Merge pull request #25 from AdvancedPhotonSource/mc_dev

Mc dev

Author: AZjk

.github/workflows/publish.yml

@@ -0,0 +1,37 @@
+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

LICENSE

@@ -1,22 +1,42 @@
-MIT License
+Copyright (c) 2026, UChicago Argonne, LLC. All rights reserved.
 
-Copyright (c) 2024, Miaoqi Chu
+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.
 
-Permission is hereby granted, free of charge, to any person obtaining a copy
-of this software and associated documentation files (the "Software"), to deal
-in the Software without restriction, including without limitation the rights
-to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
-copies of the Software, and to permit persons to whom the Software is
-furnished to do so, subject to the following conditions:
+Additionally, redistribution and use in source and binary forms, with
+or without modification, are permitted provided that the following
+conditions are met:
 
-The above copyright notice and this permission notice shall be included in all
-copies or substantial portions of the Software.
+    * Redistributions of source code must retain the above copyright
+      notice, this list of conditions and the following disclaimer.
 
-THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
-IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
-FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
-AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
-LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
-OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
-SOFTWARE.
+    * 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.

README.md

@@ -0,0 +1,78 @@
+# 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

README.rst

@@ -32,20 +32,20 @@ You can either clone the public repository:
 
 .. code-block:: console
 
-    $ git clone git://github.com/AZjk/pysimplemask
+    $ git clone https://github.com/AdvancedPhotonSource/pySimpleMask.git
 
 Or download the `tarball`_:
 
 .. code-block:: console
 
-    $ curl -OJL https://github.com/AZjk/pysimplemask/tarball/master
+    $ curl -OJL https://github.com/AdvancedPhotonSource/pySimpleMask/tarball/master
 
 Once you have a copy of the source, you can install it with:
 
 .. code-block:: console
 
-    $ python setup.py install
+    $ pip install .
 
 
-.. _Github repo: https://github.com/AZjk/pysimplemask
-.. _tarball: https://github.com/AZjk/pysimplemask/tarball/master
+.. _Github repo: https://github.com/AdvancedPhotonSource/pySimpleMask
+.. _tarball: https://github.com/AdvancedPhotonSource/pySimpleMask/tarball/master

docs/installation.rst

@@ -1 +1,24 @@
-.. include:: ../README.rst
+============
+pySimpleMask
+============
+
+**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.

docs/readme.rst

@@ -2,6 +2,10 @@
 Usage
 =====
 
-To use pySimpleMask in a project::
+To launch the pySimpleMask GUI, run::
+    
+    pysimplemask
+
+To use pySimpleMask as a library::
 
     import pysimplemask

docs/usage.rst

@@ -6,15 +6,15 @@ build-backend = "setuptools.build_meta"
 name = "pysimplemask"
 dynamic = ["version"]
 description = "A GUI for creating mask and q-partition maps for scattering patterns in preparation for SAXS/WAXS/XPCS data reduction"
-readme = "README.rst"
+readme = "README.md"
 authors = [{ name = "Miaoqi Chu", email = "mqichu@anl.gov" }]
 maintainers = [{ name = "Miaoqi Chu", email = "mqichu@anl.gov" }]
-license = { text = "MIT license" }
+license = { file = "LICENSE" }
 
 classifiers = [
   "Development Status :: 4 - Beta",
   "Intended Audience :: Science/Research",
-  "License :: OSI Approved :: MIT License",
+  "License :: OSI Approved :: BSD License",
   "Programming Language :: Python :: 3",
   "Programming Language :: Python :: 3.12",
   "Topic :: Scientific/Engineering :: Visualization",
@@ -32,7 +32,7 @@ dependencies = [
   "PySide6==6.8.3",
   "astropy",
   "imagecodecs",
-  "tiffile",
+  "tifffile",
 ]
 
 [project.optional-dependencies]
@@ -47,9 +47,9 @@ dev = [
 pysimplemask = "pysimplemask.cli:main"
 
 [project.urls]
-bugs = "https://github.com/AZjk/pysimplemask/issues"
-changelog = "https://github.com/AZjk/pysimplemask/blob/master/changelog.md"
-homepage = "https://github.com/AZjk/pysimplemask"
+bugs = "https://github.com/AdvancedPhotonSource/pySimpleMask/issues"
+changelog = "https://github.com/AdvancedPhotonSource/pySimpleMask/blob/master/changelog.md"
+homepage = "https://github.com/AdvancedPhotonSource/pySimpleMask"
 
 [tool.setuptools]
 package-dir = { "" = "src" }
@@ -60,6 +60,7 @@ local_scheme = "node-and-timestamp"
 
 [tool.setuptools.package-data]
 "*" = ["*.*"]
+"pysimplemask.resources" = ["*.svg"]
 
 # ---- Mypy ----
 [tool.mypy]

pyproject.toml

@@ -79,6 +79,16 @@ def __init__(self, path=None):
 
         self.setupUi(self)
         self.setWindowTitle(f"pySimpleMask {__version__}")
+        
+        # Set application icon
+        try:
+            from PySide6.QtGui import QIcon
+            icon_path = os.path.join(os.path.dirname(__file__), "resources", "logo.svg")
+            if os.path.exists(icon_path):
+                self.setWindowIcon(QIcon(icon_path))
+        except Exception:
+            pass
+            
         self.btn_load.clicked.connect(self.load)
         self.btn_plot.clicked.connect(self.plot)
         self.btn_compute_qpartition.clicked.connect(self.compute_partition)