eelsnmf-gui 0.0.4__tar.gz

eelsnmf_gui-0.0.4/.gitignore

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+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[cod]
+*$py.class
+
+# C extensions
+*.so
+
+# Distribution / packaging
+.Python
+env/
+build/
+develop-eggs/
+dist/
+downloads/
+eggs/
+.eggs/
+lib/
+lib64/
+parts/
+sdist/
+var/
+*.egg-info/
+.installed.cfg
+*.egg
+
+# PyInstaller
+#  Usually these files are written by a python script from a template
+#  before PyInstaller builds the exe, so as to inject date/other infos into it.
+*.manifest
+*.spec
+
+# Installer logs
+pip-log.txt
+pip-delete-this-directory.txt
+
+# Unit test / coverage reports
+htmlcov/
+.tox/
+.coverage
+.coverage.*
+.cache
+nosetests.xml
+coverage.xml
+*,cover
+.hypothesis/
+
+# Translations
+*.mo
+*.pot
+
+# Django stuff:
+*.log
+local_settings.py
+
+# Flask instance folder
+instance/
+
+# Sphinx documentation
+docs/_build/
+
+# MkDocs documentation
+/site/
+
+# PyBuilder
+target/
+
+# Pycharm and VSCode
+.idea/
+venv/
+.vscode/
+
+# IPython Notebook
+.ipynb_checkpoints
+
+# pyenv
+.python-version
+
+# OS
+.DS_Store
+

eelsnmf_gui-0.0.4/LICENSE

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+
+Copyright (c) 2026, jules-vanaret
+All rights reserved.
+
+Redistribution and use in source and binary forms, with or without
+modification, are permitted provided that the following conditions are met:
+
+* Redistributions of source code must retain the above copyright notice, this
+  list of conditions and the following disclaimer.
+
+* 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.
+
+* Neither the name of 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.

eelsnmf_gui-0.0.4/MANIFEST.in

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+include LICENSE
+include README.md
+
+recursive-exclude * __pycache__
+recursive-exclude * *.py[co]

eelsnmf_gui-0.0.4/PKG-INFO

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+Metadata-Version: 2.4
+Name: eelsnmf-gui
+Version: 0.0.4
+Summary: GUI for EELS NMF processing
+Author: jules-vanaret
+Author-email: jules.vanaret@epfl.ch
+License: 
+        Copyright (c) 2026, jules-vanaret
+        All rights reserved.
+        
+        Redistribution and use in source and binary forms, with or without
+        modification, are permitted provided that the following conditions are met:
+        
+        * Redistributions of source code must retain the above copyright notice, this
+          list of conditions and the following disclaimer.
+        
+        * 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.
+        
+        * Neither the name of 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.
+        
+Classifier: Development Status :: 2 - Pre-Alpha
+Classifier: Intended Audience :: Developers
+Classifier: License :: OSI Approved :: BSD License
+Classifier: Operating System :: OS Independent
+Classifier: Programming Language :: Python
+Classifier: Programming Language :: Python :: 3
+Classifier: Programming Language :: Python :: 3 :: Only
+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 :: Image Processing
+Requires-Python: >=3.10
+Description-Content-Type: text/markdown
+License-File: LICENSE
+Requires-Dist: numpy
+Requires-Dist: qtpy
+Requires-Dist: openpyxl
+Dynamic: license-file
+
+# eelsnmf-gui
+
+GUI for [EELS NMF](https://github.com/PauTorru/EELSNMF) processing, including a standalone Qt GUI and
+a scriptable processing API for scripts and batch workflows.
+
+## Features
+
+- Qt GUI for end-to-end EELS NMF workflows (preprocess, masking, decomposition,
+	plotting, exports).
+- `Session` API (`src/eelsnmf_gui/session.py`) exposing the same pipeline
+	stages for scripted usage outside the GUI.
+- Stage-wise caching: preprocessing, masks, and fitted decompositions are
+	reused and invalidated automatically when their inputs change.
+
+## Design Notes
+
+- The pipeline is split into explicit stages: preprocessing (folder loading,
+	ZLP alignment, despiking, common energy axis), mask building, model
+	building and decomposition, and result analysis (edges, maps, summaries).
+- `eelsnmf_gui.session.Session` owns the folders and parameters, caches each
+	stage, and self-invalidates:
+	- changing folders or the median filter size invalidates everything;
+	- changing mask parameters invalidates masks and decompositions, but
+		keeps preprocessing;
+	- changing decomposition parameters (beam, edge ranges, number of
+		components, max iterations, W init) invalidates decompositions only;
+	- colors never affect the decomposition: recoloring only re-renders.
+- The EELSNMF backend is isolated behind a loader and an engine interface, so
+	all other stages run on plain numpy arrays and are testable without
+	EELSNMF installed.
+- The GUI is a thin wrapper around the `Session`, keeping behavior consistent
+	between interactive and scripted runs.
+
+## Installation
+
+Install the EELSNMF backend from source:
+```
+pip install "EELSNMF[EML] @ git+https://github.com/PauTorru/EELSNMF.git"
+```
+
+Then install package from source:
+
+```
+git clone https://github.com/jules-vanaret/eelsnmf-gui
+cd eelsnmf-gui
+pip install -e .
+```
+
+If you want GPU support, make sure to install [cupy](https://docs.cupy.dev/en/stable/install.html) (we recommend using the conda installer or equivalent to minimize dependency issues):
+```
+conda install -c conda-forge cupy
+```
+
+## Run the GUI:
+
+Using the console entry point:
+```
+eelsnmfgui
+```
+By default the GUI assumes the loaded spectrum images are already
+preprocessed (despiked, ZLP-aligned), hides the preprocessing controls, and
+processes folders individually. To show the preprocessing controls (and
+preprocess the data on load) and/or allow joint processing of several
+folders, use:
+```
+eelsnmfgui --pre --joint
+```
+or calling the script directly (make sure to run from the package root):
+```
+python run_gui.py
+```
+
+## Testing
+
+Run the test suite with:
+```
+python -m pytest
+```
+Unit, session, and widget tests run without EELSNMF installed; the
+end-to-end tests marked `integration` run when EELSNMF is available and can
+be skipped with `pytest -m "not integration"`.
+
+## License
+
+Distributed under the terms of the BSD-3 license.

