.git_archival.txt
.gitattributes
.gitignore
.readthedocs.yaml
Dockerfile
LICENSE
README.rst
globus.svg
ptychodus.svg
pyproject.toml
.github/workflows/python-package.yml
docs/Makefile
docs/make.bat
docs/requirements.txt
docs/source/api.rst
docs/source/conf.py
docs/source/getting_started.rst
docs/source/globus.rst
docs/source/index.rst
docs/source/polaris.yaml
docs/source/ptychodus.svg
docs/source/pvapy.rst
docs/source/readers.rst
src/ptychodus/__init__.py
src/ptychodus/__main__.py
src/ptychodus/cli.py
src/ptychodus/convert_to_ptychodus.py
src/ptychodus/ptychodus_bdp.py
src/ptychodus/ptychodus_stream_processor.py
src/ptychodus.egg-info/PKG-INFO
src/ptychodus.egg-info/SOURCES.txt
src/ptychodus.egg-info/dependency_links.txt
src/ptychodus.egg-info/entry_points.txt
src/ptychodus.egg-info/requires.txt
src/ptychodus.egg-info/top_level.txt
src/ptychodus/api/__init__.py
src/ptychodus/api/common.py
src/ptychodus/api/diffraction.py
src/ptychodus/api/fluorescence.py
src/ptychodus/api/geometry.py
src/ptychodus/api/io.py
src/ptychodus/api/object.py
src/ptychodus/api/observer.py
src/ptychodus/api/parametric.py
src/ptychodus/api/plugins.py
src/ptychodus/api/probe.py
src/ptychodus/api/probe_positions.py
src/ptychodus/api/product.py
src/ptychodus/api/propagator.py
src/ptychodus/api/reconstructor.py
src/ptychodus/api/settings.py
src/ptychodus/api/tree.py
src/ptychodus/api/visualization.py
src/ptychodus/api/workflow.py
src/ptychodus/controller/__init__.py
src/ptychodus/controller/automation.py
src/ptychodus/controller/core.py
src/ptychodus/controller/data.py
src/ptychodus/controller/helpers.py
src/ptychodus/controller/image.py
src/ptychodus/controller/memory.py
src/ptychodus/controller/parametric.py
src/ptychodus/controller/ptychonn.py
src/ptychodus/controller/ptychopinn.py
src/ptychodus/controller/settings.py
src/ptychodus/controller/agent/__init__.py
src/ptychodus/controller/agent/core.py
src/ptychodus/controller/agent/item_delegate.py
src/ptychodus/controller/agent/list_model.py
src/ptychodus/controller/diffraction/__init__.py
src/ptychodus/controller/diffraction/core.py
src/ptychodus/controller/diffraction/dataset.py
src/ptychodus/controller/diffraction/dataset_layout.py
src/ptychodus/controller/diffraction/wizard/__init__.py
src/ptychodus/controller/diffraction/wizard/core.py
src/ptychodus/controller/diffraction/wizard/files.py
src/ptychodus/controller/diffraction/wizard/metadata.py
src/ptychodus/controller/diffraction/wizard/patterns.py
src/ptychodus/controller/globus/__init__.py
src/ptychodus/controller/globus/authorization.py
src/ptychodus/controller/globus/core.py
src/ptychodus/controller/globus/status.py
src/ptychodus/controller/globus/table_model.py
src/ptychodus/controller/object/__init__.py
src/ptychodus/controller/object/core.py
src/ptychodus/controller/object/editor_factory.py
src/ptychodus/controller/object/fourier.py
src/ptychodus/controller/object/frc.py
src/ptychodus/controller/object/tree_model.py
src/ptychodus/controller/object/xmcd.py
src/ptychodus/controller/probe/__init__.py
src/ptychodus/controller/probe/core.py
src/ptychodus/controller/probe/editor_factory.py
src/ptychodus/controller/probe/fluorescence.py
src/ptychodus/controller/probe/illumination.py
src/ptychodus/controller/probe/propagator.py
src/ptychodus/controller/probe/tree_model.py
src/ptychodus/controller/probe/zernike.py
src/ptychodus/controller/probe_positions/__init__.py
src/ptychodus/controller/probe_positions/core.py
