Version-1.29.0

Release Date : April 2026

Key Changes

New Features

Read/Write Directory Separation

A major architectural change allowing output files (results, CSV, cache) to be written to a separate directory from the read-only input data:

  • New DirectoryContext utility resolves the effective output directory at runtime

  • New AssociationStore persists per-user input→output directory mappings in ~/.musclex/directory_associations.json

  • New OutputDirDialog widget lets users confirm or change the output directory, with silent reuse of previously stored associations when the directory is writable

  • “Change Output Directory” option added to all major modules: AISE, AIME, Diffraction Centroids, DI Batch, Equator, Projection Traces, Quadrant Folding, X-Ray Viewer

Projection Traces – Sub-pixel Support

  • Hull range inputs and center calculations in ProjectionBoxTab now support floating-point values instead of being restricted to integers; spinboxes changed from QSpinBox to QDoubleSpinBox (0.5 step, 1 decimal place)

X-Ray Viewer – Graph Data Export

  • New “Export Graph Data to Text File…” menu action (Ctrl+Shift+E) saves the current graph profile as a two-column ASCII file (pixel index, intensity), with header metadata including image name, MuscleX version, and acquisition mode

Startup – PySide6 Environment Check

  • MuscleX now detects at startup if PySide6 is loaded from outside the active Python prefix (a common cause of ABI-mismatch segfaults on keyboard input)

  • Shows a clear error dialog (via Tkinter, independent of Qt) with step-by-step instructions for resolving the conflict; exits early instead of crashing later in C++

  • Can be bypassed with MUSCLEX_SKIP_ENV_CHECK=1

AIME – Multi-folder Input

  • Users can now add multiple experiment folders (instead of selecting one at a time)

  • “Add Folder” / “Clear List” buttons replace the previous single-folder browser

  • Duplicate folders are silently ignored; source population logic refactored accordingly

Improvements

  • X-Ray Viewer – PNG export: switched to off-screen rendering for cleaner exports; status message no longer printed after export

  • X-Ray Viewer – measurement overlay: all measurement lines, patches, and text are cleared when the distance measurement box is confirmed

  • X-Ray Viewer – output directory: CSV manager is reset automatically when the output directory changes

  • X-Ray Viewer – status bar coordinates: cursor coordinates now show d-spacing (nm) instead of q-values when calibration is available; radial distance (px) also shown

  • X-Ray Viewer – distance measurement: measured distances show both pixel count and calibrated Δq / d-spacing equivalents when calibration is available

  • UI consistency: “Fusion” style applied across all modules for a consistent look on all platforms

  • matplotlib backend: updated from Qt5Agg to QtAgg and FigureCanvasQTAgg import updated accordingly for PySide6 compatibility; canvas.draw() calls replaced with canvas.draw_idle() for improved UI responsiveness

  • Display options: gray_r (reversed grayscale) added as a colormap option

  • Blank/mask handling: all modules now use SettingsManager methods for loading blank images and masks, replacing direct file_manager calls; logic is centralized and consistent

  • User preferences: launcher and UI components migrated from configparser to QSettings for managing preferences; CollapsibleRightPanel saves its visibility state via QSettings

  • SettingsManager: extended to manage blank and mask settings in addition to geometry

  • Projection Traces – center log: center_log.csv written alongside summary.csv, recording full-precision image center and per-box centerX values

Code Cleanup

  • Removed deprecated AddIntensitiesMultExp.py, AddIntensitiesSingleExp.py (old versions), AddIntensitiesExp.py, AddIntensitiesSingleExp_bak.py, and CalibrationDialog.py

  • Removed deprecated getBlankImageAndMask / getMaskOnly functions from file_manager.py

.. note:: Version 1.29.0 is a feature release. This version has been tested on Python 3.10 on Ubuntu 22.04.

Total Changes: ~33 commits since v1.28.0