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Commit b1620a25 authored by Gröne, Tjark Leon Raphael's avatar Gröne, Tjark Leon Raphael
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Update file PDF_generator.py

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......@@ -122,15 +122,14 @@ endScan = bg.platoend_index
# Save the files for the BG subtration as .dat
bg.outputDatFile(rootdir + '/processed/' + meas_sampleName + '/Dat_files/bg_Dat/')
# Here we extract some of the data from the class to use it later,
# when we work with the sample and not the BG
# Here we extract some of the data from the background subtraction in the sample section.
bg.getRampPlatoLists(bg_heat_ranges)
bg_plato_list = bg.plato_list
bg_ramp_list = bg.ramp_list
# Save everthing done to a log file.
bg.PrintLogFile(rootdir + '/processed/' + meas_sampleName + '/Log_files/bg_Log/')
# Finish for the BG part: Now to the real sample
#-----------------------------------------------------------------------------------------#
......@@ -152,7 +151,6 @@ endScan = meas.platoend_index
# Also here we process and save to .dat
meas.outputDatFile(rootdir + '/processed/' + meas_sampleName + '/Dat_files/meas_type1_uncorrected_Dat/')
original = meas.I
# Finish loading the sample: Now to the BG subtraction and PDF generation
#-----------------------------------------------------------------------------------------#
......@@ -168,10 +166,11 @@ original = meas.I
#Background subtraction, filtering and baseline correction
meas.getRampPlatoLists(meas_heat_ranges)
meas.bgSubtraction(bg_plato_list,bg_ramp_list,meas_heat_ranges,bg_sampleName,FactorMax=FactorMax, Qmaxinst=Qmaxinst,
meas.bgSubtraction(bg.plato_list,bg.ramp_list,meas_heat_ranges,bg_sampleName,FactorMax=FactorMax, Qmaxinst=Qmaxinst,
empty_glas_int=empty_glas_int, empty_glas=empty_glas, Qmin=Qmin, use_PDF_maximization=use_PDF_maximization,
outputPath=rootdir + '/processed/' + meas_sampleName + '/PDF_files/meas_type1_uncorrected_PDF/',
single_BG_file=r'C:/Users/admin/Nextcloud/MyData/bt_1222/in_situ_reactions/varex/data/Normed_and_Averaged/lk_zns_background_insitu_oaws_1_00001_002-n=None/lk_zns_background_insitu_oaws_1_00001-17040.chi')
meas.outputMatFile(rootdir + '/processed/' + meas_sampleName + '/Mat_files/meas_type1_uncorrected_Mat/')
meas.PrintLogFile(rootdir + '/processed/' + meas_sampleName + '/Log_files/meas_type1_uncorrected_Log/')
......@@ -190,30 +189,5 @@ meas.checkPhases(check_phases_at_scan,references=references,savefig='png',output
# In addition 2D and 1D plots of the data over time can be plottet
meas.plot2dTemp(savefig='svg',outputPath=rootdir + '/processed/' + meas_sampleName + '/XRD_Plots/meas_2D_plot/')
meas.plot1dvsTime(step_width=2,maxQ=15, max_index=30, plot_temp=True,savefig='svg',outputPath=rootdir + '/processed/' + meas_sampleName + '/XRD_Plots/meas_1D_plot/')
#~~~~~~~~~~~~~~~~~ XRD Phase Check end ~~~~~~~~~~~~~~~~~~~~~#
# Now we come to the PDf generation itself (appart from the one performed for BG subtraction)
#-----------------------------------------------------------------------------------------#
# In the beginning I tried with 3 types of aproches
# 1. Giving PDFgetX3 the sample and BG file + the subtraction factor (no corrections done)
# --> This is now implemented directly in the BG subtraction, when using PDF maximization for it.
# 2. Subtracting the BG and the give PDFgetX3 just the subtracted sample file
# (This approche works not that well as PDFgetX3 accounts for the BG subtraction scale and alters the PDF in a profidable manner,
# however here one can do baseline corrections quite easily)
# 3. Doing the corrections first, then accounting for the scale of the BG and subracting the corrections from both BG and sample,
# then giving PDFgetX3 both corrected files and the scale
# (This approche can be helpfull, but in the end corrections are after the FT not that important as a good BG subtraction)
# The difference between Qmaxinst and Qmaxinst_integrate is just that one is used as a mask for the BG subtraction
# and the other as the limit for PDFgetX3. Often they can be set just to be the same,
# so I didn´t incllude 2 varibles in the class and I now set the here:
Qmaxinst = Qmaxinst_integrate
#This line is used already in the phase check but is missing if one comments it out,
# because you already now the data set and just want to reprocess the PDF.
meas.I = meas.subtracted_I
# Here we create the .dat for PDFgetX3 to take:
meas.outputDatFile(rootdir + '/processed/' + meas_sampleName + '/Dat_files/meas_type2_corrected_prior_Dat/')
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