pysimplemask 0.3.1__tar.gz

pysimplemask-0.3.1/.editorconfig

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+# http://editorconfig.org
+
+root = true
+
+[*]
+indent_style = space
+indent_size = 4
+trim_trailing_whitespace = true
+insert_final_newline = true
+charset = utf-8
+end_of_line = lf
+
+[*.bat]
+indent_style = tab
+end_of_line = crlf
+
+[LICENSE]
+insert_final_newline = false
+
+[Makefile]
+indent_style = tab

pysimplemask-0.3.1/.github/ISSUE_TEMPLATE.md

@@ -0,0 +1,15 @@
+* pySimpleMask version:
+* Python version:
+* Operating System:
+
+### Description
+
+Describe what you were trying to get done.
+Tell us what happened, what went wrong, and what you expected to happen.
+
+### What I Did
+
+```
+Paste the command(s) you ran and the output.
+If there was a crash, please include the traceback here.
+```

pysimplemask-0.3.1/.github/workflows/publish.yml

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+name: Publish to PyPI
+
+on:
+  push:
+    tags:
+      - '*'
+
+jobs:
+  pypi-publish:
+    name: Upload release to PyPI
+    runs-on: ubuntu-latest
+    environment:
+      name: pypi
+      url: https://pypi.org/p/pysimplemask
+    permissions:
+      id-token: write  # IMPORTANT: this permission is mandatory for trusted publishing
+      contents: read
+    steps:
+      - name: Checkout code
+        uses: actions/checkout@v4
+
+      - name: Set up Python
+        uses: actions/setup-python@v5
+        with:
+          python-version: '3.12'
+
+      - name: Install dependencies
+        run: |
+          python -m pip install --upgrade pip
+          pip install build twine
+
+      - name: Build package
+        run: |
+          python -m build
+
+      - name: Publish package distributions to PyPI
+        uses: pypa/gh-action-pypi-publish@release/v1

pysimplemask-0.3.1/.gitignore

@@ -0,0 +1,110 @@
+# 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/
+wheels/
+*.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/
+.pytest_cache/
+
+# Translations
+*.mo
+*.pot
+
+# Django stuff:
+*.log
+local_settings.py
+
+# Flask stuff:
+instance/
+.webassets-cache
+
+# Scrapy stuff:
+.scrapy
+
+# Sphinx documentation
+docs/_build/
+
+# PyBuilder
+target/
+
+# Jupyter Notebook
+.ipynb_checkpoints
+
+# Dask worker cache
+dask-worker-space/
+
+# pyenv
+.python-version
+
+# celery beat schedule file
+celerybeat-schedule
+
+# SageMath parsed files
+*.sage.py
+
+# dotenv
+.env
+
+# virtualenv
+.venv
+venv/
+ENV/
+
+# Spyder project settings
+.spyderproject
+.spyproject
+
+# Rope project settings
+.ropeproject
+
+# mkdocs documentation
+/site
+
+# mypy
+.mypy_cache/
+
+# IDE settings
+.vscode/
+.idea/
+

pysimplemask-0.3.1/LICENSE

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+Copyright (c) 2026, UChicago Argonne, LLC. All rights reserved.
+
+Copyright 2026. UChicago Argonne, LLC. This software was produced
+under U.S. Government contract DE-AC02-06CH11357 for Argonne National
+Laboratory (ANL), which is operated by UChicago Argonne, LLC for the
+U.S. Department of Energy. The U.S. Government has rights to use,
+reproduce, and distribute this software.  NEITHER THE GOVERNMENT NOR
+UChicago Argonne, LLC MAKES ANY WARRANTY, EXPRESS OR IMPLIED, OR
+ASSUMES ANY LIABILITY FOR THE USE OF THIS SOFTWARE.  If software is
+modified to produce derivative works, such modified software should
+be clearly marked, so as not to confuse it with the version available
+from ANL.
+
+Additionally, 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 UChicago Argonne, LLC, Argonne National
+      Laboratory, ANL, the U.S. Government, 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 UChicago Argonne, LLC 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 UChicago
+Argonne, LLC 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.

