change to pg32 machine (b746f891) · Commits · sns-hfir-scse / diffraction / powgen_live

align_focus_can.py

+2 −2

Original line number	Diff line number	Diff line
		@@ -29,9 +29,9 @@ simpleapi.LoadDiffCal(InstrumentName="PG3",
		Filename=cal_file,
		WorkspaceName="PG3")

		with open("/SNS/PG3/shared/livereduce/tmp/alignandfocuspowder.json", "r") as f:
		with open("/SNS/PG3/shared/livereduce/tmp/alignandfocuspowder_zyp.json", "r") as f:
		af_config = json.load(f)
		with open("/SNS/PG3/shared/livereduce/tmp/can.name", "r") as f:
		with open("/SNS/PG3/shared/livereduce/tmp/can_zyp.name", "r") as f:
		can = f.readline().strip()

		simpleapi.AlignAndFocusPowderFromFiles(Filename=can,

align_focus_van.py

+2 −2

Original line number	Diff line number	Diff line
		@@ -29,9 +29,9 @@ simpleapi.LoadDiffCal(InstrumentName="PG3",
		Filename=cal_file,
		WorkspaceName="PG3")

		with open("/SNS/PG3/shared/livereduce/tmp/alignandfocuspowder.json", "r") as f:
		with open("/SNS/PG3/shared/livereduce/tmp/alignandfocuspowder_zyp.json", "r") as f:
		af_config = json.load(f)
		with open("/SNS/PG3/shared/livereduce/tmp/van.name", "r") as f:
		with open("/SNS/PG3/shared/livereduce/tmp/van_zyp.name", "r") as f:
		van = f.readline().strip()

		simpleapi.LoadEventNexus(Filename=van,

align_focus_vanback.py

+2 −2

Original line number	Diff line number	Diff line
		@@ -29,9 +29,9 @@ simpleapi.LoadDiffCal(InstrumentName="PG3",
		Filename=cal_file,
		WorkspaceName="PG3")

		with open("/SNS/PG3/shared/livereduce/tmp/alignandfocuspowder.json", "r") as f:
		with open("/SNS/PG3/shared/livereduce/tmp/alignandfocuspowder_zyp.json", "r") as f:
		af_config = json.load(f)
		with open("/SNS/PG3/shared/livereduce/tmp/vanback.name", "r") as f:
		with open("/SNS/PG3/shared/livereduce/tmp/vanback_zyp.name", "r") as f:
		vanback = f.readline().strip()

		simpleapi.AlignAndFocusPowderFromFiles(Filename=vanback,

reduce_PG3_live_post_proc.py

+9 −1

Original line number	Diff line number	Diff line
		@@ -310,6 +310,14 @@ else:
		except: # noqa
		raise Exception("Failed in vanadium normalization.")

		# live_data_d = os.path.join("/SNS/PG3", ipts, "shared/livereduce")
		# if not os.path.exists(live_data_d):
		# os.makedirs(live_data_d)
		# simpleapi.SaveAscii(
		# InputWorkspace=output,
		# Filename=os.path.join(live_data_d, f"PG3_{run_num}.dat")
		# )

		div = simpleapi.SavePlot1D(
		InputWorkspace=output,
		OutputType='plotly',

reduce_PG3_live_post_proc_zyp.py

0 → 100755

+348 −0

Original line number	Diff line number	Diff line
		import json
		import mantid
		from mantid import simpleapi
		import os
		import subprocess
		import time

		# -----> Config: Conda environment to use for the reduction
		CONDA_ENV = 'mantid'
		central_config = "/SNS/PG3/shared/livereduce/live_config.json"
		# <----- Config: Conda environment to use for the reduction

		try:
		run = input.getRun()
		ipts = run.getLogData("experiment_identifier").value
		run_num = run.getLogData("run_number").value
		except: # noqa E722
		ipts = None
		run_num = None

		if not all([run_num, ipts]):
		mantid.logger.information("Live post proc run number unavailable.")
		simpleapi.CreateSampleWorkspace(OutputWorkspace=output)
		else:
		# -----> Config: Read in the config file
		with open(central_config, "r") as f:
		input_c_config = json.load(f)

		cycle = input_c_config["Cycle"]
		sam_env = input_c_config["SampleEnvironment"]
		config_file = input_c_config["ConfigFile"][sam_env]
		config_file_f = os.path.join(
		"/SNS/PG3/shared/livereduce/live_config_files",
		cycle,
		config_file
		)

		with open(config_file_f, "r") as f:
		input_config = json.load(f)
		# <----- Config: Read in the config file

		# -----> Config: Calib and char files
		must_keys = ["CalibDirectory", "InputFiles"]
		infiles_must_keys = ["CalibFile", "CharBackgrounds", "CharInPlane"]
		for key in must_keys:
		if key not in input_config.keys():
		raise Exception(f"No {key} found in {config_file_f}.")
		for key in infiles_must_keys:
		if key not in input_config["InputFiles"].keys():
		raise Exception(
		f"No {key} found under 'InputFiles' in {config_file_f}."
		)

		cal_dir = input_config["CalibDirectory"]
		cal_file = os.path.join(
		cal_dir,
		input_config["InputFiles"]["CalibFile"]
		)
		char_backgrounds = os.path.join(
		cal_dir,
		input_config["InputFiles"]["CharBackgrounds"]
		)
		char_inplane = os.path.join(
		cal_dir,
		input_config["InputFiles"]["CharInPlane"]
		)
		# <----- Config: Calib and char files

