From 25360863611726b376664a631ce06f7ae2d0b55d Mon Sep 17 00:00:00 2001 From: maestroque Date: Wed, 12 Jun 2024 18:53:52 +0300 Subject: [PATCH 01/57] Add physutils dependency placeholder --- setup.cfg | 2 ++ 1 file changed, 2 insertions(+) diff --git a/setup.cfg b/setup.cfg index 8b89352..e460ed3 100644 --- a/setup.cfg +++ b/setup.cfg @@ -27,6 +27,8 @@ install_requires = pandas scipy duecredit + # TODO: Uncomment this once it's uploaded to PyPI + # physutils tests_require = pytest >=5.3 test_suite = pytest From f047587b2327796abe7a2c931661359354f36501 Mon Sep 17 00:00:00 2001 From: maestroque Date: Wed, 12 Jun 2024 20:36:36 +0300 Subject: [PATCH 02/57] Initial Physio object integration in cardiac.py --- phys2denoise/metrics/cardiac.py | 34 +++++++++++++++++++-------------- 1 file changed, 20 insertions(+), 14 deletions(-) diff --git a/phys2denoise/metrics/cardiac.py b/phys2denoise/metrics/cardiac.py index 40ebc47..9c933c9 100644 --- a/phys2denoise/metrics/cardiac.py +++ b/phys2denoise/metrics/cardiac.py @@ -6,9 +6,10 @@ from .responses import crf from .utils import apply_function_in_sliding_window as afsw from .utils import convolve_and_rescale +from physutils import physio -def _cardiac_metrics(card, peaks, samplerate, metric, window=6, central_measure="mean"): +def _cardiac_metrics(data, metric, window=6, central_measure="mean"): """ Compute cardiac metrics. @@ -71,8 +72,11 @@ def _cardiac_metrics(card, peaks, samplerate, metric, window=6, central_measure= Annual International Conference of the IEEE Engineering in Medicine and Biology Society (EMBC), doi: 10.1109/EMBC.2016.7591347. """ + # Initialize physio object + data = physio.check_physio(data, ensure_fs=True) + # Convert window to samples, but halves it. - halfwindow_samples = int(round(window * samplerate / 2)) + halfwindow_samples = int(round(window * data.fs / 2)) if central_measure in ["mean", "average", "avg"]: central_measure_operator = np.mean @@ -85,14 +89,14 @@ def _cardiac_metrics(card, peaks, samplerate, metric, window=6, central_measure= f" {central_measure} is not a supported metric of centrality." ) - idx_arr = np.arange(len(card)) + idx_arr = np.arange(len(data)) idx_min = afsw(idx_arr, np.min, halfwindow_samples) idx_max = afsw(idx_arr, np.max, halfwindow_samples) - card_met = np.empty_like(card) + card_met = np.empty_like(data) for n, i in enumerate(idx_min): diff = ( - np.diff(peaks[np.logical_and(peaks >= i, peaks <= idx_max[n])]) / samplerate + np.diff(data.peaks[np.logical_and(data.peaks >= i, data.peaks <= idx_max[n])]) / data.fs ) if metric == "hbi": card_met[n] = central_measure_operator(diff) if diff.size > 0 else 0 @@ -109,13 +113,13 @@ def _cardiac_metrics(card, peaks, samplerate, metric, window=6, central_measure= card_met[np.isnan(card_met)] = 0.0 # Convolve with crf and rescale - card_met = convolve_and_rescale(card_met, crf(samplerate), rescale="rescale") + card_met = convolve_and_rescale(card_met, crf(data.fs), rescale="rescale") return card_met @due.dcite(references.CHANG_CUNNINGHAM_GLOVER_2009) -def heart_rate(card, peaks, samplerate, window=6, central_measure="mean"): +def heart_rate(data, window=6, central_measure="mean"): """ Compute average heart rate (HR) in a sliding window. @@ -168,12 +172,12 @@ def heart_rate(card, peaks, samplerate, window=6, central_measure="mean"): Biology Society (EMBC), doi: 10.1109/EMBC.2016.7591347. """ return _cardiac_metrics( - card, peaks, samplerate, metric="hrv", window=6, central_measure="mean" + data, metric="hrv", window=6, central_measure="mean" ) @due.dcite(references.PINHERO_ET_AL_2016) -def heart_rate_variability(card, peaks, samplerate, window=6, central_measure="mean"): +def heart_rate_variability(data, window=6, central_measure="mean"): """ Compute average heart rate variability (HRV) in a sliding window. @@ -224,12 +228,12 @@ def heart_rate_variability(card, peaks, samplerate, window=6, central_measure="m Biology Society (EMBC), doi: 10.1109/EMBC.2016.7591347. """ return _cardiac_metrics( - card, peaks, samplerate, metric="hrv", window=6, central_measure="std" + data, metric="hrv", window=6, central_measure="std" ) @due.dcite(references.CHEN_2020) -def heart_beat_interval(card, peaks, samplerate, window=6, central_measure="mean"): +def heart_beat_interval(data, window=6, central_measure="mean"): """ Compute average heart beat interval (HBI) in a sliding window. @@ -273,11 +277,11 @@ def heart_beat_interval(card, peaks, samplerate, window=6, central_measure="mean vol. 213, pp. 116707, 2020. """ return _cardiac_metrics( - card, peaks, samplerate, metric="hbi", window=6, central_measure="mean" + data, metric="hbi", window=6, central_measure="mean" ) -def cardiac_phase(peaks, sample_rate, slice_timings, n_scans, t_r): +def cardiac_phase(data, slice_timings, n_scans, t_r): """Calculate cardiac phase from cardiac peaks. Assumes that timing of cardiac events are given in same units @@ -301,11 +305,13 @@ def cardiac_phase(peaks, sample_rate, slice_timings, n_scans, t_r): phase_card : array_like Cardiac phase signal, of shape (n_scans,) """ + # Initialize physio object + data = physio.check_physio(data, ensure_fs=True) assert slice_timings.ndim == 1, "Slice times must be a 1D array" n_slices = np.size(slice_timings) phase_card = np.zeros((n_scans, n_slices)) - card_peaks_sec = peaks / sample_rate + card_peaks_sec = data.peaks / data.fs for i_slice in range(n_slices): # generate slice acquisition timings across all scans times_crSlice = t_r * np.arange(n_scans) + slice_timings[i_slice] From c7fc2eb373fe5120d56abf78c8b6d56e0b3c6c37 Mon Sep 17 00:00:00 2001 From: maestroque Date: Wed, 12 Jun 2024 20:37:57 +0300 Subject: [PATCH 03/57] Style fixes --- phys2denoise/metrics/cardiac.py | 19 ++++++++----------- 1 file changed, 8 insertions(+), 11 deletions(-) diff --git a/phys2denoise/metrics/cardiac.py b/phys2denoise/metrics/cardiac.py index 9c933c9..646d0b3 100644 --- a/phys2denoise/metrics/cardiac.py +++ b/phys2denoise/metrics/cardiac.py @@ -1,12 +1,12 @@ """Denoising metrics for cardio recordings.""" import numpy as np +from physutils import physio from .. import references from ..due import due from .responses import crf from .utils import apply_function_in_sliding_window as afsw from .utils import convolve_and_rescale -from physutils import physio def _cardiac_metrics(data, metric, window=6, central_measure="mean"): @@ -96,7 +96,10 @@ def _cardiac_metrics(data, metric, window=6, central_measure="mean"): card_met = np.empty_like(data) for n, i in enumerate(idx_min): diff = ( - np.diff(data.peaks[np.logical_and(data.peaks >= i, data.peaks <= idx_max[n])]) / data.fs + np.diff( + data.peaks[np.logical_and(data.peaks >= i, data.peaks <= idx_max[n])] + ) + / data.fs ) if metric == "hbi": card_met[n] = central_measure_operator(diff) if diff.size > 0 else 0 @@ -171,9 +174,7 @@ def heart_rate(data, window=6, central_measure="mean"): Annual International Conference of the IEEE Engineering in Medicine and Biology Society (EMBC), doi: 10.1109/EMBC.2016.7591347. """ - return _cardiac_metrics( - data, metric="hrv", window=6, central_measure="mean" - ) + return _cardiac_metrics(data, metric="hrv", window=6, central_measure="mean") @due.dcite(references.PINHERO_ET_AL_2016) @@ -227,9 +228,7 @@ def heart_rate_variability(data, window=6, central_measure="mean"): Annual International Conference of the IEEE Engineering in Medicine and Biology Society (EMBC), doi: 10.1109/EMBC.2016.7591347. """ - return _cardiac_metrics( - data, metric="hrv", window=6, central_measure="std" - ) + return _cardiac_metrics(data, metric="hrv", window=6, central_measure="std") @due.dcite(references.CHEN_2020) @@ -276,9 +275,7 @@ def heart_beat_interval(data, window=6, central_measure="mean"): .. [1] J. E. Chen et al., "Resting-state "physiological networks"", Neuroimage, vol. 213, pp. 116707, 2020. """ - return _cardiac_metrics( - data, metric="hbi", window=6, central_measure="mean" - ) + return _cardiac_metrics(data, metric="hbi", window=6, central_measure="mean") def cardiac_phase(data, slice_timings, n_scans, t_r): From ec8a3dedff409dca0ddd982cce443a375c37d207 Mon Sep 17 00:00:00 2001 From: maestroque Date: Wed, 12 Jun 2024 20:46:54 +0300 Subject: [PATCH 04/57] Minor cardiac.py physio initialization fix --- phys2denoise/metrics/cardiac.py | 42 ++++++++++----------------------- 1 file changed, 12 insertions(+), 30 deletions(-) diff --git a/phys2denoise/metrics/cardiac.py b/phys2denoise/metrics/cardiac.py index 646d0b3..7e2e686 100644 --- a/phys2denoise/metrics/cardiac.py +++ b/phys2denoise/metrics/cardiac.py @@ -22,12 +22,8 @@ def _cardiac_metrics(data, metric, window=6, central_measure="mean"): Parameters ---------- - card : list or 1D numpy.ndarray - Timeseries of recorded cardiac signal - peaks : list or 1D numpy.ndarray - array of peak indexes for card. - samplerate : float - Sampling rate for card, in Hertz. + data : Physio_like + Object containing the timeseries of the recorded cardiac signal metrics : "hbi", "hr", "hrv", string Cardiac metric(s) to calculate. window : float, optional @@ -73,7 +69,7 @@ def _cardiac_metrics(data, metric, window=6, central_measure="mean"): Biology Society (EMBC), doi: 10.1109/EMBC.2016.7591347. """ # Initialize physio object - data = physio.check_physio(data, ensure_fs=True) + data = physio.check_physio(data, ensure_fs=True, copy=True) # Convert window to samples, but halves it. halfwindow_samples = int(round(window * data.fs / 2)) @@ -132,12 +128,8 @@ def heart_rate(data, window=6, central_measure="mean"): Parameters ---------- - card : list or 1D numpy.ndarray - Timeseries of recorded cardiac signal - peaks : list or 1D numpy.ndarray - array of peak indexes for card. - samplerate : float - Sampling rate for card, in Hertz. + data : Physio_like + Object containing the timeseries of the recorded cardiac signal window : float, optional Size of the sliding window, in seconds. Default is 6. @@ -188,12 +180,8 @@ def heart_rate_variability(data, window=6, central_measure="mean"): Parameters ---------- - card : list or 1D numpy.ndarray - Timeseries of recorded cardiac signal - peaks : list or 1D numpy.ndarray - array of peak indexes for card. - samplerate : float - Sampling rate for card, in Hertz. + data : Physio_like + Object containing the timeseries of the recorded cardiac signal window : float, optional Size of the sliding window, in seconds. Default is 6. @@ -238,12 +226,8 @@ def heart_beat_interval(data, window=6, central_measure="mean"): Parameters ---------- - card : list or 1D numpy.ndarray - Timeseries of recorded cardiac signal - peaks : list or 1D numpy.ndarray - array of peak indexes for card. - samplerate : float - Sampling rate for card, in Hertz. + data : Physio_like + Object containing the timeseries of the recorded cardiac signal window : float, optional Size of the sliding window, in seconds. Default is 6. @@ -286,10 +270,8 @@ def cardiac_phase(data, slice_timings, n_scans, t_r): Parameters ---------- - peaks : 1D array_like - Cardiac peak times, in seconds. - sample_rate : float - Sample rate of physio, in Hertz. + data : Physio_like + Object containing the timeseries of the recorded cardiac signal slice_timings : 1D array_like Slice times, in seconds. n_scans : int @@ -303,7 +285,7 @@ def cardiac_phase(data, slice_timings, n_scans, t_r): Cardiac phase signal, of shape (n_scans,) """ # Initialize physio object - data = physio.check_physio(data, ensure_fs=True) + data = physio.check_physio(data, ensure_fs=True, copy=True) assert slice_timings.ndim == 1, "Slice times must be a 1D array" n_slices = np.size(slice_timings) phase_card = np.zeros((n_scans, n_slices)) From 67c4d21d2c0446376d0621072d575ee2cc079cee Mon Sep 17 00:00:00 2001 From: maestroque Date: Wed, 12 Jun 2024 21:08:51 +0300 Subject: [PATCH 05/57] Integrate Physio object for respiratory and multimodal metrics --- phys2denoise/metrics/chest_belt.py | 80 +++++++++++++++--------------- phys2denoise/metrics/multimodal.py | 20 ++++---- 2 files changed, 49 insertions(+), 51 deletions(-) diff --git a/phys2denoise/metrics/chest_belt.py b/phys2denoise/metrics/chest_belt.py index eeeb08a..5739276 100644 --- a/phys2denoise/metrics/chest_belt.py +++ b/phys2denoise/metrics/chest_belt.py @@ -1,6 +1,7 @@ """Denoising metrics for chest belt recordings.""" import numpy as np import pandas as pd +from physutils import physio from scipy.interpolate import interp1d from scipy.stats import zscore @@ -12,7 +13,7 @@ @due.dcite(references.BIRN_2006) -def respiratory_variance_time(resp, peaks, troughs, samplerate, lags=(0, 4, 8, 12)): +def respiratory_variance_time(data, lags=(0, 4, 8, 12)): """ Implement the Respiratory Variance over Time (Birn et al. 2006). @@ -20,14 +21,8 @@ def respiratory_variance_time(resp, peaks, troughs, samplerate, lags=(0, 4, 8, 1 Parameters ---------- - resp: array_like - respiratory belt data - samples x 1 - peaks: array_like - peaks found by peakdet algorithm - troughs: array_like - troughs found by peakdet algorithm - samplerate: float - sample rate in hz of respiratory belt + data : Physio_like + Object containing the timeseries of the recorded respiratory signal lags: tuple lags in seconds of the RVT output. Default is 0, 4, 8, 12. @@ -42,13 +37,15 @@ def respiratory_variance_time(resp, peaks, troughs, samplerate, lags=(0, 4, 8, 1 respiratory-variation-related fluctuations from neuronal-activity-related fluctuations in fMRI”, NeuroImage, vol.31, pp. 1536-1548, 2006. """ - timestep = 1 / samplerate + # Initialize physio object + data = physio.check_physio(data, ensure_fs=True) + timestep = 1 / data.fs # respiration belt timing - time = np.arange(0, len(resp) * timestep, timestep) - peak_vals = resp[peaks] - trough_vals = resp[troughs] - peak_time = time[peaks] - trough_time = time[troughs] + time = np.arange(0, len(data) * timestep, timestep) + peak_vals = data[data.peaks] + trough_vals = data[data.troughs] + peak_time = time[data.peaks] + trough_time = time[data.troughs] mid_peak_time = (peak_time[:-1] + peak_time[1:]) / 2 period = np.diff(peak_time) # interpolate peak values over all timepoints @@ -123,15 +120,13 @@ def respiratory_pattern_variability(resp, window): @due.dcite(references.POWER_2020) -def env(resp, samplerate, window=10): +def env(data, window=10): """Calculate respiratory pattern variability across a sliding window. Parameters ---------- - resp : (X,) :obj:`numpy.ndarray` - A 1D array with the respiratory belt time series. - samplerate : :obj:`float` - Sampling rate for resp, in Hertz. + data : Physio_like + Object containing the timeseries of the recorded respiratory signal window : :obj:`int`, optional Size of the sliding window, in seconds. Default is 10. @@ -155,13 +150,16 @@ def env(resp, samplerate, window=10): young adults scanned at rest, including systematic changes and 'missed' deep breaths," Neuroimage, vol. 204, 2020. """ + # Initialize physio object + data = physio.check_physio(data, ensure_fs=True, copy=True) + # Convert window to Hertz - window = int(window * samplerate) + window = int(window * data.fs) # Calculate RPV across a rolling window env_arr = ( - pd.Series(resp) + pd.Series(data) .rolling(window=window, center=True) .apply(respiratory_pattern_variability, args=(window,)) ) @@ -170,15 +168,13 @@ def env(resp, samplerate, window=10): @due.dcite(references.CHANG_GLOVER_2009) -def respiratory_variance(resp, samplerate, window=6): +def respiratory_variance(data, window=6): """Calculate respiratory variance. Parameters ---------- - resp : (X,) :obj:`numpy.ndarray` - A 1D array with the respiratory belt time series. - samplerate : :obj:`float` - Sampling rate for resp, in Hertz. + data : Physio_like + Object containing the timeseries of the recorded respiratory signal window : :obj:`int`, optional Size of the sliding window, in seconds. Default is 6. @@ -206,27 +202,28 @@ def respiratory_variance(resp, samplerate, window=6): end-tidal CO2, and BOLD signals in resting-state fMRI," Neuroimage, issue 4, vol. 47, pp. 1381-1393, 2009. """ + # Initialize physio object + data = physio.check_physio(data, ensure_fs=True, copy=True) + # Convert window to Hertz - halfwindow_samples = int(round(window * samplerate / 2)) + halfwindow_samples = int(round(window * data.fs / 2)) # Raw respiratory variance - rv_arr = afsw(resp, np.std, halfwindow_samples) + rv_arr = afsw(data, np.std, halfwindow_samples) # Convolve with rrf - rv_out = convolve_and_rescale(rv_arr, rrf(samplerate), rescale="zscore") + rv_out = convolve_and_rescale(rv_arr, rrf(data.fs), rescale="zscore") return rv_out -def respiratory_phase(resp, sample_rate, n_scans, slice_timings, t_r): +def respiratory_phase(data, n_scans, slice_timings, t_r): """Calculate respiratory phase from respiratory signal. Parameters ---------- - resp : 1D array_like - Respiratory signal. - sample_rate : float - Sample rate of physio, in Hertz. + data : Physio_like + Object containing the timeseries of the recorded respiratory signal n_scans Number of volumes in the imaging run. slice_timings @@ -239,16 +236,19 @@ def respiratory_phase(resp, sample_rate, n_scans, slice_timings, t_r): phase_resp : array_like Respiratory phase signal, of shape (n_scans, n_slices). """ + # Initialize physio object + data = physio.check_physio(data, ensure_fs=True, copy=True) + assert slice_timings.ndim == 1, "Slice times must be a 1D array" n_slices = np.size(slice_timings) phase_resp = np.zeros((n_scans, n_slices)) # generate histogram from respiratory signal # TODO: Replace with numpy.histogram - resp_hist, resp_hist_bins = np.histogram(resp, bins=100) + resp_hist, resp_hist_bins = np.histogram(data, bins=100) # first compute derivative of respiration signal - resp_diff = np.diff(resp, n=1) + resp_diff = np.diff(data, n=1) for i_slice in range(n_slices): # generate slice acquisition timings across all scans @@ -256,13 +256,13 @@ def respiratory_phase(resp, sample_rate, n_scans, slice_timings, t_r): phase_resp_crSlice = np.zeros(n_scans) for j_scan in range(n_scans): iphys = int( - max([1, round(times_crSlice[j_scan] * sample_rate)]) + max([1, round(times_crSlice[j_scan] * data.fs)]) ) # closest idx in resp waveform iphys = min([iphys, len(resp_diff)]) # cannot be longer than resp_diff - thisBin = np.argmin(abs(resp[iphys] - resp_hist_bins)) + thisBin = np.argmin(abs(data[iphys] - resp_hist_bins)) numerator = np.sum(resp_hist[0:thisBin]) phase_resp_crSlice[j_scan] = ( - np.math.pi * np.sign(resp_diff[iphys]) * (numerator / len(resp)) + np.math.pi * np.sign(resp_diff[iphys]) * (numerator / len(data)) ) phase_resp[:, i_slice] = phase_resp_crSlice diff --git a/phys2denoise/metrics/multimodal.py b/phys2denoise/metrics/multimodal.py index 7a298b2..3717f78 100644 --- a/phys2denoise/metrics/multimodal.py +++ b/phys2denoise/metrics/multimodal.py @@ -1,6 +1,7 @@ """These functions compute RETROICOR regressors (Glover et al. 2000).""" import numpy as np +from physutils import physio from .. import references from ..due import