pysimplemask-0.3.1/PKG-INFO

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+Metadata-Version: 2.4
+Name: pysimplemask
+Version: 0.3.1
+Summary: A GUI for creating mask and q-partition maps for scattering patterns in preparation for SAXS/WAXS/XPCS data reduction
+Author-email: Miaoqi Chu <mqichu@anl.gov>
+Maintainer-email: Miaoqi Chu <mqichu@anl.gov>
+License: Copyright (c) 2026, UChicago Argonne, LLC. All rights reserved.
+        
+        Copyright 2026. UChicago Argonne, LLC. This software was produced
+        under U.S. Government contract DE-AC02-06CH11357 for Argonne National
+        Laboratory (ANL), which is operated by UChicago Argonne, LLC for the
+        U.S. Department of Energy. The U.S. Government has rights to use,
+        reproduce, and distribute this software.  NEITHER THE GOVERNMENT NOR
+        UChicago Argonne, LLC MAKES ANY WARRANTY, EXPRESS OR IMPLIED, OR
+        ASSUMES ANY LIABILITY FOR THE USE OF THIS SOFTWARE.  If software is
+        modified to produce derivative works, such modified software should
+        be clearly marked, so as not to confuse it with the version available
+        from ANL.
+        
+        Additionally, 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 UChicago Argonne, LLC, Argonne National
+              Laboratory, ANL, the U.S. Government, 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 UChicago Argonne, LLC 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 UChicago
+        Argonne, LLC 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: bugs, https://github.com/AdvancedPhotonSource/pySimpleMask/issues
+Project-URL: changelog, https://github.com/AdvancedPhotonSource/pySimpleMask/blob/master/changelog.md
+Project-URL: homepage, https://github.com/AdvancedPhotonSource/pySimpleMask
+Classifier: Development Status :: 4 - Beta
+Classifier: Intended Audience :: Science/Research
+Classifier: License :: OSI Approved :: BSD License
+Classifier: Programming Language :: Python :: 3
+Classifier: Programming Language :: Python :: 3.12
+Classifier: Topic :: Scientific/Engineering :: Visualization
+Classifier: Operating System :: OS Independent
+Description-Content-Type: text/markdown
+License-File: LICENSE
+Requires-Dist: numpy
+Requires-Dist: scipy
+Requires-Dist: h5py
+Requires-Dist: hdf5plugin
+Requires-Dist: scikit-image
+Requires-Dist: matplotlib
+Requires-Dist: pyqtgraph
+Requires-Dist: PySide6==6.8.3
+Requires-Dist: astropy
+Requires-Dist: imagecodecs
+Requires-Dist: tifffile
+Provides-Extra: dev
+Requires-Dist: coverage; extra == "dev"
+Requires-Dist: mypy; extra == "dev"
+Requires-Dist: pytest; extra == "dev"
+Requires-Dist: ruff; extra == "dev"
+Dynamic: license-file
+
+# pySimpleMask
+
+[![PyPI version](https://img.shields.io/pypi/v/pysimplemask.svg)](https://pypi.python.org/pypi/pysimplemask)
+[![Build Status](https://img.shields.io/travis/AdvancedPhotonSource/pySimpleMask.svg)](https://travis-ci.com/AdvancedPhotonSource/pySimpleMask)
+[![Documentation Status](https://readthedocs.org/projects/pysimplemask/badge/?version=latest)](https://pysimplemask.readthedocs.io/en/latest/?version=latest)
+
+**pySimpleMask** is a graphical user interface (GUI) tool designed for creating masks and Q-partition maps for scattering patterns, specifically facilitating SAXS, WAXS, and XPCS data reduction.
+
+## Features
+
+*   **Versatile Data Support**: Load scattering data from various formats including HDF5, IMM, TIFF, and binary files.
+*   **Interactive Masking**:
+    *   **Drawing Tools**: Create masks using polygons, circles, rectangles, and lines.
+    *   **Thresholding**: Automatically mask pixels based on intensity limits (low/high).
+    *   **Blemish Maps**: Apply pre-existing blemish (bad pixel) files.
+    *   **Outlier Removal**: Automatically detect and mask outliers using SAXS 1D azimuthal average comparisons.
+    *   **Manual Selection**: Click to mask specific pixels or regions.
+*   **Partition Generation**:
+    *   Compute Q-Phi partitions (Dynamic/Static).
+    *   Generate X-Y partitions.
+    *   Support for custom mapping modes.
+*   **Visualization**: Real-time visualization of scattering patterns, masks, and SAXS 1D profiles.
+*   **Output**:
+    *   Save generated masks as TIFF files.
+    *   Save full partition maps and metadata in Nexus-compatible HDF5/XPCS formats.
+
+## Installation
+
+### From PyPI
+```bash
+pip install pysimplemask
+```
+
+### From Source
+1. Clone the repository:
+   ```bash
+   git clone https://github.com/AdvancedPhotonSource/pySimpleMask.git
+   cd pysimplemask
+   ```
+2. Install the package:
+   ```bash
+   pip install .
+   ```
+
+## Usage
+
+To launch the GUI, simply run the following command in your terminal:
+
+```bash
+pysimplemask
+```
+
+You can also specify a starting path for data loading:
+
+```bash
+pysimplemask --path /path/to/your/data
+```
+
+## Workflow
+
+1.  **Load Data**: Click "Select Raw" or "Load" to open your scattering data file.
+2.  **Define Mask**:
+    *   Use the "Mask" tabs to apply different masking techniques (Draw, Threshold, Blemish, etc.).
+    *   Combine multiple masking methods as needed.
+    *   Use "Evaluate" to preview the mask and "Apply" to finalize it.
+3.  **Compute Partition**:
+    *   Go to the "Partition" tab.
+    *   Select the desired mode (e.g., Q-Phi) and configure parameters (number of bins, symmetry).
+    *   Click "Compute Partition" to generate the maps.
+4.  **Save Results**:
+    *   Click "Save" to export the mask (TIFF) or the full partition data (HDF5).
+
+## Credits
+
+This package was created with [Cookiecutter](https://github.com/audreyr/cookiecutter) and the [audreyr/cookiecutter-pypackage](https://github.com/audreyr/cookiecutter-pypackage) project template.
+
+*   **Author**: Miaoqi Chu (mqichu@anl.gov)
+*   **License**: BSD 3-Clause license

