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DNM: Detrend optimally combined data before running PCA #1090

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DNM: Detrend optimally combined data before running PCA #1090

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a379230
Detrend data before running PCA.
tsalo Apr 27, 2024
55e161d
Update pca.py
tsalo Apr 27, 2024
9874ede
Simplify code.
tsalo Apr 28, 2024
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23 changes: 14 additions & 9 deletions tedana/decomposition/pca.py
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Original file line number Diff line number Diff line change
Expand Up @@ -6,6 +6,7 @@
import numpy as np
import pandas as pd
from mapca import MovingAveragePCA
from nilearn.signal import standardize_signal
from scipy import stats
from sklearn.decomposition import PCA

Expand Down Expand Up @@ -143,9 +144,9 @@ def tedpca(

- Nonsignificant :math:`{\kappa}` and :math:`{\rho}`.
- Nonsignificant variance explained.

Generated Files
---------------

=========================== =============================================
Default Filename Content
=========================== =============================================
Expand Down Expand Up @@ -204,9 +205,13 @@ def tedpca(
f"Computing PCA of optimally combined multi-echo data with selection criteria: {algorithm}"
)
data = data_oc[mask, :]

data_z = ((data.T - data.T.mean(axis=0)) / data.T.std(axis=0)).T # var normalize ts
data_z = (data_z - data_z.mean()) / data_z.std() # var normalize everything
if algorithm in ["mdl", "aic", "kic"]:
# Detrend the data, but don't z-score, if using MAPCA
data = standardize_signal(data.T, detrend=True, standardize=False).T
else:
# Z-score the data otherwise
data = standardize_signal(data.T, detrend=True, standardize="zscore_sample").T
data = (data - data.mean()) / data.std() # var normalize everything

if algorithm in ["mdl", "aic", "kic"]:
data_img = io.new_nii_like(io_generator.reference_img, utils.unmask(data, mask))
Expand Down Expand Up @@ -315,23 +320,23 @@ def tedpca(

elif isinstance(algorithm, Number):
ppca = PCA(copy=False, n_components=algorithm, svd_solver="full")
ppca.fit(data_z)
ppca.fit(data)
comp_ts = ppca.components_.T
varex = ppca.explained_variance_
voxel_comp_weights = np.dot(np.dot(data_z, comp_ts), np.diag(1.0 / varex))
voxel_comp_weights = np.dot(np.dot(data, comp_ts), np.diag(1.0 / varex))
varex_norm = ppca.explained_variance_ratio_
elif low_mem:
voxel_comp_weights, varex, varex_norm, comp_ts = low_mem_pca(data_z)
voxel_comp_weights, varex, varex_norm, comp_ts = low_mem_pca(data)
else:
# If algorithm is kundu or kundu-stablize component metrics
# are calculated without dimensionality estimation and
# reduction and then kundu identifies components that are
# to be accepted or rejected
ppca = PCA(copy=False, n_components=(n_vols - 1))
ppca.fit(data_z)
ppca.fit(data)
comp_ts = ppca.components_.T
varex = ppca.explained_variance_
voxel_comp_weights = np.dot(np.dot(data_z, comp_ts), np.diag(1.0 / varex))
voxel_comp_weights = np.dot(np.dot(data, comp_ts), np.diag(1.0 / varex))
varex_norm = ppca.explained_variance_ratio_

# Compute Kappa and Rho for PCA comps
Expand Down