def main(): """ NAME thellier_magic_redo.py DESCRIPTION Calculates paleointensity parameters for thellier-thellier type data using bounds stored in the "redo" file SYNTAX thellier_magic_redo [command line options] OPTIONS -h prints help message -usr USER: identify user, default is "" -fcr CRIT, set criteria for grading -f IN: specify input file, default is magic_measurements.txt -fre REDO: specify redo file, default is "thellier_redo" -F OUT: specify output file, default is thellier_specimens.txt -leg: attaches "Recalculated from original measurements; supercedes published results. " to comment field -CR PERC TYPE: apply a cooling rate correction. PERC should be a percentage of original (say reduce to 90%) TYPE should be one of the following: EG (for educated guess); PS (based on pilots); TRM (based on comparison of two TRMs) -Fcr CRout: specify pmag_specimen format file for cooling rate corrected data -ANI: there are anisotropy data to correct thellier results -fan ANIFILE: specify rmag_anisotropy format file, default is rmag_anisotropy.txt -Fac ACout: specify pmag_specimen format file for anisotropy corrected data default is AC_specimens.txt -NLT: there are non-linear trm data in the measurements file to correct thellier results -fnl NLTFILE: specify magic_measurments format file, default is magic_measurements.txt -Fnl NLTout: specify pmag_specimen format file for non-linear trm corrected data default is NLT_specimens.txt -z use z component differenences for pTRM calculation """ dir_path='.' critout="" version_num=pmag.get_version() field,first_save=-1,1 spec,recnum,start,end=0,0,0,0 frac=0 NltRecs,PmagSpecs,AniSpecRecs,NltSpecRecs,CRSpecs=[],[],[],[],[] meas_file,pmag_file,mk_file="magic_measurements.txt","thellier_specimens.txt","thellier_redo" anis_file="rmag_anisotropy.txt" anisout,nltout="AC_specimens.txt","NLT_specimens.txt" crout="CR_specimens.txt" nlt_file="" comment,user="","unknown" anis,nltrm=0,0 jackknife=0 # maybe in future can do jackknife args=sys.argv Zdiff=0 if '-WD' in args: ind=args.index('-WD') dir_path=args[ind+1] if "-h" in args: print main.__doc__ sys.exit() if "-usr" in args: ind=args.index("-usr") user=sys.argv[ind+1] if "-leg" in args: comment="Recalculated from original measurements; supercedes published results. " if "-CR" in args: ind=args.index("-CR") frac=.01*float(sys.argv[ind+1]) crtype=sys.argv[ind+2] if "-Fcr" in args: ind=args.index("-Fcr") crout=sys.argv[ind+1] if "-f" in args: ind=args.index("-f") meas_file=sys.argv[ind+1] if "-F" in args: ind=args.index("-F") pmag_file=sys.argv[ind+1] if "-fre" in args: ind=args.index("-fre") mk_file=args[ind+1] # # if "-ANI" in args: anis=1 ind=args.index("-ANI") if "-Fac" in args: ind=args.index("-Fac") anisout=args[ind+1] if "-fan" in args: ind=args.index("-fan") anis_file=args[ind+1] # if "-NLT" in args: nltrm=1 if "-Fnl" in args: ind=args.index("-Fnl") nltout=args[ind+1] if "-fnl" in args: ind=args.index("-fnl") nlt_file=args[ind+1] if "-z" in args: Zdiff=1 if '-fcr' in sys.argv: ind=args.index("-fcr") critout=sys.argv[ind+1] # # start reading in data: # meas_file=dir_path+"/"+meas_file mk_file=dir_path+"/"+mk_file critout=dir_path+"/"+critout try: open(critout,'rU') accept_keys=['specimen_int_ptrm_n','specimen_md','specimen_fvds','specimen_b_beta','specimen_dang','specimen_drats','specimen_Z'] crit_data,file_type=pmag.magic_read(critout) print "Acceptance criteria read in from ", critout accept={} accept['specimen_int_ptrm_n']=2.0 for critrec in crit_data: if critrec["pmag_criteria_code"]=="IE-SPEC": for key in accept_keys: if key not in critrec.keys(): accept[key]=-1 else: accept[key]=float(critrec[key]) except: critout="" # no acceptance criteria specified meas_data,file_type=pmag.magic_read(meas_file) if file_type != 'magic_measurements': print file_type print file_type,"This is not a valid magic_measurements file " sys.exit() try: mk_f=open(mk_file,'rU') except: print "Bad redo file" sys.exit() mkspec=[] speclist=[] for line in mk_f.readlines(): tmp=line.split() mkspec.append(tmp) speclist.append(tmp[0]) if anis==1: anis_file=dir_path+"/"+anis_file anis_data,file_type=pmag.magic_read(anis_file) if file_type != 'rmag_anisotropy': print file_type print file_type,"This is not a valid rmag_anisotropy file " sys.exit() if nlt_file=="": nlt_data=meas_data # look for trm acquisition data in the meas_data file else: nlt_file=dir_path+"/"+nlt_file nlt_data,file_type=pmag.magic_read(nlt_file) # # sort the specimen names and step through one by one # sids=pmag.get_specs(meas_data) # print 'Processing ',len(speclist),' specimens - please wait ' while spec < len(speclist): s=speclist[spec] recnum=0 datablock=[] PmagSpecRec={} PmagSpecRec["er_analyst_mail_names"]=user PmagSpecRec["er_citation_names"]="This study" PmagSpecRec["magic_software_packages"]=version_num methcodes,inst_code=[],"" # # find the data from the meas_data file for this specimen # for rec in meas_data: if rec["er_specimen_name"].lower()==s.lower(): if "magic_instrument_codes" not in rec.keys(): rec["magic_instrument_codes"]="unknown" meths=rec["magic_method_codes"] for meth in meths:meth.strip() # get rid of annoying spaces in method codes if "LP-PI-TRM" in meths: datablock.append(rec) # # collect info for the PmagSpecRec dictionary # if len(datablock)>0: rec=datablock[0] PmagSpecRec["er_specimen_name"]=s PmagSpecRec["er_sample_name"]=rec["er_sample_name"] PmagSpecRec["er_site_name"]=rec["er_site_name"] PmagSpecRec["er_location_name"]=rec["er_location_name"] PmagSpecRec["measurement_step_unit"]="K" PmagSpecRec["specimen_correction"]='u' if "magic_instrument_codes" not in rec.keys(): PmagSpecRec["magic_instrument_codes"]="unknown" else: PmagSpecRec["magic_instrument_codes"]=rec["magic_instrument_codes"] if "magic_experiment_name" not in rec.keys(): rec["magic_experiment_name"]="" else: PmagSpecRec["magic_experiment_names"]=rec["magic_experiment_name"] meths=rec["magic_experiment_name"].split(":") for meth in meths: if meth.strip() not in methcodes and "LP-" in meth:methcodes.append(meth.strip()) # # sort out the data into first_Z, first_I, ptrm_check, ptrm_tail # araiblock,field=pmag.sortarai(datablock,s,Zdiff) first_Z=araiblock[0] first_I=araiblock[1] ptrm_check=araiblock[2] ptrm_tail=araiblock[3] if len(first_I)<3 or len(first_Z)<4: spec+=1 print 'skipping specimen ', s else: # # get start, end # for redospec in mkspec: if redospec[0]==s: b,e=float(redospec[1]),float(redospec[2]) break if e > float(first_Z[-1][0]):e=float(first_Z[-1][0]) for recnum in range(len(first_Z)): if first_Z[recnum][0]==b:start=recnum if first_Z[recnum][0]==e:end=recnum nsteps=end-start if nsteps>2: zijdblock,units=pmag.find_dmag_rec(s,meas_data) pars,errcode=pmag.PintPars(araiblock,zijdblock,start,end) pars['measurement_step_unit']=units pars["specimen_lab_field_dc"]=field pars["specimen_int"]=-1*field*pars["specimen_b"] PmagSpecRec["measurement_step_min"]='%8.3e' % (pars["measurement_step_min"]) PmagSpecRec["measurement_step_max"]='%8.3e' % (pars["measurement_step_max"]) PmagSpecRec["specimen_int_n"]='%i'%(pars["specimen_int_n"]) PmagSpecRec["specimen_lab_field_dc"]='%8.3e'%(pars["specimen_lab_field_dc"]) PmagSpecRec["specimen_int"]='%9.4e '%(pars["specimen_int"]) PmagSpecRec["specimen_b"]='%5.3f '%(pars["specimen_b"]) PmagSpecRec["specimen_q"]='%5.1f '%(pars["specimen_q"]) PmagSpecRec["specimen_f"]='%5.3f '%(pars["specimen_f"]) PmagSpecRec["specimen_fvds"]='%5.3f'%(pars["specimen_fvds"]) PmagSpecRec["specimen_b_beta"]='%5.3f'%(pars["specimen_b_beta"]) PmagSpecRec["specimen_int_mad"]='%7.1f'%(pars["specimen_int_mad"]) PmagSpecRec["specimen_Z"]='%7.1f'%(pars["specimen_Z"]) PmagSpecRec["specimen_gamma"]='%7.1f'%(pars["specimen_gamma"]) if pars["method_codes"]!="" and pars["method_codes"] not in methcodes: methcodes.append(pars["method_codes"]) PmagSpecRec["specimen_dec"]='%7.1f'%(pars["specimen_dec"]) PmagSpecRec["specimen_inc"]='%7.1f'%(pars["specimen_inc"]) PmagSpecRec["specimen_tilt_correction"]='-1' PmagSpecRec["specimen_direction_type"]='l' PmagSpecRec["direction_type"]='l' # this is redudant, but helpful - won't be imported PmagSpecRec["specimen_dang"]='%7.1f '%(pars["specimen_dang"]) PmagSpecRec["specimen_drats"]='%7.1f '%(pars["specimen_drats"]) PmagSpecRec["specimen_int_ptrm_n"]='%i '%(pars["specimen_int_ptrm_n"]) PmagSpecRec["specimen_rsc"]='%6.4f '%(pars["specimen_rsc"]) PmagSpecRec["specimen_md"]='%i '%(int(pars["specimen_md"])) if PmagSpecRec["specimen_md"]=='-1':PmagSpecRec["specimen_md"]="" PmagSpecRec["specimen_b_sigma"]='%5.3f '%(pars["specimen_b_sigma"]) if "IE-TT" not in methcodes:methcodes.append("IE-TT") methods="" for meth in methcodes: methods=methods+meth+":" PmagSpecRec["magic_method_codes"]=methods[:-1] PmagSpecRec["magic_software_packages"]=version_num PmagSpecRec["specimen_description"]=comment if critout!="": score,kill=pmag.grade(PmagSpecRec,accept) Grade="" if score==len(accept.keys()):Grade='A' if score==len(accept.keys())-1:Grade='B' if score==len(accept.keys())-2:Grade='C' if score==len(accept.keys())-3:Grade='D' if score<=len(accept.keys())-4:Grade='F' PmagSpecRec["specimen_grade"]=Grade else: PmagSpecRec["specimen_grade"]="" if nltrm==0 and anis==0 and frac!=0: # apply cooling rate correction CrSpecRec={} for key in PmagSpecRec.keys():CrSpecRec[key]=PmagSpecRec[key] inten=frac*float(CrSpecRec['specimen_int']) CrSpecRec["specimen_int"]='%9.4e '%(inten) # adjust specimen intensity by cooling rate correction CrSpecRec['magic_method_codes'] = CrSpecRec['magic_method_codes']+':DA-CR-'+crtype CrSpecRec["specimen_correction"]='c' CRSpecs.append(CrSpecRec) PmagSpecs.append(PmagSpecRec) NltSpecRec="" # # check on non-linear TRM correction # if nltrm==1: # # find the data from the nlt_data list for this specimen # TRMs,Bs=[],[] NltSpecRec="" NltRecs=[] for NltRec in nlt_data: if NltRec['er_specimen_name']==PmagSpecRec["er_specimen_name"]: meths=NltRec["magic_method_codes"].split(":") for meth in meths:meth.strip() if "LP-TRM" in meths: NltRecs.append(NltRec) if len(NltRecs) > 2: for NltRec in NltRecs: Bs.append(float(NltRec['treatment_dc_field'])) TRMs.append(float(NltRec['measurement_magn_moment'])) NLTpars=nlt.NLtrm(Bs,TRMs,float(PmagSpecRec['specimen_int']),float(PmagSpecRec['specimen_lab_field_dc']),0) if NLTpars['banc']>0: NltSpecRec={} for key in PmagSpecRec.keys(): NltSpecRec[key]=PmagSpecRec[key] NltSpecRec['specimen_int']='%9.4e'%(NLTpars['banc']) NltSpecRec['magic_method_codes']=PmagSpecRec["magic_method_codes"]+":DA-NL" NltSpecRec["specimen_correction"]='c' NltSpecRec['specimen_grade']=PmagSpecRec['specimen_grade'] NltSpecRec["magic_software_packages"]=version_num print NltSpecRec['er_specimen_name'], ' Banc= ',float(NLTpars['banc'])*1e6 if anis==0 and frac!=0: CrSpecRec={} for key in NltSpecRec.keys():CrSpecRec[key]=NltSpecRec[key] inten=frac*float(CrSpecRec['specimen_int']) CrSpecRec["specimen_int"]='%9.4e '%(inten) # adjust specimen intensity by cooling rate correction CrSpecRec['magic_method_codes'] = CrSpecRec['magic_method_codes']+':DA-CR-'+crtype CRSpecs.append(CrSpecRec) NltSpecRecs.append(NltSpecRec) # # check on anisotropy correction if anis==1: if NltSpecRec!="": Spc=NltSpecRec else: # find uncorrected data Spc=PmagSpecRec for AniSpec in anis_data: if AniSpec["er_specimen_name"]==PmagSpecRec["er_specimen_name"]: AniSpecRec=pmag.thellier_anis_corr(Spc,AniSpec) AniSpecRec['specimen_grade']=PmagSpecRec['specimen_grade'] inst_codes=Spc["magic_instrument_codes"] if "magic_instrument_codes" in AniSpec.keys(): if inst_codes=="unknown": inst_codes=AniSpec["magic_instrument_codes"] else: inst_codes=inst_codes+":"+AniSpec["magic_instrument_codes"] AniSpecRec["magic_instrument_codes"]=inst_codes AniSpecRec["specimen_correction"]='c' AniSpecRec["magic_software_packages"]=version_num if frac!=0: CrSpecRec={} for key in AniSpecRec.keys():CrSpecRec[key]=AniSpecRec[key] inten=frac*float(CrSpecRec['specimen_int']) CrSpecRec["specimen_int"]='%9.4e '%(inten) # adjust specimen intensity by cooling rate correction CrSpecRec['magic_method_codes'] = CrSpecRec['magic_method_codes']+':DA-CR-'+crtype CRSpecs.append(CrSpecRec) AniSpecRecs.append(AniSpecRec) break elif anis==1: for AniSpec in anis_data: if AniSpec["er_specimen_name"]==PmagSpecRec["er_specimen_name"]: AniSpecRec=pmag.thellier_anis_corr(PmagSpecRec,AniSpec) AniSpecRec['specimen_grade']=PmagSpecRec['specimen_grade'] inst_codes=PmagSpecRec["magic_instrument_codes"] if "magic_instrument_codes" in AniSpec.keys(): if inst_codes=="unknown": inst_codes=AniSpec["magic_instrument_codes"] else: inst_codes=inst_codes+":"+AniSpec["magic_instrument_codes"] AniSpecRec["magic_instrument_codes"]=inst_codes AniSpecRec["specimen_correction"]='c' AniSpecRec["magic_software_packages"]=version_num if frac!=0: CrSpecRec={} for key in AniSpecRec.keys():CrSpecRec[key]=AniSpecRec[key] inten=frac*float(CrSpecRec['specimen_int']) CrSpecRec["specimen_int"]='%9.4e '%(inten) # adjust specimen intensity by cooling rate correction CrSpecRec['magic_method_codes'] = CrSpecRec['magic_method_codes']+':DA-CR-'+crtype CRSpecs.append(CrSpecRec) AniSpecRecs.append(AniSpecRec) break spec +=1 else: print "skipping ",s spec+=1 pmag_file=dir_path+'/'+pmag_file pmag.magic_write(pmag_file,PmagSpecs,'pmag_specimens') if anis==1: anisout=dir_path+'/'+anisout pmag.magic_write(anisout,AniSpecRecs,'pmag_specimens') if nltrm==1: nltout=dir_path+'/'+nltout pmag.magic_write(nltout,NltSpecRecs,'pmag_specimens') if frac!=0: crout=dir_path+'/'+crout pmag.magic_write(crout,CRSpecs,'pmag_specimens')
