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Code clenaup
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Andrey Gruzinov committed Mar 5, 2024
1 parent fa58b8b commit b49250c
Showing 1 changed file with 42 additions and 89 deletions.
131 changes: 42 additions & 89 deletions mxcubecore/HardwareObjects/DESY/P11Collect.py
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Original file line number Diff line number Diff line change
Expand Up @@ -66,6 +66,9 @@ def init(self):
self.acq_off_cmd = self.get_command_object("acq_off")
self.acq_window_off_cmd = self.get_command_object("acq_window_off")

self.latest_frames = None
self.acq_speed = None

if None in [
self.lower_bound_ch,
self.upper_bound_ch,
Expand All @@ -89,15 +92,14 @@ def move_motors(self, motor_position_dict):
HWR.beamline.diffractometer.move_motors(motor_position_dict)

def _take_crystal_snapshot(self, filename):
diffr = HWR.beamline.diffractometer
self.log.debug("#COLLECT# taking crystal snapshot.")

if not diffr.is_centring_phase():
if not HWR.beamline.diffractometer.is_centring_phase():
self.log.debug("#COLLECT# take_snapshot. moving to centring phase")
diffr.goto_centring_phase(wait=True)
HWR.beamline.diffractometer.goto_centring_phase(wait=True)

time.sleep(0.3)
if not diffr.is_centring_phase():
if not HWR.beamline.diffractometer.is_centring_phase():
raise RuntimeError(
"P11Collect. cannot reach centring phase for acquiring snapshots"
)
Expand Down Expand Up @@ -155,7 +157,7 @@ def do_collect(self, owner):
)

logging.getLogger("HWR").info(
"Collection parameters: %s" % str(self.current_dc_parameters)
"Collection parameters: %s", str(self.current_dc_parameters)
)

log.info("Collection: Storing data collection in LIMS")
Expand Down Expand Up @@ -245,9 +247,8 @@ def do_collect(self, owner):
log.info("Collection: Updating data collection in LIMS")
self.update_data_collection_in_lims()

except:
exc_type, exc_value, exc_tb = sys.exc_info()
failed_msg = "Data collection failed!\n%s" % exc_value
except RuntimeError as e:
failed_msg = "Data collection failed!\n%s" % str(e)
self.collection_failed(failed_msg)
else:
self.collection_finished()
Expand All @@ -260,9 +261,6 @@ def data_collection_hook(self):
"P11Collect. - object initialization failed. COLLECTION not possible"
)

self.diffr = HWR.beamline.diffractometer
detector = HWR.beamline.detector

dc_pars = self.current_dc_parameters
collection_type = dc_pars["experiment_type"]

Expand All @@ -286,28 +284,11 @@ def data_collection_hook(self):
self.acq_speed = img_range / exp_time

if not self.diffractometer_prepare_collection():
raise BaseException("Cannot prepare diffractometer for collection")

if collection_type == "Characterization":
self.log.debug("P11Collect. Characterization")
ret = self.prepare_characterization()
else:
stop_angle = start_angle + img_range * nframes

self.log.debug("P11Collect. Standard Collection")
self.log.debug(
" - collection starts at: %3.2f - ends at: %3.2f "
% (start_angle, stop_angle)
)

ret = self.prepare_std_collection(start_angle, img_range)

if not ret:
raise BaseException("Cannot set prepare collection . Aborting")
raise RuntimeError("Cannot prepare diffractometer for collection")

try:
self.log.debug("############# #COLLECT# Opening detector cover")
self.diffr.detector_cover_open(wait=True)
HWR.beamline.diffractometer.detector_cover_open(wait=True)
self.log.debug(
"############ #COLLECT# detector cover is now open. Wait 2 more seconds"
)
Expand Down Expand Up @@ -361,14 +342,11 @@ def data_collection_hook(self):
+ "======================================="
)

overlap = osc_pars["overlap"]
angle_inc = 90.0
detector.prepare_characterisation(
HWR.beamline.detector.prepare_characterisation(
exp_time, nframes, angle_inc, filepath
)
else:
# AG: Create rotational_001, etc the same way as for CC in case of characterisation

