nionswift-instrumentation

Nion Swift Instrumentation

The Nion Swift Instrumentation library (used in Nion Swift)

The instrumentation library provides base classes for STEM instrumentation including cameras and scanners.

.. start-badges

.. list-table:: :stub-columns: 1

* - package
  - |version|

.. |version| image:: https://img.shields.io/pypi/v/nionswift-instrumentation.svg :target: https://pypi.org/project/nionswift-instrumentation/ :alt: Latest PyPI version

.. end-badges

More Information

• Changelog <https://github.com/nion-software/nionswift-instrumentation-kit/blob/master/CHANGES.rst>_

• Documentation (stable) <https://nionswift-instrumentation.readthedocs.io/en/stable/>_

• Documentation (latest) <https://nionswift-instrumentation.readthedocs.io/en/latest/>_

Changelog (nionswift-instrumentation)

23.1.0 (2024-10-27)

• Add unique index to session metadata and use in acquisition output data items.
• Fix data handling when single camera frame produced. Add tests.
• Require Numpy 2. Add Python 3.13 support. Drop Python 3.9, 3.10 support.

23.0.0 (2024-06-14)

• Fix #179. Record metadata about collections for acquisitions initiated by acquisition panel.
• Fix #173. Fix issue with using subscan during scan sequence acquisition.
• Add calibration provider to provide alternate display calibrations for acquired data.
• Eliminate possible deadlock during scan view when creating data items (new project).
• Increase precision of current readout in camera panel when current less than 10 pA.
• Fixed issue where acquisition panel would not update properly after changing camera.
• Internal improvements to acquisition data flow to improve reliability and performance.

22.2.0 (2024-02-04)

• Added single frame variants to camera device, utilize when recording.
• Improve error reporting during acquisition panel errors.
• Fix some display issues in the acquisition preferences panel.
• Improve handling of malformed calibrations from instrument.
• General performance and reliability improvements.
• Fix #166. Multi acquire now properly sets exposure time on camera.
• Fix #170. Improve handling of 1D recording data.

22.1.1 (2023-10-25)

• Fix multiple issues with drift correction during scans.
• Fix issue with new acquisition API (still a work in progress)
• Fix issue with 1D and 2D ramp acquisition using wrong device (scan) values.

22.1.0 (2023-10-23)

• Add console startup component to define stem_controller.
• Fix #161. Ensures proper scan after low level changes.
• Allow enabled channels to be set with frame parameters.
• Fix issue where acquisition control being set past last index.
• Begin work on new acquisition API (work in progress).
• Python 3.12 compatibility.

22.0.0 (2023-09-14)

• Fix issues with intermittent errors during synchronized acquisition.
• Fix #13. Scan recorder allows limited-only-by-memory frame count on scan devices.
• Fix #160. Introduce RecordingTask to allow synchronization of recording with other tasks.
• Eliminate special crop region on summed camera acquisition (EELS). Crop region now determined by camera readout area.
• Many improvements to improve ability to replace default scan device; work in progress.
• Simplify acquisition panel slightly (radio button to select mode); work in progress.
• Improvements to metadata handling during acquisition; work in progress.
• Fix 1D ramp acquisition using FOV; add ability to control rotation, too.
• Raise max scan size to 16384x16384 and correctly reduce it when required.
• Performance improvements (latency and frame rate).
• Performance improvements (scan recorder).
• Add Python 3.11 support. Drop 3.8. This will be the last Python 3.9 release, too.
• Fix some issues with subscan handling during synchronized acquisition.

0.21.1 (2023-02-28)

• Fix #151. Properly calibrate subscan/line-scan during synchronized acquisition.
• Improve handling of partial acquisition, directing data to desired data item.
• Fix more acquisition graphic edge cases: graphics only on enabled context displays.
• Fix issue where acquisition graphics would not appear on new channels.

0.21.0 (2022-12-07)

• Fix sync issue with SI (prep scan after camera stopped).
• Require scan_module (scan device and settings) rather than scan_device to be registered.
• Improve progress bars for 1D line scans.
• Only remove graphics from active acquisition data items (fix #127).
• Enable graphics properly when switching projects (fix #133).
• Only invalidate context field of view, rotation, or center changes (fix #140).
• Retain probe position when disabling and re-enabling (fix #139).
• Check channel states for changes before rebuilding thumbnails to avoid flashing.
• Allow scan modules to supply their own control panel UI.
• Make fov_size_nm be a computed property representing fov with aspect ratio applied.
• Add pixel_size_nm and subscan_pixel_size_nm computed properties to frame parameters.
• Handle scan data calibrations when scan data is 1D. Pass through 3D.
• Add channel_indexes_enabled to frame parameters for future use.
• Enable support for Python 3.11.

0.20.8 (2022-09-13)

• Replace flyback_pixels property with calculate_flyback_pixels method.
• Change 2D ramp (tableau) to use relative control values, like 1D ramp.
• Fix regression in multiple shift EELS acquisition.
• Ensure live view calibrations are correct during synchronized acquisition.

0.20.7 (2022-07-26)

• Drift correction improvements, simplified UI. Work in progress.
• Performance and reliability improvements.

0.20.6 (2022-06-06)

• Fix calibration issue on view modes.

0.20.5 (2022-05-28)

• Improve error handling and reporting.
• Use a target size of 64x64 for drift tracking area.
• Allow camera device to supply its own calibrator object.
• Fix PMT issue when index >= 2.
• Allow camera device to specify desired exposure precision.
• Improve support for axis handling in STEM controller.

0.20.4 (2022-02-18)

• Fix sequence/series/tableau when used with a synchronized acquistiion.
• Add optional method to validate camera frame parameters.
• Improve compatibility with older CameraDevice implementations.
• Ensure low level data is not directly used in data items. Fixes phantom data issue.
• Add methods to instrument to get/set configuration parameters.

