Add affine transformations of ROI shapes

ezomero/_gets.py

@@ -14,6 +14,7 @@
 from omero.model import enums as omero_enums
 from .rois import Point, Line, Rectangle
 from .rois import Ellipse, Polygon, Polyline, Label, ezShape
+from .rois import AffineTransform
 import importlib.util
 
 if (importlib.util.find_spec('pandas')):
@@ -1761,55 +1762,68 @@ def _omero_shape_to_shape(omero_shape: Shape
         mk_end = omero_shape.markerEnd
     except AttributeError:
         mk_end = None
+    try:
+        transform = omero_shape.transform
+    except AttributeError:
+        transform = None
+    if transform is not None:
+        transform = AffineTransform(
+            transform.a00.val,
+            transform.a10.val,
+            transform.a01.val,
+            transform.a11.val,
+            transform.a02.val,
+            transform.a12.val,
+        )
     shape: Union[Point, Line, Rectangle, Ellipse, Polygon, Polyline, Label]
     if shape_type == "Point":
         x = omero_shape.x
         y = omero_shape.y
         shape = Point(x, y, z_val, c_val, t_val, text, fill_color,
-                      stroke_color, stroke_width)
+                      stroke_color, stroke_width, transform=transform)
     elif shape_type == "Line":
         x1 = omero_shape.x1
         x2 = omero_shape.x2
         y1 = omero_shape.y1
         y2 = omero_shape.y2
         shape = Line(x1, y1, x2, y2, z_val, c_val, t_val, mk_start, mk_end,
-                     text, fill_color, stroke_color, stroke_width)
+                     text, fill_color, stroke_color, stroke_width, transform=transform)
     elif shape_type == "Rectangle":
         x = omero_shape.x
         y = omero_shape.y
         width = omero_shape.width
         height = omero_shape.height
         shape = Rectangle(x, y, width, height, z_val, c_val, t_val, text,
-                          fill_color, stroke_color, stroke_width)
+                          fill_color, stroke_color, stroke_width, transform=transform)
     elif shape_type == "Ellipse":
         x = omero_shape.x
         y = omero_shape.y
         radiusX = omero_shape.radiusX
         radiusY = omero_shape.radiusY
         shape = Ellipse(x, y, radiusX, radiusY, z_val, c_val, t_val, text,
-                        fill_color, stroke_color, stroke_width)
+                        fill_color, stroke_color, stroke_width, transform=transform)
     elif shape_type == "Polygon":
         omero_points = omero_shape.points.split()
         points = []
         for point in omero_points:
             coords = point.split(',')
             points.append((float(coords[0]), float(coords[1])))
         shape = Polygon(points, z_val, c_val, t_val, text, fill_color,
-                        stroke_color, stroke_width)
+                        stroke_color, stroke_width, transform=transform)
     elif shape_type == "Polyline":
         omero_points = omero_shape.points.split()
         points = []
         for point in omero_points:
             coords = point.split(',')
             points.append((float(coords[0]), float(coords[1])))
         shape = Polyline(points, z_val, c_val, t_val, text, fill_color,
-                         stroke_color, stroke_width)
+                         stroke_color, stroke_width, transform=transform)
     elif shape_type == "Label":
         x = omero_shape.x
         y = omero_shape.y
         fsize = omero_shape.getFontSize().getValue()
         shape = Label(x, y, text, fsize, z_val, c_val, t_val, fill_color,
-                      stroke_color, stroke_width)
+                      stroke_color, stroke_width, transform=transform)
     else:
         err = 'The shape passed for the roi is not a valid shape type'
         raise TypeError(err)

ezomero/_posts.py

@@ -8,7 +8,7 @@
 from omero.gateway import BlitzGateway
 from omero.model import RoiI, PointI, LineI, RectangleI, EllipseI
 from omero.model import PolygonI, PolylineI, LabelI, LengthI, enums
-from omero.model import DatasetI, ProjectI, ScreenI, Shape
+from omero.model import DatasetI, ProjectI, ScreenI, Shape, AffineTransformI
 from omero.grid import BoolColumn, LongColumn
 from omero.grid import StringColumn, DoubleColumn, Column
 from omero.gateway import ProjectWrapper, DatasetWrapper
@@ -752,6 +752,17 @@ def create_columns(table: Any,
     return cols
 
 
+def _omero_affine(a00, a10, a01, a11, a02, a12):
+    affine = AffineTransformI()
+    affine.a00 = rdouble(a00)
+    affine.a10 = rdouble(a10)
+    affine.a01 = rdouble(a01)
+    affine.a11 = rdouble(a11)
+    affine.a02 = rdouble(a02)
+    affine.a12 = rdouble(a12)
+    return affine
+
+
 def _shape_to_omero_shape(shape: Union[Point, Line, Rectangle, Ellipse,
                                        Polygon, Polyline, Label]) -> Shape:
     """ Helper function to convert ezomero shapes into omero shapes"""
@@ -822,6 +833,10 @@ def _shape_to_omero_shape(shape: Union[Point, Line, Rectangle, Ellipse,
                                            enums.UnitsLength.PIXEL))
     else:
         omero_shape.setStrokeWidth(LengthI(1.0, enums.UnitsLength.PIXEL))
+    if shape.transform is not None:
+        t_ = shape.transform
+        omero_shape.transform = _omero_affine(t_.a00, t_.a10, t_.a01,
+                                              t_.a11, t_.a02, t_.a12)
     return omero_shape
 
 

ezomero/rois.py

@@ -8,7 +8,19 @@
            "Polygon",
            "Polyline",
            "Label",
-           "ezShape"]
+           "ezShape",
+           "AffineTransform"]
+
+
+@dataclass(frozen=True)
+class AffineTransform():
+    """A dataclss for affine transformation matrix of shapes"""
+    a00: float = field(default=1.0)
+    a10: float = field(default=0.0)
+    a01: float = field(default=0.0)
+    a11: float = field(default=1.0)
+    a02: float = field(default=0.0)
+    a12: float = field(default=0.0)
 
 
 @dataclass(frozen=True)
@@ -20,6 +32,7 @@ class ezShape:
     This dataclass is frozen and should not be modified after instantiation
 
     """
+    transform: Union[AffineTransform, None] = field(default=None, kw_only=True)
 
 
 @dataclass(frozen=True)