openflexure_microscope_server.stitching.FinalStitcher

class documentation

class FinalStitcher(BaseStitcher): (source)

Constructor: FinalStitcher(images_dir, logger, overlap, correlation_resize, ...)

A class to handle the final stitch for a scan.

Method	`__init__`	Initialise a final stitcher, this has more args than the base class.
Method	`log_buffer`	Log everything in the buffer at INFO level.
Method	`run`	Run the final stitch logging any output.
Instance Variable	`logger`	Undocumented
Method	`_log_ongoing`	Log the ongoing process unless it is cancelled.
Method	`_process_inputs`	Process inputs to ensure `overlap` and `correlation_resize` have values.
Instance Variable	`_extra_args`	Undocumented
Instance Variable	`_mode`	Undocumented

Inherited from BaseStitcher:

Method	`validate_path`	Check path is safe before making a command to run with subprocess.
Instance Variable	`correlation_resize`	Undocumented
Instance Variable	`images_dir`	Undocumented
Instance Variable	`min_overlap`	Undocumented
Property	`command`	The command to run with subprocess.Popen.

def __init__(self, images_dir, *, logger: lt.deps.InvocationLogger, overlap: float | None = None, correlation_resize: float | None = None, stitch_tiff: bool = False, scan_data_dict: dict[str, Any] | None = None): (source) ¶

overrides openflexure_microscope_server.stitching.BaseStitcher.__init__

Initialise a final stitcher, this has more args than the base class.

All args except images_dir are positional only.

Parameters
images_dir	The images directory of the scan to stitch.
logger:`lt.deps.InvocationLogger`	The invocation logger for this stitch process.
overlap:`float \| None`	The scan overlap, if not known enter None. A value will be chosen from the scan_data_dict, or set to a default value if no value is available in the scan_data.
correlation_resize:`float \| None`	The fraction to resize images by when correlating, if not known enter None. A value will be chosen from the scan_data_dict, or set to a default value if no value is available in the scan_data.
stitch_tiff:`bool`	Whether to stitch a pyramidal TIFF.
scan_data_dict:`dict[str, Any] \| None`	The ScanData for this scan as a dictionary. This is used to read/calculate overlap and correlation_resize if they are not provided.

def log_buffer(self, buffer: TextIOWrapper): (source) ¶

Log everything in the buffer at INFO level.

def run(self, cancel: lt.deps.CancelHook): (source) ¶

Run the final stitch logging any output.

Raises
`ChildProcessError`	if exit code is not zero
`InvocationCancelledError`	if the action is cancelled.

logger = (source) ¶

Undocumented

def _log_ongoing(self, process: subprocess.Popen, cancel: lt.deps.CancelHook): (source) ¶

Log the ongoing process unless it is cancelled.

def _process_inputs(self, overlap: float, correlation_resize: float, scan_data_dict: dict[str, Any] | None) -> tuple[float, float]: (source) ¶

Process inputs to ensure overlap and correlation_resize have values.

First the scan_data_dict is inspected for values to allow overlap and correlation_resize to be set correctly, if these values are not available then default values are used, and a warning is logged to the invocation logger.

Parameters
overlap:`float`	overlap as input to __init__
correlation_resize:`float`	correlation_resize as input to __init__
scan_data_dict:`dict[str, Any] \| None`	scan_data_dict as input to __init__

Returns
`tuple[float, float]`	overlap and correlation_resize as floats.

_extra_args = (source) ¶

overrides openflexure_microscope_server.stitching.BaseStitcher._extra_args

Undocumented

_mode: str = (source) ¶

overrides openflexure_microscope_server.stitching.BaseStitcher._mode

Undocumented