Merge pull request #48 from danforthcenter/napari-points-sam

Napari points sam

Author: k034b363

docs/napari_naive_bayes_colors.md

@@ -9,7 +9,7 @@ to get data for naive bayes functions. Collect pixel training data in Napari, ra
 
 - **Parameters:**
     - img - RGB image to extract color information from
-    - maskdict - dictionary of masks, output of [`napari_points_mask`](docs/napari_points_mask.md) for example
+    - maskdict - dictionary of masks, output of [`napari_points_mask`](napari_points_mask.md) for example
     - filename - filename to save data, formatted to work with [Naive Bayes segmentation](https://plantcv.readthedocs.io/en/latest/tutorials/machine_learning_tutorial/)
 
 - **Context:**

docs/napari_read_coor.md

@@ -1,17 +1,18 @@
 ## Read point data into Napari Format
 
-Save Points Labeled in Napari to a File
+Read points from a file or dictionary into Napari format 
 
 **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
+    - dataformat - either 'yx', 'xy', or 'sam', Napari takes data as y,x format. If data is 'xy' data is converted from x,y to y,x.
+    If data is 'sam' point data is formatted for input into ultralytics sam3 functions. If 'sam' format is selected the function does expect a dictionary with 'pos' and 'neg' points as labelled classes.
 
 - **Context:**
-    - Import previously labeled points, or points from other functions (e.g. [`pcvan.napari_read_coor`](napari_read_coor.md))
+    - Import previously labeled points, or points from other functions (e.g. [`pcvan.napari_save_coor`](napari_save_coor.md))
 
 - **Example use:**
     - Below
@@ -27,4 +28,18 @@ data = pcvan.napari_read_coor(coor ='coor.json', dataformat = 'xy')
 
 ```
 
+- **Example use for training Segment Anything Model:**
+    - Below
+
+```python
+from ultralytics import SAM
+
+model = SAM("sam3.pt")
+results = model.predict(source="./Example_image.jpg", 
+                        points=data["points"], 
+                        labels=data["labels"])
+results[0].show()
+
+```
+
 **Source Code:** [Here](https://github.com/danforthcenter/plantcv-annotate/blob/main/plantcv/annotate/napari_read_coor.py)

plantcv/annotate/napari_read_coor.py

@@ -4,22 +4,21 @@
 
 
 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
-
+    """Open img in napari and label classes
+
+    Parameters
+    ----------
+    coor : dict or str
+        Either a dictionary or path to json file of points and label classes.
+    dataformat : str
+        Use 'xy' for points function outputs, 'yx' for Napari outputs, and 'sam' for
+        Segment Anything Model, which includes "pos" and "neg" labeled classes;
+        defaults to 'yx'.
+
+    Returns
+    ----------
+    dict
+        Dictionary of points data.
     """
     if isinstance(coor, dict):
         data = coor
@@ -34,4 +33,22 @@ def napari_read_coor(coor, dataformat='yx'):
             data1.update({key: data2})
         data = data1
 
+    if dataformat == 'sam':
+        pointslist = []
+        pointslabel = []
+
+        for i in enumerate(data['pos']):
+            x, y = i[1]
+            pointslist.append([x, y])
+            pointslabel.append(1)
+
+        for i in enumerate(data['neg']):
+            x, y = i[1]
+            pointslist.append([x, y])
+            pointslabel.append(0)
+
+        data1['points'] = [pointslist]
+        data1['labels'] = [pointslabel]
+        data = data1
+
     return data

tests/test_napari_read_coor.py

@@ -4,15 +4,15 @@
 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')
+    data = napari_read_coor(test_data.coor_data, dataformat='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')
+    data = napari_read_coor(test_data.coor_data, dataformat='xy')
 
     assert data['germinated'][0] == (10, 25)
 
@@ -21,6 +21,15 @@ def test_napari_read_coor_flip():
     """Test for PlantCV.Annotate"""
     # Read in test data
     coor = {"germinated": [[25, 10]]}
-    data = napari_read_coor(coor, 'xy')
+    data = napari_read_coor(coor, dataformat='xy')
 
     assert data['germinated'][0] == (10, 25)
+
+
+def test_napari_read_coor_sam(test_data):
+    """Test for PlantCV.Annotate"""
+    # Read in test data
+    coor = {'pos': [(284, 451)], 'neg': [(206, 160)]}
+    data = napari_read_coor(coor, dataformat='sam')
+
+    assert data['points'][0][0][0] == 451