improved masking for bragg_peaks_persistence (#43)

* updated masking for `bragg_peaks_persistence`

In the function `bragg_peaks_persistence` from @trbritt the hard edges of the mask are resulting in peaks being detected at those edges. I propose to scan the full image for peaks and throw away the peaks that are in the masked area later. Resulted in improved results on my end.
`autocenter` is still done with the mask in place.

* Update CHANGELOG.rst

* Update indexing.py

* version bump

CHANGELOG.rst

@@ -1,6 +1,11 @@
 Changelog
 =========
 
+Release 2.1.12
+--------------
+
+* Improved the masking functionality in `bragg_peaks_persistence`.
+
 Release 2.1.11
 --------------
 

skued/__init__.py

@@ -2,7 +2,7 @@
 __author__ = "Laurent P. René de Cotret"
 __email__ = "[email protected]"
 __license__ = "GPLv3"
-__version__ = "2.1.10"
+__version__ = "2.1.12"
 
 from .affine import (
     affine_map,

skued/image/indexing.py

@@ -190,10 +190,8 @@ def bragg_peaks_persistence(
     """
     if mask is None:
         mask = np.ones_like(im, dtype=bool)
-    im[~mask] = 0.0
     if center is None:
         center = autocenter(im=im, mask=mask)
-    image = im
 
     g0 = Persistence(im).persistence
     birth_death = list()
@@ -237,6 +235,19 @@ def bragg_peaks_persistence(
         sorted(candidates, key=lambda p: np.linalg.norm(p - center))
     ).reshape(-1, 2)
     birth_death = np.array(birth_death).reshape(-1, 2)
+
+    # remove peaks that are within the masked area
+    if mask.sum() != mask.shape[0] * mask.shape[1]:
+        peaks = np.array([p for p in peaks if mask[p[1], p[0]]])
+        birth_death = np.array(
+            [bd for p, bd in zip(peaks, birth_death) if mask[p[1], p[0]]]
+        )
+        birth_death_indices = np.array(
+            [bdi for p, bdi in zip(peaks, birth_death_indices) if mask[p[1], p[0]]]
+        )
+        persistencies = np.array(
+            [pers for p, pers in zip(peaks, persistencies) if mask[p[1], p[0]]]
+        )
     return peaks, birth_death, birth_death_indices, persistencies