def main(): """ NAME aarm_magic.py DESCRIPTION Converts AARM data to best-fit tensor (6 elements plus sigma) Original program ARMcrunch written to accomodate ARM anisotropy data collected from 6 axial directions (+X,+Y,+Z,-X,-Y,-Z) using the off-axis remanence terms to construct the tensor. A better way to do the anisotropy of ARMs is to use 9,12 or 15 measurements in the Hext rotational scheme. SYNTAX aarm_magic.py [-h][command line options] OPTIONS -h prints help message and quits -usr USER: identify user, default is "" -f FILE: specify input file, default is aarm_measurements.txt -crd [s,g,t] specify coordinate system, requires er_samples.txt file -fsa FILE: specify er_samples.txt file, default is er_samples.txt -Fa FILE: specify anisotropy output file, default is arm_anisotropy.txt -Fr FILE: specify results output file, default is aarm_results.txt INPUT Input for the present program is a series of baseline, ARM pairs. The baseline should be the AF demagnetized state (3 axis demag is preferable) for the following ARM acquisition. The order of the measurements is: positions 1,2,3, 6,7,8, 11,12,13 (for 9 positions) positions 1,2,3,4, 6,7,8,9, 11,12,13,14 (for 12 positions) positions 1-15 (for 15 positions) """ # initialize some parameters args = sys.argv user = "" meas_file = "aarm_measurements.txt" samp_file = "er_samples.txt" rmag_anis = "arm_anisotropy.txt" rmag_res = "aarm_results.txt" dir_path = '.' # # get name of file from command line # 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 "-f" in args: ind = args.index("-f") meas_file = sys.argv[ind + 1] coord = '-1' if "-crd" in sys.argv: ind = sys.argv.index("-crd") coord = sys.argv[ind + 1] if coord == 's': coord = '-1' if coord == 'g': coord = '0' if coord == 't': coord = '100' if "-fsa" in args: ind = args.index("-fsa") samp_file = sys.argv[ind + 1] if "-Fa" in args: ind = args.index("-Fa") rmag_anis = args[ind + 1] if "-Fr" in args: ind = args.index("-Fr") rmag_res = args[ind + 1] meas_file = dir_path + '/' + meas_file samp_file = dir_path + '/' + samp_file rmag_anis = dir_path + '/' + rmag_anis rmag_res = dir_path + '/' + rmag_res # read in data meas_data, file_type = pmag.magic_read(meas_file) meas_data = pmag.get_dictitem(meas_data, 'magic_method_codes', 'LP-AN-ARM', 'has') if file_type != 'magic_measurements': print file_type print file_type, "This is not a valid magic_measurements file " sys.exit() if coord != '-1': # need to read in sample data samp_data, file_type = pmag.magic_read(samp_file) if file_type != 'er_samples': print file_type print file_type, "This is not a valid er_samples file " print "Only specimen coordinates will be calculated" coord = '-1' # # sort the specimen names # ssort = [] for rec in meas_data: spec = rec["er_specimen_name"] if spec not in ssort: ssort.append(spec) if len(ssort) > 1: sids = sorted(ssort) else: sids = ssort # # work on each specimen # specimen = 0 RmagSpecRecs, RmagResRecs = [], [] while specimen < len(sids): s = sids[specimen] data = [] RmagSpecRec = {} RmagResRec = {} method_codes = [] # # find the data from the meas_data file for this sample # data = pmag.get_dictitem(meas_data, 'er_specimen_name', s, 