default=1.0, help="Time (in seconds) to wait at each point") parser.add_argument( "--return_to_start", dest="return_to_start", action="store_true", help="Return to the origin at the beginning of each run") parser.add_argument("--output", help="HDF5 file to save to", default="linear_motion.hdf5") parser.add_argument("--settings_file", help="File where the microscope settings are stored.", default="microscope_settings.npz") args = parser.parse_args() with load_microscope(args.settings_file, dummy_stage = False) as ms, \ closing(data_file.Datafile(filename = args.output)) as df: assert picamera_supports_lens_shading( ), "You need the updated picamera module with lens shading!" camera = ms.camera stage = ms.stage N_frames = args.n_frames N_repeats = args.n_repeats step = args.step framerate = args.framerate dwell_time = args.dwell_time backlash = 256 return_to_start = args.return_to_start
return_corr=True, fraction=0.5) return data def random_point(move_dist): angle = random.randrange(0, 360) * np.pi / 180 vector = np.array( [move_dist * np.cos(angle), 0, move_dist * np.sin(angle)]) vector = np.rint(vector) return vector if __name__ == "__main__": with load_microscope("microscope_settings.npz", dummy_stage = False) as ms, \ closing(data_file.Datafile(filename = "repeat.hdf5")) as df: assert picamera_supports_lens_shading( ), "You need the updated picamera module with lens shading!" camera = ms.camera stage = ms.stage backlash = 256 camera.resolution = (640, 480) stage.backlash = backlash n_moves = 10
import queue def image_capture(start_t, event, ms, q): while event.is_set(): frame = ms.rgb_image().astype(np.float32) capture_t = time.time() frame = cv2.cvtColor(frame, cv2.COLOR_BGR2GRAY) q.put(frame) tim = capture_t - start_t q.put(tim) print('Number of itms in the queue: {}'.format(q.qsize())) time.sleep(0.2) if __name__ == "__main__": with load_microscope("microscope_settings.npz") as ms, \ closing(data_file.Datafile(filename = "drift.hdf5")) as df: assert picamera_supports_lens_shading(), "You need the updated picamera module with lens shading!" camera = ms.camera stage = ms.stage camera.resolution=(640,480) cam_pos = df.new_group("data", "drift") N_frames = 500 #need to be consistant between drift.py and drift_plot.py camera.start_preview(resolution=(640,480))