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+

v1.0.1

What's Changed

• Workflow API Improvements by @stevehenke in #109

Full Changelog: v1.0...v1.0.1

v1.0: pty-chi (#103)

• Add integrations for pty-chi and ptychopinn
• Updated template globus configuration file for ALCF Polaris
• New file readers: cSAXS, NSLS-II, SLAC, CSSI, ISN
• Improve diffraction pattern loading: enable binning, padding, and update wizard
• Add diffraction pattern counts meter to GUI
• Implement minimal support for spatially varying probes
• Added ability to rescale model probe power when specified photon count > 0
• Add ability to estimate probe photon count from diffraction data
• Packaging: Update packaging to support wheels and create Dockerfile
• Add position/probe/object file reader adapters for product file readers
• Update analysis dialogs
• Add macro to attempt reconstructions using all standard scan transforms
• Support auto-loading data products from file
• Reconstructions: execute in different thread, add status widget so GUI doesn’t lock up during reconstructions
• Update memory usage display to use LCD widget

v0.7.7

• Update packaging

v0.7.6: Ptycho+XRF Demo (#101)

• Added file readers for LCLS XPP instrument
• Implemented VSPI algorithm for ptycho-enhanced XRF
• Added BDP hooks for ptycho-enhanced XRF
• Extracted reconstructor API
• Added APS S31 batch reconstruction workflow
• Added Ptychoshelves product file reader
• Implemented fix needed to support numpy 2.0
• Added workflow to auto-load product files as they appear
• Cleaned up timers
• Fixed crash when selecting zero-sized region with rectangle tool
• Refactored settings classes to use parametric classes
• Refactor Tike GUI to use parametric view controllers
• Enable syncing product/scan/probe/object parameters to settings
• Make default product name configurable and validate renaming
• Implemented requested GUI change: Start on diffraction patterns view
• Implemented requested GUI change: Renamed HDF5 diffraction file reader
• Implemented requested GUI change: Prompt user to choose diffraction file format
• Reformatted repository using ruff format

v0.7.5

• Update PtychoNN integration to 0.3.x API
• Set default logging level to INFO
• Prototype STXM simulator and probe propagation dialog
• Add defocus distance to disk and rect probe builders
• Fix nanomax scan reader