Script execution
This commit is contained in:
gac-x03da
374
script/users/msft-constantinou_p/MultiRegionScan_msft_AllXPS.py
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374
script/users/msft-constantinou_p/MultiRegionScan_msft_AllXPS.py
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"""
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repeated xps scans with reference sample
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usage
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=====
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1. set the NUMBER_OF_ITERATIONS
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2. set the REFERENCE_POSITION and SAMPLE_POSITION
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3. set the REGION parameters
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troubleshooting
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===============
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if the script runs through very quickly without measuring anything:
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check that all position values include a decimal point!!!
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"""
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# dummy scan (time series)
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MOTORS = [dummy]
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# number of cycles (integer - not decimal point!)
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# (actual number of cycles is + 1)
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NUMBER_OF_CYCLES = 1
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POSITIONS = [1., 10., NUMBER_OF_CYCLES]
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SCAN = 'lscan'
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# seconds to wait between positioning command and triggering the detector
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LATENCY = 0.0
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# region setup
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#
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# for each region, define a python dictionary with the following items.
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# optional items can be left unspecified and will default to the indicated values.
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# for swept mode, include 'elo', 'ehi', 'estep', 'iter' values, but do not include 'efix'.
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# for fixed mode, include 'efix' value, but do not include 'elo', 'ehi', 'estep', 'iter'.
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#
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# 'name': user-specific name of the region (for graph title and RegionName attribute in data file)
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# 'elo': lower kinetic energy boundary of the spectrum
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# 'ehi': upper kinetic energy boundary of the spectrum
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# 'estep': energy step size
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# 'efix': center kinetic energy in fixed mode
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# 'epass': pass energy
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# 'ephot': photon energy (default: unchanged)
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# 'tstep': dwell time in seconds
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# 'iter': number of iterations/sweeps (default 1)
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# 'cis': True = constant initial state (photoemission line), False = constant final state (Auger peak), (default False)
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# 'slit': exit slit (default: unchanged)
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# 'position': 'reference' or 'sample'
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REFERENCE_POSITION = {'X': 3.40,'Y': 8.17, 'Z': 113.50, 'Theta': -9., 'Tilt': -2.0, 'Phi': -90.}
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SAMPLE_POSITION = {'X': 3.45,'Y': 3.00, 'Z': 113.50, 'Theta': -9., 'Tilt': -2.0, 'Phi': -90.}
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# DEFINE THE REGIONS
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# -- Region A @ 70 eV (G1 600)
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REGION_A1 = {'name': 'MoEF', 'ephot': 70., 'elo': 64., 'ehi':67., 'estep': 0.02, 'epass': 20., 'tstep': 2.0, 'iter': 1, 'cis': False, 'position': 'reference'}
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REGION_A2 = {'name': 'In4d', 'elo': 44., 'ehi':51., 'estep':0.02, 'epass': 20., 'tstep': 1.0, 'iter': 1, 'cis': False, 'position': 'sample'}
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REGION_A3 = {'name': 'As3d', 'elo': 21., 'ehi':27., 'estep':0.02, 'epass': 20., 'tstep': 1.0, 'iter': 1, 'cis': False, 'position': 'sample'}
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REGION_A4 = {'name': 'Survey', 'elo': 10., 'ehi':70., 'estep':0.10, 'epass': 20., 'tstep': 1.0, 'iter': 1, 'cis': False, 'position': 'sample'}
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# -- Region B @ 578 eV (G2 1200)
