SIM Reconstruction

API

3D-SIM recontrustrion.

class pycudasirecon.SIMReconstructor(arg0, config)[source]

Bases: object

Main class for SIM reconstruction.

Parameters:

  • arg0 (Union[np.ndarray, Tuple[int, int, int]]) – Either a numpy array of raw data, or a shape tuple (3 integers) that indicate the size of raw data (to be provided later with set_raw).

  • config (str, optional) – Config file path. Currently, the config file must include the otf-file key. by default None

Raises:

ValueError – If the array is not ndim==3 or shape is not a 3-tuple

get_image_params()[source]

Return the current image parameters.

Return type:

ImageParams

get_recon_params()[source]

Return the current reconstruction parameters.

Return type:

ReconParams

get_result()[source]

Return the current reconstruction result.

Return type:

ndarray

process_volume()[source]

Process the current volume.

Return type:

None

set_raw(img)[source]

Assign img as the raw data to be reconstructed.

Return type:

None

pycudasirecon.reconstruct(array, otf=None, psf=None, makeotf_kwargs=None, otf_file=None, **kwargs)[source]

Perform SIM reconstruction on array.

Parameters:

  • array (np.ndarray) – The array to reconstruct

  • otf (array or str or Path, optional) – OTF to use for reconstruction. Either PSF or OTF must be provided, by default None

  • psf (array or str or Path, optional) – PSF to use for reconstruction. Either PSF or OTF must be provided, by default None

  • makeotf_kwargs (dict) – If psf is provided, these kwargs will be passed to the make_otf() function when generating the OTF. See make_otf docstring for details.

  • otf_file (str or Path, optional) – OTF file to use for reconstruction. Either PSF or OTF must be provided, by default None

  • **kwargs (Any) – Reconstruction parameters. See ReconParams for valid keys.

Returns:

The reconstructed array.

Return type:

np.ndarray