Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Print optimal number of maPCA components and plot optimization curves #839

Merged
merged 17 commits into from
May 17, 2022
Merged
Show file tree
Hide file tree
Changes from 11 commits
Commits
File filter

Filter by extension

Filter by extension

Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
90 changes: 87 additions & 3 deletions tedana/decomposition/pca.py
Original file line number Diff line number Diff line change
Expand Up @@ -6,11 +6,12 @@

import numpy as np
import pandas as pd
from mapca import ma_pca
from mapca import MovingAveragePCA
from scipy import stats
from sklearn.decomposition import PCA

from tedana import io, metrics, utils
from tedana.reporting import pca_results as plot_pca_results
from tedana.selection import kundu_tedpca
from tedana.stats import computefeats2

Expand Down Expand Up @@ -234,9 +235,92 @@ def tedpca(
if algorithm in ["mdl", "aic", "kic"]:
data_img = io.new_nii_like(io_generator.reference_img, utils.unmask(data, mask))
mask_img = io.new_nii_like(io_generator.reference_img, mask.astype(int))
voxel_comp_weights, varex, varex_norm, comp_ts = ma_pca(
data_img, mask_img, algorithm, normalize=True
ma_pca = MovingAveragePCA(criterion=algorithm, normalize=True)
_ = ma_pca.fit_transform(data_img, mask_img)

# Extract results from maPCA
voxel_comp_weights = ma_pca.u_
varex = ma_pca.explained_variance_
varex_norm = ma_pca.explained_variance_ratio_
comp_ts = ma_pca.components_.T
Copy link
Collaborator

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

This looks like we're accessing private components of the object. Could we either link to some documentation about the returned object or elaborate on what we're accessing here?

Copy link
Member

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

The trailing underscore indicates that the attribute is estimated from the data (via fit), rather than that it's private. We adopted this convention from scikit-learn.

Copy link
Collaborator

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

Ah, that makes sense. Sorry had a momentary flip in my brain, where I put the underscore on the wrong side. I do think it's worth a quick reference to the docs.

aic = ma_pca.aic_
kic = ma_pca.kic_
mdl = ma_pca.mdl_
varex_90 = ma_pca.varexp_90_
varex_95 = ma_pca.varexp_95_
all_comps = ma_pca.all_

# Extract number of components and variance explained for logging and plotting
n_aic = aic["n_components"]
aic_varexp = np.round(aic["explained_variance_total"], 3)
n_kic = kic["n_components"]
kic_varexp = np.round(kic["explained_variance_total"], 3)
n_mdl = mdl["n_components"]
mdl_varexp = np.round(mdl["explained_variance_total"], 3)
n_varex_90 = varex_90["n_components"]
varex_90_varexp = np.round(varex_90["explained_variance_total"], 3)
n_varex_95 = varex_95["n_components"]
varex_95_varexp = np.round(varex_95["explained_variance_total"], 3)
all_varex = np.round(all_comps["explained_variance_total"], 3)

# Print out the results
LGR.info("Optimal number of components based on different criteria:")
LGR.info(
f"AIC: {n_aic} | KIC: {n_kic} | MDL: {n_mdl} | 90% varexp: {n_varex_90} "
f"| 95% varexp: {n_varex_95}"
)

LGR.info("Explained variance based on different criteria:")
LGR.info(
f"AIC: {aic_varexp}% | KIC: {kic_varexp}% | MDL: {mdl_varexp}% | "
f"90% varexp: {varex_90_varexp}% | 95% varexp: {varex_95_varexp}%"
)

pca_optimization_curves = np.array([aic["value"], kic["value"], mdl["value"]])
pca_criteria_components = np.array(
[
n_aic,
n_kic,
n_mdl,
n_varex_90,
n_varex_95,
]
)

# Plot maPCA optimization curves
LGR.info("Plotting maPCA optimization curves")
plot_pca_results(pca_optimization_curves, pca_criteria_components, all_varex, io_generator)

# Save maPCA results into a dictionary
mapca_results = {
"aic": {
"n_components": n_aic,
"explained_variance_total": aic_varexp,
"curve": aic["value"],
},
"kic": {
"n_components": n_kic,
"explained_variance_total": kic_varexp,
"curve": kic["value"],
},
"mdl": {
"n_components": n_mdl,
"explained_variance_total": mdl_varexp,
"curve": mdl["value"],
},
"varex_90": {
"n_components": n_varex_90,
"explained_variance_total": varex_90_varexp,
},
"varex_95": {
"n_components": n_varex_95,
"explained_variance_total": varex_95_varexp,
},
}

# Save dictionary
io_generator.save_file(mapca_results, "PCA cross component metrics json")

elif isinstance(algorithm, Number):
ppca = PCA(copy=False, n_components=algorithm, svd_solver="full")
ppca.fit(data_z)
Expand Down
2 changes: 1 addition & 1 deletion tedana/info.py
Original file line number Diff line number Diff line change
Expand Up @@ -29,7 +29,7 @@

REQUIRES = [
"bokeh<2.3.0",
"mapca~=0.0.1",
"mapca>=0.0.2",
Copy link
Collaborator

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

Unfortunately we'll need to resolve the conflict with main where we've moved everything into a different setup organization (in particular, setup.cfg in the install_requires section).

