284 lines
10 KiB
Python
284 lines
10 KiB
Python
import datetime
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import io
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import os
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from typing import List, Optional
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import aareDBclient
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import cv2
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import numpy as np
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import requests
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from aareDBclient import (
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SetTellPosition,
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SampleEventCreate,
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SetTellPositionRequest,
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RotationParameters,
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GridScanParameters,
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Detector as DetectorParameters,
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BeamlineParameters,
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ExperimentParametersCreate)
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from aaredaqlib.diffraction_geometry import DiffractionGeometry
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from aaredaqlib.models import (
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SampleShortInfo,
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PuckLoadedInfo,
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DewarAddress,
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SampleShortInfoList,
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DAQStatusModel,
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)
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from aaredaqlib.beamline import MXBeamline
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from aaredaqlib.raster_grid import RasterGridRequest, CompletedRasterGrid
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from aaredaqlib.rotation_scan import RotationScanRequest
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from aaredaqlib.sample_geometry import SampleGeometryModel
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class AareWrapper:
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def __init__(
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self,
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bl: MXBeamline,
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host: str = "https://mx-db-01.psi.ch/dispatcher",
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):
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configuration = aareDBclient.Configuration(host=host)
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configuration.verify_ssl = False # Disable SSL verification
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self.client = aareDBclient.ApiClient(configuration)
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self.client.default_headers["X-Shared-Password"] = os.getenv("AAREDB_SHARED_PASSWORD")
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self.__host = host
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self.__tell_api = aareDBclient.TellsRunnerApi(self.client)
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self.__sample_api = aareDBclient.SamplesRunnerApi(self.client)
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self.__proc_api = aareDBclient.ProcessingsRunnerApi(self.client)
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self.__bl = bl
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def set_pucks_beamline(self, input_list: List[PuckLoadedInfo]):
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o = []
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for i in input_list:
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t = SetTellPosition(
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puck_name=i.puck_name,
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segment=i.location.segment,
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puck_in_segment=i.location.pos,
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)
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o.append(t)
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payload = SetTellPositionRequest(pucks = o, tell=self.__bl.value.upper())
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ret = self.__tell_api.set_tell_positions(
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set_tell_position_request=payload,
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)
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print(ret)
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def get_sample_info(self) -> SampleShortInfoList:
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sample_list = (
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self.__tell_api.get_pucks_with_tell_position(tell=self.__bl.value.upper())
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)
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ret = []
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for p in sample_list:
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for s in p.samples:
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dewar_address = None
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if p.tell_position is not None and len(p.tell_position) == 2:
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dewar_address = DewarAddress(
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segment=p.tell_position[0], pos=p.tell_position[1]
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)
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ret.append(
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SampleShortInfo(
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db_id=s.id,
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puck_name=p.puck_name,
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dewar_name="Unknown" if p.dewar_name is None else p.dewar_name,
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sample_name=s.sample_name,
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user=p.pgroup,
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pin=s.position,
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location=dewar_address,
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priority=1.0 if s.priority is None else s.priority,
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comment=s.comments,
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mount_count=s.mount_count or 0
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)
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)
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return SampleShortInfoList(s=ret)
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def sample_mounted(self, s: Optional[SampleShortInfo]):
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if s is not None:
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try:
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self.__sample_api.create_sample_event(
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sample_id=s.db_id,
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sample_event_create=SampleEventCreate(event_type="Mounted"),
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)
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except Exception as e:
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print(e)
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def sample_unmounted(self, s: Optional[SampleShortInfo]):
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if s is not None:
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try:
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self.__sample_api.create_sample_event(
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sample_id=s.db_id,
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sample_event_create=SampleEventCreate(event_type="Unmounted"),
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)
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except Exception as e:
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print(e)
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def sample_centered(self, s: Optional[SampleShortInfo]):
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if s is not None:
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try:
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self.__sample_api.create_sample_event(
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sample_id=s.db_id,
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sample_event_create=SampleEventCreate(event_type="Centered"),
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)
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except Exception as e:
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print(e)
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def sample_collected(self, s: Optional[SampleShortInfo]):
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if s is None:
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return
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try:
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self.__sample_api.create_sample_event(
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sample_id=s.db_id,
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sample_event_create=SampleEventCreate(event_type="Collected"),
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)
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except Exception as e:
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print(e)
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def upload_image(self, sample_id: int, filename: str, bgr_image: np.ndarray):
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_, buffer = cv2.imencode('.jpg', bgr_image)
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jpeg_bytes = io.BytesIO(buffer)
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url = f"{self.__host}/samples/{sample_id}/upload-images"
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headers = {
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"accept": "application/json"
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}
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response = requests.post(url,
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files={'uploaded_file': (filename + ".jpg", jpeg_bytes, "image/jpeg")},
