openflexure_microscope_server.things.smart

class documentation

class SmartScanThing(OFMThing): (source)

Constructor: SmartScanThing(thing_server_interface, default_workflow)

A Thing for scanning samples and interacting with past scans.

SmartScanThing exposes all functionality for automatically scanning samples, previewing live stitching, retrieving data from past scans, and for deleting past scans.

Method	`__enter__`	Open hardware connection when the Thing context manager is opened.
Method	`__exit__`	Clean up after context manager is closed.
Method	`__init__`	Initialise a SmartScanThing saving to and loading from the input directory.
Method	`delete_all_gallery_items`	Delete all the scans on the microscope.
Method	`delete_scan`	Delete the folder for the specified scan.
Method	`download_zip`	Return zip after including any files left until the end.
Method	`get_gallery_bulk_actions`	Return the bulk gallery actions for smart scan.
Method	`get_latest_preview`	Retrieve the latest preview image.
Method	`purge_empty_scans`	Delete all scan folders containing no images at the top level.
Method	`sample_scan`	Move the stage to cover an area, taking images.
Method	`stitch_all_scans`	Check the list of scans, and stitch any that don't have a DZI associated with it.
Method	`stitch_scan`	Generate a stitched image based on stage position metadata.
Method	`workflow_name`	The name of the scan workflow selector.
Method	`workflow_name.setter`	Validate and set workflow_name.
Class Variable	`stitch_automatically`	Whether to run a final stitch at the end of a successful scan.
Class Variable	`stitch_tiff`	Whether or not to also produce a pyramidal tiff at the end of a scan.
Property	`all_workflow_names`	Return a list of all available Scan Workflows.
Property	`gallery_db_engine`	The database engine.
Property	`latest_preview_stitch_path`	The path of the latest preview stitched image, or None if not available.
Property	`latest_preview_stitch_time`	The modification time of the latest preview image, to allow live updating.
Property	`latest_scan_live_details`	The details of any ongoing scan, or the previous scan if no scan ongoing.
Property	`ongoing_scan`	The ScanDirectory object of the ongoing scan.
Property	`scan_data`	The ActiveScanData object holding information about the of the ongoing scan.
Property	`thing_state`	Return a metadata dict for ongoing scan to populate.
Property	`workflow_display_names`	Return a list of the display names of all available Scan Workflows.
Method	`_collect_scan_data`	Collect and return the data for this scan so it cannot be changed mid-scan.
Method	`_delete_scan`	Delete a scan.
Method	`_get_scan_dir`	Undocumented
Method	`_main_scan_loop`	Run the main loop of the scan.
Method	`_manage_stitching_threads`	Manage the stitching threads, starting them if needed and not already running.
Method	`_move_to_next_point`	Move the stage to the next position.
Method	`_perform_final_stitch`	Update the scan zip and perform final stitch of the data.
Method	`_return_to_starting_position`	Return to the initial scan position, if set.
Method	`_run_scan`	Prepare and run the main scan, and perform final actions on completion.
Method	`_save_final_scan_data`	Update scan data JSON file with data only known at the end of the scan.
Class Variable	`_all_workflows`	Undocumented
Class Variable	`_cam`	Undocumented
Class Variable	`_class_settings`	Undocumented
Class Variable	`_show_data_in_gallery`	Undocumented
Class Variable	`_stage`	Undocumented
Instance Variable	`_default_workflow`	Undocumented
Instance Variable	`_gallery_db_engine`	Undocumented
Instance Variable	`_latest_scan_live_details`	Undocumented
Instance Variable	`_ongoing_scan`	Undocumented
Instance Variable	`_preview_stitcher`	Undocumented
Instance Variable	`_scan_data`	Undocumented
Instance Variable	`_scan_lock`	Undocumented
Instance Variable	`_workflow_name`	Undocumented
Property	`_workflow`	The active scan workflow object.

Inherited from OFMThing:

Method	`create_data_path`	Create a `RelativeDataPath` object with this Thing set as the saving Thing.
Property	`data_dir`	The data directory for this thing.
Property	`show_data_in_gallery`	Whether to show in the Gallery.
Instance Variable	`_data_dir`	Undocumented

def __enter__(self) -> Self: (source) ¶

overrides openflexure_microscope_server.things.OFMThing.__enter__

Open hardware connection when the Thing context manager is opened.

def __exit__(self, _exc_type: type[BaseException], _exc_value: BaseException | None, _traceback: TracebackType | None): (source) ¶

overrides openflexure_microscope_server.things.OFMThing.__exit__

Clean up after context manager is closed.

def __init__(self, thing_server_interface: lt.ThingServerInterface, default_workflow: str): (source) ¶

Initialise a SmartScanThing saving to and loading from the input directory.

Parameters
thing_server_interface:`lt.ThingServerInterface`	Undocumented
default_workflow:`str`	The default workflows that smart scan uses if nothing is set in settings.

def delete_all_gallery_items(self): (source) ¶

Delete all the scans on the microscope.

This will irreversibly remove all scanned data from the microscope!

Use with extreme caution.

@lt.endpoint('delete', 'scans/{scan_name}', responses={200: {'description': 'Successfully deleted scan'}, 400: {'description': 'An error occurred while trying to delete scan'}})

def delete_scan(self, scan_name: str): (source) ¶

Delete the folder for the specified scan.

This endpoint allows scans to be deleted from disk.

