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first adjustments towards scanning

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This commit is contained in:
Holler Mirko
2024-10-01 16:32:52 +02:00
committed by wakonig_k
parent d3c86b07a0
commit 86e71ca255
4 changed files with 46 additions and 67 deletions
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12
csaxs_bec/bec_ipython_client/plugins/flomni/flomni.py
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@@ -424,18 +424,18 @@ class FlomniSampleTransferMixin:
def show_signal_strength_interferometer(self):
dev.rtx.controller.show_signal_strength_interferometer()
def rt_feedback_disable(self):
def feedback_disable(self):
self.device_manager.devices.rtx.controller.feedback_disable()
def rt_feedback_enable_with_reset(self):
def 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):
def feedback_enable_without_reset(self):
self.device_manager.devices.rtx.controller.feedback_enable_without_reset()
self.rt_feedback_status()
def rt_feedback_status(self):
def 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.")
@@ -455,7 +455,7 @@ class FlomniSampleTransferMixin:
umv(dev.fsamroy, 0)
self.rt_feedback_disable()
self.feedback_disable()
self.ensure_fheater_up()
@@ -1142,7 +1142,7 @@ class Flomni(
fsamx_in = self._get_user_param_safe(dev.fsamx, "in")
if np.isclose(fsamx_in, dev.fsamx.readback.get(), 0.5):
print("Stopping alignment. Returning to fsamx in position.")
self.rt_feedback_disable()
self.feedback_disable()
umv(dev.fsamx, fsamx_in)
raise exc

14
csaxs_bec/bec_ipython_client/plugins/flomni/x_ray_eye_align.py
View File

@@ -100,7 +100,7 @@ class XrayEyeAlign:
self.flomni.laser_tracker_on()
self.flomni.rt_feedback_enable_with_reset()
self.flomni.feedback_enable_with_reset()
# disable movement buttons
self.movement_buttons_enabled = False
@@ -109,7 +109,7 @@ class XrayEyeAlign:
epics_put("XOMNYI-XEYE-SAMPLENAME:0.DESC", sample_name)
# this makes sure we are in a defined state
self.flomni.rt_feedback_disable()
self.flomni.feedback_disable()
epics_put("XOMNYI-XEYE-PIXELSIZE:0", self.PIXEL_CALIBRATION)
@@ -143,13 +143,13 @@ class XrayEyeAlign:
self.movement_buttons_enabled = False
epics_put("XOMNYI-XEYE-SUBMIT:0", -1) # disable submit button
self.flomni.rt_feedback_disable()
self.flomni.feedback_disable()
fsamx_in = self.flomni._get_user_param_safe("fsamx", "in")
umv(dev.fsamx, fsamx_in)
self.flomni.foptics_out()
self.flomni.rt_feedback_disable()
self.flomni.feedback_disable()
umv(dev.fsamx, fsamx_in - 0.25)
self.update_frame()
@@ -160,7 +160,7 @@ class XrayEyeAlign:
umv(dev.fsamx, fsamx_in)
time.sleep(0.5)
self.flomni.rt_feedback_enable_with_reset()
self.flomni.feedback_enable_with_reset()
self.update_frame()
self.send_message("Adjust sample height and submit center")
@@ -205,11 +205,11 @@ class XrayEyeAlign:
# allow movements, store movements to calculate center
_xrayeyalignmvy = epics_get("XOMNYI-XEYE-MVY:0")
if _xrayeyalignmvy != 0:
self.flomni.rt_feedback_disable()
self.flomni.feedback_disable()
umvr(dev.fsamy, _xrayeyalignmvy / 1000)
time.sleep(2)
epics_put("XOMNYI-XEYE-MVY:0", 0)
self.flomni.rt_feedback_enable_with_reset()
self.flomni.feedback_enable_with_reset()
self.update_frame()
time.sleep(0.2)

