Update file PDF_generator.py

pure code not instalable as environment/PDF_generator.py

@@ -31,35 +31,10 @@ meas_sampleName = 'lk_zns_insitu_1_00001'  #filename
 meas_path = r'C:\Users\admin\Nextcloud\MyData\bt_1222\in_situ_reactions\varex\data\Original\lk_zns_insitu_1_00001\\' #integrated data path
 meas_tempPath =  r'C:\Users\admin\Nextcloud\MyData\bt_1222\in_situ_reactions\varex\metadata\lk_zns_insitu_1_00001\\' #metadat path
 
-# # BG file name (directories for integrated data and metadata should be keept constant throughout the beamtime)
-# bg_sampleName = 'fc_bg_zns_1cm_1' #filename 
-# bg_path = None #integrated data path
-# bg_tempPath = None #metadat path
-
-# # Measurment file name (directories for integrated data and metadata should be keept constant throughout the beamtime)
-# meas_sampleName = 'fc_zns_1cm_3'  #filename
-# meas_path = None #integrated data path
-# meas_tempPath = None #metadat path
-
-# # BG file name (directories for integrated data and metadata should be keept constant throughout the beamtime)
-# bg_sampleName = 'background_zns_2p_10_2' #filename
-# bg_path = '/home/groenetj/Documents/Beamtime0423/processed/' + bg_sampleName + "/" #integrated data path
-# bg_tempPath = '/asap3/petra3/gpfs/p21.1/2023/data/11017732/raw/pe/ac_cell/' + bg_sampleName + "/" #metadat path
-
-# # Measurment file name (directories for integrated data and metadata should be keept constant throughout the beamtime)
-# meas_sampleName = 'zns_2p_10_2'  #filename
-# meas_path = '/home/groenetj/Documents/Beamtime0423/processed/' + meas_sampleName + "/" #integrated data path
-# meas_tempPath = '/asap3/petra3/gpfs/p21.1/2023/data/11017732/raw/pe/ac_cell/' + meas_sampleName + "/" #metadat path
-
-# # path and temp_path could also be set to None if reload .mat files are used.
-# bg_Reload = rootdir + '/Testsets/' + meas_sampleName + '/Reload_files/bg_Reload/' + bg_sampleName + '.mat' 
-# meas_Reload = rootdir + '/Testsets/' + meas_sampleName + '/Reload_files/meas_Reload/' + meas_sampleName + '.mat'
-
 # path and temp_path could also be set to None if reload .mat files are used.
 bg_Reload = None #rootdir + '/processed/' + meas_sampleName + '/Reload_files/bg_Reload/' + bg_sampleName + '.mat' 
 meas_Reload = None #rootdir + '/processed/' + meas_sampleName + '/Reload_files/meas_Reload/' + meas_sampleName + '.mat'
 
-
 # Correction factors to subtract as well empty glas to counter deviations in cell manufacturing
 empty_glas_int =0 # -0.0009683967395722652#-0.01#*(1/120) #0.01 # 0.014 #0.0210336
 empty_glas = None #'C:/Users/admin/Nextcloud/Beamtimes/bt_0423/XRD_detailed/empty_ac_cell_inlet_180_10_Av120.chi'
@@ -90,23 +65,7 @@ references = {  'ZnS Sph': {'path': rootdir + "/References/ZnS Sphalerite.cif",
                             'decay_rate': 0.8},} #you an add more if nessicarry, just add another three lined block 
 
 
-# Prior to .cif I used .int files generated by Vesta for 100 keV like this:
-
-#references = {  'Fe3S4 cb': {'path': rootdir + "/References/Fe3S4 cubic.int", #Change here references name (Copper) and path (/References/cu.int) to acces other references
- #                           'skiprows': 2,  #skiprows and Energy are all normed to be the same 
-  #                          'energy': 100} , 
-   #             'Fe3O4':{'path': rootdir + "/References/Fe3O4.int",
-    #                        'skiprows': 2,
-     #                       'energy': 100},
-      #           'Fe2O3': {'path': rootdir + "/References/fe2o3.int",
-       #                     'skiprows': 2,
-        #                    'energy': 100} ,
-         #       'Fe':{'path': rootdir + "/References/Fe.int",
-          #                  'skiprows': 2,
-           #                 'energy': 100},
-            #    'Fe3S4 trig': {'path': rootdir + "/References/Fe3S4 trigonal.int",
-             #               'skiprows': 2,
-              #              'energy': 100} ,} #you an add more if nessicarry, just add another three lined block 6
+# Legacy note: Prior to .cif I used .int files generated by Vesta for 100 keV
 
 ends_with = '.dat' # this can differe for differnet live integrations used, but should be the same for one beamtime
 
@@ -264,32 +223,3 @@ 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/')
-
-
-#~~~~~~~~~~~~~~~~~~~ PDF Type 2 ~~~~~~~~~~~~~~~~~~~~~~#
-#Set the directorys:
-outputPath = rootdir + '/processed/' + meas_sampleName + '/PDF_files/meas_type2_corrected_prior_PDF'
-dataPath = rootdir + '/processed/' + meas_sampleName + '/Dat_files/meas_type2_corrected_prior_Dat/'
-bgPath = None # Data is here already subtracted
-
-# Generate the PDF and log.
-meas.generatePDF(dataPath, bgPath, outputPath, Composition, Qmaxinst, Qmax, Qmin, Rmax, Rpoly)
-meas.PrintLogFile(rootdir + '/processed/' + meas_sampleName + '/Log_files/meas_type2_corrected_prior_Log/')
-#~~~~~~~~~~~~~~~~~ PDF Type 2 end ~~~~~~~~~~~~~~~~~~~~~~#
-
-
-
-#~~~~~~~~~~~~~~~~~~~ PDF Type 3 ~~~~~~~~~~~~~~~~~~~~~~#
-# If commented out above:
-Qmaxinst = Qmaxinst_integrate
-
-#Set the directorys:
-# Here we corrected both BG and sample by filtering, baseline subtraction or both
-outputPath = rootdir + '/processed/' + meas_sampleName + '/PDF_files/meas_type3_corrected_after_PDF'
-dataPath = rootdir + '/processed/' + meas_sampleName + '/Dat_files/meas_type3_corrected_after_Dat/'
-bgPath = rootdir + '/processed/' + meas_sampleName + '/Dat_files/bg_type3_corrected_after_Dat/'
-
-# Generate the PDF and log.
-meas.generatePDF(dataPath, bgPath, outputPath, Composition, Qmaxinst, Qmax, Qmin, Rmax, Rpoly)
-meas.PrintLogFile(rootdir + '/processed/' + meas_sampleName + '/Log_files/meas_type3_corrected_after_Log/')
-#~~~~~~~~~~~~~~~~~ PDF Type 3 end ~~~~~~~~~~~~~~~~~~~~~~#
\ No newline at end of file