tedana.utils.io

Functions to handle file input/output

Functions

ctabsel(ctabfile) Loads a pre-existing component table file
gscontrol_mmix(OCcatd, mmix, mask, acc, rej, …) Perform global signal regression.
split_ts(data, mmix, mask, acc) Splits data time series into accepted component time series and remainder
write_split_ts(data, mmix, mask, acc, rej, …) Splits data into denoised / noise / ignored time series and saves to disk
writect(comptable, n_vols, acc, rej, midk, empty) Saves component table to disk
writefeats(data, mmix, mask, ref_img[, suffix]) Converts data to component space with mmix and saves to disk
writeresults(ts, mask, comptable, mmix, …) Denoises ts and saves all resulting files to disk
writeresults_echoes(catd, mmix, mask, acc, …) Saves individually denoised echos to disk
ctabsel(ctabfile)[source]

Loads a pre-existing component table file

Parameters:ctabfile (str) – Filepath to existing component table
Returns:ctab – Tuple containing arrays of (1) accepted, (2) rejected, (3) mid, and (4) ignored components
Return type:(4,) tuple of numpy.ndarray
gscontrol_mmix(OCcatd, mmix, mask, acc, rej, midk, ref_img)[source]

Perform global signal regression.

Parameters:
  • OCcatd ((S x T) array_like) – Optimally-combined time series data
  • mmix ((C x T) array_like) – Mixing matrix for converting input data to component space, where C is components and T is the same as in OCcatd
  • mask ((S,) array_like) – Boolean mask array
  • acc (list) – Indices of accepted (BOLD) components in mmix
  • rej (list) – Indices of rejected (non-BOLD) components in mmix
  • midk (list) – Indices of mid-K (questionable) components in mmix
  • ref_img (str or img_like) – Reference image to dictate how outputs are saved to disk
split_ts(data, mmix, mask, acc)[source]

Splits data time series into accepted component time series and remainder

Parameters:
  • data ((S x T) array_like) – Input data, where S is samples and T is time
  • mmix ((T x C) array_like) – Mixing matrix for converting input data to component space, where C is components and T is the same as in data
  • mask ((S,) array_like) – Boolean mask array
  • acc (list) – List of accepted components used to subset mmix
Returns:

  • hikts ((S x T) numpy.ndarray) – Time series reconstructed using only components in acc
  • rest ((S x T) numpy.ndarray) – Original data with hikts removed
write_split_ts(data, mmix, mask, acc, rej, midk, ref_img, suffix='')[source]

Splits data into denoised / noise / ignored time series and saves to disk

Parameters:
  • data ((S x T) array_like) – Input time series
  • mmix ((C x T) array_like) – Mixing matrix for converting input data to component space, where C is components and T is the same as in data
  • mask ((S,) array_like) – Boolean mask array
  • acc (list) – Indices of accepted (BOLD) components in mmix
  • rej (list) – Indices of rejected (non-BOLD) components in mmix
  • midk (list) – Indices of mid-K (questionable) components in mmix
  • ref_img (str or img_like) – Reference image to dictate how outputs are saved to disk
  • suffix (str, optional) – Appended to name of saved files (before extension). Default: ‘’
Returns:

varexpl – Percent variance of data explained by extracted + retained components
Return type:

float
writect(comptable, n_vols, acc, rej, midk, empty, ctname='comp_table.txt', varexpl='-1')[source]

Saves component table to disk

Parameters:
  • comptable ((N x 5) array_like) – Array with columns denoting (1) index of component, (2) Kappa score of component, (3) Rho score of component, (4) variance explained by component, and (5) normalized variance explained by component
  • n_vols (int) – Number of volumes in original time series
  • acc (list) – Indices of accepted (BOLD) components in mmix
  • rej (list) – Indices of rejected (non-BOLD) components in mmix
  • midk (list) – Indices of mid-K (questionable) components in mmix
  • empty (list) – Indices of ignored components in mmix
  • ctname (str, optional) – Filename to save comptable to disk. Default ‘comp_table.txt’
  • varexpl (str) – Variance explained by original data
writefeats(data, mmix, mask, ref_img, suffix='')[source]

Converts data to component space with mmix and saves to disk

Parameters:
  • data ((S x T) array_like) – Input time series
  • mmix ((C x T) array_like) – Mixing matrix for converting input data to component space, where C is components and T is the same as in data
  • mask ((S,) array_like) – Boolean mask array
  • ref_img (str or img_like) – Reference image to dictate how outputs are saved to disk
  • suffix (str, optional) – Appended to name of saved files (before extension). Default: ‘’
Returns:

fname – Filepath to saved file
Return type:

str
writeresults(ts, mask, comptable, mmix, n_vols, acc, rej, midk, empty, ref_img)[source]

Denoises ts and saves all resulting files to disk

Parameters:
  • ts ((S x T) array_like) – Time series to denoise and save to disk
  • mask ((S,) array_like) – Boolean mask array
  • comptable ((N x 5) array_like) – Array with columns denoting (1) index of component, (2) Kappa score of component, (3) Rho score of component, (4) variance explained by component, and (5) normalized variance explained by component
  • mmix ((C x T) array_like) – Mixing matrix for converting input data to component space, where C is components and T is the same as in data
  • acc (list) – Indices of accepted (BOLD) components in mmix
  • rej (list) – Indices of rejected (non-BOLD) components in mmix
  • midk (list) – Indices of mid-K (questionable) components in mmix
  • empty (list) – Indices of ignored components in mmix
  • ref_img (str or img_like) – Reference image to dictate how outputs are saved to disk
writeresults_echoes(catd, mmix, mask, acc, rej, midk, ref_img)[source]

Saves individually denoised echos to disk

Parameters:
  • catd ((S x E x T) array_like) – Input data time series
  • mmix ((C x T) array_like) – Mixing matrix for converting input data to component space, where C is components and T is the same as in data
  • mask ((S,) array_like) – Boolean mask array
  • acc (list) – Indices of accepted (BOLD) components in mmix
  • rej (list) – Indices of rejected (non-BOLD) components in mmix
  • midk (list) – Indices of mid-K (questionable) components in mmix
  • ref_img (str or img_like) – Reference image to dictate how outputs are saved to disk