MossView

MossView is a command-line tool for reading Mössbauer spectra and plotting relative transmission. The main application is core-app/mossview.py. It reads counts from a .mos file and, when it finds an associated .job file, uses its metadata for the plot title and velocity scale.

Requirements

• Python 3.8 or later, as declared in pyproject.toml.
• Dependencies listed in requirements.txt: NumPy and Matplotlib, with their transitive dependencies pinned there.

Install the dependencies in a virtual environment if desired:

python -m venv .venv
# Windows PowerShell
.venv\Scripts\Activate.ps1
# macOS or Linux
source .venv/bin/activate
python -m pip install -r requirements.txt

Usage

Run from the repository root and pass a .mos or .job file:

python core-app/mossview.py data-control/b025a-26.mos
python core-app/mossview.py data-control/b025adi.job

When given a .job, MossView tries to locate the .mos file named near the beginning of the job file, then falls back to a file with the same base name. When given a .mos, it looks for a .job that references it or has the same base name. Paths are checked as provided, then relative to the script directory.

The program prints progress and saves a PNG beside the .mos file with the same base name. It also opens an interactive Matplotlib window; close the window to end the process.

Processing flow

1. Resolves the input path and finds the associated .mos and .job files.
2. Reads recognized metadata from the .job's &DATA ... &END block: VMAX (absolute value), ND, and TRIANG. The plot uses VMAX, defaulting to 10 mm/s when unavailable. ND and TRIANG are read but do not affect current processing.
3. Reads counts from the .mos. The parser accepts XML containing a <data> element, as well as text containing numbers. It can read the XML time attribute, but does not currently use it in the plot.
4. Builds a linear velocity scale from -VMAX to +VMAX, with one point per count.
5. Calculates relative transmission as count / maximum_count × 100 and plots Poisson error bars as √count / maximum_count × 100.
6. Saves and displays the plot.

&PARAM block validation

When a .job file is available, the program examines assignments only inside the &PARAM ... &END block. It compares selected parameters with final values found in tables in the same file. It also checks ARX values above 0.5 mm/s when no applicable reference is available. If it finds discrepancies, it writes a copy with the -updated.job suffix, reports the changes, and uses that copy. The original .job is not overwritten by this process.

This correction is a heuristic for numeric discrepancies and ARX values. It is not a complete NORMOS format validator or a guarantee of physical correctness. Review the -updated.job file before using it with another program.

Repository components

Current scope and limitations

• The available interface is a CLI with an interactive plot; there is no dedicated GUI or web application.
• The velocity axis is always linear and symmetric. The program does not use ND or TRIANG to reconstruct other acquisition geometries.
• The permissive text parser extracts numeric tokens but does not support every possible .mos format.
• pyproject.toml sets packages = [] and defines no console command. Run the script directly as shown above; the publishing configuration alone does not provide an installed CLI.
• legado/README.md describes a historical system and its executables, not the current implementation.

Development and releases

Automatic versioning is configured for the main and beta branches with Python Semantic Release. The publishing workflow builds and uploads the package to PyPI when a GitHub release is published. Packaging configuration and workflows are still evolving; to run the tool locally, use the commands in the Usage section.

License

Distributed under the MIT License. See LICENSE.