def main(): """ NAME zeq_magic_redo.py DESCRIPTION Calculate principal components through demagnetization data using bounds and calculation type stored in "redo" file SYNTAX zeq_magic_redo.py [command line options] OPTIONS -h prints help message -usr USER: identify user, default is "" -f: specify input file, default is magic_measurements.txt -F: specify output file, default is zeq_specimens.txt -fre REDO: specify redo file, default is "zeq_redo" -fsa SAMPFILE: specify er_samples format file, default is "er_samples.txt" -A : don't average replicate measurements, default is yes -crd [s,g,t] : specify coordinate system [s,g,t] [default is specimen coordinates] are specimen, geographic, and tilt corrected respectively NB: you must have a SAMPFILE in this directory to rotate from specimen coordinates -leg: attaches "Recalculated from original measurements; supercedes published results. " to comment field INPUTS zeq_redo format file is: specimen_name calculation_type[DE-BFL,DE-BFL-A,DE-BFL-O,DE-BFP,DE-FM] step_min step_max component_name[A,B,C] """ dir_path='.' INCL=["LT-NO","LT-AF-Z","LT-T-Z","LT-M-Z"] # looking for demag data beg,end,pole,geo,tilt,askave,save=0,0,[],0,0,0,0 user,doave,comment= "",1,"" geo,tilt=0,0 version_num=pmag.get_version() args=sys.argv if '-WD' in args: ind=args.index('-WD') dir_path=args[ind+1] meas_file,pmag_file,mk_file= dir_path+"/"+"magic_measurements.txt",dir_path+"/"+"zeq_specimens.txt",dir_path+"/"+"zeq_redo" samp_file,coord=dir_path+"/"+"er_samples.txt","" if "-h" in args: print main.__doc__ sys.exit() if "-usr" in args: ind=args.index("-usr") user=sys.argv[ind+1] if "-A" in args:doave=0 if "-leg" in args: comment="Recalculated from original measurements; supercedes published results. " if "-f" in args: ind=args.index("-f") meas_file=dir_path+'/'+sys.argv[ind+1] if "-F" in args: ind=args.index("-F") pmag_file=dir_path+'/'+sys.argv[ind+1] if "-fre" in args: ind=args.index("-fre") mk_file=dir_path+"/"+args[ind+1] try: mk_f=open(mk_file,'rU') except: print "Bad redo file" sys.exit() mkspec,skipped=[],[] speclist=[] for line in mk_f.readlines(): tmp=line.split() mkspec.append(tmp) speclist.append(tmp[0]) if "-fsa" in args: ind=args.index("-fsa") samp_file=dir_path+'/'+sys.argv[ind+1] if "-crd" in args: ind=args.index("-crd") coord=sys.argv[ind+1] if coord=="g":geo,tilt=1,0 if coord=="t":geo,tilt=1,1 # # now get down to bidness if geo==1: samp_data,file_type=pmag.magic_read(samp_file) if file_type != 'er_samples': print file_type print "This is not a valid er_samples file " sys.exit() # set orientation priorities SO_methods=[] for rec in samp_data: if "magic_method_codes" in rec: methlist=rec["magic_method_codes"] for meth in methlist.split(":"): if "SO" in meth and "SO-POM" not in meth.strip(): if meth.strip() not in SO_methods: SO_methods.append(meth.strip()) SO_priorities=pmag.set_priorities(SO_methods,0) # # # meas_data,file_type=pmag.magic_read(meas_file) if file_type != 'magic_measurements': print file_type print file_type,"This is not a valid magic_measurements file " sys.exit() # # sort the specimen names # k = 0 print 'Processing ',len(speclist), ' specimens - please wait' PmagSpecs=[] while k < len(speclist): s=speclist[k] recnum=0 PmagSpecRec={} method_codes,inst_codes=[],[] # find the data from the meas_data file for this sample # # collect info for the PmagSpecRec dictionary # meas_meth=[] for rec in meas_data: # copy of vital stats to PmagSpecRec from first spec record in demag block skip=1 if rec["er_specimen_name"]==s: methods=rec["magic_method_codes"].split(":") if len(set(methods) & set(INCL))>0: PmagSpecRec["er_analyst_mail_names"]=user PmagSpecRec["magic_software_packages"]=version_num PmagSpecRec["er_specimen_name"]=s PmagSpecRec["er_sample_name"]=rec["er_sample_name"] PmagSpecRec["er_site_name"]=rec["er_site_name"] PmagSpecRec["er_location_name"]=rec["er_location_name"] PmagSpecRec["er_citation_names"]="This study" if "magic_experiment_name" not in rec.keys(): rec["magic_experiment_name"]="" PmagSpecRec["magic_experiment_names"]=rec["magic_experiment_name"] if "magic_instrument_codes" not in rec.keys(): rec["magic_instrument_codes"]="" inst=rec['magic_instrument_codes'].split(":") for I in inst: if I not in inst_codes: # copy over instruments inst_codes.append(I) meths=rec["magic_method_codes"].split(":") for meth in meths: if meth.strip() not in meas_meth:meas_meth.append(meth) if "LP-DIR-AF" in meas_meth or "LT-AF-Z" in meas_meth: PmagSpecRec["measurement_step_unit"]="T" if "LP-DIR-AF" not in method_codes:method_codes.append("LP-DIR-AF") if "LP-DIR-T" in meas_meth or "LT-T-Z" in meas_meth: PmagSpecRec["measurement_step_unit"]="K" if "LP-DIR-T" not in method_codes:method_codes.append("LP-DIR-T") if "LP-DIR-M" in meas_meth or "LT-M-Z" in meas_meth: PmagSpecRec["measurement_step_unit"]="J" if "LP-DIR-M" not in method_codes:method_codes.append("LP-DIR-M") if PmagSpecRec=={}: print 'no data found for specimen: ',s print 'delete from zeq_redo input file...., then try again' sys.exit() # # data,units=pmag.find_dmag_rec(s,meas_data) # datablock=data noskip=1 if len(datablock) <2 or s not in speclist : noskip=0 k+=1 # print 'skipping ', s,len(datablock) if noskip: # # find replicate measurements at given treatment step and average them # # step_meth,avedata=pmag.vspec(data) # # if len(avedata) != len(datablock): # if doave==1: # method_codes.append("DE-VM") # datablock=avedata # # do geo or stratigraphic correction now # if geo==1: # find top priority orientation method redo,p=1,0 if len(SO_methods)<=1: az_type=SO_methods[0] orient=pmag.find_samp_rec(PmagSpecRec["er_sample_name"],samp_data,az_type) if orient["sample_azimuth"] !="": method_codes.append(az_type) redo=0 while redo==1: if p>=len(SO_priorities): print "no orientation data for ",s orient["sample_azimuth"]="" orient["sample_dip"]="" method_codes.append("SO-NO") redo=0 else: az_type=SO_methods[SO_methods.index(SO_priorities[p])] orient=pmag.find_samp_rec(PmagSpecRec["er_sample_name"],samp_data,az_type) if orient["sample_azimuth"] !="": method_codes.append(az_type) redo=0 p+=1 # # if tilt selected, get stratigraphic correction # tiltblock,geoblock=[],[] for rec in datablock: if "sample_azimuth" in orient.keys() and orient["sample_azimuth"]!="": d_geo,i_geo=pmag.dogeo(rec[1],rec[2],orient["sample_azimuth"],orient["sample_dip"]) geoblock.append([rec[0],d_geo,i_geo,rec[3],rec[4],rec[5]]) if tilt==1 and "sample_bed_dip_direction" in orient.keys(): d_tilt,i_tilt=pmag.dotilt(d_geo,i_geo,orient["sample_bed_dip_direction"],orient["sample_bed_dip"]) tiltblock.append([rec[0],d_tilt,i_tilt,rec[3],rec[4],rec[5]]) elif tilt==1: if PmagSpecRec["er_sample_name"] not in skipped: print 'no tilt correction for ', PmagSpecRec["er_sample_name"],' skipping....' skipped.append(PmagSpecRec["er_sample_name"]) else: if PmagSpecRec["er_sample_name"] not in skipped: print 'no geographic correction for ', PmagSpecRec["er_sample_name"],' skipping....' skipped.append(PmagSpecRec["er_sample_name"]) # # get beg_pca, end_pca, pca if PmagSpecRec['er_sample_name'] not in skipped: compnum=-1 for spec in mkspec: if spec[0]==s: CompRec={} for key in PmagSpecRec.keys():CompRec[key]=PmagSpecRec[key] compnum+=1 calculation_type=spec[1] beg=float(spec[2]) end=float(spec[3]) if len(spec)>4: comp_name=spec[4] else: comp_name=string.uppercase[compnum] CompRec['specimen_comp_name']=comp_name if beg < float(datablock[0][0]):beg=float(datablock[0][0]) if end > float(datablock[-1][0]):end=float(datablock[-1][0]) for l in range(len(datablock)): if datablock[l][0]==beg:beg_pca=l if datablock[l][0]==end:end_pca=l if geo==1 and tilt==0: mpars=pmag.domean(geoblock,beg_pca,end_pca,calculation_type) if mpars["specimen_direction_type"]!="Error": CompRec["specimen_dec"]='%7.1f ' %(mpars["specimen_dec"]) CompRec["specimen_inc"]='%7.1f ' %(mpars["specimen_inc"]) CompRec["specimen_tilt_correction"]='0' if geo==1 and tilt==1: mpars=pmag.domean(tiltblock,beg_pca,end_pca,calculation_type) if mpars["specimen_direction_type"]!="Error": CompRec["specimen_dec"]='%7.1f ' %(mpars["specimen_dec"]) CompRec["specimen_inc"]='%7.1f ' %(mpars["specimen_inc"]) CompRec["specimen_tilt_correction"]='100' if geo==0 and tilt==0: mpars=pmag.domean(datablock,beg_pca,end_pca,calculation_type) if mpars["specimen_direction_type"]!="Error": CompRec["specimen_dec"]='%7.1f ' %(mpars["specimen_dec"]) CompRec["specimen_inc"]='%7.1f ' %(mpars["specimen_inc"]) CompRec["specimen_tilt_correction"]='-1' if mpars["specimen_direction_type"]=="Error": pass else: CompRec["measurement_step_min"]='%8.3e '%(datablock[beg_pca][0]) try: CompRec["measurement_step_max"]='%8.3e '%(datablock[end_pca][0] ) except: print 'error in end_pca ',PmagSpecRec['er_specimen_name'] CompRec["specimen_correction"]='u' if calculation_type!='DE-FM': CompRec["specimen_mad"]='%7.1f '%(mpars["specimen_mad"]) CompRec["specimen_alpha95"]="" else: CompRec["specimen_mad"]="" CompRec["specimen_alpha95"]='%7.1f '%(mpars["specimen_alpha95"]) CompRec["specimen_n"]='%i '%(mpars["specimen_n"]) CompMeths=[] for meth in method_codes: if meth not in CompMeths:CompMeths.append(meth) if calculation_type not in CompMeths:CompMeths.append(calculation_type) if geo==1: CompMeths.append("DA-DIR-GEO") if tilt==1: CompMeths.append("DA-DIR-TILT") if "DE-BFP" not in calculation_type: CompRec["specimen_direction_type"]='l' else: CompRec["specimen_direction_type"]='p' CompRec["magic_method_codes"]="" if len(CompMeths) != 0: methstring="" for meth in CompMeths: methstring=methstring+ ":" +meth CompRec["magic_method_codes"]=methstring.strip(':') CompRec["specimen_description"]=comment if len(inst_codes) != 0: inststring="" for inst in inst_codes: inststring=inststring+ ":" +inst CompRec["magic_instrument_codes"]=inststring.strip(':') PmagSpecs.append(CompRec) k+=1 pmag.magic_write(pmag_file,PmagSpecs,'pmag_specimens') print "Recalculated specimen data stored in ",pmag_file
def main(): """ NAME thellier_magic_redo.py DESCRIPTION Calculates paleointensity parameters for thellier-thellier type data using bounds stored in the "redo" file SYNTAX thellier_magic_redo [command line options] OPTIONS -h prints help message -usr USER: identify user, default is "" -fcr CRIT, set criteria for grading -f IN: specify input file, default is magic_measurements.txt -fre REDO: specify redo file, default is "thellier_redo" -F OUT: specify output file, default is thellier_specimens.txt -leg: attaches "Recalculated from original measurements; supercedes published results. " to comment field -CR PERC TYPE: apply a blanket cooling rate correction if none supplied in the er_samples.txt file PERC should be a percentage of original (say reduce to 90%) TYPE should be one of the following: EG (for educated guess); PS (based on pilots); TRM (based on comparison of two TRMs) -ANI: perform anisotropy correction -fsa SAMPFILE: er_samples.txt file with cooling rate correction information, default is NO CORRECTION -Fcr CRout: specify pmag_specimen format file for cooling rate corrected data -fan ANIFILE: specify rmag_anisotropy format file, default is rmag_anisotropy.txt -Fac ACout: specify pmag_specimen format file for anisotropy corrected data default is AC_specimens.txt -fnl NLTFILE: specify magic_measurments format file, default is magic_measurements.txt -Fnl NLTout: specify pmag_specimen format file for non-linear trm corrected data default is NLT_specimens.txt -z use z component differenences for pTRM calculation INPUT a thellier_redo file is Specimen_name Tmin Tmax (where Tmin and Tmax are in Centigrade) """ dir_path = "." critout = "" version_num = pmag.get_version() field, first_save = -1, 1 spec, recnum, start, end = 0, 0, 0, 0 crfrac = 0 NltRecs, PmagSpecs, AniSpecRecs, NltSpecRecs, CRSpecs = [], [], [], [], [] meas_file, pmag_file, mk_file = "magic_measurements.txt", "thellier_specimens.txt", "thellier_redo" anis_file = "rmag_anisotropy.txt" anisout, nltout = "AC_specimens.txt", "NLT_specimens.txt" crout = "CR_specimens.txt" nlt_file = "" samp_file = "" comment, user = "", "unknown" anis, nltrm = 0, 0 jackknife = 0 # maybe in future can do jackknife args = sys.argv Zdiff = 0 if "-WD" in args: ind = args.index("-WD") dir_path = args[ind + 1] if "-h" in args: print main.