From 22814516a14c4bc3dc62df256b030ae471f26a1f Mon Sep 17 00:00:00 2001
From: Malia Gehan <mgehan@danforthcenter.org>
Date: Thu, 22 Aug 2024 21:10:59 -0500
Subject: [PATCH] update napari_open

update napari_open function tests and docs so the default behavior is not to colorize gray images by adding  a mode option.
---
 docs/napari_open.md             |  5 +++--
 plantcv/annotate/napari_open.py | 10 ++++++----
 tests/test_napari_open.py       | 13 +++++++++++++
 3 files changed, 22 insertions(+), 6 deletions(-)

diff --git a/docs/napari_open.md b/docs/napari_open.md
index c699a85..30fef49 100644
--- a/docs/napari_open.md
+++ b/docs/napari_open.md
@@ -2,12 +2,13 @@
 
 Open image data (e.g. RGB, gray, hyperspectral) with an interactive Napari viewer. If a gray image is opened, the image will be pseudocolored for better visualization.
 
-**plantcv.annotate.napari_open**(*img, show=True*)
+**plantcv.annotate.napari_open**(*img, mode = 'native', show=True*)
 
 **returns** napari viewer object
 
 - **Parameters:**
     - img - image data (compatible with gray, RGB, and hyperspectral data. If data is hyperspecral it should be the array e.g. hyperspectral.array_data)
+    - mode - 'native' or 'colorize'. If 'colorized' is selected grayimages will be colorized.
     - show - if show = True, viewer is launched. False setting is useful for test purposes.
 
 - **Context:**
@@ -24,7 +25,7 @@ import plantcv.annotate as pcvan
 # Create an instance of the Points class
 img, path, name = pcv.readimage("./grayimg.png")
 
-viewer = pcvan.napari_open(img=img)
+viewer = pcvan.napari_open(img=img, mode='colorize')
 
 # Should open interactive napari viewer
 
diff --git a/plantcv/annotate/napari_open.py b/plantcv/annotate/napari_open.py
index 59fa317..e2c56ff 100755
--- a/plantcv/annotate/napari_open.py
+++ b/plantcv/annotate/napari_open.py
@@ -6,13 +6,14 @@
 import napari
 
 
-def napari_open(img, show=True):
+def napari_open(img, mode='native', show=True):
     """
     open img in napari
 
     Inputs:
     img  = img  (grayimg, rgbimg, or hyperspectral image array data e.g.
     hyperspectraldata.array_data)
+    mode = 'native or 'colorize'
     show = if show is True the viewer is launched. This option is useful for
     running tests without triggering the viewer.
 
@@ -25,9 +26,10 @@ def napari_open(img, show=True):
     """
     shape = np.shape(img)
     if len(shape) == 2:
-        colorful = label2rgb(img)
-        img = (255*colorful).astype(np.uint8)
-        img = cv2.cvtColor(img, cv2.COLOR_BGR2RGB)
+        if mode == 'colorize':
+            colorful = label2rgb(img)
+            img = (255*colorful).astype(np.uint8)
+            img = cv2.cvtColor(img, cv2.COLOR_BGR2RGB)
     if len(shape) == 3:
         if shape[2] == 3:
             img = cv2.cvtColor(img, cv2.COLOR_BGR2RGB)
diff --git a/tests/test_napari_open.py b/tests/test_napari_open.py
index 602e3ef..c6d1376 100644
--- a/tests/test_napari_open.py
+++ b/tests/test_napari_open.py
@@ -29,6 +29,19 @@ def test_napari_open_gray(test_data):
     viewer.close()
 
 
+def test_napari_open_gray1(test_data):
+    """Test for PlantCV.Annotate"""
+    # Read in test data
+    img, _, _ = readimage(test_data.kmeans_seed_gray_img)
+    viewer = napari_open(img, mode='colorize', show=False)
+    coor = [(25, 25), (50, 50)]
+    viewer.add_points(np.array(coor), symbol="o", name="total",
+                      face_color="red", size=1)
+
+    assert len(viewer.layers['total'].data) == 2
+    viewer.close()
+
+
 def test_napari_open_envi(test_data):
     """Test for PlantCV.Annotate"""
     # Read in test data