Support Rectangle ROIs

README.md

@@ -96,7 +96,7 @@ The following fields are available:
 - `Config file name`    (optional, "VitessceConfig-YYYY.MM.DD_HHMMSS.json"):   Name of the config file to attach, a ".json" extension is added if missing. 	
 - `Images`               (required): 	                                       OMERO Image(s) to view, assumes the same pixel size for all images.
 - `Segmentation`        (optional, `None`): 	                               Label image to overlay on the image, pixel values correspond to cell identities.
-- `ROIs`                (optional, `False`):                                   Use the ROIs from OMERO as a cell segmentation. Assumes 1 polygon shape per ROI, whose text value is the cell identity.
+- `ROIs`                (optional, `False`):                                   Use the ROIs from OMERO as a cell segmentation. Assumes 1 polygon/rectangle shape per ROI, whose text value is the cell identity.
 - `Cell identities`     (optional, `None`): 	                               `.csv` file with at least 2 columns: `Cell id column` and `Label column` defined in the 2 fields below. 
 - `Cell id column`      (optional, "cell_id"):   	                           Name of the `Cell id column` used in `Cell identities`, `Expression`, `Embeddings`.
 - `Label column`        (optional, "label"): 	                               Name of the `Label` used in `Cell identities`.
@@ -121,6 +121,9 @@ The `Embeddings` file is necessary to show the cells in a scatterplot.
 The `Molecules` file is used to overlay molecules on the image. All molecules are displayed and selecting by gene is not yet possible.  
 The `Status` panel will be empty unless a `Segmentation` or `Embeddings` are provided.  
 
+The `ROIs` are used as cells. Only the first shape is considered, and only polygons and rectangles are kept (TO DO: add support for ellipses). Other shapes are skipped.
+The text value of the shape is used as a cell identity to link with expression/labels/embeddings, if there is no text value the ROI is skipped.
+
 #### Attaching preexisting config files
 Custom config files should have a `.json` extension and added as attachements to a dataset or an image.
 The configuration files does not need to refer to the dataset / image it is attached to and can refer to other images.

omero_vitessce/utils.py

@@ -17,6 +17,10 @@
 # Get the address of omeroweb from the config
 SERVER = omero_vitessce_settings.SERVER_ADDRESS[1:-1]
 
+# Valid ROI shapes for representing cells
+VALID_SHAPES = ["ome.model.roi.Polygon_roi",
+                "ome.model.roi.Rectangle_roi"]
+
 
 def get_files_images(obj_type, obj_id, conn):
     """ Gets all the non config files attached to an object,
@@ -168,28 +172,41 @@ def add_cell_identities(config_args, vc_dataset):
 
 class VitessceShape():
     """
-    Converts an OMERO ROI shape to a vitessce compatibel represetnation
+    Converts an OMERO ROI shape to a vitessce compatible representation
     https://github.com/will-moore/omero-vitessce/blob/master/omero_vitessce/views.py
     """
     def __init__(self, shape):
-        self.shape = self.to_shapely(shape)
+        self.type = shape.ROI
+        self.polygon = self.to_shapely(shape)
         self.name = shape.getTextValue().getValue()
 
     def to_shapely(self, omero_shape):
         encoder = get_encoder(omero_shape.__class__)
         shape_json = encoder.encode(omero_shape)
 
-        if "Points" in shape_json:
+        coords = []
+
+        if self.type == "ome.model.roi.Polygon_roi":
             xy = shape_json["Points"].split(" ")
-            coords = []
             for coord in xy:
                 c = coord.split(",")
                 coords.append((float(c[0]), float(c[1])))
-            return Polygon(coords)
+
+        elif self.type == "ome.model.roi.Rectangle_roi":
+            # X and Y are the top-left corner
+            x = omero_shape.getX().getValue()
+            y = omero_shape.getY().getValue()
+            w = omero_shape.getWidth().getValue()
+            h = omero_shape.getHeight().getValue()
+            coords.append((x, y))
+            coords.append((x + w, y))
+            coords.append((x + w, y + h))
+            coords.append((x, y + h))
+        return Polygon(coords)
 
     def poly(self):
         # Use 2 to get e.g. 8 points from 56.
-        return list(self.shape.simplify(2).exterior.coords)
+        return list(self.polygon.simplify(2).exterior.coords)
 
 
 def process_rois(img_ids, conn):
@@ -203,7 +220,12 @@ def process_rois(img_ids, conn):
         if not img:
             continue
         rois += img.getROIs()
-    shapes = [VitessceShape(r.getShape(0)) for r in rois]
+    shapes = [r.getShape(0) for r in rois]
+    # Exclude non closed shapes
+    shapes = filter(lambda x: x.ROI in VALID_SHAPES, shapes)
+    # Exclude shapes whithout a text value = No Cell ID
+    shapes = filter(lambda x: x.getTextValue() is not None, shapes)
+    shapes = [VitessceShape(s) for s in shapes]
     return shapes
 
