts = "--cov=src/nema_quant --cov-report=term-missing --cov-report=html"
+testpaths = [
+  "tests",
+]
+pythonpath = [
+  "src",
+  "."
+]
+filterwarnings = [
+    "ignore:builtin type SwigPyPacked has no __module__ attribute:DeprecationWarning",
+    "ignore:builtin type SwigPyObject has no __module__ attribute:DeprecationWarning",
+    "ignore:builtin type swigvarlink has no __module__ attribute:DeprecationWarning"
+]
+
+[tool.mypy]
+mypy_path = "nema-analysis-tool"
+explicit_package_bases = true
+check_untyped_defs = true
+disallow_any_generics = true
+ignore_missing_imports = true
+no_implicit_optional = true
+show_error_codes = true
+strict_equality = true
+warn_redundant_casts = true
+warn_return_any = true
+warn_unused_configs = true
+no_implicit_reexport = true
+
+
+[[tool.mypy.overrides]]
+module = "yacs.*"
+ignore_missing_imports = true
+
+[tool.isort]
+profile = "black"

chameleoniq-1.0.0/setup.cfg

@@ -0,0 +1,49 @@
+[metadata]
+name = Nema Analysis Tool
+description = A Python tool for automated PET image quality analysis based on NEMA NU 2-2018 standard, focusing on Section 7.4.1 with features for calculating Percent Contrast, Background Variability, and Accuracy of Corrections using 3D ROIs.
+author = Edwing Ulin-Briseno
+license = MIT
+license_file = LICENSE.txt
+platforms = unix, linux, osx, cygwin, win32
+classifiers = 
+	Programming Language :: Python :: 3
+	Programming Language :: Python :: 3 :: Only
+	Programming Language :: Python :: 3.9
+	Programming Language :: Python :: 3.10
+	Programming Language :: Python :: 3.11
+	Programming Language :: Python :: 3.12
+
+[options]
+packages = 
+	nema_quant
+install_requires = 
+	matplotlib>=3.10
+	numpy>=2.3
+	PyYAML>=6.0
+	reportlab>=4.4
+	scipy>=1.16
+	SimpleITK>=2.0.0
+	yacs>0.1
+	setuptools>=80.9
+	statsmodels>=0.14.5
+	rich>=14.2.0
+python_requires = >=3.9
+package_dir = 
+	= src
+zip_safe = no
+
+[options.extras_require]
+testing = 
+	tox>=4.27
+	pytest>=8.4
+	pytest-cov>=6.2
+	mypy>=1.16
+	flake8>=7.3
+
+[flake8]
+max-line-length = 160
+
+[egg_info]
+tag_build = 
+tag_date = 0
+

chameleoniq-1.0.0/setup.py

@@ -0,0 +1,4 @@
+from setuptools import setup
+
+if __name__ == "__main__":
+    setup()

