Commit 53987619 authored by Zhang, Yuanpeng's avatar Zhang, Yuanpeng ⭐
Browse files

updating to the 2024 cycle

parent 298c66d1

dev_version/reduce_PG3_live_post_proc_dirty_08132023.py

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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-qa'

central_config = "/SNS/PG3/shared/livereduce/live_config.json"

# <----- Config: Conda environment to use for the reduction



# -----> 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: 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



simpleapi.CompressEvents(InputWorkspace=input, OutputWorkspace=output)

# simpleapi.LoadNexus(Filename="/SNS/PG3/shared/livereduce/tmp/result.nxs",

#                     OutputWorkspace=output)

if simpleapi.mtd[str(input)].run().getProtonCharge() > 0.:

    simpleapi.NormaliseByCurrent(InputWorkspace=input, OutputWorkspace=output)

# if simpleapi.mtd[output].run().getProtonCharge() > 0.:

#     simpleapi.NormaliseByCurrent(InputWorkspace=output, OutputWorkspace=output)



simpleapi.SaveNexus(InputWorkspace=output,

                    Filename="/SNS/PG3/shared/livereduce/tmp/output.nxs")

simpleapi.LoadNexus(Filename=f"/SNS/PG3/shared/livereduce/tmp/output.nxs",

                    OutputWorkspace="output_reloaded")



# simpleapi.PDDetermineCharacterizations(InputWorkspace=output,

#                                        Characterizations='characterizations',

#                                        ReductionProperties='__pd_reduction_properties')

simpleapi.PDDetermineCharacterizations(InputWorkspace="output_reloaded",

                                       Characterizations='characterizations',

                                       ReductionProperties='__pd_reduction_properties')

manager = mantid.PropertyManagerDataService.retrieve('__pd_reduction_properties')

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': False,

                    'CompressTolerance': 0.}



can = getRunId(manager, 'container')

with open("/SNS/PG3/shared/livereduce/tmp/alignandfocuspowder.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.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:

    simpleapi.RebinToWorkspace(WorkspaceToRebin=can,

                               WorkspaceToMatch=output,

                               OutputWorkspace=can)

    simpleapi.Minus(LHSWorkspace=output,

                    RHSWorkspace=can,

                    OutputWorkspace=output)



van = getRunId(manager, 'vanadium')

if van is not None and not simpleapi.mtd.doesExist(van):

    with open("/SNS/PG3/shared/livereduce/tmp/van.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.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")

        simpleapi.RebinToWorkspace(WorkspaceToRebin=vanback,

                                   WorkspaceToMatch=van,

                                   OutputWorkspace=vanback)

        simpleapi.Minus(LHSWorkspace=van,

                        RHSWorkspace=vanback,

                        OutputWorkspace=van,

                        ClearRHSWorkspace=True)



        simpleapi.DeleteWorkspace(Workspace=vanback)



    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)



if van is not None:

    simpleapi.RebinToWorkspace(WorkspaceToRebin=van,

                               WorkspaceToMatch=output,

                               OutputWorkspace=van)

    simpleapi.Divide(LHSWorkspace=output,

                     RHSWorkspace=van,

                     OutputWorkspace=output)



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



    request = publish_plot('PG3', runNumber, files={'file': div})



    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)

dev_version/reduce_PG3_live_proc_dirty_08132023.py

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import mantid

from mantid import simpleapi

import os

import json



# -----> Config: Conda environment to use for the reduction

CONDA_ENV = 'mantid-qa'

central_config = "/SNS/PG3/shared/livereduce/live_config.json"

# <----- Config: Conda environment to use for the reduction



# -----> 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 reduction parameters

tof_bin_width_init = input_config["Params"]["Proc"]["TOFBinWidthInit"]

tof_bin_width_proc = input_config["Params"]["Proc"]["TOFBinWidthProc"]

rppw = input_config["Params"]["Proc"]["RemovePromptPulseWidth"]

# <----- Config: Live reduction parameters



mantid.logger.information('Number events = %d' % input.getNumberEvents())



simpleapi.PDLoadCharacterizations(Filename=char_backgrounds + ',' + char_inplane,

                                  OutputWorkspace='characterizations')

simpleapi.SaveNexus(InputWorkspace=input,

                    Filename="/SNS/PG3/shared/livereduce/tmp/input.nxs")

simpleapi.LoadNexus(Filename=f"/SNS/PG3/shared/livereduce/tmp/input.nxs",

                    OutputWorkspace="input_reloaded")

simpleapi.PDDetermineCharacterizations(InputWorkspace="input_reloaded",

                                       Characterizations='characterizations',

                                       ReductionProperties='__pd_reduction_properties')