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verify=False, headers=headers)
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print(response.status_code)
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def create_rotation_run(self, s: Optional[SampleShortInfo], r:RotationScanRequest, d:DAQStatusModel, sg:SampleGeometryModel):
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if s is None:
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return
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try:
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rotation = RotationParameters(
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omegaStart_deg=r.start_omega_deg,
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omegaStep=r.incr_omega_deg,
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phi=r.start.phi_deg,
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chi=r.start.chi_deg,
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numberOfImages=r.steps,
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exposureTime_s=r.exp_time_s,
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)
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detector_data = DetectorParameters(
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manufacturer="DECTRIS",
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model=d.diffraction.detector_description,
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type="photon-counting",
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serialNumber=d.detector_serial_number,
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detectorDistance_mm=r.dtz,
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beamCenterX_px=d.diffraction.beam_center_pxl[0],
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beamCenterY_px=d.diffraction.beam_center_pxl[1],
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pixelSizeX_um=d.diffraction.pixel_size_mm * 1000,
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pixelSizeY_um=d.diffraction.pixel_size_mm * 1000,
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)
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beamline_params = BeamlineParameters(
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synchrotron="Swiss Light Source",
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beamline=d.bl.name,
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detector=detector_data,
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energy_keV=d.diffraction.energy_keV,
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wavelength_Ang=d.diffraction.wavelength_angstrom,
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ringCurrent_mA=d.bl.ring_current_mA,
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ringMode="Beamline Development",
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monochromator="Si111",
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transmission=r.transmission,
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focusingOptic="Kirkpatrick-Baez",
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beamlineFluxAtSample_ph_s=d.flux_ph_s,
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beamSizeWidth=sg.beam_size_mm * 100,
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beamSizeHeight=sg.beam_size_mm * 100,
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cryojetTemperature_K=d.bl.cryojet_K,
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rotation=rotation
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)
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experiment_params_payload = ExperimentParametersCreate(
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type="standard",
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beamline_parameters=beamline_params,
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sample_id=s.db_id
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)
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response = self.__sample_api.create_experiment_parameters_for_sample(
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sample_id=s.db_id,
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experiment_parameters_create=experiment_params_payload
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)
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print("Experiment parameters created:", response)
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except Exception as e:
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print(e)
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def create_gridscan_run(self, s: Optional[SampleShortInfo], r:RasterGridRequest, d:DAQStatusModel, sg:SampleGeometryModel):
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if s is None:
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return
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try:
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gridscan = GridScanParameters(
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#xStart=90.0,
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xStep=0.1,
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#yStart=0.0,
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yStep= 0.1,
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x_col=r.n_x,
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y_row=r.n_y,
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omegaStart_deg=r.omega_deg,
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numberOfImages=r.get_image_number,
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exposureTime_s=r.exp_time_s,
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)
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detector_data = DetectorParameters(
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manufacturer="DECTRIS",
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model=d.diffraction.detector_description,
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type="photon-counting",
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serialNumber=d.detector_serial_number,
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detectorDistance_mm=r.dtz,
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beamCenterX_px=d.diffraction.beam_center_pxl[0],
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beamCenterY_px=d.diffraction.beam_center_pxl[1],
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pixelSizeX_um=d.diffraction.pixel_size_mm * 1000,
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pixelSizeY_um=d.diffraction.pixel_size_mm * 1000,
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)
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beamline_params = BeamlineParameters(
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synchrotron="Swiss Light Source",
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beamline=d.bl.name,
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detector=detector_data,
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energy_keV=d.diffraction.energy_keV,
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wavelength_Ang=d.diffraction.wavelength_angstrom,
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ringCurrent_mA=d.bl.ring_current_mA,
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ringMode="Beamline Development",
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monochromator="Si111",
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transmission=r.transmission,
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focusingOptic="Kirkpatrick-Baez",
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beamlineFluxAtSample_ph_s=d.flux_ph_s,
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beamSizeWidth=sg.beam_size_mm * 100,
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beamSizeHeight=sg.beam_size_mm * 100,
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cryojetTemperature_K=d.bl.cryojet_K,
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gridScan=gridscan
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)
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experiment_params_payload = ExperimentParametersCreate(
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type="standard",
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beamline_parameters=beamline_params,
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sample_id=s.db_id
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)
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response = self.__sample_api.create_experiment_parameters_for_sample(
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sample_id=s.db_id,
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experiment_parameters_create=experiment_params_payload
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)
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print("Experiment parameters created:", response)
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except Exception as e:
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print(e)
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def confirm_image_written(self, s: Optional[SampleShortInfo], r:RotationScanRequest):
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if s is None:
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return
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try:
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response = self.__sample_api.update_dataset_for_experiment_run(
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filepath=r.file_prefix, #need to check if this is correct
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status="written",
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written_at=datetime.datetime.now().isoformat(),
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)
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print("Experiment run updated:", response)
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except Exception as e:
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print(e)
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#def send_gridscan_result(self, s: Optional[SampleShortInfo], c: CompletedRasterGrid):
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# if s is None:
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# return
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#
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# try:
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# response = self.__proc_api.create_result(
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#
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# ) |