Autofocus verify based on sharpness range, removed repetitive logging

src/openflexure_microscope_server/things/autofocus.py

@@ -238,15 +238,15 @@ class AutofocusThing(Thing):
             return heights.tolist(), sizes.tolist()
 
     @thing_action
-    def verify_focus_sharpness(self, sweep_sizes: list, camera: WrappedCamera, leniency: int = 1):
+    def verify_focus_sharpness(self, sweep_sizes: list, camera: WrappedCamera, threshold: float = 0.95):
         '''Take the sharpness curve of the autofocus, and the size of the current frame
         to see if the autofocus completed successfully. Returns True if current sharpness
         is within "leniency" number of frames from the peak of the autofocus'''
 
         current_sharpness = camera.grab_jpeg_size(stream_name='lores')
 
-        peak = np.argmax(sweep_sizes)
+        peak = np.max(sweep_sizes)
-        accepted_range = [peak - leniency, peak + leniency]
+        base = np.min(sweep_sizes)
+        cutoff = threshold * (peak - base)
 
-        sharpness_range = [sweep_sizes[i] for i in accepted_range]
+        return current_sharpness >= base + cutoff
-        return current_sharpness >= min(sharpness_range)

src/openflexure_microscope_server/things/smart_scan.py

@@ -642,7 +642,7 @@ class SmartScanThing(Thing):
                         while True:
                             jpeg_zs, jpeg_sizes = autofocus.looping_autofocus(dz=self.autofocus_dz, start = 'base')
                             current_height = stage.position["z"]
-                            autofocus_success = autofocus.verify_focus_sharpness(sweep_sizes = jpeg_sizes, camera = CamDep, leniency = 1)
+                            autofocus_success = autofocus.verify_focus_sharpness(sweep_sizes = jpeg_sizes, camera = CamDep, threshold = 0.92)
                             logger.info(f"We just tested the focus! Result was {autofocus_success}")
 
                             if autofocus_success:
@@ -655,7 +655,7 @@ class SmartScanThing(Thing):
                                         nearest_focused_site[-1],
                                         loc[0:2],
                                         current_height,
-                                        0.3,
+                                        0.5,
                                     )
 
                                 # if there haven't been any previous autofocuses, we have to assume this one worked
@@ -721,6 +721,7 @@ class SmartScanThing(Thing):
                         logger.info(f'Rejected moving to {i} as it is out of range')
                 path = temp_path.copy()
                 path = sorted(path, key=lambda x: (steps_from_centre(x, true_path[0][:2], dx, dy), distance_to_site(loc[:2], x)))
+                self.create_zip_of_scan(logger = logger, scan_name = scan_folder.split('scans/')[1], download_zip = False)
 
         except InvocationCancelledError:
             logger.error("Stopping scan because it was cancelled.")
@@ -1036,7 +1037,12 @@ class SmartScanThing(Thing):
             )
         if not os.path.isdir(images_folder):
             raise FileNotFoundError(f"Tried to make a zip archive of {images_folder} but it does not exist.")
-        logger.info("Creating zip archive of images (may take some time)...")
+        # logger.info("Creating zip archive of images (may take some time)...")
+
+        from pathlib import Path
+
+        root_directory = Path(images_folder)
+        print(sum(f.stat().st_size for f in root_directory.glob('**/*') if f.is_file()))
 
         zip_fname = f'{os.path.join(scan_folder, "images")}.zip'
 
@@ -1050,8 +1056,6 @@ class SmartScanThing(Thing):
         # get a list of files in the existing zip    
         current_zip = self.get_files_in_zip(zip_fname)
 
-        logger.info(current_zip)
-
         # get a list of files in the folder we're zipping
         folder_path = self.scan_folder_path(scan_name)
         files = glob.glob(folder_path + '/**/*', recursive=True)
@@ -1065,11 +1069,14 @@ class SmartScanThing(Thing):
         with zipfile.ZipFile(zip_fname, mode="a") as zip:
             for file in files:
                 if any(banned_name in file for banned_name in files_to_delay):
-                    logger.info(f'we only add {file} into zip at the end of the scan')
+                    # logger.info(f'we only add {file} into zip at the end of the scan')
+                    pass
                 elif file in current_zip:
-                    logger.info(f'{file} is already in zip')
+                    # logger.info(f'{file} is already in zip')
-                elif ".zip" in file:
+                    pass
-                    logger.info('Not adding the .zip to itself')
+                elif ".zip" in file or 'raw' in file:
+                    # logger.info('Not adding the .zip to itself')
+                    pass
                 else:
                     logger.info(f'appending {file} to zip')
                     zip.write(os.path.join(folder_path, file), arcname=file)
@@ -1090,7 +1097,7 @@ class SmartScanThing(Thing):
                     if any(banned_name in file for banned_name in files_to_delay):
                         logger.info(f'we are finally adding {file} into zip')
                         zip.write(os.path.join(folder_path, file), arcname=file)
-
+            logger.info('about to download zip')
             return ZipBlob.from_file(zip_fname)
 
     @thing_action