pysimplemask-0.3.1/README.md

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+# pySimpleMask
+
+[![PyPI version](https://img.shields.io/pypi/v/pysimplemask.svg)](https://pypi.python.org/pypi/pysimplemask)
+[![Build Status](https://img.shields.io/travis/AdvancedPhotonSource/pySimpleMask.svg)](https://travis-ci.com/AdvancedPhotonSource/pySimpleMask)
+[![Documentation Status](https://readthedocs.org/projects/pysimplemask/badge/?version=latest)](https://pysimplemask.readthedocs.io/en/latest/?version=latest)
+
+**pySimpleMask** is a graphical user interface (GUI) tool designed for creating masks and Q-partition maps for scattering patterns, specifically facilitating SAXS, WAXS, and XPCS data reduction.
+
+## Features
+
+*   **Versatile Data Support**: Load scattering data from various formats including HDF5, IMM, TIFF, and binary files.
+*   **Interactive Masking**:
+    *   **Drawing Tools**: Create masks using polygons, circles, rectangles, and lines.
+    *   **Thresholding**: Automatically mask pixels based on intensity limits (low/high).
+    *   **Blemish Maps**: Apply pre-existing blemish (bad pixel) files.
+    *   **Outlier Removal**: Automatically detect and mask outliers using SAXS 1D azimuthal average comparisons.
+    *   **Manual Selection**: Click to mask specific pixels or regions.
+*   **Partition Generation**:
+    *   Compute Q-Phi partitions (Dynamic/Static).
+    *   Generate X-Y partitions.
+    *   Support for custom mapping modes.
+*   **Visualization**: Real-time visualization of scattering patterns, masks, and SAXS 1D profiles.
+*   **Output**:
+    *   Save generated masks as TIFF files.
+    *   Save full partition maps and metadata in Nexus-compatible HDF5/XPCS formats.
+
+## Installation
+
+### From PyPI
+```bash
+pip install pysimplemask
+```
+
+### From Source
+1. Clone the repository:
+   ```bash
+   git clone https://github.com/AdvancedPhotonSource/pySimpleMask.git
+   cd pysimplemask
+   ```
+2. Install the package:
+   ```bash
+   pip install .
+   ```
+
+## Usage
+
+To launch the GUI, simply run the following command in your terminal:
+
+```bash
+pysimplemask
+```
+
+You can also specify a starting path for data loading:
+
+```bash
+pysimplemask --path /path/to/your/data
+```
+
+## Workflow
+
+1.  **Load Data**: Click "Select Raw" or "Load" to open your scattering data file.
+2.  **Define Mask**:
+    *   Use the "Mask" tabs to apply different masking techniques (Draw, Threshold, Blemish, etc.).
+    *   Combine multiple masking methods as needed.
+    *   Use "Evaluate" to preview the mask and "Apply" to finalize it.
+3.  **Compute Partition**:
+    *   Go to the "Partition" tab.
+    *   Select the desired mode (e.g., Q-Phi) and configure parameters (number of bins, symmetry).
+    *   Click "Compute Partition" to generate the maps.
+4.  **Save Results**:
+    *   Click "Save" to export the mask (TIFF) or the full partition data (HDF5).
+
+## Credits
+
+This package was created with [Cookiecutter](https://github.com/audreyr/cookiecutter) and the [audreyr/cookiecutter-pypackage](https://github.com/audreyr/cookiecutter-pypackage) project template.
+
+*   **Author**: Miaoqi Chu (mqichu@anl.gov)
+*   **License**: BSD 3-Clause license

