From c9704b4cf0687b95a322109be4281376c72a467c Mon Sep 17 00:00:00 2001
From: Jeremy Muhlich <jmuhlich@bitflood.org>
Date: Mon, 8 Jul 2024 10:38:36 -0400
Subject: [PATCH] Add identify_foreground to EdgeAligner

---
 ashlar/reg.py | 10 ++++++++++
 1 file changed, 10 insertions(+)

diff --git a/ashlar/reg.py b/ashlar/reg.py
index 54dee816..5f821c20 100644
--- a/ashlar/reg.py
+++ b/ashlar/reg.py
@@ -12,6 +12,7 @@
 import skimage.util.dtype
 import skimage.io
 import skimage.exposure
+import skimage.filters
 import skimage.transform
 import sklearn.linear_model
 import networkx as nx
@@ -504,6 +505,7 @@ def __init__(
     def run(self):
         self.make_thumbnail()
         self.check_overlaps()
+        self.identify_foreground()
         self.compute_threshold()
         self.register_all()
         self.build_spanning_tree()
@@ -533,6 +535,14 @@ def check_overlaps(self):
         elif any(failures):
             warn_data("Some neighboring tiles have zero overlap.")
 
+    def identify_foreground(self):
+        energies = np.array([
+            np.linalg.norm(utils.whiten(self.reader.read(i, self.channel), 0))
+            for i in range(self.metadata.num_images)
+        ])
+        threshold = skimage.filters.threshold_otsu(energies)
+        self.foreground = energies > threshold
+
     def compute_threshold(self):
         if self.max_error is not None:
             if self.verbose: