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Bug fixes in cpac_correlations #8

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merged 1 commit into from
Dec 13, 2023
Merged

Bug fixes in cpac_correlations #8

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16 changes: 8 additions & 8 deletions cpac_correlations.py
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Original file line number Diff line number Diff line change
Expand Up @@ -158,20 +158,20 @@ def batch_correlate(
https://en.wikipedia.org/wiki/Concordance_correlation_coefficient
"""
# Summary stats for x
x_mean = np.mean(x, axis=axis, keepdims=True)
x_var = np.var(x, axis=axis, keepdims=True)
x_mean = np.mean(x, axis=axis)
x_var = np.var(x, axis=axis)
x_std = np.sqrt(x_var)
# NOTE: Not trying to fix NaNs
x_norm = (x - x_mean) / x_std

# Summary stats for y
y_mean = np.mean(y, axis=axis, keepdims=True)
y_var = np.var(y, axis=axis, keepdims=True)
y_mean = np.mean(y, axis=axis)
y_var = np.var(y, axis=axis)
y_std = np.sqrt(y_var)
y_norm = (y - y_mean) / y_std

# Correlation coefficients
pearson = np.mean(x_norm * y_norm, axis=axis, keepdims=True)
pearson = np.mean(x_norm * y_norm, axis=axis)
concor = 2 * pearson * x_std * y_std / (x_var + y_var + (x_mean - y_mean) ** 2)

# Squeeze reduced singleton dimensions
Expand Down Expand Up @@ -558,8 +558,8 @@ def calculate_correlation(args_tuple):
old_file_dims = old_file_hdr.get_zooms()
new_file_dims = new_file_hdr.get_zooms()

data_1 = nb.load(old_path).get_data()
data_2 = nb.load(new_path).get_data()
data_1 = nb.load(old_path).get_fdata()
data_2 = nb.load(new_path).get_fdata()

except Exception as e:
corr_tuple = ("file reading problem: {0}".format(e),
Expand Down Expand Up @@ -858,7 +858,7 @@ def create_boxplot(corr_group, corr_group_name, pipeline_names=None,
if "file reading problem" in label:
continue
try:
allData.append(np.asarray(corr_group[label]).astype(np.float))
allData.append(np.asarray(corr_group[label]).astype(float))
except ValueError as ve:
continue
#raise Exception(ve)
Expand Down