def overhead_per_point(self, element, edge=None): a = json.load(open(self.json)) element = element_symbol(element) if edge is not None and edge.lower() in ('l2', 'l1'): return ([self.interpolate(edge_energy(element, edge)), 0]) if element in a and 'dpp' in a[element]: return (a[element]['dpp']) else: if edge is None or edge.lower() not in ('l2', 'l1'): edge = 'k' if Z_number(element) > 45: edge = 'l3' return ([self.interpolate(edge_energy(element, edge)), 0])
def interpolate(self, energy): a = json.load(open(self.json)) e, t = numpy.array([]), numpy.array([]) for z in self.all_elements: if 'count' not in a[element_symbol(z)]: continue if a[element_symbol(z)]['count'] < self.reliability: continue t = numpy.append(t, a[element_symbol(z)]['dpp'][0]) if z < 46: e = numpy.append(e, edge_energy(z, 'k')) else: e = numpy.append(e, edge_energy(z, 'l3')) s = numpy.argsort(e) return (numpy.interp(energy, e[s], t[s]))
def estimate_time(self, m, el, ed): '''Approximate the time contribution from the current row''' if type(m['bounds']) is str: b = re.split('[ ,]+', m['bounds'].strip()) else: b = re.split('[ ,]+', self.measurements[0]['bounds'].strip()) if type(m['steps']) is str: s = re.split('[ ,]+', m['steps'].strip()) else: s = re.split('[ ,]+', self.measurements[0]['steps'].strip()) if type(m['times']) is str: t = re.split('[ ,]+', m['times'].strip()) else: t = re.split('[ ,]+', self.measurements[0]['times'].strip()) b = [float(x) if isfloat(x) else x for x in b] s = [float(x) if isfloat(x) else x for x in s] t = [float(x) if isfloat(x) else x for x in t] (e, t, at, delta) = conventional_grid(bounds=b, steps=s, times=t, e0=edge_energy(el, ed), element=el, edge=ed, ththth=False) if type(m['nscans']) is int: nsc = m['nscans'] else: nsc = self.measurements[0]['nscans'] self.totaltime += at * nsc self.deltatime += delta * delta
def from_json(self, filename): rkvs = user_ns['rkvs'] if os.path.isfile(filename): with open(filename, 'r') as jsonfile: config = json.load(jsonfile) for k in config.keys(): setattr(self, k, config[k]) user_ns['rois'].trigger = True rkvs.set('BMM:pds:edge', str(config['edge'])) rkvs.set('BMM:pds:element', str(config['element'])) rkvs.set('BMM:pds:edge_energy', edge_energy(config['element'], config['edge']))
def from_json(self, filename): if os.path.isfile(filename): with open(filename, 'r') as jsonfile: config = json.load(jsonfile) for k in config.keys(): if k in ('cycle', ): continue setattr(self, k, config[k]) #rois.trigger = True from BMM.workspace import rkvs try: #rkvs.set('BMM:pds:edge', str(config['edge'])) #rkvs.set('BMM:pds:element', str(config['element'])) rkvs.set('BMM:pds:edge_energy', edge_energy(config['element'], config['edge'])) BMMuser.element = rkvs.get('BMM:pds:element').decode('utf-8') BMMuser.edge = rkvs.get('BMM:pds:edge').decode('utf-8') except: pass
def change_edge(el, focus=False, edge='K', energy=None, slits=True, target=300., xrd=False, bender=True): '''Change edge energy by: 1. Moving the DCM above the edge energy 2. Moving the photon delivery system to the correct mode 3. Running a rocking curve scan 4. Running a slits_height scan Parameters ---------- el : str one- or two-letter symbol focus : bool, optional T=focused or F=unfocused beam [False, unfocused] edge : str, optional edge symbol ['K'] energy : float, optional e0 value [None, determined from el/edge] slits : bool, optional perform slit_height() scan [False] target : float, optional energy where rocking curve is measured [300] xrd : boolean, optional force photon delivery system to XRD [False] Examples -------- Normal use, unfocused beam: >>> RE(change_edge('Fe')) Normal use, focused beam: >>> RE(change_edge('Fe', focus=True)) L2 or L1 edge: >>> RE(change_edge('Re', edge='L2')) Measure rocking curve at edge energy: >>> RE(change_edge('Fe', target=0)) XRD, new energy: >>> RE(change_edge('Fe', xrd=True, energy=8600)) note that you must specify an element, but it doesn't matter which one the energy will be moved to the specified energy xrd=True implies focus=True and target=0 ''' BMMuser, RE, dcm, dm3_bct = user_ns['BMMuser'], user_ns['RE'], user_ns[ 'dcm'], user_ns['dm3_bct'] dcm_pitch, dcm_bragg = user_ns['dcm_pitch'], user_ns['dcm_bragg'] rkvs = user_ns['rkvs'] try: xs = user_ns['xs'] except: pass #BMMuser.prompt = True el = el.capitalize() ###################################################################### # this is a tool for verifying a macro. this replaces an xafsmod scan # # with a sleep, allowing the user to easily map out motor motions in # # a macro # if BMMuser.macro_dryrun: print( info_msg( '\nBMMuser.macro_dryrun is True. Sleeping for %.1f seconds rather than changing to the %s edge.\n' % (BMMuser.macro_sleep, el))) countdown(BMMuser.macro_sleep) return (yield from null()) ###################################################################### if pds_motors_ready() is False: print( error_msg( '\nOne or more motors are showing amplifier faults.\nToggle the correct kill switch, then re-enable the faulted motor.' )) return (yield from null()) (ok, text) = BMM_clear_to_start() if ok is False: print( error_msg('\n' + text) + bold_msg('Quitting change_edge() macro....