diff --git a/script/users/X-Treme users/Tests_Nieli.py b/script/users/X-Treme users/Tests_Nieli.py new file mode 100644 index 00000000..219a8c5d --- /dev/null +++ b/script/users/X-Treme users/Tests_Nieli.py @@ -0,0 +1,321 @@ +""" +Line scan of multiple spectral regions + +1. uncomment one of the scan blocks and adjust the parameters. + add another block if necessary. +2. declare the regions. +3. add the regions to the REGIONS list. +4. run the script. +""" + +# photon energy scan (do not include 'ephot' in regions in this case!) +MOTORS = [Eph] + +# line scan [start, stop, step] +POSITIONS = [0., 5., 0.5] +SCAN = 'lscan' + +# region setup +# +# for each region, define a python dictionary with the following items. +# optional items can be left unspecified and will default to the indicated values. +# for swept mode, include 'elo', 'ehi', 'estep', 'iter' values, but do not include 'efix'. +# for fixed mode, include 'efix' value, but do not include 'elo', 'ehi', 'estep', 'iter'. +# +# 'name': user-specific name of the region (for graph title and RegionName attribute in data file) +# 'elo': lower kinetic energy boundary of the spectrum +# 'ehi': upper kinetic energy boundary of the spectrum +# 'estep': energy step size +# 'efix': center kinetic energy in fixed mode +# 'epass': pass energy +# 'ephot': photon energy (default: unchanged) +# 'tstep': dwell time in seconds +# 'iter': number of iterations/sweeps (default 1) +# 'cis': True = constant initial state (photoemission line), False = constant final state (Auger peak), (default False) +# 'slit': exit slit (default: unchanged) + + +# VB 62 eV fine scan exit slit 100 +ExitSlit.write(100) +rs = RangeSelection(53.0,58.0) +rs.setVars([0.5, 0.02, 20, 62.0]) #Time, Size, Iteration, photon energy +run("XPSSpectrum", {"save_scienta_image":True, "ranges":[rs, ], "ENDSCAN":True, "pass_energy":20}) + +REGION1 = {'name': 'survey_scan', 'elo': 100., 'ehi':800., 'epass': 50., 'tstep': 0.5, 'estep': 0.5, 'iter': 1, 'cis': False} +REGION2 = {'name': 'O_1s', 'elo': 250., 'ehi':275., 'epass': 50., 'tstep': 0.5, 'estep': 0.05, 'iter': 3, 'cis': False} +REGION3 = {'name': 'C_1s', 'elo': 495., 'ehi':521., 'epass': 50., 'tstep': 0.5, 'estep': 0.05, 'iter': 3, 'cis': False} +REGION3 = {'name': 'C_1s', 'elo': 495., 'ehi':521., 'epass': 50., 'tstep': 0.5, 'estep': 0.05, 'iter': 3, 'cis': False} + +# list of region dictionaries to execute at each scan position +REGIONS = [REGION1, REGION2] + +# close beam shutter and turn off analyser at the end of the scan +CLOSE_SHUTTER_AT_END = True + + + +# --- DO NOT EDIT BELOW THIS LINE! --- + +set_exec_pars(keep=False) +set_exec_pars(compression=True) + +def check_region(region): + """ + check region dictionary items and apply defaults where necessary + """ + region['fixed'] = 'efix' in region + if region['fixed']: + region['elo'] = region['efix'] + region['ehi'] = region['efix'] + if 'iter' not in region: + region['iter'] = 1 + print("region {0}: setting default iter = {1}".format(region['name'], region['iter'])) + if 'cis' not in region: + region['cis'] = False + print("region {0}: setting default cis = {1}".format(region['name'], region['cis'])) + +class SpectrumReader(ReadonlyRegisterBase, ReadonlyRegisterArray): + """ + pseudo-device class to acquire and read out a Scienta spectrum per region. + + this devices starts the spectrum acquisition and organises the data file. + """ + def initialize(self): + #super(SpectrumReader, self).initialize() + self.scan_index = -1 + + def create_datasets(self): + path = get_exec_pars().scanPath + self.region_name + "/" + + self.channel_begin_dataset_name = path + "ScientaChannelBegin" + self.channel_end_dataset_name = path + "ScientaChannelEnd" + create_dataset(self.channel_begin_dataset_name, 'd') + create_dataset(self.channel_end_dataset_name, 'd') + if self.region['fixed']: + self.channel_center_dataset_name = path + "ScientaChannelCenter" + create_dataset(self.channel_center_dataset_name, 'd') + else: + self.step_energy_dataset_name = path + "ScientaStepEnergy" + create_dataset(self.step_energy_dataset_name, 'd') + + if 'epass' in self.region: + self.pass_energy_dataset_name = path + "ScientaPassEnergy" + create_dataset(self.pass_energy_dataset_name, 'd') + if 'tstep' in self.region: + self.step_time_dataset_name = path + "ScientaStepTime" + create_dataset(self.step_time_dataset_name, 'd') + if 'iter' in self.region: + self.iterations_dataset_name = path + "ScientaIterations" + create_dataset(self.iterations_dataset_name, 'd') + if 'slit' in self.region: + self.slit_dataset_name = path + "ExitSlit" + create_dataset(self.slit_dataset_name, 'd') + + def setup(self): + # print("spectrum.setup") + if self.scan_index != get_exec_pars().index: + self.scan_index = get_exec_pars().index + self.create_datasets() + + print "scan {0}, region {1} ({2})".format(self.scan_index, self.region_index, self.region['name']) + + edelta = 0.0 + try: + ephot = self.region['ephot'] + Eph.move(ephot) + except KeyError: + ephot = Eph.take(100) + + if isinstance(ephot, float) and ephot > 0.: + try: + if self.region['cis']: + edelta = ephot - self.ephot_start + except AttributeError: + self.ephot_start = ephot + + elo = self.region['elo'] + edelta + ehi = self.region['ehi'] + edelta + + if self.region['fixed']: + Scienta.setAcquisitionMode(ch.psi.pshell.epics.Scienta.AcquisitionMode.Fixed) + Scienta.centerEnergy.write(elo) + append_dataset(self.channel_center_dataset_name, elo) + else: + Scienta.setAcquisitionMode(ch.psi.pshell.epics.Scienta.AcquisitionMode.Swept) + Scienta.lowEnergy.write(elo) + Scienta.highEnergy.write(ehi) + Scienta.stepSize.write(self.region['estep']) + append_dataset(self.step_energy_dataset_name, self.region['estep']) + + try: + Scienta.setPassEnergy(int(self.region['epass'])) + append_dataset(self.pass_energy_dataset_name, self.region['epass']) + except KeyError: + pass + + try: + Scienta.stepTime.write(self.region['tstep']) + append_dataset(self.step_time_dataset_name, self.region['tstep']) + except KeyError: + pass + + try: + Scienta.setIterations(self.region['iter']) + append_dataset(self.iterations_dataset_name, self.region['iter']) + except KeyError: + pass + + try: + ExitSlit.write(self.region['slit']) + append_dataset(self.slit_dataset_name, self.region['slit']) + except KeyError: + pass + + Scienta.update() + + def read(self): + # print("spectrum.read") + global current_region_index + current_region_index = self.region_index + self.setup() + # print("Acquiring region {0}.".format(self.region['name'])) + trig_scienta() + time.sleep(0.1) + sp = Scienta.getSpectrum().read() + append_dataset(self.channel_begin_dataset_name, Scienta.getChannelBegin().getValue()) + append_dataset(self.channel_end_dataset_name, Scienta.getChannelEnd().getValue()) + return sp + + def getSize(self): + # this is called before the scan starts - we have to predict the spectrum size + # wrong values don't seem to affect the data files, however + if self.region['fixed']: + nx = 1066 + else: + nx = int((self.region['ehi'] - self.region['elo']) / self.region['estep']) + 1 + return nx + + +class ImageReader(ReadonlyRegisterBase, ReadonlyRegisterMatrix): + """ + pseudo-device class to read out the Scienta image per region. + + this device just reads out the Scienta image that has been acquired by