From f7f966ff67cee54aa569c2e2bf9158dc95b7448a Mon Sep 17 00:00:00 2001
From: Laurenz Kremeyer <laurenz.kremeyer@mail.mcgill.ca>
Date: Sat, 27 Aug 2022 10:31:21 -0400
Subject: [PATCH] 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           |  5 +++++
 skued/__init__.py       |  2 +-
 skued/image/indexing.py | 15 +++++++++++++--
 3 files changed, 19 insertions(+), 3 deletions(-)

diff --git a/CHANGELOG.rst b/CHANGELOG.rst
index 165923f0..92ed841b 100644
--- a/CHANGELOG.rst
+++ b/CHANGELOG.rst
@@ -1,6 +1,11 @@
 Changelog
 =========
 
+Release 2.1.12
+--------------
+
+* Improved the masking functionality in `bragg_peaks_persistence`.
+
 Release 2.1.11
 --------------
 
diff --git a/skued/__init__.py b/skued/__init__.py
index 09e3d909..31df6efa 100644
--- a/skued/__init__.py
+++ b/skued/__init__.py
@@ -2,7 +2,7 @@
 __author__ = "Laurent P. René de Cotret"
 __email__ = "laurent.renedecotret@mail.mcgill.ca"
 __license__ = "GPLv3"
-__version__ = "2.1.10"
+__version__ = "2.1.12"
 
 from .affine import (
     affine_map,
diff --git a/skued/image/indexing.py b/skued/image/indexing.py
index 4a1a6422..0d41e0a9 100644
--- a/skued/image/indexing.py
+++ b/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