From ce5a3c483c443a80ec06eaccdffb3f7e8969ced1 Mon Sep 17 00:00:00 2001
From: Noah Fahlgren <noahfahlgren@gmail.com>
Date: Thu, 28 Mar 2024 21:25:15 -0500
Subject: [PATCH] Test tests

---
 plantcv/annotate/__init__.py    |  3 +++
 plantcv/annotate/napari_open.py | 36 +++++++++++++++++++++++++++++++++
 tests/test_annotate.py          | 18 +++++++++++------
 3 files changed, 51 insertions(+), 6 deletions(-)
 create mode 100644 plantcv/annotate/napari_open.py

diff --git a/plantcv/annotate/__init__.py b/plantcv/annotate/__init__.py
index e69de29..d18cd53 100644
--- a/plantcv/annotate/__init__.py
+++ b/plantcv/annotate/__init__.py
@@ -0,0 +1,3 @@
+from plantcv.annotate.napari_open import napari_open
+
+__all__ = ["napari_open"]
diff --git a/plantcv/annotate/napari_open.py b/plantcv/annotate/napari_open.py
new file mode 100644
index 0000000..6b7c490
--- /dev/null
+++ b/plantcv/annotate/napari_open.py
@@ -0,0 +1,36 @@
+# Use Napari to Label
+
+import napari
+import cv2
+import numpy as np
+from skimage.color import label2rgb
+
+
+def napari_open(img, show=True):
+    """
+    open img in napari and label classes
+    Inputs:
+    img  = img  (grayimg, rgbimg, or hyperspectral image array data e.g.
+    hyperspectraldata.array_data)
+    show = if show is True the viewer is launched. This opetion is useful for
+    running tests without triggering the viewer.
+    Returns:
+    viewer  = napari viewer object
+    :param img: numpy.ndarray
+    :return viewer: napari viewer object
+    """
+    shape = np.shape(img)
+    showcall = show
+    if len(shape) == 2:
+        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)
+        if shape[2] > 3:
+            img = img.transpose(2, 0, 1)
+
+    viewer = napari.view_image(img, show=showcall)
+
+    return viewer
diff --git a/tests/test_annotate.py b/tests/test_annotate.py
index ab22976..8f99900 100644
--- a/tests/test_annotate.py
+++ b/tests/test_annotate.py
@@ -1,11 +1,17 @@
-from plantcv import annotate as an
+import numpy as np
+from plantcv.annotate import napari_open
 
 
-def test_annotate():
+def test_napari(qtbot):
     """PlantCV Test"""
-    assert an.__name__ == "plantcv.annotate"
+    img = np.zeros((100, 100, 3), dtype=np.uint8)
+    viewer = napari_open(img, show=False)
+    coor = [(25, 25), (75, 75)]
+    viewer.add_points(np.array(coor), symbol="o", name="total", face_color="red", size=1)
 
+    def check_open():
+        assert np.shape(viewer.layers['total'].data) != (0, 2)
 
-def test_napari(make_napari_viewer):
-    """PlantCV Test"""
-    viewer = make_napari_viewer(show=False)
+    qtbot.waitUntil(check_open, timeout=60_000)
+
+    assert len(viewer.layers["total"].data) == 2