Commit 81989358 authored by Yakubov, Sergey's avatar Yakubov, Sergey
Browse files

accept directory with run files

parent 9f6b5fd9

.gitlab-ci.yml

+1 −1
Original line number Diff line number Diff line
@@ -20,7 +20,7 @@ after_script: 
build-image:

  stage: build

  variables:

    TAG: "0.1"

    TAG: "0.2"

    FORCE_TAGS: "false"

  when: manual

  script:

src/ReduceDictionary.py

+62 −39
Original line number Diff line number Diff line
@@ -13,12 +13,15 @@ 
# individual run numbers, or ranges specified with a colon separator.

#

# shlex splits line space while ignoring spaces within quotes. May 2018

import os

import shlex





def LoadDictionary(filename):

    params_dictionary = {}

    run_nums = []

    file = open(filename)

    add_all_runs_from_data_directory = False

    for line in file:

        line = line.strip();

        line = line.rstrip();
@@ -32,22 +35,43 @@ def LoadDictionary( filename ): 
                elif words[1] == "False":

                    params_dictionary[words[0]] = False

                elif words[0] == "run_nums":

                    if words[1] == "data_directory":

                        add_all_runs_from_data_directory = True

                    else:

                        run_list = ParseRunList(words[1])

          for i in range(0,len(run_list)):

            run_nums.append(run_list[i])

                        run_nums = run_nums + run_list

                else:

                    params_dictionary[words[0]] = words[1]

            else:

                print(("Syntax Error On Line: " + line))



    if add_all_runs_from_data_directory:

        if len(run_nums) > 0:

            raise Exception("cannot mix run_nums as range and data_directory")

        if params_dictionary["data_directory"]:

            run_nums = ParseRunListFromFolder(params_dictionary["data_directory"])

        else:

            raise Exception("data_directory must be set when using run_nums from data_directory")



    params_dictionary["run_nums"] = run_nums

  return params_dictionary;

    return params_dictionary





#

# Return a list of run numbers from a string containing a comma separated

# list of individual run numbers, and/or ranges of run numbers specified 

# with a colon separator.

#



def ParseRunListFromFolder(folder):

    files = []

    for f in os.listdir(folder):

        full_path = os.path.join(folder, f)

        if os.path.isfile(full_path):

            files.append(full_path)

    return files





def ParseRunList(run_string):

    run_list = []

    groups = run_string.split(",")
@@ -62,4 +86,3 @@ def ParseRunList( run_string ): 
                run_list.append(str(run))



    return run_list

src/ReduceSCD_OneRun.py

+5 −6
Original line number Diff line number Diff line
@@ -175,7 +175,6 @@ cylinder_length = params_dictionary[ "cylinder_length" ] 
read_UB                   = params_dictionary[ "read_UB" ]

UB_filename               = params_dictionary[ "UB_filename" ]



shared_folder = os.environ.get("SNS_TOPAZ_SHARED_FOLDER", "/SNS/TOPAZ/shared")

shared_folder = os.environ.get("SNS_TOPAZ_SHARED_FOLDER", "/SNS/TOPAZ/shared")

fname = shared_folder+'/ProfileFitting/franz_coefficients_2017.dat'
@@ -278,9 +277,9 @@ run_niggli_fit_profile_file = output_directory + "/" + str(run)+ "_Niggli_profil 


#

#ipts_folder_name = GetIPTS(INSTRUMENT='TOPAZ', RunNumber=run)

location = full_name.find("IPTS")

location = full_name.find("/", location)

ipts_folder_name = full_name[0: location + 1]

#location = full_name.find("IPTS")

#location = full_name.find("/", location)

#ipts_folder_name = full_name[0: location + 1]

#

# Load the run data and find the total monitor counts
@@ -292,11 +291,11 @@ if subtract_bkg is not True: 
  event_ws = FilterBadPulses(InputWorkspace=event_ws, LowerCutoff = 95)

  proton_charge = event_ws.getRun().getProtonCharge() * 1000.0  # get proton charge



  print("\n", run, " has integrated proton charge x 1000 of", proton_charge, "\n")

  print("\n", run, " has integrted proton charge x 1000 of", proton_charge, "\n")



else:

  # Subtract no-sample background

  bkg_subtracted_event_fname =  ipts_folder_name + "shared/bkg_data/" + short_filename + "_event_bkg.nxs"

  bkg_subtracted_event_fname =  shared_folder + "/bkg_data/" + short_filename + "_event_bkg.nxs"

  if os.path.exists(bkg_subtracted_event_fname):

    print("\nProcessing File: " + bkg_subtracted_event_fname + " ......\n")

    event_ws=Load(Filename=bkg_subtracted_event_fname, LoadHistory=False)

src/topaz_reduction.py

+2 −2
Original line number Diff line number Diff line
@@ -321,7 +321,7 @@ list=[] 
index = 0

for r_num in run_nums:

  list.append( ProcessThread() )

  cmd = 'mantidpython ' + reduce_one_run_script + ' ' + config_file_name + ' ' + str(r_num)

  cmd = 'mantidpython -u ' + reduce_one_run_script + ' ' + config_file_name + ' ' + str(r_num)

  if slurm_queue_name is not None:

    console_file = output_directory + "/" + str(r_num) + "_output.txt"

    cmd =  'srun -p ' + slurm_queue_name + \
@@ -352,4 +352,4 @@ print("\n*********************************************************************** 
print("****************************** All DONE **********************************************")

print("**************************************************************************************\n")



print('Connfig file: ' + config_file_name) 
print('Config file: ' + config_file_name)