def determine_rotation_axis(camera, shutter, flat_motor, rotation_motor, flat_position,
radio_position):
"""Determine tomographic rotation axis using *camera*, *shutter*, *rotation_motor* and
*flat_motor* devices. *flat_position* is the position for making a flat field, *radio_position*
is the position with the sample in the field of view.
"""
dark = acquire_dark(camera, shutter).result().astype(np.float32)
flat = acquire_image_with_beam(camera, shutter, flat_motor, flat_position).result()
first = acquire_image_with_beam(camera, shutter, flat_motor, radio_position).result()
rotation_motor.move(180 * q.deg).join()
last = acquire_image_with_beam(camera, shutter, flat_motor, radio_position).result()
# flat correct
flat_corr_first = flat_correct(first, flat, dark=dark)
flat_corr_last = flat_correct(last, flat, dark=dark)
return compute_rotation_axis(flat_corr_first, flat_corr_last)
def determine_rotation_axis(camera, shutter, flat_motor, rotation_motor,
flat_position, radio_position):
"""Determine tomographic rotation axis using *camera*, *shutter*, *rotation_motor* and
*flat_motor* devices. *flat_position* is the position for making a flat field, *radio_position*
is the position with the sample in the field of view.
"""
dark = acquire_dark(camera, shutter).result().astype(np.float32)
flat = acquire_image_with_beam(camera, shutter, flat_motor,
flat_position).result()
first = acquire_image_with_beam(camera, shutter, flat_motor,
radio_position).result()
rotation_motor.move(180 * q.deg).join()
last = acquire_image_with_beam(camera, shutter, flat_motor,
radio_position).result()
# flat correct
flat_corr_first = flat_correct(first, flat, dark=dark)
flat_corr_last = flat_correct(last, flat, dark=dark)
return compute_rotation_axis(flat_corr_first, flat_corr_last)
def get_frames():
frames = []
for i in range(num_frames):
rotation_motor.move(step).join()
camera.trigger()
frame = camera.grab().astype(np.float)
if flat is not None:
frame = flat_correct(frame, flat, dark=dark)
if frame_consumer:
frame_consumer.send(frame)
frames.append(frame)
return frames
def get_frames():
frames = []
for i in range(num_frames):
rotation_motor.move(step).join()
camera.trigger()
frame = camera.grab().astype(np.float)
if flat is not None:
frame = flat_correct(frame, flat, dark=dark)
if frame_consumer:
frame_consumer.send(frame)
frames.append(frame)
return frames
async def acquire_frames_360(camera,
rotation_motor,
num_frames,
shutter=None,
flat_motor=None,
flat_position=None,
y_0=0,
y_1=None):
"""
acquire_frames_360(camera, rotation_motor, num_frames, shutter=None, flat_motor=None,
flat_position=None, y_0=0, y_1=None)
Acquire frames around a circle.
"""
flat = None
if await camera.get_state() == 'recording':
await camera.stop_recording()
await camera['trigger_source'].stash()
await camera.set_trigger_source(camera.trigger_sources.SOFTWARE)
try:
async with camera.recording():
if shutter:
if await shutter.get_state() != 'closed':
await shutter.close()
await camera.trigger()
dark = (await camera.grab())[y_0:y_1]
await shutter.open()
if flat_motor and flat_position is not None:
radio_position = await flat_motor.get_position()
await flat_motor.set_position(flat_position)
await camera.trigger()
flat = (await camera.grab())[y_0:y_1]
await flat_motor.set_position(radio_position)
for i in range(num_frames):
await rotation_motor.move(2 * np.pi / num_frames * q.rad)
await camera.trigger()
frame = (await camera.grab())[y_0:y_1].astype(np.float)
if flat is not None:
frame = flat_correct(frame, flat, dark=dark)
frame = np.nan_to_num(-np.log(frame))
# Huge numbers can also cause trouble
frame[np.abs(frame) > 1e6] = 0
else:
frame = frame.max() - frame
yield frame
finally:
# No side effects
await camera['trigger_source'].restore()