__doc__ sys.exit() if "-usr" in args: ind = args.index("-usr") user = sys.argv[ind + 1] if "-leg" in args: comment = "Recalculated from original measurements; supercedes published results. " cool = 0 if "-CR" in args: cool = 1 ind = args.index("-CR") crfrac = 0.01 * float(sys.argv[ind + 1]) crtype = "DA-CR-" + sys.argv[ind + 2] if "-Fcr" in args: ind = args.index("-Fcr") crout = sys.argv[ind + 1] if "-f" in args: ind = args.index("-f") meas_file = sys.argv[ind + 1] if "-F" in args: ind = args.index("-F") pmag_file = sys.argv[ind + 1] if "-fre" in args: ind = args.index("-fre") mk_file = args[ind + 1] if "-fsa" in args: ind = args.index("-fsa") samp_file = dir_path + "/" + args[ind + 1] Samps, file_type = pmag.magic_read(samp_file) SampCRs = pmag.get_dictitem(Samps, "cooling_rate_corr", "", "F") # get samples cooling rate corrections cool = 1 if file_type != "er_samples": print "not a valid er_samples.txt file" sys.exit() # # if "-ANI" in args: anis = 1 ind = args.index("-ANI") if "-Fac" in args: ind = args.index("-Fac") anisout = args[ind + 1] if "-fan" in args: ind = args.index("-fan") anis_file = args[ind + 1] # if "-NLT" in args: if "-Fnl" in args: ind = args.index("-Fnl") nltout = args[ind + 1] if "-fnl" in args: ind = args.index("-fnl") nlt_file = args[ind + 1] if "-z" in args: Zdiff = 1 if "-fcr" in sys.argv: ind = args.index("-fcr") critout = sys.argv[ind + 1] # # start reading in data: # meas_file = dir_path + "/" + meas_file mk_file = dir_path + "/" + mk_file accept = pmag.default_criteria(1)[0] # set criteria to none if critout != "": critout = dir_path + "/" + critout crit_data, file_type = pmag.magic_read(critout) if file_type != "pmag_criteria": print "bad pmag_criteria file, using no acceptance criteria" print "Acceptance criteria read in from ", critout for critrec in crit_data: if "sample_int_sigma_uT" in critrec.keys(): # accommodate Shaar's new criterion critrec["sample_int_sigma"] = "%10.3e" % (eval(critrec["sample_int_sigma_uT"]) * 1e-6) for key in critrec.keys(): if key not in accept.keys() and critrec[key] != "": accept[key] = critrec[key] meas_data, file_type = pmag.magic_read(meas_file) if file_type != "magic_measurements": print file_type print file_type, "This is not a valid magic_measurements file " sys.exit() try: mk_f = open(mk_file, "rU") except: print "Bad redo file" sys.exit() mkspec = [] speclist = [] for line in mk_f.readlines(): tmp = line.split() mkspec.append(tmp) speclist.append(tmp[0]) if anis == 1: anis_file = dir_path + "/" + anis_file anis_data, file_type = pmag.magic_read(anis_file) if file_type != "rmag_anisotropy": print file_type print file_type, "This is not a valid rmag_anisotropy file " sys.exit() if nlt_file == "": nlt_data = pmag.get_dictitem( meas_data, "magic_method_codes", "LP-TRM", "has" ) # look for trm acquisition data in the meas_data file else: nlt_file = dir_path + "/" + nlt_file nlt_data, file_type = pmag.magic_read(nlt_file) if len(nlt_data) > 0: nltrm = 1 # # sort the specimen names and step through one by one # sids = pmag.get_specs(meas_data) # print "Processing ", len(speclist), " specimens - please wait " while spec < len(speclist): s = speclist[spec] recnum = 0 datablock = [] PmagSpecRec = {} PmagSpecRec["er_analyst_mail_names"] = user PmagSpecRec["er_citation_names"] = "This study" PmagSpecRec["magic_software_packages"] = version_num methcodes, inst_code = [], "" # # find the data from the meas_data file for this specimen # datablock = pmag.get_dictitem(meas_data, "er_specimen_name", s, "T") datablock = pmag.get_dictitem( datablock, "magic_method_codes", "LP-PI-TRM", "has" ) # pick out the thellier experiment data if len(datablock) > 0: for rec in datablock: if "magic_instrument_codes" not in rec.keys(): rec["magic_instrument_codes"] = "unknown" # # collect info for the PmagSpecRec dictionary # rec = datablock[0] PmagSpecRec["er_specimen_name"] = s PmagSpecRec["er_sample_name"] = rec["er_sample_name"] PmagSpecRec["er_site_name"] = rec["er_site_name"] PmagSpecRec["er_location_name"] = rec["er_location_name"] PmagSpecRec["measurement_step_unit"] = "K" PmagSpecRec["specimen_correction"] = "u" if "er_expedition_name" in rec.keys(): PmagSpecRec["er_expedition_name"] = rec["er_expedition_name"] if "magic_instrument_codes" not in rec.keys(): PmagSpecRec["magic_instrument_codes"] = "unknown" else: PmagSpecRec["magic_instrument_codes"] = rec["magic_instrument_codes"] if "magic_experiment_name" not in rec.keys(): rec["magic_experiment_name"] = "" else: PmagSpecRec["magic_experiment_names"] = rec["magic_experiment_name"] meths = rec["magic_experiment_name"].split(":") for meth in meths: if meth.strip() not in methcodes and "LP-" in meth: methcodes.append(meth.strip()) # # sort out the data into first_Z, first_I, ptrm_check, ptrm_tail # araiblock, field = pmag.sortarai(datablock, s, Zdiff) first_Z = araiblock[0] first_I = araiblock[1] ptrm_check = araiblock[2] ptrm_tail = araiblock[3] if len(first_I) < 3 or len(first_Z) < 4: spec += 1 print "skipping specimen ", s else: # # get start, end # for redospec in mkspec: if redospec[0] == s: b, e = float(redospec[1]), float(redospec[2]) break if e > float(first_Z[-1][0]): e = float(first_Z[-1][0]) for recnum in range(len(first_Z)): if first_Z[recnum][0] == b: start = recnum if first_Z[recnum][0] == e: end = recnum nsteps = end - start if nsteps > 2: zijdblock, units = pmag.find_dmag_rec(s, meas_data) pars, errcode = pmag.PintPars(datablock, araiblock, zijdblock, start, end, accept) if "specimen_scat" in pars.keys(): PmagSpecRec["specimen_scat"] = pars["specimen_scat"] if "specimen_frac" in pars.keys(): PmagSpecRec["specimen_frac"] = "%5.3f" % (pars["specimen_frac"]) if "specimen_gmax" in pars.keys(): PmagSpecRec["specimen_gmax"] = "%5.3f" % (pars["specimen_gmax"]) pars["measurement_step_unit"] = units pars["specimen_lab_field_dc"] = field pars["specimen_int"] = -1 * field * pars["specimen_b"] PmagSpecRec["measurement_step_min"] = "%8.3e" % (pars["measurement_step_min"]) PmagSpecRec["measurement_step_max"] = "%8.3e" % (pars["measurement_step_max"]) PmagSpecRec["specimen_int_n"] = "%i" % (pars["specimen_int_n"]) PmagSpecRec["specimen_lab_field_dc"] = "%8.3e" % (pars["specimen_lab_field_dc"]) PmagSpecRec["specimen_int"] = "%9.4e " % (pars["specimen_int"]) PmagSpecRec["specimen_b"] = "%5.3f " % (pars["specimen_b"]) PmagSpecRec["specimen_q"] = "%5.1f " % (pars["specimen_q"]) PmagSpecRec["specimen_f"] = "%5.3f " % (pars["specimen_f"]) PmagSpecRec["specimen_fvds"] = "%5.3f" % (pars["specimen_fvds"]) PmagSpecRec["specimen_b_beta"] = "%5.3f" % (pars["specimen_b_beta"]) PmagSpecRec["specimen_int_mad"] = "%7.1f" % (pars["specimen_int_mad"]) PmagSpecRec["specimen_Z"] = "%7.1f" % (pars["specimen_Z"]) PmagSpecRec["specimen_gamma"] = "%7.1f" % (pars["specimen_gamma"]) if pars["method_codes"] != "" and pars["method_codes"] not in methcodes: methcodes.append(pars["method_codes"]) PmagSpecRec["specimen_dec"] = "%7.1f" % (pars["specimen_dec"]) PmagSpecRec["specimen_inc"] = "%7.1f" % (pars["specimen_inc"]) PmagSpecRec["specimen_tilt_correction"] = "-1" PmagSpecRec["specimen_direction_type"] = "l" PmagSpecRec["direction_type"] = "l" # this is redudant, but helpful - won't be imported PmagSpecRec["specimen_dang"] = "%7.1f " % (pars["specimen_dang"]) PmagSpecRec["specimen_drats"] = "%7.1f " % (pars["specimen_drats"]) PmagSpecRec["specimen_drat"] = "%7.1f " % (pars["specimen_drat"]) PmagSpecRec["specimen_int_ptrm_n"] = "%i " % (pars["specimen_int_ptrm_n"]) PmagSpecRec["specimen_rsc"] = "%6.4f " % (pars["specimen_rsc"]) PmagSpecRec["specimen_md"] = "%i " % (int(pars["specimen_md"])) if PmagSpecRec["specimen_md"] == "-1": PmagSpecRec["specimen_md"] = "" PmagSpecRec["specimen_b_sigma"] = "%5.3f " % (pars["specimen_b_sigma"]) if "IE-TT" not in methcodes: methcodes.append("IE-TT") methods = "" for meth in methcodes: methods = methods + meth + ":" PmagSpecRec["magic_method_codes"] = methods.strip(":") PmagSpecRec["magic_software_packages"] = version_num PmagSpecRec["specimen_description"] = comment if critout != "": kill = pmag.grade(PmagSpecRec, accept, "specimen_int") if len(kill) > 0: Grade = "F" # fails else: Grade = "A" # passes PmagSpecRec["specimen_grade"] = Grade else: PmagSpecRec["specimen_grade"] = "" # not graded if nltrm == 0 and anis == 0 and cool != 0: # apply cooling rate correction SCR = pmag.get_dictitem( SampCRs, "er_sample_name", PmagSpecRec["er_sample_name"], "T" ) # get this samples, cooling rate correction CrSpecRec = pmag.cooling_rate(PmagSpecRec, SCR, crfrac, crtype) if CrSpecRec["er_specimen_name"] != "none": CrSpecs.append(CrSpecRec) PmagSpecs.append(PmagSpecRec) NltSpecRec = "" # # check on non-linear TRM correction # if nltrm == 1: # # find the data from the nlt_data list for this specimen # TRMs, Bs = [], [] NltSpecRec = "" NltRecs = pmag.get_dictitem( nlt_data, "er_specimen_name", PmagSpecRec["er_specimen_name"], "has" ) # fish out all the NLT data for this specimen if len(NltRecs) > 2: for NltRec in NltRecs: Bs.append(float(NltRec["treatment_dc_field"])) TRMs.append(float(NltRec["measurement_magn_moment"])) NLTpars = nlt.NLtrm( Bs, TRMs, float(PmagSpecRec["specimen_int"]), float(PmagSpecRec["specimen_lab_field_dc"]), 0, ) if NLTpars["banc"] > 0: NltSpecRec = {} for key in PmagSpecRec.keys(): NltSpecRec[key] = PmagSpecRec[key] NltSpecRec["specimen_int"] = "%9.4e" % (NLTpars["banc"]) NltSpecRec["magic_method_codes"] = PmagSpecRec["magic_method_codes"] + ":DA-NL" NltSpecRec["specimen_correction"] = "c" NltSpecRec["specimen_grade"] = PmagSpecRec["specimen_grade"] NltSpecRec["magic_software_packages"] = version_num print NltSpecRec["er_specimen_name"], " Banc= ", float(NLTpars["banc"]) * 1e6 if anis == 0 and cool != 0: SCR = pmag.get_dictitem( SampCRs, "er_sample_name", NltSpecRec["er_sample_name"], "T" ) # get this samples, cooling rate correction CrSpecRec = pmag.cooling_rate(NltSpecRec, SCR, crfrac, crtype) if CrSpecRec["er_specimen_name"] != "none": CrSpecs.append(CrSpecRec) NltSpecRecs.append(NltSpecRec) # # check on anisotropy correction if anis == 1: if NltSpecRec != "": Spc = NltSpecRec else: # find uncorrected data Spc = PmagSpecRec AniSpecs = pmag.get_dictitem( anis_data, "er_specimen_name", PmagSpecRec["er_specimen_name"], "T" ) if len(AniSpecs) > 0: AniSpec = AniSpecs[0] AniSpecRec = pmag.doaniscorr(Spc, AniSpec) AniSpecRec["specimen_grade"] = PmagSpecRec["specimen_grade"] AniSpecRec["magic_instrument_codes"] = PmagSpecRec["magic_instrument_codes"] AniSpecRec["specimen_correction"] = "c" AniSpecRec["magic_software_packages"] = version_num if cool != 0: SCR = pmag.get_dictitem( SampCRs, "er_sample_name", AniSpecRec["er_sample_name"], "T" ) # get this samples, cooling rate correction CrSpecRec = pmag.cooling_rate(AniSpecRec, SCR, crfrac, crtype) if CrSpecRec["er_specimen_name"] != "none": CrSpecs.append(CrSpecRec) AniSpecRecs.append(AniSpecRec) elif anis == 1: AniSpecs = pmag.get_dictitem( anis_data, "er_specimen_name", PmagSpecRec["er_specimen_name"], "T" ) if len(AniSpecs) > 0: AniSpec = AniSpecs[0] AniSpecRec = pmag.doaniscorr(PmagSpecRec, AniSpec) AniSpecRec["specimen_grade"] = PmagSpecRec["specimen_grade"] AniSpecRec["magic_instrument_codes"] = PmagSpecRec["magic_instrument_codes"] AniSpecRec["specimen_correction"] = "c" AniSpecRec["magic_software_packages"] = version_num if crfrac != 0: CrSpecRec = {} for key in AniSpecRec.keys(): CrSpecRec[key] = AniSpecRec[key] inten = frac * float(CrSpecRec["specimen_int"]) CrSpecRec["specimen_int"] = "%9.4e " % ( inten ) # adjust specimen intensity by cooling rate correction CrSpecRec["magic_method_codes"] = CrSpecRec["magic_method_codes"] + ":DA-CR-" + crtype CRSpecs.append(CrSpecRec) AniSpecRecs.append(AniSpecRec) spec += 1 else: print "skipping ", s spec += 1 pmag_file = dir_path + "/" + pmag_file pmag.magic_write(pmag_file, PmagSpecs, "pmag_specimens") print "uncorrected thellier data saved in: ", pmag_file if anis == 1 and len(AniSpecRecs) > 0: anisout = dir_path + "/" + anisout pmag.magic_write(anisout, AniSpecRecs, "pmag_specimens") print "anisotropy corrected data saved in: ", anisout if nltrm == 1 and len(NltSpecRecs) > 0: nltout = dir_path + "/" + nltout pmag.magic_write(nltout, NltSpecRecs, "pmag_specimens") print "non-linear TRM corrected data saved in: ", nltout if crfrac != 0: crout = dir_path + "/" + crout pmag.magic_write(crout, CRSpecs, "pmag_specimens") print "cooling rate corrected data saved in: ", crout
def main(): """ NAME thellier_magic.py DESCRIPTION plots Thellier-Thellier, allowing interactive setting of bounds and customizing of selection criteria. Saves and reads interpretations from a pmag_specimen formatted table, default: thellier_specimens.txt SYNTAX thellier_magic.py [command line options] OPTIONS -h prints help message and quits -f MEAS, set magic_measurements input file -fsp PRIOR, set pmag_specimen prior interpretations file -fan ANIS, set rmag_anisotropy file for doing the anisotropy corrections -fcr CRIT, set criteria file for grading. -fmt [svg,png,jpg], format for images - default is svg -sav, saves plots with out review (default format) -spc SPEC, plots single specimen SPEC, saves plot with specified format with optional -b bounds adn quits -b BEG END: sets bounds for calculation BEG: starting step for slope calculation END: ending step for slope calculation -z use only z component difference for pTRM calculation DEFAULTS MEAS: magic_measurements.txt REDO: thellier_redo CRIT: NONE PRIOR: NONE OUTPUT figures: ALL: numbers refer to temperature steps in command line window 1) Arai plot: closed circles are zero-field first/infield open circles are infield first/zero-field triangles are pTRM checks squares are pTRM tail checks VDS is vector difference sum diamonds are bounds for interpretation 2) Zijderveld plot: closed (open) symbols are X-Y (X-Z) planes X rotated to NRM direction 3) (De/Re)Magnetization diagram: circles are NRM remaining squares are pTRM gained 4) equal area projections: green triangles are pTRM gained direction red (purple) circles are lower(upper) hemisphere of ZI step directions blue (cyan) squares are lower(upper) hemisphere IZ step directions 5) Optional: TRM acquisition 6) Optional: TDS normalization command line window: list is: temperature step numbers, temperatures (C), Dec, Inc, Int (units of magic_measuements) list of possible commands: type letter followed by return to select option saving of plots creates .svg format files with specimen_name, plot type as name """ # # initializations # meas_file,critout,inspec="magic_measurements.txt","","thellier_specimens.txt" first=1 inlt=0 version_num=pmag.get_version() TDinit,Tinit,field,first_save=0,0,-1,1 user,comment,AniSpec,locname="",'',"","" ans,specimen,recnum,start,end=0,0,0,0,0 plots,pmag_out,samp_file,style=0,"","","svg" verbose=pmagplotlib.verbose fmt='.'+style # # default acceptance criteria # accept=pmag.default_criteria(0)[0] # set the default criteria # # parse command line options # Zdiff,anis=0,0 spc,BEG,END="","","" if '-h' in sys.argv: print main.