20240322_hotfix

src/decolace/acquisition/acquisition_area.py

@@ -178,7 +178,16 @@ def load_from_disk(self):
         most_recent = sorted(potential_files)[-1]
         self.state = np.load(most_recent, allow_pickle=True).item()
 
-
+    def save_map(self, map):
+        import mrcfile
+
+        mrcfile.new(os.path.join(self.directory, self.name + "_map.mrc"), map)
+
+    def load_map(self):
+        import mrcfile
+
+        return mrcfile.read(os.path.join(self.directory, self.name + "_map.mrc"))
+
     def initialize_from_napari(
         self, map_navigator_id: int, center_coordinate, corner_coordinates, affine= None
     ):
@@ -402,24 +411,28 @@ def acquire(
                 fraction_of_gradient = (np.cos((index % self.state.defocus_steps)/self.state.defocus_steps * 2* np.pi) + 1) /2
                 self.state.desired_defocus = self.state.low_defocus + fraction_of_gradient * (self.state.high_defocus-self.state.low_defocus)
             offset = self.state.desired_defocus - measured_defocus
-
+            true_offset = offset
 
             if abs(offset) > self.state.ctf_max_step and established_lock:
                 offset = self.state.ctf_max_step * np.sign(offset)
                 if num_max_correction == 0:
-                    offset_before_max_correction = abs(offset)
+                    offset_before_max_correction = abs(true_offset)
                 num_max_correction += 1
 
             else:
                 if abs(offset) > self.state.ctf_max_step_initially:
                     offset = self.state.ctf_max_step_initially * np.sign(offset)
                     if num_max_correction == 0:
-                        offset_before_max_correction = abs(offset)
+                        offset_before_max_correction = abs(true_offset)
                     num_max_correction += 1
                 else:
                     num_max_correction = 0
-            if num_max_correction > 3 and abs(offset) > offset_before_max_correction:
-                report["potential_overfocus"] = True
+            if num_max_correction > 2 and abs(true_offset) > offset_before_max_correction:
+                correction_attempt = -1.6 * true_offset
+                print(f"Overfocus, trying to correct by {correction_attempt} instead of {offset}")
+                offset = correction_attempt
+
+                #report["potential_overfocus"] = True
 
             if abs(offset) < 0.1 and not established_lock and last_bs_correction < 0.06:
                 established_lock = True

src/decolace/acquisition/cli_acquisition.py

@@ -139,6 +139,19 @@ def print_aa_state(
     for aa in session_o.active_grid.acquisition_areas:
         print(aa.state)
 
+@app.command()
+def set_aa_state_abort(
+    name: str = typer.Option(None, help="Name of the session"),
+    directory: str = typer.Option(None , help="Directory to save session in"),
+    id: int = typer.Option(...),
+): 
+    session_o = load_session(name, directory)
+    for i, aa in enumerate(session_o.active_grid.acquisition_areas):
+        if i == id:
+            aa.state.aborted = True
+            aa.write_to_disk()
+        print(aa.state.aborted)
+
 @app.command()
 def set_session_state(
     name: str = typer.Option(None, help="Name of the session"),
@@ -454,7 +467,15 @@ def nice_view_button() -> napari.types.LayerDataTuple:
         pool = Pool(processes=1)
         image = pool.map(get_nice_view,[session_o])[0]
         existing_data = viewer.layers
-
+
+@app.command()
+def monitor(
+    session_name: str = typer.Option(None, help="Name of the session"),
+    directory: str = typer.Option(None, help="Directory to save session in"),
+):
+    serialem = connect_sem()
+    session_o = load_session(session_name, directory)
+
 
 @app.command()
 def setup_areas(
@@ -508,6 +529,7 @@ def my_widget(shapes: Shapes, use_square_beam: bool = False, start_from_bottom:
             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, use_square_beam=use_square_beam, start_from_bottom=start_from_bottom)
             aa.write_to_disk()
+            aa.save_map(maps[int(map_id)])
             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()
@@ -585,11 +607,13 @@ def acquire(
         def progress_callback(grid, report, acquisition_area, type=None):
             global numbad
             if type == "start_new_area":
+                numbad = 0
                 progress.console.log(
                     f"Starting acquisition of area {acquisition_area.name} in grid {grid.name}"
                 )
 
             elif type == "resume_area":
+                numbad = 0
                 progress.console.log(
                     f"Resuming acquisition of area {acquisition_area.name} in grid {grid.name}"
                 )

src/decolace/acquisition/grid.py

@@ -55,7 +55,7 @@ def write_to_disk(self, save_areas=False):
     def load_from_disk(self):
         potential_files = glob.glob(os.path.join(self.directory, self.name + "_*.npy"))
         if len(potential_files) < 1:
-            raise (FileNotFoundError("Couldn't find saved files"))
+            raise (FileNotFoundError("Couldn't find saved files grid"))
         most_recent = sorted(potential_files)[-1]
         self.state = np.load(most_recent, allow_pickle=True).item()
         #self.state = GridState(**self.state)
@@ -145,6 +145,8 @@ def start_acquisition(self, initial_defocus, progress_callback=None):
                 aa.state.positions_acquired
             ):
                 continue
+            if aa.state.aborted:
+                continue
             serialem.SetImageShift(0.0, 0.0)
             if np.sum(aa.state.positions_acquired) == 0:
                 progress_callback(

src/decolace/acquisition/session.py

@@ -22,8 +22,8 @@ class SessionState(BaseModel):
     active_grid: Optional[int] = None
     beam_radius: Optional[float] = None
     fringe_free_focus_vacuum: Optional[float] = None
-    min_defocus_for_ffsearch: Optional[float] = 30
-    max_defocus_for_ffsearch: Optional[float] = 80
+    min_defocus_for_ffsearch: Optional[float] = -10
+    max_defocus_for_ffsearch: Optional[float] = 10
     fringe_free_focus_cross_grating: Optional[float] = None
     dose_rate_e_per_pix_s: Optional[float] = None
     unbinned_pixel_size_A: Optional[float] = None
@@ -69,8 +69,8 @@ def load_from_disk(self):
                 new_grid = grid(grid_info[0], grid_info[1])
                 new_grid.load_from_disk()
                 self.grids.append(new_grid)
-            except FileNotFoundError:
-                print(f"Can't load grid {grid_info[0]}")
+            except FileNotFoundError as e:
+                print(f"Can't load grid {grid_info[0]} {e}")
 
 
     def add_grid(self, name, tilt):
@@ -160,9 +160,13 @@ def prepare_beam_cross_final(self):
                 print(f"Error could not center beam")
                 return
 
-        #serialem.MoveStage(0,0, -50.0)
-        wanted_defocus = -1.0    
-
+        #serialem.MoveStage(0,0, 10.0)
+        wanted_defocus = -1.0
+        # Get Focus using record mode wihtout adjusting focus    
+        #measured_defocus = serialem.G(-1,-1)
+        #defocus_error = wanted_defocus - measured_defocus
+        #serialem.MoveStage(0,0,defocus_error)
+
         serialem.Record()
         serialem.FFT("A")
         powerspectrum = np.asarray(serialem.bufferImage("AF"))