0.20.3 (2021-12-21)

• Fix issue handling partial acquisition during synchronized/sequence acquisition.
• Improve error handling and notifications after errors.

0.20.2 (2021-12-13)

• Fix issue assembling scan channels during synchronized acquisition when split into sections (drift).
• Add support for camera device 3 (no prepare methods).
• Fix issue with camera state being incorrect in display panel control bar.
• Make auto drift tracker during synchronized acquisition optional (default off).
• Improve error recovery and notification during acquisition errors.
• Improve handling of subscan/drift graphics when switching projects.
• Fix sequence of spectra acquisition when optimized on device.
• Show acquisition activity in activity panel.
• Enable support for Python 3.10.

0.20.0 (2021-11-12)

• Add preliminary acquisition panel for more complex sequence/collection acquisitions.
• Acquisition panel includes 1D ramp (series), 2D ramp (tableau), and other options.
• Add preliminary drift tracker, both manual and automatic. Work in progress.
• Add virtual detector option to MultiAcquire.
• Add option to apply shift for each frame in MultiAcquire.
• Remove unused and incomplete monitor button in camera panel.
• Improve internal documentation by utilizing Python protocols for various interfaces.
• Improve reliability and code quality by enabling Python strict typing.
• Drop support for Python 3.7.

0.19.5 (2021-04-12)

• Improve multiple shift EELS acquire by allowing disabling of dark subtraction and alignment.
• Synchronized acquisition now attached session metadata to resulting data items.

Thanks to Isobel Bicket/McMaster University for multiple shift EELS contributions.

0.19.4 (2021-03-12)

• Compatibility with nionui 0.5.0, nionswift 0.15.5.
• Fix issue with large SI's in wrong storage format (ndata vs h5py).

0.19.3 (2021-01-17)

• Add ability to pass some metadata from camera to final synchronized acquisition data. Temporary.
• Fix issue where record did not work after running synchronized acquisition.
• Add camera base methods for setting and clearing gain reference images.

0.19.2 (2020-12-10)

• Fix issue with probe position graphic when multiple channels enabled.

0.19.1 (2020-12-08)

• Fix issue with metadata in scan recorder result data items.
• Fix issue with spectrum imaging panel Acquire button not getting enabled.
• Rework MultiAcquire to use new partial data item updates.

0.19.0 (2020-08-31)

• Add section-by-section drift correction during synchronized acquisition.
• Add support for specifying drift correction parameters (only used in synchronized acquisition).
• Add record_immediate function for scan devices.
• Add partial updating during synchronized acquisition.
• Add optional help button and ability to register delegate for camera panel to handle.
• Fix numerous issues handling the subscan and beam position graphics.
• Fix issue starting scan record immediately after another one.
• Fix issue with reloading scans with leftover probe/subscan graphics.
• Enable spectrum image acquisition for MultiAcquire.
• Removed y-shift and shifter strength from MultiAcquire.
• Added a time estimate to MultiAcquire.

0.18.3 (2019-11-26)

• Fix issue with subscan handling during SI.
• Improve exception handling during camera initialization.
• Add support for time-based initial calibration style for scans.

0.18.2 (2019-07-22)

• Fix metadata handling in scan devices (was not copying it to the image).

0.18.1 (2019-06-27)

• Fix multi acquire data item calibration handling.

0.18.0 (2019-06-25)

• Change camera to use instrument controller (generalized stem controller).
• Add stubs for 2D control methods.

0.17.0 (2019-04-29)

• Add synchronized acquisition of sub areas and lines.
• Expand ability of custom devices to specify calibration and processing.
• Add multi-acquire panel for acquiring multiple summed sets of spectra with optional energy offsets.
• Support subscan rotation and subscan resolution.
• Improve handling of default stem_controller for camera, scan modules.
• Change shift output messages to match sign of change.

0.16.3 (2019-02-27)

• Change camera exposure time and scan pixel time to have two digits of precision.
• Add 'synchronized state' messages to instrument controller, invoked at start/end of synchronized acquisition.
• Limit scan device pixel time in the case of long camera exposure during synchronized acquisition.

0.16.2 (2018-01-18)

• Fix closing bug in state controller leading to errors when closing document window.

0.16.1 (2018-12-21)

• Change spectrum and 4d images to go into new data items each acquisition.

0.16.0 (2018-12-12)

• Add check mark in context menu to indicate active display panel controller.
• Use new display item capabilities in Nion Swift 0.14.

0.15.1 (2018-10-04)

• Fix race condition when scripting probe position.

0.15.0 (2018-10-03)

• Improve support for sub-scan.
• Expand API and documentation.
• Improve cancel and error handling in synchronized acquisition.
• Remove limitation of PMT to channels 0, 1.
• Add support for acquisition sequence cancellation.

0.14.1 (2018-06-25)

• Add STEM controller methods to access ronchigram camera, eels camera, and scan controller.
• Register all cameras via Registry rather than directly in HardwareSourceManager.
• Improve metadata, calibration, and naming during acquisition recording.

0.14.0 (2018-06-21)

• Introduce camera modules to replace camera devices. Allows more control of camera settings.

0.13.3 (2018-06-18)

• Minor changes to scan acquisition (ensure size is int).
• Fix handling of Ronchigram when scale calibration missing.

0.13.2 (2018-06-04)

• Improve handling of sum/project processing in acquire sequence.
• Improve handling of calibration via calibration controls.
• Fix default handling of dimensional calibrations in acquire sequence.

0.13.1 (2018-05-13)

• Fix manifest.

0.13.0 (2018-05-12)

• Initial version online.