topostats.io#
Functions for reading and writing data.
Attributes#
Classes#
Load the image and image parameters from a file path. |
Functions#
|
Read a YAML file. |
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Write a configuration (stored as a dictionary) to a YAML file. |
Module Contents#
- topostats.io.LOGGER#
- topostats.io.read_yaml(filename: str | pathlib.Path) Dict[source]#
Read a YAML file.
- Parameters:
filename (Union[str, Path]) – YAML file to read.
- Returns:
Dictionary of the file.
- Return type:
Dict
- topostats.io.write_yaml(config: dict, output_dir: str | pathlib.Path) None[source]#
Write a configuration (stored as a dictionary) to a YAML file.
- Parameters:
config (dict) – Configuration dictionary.
output_dir (Union[str, Path]) – Path to save the dictionary to as a YAML file (it will be called ‘config.yaml’).
- class topostats.io.LoadScan(img_path: str | pathlib.Path, channel: str)#
Load the image and image parameters from a file path.
- img_path#
- channel#
- channel_data = None#
- file_path#
- filename#
- suffix#
- image = None#
- pixel_to_nm_scaling = None#
- load_spm() tuple#
Extract image and pixel to nm scaling from the Bruker .spm file.
- _spm_pixel_to_nm_scaling(channel_data) float#
Extract pixel to nm scaling from the SPM image metadata.
- Parameters:
channel_data – Channel data
- Returns:
Pixel to nm scaling factor.
- Return type:
float
- load_ibw() tuple#
Loads image from Asylum Research (Igor) .ibw files
- _ibw_pixel_to_nm_scaling(scan) float#
Extract pixel to nm scaling from the IBW image metadata.
- load_jpk() None#
- static _extract_jpk(jpk: afmformats.mod_creep_compliance.AFMCreepCompliance) numpy.ndarray#
Extract data from jpk object.
- get_data() None#
Method to extract image and pixel to nm scaling.