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_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 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"