Processing

Run AFMSlicer modules.

This module provides entry points for running AFMSlicer as a command line programme.

Functions:

Name	Description
filter_scan	Filter an image and save to ''.topostats''.
process_scan	Process a single image, filtering, slicing and calculating statistics.
slicer_scan	Flatten images and save to ''.topostats''.

filter_scan

filter_scan(topostats_object, config=None)

Filter an image and save to ''.topostats''.

Runs just the first key step of flattening images to remove noise, tilt and optionally scars saving to .topostats for subsequent processing and analyses.

Parameters:

Name	Type	Description	Default
topostats_object	TopoStats	A TopoStats object.	required
config	dict	Dictionary of configuration options for running the Filter stage.	None

Returns:

Type	Description
tuple[str, bool]	Returns a tuple of topostats_object.filename and a bool of whether it successfully filtered.

process_scan

process_scan(topostats_object, config=None)

Process a single image, filtering, slicing and calculating statistics.

Parameters:

Name	Type	Description	Default
topostats_object	dict[str, Union[NDArray, Path, float]]	A dictionary with keys 'image', 'img_path' and 'pixel_to_nm_scaling' containing a file or frames' image, it's path and it's pixel to namometre scaling value.	required
config	dict	Dictionary of configuration options for processing images.	None

Returns:

Type	Description
tuple(str, bool)	Tuple of filename and whether it processed correctly.

slicer_scan

slicer_scan(topostats_object, config=None)

Flatten images and save to ''.topostats''.

Runs just the first key step of flattening images to remove noise, tilt and optionally scars saving to ''.topostats'' for subsequent processing and analyses.

Parameters:

Name	Type	Description	Default
topostats_object	TopoStats	A TopoStats object.	required
config	dict	Dictionary of configuration options for running the Slicing stage.	None

Returns:

Type	Description
tuple[str, AFMSlicer]	Returns a tuple of the AFMSlicer.filename and the processed AFMSlicer object.