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REGION_B1 = {'name': 'MoEF', 'ephot': 578., 'elo': 572., 'ehi':575., 'estep': 0.02, 'epass': 20., 'tstep': 2.0, 'iter': 1, 'cis': False, 'position': 'reference'}
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REGION_B2 = {'name': 'In4d', 'elo': 551., 'ehi':559., 'estep':0.02, 'epass': 20., 'tstep': 0.5, 'iter': 1, 'cis': False, 'position': 'sample'}
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REGION_B3 = {'name': 'As3d', 'elo': 529., 'ehi':535., 'estep':0.02, 'epass': 20., 'tstep': 0.5, 'iter': 1, 'cis': False, 'position': 'sample'}
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REGION_B4 = {'name': 'In3d', 'elo': 118., 'ehi':133., 'estep':0.02, 'epass': 20., 'tstep': 0.1, 'iter': 1, 'cis': False, 'position': 'sample'}
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# -- Region C @ 1050 eV (G2 1200)
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REGION_C1 = {'name': 'MoEF', 'ephot': 1050., 'elo': 1045., 'ehi':1047, 'estep':0.02, 'epass': 20., 'tstep': 2.0, 'iter': 1, 'cis': False, 'position': 'reference'}
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REGION_C2 = {'name': 'In4d', 'elo': 1025., 'ehi':1031., 'estep':0.02, 'epass': 20., 'tstep': 0.5, 'iter': 1, 'cis': False, 'position': 'sample'}
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REGION_C3 = {'name': 'As3d', 'elo': 1002., 'ehi':1007., 'estep':0.02, 'epass': 20., 'tstep': 0.5, 'iter': 1, 'cis': False, 'position': 'sample'}
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REGION_C4 = {'name': 'In3d', 'elo': 590., 'ehi':605., 'estep':0.02, 'epass': 20., 'tstep': 0.1, 'iter': 1, 'cis': False, 'position': 'sample'}
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# -- Region D @ 1050 eV (G2 1200)
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REGION_D1 = {'name': 'MoEF', 'ephot': 1050., 'elo': 1045., 'ehi':1047, 'estep':0.02, 'epass': 50., 'tstep': 2.0, 'iter': 1, 'cis': False, 'position': 'reference'}
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REGION_D2 = {'name': 'Survey', 'elo': 300., 'ehi':1050., 'estep':0.20, 'epass': 50., 'tstep': 0.1, 'iter': 1, 'cis': False, 'position': 'sample'}
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# CHOOSE THE REGIONS TO RUN
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## (G1 600)
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# REGIONS = [REGION_A1,REGION_A2,REGION_A3,REGION_A4]
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## (G2 1200)
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REGIONS = [REGION_B1,REGION_B2,REGION_B3,REGION_B4,REGION_C1,REGION_C2,REGION_C3,REGION_C4,REGION_D1,REGION_D2]
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# close beam shutter and turn off analyser at the end of the scan
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# True or False
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CLOSE_SHUTTER_AT_END = False
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# --- DO NOT EDIT BELOW THIS LINE! ---
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set_exec_pars(keep=False)
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set_exec_pars(compression=True)
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def check_region(region):
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"""
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check region dictionary items and apply defaults where necessary
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"""
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region['fixed'] = 'efix' in region
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if region['fixed']:
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region['elo'] = region['efix']
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region['ehi'] = region['efix']
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if 'iter' not in region:
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region['iter'] = 1
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print("region {0}: setting default iter = {1}".format(region['name'], region['iter']))
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if 'cis' not in region:
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region['cis'] = False
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print("region {0}: setting default cis = {1}".format(region['name'], region['cis']))
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def move_to_position(pdict):
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ManipulatorX.move(pdict['X'])
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ManipulatorY.move(pdict['Y'])
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ManipulatorZ.move(pdict['Z'])
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ManipulatorTheta.move(pdict['Theta'])
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ManipulatorTilt.move(pdict['Tilt'])
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ManipulatorPhi.move(pdict['Phi'])
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class SpectrumReader(ReadonlyRegisterBase, ReadonlyRegisterArray):
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"""
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pseudo-device class to acquire and read out a Scienta spectrum per region.
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this devices starts the spectrum acquisition and organises the data file.