src/ptychodus/controller/probe_positions/editor_factory.py
src/ptychodus/controller/probe_positions/table_model.py
src/ptychodus/controller/processing/__init__.py
src/ptychodus/controller/processing/core.py
src/ptychodus/controller/processing/parameters.py
src/ptychodus/controller/product/__init__.py
src/ptychodus/controller/product/core.py
src/ptychodus/controller/product/editor.py
src/ptychodus/controller/product/list_model.py
src/ptychodus/controller/ptychi/__init__.py
src/ptychodus/controller/ptychi/core.py
src/ptychodus/controller/ptychi/object.py
src/ptychodus/controller/ptychi/opr.py
src/ptychodus/controller/ptychi/optimizer.py
src/ptychodus/controller/ptychi/probe.py
src/ptychodus/controller/ptychi/probe_positions.py
src/ptychodus/controller/ptychi/reconstructor.py
src/ptychodus/controller/visualization/__init__.py
src/ptychodus/controller/visualization/controller.py
src/ptychodus/controller/visualization/parameters.py
src/ptychodus/controller/visualization/widget.py
src/ptychodus/model/__init__.py
src/ptychodus/model/core.py
src/ptychodus/model/memory.py
src/ptychodus/model/metadata.py
src/ptychodus/model/phase_unwrapper.py
src/ptychodus/model/task_manager.py
src/ptychodus/model/workflow.py
src/ptychodus/model/agent/__init__.py
src/ptychodus/model/agent/argo.py
src/ptychodus/model/agent/chat.py
src/ptychodus/model/agent/core.py
src/ptychodus/model/agent/properties.py
src/ptychodus/model/agent/settings.py
src/ptychodus/model/analysis/__init__.py
src/ptychodus/model/analysis/affine.py
src/ptychodus/model/analysis/core.py
src/ptychodus/model/analysis/diffraction.py
src/ptychodus/model/analysis/fourier.py
src/ptychodus/model/analysis/frc.py
src/ptychodus/model/analysis/illumination.py
src/ptychodus/model/analysis/interpolators.py
src/ptychodus/model/analysis/propagator.py
src/ptychodus/model/analysis/settings.py
src/ptychodus/model/analysis/xmcd.py
src/ptychodus/model/automation/__init__.py
src/ptychodus/model/automation/buffer.py
src/ptychodus/model/automation/core.py
src/ptychodus/model/automation/repository.py
src/ptychodus/model/automation/settings.py
src/ptychodus/model/automation/watcher.py
src/ptychodus/model/diffraction/__init__.py
src/ptychodus/model/diffraction/_loader.py
src/ptychodus/model/diffraction/api.py
src/ptychodus/model/diffraction/bad_pixels.py
src/ptychodus/model/diffraction/core.py
src/ptychodus/model/diffraction/dataset.py
src/ptychodus/model/diffraction/processor.py
src/ptychodus/model/diffraction/settings.py
src/ptychodus/model/diffraction/sizer.py
src/ptychodus/model/fluorescence/__init__.py
src/ptychodus/model/fluorescence/core.py
src/ptychodus/model/fluorescence/settings.py
src/ptychodus/model/fluorescence/two_step.py
src/ptychodus/model/fluorescence/vspi.py
src/ptychodus/model/globus/__init__.py
src/ptychodus/model/globus/_gladier_client.py
src/ptychodus/model/globus/_globus_client.py
src/ptychodus/model/globus/authorizer.py
src/ptychodus/model/globus/client.py
src/ptychodus/model/globus/core.py
src/ptychodus/model/globus/executor.py
src/ptychodus/model/globus/settings.py
src/ptychodus/model/globus/status.py
src/ptychodus/model/processing/__init__.py
src/ptychodus/model/processing/api.py
src/ptychodus/model/processing/context.py
src/ptychodus/model/processing/core.py
src/ptychodus/model/processing/settings.py
src/ptychodus/model/product/__init__.py
src/ptychodus/model/product/api.py
src/ptychodus/model/product/core.py