due @@ -10,8 +11,7 @@ @due.dcite(references.GLOVER_2000) def retroicor( - physio, - sample_rate, + data, t_r, n_scans, slice_timings, @@ -23,12 +23,8 @@ def retroicor( Parameters ---------- - physio : array_like - 1D array, whether cardiac or respiratory signal. - If cardiac, the array is a set of peaks in seconds. - If respiratory, the array is the actual respiratory signal. - sample_rate : float - Physio sample rate, in Hertz. + data : Physio_like + Object containing the timeseries of the recorded respiratory or cardiac signal t_r : float Imaging sample rate, in seconds. n_scans : int @@ -59,6 +55,9 @@ def retroicor( correction of physiological motion effects in fMRI: RETROICOR“, Magn. Reson. Med., issue 1, vol. 44, pp. 162-167, 2000. """ + # Initialize physio object + data = physio.check_physio(data, ensure_fs=True, copy=True) + n_slices = np.shape(slice_timings) # number of slices # initialize output variables @@ -75,7 +74,7 @@ def retroicor( # slice sampling times if card: phase[:, i_slice] = cardiac_phase( - physio, + data, crslice_timings, n_scans, t_r, @@ -83,8 +82,7 @@ def retroicor( if resp: phase[:, i_slice] = respiratory_phase( - physio, - sample_rate, + data, n_scans, slice_timings, t_r, From 2ffa46597ad1cc779c03e4d08e75971105fdb8ad Mon Sep 17 00:00:00 2001 From: maestroque Date: Thu, 13 Jun 2024 02:26:02 +0300 Subject: [PATCH 06/57] Add sample support for object and function oriented usage of metric functions --- phys2denoise/metrics/cardiac.py | 30 ++++++++++++++++++++++++++---- 1 file changed, 26 insertions(+), 4 deletions(-) diff --git a/phys2denoise/metrics/cardiac.py b/phys2denoise/metrics/cardiac.py index 7e2e686..8fb09aa 100644 --- a/phys2denoise/metrics/cardiac.py +++ b/phys2denoise/metrics/cardiac.py @@ -1,6 +1,6 @@ """Denoising metrics for cardio recordings.""" import numpy as np -from physutils import physio +from physutils import io, physio from .. import references from ..due import due @@ -262,7 +262,7 @@ def heart_beat_interval(data, window=6, central_measure="mean"): return _cardiac_metrics(data, metric="hbi", window=6, central_measure="mean") -def cardiac_phase(data, slice_timings, n_scans, t_r): +def cardiac_phase(data, slice_timings, n_scans, t_r, fs=None, peaks=None): """Calculate cardiac phase from cardiac peaks. Assumes that timing of cardiac events are given in same units @@ -284,8 +284,30 @@ def cardiac_phase(data, slice_timings, n_scans, t_r): phase_card : array_like Cardiac phase signal, of shape (n_scans,) """ - # Initialize physio object - data = physio.check_physio(data, ensure_fs=True, copy=True) + if isinstance(data, physio.Physio): + # Initialize physio object + data = physio.check_physio(data, ensure_fs=True, copy=True) + elif fs is not None and peaks is not None: + data = io.load_physio(data, fs=fs) + data._metadata["peaks"] = peaks + else: + raise ValueError( + """ + To use this function you should either provide a Physio object + with existing peaks metadata (e.g. using the peakdet module), or + by providing the physiological data timeseries, the sampling frequency, + and the peak indices separately. + """ + ) + if not data.peaks: + raise ValueError( + """ + Peaks must be a non-empty list. + Make sure to run peak detection on your physiological data first, + using the peakdet module, or other software of your choice. + """ + ) + assert slice_timings.ndim == 1, "Slice times must be a 1D array" n_slices = np.size(slice_timings) phase_card = np.zeros((n_scans, n_slices)) From 9fa3467cd30e88a37a3688c067bdf52c747cb2e6 Mon Sep 17 00:00:00 2001 From: maestroque Date: Mon, 24 Jun 2024 16:08:03 +0300 Subject: [PATCH 07/57] Make metric functions operations --- phys2denoise/metrics/cardiac.py | 4 ++++ phys2denoise/metrics/chest_belt.py | 5 +++++ phys2denoise/metrics/multimodal.py | 1 + 3 files changed, 10 insertions(+) diff --git a/phys2denoise/metrics/cardiac.py b/phys2denoise/metrics/cardiac.py index 8fb09aa..428151d 100644 --- a/phys2denoise/metrics/cardiac.py +++ b/phys2denoise/metrics/cardiac.py @@ -118,6 +118,7 @@ def _cardiac_metrics(data, metric, window=6, central_measure="mean"): @due.dcite(references.CHANG_CUNNINGHAM_GLOVER_2009) +@physio.make_operation() def heart_rate(data, window=6, central_measure="mean"): """ Compute average heart rate (HR) in a sliding window. @@ -170,6 +171,7 @@ def heart_rate(data, window=6, central_measure="mean"): @due.dcite(references.PINHERO_ET_AL_2016) +@physio.make_operation() def heart_rate_variability(data, window=6, central_measure="mean"): """ Compute average heart rate variability (HRV) in a sliding window. @@ -220,6 +222,7 @@ def heart_rate_variability(data, window=6, central_measure="mean"): @due.dcite(references.CHEN_2020) +@physio.make_operation() def heart_beat_interval(data, window=6, central_measure="mean"): """ Compute average heart beat interval (HBI) in a sliding window. @@ -262,6 +265,7 @@ def heart_beat_interval(data, window=6, central_measure="mean"): return _cardiac_metrics(data, metric="hbi", window=6, central_measure="mean") +@physio.make_operation() def cardiac_phase(data, slice_timings, n_scans, t_r, fs=None, peaks=None): """Calculate cardiac phase from cardiac peaks. diff --git a/phys2denoise/metrics/chest_belt.py b/phys2denoise/metrics/chest_belt.py index 5739276..79467bd 100644 --- a/phys2denoise/metrics/chest_belt.py +++ b/phys2denoise/metrics/chest_belt.py @@ -13,6 +13,7 @@ @due.dcite(references.BIRN_2006) +@physio.make_operation() def respiratory_variance_time(data, lags=(0, 4, 8, 12)): """ Implement the Respiratory Variance over Time (Birn et al. 2006). @@ -78,6 +79,7 @@ def respiratory_variance_time(data, lags=(0, 4, 8, 12)): @due.dcite(references.POWER_2018) +@physio.make_operation() def respiratory_pattern_variability(resp, window): """Calculate respiratory pattern variability. @@ -120,6 +122,7 @@ def respiratory_pattern_variability(resp, window): @due.dcite(references.POWER_2020) +@physio.make_operation() def env(data, window=10): """Calculate respiratory pattern variability across a sliding window. @@ -168,6 +171,7 @@ def env(data, window=10): @due.dcite(references.CHANG_GLOVER_2009) +@physio.make_operation() def respiratory_variance(data, window=6): """Calculate respiratory variance. @@ -217,6 +221,7 @@ def respiratory_variance(data, window=6): return rv_out +@physio.make_operation() def respiratory_phase(data, n_scans, slice_timings, t_r): """Calculate respiratory phase from respiratory signal. diff --git a/phys2denoise/metrics/multimodal.py b/phys2denoise/metrics/multimodal.py index 3717f78..f8c6968 100644 --- a/phys2denoise/metrics/multimodal.py +++ b/phys2denoise/metrics/multimodal.py @@ -10,6 +10,7 @@ @due.dcite(references.GLOVER_2000) +@physio.make_operation() def retroicor( data, t_r, From 380ab65739570bed7f5d9cfe91933a792a00ecb7 Mon Sep 17 00:00:00 2001 From: maestroque Date: Mon, 24 Jun 2024 16:20:28 +0300 Subject: [PATCH 08/57] Add Physio and non-Physio compatibility to cardiac.py --- phys2denoise/metrics/cardiac.py | 67 ++++++++++++++++++++++++++++----- 1 file changed, 58 insertions(+), 9 deletions(-) diff --git a/phys2denoise/metrics/cardiac.py b/phys2denoise/metrics/cardiac.py index 428151d..00fe312 100644 --- a/phys2denoise/metrics/cardiac.py +++ b/phys2denoise/metrics/cardiac.py @@ -9,7 +9,9 @@ from .utils import convolve_and_rescale -def _cardiac_metrics(data, metric, window=6, central_measure="mean"): +def _cardiac_metrics( + data, metric, fs=None, peaks=None, window=6, central_measure="mean" +): """ Compute cardiac metrics. @@ -26,6 +28,10 @@ def _cardiac_metrics(data, metric, window=6, central_measure="mean"): Object containing the timeseries of the recorded cardiac signal metrics : "hbi", "hr", "hrv", string Cardiac metric(s) to calculate. + fs : float, optional if data is a physutils.Physio + Sampling rate of `data` in Hz + peaks : :obj:`numpy.ndarray`, optional if data is a physutils.Physio + Indices of peaks in `data` window : float, optional Size of the sliding window, in seconds. Default is 6. @@ -68,8 +74,29 @@ def _cardiac_metrics(data, metric, window=6, central_measure="mean"): Annual International Conference of the IEEE Engineering in Medicine and Biology Society (EMBC), doi: 10.1109/EMBC.2016.7591347. """ - # Initialize physio object - data = physio.check_physio(data, ensure_fs=True, copy=True) + if isinstance(data, physio.Physio): + # Initialize physio object + data = physio.check_physio(data, ensure_fs=True, copy=True) + elif fs is not None and peaks is not None: + data = io.load_physio(data, fs=fs) + data._metadata["peaks"] = peaks + else: + raise ValueError( + """ + To use this function you should either provide a Physio object + with existing peaks metadata (e.g. using the peakdet module), or + by providing the physiological data timeseries, the sampling frequency, + and the peak indices separately. + """ + ) + if not data.peaks: + raise ValueError( + """ + Peaks must be a non-empty list. + Make sure to run peak detection on your physiological data first, + using the peakdet module, or other software of your choice. + """ + ) # Convert window to samples, but halves it. halfwindow_samples = int(round(window * data.fs / 2)) @@ -119,7 +146,7 @@ def _cardiac_metrics(data, metric, window=6, central_measure="mean"): @due.dcite(references.CHANG_CUNNINGHAM_GLOVER_2009) @physio.make_operation() -def heart_rate(data, window=6, central_measure="mean"): +def heart_rate(data, fs=None, peaks=None, window=6, central_measure="mean"): """ Compute average heart rate (HR) in a sliding window. @@ -131,6 +158,10 @@ def heart_rate(data, window=6, central_measure="mean"): ---------- data : Physio_like Object containing the timeseries of the recorded cardiac signal + fs : float, optional if data is a physutils.Physio + Sampling rate of `data` in Hz + peaks : :obj:`numpy.ndarray`, optional if data is a physutils.Physio + Indices of peaks in `data` window : float, optional Size of the sliding window, in seconds. Default is 6. @@ -167,12 +198,14 @@ def heart_rate(data, window=6, central_measure="mean"): Annual International Conference of the IEEE Engineering in Medicine and Biology Society (EMBC), doi: 10.1109/EMBC.2016.7591347. """ - return _cardiac_metrics(data, metric="hrv", window=6, central_measure="mean") + return _cardiac_metrics( + data, metric="hrv", fs=fs, peaks=peaks, window=6, central_measure="mean" + ) @due.dcite(references.PINHERO_ET_AL_2016) @physio.make_operation() -def heart_rate_variability(data, window=6, central_measure="mean"): +def heart_rate_variability(data, fs=None, peaks=None, window=6, central_measure="mean"): """ Compute average heart rate variability (HRV) in a sliding window. @@ -184,6 +217,10 @@ def heart_rate_variability(data, window=6, central_measure="mean"): ---------- data : Physio_like Object containing the timeseries of the recorded cardiac signal + fs : float, optional if data is a physutils.Physio + Sampling rate of `data` in Hz + peaks : :obj:`numpy.ndarray`, optional if data is a physutils.Physio + Indices of peaks in `data` window : float, optional Size of the sliding window, in seconds. Default is 6. @@ -218,12 +255,14 @@ def heart_rate_variability(data, window=6, central_measure="mean"): Annual International Conference of the IEEE Engineering in Medicine and Biology Society (EMBC), doi: 10.1109/EMBC.2016.7591347. """ - return _cardiac_metrics(data, metric="hrv", window=6, central_measure="std") + return _cardiac_metrics( + data, metric="hrv", fs=None, peaks=None, window=6, central_measure="std" + ) @due.dcite(references.CHEN_2020) @physio.make_operation() -def heart_beat_interval(data, window=6, central_measure="mean"): +def heart_beat_interval(data, fs=None, peaks=None, window=6, central_measure="mean"): """ Compute average heart beat interval (HBI) in a sliding window. @@ -231,6 +270,10 @@ def heart_beat_interval(data, window=6, central_measure="mean"): ---------- data : Physio_like Object containing the timeseries of the recorded cardiac signal + fs : float, optional if data is a physutils.Physio + Sampling rate of `data` in Hz + peaks : :obj:`numpy.ndarray`, optional if data is a physutils.Physio + Indices of peaks in `data` window : float, optional Size of the sliding window, in seconds. Default is 6. @@ -262,7 +305,9 @@ def heart_beat_interval(data, window=6, central_measure="mean"): .. [1] J. E. Chen et al., "Resting-state "physiological networks"", Neuroimage, vol. 213, pp. 116707, 2020. """ - return _cardiac_metrics(data, metric="hbi", window=6, central_measure="mean") + return _cardiac_metrics( + data, metric="hbi", fs=None, peaks=None, window=6, central_measure="mean" + ) @physio.make_operation() @@ -282,6 +327,10 @@ def cardiac_phase(data, slice_timings, n_scans, t_r, fs=None, peaks=None): Number of volumes in the imaging run. t_r : float Sampling rate of the imaging run, in seconds. + fs : float, optional if data is a physutils.Physio + Sampling rate of `data` in Hz + peaks : :obj:`numpy.ndarray`, optional if data is a physutils.Physio + Indices of peaks in `data` Returns ------- From 59ee6c8aa11b2eeb43dfa4ea7f37d2b65dbe693f Mon Sep 17 00:00:00 2001 From: maestroque Date: Mon, 24 Jun 2024 18:27:55 +0300 Subject: [PATCH 09/57] Add Physio and non-Physio compatibility to chest_belt.py --- phys2denoise/metrics/chest_belt.py | 110 ++++++++++++++++++++++++----- 1 file changed, 93 insertions(+), 17 deletions(-) diff --git a/phys2denoise/metrics/chest_belt.py b/phys2denoise/metrics/chest_belt.py index 79467bd..e48865a 100644 --- a/phys2denoise/metrics/chest_belt.py +++ b/phys2denoise/metrics/chest_belt.py @@ -1,7 +1,7 @@ """Denoising metrics for chest belt recordings.""" import numpy as np import pandas as pd -from physutils import physio +from physutils import io, physio from scipy.interpolate import interp1d from scipy.stats import zscore @@ -14,7 +14,9 @@ @due.dcite(references.BIRN_2006) @physio.make_operation() -def respiratory_variance_time(data, lags=(0, 4, 8, 12)): +def respiratory_variance_time( + data, fs=None, peaks=None, troughs=None, lags=(0, 4, 8, 12) +): """ Implement the Respiratory Variance over Time (Birn et al. 2006). @@ -24,6 +26,12 @@ def respiratory_variance_time(data, lags=(0, 4, 8, 12)): ---------- data : Physio_like Object containing the timeseries of the recorded respiratory signal + fs : float, optional if data is a physutils.Physio + Sampling rate of `data` in Hz + peaks : :obj:`numpy.ndarray`, optional if data is a physutils.Physio + Indices of peaks in `data` + troughs : :obj:`numpy.ndarray`, optional if data is a physutils.Physio + Indices of troughs in `data` lags: tuple lags in seconds of the RVT output. Default is 0, 4, 8, 12. @@ -38,8 +46,31 @@ def respiratory_variance_time(data, lags=(0, 4, 8, 12)): respiratory-variation-related fluctuations from neuronal-activity-related fluctuations in fMRI”, NeuroImage, vol.31, pp. 1536-1548, 2006. """ - # Initialize physio object - data = physio.check_physio(data, ensure_fs=True) + if isinstance(data, physio.Physio): + # Initialize physio object + data = physio.check_physio(data, ensure_fs=True, copy=True) + elif fs is not None and peaks is not None and troughs is not None: + data = io.load_physio(data, fs=fs) + data._metadata["peaks"] = peaks + data._metadata["troughs"] = troughs + else: + raise ValueError( + """ + To use this function you should either provide a Physio object + with existing peaks and troughs metadata (e.g. using the peakdet module), or + by providing the physiological data timeseries, the sampling frequency, + and the peak and trough indices separately. + """ + ) + if not data.peaks or not data.troughs: + raise ValueError( + """ + Peaks and troughs must be non-empty lists. + Make sure to run peak/trough detection on your physiological data first, + using the peakdet module, or other software of your choice. + """ + ) + timestep = 1 / data.fs # respiration belt timing time = np.arange(0, len(data) * timestep, timestep) @@ -80,13 +111,13 @@ def respiratory_variance_time(data, lags=(0, 4, 8, 12)): @due.dcite(references.POWER_2018) @physio.make_operation() -def respiratory_pattern_variability(resp, window): +def respiratory_pattern_variability(data, window): """Calculate respiratory pattern variability. Parameters ---------- - resp : str or 1D numpy.ndarray - Tiemseries representing respiration activity. + data : Physio_like + Object containing the timeseries of the recorded respiratory signal window : int Window length in samples. @@ -110,8 +141,11 @@ def respiratory_pattern_variability(resp, window): data," Proceedings of the National Academy of Sciences, issue 9, vol. 115, pp. 2105-2114, 2018. """ + # Initialize physio object + data = physio.check_physio(data, ensure_fs=True, copy=True) + # First, z-score respiratory traces - resp_z = zscore(resp) + resp_z = zscore(data.data) # Collect upper envelope rpv_upper_env = rms_envelope_1d(resp_z, window) @@ -123,13 +157,15 @@ def respiratory_pattern_variability(resp, window): @due.dcite(references.POWER_2020) @physio.make_operation() -def env(data, window=10): +def env(data, fs=None, window=10): """Calculate respiratory pattern variability across a sliding window. Parameters ---------- data : Physio_like Object containing the timeseries of the recorded respiratory signal + fs : float, optional if data is a physutils.Physio + Sampling rate of `data` in Hz window : :obj:`int`, optional Size of the sliding window, in seconds. Default is 10. @@ -153,8 +189,20 @@ def env(data, window=10): young adults scanned at rest, including systematic changes and 'missed' deep breaths," Neuroimage, vol. 204, 2020. """ - # Initialize physio object - data = physio.check_physio(data, ensure_fs=True, copy=True) + if isinstance(data, physio.Physio): + # Initialize physio object + data = physio.check_physio(data, ensure_fs=True, copy=True) + elif fs is not None: + data = io.load_physio(data, fs=fs) + else: + raise ValueError( + """ + To use this function you should either provide a Physio object + with the sampling frequency encapsulated, or + by providing the physiological data timeseries and the sampling + frequency separately. + """ + ) # Convert window to Hertz window = int(window * data.fs) @@ -172,13 +220,15 @@ def env(data, window=10): @due.dcite(references.CHANG_GLOVER_2009) @physio.make_operation() -def respiratory_variance(data, window=6): +def respiratory_variance(data, fs=None, window=6): """Calculate respiratory variance. Parameters ---------- data : Physio_like Object containing the timeseries of the recorded respiratory signal + fs : float, optional if data is a physutils.Physio + Sampling rate of `data` in Hz window : :obj:`int`, optional Size of the sliding window, in seconds. Default is 6. @@ -206,8 +256,20 @@ def respiratory_variance(data, window=6): end-tidal CO2, and BOLD signals in resting-state fMRI," Neuroimage, issue 4, vol. 47, pp. 1381-1393, 2009. """ - # Initialize physio object - data = physio.check_physio(data, ensure_fs=True, copy=True) + if