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))