		# -----> Config: Live post processing parameters
		tof_bin_width_pproc = input_config["Params"]["PostProc"]["TOFBinWidthPProc"]
		rppw_pproc = input_config["Params"]["PostProc"]["RemovePromptPulseWidth"]
		strip_v_pp_tol = input_config["Params"]["PostProc"]["StripVPeaksPosTol"]
		strip_v_bt = input_config["Params"]["PostProc"]["StripVPeaksBkgType"]
		# <----- Config: Live post processing parameters

		try:
		accum_prtc = simpleapi.mtd[str(input)].run().getProtonCharge()
		if accum_prtc > 0.:
		mantid.logger.information(f"Accumulated proton charge: {accum_prtc}")
		simpleapi.NormaliseByCurrent(
		InputWorkspace=input,
		OutputWorkspace=output,
		RecalculatePCharge=True
		)
		except:
		raise Exception("Failed in proton charge normalization.")

		simpleapi.SaveNexus(
		InputWorkspace=input,
		Filename=f"/SNS/PG3/shared/livereduce/tmp/pproc_zyp_tmp.nxs")
		simpleapi.LoadNexus(
		Filename="/SNS/PG3/shared/livereduce/tmp/pproc_zyp_tmp.nxs",
		OutputWorkspace="pproc_in"
		)

		try:
		simpleapi.PDLoadCharacterizations(
		Filename=char_backgrounds + ',' + char_inplane,
		OutputWorkspace='characterizations'
		)
		simpleapi.PDDetermineCharacterizations(
		InputWorkspace="pproc_in",
		Characterizations='characterizations',
		ReductionProperties='__pd_reduction_properties'
		)
		manager = mantid.PropertyManagerDataService.retrieve(
		'__pd_reduction_properties'
		)
		except:
		raise Exception("Failed in characterization determination.")

		mantid.logger.information("In post processing ...")

		def getRunId(manager, key):
		value = manager[key].value[0]
		if value == 0:
		return None
		else:
		return 'PG3_' + str(value)

		def smooth(wksp):
		simpleapi.ConvertUnits(InputWorkspace=wksp, OutputWorkspace=wksp,
		Target='TOF', EMode='Elastic')
		simpleapi.FFTSmooth(InputWorkspace=wksp,
		OutputWorkspace=wksp,
		Filter="Butterworth",
		Params='20,2',
		IgnoreXBins=True,
		AllSpectra=True)
		simpleapi.ConvertUnits(InputWorkspace=wksp, OutputWorkspace=wksp,
		Target='dSpacing', EMode='Elastic')

		processingParams = {'CalibrationWorkspace': 'PG3_cal',
		'GroupingWorkspace': 'PG3_group',
		'MaskWorkspace': 'PG3_mask',
		'Params': [tof_bin_width_pproc],
		'RemovePromptPulseWidth': rppw_pproc,
		'ReductionProperties': '__pd_reduction_properties',
		'PreserveEvents': True,
		'CompressTolerance': 0.}

		can = getRunId(manager, 'container')
		with open(
		"/SNS/PG3/shared/livereduce/tmp/alignandfocuspowder_zyp.json",
		"w"
		) as f:
		json.dump(processingParams, f, indent=4)

		if can is not None and not simpleapi.mtd.doesExist(can):
		with open("/SNS/PG3/shared/livereduce/tmp/can_zyp.name", "w") as f:
		f.write(can)
		mantid.logger.information("processing container '%s'" % can)
		subprocess.run(
		[
		"mantidpython",
		"/SNS/PG3/shared/livereduce/align_focus_can.py"
		]
		)
		while not os.path.exists(
		f"/SNS/PG3/shared/livereduce/tmp/can_{can}.nxs"
		):
		time.sleep(1)
		simpleapi.LoadNexus(
		Filename=f"/SNS/PG3/shared/livereduce/tmp/can_{can}.nxs",
		OutputWorkspace=can
		)
		simpleapi.ConvertUnits(
		InputWorkspace=can,
		OutputWorkspace=can,
		Target='dSpacing',
		EMode='Elastic'
		)
		simpleapi.NormaliseByCurrent(
		InputWorkspace=can,
		OutputWorkspace=can
		)


		if can is not None:
		try:
		simpleapi.RebinToWorkspace(
		WorkspaceToRebin=can,
		WorkspaceToMatch=output,
		OutputWorkspace=can
		)
		except: # noqa
		raise Exception("Failed in rebinning.")