# Filepath to work with presenterd
filepath = os.path.join(
basepath,
Expand All @@ -394,10 +372,12 @@ def data_collection_hook(self):
+ "======================================="
)

detector.prepare_std_collection(exp_time, nframes, filepath)
HWR.beamline.detector.prepare_std_collection(
exp_time, nframes, filepath
)

self.log.debug("#COLLECT# Starting detector")
detector.start_acquisition()
HWR.beamline.detector.start_acquisition()

if collection_type == "Characterization":
print("STARTING CHARACTERISATION")
Expand Down Expand Up @@ -464,8 +444,6 @@ def collect_characterisation(
:param exp_time: The `exp_time` parameter represents the exposure time for each image
"""

diffr = HWR.beamline.diffractometer

self.log.debug(
"#COLLECT# Running OMEGA through the characteristation acquisition"
)
Expand All @@ -476,16 +454,10 @@ def collect_characterisation(
print("collecting image %s" % img_no)
start_at = start_angle + angle_inc * img_no
stop_angle = start_at + img_range * 1.0
# print("======= CHARACTERISATION Adding angle and range to the header...")
# Add start angle to the header
# detector = HWR.beamline.detector
# detector.set_eiger_start_angle(start_at)

# Add angle increment to the header
# detector.set_eiger_angle_increment(angle_inc)

print("collecting image %s, angle %f" % (img_no, start_at))

# Keep it here for now. It is not clear if it is needed.
if start_at >= stop_angle:
init_pos = start_at # - self.acq_speed * self.turnback_time
# init_pos = start_at - 1.5
Expand All @@ -495,19 +467,6 @@ def collect_characterisation(

# self.omega_mv(init_pos, self.default_speed)
self.collect_std_collection(start_at, stop_angle)

# This part goes to standard collection. Otherwise it produces phantom openings.
# diffr.set_omega_velocity(self.default_speed)
# self.acq_window_off_cmd()
# self.acq_off_cmd()
self.log.debug(
"======= collect_characterisation Waiting ======================================="
)

# This part goes to standard collection. Otherwise it produces phantom openings.
# diffr.set_omega_velocity(self.default_speed)
# self.acq_window_off_cmd()
# self.acq_off_cmd()
self.log.debug(
"======= collect_characterisation Waiting ======================================="
)
Expand Down Expand Up @@ -546,18 +505,16 @@ def acquisition_cleanup(self):
detector cover, and stopping the acquisition.
"""
try:
diffr = HWR.beamline.diffractometer
detector = HWR.beamline.detector
detector.stop_acquisition()
diffr.wait_omega()
HWR.beamline.detector.stop_acquisition()
HWR.beamline.diffractometer.wait_omega()
# =================
# It is probably already finished in a standard collection.
self.acq_off_cmd()
self.acq_window_off_cmd()
# ==================
diffr.set_omega_velocity(self.default_speed)
HWR.beamline.diffractometer.set_omega_velocity(self.default_speed)
self.log.debug("#COLLECT# Closing detector cover")
diffr.detector_cover_close(wait=True)
HWR.beamline.diffractometer.detector_cover_close(wait=True)

# Move omega to 0 at the end
self.omega_mv(0, self.default_speed)
Expand Down Expand Up @@ -620,7 +577,8 @@ def add_h5_info(self, h5file):
self.get_filter_transmission(),
)

# # Set attributes for certain nodes
# Keep it here as it is not clear if it is needed.
# It was used in CC to fix the issue with the data processing
# h5fd["entry/sample/transformations/omega"].attrs["vector"] = [
# 1.0,
# 0.0,
Expand All @@ -643,7 +601,7 @@ def add_h5_info(self, h5file):
for node in unwanted_nodes:
if node in h5fd:
del h5fd[node]
except Exception as err_msg:
except RuntimeWarning as err_msg:
self.log.debug(f"Error while adding info to HDF5 file: {str(err_msg)}")
self.log.debug(traceback.format_exc())

Expand Down Expand Up @@ -816,8 +774,9 @@ def trigger_auto_processing(self, process_event=None, frame_number=None):
open(datasets_file, "a").write(
mosflm_path_local.split("/gpfs/current/processed/")[1] + "\n"
)
except:
print(sys.exc_info())
except RuntimeWarning as err_msg:
self.log.debug("Cannot write to datasets.txt")
self.log.debug(sys.exc_info(), err_msg)

# create call
ssh = btHelper.get_ssh_command()
Expand Down Expand Up @@ -859,7 +818,7 @@ def trigger_auto_processing(self, process_event=None, frame_number=None):
else:
if collection_type == "OSC":
self.log.debug(
"==== AUTOPROCESSING STANDARD PROCESSING IN PROGRESS =========="
"==== AUTOPROCESSING STANDARD PROCESSING IS IN PROGRESS =========="
)

try:
Expand Down Expand Up @@ -951,16 +910,18 @@ def trigger_auto_processing(self, process_event=None, frame_number=None):
)

def diffractometer_prepare_collection(self):
diffr = HWR.beamline.diffractometer

self.log.debug("#COLLECT# preparing collection ")
if not diffr.is_collect_phase():
if not HWR.beamline.diffractometer.is_collect_phase():
self.log.debug("#COLLECT# going to collect phase")
diffr.goto_collect_phase(wait=True)
HWR.beamline.diffractometer.goto_collect_phase(wait=True)

self.log.debug("#COLLECT# now in collect phase: %s" % diffr.is_collect_phase())
self.log.debug(
"#COLLECT# now in collect phase: %s"
% HWR.beamline.diffractometer.is_collect_phase()
)

return diffr.is_collect_phase()
return HWR.beamline.diffractometer.is_collect_phase()

def prepare_std_collection(self, start_angle, img_range):
"""
Expand All @@ -977,16 +938,12 @@ def prepare_std_collection(self, start_angle, img_range):
# Add start angle to the header
osc_pars = self.current_dc_parameters["oscillation_sequence"][0]
start_angle = osc_pars["start"]

detector = HWR.beamline.detector
detector.set_eiger_start_angle(start_angle)
HWR.beamline.detector.set_eiger_start_angle(start_angle)

# Add angle increment to the header
osc_pars = self.current_dc_parameters["oscillation_sequence"][0]
img_range = osc_pars["range"]
detector.set_eiger_angle_increment(img_range)

return True
HWR.beamline.detector.set_eiger_angle_increment(img_range)

def omega_mv(self, target, speed):
"""
Expand All @@ -997,9 +954,9 @@ def omega_mv(self, target, speed):
motor to move to.
:param speed: The speed parameter is the desired velocity at which the omega motor should move
"""
self.diffr.set_omega_velocity(speed)
self.diffr.move_omega(target)
self.diffr.wait_omega()
HWR.beamline.diffractometer.set_omega_velocity(speed)
HWR.beamline.diffractometer.move_omega(target)
HWR.beamline.diffractometer.wait_omega()

def prepare_characterization(self):
"""
Expand All @@ -1012,16 +969,12 @@ def prepare_characterization(self):
# Add start angle to the header
osc_pars = self.current_dc_parameters["oscillation_sequence"][0]
start_angle = osc_pars["start"]

detector = HWR.beamline.detector
detector.set_eiger_start_angle(start_angle)
HWR.beamline.detector.set_eiger_start_angle(start_angle)

# Add angle increment to the header
osc_pars = self.current_dc_parameters["oscillation_sequence"][0]
img_range = osc_pars["range"]
detector.set_eiger_angle_increment(img_range)

return True
HWR.beamline.detector.set_eiger_angle_increment(img_range)

def get_relative_path(self, path1, path2):
"""
Expand Down

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