chameleoniq-1.0.0/src/ChameleonIQ.egg-info/PKG-INFO

@@ -0,0 +1,110 @@
+Metadata-Version: 2.4
+Name: ChameleonIQ
+Version: 1.0.0
+Summary: A tool for NEMA NU 2-2018 Image Quality analysis.
+Author: Edwing Ulin-Briseno
+Author-email: EdAlita <eyulibri@i3m.upv.es>
+Platform: unix
+Platform: linux
+Platform: osx
+Platform: cygwin
+Platform: win32
+Classifier: Programming Language :: Python :: 3
+Classifier: License :: OSI Approved :: MIT License
+Classifier: Operating System :: OS Independent
+Classifier: Topic :: Scientific/Engineering :: Medical Science Apps.
+Requires-Python: >=3.8
+Description-Content-Type: text/markdown
+Requires-Dist: numpy==2.2.6
+Requires-Dist: scipy==1.16.0
+Requires-Dist: scipy-stubs==1.16.0.2
+Requires-Dist: nibabel==5.3.2
+Requires-Dist: matplotlib==3.10.3
+Requires-Dist: seaborn==0.13.2
+Requires-Dist: pandas==2.3.1
+Requires-Dist: yacs==0.1.8
+Requires-Dist: opencv-python==4.12.0.88
+Requires-Dist: pillow==11.3.0
+Requires-Dist: reportlab==4.4.2
+Requires-Dist: types-reportlab==4.4.1.20250602
+Requires-Dist: SimpleITK==2.5.2
+Requires-Dist: scikit-image==0.25.2
+Requires-Dist: rich==14.2.0
+Provides-Extra: dev
+Requires-Dist: pytest==8.4.1; extra == "dev"
+Requires-Dist: pytest-cov==6.2.1; extra == "dev"
+Requires-Dist: mypy==1.16.1; extra == "dev"
+Requires-Dist: mypy_extensions==1.1.0; extra == "dev"
+Requires-Dist: flake8==7.3.0; extra == "dev"
+
+<p align="center">
+  <img alt="Logo Banner" src="data/banner.png">
+</p>
+
+<p align="center">
+  <a href="https://github.com/EdAlita/nema_analysis_tool/actions/workflows/tests.yml">
+    <img alt="Tests" src="https://github.com/EdAlita/nema_analysis_tool/actions/workflows/tests.yml/badge.svg?branch=main">
+  </a>
+  <a href="https://github.com/psf/black">
+    <img alt="Code style: black" src="https://img.shields.io/badge/code%20style-black-000000.svg">
+  </a>
+  <a href="https://github.com/EdAlita/nema_analysis_tool/blob/main/LICENSE">
+    <img alt="License: Apache-2.0" src="https://img.shields.io/badge/License-Apache_2.0-blue.svg">
+  </a>
+  <a>
+    <img alt="Python" src="https://img.shields.io/badge/language-Python-blue?logo=python">
+  </a>
+  <a>
+    <img alt="Git Download" src="https://img.shields.io/github/downloads/EdAlita/nema_analysis_tool/total">
+  </a>
+  <a>
+    <img alt="Git Release" src="https://img.shields.io/github/v/release/EdAlita/ChameleonIQ">
+  </a>
+</p>
+
+
+# ChameleonIQ: Nema-aware Image Quality Tool for Python
+
+This project is a Python-based tool for the automated analysis of PET image quality based on the NEMA NU 2-2018 standard, specifically focusing on Section 7.4.1.
+
+## Features
+
+*   Calculates Percent Contrast (Q_H,j), Percent Background Variability (N_j), and Accuracy of Corrections (ΔC_lung,i).
+*   Utilizes 3D Regions of Interest (ROIs) based on the NEMA Body Phantom.
+*   Loads nii image data with user-defined dimensions and voxel spacing.
+*   Automatic postions of ROIs on given centers
+
+## Project Structure
+
+```bash
+nema-analysis-tool
+├── data
+├── documentation
+├── src
+│  ├── config
+│  ├── nema_merge
+│  ├── nema_quant
+│  └── nema_quant_iter
+└── tests
+```
+
+- [**Config**](src/config): configuration files to run the tool
+- [**Data**](src/data): Data for testing and logos used for PDF reports
+- [**Documentation**](src/nema_quant_iter): Documentation, wikis and how to install the tool
+- [**nema_merge**](src/nema_merge): scripts for creating fusing of individuals runs
+- [**nema_quant**](src/nema_quant): scripts for individuals test runs
+- [**nema_quant_iter**](src/nema_quant_iter): scripts for a iteration based analysis
+
+## How to get Started?
+Read these:
+- [**Installation instructions**](documentation/INSTALLATION.md)
+- [**Usage instructions**](documentation/USAGE.md)
+- [**How it works?**](documentation/HOW_IT_WORKS.md)
+
+Additional information:
+- [**What will change?**](documentation/CHANGELOG.md)
+
+## License
+This project is licensed under the Apache Lincese 2.0 - see the [LICENSE.md](LICENSE) file for details.
+
+[//]: # (- [Ignore label]&#40;documentation/ignore_label.md&#41;)