pysimplemask-0.3.1/docs/Makefile

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+# Minimal makefile for Sphinx documentation
+#
+
+# You can set these variables from the command line.
+SPHINXOPTS    =
+SPHINXBUILD   = python -msphinx
+SPHINXPROJ    = pysimplemask
+SOURCEDIR     = .
+BUILDDIR      = _build
+
+# Put it first so that "make" without argument is like "make help".
+help:
+	@$(SPHINXBUILD) -M help "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
+
+.PHONY: help Makefile
+
+# Catch-all target: route all unknown targets to Sphinx using the new
+# "make mode" option.  $(O) is meant as a shortcut for $(SPHINXOPTS).
+%: Makefile
+	@$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)

pysimplemask-0.3.1/docs/authors.rst

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+.. include:: ../AUTHORS.rst

pysimplemask-0.3.1/docs/conf.py

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+#!/usr/bin/env python
+#
+# pysimplemask documentation build configuration file, created by
+# sphinx-quickstart on Fri Jun  9 13:47:02 2017.
+#
+# This file is execfile()d with the current directory set to its
+# containing dir.
+#
+# Note that not all possible configuration values are present in this
+# autogenerated file.
+#
+# All configuration values have a default; values that are commented out
+# serve to show the default.
+
+# If extensions (or modules to document with autodoc) are in another
+# directory, add these directories to sys.path here. If the directory is
+# relative to the documentation root, use os.path.abspath to make it
+# absolute, like shown here.
+#
+import os
+import sys
+sys.path.insert(0, os.path.abspath('..'))
+
+import pysimplemask
+
+# -- General configuration ---------------------------------------------
+
+# If your documentation needs a minimal Sphinx version, state it here.
+#
+# needs_sphinx = '1.0'
+
+# Add any Sphinx extension module names here, as strings. They can be
+# extensions coming with Sphinx (named 'sphinx.ext.*') or your custom ones.
+extensions = ['sphinx.ext.autodoc', 'sphinx.ext.viewcode']
+
+# Add any paths that contain templates here, relative to this directory.
+templates_path = ['_templates']
+
+# The suffix(es) of source filenames.
+# You can specify multiple suffix as a list of string:
+#
+# source_suffix = ['.rst', '.md']
+source_suffix = '.rst'
+
+# The master toctree document.
+master_doc = 'index'
+
+# General information about the project.
+project = 'pySimpleMask'
+copyright = "2024, Miaoqi Chu"
+author = "Miaoqi Chu"
+
+# The version info for the project you're documenting, acts as replacement
+# for |version| and |release|, also used in various other places throughout
+# the built documents.
+#
+# The short X.Y version.
+version = pysimplemask.__version__
+# The full version, including alpha/beta/rc tags.
+release = pysimplemask.__version__
+
+# The language for content autogenerated by Sphinx. Refer to documentation
+# for a list of supported languages.
+#
+# This is also used if you do content translation via gettext catalogs.
+# Usually you set "language" from the command line for these cases.
+language = None
+
+# List of patterns, relative to source directory, that match files and