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"""
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def initialize(self):
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#super(SpectrumReader, self).initialize()
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self.scan_index = -1
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def create_datasets(self):
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path = get_exec_pars().scanPath + self.region_name + "/"
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self.channel_begin_dataset_name = path + "ScientaChannelBegin"
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self.channel_end_dataset_name = path + "ScientaChannelEnd"
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create_dataset(self.channel_begin_dataset_name, 'd')
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create_dataset(self.channel_end_dataset_name, 'd')
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if self.region['fixed']:
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self.channel_center_dataset_name = path + "ScientaChannelCenter"
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create_dataset(self.channel_center_dataset_name, 'd')
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else:
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self.step_energy_dataset_name = path + "ScientaStepEnergy"
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create_dataset(self.step_energy_dataset_name, 'd')
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if 'epass' in self.region:
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self.pass_energy_dataset_name = path + "ScientaPassEnergy"
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create_dataset(self.pass_energy_dataset_name, 'd')
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if 'tstep' in self.region:
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self.step_time_dataset_name = path + "ScientaStepTime"
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create_dataset(self.step_time_dataset_name, 'd')
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if 'iter' in self.region:
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self.iterations_dataset_name = path + "ScientaIterations"
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create_dataset(self.iterations_dataset_name, 'd')
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if 'slit' in self.region:
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self.slit_dataset_name = path + "ExitSlit"
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create_dataset(self.slit_dataset_name, 'd')
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if 'position' in self.region:
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position_names = {key:path + "Position"+ key for key in ['X','Y','Z','Theta','Tilt','Phi']}
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self.position_dataset_names = position_names
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for datanames in self.position_dataset_names.values():
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create_dataset(datanames, 'd')
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def setup(self):
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# print("spectrum.setup")
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if self.scan_index != get_exec_pars().index:
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self.scan_index = get_exec_pars().index
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self.create_datasets()
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print "scan {0}, region {1} ({2})".format(self.scan_index, self.region_index, self.region['name'])
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edelta = 0.0
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try:
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ephot = self.region['ephot']
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Eph.move(ephot)
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except KeyError:
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ephot = Eph.take(100)
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if isinstance(ephot, float) and ephot > 0.:
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try:
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if self.region['cis']:
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edelta = ephot - self.ephot_start
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except AttributeError:
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self.ephot_start = ephot
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elo = self.region['elo'] + edelta
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ehi = self.region['ehi'] + edelta
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if self.region['fixed']:
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Scienta.setAcquisitionMode(ch.psi.pshell.epics.Scienta.AcquisitionMode.Fixed)
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Scienta.centerEnergy.write(elo)
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append_dataset(self.channel_center_dataset_name, elo)
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else:
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Scienta.setAcquisitionMode(ch.psi.pshell.epics.Scienta.AcquisitionMode.Swept)
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Scienta.lowEnergy.write(elo)
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Scienta.highEnergy.write(ehi)
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Scienta.stepSize.write(self.region['estep'])
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append_dataset(self.step_energy_dataset_name, self.region['estep'])
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try:
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Scienta.setPassEnergy(int(self.region['epass']))
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append_dataset(self.pass_energy_dataset_name, self.region['epass'])
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except KeyError:
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pass
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try:
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Scienta.stepTime.write(self.region['tstep'])
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append_dataset(self.step_time_dataset_name, self.region['tstep'])
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except KeyError:
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pass
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try:
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Scienta.setIterations(self.region['iter'])
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append_dataset(self.iterations_dataset_name, self.region['iter'])
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except KeyError:
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pass
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try:
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ExitSlit.write(self.region['slit'])
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append_dataset(self.slit_dataset_name, self.region['slit'])
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except KeyError:
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pass
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if self.region['position'] == 'sample':
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move_to_position(SAMPLE_POSITION)
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for name in SAMPLE_POSITION.keys():
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append_dataset(self.position_dataset_names[name], SAMPLE_POSITION[name])
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elif self.region['position'] == 'reference':
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move_to_position(REFERENCE_POSITION)
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for name in REFERENCE_POSITION.keys():
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append_dataset(self.position_dataset_names[name], SAMPLE_POSITION[name])
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Scienta.update()
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def read(self):
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# print("spectrum.read")
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global current_region_index
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current_region_index = self.region_index
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self.setup()
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# print("Acquiring region {0}.".format(self.region['name']))
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trig_scienta()
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time.sleep(0.1)
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sp = Scienta.getSpectrum().read()
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append_dataset(self.channel_begin_dataset_name, Scienta.getChannelBegin().getValue())
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append_dataset(self.channel_end_dataset_name, Scienta.getChannelEnd().getValue())
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return sp
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def getSize(self):
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# this is called before the scan starts - we have to predict the spectrum size
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# wrong values don't seem to affect the data files, however
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if self.region['fixed']:
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nx = 1066
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else:
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nx = int((self.region['ehi'] - self.region['elo']) / self.region['estep']) + 1
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return nx
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class ImageReader(ReadonlyRegisterBase, ReadonlyRegisterMatrix):
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"""
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pseudo-device class to read out the Scienta image per region.
