Sqaure beam setup

src/decolace/acquisition/acquisition_area.py

@@ -70,10 +70,10 @@ def _hexagonal_cover(polygon, radius):
 def rectangular_cover(polygon, radius):
 
     # Define a regular hexagon with side length equal to the sphere radius
-    sqaure = Polygon(
+    square = Polygon(
         [
             (-radius,radius),
-            {-radius,-radius},
+            (-radius,-radius),
             (radius,-radius),
             (radius,radius),
             (-radius,radius)
@@ -84,8 +84,8 @@ def rectangular_cover(polygon, radius):
     minx, miny, maxx, maxy = polygon.bounds
 
     # Compute the offset required to center the hexagonal grid within the bounding box
-    dx = sqaure.bounds[2] - square.bounds[0]
-    dy = sqaure.bounds[3] - sqaure.bounds[1]
+    dx = square.bounds[2] - square.bounds[0]
+    dy = square.bounds[3] - square.bounds[1]
     offsetx = (maxx - minx - dx) / 2
     offsety = (maxy - miny - dy) / 2
 
@@ -105,9 +105,9 @@ def rectangular_cover(polygon, radius):
                 minx
                 + offsetx
                 + (i * 2 * radius)
-                + (j % 2) * radius
+
             )
-            if polygon.intersects(affinity.translate(sqaure, xoff=x, yoff=y)):
+            if polygon.intersects(affinity.translate(square, xoff=x, yoff=y)):
                 centers.append((x, y))
 
     return np.array(centers)
@@ -177,7 +177,7 @@ def load_from_disk(self):
 
 
     def initialize_from_napari(
-        self, map_navigator_id: int, center_coordinate, corner_coordinates
+        self, map_navigator_id: int, center_coordinate, corner_coordinates, affine= None
     ):
         serialem = connect_sem()
         serialem.LoadOtherMap(map_navigator_id, "A")
@@ -220,13 +220,19 @@ def initialize_from_napari(
         )
         self.state.corner_positions_image = np.array(corner_coordinates)
 
-    def calculate_acquisition_positions_from_napari(self, beam_radius, add_overlap=0.05):
+    def calculate_acquisition_positions_from_napari(self, beam_radius, add_overlap=0.05,  use_square_beam=False):
 
         polygon = Polygon(self.state.corner_positions_specimen)
 
-        center = _hexagonal_cover(
-            polygon, beam_radius * (1 - add_overlap)
-        )
+
+        if use_square_beam:
+            center = rectangular_cover(
+                polygon, beam_radius * (1 - add_overlap)
+            )
+        else:
+            center = _hexagonal_cover(
+                polygon, beam_radius * (1 - add_overlap)
+            )
 
         self.state.acquisition_positions = center
         self.state.positions_acquired = np.zeros(

src/decolace/acquisition/cli_acquisition.py

@@ -369,10 +369,20 @@ def setup_areas(
     import napari
     from napari.layers import Shapes
     from magicgui import magicgui
+
     viewer = napari.view_image(np.array(maps))
+
+    # Now test if there are already areas set up
+    existing_acquisiton_positions = False
+    if len(session_o.active_grid.state.acquisition_areas) > 0:
+        if sum([len(aa.state.acquisition_positions) for aa in session_o.active_grid.acquisition_areas]) > 0:
+            existing_acquisiton_positions = True
+
+    if existing_acquisiton_positions:
+        affine = session_o.active_grid.draw_acquisition_positions_into_napari(viewer, map_navids, session_o.state.beam_radius)
 
     @magicgui(shapes={'label': 'Setup areas'})
-    def my_widget(shapes: Shapes, use_rectangular_grid: bool = False):
+    def my_widget(shapes: Shapes, use_square_beam: bool = False):
         points = []
         areas = shapes.data
         for area in areas:
@@ -382,14 +392,14 @@ def my_widget(shapes: Shapes, use_rectangular_grid: bool = False):
             name = f"area{len(session_o.active_grid.state.acquisition_areas)+2}"
             polygon = shapely.geometry.Polygon(area[:,1:3])
             aa = AcquisitionAreaSingle(name,Path(session_o.active_grid.directory,name).as_posix(),tilt=session_o.active_grid.state.tilt)   
-            aa.initialize_from_napari(map_navids[int(map_id)], [polygon.centroid.y, polygon.centroid.x], area[:,1:3])
-            aa.calculate_acquisition_positions_from_napari(beam_radius=session_o.state.beam_radius)
+            aa.initialize_from_napari(map_navids[int(map_id)], [polygon.centroid.y, polygon.centroid.x], area[:,1:3],affine=affine)
+            aa.calculate_acquisition_positions_from_napari(beam_radius=session_o.state.beam_radius, use_square_beam=use_square_beam)
             aa.write_to_disk()
             session_o.active_grid.state.acquisition_areas.append([aa.name,aa.directory])
+            session_o.active_grid.acquisition_areas.append(aa)
         session_o.active_grid.write_to_disk()
         session_o.active_grid.save_navigator()
-
-
+        session_o.active_grid.draw_acquisition_positions_into_napari(viewer, map_navids, session_o.state.beam_radius,use_square_beam=use_square_beam)
 