'T') # # find out the number of measurements (9, 12 or 15) # npos = len(data) / 2 if npos == 9: # # get dec, inc, int and convert to x,y,z # B, H, tmpH = pmag.designAARM( npos) # B matrix made from design matrix for positions X = [] for rec in data: Dir = [] Dir.append(float(rec["measurement_dec"])) Dir.append(float(rec["measurement_inc"])) Dir.append(float(rec["measurement_magn_moment"])) X.append(pmag.dir2cart(Dir)) # # subtract baseline and put in a work array # work = numpy.zeros((npos, 3), 'f') for i in range(npos): for j in range(3): work[i][j] = X[2 * i + 1][j] - X[2 * i][j] # # calculate tensor elements # first put ARM components in w vector # w = numpy.zeros((npos * 3), 'f') index = 0 for i in range(npos): for j in range(3): w[index] = work[i][j] index += 1 s = numpy.zeros((6), 'f') # initialize the s matrix for i in range(6): for j in range(len(w)): s[i] += B[i][j] * w[j] trace = s[0] + s[1] + s[2] # normalize by the trace for i in range(6): s[i] = s[i] / trace a = pmag.s2a(s) #------------------------------------------------------------ # Calculating dels is different than in the Kappabridge # routine. Use trace normalized tensor (a) and the applied # unit field directions (tmpH) to generate model X,Y,Z # components. Then compare these with the measured values. #------------------------------------------------------------ S = 0. comp = numpy.zeros((npos * 3), 'f') for i in range(npos): for j in range(3): index = i * 3 + j compare = a[j][0] * tmpH[i][0] + a[j][1] * tmpH[i][1] + a[ j][2] * tmpH[i][2] comp[index] = compare for i in range(npos * 3): d = w[i] / trace - comp[i] # del values S += d * d nf = float(npos * 3 - 6) # number of degrees of freedom if S > 0: sigma = numpy.sqrt(S / nf) else: sigma = 0 RmagSpecRec["rmag_anisotropy_name"] = data[0]["er_specimen_name"] RmagSpecRec["er_location_name"] = data[0]["er_location_name"] RmagSpecRec["er_specimen_name"] = data[0]["er_specimen_name"] RmagSpecRec["er_sample_name"] = data[0]["er_sample_name"] RmagSpecRec["er_site_name"] = data[0]["er_site_name"] RmagSpecRec["magic_experiment_names"] = RmagSpecRec[ "rmag_anisotropy_name"] + ":AARM" RmagSpecRec["er_citation_names"] = "This study" RmagResRec[ "rmag_result_name"] = data[0]["er_specimen_name"] + ":AARM" RmagResRec["er_location_names"] = data[0]["er_location_name"] RmagResRec["er_specimen_names"] = data[0]["er_specimen_name"] RmagResRec["er_sample_names"] = data[0]["er_sample_name"] RmagResRec["er_site_names"] = data[0]["er_site_name"] RmagResRec["magic_experiment_names"] = RmagSpecRec[ "rmag_anisotropy_name"] + ":AARM" RmagResRec["er_citation_names"] = "This study" if "magic_instrument_codes" in data[0].keys(): RmagSpecRec["magic_instrument_codes"] = data[0][ "magic_instrument_codes"] else: RmagSpecRec["magic_instrument_codes"] = "" RmagSpecRec["anisotropy_type"] = "AARM" RmagSpecRec[ "anisotropy_description"] = "Hext statistics adapted to AARM" if coord != '-1': # need to rotate s # set orientation priorities SO_methods = [] for rec in samp_data: if "magic_method_codes" not in rec: rec['magic_method_codes'] = 'SO-NO' 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) # continue here redo, p = 1, 0 if len(SO_methods) <= 