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Dependency updates #9

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Dependency updates #9

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0ace5ed
update example script
Mar 19, 2024
4511ff3
Updates to conform with new dependency behavior and use nilearn for m…
Mar 19, 2024
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13 changes: 6 additions & 7 deletions example_script.ipynb
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2 changes: 1 addition & 1 deletion neuropower/cluster.py
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Original file line number Diff line number Diff line change
Expand Up @@ -58,7 +58,7 @@ def PeakTable(spm, exc, mask):
res = pd.DataFrame(
data=[[m - r, n - r, o - r, spm_ext[m, n, o]]], columns=labels
)
peak_df = peak_df.append(res)
peak_df = pd.concat([peak_df, res], ignore_index=True)

# Peak-level p-values (not the same as simple z-to-p conversion)
p_values = np.exp(-float(exc) * (np.array(peak_df["zval"]) - float(exc)))
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9 changes: 5 additions & 4 deletions neuropower/neuropowermodels.py
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Original file line number Diff line number Diff line change
Expand Up @@ -13,6 +13,7 @@
from scipy.optimize import minimize
from scipy.stats import beta, norm, t as tdist

from nilearn.image import math_img
from neuropower import BUM, cluster, peakdistribution


Expand Down Expand Up @@ -418,10 +419,10 @@ def run_power_analysis(
DataFrame of power estimates using different multiple comparisons
correction methods for different sample sizes.
"""
spm = input_img.get_data()
spm = input_img.get_fdata()
affine = input_img.affine
voxel_size = input_img.header.get_zooms()
mask = mask_img.get_data() if mask_img is not None else (spm != 0).astype(int)
mask = mask_img.get_fdata() if mask_img is not None else math_img('(img != 0)', img=input_img).get_fdata()
n_voxels = np.sum(mask)

if design == "one-sample":
Expand Down Expand Up @@ -531,7 +532,7 @@ def generate_figure(peak_df, params, method="RFT"):
axes[0].hist(
p_values,
bins=np.arange(0, 1.1, 0.1),
normed=True,
density=True,
alpha=0.6,
label="observed distribution",
)
Expand All @@ -557,7 +558,7 @@ def generate_figure(peak_df, params, method="RFT"):
y, _, _ = axes[1].hist(
z_values,
bins=np.arange(min(z_values), 30, 0.3),
normed=True,
density=True,
alpha=0.6,
label="observed distribution",
)
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3 changes: 2 additions & 1 deletion pyproject.toml
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Expand Up @@ -27,7 +27,8 @@ dependencies = [
"nibabel>=2.0.2",
"pandas>=0.18.1",
"nose>=1.3.7",
"matplotlib"
"matplotlib",
"nilearn"
]
description = "A package to perform power analyses for neuroimaging data"
# Version from setuptools_scm
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