+# directories to ignore when looking for source files.
+# This patterns also effect to html_static_path and html_extra_path
+exclude_patterns = ['_build', 'Thumbs.db', '.DS_Store']
+
+# The name of the Pygments (syntax highlighting) style to use.
+pygments_style = 'sphinx'
+
+# If true, `todo` and `todoList` produce output, else they produce nothing.
+todo_include_todos = False
+
+
+# -- Options for HTML output -------------------------------------------
+
+# The theme to use for HTML and HTML Help pages.  See the documentation for
+# a list of builtin themes.
+#
+html_theme = 'alabaster'
+
+# Theme options are theme-specific and customize the look and feel of a
+# theme further.  For a list of options available for each theme, see the
+# documentation.
+#
+# html_theme_options = {}
+
+# Add any paths that contain custom static files (such as style sheets) here,
+# relative to this directory. They are copied after the builtin static files,
+# so a file named "default.css" will overwrite the builtin "default.css".
+html_static_path = ['_static']
+
+
+# -- Options for HTMLHelp output ---------------------------------------
+
+# Output file base name for HTML help builder.
+htmlhelp_basename = 'pysimplemaskdoc'
+
+
+# -- Options for LaTeX output ------------------------------------------
+
+latex_elements = {
+    # The paper size ('letterpaper' or 'a4paper').
+    #
+    # 'papersize': 'letterpaper',
+
+    # The font size ('10pt', '11pt' or '12pt').
+    #
+    # 'pointsize': '10pt',
+
+    # Additional stuff for the LaTeX preamble.
+    #
+    # 'preamble': '',
+
+    # Latex figure (float) alignment
+    #
+    # 'figure_align': 'htbp',
+}
+
+# Grouping the document tree into LaTeX files. List of tuples
+# (source start file, target name, title, author, documentclass
+# [howto, manual, or own class]).
+latex_documents = [
+    (master_doc, 'pysimplemask.tex',
+     'pySimpleMask Documentation',
+     'Miaoqi Chu', 'manual'),
+]
+
+
+# -- Options for manual page output ------------------------------------
+
+# One entry per manual page. List of tuples
+# (source start file, name, description, authors, manual section).
+man_pages = [
+    (master_doc, 'pysimplemask',
+     'pySimpleMask Documentation',
+     [author], 1)
+]
+
+
+# -- Options for Texinfo output ----------------------------------------
+
+# Grouping the document tree into Texinfo files. List of tuples
+# (source start file, target name, title, author,
+#  dir menu entry, description, category)
+texinfo_documents = [
+    (master_doc, 'pysimplemask',
+     'pySimpleMask Documentation',
+     author,
+     'pysimplemask',
+     'One line description of project.',
+     'Miscellaneous'),
+]
+
+
+

pysimplemask-0.3.1/docs/contributing.rst

@@ -0,0 +1 @@
+.. include:: ../CONTRIBUTING.rst

pysimplemask-0.3.1/docs/history.rst

@@ -0,0 +1 @@
+.. include:: ../HISTORY.rst

pysimplemask-0.3.1/docs/index.rst

@@ -0,0 +1,20 @@
+Welcome to pySimpleMask's documentation!
+======================================
+
+.. toctree::
+   :maxdepth: 2
+   :caption: Contents:
+
+   readme
+   installation
+   usage
+   modules
+   contributing
+   authors
+   history
+
+Indices and tables
+==================
+* :ref:`genindex`
+* :ref:`modindex`
+* :ref:`search`