From b931d9e852da1205084885dab6fdfbd0c72cfca6 Mon Sep 17 00:00:00 2001
From: volker-baecker <volker.baecker@mri.cnrs>
Date: Wed, 11 Dec 2024 18:58:16 +0100
Subject: [PATCH] make it work with the input images from the czi plugin which
 technially have 4 dimensions

---
 src/napari_bigfish/_widget.py | 14 ++++++++++++--
 1 file changed, 12 insertions(+), 2 deletions(-)

diff --git a/src/napari_bigfish/_widget.py b/src/napari_bigfish/_widget.py
index 1d37cdc..383f53c 100644
--- a/src/napari_bigfish/_widget.py
+++ b/src/napari_bigfish/_widget.py
@@ -603,9 +603,19 @@ def addDetectedSpots(self, data):
 
 
     def detectSpots(self):
-        self.model.setData(self.data)
-        self.model.detectSpots(tuple(self.scale))
+        data = self.data
+        if len(data.shape) > 3:
+            data = np.squeeze(data)
+        if np.amax(data) > 1:
+            data = data / np.amax(data)
+        scale = self.scale
+        if len(scale) > 3:
+            scale = scale[1:len(scale)]
+        self.model.setData(data)
+        self.model.detectSpots(tuple(scale))
         result = self.model.getSpots()
+        if len(result.shape) < len(data.shape):
+            return np.hstack((np.zeros((len(result), 1), dtype=result.dtype), result))
         return result