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from mantid.api import *
from mantid.simpleapi import *
import csv, math
from itertools import product
mtd.importAll()
#######################################################################################
# REDUCTION #######################################################################################
#######################################################################################
def string_boolean(line):
""" Convert string to boolean; needed to read "true" and "false" from the csv Data reduction settings table """
if line == 'false':
bool_string = False
elif line == 'true':
bool_string = True
else:
print "Check value of ", line
print "It must be either True or False"
sys.exit()
return bool_string
#######################################################################################
def read_convert_to_float(array_strings):
""" Needed to convert binning parameters from the csv file into the float numbers """
array = [x.strip() for x in array_strings.split(',')]
array = [float(x) for x in array]
if (len(array) != 3):
print "Check input parameters; binning parameters shall be given in a format left_value, step, right_value."
sys.exit()
return array
###########################################################################################
def FilesListReduce (filename):
""" Creat array of input reduction settings """
parameters = []
with open(filename) as csv_file:
reader = csv.DictReader(csv_file)
for row in reader:
if row['index'] == '':
continue
if row['index'] == 'END':
break
parameters.append(row)
return parameters
#######################################################################################
#===============================================================
# Function to extract list of lines in the csv file to be processed; input format is a combination of digits, '-' ,',' or empty space
# returns list of numbers to be processed
def evaluate_files_list(numbers):
""" Needed for FilesToReduce, see below """
expanded = []
for number in numbers.split(","):
if "-" in number:
start, end = number.split("-")
nrs = range(int(start), int(end) + 1)
expanded.extend(nrs)
else:
expanded.append(int(number))
return expanded
#######################################################################################
def FilesToReduce(parameters, evaluate_files):
""" Create list of the files to reduce """
files_to_reduce = []
if len(evaluate_files) == 0:
files_to_reduce.extend(parameters)
else:
evaluate_files_l = evaluate_files_list(evaluate_files) # call funciton for retrieve the IDs list
for parameter in parameters:
if int(parameter['index']) in evaluate_files_l:
files_to_reduce.append(parameter)
return files_to_reduce
#######################################################################################
def strip_NaNs(output_workspace, base_output_name):
""" Strip NaNs from the 1D OutputWorkspace """ #add isinf
data = output_workspace.readY(0)
start_index = next((index for index in range(len(data)) if not math.isnan(data[index])), None)
end_index = next((index for index in range(len(data)-1, -1, -1) if not math.isnan(data[index])), None)
q_values = output_workspace.readX(0)
start_q = q_values[start_index]
end_q = q_values[end_index]
CropWorkspace(InputWorkspace = output_workspace, XMin = start_q, XMax = end_q, OutputWorkspace = base_output_name)
return base_output_name
#######################################################################################
# GENERAL #########################################################################################
#######################################################################################
def GetPixelSize(): # reads current IDF and get pixelsize from there
""" To get pixel size for Bilby detectors from the Bilby_Definition.xml file """
from mantid.api import ExperimentInfo
import xml.etree.cElementTree as ET
currentIDF = ExperimentInfo.getInstrumentFilename("Bilby")
#print currentIDF
tree = ET.parse(currentIDF)
for node in tree.iter():
if node.tag=="{http://www.mantidproject.org/IDF/1.0}height":
name = node.attrib.get('val')
break
pixelsize = float(name)
return pixelsize
#######################################################################################
def ReadCSV(filename):
""" Read cvs... """
parameters = []
with open(filename) as csvfile:
reader = csv.reader(csvfile)
for row in reader:
parameters.append(row)
return parameters
#######################################################################################
def AttenuationCorrection(att_pos, data_before_May_2016):
""" Bilby has four attenuators; before May 2016 there were only two. Value of the attenuators are hard coded here and being used for the I(Q) scaling in Q1D """
if (data_before_May_2016):
print "You stated data have been collected before May, 2016, i.e. using old attenuators. Please double check."
