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refactor(read_device): skip return calibration coefficients by default #45

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merged 2 commits into from
Jul 24, 2024
Merged

refactor(read_device): skip return calibration coefficients by default #45

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4cedf42
feat(calibrate_gravity): add return_coeffs option whether return cali…
chanshing Jul 24, 2024
d9fb2d7
refactor(read_device): set return_coeffs=False in calibrate_gravity
chanshing Jul 24, 2024
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37 changes: 21 additions & 16 deletions src/actipy/processing.py
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Original file line number Diff line number Diff line change
Expand Up @@ -229,7 +229,7 @@ def detect_nonwear(data, patience='90m', window='10s', stdtol=15 / 1000):
return data, info


def calibrate_gravity(data, calib_cube=0.3, calib_min_samples=50, window='10s', stdtol=15 / 1000, chunksize=1_000_000): # noqa: C901
def calibrate_gravity(data, calib_cube=0.3, calib_min_samples=50, window='10s', stdtol=15 / 1000, return_coeffs=True, chunksize=1_000_000): # noqa: C901
"""
Gravity calibration method of van Hees et al. 2014 (https://pubmed.ncbi.nlm.nih.gov/25103964/)

Expand Down Expand Up @@ -283,10 +283,12 @@ def calibrate_gravity(data, calib_cube=0.3, calib_min_samples=50, window='10s',
del stationary_indicator
del nonzero

info['CalibNumSamples'] = len(xyz)

if len(xyz) < calib_min_samples:
info['CalibOK'] = 0
info['CalibErrorBefore(mg)'] = np.nan
info['CalibErrorAfter(mg)'] = np.nan
info['CalibOK'] = 0
warnings.warn(f"Skipping calibration: Insufficient stationary samples: {len(xyz)} < {calib_min_samples}")
return data, info

Expand Down Expand Up @@ -316,15 +318,17 @@ def calibrate_gravity(data, calib_cube=0.3, calib_min_samples=50, window='10s',
# Check that we have sufficiently uniformly distributed points:
# need at least one point outside each face of the cube
if (np.max(xyz, axis=0) < calib_cube).any() or (np.min(xyz, axis=0) > -calib_cube).any():
info['CalibOK'] = 0
info['CalibErrorAfter(mg)'] = init_err * 1000
info['CalibNumIters'] = 0
info['CalibOK'] = 0

return data, info

# If initial error is already below threshold, skip and return
if init_err < ERR_TOL:
info['CalibOK'] = 1
info['CalibErrorAfter(mg)'] = init_err * 1000
info['CalibNumIters'] = 0
info['CalibOK'] = 1

return data, info

Expand Down Expand Up @@ -374,6 +378,7 @@ def calibrate_gravity(data, calib_cube=0.3, calib_min_samples=50, window='10s',
break

info['CalibErrorAfter(mg)'] = best_err * 1000
info['CalibNumIters'] = it + 1

if (best_err >= ERR_TOL) or (it + 1 >= MAXITER):
info['CalibOK'] = 0
Expand Down Expand Up @@ -427,18 +432,18 @@ def calibrate_gravity(data, calib_cube=0.3, calib_min_samples=50, window='10s',
del data_mmap

info['CalibOK'] = 1
info['CalibNumIters'] = it + 1
info['CalibNumSamples'] = len(xyz)
info['CalibxIntercept'] = best_intercept[0]
info['CalibyIntercept'] = best_intercept[1]
info['CalibzIntercept'] = best_intercept[2]
info['CalibxSlope'] = best_slope[0]
info['CalibySlope'] = best_slope[1]
info['CalibzSlope'] = best_slope[2]
if hasT:
info['CalibxSlopeT'] = best_slopeT[0]
info['CalibySlopeT'] = best_slopeT[1]
info['CalibzSlopeT'] = best_slopeT[2]

if return_coeffs:
info['CalibxIntercept'] = best_intercept[0]
info['CalibyIntercept'] = best_intercept[1]
info['CalibzIntercept'] = best_intercept[2]
info['CalibxSlope'] = best_slope[0]
info['CalibySlope'] = best_slope[1]
info['CalibzSlope'] = best_slope[2]
if hasT:
info['CalibxSlopeT'] = best_slopeT[0]
info['CalibySlopeT'] = best_slopeT[1]
info['CalibzSlopeT'] = best_slopeT[2]

return data, info

Expand Down
2 changes: 1 addition & 1 deletion src/actipy/reader.py
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Original file line number Diff line number Diff line change
Expand Up @@ -73,7 +73,7 @@ def read_device(input_file,

if calibrate_gravity:
timer.start("Gravity calibration...")
data, info_calib = P.calibrate_gravity(data)
data, info_calib = P.calibrate_gravity(data, return_coeffs=False)
info.update(info_calib)
timer.stop()

Expand Down
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