\n')) return (yield from null()) if energy is None: energy = edge_energy(el, edge) if energy is None: print( error_msg('\nEither %s or %s is not a valid symbol\n' % (el, edge))) return (yield from null()) if energy > 23500: edge = 'L3' energy = edge_energy(el, 'L3') if energy < 4000: print(warning_msg('The %s edge energy is below 4950 eV' % el)) print(warning_msg('You have to change energy by hand.')) return (yield from null()) if energy > 23500: print( warning_msg( 'The %s edge energy is outside the range of this beamline!' % el)) return (yield from null()) BMMuser.edge = edge BMMuser.element = el BMMuser.edge_energy = energy rkvs.set('BMM:pds:edge', edge) rkvs.set('BMM:pds:element', el) rkvs.set('BMM:pds:edge_energy', energy) if energy > 8000: mode = 'A' if focus else 'D' elif energy < 6000: #mode = 'B' if focus else 'F' ## mode B currently is inaccessible :( mode = 'C' if focus else 'F' else: mode = 'C' if focus else 'E' if xrd: mode = 'XRD' focus = True target = 0.0 current_mode = get_mode() if mode in ('D', 'E', 'F') and current_mode in ('D', 'E', 'F'): with_m2 = False elif mode in ('A', 'B', 'C') and current_mode in ('A', 'B', 'C'): # no need to move M2 with_m2 = False else: with_m2 = True if all_connected(with_m2) is False: print(warning_msg('Ophyd connection failure' % el)) return (yield from null()) ################################ # confirm configuration change # ################################ print(bold_msg('\nEnergy change:')) print(' %s: %s %s' % (list_msg('edge'), el.capitalize(), edge.capitalize())) print(' %s: %.1f' % (list_msg('edge energy'), energy)) print(' %s: %.1f' % (list_msg('target energy'), energy + target)) print(' %s: %s' % (list_msg('focus'), str(focus))) print(' %s: %s' % (list_msg('photon delivery mode'), mode)) print(' %s: %s' % (list_msg('optimizing slits height'), str(slits))) if BMMuser.prompt: action = input("\nBegin energy change? [Y/n then Enter] ") if action.lower() == 'q' or action.lower() == 'n': return (yield from null()) if mode == 'C' and energy < 6000: print( warning_msg( '\nMoving to mode C for focused beam and an edge energy below 6 keV.' )) action = input( "You will not get optimal harmonic rejection. Continue anyway? [Y/n then Enter] " ) if action.lower() == 'q' or action.lower() == 'n': return (yield from null()) start = time.time() if mode == 'XRD': report('Configuring beamline for XRD', level='bold', slack=True) else: report( f'Configuring beamline for {el.capitalize()} {edge.capitalize()} edge', level='bold', slack=True) yield from dcm.kill_plan() ################################################ # change to the correct photon delivery mode # # + move mono to correct energy # # + move reference holder to correct slot # ################################################ # if not calibrating and mode != current_mode: # print('Moving to photon delivery mode %s...' % mode) yield from mv(dcm_bragg.acceleration, BMMuser.acc_slow) yield from change_mode(mode=mode, prompt=False, edge=energy + target, reference=el, bender=bender) yield from mv(dcm_bragg.acceleration, BMMuser.acc_fast) if arrived_in_mode(mode=mode) is False: print(error_msg(f'\nFailed to arrive in Mode {mode}')) print( 'Fixing this is often as simple as re-running the change_mode() command.' ) print('Or try dm3_bct.kill() the re-run the change_mode() command.') print('If that doesn\'t work, call for help') return (yield from null()) yield from user_ns['kill_mirror_jacks']() yield from sleep(1) if BMMuser.motor_fault is not None: print( error_msg('\nSome motors are reporting amplifier faults: %s' % BMMuser.motor_fault)) print( 'Clear the faults and try running the same change_edge() command again.' ) print('Troubleshooting: ' + url_msg( 'https://nsls-ii-bmm.github.io/BeamlineManual/trouble.html#amplifier-fault' )) BMMuser.motor_fault = None return (yield from null()) BMMuser.motor_fault = None ############################ # run a rocking curve scan # ############################ print('Optimizing rocking curve...') yield from abs_set(dcm_pitch.kill_cmd, 1, wait=True) yield from mv(dcm_pitch, approximate_pitch(energy + target)) yield from sleep(1) yield from abs_set(dcm_pitch.kill_cmd, 1, wait=True) yield from rocking_curve() close_last_plot() ########################## # run a slit height scan # ########################## if slits: print('Optimizing slits height...') yield from slit_height(move=True) close_last_plot() ## redo rocking curve? ################################## # set reference and roi channels # ################################## if not xrd: ## reference channel rois = user_ns['rois'] print('Moving reference foil...') yield from rois.select_plan(el) ## Xspress3 BMMuser.verify_roi(xs, el, edge) ## feedback show_edges() if mode == 'XRD': report('Finished configuring for XRD', level='bold', slack=True) else: report( f'Finished configuring for {el.capitalize()} {edge.capitalize()} edge', level='bold', slack=True) if slits is False: print( ' * You may need to verify the slit position: RE(slit_height())') self.to_json(os.path.join(self.DATA, '.BMMuser')) yield from dcm.kill_plan() end = time.time() print('\n\nThat took %.1f min' % ((end - start) / 60)) return ()