# simpleapi.PDDetermineCharacterizations(InputWorkspace=input,

#                                        Characterizations='characterizations',

#                                        ReductionProperties='__pd_reduction_properties')

manager = mantid.PropertyManagerDataService.retrieve('__pd_reduction_properties')



simpleapi.Rebin(InputWorkspace=input,

                OutputWorkspace=input,

                Params=(manager['tof_min'].value,

                        tof_bin_width_init,

                        manager['tof_max'].value))



if True:

    simpleapi.AlignAndFocusPowder(InputWorkspace=input,

                                  OutputWorkspace=output,

                                  CalFilename=cal_file,

                                  Params=[tof_bin_width_proc],

                                  RemovePromptPulseWidth=rppw,

                                  ReductionProperties='__pd_reduction_properties')

    simpleapi.ConvertUnits(InputWorkspace=output, OutputWorkspace=output,

                           Target='dSpacing', EMode='Elastic')

    # simpleapi.Rebin(InputWorkspace=output, OutputWorkspace=output,

    #                 Params="0, 0.0001, 10.0")

    # simpleapi.SaveNexus(InputWorkspace=output,

    #                     Filename="/SNS/PG3/shared/livereduce/tmp/result.nxs")

live_config.json

+5 −3
Original line number Diff line number Diff line 
{

    "Cycle": "2023-1_11A_CAL",

    "Cycle": "2024-2_11A_CAL",

    "SampleEnvironment": "PAC",

    "OverwriteUserJsonFile": "N",

         "ConfigFile": {

        "PAC": "PAC_default.json",

        "HTJANIS": "HTJANIS_default.json",
@@ -11,6 +12,7 @@ 
        "JANIS_GAS_noscale":"JANIS_GAS_noscale.json",

        "GASJANIS":"GASJANIS_Default.json",

        "JANIS_GAS_intensifier_no_scale":"LTJANIS_intensifier.json",

        "LTJANIS_GAS_Dec":"LTJANIS_GAS_Dec_2022.json"

        "LTJANIS_GAS_Dec":"LTJANIS_GAS_Dec_2022.json",

          "MAG": "MAG_default.json"

    }

}

live_config_files/2023-1_11A_CAL/MAG_default.json

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{

    "CalibDirectory": "/SNS/PG3/shared/CALIBRATION/2023-1_11A_CAL/",

    "InputFiles": {

        "CalibFile": "PG3_Mag08_d56237_2023_08_11.h5",

        "CharBackgrounds": "PG3_char_2023_8_11-HighRes_Mag.txt",

        "CharInPlane": "PG3_char_2023_8_11_MAG_limit.txt",

        "GroupInPlane": "grouping/PG3_Grouping-IP.xml"

    },

    "Params": {

        "Proc": {

            "TOFBinWidthInit": 100.0,

            "TOFBinWidthProc": -0.0008,

            "RemovePromptPulseWidth": 0

        },

        "PostProc": {

            "TOFBinWidthPProc": -0.0008,

            "RemovePromptPulseWidth": 0,

            "StripVPeaksPosTol": 0.05,

            "StripVPeaksBkgType": "Quadratic"

        }

    }

}

live_config_files/2023-1_11A_CAL/MAG_default_new.json

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{

    "CalibDirectory": "/SNS/PG3/shared/CALIBRATION/2023-1_11A_CAL/",

    "InputFiles": {

        "CalibFile": "PG3_Mag08_d56237_2023_08_11.h5",

        "CharBackgrounds": "PG3_char_2023_8_11-HighRes_Mag.txt",

        "CharInPlane": "PG3_char_2023_8_11_MAG_limit.txt",

        "GroupInPlane": "grouping/PG3_Grouping-IP.xml"

    },

    "Params": {

        "Proc": {

            "TOFBinWidthInit": 100.0,

            "TOFBinWidthProc": -0.0008,

            "RemovePromptPulseWidth": 0

        },

        "PostProc": {

            "TOFBinWidthPProc": -0.0008,

            "RemovePromptPulseWidth": 0,

            "StripVPeaksPosTol": 0.05,

            "StripVPeaksBkgType": "Quadratic"

        }

    }

}