1: az_type = SO_methods[0] orient = pmag.find_samp_rec(RmagSpecRec["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 az, pl = orient['sample_azimuth'], orient['sample_dip'] s = pmag.dosgeo(s, az, pl) # rotate to geographic coordinates if coord == '100': sampe_bed_dir, sample_bed_dip = orient[ 'sample_bed_dip_direction'], orient['sample_bed_dip'] s = pmag.dostilt( s, bed_dir, bed_dip) # rotate to geographic coordinates hpars = pmag.dohext(nf, sigma, s) # # prepare for output # RmagSpecRec["anisotropy_s1"] = '%8.6f' % (s[0]) RmagSpecRec["anisotropy_s2"] = '%8.6f' % (s[1]) RmagSpecRec["anisotropy_s3"] = '%8.6f' % (s[2]) RmagSpecRec["anisotropy_s4"] = '%8.6f' % (s[3]) RmagSpecRec["anisotropy_s5"] = '%8.6f' % (s[4]) RmagSpecRec["anisotropy_s6"] = '%8.6f' % (s[5]) RmagSpecRec["anisotropy_mean"] = '%8.3e' % (trace / 3) RmagSpecRec["anisotropy_sigma"] = '%8.6f' % (sigma) RmagSpecRec["anisotropy_unit"] = "Am^2" RmagSpecRec["anisotropy_n"] = '%i' % (npos) RmagSpecRec["anisotropy_tilt_correction"] = coord RmagSpecRec["anisotropy_F"] = '%7.1f ' % ( hpars["F"] ) # used by thellier_gui - must be taken out for uploading RmagSpecRec["anisotropy_F_crit"] = hpars[ "F_crit"] # used by thellier_gui - must be taken out for uploading RmagResRec["anisotropy_t1"] = '%8.6f ' % (hpars["t1"]) RmagResRec["anisotropy_t2"] = '%8.6f ' % (hpars["t2"]) RmagResRec["anisotropy_t3"] = '%8.6f ' % (hpars["t3"]) RmagResRec["anisotropy_v1_dec"] = '%7.1f ' % (hpars["v1_dec"]) RmagResRec["anisotropy_v2_dec"] = '%7.1f ' % (hpars["v2_dec"]) RmagResRec["anisotropy_v3_dec"] = '%7.1f ' % (hpars["v3_dec"]) RmagResRec["anisotropy_v1_inc"] = '%7.1f ' % (hpars["v1_inc"]) RmagResRec["anisotropy_v2_inc"] = '%7.1f ' % (hpars["v2_inc"]) RmagResRec["anisotropy_v3_inc"] = '%7.1f ' % (hpars["v3_inc"]) RmagResRec["anisotropy_ftest"] = '%7.1f ' % (hpars["F"]) RmagResRec["anisotropy_ftest12"] = '%7.1f ' % (hpars["F12"]) RmagResRec["anisotropy_ftest23"] = '%7.1f ' % (hpars["F23"]) RmagResRec["result_description"] = 'Critical F: ' + hpars[ "F_crit"] + ';Critical F12/F13: ' + hpars["F12_crit"] if hpars["e12"] > hpars["e13"]: RmagResRec["anisotropy_v1_zeta_semi_angle"] = '%7.1f ' % ( hpars['e12']) RmagResRec["anisotropy_v1_zeta_dec"] = '%7.1f ' % ( hpars['v2_dec']) RmagResRec["anisotropy_v1_zeta_inc"] = '%7.1f ' % ( hpars['v2_inc']) RmagResRec["anisotropy_v2_zeta_semi_angle"] = '%7.1f ' % ( hpars['e12']) RmagResRec["anisotropy_v2_zeta_dec"] = '%7.1f ' % ( hpars['v1_dec']) RmagResRec["anisotropy_v2_zeta_inc"] = '%7.1f ' % ( hpars['v1_inc']) RmagResRec["anisotropy_v1_eta_semi_angle"] = '%7.1f ' % ( hpars['e13']) RmagResRec["anisotropy_v1_eta_dec"] = '%7.1f ' % ( hpars['v3_dec']) RmagResRec["anisotropy_v1_eta_inc"] = '%7.1f ' % ( hpars['v3_inc']) RmagResRec["anisotropy_v3_eta_semi_angle"] = '%7.1f ' % ( hpars['e13']) RmagResRec["anisotropy_v3_eta_dec"] = '%7.1f ' % ( hpars['v1_dec']) RmagResRec["anisotropy_v3_eta_inc"] = '%7.1f ' % ( hpars['v1_inc']) else: RmagResRec["anisotropy_v1_zeta_semi_angle"] = '%7.1f ' % ( hpars['e13']) RmagResRec["anisotropy_v1_zeta_dec"] = '%7.1f ' % ( hpars['v3_dec']) RmagResRec["anisotropy_v1_zeta_inc"] = '%7.1f ' % ( hpars['v3_inc']) RmagResRec["anisotropy_v3_zeta_semi_angle"] = '%7.1f ' % ( hpars['e13']) RmagResRec["anisotropy_v3_zeta_dec"] = '%7.1f ' % ( hpars['v1_dec']) RmagResRec["anisotropy_v3_zeta_inc"] = '%7.1f ' % ( hpars['v1_inc']) RmagResRec["anisotropy_v1_eta_semi_angle"] = '%7.1f ' % ( hpars['e12']) RmagResRec["anisotropy_v1_eta_dec"] = '%7.1f ' % ( hpars['v2_dec']) RmagResRec["anisotropy_v1_eta_inc"] = '%7.1f ' % ( hpars['v2_inc']) RmagResRec["anisotropy_v2_eta_semi_angle"] = '%7.1f ' % ( hpars['e12']) RmagResRec["anisotropy_v2_eta_dec"] = '%7.1f ' % ( hpars['v1_dec']) RmagResRec["anisotropy_v2_eta_inc"] = '%7.1f ' % ( hpars['v1_inc']) if hpars["e23"] > hpars['e12']: RmagResRec["anisotropy_v2_zeta_semi_angle"] = '%7.1f ' % ( hpars['e23']) RmagResRec["anisotropy_v2_zeta_dec"] = '%7.1f ' % ( hpars['v3_dec']) RmagResRec["anisotropy_v2_zeta_inc"] = '%7.1f ' % ( hpars['v3_inc']) RmagResRec["anisotropy_v3_zeta_semi_angle"] = '%7.1f ' % ( hpars['e23']) RmagResRec["anisotropy_v3_zeta_dec"] = '%7.1f ' % ( hpars['v2_dec']) RmagResRec["anisotropy_v3_zeta_inc"] = '%7.1f ' % ( hpars['v2_inc']) RmagResRec["anisotropy_v3_eta_semi_angle"] = '%7.1f ' % ( hpars['e13']) RmagResRec["anisotropy_v3_eta_dec"] = '%7.1f ' % ( hpars['v1_dec']) RmagResRec["anisotropy_v3_eta_inc"] = '%7.1f ' % ( hpars['v1_inc']) RmagResRec["anisotropy_v2_eta_semi_angle"] = '%7.1f ' % ( hpars['e12']) RmagResRec["anisotropy_v2_eta_dec"] = '%7.1f ' % ( hpars['v1_dec']) RmagResRec["anisotropy_v2_eta_inc"] = '%7.1f ' % ( hpars['v1_inc']) else: RmagResRec["anisotropy_v2_zeta_semi_angle"] = '%7.1f ' % ( hpars['e12']) RmagResRec["anisotropy_v2_zeta_dec"] = '%7.1f ' % ( hpars['v1_dec']) RmagResRec["anisotropy_v2_zeta_inc"] = '%7.1f ' % ( hpars['v1_inc']) RmagResRec["anisotropy_v3_eta_semi_angle"] = '%7.1f ' % ( hpars['e23']) RmagResRec["anisotropy_v3_eta_dec"] = '%7.1f ' % ( hpars['v2_dec']) RmagResRec["anisotropy_v3_eta_inc"] = '%7.1f ' % ( hpars['v2_inc']) RmagResRec["anisotropy_v3_zeta_semi_angle"] = '%7.1f ' % ( hpars['e13']) RmagResRec["anisotropy_v3_zeta_dec"] = '%7.1f ' % ( hpars['v1_dec']) RmagResRec["anisotropy_v3_zeta_inc"] = '%7.1f ' % ( hpars['v1_inc']) RmagResRec["anisotropy_v2_eta_semi_angle"] = '%7.1f ' % ( hpars['e23']) RmagResRec["anisotropy_v2_eta_dec"] = '%7.1f ' % ( hpars['v3_dec']) RmagResRec["anisotropy_v2_eta_inc"] = '%7.1f ' % ( hpars['v3_inc']) RmagResRec["tilt_correction"] = '-1' RmagResRec["anisotropy_type"] = 'AARM' RmagResRec["magic_method_codes"] = 'LP-AN-ARM:AE-H' RmagSpecRec["magic_method_codes"] = 'LP-AN-ARM:AE-H' RmagResRec["magic_software_packages"] = pmag.get_version() RmagSpecRec["magic_software_packages"] = pmag.get_version() specimen += 1 RmagSpecRecs.append(RmagSpecRec) RmagResRecs.append(RmagResRec) else: print 'skipping specimen ', s, ' only 9 positions supported', '; this has ', npos specimen += 1 if rmag_anis == "": rmag_anis = "rmag_anisotropy.txt" pmag.magic_write(rmag_anis, RmagSpecRecs, 'rmag_anisotropy') print "specimen tensor elements stored in ", rmag_anis if rmag_res == "": rmag_res = "rmag_results.txt" pmag.magic_write(rmag_res, RmagResRecs, 'rmag_results') print "specimen statistics and eigenparameters stored in ", rmag_res
