Loading openflexure_microscope/plugins/default/stack/__init__.py 0 → 100644 +1 −0 Original line number Diff line number Diff line from .plugin import StackPlugin openflexure_microscope/plugins/default/stack/plugin.py 0 → 100644 +147 −0 Original line number Diff line number Diff line import time import numpy as np from typing import Tuple import uuid from openflexure_microscope.camera.base import generate_basename from openflexure_microscope.plugins import MicroscopePlugin from openflexure_microscope.utilities import set_properties class StackPlugin(MicroscopePlugin): """ Stack and tile plugin """ api_views = {} def do_capture(self, basename, scan_id, use_video_port: bool = False, resize: Tuple[int, int] = None, bayer: bool = False): # Construct a tile filename filename = "{}_{}_{}_{}".format(basename, *self.microscope.stage.position) foldername = "SCAN_{}".format(basename) # Create output object output = self.microscope.camera.new_image( write_to_file=True, temporary=False, filename=filename, folder=foldername) # Capture self.microscope.camera.capture( output, use_video_port=use_video_port, resize=resize, bayer=bayer) # Affix metadata metadata = {} tags = ['stack'] metadata.update({ 'Position': self.microscope.state['stage']['position'], 'Stack ID': scan_id }) output.put_metadata(metadata) output.put_tags(tags) def tile( self, basename: str = None, step_size: int = [2000, 1500], grid: list = [3, 3], autofocus_dz: int = 20, use_video_port: bool = False, resize: Tuple[int, int] = None, bayer: bool = False): # Generate a basename if none given if not basename: basename = generate_basename() # Generate a stack ID scan_id = uuid.uuid4().hex # Store initial position initial_position = self.microscope.stage.position # Check if autofocus is enabled if autofocus_dz and hasattr(self.microscope.plugin, 'default_autofocus'): autofocus_enabled = True else: autofocus_enabled = False xdirection = 1 with self.microscope.lock: for i in range(grid[0]): for j in range(grid[1]): if autofocus_enabled: self.microscope.plugin.default_autofocus.autofocus(range(-2*autofocus_dz, 3*autofocus_dz, autofocus_dz)) self.do_capture( basename, scan_id, use_video_port=use_video_port, resize=resize, bayer=bayer ) if j != grid[0] - 1: self.microscope.stage.move_rel([step_size[0]*xdirection, 0, 0]) xdirection *= -1 if i != grid[1] - 1: self.microscope.stage.move_rel([256*xdirection, step_size[1], 0]) self.microscope.stage.move_abs(initial_position) def stack( self, basename: str = None, step_size: int = 100, steps: list = 5, center: bool = True, use_video_port: bool = False, resize: Tuple[int, int] = None, bayer: bool = False): # Generate a basename if none given if not basename: basename = generate_basename() # Generate a stack ID scan_id = uuid.uuid4().hex # Store initial position initial_position = self.microscope.stage.position # Move to center scan if center: self.microscope.stage.move_rel([0, 0, int((-step_size * steps)/2)]) with self.microscope.lock: for i in range(steps): self.do_capture( basename, scan_id, use_video_port=use_video_port, resize=resize, bayer=bayer ) if i != steps - 1: self.microscope.stage.move_rel([0, 0, step_size]) self.microscope.stage.move_abs(initial_position) Loading
openflexure_microscope/plugins/default/stack/__init__.py 0 → 100644 +1 −0 Original line number Diff line number Diff line from .plugin import StackPlugin
openflexure_microscope/plugins/default/stack/plugin.py 0 → 100644 +147 −0 Original line number Diff line number Diff line import time import numpy as np from typing import Tuple import uuid from openflexure_microscope.camera.base import generate_basename from openflexure_microscope.plugins import MicroscopePlugin from openflexure_microscope.utilities import set_properties class StackPlugin(MicroscopePlugin): """ Stack and tile plugin """ api_views = {} def do_capture(self, basename, scan_id, use_video_port: bool = False, resize: Tuple[int, int] = None, bayer: bool = False): # Construct a tile filename filename = "{}_{}_{}_{}".format(basename, *self.microscope.stage.position) foldername = "SCAN_{}".format(basename) # Create output object output = self.microscope.camera.new_image( write_to_file=True, temporary=False, filename=filename, folder=foldername) # Capture self.microscope.camera.capture( output, use_video_port=use_video_port, resize=resize, bayer=bayer) # Affix metadata metadata = {} tags = ['stack'] metadata.update({ 'Position': self.microscope.state['stage']['position'], 'Stack ID': scan_id }) output.put_metadata(metadata) output.put_tags(tags) def tile( self, basename: str = None, step_size: int = [2000, 1500], grid: list = [3, 3], autofocus_dz: int = 20, use_video_port: bool = False, resize: Tuple[int, int] = None, bayer: bool = False): # Generate a basename if none given if not basename: basename = generate_basename() # Generate a stack ID scan_id = uuid.uuid4().hex # Store initial position initial_position = self.microscope.stage.position # Check if autofocus is enabled if autofocus_dz and hasattr(self.microscope.plugin, 'default_autofocus'): autofocus_enabled = True else: autofocus_enabled = False xdirection = 1 with self.microscope.lock: for i in range(grid[0]): for j in range(grid[1]): if autofocus_enabled: self.microscope.plugin.default_autofocus.autofocus(range(-2*autofocus_dz, 3*autofocus_dz, autofocus_dz)) self.do_capture( basename, scan_id, use_video_port=use_video_port, resize=resize, bayer=bayer ) if j != grid[0] - 1: self.microscope.stage.move_rel([step_size[0]*xdirection, 0, 0]) xdirection *= -1 if i != grid[1] - 1: self.microscope.stage.move_rel([256*xdirection, step_size[1], 0]) self.microscope.stage.move_abs(initial_position) def stack( self, basename: str = None, step_size: int = 100, steps: list = 5, center: bool = True, use_video_port: bool = False, resize: Tuple[int, int] = None, bayer: bool = False): # Generate a basename if none given if not basename: basename = generate_basename() # Generate a stack ID scan_id = uuid.uuid4().hex # Store initial position initial_position = self.microscope.stage.position # Move to center scan if center: self.microscope.stage.move_rel([0, 0, int((-step_size * steps)/2)]) with self.microscope.lock: for i in range(steps): self.do_capture( basename, scan_id, use_video_port=use_video_port, resize=resize, bayer=bayer ) if i != steps - 1: self.microscope.stage.move_rel([0, 0, step_size]) self.microscope.stage.move_abs(initial_position)
