Split up z stack function
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jaknapper
parent
c0677858a1
commit
6acfbaefd6
2 changed files with 143 additions and 57 deletions
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@ -288,7 +288,7 @@ class AutofocusThing(Thing):
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self.thing_settings["stack_dz"] = value
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@thing_action
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def run_z_stack(
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def run_smart_stack(
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self,
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cam: WrappedCamera,
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stage: Stage,
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@ -305,72 +305,75 @@ class AutofocusThing(Thing):
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images_to_capture = self.stack_images_to_capture
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images_to_test = self.stack_images_to_test
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if images_to_test < images_to_capture:
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raise RuntimeError(
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"Can't capture more images than are tested. Please increase number to test, or decrease number to capture"
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)
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if images_to_test % 2 == 0:
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raise RuntimeError("Images to test should be odd")
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stack_z_range = stack_dz * (images_to_test - 1)
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overshoot = stack_dz * 5
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# Move down by the height of the z stack, plus an overshoot
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# Better to start too low and take too many images than too high and need to refocus
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stage.move_relative(z=-(overshoot + BACKLASH_CORRECTION + stack_z_range / 2))
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stage.move_relative(z=BACKLASH_CORRECTION)
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self.validate_scan_inputs(images_to_test, images_to_capture)
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continue_stack = True
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captures = []
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sharpnesses = []
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heights = []
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capture_count = 0
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starting_height = stage.position["z"]
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while continue_stack:
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time.sleep(SETTLING_TIME)
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stage_location = stage.position
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jpeg_path = os.path.join(
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success = False
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while not success:
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result, heights, captures, sharpest_index = self.z_stack(
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stack_dz,
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images_to_test,
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images_dir,
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f"{stage_location['x']}_{stage_location['y']}_{stage_location['z']}.jpeg",
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stack_z_range,
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overshoot,
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stage,
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cam,
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capture,
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metadata_getter,
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logger,
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)
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image, metadata = capture._capture_image(
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cam=cam,
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metadata_getter=metadata_getter,
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if result == "success":
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success = True
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break
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# If result remains as "restart", move to the start and autofocus
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self.reset_stack(
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heights,
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stack_z_range,
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overshoot,
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autofocus_dz,
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stage,
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sharpness_monitor,
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)
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captures.append([jpeg_path, image, metadata])
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sharpnesses.append(cam.grab_jpeg_size(stream_name="lores"))
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heights.append(stage.position["z"])
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capture_count += 1
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# If the stack isn't complete yet, move
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if capture_count >= images_to_test:
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stack_result = self.test_stack(sharpnesses[-images_to_test:])
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self.save_stack(
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sharpest_index,
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captures,
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images_to_test,
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images_to_capture,
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logger,
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capture,
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)
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if stack_result == "success":
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continue_stack = False
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return heights[-images_to_test:][sharpest_index]
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# These are signs of overshooting. Autofocus and retry
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elif stack_result == "restart" or capture_count > 20:
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captures = []
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sharpnesses = []
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heights = []
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capture_count = 0
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stage.move_absolute(z=starting_height - stack_z_range)
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self.looping_autofocus(
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stage=stage,
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sharpness_monitor=sharpness_monitor,
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dz=autofocus_dz,
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)
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stage.move_relative(
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z=-(overshoot + BACKLASH_CORRECTION + stack_z_range / 2)
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)
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stage.move_relative(z=BACKLASH_CORRECTION)
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stage.move_relative(z=stack_dz)
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def reset_stack(
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self,
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heights,
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autofocus_dz,
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stage,
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sharpness_monitor,
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):
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stage.move_absolute(z=heights[0])
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self.looping_autofocus(
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stage=stage,
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sharpness_monitor=sharpness_monitor,
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dz=autofocus_dz,
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)
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def save_stack(
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self,
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sharpest_index,
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captures,
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images_to_test,
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images_to_capture,
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logger,
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capture,
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):
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# Find the range of images from the stack to capture
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sharpest_index = np.argmax(sharpnesses[-images_to_test:])
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stack_extent = int((images_to_capture - 1) / 2)
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stack_range = range(
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sharpest_index - stack_extent, sharpest_index + stack_extent + 1
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@ -384,8 +387,91 @@ class AutofocusThing(Thing):
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metadata=captures[-images_to_test:][capture_index][2],
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logger=logger,
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)
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return sharpest_index
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return heights[-images_to_test:][sharpest_index]
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def z_stack(
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self,
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stack_dz,
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images_to_test,
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images_dir,
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stack_z_range,
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overshoot,
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stage,
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cam,
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capture,
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metadata_getter,
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):
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# Move down by the height of the z stack, plus an overshoot
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# Better to start too low and take too many images than too high and need to refocus
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stage.move_relative(z=-(overshoot + BACKLASH_CORRECTION + stack_z_range / 2))
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stage.move_relative(z=BACKLASH_CORRECTION)
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captures = []
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sharpnesses = []
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heights = []
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while len(captures) <= 20:
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time.sleep(SETTLING_TIME)
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captures, heights, sharpnesses = self.capture_stack_image(
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captures,
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heights,
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sharpnesses,
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images_dir,
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cam,
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stage,
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capture,
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metadata_getter,
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)
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# If the number of images is enough to test, test them
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if len(captures) >= images_to_test:
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stack_result = self.test_stack(sharpnesses[-images_to_test:])
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if stack_result == "success":
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sharpest_index = np.argmax(sharpnesses[-images_to_test:])
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return "success", heights, captures, sharpest_index
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if stack_result == "restart":
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return "restart", heights, None, None
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stage.move_relative(z=stack_dz)
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return "restart", heights, None, None
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def capture_stack_image(
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self,
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captures,
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heights,
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sharpnesses,
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images_dir,
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cam,
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stage,
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capture,
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metadata_getter,
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):
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stage_location = stage.position
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jpeg_path = os.path.join(
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images_dir,
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f"{stage_location['x']}_{stage_location['y']}_{stage_location['z']}.jpeg",
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)
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image, metadata = capture._capture_image(
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cam=cam,
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metadata_getter=metadata_getter,
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)
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captures.append([jpeg_path, image, metadata])
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sharpnesses.append(cam.grab_jpeg_size(stream_name="lores"))
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heights.append(stage_location["z"])
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return captures, heights, sharpnesses
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def validate_scan_inputs(self, images_to_test, images_to_capture):
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if images_to_test < images_to_capture:
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raise RuntimeError(
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"Can't capture more images than are tested. Please increase number to test, or decrease number to capture"
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)
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if images_to_test % 2 == 0:
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raise RuntimeError("Images to test should be odd")
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def test_stack(self, sharpnesses: list):
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"""Test a list of sharpnesses, to decide whether the sharpest image from a stack is within them
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@ -642,7 +642,7 @@ class SmartScanThing(Thing):
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self._scan_logger.info(msg)
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continue
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focused_height = self._autofocus.run_z_stack(
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focused_height = self._autofocus.run_smart_stack(
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images_dir=self._ongoing_scan_images_dir,
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autofocus_dz=self._scan_data["autofocus_dz"],
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)
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