		simpleapi.SaveNexus(
		InputWorkspace=can,
		Filename=f"/SNS/PG3/shared/livereduce/tmp/can_{can}_final.nxs")
		simpleapi.SaveNexus(
		InputWorkspace=output,
		Filename=f"/SNS/PG3/shared/livereduce/tmp/live_check.nxs")

		try:
		simpleapi.Minus(
		LHSWorkspace=output,
		RHSWorkspace=can,
		OutputWorkspace=output
		)
		except: # noqa
		raise Exception("Failed in background subtraction.")

		van = getRunId(manager, 'vanadium')
		if van is not None and not simpleapi.mtd.doesExist(van):
		with open("/SNS/PG3/shared/livereduce/tmp/van_zyp.name", "w") as f:
		f.write(van)
		mantid.logger.information("processing vanadium '%s'" % van)
		subprocess.run(
		[
		"mantidpython",
		"/SNS/PG3/shared/livereduce/align_focus_van.py"
		]
		)
		while not os.path.exists(
		f"/SNS/PG3/shared/livereduce/tmp/van_{van}.nxs"
		):
		time.sleep(1)
		simpleapi.LoadNexus(
		Filename=f"/SNS/PG3/shared/livereduce/tmp/van_{van}.nxs",
		OutputWorkspace=van
		)
		simpleapi.NormaliseByCurrent(
		InputWorkspace=van,
		OutputWorkspace=van
		)

		vanback = getRunId(manager, 'vanadium_background')
		with open("/SNS/PG3/shared/livereduce/tmp/vanback_zyp.name", "w") as f:
		f.write(vanback)
		if vanback is not None:
		mantid.logger.information(
		"processing vanadium background '%s'" % vanback
		)
		subprocess.run(
		[
		"mantidpython",
		"/SNS/PG3/shared/livereduce/align_focus_vanback.py"
		]
		)
		while not os.path.exists(
		f"/SNS/PG3/shared/livereduce/tmp/vanback_{vanback}.nxs"
		):
		time.sleep(1)
		simpleapi.LoadNexus(
		Filename=f"/SNS/PG3/shared/livereduce/tmp/vanback_{vanback}.nxs",
		OutputWorkspace="__vanback"
		)
		vanback = '__vanback'
		simpleapi.NormaliseByCurrent(
		InputWorkspace=vanback,
		OutputWorkspace=vanback
		)

		mantid.logger.information("subtracting vanadium background")

		try:
		simpleapi.RebinToWorkspace(
		WorkspaceToRebin=vanback,
		WorkspaceToMatch=van,
		OutputWorkspace=vanback
		)
		simpleapi.Minus(
		LHSWorkspace=van,
		RHSWorkspace=vanback,
		OutputWorkspace=van,
		ClearRHSWorkspace=True
		)
		except: # noqa
		raise Exception("Failed in bkg subtraction for vanadium.")

		simpleapi.DeleteWorkspace(Workspace=vanback)

		try:
		simpleapi.ConvertUnits(
		InputWorkspace=van,
		OutputWorkspace=van,
		Target='dSpacing',
		EMode='Elastic'
		)

		simpleapi.StripVanadiumPeaks(
		InputWorkspace=van,
		OutputWorkspace=van,
		BackgroundType=strip_v_bt,
		PeakPositionTolerance=strip_v_pp_tol
		)
		smooth(van)
		except: # noqa
		raise Exception("Failed in preparing vanadium normalization.")

		if van is not None:
		try:
		simpleapi.RebinToWorkspace(
		WorkspaceToRebin=van,
		WorkspaceToMatch=output,
		OutputWorkspace=van
		)
		except: # noqa
		raise Exception("Failed in rebinning vanadium.")

		simpleapi.SaveNexus(
		InputWorkspace=van,
		Filename=f"/SNS/PG3/shared/livereduce/tmp/van_{van}_final.nxs")

		try:
		simpleapi.Divide(
		LHSWorkspace=output,
		RHSWorkspace=van,
		OutputWorkspace=output
		)
		except: # noqa
		raise Exception("Failed in vanadium normalization.")

		# live_data_d = os.path.join("/SNS/PG3", ipts, "shared/livereduce")
		# if not os.path.exists(live_data_d):
		# os.makedirs(live_data_d)
		# simpleapi.SaveAscii(
		# InputWorkspace=output,
		# Filename=os.path.join(live_data_d, f"PG3_{run_num}.dat")
		# )

		div = simpleapi.SavePlot1D(
		InputWorkspace=output,
		OutputType='plotly',
		XLabel='d-spacing (A)'
		)
		runNumber = simpleapi.mtd[output].getRunNumber()
		if runNumber > 0:
		mantid.logger.information('Posting plot of PG3_%s' % runNumber)
		try:
		from postprocessing.publish_plot import publish_plot
		except ImportError:
		from finddata import publish_plot

		try:
		request = publish_plot('PG3', runNumber, files={'file': div})
		except: # noqa
		raise Exception("Failed in data plot publishing.")

		mantid.logger.information("post returned %d" % request.status_code)
		mantid.logger.information("resulting document:")
		mantid.logger.information(str(request.text))
		else:
		s_part1 = "Not posting becuase run number is "
		s_part2 = "not greater than zero: %s" % runNumber
		mantid.logger.information(s_part1 + s_part2)