isinstance(data, physio.Physio): + # Initialize physio object + data = physio.check_physio(data, ensure_fs=True, copy=True) + elif fs is not None: + data = io.load_physio(data, fs=fs) + else: + raise ValueError( + """ + To use this function you should either provide a Physio object + with the sampling frequency encapsulated, or + by providing the physiological data timeseries and the sampling + frequency separately. + """ + ) # Convert window to Hertz halfwindow_samples = int(round(window * data.fs / 2)) @@ -222,7 +284,7 @@ def respiratory_variance(data, window=6): @physio.make_operation() -def respiratory_phase(data, n_scans, slice_timings, t_r): +def respiratory_phase(data, n_scans, slice_timings, t_r, fs=None): """Calculate respiratory phase from respiratory signal. Parameters @@ -235,14 +297,28 @@ def respiratory_phase(data, n_scans, slice_timings, t_r): Slice times, in seconds. t_r Sample rate of the imaging run, in seconds. + fs : float, optional if data is a physutils.Physio + Sampling rate of `data` in Hz Returns ------- phase_resp : array_like Respiratory phase signal, of shape (n_scans, n_slices). """ - # Initialize physio object - data = physio.check_physio(data, ensure_fs=True, copy=True) + if isinstance(data, physio.Physio): + # Initialize physio object + data = physio.check_physio(data, ensure_fs=True, copy=True) + elif fs is not None: + data = io.load_physio(data, fs=fs) + else: + raise ValueError( + """ + To use this function you should either provide a Physio object + with the sampling frequency encapsulated, or + by providing the physiological data timeseries and the sampling + frequency separately. + """ + ) assert slice_timings.ndim == 1, "Slice times must be a 1D array" n_slices = np.size(slice_timings) From 56abb720a83ef9fb969b32402dcdd91750d2b19a Mon Sep 17 00:00:00 2001 From: maestroque Date: Mon, 24 Jun 2024 18:56:55 +0300 Subject: [PATCH 10/57] Add Physio and non-Physio compatibility to retroicor --- phys2denoise/metrics/multimodal.py | 50 +++++++++++++++++++++++++----- 1 file changed, 43 insertions(+), 7 deletions(-) diff --git a/phys2denoise/metrics/multimodal.py b/phys2denoise/metrics/multimodal.py index f8c6968..0f3f076 100644 --- a/phys2denoise/metrics/multimodal.py +++ b/phys2denoise/metrics/multimodal.py @@ -1,7 +1,7 @@ """These functions compute RETROICOR regressors (Glover et al. 2000).""" import numpy as np -from physutils import physio +from physutils import io, physio from .. import references from ..due import due @@ -17,8 +17,9 @@ def retroicor( n_scans, slice_timings, n_harmonics, - card=False, - resp=False, + physio_type=None, + fs=None, + cardiac_peaks=None, ): """Compute RETROICOR regressors. @@ -56,8 +57,43 @@ def retroicor( correction of physiological motion effects in fMRI: RETROICOR“, Magn. Reson. Med., issue 1, vol. 44, pp. 162-167, 2000. """ - # Initialize physio object - data = physio.check_physio(data, ensure_fs=True, copy=True) + if isinstance(data, physio.Physio): + # Initialize physio object + data = physio.check_physio(data, ensure_fs=True, copy=True) + if data.physio_type is None and physio_type is not None: + data._physio_type = physio_type + elif data.physio_type is None and physio_type is None: + raise ValueError( + """ + Since the provided Physio object does not specify a `physio_type`, + this function's `physio_type` parameter must be specified as a + value from {'cardiac', 'respiratory'} + """ + ) + + elif fs is not None and physio_type is not None: + data = io.load_physio(data, fs=fs) + data._physio_type = physio_type + if data.physio_type == "cardiac": + data._metadata["peaks"] = cardiac_peaks + else: + raise ValueError( + """ + To use this function you should either provide a Physio object + with existing peaks metadata if it describes a cardiac signal + (e.g. using the peakdet module), or + by providing the physiological data timeseries, the sampling frequency, + the physio_type and the peak indices separately. + """ + ) + if not data.peaks and data.physio_type == "cardiac": + raise ValueError( + """ + Peaks must be a non-empty list for cardiac data. + Make sure to run peak detection on your cardiac data first, + using the peakdet module, or other software of your choice. + """ + ) n_slices = np.shape(slice_timings) # number of slices @@ -73,7 +109,7 @@ def retroicor( # Compute physiological phases using the timings of physio events (e.g. peaks) # slice sampling times - if card: + if data.physio_type == "cardiac": phase[:, i_slice] = cardiac_phase( data, crslice_timings, @@ -81,7 +117,7 @@ def retroicor( t_r, ) - if resp: + if data.physio_type == "respiratory": phase[:, i_slice] = respiratory_phase( data, n_scans, From 2c19a65a5b0b7795994e86ce127374b5634e1a7a Mon Sep 17 00:00:00 2001 From: maestroque Date: Mon, 24 Jun 2024 22:26:00 +0300 Subject: [PATCH 11/57] Fix CRF, iCRF and RRF calculation --- phys2denoise/metrics/responses.py | 7 +++++-- phys2denoise/tests/conftest.py | 15 +++++++++++++++ phys2denoise/tests/test_metrics_cardiac.py | 11 +++-------- 3 files changed, 23 insertions(+), 10 deletions(-) diff --git a/phys2denoise/metrics/responses.py b/phys2denoise/metrics/responses.py index aabcec9..1a2aeee 100644 --- a/phys2denoise/metrics/responses.py +++ b/phys2denoise/metrics/responses.py @@ -2,6 +2,7 @@ import logging import numpy as np +from loguru import logger from .. import references from ..due import due @@ -56,10 +57,12 @@ def _crf(t): ) * np.exp(-0.5 * (((t - 12) ** 2) / 9)) return rf - time_stamps = np.arange(0, time_length, 1 / samplerate) + time_stamps = np.arange(0, time_length, samplerate) time_stamps -= onset + logger.debug(f"Time stamps: {time_stamps}") crf_arr = _crf(time_stamps) crf_arr = crf_arr / max(abs(crf_arr)) + logger.debug(f"CRF: {crf_arr}") if inverse: return -crf_arr @@ -135,7 +138,7 @@ def _rrf(t): rf = 0.6 * t**2.1 * np.exp(-t / 1.6) - 0.0023 * t**3.54 * np.exp(-t / 4.25) return rf - time_stamps = np.arange(0, time_length, 1 / samplerate) + time_stamps = np.arange(0, time_length, samplerate) time_stamps -= onset rrf_arr = _rrf(time_stamps) rrf_arr = rrf_arr / max(abs(rrf_arr)) diff --git a/phys2denoise/tests/conftest.py b/phys2denoise/tests/conftest.py index fcf05f3..757a071 100644 --- a/phys2denoise/tests/conftest.py +++ b/phys2denoise/tests/conftest.py @@ -1,5 +1,20 @@ import numpy as np import pytest +from _pytest.logging import LogCaptureFixture +from loguru import logger + + +@pytest.fixture +def caplog(caplog: LogCaptureFixture): + handler_id = logger.add( + caplog.handler, + format="{message}", + level=20, + filter=lambda record: record["level"].no >= caplog.handler.level, + enqueue=False, + ) + yield caplog + logger.remove(handler_id) @pytest.fixture(scope="module") diff --git a/phys2denoise/tests/test_metrics_cardiac.py b/phys2denoise/tests/test_metrics_cardiac.py index bb10d76..2206030 100644 --- a/phys2denoise/tests/test_metrics_cardiac.py +++ b/phys2denoise/tests/test_metrics_cardiac.py @@ -7,20 +7,15 @@ def test_crf_smoke(): """Basic smoke test for CRF calculation.""" samplerate = 0.01 # in seconds - oversampling = 20 time_length = 20 onset = 0 tr = 0.72 crf_arr = cardiac.crf( - samplerate, - oversampling=oversampling, - time_length=time_length, - onset=onset, - tr=tr, + samplerate, time_length=time_length, onset=onset, inverse=False ) - pred_len = np.rint(time_length / (tr / oversampling)) + pred_len = np.rint(time_length * 1 / samplerate) assert crf_arr.ndim == 1 - assert crf_arr.shape == pred_len + assert len(crf_arr) == pred_len def test_cardiac_phase_smoke(): From c28914c5eda8f0b9187a58daa58481d3e8a80113 Mon Sep 17 00:00:00 2001 From: maestroque Date: Mon, 24 Jun 2024 23:09:33 +0300 Subject: [PATCH 12/57] Fix cardiac_phase test, return Physio object and metric to update history --- phys2denoise/metrics/cardiac.py | 9 +++++---- phys2denoise/tests/test_metrics_cardiac.py | 9 ++++++--- 2 files changed, 11 insertions(+), 7 deletions(-) diff --git a/phys2denoise/metrics/cardiac.py b/phys2denoise/metrics/cardiac.py index 00fe312..3e217d7 100644 --- a/phys2denoise/metrics/cardiac.py +++ b/phys2denoise/metrics/cardiac.py @@ -1,5 +1,6 @@ """Denoising metrics for cardio recordings.""" import numpy as np +from loguru import logger from physutils import io, physio from .. import references @@ -89,7 +90,7 @@ def _cardiac_metrics( and the peak indices separately. """ ) - if not data.peaks: + if data.peaks.size == 0: raise ValueError( """ Peaks must be a non-empty list. @@ -141,7 +142,7 @@ def _cardiac_metrics( # Convolve with crf and rescale card_met = convolve_and_rescale(card_met, crf(data.fs), rescale="rescale") - return card_met + return data, card_met @due.dcite(references.CHANG_CUNNINGHAM_GLOVER_2009) @@ -352,7 +353,7 @@ def cardiac_phase(data, slice_timings, n_scans, t_r, fs=None, peaks=None): and the peak indices separately. """ ) - if not data.peaks: + if data.peaks.size == 0: raise ValueError( """ Peaks must be a non-empty list. @@ -392,4 +393,4 @@ def cardiac_phase(data, slice_timings, n_scans, t_r, fs=None, peaks=None): ) / (t2 - t1) phase_card[:, i_slice] = phase_card_crSlice - return phase_card + return data, phase_card diff --git a/phys2denoise/tests/test_metrics_cardiac.py b/phys2denoise/tests/test_metrics_cardiac.py index 2206030..cf125e2 100644 --- a/phys2denoise/tests/test_metrics_cardiac.py +++ b/phys2denoise/tests/test_metrics_cardiac.py @@ -1,5 +1,6 @@ """Tests for phys2denoise.metrics.cardiac.""" import numpy as np +from loguru import logger from phys2denoise.metrics import cardiac @@ -25,9 +26,11 @@ def test_cardiac_phase_smoke(): sample_rate = 1 / 0.01 slice_timings = np.linspace(0, t_r, 22)[1:-1] peaks = np.array([0.534, 0.577, 10.45, 20.66, 50.55, 90.22]) - card_phase = cardiac.cardiac_phase( - peaks, - sample_rate=sample_rate, + data = np.zeros(peaks.shape) + _, card_phase = cardiac.cardiac_phase( + data, + peaks=peaks, + fs=sample_rate, slice_timings=slice_timings, n_scans=n_scans, t_r=t_r, From 625d45f0e9b149c9af31489f02d538772178bbd2 Mon Sep 17 00:00:00 2001 From: maestroque Date: Mon, 24 Jun 2024 23:40:31 +0300 Subject: [PATCH 13/57] Fix chest_belt tests, return Physio object and metric to update history with each operation --- phys2denoise/metrics/chest_belt.py | 35 ++++++++++++++----- phys2denoise/tests/test_metrics_chest_belt.py | 12 +++---- 2 files changed, 32 insertions(+), 15 deletions(-) diff --git a/phys2denoise/metrics/chest_belt.py b/phys2denoise/metrics/chest_belt.py index e48865a..e29eccb 100644 --- a/phys2denoise/metrics/chest_belt.py +++ b/phys2denoise/metrics/chest_belt.py @@ -62,7 +62,7 @@ def respiratory_variance_time( and the peak and trough indices separately. """ ) - if not data.peaks or not data.troughs: + if data.peaks.size == 0 or data.troughs.size == 0: raise ValueError( """ Peaks and troughs must be non-empty lists. @@ -106,7 +106,7 @@ def respiratory_variance_time( ) rvt_lags[:, ind] = temp_rvt - return rvt_lags + return data, rvt_lags @due.dcite(references.POWER_2018) @@ -142,7 +142,7 @@ def respiratory_pattern_variability(data, window): 115, pp. 2105-2114, 2018. """ # Initialize physio object - data = physio.check_physio(data, ensure_fs=True, copy=True) + data = physio.check_physio(data, ensure_fs=False, copy=True) # First, z-score respiratory traces resp_z = zscore(data.data) @@ -152,7 +152,7 @@ def respiratory_pattern_variability(data, window): # Calculate standard deviation rpv_val = np.std(rpv_upper_env) - return rpv_val + return data, rpv_val @due.dcite(references.POWER_2020) @@ -189,6 +189,25 @@ def env(data, fs=None, window=10): young adults scanned at rest, including systematic changes and 'missed' deep breaths," Neuroimage, vol. 204, 2020. """ + + def _respiratory_pattern_variability(data, window): + """ + Respiratory pattern variability function without utilizing + the physutils.Physio object history, only to be used within + the context of this function. This is done to only store the + chest_belt.env operation call to the history and not all the + subsequent sub-operations + """ + # First, z-score respiratory traces + resp_z = zscore(data) + + # Collect upper envelope + rpv_upper_env = rms_envelope_1d(resp_z, window) + + # Calculate standard deviation + rpv_val = np.std(rpv_upper_env) + return rpv_val + if isinstance(data, physio.Physio): # Initialize physio object data = physio.check_physio(data, ensure_fs=True, copy=True) @@ -210,12 +229,12 @@ def env(data, fs=None, window=10): # Calculate RPV across a rolling window env_arr = ( - pd.Series(data) + pd.Series(data.data) .rolling(window=window, center=True) - .apply(respiratory_pattern_variability, args=(window,)) + .apply(_respiratory_pattern_variability, args=(window,)) ) env_arr[np.isnan(env_arr)] = 0.0 - return env_arr + return data, env_arr @due.dcite(references.CHANG_GLOVER_2009) @@ -280,7 +299,7 @@ def respiratory_variance(data, fs=None, window=6): # Convolve with rrf rv_out = convolve_and_rescale(rv_arr, rrf(data.fs), rescale="zscore") - return rv_out + return data, rv_out @physio.make_operation() diff --git a/phys2denoise/tests/test_metrics_chest_belt.py b/phys2denoise/tests/test_metrics_chest_belt.py index 1250d85..27179e4 100644 --- a/phys2denoise/tests/test_metrics_chest_belt.py +++ b/phys2denoise/tests/test_metrics_chest_belt.py @@ -14,12 +14,10 @@ def test_rrf_smoke(): tr = 0.72 rrf_arr = chest_belt.rrf( samplerate, - oversampling=oversampling, time_length=time_length, onset=onset, - tr=tr, ) - pred_len = int(np.rint(time_length / (tr / oversampling))) + pred_len = int(np.rint(time_length * (1 / samplerate))) assert rrf_arr.ndim == 1 assert rrf_arr.size == pred_len @@ -33,7 +31,7 @@ def test_respiratory_phase_smoke(): slice_timings = np.linspace(0, t_r, 22)[1:-1] n_samples = int(np.rint((n_scans * t_r) * sample_rate)) resp = np.random.normal(size=n_samples) - resp_phase = chest_belt.respiratory_phase( + _, resp_phase = chest_belt.respiratory_phase( resp, sample_rate=sample_rate, slice_timings=slice_timings, @@ -49,7 +47,7 @@ def test_respiratory_pattern_variability_smoke(): n_samples = 2000 resp = np.random.normal(size=n_samples) window = 50 - rpv_val = chest_belt.respiratory_pattern_variability(resp, window) + _, rpv_val = chest_belt.respiratory_pattern_variability(resp, window) assert isinstance(rpv_val, float) @@ -59,7 +57,7 @@ def test_env_smoke(): resp = np.random.normal(size=n_samples) samplerate = 1 / 0.01 window = 6 - env_arr = chest_belt.env(resp, samplerate=samplerate, window=window) + _, env_arr = chest_belt.env(resp, fs=samplerate, window=window) assert env_arr.ndim == 1 assert env_arr.shape == (n_samples,) @@ -70,6 +68,6 @@ def test_respiratory_variance_smoke(): resp = np.random.normal(size=n_samples) samplerate = 1 / 0.01 window = 6 - rv_arr = chest_belt.respiratory_variance(resp, samplerate=samplerate, window=window) + _, rv_arr = chest_belt.respiratory_variance(resp, fs=samplerate, window=window) assert rv_arr.ndim == 2 assert rv_arr.shape == (n_samples, 2) From acf960d792ae64074dae72d680d7bfcd1dfad834 Mon Sep 17 00:00:00 2001 From: maestroque Date: Mon, 24 Jun 2024 23:57:00 +0300 Subject: [PATCH 14/57] Update RVT test --- phys2denoise/metrics/chest_belt.py | 2 +- phys2denoise/tests/test_rvt.py | 7 +++++-- 2 files changed, 6 insertions(+), 3 deletions(-) diff --git a/phys2denoise/metrics/chest_belt.py b/phys2denoise/metrics/chest_belt.py index e29eccb..4e83b7d 100644 --- a/phys2denoise/metrics/chest_belt.py +++ b/phys2denoise/metrics/chest_belt.py @@ -367,4 +367,4 @@ def respiratory_phase(data, n_scans, slice_timings, t_r, fs=None): phase_resp[:, i_slice] = phase_resp_crSlice - return phase_resp + return data, phase_resp diff --git a/phys2denoise/tests/test_rvt.py b/phys2denoise/tests/test_rvt.py index 13e27d8..67a7bf9 100644 --- a/phys2denoise/tests/test_rvt.py +++ b/phys2denoise/tests/test_rvt.py @@ -15,8 +15,11 @@ def test_respiratory_variance_time(fake_phys): phys = peakdet.Physio(fake_phys, fs=62.5) phys = peakdet.operations.filter_physio(phys, cutoffs=3, method="lowpass") phys = peakdet.operations.peakfind_physio(phys) - r = test_respiratory_variance_time( - phys.data, phys.peaks, phys.troughs, samplerate=phys.fs + + # TODO: Change to a simpler call once physutils are + # integrated to peakdet + phys, r = respiratory_variance_time( + phys.data, fs=phys.fs, peaks=phys.peaks, troughs=phys.troughs ) assert r is not None assert len(r) == 18750 From 62e4b6f93fb0c6073736313469cac8a6be6ea0ce Mon Sep 17 00:00:00 2001 From: maestroque Date: Tue, 25 Jun 2024 00:00:17 +0300 Subject: [PATCH 15/57] Fix respiratory_phase_smoke test --- phys2denoise/tests/test_metrics_chest_belt.py | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/phys2denoise/tests/test_metrics_chest_belt.py b/phys2denoise/tests/test_metrics_chest_belt.py index 27179e4..5e5bfd1 100644 --- a/phys2denoise/tests/test_metrics_chest_belt.py +++ b/phys2denoise/tests/test_metrics_chest_belt.py @@ -22,7 +22,6 @@ def test_rrf_smoke(): assert rrf_arr.size == pred_len -@mark.xfail def test_respiratory_phase_smoke(): """Basic smoke test for respiratory phase calculation.""" t_r = 1.0 @@ -33,7 +32,7 @@ def test_respiratory_phase_smoke(): resp = np.random.normal(size=n_samples) _, resp_phase = chest_belt.respiratory_phase( resp, - sample_rate=sample_rate, + fs=sample_rate, slice_timings=slice_timings, n_scans=n_scans, t_r=t_r, From e60d49ec41ef0e92b09869a2b28a33380c3fc626 Mon Sep 17 00:00:00 2001 From: maestroque Date: Tue, 25 Jun 2024 00:07:59 +0300 Subject: [PATCH 16/57] Return physio in retroicor and specify raised error type in test_mirrorpad_exception --- phys2denoise/metrics/multimodal.py | 2 +- phys2denoise/tests/test_metrics_utils.py | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/phys2denoise/metrics/multimodal.py b/phys2denoise/metrics/multimodal.py index 0f3f076..f5b479e 100644 --- a/phys2denoise/metrics/multimodal.py +++ b/phys2denoise/metrics/multimodal.py @@ -134,4 +134,4 @@ def retroicor( (j_harm + 1) * phase[i_slice] ) - return retroicor_regressors, phase + return data, retroicor_regressors, phase diff --git a/phys2denoise/tests/test_metrics_utils.py b/phys2denoise/tests/test_metrics_utils.py index 916c485..d7e1b46 100644 --- a/phys2denoise/tests/test_metrics_utils.py +++ b/phys2denoise/tests/test_metrics_utils.py @@ -20,7 +20,7 @@ def test_mirrorpad_exception(short_arr): """When passing array that is too short to perform mirrorpadding, the function should give an error.""" arr = np.array(short_arr) - with pytest.raises(Exception) as e_info: + with pytest.raises(IndexError): arr_mirror = mirrorpad_1d(short_arr) From 3dbf65612629873114509752e924cbf569646894 Mon Sep 17 00:00:00 2001 From: maestroque Date: Tue, 25 Jun 2024 00:13:05 +0300 Subject: [PATCH 17/57] Add loguru as a dependency --- setup.cfg | 1 + 1 file changed, 1 insertion(+) diff --git a/setup.cfg b/setup.cfg index e460ed3..6f9e718 100644 --- a/setup.cfg +++ b/setup.cfg @@ -27,6 +27,7 @@ install_requires = pandas scipy duecredit + loguru # TODO: Uncomment this once it's uploaded