     viewer.window.add_dock_widget(my_widget)
     napari.run()

src/decolace/acquisition/grid.py

@@ -13,7 +13,7 @@
 from .acquisition_area import AcquisitionAreaSingle
 
 class GridState(BaseModel):
-    acquisition_areas: List[str] = []
+    acquisition_areas: List[List] = []
     desired_defocus: float = -1.0
     tilt: float = 0.0
     view_file: Optional[str] = None
@@ -58,6 +58,7 @@ def load_from_disk(self):
             raise (FileNotFoundError("Couldn't find saved files"))
         most_recent = sorted(potential_files)[-1]
         self.state = np.load(most_recent, allow_pickle=True).item()
+        #self.state = GridState(**self.state)
         self.acquisition_areas = []
         for area in self.state.acquisition_areas:
             self.acquisition_areas.append(AcquisitionAreaSingle(area[0], Path(self.directory) / area[0]))
@@ -172,3 +173,48 @@ def start_acquisition(self, initial_defocus, progress_callback=None):
             aa.acquire(initial_defocus=initial_defocus, progress_callback=callback,initial_beamshift=initial_beamshift)
             aa.write_to_disk()
         serialem.SetColumnOrGunValve(0)
+
+    def draw_acquisition_positions_into_napari(self, viewer, map_navids, beam_radius, use_square_beam=False):
+        from skimage.transform import AffineTransform
+        write_to_disktext = {
+                'string': '{order}',
+                'size': 10,
+                'color': 'white',
+                'translation': np.array([0, 0]),
+             }
+        order = [[] for a in map_navids]
+        positions = [[] for a in map_navids]
+        corner_positions = []
+        for i, aa in enumerate(self.acquisition_areas):
+
+            map_index = map_navids.index(aa.state.navigator_map_index)
+
+            # Get the affine matrix converting aa.state.corner_positions_specimen into aa.state.corner_positions_image
+            affine = AffineTransform()
+            affine.estimate(aa.state.corner_positions_specimen, aa.state.corner_positions_image)
+
+
+            pos = affine(aa.state.acquisition_positions[:, ::1])
+            # Concatenat i to pos along axis 1
+            pos = np.concatenate((np.ones((len(pos), 1)) * map_index, pos), axis=1)
+            # Find position of aa.navigator_map_index in nav_ids
+
+            positions[map_index].extend(pos)
+            order[map_index].extend(np.array(range(len(aa.state.acquisition_positions))))
+        pos = np.concatenate(positions, axis = 0)
+        order = np.concatenate(order, axis = 0)
+
+        if use_square_beam:
+            symbol='square'
+        else:
+            symbol='o'
+        viewer.add_points(
+            pos,
+            name="exposures",
+            symbol=symbol,
+            size=beam_radius * 2 * affine.scale[0],
+            face_color="#00000000",
+            features={"order":np.array(order)},
+            text=write_to_disktext
+        )
+        return affine

src/decolace/acquisition/session.py

@@ -12,7 +12,7 @@
 from .grid import grid
 
 class SessionState(BaseModel):
-    grids: List[grid] = []
+    grids: List[List] = []
     microscope_settings: dict = {}
     active_grid: Optional[int] = None
     beam_radius: Optional[float] = None
@@ -50,6 +50,7 @@ def load_from_disk(self):
         most_recent = sorted(potential_files)[-1]
         #print(f"Loading file {most_recent}")
         self.state = np.load(most_recent, allow_pickle=True).item()
+        #self.state = SessionState(**self.state)
         for grid_info in self.state.grids:
             if not Path(grid_info[1]).exists():
                 grid_info[1] = Path(self.directory) / Path(grid_info[1]).parts[-1]