__doc__ sys.exit() if '-f' in sys.argv: ind=sys.argv.index('-f') meas_file=sys.argv[ind+1] if '-fsp' in sys.argv: ind=sys.argv.index('-fsp') inspec=sys.argv[ind+1] if '-fan' in sys.argv: ind=sys.argv.index('-fan') anisfile=sys.argv[ind+1] anis=1 anis_data,file_type=pmag.magic_read(anisfile) if verbose: print "Anisotropy data read in from ", anisfile if '-fmt' in sys.argv: ind=sys.argv.index('-fmt') fmt='.'+sys.argv[ind+1] if '-sav' in sys.argv: plots=1 verbose=0 if '-z' in sys.argv: Zdiff=1 if '-spc' in sys.argv: ind=sys.argv.index('-spc') spc=sys.argv[ind+1] if '-b' in sys.argv: ind=sys.argv.index('-b') BEG=int(sys.argv[ind+1]) END=int(sys.argv[ind+2]) if '-fcr' in sys.argv: ind=sys.argv.index('-fcr') critout=sys.argv[ind+1] crit_data,file_type=pmag.magic_read(critout) if file_type!='pmag_criteria': if verbose: print 'bad pmag_criteria file, using no acceptance criteria' accept=pmag.default_criteria(1)[0] else: if verbose: print "Acceptance criteria read in from ", critout accept={'pmag_criteria_code':'ACCEPTANCE','er_citation_names':'This study'} for critrec in crit_data: if 'sample_int_sigma_uT' in critrec.keys(): # accommodate Shaar's new criterion critrec['sample_int_sigma']='%10.3e'%(eval(critrec['sample_int_sigma_uT'])*1e-6) for key in critrec.keys(): if key not in accept.keys() and critrec[key]!='': accept[key]=critrec[key] try: open(inspec,'rU') PriorRecs,file_type=pmag.magic_read(inspec) if file_type != 'pmag_specimens': print file_type print file_type,inspec," is not a valid pmag_specimens file " sys.exit() for rec in PriorRecs: if 'magic_software_packages' not in rec.keys():rec['magic_software_packages']="" except IOError: PriorRecs=[] if verbose:print "starting new specimen interpretation file: ",inspec meas_data,file_type=pmag.magic_read(meas_file) if file_type != 'magic_measurements': print file_type print file_type,"This is not a valid magic_measurements file " sys.exit() backup=0 # define figure numbers for arai, zijderveld and # de-,re-magization diagrams AZD={} AZD['deremag'], AZD['zijd'],AZD['arai'],AZD['eqarea']=1,2,3,4 pmagplotlib.plot_init(AZD['arai'],5,5) pmagplotlib.plot_init(AZD['zijd'],5,5) pmagplotlib.plot_init(AZD['deremag'],5,5) pmagplotlib.plot_init(AZD['eqarea'],5,5) # # # # get list of unique specimen names # CurrRec=[] sids=pmag.get_specs(meas_data) # get plots for specimen s - default is just to step through arai diagrams # if spc!="": specimen =sids.index(spc) while specimen < len(sids): methcodes=[] if verbose: print sids[specimen],specimen+1, 'of ', len(sids) MeasRecs=[] s=sids[specimen] datablock,trmblock,tdsrecs=[],[],[] PmagSpecRec={} if first==0: for key in keys:PmagSpecRec[key]="" # make sure all new records have same set of keys PmagSpecRec["er_analyst_mail_names"]=user PmagSpecRec["specimen_correction"]='u' # # find the data from the meas_data file for this specimen # for rec in meas_data: if rec["er_specimen_name"]==s: MeasRecs.append(rec) if "magic_method_codes" not in rec.keys(): rec["magic_method_codes"]="" methods=rec["magic_method_codes"].split(":") meths=[] for meth in methods: meths.append(meth.strip()) # take off annoying spaces methods="" for meth in meths: if meth.strip() not in methcodes and "LP-" in meth:methcodes.append(meth.strip()) methods=methods+meth+":" methods=methods[:-1] rec["magic_method_codes"]=methods if "LP-PI-TRM" in meths: datablock.append(rec) if "LP-TRM" in meths: trmblock.append(rec) if "LP-TRM-TD" in meths: tdsrecs.append(rec) if len(trmblock)>2 and inspec!="": if Tinit==0: Tinit=1 AZD['TRM']=5 pmagplotlib.plot_init(AZD['TRM'],5,5) elif Tinit==1: # clear the TRM figure if not needed pmagplotlib.clearFIG(AZD['TRM']) if len(tdsrecs)>2: if TDinit==0: TDinit=1 AZD['TDS']=6 pmagplotlib.plot_init(AZD['TDS'],5,5) elif TDinit==1: # clear the TDS figure if not needed pmagplotlib.clearFIG(AZD['TDS']) if len(datablock) <4: if backup==0: specimen+=1 if verbose: print 'skipping specimen - moving forward ', s else: specimen-=1 if verbose: print 'skipping specimen - moving backward ', s # # collect info for the PmagSpecRec dictionary # else: rec=datablock[0] PmagSpecRec["er_citation_names"]="This study" PmagSpecRec["er_specimen_name"]=s PmagSpecRec["er_sample_name"]=rec["er_sample_name"] PmagSpecRec["er_site_name"]=rec["er_site_name"] PmagSpecRec["er_location_name"]=rec["er_location_name"] locname=rec['er_location_name'].replace('/','-') if "er_expedition_name" in rec.keys():PmagSpecRec["er_expedition_name"]=rec["er_expedition_name"] if "magic_instrument_codes" not in rec.keys():rec["magic_instrument_codes"]="" PmagSpecRec["magic_instrument_codes"]=rec["magic_instrument_codes"] PmagSpecRec["measurement_step_unit"]="K" if "magic_experiment_name" not in rec.keys(): rec["magic_experiment_name"]="" else: PmagSpecRec["magic_experiment_names"]=rec["magic_experiment_name"] meths=rec["magic_method_codes"].split() # sort data into types araiblock,field=pmag.sortarai(datablock,s,Zdiff) first_Z=araiblock[0] GammaChecks=araiblock[5] if len(first_Z)<3: if backup==0: specimen+=1 if verbose: print 'skipping specimen - moving forward ', s else: specimen-=1 if verbose: print 'skipping specimen - moving backward ', s else: backup=0 zijdblock,units=pmag.find_dmag_rec(s,meas_data) recnum=0 if verbose: print "index step Dec Inc Int Gamma" for plotrec in zijdblock: if GammaChecks!="": gamma="" for g in GammaChecks: if g[0]==plotrec[0]-273: gamma=g[1] break if gamma!="": print '%i %i %7.1f %7.1f %8.3e %7.1f' % (recnum,plotrec[0]-273,plotrec[1],plotrec[2],plotrec[3],gamma) else: print '%i %i %7.1f %7.1f %8.3e ' % (recnum,plotrec[0]-273,plotrec[1],plotrec[2],plotrec[3]) recnum += 1 pmagplotlib.plotAZ(AZD,araiblock,zijdblock,s,units[0]) if verbose:pmagplotlib.drawFIGS(AZD) if len(tdsrecs)>2: # a TDS experiment tdsblock=[] # make a list for the TDS data Mkeys=['measurement_magnitude','measurement_magn_moment','measurement_magn_volume','measuruement_magn_mass'] mkey,k="",0 while mkey=="" and k<len(Mkeys)-1: # find which type of intensity key= Mkeys[k] if key in tdsrecs[0].keys() and tdsrecs[0][key]!="": mkey=key k+=1 if mkey=="":break # get outta here Tnorm="" for tdrec in tdsrecs: meths=tdrec['magic_method_codes'].split(":") for meth in meths: meth.replace(" ","") # strip off potential nasty spaces if 'LT-T-I' in meths and Tnorm=="": # found first total TRM Tnorm=float(tdrec[mkey]) # normalize by total TRM tdsblock.append([273,zijdblock[0][3]/Tnorm,1.]) # put in the zero step if 'LT-T-Z' in meths and Tnorm!="": # found a LP-TRM-TD demag step, now need complementary LT-T-Z from zijdblock step=float(tdrec['treatment_temp']) Tint="" if mkey!="": Tint=float(tdrec[mkey]) if Tint!="": for zrec in zijdblock: if zrec[0]==step: # found matching tdsblock.append([step,zrec[3]/Tnorm,Tint/Tnorm]) break if len(tdsblock)>2: pmagplotlib.plotTDS(AZD['TDS'],tdsblock,s+':LP-PI-TDS:') if verbose:pmagplotlib(drawFIGS(AZD)) else: print "Something wrong here" if anis==1: # look up anisotropy data for this specimen AniSpec="" for aspec in anis_data: if aspec["er_specimen_name"]==PmagSpecRec["er_specimen_name"]: AniSpec=aspec if verbose: print 'Found anisotropy record...' break if inspec !="": if verbose: print 'Looking up saved interpretation....' found = 0 for k in range(len(PriorRecs)): try: if PriorRecs[k]["er_specimen_name"]==s: found =1 CurrRec.append(PriorRecs[k]) for j in range(len(zijdblock)): if float(zijdblock[j][0])==float(PriorRecs[k]["measurement_step_min"]):start=j if float(zijdblock[j][0])==float(PriorRecs[k]["measurement_step_max"]):end=j pars,errcode=pmag.PintPars(datablock,araiblock,zijdblock,start,end,accept) pars['measurement_step_unit']="K" pars['experiment_type']='LP-PI-TRM' del PriorRecs[k] # put in CurrRec, take out of PriorRecs if errcode!=1: pars["specimen_lab_field_dc"]=field pars["specimen_int"]=-1*field*pars["specimen_b"] pars["er_specimen_name"]=s if verbose: print 'Saved interpretation: ' pars,kill=pmag.scoreit(pars,PmagSpecRec,accept,'',verbose) pmagplotlib.plotB(AZD,araiblock,zijdblock,pars) if verbose:pmagplotlib.drawFIGS(AZD) if len(trmblock)>2: blab=field best=pars["specimen_int"] Bs,TRMs=[],[] for trec in trmblock: Bs.append(float(trec['treatment_dc_field'])) TRMs.append(float(trec['measurement_magn_moment'])) NLpars=nlt.NLtrm(Bs,TRMs,best,blab,0) # calculate best fit parameters through TRM acquisition data, and get new banc Mp,Bp=[],[] for k in range(int(max(Bs)*1e6)): Bp.append(float(k)*1e-6) npred=nlt.TRM(Bp[-1],NLpars['xopt'][0],NLpars['xopt'][1]) # predicted NRM for this field Mp.append(npred) pmagplotlib.plotTRM(AZD['TRM'],Bs,TRMs,Bp,Mp,NLpars,trec['magic_experiment_name']) PmagSpecRec['specimen_int']=NLpars['banc'] if verbose: print 'Banc= ',float(NLpars['banc'])*1e6 pmagplotlib.drawFIGS(AZD) mpars=pmag.domean(araiblock[1],start,end,'DE-BFL') if verbose: print 'pTRM direction= ','%7.1f'%(mpars['specimen_dec']),' %7.1f'%(mpars['specimen_inc']),' MAD:','%7.1f'%(mpars['specimen_mad']) if AniSpec!="": CpTRM=pmag.Dir_anis_corr([mpars['specimen_dec'],mpars['specimen_inc']],AniSpec) AniSpecRec=pmag.doaniscorr(PmagSpecRec,AniSpec) if verbose: print 'Anisotropy corrected TRM direction= ','%7.1f'%(CpTRM[0]),' %7.1f'%(CpTRM[1]) print 'Anisotropy corrected intensity= ',float(AniSpecRec['specimen_int'])*1e6 else: print 'error on specimen ',s except: pass if verbose and found==0: print ' None found :( ' if spc!="": if BEG!="": pars,errcode=pmag.PintPars(datablock,araiblock,zijdblock,BEG,END,accept) pars['measurement_step_unit']="K" pars["specimen_lab_field_dc"]=field pars["specimen_int"]=-1*field*pars["specimen_b"] pars["er_specimen_name"]=s pars['specimen_grade']='' # ungraded pmagplotlib.plotB(AZD,araiblock,zijdblock,pars) if verbose:pmagplotlib.drawFIGS(AZD) if len(trmblock)>2: if inlt==0: inlt=1 blab=field best=pars["specimen_int"] Bs,TRMs=[],[] for trec in trmblock: Bs.append(float(trec['treatment_dc_field'])) TRMs.append(float(trec['measurement_magn_moment'])) NLpars=nlt.NLtrm(Bs,TRMs,best,blab,0) # calculate best fit parameters through TRM acquisition data, and get new banc # Mp,Bp=[],[] for k in range(int(max(Bs)*1e6)): Bp.append(float(k)*1e-6) npred=nlt.TRM(Bp[-1],NLpars['xopt'][0],NLpars['xopt'][1]) # predicted NRM for this field files={} for key in AZD.keys(): files[key]=s+'_'+key+fmt pmagplotlib.saveP(AZD,files) sys.exit() if verbose: ans='b' while ans != "": print """ s[a]ve plot, set [b]ounds for calculation, [d]elete current interpretation, [p]revious, [s]ample, [q]uit: """ ans=raw_input('Return for next specimen \n') if ans=="": specimen +=1 if ans=="d": save_redo(PriorRecs,inspec) CurrRec=[] pmagplotlib.plotAZ(AZD,araiblock,zijdblock,s,units[0]) if verbose:pmagplotlib.drawFIGS(AZD) if ans=='a': files={} for key in AZD.keys(): files[key]="LO:_"+locname+'_SI:_'+PmagSpecRec['er_site_name']+'_SA:_'+PmagSpecRec['er_sample_name']+'_SP:_'+s+'_CO:_s_TY:_'+key+fmt pmagplotlib.saveP(AZD,files) ans="" if ans=='q': print "Good bye" sys.exit() if ans=='p': specimen =specimen -1 backup = 1 ans="" if ans=='s': keepon=1 spec=raw_input('Enter desired specimen name (or first part there of): ') while keepon==1: try: specimen =sids.index(spec) keepon=0 except: tmplist=[] for qq in range(len(sids)): if spec in sids[qq]:tmplist.append(sids[qq]) print specimen," not found, but this was: " print tmplist spec=raw_input('Select one or try again\n ') ans="" if ans=='b': if end==0 or end >=len(zijdblock):end=len(zijdblock)-1 GoOn=0 while GoOn==0: answer=raw_input('Enter index of first point for calculation: ['+str(start)+'] ') try: start=int(answer) answer=raw_input('Enter index of last point for calculation: ['+str(end)+'] ') end=int(answer) if start >=0 and start <len(zijdblock)-2 and end >0 and end <len(zijdblock) or start>=end: GoOn=1 else: print "Bad endpoints - try again! " start,end=0,len(zijdblock) except ValueError: print "Bad endpoints - try again! " start,end=0,len(zijdblock) s=sids[specimen] pars,errcode=pmag.PintPars(datablock,araiblock,zijdblock,start,end,accept) pars['measurement_step_unit']="K" pars["specimen_lab_field_dc"]=field pars["specimen_int"]=-1*field*pars["specimen_b"] pars["er_specimen_name"]=s pars,kill=pmag.scoreit(pars,PmagSpecRec,accept,'',0) PmagSpecRec['specimen_scat']=pars['specimen_scat'] PmagSpecRec['specimen_frac']='%5.3f'%(pars['specimen_frac']) PmagSpecRec['specimen_gmax']='%5.3f'%(pars['specimen_gmax']) PmagSpecRec["measurement_step_min"]='%8.3e' % (pars["measurement_step_min"]) PmagSpecRec["measurement_step_max"]='%8.3e' % (pars["measurement_step_max"]) PmagSpecRec["measurement_step_unit"]="K" PmagSpecRec["specimen_int_n"]='%i'%(pars["specimen_int_n"]) PmagSpecRec["specimen_lab_field_dc"]='%8.3e'%(pars["specimen_lab_field_dc"]) PmagSpecRec["specimen_int"]='%9.4e '%(pars["specimen_int"]) PmagSpecRec["specimen_b"]='%5.3f '%(pars["specimen_b"]) PmagSpecRec["specimen_q"]='%5.1f '%(pars["specimen_q"]) PmagSpecRec["specimen_f"]='%5.3f '%(pars["specimen_f"]) PmagSpecRec["specimen_fvds"]='%5.3f'%(pars["specimen_fvds"]) PmagSpecRec["specimen_b_beta"]='%5.3f'%(pars["specimen_b_beta"]) PmagSpecRec["specimen_int_mad"]='%7.1f'%(pars["specimen_int_mad"]) PmagSpecRec["specimen_Z"]='%7.1f'%(pars["specimen_Z"]) PmagSpecRec["specimen_gamma"]='%7.1f'%(pars["specimen_gamma"]) PmagSpecRec["specimen_grade"]=pars["specimen_grade"] if pars["method_codes"]!