eelsnmf_gui-0.0.4/README.md

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+# eelsnmf-gui
+
+GUI for [EELS NMF](https://github.com/PauTorru/EELSNMF) processing, including a standalone Qt GUI and
+a scriptable processing API for scripts and batch workflows.
+
+## Features
+
+- Qt GUI for end-to-end EELS NMF workflows (preprocess, masking, decomposition,
+	plotting, exports).
+- `Session` API (`src/eelsnmf_gui/session.py`) exposing the same pipeline
+	stages for scripted usage outside the GUI.
+- Stage-wise caching: preprocessing, masks, and fitted decompositions are
+	reused and invalidated automatically when their inputs change.
+
+## Design Notes
+
+- The pipeline is split into explicit stages: preprocessing (folder loading,
+	ZLP alignment, despiking, common energy axis), mask building, model
+	building and decomposition, and result analysis (edges, maps, summaries).
+- `eelsnmf_gui.session.Session` owns the folders and parameters, caches each
+	stage, and self-invalidates:
+	- changing folders or the median filter size invalidates everything;
+	- changing mask parameters invalidates masks and decompositions, but
+		keeps preprocessing;
+	- changing decomposition parameters (beam, edge ranges, number of
+		components, max iterations, W init) invalidates decompositions only;
+	- colors never affect the decomposition: recoloring only re-renders.
+- The EELSNMF backend is isolated behind a loader and an engine interface, so
+	all other stages run on plain numpy arrays and are testable without
+	EELSNMF installed.
+- The GUI is a thin wrapper around the `Session`, keeping behavior consistent
+	between interactive and scripted runs.
+
+## Installation
+
+Install the EELSNMF backend from source:
+```
+pip install "EELSNMF[EML] @ git+https://github.com/PauTorru/EELSNMF.git"
+```
+
+Then install package from source:
+
+```
+git clone https://github.com/jules-vanaret/eelsnmf-gui
+cd eelsnmf-gui
+pip install -e .
+```
+
+If you want GPU support, make sure to install [cupy](https://docs.cupy.dev/en/stable/install.html) (we recommend using the conda installer or equivalent to minimize dependency issues):
+```
+conda install -c conda-forge cupy
+```
+
+## Run the GUI:
+
+Using the console entry point:
+```
+eelsnmfgui
+```
+By default the GUI assumes the loaded spectrum images are already
+preprocessed (despiked, ZLP-aligned), hides the preprocessing controls, and
+processes folders individually. To show the preprocessing controls (and
+preprocess the data on load) and/or allow joint processing of several
+folders, use:
+```
+eelsnmfgui --pre --joint
+```
+or calling the script directly (make sure to run from the package root):
+```
+python run_gui.py
+```
+
+## Testing
+
+Run the test suite with:
+```
+python -m pytest
+```
+Unit, session, and widget tests run without EELSNMF installed; the
+end-to-end tests marked `integration` run when EELSNMF is available and can
+be skipped with `pytest -m "not integration"`.
+
+## License
+
+Distributed under the terms of the BSD-3 license.

