darsia.AnalysisBase

class AnalysisBase(baseline, config, update_setup=False)

Bases: object

Standard setup for an image analysis, in particular useful when analyzing a larger set of images in a time series.

Constructor.

Sets up fixed config file required for preprocessing.

Parameters:

baselinestr, Path or list of such

Baseline images, used to set up analysis tools and cleaning tools.

configstr or Path

Path to config dict.

update_setupbool

Flag controlling whether cache in setup routines is emptied.

Methods

batch_analysis(images, **kwargs)	Standard batch analysis.
load_and_process_image(path)	Load image for further analysis.
single_image_analysis(img, **kwargs)	Standard workflow to analyze CO2 phases.

Attributes

config	Config dict from file.
width	Physical width of image.
height	Physical height of image.
origin	Physical origin of origin voxel.
processed_baseline_images	List of corrected baseline images.
drift_correction	Drift correction wrt.
deformation_correction	Local deformation correction wrt.
color_correction	Color correction based on reference colors.
translation_correction	Translation correction based on fixed absolute translation.
curvature_correction	Curvature correction.
uncorrected_base	Baseline image stored as physical image but without corrections.
drift_corrected_base	Baseline image corrected for drift only.

batch_analysis(images, **kwargs)

Standard batch analysis.

Parameters:

imageslist of Path

Paths to batch of images.

**kwargs

Optional keyword arguments used in single_image_analysis.

load_and_process_image(path)

Load image for further analysis. Do all corrections and processing needed.

Parameters:

pathstr or Path

Path to image.

Returns:

darsia.Image

Processed image.

single_image_analysis(img, **kwargs)

Standard workflow to analyze CO2 phases.

Parameters:

imgPath or Image

Path to single image.

**kwargs

Optional keyword arguments.

color_correction

Color correction based on reference colors.

config

Config dict from file.

curvature_correction

Curvature correction.

deformation_correction

Local deformation correction wrt. baseline image.

drift_corrected_base

Baseline image corrected for drift only.

drift_correction

Drift correction wrt. baseline image.

height

Physical height of image.

origin

Physical origin of origin voxel.

processed_baseline_images

List of corrected baseline images.

translation_correction

Translation correction based on fixed absolute translation.

uncorrected_base

Baseline image stored as physical image but without corrections.

width

Physical width of image.