to PyPI # physutils tests_require = From f7d781116e9948b5403386bae037022a4d4104c5 Mon Sep 17 00:00:00 2001 From: maestroque Date: Tue, 25 Jun 2024 12:38:58 +0300 Subject: [PATCH 18/57] Add Physio object use cardiac phase unit test --- phys2denoise/tests/test_metrics_cardiac.py | 23 ++++++++++++++++++++++ 1 file changed, 23 insertions(+) diff --git a/phys2denoise/tests/test_metrics_cardiac.py b/phys2denoise/tests/test_metrics_cardiac.py index cf125e2..6a7be8c 100644 --- a/phys2denoise/tests/test_metrics_cardiac.py +++ b/phys2denoise/tests/test_metrics_cardiac.py @@ -1,6 +1,7 @@ """Tests for phys2denoise.metrics.cardiac.""" import numpy as np from loguru import logger +from physutils import physio from phys2denoise.metrics import cardiac @@ -37,3 +38,25 @@ def test_cardiac_phase_smoke(): ) assert card_phase.ndim == 2 assert card_phase.shape == (n_scans, slice_timings.size) + + +def test_cardiac_phase_smoke_physio_obj(): + """Basic smoke test for cardiac phase calculation.""" + t_r = 1.0 + n_scans = 200 + sample_rate = 1 / 0.01 + slice_timings = np.linspace(0, t_r, 22)[1:-1] + peaks = np.array([0.534, 0.577, 10.45, 20.66, 50.55, 90.22]) + data = np.zeros(peaks.shape) + phys = physio.Physio(data, sample_rate, physio_type="cardiac") + phys._metadata["peaks"] = peaks + phys, card_phase = cardiac.cardiac_phase( + phys, + slice_timings=slice_timings, + n_scans=n_scans, + t_r=t_r, + ) + logger.debug(f"History: {phys.history}") + assert phys.history[0][0] == "phys2denoise.metrics.cardiac.cardiac_phase" + assert card_phase.ndim == 2 + assert card_phase.shape == (n_scans, slice_timings.size) From 907faba7d592bd5700ed1048687722daa09ef88c Mon Sep 17 00:00:00 2001 From: maestroque Date: Tue, 25 Jun 2024 12:39:28 +0300 Subject: [PATCH 19/57] Remove test log --- phys2denoise/tests/test_metrics_cardiac.py | 1 - 1 file changed, 1 deletion(-) diff --git a/phys2denoise/tests/test_metrics_cardiac.py b/phys2denoise/tests/test_metrics_cardiac.py index 6a7be8c..25faa9a 100644 --- a/phys2denoise/tests/test_metrics_cardiac.py +++ b/phys2denoise/tests/test_metrics_cardiac.py @@ -56,7 +56,6 @@ def test_cardiac_phase_smoke_physio_obj(): n_scans=n_scans, t_r=t_r, ) - logger.debug(f"History: {phys.history}") assert phys.history[0][0] == "phys2denoise.metrics.cardiac.cardiac_phase" assert card_phase.ndim == 2 assert card_phase.shape == (n_scans, slice_timings.size) From e61cf3d6965b4391bc599d1434a7a35427e4ef7b Mon Sep 17 00:00:00 2001 From: maestroque Date: Wed, 3 Jul 2024 01:21:05 +0300 Subject: [PATCH 20/57] docs: Add API page --- docs/Makefile | 20 ++++++ docs/api.rst | 29 +++++++++ docs/conf.py | 113 +++++++++++++++++++++++++++++++++ docs/index.rst | 11 ++++ docs/installation.rst | 19 ++++++ docs/requirements.txt | 3 + docs/usage.rst | 12 ++++ docs/user_guide/loading.rst | 0 docs/user_guide/metrics.rst | 0 docs/user_guide/processing.rst | 0 docs/user_guide/saving.rst | 0 11 files changed, 207 insertions(+) create mode 100644 docs/Makefile create mode 100644 docs/api.rst create mode 100644 docs/conf.py create mode 100644 docs/index.rst create mode 100644 docs/installation.rst create mode 100644 docs/requirements.txt create mode 100644 docs/usage.rst create mode 100644 docs/user_guide/loading.rst create mode 100644 docs/user_guide/metrics.rst create mode 100644 docs/user_guide/processing.rst create mode 100644 docs/user_guide/saving.rst diff --git a/docs/Makefile b/docs/Makefile new file mode 100644 index 0000000..f610428 --- /dev/null +++ b/docs/Makefile @@ -0,0 +1,20 @@ +# Minimal makefile for Sphinx documentation +# + +# You can set these variables from the command line. +SPHINXOPTS = +SPHINXBUILD = sphinx-build +SPHINXPROJ = phys2denoise +SOURCEDIR = . +BUILDDIR = _build + +# Put it first so that "make" without argument is like "make help". +help: + @$(SPHINXBUILD) -M help "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O) + +.PHONY: help Makefile + +# Catch-all target: route all unknown targets to Sphinx using the new +# "make mode" option. $(O) is meant as a shortcut for $(SPHINXOPTS). +%: Makefile + @$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O) diff --git a/docs/api.rst b/docs/api.rst new file mode 100644 index 0000000..676c368 --- /dev/null +++ b/docs/api.rst @@ -0,0 +1,29 @@ +.. _api_ref: + +API +=== + +.. py:module:: phys2denoise + +Cardiac data +------------------ + +.. automodule:: phys2denoise.metrics.cardiac + :members: heart_rate, heart_rate_variability, heart_beat_interval, cardiac_phase + +Respiratory data +------------ + +.. automodule:: phys2denoise.metrics.chest_belt + :members: respiratory_cariance_time, respiratory_pattern_variability, env, respiratory_variance, respiratory_phase + +Multimodal data +--------------- + +.. autofunction:: phys2denoise.multimodal.retroicor + +Response functions +----------- + +.. automodule:: phys2denoise.metrics.responses + :members: crf, icrf, rrf diff --git a/docs/conf.py b/docs/conf.py new file mode 100644 index 0000000..e42ac87 --- /dev/null +++ b/docs/conf.py @@ -0,0 +1,113 @@ +#!/usr/bin/env python3 +# -*- coding: utf-8 -*- +# +# Configuration file for the Sphinx documentation builder. + +# -- Path setup -------------------------------------------------------------- + +# If extensions (or modules to document with autodoc) are in another directory, +# add these directories to sys.path here. If the directory is relative to the +# documentation root, use os.path.abspath to make it absolute, like shown here. +import os +import sys + +import matplotlib as mpl + +mpl.use("Agg") + +# -- Project information ----------------------------------------------------- + +# Add project name, copyright holder, and author(s) +project = "phys2denoise" +copyright = "2024, physiopy" +author = "physiopy" + +# Import project to get version info +sys.path.insert(0, os.path.abspath(os.path.pardir)) +import phys2denoise # noqa + +# The short X.Y version +version = phys2denoise.__version__ +# The full version, including alpha/beta/rc tags +release = phys2denoise.__version__ + +# -- General configuration --------------------------------------------------- + +# Add any Sphinx extension module names here, as strings. They can be +# extensions coming with Sphinx (named 'sphinx.ext.*') or your custom +# ones. +extensions = [ + "matplotlib.sphinxext.plot_directive", + "sphinx.ext.autodoc", + "sphinx.ext.autosummary", + "sphinx.ext.doctest", + "sphinx.ext.intersphinx", + "sphinx.ext.mathjax", + "sphinx.ext.napoleon", + "sphinx.ext.viewcode", +] + +# Generate the API documentation when building +autosummary_generate = True +numpydoc_show_class_members = False +autoclass_content = "class" + +# Add any paths that contain templates here, relative to this directory. +templates_path = ["_templates"] + +# The suffix(es) of source filenames. +source_suffix = ".rst" + +# The master toctree document. +master_doc = "index" + +# The language for content autogenerated by Sphinx. Refer to documentation +# for a list of supported languages. +# +# This is also used if you do content translation via gettext catalogs. +# Usually you set "language" from the command line for these cases. +language = None + +# List of patterns, relative to source directory, that match files and +# directories to ignore when looking for source files. +# This pattern also affects html_static_path and html_extra_path . +exclude_patterns = ["_build", "Thumbs.db", ".DS_Store"] + +# The name of the Pygments (syntax highlighting) style to use. +pygments_style = "sphinx" + +# -- Options for HTML output ------------------------------------------------- + +# The theme to use for HTML and HTML Help pages. See the documentation for +# a list of builtin themes. +import sphinx_rtd_theme # noqa + +html_theme = "sphinx_rtd_theme" +html_show_sourcelink = False + +# Theme options are theme-specific and customize the look and feel of a theme +# further. For a list of options available for each theme, see the +# documentation. +html_theme_options = {} + +# Add any paths that contain custom static files (such as style sheets) here, +# relative to this directory. They are copied after the builtin static files, +# so a file named "default.css" will overwrite the builtin "default.css". +html_static_path = ["_static"] + +# -- Options for HTMLHelp output --------------------------------------------- + +# Output file base name for HTML help builder. +htmlhelp_basename = "peakdetdoc" + +# -- Extension configuration ------------------------------------------------- +intersphinx_mapping = { + "matplotlib": ("https://matplotlib.org", None), + "numpy": ("https://docs.scipy.org/doc/numpy", None), + "scipy": ("https://docs.scipy.org/doc/scipy/reference", None), +} + +plot_include_source = True +plot_formats = [("png", 90)] +plot_html_show_formats = False +plot_html_show_source_link = False diff --git a/docs/index.rst b/docs/index.rst new file mode 100644 index 0000000..590f394 --- /dev/null +++ b/docs/index.rst @@ -0,0 +1,11 @@ +.. include:: ../README.rst + +Contents +-------- + +.. toctree:: + :maxdepth: 1 + + installation + usage + api diff --git a/docs/installation.rst b/docs/installation.rst new file mode 100644 index 0000000..709983c --- /dev/null +++ b/docs/installation.rst @@ -0,0 +1,19 @@ +.. _installation_setup: + +Installation and setup +====================== + +.. _basic_installation: + +Developer installation +-------------------- + +This package requires Python >= 3.6. Assuming you have the correct version of +Python installed, you can install ``phys2denoise`` by opening a terminal and running +the following: + +.. code-block:: bash + + git clone https://github.com/physiopy/phys2denoise.git + cd phys2denoise + pip install -e .[dev] diff --git a/docs/requirements.txt b/docs/requirements.txt new file mode 100644 index 0000000..ed30bc9 --- /dev/null +++ b/docs/requirements.txt @@ -0,0 +1,3 @@ +-r ../requirements.txt +sphinx>=1.2 +sphinx_rtd_theme diff --git a/docs/usage.rst b/docs/usage.rst new file mode 100644 index 0000000..27eab4b --- /dev/null +++ b/docs/usage.rst @@ -0,0 +1,12 @@ +.. _usage: + +User guide +========== + +.. toctree:: + :numbered: + + user_guide/loading.rst + user_guide/processing.rst + user_guide/saving.rst + user_guide/metrics.rst diff --git a/docs/user_guide/loading.rst b/docs/user_guide/loading.rst new file mode 100644 index 0000000..e69de29 diff --git a/docs/user_guide/metrics.rst b/docs/user_guide/metrics.rst new file mode 100644 index 0000000..e69de29 diff --git a/docs/user_guide/processing.rst b/docs/user_guide/processing.rst new file mode 100644 index 0000000..e69de29 diff --git a/docs/user_guide/saving.rst b/docs/user_guide/saving.rst new file mode 100644 index 0000000..e69de29 From 2534b50182312361c2c98e8f1faf67be4ef4a600 Mon Sep 17 00:00:00 2001 From: maestroque Date: Wed, 17 Jul 2024 11:21:36 +0300 Subject: [PATCH 21/57] docs: Minor additions --- docs/usage.rst | 4 +--- docs/user_guide/exporting.rst | 4 ++++ docs/user_guide/loading.rst | 0 docs/user_guide/metrics.rst | 14 ++++++++++++++ docs/user_guide/processing.rst | 0 docs/user_guide/saving.rst | 0 6 files changed, 19 insertions(+), 3 deletions(-) create mode 100644 docs/user_guide/exporting.rst delete mode 100644 docs/user_guide/loading.rst delete mode 100644 docs/user_guide/processing.rst delete mode 100644 docs/user_guide/saving.rst diff --git a/docs/usage.rst b/docs/usage.rst index 27eab4b..58b7c89 100644 --- a/docs/usage.rst +++ b/docs/usage.rst @@ -6,7 +6,5 @@ User guide .. toctree:: :numbered: - user_guide/loading.rst - user_guide/processing.rst - user_guide/saving.rst user_guide/metrics.rst + user_guide/exporting.rst diff --git a/docs/user_guide/exporting.rst b/docs/user_guide/exporting.rst new file mode 100644 index 0000000..2a9a7bb --- /dev/null +++ b/docs/user_guide/exporting.rst @@ -0,0 +1,4 @@ +.. _usage_exporting: + +Exporting physiological data metrics +------------------------------------ diff --git a/docs/user_guide/loading.rst b/docs/user_guide/loading.rst deleted file mode 100644 index e69de29..0000000 diff --git a/docs/user_guide/metrics.rst b/docs/user_guide/metrics.rst index e69de29..81edc89 100644 --- a/docs/user_guide/metrics.rst +++ b/docs/user_guide/metrics.rst @@ -0,0 +1,14 @@ +.. _usage_metrics: + +Computing physiological data metrics +------------------------------------ + + 1. :ref:`_usage_metrics_physio`, + +.. _usage_metrics_physio: + +Using a Physio object +--------------------- + +Physiological data metrics can be easily computed using Physio objects, from :py:mod:`physutils`, +on which the physiological data will be loaded. diff --git a/docs/user_guide/processing.rst b/docs/user_guide/processing.rst deleted file mode 100644 index e69de29..0000000 diff --git a/docs/user_guide/saving.rst b/docs/user_guide/saving.rst deleted file mode 100644 index e69de29..0000000 From 7b4dc311f48b17e186a4ecfa20b7e47905b8648e Mon Sep 17 00:00:00 2001 From: maestroque Date: Wed, 17 Jul 2024 13:58:56 +0300 Subject: [PATCH 22/57] docs: Add computing metrics page --- docs/api.rst | 1 - docs/user_guide/metrics.rst | 72 ++++++++++++++++++++++++++++++++++--- 2 files changed, 67 insertions(+), 6 deletions(-) diff --git a/docs/api.rst b/docs/api.rst index 676c368..c033d58 100644 --- a/docs/api.rst +++ b/docs/api.rst @@ -1,5 +1,4 @@ .. _api_ref: - API === diff --git a/docs/user_guide/metrics.rst b/docs/user_guide/metrics.rst index 81edc89..402fe0c 100644 --- a/docs/user_guide/metrics.rst +++ b/docs/user_guide/metrics.rst @@ -1,14 +1,76 @@ .. _usage_metrics: Computing physiological data metrics ------------------------------------- +------------------------------------- +The :py:mod:`phys2denoise` package provides a set of functions to compute physiological data metrics. The set of supported metrics +includes: - 1. :ref:`_usage_metrics_physio`, +- Cardiac metrics + - Cardiac phase + - Heart rate + - Heart rate variability + - Heart beat interval +- Respiratory metrics + - Respiratory phase + - Respiratory variance + - Respiratory pattern variability + - Envelope +- Multimodal metrics + - RETROICOR + +All of the metrics computation function definitions, descriptions and references can be found in :ref:`api_ref`. -.. _usage_metrics_physio: Using a Physio object ---------------------- +##################### -Physiological data metrics can be easily computed using Physio objects, from :py:mod:`physutils`, +Physiological data metrics can be easily computed using Physio objects, from the :py:mod:`physutils` module, on which the physiological data will be loaded. + +The following example shows how to compute the respiratory variance time using a Physio object. + +.. code-block:: python + + from physutils import io + from phys2denoise.metrics.chest_belt import respiratory_variance_time + # peakdet is an example package that provides peak/trough detection for the respiratory signal + from peakdet import operations + + # Load the physiological data + sample_rate = 1000 + physio = io.load_physio('path/to/physiological/data', fs=sample_rate) + + # Peak/trough detection for the respiratory signal, using the peakdet package + physio = operations.peakfind_physio(physio) + + # Compute RVT + physio, rvt = respiratory_variance_time(physio) + +:py:func:`respiratory_variance_time` returns a tuple with the updated Physio object and the computed respiratory variance time. + +:py:mod:`peakdet` is used in this example as it is also compatible with the Physio object. However, any other peak/trough detection +package can be used. In this case, the peak and trough values should be stored in the Physio object manually as follows: + +.. code-block:: python + + # Store the peak and trough values in the Physio object + physio._metadata["peaks"] = peaks + physio._metadata["troughs"] = troughs + +The benefit of using a Physio object other than the encapsulation of all the desired parameters in a single object is the fact that +the object retains a history of all the operations performed on it. This allows for easy debugging and reproducibility of the results. +For further information refer to the :py:mod:`physutils` documentation. + +Without using a Physio object +############################# + +However, if the use of :py:mod:`physutils` is not preferred, the metrics can be also computed without it. The following +example shows how to compute the heart rate and the heart rate variability using the :py:mod:`phys2denoise` package. + +.. code-block:: python + + from phys2denoise.metrics.chest_belt import respiratory_variance_time + + # Given that the respiratory signal is stored in `data`, the peaks in `peaks`, the troughs in `troughs` + # and the sample rate in `sample_rate` + _, rvt = respiratory_variance_time(physio, peaks, troughs, sample_rate) From 83662c9452f68b706132c69d40a10b11fdfd0d42 Mon Sep 17 00:00:00 2001 From: maestroque Date: Thu, 18 Jul 2024 15:15:38 +0300 Subject: [PATCH 23/57] docs: Add utils to API --- docs/api.rst | 6 ++++++ 1 file changed, 6 insertions(+) diff --git a/docs/api.rst b/docs/api.rst index c033d58..da73600 100644 --- a/docs/api.rst +++ b/docs/api.rst @@ -26,3 +26,9 @@ Response functions .. automodule:: phys2denoise.metrics.responses :members: crf, icrf, rrf + +Utilities +----------- + +.. automodule:: phys2denoise.metrics.utils + :members: print_metric_call, mirrorpad_1d, rms_envelope_1d, apply_lags, apply_function_in_sliding_window, convolve_and_rescale, export_metric \ No newline at end of file From 9004c11d74342d6ef79152d0d4b1faa1355a3423 Mon Sep 17 00:00:00 2001 From: maestroque Date: Thu, 18 Jul 2024 15:31:53 +0300 Subject: [PATCH 24/57] docs: Add exporting metrics page --- docs/api.rst | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/api.rst b/docs/api.rst index da73600..dde3b05 100644 --- a/docs/api.rst +++ b/docs/api.rst @@ -31,4 +31,4 @@ Utilities ----------- .. automodule:: phys2denoise.metrics.utils - :members: print_metric_call, mirrorpad_1d, rms_envelope_1d, apply_lags, apply_function_in_sliding_window, convolve_and_rescale, export_metric \ No newline at end of file + :members: print_metric_call, mirrorpad_1d, rms_envelope_1d, apply_lags, apply_function_in_sliding_window, convolve_and_rescale, export_metric From d31a19c32b3a84ca0861211b72a3e92bc4ad4915 Mon Sep 17 00:00:00 2001 From: maestroque Date: Thu, 18 Jul 2024 15:32:34 +0300 Subject: [PATCH 25/57] docs: Add exporting metrics page --- docs/user_guide/exporting.rst | 25 +++++++++++++++++++++++++ 1 file changed, 25 insertions(+) diff --git a/docs/user_guide/exporting.rst b/docs/user_guide/exporting.rst index 2a9a7bb..6e1d8db 100644 --- a/docs/user_guide/exporting.rst +++ b/docs/user_guide/exporting.rst @@ -2,3 +2,28 @@ Exporting physiological data metrics ------------------------------------ +Another feature of the :py:mod:`phys2denoise` package is the ability to export the computed physiological data metrics to a file, with various parameters. +This can be done using the :py:func:`export_metric` function, which provides the following capabilities: + +- Exporting the computed metrics, resampled at the TR of the fMRI data, along with the original data. +- Flagging if the exported data is the convolved version or if the metric contains lags of itself, resulting in appropriate file naming. +- Defining the output file extension and file prefix. +- Defining the number of timepoints to be considered. + +The following example shows how to export the computed respiratory variance time using a Physio object. + +.. code-block:: python + + RVT = respiratory_variance_time( + resp.data, resp.peaks, resp.troughs, resp.fs, lags=(0, 4, 8, 12) + ) + + export_metric( + RVT, + resp.fs, + tr=1.5, + fileprefix="data/pk-p2d/sub-007_ses-05_task-rest_run-01_RVT", + ntp=400, + is_convolved=False, + has_lags=True, + ) From 34a2e7662e71e30f2aeadc4523c693b795d2a1ac Mon Sep 17 00:00:00 2001 From: maestroque Date: Thu, 18 Jul 2024 15:35:07 +0300 Subject: [PATCH 26/57] docs: Remove README.rst reference --- docs/index.rst | 1 - 1 file changed, 1 deletion(-) diff --git a/docs/index.rst b/docs/index.rst index 590f394..0651d73 100644 --- a/docs/index.rst +++ b/docs/index.rst @@ -1,4 +1,3 @@ -.. include:: ../README.rst Contents -------- From 8c3f1bd7f25c309d3b7655051e82f12a233bf8fe Mon Sep 17 00:00:00 2001 From: maestroque Date: Thu, 18 Jul 2024 15:37:15 +0300 Subject: [PATCH 27/57] docs: Minor codeblock fix --- docs/user_guide/exporting.rst | 26 ++++++++++++++------------ 1 file changed, 14 insertions(+), 12 deletions(-) diff --git a/docs/user_guide/exporting.rst b/docs/user_guide/exporting.rst index 6e1d8db..61f6522 100644 --- a/docs/user_guide/exporting.rst +++ b/docs/user_guide/exporting.rst @@ -13,17 +13,19 @@ This can be done using the :py:func:`export_metric` function, which provides the The following example shows how to export the computed respiratory variance time using a Physio object. .. code-block:: python + from phys2denoise.metrics.chest_belt import respiratory_variance_time + from phys2denoise.metrics.utils import export_metric - RVT = respiratory_variance_time( - resp.data, resp.peaks, resp.troughs, resp.fs, lags=(0, 4, 8, 12) - ) + RVT = respiratory_variance_time( + resp.data, resp.peaks, resp.troughs, resp.fs, lags=(0, 4, 8, 12) + ) - export_metric( - RVT, - resp.fs, - tr=1.5, - fileprefix="data/pk-p2d/sub-007_ses-05_task-rest_run-01_RVT", - ntp=400, - is_convolved=False, - has_lags=True, - ) + export_metric( + RVT, + resp.fs, + tr=1.5, + fileprefix="data/sub-002_ses-01_task-rest_run-01_RVT", + ntp=400, + is_convolved=False, + has_lags=True, + ) From 3af24c7a535f6262394d85a056de97687152d3de Mon Sep 17 00:00:00 2001 From: maestroque Date: Thu, 18 Jul 2024 15:37:51 +0300 Subject: [PATCH 28/57] docs: Minor codeblock fix --- docs/user_guide/exporting.rst | 1 + 1 file changed, 1 insertion(+) diff --git a/docs/user_guide/exporting.rst b/docs/user_guide/exporting.rst index 61f6522..1a9421f 100644 --- a/docs/user_guide/exporting.rst +++ b/docs/user_guide/exporting.rst @@ -13,6 +13,7 @@ This can be done using the :py:func:`export_metric` function, which provides the The following example shows how to export the computed respiratory variance time using a Physio object. .. code-block:: python + from phys2denoise.metrics.chest_belt import respiratory_variance_time from phys2denoise.metrics.utils import export_metric From 2d9fd750197377c14afebda8394551f91f1c080a Mon Sep 17 00:00:00 2001 From: maestroque Date: Thu, 18 Jul 2024 15:43:35 +0300 Subject: [PATCH 29/57] Add physutils dependency and peakdet version --- setup.cfg | 5 ++--- 1 file changed, 2 insertions(+), 3 deletions(-) diff --git a/setup.cfg b/setup.cfg index 6f9e718..82a5696 100644 --- a/setup.cfg +++ b/setup.cfg @@ -28,8 +28,7 @@ install_requires = scipy duecredit loguru - # TODO: Uncomment this once it's uploaded to PyPI - # physutils + physutils tests_require = pytest >=5.3 test_suite = pytest @@ -52,7 +51,7 @@ test = %(style)s pytest >=5.3 pytest-cov - peakdet + peakdet>=0.4.0 coverage devtools = pre-commit From 366175a5a153146f17dec605869046039264aab5 Mon Sep 17 00:00:00 2001 From: maestroque Date: Sat, 20 Jul 2024 00:48:56 +0300 Subject: [PATCH 30/57] Update peakdet dependency --- setup.cfg | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/setup.cfg b/setup.cfg index 82a5696..562bae4 100644 --- a/setup.cfg +++ b/setup.cfg @@ -51,7 +51,7 @@ test = %(style)s pytest >=5.3 pytest-cov - peakdet>=0.4.0 + peakdet>=0.5.0 coverage devtools = pre-commit From 533c80e055af0fd8de104f99cffeda46874abcef Mon Sep 17 00:00:00 2001 From: maestroque Date: Mon, 22 Jul 2024 10:27:00 +0300 Subject: [PATCH 31/57] Minor fix --- setup.cfg | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/setup.cfg b/setup.cfg index 562bae4..23813a9 100644 --- a/setup.cfg +++ b/setup.cfg @@ -23,7 +23,7 @@ provides = python_requires = >=3.6.1 install_requires = numpy >=1.9.3 - matplotlib >=3.1.1 + matplotlib>=3.9 pandas scipy duecredit From 3fba78c1ab7752c7f267eee14960f5027af1c4f9 Mon Sep 17 00:00:00 2001 From: maestroque Date: Mon, 22 Jul 2024 10:44:55 +0300 Subject: [PATCH 32/57] circleci: python version upgrade --- .circleci/config.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.circleci/config.yml b/.circleci/config.yml index fc36d30..176c0a7 100644 --- a/.circleci/config.yml +++ b/.circleci/config.yml @@ -85,7 +85,7 @@ jobs: style_check: docker: - - image: cimg/python:3.7 + - image: cimg/python:3.10 working_directory: /tmp/src/phys2denoise resource_class: small steps: From 43576d0edee92c1678a2c77222fd0630ae431684 Mon Sep 17 00:00:00 2001 From: maestroque Date: Mon, 22 Jul 2024 11:22:25 +0300 Subject: [PATCH 33/57] circleci: python version migration to 3.8 and 3.12 --- .circleci/config.yml | 24 ++++++++++++------------ setup.cfg | 2 +- 2 files changed, 13 insertions(+), 13 deletions(-) diff --git a/.circleci/config.yml b/.circleci/config.yml index 176c0a7..071888b 100644 --- a/.circleci/config.yml +++ b/.circleci/config.yml @@ -15,14 +15,14 @@ orbs: # Define a job to be invoked later in a workflow. # See: https://circleci.com/docs/2.0/configuration-reference/#jobs jobs: - test37: # This is the name of the job, feel free to change it to better match what you're trying to do! + test38: # This is the name of the job, feel free to change it to better match what you're trying to do! # These next lines defines a Docker executors: https://circleci.com/docs/2.0/executor-types/ # You can specify an image from Dockerhub or use one of the convenience images from CircleCI's Developer Hub # A list of available CircleCI Docker convenience images are available here: https://circleci.com/developer/images/image/cimg/python # The executor is the environment in which the steps below will be executed - below will use a python 3.6.14 container # Change the version below to your required version of python docker: - - image: cimg/python:3.7 + - image: cimg/python:3.8 working_directory: /tmp/src/phys2denoise resource_class: medium # Checkout the code as the first step. This is a dedicated CircleCI step. @@ -46,7 +46,7 @@ jobs: command: | pytest --cov=./phys2denoise mkdir /tmp/src/coverage - mv ./.coverage /tmp/src/coverage/.coverage.py37 + mv ./.coverage /tmp/src/coverage/.coverage.py38 - store_artifacts: path: /tmp/src/coverage # Persist the specified paths (workspace/echo-output) into the workspace for use in downstream job. @@ -56,11 +56,11 @@ jobs: root: /tmp # Must be relative path from root paths: - - src/coverage/.coverage.py37 + - src/coverage/.coverage.py38 - test310: + test312: docker: - - image: cimg/python:3.10 + - image: cimg/python:3.12 working_directory: /tmp/src/phys2denoise resource_class: medium steps: @@ -75,17 +75,17 @@ jobs: command: | pytest --cov=./phys2denoise mkdir /tmp/src/coverage - mv ./.coverage /tmp/src/coverage/.coverage.py310 + mv ./.coverage /tmp/src/coverage/.coverage.py312 - store_artifacts: path: /tmp/src/coverage - persist_to_workspace: root: /tmp paths: - - src/coverage/.coverage.py310 + - src/coverage/.coverage.py312 style_check: docker: - - image: cimg/python:3.10 + - image: cimg/python:3.8 working_directory: /tmp/src/phys2denoise resource_class: small steps: @@ -105,7 +105,7 @@ jobs: merge_coverage: working_directory: /tmp/src/phys2denoise docker: - - image: cimg/python:3.10 + - image: cimg/python:3.12 resource_class: small steps: - attach_workspace: @@ -141,5 +141,5 @@ workflows: - style_check - merge_coverage: requires: - - test37 - - test310 + - test38 + - test312 diff --git a/setup.cfg b/setup.cfg index 23813a9..7568f5d 100644 --- a/setup.cfg +++ b/setup.cfg @@ -20,7 +20,7 @@ provides = phys2denoise [options] -python_requires = >=3.6.1 +python_requires = >=3.8 install_requires = numpy >=1.9.3 matplotlib>=3.9 From e2f22419bbde7ea5692bad68352318d4f75fb91e Mon Sep 17 00:00:00 2001 From: maestroque Date: Mon, 22 Jul 2024 11:23:29 +0300 Subject: [PATCH 34/57] Minor CI fix --- .circleci/config.yml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/.circleci/config.yml b/.circleci/config.yml index 071888b..a392ad0 100644 --- a/.circleci/config.yml +++ b/.circleci/config.yml @@ -133,10 +133,10 @@ workflows: # Inside the workflow, you define the jobs you want to run. jobs: - style_check - - test37: + - test38: requires: - style_check - - test310: + - test312: requires: - style_check - merge_coverage: From 9efbf5fe1065e9da7c15dbdec52bd20c970b4032 Mon Sep 17 00:00:00 2001 From: maestroque Date: Mon, 22 Jul 2024 11:43:17 +0300 Subject: [PATCH 35/57] CI: Change minimum python version to 3.9 --- .circleci/config.yml | 14 +++++++------- setup.cfg | 2 +- 2 files changed, 8 insertions(+), 8 deletions(-) diff --git a/.circleci/config.yml b/.circleci/config.yml index a392ad0..5508e83 100644 --- a/.circleci/config.yml +++ b/.circleci/config.yml @@ -15,14 +15,14 @@ orbs: # Define a job to be invoked later in a workflow. # See: https://circleci.com/docs/2.0/configuration-reference/#jobs jobs: - test38: # This is the name of the job, feel free to change it to better match what you're trying to do! + test39: # This is the name of the job, feel free to change it to better match what you're trying to do! # These next lines defines a Docker executors: https://circleci.com/docs/2.0/executor-types/ # You can specify an image from Dockerhub or use one of the convenience images from CircleCI's Developer Hub # A list of available CircleCI Docker convenience images are available here: https://circleci.com/developer/images/image/cimg/python # The executor is the environment in which the steps below will be executed - below will use a python 3.6.14 container # Change the version below to your required version of python docker: - - image: cimg/python:3.8 + - image: cimg/python:3.9 working_directory: /tmp/src/phys2denoise resource_class: medium # Checkout the code as the first step. This is a dedicated CircleCI step. @@ -46,7 +46,7 @@ jobs: command: | pytest --cov=./phys2denoise mkdir /tmp/src/coverage - mv ./.coverage /tmp/src/coverage/.coverage.py38 + mv ./.coverage /tmp/src/coverage/.coverage.py39 - store_artifacts: path: /tmp/src/coverage # Persist the specified paths (workspace/echo-output) into the workspace for use in downstream job. @@ -56,7 +56,7 @@ jobs: root: /tmp # Must be relative path from root paths: - - src/coverage/.coverage.py38 + - src/coverage/.coverage.py39 test312: docker: @@ -85,7 +85,7 @@ jobs: style_check: docker: - - image: cimg/python:3.8 + - image: cimg/python:3.9 working_directory: /tmp/src/phys2denoise resource_class: small steps: @@ -133,7 +133,7 @@ workflows: # Inside the workflow, you define the jobs you want to run. jobs: - style_check - - test38: + - test39: requires: - style_check - test312: @@ -141,5 +141,5 @@ workflows: - style_check - merge_coverage: requires: - - test38 + - test39 - test312 diff --git a/setup.cfg b/setup.cfg index 7568f5d..11316bc 100644 --- a/setup.cfg +++ b/setup.cfg @@ -20,7 +20,7 @@ provides = phys2denoise [options] -python_requires = >=3.8 +python_requires = >=3.9 install_requires = numpy >=1.9.3 matplotlib>=3.9 From ba5dcbc33db27cd67ce7ab5d6a698e378be44c01 Mon Sep 17 00:00:00 2001 From: maestroque Date: Mon, 22 Jul 2024 11:57:43 +0300 Subject: [PATCH 36/57] CI: Test for python 3.9 and 3.11 --- .circleci/config.yml | 14 +++++++------- 1 file changed, 7 insertions(+), 7 deletions(-) diff --git a/.circleci/config.yml b/.circleci/config.yml index 5508e83..dd45175 100644 --- a/.circleci/config.yml +++ b/.circleci/config.yml @@ -58,9 +58,9 @@ jobs: paths: - src/coverage/.coverage.py39 - test312: + test311: docker: - - image: cimg/python:3.12 + - image: cimg/python:3.11 working_directory: /tmp/src/phys2denoise resource_class: medium steps: @@ -75,13 +75,13 @@ jobs: command: | pytest --cov=./phys2denoise mkdir /tmp/src/coverage - mv ./.coverage /tmp/src/coverage/.coverage.py312 + mv ./.coverage /tmp/src/coverage/.coverage.py311 - store_artifacts: path: /tmp/src/coverage - persist_to_workspace: root: /tmp paths: - - src/coverage/.coverage.py312 + - src/coverage/.coverage.py311 style_check: docker: @@ -105,7 +105,7 @@ jobs: merge_coverage: working_directory: /tmp/src/phys2denoise docker: - - image: cimg/python:3.12 + - image: cimg/python:3.11 resource_class: small steps: - attach_workspace: @@ -136,10 +136,10 @@ workflows: - test39: requires: - style_check - - test312: + - test311: requires: - style_check - merge_coverage: requires: - test39 - - test312 + - test311 From 9f5e1629fc3f501c33978594d55e7b5f57013bff Mon Sep 17 00:00:00 2001 From: maestroque Date: Mon, 22 Jul 2024 19:57:13 +0300 Subject: [PATCH 37/57] Store computed metrics inside the Physio object --- phys2denoise/metrics/cardiac.py | 19 +++++++++++++++---- phys2denoise/metrics/chest_belt.py | 9 +++++++++ phys2denoise/metrics/multimodal.py | 3 +++ 3 files changed, 27 insertions(+), 4 deletions(-) diff --git a/phys2denoise/metrics/cardiac.py b/phys2denoise/metrics/cardiac.py index 3e217d7..06d8b50 100644 --- a/phys2denoise/metrics/cardiac.py +++ b/phys2denoise/metrics/cardiac.py @@ -199,9 +199,12 @@ def heart_rate(data, fs=None, peaks=None, window=6, central_measure="mean"): Annual International Conference of the IEEE Engineering in Medicine and Biology Society (EMBC), doi: 10.1109/EMBC.2016.7591347. """ - return _cardiac_metrics( - data, metric="hrv", fs=fs, peaks=peaks, window=6, central_measure="mean" + data, hr = _cardiac_metrics( + data, metric="hr", fs=fs, peaks=peaks, window=6, central_measure="mean" ) + data._computed_metrics["heart_rate"] = dict(metric=hr, has_lags=False) + + return data, hr @due.dcite(references.PINHERO_ET_AL_2016) @@ -256,9 +259,12 @@ def heart_rate_variability(data, fs=None, peaks=None, window=6, central_measure= Annual International Conference of the IEEE Engineering in Medicine and Biology Society (EMBC), doi: 10.1109/EMBC.2016.7591347. """ - return _cardiac_metrics( + data, hrv = _cardiac_metrics( data, metric="hrv", fs=None, peaks=None, window=6, central_measure="std" ) + data._computed_metrics["heart_rate_variability"] = dict(metric=hrv) + + return data, hrv @due.dcite(references.CHEN_2020) @@ -306,9 +312,12 @@ def heart_beat_interval(data, fs=None, peaks=None, window=6, central_measure="me .. [1] J. E. Chen et al., "Resting-state "physiological networks"", Neuroimage, vol. 213, pp. 116707, 2020. """ - return _cardiac_metrics( + data, hbi = _cardiac_metrics( data, metric="hbi", fs=None, peaks=None, window=6, central_measure="mean" ) + data._computed_metrics["heart_beat_interval"] = dict(metric=hbi) + + return data, hbi @physio.make_operation() @@ -393,4 +402,6 @@ def cardiac_phase(data, slice_timings, n_scans, t_r, fs=None, peaks=None): ) / (t2 - t1) phase_card[:, i_slice] = phase_card_crSlice + data._computed_metrics["cardiac_phase"] = dict(metric=phase_card) + return data, phase_card diff --git a/phys2denoise/metrics/chest_belt.py b/phys2denoise/metrics/chest_belt.py index 4e83b7d..1c20aeb 100644 --- a/phys2denoise/metrics/chest_belt.py +++ b/phys2denoise/metrics/chest_belt.py @@ -106,6 +106,7 @@ def respiratory_variance_time( ) rvt_lags[:, ind] = temp_rvt + data._computed_metrics["rvt"] = dict(metric=rvt_lags, has_lags=True) return data, rvt_lags @@ -152,6 +153,8 @@ def respiratory_pattern_variability(data, window): # Calculate standard deviation rpv_val = np.std(rpv_upper_env) + + data._computed_metrics["rpv"] = dict(metric=rpv_val) return data, rpv_val @@ -234,6 +237,8 @@ def _respiratory_pattern_variability(data, window): .apply(_respiratory_pattern_variability, args=(window,)) ) env_arr[np.isnan(env_arr)] = 0.0 + + data._computed_metrics["env"] = dict(metric=env_arr) return data, env_arr @@ -299,6 +304,8 @@ def respiratory_variance(data, fs=None, window=6): # Convolve with rrf rv_out = convolve_and_rescale(rv_arr, rrf(data.fs), rescale="zscore") + data._computed_metrics["respiratory_variance"] = dict(metric=rv_out) + return data, rv_out @@ -367,4 +374,6 @@ def respiratory_phase(data, n_scans, slice_timings, t_r, fs=None): phase_resp[:, i_slice] = phase_resp_crSlice + data._computed_metrics["respiratory_phase"] = dict(metric=phase_resp) + return data, phase_resp diff --git a/phys2denoise/metrics/multimodal.py b/phys2denoise/metrics/multimodal.py index f5b479e..fc48213 100644 --- a/phys2denoise/metrics/multimodal.py +++ b/phys2denoise/metrics/multimodal.py @@ -134,4 +134,7 @@ def retroicor( (j_harm + 1) * phase[i_slice] ) + data._computed_metrics["retroicor_regressors"] = dict( + metrics=retroicor_regressors, phase=phase + ) return data, retroicor_regressors, phase From daaed9c86adb650e29e0e5865f9410256786262d Mon Sep 17 00:00:00 2001 From: maestroque Date: Tue, 23 Jul 2024 16:07:46 +0300 Subject: [PATCH 38/57] Update .all-contributorsrc --- .all-contributorsrc | 12 ++++++++++++ 1 file changed, 12 insertions(+) diff --git a/.all-contributorsrc b/.all-contributorsrc index 46f9a58..e8b53b1 100644 --- a/.all-contributorsrc +++ b/.all-contributorsrc @@ -110,6 +110,18 @@ "review", "userTesting" ] + }, + { + "login": "maestroque", + "name": "George Kikas", + "avatar_url": "https://avatars.githubusercontent.com/u/74024609?v=4", + "profile": "https://github.com/maestroque", + "contributions": [ + "code", + "ideas", + "bug", + "review" + ] } ], "contributorsPerLine": 8, From 931207754d63bdc0a2929cf8dd6c798db8f7061b Mon Sep 17 00:00:00 2001 From: maestroque Date: Thu, 8 Aug 2024 21:47:56 +0300 Subject: [PATCH 39/57] Add basic installation, README.rst in index page and minor fixes --- README.rst | 22 ++++++++++++++++++++++ docs/index.rst | 1 + docs/installation.rst | 11 +++++++++++ docs/user_guide/exporting.rst | 3 ++- docs/user_guide/metrics.rst | 4 ++-- 5 files changed, 38 insertions(+), 3 deletions(-) create mode 100644 README.rst diff --git a/README.rst b/README.rst new file mode 100644 index 0000000..d247555 --- /dev/null +++ b/README.rst @@ -0,0 +1,22 @@ +phys2denoise: A toolbox for physiological metrics calculation +============================================================= + +This package is designed for use in the metrics calculation of physiological