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Let's roll it out and come back to this if @effigies disagrees. |
effigies
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Aug 19, 2024
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| # Read slope and intercept (see #1315) | ||
| slope, intercept = full_img.header.get_slope_inter() | ||
| slope = slope if slope is not None else 1.0 | ||
| intercept = intercept if intercept is not None else 0.0 | ||
| corrected = ( | ||
| full_img.get_fdata() * fitted[np.newaxis, np.newaxis, np.newaxis, :] / slope | ||
| - intercept | ||
| ) | ||
| full_img.__class__( | ||
| (full_img.get_fdata() * fitted[np.newaxis, np.newaxis, np.newaxis, :]).astype( | ||
| full_img.header.get_data_dtype() | ||
| ), | ||
| corrected.astype(full_img.header.get_data_dtype()), | ||
| full_img.affine, | ||
| full_img.header, | ||
| ).to_filename(self._results['out_full_file']) |
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Sorry for the delay. No, you just want:
full_img.__class__(
full_img.get_fdata() * fitted[np.newaxis, np.newaxis, np.newaxis, :],
full_img.affine
full_img.header
).to_filename(self._results['out_full_file'])You pretty much never want to dynamically coerce the type. All of nibabel's machinery assumes that the data is valid and that the header encodes the intent, and will perform scaling on your behalf if continuous data needs to be discretized into an integer dtype.
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I assume that applies the slope and intercept when generating the spatialimage object, correct?
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Yes, it will calculate a new slope and intercept based on the min/max values of the data array.
oesteban
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Aug 19, 2024
Co-authored-by: Chris Markiewicz <effigies@gmail.com>
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Addresses the issue reported by @psadil with his proposed solution 1 (considering the slope and intercept).
cc/ @effigies for a correctness check.
Resolves: #1315.