def main(): """ NAME atrm_magic.py DESCRIPTION Converts ATRM data to best-fit tensor (6 elements plus sigma) Original program ARMcrunch written to accomodate ARM anisotropy data collected from 6 axial directions (+X,+Y,+Z,-X,-Y,-Z) using the off-axis remanence terms to construct the tensor. A better way to do the anisotropy of ARMs is to use 9,12 or 15 measurements in the Hext rotational scheme. SYNTAX atrm_magic.py [-h][command line options] OPTIONS -h prints help message and quits -usr USER: identify user, default is "" -f FILE: specify input file, default is atrm_measurements.txt -Fa FILE: specify anisotropy output file, default is trm_anisotropy.txt -Fr FILE: specify results output file, default is atrm_results.txt INPUT Input for the present program is a TRM acquisition data with an optional baseline. The order of the measurements is: Decs=[0,90,0,180,270,0,0,90,0] Incs=[0,0,90,0,0,-90,0,0,90] The last two measurements are optional """ # initialize some parameters args=sys.argv user="" meas_file="atrm_measurements.txt" rmag_anis="trm_anisotropy.txt" rmag_res="atrm_results.txt" dir_path='.' # # get name of file from command line # 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 "-f" in args: ind=args.index("-f") meas_file=sys.argv[ind+1] if "-Fa" in args: ind=args.index("-Fa") rmag_anis=args[ind+1] if "-Fr" in args: ind=args.index("-Fr") rmag_res=args[ind+1] meas_file=dir_path+'/'+meas_file rmag_anis=dir_path+'/'+rmag_anis rmag_res=dir_path+'/'+rmag_res # read in data meas_data,file_type=pmag.magic_read(meas_file) meas_data=pmag.get_dictitem(meas_data,'magic_method_codes','LP-AN-TRM','has') if file_type != 'magic_measurements': print file_type print file_type,"This is not a valid magic_measurements file " sys.exit() # # # get sorted list of unique specimen names ssort=[] for rec in meas_data: spec=rec["er_specimen_name"] if spec not in ssort:ssort.append(spec) sids=sorted(ssort) # # # work on each specimen # specimen,npos=0,6 RmagSpecRecs,RmagResRecs=[],[] while specimen < len(sids): nmeas=0 s=sids[specimen] RmagSpecRec={} RmagResRec={} BX,X=[],[] method_codes=[] Spec0="" # # find the data from the meas_data file for this sample # and get dec, inc, int and convert to x,y,z # data=pmag.get_dictitem(meas_data,'er_specimen_name',s,'T') # fish out data for this specimen name if len(data)>5: RmagSpecRec["rmag_anisotropy_name"]=data[0]["er_specimen_name"] RmagSpecRec["er_location_name"]=data[0]["er_location_name"] RmagSpecRec["er_specimen_name"]=data[0]["er_specimen_name"] RmagSpecRec["er_sample_name"]=data[0]["er_sample_name"] RmagSpecRec["er_site_name"]=data[0]["er_site_name"] RmagSpecRec["magic_experiment_names"]=RmagSpecRec["rmag_anisotropy_name"]+":ATRM" RmagSpecRec["er_citation_names"]="This study" RmagResRec["rmag_result_name"]=data[0]["er_specimen_name"]+":ATRM" RmagResRec["er_location_names"]=data[0]["er_location_name"] RmagResRec["er_specimen_names"]=data[0]["er_specimen_name"] RmagResRec["er_sample_names"]=data[0]["er_sample_name"] RmagResRec["er_site_names"]=data[0]["er_site_name"] RmagResRec["magic_experiment_names"]=RmagSpecRec["rmag_anisotropy_name"]+":ATRM" RmagResRec["er_citation_names"]="This study" RmagSpecRec["anisotropy_type"]="ATRM" if "magic_instrument_codes" in data[0].keys(): RmagSpecRec["magic_instrument_codes"]=data[0]["magic_instrument_codes"] else: RmagSpecRec["magic_instrument_codes"]="" RmagSpecRec["anisotropy_description"]="Hext statistics adapted to ATRM" for rec in data: meths=rec['magic_method_codes'].strip().split(':') Dir=[] Dir.append(float(rec["measurement_dec"])) Dir.append(float(rec["measurement_inc"])) Dir.append(float(rec["measurement_magn_moment"])) if "LT-T-Z" in meths: BX.append(pmag.dir2cart(Dir)) # append baseline steps elif "LT-T-I" in meths: X.append(pmag.dir2cart(Dir)) nmeas+=1 # if len(BX)==1: for i in range(len(X)-1):BX.append(BX[0]) # assume first 0 field step as baseline elif len(BX)== 0: # assume baseline is zero for i in range(len(X)):BX.append([0.,0.,0.]) # assume baseline of 0 elif len(BX)!= len(X): # if BX isn't just one measurement or one in between every infield step, just assume it is zero print 'something odd about the baselines - just assuming zero' for i in range(len(X)):BX.append([0.,0.,0.]) # assume baseline of 0 if nmeas<6: # must have at least 6 measurements right now - print 'skipping specimen ',s,' too few measurements' specimen+=1 else: B,H,tmpH=pmag.designATRM(npos) # B matrix made from design matrix for positions # # subtract optional baseline and put in a work array # work=numpy.zeros((nmeas,3),'f') for i in range(nmeas): for j in range(3): work[i][j]=X[i][j]-BX[i][j] # subtract baseline, if available # # calculate tensor elements # first put ARM components in w vector # w=numpy.zeros((npos*3),'f') index=0 for i in range(npos): for j in range(3): w[index]=work[i][j] index+=1 s=numpy.zeros((6),'f') # initialize the s matrix for i in range(6): for j in range(len(w)): s[i]+=B[i][j]*w[j] trace=s[0]+s[1]+s[2] # normalize by the trace for i in range(6): s[i]=s[i]/trace a=pmag.s2a(s) #------------------------------------------------------------ # Calculating dels is different than in the Kappabridge # routine. Use trace normalized tensor (a) and the applied # unit field directions (tmpH) to generate model X,Y,Z # components. Then compare these with the measured values. #------------------------------------------------------------ S=0. comp=numpy.zeros((npos*3),'f') for i in range(npos): for j in range(3): index=i*3+j compare=a[j][0]*tmpH[i][0]+a[j][1]*tmpH[i][1]+a[j][2]*tmpH[i][2] comp[index]=compare for i in range(npos*3): d=w[i]/trace - comp[i] # del values S+=d*d nf=float(npos*3.-6.) # number of degrees of freedom if S >0: sigma=numpy.sqrt(S/nf) else: sigma=0 hpars=pmag.dohext(nf,sigma,s) # # prepare for output # RmagSpecRec["anisotropy_s1"]='%8.6f'%(s[0]) RmagSpecRec["anisotropy_s2"]='%8.6f'%(s[1]) RmagSpecRec["anisotropy_s3"]='%8.6f'%(s[2]) RmagSpecRec["anisotropy_s4"]='%8.6f'%(s[3]) RmagSpecRec["anisotropy_s5"]='%8.6f'%(s[4]) RmagSpecRec["anisotropy_s6"]='%8.6f'%(s[5]) RmagSpecRec["anisotropy_mean"]='%8.3e'%(trace/3) RmagSpecRec["anisotropy_sigma"]='%8.6f'%(sigma) RmagSpecRec["anisotropy_unit"]="Am^2" RmagSpecRec["anisotropy_n"]='%i'%(npos) RmagSpecRec["anisotropy_tilt_correction"]='-1' RmagSpecRec["anisotropy_F"]='%7.1f '%(hpars["F"]) # used by thellier_gui - must be taken out for uploading