Merge pull request #36 from danforthcenter/35-update-napari_open

update napari_open

docs/changelog.md

@@ -1,3 +1,27 @@
 ## Changelog
 
 All notable changes to this project will be documented below.
+
+#### annotate.get_centroids
+
+* v0.1dev: coords_list = **annotate.get_centroids**(*bin_img*)
+
+#### annotate.napari_classes
+
+* v0.1dev: class_list = **annotate.napari_classes**(*viewer*)
+
+#### annotate.napari_join_labels
+
+* v0.1dev: relabeled_mask, mask_dict = **annotate.napari_join_labels**(*img, viewer*)
+
+#### annotate.napari_label_classes
+
+* v0.1dev: viewer = **annotate.napari_label_classes**(*img, classes, show=True*)
+
+#### annotate.napari_open
+
+* v0.1dev: viewer = **annotate.napari_open**(*img, mode = 'native', show=True*)
+
+#### annotate.Points
+
+* v0.1dev: viewer = **annotate.Points**(*img, figsize=(12,6), label="dafault"*)

docs/napari_open.md

@@ -1,13 +1,14 @@
 ## Open Image with Napari
 
-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.
+Open image data (e.g. RGB, gray, hyperspectral) with an interactive Napari viewer. Labeled masks may be colorized 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)
+    - 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 gray images 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
 

plantcv/annotate/napari_open.py

@@ -6,25 +6,26 @@
 import napari
 
 
-def napari_open(img, show=True):
-    """
-    open img in napari
+def napari_open(img, mode='native', show=True):
+    """Open an image with a napari interactive viewer
 
-    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 option is useful for
+    Parameters
+    ----------
+    img : numpy.ndarray
+        Image to be opened, img can be gray, rgb, or multispectral
+    mode: str
+        Viewing mode, either 'native' (default) or 'colorize'
+    show: bool
+        if show is True the viewer is launched. This option is useful for
     running tests without triggering the viewer.
 
-    Returns:
-    viewer  = napari viewer object
-
-    :param img: numpy.ndarray
-    :return viewer: napari viewer object
-
+    Returns
+    -------
+    napari.viewer.Viewer
+        Napari viewer object
     """
     shape = np.shape(img)
-    if len(shape) == 2:
+    if len(shape) == 2 and mode == 'colorize':
         colorful = label2rgb(img)
         img = (255*colorful).astype(np.uint8)
         img = cv2.cvtColor(img, cv2.COLOR_BGR2RGB)

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