napari save

.github/PULL_REQUEST_TEMPLATE.md

@@ -23,6 +23,6 @@ See [this page](https://plantcv.readthedocs.io/en/latest/pr_review_process/) for
 - [ ] Test coverage remains 100%
 - [ ] Documentation tested
 - [ ] New documentation pages added to `plantcv/mkdocs.yml`
-- [ ] Changes to function input/output signatures added to `updating.md`
+- [ ] Changes to function input/output signatures added to `changelog.md`
 - [ ] Code reviewed
 - [ ] PR approved

docs/changelog.md

@@ -22,6 +22,10 @@ All notable changes to this project will be documented below.
 
 * v0.1dev: viewer = **annotate.napari_open**(*img, mode = 'native', show=True*)
 
+#### annotate.napari_save_coor
+
+* v0.1dev: datadict = **annotate.napari_save_coor**(*viewer, filepath*)
+
 #### annotate.Points
 
 * v0.1dev: viewer = **annotate.Points**(*img, figsize=(12,6), label="dafault"*)

docs/napari_save_coor.md

@@ -0,0 +1,39 @@
+## Save Napari Labels to File
+
+Save Points Labeled in Napari to a File
+
+**plantcv.annotate.napari_save_coor**(*viewer, filepath*)
+
+**returns** dictionary of points labeled by class
+
+- **Parameters:**
+    - viewer - Napari Viewer Object
+    - Filepath - File to save data. If the file exits an extension will be added.
+
+- **Context:**
+    - Save points labeled in Napari to a file to checkpoint annotation progress or reuse.
+
+- **Example use:**
+    - Save points labeled to a file 
+
+
+```python
+import plantcv.plantcv as pcv 
+import plantcv.annotate as pcvan
+
+# Create an instance of the Points class
+img, path, name = pcv.readimage("./grayimg.png")
+# Should open interactive napari viewer
+viewer = pcvan.napari_label_classes(img=img, classes=['background', 'wing','seed'])
+
+dictobj = pcvan.napari_save_coor(viewer, 'testdata.txt')
+
+```
+
+![Screenshot](img/documentation_images/napari_label_classes/napari_label_classes.png)
+
+![Screenshot](img/documentation_images/napari_save_coor/napari_save.png)
+
+
+
+**Source Code:** [Here](https://github.com/danforthcenter/plantcv-annotate/blob/main/plantcv/annotate/napari_save_coor.py)

mkdocs.yml

@@ -21,6 +21,7 @@ nav:
       - Napari Join: napari_join_labels.md
       - Napari Label: napari_label_classes.md
       - Napari Open: napari_open.md
+      - Napari Save: napari_save_coor.md
       - Points: Points.md
       - Get Centroids: get_centroids.md
 markdown_extensions:

plantcv/annotate/__init__.py

@@ -5,6 +5,7 @@
 from plantcv.annotate.napari_open import napari_open
 from plantcv.annotate.napari_label_classes import napari_label_classes
 from plantcv.annotate.napari_join_labels import napari_join_labels
+from plantcv.annotate.napari_save_coor import napari_save_coor
 
 # Auto versioning
 __version__ = version("plantcv-annotate")
@@ -15,5 +16,6 @@
     "napari_classes",
     "napari_open",
     "napari_label_classes",
-    "napari_join_labels"
-    ]
+    "napari_join_labels",
+    "napari_save_coor"
+]

plantcv/annotate/napari_save_coor.py

@@ -0,0 +1,40 @@
+# Save Napari Data to a File
+
+import json
+import os
+from plantcv.annotate import napari_classes
+
+
+def napari_save_coor(viewer, filepath):
+    """
+    save napari labeled points to a file
+
+    Inputs:
+    viewer = Napari viewer object
+    filepath = path to file to save data to
+
+    Returns:
+    dictionary  = dictionary of saved data points
+
+    :param viewer: napari viewer object
+    :param filepath: str
+    :return dictionary: dictionary
+
+    """
+    classes = napari_classes(viewer)
+    datadict = {}
+
+    for label in classes:
+        coordict = []
+        for _, (x, y) in enumerate(viewer.layers[label].data):
+            x = int(x)
+            y = int(y)
+            coordict.append((x, y))
+        datadict.update({label: coordict})
+
+    if os.path.exists(filepath):
+        filepath = str(filepath)+"_1.txt"
+    with open(filepath, 'w') as fp:
+        json.dump(datadict, fp)
+
+    return datadict

tests/test_napari_save_coor.py

@@ -0,0 +1,25 @@
+import numpy as np
+import os
+from plantcv.annotate import napari_label_classes
+from plantcv.plantcv import readimage
+from plantcv.annotate import napari_save_coor
+
+
+def test_napari_save_coor(test_data, tmpdir):
+    """Test for PlantCV.Annotate"""
+    # Read in test data
+    cache_dir = tmpdir.mkdir("cache")
+    img, _, _ = readimage(test_data.kmeans_seed_gray_img)
+    viewer = napari_label_classes(img, ['seed'], show=False)
+    coor = [(25, 25)]
+    viewer.add_points(np.array(coor), symbol="o", name='background',
+                      face_color="red", size=1)
+
+    filename = os.path.join(cache_dir, 'tempfile.txt')
+    # Assert that the file was created
+    _ = napari_save_coor(viewer, filename)
+    # Triggers addtion of _1 since filename previously exists
+    _ = napari_save_coor(viewer, filename)
+
+    assert os.path.exists(filename)
+    viewer.close()