Version-2.0.0

Release Date : May 2026

This is a major release that consolidates all development since v1.27.5. Versions 1.28.0, 1.29.0, and 1.30.0 were beta milestones leading to this release.

New Features

Add Intensities Single Experiment (AISE) – Major Overhaul

  • Complete rewrite with a new, workflow-oriented UI

  • Built-in workflow guide dialog to walk users through the alignment and summation process

  • Image alignment table (ImageAlignmentTable) with columns for center, rotation, image difference, and transform status; misaligned rows highlighted in red

  • Auto-detection of misaligned images with configurable distance and image-difference thresholds

  • Per-image transform flag: apply (or skip) affine correction to individual images before summation

  • Auto-rotation and auto-center modes; propagate global base correction to subsequent images

  • Global settings dialog for managing the reference (base) image center and rotation

  • Blank image support applied during summation; CSV output of per-image intensity statistics

  • Multiprocessing support for geometry calculations; start/stop toggle on the “Sum Images” button

  • Center overlay visualization in the image viewer

Add Intensities Multiple Experiments (AIME) – New Module

  • New window for combining images across multiple experiment directories

  • Multiple experiment folders can be added at once (“Add Folder” / “Clear List” buttons)

  • Cartesian row-mapping strategy groups images by frame index across experiments

  • Tab-based experiment management with per-tab table views

  • Base name input dialog for naming output files; default base name appends _folded when source filenames contain folded

  • Workflow guide dialog accessible via a “Workflow Guide” button; can be suppressed for future sessions

Quadrant Folding – Background Subtraction Overhaul

  • New BackgroundSubtractionDialog: dedicated popup for all background subtraction controls

  • New background_search.py engine: automated parameter search with optimization cache (optimization_cache.py) to reuse best configurations across images

  • Manual background assignment dialog (ManualBackgroundAssignmentDialog) for per-image overrides

  • Background configurations table: stores multiple named configurations; best match auto-selected during batch processing

  • Optimization timeout feature: cap per-image search time to prevent runaway computations

  • Synthetic Gaussian data generation for quantitative evaluation of background subtraction quality

  • Full evaluation metric suite: MSE against synthetic data, equator metrics, symmetry score, and composite loss; metrics exported to background_metrics.csv

  • Evaluation baseline persistence: optionally fix a reference baseline across the dataset

  • “Optimize each image” mode: run parameter search independently per image

  • Layer-line mask support added to QF processing

  • ROI (Region of Interest) support with ROI translation for headless processing

  • “Save Cropped Image” option removed; only full-size folded images are saved

Quadrant Folding – Image Alignment Detection

  • New QFAlignmentDialog: non-modal dialog reusing the AISE ImageAlignmentWidget for detecting misaligned images within a QF dataset

  • “Detect Image Alignment” button added to QuadrantFoldingGUI

  • Fold symmetry scoring (fold_symmetry.py): quantitative metric exported to CSV and surfaced in the alignment table

Quadrant Folding – Batch Processing

  • Batch processing rewritten to use ProcessPoolExecutor for true parallel execution

  • New process_one_qf_image headless function in mp_executor.py for GUI-free batch processing

  • User-initiated stop: “Stop” button cleanly cancels in-flight tasks with an indeterminate progress dialog

  • Progress bar logic refactored to use taskManager statistics as the single source of truth

Projection Traces – Fitting Performance

  • Analytical Jacobian fast-path for GMM fitting (scipy.optimize.least_squares): significant speedup for ≥ 10 peaks

  • Vectorised L3 batch Gaussian evaluation applied to production layerlineModel

  • Hull-range slicing: fit arrays are cropped to the hull range before fitting

  • ProjectionProcessor refactored to use least_squares (TRF) solver

X-Ray Viewer – New Tools

  • Box Intensity Stats tool (BoxStatsTool): multi-shot rectangular ROI tool for region intensity statistics; boxes are editable and numbered

  • Radius tool (RadiusTool): interactive radial selection on the image

  • Unit selection for calibrated distance display (nm or q-space)

  • Center marker overlay on the image

  • “Export Graph Data to Text File…” (Ctrl+Shift+E): saves current graph profile as a two-column ASCII file

  • XRayViewerGUI integrated with ProcessingWorkspace for consistent file management, display options, navigation, and calibration

