phys2cvr package

phys2cvr.workflows - Primary workflows

phys2cvr(fname_func[, fname_co2, ...])

Run main workflow of phys2cvr.

phys2cvr.regressors - Create regressors

create_legendre(degree, length)	Produce the Legendre polynomials of order degree.
compute_bulk_shift(func_upsampled, ...[, ...])	Compute (initial) bulk shift of regressor.
create_fine_shift_regressors(petco2hrf, ...)	Compute fine shifts to further optimize shifts.
create_physio_regressor(func_avg, petco2hrf, ...)	Create regressor(s) of interest for nifti GLM.

phys2cvr.stats - Statistics

R2MODEL	Built-in mutable sequence.
x_corr(func, co2[, n_shifts, offset, abs_xcorr])	Compute cross correlation between func and co2.
ols(Ymat, Xmat[, r2model, residuals, demean])	Perform Ordinary Least Squares (OLS) regression.
regression(data, regr[, denoise_mat, ...])	Estimate regression parameters.

phys2cvr.signal - Signal processing related

spc(ts)	Compute signal percentage change over time series (ts).
create_hrf([freq])	Create a canonical haemodynamic response function sampled at the given freq.
filter_signal(data, tr[, lowcut, highcut, ...])	Create a bandpass filter within lower and upper threshold, then filter.
resample_signal_samples(ts, samples[, axis])	Resample timeseries based on desired number of samples.
resample_signal_freqs(ts, freq1, freq2[, axis])	Resample timeseries based on current and desired frequency.

phys2cvr.io - I/O functions: load

load_nifti_get_mask(fname[, is_mask, dim])	Load a nifti-like file and returns its data, its image, and a 3d mask.
load_txt(fname[, shape])	Read files in textual format.
load_mat(fname[, shape])	Read files in MATLAB format.
load_xls(fname[, shape])	Read files in xls format.
load_array(fname[, shape])	Read files in text-like format.
load_physio(fname)	Read peakdet and physiopy objects.

phys2cvr.io - I/O functions: export

export_regressor(regressors_matrix, ntp, ...)	Export generated regressors for fMRI analysis.
export_nifti(data, img, fname)	Export a nifti file.

phys2cvr.io - I/O functions: supported extensions

EXT_1D	Built-in mutable sequence.
EXT_MAT	Built-in mutable sequence.
EXT_ARRAY	Built-in mutable sequence.
EXT_PHYS	Built-in mutable sequence.
EXT_NIFTI	Built-in mutable sequence.
EXT_GIFTI	Built-in mutable sequence.
EXT_NIMG	Built-in mutable sequence.
EXT_ALL	Built-in mutable sequence.

phys2cvr.viz - Visualisations

plot_two_timeseries(ts1, ts2, outname[, ...])	Plot two timeseries.
plot_xcorr(xcorr, outprefix[, freq])	Plot Cross Correlation max and abs max values.

phys2cvr.utils - Utility functions

if_declared_force_type(var, dtype[, ...])	Make sure var is of type dtype.
check_ext(all_ext, fname[, scan, remove])	Check which extension a file has, and possibly remove it.
check_nifti_dim(fname, data[, dim])	Remove extra dimensions.
check_array_dim(fname, data[, shape])	Check dimensions of a matrix.
save_bash_call(fname, outdir)	Save the bash call into file p2d_call.sh.