data, more specifically of cardiac and respiratory signals, to be used in fMRI denoising. + + +.. image:: https://readthedocs.org/projects/phys2denoise/badge/?version=latest + :target: http://phys2denoise.readthedocs.io/en/latest +.. image:: https://img.shields.io/badge/license-Apache%202-blue.svg + :target: http://www.apache.org/licenses/LICENSE-2.0 +.. image:: https://img.shields.io/badge/python-3.6+-blue.svg + :target: https://www.python.org/downloads/ + + +.. _licensing: + +License Information +------------------- + +This codebase is licensed under the Apache License, Version 2.0. The full +license can be found in the `LICENSE `_ file in the ``phys2denoise`` distribution. You may also +obtain a copy of the license at: http://www.apache.org/licenses/LICENSE-2.0. diff --git a/docs/index.rst b/docs/index.rst index 0651d73..590f394 100644 --- a/docs/index.rst +++ b/docs/index.rst @@ -1,3 +1,4 @@ +.. include:: ../README.rst Contents -------- diff --git a/docs/installation.rst b/docs/installation.rst index 709983c..a647649 100644 --- a/docs/installation.rst +++ b/docs/installation.rst @@ -5,6 +5,17 @@ Installation and setup .. _basic_installation: +Basic installation +------------------ + +The easiest way to install ``phys2denoise`` is to use ``pip``. Assuming you have +Python >= 3.6 installed, you can install ``phys2denoise`` by opening a terminal +and running the following: + +.. code-block:: bash + + pip install phys2denoise + Developer installation -------------------- diff --git a/docs/user_guide/exporting.rst b/docs/user_guide/exporting.rst index 1a9421f..5674a34 100644 --- a/docs/user_guide/exporting.rst +++ b/docs/user_guide/exporting.rst @@ -10,7 +10,8 @@ This can be done using the :py:func:`export_metric` function, which provides the - Defining the output file extension and file prefix. - Defining the number of timepoints to be considered. -The following example shows how to export the computed respiratory variance time using a Physio object. +The following example shows how to export the computed respiratory variance time using a Physio object. In the following example, +we consider that the Physio object is ``resp``, containing the respiratory data, peaks and troughs. .. code-block:: python diff --git a/docs/user_guide/metrics.rst b/docs/user_guide/metrics.rst index 402fe0c..7b1c5dc 100644 --- a/docs/user_guide/metrics.rst +++ b/docs/user_guide/metrics.rst @@ -64,7 +64,7 @@ For further information refer to the :py:mod:`physutils` documentation. Without using a Physio object ############################# -However, if the use of :py:mod:`physutils` is not preferred, the metrics can be also computed without it. The following +However, if the use of the ``Physio`` object of the :py:mod:`physutils` module is not preferred, the metrics can be also computed without it. The following example shows how to compute the heart rate and the heart rate variability using the :py:mod:`phys2denoise` package. .. code-block:: python @@ -73,4 +73,4 @@ example shows how to compute the heart rate and the heart rate variability using # Given that the respiratory signal is stored in `data`, the peaks in `peaks`, the troughs in `troughs` # and the sample rate in `sample_rate` - _, rvt = respiratory_variance_time(physio, peaks, troughs, sample_rate) + _, rvt = respiratory_variance_time(data, peaks, troughs, sample_rate) From 9b6a03c92781e2c7e6723ceef64d40c6fee1d6c1 Mon Sep 17 00:00:00 2001 From: Marie-Eve Picard Date: Thu, 8 Aug 2024 15:24:43 -0400 Subject: [PATCH 40/57] FIX typos and layout --- README.rst | 2 +- docs/api.rst | 8 ++++---- docs/installation.rst | 7 ++++++- docs/user_guide/metrics.rst | 2 +- 4 files changed, 12 insertions(+), 7 deletions(-) diff --git a/README.rst b/README.rst index d247555..4316096 100644 --- a/README.rst +++ b/README.rst @@ -1,7 +1,7 @@ phys2denoise: A toolbox for physiological metrics calculation ============================================================= -This package is designed for use in the metrics calculation of physiological data, more specifically of cardiac and respiratory signals, to be used in fMRI denoising. +This package is designed for calculating physiological metrics, derived specifically cardiac and respiratory signals, to use in fMRI denoising. .. image:: https://readthedocs.org/projects/phys2denoise/badge/?version=latest diff --git a/docs/api.rst b/docs/api.rst index dde3b05..b419f38 100644 --- a/docs/api.rst +++ b/docs/api.rst @@ -5,13 +5,13 @@ API .. py:module:: phys2denoise Cardiac data ------------------- +------------ .. automodule:: phys2denoise.metrics.cardiac :members: heart_rate, heart_rate_variability, heart_beat_interval, cardiac_phase Respiratory data ------------- +---------------- .. automodule:: phys2denoise.metrics.chest_belt :members: respiratory_cariance_time, respiratory_pattern_variability, env, respiratory_variance, respiratory_phase @@ -22,13 +22,13 @@ Multimodal data .. autofunction:: phys2denoise.multimodal.retroicor Response functions ------------ +------------------ .. automodule:: phys2denoise.metrics.responses :members: crf, icrf, rrf Utilities ------------ +--------- .. automodule:: phys2denoise.metrics.utils :members: print_metric_call, mirrorpad_1d, rms_envelope_1d, apply_lags, apply_function_in_sliding_window, convolve_and_rescale, export_metric diff --git a/docs/installation.rst b/docs/installation.rst index a647649..8e5fe3a 100644 --- a/docs/installation.rst +++ b/docs/installation.rst @@ -16,8 +16,13 @@ and running the following: pip install phys2denoise +.. warning:: + + If you encounter an ImportError related to numpy.core.multiarray, please try to update + your matplotlib version to 3.9. + Developer installation --------------------- +---------------------- This package requires Python >= 3.6. Assuming you have the correct version of Python installed, you can install ``phys2denoise`` by opening a terminal and running diff --git a/docs/user_guide/metrics.rst b/docs/user_guide/metrics.rst index 7b1c5dc..e387600 100644 --- a/docs/user_guide/metrics.rst +++ b/docs/user_guide/metrics.rst @@ -64,7 +64,7 @@ For further information refer to the :py:mod:`physutils` documentation. Without using a Physio object ############################# -However, if the use of the ``Physio`` object of the :py:mod:`physutils` module is not preferred, the metrics can be also computed without it. The following +However, if the use of the ``Physio`` object from the :py:mod:`physutils` module is not preferred, the metrics can be also computed without it. The following example shows how to compute the heart rate and the heart rate variability using the :py:mod:`phys2denoise` package. .. code-block:: python From a596838137384e963268a9e9183912783f409924 Mon Sep 17 00:00:00 2001 From: "pre-commit-ci[bot]" <66853113+pre-commit-ci[bot]@users.noreply.github.com> Date: Thu, 8 Aug 2024 19:25:08 +0000 Subject: [PATCH 41/57] [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci --- docs/installation.rst | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/installation.rst b/docs/installation.rst index 8e5fe3a..fc61add 100644 --- a/docs/installation.rst +++ b/docs/installation.rst @@ -18,7 +18,7 @@ and running the following: .. warning:: - If you encounter an ImportError related to numpy.core.multiarray, please try to update + If you encounter an ImportError related to numpy.core.multiarray, please try to update your matplotlib version to 3.9. Developer installation From 9bb94bd2dbe9d01c60571d90f616dc3dde95bbba Mon Sep 17 00:00:00 2001 From: Marie-Eve Picard Date: Fri, 9 Aug 2024 09:20:00 -0400 Subject: [PATCH 42/57] Fix docs --- .readthedocs.yml | 1 - 1 file changed, 1 deletion(-) diff --git a/.readthedocs.yml b/.readthedocs.yml index bc99c2a..86e7464 100644 --- a/.readthedocs.yml +++ b/.readthedocs.yml @@ -20,4 +20,3 @@ python: path: . extra_requirements: - doc - system_packages: true From bc300f046c69e8315668234bd82a4e66107512a8 Mon Sep 17 00:00:00 2001 From: maestroque Date: Sat, 10 Aug 2024 20:40:18 +0300 Subject: [PATCH 43/57] Add wrapper to determine whether to return a metric or a physio object --- phys2denoise/metrics/cardiac.py | 40 ++++++++++++++----- phys2denoise/metrics/chest_belt.py | 14 +++---- phys2denoise/metrics/utils.py | 38 ++++++++++++++++++ phys2denoise/tests/test_metrics_cardiac.py | 2 +- phys2denoise/tests/test_metrics_chest_belt.py | 8 ++-- phys2denoise/tests/test_rvt.py | 4 +- 6 files changed, 81 insertions(+), 25 deletions(-) diff --git a/phys2denoise/metrics/cardiac.py b/phys2denoise/metrics/cardiac.py index 06d8b50..72c7e8d 100644 --- a/phys2denoise/metrics/cardiac.py +++ b/phys2denoise/metrics/cardiac.py @@ -7,11 +7,17 @@ from ..due import due from .responses import crf from .utils import apply_function_in_sliding_window as afsw -from .utils import convolve_and_rescale +from .utils import convolve_and_rescale, return_physio_or_metric def _cardiac_metrics( - data, metric, fs=None, peaks=None, window=6, central_measure="mean" + data, + metric, + fs=None, + peaks=None, + window=6, + central_measure="mean", + return_physio=False, ): """ Compute cardiac metrics. @@ -146,6 +152,7 @@ def _cardiac_metrics( @due.dcite(references.CHANG_CUNNINGHAM_GLOVER_2009) +@return_physio_or_metric() @physio.make_operation() def heart_rate(data, fs=None, peaks=None, window=6, central_measure="mean"): """ @@ -200,14 +207,19 @@ def heart_rate(data, fs=None, peaks=None, window=6, central_measure="mean"): Biology Society (EMBC), doi: 10.1109/EMBC.2016.7591347. """ data, hr = _cardiac_metrics( - data, metric="hr", fs=fs, peaks=peaks, window=6, central_measure="mean" + data, + metric="hr", + fs=fs, + peaks=peaks, + window=window, + central_measure=central_measure, ) - data._computed_metrics["heart_rate"] = dict(metric=hr, has_lags=False) return data, hr @due.dcite(references.PINHERO_ET_AL_2016) +@return_physio_or_metric() @physio.make_operation() def heart_rate_variability(data, fs=None, peaks=None, window=6, central_measure="mean"): """ @@ -260,14 +272,19 @@ def heart_rate_variability(data, fs=None, peaks=None, window=6, central_measure= Biology Society (EMBC), doi: 10.1109/EMBC.2016.7591347. """ data, hrv = _cardiac_metrics( - data, metric="hrv", fs=None, peaks=None, window=6, central_measure="std" + data, + metric="hrv", + fs=fs, + peaks=peaks, + window=window, + central_measure=central_measure, ) - data._computed_metrics["heart_rate_variability"] = dict(metric=hrv) return data, hrv @due.dcite(references.CHEN_2020) +@return_physio_or_metric() @physio.make_operation() def heart_beat_interval(data, fs=None, peaks=None, window=6, central_measure="mean"): """ @@ -313,13 +330,18 @@ def heart_beat_interval(data, fs=None, peaks=None, window=6, central_measure="me vol. 213, pp. 116707, 2020. """ data, hbi = _cardiac_metrics( - data, metric="hbi", fs=None, peaks=None, window=6, central_measure="mean" + data, + metric="hbi", + fs=fs, + peaks=peaks, + window=window, + central_measure=central_measure, ) - data._computed_metrics["heart_beat_interval"] = dict(metric=hbi) return data, hbi +@return_physio_or_metric() @physio.make_operation() def cardiac_phase(data, slice_timings, n_scans, t_r, fs=None, peaks=None): """Calculate cardiac phase from cardiac peaks. @@ -402,6 +424,4 @@ def cardiac_phase(data, slice_timings, n_scans, t_r, fs=None, peaks=None): ) / (t2 - t1) phase_card[:, i_slice] = phase_card_crSlice - data._computed_metrics["cardiac_phase"] = dict(metric=phase_card) - return data, phase_card diff --git a/phys2denoise/metrics/chest_belt.py b/phys2denoise/metrics/chest_belt.py index 1c20aeb..0a7b800 100644 --- a/phys2denoise/metrics/chest_belt.py +++ b/phys2denoise/metrics/chest_belt.py @@ -9,10 +9,11 @@ from ..due import due from .responses import rrf from .utils import apply_function_in_sliding_window as afsw -from .utils import convolve_and_rescale, rms_envelope_1d +from .utils import convolve_and_rescale, return_physio_or_metric, rms_envelope_1d @due.dcite(references.BIRN_2006) +@return_physio_or_metric() @physio.make_operation() def respiratory_variance_time( data, fs=None, peaks=None, troughs=None, lags=(0, 4, 8, 12) @@ -106,11 +107,11 @@ def respiratory_variance_time( ) rvt_lags[:, ind] = temp_rvt - data._computed_metrics["rvt"] = dict(metric=rvt_lags, has_lags=True) return data, rvt_lags @due.dcite(references.POWER_2018) +@return_physio_or_metric() @physio.make_operation() def respiratory_pattern_variability(data, window): """Calculate respiratory pattern variability. @@ -154,11 +155,11 @@ def respiratory_pattern_variability(data, window): # Calculate standard deviation rpv_val = np.std(rpv_upper_env) - data._computed_metrics["rpv"] = dict(metric=rpv_val) return data, rpv_val @due.dcite(references.POWER_2020) +@return_physio_or_metric() @physio.make_operation() def env(data, fs=None, window=10): """Calculate respiratory pattern variability across a sliding window. @@ -238,11 +239,11 @@ def _respiratory_pattern_variability(data, window): ) env_arr[np.isnan(env_arr)] = 0.0 - data._computed_metrics["env"] = dict(metric=env_arr) return data, env_arr @due.dcite(references.CHANG_GLOVER_2009) +@return_physio_or_metric() @physio.make_operation() def respiratory_variance(data, fs=None, window=6): """Calculate respiratory variance. @@ -304,11 +305,10 @@ def respiratory_variance(data, fs=None, window=6): # Convolve with rrf rv_out = convolve_and_rescale(rv_arr, rrf(data.fs), rescale="zscore") - data._computed_metrics["respiratory_variance"] = dict(metric=rv_out) - return data, rv_out +@return_physio_or_metric() @physio.make_operation() def respiratory_phase(data, n_scans, slice_timings, t_r, fs=None): """Calculate respiratory phase from respiratory signal. @@ -374,6 +374,4 @@ def respiratory_phase(data, n_scans, slice_timings, t_r, fs=None): phase_resp[:, i_slice] = phase_resp_crSlice - data._computed_metrics["respiratory_phase"] = dict(metric=phase_resp) - return data, phase_resp diff --git a/phys2denoise/metrics/utils.py b/phys2denoise/metrics/utils.py index 34fb21b..4378866 100644 --- a/phys2denoise/metrics/utils.py +++ b/phys2denoise/metrics/utils.py @@ -1,8 +1,11 @@ """Miscellaneous utility functions for metric calculation.""" +import functools import logging import numpy as np +from loguru import logger from numpy.lib.stride_tricks import sliding_window_view as swv +from physutils.physio import Physio from scipy.interpolate import interp1d from scipy.stats import zscore @@ -332,3 +335,38 @@ def export_metric( ) return fileprefix + + +def return_physio_or_metric(*, return_physio=True): + """ + Decorator to check if the input is a Physio object. + + Parameters + ---------- + func : function + Function to be decorated + + Returns + ------- + function + Decorated function + """ + + def determine_return_type(func): + @functools.wraps(func) + def wrapper(*args, **kwargs): + physio, metric = func(*args, **kwargs) + if isinstance(args[0], Physio): + physio._computed_metrics[func.__name__] = dict( + metric=metric, args=kwargs + ) + if return_physio: + return physio, metric + else: + return metric + else: + return metric + + return wrapper + + return determine_return_type diff --git a/phys2denoise/tests/test_metrics_cardiac.py b/phys2denoise/tests/test_metrics_cardiac.py index 25faa9a..f9b69ad 100644 --- a/phys2denoise/tests/test_metrics_cardiac.py +++ b/phys2denoise/tests/test_metrics_cardiac.py @@ -28,7 +28,7 @@ def test_cardiac_phase_smoke(): slice_timings = np.linspace(0, t_r, 22)[1:-1] peaks = np.array([0.534, 0.577, 10.45, 20.66, 50.55, 90.22]) data = np.zeros(peaks.shape) - _, card_phase = cardiac.cardiac_phase( + card_phase = cardiac.cardiac_phase( data, peaks=peaks, fs=sample_rate, diff --git a/phys2denoise/tests/test_metrics_chest_belt.py b/phys2denoise/tests/test_metrics_chest_belt.py index 5e5bfd1..a4257ec 100644 --- a/phys2denoise/tests/test_metrics_chest_belt.py +++ b/phys2denoise/tests/test_metrics_chest_belt.py @@ -30,7 +30,7 @@ def test_respiratory_phase_smoke(): slice_timings = np.linspace(0, t_r, 22)[1:-1] n_samples = int(np.rint((n_scans * t_r) * sample_rate)) resp = np.random.normal(size=n_samples) - _, resp_phase = chest_belt.respiratory_phase( + resp_phase = chest_belt.respiratory_phase( resp, fs=sample_rate, slice_timings=slice_timings, @@ -46,7 +46,7 @@ def test_respiratory_pattern_variability_smoke(): n_samples = 2000 resp = np.random.normal(size=n_samples) window = 50 - _, rpv_val = chest_belt.respiratory_pattern_variability(resp, window) + rpv_val = chest_belt.respiratory_pattern_variability(resp, window) assert isinstance(rpv_val, float) @@ -56,7 +56,7 @@ def test_env_smoke(): resp = np.random.normal(size=n_samples) samplerate = 1 / 0.01 window = 6 - _, env_arr = chest_belt.env(resp, fs=samplerate, window=window) + env_arr = chest_belt.env(resp, fs=samplerate, window=window) assert env_arr.ndim == 1 assert env_arr.shape == (n_samples,) @@ -67,6 +67,6 @@ def test_respiratory_variance_smoke(): resp = np.random.normal(size=n_samples) samplerate = 1 / 0.01 window = 6 - _, rv_arr = chest_belt.respiratory_variance(resp, fs=samplerate, window=window) + rv_arr = chest_belt.respiratory_variance(resp, fs=samplerate, window=window) assert rv_arr.ndim == 2 assert rv_arr.shape == (n_samples, 2) diff --git a/phys2denoise/tests/test_rvt.py b/phys2denoise/tests/test_rvt.py index 67a7bf9..20d1690 100644 --- a/phys2denoise/tests/test_rvt.py +++ b/phys2denoise/tests/test_rvt.py @@ -17,8 +17,8 @@ def test_respiratory_variance_time(fake_phys): phys = peakdet.operations.peakfind_physio(phys) # TODO: Change to a simpler call once physutils are - # integrated to peakdet - phys, r = respiratory_variance_time( + # integrated to peakdet/prep4phys + r = respiratory_variance_time( phys.data, fs=phys.fs, peaks=phys.peaks, troughs=phys.troughs ) assert r is not None From 9883ce296f7824faa757d9feeeb3c01c912374ea Mon Sep 17 00:00:00 2001 From: maestroque Date: Sat, 10 Aug 2024 20:40:48 +0300 Subject: [PATCH 44/57] [deps] Cap numpy to <2.0 --- setup.cfg | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/setup.cfg b/setup.cfg index 9f26a68..f1a08fd 100644 --- a/setup.cfg +++ b/setup.cfg @@ -21,8 +21,8 @@ provides = [options] python_requires = >=3.9 install_requires = - numpy >=1.9.3 - matplotlib>=3.9 + numpy >=1.9.3, <2 + matplotlib pandas scipy duecredit From 181304fe10d6b785b4577cf8ac1883b276bd37c8 Mon Sep 17 00:00:00 2001 From: maestroque Date: Sat, 10 Aug 2024 20:51:09 +0300 Subject: [PATCH 45/57] [docs]: Update computing metrics --- docs/user_guide/metrics.rst | 8 ++++++-- 1 file changed, 6 insertions(+), 2 deletions(-) diff --git a/docs/user_guide/metrics.rst b/docs/user_guide/metrics.rst index e387600..779f31b 100644 --- a/docs/user_guide/metrics.rst +++ b/docs/user_guide/metrics.rst @@ -71,6 +71,10 @@ example shows how to compute the heart rate and the heart rate variability using from phys2denoise.metrics.chest_belt import respiratory_variance_time - # Given that the respiratory signal is stored in `data`, the peaks in `peaks`, the troughs in `troughs` + # Given that the respiratory signal is stored in `data` (which is not a physio.Physio instance), the peaks in `peaks`, the troughs in `troughs` # and the sample rate in `sample_rate` - _, rvt = respiratory_variance_time(data, peaks, troughs, sample_rate) + rvt = respiratory_variance_time(data, peaks, troughs, sample_rate) + +The computed respiratory variance time is stored in the variable ``rvt``. An internal check is performed to verify if the input data is a Physio object or not +determining the appropriate output format. If the input is not a ``Physio`` object, the output will be a numpy array only containing the computed metric. Otherwise, +the output will be a tuple with the updated Physio object and the computed metric. From 43107db3d956f316255e44a934d28edc7eba5a0e Mon Sep 17 00:00:00 2001 From: maestroque Date: Sun, 11 Aug 2024 21:35:19 +0300 Subject: [PATCH 46/57] Metric or Physio returning optimization --- phys2denoise/metrics/cardiac.py | 17 ++++++++++++----- phys2denoise/metrics/chest_belt.py | 10 +++++----- phys2denoise/metrics/multimodal.py | 1 + phys2denoise/metrics/utils.py | 5 +++-- phys2denoise/tests/test_metrics_cardiac.py | 18 +++++++++++++++++- 5 files changed, 38 insertions(+), 13 deletions(-) diff --git a/phys2denoise/metrics/cardiac.py b/phys2denoise/metrics/cardiac.py index 72c7e8d..63f1475 100644 --- a/phys2denoise/metrics/cardiac.py +++ b/phys2denoise/metrics/cardiac.py @@ -17,7 +17,7 @@ def _cardiac_metrics( peaks=None, window=6, central_measure="mean", - return_physio=False, + **kwargs, ): """ Compute cardiac metrics. @@ -154,7 +154,7 @@ def _cardiac_metrics( @due.dcite(references.CHANG_CUNNINGHAM_GLOVER_2009) @return_physio_or_metric() @physio.make_operation() -def heart_rate(data, fs=None, peaks=None, window=6, central_measure="mean"): +def heart_rate(data, fs=None, peaks=None, window=6, central_measure="mean", **kwargs): """ Compute average heart rate (HR) in a sliding window. @@ -213,6 +213,7 @@ def heart_rate(data, fs=None, peaks=None, window=6, central_measure="mean"): peaks=peaks, window=window, central_measure=central_measure, + **kwargs, ) return data, hr @@ -221,7 +222,9 @@ def heart_rate(data, fs=None, peaks=None, window=6, central_measure="mean"): @due.dcite(references.PINHERO_ET_AL_2016) @return_physio_or_metric() @physio.make_operation() -def heart_rate_variability(data, fs=None, peaks=None, window=6, central_measure="mean"): +def heart_rate_variability( + data, fs=None, peaks=None, window=6, central_measure="mean", **kwargs +): """ Compute average heart rate variability (HRV) in a sliding window. @@ -278,6 +281,7 @@ def heart_rate_variability(data, fs=None, peaks=None, window=6, central_measure= peaks=peaks, window=window, central_measure=central_measure, + **kwargs, ) return data, hrv @@ -286,7 +290,9 @@ def heart_rate_variability(data, fs=None, peaks=None, window=6, central_measure= @due.dcite(references.CHEN_2020) @return_physio_or_metric() @physio.make_operation() -def heart_beat_interval(data, fs=None, peaks=None, window=6, central_measure="mean"): +def heart_beat_interval( + data, fs=None, peaks=None, window=6, central_measure="mean", **kwargs +): """ Compute average heart beat interval (HBI) in a sliding window. @@ -336,6 +342,7 @@ def heart_beat_interval(data, fs=None, peaks=None, window=6, central_measure="me peaks=peaks, window=window, central_measure=central_measure, + **kwargs, ) return data, hbi @@ -343,7 +350,7 @@ def heart_beat_interval(data, fs=None, peaks=None, window=6, central_measure="me @return_physio_or_metric() @physio.make_operation() -def cardiac_phase(data, slice_timings, n_scans, t_r, fs=None, peaks=None): +def cardiac_phase(data, slice_timings, n_scans, t_r, fs=None, peaks=None, **kwargs): """Calculate cardiac phase from cardiac peaks. Assumes that timing of cardiac events are given in same units diff --git a/phys2denoise/metrics/chest_belt.py b/phys2denoise/metrics/chest_belt.py index 0a7b800..deae46f 100644 --- a/phys2denoise/metrics/chest_belt.py +++ b/phys2denoise/metrics/chest_belt.py @@ -16,7 +16,7 @@ @return_physio_or_metric() @physio.make_operation() def respiratory_variance_time( - data, fs=None, peaks=None, troughs=None, lags=(0, 4, 8, 12) + data, fs=None, peaks=None, troughs=None, lags=(0, 4, 8, 12), **kwargs ): """ Implement the Respiratory Variance over Time (Birn et al. 2006). @@ -113,7 +113,7 @@ def respiratory_variance_time( @due.dcite(references.POWER_2018) @return_physio_or_metric() @physio.make_operation() -def respiratory_pattern_variability(data, window): +def respiratory_pattern_variability(data, window, **kwargs): """Calculate respiratory pattern variability. Parameters @@ -161,7 +161,7 @@ def respiratory_pattern_variability(data, window): @due.dcite(references.POWER_2020) @return_physio_or_metric() @physio.make_operation() -def env(data, fs=None, window=10): +def env(data, fs=None, window=10, **kwargs): """Calculate respiratory pattern variability across a sliding window. Parameters @@ -245,7 +245,7 @@ def _respiratory_pattern_variability(data, window): @due.dcite(references.CHANG_GLOVER_2009) @return_physio_or_metric() @physio.make_operation() -def respiratory_variance(data, fs=None, window=6): +def respiratory_variance(data, fs=None, window=6, **kwargs): """Calculate respiratory variance. Parameters @@ -310,7 +310,7 @@ def respiratory_variance(data, fs=None, window=6): @return_physio_or_metric() @physio.make_operation() -def respiratory_phase(data, n_scans, slice_timings, t_r, fs=None): +def respiratory_phase(data, n_scans, slice_timings, t_r, fs=None, **kwargs): """Calculate respiratory phase from respiratory signal. Parameters diff --git a/phys2denoise/metrics/multimodal.py b/phys2denoise/metrics/multimodal.py index fc48213..85f168f 100644 --- a/phys2denoise/metrics/multimodal.py +++ b/phys2denoise/metrics/multimodal.py @@ -20,6 +20,7 @@ def retroicor( physio_type=None, fs=None, cardiac_peaks=None, + **kwargs, ): """Compute RETROICOR regressors. diff --git a/phys2denoise/metrics/utils.py b/phys2denoise/metrics/utils.py index 4378866..edd66ec 100644 --- a/phys2denoise/metrics/utils.py +++ b/phys2denoise/metrics/utils.py @@ -360,8 +360,9 @@ def wrapper(*args, **kwargs): physio._computed_metrics[func.__name__] = dict( metric=metric, args=kwargs ) - if return_physio: - return physio, metric + return_physio_value = kwargs.get("return_physio", return_physio) + if return_physio_value: + return physio else: return metric else: diff --git a/phys2denoise/tests/test_metrics_cardiac.py b/phys2denoise/tests/test_metrics_cardiac.py index f9b69ad..839b040 100644 --- a/phys2denoise/tests/test_metrics_cardiac.py +++ b/phys2denoise/tests/test_metrics_cardiac.py @@ -50,12 +50,28 @@ def test_cardiac_phase_smoke_physio_obj(): data = np.zeros(peaks.shape) phys = physio.Physio(data, sample_rate, physio_type="cardiac") phys._metadata["peaks"] = peaks - phys, card_phase = cardiac.cardiac_phase( + + # Test where the physio object is returned + phys = cardiac.cardiac_phase( phys, slice_timings=slice_timings, n_scans=n_scans, t_r=t_r, ) assert phys.history[0][0] == "phys2denoise.metrics.cardiac.cardiac_phase" + assert phys.computed_metrics["cardiac_phase"]["metric"].ndim == 2 + assert phys.computed_metrics["cardiac_phase"]["metric"].shape == ( + n_scans, + slice_timings.size, + ) + + # Test where the metric is returned + card_phase = cardiac.cardiac_phase( + phys, + slice_timings=slice_timings, + n_scans=n_scans, + t_r=t_r, + return_physio=False, + ) assert card_phase.ndim == 2 assert card_phase.shape == (n_scans, slice_timings.size) From b0f411017b646e421be11fefd010e796b35d73c9 Mon Sep 17 00:00:00 2001 From: maestroque Date: Sun, 11 Aug 2024 22:06:47 +0300 Subject: [PATCH 47/57] Add Metric class for easier properties accessing --- phys2denoise/metrics/utils.py | 62 +++++++++++++++++++++- phys2denoise/tests/test_metrics_cardiac.py | 8 ++- 2 files changed, 66 insertions(+), 4 deletions(-) diff --git a/phys2denoise/metrics/utils.py b/phys2denoise/metrics/utils.py index edd66ec..eab3e7a 100644 --- a/phys2denoise/metrics/utils.py +++ b/phys2denoise/metrics/utils.py @@ -353,13 +353,29 @@ def return_physio_or_metric(*, return_physio=True): """ def determine_return_type(func): + metrics_with_lags = ["respiratory_variance_time"] + convolved_metrics = [ + "respiratory_variance", + "heart_rate", + "heart_rate_variability", + "heart_beat_interval", + ] + @functools.wraps(func) def wrapper(*args, **kwargs): physio, metric = func(*args, **kwargs) if isinstance(args[0], Physio): - physio._computed_metrics[func.__name__] = dict( - metric=metric, args=kwargs + has_lags = True if func.__name__ in metrics_with_lags else False + is_convolved = True if func.__name__ in convolved_metrics else False + + physio._computed_metrics[func.__name__] = Metric( + func.__name__, + metric, + kwargs, + has_lags=has_lags, + is_convolved=is_convolved, ) + return_physio_value = kwargs.get("return_physio", return_physio) if return_physio_value: return physio @@ -371,3 +387,45 @@ def wrapper(*args, **kwargs): return wrapper return determine_return_type + + +class Metric: + def __init__(self, name, data, args, has_lags=False, is_convolved=False): + self.name = name + self._data = data + self._args = args + self._has_lags = has_lags + self._is_convolved = is_convolved + + def __array__(self): + return self.data + + def __getitem__(self, slicer): + return self.data[slicer] + + def __len__(self): + return len(self.data) + + @property + def ndim(self): + return self.data.ndim + + @property + def shape(self): + return self.data.shape + + @property + def data(self): + return self._data + + @property + def args(self): + return self._args + + @property + def has_lags(self): + return self._has_lags + + @property + def is_convolved(self): + return self._is_convolved diff --git a/phys2denoise/tests/test_metrics_cardiac.py b/phys2denoise/tests/test_metrics_cardiac.py index 839b040..2d776cf 100644 --- a/phys2denoise/tests/test_metrics_cardiac.py +++ b/phys2denoise/tests/test_metrics_cardiac.py @@ -58,12 +58,16 @@ def test_cardiac_phase_smoke_physio_obj(): n_scans=n_scans, t_r=t_r, ) + assert phys.history[0][0] == "phys2denoise.metrics.cardiac.cardiac_phase" - assert phys.computed_metrics["cardiac_phase"]["metric"].ndim == 2 - assert phys.computed_metrics["cardiac_phase"]["metric"].shape == ( + assert phys.computed_metrics["cardiac_phase"].ndim == 2 + assert phys.computed_metrics["cardiac_phase"].shape == ( n_scans, slice_timings.size, ) + assert phys.computed_metrics["cardiac_phase"].args["slice_timings"] is not None + assert phys.computed_metrics["cardiac_phase"].args["n_scans"] is not None + assert phys.computed_metrics["cardiac_phase"].args["t_r"] is not None # Test where the metric is returned card_phase = cardiac.cardiac_phase( From 10509bd43b843480d19121e60e16340300d498e6 Mon Sep 17 00:00:00 2001 From: maestroque Date: Wed, 21 Aug 2024 17:13:49 +0200 Subject: [PATCH 48/57] More unit tests, physio/metric wrapper optimization, doc fixes --- .all-contributorsrc | 2 ++ phys2denoise/metrics/cardiac.py | 10 ++++---- phys2denoise/metrics/chest_belt.py | 10 ++++---- phys2denoise/metrics/multimodal.py | 8 ++++-- phys2denoise/metrics/utils.py | 25 +++++++++++++++++-- phys2denoise/tests/test_rvt.py | 39 ++++++++++++++++++++++++++++++ 6 files changed, 80 insertions(+), 14 deletions(-) diff --git a/.all-contributorsrc b/.all-contributorsrc index e8b53b1..1e8e6aa 100644 --- a/.all-contributorsrc +++ b/.all-contributorsrc @@ -119,6 +119,8 @@ "contributions": [ "code", "ideas", + "infra", + "docs", "bug", "review" ] diff --git a/phys2denoise/metrics/cardiac.py b/phys2denoise/metrics/cardiac.py index 63f1475..711aacb 100644 --- a/phys2denoise/metrics/cardiac.py +++ b/phys2denoise/metrics/cardiac.py @@ -31,7 +31,7 @@ def _cardiac_metrics( Parameters ---------- - data : Physio_like + data : physutils.Physio, np.ndarray, or array-like object Object containing the timeseries of the recorded cardiac signal metrics : "hbi", "hr", "hrv", string Cardiac metric(s) to calculate. @@ -164,7 +164,7 @@ def heart_rate(data, fs=None, peaks=None, window=6, central_measure="mean", **kw Parameters ---------- - data : Physio_like + data : physutils.Physio, np.ndarray, or array-like object Object containing the timeseries of the recorded cardiac signal fs : float, optional if data is a physutils.Physio Sampling rate of `data` in Hz @@ -234,7 +234,7 @@ def heart_rate_variability( Parameters ---------- - data : Physio_like + data : physutils.Physio, np.ndarray, or array-like object Object containing the timeseries of the recorded cardiac signal fs : float, optional if data is a physutils.Physio Sampling rate of `data` in Hz @@ -298,7 +298,7 @@ def heart_beat_interval( Parameters ---------- - data : Physio_like + data : physutils.Physio, np.ndarray, or array-like object Object containing the timeseries of the recorded cardiac signal fs : float, optional if data is a physutils.Physio Sampling rate of `data` in Hz @@ -358,7 +358,7 @@ def cardiac_phase(data, slice_timings, n_scans, t_r, fs=None, peaks=None, **kwar Parameters ---------- - data : Physio_like + data : physutils.Physio, np.ndarray, or array-like object Object containing the timeseries of the recorded cardiac signal slice_timings : 1D array_like Slice times, in seconds. diff --git a/phys2denoise/metrics/chest_belt.py b/phys2denoise/metrics/chest_belt.py index deae46f..4f7fc2c 100644 --- a/phys2denoise/metrics/chest_belt.py +++ b/phys2denoise/metrics/chest_belt.py @@ -25,7 +25,7 @@ def respiratory_variance_time( Parameters ---------- - data : Physio_like + data : physutils.Physio, np.ndarray, or array-like object Object containing the timeseries of the recorded respiratory signal fs : float, optional if data is a physutils.Physio Sampling rate of `data` in Hz @@ -118,7 +118,7 @@ def respiratory_pattern_variability(data, window, **kwargs): Parameters ---------- - data : Physio_like + data : physutils.Physio, np.ndarray, or array-like object Object containing the timeseries of the recorded respiratory signal window : int Window length in samples. @@ -166,7 +166,7 @@ def env(data, fs=None, window=10, **kwargs): Parameters ---------- - data : Physio_like + data : physutils.Physio, np.ndarray, or array-like object Object containing the timeseries of the recorded respiratory signal fs : float, optional if data is a physutils.Physio Sampling rate of `data` in Hz @@ -250,7 +250,7 @@ def respiratory_variance(data, fs=None, window=6, **kwargs): Parameters ---------- - data : Physio_like + data : physutils.Physio, np.ndarray, or array-like object Object containing the timeseries of the recorded respiratory signal fs : float, optional if data is a physutils.Physio Sampling rate of `data` in Hz @@ -315,7 +315,7 @@ def respiratory_phase(data, n_scans, slice_timings, t_r, fs=None, **kwargs): Parameters ---------- - data : Physio_like + data : physutils.Physio, np.ndarray, or array-like object Object containing the timeseries of the recorded respiratory signal n_scans Number of volumes in the imaging run. diff --git a/phys2denoise/metrics/multimodal.py b/phys2denoise/metrics/multimodal.py index 85f168f..fa28bae 100644 --- a/phys2denoise/metrics/multimodal.py +++ b/phys2denoise/metrics/multimodal.py @@ -7,9 +7,11 @@ from ..due import due from .cardiac import cardiac_phase from .chest_belt import respiratory_phase +from .utils import return_physio_or_metric @due.dcite(references.GLOVER_2000) +@return_physio_or_metric() @physio.make_operation() def retroicor( data, @@ -26,7 +28,7 @@ def retroicor( Parameters ---------- - data : Physio_like + data : physutils.Physio, np.ndarray, or array-like object Object containing the timeseries of the recorded respiratory or cardiac signal t_r : float Imaging sample rate, in seconds. @@ -138,4 +140,6 @@ def retroicor( data._computed_metrics["retroicor_regressors"] = dict( metrics=retroicor_regressors, phase=phase ) - return data, retroicor_regressors, phase + retroicor_regressors = dict(metrics=retroicor_regressors, phase=phase) + + return data, retroicor_regressors diff --git a/phys2denoise/metrics/utils.py b/phys2denoise/metrics/utils.py index eab3e7a..cf14ef6 100644 --- a/phys2denoise/metrics/utils.py +++ b/phys2denoise/metrics/utils.py @@ -1,5 +1,6 @@ """Miscellaneous utility functions for metric calculation.""" import functools +import inspect import logging import numpy as np @@ -353,7 +354,6 @@ def return_physio_or_metric(*, return_physio=True): """ def determine_return_type(func): - metrics_with_lags = ["respiratory_variance_time"] convolved_metrics = [ "respiratory_variance", "heart_rate", @@ -364,8 +364,15 @@ def determine_return_type(func): @functools.wraps(func) def wrapper(*args, **kwargs): physio, metric = func(*args, **kwargs) + default_args = get_default_args(func) if isinstance(args[0], Physio): - has_lags = True if func.__name__ in metrics_with_lags else False + if "lags" in kwargs: + has_lags = True if len(kwargs["lags"]) > 1 else False + elif "lags" in default_args: + has_lags = True if len(default_args["lags"]) > 1 else False + else: + has_lags = False + is_convolved = True if func.__name__ in convolved_metrics else False physio._computed_metrics[func.