Merge pull request #20 from danforthcenter/18-napari-import-data

napari read coor

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_read_coor
+
+* v0.1dev: data = **annotate.napari_read_coor**(*coor, dataformat='yx'*)
+
 #### annotate.napari_save_coor
 
 * v0.1dev: datadict = **annotate.napari_save_coor**(*viewer, filepath*)

docs/napari_read_coor.md

@@ -0,0 +1,30 @@
+## Read point data into Napari Format
+
+Save Points Labeled in Napari to a File
+
+**plantcv.napari_read_coor**(*coor, dataformat = 'yx'*)
+
+**returns** dictionary of points labeled by class
+
+- **Parameters:**
+    - coor - dictionary object of coordinates, or a path to json datafile with dictionary of point coordinates
+    - dataformat - either 'yx' or 'xy', Napari takes data as y,x format. If data is 'xy' data is converted from x,y to y,x
+
+- **Context:**
+    - Import previously labeled points, or points from other functions (e.g. [`pcvan.napari_read_coor`](napari_read_coor.md))
+
+- **Example use:**
+    - Below
+
+
+```python
+import plantcv.plantcv as pcv 
+import plantcv.annotate as pcvan
+
+# read in data
+
+data = pcvan.napari_read_points(coor ='coor.json', dataformat = 'xy')
+
+```
+
+**Source Code:** [Here](https://github.com/danforthcenter/plantcv-annotate/blob/main/plantcv/annotate/napari_read_coor.py)

mkdocs.yml

@@ -21,7 +21,8 @@ nav:
       - Napari Join: napari_join_labels.md
       - Napari Label: napari_label_classes.md
       - Napari Open: napari_open.md
-      - Napari Save: napari_save_coor.md
+      - Napari Read Coor: napari_read_coor.md
+      - Napari Save Coor: napari_save_coor.md
       - Points: Points.md
       - Get Centroids: get_centroids.md
 markdown_extensions:

plantcv/annotate/__init__.py

@@ -6,6 +6,7 @@
 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
+from plantcv.annotate.napari_read_coor import napari_read_coor
 
 # Auto versioning
 __version__ = version("plantcv-annotate")
@@ -17,5 +18,6 @@
     "napari_open",
     "napari_label_classes",
     "napari_join_labels",
-    "napari_save_coor"
+    "napari_save_coor",
+    "napari_read_coor"
 ]

plantcv/annotate/napari_read_coor.py

@@ -0,0 +1,37 @@
+# Import points from json file
+
+import json
+
+
+def napari_read_coor(coor, dataformat='yx'):
+    """
+    open img in napari and label classes
+
+    Inputs:
+    coor  = either a dictionary of data or a path to a json file
+    with dictionary of point coordinates
+    dataformat = either 'yx' or 'xy'. Output of points function is in
+    x,y format and Napari is in y,x format.
+
+    Returns:
+    data  = dictionary of data
+
+    :param coor: dict or str
+    :param dataformat: str
+    :return data: dictionary of data in y,x format for napari
+
+    """
+    if isinstance(coor, dict):
+        data = coor
+    else:
+        with open(coor) as json_file:
+            data = json.load(json_file)
+    data1 = {}
+    if dataformat != 'yx':
+        keys = list(data.keys())
+        for key in keys:
+            data2 = [(sub[1], sub[0]) for sub in data[key]]
+            data1.update({key: data2})
+        data = data1
+
+    return data

tests/conftest.py

@@ -23,7 +23,12 @@ def __init__(self):
         # Kmeans Clustered Gray image
         self.kmeans_seed_gray_img = os.path.join(self.datadir, "silphium_seed_labeled_example.png")
         # Small Hyperspectral image
-        self.envi_sample_data = os.path.join(self.datadir, "corn-kernel-hyperspectral.raw")
+        filename_hyper = "corn-kernel-hyperspectral.raw"
+        self.envi_sample_data = os.path.join(self.datadir, filename_hyper)
+        # Coordinates File
+        filename_coor = "germinated.txt"
+        self.coor_data = os.path.join(self.datadir, filename_coor)
+
 
 
 @pytest.fixture(scope="session")

tests/test_napari_read_coor.py

@@ -0,0 +1,26 @@
+from plantcv.annotate import napari_read_coor
+
+
+def test_napari_read_coor_napari(test_data):
+    """Test for PlantCV.Annotate"""
+    # Read in test data
+    data = napari_read_coor(test_data.coor_data, 'yx')
+
+    assert isinstance(data, dict)
+
+
+def test_napari_read_coor_other(test_data):
+    """Test for PlantCV.Annotate"""
+    # Read in test data
+    data = napari_read_coor(test_data.coor_data, 'xy')
+
+    assert data['germinated'][0] == (10, 25)
+
+
+def test_napari_read_coor_flip():
+    """Test for PlantCV.Annotate"""
+    # Read in test data
+    coor = {"germinated": [[25, 10]]}
+    data = napari_read_coor(coor, 'xy')
+
+    assert data['germinated'][0] == (10, 25)

tests/testdata/germinated.txt

@@ -0,0 +1 @@
+{"germinated": [[25, 10]]}