openflexure_microscope_server.stitching.FinalStitcher

class documentation

class FinalStitcher(BaseStitcher): (source)

Constructor: FinalStitcher(images_dir, logger, stitching_settings, stitch_tiff)

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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.
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: str, *, logger: logging.Logger, stitching_settings: StitchingSettings, stitch_tiff: bool = False): (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:strThe images directory of the scan to stitch.
logger:logging.LoggerThe logger from the Thing that created this stitcher.
stitching_settings:StitchingSettingsA StitchingSettings model this can be loaded from a HistoricScanData for this scan as a dictionary.
stitch_tiff:boolWhether to stitch a pyramidal TIFF.
def log_buffer(self, buffer: IO[str]): (source)

Log everything in the buffer at INFO level.

def run(self): (source)

Run the final stitch logging any output.

Raises
ChildProcessErrorif exit code is not zero
InvocationCancelledErrorif the action is cancelled.
logger = (source)

Undocumented

def _log_ongoing(self, process: subprocess.Popen[str]): (source)

Log the ongoing process unless it is cancelled.

_extra_args = (source)
overrides openflexure_microscope_server.stitching.BaseStitcher._extra_args

Undocumented

_mode: str = (source)
overrides openflexure_microscope_server.stitching.BaseStitcher._mode

Undocumented