="": tmpcodes=pars["method_codes"].split(":") for t in tmpcodes: if t.strip() not in methcodes:methcodes.append(t.strip()) PmagSpecRec["specimen_dec"]='%7.1f'%(pars["specimen_dec"]) PmagSpecRec["specimen_inc"]='%7.1f'%(pars["specimen_inc"]) PmagSpecRec["specimen_tilt_correction"]='-1' PmagSpecRec["specimen_direction_type"]='l' PmagSpecRec["direction_type"]='l' # this is redundant, but helpful - won't be imported PmagSpecRec["specimen_int_dang"]='%7.1f '%(pars["specimen_int_dang"]) PmagSpecRec["specimen_drats"]='%7.1f '%(pars["specimen_drats"]) PmagSpecRec["specimen_drat"]='%7.1f '%(pars["specimen_drat"]) PmagSpecRec["specimen_int_ptrm_n"]='%i '%(pars["specimen_int_ptrm_n"]) PmagSpecRec["specimen_rsc"]='%6.4f '%(pars["specimen_rsc"]) PmagSpecRec["specimen_md"]='%i '%(int(pars["specimen_md"])) if PmagSpecRec["specimen_md"]=='-1':PmagSpecRec["specimen_md"]="" PmagSpecRec["specimen_b_sigma"]='%5.3f '%(pars["specimen_b_sigma"]) if "IE-TT" not in methcodes:methcodes.append("IE-TT") methods="" for meth in methcodes: methods=methods+meth+":" PmagSpecRec["magic_method_codes"]=methods[:-1] PmagSpecRec["specimen_description"]=comment PmagSpecRec["magic_software_packages"]=version_num pmagplotlib.plotAZ(AZD,araiblock,zijdblock,s,units[0]) pmagplotlib.plotB(AZD,araiblock,zijdblock,pars) if verbose:pmagplotlib.drawFIGS(AZD) if len(trmblock)>2: blab=field best=pars["specimen_int"] Bs,TRMs=[],[] for trec in trmblock: Bs.append(float(trec['treatment_dc_field'])) TRMs.append(float(trec['measurement_magn_moment'])) NLpars=nlt.NLtrm(Bs,TRMs,best,blab,0) # calculate best fit parameters through TRM acquisition data, and get new banc Mp,Bp=[],[] for k in range(int(max(Bs)*1e6)): Bp.append(float(k)*1e-6) npred=nlt.TRM(Bp[-1],NLpars['xopt'][0],NLpars['xopt'][1]) # predicted NRM for this field Mp.append(npred) pmagplotlib.plotTRM(AZD['TRM'],Bs,TRMs,Bp,Mp,NLpars,trec['magic_experiment_name']) if verbose: print 'Non-linear TRM corrected intensity= ',float(NLpars['banc'])*1e6 if verbose:pmagplotlib.drawFIGS(AZD) pars["specimen_lab_field_dc"]=field pars["specimen_int"]=-1*field*pars["specimen_b"] pars,kill=pmag.scoreit(pars,PmagSpecRec,accept,'',verbose) saveit=raw_input("Save this interpretation? [y]/n \n") if saveit!='n': PriorRecs.append(PmagSpecRec) # put back an interpretation specimen+=1 save_redo(PriorRecs,inspec) ans="" elif plots==1: specimen+=1 if fmt != ".pmag": files={} for key in AZD.keys(): files[key]="LO:_"+locname+'_SI:_'+PmagSpecRec['er_site_name']+'_SA:_'+PmagSpecRec['er_sample_name']+'_SP:_'+s+'_CO:_s_TY:_'+key+'_'+fmt if pmagplotlib.isServer: black = '#000000' purple = '#800080' titles={} titles['deremag']='DeReMag Plot' titles['zijd']='Zijderveld Plot' titles['arai']='Arai Plot' AZD = pmagplotlib.addBorders(AZD,titles,black,purple) pmagplotlib.saveP(AZD,files) # pmagplotlib.combineFigs(s,files,3) else: # save in pmag format script="grep "+s+" output.mag | thellier -mfsi" script=script+' %8.4e'%(field) min='%i'%((pars["measurement_step_min"]-273)) Max='%i'%((pars["measurement_step_max"]-273)) script=script+" "+min+" "+Max script=script+" |plotxy;cat mypost >>thellier.ps\n" pltf.write(script) pmag.domagicmag(outf,MeasRecs) if len(CurrRec)>0: for rec in CurrRec: PriorRecs.append(rec) CurrRec=[] if plots!=1 and verbose: ans=raw_input(" Save last plot? 1/[0] ") if ans=="1": if fmt != ".pmag": files={} for key in AZD.keys(): files[key]=s+'_'+key+fmt pmagplotlib.saveP(AZD,files) else: print "\n Good bye\n" sys.exit() if len(CurrRec)>0:PriorRecs.append(CurrRec) # put back an interpretation if len(PriorRecs)>0: save_redo(PriorRecs,inspec) print 'Updated interpretations saved in ',inspec if verbose: print "Good bye"
def main(): """ NAME nrm_specimens_magic.py DESCRIPTION converts NRM data in a magic_measurements type file to geographic and tilt corrected data in a pmag_specimens type file SYNTAX nrm_specimens_magic.py [-h][command line options] OPTIONS: -h prints the help message and quits -f MFILE: specify input file -fsa SFILE: specify er_samples format file [with orientations] -F PFILE: specify output file -A do not average replicate measurements -crd [g, t]: specify coordinate system ([g]eographic or [t]ilt adjusted) NB: you must have the SFILE in this directory DEFAULTS MFILE: magic_measurements.txt PFILE: nrm_specimens.txt SFILE: er_samples.txt coord: specimen average replicate measurements?: YES """ # # define some variables # beg,end,pole,geo,tilt,askave,save=0,0,[],0,0,0,0 samp_file=1 args=sys.argv geo,tilt,orient=0,0,0 doave=1 user,comment,doave,coord="","",1,"" meas_file="magic_measurements.txt" pmag_file="nrm_specimens.txt" samp_file="er_samples.txt" if "-h" in args: print main.__doc__ sys.exit() if "-A" in args: doave=0 if "-f" in args: ind=args.index("-f") meas_file=sys.argv[ind+1] if "-F" in args: ind=args.index("-F") pmag_file=sys.argv[ind+1] speclist=[] if "-fsa" in args: ind=args.index("-fsa") samp_file=sys.argv[ind+1] if "-crd" in args: ind=args.index("-crd") coord=sys.argv[ind+1] if coord=="g": geo,orient=1,1 if coord=="t": tilt,orient,geo=1,1,1 # # read in data if samp_file!="": samp_data,file_type=pmag.magic_read(samp_file) if file_type != 'er_samples': print file_type print "This is not a valid er_samples file " sys.exit() else: print samp_file,' read in with ',len(samp_data),' records' else: print 'no orientations - will create file in specimen coordinates' geo,tilt,orient=0,0,0 # # meas_data,file_type=pmag.magic_read(meas_file) if file_type != 'magic_measurements': print file_type print file_type,"This is not a valid magic_measurements file " sys.exit() # if orient==1: # set orientation priorities SO_methods=[] orientation_priorities={'0':'SO-SUN','1':'SO-GPS-DIFF','2':'SO-SIGHT-BACK','3':'SO-CMD-NORTH','4':'SO-MAG'} for rec in samp_data: if "magic_method_codes" in rec: methlist=rec["magic_method_codes"] for meth in methlist.split(":"): if "SO" in meth and "SO-POM" not in meth.strip(): if meth.strip() not in SO_methods: SO_methods.append(meth.strip()) # # sort the sample names # sids=pmag.get_specs(meas_data) # # PmagSpecRecs=[] for s in sids: skip=0 recnum=0 PmagSpecRec={} PmagSpecRec["er_analyst_mail_names"]=user method_codes,inst_code=[],"" # find the data from the meas_data file for this sample # # collect info for the PmagSpecRec dictionary # meas_meth=[] for rec in meas_data: # copy of vital stats to PmagSpecRec from first spec record if rec["er_specimen_name"]==s: PmagSpecRec["er_specimen_name"]=s PmagSpecRec["er_sample_name"]=rec["er_sample_name"] PmagSpecRec["er_site_name"]=rec["er_site_name"] PmagSpecRec["er_location_name"]=rec["er_location_name"] PmagSpecRec["er_citation_names"]="This study" PmagSpecRec["magic_instrument_codes"]="" if "magic_experiment_name" not in rec.keys(): rec["magic_experiment_name"]="" if "magic_instrument_codes" not in rec.keys(): rec["magic_instrument_codes"]="" else: PmagSpecRec["magic_experiment_names"]=rec["magic_experiment_name"] if len(rec["magic_instrument_codes"]) > len(inst_code): inst_code=rec["magic_instrument_codes"] PmagSpecRec["magic_instrument_codes"]=inst_code # copy over instruments break # # now check for correct method labels for all measurements # nrm_data=[] for meas_rec in meas_data: if meas_rec['er_specimen_name']==PmagSpecRec['er_specimen_name']: meths=meas_rec["magic_method_codes"].split(":") for meth in meths: if meth.strip() not in meas_meth:meas_meth.append(meth) if "LT-NO" in meas_meth:nrm_data.append(meas_rec) # data,units=pmag.find_dmag_rec(s,nrm_data) # datablock=data # # find replicate measurements at NRM step and average them # Specs=[] if doave==1: step_meth,avedata=pmag.vspec(data) if len(avedata) != len(datablock): method_codes.append("DE-VM") SpecRec=avedata[0] print 'averaging data ' else: SpecRec=data[0] Specs.append(SpecRec) else: for spec in data:Specs.append(spec) for SpecRec in Specs: # # do geo or stratigraphic correction now # if geo==1: # # find top priority orientation method redo,p=1,0 if len(SO_methods)<=1: az_type=SO_methods[0] orient=pmag.find_samp_rec(PmagSpecRec["er_sample_name"],samp_data,az_type) if orient["sample_azimuth"] !="": method_codes.append(az_type) redo=0 while redo==1: if p>=len(orientation_priorities): print "no orientation data for ",s skip,redo=1,0 break az_type=orientation_priorities[str(p)] orient=pmag.find_samp_rec(PmagSpecRec["er_sample_name"],samp_data,az_type) if orient["sample_azimuth"] !="": method_codes.append(az_type.strip()) redo=0 elif orient["sample_azimuth"] =="": p+=1 # # if stratigraphic selected, get stratigraphic correction # if skip==0 and orient["sample_azimuth"]!="" and orient["sample_dip"]!="": d_geo,i_geo=pmag.dogeo(SpecRec[1],SpecRec[2],orient["sample_azimuth"],orient["sample_dip"]) SpecRec[1]=d_geo SpecRec[2]=i_geo if tilt==1 and "sample_bed_dip" in orient.keys() and orient['sample_bed_dip']!="": d_tilt,i_tilt=pmag.dotilt(d_geo,i_geo,orient["sample_bed_dip_direction"],orient["sample_bed_dip"]) SpecRec[1]=d_tilt SpecRec[2]=i_tilt if skip==0: PmagSpecRec["specimen_dec"]='%7.1f ' %(SpecRec[1]) PmagSpecRec["specimen_inc"]='%7.1f ' %(SpecRec[2]) if geo==1 and tilt==0:PmagSpecRec["specimen_tilt_correction"]='0' if geo==1 and tilt==1: PmagSpecRec["specimen_tilt_correction"]='100' if geo==0 and tilt==0: PmagSpecRec["specimen_tilt_correction"]='-1' PmagSpecRec["specimen_direction_type"]='l' PmagSpecRec["magic_method_codes"]="LT-NO" if len(method_codes) != 0: methstring="" for meth in method_codes: methstring=methstring+ ":" +meth PmagSpecRec["magic_method_codes"]=methstring[1:] PmagSpecRec["specimen_description"]="NRM data" PmagSpecRecs.append(PmagSpecRec) pmag.magic_write(pmag_file,PmagSpecRecs,'pmag_specimens') print "Data saved in ",pmag_file
def main(): """ NAME zeq_magic.py DESCRIPTION reads in magic_measurements formatted file, makes plots of remanence decay during demagnetization experiments. Reads in prior interpretations saved in a pmag_specimens formatted file and allows re-interpretations of best-fit lines and planes and saves (revised or new) interpretations in a pmag_specimens file. interpretations are saved in the coordinate system used. Also allows judicious editting of measurements to eliminate "bad" measurements. These are marked as such in the magic_measurements input file. they are NOT deleted, just ignored. SYNTAX zeq_magic.py [command line options] OPTIONS -h prints help message and quits -f MEASFILE: sets magic_measurements format input file, default: magic_measurements.txt -fsp SPECFILE: sets pmag_specimens format file with prior interpreations, default: zeq_specimens.txt -Fp PLTFILE: sets filename for saved plot, default is name_type.fmt (where type is zijd, eqarea or decay curve) -crd [s,g,t]: sets coordinate system, g=geographic, t=tilt adjusted, default: specimen coordinate system -fsa SAMPFILE: sets er_samples format file with orientation information, default: er_samples.txt -spc SPEC plots single specimen SPEC, saves plot with specified format with optional -dir settings and quits -dir [L,P,F][beg][end]: sets calculation type for principal component analysis, default is none beg: starting step for PCA calculation end: ending step for PCA calculation [L,P,F]: calculation type for line, plane or fisher mean must be used with -spc option -fmt FMT: set format of saved plot [png,svg,jpg] -A: suppresses averaging of replicate measurements, default is to average -sav: saves all plots without review SCREEN OUTPUT: Specimen, N, a95, StepMin, StepMax, Dec, Inc, calculation type """ # initialize some variables doave,e,b=1,0,0 # average replicates, initial end and beginning step plots,coord=0,'s' noorient=0 version_num=pmag.get_version() verbose=pmagplotlib.verbose beg_pca,end_pca,direction_type="","",'l' calculation_type,fmt="","svg" user,spec_keys,locname="",[],'' plot_file="" sfile="" plot_file="" PriorRecs=[] # empty list for prior interpretations backup=0 specimen="" # can skip everything and just plot one specimen with bounds e,b if '-h' in sys.argv: print main.__doc__ sys.exit() if '-WD' in sys.argv: ind=sys.argv.index('-WD') dir_path=sys.argv[ind+1] else: dir_path='.' inspec=dir_path+'/'+'zeq_specimens.txt' meas_file,geo,tilt,ask,samp_file=dir_path+'/magic_measurements.txt',0,0,0,dir_path+'/er_samples.txt' if '-f' in sys.argv: ind=sys.argv.index('-f') meas_file=dir_path+'/'+sys.argv[ind+1] if '-fsp' in sys.argv: ind=sys.argv.index('-fsp') inspec=dir_path+'/'+sys.argv[ind+1] if '-fsa' in sys.argv: ind=sys.argv.index('-fsa') samp_file=dir_path+'/'+sys.argv[ind+1] sfile='ok' if '-crd' in sys.argv: ind=sys.argv.index('-crd') coord=sys.argv[ind+1] if coord=='g' or coord=='t': samp_data,file_type=pmag.magic_read(samp_file) if file_type=='er_samples':sfile='ok' geo=1 if coord=='t':tilt=1 if '-spc' in sys.argv: ind=sys.argv.index('-spc') specimen=sys.argv[ind+1] if '-dir' in sys.argv: ind=sys.argv.index('-dir') direction_type=sys.argv[ind+1] beg_pca=int(sys.argv[ind+2]) end_pca=int(sys.argv[ind+3]) if direction_type=='L':calculation_type='DE-BFL' if direction_type=='P':calculation_type='DE-BFP' if direction_type=='F':calculation_type='DE-FM' if '-Fp' in sys.argv: ind=sys.argv.index('-Fp') plot_file=dir_path+'/'+sys.argv[ind+1] if '-A' in sys.argv: doave=0 if '-sav' in sys.argv: plots=1 verbose=0 if '-fmt' in sys.argv: ind=sys.argv.index('-fmt') fmt=sys.argv[ind+1] # first_save=1 meas_data,file_type=pmag.magic_read(meas_file) changeM,changeS=0,0 # check if data or interpretations have changed if file_type != 'magic_measurements': print file_type print file_type,"This is not a valid magic_measurements file " sys.exit() for rec in meas_data: if "magic_method_codes" not in rec.keys(): rec["magic_method_codes"]="" methods="" tmp=rec["magic_method_codes"].replace(" ","").split(":") for meth in tmp: methods=methods+meth+":" rec["magic_method_codes"]=methods[:-1] # get rid of annoying spaces in Anthony's export files if "magic_instrument_codes" not in rec.keys() :rec["magic_instrument_codes"]="" PriorSpecs=[] PriorRecs,file_type=pmag.magic_read(inspec) if len(PriorRecs)==0: if verbose:print "starting new file ",inspec for Rec in PriorRecs: if 'magic_software_packages' not in Rec.keys():Rec['magic_software_packages']="" if Rec['er_specimen_name'] not in PriorSpecs: if 'specimen_comp_name' not in Rec.keys():Rec['specimen_comp_name']="A" PriorSpecs.append(Rec['er_specimen_name']) else: if 'specimen_comp_name' not in Rec.keys():Rec['specimen_comp_name']="A" if "magic_method_codes" in Rec.keys(): methods=[] tmp=Rec["magic_method_codes"].replace(" ","").split(":") for meth in tmp: methods.append(meth) if 'DE-FM' in methods: Rec['calculation_type']='DE-FM' # this won't be imported but helps if 'DE-BFL' in methods: Rec['calculation_type']='DE-BFL' if 'DE-BFL-A' in methods: Rec['calculation_type']='DE-BFL-A' if 'DE-BFL-O' in methods: Rec['calculation_type']='DE-BFL-O' if 'DE-BFP' in methods: Rec['calculation_type']='DE-BFP' else: Rec['calculation_type']='DE-BFL' # default is to assume a best-fit line # # get list of unique specimen names # sids=pmag.get_specs(meas_data) # # set up plots, angle sets X axis to horizontal, direction_type 'l' is best-fit line # direction_type='p' is great circle # # # draw plots for sample s - default is just to step through zijderveld diagrams # # # define figure numbers for equal area, zijderveld, # and intensity vs. demagnetiztion step respectively ZED={} ZED['eqarea'],ZED['zijd'], ZED['demag']=1,2,3 pmagplotlib.plot_init(ZED['eqarea'],5,5) pmagplotlib.plot_init(ZED['zijd'],6,5) pmagplotlib.plot_init(ZED['demag'],5,5) save_pca=0 if specimen=="": k = 0 else: k=sids.index(specimen) angle,direction_type="","" setangle=0 CurrRecs=[] while k < len(sids): CurrRecs=[] if setangle==0:angle="" method_codes,inst_code=[],"" s=sids[k] PmagSpecRec={} PmagSpecRec["er_analyst_mail_names"]=user PmagSpecRec['magic_software_packages']=version_num PmagSpecRec['specimen_description']="" PmagSpecRec['magic_method_codes']="" if verbose and s!