 

setup.py

@@ -2,7 +2,7 @@
 
 setup(
     name="omero-vitessce",
-    version="1.1.2",
+    version="1.1.3",
     description="OMERO Vitessce multimodal data viewer plugin for OMERO.web",
     long_description=open('README.md').read(),
     long_description_content_type='text/markdown',

test/integration/test_rois.py

@@ -2,14 +2,14 @@
 import pytest
 
 import omero.model
-from omero.rtypes import rstring
+from omero.rtypes import rstring, rdouble
 from omeroweb.testlib import IWebTest
 from omero.gateway import BlitzGateway
 
 from omero_vitessce import utils
 
 
-def add_roi(img, points, name, conn):
+def add_roi_polygon(img, points, name, conn):
     polygon = omero.model.PolygonI()
     polygon.points = rstring(points)
     polygon.setTextValue(rstring(name))
@@ -20,6 +20,20 @@ def add_roi(img, points, name, conn):
     return roi.getId().getValue()
 
 
+def add_roi_rectangle(img, x, y, w, h, name, conn):
+    rect = omero.model.RectangleI()
+    rect.setX(rdouble(x))
+    rect.setY(rdouble(y))
+    rect.setWidth(rdouble(w))
+    rect.setHeight(rdouble(h))
+    rect.setTextValue(rstring(name))
+    roi = omero.model.RoiI()
+    roi.addShape(rect)
+    roi.setImage(img._obj)
+    roi = conn.getUpdateService().saveAndReturnObject(roi)
+    return roi.getId().getValue()
+
+
 class TestConfig(IWebTest):
     """Tests loading the index page."""
     USER_NAME = "test_user"
@@ -42,17 +56,27 @@ def rois(self, conn):
         """make two mock ROIs and link them to Image:1 and Image:2"""
         rois = []
         img = conn.getObject("Image", 1)
-        rois.append(add_roi(img, "10,20, 50,150, 200,200, 250,75", "A", conn))
+        rois.append(
+            add_roi_polygon(img, "10,20, 200,200, 250,75 300,250, 75,400",
+                            "A", conn))
+        rois.append(add_roi_polygon(img, "10,20, 50,150, 250,75", "B", conn))
         img = conn.getObject("Image", 2)
-        rois.append(add_roi(img, "10,20, 50,150, 250,75", "B", conn))
+        rois.append(add_roi_rectangle(img, 0, 0, 10, 5, "C", conn))
+        rois.append(add_roi_rectangle(img, 3333, 6666, 1000, 2000, "D", conn))
         yield rois
         conn.deleteObjects("Roi", rois)
 
     def test_rois(self, conn, rois):
         shapes = utils.process_rois([1, 2], conn)
-        obs_dict = utils.make_cell_json(shapes)  # We get floats from OMERO
-        exp_dict = {"A": [(10.0, 20.0), (50.0, 150.0),
-                          (200.0, 200.0), (250.0, 75.0), (10.0, 20.0)],
+        obs_dict = utils.make_cell_json(shapes)  # OMERO uses floats
+        exp_dict = {"A": [(10.0, 20.0), (200.0, 200.0),
+                          (250.0, 75.0), (300.0, 250.0),
+                          (75.0, 400.0), (10.0, 20.0)],
                     "B": [(10.0, 20.0), (50.0, 150.0),
-                          (250.0, 75.0), (10.0, 20.0)]}
+                          (250.0, 75.0), (10.0, 20.0)],
+                    "C": [(0.0, 0.0), (10.0, 0.0),
+                          (10.0, 5.0), (0.0, 5.0), (0.0, 0.0)],
+                    "D": [(3333.0, 6666.0), (4333.0, 6666.0),
+                          (4333.0, 8666.0), (3333.0, 8666.0),
+                          (3333.0, 6666.0)]}
         assert obs_dict == exp_dict