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feat(flomni): scan status for tomography

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This commit is contained in:
Holler Mirko 2024-04-10 13:59:11 +02:00 committed by wakonig_k
parent 54b139f40c
commit eca3e64fac
1 changed files with 61 additions and 1 deletions
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62
bec_client/bec_client/plugins/flomni/flomni.py
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@ -1126,6 +1126,7 @@ class Flomni(
self.corr_angle_y = []
self.corr_pos_y_2 = []
self.corr_angle_y_2 = []
self.progress = {}
self.align = XrayEyeAlign(self.client, self)
def start_x_ray_eye_alignment(self):
@ -1518,6 +1519,14 @@ class Flomni(
if not (subtomo_number % 2):
angles = np.flip(angles)
for angle in angles:
self.progress["subtomo"] = subtomo_number
self.progress["subtomo_projection"] = angles.index(angle)
self.progress["subtomo_total_projections"] = 180 / self.tomo_angle_stepsize
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["angle"] = angle
self._tomo_scan_at_angle(angle, subtomo_number)
def _tomo_scan_at_angle(self, angle, subtomo_number):
@ -1525,6 +1534,7 @@ class Flomni(
error_caught = False
if 0 <= angle < 180.05:
print(f"Starting flOMNI scan for angle {angle} in subtomo {subtomo_number}")
self._print_progress()
while not successful:
self._start_beam_check()
if not self.special_angles:
@ -1562,8 +1572,13 @@ class Flomni(
bec = builtins.__dict__.get("bec")
scans = builtins.__dict__.get("scans")
self._current_special_angles = self.special_angles.copy()
# a new tomo scan was started
if (
(self.tomo_type == 1 and subtomo_start == 1 and start_angle is None)
or (self.tomo_type == 2 and projection_number == None)
or (self.tomo_type == 3 and projection_number == None)
):
if subtomo_start == 1 and start_angle is None:
# pylint: disable=undefined-variable
if bec.active_account != "":
self.tomo_id = self.add_sample_database(
@ -1578,9 +1593,11 @@ class Flomni(
self.write_pdf_report()
else:
self.tomo_id = 0
with scans.dataset_id_on_hold:
if self.tomo_type == 1:
# 8 equally spaced sub-tomograms
self.progress["tomo_type"] = "Equally spaced sub-tomograms"
for ii in range(subtomo_start, 9):
self.sub_tomo_scan(ii, start_angle=start_angle)
start_angle = None
@ -1603,6 +1620,24 @@ class Flomni(
):
self._tomo_scan_at_angle(0, subtomo_number)
previous_subtomo_number = subtomo_number
self.progress["tomo_type"] = "Golden ratio tomography"
self.progress["subtomo"] = subtomo_number
self.progress["projection"] = ii
self.progress["angle"] = angle
if self.golden_ratio_bunch_size > 0:
self.progress["subtomo_total_projections"] = self.golden_ratio_bunch_size
self.progress["subtomo_projection"] = (
ii - (subtomo_number - 1) * self.golden_ratio_bunch_size
)
else:
self.progress["subtomo_total_projections"] = 0
self.progress["subtomo_projection"] = 0
if self.golden_max_number_of_projections > 0:
self.progress["total_projections"] = self.golden_max_number_of_projections
else:
self.progress["total_projections"] = 0
self._tomo_scan_at_angle(angle, subtomo_number)
ii += 1
if (
@ -1633,6 +1668,22 @@ class Flomni(
):
self._tomo_scan_at_angle(0, subtomo_number)
previous_subtomo_number = subtomo_number
self.progress["tomo_type"] = (
"Equally spaced tomography, golden ratio starting angle"
)
self.progress["subtomo"] = subtomo_number
self.progress["projection"] = ii
self.progress["angle"] = angle
self.progress["subtomo_total_projections"] = 180 / self.tomo_angle_stepsize
self.progress["subtomo_projection"] = (
ii - (subtomo_number - 1) * self.progress["subtomo_total_projections"]
)
if self.golden_max_number_of_projections > 0:
self.progress["total_projections"] = self.golden_max_number_of_projections
else:
self.progress["total_projections"] = 0
self._tomo_scan_at_angle(angle, subtomo_number)
ii += 1
if (
@ -1646,6 +1697,15 @@ class Flomni(
else:
raise FlomniError("undefined tomo type")
def _print_progress(self):
print("\x1b[95mProgress report:")
print(f"Tomo type: ....................... {self.progress['tomo_type']}")
print(f"Projection: ...................... {self.progress['projection']}")
print(f"Total projections expected ....... {self.progress['total_projections']}")
print(f"Angle: ........................... {self.progress['angle']}")
print(f"Current subtomo: ................. {self.progress['subtomo']}")
print(f"Current projection within subtomo: {self.progress['subtomo_projection']}\x1b[0m")
def add_sample_database(
self, samplename, date, eaccount, scan_number, setup, sample_additional_info, user
):