="":print s, k , 'out of ',len(sids) # # collect info for the PmagSpecRec dictionary # s_meas=pmag.get_dictitem(meas_data,'er_specimen_name',s,'T') # fish out this specimen s_meas=pmag.get_dictitem(s_meas,'magic_method_codes','Z','has') # fish out zero field steps if len(s_meas)>0: for rec in s_meas: # fix up a few things for the output record PmagSpecRec["magic_instrument_codes"]=rec["magic_instrument_codes"] # copy over instruments PmagSpecRec["er_citation_names"]="This study" PmagSpecRec["er_specimen_name"]=s PmagSpecRec["er_sample_name"]=rec["er_sample_name"] PmagSpecRec["er_site_name"]=rec["er_site_name"] PmagSpecRec["er_location_name"]=rec["er_location_name"] locname=rec['er_location_name'] if 'er_expedition_name' in rec.keys(): PmagSpecRec["er_expedition_name"]=rec["er_expedition_name"] PmagSpecRec["magic_method_codes"]=rec["magic_method_codes"] if "magic_experiment_name" not in rec.keys(): PmagSpecRec["magic_experiment_names"]="" else: PmagSpecRec["magic_experiment_names"]=rec["magic_experiment_name"] break # # find the data from the meas_data file for this specimen # data,units=pmag.find_dmag_rec(s,meas_data) PmagSpecRec["measurement_step_unit"]= units u=units.split(":") if "T" in units:PmagSpecRec["magic_method_codes"]=PmagSpecRec["magic_method_codes"]+":LP-DIR-AF" if "K" in units:PmagSpecRec["magic_method_codes"]=PmagSpecRec["magic_method_codes"]+":LP-DIR-T" if "J" in units:PmagSpecRec["magic_method_codes"]=PmagSpecRec["magic_method_codes"]+":LP-DIR-M" # # find prior interpretation # if len(CurrRecs)==0: # check if already in beg_pca,end_pca="","" calculation_type="" if inspec !="": if verbose: print " looking up previous interpretations..." precs=pmag.get_dictitem(PriorRecs,'er_specimen_name',s,'T') # get all the prior recs with this specimen name precs=pmag.get_dictitem(precs,'magic_method_codes','LP-DIR','has') # get the directional data PriorRecs=pmag.get_dictitem(PriorRecs,'er_specimen_name',s,'F') # take them all out of prior recs # get the ones that meet the current coordinate system for prec in precs: if 'specimen_tilt_correction' not in prec.keys() or prec['specimen_tilt_correction']=='-1': crd='s' elif prec['specimen_tilt_correction']=='0': crd='g' elif prec['specimen_tilt_correction']=='100': crd='t' else: crd='?' CurrRec={} for key in prec.keys():CurrRec[key]=prec[key] CurrRecs.append(CurrRec) # put in CurrRecs method_codes= CurrRec["magic_method_codes"].replace(" ","").split(':') calculation_type='DE-BFL' if 'DE-FM' in method_codes: calculation_type='DE-FM' if 'DE-BFP' in method_codes: calculation_type='DE-BFP' if 'DE-BFL-A' in method_codes: calculation_type='DE-BFL-A' if 'specimen_dang' not in CurrRec.keys(): if verbose:print 'Run mk_redo.py and zeq_magic_redo.py to get the specimen_dang values' CurrRec['specimen_dang']=-1 if calculation_type!='DE-FM' and crd==coord: # not a fisher mean if verbose:print "Specimen N MAD DANG start end dec inc type component coordinates" if units=='K': if verbose:print '%s %i %7.1f %7.1f %7.1f %7.1f %7.1f %7.1f %s %s %s \n' % (CurrRec["er_specimen_name"],int(CurrRec["specimen_n"]),float(CurrRec["specimen_mad"]),float(CurrRec["specimen_dang"]),float(CurrRec["measurement_step_min"])-273,float(CurrRec["measurement_step_max"])-273,float(CurrRec["specimen_dec"]),float(CurrRec["specimen_inc"]),calculation_type,CurrRec['specimen_comp_name'],crd) elif units=='T': if verbose:print '%s %i %7.1f %7.1f %7.1f %7.1f %7.1f %7.1f %s %s %s \n' % (CurrRec["er_specimen_name"],int(CurrRec["specimen_n"]),float(CurrRec["specimen_mad"]),float(CurrRec["specimen_dang"]),float(CurrRec["measurement_step_min"])*1e3,float(CurrRec["measurement_step_max"])*1e3,float(CurrRec["specimen_dec"]),float(CurrRec["specimen_inc"]),calculation_type,CurrRec['specimen_comp_name'],crd) elif 'T' in units and 'K' in units: if float(CurrRec['measurement_step_min'])<1.0 : min=float(CurrRec['measurement_step_min'])*1e3 else: min=float(CurrRec['measurement_step_min'])-273 if float(CurrRec['measurement_step_max'])<1.0 : max=float(CurrRec['measurement_step_max'])*1e3 else: max=float(CurrRec['measurement_step_max'])-273 if verbose:print '%s %i %7.1f %i %i %7.1f %7.1f %7.1f, %s %s\n' % (CurrRec["er_specimen_name"],int(CurrRec["specimen_n"]),float(CurrRec["specimen_mad"]),float(CurrRec['specimen_dang']),min,max,float(CurrRec["specimen_dec"]),float(CurrRec["specimen_inc"]),calculation_type,crd) elif 'J' in units: if verbose:print '%s %i %7.1f %7.1f %7.1f %7.1f %7.1f %7.1f %s %s %s \n' % (CurrRec["er_specimen_name"],int(CurrRec["specimen_n"]),float(CurrRec["specimen_mad"]),float(CurrRec['specimen_dang']),float(CurrRec["measurement_step_min"]),float(CurrRec["measurement_step_max"]),float(CurrRec["specimen_dec"]),float(CurrRec["specimen_inc"]),calculation_type,CurrRec['specimen_comp_name'],crd) elif calculation_type=='DE-FM' and crd==coord: # fisher mean if verbose:print "Specimen a95 DANG start end dec inc type component coordinates" if units=='K': if verbose:print '%s %i %7.1f %7.1f %7.1f %7.1f %7.1f %s %s %s \n' % (CurrRec["er_specimen_name"],int(CurrRec["specimen_n"]),float(CurrRec["specimen_alpha95"]),float(CurrRec["measurement_step_min"])-273,float(CurrRec["measurement_step_max"])-273,float(CurrRec["specimen_dec"]),float(CurrRec["specimen_inc"]),calculation_type,CurrRec['specimen_comp_name'],crd) elif units=='T': if verbose:print '%s %i %7.1f %7.1f %7.1f %7.1f %7.1f %s %s %s \n' % (CurrRec["er_specimen_name"],int(CurrRec["specimen_n"]),float(CurrRec["specimen_alpha95"]),float(CurrRec["measurement_step_min"])*1e3,float(CurrRec["measurement_step_max"])*1e3,float(CurrRec["specimen_dec"]),float(CurrRec["specimen_inc"]),calculation_type,CurrRec['specimen_comp_name'],crd) elif 'T' in units and 'K' in units: if float(CurrRec['measurement_step_min'])<1.0 : min=float(CurrRec['measurement_step_min'])*1e3 else: min=float(CurrRec['measurement_step_min'])-273 if float(CurrRec['measurement_step_max'])<1.0 : max=float(CurrRec['measurement_step_max'])*1e3 else: max=float(CurrRec['measurement_step_max'])-273 if verbose:print '%s %i %7.1f %i %i %7.1f %7.1f %s %s \n' % (CurrRec["er_specimen_name"],int(CurrRec["specimen_n"]),float(CurrRec["specimen_alpha95"]),min,max,float(CurrRec["specimen_dec"]),float(CurrRec["specimen_inc"]),calculation_type,crd) elif 'J' in units: if verbose:print '%s %i %7.1f %7.1f %7.1f %7.1f %7.1f %s %s %s \n' % (CurrRec["er_specimen_name"],int(CurrRec["specimen_n"]),float(CurrRec["specimen_mad"]),float(CurrRec["measurement_step_min"]),float(CurrRec["measurement_step_max"]),float(CurrRec["specimen_dec"]),float(CurrRec["specimen_inc"]),calculation_type,CurrRec['specimen_comp_name'],crd) if len(CurrRecs)==0:beg_pca,end_pca="","" datablock=data noskip=1 if len(datablock) <3: noskip=0 if backup==0: k+=1 else: k-=1 if len(CurrRecs)>0: for rec in CurrRecs: PriorRecs.append(rec) CurrRecs=[] else: backup=0 if noskip: # # find replicate measurements at given treatment step and average them # # step_meth,avedata=pmag.vspec(data) # if len(avedata) != len(datablock): # if doave==1: # method_codes.append("DE-VM") # datablock=avedata # # # do geo or stratigraphic correction now # if geo==1: # # find top priority orientation method orient,az_type=pmag.get_orient(samp_data,PmagSpecRec["er_sample_name"]) if az_type=='SO-NO': if verbose: print "no orientation data for ",s orient["sample_azimuth"]=0 orient["sample_dip"]=0 noorient=1 method_codes.append("SO-NO") orient["sample_azimuth"]=0 orient["sample_dip"]=0 orient["sample_bed_dip_azimuth"]=0 orient["sample_bed_dip"]=0 noorient=1 method_codes.append("SO-NO") else: noorient=0 # # if stratigraphic selected, get stratigraphic correction # tiltblock,geoblock=[],[] for rec in datablock: d_geo,i_geo=pmag.dogeo(rec[1],rec[2],float(orient["sample_azimuth"]),float(orient["sample_dip"])) geoblock.append([rec[0],d_geo,i_geo,rec[3],rec[4],rec[5],rec[6]]) if tilt==1 and "sample_bed_dip" in orient.keys() and float(orient['sample_bed_dip'])!=0: d_tilt,i_tilt=pmag.dotilt(d_geo,i_geo,float(orient["sample_bed_dip_direction"]),float(orient["sample_bed_dip"])) tiltblock.append([rec[0],d_tilt,i_tilt,rec[3],rec[4],rec[5],rec[6]]) if tilt==1: plotblock=tiltblock if geo==1 and tilt==0:plotblock=geoblock if geo==0 and tilt==0: plotblock=datablock # # set the end pca point to last point if not set if e==0 or e>len(plotblock)-1: e=len(plotblock)-1 if angle=="": angle=plotblock[0][1] # rotate to NRM declination title=s+'_s' if geo==1 and tilt==0 and noorient!=1:title=s+'_g' if tilt==1 and noorient!=1:title=s+'_t' pmagplotlib.plotZED(ZED,plotblock,angle,title,units) if verbose:pmagplotlib.drawFIGS(ZED) if len(CurrRecs)!=0: for prec in CurrRecs: if 'calculation_type' not in prec.keys(): calculation_type='' else: calculation_type=prec["calculation_type"] direction_type=prec["specimen_direction_type"] if calculation_type !="": beg_pca,end_pca="","" for j in range(len(datablock)): if data[j][0]==float(prec["measurement_step_min"]):beg_pca=j if data[j][0]==float(prec["measurement_step_max"]):end_pca=j if beg_pca=="" or end_pca=="": if verbose: print "something wrong with prior interpretation " break if calculation_type!="": if beg_pca=="":beg_pca=0 if end_pca=="":end_pca=len(plotblock)-1 if geo==1 and tilt==0: mpars=pmag.domean(geoblock,beg_pca,end_pca,calculation_type) if mpars["specimen_direction_type"]!="Error": pmagplotlib.plotDir(ZED,mpars,geoblock,angle) if verbose:pmagplotlib.drawFIGS(ZED) if geo==1 and tilt==1: mpars=pmag.domean(tiltblock,beg_pca,end_pca,calculation_type) if mpars["specimen_direction_type"]!="Error": pmagplotlib.plotDir(ZED,mpars,tiltblock,angle) if verbose:pmagplotlib.drawFIGS(ZED) if geo==0 and tilt==0: mpars=pmag.domean(datablock,beg_pca,end_pca,calculation_type) if mpars["specimen_direction_type"]!="Error": pmagplotlib.plotDir(ZED,mpars,plotblock,angle) if verbose:pmagplotlib.drawFIGS(ZED) # # print out data for this sample to screen # recnum=0 for plotrec in plotblock: if units=='T' and verbose: print '%s: %i %7.1f %s %8.3e %7.1f %7.1f %s' % (plotrec[5], recnum,plotrec[0]*1e3," mT",plotrec[3],plotrec[1],plotrec[2],plotrec[6]) if units=="K" and verbose: print '%s: %i %7.1f %s %8.3e %7.1f %7.1f %s' % (plotrec[5], recnum,plotrec[0]-273,' C',plotrec[3],plotrec[1],plotrec[2],plotrec[6]) if units=="J" and verbose: print '%s: %i %7.1f %s %8.3e %7.1f %7.1f %s' % (plotrec[5], recnum,plotrec[0],' J',plotrec[3],plotrec[1],plotrec[2],plotrec[6]) if 'K' in units and 'T' in units: if plotrec[0]>=1. and verbose: print '%s: %i %7.1f %s %8.3e %7.1f %7.1f %s' % (plotrec[5], recnum,plotrec[0]-273,' C',plotrec[3],plotrec[1],plotrec[2],plotrec[6]) if plotrec[0]<1. and verbose: print '%s: %i %7.1f %s %8.3e %7.1f %7.1f %s' % (plotrec[5], recnum,plotrec[0]*1e3," mT",plotrec[3],plotrec[1],plotrec[2],plotrec[6]) recnum += 1 if specimen!="": if plot_file=="": basename=locname+'_'+s else: basename=plot_file files={} for key in ZED.keys(): files[key]=basename+'_'+key+'.'+fmt pmagplotlib.saveP(ZED,files) sys.exit() else: # interactive if plots==0: ans='b' k+=1 changeS=0 while ans != "": if len(CurrRecs)==0: print """ g/b: indicates good/bad measurement. "bad" measurements excluded from calculation set s[a]ve plot, [b]ounds for pca and calculate, [p]revious, [s]pecimen, change [h]orizontal projection angle, change [c]oordinate systems, [e]dit data, [q]uit: """ else: print """ g/b: indicates good/bad measurement. "bad" measurements excluded from calculation set s[a]ve plot, [b]ounds for pca and calculate, [p]revious, [s]pecimen, change [h]orizontal projection angle, change [c]oordinate systems, [d]elete current interpretation(s), [e]dit data, [q]uit: """ ans=raw_input('<Return> for next specimen \n') setangle=0 if ans=='d': # delete this interpretation CurrRecs=[] k-=1 # replot same specimen ans="" changeS=1 if ans=='q': if changeM==1: ans=raw_input('Save changes to magic_measurements.txt? y/[n] ') if ans=='y': pmag.magic_write(meas_file,meas_data,'magic_measurements') print "Good bye" sys.exit() if ans=='a': if plot_file=="": basename=locname+'_'+s+'_' else: basename=plot_file files={} for key in ZED.keys(): files[key]=basename+'_'+coord+'_'+key+'.'