afmformats.afm_qmap

Functions

afmformats.afm_qmap.qmap_feature(name, unit, cache=False)[source]

Decorator for labeling AFMQMap features

The name and unit are stored as properties of the wrapped function. In addition, the return value of the function can be cached (see cache argument).

Parameters

  • name (str) – Name of the feature

  • unit (str) – Unit of the returned feature

  • cache (bool or callable) – If boolean, determines whether the feature data should be cached or not. If callable, the callable gets an instance of AFMData as an argument and should return an identifier (str) for the current value. If that identifier is the same as in the cache, then the cached value is used.

Classes

  • AFMQMap: Management of quantitative AFM data on a grid

class afmformats.afm_qmap.AFMQMap(path_or_group, meta_override=None, callback=None, modality=None, data_classes_by_modality=None)[source]

Management of quantitative AFM data on a grid

Parameters

  • path_or_group (str or pathlib.Path or afmformats.afm_group.AFMGroup) – The path to the data file or an instance of AFMGroup

  • meta_override (dict) – Dictionary with metadata that is used when loading the data in path.

  • callback (callable or None) – A method that accepts a float between 0 and 1 to externally track the process of loading the data.

  • data_classes_by_modality (dict) – Override the default AFMData class to use for managing the data (see default_data_classes_by_modality): This is e.g. used by index to pass Indentation (which is a subclass of the default AFMForceDistance) for handling “force-indentation” data.

Inheritance

Inheritance diagram of AFMQMap
static feat_core_data_height_base_point_um(afmdata)[source]

Compute the lowest height (measured)

static feat_core_data_piezo_range_um(afmdata)[source]

Compute peak-to-peak piezo range

static feat_core_data_scan_order(afmdata)[source]

Return the enumeration of the dataset

get_coords(which='px')[source]

Get the qmap coordinates for each curve in AFMQMap.group

Parameters

which (str) – “px” for pixels or “um” for microns.

get_qmap(feature, qmap_only=False)[source]

Return the quantitative map for a feature

Parameters

  • feature (str) – Feature to compute map for (see QMap.features)

  • qmap_only – Only return the quantitative map data, not the coordinates

Returns

  • x, y (1d ndarray) – Only returned if qmap_only is False; Pixel grid coordinates along x and y

  • qmap (2d ndarray) – Quantitative map

property extent

extent (x1, x2, y1, y2) [µm]

features

Available features

group

AFM data (instance of afmformats.afm_group.AFMGroup)

property shape

shape of the map [px]

Variables

afmformats.afm_qmap.unit_scales

Scale conversion helper

{'': 1, 'k': 1000.0, 'm': 0.001, 'n': 1e-09, 'p': 1e-12, 'µ': 1e-06}