From f88badf9683aff9b80e15662429a21586f7f48bf Mon Sep 17 00:00:00 2001
From: Robbi Bishop-Taylor <Robbi.BishopTaylor@ga.gov.au>
Date: Fri, 22 Mar 2024 17:47:58 +1100
Subject: [PATCH] Make max/min freq and corr configurable via CLI

---
 intertidal/elevation.py | 3 +++
 intertidal/extents.py   | 9 ++++++---
 2 files changed, 9 insertions(+), 3 deletions(-)

diff --git a/intertidal/elevation.py b/intertidal/elevation.py
index a949682..645dc31 100644
--- a/intertidal/elevation.py
+++ b/intertidal/elevation.py
@@ -1213,6 +1213,9 @@ def intertidal_cli(
             freq=ds.qa_ndwi_freq,
             corr=ds.qa_ndwi_corr,
             reclassified_aclum=reclassified_aclum,
+            min_freq=min_freq,
+            max_freq=max_freq,
+            min_correlation=min_correlation,
         )
 
         if exposure_offsets:
diff --git a/intertidal/extents.py b/intertidal/extents.py
index 4907b85..7bceb47 100644
--- a/intertidal/extents.py
+++ b/intertidal/extents.py
@@ -55,6 +55,9 @@ def extents(
     freq,
     corr,
     reclassified_aclum,
+    min_freq=0.01,
+    max_freq=0.99,
+    min_correlation=0.15,
 ):
     """
     Classify coastal ecosystems into broad classes based
@@ -128,7 +131,7 @@ def extents(
 
     """--------------------------------------------------------------------"""
     ## Set the upper and lower freq thresholds
-    upper, lower = 0.99, 0.01
+    upper, lower = max_freq, min_freq
 
     # Set NaN values (i.e. pixels masked out over deep water) in frequency to 1
     freq = freq.fillna(1)
@@ -139,10 +142,10 @@ def extents(
     wet = freq > upper
 
     ##### Separate intermittent_tidal (intertidal)
-    intertidal = intermittent & (corr >= 0.15)
+    intertidal = intermittent & (corr >= min_correlation)
 
     ##### Separate intermittent_nontidal
-    intermittent_nontidal = intermittent & (corr < 0.15)
+    intermittent_nontidal = intermittent & (corr < min_correlation)
 
     ##### Separate high and low confidence intertidal pixels
     intertidal_hc = intertidal & dem.notnull()