Parameters
scan_name:`str`	The name of the scan to delete

@lt.action(use_global_lock=False)

def download_zip(self, scan_name: str) -> ZipBlob: (source) ¶

Return zip after including any files left until the end.

The zipfile is returned as a Blob.

def get_gallery_bulk_actions(self) -> list[ActionButton]: (source) ¶

Return the bulk gallery actions for smart scan.

@lt.endpoint('get', 'latest_preview_stitch.jpg', responses={200: {'description': 'A preview-quality stitched image', 'content': {'image/jpeg': {}}}, 404: {'description': 'File not found'}})

def get_latest_preview(self) -> FileResponse: (source) ¶

Retrieve the latest preview image.

@lt.action

def purge_empty_scans(self): (source) ¶

Delete all scan folders containing no images at the top level.

@lt.action

def sample_scan(self, scan_name: str = ''): (source) ¶

Move the stage to cover an area, taking images.

The way the stage moves depends on the selected workflow. If images overlap for a scan workflow then the images can be stitched together into a larger composite image.

@lt.action(use_global_lock=False)

def stitch_all_scans(self): (source) ¶

Check the list of scans, and stitch any that don't have a DZI associated with it.

Raises
`RuntimeError`	if the microscope is currently running a scan

@lt.action(use_global_lock=False)

def stitch_scan(self, scan_name: str): (source) ¶

Generate a stitched image based on stage position metadata.

@lt.setting

def workflow_name(self) -> str: (source) ¶

The name of the scan workflow selector.

@workflow_name.setter

def workflow_name(self, name: str): (source) ¶

Validate and set workflow_name.

stitch_automatically: bool = (source) ¶

Whether to run a final stitch at the end of a successful scan.

stitch_tiff: bool = (source) ¶

Whether or not to also produce a pyramidal tiff at the end of a scan.

@lt.property

all_workflow_names: list[str] = (source) ¶

Return a list of all available Scan Workflows.

@property

gallery_db_engine: ScanGalleryDBEngine = (source) ¶

The database engine.

@property

latest_preview_stitch_path: str | None = (source) ¶

The path of the latest preview stitched image, or None if not available.

@property

latest_preview_stitch_time: float | None = (source) ¶

The modification time of the latest preview image, to allow live updating.

This will return None (null to JS) if there is no preview image to return.

This is used for two reasons:

If all caching was turned off this stitch would be sent over the network repeatedly
If caching was is on, then the stitch will not update when needed.

@lt.property

latest_scan_live_details: LiveScanDetails | None = (source) ¶

The details of any ongoing scan, or the previous scan if no scan ongoing.

@property

ongoing_scan: ScanDirectory = (source) ¶

The ScanDirectory object of the ongoing scan.

Only read this property is a scan is ongoing or it will raise an error.

@property

scan_data: ActiveScanData = (source) ¶

The ActiveScanData object holding information about the of the ongoing scan.

Only read this property is a scan is ongoing or it will raise an error.

@property

thing_state: Mapping[str, Any] = (source) ¶

Return a metadata dict for ongoing scan to populate.

@lt.property

workflow_display_names: dict[str, str] = (source) ¶

Return a list of the display names of all available Scan Workflows.

@_scan_running

def _collect_scan_data(self, workflow: ScanWorkflow) -> ActiveScanData: (source) ¶

Collect and return the data for this scan so it cannot be changed mid-scan.

def _delete_scan(self, scan_name: str) -> bool: (source) ¶

Delete a scan.

def _get_scan_dir(self, scan_name: str) -> ScanDirectory: (source) ¶

Undocumented

@_scan_running

def _main_scan_loop(self, workflow: ScanWorkflow): (source) ¶

Run the main loop of the scan.

This loop runs during a scan, until no more scan x,y positions are remaining.

@_scan_running

def _manage_stitching_threads(self): (source) ¶

Manage the stitching threads, starting them if needed and not already running.

@_scan_running

def _move_to_next_point(self, next_point: tuple[int, int], z_estimate: int | None = None) -> tuple[int, int, int]: (source) ¶

Move the stage to the next position.

If no z_estimate is given then the current stage position is used. Must move to the estimated focused position (although moving below would be marginally faster) because background detect is most reliable at the focused position.

Returns
`tuple[int, int, int]`	the (x,y,z) with the chosen z_estimate

@_scan_running

def _perform_final_stitch(self): (source) ¶

Update the scan zip and perform final stitch of the data.

@_scan_running

def _return_to_starting_position(self): (source) ¶

Return to the initial scan position, if set.

@_scan_running

def _run_scan(self, workflow: ScanWorkflow): (source) ¶

Prepare and run the main scan, and perform final actions on completion.

The result (or exception) from the main scan loop determines whether the scan should be stitched and whether the microscope should return to the starting x,y,z position.

@_scan_running

def _save_final_scan_data(self, scan_result: str): (source) ¶

Update scan data JSON file with data only known at the end of the scan.

Takes scan_result, a string that is either "success", "cancelled by user", or the error that ended the scan.

_all_workflows: Mapping[str, ScanWorkflow] = (source) ¶

Undocumented

_cam: BaseCamera = (source) ¶

Undocumented

_class_settings: dict[str, bool] = (source) ¶

Undocumented

_show_data_in_gallery: bool = (source) ¶

overrides openflexure_microscope_server.things.OFMThing._show_data_in_gallery