lcpca_denoising¶
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nighres.intensity.
lcpca_denoising
(image_list, phase_list=None, ngb_size=4, stdev_cutoff=1.05, min_dimension=0, max_dimension=-1, unwrap=True, process_2d=False, use_rmt=False, save_data=False, overwrite=False, output_dir=None, file_names=None)[source]¶ LCPCA denoising
Denoise multi-contrast data with a local complex-valued PCA-based method
Parameters: - image_list ([niimg]) – List of input images to denoise
- phase_list ([niimg], optional) – List of input phase to denoise (order must match that of image_list)
- ngb_size (int, optional) – Size of the local PCA neighborhood, to be increased with number of inputs (default is 4)
- stdev_cutoff (float, optional) – Factor of local noise level to remove PCA components. Higher values remove more components (default is 1.05)
- min_dimension (int, optional) – Minimum number of kept PCA components (default is 0)
- max_dimension (int, optional) – Maximum number of kept PCA components (default is -1 for all components)
- unwrap (bool, optional) – Whether to unwrap the phase data of keep it as is, assuming radians (default is True)
- process_2d (bool, optional) – Whether to denoise in 2D, for instance when acquiring a thin slab of data (default is False)
- use_rmt (bool, optional) – Whether to use random matrix theory rather than noise fitting to estimate the noise threshold (default is False)
- save_data (bool) – Save output data to file (default is False)
- overwrite (bool) – Overwrite existing results (default is False)
- output_dir (str, optional) – Path to desired output directory, will be created if it doesn’t exist
- file_names ([str], optional) – Desired base names for output files with file extension (suffixes will be added)
Returns: Dictionary collecting outputs under the following keys (suffix of output files in brackets)
- denoised ([niimg]): The list of denoised input images (_lcpca_den)
- dimensions (niimg): Map of the estimated local dimensions (_lcpca_dim)
- residuals (niimg): Estimated residuals between input and denoised images (_lcpca_err)
Return type: Notes
Original Java module by Pierre-Louis Bazin. Algorithm adapted from [1] with a different approach to set the adaptive noise threshold and additional processing to handle the phase data.
References
[1] Manjon, Coupe, Concha, Buades, Collins, Robles (2013). Diffusion Weighted Image Denoising Using Overcomplete Local PCA doi:10.1371/journal.pone.0073021