85
csaxs_bec/bec_ipython_client/plugins/omny/omny.py
View File

@@ -552,11 +552,11 @@ class OMNY(
try:
self.align.align()
except KeyboardInterrupt as exc:
fsamx_in = self._get_user_param_safe(dev.fsamx, "in")
if np.isclose(fsamx_in, dev.fsamx.readback.get(), 0.5):
self.OMNYTools.printgreen("Stopping alignment. Returning to fsamx in position.")
self.rt_feedback_disable()
umv(dev.fsamx, fsamx_in)
osamx_in = self._get_user_param_safe(dev.osamx, "in")
if np.isclose(osamx_in, dev.osamx.readback.get(), 0.5):
self.OMNYTools.printgreen("Stopping alignment. Returning to osamx in position.")
self.feedback_disable()
umv(dev.osamx, osamx_in)
raise exc
def xrayeye_update_frame(self):
@@ -565,10 +565,10 @@ class OMNY(
def xrayeye_alignment_start(self):
self.start_x_ray_eye_alignment()
def drive_axis_to_limit(self, device, direction):
axis_id = device._config["deviceConfig"].get("axis_Id")
axis_id_numeric = self.axis_id_to_numeric(axis_id)
device.controller.drive_axis_to_limit(axis_id_numeric, direction)
# def drive_axis_to_limit(self, device, direction):
# axis_id = device._config["deviceConfig"].get("axis_Id")
# axis_id_numeric = self.axis_id_to_numeric(axis_id)
# device.controller.drive_axis_to_limit(axis_id_numeric, direction)
def axis_id_to_numeric(self, axis_id) -> int:
return ord(axis_id.lower()) - 97
@@ -692,7 +692,7 @@ class OMNY(
@tomo_type.setter
def tomo_type(self, val: float):
if val == 1:
# equally spaced tomography with 8 sub tomograms
# equally spaced tomography with 2 sub tomograms
self.client.set_global_var("tomo_type", val)
elif val == 2:
# golden ratio tomography (sorted bunches)
@@ -853,7 +853,7 @@ class OMNY(
successful = False
error_caught = False
if 0 <= angle < 180.05:
print(f"Starting flOMNI scan for angle {angle}")
print(f"Starting OMNY scan for angle {angle}")
while not successful:
self._start_beam_check()
try:
@@ -879,7 +879,7 @@ class OMNY(
print("Alignment scan finished. Please run SPEC_ptycho_align and load the new fit.")
umv(dev.fsamroy, 0)
umv(dev.osamroy, 0)
def _write_subtomo_to_scilog(self, subtomo_number):
dev = builtins.__dict__.get("dev")
@@ -900,36 +900,13 @@ class OMNY(
subtomo_number (int): The sub tomogram number.
start_angle (float, optional): The start angle of the scan. Defaults to None.
"""
# dev = builtins.__dict__.get("dev")
# bec = builtins.__dict__.get("bec")
# if self.tomo_id > 0:
# tags = ["BEC_subtomo", self.sample_name, f"tomo_id_{self.tomo_id}"]
# else:
# tags = ["BEC_subtomo", self.sample_name]
# self.write_to_scilog(
# f"Starting subtomo: {subtomo_number}. First scan number: {bec.queue.next_scan_number}.",
# tags,
# )
self._write_subtomo_to_scilog(subtomo_number)
if start_angle is None:
if subtomo_number == 1:
start_angle = 0
elif subtomo_number == 2:
start_angle = self.tomo_angle_stepsize / 8.0 * 4
elif subtomo_number == 3:
start_angle = self.tomo_angle_stepsize / 8.0 * 2
elif subtomo_number == 4:
start_angle = self.tomo_angle_stepsize / 8.0 * 6
elif subtomo_number == 5:
start_angle = self.tomo_angle_stepsize / 8.0 * 1
elif subtomo_number == 6:
start_angle = self.tomo_angle_stepsize / 8.0 * 5
elif subtomo_number == 7:
start_angle = self.tomo_angle_stepsize / 8.0 * 3
elif subtomo_number == 8:
start_angle = self.tomo_angle_stepsize / 8.0 * 7
start_angle = self.tomo_angle_stepsize / 2.0
# _tomo_shift_angles (potential global variable)
_tomo_shift_angles = 0
@@ -940,7 +917,7 @@ class OMNY(
num=int(180 / self.tomo_angle_stepsize) + 1,
endpoint=True,
)
# reverse even sub-tomograms
# reverse even sub-tomogram
if not (subtomo_number % 2):
angles = np.flip(angles)
for angle in angles:
@@ -950,7 +927,7 @@ class OMNY(
self.progress["projection"] = (subtomo_number - 1) * self.progress[
"subtomo_total_projections"
] + self.progress["subtomo_projection"]
self.progress["total_projections"] = 180 / self.tomo_angle_stepsize * 8
self.progress["total_projections"] = 180 / self.tomo_angle_stepsize * 2
self.progress["angle"] = angle
self._tomo_scan_at_angle(angle, subtomo_number)
@@ -958,7 +935,7 @@ class OMNY(
successful = False
error_caught = False
if 0 <= angle < 180.05:
print(f"Starting flOMNI scan for angle {angle} in subtomo {subtomo_number}")
print(f"Starting OMNY scan for angle {angle} in subtomo {subtomo_number}")
self._print_progress()
while not successful:
self._start_beam_check()
@@ -1011,7 +988,7 @@ class OMNY(
str(datetime.date.today()),
