diff --git a/csaxs_bec/bec_ipython_client/plugins/flomni/docs/FZP_30nm_Tomas_Abe_2026.pdf b/csaxs_bec/bec_ipython_client/plugins/flomni/docs/FZP_30nm_Tomas_Abe_2026.pdf new file mode 100644 index 0000000..29231ef Binary files /dev/null and b/csaxs_bec/bec_ipython_client/plugins/flomni/docs/FZP_30nm_Tomas_Abe_2026.pdf differ diff --git a/csaxs_bec/bec_ipython_client/plugins/flomni/flomni.py b/csaxs_bec/bec_ipython_client/plugins/flomni/flomni.py index 773d17f..86887cd 100644 --- a/csaxs_bec/bec_ipython_client/plugins/flomni/flomni.py +++ b/csaxs_bec/bec_ipython_client/plugins/flomni/flomni.py @@ -1664,7 +1664,7 @@ class Flomni( f"Number of alignment scans: {len(alignment_scan_numbers)}\n" f"Alignment scan numbers: {scan_list_str}\n" ) - print(scliog_content) + print(scilog_content) bec.messaging.scilog.new().add_text(scilog_content.replace("\n", "
")).add_tags("alignmentscan").send() def sub_tomo_scan(self, subtomo_number, start_angle=None): @@ -2120,7 +2120,7 @@ class Flomni( f" number {bec.queue.next_scan_number}.\n" ) - scans.flomni_fermat_scan( + scan_kwargs = dict( fovx=self.fovx, fovy=self.fovy, step=self.tomo_shellstep, @@ -2129,9 +2129,13 @@ class Flomni( zshift=sum_offset_z, angle=angle, exp_time=self.tomo_countingtime, - corridor_size=corridor_size, ) + if self.corridor_size > 0: + scan_kwargs["corridor_size"] = self.corridor_size + + scans.flomni_fermat_scan(**scan_kwargs) + self.tomo_reconstruct() diff --git a/csaxs_bec/bec_ipython_client/plugins/flomni/x_ray_eye_align.py b/csaxs_bec/bec_ipython_client/plugins/flomni/x_ray_eye_align.py index 70dea21..ec80ca6 100644 --- a/csaxs_bec/bec_ipython_client/plugins/flomni/x_ray_eye_align.py +++ b/csaxs_bec/bec_ipython_client/plugins/flomni/x_ray_eye_align.py @@ -28,7 +28,7 @@ if TYPE_CHECKING: class XrayEyeAlign: # pixel calibration, multiply to get mm - test_wo_movements = True + test_wo_movements = False PIXEL_CALIBRATION = 0.1 / 113 # .2 with binning def __init__(self, client, flomni: Flomni) -> None: @@ -257,7 +257,7 @@ class XrayEyeAlign: print("After that, run the fit in Matlab and load the new fit flomni.read_alignment_offset()") def write_output(self): - file = os.path.expanduser("~/Data10/specES1/internal/xrayeye_alignmentvalues") + file = os.path.expanduser("~/data/raw/logs/xrayeye_alignmentvalues") if not os.path.exists(file): os.makedirs(os.path.dirname(file), exist_ok=True)