From e41fcb52b40551fb80e79603e27f975ffb3a47c9 Mon Sep 17 00:00:00 2001
From: jrob93 <jrobinson72@qub.ac.uk>
Date: Thu, 7 Nov 2024 14:54:29 +0000
Subject: [PATCH] update docs for new sigma_clip

---
 docs/notebooks/outlier_detection_example.ipynb | 6 +++---
 src/adler/utilities/science_utilities.py       | 7 +++++--
 2 files changed, 8 insertions(+), 5 deletions(-)

diff --git a/docs/notebooks/outlier_detection_example.ipynb b/docs/notebooks/outlier_detection_example.ipynb
index f3af189..82ef920 100644
--- a/docs/notebooks/outlier_detection_example.ipynb
+++ b/docs/notebooks/outlier_detection_example.ipynb
@@ -177,7 +177,7 @@
    "outputs": [],
    "source": [
     "# astropy sigma_clip normally uses the median as the central function\n",
-    "utils.sigma_clip(res, {\"cenfunc\": \"median\"})"
+    "utils.sigma_clip(res, cenfunc=\"median\", maxiters=1)"
    ]
   },
   {
@@ -188,7 +188,7 @@
    "outputs": [],
    "source": [
     "# assuming that the model is the ground truth, we use zero as the centroid for the residuals\n",
-    "utils.sigma_clip(res, {\"cenfunc\": utils.zero_func})"
+    "utils.sigma_clip(res, cenfunc=utils.zero_func, maxiters=1)"
    ]
   },
   {
@@ -296,7 +296,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.10.13"
+   "version": "3.9.19"
   }
  },
  "nbformat": 4,
diff --git a/src/adler/utilities/science_utilities.py b/src/adler/utilities/science_utilities.py
index 146f9c0..7bcf46a 100644
--- a/src/adler/utilities/science_utilities.py
+++ b/src/adler/utilities/science_utilities.py
@@ -78,7 +78,6 @@ def zero_func(x, axis=None):
     return 0
 
 
-# def sigma_clip(data_res, kwargs={"sigma":3, "maxiters": 1, "cenfunc": zero_func}):
 def sigma_clip(data_res, **kwargs):
     """Wrapper function for astropy.stats.sigma_clip, here we define the default centre of the data (the data - model residuals) to be zero
 
@@ -88,7 +87,11 @@ def sigma_clip(data_res, **kwargs):
     data_res: array
         The residuals of the data compared to the model.
     kwargs: dict
-        Dictionary of keyword arguments from astropy.stats.sigma_clip
+        Dictionary of keyword arguments from astropy.stats.sigma_clip, namely:
+        sigma : default 3
+        maxiters: default 5
+        cenfunc: default 'median'
+
 
     Returns
     -----------