usov_i-org/bec
1
0
Fork 0
mirror of https://github.com/ivan-usov-org/bec.git synced 2025-04-22 02:20:02 +02:00
Code Issues Actions Packages Projects Releases Wiki Activity

flomni-improvements

Browse Source
This commit is contained in:
Holler Mirko 2024-03-21 10:12:46 +01:00 committed by wakonig_k
parent 990738431e
commit cf90614bb2
2 changed files with 77 additions and 22 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

96
bec_client/bec_client/plugins/flomni/flomni.py
View File

@ -344,6 +344,9 @@ class FlomniSampleTransferMixin:
if not curtain_is_triggered:
raise FlomniError("Fosaz did not reach light curtain")
def move_fheater_up(self):
self.ensure_fheater_up()
def ensure_fheater_up(self):
axis_id = dev.fheater._config["deviceConfig"].get("axis_Id")
axis_id_numeric = self.axis_id_to_numeric(axis_id)
@ -423,17 +426,19 @@ class FlomniSampleTransferMixin:
def rt_feedback_enable_with_reset(self):
self.device_manager.devices.rtx.controller.feedback_enable_with_reset()
self.rt_feedback_status()
def rt_feedback_enable_without_reset(self):
self.device_manager.devices.rtx.controller.feedback_enable_without_reset()
self.rt_feedback_status()
def rt_feedback_status(self):
feedback_status = self.device_manager.devices.rtx.controller.feedback_is_running()
if feedback_status == True:
print("The rt feedback is \x1b[92mrunning\x1b[0m.")
else:
print("The rt feedback is \x1b[91mNOT\x1b[0m running.")
def rt_feedback_status(self):
self
def lights_off(self):
self.device_manager.devices.fsamx.controller.lights_off()
@ -1002,7 +1007,6 @@ class FlomniAlignmentMixin:
with open(correction_file, "r") as f:
num_elements = f.readline()
int_num_elements = int(num_elements.split(" ")[2])
print(int_num_elements)
corr_pos = []
corr_angle = []
for j in range(int_num_elements * 2):
@ -1013,6 +1017,9 @@ class FlomniAlignmentMixin:
corr_pos.append(float(value) / 1000)
elif name == "corr_angle":
corr_angle.append(float(value))
print(
f"Loading default mirror correction from file {correction_file} containing {int_num_elements} elements."
)
return corr_pos, corr_angle
def read_additional_correction_y(self, correction_file: str):
@ -1067,9 +1074,9 @@ class Flomni(
super().__init__()
self.client = client
self.device_manager = client.device_manager
self.check_shutter = True
self.check_light_available = True
self.check_fofb = True
self.check_shutter = False
self.check_light_available = False
self.check_fofb = False
self._check_msgs = []
self.tomo_id = -1
self.special_angles = []
@ -1309,6 +1316,56 @@ class Flomni(
except Exception:
logger.warning("Failed to write to scilog.")
def tomo_alignment_scan(self):
"""
Performs a tomogram alignment scan.
"""
if self.get_alignment_offset(0) == (0, 0, 0):
print("It appears that the xrayeye alignemtn was not performend or loaded. Aborting.")
return
dev = builtins.__dict__.get("dev")
bec = builtins.__dict__.get("bec")
tags = ["alignment", self.sample_name]
self.write_to_scilog(
f"Starting alignment scan. First scan number: {bec.queue.next_scan_number}.", tags
)
start_angle = 0
angle_end = start_angle + 180
for angle in np.linspace(start_angle, angle_end, num=int(180 / 45) + 1, endpoint=True):
successful = False
error_caught = False
if 0 <= angle < 180.05:
print(f"Starting flOMNI scan for angle {angle}")
while not successful:
self._start_beam_check()
try:
start_scan_number = bec.queue.next_scan_number
self.tomo_scan_projection(angle)
self.tomo_reconstruct()
error_caught = False
except AlarmBase as exc:
if exc.alarm_type == "TimeoutError":
bec.queue.request_queue_reset()
time.sleep(2)
error_caught = True
else:
raise exc
if self._was_beam_okay() and not error_caught:
successful = True
else:
self._wait_for_beamline_checks()
end_scan_number = bec.queue.next_scan_number
for scan_nr in range(start_scan_number, end_scan_number):
self._write_tomo_scan_number(scan_nr, angle, 0)
print("Alignment scan finished. Please run SPEC_ptycho_align and load the new fit.")
umv(dev.fsamroy, 0)
def sub_tomo_scan(self, subtomo_number, start_angle=None):
"""
Performs a sub tomogram scan.
@ -1458,7 +1515,7 @@ class Flomni(
with open(tomo_scan_numbers_file, "a+") as out_file:
# pylint: disable=undefined-variable
out_file.write(
f"{scan_number} {angle} {dev.lsamrot.read()['lsamrot']['value']:.3f} {self.tomo_id} {subtomo_number} {0} {'lamni'}\n"
f"{scan_number} {angle} {dev.fsamroy.read()['fsamroy']['value']:.3f} {self.tomo_id} {subtomo_number} {0} {self.sample_name}\n"
)
def tomo_scan_projection(self, angle: float):
@ -1551,17 +1608,18 @@ class Flomni(
def write_pdf_report(self):
"""create and write the pdf report with the current flomni settings"""
dev = builtins.__dict__.get("dev")
header = ""
# header = (
# " \n" * 3
# + " ::: ::: ::: ::: :::: ::: ::::::::::: \n"
# + " :+: :+: :+: :+:+: :+:+: :+:+: :+: :+: \n"
# + " +:+ +:+ +:+ +:+ +:+:+ +:+ :+:+:+ +:+ +:+ \n"
# + " +#+ +#++:++#++: +#+ +:+ +#+ +#+ +:+ +#+ +#+ \n"
# + " +#+ +#+ +#+ +#+ +#+ +#+ +#+#+# +#+ \n"
# + " #+# #+# #+# #+# #+# #+# #+#+# #+# \n"
# + " ########## ### ### ### ### ### #### ########### \n"
# )
# header = ""
header = (
" \n" * 3
+ " .d888 888 .d88888b. 888b d888 888b 888 8888888 \n"
+ ' d88P" 888 d88P" "Y88b 8888b d8888 8888b 888 888 \n'
+ " 888 888 888 888 88888b.d88888 88888b 888 888 \n"
+ " 888888 888 888 888 888Y88888P888 888Y88b 888 888 \n"
+ " 888 888 888 888 888 Y888P 888 888 Y88b888 888 \n"
+ " 888 888 888 888 888 Y8P 888 888 Y88888 888 \n"
+ ' 888 888 Y88b. .d88P 888 " 888 888 Y8888 888 \n'
+ ' 888 888 "Y88888P" 888 888 888 Y888 8888888 \n'
)
padding = 20
fovxy = f"{self.fovx:.2f}/{self.fovy:.2f}"
stitching = f"{self.stitch_x:.2f}/{self.stitch_y:.2f}"

3
bec_client/bec_client/plugins/flomni/x_ray_eye_align.py
View File

@ -33,9 +33,6 @@ class XrayEyeAlign:
self.flomni.reset_correction()
self.flomni.reset_tomo_alignment_fit()
def reset_xray_eye_correction(self):
self.client.delete_global_var("tomo_fit_xray_eye")
def _reset_init_values(self):
self.shift_xy = [0, 0]
self._xray_fov_xy = [0, 0]