From d37f5bb5d35d7c4b3d4c3236a1214d209d19a92c Mon Sep 17 00:00:00 2001
From: Jan Eglinger <jan.eglinger@fmi.ch>
Date: Fri, 15 Dec 2023 13:33:09 +0100
Subject: [PATCH 1/2] threshold: add option of gaussian filtering

---
 src/faim_wako_searchfirst/segment.py | 4 ++++
 tests/test_main.py                   | 9 +++++++++
 2 files changed, 13 insertions(+)

diff --git a/src/faim_wako_searchfirst/segment.py b/src/faim_wako_searchfirst/segment.py
index 48eeaf4..a7c8453 100644
--- a/src/faim_wako_searchfirst/segment.py
+++ b/src/faim_wako_searchfirst/segment.py
@@ -15,6 +15,7 @@
 import numpy as np
 from cellpose import models
 from scipy.ndimage import binary_fill_holes
+from skimage.filters import gaussian
 from skimage.measure import label, regionprops
 
 
@@ -22,6 +23,7 @@ def threshold(
     img,
     threshold: int,
     include_holes: bool,
+    gaussian_sigma: float = 0.0,
     logger=logging,
 ):
     """Segment a given image by global thresholding.
@@ -33,6 +35,8 @@ def threshold(
 
     :return: a label image representing the detected objects
     """
+    if gaussian_sigma > 0:
+        img = gaussian(img, sigma=gaussian_sigma, preserve_range=True)
     mask = img > threshold
     if include_holes:
         mask = binary_fill_holes(mask)
diff --git a/tests/test_main.py b/tests/test_main.py
index 54b7688..2f88266 100644
--- a/tests/test_main.py
+++ b/tests/test_main.py
@@ -55,6 +55,15 @@ def test_partial(_image, tmp_path):
     )
     assert np.max(labels) == 7
 
+    # segment with gaussian
+    labels_blurred: np.ndarray = threshold(
+        _image,
+        threshold=128,
+        include_holes=True,
+        gaussian_sigma=5.5,
+    )
+    assert np.max(labels_blurred) == 4
+
     # filter
     label2 = labels.copy()
     bounding_box(

From 0826d4e64ed37d5ecec255ac804d3c36b23984c8 Mon Sep 17 00:00:00 2001
From: Jan Eglinger <jan.eglinger@fmi.ch>
Date: Fri, 15 Dec 2023 13:40:57 +0100
Subject: [PATCH 2/2] README: add optional gaussian_sigma parameter

---
 README.md | 1 +
 1 file changed, 1 insertion(+)

diff --git a/README.md b/README.md
index bbcd906..73fb6a8 100644
--- a/README.md
+++ b/README.md
@@ -44,6 +44,7 @@ process:  # choose method how to segment, filter, and sample the objects
 threshold:
     threshold: 128
     include_holes: yes
+    gaussian_sigma: 2.0 # optional 
 bounding_box:
     min_x: 64
     min_y: 0