__name__] = Metric( @@ -389,6 +396,20 @@ def wrapper(*args, **kwargs): return determine_return_type +def get_default_args(func): + # Get the signature of the function + sig = inspect.signature(func) + + # Extract default values for each parameter + defaults = { + k: v.default + for k, v in sig.parameters.items() + if v.default is not inspect.Parameter.empty + } + + return defaults + + class Metric: def __init__(self, name, data, args, has_lags=False, is_convolved=False): self.name = name diff --git a/phys2denoise/tests/test_rvt.py b/phys2denoise/tests/test_rvt.py index 20d1690..0bc4066 100644 --- a/phys2denoise/tests/test_rvt.py +++ b/phys2denoise/tests/test_rvt.py @@ -1,4 +1,5 @@ import peakdet +from physutils import io, physio from phys2denoise.metrics.chest_belt import respiratory_variance_time @@ -23,3 +24,41 @@ def test_respiratory_variance_time(fake_phys): ) assert r is not None assert len(r) == 18750 + + +def test_respiratory_variance_time(fake_phys): + phys = peakdet.Physio(fake_phys, fs=62.5) + phys = peakdet.operations.filter_physio(phys, cutoffs=3, method="lowpass") + phys = peakdet.operations.peakfind_physio(phys) + + # TODO: Change to a simpler call once physutils are + # integrated to peakdet/prep4phys + r = respiratory_variance_time( + phys.data, fs=phys.fs, peaks=phys.peaks, troughs=phys.troughs + ) + assert r is not None + assert len(r) == 18750 + + +def test_respiratory_variance_time_physio_obj(fake_phys): + phys = peakdet.Physio(fake_phys, fs=62.5) + phys = peakdet.operations.filter_physio(phys, cutoffs=3, method="lowpass") + phys = peakdet.operations.peakfind_physio(phys) + + # TODO: Change to a simpler call once physutils are + # integrated to peakdet/prep4phys + physio_obj = physio.Physio(phys.data, phys.fs) + physio_obj._metadata["peaks"] = phys.peaks + physio_obj._metadata["troughs"] = phys.troughs + physio_obj = respiratory_variance_time(physio_obj) + + assert ( + physio_obj.history[0][0] + == "phys2denoise.metrics.chest_belt.respiratory_variance_time" + ) + assert physio_obj.computed_metrics["respiratory_variance_time"].ndim == 2 + assert physio_obj.computed_metrics["respiratory_variance_time"].shape == (18750, 4) + assert physio_obj.computed_metrics["respiratory_variance_time"].has_lags == True + + # assert r is not None + # assert len(r) == 18750 From 612c616f3ba26d3048f6d80fbe25a17b27322d25 Mon Sep 17 00:00:00 2001 From: maestroque Date: Wed, 21 Aug 2024 17:48:09 +0200 Subject: [PATCH 49/57] Minor fix --- phys2denoise/metrics/cardiac.py | 16 ++++++++-------- phys2denoise/metrics/chest_belt.py | 2 +- 2 files changed, 9 insertions(+), 9 deletions(-) diff --git a/phys2denoise/metrics/cardiac.py b/phys2denoise/metrics/cardiac.py index 711aacb..5b7588d 100644 --- a/phys2denoise/metrics/cardiac.py +++ b/phys2denoise/metrics/cardiac.py @@ -13,8 +13,8 @@ def _cardiac_metrics( data, metric, - fs=None, peaks=None, + fs=None, window=6, central_measure="mean", **kwargs, @@ -154,7 +154,7 @@ def _cardiac_metrics( @due.dcite(references.CHANG_CUNNINGHAM_GLOVER_2009) @return_physio_or_metric() @physio.make_operation() -def heart_rate(data, fs=None, peaks=None, window=6, central_measure="mean", **kwargs): +def heart_rate(data, peaks=None, fs=None, window=6, central_measure="mean", **kwargs): """ Compute average heart rate (HR) in a sliding window. @@ -209,8 +209,8 @@ def heart_rate(data, fs=None, peaks=None, window=6, central_measure="mean", **kw data, hr = _cardiac_metrics( data, metric="hr", - fs=fs, peaks=peaks, + fs=fs, window=window, central_measure=central_measure, **kwargs, @@ -223,7 +223,7 @@ def heart_rate(data, fs=None, peaks=None, window=6, central_measure="mean", **kw @return_physio_or_metric() @physio.make_operation() def heart_rate_variability( - data, fs=None, peaks=None, window=6, central_measure="mean", **kwargs + data, peaks=None, fs=None, window=6, central_measure="mean", **kwargs ): """ Compute average heart rate variability (HRV) in a sliding window. @@ -277,8 +277,8 @@ def heart_rate_variability( data, hrv = _cardiac_metrics( data, metric="hrv", - fs=fs, peaks=peaks, + fs=fs, window=window, central_measure=central_measure, **kwargs, @@ -291,7 +291,7 @@ def heart_rate_variability( @return_physio_or_metric() @physio.make_operation() def heart_beat_interval( - data, fs=None, peaks=None, window=6, central_measure="mean", **kwargs + data, peaks=None, fs=None, window=6, central_measure="mean", **kwargs ): """ Compute average heart beat interval (HBI) in a sliding window. @@ -338,8 +338,8 @@ def heart_beat_interval( data, hbi = _cardiac_metrics( data, metric="hbi", - fs=fs, peaks=peaks, + fs=fs, window=window, central_measure=central_measure, **kwargs, @@ -350,7 +350,7 @@ def heart_beat_interval( @return_physio_or_metric() @physio.make_operation() -def cardiac_phase(data, slice_timings, n_scans, t_r, fs=None, peaks=None, **kwargs): +def cardiac_phase(data, slice_timings, n_scans, t_r, peaks=None, fs=None, **kwargs): """Calculate cardiac phase from cardiac peaks. Assumes that timing of cardiac events are given in same units diff --git a/phys2denoise/metrics/chest_belt.py b/phys2denoise/metrics/chest_belt.py index 4f7fc2c..4e080fc 100644 --- a/phys2denoise/metrics/chest_belt.py +++ b/phys2denoise/metrics/chest_belt.py @@ -16,7 +16,7 @@ @return_physio_or_metric() @physio.make_operation() def respiratory_variance_time( - data, fs=None, peaks=None, troughs=None, lags=(0, 4, 8, 12), **kwargs + data, peaks=None, troughs=None, fs=None, lags=(0, 4, 8, 12), **kwargs ): """ Implement the Respiratory Variance over Time (Birn et al. 2006). From e528d216883dde68447837ab25cdb18713e06f7f Mon Sep 17 00:00:00 2001 From: maestroque Date: Sun, 25 Aug 2024 15:06:04 +0200 Subject: [PATCH 50/57] [test] Fix failing warning assertion --- phys2denoise/metrics/utils.py | 8 ++++++-- phys2denoise/tests/test_metrics_utils.py | 6 +++--- 2 files changed, 9 insertions(+), 5 deletions(-) diff --git a/phys2denoise/metrics/utils.py b/phys2denoise/metrics/utils.py index cf14ef6..e21a085 100644 --- a/phys2denoise/metrics/utils.py +++ b/phys2denoise/metrics/utils.py @@ -37,7 +37,7 @@ def print_metric_call(metric, args): msg = f"{msg}\n" - LGR.info(msg) + logger.info(msg) def mirrorpad_1d(arr, buffer=250): @@ -62,7 +62,11 @@ def mirrorpad_1d(arr, buffer=250): post_mirror = np.take(mirror, idx, axis=0) except IndexError: len(arr) - LGR.warning( + # LGR.warning( + # f"Requested buffer size ({buffer}) is longer than input array length " + # f"({len(arr)}). Fixing buffer size to array length." + # ) + logger.warning( f"Requested buffer size ({buffer}) is longer than input array length " f"({len(arr)}). Fixing buffer size to array length." ) diff --git a/phys2denoise/tests/test_metrics_utils.py b/phys2denoise/tests/test_metrics_utils.py index d7e1b46..1995aaf 100644 --- a/phys2denoise/tests/test_metrics_utils.py +++ b/phys2denoise/tests/test_metrics_utils.py @@ -16,12 +16,12 @@ def test_mirrorpad(short_arr): assert all(arr_mirror == expected_arr_mirror) -def test_mirrorpad_exception(short_arr): +def test_mirrorpad_exception(short_arr, caplog): """When passing array that is too short to perform mirrorpadding, the function should give an error.""" arr = np.array(short_arr) - with pytest.raises(IndexError): - arr_mirror = mirrorpad_1d(short_arr) + arr_mirror = mirrorpad_1d(arr) + assert caplog.text.count("Fixing buffer size to array length.") > 0 def test_rms_envelope(): From 6266b6f78950d3c924a97249272fb4acb6c1264d Mon Sep 17 00:00:00 2001 From: maestroque Date: Sun, 25 Aug 2024 15:36:26 +0200 Subject: [PATCH 51/57] Add updated physutils version --- setup.cfg | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/setup.cfg b/setup.cfg index f1a08fd..81268a1 100644 --- a/setup.cfg +++ b/setup.cfg @@ -27,7 +27,7 @@ install_requires = scipy duecredit loguru - physutils + physutils >=0.2.1 tests_require = pytest >=5.3 test_suite = pytest From 34be77289db02c08c2a4ae1ef7d7dd3d00fa042e Mon Sep 17 00:00:00 2001 From: maestroque Date: Sun, 25 Aug 2024 15:44:27 +0200 Subject: [PATCH 52/57] Fix all-contributors.rc --- .all-contributorsrc | 1 - 1 file changed, 1 deletion(-) diff --git a/.all-contributorsrc b/.all-contributorsrc index 1e8e6aa..50ffa6d 100644 --- a/.all-contributorsrc +++ b/.all-contributorsrc @@ -120,7 +120,6 @@ "code", "ideas", "infra", - "docs", "bug", "review" ] From 1a7338735885df1d36afdafef2dcd4667afde6ef Mon Sep 17 00:00:00 2001 From: Stefano Moia Date: Sun, 25 Aug 2024 13:48:59 +0000 Subject: [PATCH 53/57] Update CHANGELOG.md [skip ci] --- CHANGELOG.md | 34 ++++++++++++++++++++++++++++++++++ 1 file changed, 34 insertions(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index 05c3a8d..9819170 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -1,3 +1,37 @@ +# 0.5.0 (Sun Aug 25 2024) + +:tada: This release contains work from new contributors! :tada: + +Thanks for all your work! + +:heart: George Kikas ([@maestroque](https://github.com/maestroque)) + +:heart: Marie-Eve Picard ([@me-pic](https://github.com/me-pic)) + +#### 💥 Breaking Change during development + +- Release Fix [#63](https://github.com/physiopy/phys2denoise/pull/63) ([@maestroque](https://github.com/maestroque)) +- Integrate physutils - Physio object usage [#54](https://github.com/physiopy/phys2denoise/pull/54) ([@maestroque](https://github.com/maestroque)) + +#### 📝 Documentation + +- Fix readthedocs config [#61](https://github.com/physiopy/phys2denoise/pull/61) ([@me-pic](https://github.com/me-pic)) +- Generate docs [#56](https://github.com/physiopy/phys2denoise/pull/56) ([@maestroque](https://github.com/maestroque) [@me-pic](https://github.com/me-pic) [@pre-commit-ci[bot]](https://github.com/pre-commit-ci[bot])) + +#### 🏠 Internal + +- Update description in setup [#59](https://github.com/physiopy/phys2denoise/pull/59) ([@me-pic](https://github.com/me-pic)) +- Add auto-author and auto-label to github workflow [#52](https://github.com/physiopy/phys2denoise/pull/52) ([@RayStick](https://github.com/RayStick)) + +#### Authors: 4 + +- [@pre-commit-ci[bot]](https://github.com/pre-commit-ci[bot]) +- George Kikas ([@maestroque](https://github.com/maestroque)) +- Marie-Eve Picard ([@me-pic](https://github.com/me-pic)) +- Rachael Stickland ([@RayStick](https://github.com/RayStick)) + +--- + # 0.4.0 (Mon Jul 15 2024) :tada: This release contains work from a new contributor! :tada: From c14d232b66ca04783594ef59f12ddfd00104fbf7 Mon Sep 17 00:00:00 2001 From: Stefano Moia Date: Sun, 25 Aug 2024 13:49:13 +0000 Subject: [PATCH 54/57] Update contributors [skip ci] --- .all-contributorsrc | 10 ++++++++++ README.md | 2 ++ 2 files changed, 12 insertions(+) diff --git a/.all-contributorsrc b/.all-contributorsrc index 50ffa6d..be7af4b 100644 --- a/.all-contributorsrc +++ b/.all-contributorsrc @@ -123,6 +123,16 @@ "bug", "review" ] + }, + { + "login": "RayStick", + "name": "Rachael Stickland", + "avatar_url": "https://avatars.githubusercontent.com/u/50215726?v=4", + "profile": "https://github.com/RayStick", + "contributions": [ + "doc", + "infra" + ] } ], "contributorsPerLine": 8, diff --git a/README.md b/README.md index 88ba380..7b46a51 100644 --- a/README.md +++ b/README.md @@ -39,6 +39,8 @@ Thanks goes to these wonderful people ([emoji key](https://allcontributors.org/d
Inés Chavarría
🚇
Kristina Zvolanek
🚇 👀 📓 +
George Kikas
💻 🤔 🚇 🐛 👀 +
Rachael Stickland
📖 🚇 From 066243a612addf135ccc7621ee6ecfa26a645f88 Mon Sep 17 00:00:00 2001 From: Marie-Eve Picard Date: Mon, 26 Aug 2024 17:15:50 -0400 Subject: [PATCH 55/57] Add contribution --- .zenodo.json | 5 +++++ 1 file changed, 5 insertions(+) diff --git a/.zenodo.json b/.zenodo.json index 54425df..c17fe0c 100644 --- a/.zenodo.json +++ b/.zenodo.json @@ -16,6 +16,11 @@ "orcid": "0000-0002-2553-3327", "affiliation": "BCBL - Basque Center on Cognition, Brain and Language", "name": "Stefano Moia" + }, + { + "orcid": "0009-0001-2412-7829", + "affiliation": "Département de psychologie, Université de Montréal", + "name": "Marie-Eve Picard" } ] } From 39c93a66b5c94c7b7cb61a092cfee845d79cd986 Mon Sep 17 00:00:00 2001 From: Stefano Moia Date: Tue, 27 Aug 2024 17:33:58 +0200 Subject: [PATCH 56/57] Update allcontributors --- .all-contributorsrc | 77 ++++++++++++++++++++++++++++----------------- README.md | 36 +++++++++++---------- 2 files changed, 69 insertions(+), 44 deletions(-) diff --git a/.all-contributorsrc b/.all-contributorsrc index be7af4b..17ea5fe 100644 --- a/.all-contributorsrc +++ b/.all-contributorsrc @@ -15,6 +15,15 @@ "ideas" ] }, + { + "login": "ineschh", + "name": "Inés Chavarría", + "avatar_url": "https://avatars.githubusercontent.com/u/72545702?v=4", + "profile": "https://github.com/ineschh", + "contributions": [ + "infra" + ] + }, { "login": "eril892", "name": "Raphaël Fournier", @@ -26,6 +35,20 @@ "doc" ] }, + { + "login": "maestroque", + "name": "George Kikas", + "avatar_url": "https://avatars.githubusercontent.com/u/74024609?v=4", + "profile": "https://github.com/maestroque", + "contributions": [ + "code", + "ideas", + "infra", + "bug", + "test", + "review" + ] + }, { "login": "TomasLenc", "name": "Tomas Lenc", @@ -56,6 +79,16 @@ "mentoring" ] }, + { + "login": "m-miedema", + "name": "m-miedema", + "avatar_url": "https://avatars.githubusercontent.com/u/39968233?v=4", + "profile": "https://github.com/m-miedema", + "contributions": [ + "review", + "mentoring" + ] + }, { "login": "smoia", "name": "Stefano Moia", @@ -80,6 +113,16 @@ "code" ] }, + { + "login": "me-pic", + "name": "Marie-Eve Picard", + "avatar_url": "https://avatars.githubusercontent.com/u/77584086?v=4", + "profile": "https://github.com/me-pic", + "contributions": [ + "review", + "infra" + ] + }, { "login": "tsalo", "name": "Taylor Salo", @@ -92,12 +135,13 @@ ] }, { - "login": "ineschh", - "name": "Inés Chavarría", - "avatar_url": "https://avatars.githubusercontent.com/u/72545702?v=4", - "profile": "https://github.com/ineschh", + "login": "RayStick", + "name": "Rachael Stickland", + "avatar_url": "https://avatars.githubusercontent.com/u/50215726?v=4", + "profile": "https://github.com/RayStick", "contributions": [ - "infra" + "infra", + "doc" ] }, { @@ -110,29 +154,6 @@ "review", "userTesting" ] - }, - { - "login": "maestroque", - "name": "George Kikas", - "avatar_url": "https://avatars.githubusercontent.com/u/74024609?v=4", - "profile": "https://github.com/maestroque", - "contributions": [ - "code", - "ideas", - "infra", - "bug", - "review" - ] - }, - { - "login": "RayStick", - "name": "Rachael Stickland", - "avatar_url": "https://avatars.githubusercontent.com/u/50215726?v=4", - "profile": "https://github.com/RayStick", - "contributions": [ - "doc", - "infra" - ] } ], "contributorsPerLine": 8, diff --git a/README.md b/README.md index 7b46a51..dcdb208 100644 --- a/README.md +++ b/README.md @@ -26,22 +26,26 @@ Thanks goes to these wonderful people ([emoji key](https://allcontributors.org/d - - - - - - - - - - - - - - - - + + + + + + + + + + + + + + + + + + + +

Cesar Caballero Gaudes
💻 🤔
Raphaël Fournier
💻 📓 📖
Tomas Lenc
🐛 ⚠️
rzlim08
💻 ⚠️
Ross Markello
🚇 🧑‍🏫
Stefano Moia
🔣 🚇 📆 💻 🤔 📖 🧑‍🏫
Alice Patin
💻
Taylor Salo
💻 🤔 👀

Inés Chavarría
🚇
Kristina Zvolanek
🚇 👀 📓
George Kikas
💻 🤔 🚇 🐛 👀
Rachael Stickland
📖 🚇
Cesar Caballero Gaudes
Cesar Caballero Gaudes
💻 🤔		Inés Chavarría
Inés Chavarría
🚇		Raphaël Fournier
Raphaël Fournier
💻 📓 📖		George Kikas
George Kikas
💻 🤔 🚇 🐛 ⚠️ 👀		Tomas Lenc
Tomas Lenc
🐛 ⚠️		rzlim08
rzlim08
💻 ⚠️		Ross Markello
Ross Markello
🚇 🧑‍🏫		m-miedema
m-miedema
👀 🧑‍🏫
Stefano Moia
Stefano Moia
🔣 🚇 📆 💻 🤔 📖 🧑‍🏫		Alice Patin
Alice Patin
💻		Marie-Eve Picard
Marie-Eve Picard
👀 🚇		Taylor Salo
Taylor Salo
💻 🤔 👀		Rachael Stickland
Rachael Stickland
🚇 📖		Kristina Zvolanek
Kristina Zvolanek
🚇 👀 📓
From e6fe80fc6689ece1fe258182eb349647b2f8dbcd Mon Sep 17 00:00:00 2001 From: Stefano Moia Date: Tue, 27 Aug 2024 17:35:30 +0200 Subject: [PATCH 57/57] Update zenodo --- .zenodo.json | 253 +++++++++++++++++++++++++++++++++++++++++++++++++-- 1 file changed, 243 insertions(+), 10 deletions(-) diff --git a/.zenodo.json b/.zenodo.json index c17fe0c..99bdb75 100644 --- a/.zenodo.json +++ b/.zenodo.json @@ -5,22 +5,255 @@ "access_right":"open", "creators": [ { - "affiliation": "BCBL - Basque Center on Cognition, Brain and Language", - "name": "C\u00e9sar Caballero Gaudes" + "affiliations": [ + { + "name": "University of Southern California" + } + ], + "person_or_org": { + "family_name": "Bottenhorn", + "given_name": "Katherine", + "identifiers": [ + { + "identifier": "0000-0002-7796-8795", + "scheme": "orcid" + } + ], + "name": "Bottenhorn, Katherine", + "type": "personal" + } }, { - "affiliation": "McGill University", - "name": "Ross Markello" + "affiliations": [ + { + "name": "BCBL - Basque Center on Cognition, Brain and Language" + } + ], + "person_or_org": { + "family_name": "Caballero Gaudes", + "given_name": "C\u00e9sar", + "identifiers": [ + { + "identifier": "0000-0002-9068-5810", + "scheme": "orcid" + } + ], + "name": "Caballero Gaudes, C\u00e9sar", + "type": "personal" + } }, { - "orcid": "0000-0002-2553-3327", - "affiliation": "BCBL - Basque Center on Cognition, Brain and Language", - "name": "Stefano Moia" + "affiliations": [ + { + "id": "01a28zg77", + "name": "Basque Center on Cognition, Brain and Language" + } + ], + "person_or_org": { + "family_name": "Chavarria", + "given_name": "In\u00e9s", + "name": "Chavarria, In\u00e9s", + "type": "personal" + } }, { - "orcid": "0009-0001-2412-7829", - "affiliation": "Département de psychologie, Université de Montréal", - "name": "Marie-Eve Picard" + "affiliations": [ + { + "id": "05a28rw58", + "name": "ETH Zurich" + } + ], + "person_or_org": { + "family_name": "Fournier", + "given_name": "Rapha\u00ebl", + "name": "Fournier, Rapha\u00ebl", + "type": "personal" + } + }, + { + "affiliations": [ + { + "id": "02j61yw88", + "name": "Aristotle University of Thessaloniki" + } + ], + "person_or_org": { + "family_name": "Kikas", + "given_name": "Georgios", + "name": "Kikas, Georgios", + "type": "personal" + } + }, + { + "affiliations": [ + { + "name": "Universit\u00e9 catholique de Louvain" + } + ], + "person_or_org": { + "family_name": "Lenc", + "given_name": "Tomas", + "identifiers": [ + { + "identifier": "0000-0001-5796-1388", + "scheme": "orcid" + } + ], + "name": "Lenc, Tomas", + "type": "personal" + } + }, + { + "person_or_org": { + "family_name": "Lim", + "given_name": "Ryan", + "name": "Lim, Ryan", + "type": "personal" + } + }, + { + "affiliations": [ + { + "name": "McGill University" + } + ], + "person_or_org": { + "family_name": "Markello", + "given_name": "Ross", + "identifiers": [ + { + "identifier": "0000-0003-1057-1336", + "scheme": "orcid" + } + ], + "name": "Markello, Ross", + "type": "personal" + } + }, + { + "affiliations": [ + { + "id": "01pxwe438", + "name": "McGill University" + } + ], + "person_or_org": { + "family_name": "Miedema", + "given_name": "Mary", + "identifiers": [ + { + "identifier": "0009-0008-3263-731X", + "scheme": "orcid" + } + ], + "name": "Miedema, Mary", + "type": "personal" + } + }, + { + "affiliations": [ + { + "id": "02jz4aj89", + "name": "Maastricht University" + } + ], + "person_or_org": { + "family_name": "Moia", + "given_name": "Stefano", + "identifiers": [ + { + "identifier": "0000-0002-2553-3327", + "scheme": "orcid" + } + ], + "name": "Moia, Stefano", + "type": "personal" + } + }, + { + "person_or_org": { + "family_name": "Patin", + "given_name": "Alice", + "name": "Patin, Alice", + "type": "personal" + } + }, + { + "affiliations": [ + { + "name": "Universit\u00e9 de Montr\u00e9al" + } + ], + "person_or_org": { + "family_name": "Picard", + "given_name": "Marie-Eve", + "identifiers": [ + { + "identifier": "0009-0001-2412-7829", + "scheme": "orcid" + } + ], + "name": "Picard, Marie-Eve", + "type": "personal" + } + }, + { + "affiliations": [ + { + "name": "University of Pennsylvania" + } + ], + "person_or_org": { + "family_name": "Salo", + "given_name": "Taylor", + "identifiers": [ + { + "identifier": "0000-0001-9813-3167", + "scheme": "orcid" + } + ], + "name": "Salo, Taylor", + "type": "personal" + } + }, + { + "affiliations": [ + { + "name": "Northwestern University" + } + ], + "person_or_org": { + "family_name": "Stickland", + "given_name": "Rachael", + "identifiers": [ + { + "identifier": "0000-0003-3398-4272", + "scheme": "orcid" + } + ], + "name": "Stickland, Rachael", + "type": "personal" + } + }, + { + "affiliations": [ + { + "id": "00m6w7z96", + "name": "Northwestern University" + } + ], + "person_or_org": { + "family_name": "Zvolanek", + "given_name": "Kristina", + "identifiers": [ + { + "identifier": "0000-0003-2239-7902", + "scheme": "orcid" + } + ], + "name": "Zvolanek, Kristina", + "type": "personal" + } } ] }