"matplotlib",
"nibabel>=2.5.1",
"nilearn>=0.7",
Expand Down
4 changes: 2 additions & 2 deletions tedana/reporting/__init__.py
Original file line number Diff line number Diff line change
Expand Up @@ -3,6 +3,6 @@
"""

from .html_report import generate_report
from .static_figures import comp_figures
from .static_figures import comp_figures, pca_results

__all__ = ["generate_report", "comp_figures"]
__all__ = ["generate_report", "comp_figures", "pca_results"]
141 changes: 141 additions & 0 deletions tedana/reporting/static_figures.py
Original file line number Diff line number Diff line change
Expand Up @@ -288,3 +288,144 @@ def comp_figures(ts, mask, comptable, mmix, io_generator, png_cmap):
compplot_name = os.path.join(io_generator.out_dir, "figures", plot_name)
plt.savefig(compplot_name)
plt.close()


def pca_results(criteria, n_components, all_varex, io_generator):
Copy link
Collaborator

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

This function has a large amount of repetition. Could we break it into smaller functions, parametrized perhaps by something like the input data and the label only, and if matplotlib requires this, the figure itself?

"""
Plot the PCA optimization curve for each criteria, and the variance explained curve.

Parameters
----------
criteria : array-like
AIC, KIC, and MDL optimization values for increasing number of components.
n_components : array-like
Number of optimal components given by each criteria.
io_generator : object
An object containing all the information needed to generate the output.
"""

# Plot the PCA optimization curve for each criteria
plt.figure(figsize=(10, 9))
plt.title("PCA Criteria")
plt.xlabel("PCA components")
plt.ylabel("Arbitrary Units")

# AIC curve
plt.plot(criteria[0, :], color="tab:blue", label="AIC")
# KIC curve
plt.plot(criteria[1, :], color="tab:orange", label="KIC")
# MDL curve
plt.plot(criteria[2, :], color="tab:green", label="MDL")

# Vertical line depicting the optimal number of components given by AIC
plt.vlines(
n_components[0],
ymin=np.min(criteria),
ymax=np.max(criteria),
color="tab:blue",
linestyles="dashed",
)
# Vertical line depicting the optimal number of components given by KIC
plt.vlines(
n_components[1],
ymin=np.min(criteria),
ymax=np.max(criteria),
color="tab:orange",
linestyles="dashed",
)
# Vertical line depicting the optimal number of components given by MDL
plt.vlines(
n_components[2],
ymin=np.min(criteria),
ymax=np.max(criteria),
color="tab:green",
linestyles="dashed",
)
# Vertical line depicting the optimal number of components for 90% variance explained
plt.vlines(
n_components[3],
ymin=np.min(criteria),
ymax=np.max(criteria),
color="tab:red",
linestyles="dashed",
label="90% varexp",
)
# Vertical line depicting the optimal number of components for 95% variance explained
plt.vlines(
n_components[4],
ymin=np.min(criteria),
ymax=np.max(criteria),
color="tab:purple",
linestyles="dashed",
label="95% varexp",
)

plt.legend()

#  Save the plot
plot_name = "pca_criteria.png"
pca_criteria_name = os.path.join(io_generator.out_dir, "figures", plot_name)
plt.savefig(pca_criteria_name)
plt.close()

# Plot the variance explained curve
plt.figure(figsize=(10, 9))
plt.title("Variance Explained")
plt.xlabel("PCA components")
plt.ylabel("Variance Explained")

plt.plot(all_varex, color="black", label="Variance Explained")

# Vertical line depicting the optimal number of components given by AIC
plt.vlines(
n_components[0],
ymin=np.min(criteria),
ymax=np.max(criteria),
color="tab:blue",
linestyles="dashed",
label="AIC",
)
# Vertical line depicting the optimal number of components given by KIC
plt.vlines(
n_components[1],
ymin=np.min(criteria),
ymax=np.max(criteria),
color="tab:orange",
linestyles="dashed",
label="KIC",
)
# Vertical line depicting the optimal number of components given by MDL
plt.vlines(
n_components[2],
ymin=np.min(criteria),
ymax=np.max(criteria),
color="tab:green",
linestyles="dashed",
label="MDL",
)
# Vertical line depicting the optimal number of components for 90% variance explained
plt.vlines(
n_components[3],
ymin=np.min(criteria),
ymax=np.max(criteria),
color="tab:red",
linestyles="dashed",
label="90% varexp",
)
# Vertical line depicting the optimal number of components for 95% variance explained
plt.vlines(
n_components[4],
ymin=np.min(criteria),
ymax=np.max(criteria),
color="tab:purple",
linestyles="dashed",
label="95% varexp",
)

plt.legend()

#  Save the plot
plot_name = "pca_variance_explained.png"
pca_variance_explained_name = os.path.join(io_generator.out_dir, "figures", plot_name)
plt.savefig(pca_variance_explained_name)
plt.close()
4 changes: 4 additions & 0 deletions tedana/resources/config/outputs.json
Original file line number Diff line number Diff line change
Expand Up @@ -147,6 +147,10 @@
"orig": "pca_metrics",
"bidsv1.5.0": "desc-PCA_metrics"
},
"PCA cross component metrics json": {
"orig": "pca_cross_component_metrics",
"bidsv1.5.0": "desc-PCA_cross_component_metrics"
},
"ICA decomposition json": {
"orig": "ica_decomposition",
"bidsv1.5.0": "desc-ICA_decomposition"
Expand Down
1 change: 1 addition & 0 deletions tedana/tests/data/cornell_three_echo_outputs.txt
Original file line number Diff line number Diff line change
Expand Up @@ -91,3 +91,4 @@ figures/comp_061.png
figures/comp_062.png
figures/comp_063.png
figures/comp_064.png
figures/pca_criteria.png