+fmt pmagplotlib.saveP(ZED,files) ans="" if ans=='p': k-=2 ans="" backup=1 if ans=='c': k-=1 # replot same block if tilt==0 and geo ==1:print "You are currently viewing geographic coordinates " if tilt==1 and geo ==1:print "You are currently viewing stratigraphic coordinates " if tilt==0 and geo ==0: print "You are currently viewing sample coordinates " print "\n Which coordinate system do you wish to view? " coord=raw_input(" <Return> specimen, [g] geographic, [t] tilt corrected ") if coord=="g":geo,tilt=1,0 if coord=="t": geo=1 tilt=1 if coord=="": coord='s' geo=0 tilt=0 if geo==1 and sfile=="": samp_file=raw_input(" Input er_samples file for sample orientations [er_samples.txt] " ) if samp_file=="":samp_file="er_samples.txt" samp_data,file_type=pmag.magic_read(samp_file) if file_type != 'er_samples': print file_type print "This is not a valid er_samples file - coordinate system not changed" else: sfile="ok" ans="" if ans=='s': keepon=1 sample=raw_input('Enter desired specimen name (or first part there of): ') while keepon==1: try: k =sids.index(sample) keepon=0 except: tmplist=[] for qq in range(len(sids)): if sample in sids[qq]:tmplist.append(sids[qq]) print sample," not found, but this was: " print tmplist sample=raw_input('Select one or try again\n ') angle,direction_type="","" setangle=0 ans="" if ans=='h': k-=1 angle=raw_input("Enter desired declination for X axis 0-360 ") angle=float(angle) if angle==0:angle=0.001 s=sids[k] setangle=1 ans="" if ans=='e': k-=1 ans="" recnum=0 for plotrec in plotblock: if plotrec[0]<=200 and verbose: print '%s: %i %7.1f %s %8.3e %7.1f %7.1f ' % (plotrec[5], recnum,plotrec[0]*1e3," mT",plotrec[3],plotrec[1],plotrec[2]) if plotrec[0]>200 and verbose: print '%s: %i %7.1f %s %8.3e %7.1f %7.1f ' % (plotrec[5], recnum,plotrec[0]-273,' C',plotrec[3],plotrec[1],plotrec[2]) recnum += 1 answer=raw_input('Enter index of point to change from bad to good or vice versa: ') try: ind=int(answer) meas_data=pmag.mark_dmag_rec(s,ind,meas_data) changeM=1 except: 'bad entry, try again' if ans=='b': if end_pca=="":end_pca=len(plotblock)-1 if beg_pca=="":beg_pca=0 k-=1 # stay on same sample until through GoOn=0 while GoOn==0: print 'Enter index of first point for pca: ','[',beg_pca,']' answer=raw_input('return to keep default ') if answer != "": beg_pca=int(answer) print 'Enter index of last point for pca: ','[',end_pca,']' answer=raw_input('return to keep default ') try: end_pca=int(answer) if plotblock[beg_pca][5]=='b' or plotblock[end_pca][5]=='b': print "Can't select 'bad' measurement for PCA bounds -try again" end_pca=len(plotblock)-1 beg_pca=0 elif beg_pca >=0 and beg_pca<=len(plotblock)-2 and end_pca>0 and end_pca<len(plotblock): GoOn=1 else: print beg_pca,end_pca, " are bad entry of indices - try again" end_pca=len(plotblock)-1 beg_pca=0 except: print beg_pca,end_pca, " are bad entry of indices - try again" end_pca=len(plotblock)-1 beg_pca=0 GoOn=0 while GoOn==0: if calculation_type!="": print "Prior calculation type = ",calculation_type ct=raw_input('Enter new Calculation Type: best-fit line, plane or fisher mean [l]/p/f : ' ) if ct=="" or ct=="l": direction_type="l" calculation_type="DE-BFL" GoOn=1 elif ct=='p': direction_type="p" calculation_type="DE-BFP" GoOn=1 elif ct=='f': direction_type="l" calculation_type="DE-FM" GoOn=1 else: print "bad entry of calculation type: try again. " pmagplotlib.plotZED(ZED,plotblock,angle,s,units) if verbose:pmagplotlib.drawFIGS(ZED) if geo==1 and tilt==0: mpars=pmag.domean(geoblock,beg_pca,end_pca,calculation_type) if mpars['specimen_direction_type']=='Error':break PmagSpecRec["specimen_dec"]='%7.1f ' %(mpars["specimen_dec"]) PmagSpecRec["specimen_inc"]='%7.1f ' %(mpars["specimen_inc"]) if "SO-NO" not in method_codes: PmagSpecRec["specimen_tilt_correction"]='0' method_codes.append("DA-DIR-GEO") else: PmagSpecRec["specimen_tilt_correction"]='-1' pmagplotlib.plotDir(ZED,mpars,geoblock,angle) if verbose:pmagplotlib.drawFIGS(ZED) if geo==1 and tilt==1: mpars=pmag.domean(tiltblock,beg_pca,end_pca,calculation_type) if mpars['specimen_direction_type']=='Error':break PmagSpecRec["specimen_dec"]='%7.1f ' %(mpars["specimen_dec"]) PmagSpecRec["specimen_inc"]='%7.1f ' %(mpars["specimen_inc"]) if "SO-NO" not in method_codes: PmagSpecRec["specimen_tilt_correction"]='100' method_codes.append("DA-DIR-TILT") else: PmagSpecRec["specimen_tilt_correction"]='-1' pmagplotlib.plotDir(ZED,mpars,tiltblock,angle) if verbose:pmagplotlib.drawFIGS(ZED) if geo==0 and tilt==0: mpars=pmag.domean(datablock,beg_pca,end_pca,calculation_type) if mpars['specimen_direction_type']=='Error':break PmagSpecRec["specimen_dec"]='%7.1f ' %(mpars["specimen_dec"]) PmagSpecRec["specimen_inc"]='%7.1f ' %(mpars["specimen_inc"]) PmagSpecRec["specimen_tilt_correction"]='-1' pmagplotlib.plotDir(ZED,mpars,plotblock,angle) if verbose:pmagplotlib.drawFIGS(ZED) PmagSpecRec["measurement_step_min"]='%8.3e ' %(mpars["measurement_step_min"]) PmagSpecRec["measurement_step_max"]='%8.3e ' %(mpars["measurement_step_max"]) PmagSpecRec["specimen_correction"]='u' PmagSpecRec["specimen_dang"]='%7.1f ' %(mpars['specimen_dang']) print 'DANG: ',PmagSpecRec["specimen_dang"] if calculation_type!='DE-FM': PmagSpecRec["specimen_mad"]='%7.1f ' %(mpars["specimen_mad"]) PmagSpecRec["specimen_alpha95"]="" else: PmagSpecRec["specimen_alpha95"]='%7.1f ' %(mpars["specimen_alpha95"]) PmagSpecRec["specimen_mad"]="" PmagSpecRec["specimen_n"]='%i ' %(mpars["specimen_n"]) PmagSpecRec["specimen_direction_type"]=direction_type PmagSpecRec["calculation_type"]=calculation_type # redundant and won't be imported - just for convenience method_codes=PmagSpecRec["magic_method_codes"].split(':') if len(method_codes) != 0: methstring="" for meth in method_codes: ctype=meth.split('-') if 'DE' not in ctype:methstring=methstring+ ":" +meth # don't include old direction estimation methods methstring=methstring+':'+calculation_type PmagSpecRec["magic_method_codes"]= methstring.strip(':') print 'Method codes: ',PmagSpecRec['magic_method_codes'] if calculation_type!='DE-FM': if units=='K': print '%s %i %7.1f %7.1f %7.1f %7.1f %7.1f %7.1f, %s \n' % (PmagSpecRec["er_specimen_name"],int(PmagSpecRec["specimen_n"]),float(PmagSpecRec["specimen_mad"]),float(PmagSpecRec["specimen_dang"]),float(PmagSpecRec["measurement_step_min"])-273,float(PmagSpecRec["measurement_step_max"])-273,float(PmagSpecRec["specimen_dec"]),float(PmagSpecRec["specimen_inc"]),calculation_type) elif units== 'T': print '%s %i %7.1f %7.1f %7.1f %7.1f %7.1f %7.1f, %s \n' % (PmagSpecRec["er_specimen_name"],int(PmagSpecRec["specimen_n"]),float(PmagSpecRec["specimen_mad"]),float(PmagSpecRec["specimen_dang"]),float(PmagSpecRec["measurement_step_min"])*1e3,float(PmagSpecRec["measurement_step_max"])*1e3,float(PmagSpecRec["specimen_dec"]),float(PmagSpecRec["specimen_inc"]),calculation_type) elif 'T' in units and 'K' in units: if float(PmagSpecRec['measurement_step_min'])<1.0 : min=float(PmagSpecRec['measurement_step_min'])*1e3 else: min=float(PmagSpecRec['measurement_step_min'])-273 if float(PmagSpecRec['measurement_step_max'])<1.0 : max=float(PmagSpecRec['measurement_step_max'])*1e3 else: max=float(PmagSpecRec['measurement_step_max'])-273 print '%s %i %7.1f %i %i %7.1f %7.1f %7.1f, %s \n' % (PmagSpecRec["er_specimen_name"],int(PmagSpecRec["specimen_n"]),float(PmagSpecRec["specimen_mad"]),float(PmagSpecRec["specimen_dang"]),min,max,float(PmagSpecRec["specimen_dec"]),float(PmagSpecRec["specimen_inc"]),calculation_type) else: print '%s %i %7.1f %7.1f %7.1f %7.1f %7.1f %7.1f, %s \n' % (PmagSpecRec["er_specimen_name"],int(PmagSpecRec["specimen_n"]),float(PmagSpecRec["specimen_mad"]),float(PmagSpecRec["specimen_dang"]),float(PmagSpecRec["measurement_step_min"]),float(PmagSpecRec["measurement_step_max"]),float(PmagSpecRec["specimen_dec"]),float(PmagSpecRec["specimen_inc"]),calculation_type) else: if 'K' in units: print '%s %i %7.1f %7.1f %7.1f %7.1f %7.1f %7.1f, %s \n' % (PmagSpecRec["er_specimen_name"],int(PmagSpecRec["specimen_n"]),float(PmagSpecRec["specimen_alpha95"]),float(PmagSpecRec["specimen_dang"]),float(PmagSpecRec["measurement_step_min"])-273,float(PmagSpecRec["measurement_step_max"])-273,float(PmagSpecRec["specimen_dec"]),float(PmagSpecRec["specimen_inc"]),calculation_type) elif 'T' in units: print '%s %i %7.1f %7.1f %7.1f %7.1f %7.1f %7.1f, %s \n' % (PmagSpecRec["er_specimen_name"],int(PmagSpecRec["specimen_n"]),float(PmagSpecRec["specimen_alpha95"]),float(PmagSpecRec["specimen_dang"]),float(PmagSpecRec["measurement_step_min"])*1e3,float(PmagSpecRec["measurement_step_max"])*1e3,float(PmagSpecRec["specimen_dec"]),float(PmagSpecRec["specimen_inc"]),calculation_type) elif 'T' in units and 'K' in units: if float(PmagSpecRec['measurement_step_min'])<1.0 : min=float(PmagSpecRec['measurement_step_min'])*1e3 else: min=float(PmagSpecRec['measurement_step_min'])-273 if float(PmagSpecRec['measurement_step_max'])<1.0 : max=float(PmagSpecRec['measurement_step_max'])*1e3 else: max=float(PmagSpecRec['measurement_step_max'])-273 print '%s %i %7.1f %i %i %7.1f %7.1f, %s \n' % (PmagSpecRec["er_specimen_name"],int(PmagSpecRec["specimen_n"]),float(PmagSpecRec["specimen_alpha95"]),min,max,float(PmagSpecRec["specimen_dec"]),float(PmagSpecRec["specimen_inc"]),calculation_type) else: print '%s %i %7.1f %7.1f %7.1f %7.1f %7.1f, %s \n' % (PmagSpecRec["er_specimen_name"],int(PmagSpecRec["specimen_n"]),float(PmagSpecRec["specimen_alpha95"]),float(PmagSpecRec["measurement_step_min"]),float(PmagSpecRec["measurement_step_max"]),float(PmagSpecRec["specimen_dec"]),float(PmagSpecRec["specimen_inc"]),calculation_type) saveit=raw_input("Save this interpretation? [y]/n \n") if saveit!="n": changeS=1 # # put in details # angle,direction_type,setangle="","",0 if len(CurrRecs)>0: replace=raw_input(" [0] add new component, or [1] replace existing interpretation(s) [default is replace] ") if replace=="1" or replace=="": CurrRecs=[] PmagSpecRec['specimen_comp_name']='A' CurrRecs.append(PmagSpecRec) else: print 'These are the current component names for this specimen: ' for trec in CurrRecs:print trec['specimen_comp_name'] compnum=raw_input("Enter new component name: ") PmagSpecRec['specimen_comp_name']=compnum print "Adding new component: ",PmagSpecRec['specimen_comp_name'] CurrRecs.append(PmagSpecRec) else: PmagSpecRec['specimen_comp_name']='A' CurrRecs.append(PmagSpecRec) k+=1 ans="" else: ans="" else: # plots=1 k+=1 files={} locname.replace('/','-') print PmagSpecRec for key in ZED.keys(): files[key]="LO:_"+locname+'_SI:_'+PmagSpecRec['er_site_name']+'_SA:_'+PmagSpecRec['er_sample_name']+'_SP:_'+s+'_CO:_'+coord+'_TY:_'+key+'_.'+fmt if pmagplotlib.isServer: black = '#000000' purple = '#800080' titles={} titles['demag']='DeMag Plot' titles['zijd']='Zijderveld Plot' titles['eqarea']='Equal Area Plot' ZED = pmagplotlib.addBorders(ZED,titles,black,purple) pmagplotlib.saveP(ZED,files) if len(CurrRecs)>0: for rec in CurrRecs: PriorRecs.append(rec) if changeS==1: if len(PriorRecs)>0: save_redo(PriorRecs,inspec) else: os.system('rm '+inspec) CurrRecs,beg_pca,end_pca=[],"","" # next up changeS=0 else: k+=1 # skip record - not enough data if changeM==1: pmag.magic_write(meas_file,meas_data,'magic_measurements')
def main(): """ NAME microwave_magic.py DESCRIPTION plots microwave paleointensity data, allowing interactive setting of bounds. Saves and reads interpretations from a pmag_specimen formatted table, default: microwave_specimens.txt SYNTAX microwave_magic.py [command line options] OPTIONS -h prints help message and quits -f MEAS, set magic_measurements input file -fsp PRIOR, set pmag_specimen prior interpretations file -fcr CRIT, set criteria file for grading. -fmt [svg,png,jpg], format for images - default is svg -sav, saves plots with out review (default format) -spc SPEC, plots single specimen SPEC, saves plot with specified format with optional -b bounds adn quits -b BEG END: sets bounds for calculation BEG: starting step for slope calculation END: ending step for slope calculation DEFAULTS MEAS: magic_measurements.txt CRIT: NONE PRIOR: microwave_specimens.txt OUTPUT figures: ALL: numbers refer to temperature steps in command line window 1) Arai plot: closed circles are zero-field first/infield open circles are infield first/zero-field triangles are pTRM checks squares are pTRM tail checks VDS is vector difference sum diamonds are bounds for interpretation 2) Zijderveld plot: closed (open) symbols are X-Y (X-Z) planes X rotated to NRM direction 3) (De/Re)Magnetization diagram: circles are NRM remaining squares are pTRM gained command line window: list is: temperature step numbers, power (J), Dec, Inc, Int (units of magic_measuements) list of possible commands: type letter followed by return to select option saving of plots creates .svg format files with specimen_name, plot type as name """ # # initializations # meas_file,critout,inspec="magic_measurements.txt","","microwave_specimens.txt" inlt=0 version_num=pmag.get_version() Tinit,DCZ,field,first_save=0,0,-1,1 user,comment="",'' ans,specimen,recnum,start,end=0,0,0,0,0 plots,pmag_out,samp_file,style=0,"","","svg" fmt='.'