bec.active_account.decode(),
bec.queue.next_scan_number,
"flomni",
"OMNY",
"test additional info",
"BEC",
)
@@ -1021,9 +998,9 @@ class OMNY(
with scans.dataset_id_on_hold:
if self.tomo_type == 1:
# 8 equally spaced sub-tomograms
# 2 equally spaced sub-tomograms
self.progress["tomo_type"] = "Equally spaced sub-tomograms"
for ii in range(subtomo_start, 9):
for ii in range(subtomo_start, 3):
self.sub_tomo_scan(ii, start_angle=start_angle)
start_angle = None
@@ -1073,6 +1050,7 @@ class OMNY(
f"Golden ratio tomography stopped automatically after the requested {self.golden_max_number_of_projections} projections"
)
break
elif self.tomo_type == 3:
# Equally spaced tomography, golden ratio starting angle
previous_subtomo_number = -1
@@ -1144,9 +1122,9 @@ class OMNY(
return tomo_number
def _at_each_angle(self, angle: float) -> None:
if "flomni_at_each_angle" in builtins.__dict__:
if "omny_at_each_angle" in builtins.__dict__:
# pylint: disable=undefined-variable
flomni_at_each_angle(self, angle)
omny_at_each_angle(self, angle)
return
self.tomo_scan_projection(angle)
@@ -1253,18 +1231,18 @@ class OMNY(
cenx = sum_offset_x + stitch_x * (self.fovx - self.tomo_stitch_overlap)
ceny = sum_offset_y + stitch_y * (self.fovy - self.tomo_stitch_overlap)
logger.info(
f"scans.flomni_fermat_scan(fovx={self.fovx}, fovy={self.fovy},"
f"scans.omny_fermat_scan(fovx={self.fovx}, fovy={self.fovy},"
f" step={self.tomo_shellstep}, cenx={cenx}, ceny={ceny},"
f" zshift={sum_offset_z}, angle={angle},"
f" exp_time={self.tomo_countingtime}, corridor_size={corridor_size})"
)
log_message = (
f"{str(datetime.datetime.now())}: flomni scan projection at angle {angle}, scan"
f"{str(datetime.datetime.now())}: omny scan projection at angle {angle}, scan"
f" number {bec.queue.next_scan_number}.\n"
)
self.write_to_spec_log(log_message)
# self.write_to_scilog(log_message, ["BEC_scans", self.sample_name])
scans.flomni_fermat_scan(
scans.omny_fermat_scan(
fovx=self.fovx,
fovy=self.fovy,
step=self.tomo_shellstep,
@@ -1288,8 +1266,8 @@ class OMNY(
print(f" _manual_shift_y <mm> = {self.manual_shift_y}")
print("")
if self.tomo_type == 1:
print("\x1b[1mTomo type 1:\x1b[0m 8 equally spaced sub-tomograms")
print(f"Total number of projections: {180/self.tomo_angle_stepsize*8}")
print("\x1b[1mTomo type 1:\x1b[0m 2 equally spaced sub-tomograms")
print(f"Total number of projections: {180/self.tomo_angle_stepsize*2}")
print(f"Angular step within sub-tomogram: {self.tomo_angle_stepsize} degrees")
if self.tomo_type == 2:
print("\x1b[1mTomo type 2:\x1b[0m Golden ratio tomography")
@@ -1332,17 +1310,17 @@ class OMNY(
)
print("Tomography type:")
print(" 1: 8 equally spaced sub-tomograms")
print(" 1: 2 equally spaced sub-tomograms")
print(" 2: Golden ratio tomography")
print(" 3: Equally spaced tomography, golden ratio starting angle")
self.tomo_type = self._get_val("Tomography type", self.tomo_type, int)
if self.tomo_type == 1:
tomo_numberofprojections = self._get_val(
"Total number of projections", 180 / self.tomo_angle_stepsize * 8, int
"Total number of projections", 180 / self.tomo_angle_stepsize * 2, int
)
print(f"The angular step will be {180/tomo_numberofprojections}")
self.tomo_angle_stepsize = 180 / tomo_numberofprojections * 8
self.tomo_angle_stepsize = 180 / tomo_numberofprojections * 2
print(f"The angular step in a subtomogram it will be {self.tomo_angle_stepsize}")
if self.tomo_type == 2:
@@ -1399,7 +1377,7 @@ class OMNY(
print("failed to enable rt")
def write_pdf_report(self):
"""create and write the pdf report with the current flomni settings"""
"""create and write the pdf report with the current OMNY settings"""
dev = builtins.__dict__.get("dev")
# header = ""
header = (
@@ -1435,6 +1413,7 @@ class OMNY(
f"{'Stitching:':<{padding}}{stitching:>{padding}}\n",
f"{'Number of individual sub-tomograms:':<{padding}}{8:>{padding}}\n",
f"{'Angular step within sub-tomogram:':<{padding}}{self.tomo_angle_stepsize:>{padding}.2f}\n",
"Add current temperature and pressure status"
]
content = "".join(content)
user_target = os.path.expanduser(f"~/Data10/documentation/tomo_scan_ID_{self.tomo_id}.pdf")

2
csaxs_bec/device_configs/omny_config.yaml
View File

@@ -283,7 +283,7 @@ osamx:
readOnly: false
readoutPriority: baseline
userParameter:
in: 0
in: -0.1
osamz:
description: Sample Z
deviceClass: csaxs_bec.devices.omny.galil.ogalil_ophyd.OMNYGalilMotor