src/ptychodus/model/product/geometry.py
src/ptychodus/model/product/item.py
src/ptychodus/model/product/item_factory.py
src/ptychodus/model/product/metadata.py
src/ptychodus/model/product/object_repository.py
src/ptychodus/model/product/probe_repository.py
src/ptychodus/model/product/repository.py
src/ptychodus/model/product/scan_repository.py
src/ptychodus/model/product/settings.py
src/ptychodus/model/product/validator.py
src/ptychodus/model/product/object/__init__.py
src/ptychodus/model/product/object/builder.py
src/ptychodus/model/product/object/builder_factory.py
src/ptychodus/model/product/object/dead_leaves.py
src/ptychodus/model/product/object/item.py
src/ptychodus/model/product/object/item_factory.py
src/ptychodus/model/product/object/random.py
src/ptychodus/model/product/object/settings.py
src/ptychodus/model/product/object/stxm.py
src/ptychodus/model/product/probe/__init__.py
src/ptychodus/model/product/probe/average_pattern.py
src/ptychodus/model/product/probe/builder.py
src/ptychodus/model/product/probe/builder_factory.py
src/ptychodus/model/product/probe/disk.py
src/ptychodus/model/product/probe/fzp.py
src/ptychodus/model/product/probe/item.py
src/ptychodus/model/product/probe/item_factory.py
src/ptychodus/model/product/probe/multimodal.py
src/ptychodus/model/product/probe/rect.py
src/ptychodus/model/product/probe/settings.py
src/ptychodus/model/product/probe/super_gaussian.py
src/ptychodus/model/product/probe/zernike.py
src/ptychodus/model/product/probe_positions/__init__.py
src/ptychodus/model/product/probe_positions/bounding_box.py
src/ptychodus/model/product/probe_positions/builder.py
src/ptychodus/model/product/probe_positions/builder_factory.py
src/ptychodus/model/product/probe_positions/cartesian.py
src/ptychodus/model/product/probe_positions/concentric.py
src/ptychodus/model/product/probe_positions/item.py
src/ptychodus/model/product/probe_positions/item_factory.py
src/ptychodus/model/product/probe_positions/lissajous.py
src/ptychodus/model/product/probe_positions/settings.py
src/ptychodus/model/product/probe_positions/spiral.py
src/ptychodus/model/product/probe_positions/streaming.py
src/ptychodus/model/product/probe_positions/transform.py
src/ptychodus/model/ptychi/__init__.py
src/ptychodus/model/ptychi/affine.py
src/ptychodus/model/ptychi/autodiff.py
src/ptychodus/model/ptychi/core.py
src/ptychodus/model/ptychi/device.py
src/ptychodus/model/ptychi/dm.py
src/ptychodus/model/ptychi/enums.py
src/ptychodus/model/ptychi/epie.py
src/ptychodus/model/ptychi/helper.py
src/ptychodus/model/ptychi/lsqml.py
src/ptychodus/model/ptychi/pie.py
src/ptychodus/model/ptychi/rpie.py
src/ptychodus/model/ptychi/settings.py
src/ptychodus/model/ptychonn/__init__.py
src/ptychodus/model/ptychonn/buffers.py
src/ptychodus/model/ptychonn/core.py
src/ptychodus/model/ptychonn/model.py
src/ptychodus/model/ptychonn/reconstructor.py
src/ptychodus/model/ptychonn/settings.py
src/ptychodus/model/ptychopinn/__init__.py
src/ptychodus/model/ptychopinn/core.py
src/ptychodus/model/ptychopinn/enums.py
src/ptychodus/model/ptychopinn/reconstructor.py
src/ptychodus/model/ptychopinn/settings.py
src/ptychodus/model/visualization/__init__.py
src/ptychodus/model/visualization/color_axis.py
src/ptychodus/model/visualization/color_model.py
src/ptychodus/model/visualization/color_model_renderer.py
src/ptychodus/model/visualization/colormap.py
src/ptychodus/model/visualization/colormap_renderer.py
