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.

Installation

From PyPI

pip install pysimplemask

From Source

1. Clone the repository:

   git clone https://github.com/AdvancedPhotonSource/pySimpleMask.git
   cd pysimplemask

2. Install the package:

   pip install .

Usage

To launch the GUI, simply run the following command in your terminal:

pysimplemask

You can also specify a starting path for data loading:

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 and the audreyr/cookiecutter-pypackage project template.

• Author: Miaoqi Chu (mqichu@anl.gov)
• License: BSD 3-Clause license