MossView

MossView is a command-line tool for reading Mössbauer spectra and plotting relative transmission. The main application is src/mossview/cli.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

After installing the package, pass a .mos or .job file to either the mossview command or the module:

mossview data-control/b025a-26.mos
python -m mossview 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.
• The package provides both the mossview console command and python -m mossview.
• legado/README.md describes a historical system and its executables, not the current implementation.

Development and releases

Release versions are controlled by .github/version.txt:

• main uses the release entry and creates a stable PyPI release.
• beta uses the pre-release entry and creates a prerelease. If the entry has no prerelease suffix, the workflow adds b0 automatically (for example, 1.0.3 becomes 1.0.3b0).

When the selected version already exists on PyPI or as a Git tag, the release workflow increments it automatically, updates version.txt and pyproject.toml, commits those changes, and publishes the new version.

License

Distributed under the MIT License. See LICENSE.