if (att_pos == 2.0 or att_pos == 4.0):
print "Wrong attenuators value; Either data have been collected after May, 2016, or something is wrong with hdf file"
sys.exit()
if att_pos == 1.0:
scale = 0.007655 # att 130
elif att_pos == 3.0:
scale = 1.0
elif att_pos == 5.0:
scale = 0.005886 # att 170
else:
if att_pos == 1.0:
scale = 1.0
elif att_pos == 2.0:
scale = 0.00955
elif att_pos == 3.0:
scale = 0.005886
elif att_pos == 4.0:
scale = 0.00290
elif att_pos == 5.0:
scale = 0.00062
return scale
#######################################################################################
# FOR WAVELENGTH SLICES ##############################################################################
#######################################################################################
# To create a set of wavelength slices, if requested by reduction settings
def wavelengh_slices(wavelength_intervals, binning_wavelength_ini, wav_delta):
""" This function defined number of wavelenth slices and creates array of the binning parameters for each slice """
binning_wavelength = []
if not wavelength_intervals:
binning_wavelength.append(binning_wavelength_ini)
n = 1 # in this case, number of wavelength range intervals always will be 1
else: # reducing data on a several intervals of wavelengths
wav1 = float(binning_wavelength_ini[0])
wv_ini_step = float(binning_wavelength_ini[1])
wav2 = float(binning_wavelength_ini[2])
# check if chosen wavelenth interval is feasible
if (wav1 + wav_delta) > wav2:
raise ValueError("wav_delta is too large for the upper range of wavelength")
if math.fmod((wav2 - wav1), wav_delta) == 0.0: # if reminder is 0
n = (wav2 - wav1)/wav_delta
else: # if reminder is greater than 0, to trancate the maximum wavelength in the range
n = math.floor((wav2 - wav1)/wav_delta)
max_wave_length = wav1 + n*wav_delta
print ('\n WARNING: because of your set-up, maximum wavelength to consider for partial reduction is only %4.2f \n' %max_wave_length)
# number of wavelength range intervals
n = int(n)
binning_wavelength_interm = []
binning_wavelength_interm_1 = wv_ini_step # binning step is always the same
for i in range (n):
binning_wavelength_interm_0 = wav1 + wav_delta * i # left range
binning_wavelength_interm_2 = binning_wavelength_interm_0 + wav_delta # right range
binning_wavelength_interm = [binning_wavelength_interm_0, binning_wavelength_interm_1, binning_wavelength_interm_2]
binning_wavelength.append(binning_wavelength_interm)
binning_wavelength.append(binning_wavelength_ini) # reduce data on the full range
n = n + 1 # to include full range
return binning_wavelength, n
###############################################################
#######################################################################################
# FOR TUBE ADJUSTMENT ###############################################################################
#######################################################################################
def CorrectionTubesShift(ws_to_correct, path_to_shifts_file):
""" This function moves each tube and then rear panels as a whole as per numbers recorded in the path_to_shifts_file csv file.
The values in the file are obtained from fitting of a few data sets collected using different masks.