SpectrumReader. + """ + def read(self): + # print("image.read") + return Scienta.getDataMatrix().read() + + def getWidth(self): + # this is called before the scan starts - we have to predict the spectrum size + # wrong values don't seem to affect the data files, however + if self.region['fixed']: + nx = 1066 + else: + nx = int((self.region['ehi'] - self.region['elo']) / self.region['estep']) + 1 + return nx + + def getHeight(self): + # this is called before the scan starts - the number of slices is an independent parameter + ny = Scienta.slices.read() + return ny + +class SimpleDeviceReader(Readable): + """ + pseudo-device class to read out another device once per region. + + the device must be set assigned to the source attribute. + """ + def read(self): + return self.source.read() + + +def setup_live_plots(regions): + global live_plots + global current_region_index + names = [region['name'] for region in regions] + live_plots = plot(None, names, title="Live Spectra") + current_region_index = 0 + +def update_live_plots(): + global live_plots + global current_region_index + try: + while get_context().state.running: + y = Scienta.spectrum.take(100) + x = Scienta.spectrumX + try: + series = live_plots[current_region_index].getSeries(0) + series.setData(x, y) + except IndexError: + pass + time.sleep(1.0) + finally: + print "Stopping live spectra" + +def do_scan(scan, motors, positions, regions, latency): + """ + set up detectors and run the scan + + for each region we have to add a SpectrumReader and an ImageReader pseudo-device to the SENSORS list. + the order SpectrumReader, ImageReader is important because the SpectrumReader triggers the Scienta, + whereafter the ImageReader reads the image. + """ + global SENSORS + + SENSORS = [] + + for (index, region) in enumerate(regions): + check_region(region) + + reader = SpectrumReader() + reader.region_index = index + reader.region_name = "region{0}".format(index + 1) + reader.region = region + reader.initialize() + set_device_alias(reader, reader.region_name + "/ScientaSpectrum") + SENSORS.append(reader) + + image = ImageReader() + image.region_index = index + image.region = region + image.initialize() + set_device_alias(image, reader.region_name + "/ScientaImage") + SENSORS.append(image) + + dev = SimpleDeviceReader() + dev.source = SampleCurrent + set_device_alias(dev, reader.region_name + "/SampleCurrent") + SENSORS.append(dev) + + dev = SimpleDeviceReader() + dev.source = RefCurrent + set_device_alias(dev, reader.region_name + "/RefCurrent") + SENSORS.append(dev) + + adjust_sensors() + set_adc_averaging() + + if scan == 'ascan': + ascan(motors, SENSORS, positions[0], positions[1], positions[2], latency, False, zigzag = True, before_read=wait_beam, after_read = after_readout) + elif scan == 'lscan': + lscan(motors, SENSORS, positions[0], positions[1], positions[2], latency, False, before_read=wait_beam, after_read = after_readout) + elif scan == 'vscan': + vscan(motors, SENSORS, positions, True, latency,False, before_read=wait_beam, after_read = after_readout) + else: + print('unknown scan mode {}'.format(scan)) + + for (index, region) in enumerate(regions): + set_attribute(get_exec_pars().scanPath + "region{0}/ScientaSpectrum".format(index + 1), "RegionName", region['name']) + set_attribute(get_exec_pars().scanPath + "region{0}/ScientaImage".format(index + 1), "RegionName", region['name']) + set_attribute(get_exec_pars().scanPath, "Regions", [region['name'] for region in regions]) + +try: + setup_live_plots(REGIONS) + task = fork(update_live_plots) + do_scan(SCAN, MOTORS, POSITIONS, REGIONS, LATENCY) +finally: + if CLOSE_SHUTTER_AT_END: + after_scan() + +