Merge pull request #16 from mjt320/develop

*roi_measure* exclude NaNs when calculating percentiles

Author: mjt320

README.md

@@ -42,6 +42,7 @@ Most functionality is demonstrated in Jupyter notebook format in ./demo
 ---
 
 ### Updates
+Release 1.1.1 - *roi_measure* exclude NaNs when calculating percentiles
 Release 1.1.0 - *roi_measure* modified to generate more ROI statistics
 Release 1.0.3 - Add exception handling for some zero/negative inputs.  
 Release 1.0.2 - Changed AIF interpolation method to linear to further reduce oscillations.  

pyproject.toml

@@ -6,7 +6,7 @@ build-backend = "setuptools.build_meta"
 
 [project]
 name = "sepal"
-version = "1.1.0"
+version = "1.1.1"
 description = "Quantitative MRI processing"
 readme = "README.md"
 authors = [{ name = "Michael Thrippleton", email = "mjt320@googlemail.com" }]

src/sepal/utils/imaging.py

@@ -96,7 +96,7 @@ def roi_measure(image, mask_image):
     # measure statistics for masked voxels
     masked_voxels = data_2d[mask_1d == 1, :]
     stats = [(np.nanmean(m_d), np.nanmedian(m_d), np.nanstd(m_d), np.nanmin(m_d), np.nanmax(m_d),
-              np.percentile(m_d, 25), np.percentile(m_d, 75))
+              np.nanpercentile(m_d, 25), np.nanpercentile(m_d, 75))
              for m_d in masked_voxels.transpose()]
     mean, median, sd, mini, maxi, pct25, pct75 = zip(*stats)