eelsnmf_gui-0.0.4/pyproject.toml

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+[project]
+name = "eelsnmf-gui"
+version = "0.0.4"
+description = "GUI for EELS NMF processing"
+readme = "README.md"
+license = {file = "LICENSE"}
+authors = [
+  {name = "jules-vanaret"},
+  {email = "jules.vanaret@epfl.ch"},
+]
+classifiers = [
+    "Development Status :: 2 - Pre-Alpha",
+    "Intended Audience :: Developers",
+    "License :: OSI Approved :: BSD License",
+    "Operating System :: OS Independent",
+    "Programming Language :: Python",
+    "Programming Language :: Python :: 3",
+    "Programming Language :: Python :: 3 :: Only",
+    "Programming Language :: Python :: 3.10",
+    "Programming Language :: Python :: 3.11",
+    "Programming Language :: Python :: 3.12",
+    "Programming Language :: Python :: 3.13",
+    "Topic :: Scientific/Engineering :: Image Processing",
+]
+requires-python = ">=3.10"
+dependencies = [
+    "numpy",
+    "qtpy",
+    "openpyxl",
+    # "EELSNMF[EML] @ git+https://github.com/PauTorru/EELSNMF.git",
+]
+
+[project.scripts]
+eelsnmfgui = "eelsnmf_gui.cli:main"
+
+[dependency-groups]
+dev = [
+    "tox-uv",
+    "pytest",  # https://docs.pytest.org/en/latest/contents.html
+    "pytest-cov",  # https://pytest-cov.readthedocs.io/en/latest/
+    "pytest-qt",  # https://pytest-qt.readthedocs.io/en/latest/
+]
+
+
+
+[build-system]
+requires = ["setuptools>=42.0.0"]
+build-backend = "setuptools.build_meta"
+
+[tool.setuptools]
+include-package-data = true
+
+[tool.setuptools.packages.find]
+where = ["src"]
+
+[tool.pytest.ini_options]
+minversion = "6.0"
+addopts = ["-ra", "--showlocals", "--strict-markers", "--strict-config"]
+xfail_strict = true
+# filterwarnings = ["error"]  # recommended by PP309; deprecation warnings cause failures so leaving for the user to enable if desired
+log_cli_level = "INFO"
+testpaths = ["tests"]
+markers = [
+    "integration: end-to-end tests that require the EELSNMF backend (deselect with '-m \"not integration\"')",
+]
+
+[tool.black]
+line-length = 79
+target-version = ['py310', 'py311', 'py312', 'py313']
+
+[tool.ruff]
+line-length = 79
+lint.select = [
+    "E", "F", "W", #flake8
+    "UP", # pyupgrade
+    "I", # isort
+    "BLE", # flake8-blind-exception
+    "B", # flake8-bugbear
+    "A", # flake8-builtins
+    "C4", # flake8-comprehensions
+    "ISC", # flake8-implicit-str-concat
+    "G", # flake8-logging-format
+    "PIE", # flake8-pie
+    "SIM", # flake8-simplify
+]
+lint.ignore = [
+    "E501", # line too long. let black handle this
+    "UP006", "UP007", # type annotation. As using magicgui require runtime type annotation then we disable this.
+]
+
+exclude = [
+    ".bzr",
+    ".direnv",
+    ".eggs",
+    ".git",
+    ".mypy_cache",
+    ".pants.d",
+    ".ruff_cache",
+    ".svn",
+    ".tox",
+    ".venv",
+    "__pypackages__",
+    "_build",
+    "buck-out",
+    "build",
+    "dist",
+    "node_modules",
+    "venv",
+    "*vendored*",
+    "*_vendor*",
+]
+fix = true

eelsnmf_gui-0.0.4/run_gui.py

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+from eelsnmf_gui.cli import main
+
+
+if __name__ == "__main__":
+    main()

eelsnmf_gui-0.0.4/setup.cfg

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+[egg_info]
+tag_build = 
+tag_date = 0
+

eelsnmf_gui-0.0.4/src/eelsnmf_gui/__init__.py

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+from importlib.metadata import PackageNotFoundError, version
+
+try:
+    __version__ = version("eelsnmf-gui")
+except PackageNotFoundError:  # running from source without installation
+    __version__ = "unknown"
+
+from ._results import (
+    BeamParams,
+    DecoBundle,
+    EdgeCollection,
+    EdgeSeries,
+    ImageCollection,
+    MaskParams,
+    MaskResult,
+    PreprocessedData,
+    PreprocessedSI,
+    ProcessFoldersResult,
+    ProcessingResult,
+)
+from ._widget import EELSProcessingWidget
+from .session import Session
+
+__all__ = (
+    "EELSProcessingWidget",
+    "Session",
+    "BeamParams",
+    "MaskParams",
+    "PreprocessedData",
+    "PreprocessedSI",
+    "MaskResult",
+    "DecoBundle",
+    "ProcessingResult",
+    "ProcessFoldersResult",
+    "EdgeCollection",
+    "EdgeSeries",
+    "ImageCollection",
+)