v1.4.1

• Improve error when no plugins are registered
• Handle case when no Genesis facility/transfer entries are provided
• Animate navigation panel

v1.4.0

• New AmSC IRI client with facility, status, account, and compute APIs
• Facility adapters for ALCF, NERSC, and OLCF; choose compute resource by name; facility shown in Genesis status table
- New AmSC transfer client
• Live status monitoring and shared task-progress reporting for processing and fluorescence pipelines
• New token-management CLIs: ptychodus-iri-tokens and ptychodus-transfer-tokens
• Per-facility helper scripts under src/ptychodus/scripts/genesis/{alcf,nersc,olcf}/
• Update to pty-chi 1.4.0; add Bilinear Hessian reconstructor backend and expose new probe-support methods and magnitude/phase optimization components
• Update PtychoPINN-Torch integration: in-memory prediction, multiple-probe-mode export, sync to upstream API
• Per-reconstructor model autosave / autoload, wired through the Genesis workflow
• Support APS 31-ID LYNX area-detector file format
• ptychodus-bdp: load bad-pixel masks from file
• Clean up diffraction-pattern / probe-position association so pairing is driven strictly by diffraction pattern index, with duplicate-index averaging and interpolation for missing positions; out-of-range patterns are dropped rather than extrapolated
• Paganin object builder (single-material phase retrieval from the central diffraction pattern)
• Hermite probe builder
• Estimate diffraction-pattern crop center and probe-size metrics from raw data
• New ReconstructionAmbiguities estimator (global complex scale, linear phase ramp, sub-pixel shift) so quality metrics compare reconstructions on equal footing
• FRC (Fourier ring correlation) preprocessing, metrics, and GUI panel
• Visualize reconstruction residuals (per-pattern modeled-vs-measured diffraction)
• Revise affine-transform estimator for probe-position correction (RANSAC, Hodges–Lehmann centering)
• Propagator view: improved layout and on-the-fly probe-size metrics
• XMCD dialog fixes
• Allow and gracefully render NaN values in visualizations
• Group navigation subviews in the left-panel toolbar
• Diffraction loading progress monitor
• Fluorescence enhancer progress monitor (shared TaskMonitor) with enhance_fluorescence_local workflow API
• Auto-size item-view columns
• Split the single Dockerfile into per-accelerator variants: Dockerfile.cpu, Dockerfile.cuda, Dockerfile.rocm, Dockerfile.xpu, each with build-arg knobs (CUDA / ROCm / PyTorch versions, XPU base tag)
• Add a podman wrapper script (src/ptychodus/scripts/podman/ptychodus) that builds, runs, and mounts the container with the right GPU / display / volume flags
• New ptychodus-system-check CLI for smoke-checking the installed environment
• Improved documentation and test coverage

v1.3.2

• migrate from gladier and fair-research-login to directly use globus-sdk
• fix probe orthogonalization bug that was introduced in previous release
• move data visualization methods to API
• switch to colorcet for perceptually uniform color maps
• improve forward model for synthetic diffraction pattern generation
• improve API documentation & test coverage

v1.3.1: Expand Python API

• Added position/probe/object generator methods to API
• Cleaned up Globus module
• Updated LYNX automation plugin
• Fix hidden pty-chi widgets
• Added detector pixel geometry to assembled diffraction data
• Added user prompt to sync parameters on settings save
• Bugfix: refresh diffraction info text after allocating patterns array
• Added procedural object builders: Gaussian random field and fractal/simplex noise

v1.3: Remote training & inference

• update packaging
• improve API documentation & update docs
• add diffraction and product file I/O to API
• reduce default logging verbosity
• update trainable reconstructor interface
• grow workflow API to expose more actions, including registering products and transforming probe positions
• update automation modules to use task manager
• update globus modules to use task manager; add remote inference & training workflows
• update processing modules to support background training tasks
• update processing view to simplify GUI
• consolidate controller timers to simplify synchronization tasks
• add diffraction pattern simulator
• add dead leaves procedural object builder
• illumination dialog can display different quantities
• improve numerics in XMCD analyzer
• improve HDF5 file filtering in LYNX automation plugin
• bugfix: diffraction metadata is now applied before assembling array
• random object builder supports blur
• add fallback data source to Polar position file reader
• update PtychoPINN integration and enahance SLAC file readers

v1.2: Improve background task handling (#116)

• introduce “task manager” to improve synchronization of data loading and reconstruction tasks; implement blocking option for diffraction data loading and reconstruction tasks
• several breaking API changes: renamed scan -> probe positions based on user feedback, add option to disable diffraction pattern processing
• implement reconstruction progress monitoring
• fix bad pixels handling and add documentation for good/bad pixel masks
• simplify behavior of crop center editing widgets
• closing diffraction dataset clears visualization
• rework stxm analysis dialog to stxm object builder
• improve object fourier analysis dialog and promote from developer mode
• extract globus integration from workflow module
• rename ptychoshelves readers -> fold_slice readers; fix loss value loading
• change default hdf5 file writer compression method to lzf
• fix fresnel zone plate probe builder for rectangular probes
• display current object and probe pixel sizes in GUI
• remove tike integration
• add convert-to-ptychodus script for translating prepared datasets to ptychodus file format
• update ptychouds-bdp script and batch mode actions to use standard directory layout
• standardize argument naming across scripts
• add convert-to-ptychodus and ptychodus-bdp to project scripts

v1.1.2

What's Changed

• Fix bad pixels implementation by @stevehenke in #114

Full Changelog: v1.1.1...v1.1.2

v1.1.1

• prototype object Fourier analysis dialog
• change background of editable fields in item views
• make diffraction view more responsive by caching diffraction pattern summaries
• update PtychoPINN integration to match recent API changes
• update file readers: APS Polar, APS ISN, LCLS XPP, MAX-IV NanoMax
• better debugging information for troubleshooting HDF5 compression plugins
• fix loss values I/O in HDF5 & NPZ product reader/writer

v1.1.0: v1.1 (#111)

• fix issue with numpy 2.3 vectorize
• changed default file format from NPZ to HDF5
• add readthedocs documentation: ptychodus.readthedocs.io
• update pty-chi integration to support v1.2 api
• add readers for multiple NSLS-II data formats
• read new metadata in ISN diffraction file reader
• read new metadata in LYNX diffraction file reader
• display depth of field and detector numerical aperture in product editor
• renamed "patterns" modules to "diffraction"
• python api changes
  • product api
    • rename costs to losses and use LossValue to record epoch with value
    • add exposure_time_s to metadata
  • reconstruction api
    • add logging to ReconstructorLibrary interface
    • update train output to return training loss and validation loss with epochs
  • workflow api
    • added method to get prepared reconstruct input
    • added method to train reconstructor
• prototype object fourier analysis dialog

v1.0.2: Update to pty-chi 1.1 (#110)

• Update to pty-chi v1.1 api
• Enable loading bad pixels masks from file
• Add sphinx documentation
• Add file readers for APS Polar (4-ID), Ptycho-SAXS (12-ID-E), and ISN (19-ID) instruments
• Update file reader names to be more consistent
• Add support for transposing diffraction patterns
• Bundle xdrlib so MDA file readers work with python 3.13+