v0.6.6

What's Changed

• NEW: Use matplotlib fill_between to show object function uncertainty for multi-batch reconstructions by @carterbox in #70
• BUG: Use average (measured) scan positions in Orchestra dataloader by @carterbox in #71

Full Changelog: v0.6.5...v0.6.6

v0.6.5

• Implement NanoMax DiffractionEndStation file readers

v0.6.4

• Support PtychoNN amplitude+phase model

v0.6.3

• Update to support Tike v0.25 interface
• Update to support Gladier v0.9 interface

v0.6.2: Multislice & Object Comparisons

• Add support for even/odd split reconstructions
• Support object comparisons and Fourier Ring Correlation (FRC)
• Support loading and viewing multi-layer (multislice) objects including layer distance
• Relocate diffraction pattern loading to wizard in detectors view
• Simplify behavior of diffraction pattern crop widgets
• Add new mouse tools to image view: move, ruler, rectangle, line-cut
• Add option to view complex array intensity
• Add color legends for acyclic and cyclic quantities to image view
• Fix tike cost function plots
• Add memory usage monitor widget
• Add Fourier Zone Plate (FZP) presets for several Advanced Photon Source (APS) instruments
• Add space-deliminated scan position reader to support format used for NXSchool IC datasets
• Update interface to support PtychoNN v0.2
• Extract probe/object classes and refactor

v0.6.1: Misc requested fixes (#60)

• Support replacing saturated (bad) pixel values in diffraction patterns
• Change diffraction data directory widget to editable combobox
• Add controls and settings for detector bit depth
• Add data readers for APS 2-ID beamlines: diffraction patterns & scan positions
• Avoid rescaling additional probe mode power when loading from file
• Make scan centroid override behavior more intuitive
• Fix how dimensions are transposed for MATLAB probe and object readers
• Update required PtychoNN version; mention pytorch-gpu package needed for GPU support
• Clean up extraneous log messages

Improve Reconstructor & PtychoNN Training

• Update dependency versions
• Refactor to simplify plugins
• Use floats for scan positions
• Display message dialog when attempting to edit item without parameters
• Include initializer name in probe/object table views
• Handle exceptions when file saving fails
• Support saving multi-mode probes to CSV
• Transpose array dimensions when reading/writing MATLAB files
• Add reader for Bionanoprobe MDA scan files
• Support power decay and orthogonalization when initializing additional probe modes
• Change scan/object mapping: midpoint of scan bounding box now anchored to center of object array
• Object padding is customizable; object grows to maintain center point
• Refactor state data input/output: output now includes object center
• Refactor model to reduce code duplication between reconstructor library adapters
• Reconstruction results are only added to the scan/probe/object repositories when changed
• Add support for extracting object patches via interpolation
• Add controls for changing tike log level
• PtychoNN training and inference are now working
• Implement circular buffers to support PtychoNN continual training workflows
• Can save PtychoNN training data to NPZ file
• Display loss plot in reconstructor view after training
• Add batch mode training hook for workflows
• Add reconstructor API for workflows
• Click to display image view coordinates

Multiprobe & Multiobject Workflows

• Add ability to work with multiple probes and objects simultaneously
• Refactor scan M/V/C to extract item repository classes that are now shared with probe and object M/V/C
• Fix bug with autoloading diffraction data from settings file
• Prevent file type combo box on diffraction data screen from updating too often
• Add ability to specify scan bounding box to use with object array size calculations (needed for consistent reconstructions during data acquisition)
• Add support for generating centered rectangular and concentric scan paths, specialize spiral scan
• Merge random and uniform object initializers and padding options
• Update Tike reconstructor interfaces to work with Tike 0.24.x
• Remove Tike MPI option (not straightforward to support in ptychodus)
• Add mechanism for exporting PtychoNN training data
• Introduce PtychoNN phase centering plugins
• Prototype data reprocessing automation with ability to add delay between processing jobs
• Add model API classes to facilitate writing automation plugins
• Add file readers for CXI diffraction/scan/probe data
• BUG: Combine adjacent whitespace delimiters in LYNX Orchestra loader
• Update detector view to present diffraction dataset as a tree; selecting root displays sum of child diffraction patterns
• Add probe initializer for disk and test patterns
• Reparameterize supergaussian probe initializer using FWHM
• Probe/object controllers live update views while editing parameters
• Autoselect new scan/probe/object after reconstruction
• Add NPZ scan plugin

Workflows & Automation

• Implement Globus flows support using Gladier interface
• Provide an example FuncX endpoint config file for ALCF Polaris
• Add support for dumping/restoring loaded datasets to/from a restart file
• Batch mode reconstruction output file moved from settings file to command line option
• Add support for filtering odd/even scan positions
• Show workflows tab when supporting packages are installed
• Update PtychoNN interface to support training, latest API, and reconstruction parameters
• Update Tike interface to support, multigrid, latest API, and reconstruction parameters
• Add dialog for editing tabular scan parameters
• Fix automatic visualization data range when transformations are applied
• Code now passes all default mypy checks
• Add LYNX Orchestra scan file reader
• Add support for reading processed scan data to LYNX SoftGlueZynq scan file reader
• Add LYNX diffraction data file reader
• Disable GIT LFS
• Fix diffraction pattern image processing pipeline
• Add GUI controls for memory mapping options
• Update diffraction file readers to include detector size metadata
• Fix loading of uncropped diffraction patterns
• Add documentation for globus workflows
• Add prototype automation capability to developer mode
• Fix behavior of dataset file controller file type combo box
• Add readers for PtychoShelves formatted diffraction patterns and scan positions
• Implement prototype automation capability
• Add widget to display Fresnel number

v0.3.1

What's Changed

• REL: Do not include test files in git release archive by @carterbox in #49

Full Changelog: v0.3.0...v0.3.1