src/ptychodus/model/visualization/components.py
src/ptychodus/model/visualization/core.py
src/ptychodus/model/visualization/renderer.py
src/ptychodus/model/visualization/transformation.py
src/ptychodus/plugins/aps02id_diffraction_file.py
src/ptychodus/plugins/aps04id_polar_diffraction_file.py
src/ptychodus/plugins/aps04id_polar_position_file.py
src/ptychodus/plugins/aps09id_cssi_position_file.py
src/ptychodus/plugins/aps12id_diffraction_file.py
src/ptychodus/plugins/aps12id_position_file.py
src/ptychodus/plugins/aps19id_isn_diffraction_file.py
src/ptychodus/plugins/aps31id_lynx_diffraction_file.py
src/ptychodus/plugins/aps31id_lynx_orchestra_position_file.py
src/ptychodus/plugins/aps31id_lynx_sgz_position_file.py
src/ptychodus/plugins/bad_pixels.py
src/ptychodus/plugins/csv_object_file.py
src/ptychodus/plugins/csv_probe_file.py
src/ptychodus/plugins/cxi_file.py
src/ptychodus/plugins/deconvolution.py
src/ptychodus/plugins/delimited_position_file.py
src/ptychodus/plugins/fold_slice_position_file.py
src/ptychodus/plugins/fold_slice_product_file.py
src/ptychodus/plugins/fresnel_zone_plate.py
src/ptychodus/plugins/h5_diffraction_file.py
src/ptychodus/plugins/h5_product_file.py
src/ptychodus/plugins/lcls_file_readers.py
src/ptychodus/plugins/max_iv_nanomax_diffraction_file.py
src/ptychodus/plugins/max_iv_nanomax_position_file.py
src/ptychodus/plugins/mda_position_file.py
src/ptychodus/plugins/npy_diffraction_file.py
src/ptychodus/plugins/npy_object_file.py
src/ptychodus/plugins/npy_probe_file.py
src/ptychodus/plugins/npz_diffraction_file.py
src/ptychodus/plugins/npz_product_file.py
src/ptychodus/plugins/nsls2_diffraction_file.py
src/ptychodus/plugins/nsls2_position_file.py
src/ptychodus/plugins/nsls2_product_file.py
src/ptychodus/plugins/slac_npz_file.py
src/ptychodus/plugins/sls_csaxs_diffraction_file.py
src/ptychodus/plugins/tiff_diffraction_file.py
src/ptychodus/plugins/upscaling.py
src/ptychodus/plugins/workflow.py
src/ptychodus/plugins/xrf_maps_file.py
src/ptychodus/plugins/_xdrlib/LICENSE
src/ptychodus/plugins/_xdrlib/xdrlib.py
src/ptychodus/plugins/aps33id_velociprobe/__init__.py
src/ptychodus/plugins/aps33id_velociprobe/aps33id_velociprobe_diffraction_file.py
src/ptychodus/plugins/aps33id_velociprobe/aps33id_velociprobe_position_file.py
src/ptychodus/scripts/__init__.py
src/ptychodus/scripts/ptychopinn_tf_test.py
src/ptychodus/view/__init__.py
src/ptychodus/view/agent.py
src/ptychodus/view/core.py
src/ptychodus/view/diffraction.py
src/ptychodus/view/globus.svg
src/ptychodus/view/image.py
src/ptychodus/view/make_qrc.sh
src/ptychodus/view/object.py
src/ptychodus/view/probe.py
src/ptychodus/view/probe_positions.py
src/ptychodus/view/processing.py
src/ptychodus/view/product.py
src/ptychodus/view/ptychodus.svg
src/ptychodus/view/repository.py
src/ptychodus/view/resources.py
src/ptychodus/view/resources.qrc
src/ptychodus/view/settings.py
src/ptychodus/view/visualization.py
src/ptychodus/view/widgets/__init__.py
src/ptychodus/view/widgets/angle_widget.py
src/ptychodus/view/widgets/combo_box_item_delegate.py
src/ptychodus/view/widgets/decimal_line_edit.py
src/ptychodus/view/widgets/decimal_slider.py
src/ptychodus/view/widgets/exception_dialog.py
src/ptychodus/view/widgets/group_box.py
src/ptychodus/view/widgets/length_widget.py
src/ptychodus/view/widgets/progress_bar_item_delegate.py
src/ptychodus/view/widgets/uuid_line_edit.py
tests/aperture.py
tests/test_phase_unwrap.py
tests/test_zernike.py