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this device just reads out the Scienta image that has been acquired by SpectrumReader.
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"""
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def read(self):
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# print("image.read")
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return Scienta.getDataMatrix().read()
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def getWidth(self):
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# this is called before the scan starts - we have to predict the spectrum size
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# wrong values don't seem to affect the data files, however
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if self.region['fixed']:
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nx = 1066
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else:
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nx = int((self.region['ehi'] - self.region['elo']) / self.region['estep']) + 1
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return nx
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def getHeight(self):
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# this is called before the scan starts - the number of slices is an independent parameter
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ny = Scienta.slices.read()
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return ny
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class SimpleDeviceReader(Readable):
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"""
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pseudo-device class to read out another device once per region.
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the device must be set assigned to the source attribute.
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"""
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def read(self):
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return self.source.read()
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def setup_live_plots(regions):
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global live_plots
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global current_region_index
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names = [region['name'] for region in regions]
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live_plots = plot(None, names, title="Live Spectra")
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current_region_index = 0
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def update_live_plots():
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global live_plots
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global current_region_index
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try:
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while get_context().state.running:
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y = Scienta.spectrum.take(100)
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x = Scienta.spectrumX
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try:
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series = live_plots[current_region_index].getSeries(0)
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series.setData(x, y)
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except IndexError:
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pass
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time.sleep(1.0)
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finally:
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print "Stopping live spectra"
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def do_scan(scan, motors, positions, regions, latency):
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"""
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set up detectors and run the scan
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for each region we have to add a SpectrumReader and an ImageReader pseudo-device to the SENSORS list.
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the order SpectrumReader, ImageReader is important because the SpectrumReader triggers the Scienta,
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whereafter the ImageReader reads the image.
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"""
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global SENSORS
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SENSORS = []
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for (index, region) in enumerate(regions):
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check_region(region)
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reader = SpectrumReader()
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reader.region_index = index
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reader.region_name = "region{0}".format(index + 1)
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reader.region = region
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reader.initialize()
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set_device_alias(reader, reader.region_name + "/ScientaSpectrum")
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SENSORS.append(reader)
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image = ImageReader()
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image.region_index = index
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image.region = region
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image.initialize()
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set_device_alias(image, reader.region_name + "/ScientaImage")
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SENSORS.append(image)
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dev = SimpleDeviceReader()
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dev.source = SampleCurrent
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set_device_alias(dev, reader.region_name + "/SampleCurrent")
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SENSORS.append(dev)
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dev = SimpleDeviceReader()
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dev.source = RefCurrent
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set_device_alias(dev, reader.region_name + "/RefCurrent")
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SENSORS.append(dev)
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adjust_sensors()
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set_adc_averaging()
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if scan == 'ascan':
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ascan(motors, SENSORS, positions[0], positions[1], positions[2], latency, False, zigzag = True, before_read=wait_beam, after_read = after_readout)
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elif scan == 'lscan':
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lscan(motors, SENSORS, positions[0], positions[1], positions[2], latency, False, before_read=wait_beam, after_read = after_readout)
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elif scan == 'vscan':
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vscan(motors, SENSORS, positions, True, latency,False, before_read=wait_beam, after_read = after_readout)
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else:
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print('unknown scan mode {}'.format(scan))
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for (index, region) in enumerate(regions):
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set_attribute(get_exec_pars().scanPath + "region{0}/ScientaSpectrum".format(index + 1), "RegionName", region['name'])
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set_attribute(get_exec_pars().scanPath + "region{0}/ScientaImage".format(index + 1), "RegionName", region['name'])
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set_attribute(get_exec_pars().scanPath, "Regions", [region['name'] for region in regions])
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try:
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setup_live_plots(REGIONS)
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task = fork(update_live_plots)
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do_scan(SCAN, MOTORS, POSITIONS, REGIONS, LATENCY)
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finally:
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if CLOSE_SHUTTER_AT_END:
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after_scan()
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