+style # # default acceptance criteria # accept_keys=['specimen_int_ptrm_n','specimen_md','specimen_fvds','specimen_b_beta','specimen_dang','specimen_drats','specimen_Z'] accept={} accept['specimen_int_ptrm_n']=2 accept['specimen_md']=10 accept['specimen_fvds']=0.35 accept['specimen_b_beta']=.1 accept['specimen_int_mad']=7 accept['specimen_dang']=10 accept['specimen_drats']=10 accept['specimen_Z']=10 # # parse command line options # spc,BEG,END="","","" if '-h' in sys.argv: print main.__doc__ sys.exit() if '-f' in sys.argv: ind=sys.argv.index('-f') meas_file=sys.argv[ind+1] if '-fsp' in sys.argv: ind=sys.argv.index('-fsp') inspec=sys.argv[ind+1] if '-fcr' in sys.argv: ind=sys.argv.index('-fcr') critout=sys.argv[ind+1] if '-fmt' in sys.argv: ind=sys.argv.index('-fmt') fmt='.'+sys.argv[ind+1] if '-spc' in sys.argv: ind=sys.argv.index('-spc') spc=sys.argv[ind+1] if '-b' in sys.argv: ind=sys.argv.index('-b') BEG=int(sys.argv[ind+1]) END=int(sys.argv[ind+2]) if critout!="": crit_data,file_type=pmag.magic_read(critout) if pmagplotlib.verbose: print "Acceptance criteria read in from ", critout accept={} accept['specimen_int_ptrm_n']=2.0 for critrec in crit_data: if critrec["pmag_criteria_code"]=="IE-SPEC": for key in accept_keys: if key not in critrec.keys(): accept[key]=-1 else: accept[key]=float(critrec[key]) try: open(inspec,'rU') PriorRecs,file_type=pmag.magic_read(inspec) if file_type != 'pmag_specimens': print file_type print file_type,inspec," is not a valid pmag_specimens file " sys.exit() for rec in PriorRecs: if 'magic_software_packages' not in rec.keys():rec['magic_software_packages']="" except IOError: PriorRecs=[] if pmagplotlib.verbose:print "starting new specimen interpretation file: ",inspec meas_data,file_type=pmag.magic_read(meas_file) if file_type != 'magic_measurements': print file_type print file_type,"This is not a valid magic_measurements file " sys.exit() backup=0 # define figure numbers for arai, zijderveld and # de-,re-magization diagrams AZD={} AZD['deremag'], AZD['zijd'],AZD['arai'],AZD['eqarea']=1,2,3,4 pmagplotlib.plot_init(AZD['arai'],4,4) pmagplotlib.plot_init(AZD['zijd'],4,4) pmagplotlib.plot_init(AZD['deremag'],4,4) pmagplotlib.plot_init(AZD['eqarea'],4,4) # # # # get list of unique specimen names # CurrRec=[] sids=pmag.get_specs(meas_data) # get plots for specimen s - default is just to step through arai diagrams # if spc!="": specimen =sids.index(spc) while specimen < len(sids): methcodes=[] if pmagplotlib.verbose and spc!="": print sids[specimen],specimen+1, 'of ', len(sids) MeasRecs=[] s=sids[specimen] datablock,trmblock=[],[] PmagSpecRec={} PmagSpecRec["er_analyst_mail_names"]=user PmagSpecRec["specimen_correction"]='u' # # find the data from the meas_data file for this specimen # for rec in meas_data: if rec["er_specimen_name"]==s: MeasRecs.append(rec) methods=rec["magic_method_codes"].split(":") meths=[] for meth in methods: meths.append(meth.strip()) # take off annoying spaces methods="" for meth in meths: if meth.strip() not in methcodes and "LP-" in meth:methcodes.append(meth.strip()) methods=methods+meth+":" methods=methods[:-1] rec["magic_method_codes"]=methods if "LP-PI-M" in meths: datablock.append(rec) if "LP-MRM" in meths: trmblock.append(rec) if len(trmblock)>2 and inspec!="": if Tinit==0: Tinit=1 AZD['MRM']=4 pmagplotlib.plot_init(AZD['MRM'],4,4) elif Tinit==1: pmagplotlib.clearFIG(AZD['MRM']) if len(datablock) <4: if backup==0: specimen+=1 if pmagplotlib.verbose: print 'skipping specimen - moving forward ', s else: specimen-=1 if pmagplotlib.verbose: print 'skipping specimen - moving backward ', s # # collect info for the PmagSpecRec dictionary # else: rec=datablock[0] PmagSpecRec["er_citation_names"]="This study" PmagSpecRec["er_specimen_name"]=s PmagSpecRec["er_sample_name"]=rec["er_sample_name"] PmagSpecRec["er_site_name"]=rec["er_site_name"] PmagSpecRec["er_location_name"]=rec["er_location_name"] if "magic_instrument_codes" not in rec.keys():rec["magic_instrument_codes"]="" PmagSpecRec["magic_instrument_codes"]=rec["magic_instrument_codes"] PmagSpecRec["measurement_step_unit"]="J" if "magic_experiment_name" not in rec.keys(): rec["magic_experiment_name"]="" else: PmagSpecRec["magic_experiment_names"]=rec["magic_experiment_name"] meths=rec["magic_method_codes"].split(':') # sort data into types if "LP-PI-M-D" in meths: # this is a double heating experiment exp_type="LP-PI-M-D" elif "LP-PI-M-S" in meths: exp_type="LP-PI-M-S" else: print "experiment type not supported yet " break araiblock,field=pmag.sortmwarai(datablock,exp_type) first_Z=araiblock[0] first_I=araiblock[1] GammaChecks=araiblock[-3] ThetaChecks=araiblock[-2] DeltaChecks=araiblock[-1] if len(first_Z)<3: if backup==0: specimen+=1 if pmagplotlib.verbose: print 'skipping specimen - moving forward ', s else: specimen-=1 if pmagplotlib.verbose: print 'skipping specimen - moving backward ', s else: backup=0 zijdblock,units=pmag.find_dmag_rec(s,meas_data) if exp_type=="LP-PI-M-D": recnum=0 print "ZStep Watts Dec Inc Int" for plotrec in zijdblock: if pmagplotlib.verbose: print '%i %i %7.1f %7.1f %8.3e ' % (recnum,plotrec[0],plotrec[1],plotrec[2],plotrec[3]) recnum += 1 recnum = 1 if GammaChecks!="": print "IStep Watts Gamma" for gamma in GammaChecks: if pmagplotlib.verbose: print '%i %i %7.1f ' % (recnum, gamma[0],gamma[1]) recnum += 1 if exp_type=="LP-PI-M-S": if pmagplotlib.verbose: print "IStep Watts Theta" kk=0 for theta in ThetaChecks: kk+=1 print '%i %i %7.1f ' % (kk,theta[0],theta[1]) if pmagplotlib.verbose: print "Watts Delta" for delta in DeltaChecks: print '%i %7.1f ' % (delta[0],delta[1]) pmagplotlib.plotAZ(AZD,araiblock,zijdblock,s,units[0]) if inspec !="": if pmagplotlib.verbose: print 'Looking up saved interpretation....' found = 0 for k in range(len(PriorRecs)): try: if PriorRecs[k]["er_specimen_name"]==s: found =1 CurrRec.append(PriorRecs[k]) for j in range(len(araiblock[0])): if float(araiblock[0][j][0])==float(PriorRecs[k]["measurement_step_min"]):start=j if float(araiblock[0][j][0])==float(PriorRecs[k]["measurement_step_max"]):end=j pars,errcode=pmag.PintPars(araiblock,zijdblock,start,end) pars['measurement_step_unit']="J" del PriorRecs[k] # put in CurrRec, take out of PriorRecs if errcode!=1: pars["specimen_lab_field_dc"]=field pars["specimen_int"]=-1*field*pars["specimen_b"] pars["er_specimen_name"]=s if pmagplotlib.verbose: print 'Saved interpretation: ' pars=pmag.scoreit(pars,PmagSpecRec,accept,'',0) pmagplotlib.plotB(AZD,araiblock,zijdblock,pars) if len(trmblock)>2: blab=field best=pars["specimen_int"] Bs,TRMs=[],[] for trec in trmblock: Bs.append(float(trec['treatment_dc_field'])) TRMs.append(float(trec['measurement_magn_moment'])) NLpars=nlt.NLtrm(Bs,TRMs,best,blab,0) # calculate best fit parameters through TRM acquisition data, and get new banc Mp,Bp=[],[] for k in range(int(max(Bs)*1e6)): Bp.append(float(k)*1e-6) npred=nlt.TRM(Bp[-1],NLpars['xopt'][0],NLpars['xopt'][1]) # predicted NRM for this field Mp.append(npred) pmagplotlib.plotTRM(AZD['MRM'],Bs,TRMs,Bp,Mp,NLpars,trec['magic_experiment_name']) print npred print 'Banc= ',float(NLpars['banc'])*1e6 if pmagplotlib.verbose: print 'Banc= ',float(NLpars['banc'])*1e6 pmagplotlib.drawFIGS(AZD) else: print 'error on specimen ',s except: pass if pmagplotlib.verbose and found==0: print ' None found :( ' if spc!="": if BEG!="": pars,errcode=pmag.PintPars(araiblock,zijdblock,BEG,END) pars['measurement_step_unit']="J" pars["specimen_lab_field_dc"]=field pars["specimen_int"]=-1*field*pars["specimen_b"] pars["er_specimen_name"]=s pars['specimen_grade']='' # ungraded pmagplotlib.plotB(AZD,araiblock,zijdblock,pars) if len(trmblock)>2: if inlt==0: donlt() inlt=1 blab=field best=pars["specimen_int"] Bs,TRMs=[],[] for trec in trmblock: Bs.append(float(trec['treatment_dc_field'])) TRMs.append(float(trec['measurement_magn_moment'])) NLpars=nlt.NLtrm(Bs,TRMs,best,blab,0) # calculate best fit parameters through TRM acquisition data, and get new banc # Mp,Bp=[],[] for k in range(int(max(Bs)*1e6)): Bp.append(float(k)*1e-6) npred=nlt.TRM(Bp[-1],NLpars['xopt'][0],NLpars['xopt'][1]) # predicted NRM for this field files={} for key in AZD.keys(): files[key]=s+'_'+key+fmt pmagplotlib.saveP(AZD,files) sys.exit() if plots==0: ans='b' while ans != "": print """ s[a]ve plot, set [b]ounds for calculation, [d]elete current interpretation, [p]revious, [s]ample, [q]uit: """ ans=raw_input('Return for next specimen \n') if ans=="": specimen +=1 if ans=="d": save_redo(PriorRecs,inspec) CurrRec=[] pmagplotlib.plotAZ(AZD,araiblock,zijdblock,s,units[0]) pmagplotlib.drawFIGS(AZD) if ans=='a': files={} for key in AZD.keys(): files[key]=s+'_'+key+fmt pmagplotlib.saveP(AZD,files) ans="" if ans=='q': print "Good bye" sys.exit() if ans=='p': specimen =specimen -1 backup = 1 ans="" if ans=='s': keepon=1 spec=raw_input('Enter desired specimen name (or first part there of): ') while keepon==1: try: specimen =sids.index(spec) keepon=0 except: tmplist=[] for qq in range(len(sids)): if spec in sids[qq]:tmplist.append(sids[qq]) print specimen," not found, but this was: " print tmplist spec=raw_input('Select one or try again\n ') ans="" if ans=='b': if end==0 or end >=len(araiblock[0]):end=len(araiblock[0])-1 GoOn=0 while GoOn==0: print 'Enter index of first point for calculation: ','[',start,']' answer=raw_input('return to keep default ') if answer != "":start=int(answer) print 'Enter index of last point for calculation: ','[',end,']' answer=raw_input('return to keep default ') if answer != "": end=int(answer) if start >=0 and start <len(araiblock[0])-2 and end >0 and end <len(araiblock[0]) and start<end: GoOn=1 else: print "Bad endpoints - try again! " start,end=0,len(araiblock) s=sids[specimen] pars,errcode=pmag.PintPars(araiblock,zijdblock,start,end) pars['measurement_step_unit']="J" pars["specimen_lab_field_dc"]=field pars["specimen_int"]=-1*field*pars["specimen_b"] pars["er_specimen_name"]=s pars=pmag.scoreit(pars,PmagSpecRec,accept,'',0) PmagSpecRec["measurement_step_min"]='%8.3e' % (pars["measurement_step_min"]) PmagSpecRec["measurement_step_max"]='%8.3e' % (pars["measurement_step_max"]) PmagSpecRec["measurement_step_unit"]="J" PmagSpecRec["specimen_int_n"]='%i'%(pars["specimen_int_n"]) PmagSpecRec["specimen_lab_field_dc"]='%8.3e'%(pars["specimen_lab_field_dc"]) PmagSpecRec["specimen_int"]='%8.3e '%(pars["specimen_int"]) PmagSpecRec["specimen_b"]='%5.3f '%(pars["specimen_b"]) PmagSpecRec["specimen_q"]='%5.1f '%(pars["specimen_q"]) PmagSpecRec["specimen_f"]='%5.3f '%(pars["specimen_f"]) PmagSpecRec["specimen_fvds"]='%5.3f'%(pars["specimen_fvds"]) PmagSpecRec["specimen_b_beta"]='%5.3f'%(pars["specimen_b_beta"]) PmagSpecRec["specimen_int_mad"]='%7.1f'%(pars["specimen_int_mad"]) PmagSpecRec["specimen_Z"]='%7.1f'%(pars["specimen_Z"]) if pars["method_codes"]!="": tmpcodes=pars["method_codes"].split(":") for t in tmpcodes: if t.strip() not in methcodes:methcodes.append(t.strip()) PmagSpecRec["specimen_dec"]='%7.1f'%(pars["specimen_dec"]) PmagSpecRec["specimen_inc"]='%7.1f'%(pars["specimen_inc"]) PmagSpecRec["specimen_tilt_correction"]='-1' PmagSpecRec["specimen_direction_type"]='l' PmagSpecRec["direction_type"]='l' # this is redudant, but helpful - won't be imported PmagSpecRec["specimen_dang"]='%7.1f '%(pars["specimen_dang"]) PmagSpecRec["specimen_drats"]='%7.1f '%(pars["specimen_drats"]) PmagSpecRec["specimen_int_ptrm_n"]='%i '%(pars["specimen_int_ptrm_n"]) PmagSpecRec["specimen_rsc"]='%6.4f '%(pars["specimen_rsc"]) PmagSpecRec["specimen_md"]='%i '%(int(pars["specimen_md"])) if PmagSpecRec["specimen_md"]=='-1':PmagSpecRec["specimen_md"]="" PmagSpecRec["specimen_b_sigma"]='%5.3f '%(pars["specimen_b_sigma"]) if "IE-TT" not in methcodes:methcodes.append("IE-TT") methods="" for meth in methcodes: methods=methods+meth+":" PmagSpecRec["magic_method_codes"]=methods[:-1] PmagSpecRec["specimen_description"]=comment PmagSpecRec["magic_software_packages"]=version_num pmagplotlib.plotAZ(AZD,araiblock,zijdblock,s,units[0]) pmagplotlib.plotB(AZD,araiblock,zijdblock,pars) if len(trmblock)>2: blab=field best=pars["specimen_int"] Bs,TRMs=[],[] for trec in trmblock: Bs.append(float(trec['treatment_dc_field'])) TRMs.append(float(trec['measurement_magn_moment'])) NLpars=nlt.NLtrm(Bs,TRMs,best,blab,0) # calculate best fit parameters through TRM acquisition data, and get new banc Mp,Bp=[],[] for k in range(int(max(Bs)*1e6)): Bp.append(float(k)*1e-6) npred=nlt.TRM(Bp[-1],NLpars['xopt'][0],NLpars['xopt'][1]) # predicted NRM for this field Mp.append(npred) pmagplotlib.plotTRM(AZD['MRM'],Bs,TRMs,Bp,Mp,NLpars,trec['magic_experiment_name']) print 'Banc= ',float(NLpars['banc'])*1e6 pmagplotlib.drawFIGS(AZD) pars["specimen_lab_field_dc"]=field pars["specimen_int"]=-1*field*pars["specimen_b"] saveit=raw_input("Save this interpretation? [y]/n \n") if saveit!='n': specimen+=1 PriorRecs.append(PmagSpecRec) # put back an interpretation save_redo(PriorRecs,inspec) ans="" else: specimen+=1 if fmt != ".pmag": basename=s+'_microwave'+fmt files={} for key in AZD.keys(): files[key]=s+'_'+key+fmt if pmagplotlib.isServer: black = '#000000' purple = '#800080' titles={} titles['deremag']='DeReMag Plot' titles['zijd']='Zijderveld Plot' titles['arai']='Arai Plot' AZD = pmagplotlib.addBorders(AZD,titles,black,purple) pmagplotlib.saveP(AZD,files) # pmagplotlib.combineFigs(s,files,3) if len(CurrRec)>0: for rec in CurrRec: PriorRecs.append(rec) CurrRec=[] if plots!=1: ans=raw_input(" Save last plot? 1/[0] ") if ans=="1": if fmt != ".pmag": files={} for key in AZD.keys(): files[key]=s+'_'+key+fmt pmagplotlib.saveP(AZD,files) if len(CurrRec)>0:PriorRecs.append(CurrRec) # put back an interpretation if len(PriorRecs)>0: save_redo(PriorRecs,inspec) print 'Updated interpretations saved in ',inspec if pmagplotlib.verbose: print "Good bye"