chameleoniq-1.0.0/src/ChameleonIQ.egg-info/SOURCES.txt

@@ -0,0 +1,53 @@
+README.md
+pyproject.toml
+setup.cfg
+setup.py
+src/ChameleonIQ.egg-info/PKG-INFO
+src/ChameleonIQ.egg-info/SOURCES.txt
+src/ChameleonIQ.egg-info/dependency_links.txt
+src/ChameleonIQ.egg-info/entry_points.txt
+src/ChameleonIQ.egg-info/not-zip-safe
+src/ChameleonIQ.egg-info/requires.txt
+src/ChameleonIQ.egg-info/top_level.txt
+src/config/__init__.py
+src/config/defaults.py
+src/nema_merge/__init__.py
+src/nema_merge/__main__.py
+src/nema_merge/cli.py
+src/nema_merge/reporting.py
+src/nema_quant/__init__.py
+src/nema_quant/__main__.py
+src/nema_quant/analysis.py
+src/nema_quant/cli.py
+src/nema_quant/io.py
+src/nema_quant/metrics.py
+src/nema_quant/phantom.py
+src/nema_quant/reporting.py
+src/nema_quant/utils.py
+src/nema_quant_iter/__init__.py
+src/nema_quant_iter/__main__.py
+src/nema_quant_iter/cli.py
+src/nema_quant_iter/reporting.py
+tests/test_analysis.py
+tests/test_analysis_comprehensive.py
+tests/test_analysis_edge_cases.py
+tests/test_analysis_missing_lines.py
+tests/test_analysis_specific_lines.py
+tests/test_analysis_visualizations.py
+tests/test_cli.py
+tests/test_cli_comprehensive.py
+tests/test_cli_key_error_handling.py
+tests/test_cli_missing_lines.py
+tests/test_cli_remaining_coverage.py
+tests/test_direct_coverage.py
+tests/test_final_analysis_push.py
+tests/test_force_real_coverage.py
+tests/test_function_signatures.py
+tests/test_integration.py
+tests/test_io.py
+tests/test_main.py
+tests/test_phantom.py
+tests/test_remaining_analysis_lines.py
+tests/test_reporting_comprehensive.py
+tests/test_reporting_missing_lines.py
+tests/test_utils_comprehensive.py

chameleoniq-1.0.0/src/ChameleonIQ.egg-info/dependency_links.txt

@@ -0,0 +1 @@
+

chameleoniq-1.0.0/src/ChameleonIQ.egg-info/entry_points.txt

@@ -0,0 +1,9 @@
+[console_scripts]
+chameleoniq_coord = nema_quant.utils:main
+chameleoniq_merge = nema_merge.__main__:main
+chameleoniq_quant = nema_quant.__main__:main
+chameleoniq_quant_iter = nema_quant_iter.__main__:main
+nema_coord = nema_quant.utils:main
+nema_merge = nema_merge.__main__:main
+nema_quant = nema_quant.__main__:main
+nema_quant_iter = nema_quant_iter.__main__:main

chameleoniq-1.0.0/src/ChameleonIQ.egg-info/not-zip-safe

@@ -0,0 +1 @@
+

chameleoniq-1.0.0/src/ChameleonIQ.egg-info/requires.txt

@@ -0,0 +1,22 @@
+numpy==2.2.6
+scipy==1.16.0
+scipy-stubs==1.16.0.2
+nibabel==5.3.2
+matplotlib==3.10.3
+seaborn==0.13.2
+pandas==2.3.1
+yacs==0.1.8
+opencv-python==4.12.0.88
+pillow==11.3.0
+reportlab==4.4.2
+types-reportlab==4.4.1.20250602
+SimpleITK==2.5.2
+scikit-image==0.25.2
+rich==14.2.0
+
+[dev]
+pytest==8.4.1
+pytest-cov==6.2.1
+mypy==1.16.1
+mypy_extensions==1.1.0
+flake8==7.3.0

chameleoniq-1.0.0/src/ChameleonIQ.egg-info/top_level.txt

@@ -0,0 +1,4 @@
+config
+nema_merge
+nema_quant
+nema_quant_iter