It is a very good idea do not change the file. """
shifts = []
shifts = ReadCSV(path_to_shifts_file) # shall be precisely sevel lines; shifts for rear left, rear right, left, right, top, bottom curtains [calculated from 296_Cd_lines_setup1 file] + value for symmetrical shift for entire rear panels
pixelsize = GetPixelSize()
CorrectElementOneStripe("BackDetectorLeft", pixelsize, shifts[0], ws_to_correct)
CorrectElementOneStripe("BackDetectorRight", pixelsize, shifts[1], ws_to_correct)
CorrectElementOneStripe("CurtainLeft", pixelsize, shifts[2], ws_to_correct)
CorrectElementOneStripe("CurtainRight", pixelsize, shifts[3], ws_to_correct)
CorrectElementOneStripe("CurtainTop", pixelsize, shifts[4], ws_to_correct)
CorrectElementOneStripe("CurtainBottom", pixelsize, shifts[5], ws_to_correct)
MoveRearPanels (shifts[6][0], pixelsize, ws_to_correct)
CorrectionBasedOnExperiment(ws_to_correct)
return
#######################################################################################
def CorrectElementOneStripe (panel, pixelsize, shift, ws): # sutable for one Cd stripe correction and for the stripes on BorAl mask on left curtain
""" Technical for CorrectionTubesShift """
eightpack = ['eight_pack1','eight_pack2','eight_pack3','eight_pack4','eight_pack5']
tube = ['tube1','tube2','tube3','tube4','tube5','tube6','tube7','tube8']
i = 0
for ei_pack, t_tube in product(eightpack, tube):
if (panel== "BackDetectorLeft" or panel== "CurtainLeft"):
direction = 1.0
MoveInstrumentComponent(ws, panel + '/' + ei_pack + '/' + t_tube, X=0, Y=-float(shift[i])*pixelsize*direction, Z=0)
if (panel== "BackDetectorRight" or panel== "CurtainRight"):
direction = -1.0
MoveInstrumentComponent(ws, panel + '/' + ei_pack + '/' + t_tube, X=0, Y=-float(shift[i])*pixelsize*direction, Z=0)
if (panel== "CurtainBottom"):
direction = 1.0
MoveInstrumentComponent(ws, panel + '/' + ei_pack + '/' + t_tube, X=-float(shift[i])*pixelsize*direction, Y=0, Z=0)
if (panel== "CurtainTop"):
direction = -1.0
MoveInstrumentComponent(ws, panel + '/' + ei_pack + '/' + t_tube, X=-float(shift[i])*pixelsize*direction, Y=0, Z=0)
i = i + 1
return ws
#######################################################################################
def MoveRearPanels (shift, pixelsize, ws): # moves only rear left and rear right, each on shift; +1 to the right panel to make them symmetrical
""" Technical for CorrectionTubesShift """
panel = "BackDetectorLeft"
direction = 1.0
MoveInstrumentComponent(ws, panel, X=0, Y=-float(shift)*pixelsize*direction, Z=0)
panel = "BackDetectorRight"
direction = -1.0
MoveInstrumentComponent(ws, panel, X=0, Y=-float(shift)*pixelsize*direction, Z=0)
return ws
#######################################################################################
def CorrectionBasedOnExperiment(ws_to_correct):
""" The function to move curtains, based on fits/analysis of a massive set of AgBeh and liquid crystals data.
Laser tracker has not picked up these imperfections.
Added on October, 6th, 2016 """
MoveInstrumentComponent(ws_to_correct, 'CurtainLeft', X=-5.3/1000, Y=0, Z=13.0/1000)
MoveInstrumentComponent(ws_to_correct, 'CurtainRight', X=5.5/1000, Y=0, Z=17.0/1000)
MoveInstrumentComponent(ws_to_correct, 'CurtainTop', X=0, Y=-4.0/1000, Z=0)
MoveInstrumentComponent(ws_to_correct, 'CurtainBottom', X=0, Y=6.0/1000, Z=0)
MoveInstrumentComponent(ws_to_correct, 'BackDetectorRight', X=0, Y=-2.0/1000, Z=0)
MoveInstrumentComponent(ws_to_correct, 'BackDetectorLeft', X=0, Y=-2.0/1000, Z=0)
return
#######################################################################################
def DetShift_before2016 (ws_to_correct):
""" Final detectors' alignement has been done using laser tracker in January, 2016. To correct data collected before that, some extra shift hardcoded here, shall be applied """
shift_curtainl = 0.74/1000
shift_curtainr = 6.92/1000
shift_curtainu = -7.50/1000
shift_curtaind = -1.59/1000
MoveInstrumentComponent(ws_to_correct, 'CurtainLeft', X = shift_curtainl, Y = 0 , Z = 0)
MoveInstrumentComponent(ws_to_correct, 'CurtainRight', X = shift_curtainr, Y = 0 , Z = 0)
MoveInstrumentComponent(ws_to_correct, 'CurtainTop', X = 0, Y=shift_curtainu , Z = 0)
MoveInstrumentComponent(ws_to_correct, 'CurtainBottom', X = 0, Y=shift_curtaind , Z = 0)
CorrectionBasedOnExperiment(ws_to_correct)
return ws
#######################################################################################