Total Diffraction Intensity – Refactored

  • Renamed from TotalDisplayIntensity to TotalDiffractionIntensity across the project

  • Rebuilt UI around ProcessingWorkspace for consistency with other modules

  • Radial range selection added via RadiusTool

Equator – Settings Bindings

  • New eq_settings_bindings.py: centralized loading/saving of Equator settings

  • Settings loaded from and bound to <dataset>/settings/calibration.info; headless path uses the same file

  • New EQ_FittingTab: dedicated fitting settings tab

  • Inpainting option: fill invalid/masked pixels using pyFAI before processing

  • Process pool uses spawn context to avoid Qt fork-safety issues on Linux

Read/Write Directory Separation

  • 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; “Change Output Directory” option added to all major modules

  • Headless modules now validate and respect output directory settings

Architecture

  • New SettingsManager: centralized, Qt-free manager for geometry, auto-geometry cache, blank/mask settings

  • FileManager extended with load_from_sources() and load_from_directories()

  • Cache file naming uses relative paths; ImageData no longer stores raw images to reduce cache size

  • configparser replaced with QSettings for user preferences across launcher and UI components

  • “Fusion” style applied across all modules for consistent UI on all platforms

  • matplotlib backend updated from Qt5Agg to QtAgg; canvas.draw() replaced with canvas.draw_idle()

Startup – PySide6 Environment Check

  • Detects at startup if PySide6 is loaded from outside the active Python prefix

  • Shows a Tkinter error dialog with resolution steps; exits before crashing in C++

  • Bypass with MUSCLEX_SKIP_ENV_CHECK=1

Improvements

  • Projection Traces – sub-pixel support: hull range inputs use QDoubleSpinBox (0.5 step); center calculations no longer rounded to integers; center_log.csv records full-precision center and per-box centerX values

  • QF CSV: summary.csv extended with version, date, blank_enabled, mask_enabled, blank_weight, detector, lambda_sdd; ROI columns standardized; processing flags included

  • QF headless consistency: QuadrantFoldingh applies blank/mask preprocessing from SettingsManager, matching GUI behavior

  • X-Ray Viewer – status bar: d-spacing (nm) shown instead of q-values when calibration available; distance measurements show calibrated Δq / d equivalents

  • X-Ray Viewer – PNG export: off-screen rendering; overlays excluded; playback returns to starting image after completion

  • Status bar: cursor coordinates and radial distance (r_px) shown across all modules

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

  • EquatorImage: interpolation for ignored hull values; mask threshold allows negative values

  • Headless: EquatorWindowh, QuadrantFoldingh, ProjectionTracesh use SettingsManager for center/rotation; CPU worker count limitable

  • Image Blank Dialog: integrated ImageViewerWidget for preview

  • Tooltips: added across AISE, AIME, QF, PT, navigation controls, image mask tool, and center/rotation settings widgets

  • Draw Mask: cross-environment launcher (drawmask_launcher.py) handles venv, pip, and PyInstaller-frozen .deb; PyInstaller hooks for pyFAI and silx collect all required resources

  • macOS installer: .dmg builds restored; multiprocessing.freeze_support() added for frozen apps

  • Launcher – environment check: version mismatch messages clarified; output label changed from “Test results” to “Log excerpt”

Documentation Overhaul

  • All major module docs refreshed: Equator, Quadrant Folding, Projection Traces, X-Ray Viewer, Add Intensities, Scanning Diffraction, Total Diffracted Intensity

  • New dedicated Quadrant Folding – Background Subtraction reference page

  • New Common Settings page consolidating shared configuration across modules

  • Utilities section reorganised; DDF Processor and Convert Rectangle Image to Square Images entries added

  • Deprecated/outdated doc files removed

Code Cleanup

  • Removed deprecated AddIntensitiesMultExp.py, AddIntensitiesExp.py, AddIntensitiesSingleExp_bak.py, CalibrationDialog.py, TotalDisplayIntensity.py

  • Removed deprecated getBlankImageAndMask / getMaskOnly from file_manager.py

  • Background subtraction functions removed from QuadrantFoldingGUI and centralized in BackgroundSubtractionDialog

.. note:: Version 2.0.0 is a major release. This version has been tested on Python 3.10 on Ubuntu 22.04.

Total Changes: ~400 commits since v1.27.5