RmagSpecRec["anisotropy_F_crit"]=hpars["F_crit"] # used by thellier_gui - must be taken out for uploading RmagResRec["anisotropy_t1"]='%8.6f '%(hpars["t1"]) RmagResRec["anisotropy_t2"]='%8.6f '%(hpars["t2"]) RmagResRec["anisotropy_t3"]='%8.6f '%(hpars["t3"]) RmagResRec["anisotropy_v1_dec"]='%7.1f '%(hpars["v1_dec"]) RmagResRec["anisotropy_v2_dec"]='%7.1f '%(hpars["v2_dec"]) RmagResRec["anisotropy_v3_dec"]='%7.1f '%(hpars["v3_dec"]) RmagResRec["anisotropy_v1_inc"]='%7.1f '%(hpars["v1_inc"]) RmagResRec["anisotropy_v2_inc"]='%7.1f '%(hpars["v2_inc"]) RmagResRec["anisotropy_v3_inc"]='%7.1f '%(hpars["v3_inc"]) RmagResRec["anisotropy_ftest"]='%7.1f '%(hpars["F"]) RmagResRec["anisotropy_ftest12"]='%7.1f '%(hpars["F12"]) RmagResRec["anisotropy_ftest23"]='%7.1f '%(hpars["F23"]) RmagResRec["result_description"]='Critical F: '+hpars["F_crit"]+';Critical F12/F13: '+hpars["F12_crit"] if hpars["e12"]>hpars["e13"]: RmagResRec["anisotropy_v1_zeta_semi_angle"]='%7.1f '%(hpars['e12']) RmagResRec["anisotropy_v1_zeta_dec"]='%7.1f '%(hpars['v2_dec']) RmagResRec["anisotropy_v1_zeta_inc"]='%7.1f '%(hpars['v2_inc']) RmagResRec["anisotropy_v2_zeta_semi_angle"]='%7.1f '%(hpars['e12']) RmagResRec["anisotropy_v2_zeta_dec"]='%7.1f '%(hpars['v1_dec']) RmagResRec["anisotropy_v2_zeta_inc"]='%7.1f '%(hpars['v1_inc']) RmagResRec["anisotropy_v1_eta_semi_angle"]='%7.1f '%(hpars['e13']) RmagResRec["anisotropy_v1_eta_dec"]='%7.1f '%(hpars['v3_dec']) RmagResRec["anisotropy_v1_eta_inc"]='%7.1f '%(hpars['v3_inc']) RmagResRec["anisotropy_v3_eta_semi_angle"]='%7.1f '%(hpars['e13']) RmagResRec["anisotropy_v3_eta_dec"]='%7.1f '%(hpars['v1_dec']) RmagResRec["anisotropy_v3_eta_inc"]='%7.1f '%(hpars['v1_inc']) else: RmagResRec["anisotropy_v1_zeta_semi_angle"]='%7.1f '%(hpars['e13']) RmagResRec["anisotropy_v1_zeta_dec"]='%7.1f '%(hpars['v3_dec']) RmagResRec["anisotropy_v1_zeta_inc"]='%7.1f '%(hpars['v3_inc']) RmagResRec["anisotropy_v3_zeta_semi_angle"]='%7.1f '%(hpars['e13']) RmagResRec["anisotropy_v3_zeta_dec"]='%7.1f '%(hpars['v1_dec']) RmagResRec["anisotropy_v3_zeta_inc"]='%7.1f '%(hpars['v1_inc']) RmagResRec["anisotropy_v1_eta_semi_angle"]='%7.1f '%(hpars['e12']) RmagResRec["anisotropy_v1_eta_dec"]='%7.1f '%(hpars['v2_dec']) RmagResRec["anisotropy_v1_eta_inc"]='%7.1f '%(hpars['v2_inc']) RmagResRec["anisotropy_v2_eta_semi_angle"]='%7.1f '%(hpars['e12']) RmagResRec["anisotropy_v2_eta_dec"]='%7.1f '%(hpars['v1_dec']) RmagResRec["anisotropy_v2_eta_inc"]='%7.1f '%(hpars['v1_inc']) if hpars["e23"]>hpars['e12']: RmagResRec["anisotropy_v2_zeta_semi_angle"]='%7.1f '%(hpars['e23']) RmagResRec["anisotropy_v2_zeta_dec"]='%7.1f '%(hpars['v3_dec']) RmagResRec["anisotropy_v2_zeta_inc"]='%7.1f '%(hpars['v3_inc']) RmagResRec["anisotropy_v3_zeta_semi_angle"]='%7.1f '%(hpars['e23']) RmagResRec["anisotropy_v3_zeta_dec"]='%7.1f '%(hpars['v2_dec']) RmagResRec["anisotropy_v3_zeta_inc"]='%7.1f '%(hpars['v2_inc']) RmagResRec["anisotropy_v3_eta_semi_angle"]='%7.1f '%(hpars['e13']) RmagResRec["anisotropy_v3_eta_dec"]='%7.1f '%(hpars['v1_dec']) RmagResRec["anisotropy_v3_eta_inc"]='%7.1f '%(hpars['v1_inc']) RmagResRec["anisotropy_v2_eta_semi_angle"]='%7.1f '%(hpars['e12']) RmagResRec["anisotropy_v2_eta_dec"]='%7.1f '%(hpars['v1_dec']) RmagResRec["anisotropy_v2_eta_inc"]='%7.1f '%(hpars['v1_inc']) else: RmagResRec["anisotropy_v2_zeta_semi_angle"]='%7.1f '%(hpars['e12']) RmagResRec["anisotropy_v2_zeta_dec"]='%7.1f '%(hpars['v1_dec']) RmagResRec["anisotropy_v2_zeta_inc"]='%7.1f '%(hpars['v1_inc']) RmagResRec["anisotropy_v3_eta_semi_angle"]='%7.1f '%(hpars['e23']) RmagResRec["anisotropy_v3_eta_dec"]='%7.1f '%(hpars['v2_dec']) RmagResRec["anisotropy_v3_eta_inc"]='%7.1f '%(hpars['v2_inc']) RmagResRec["anisotropy_v3_zeta_semi_angle"]='%7.1f '%(hpars['e13']) RmagResRec["anisotropy_v3_zeta_dec"]='%7.1f '%(hpars['v1_dec']) RmagResRec["anisotropy_v3_zeta_inc"]='%7.1f '%(hpars['v1_inc']) RmagResRec["anisotropy_v2_eta_semi_angle"]='%7.1f '%(hpars['e23']) RmagResRec["anisotropy_v2_eta_dec"]='%7.1f '%(hpars['v3_dec']) RmagResRec["anisotropy_v2_eta_inc"]='%7.1f '%(hpars['v3_inc']) RmagResRec["tilt_correction"]='-1' RmagResRec["anisotropy_type"]='ATRM' RmagResRec["magic_method_codes"]='LP-AN-TRM:AE-H' RmagSpecRec["magic_method_codes"]='LP-AN-TRM:AE-H' RmagResRec["magic_software_packages"]=pmag.get_version() RmagSpecRec["magic_software_packages"]=pmag.get_version() RmagSpecRecs.append(RmagSpecRec) RmagResRecs.append(RmagResRec) specimen+=1 pmag.magic_write(rmag_anis,RmagSpecRecs,'rmag_anisotropy') print "specimen tensor elements stored in ",rmag_anis pmag.magic_write(rmag_res,RmagResRecs,'rmag_results') print "specimen statistics and eigenparameters stored in ",rmag_res
def main(): """ NAME atrm_magic.py DESCRIPTION Converts ATRM data to best-fit tensor (6 elements plus sigma) Original program ARMcrunch written to accomodate ARM anisotropy data collected from 6 axial directions (+X,+Y,+Z,-X,-Y,-Z) using the off-axis remanence terms to construct the tensor. A better way to do the anisotropy of ARMs is to use 9,12 or 15 measurements in the Hext rotational scheme. SYNTAX atrm_magic.py [-h][command line options] OPTIONS -h prints help message and quits -usr USER: identify user, default is "" -f FILE: specify input file, default is atrm_measurements.txt -Fa FILE: specify anisotropy output file, default is trm_anisotropy.txt -Fr FILE: specify results output file, default is atrm_results.txt INPUT Input for the present program is a TRM acquisition data with an optional baseline. The order of the measurements is: Decs=[0,90,0,180,270,0,0,90,0] Incs=[0,0,90,0,0,-90,0,0,90] The last two measurements are optional """ # initialize some parameters args = sys.argv user = "" meas_file = "atrm_measurements.txt" rmag_anis = "trm_anisotropy.txt" rmag_res = "atrm_results.txt" dir_path = '.' # # get name of file from command line # 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 "-f" in args: ind = args.index("-f") meas_file = sys.argv[ind + 1] if "-Fa" in args: ind = args.index("-Fa") rmag_anis = args[ind + 1] if "-Fr" in args: ind = args.index("-Fr") rmag_res = args[ind + 1] meas_file = dir_path + '/' + meas_file rmag_anis = dir_path + '/' + rmag_anis rmag_res = dir_path + '/' + rmag_res # read in data meas_data, file_type = pmag.magic_read(meas_file) meas_data = pmag.get_dictitem(meas_data, 'magic_method_codes', 'LP-AN-TRM', 'has') if file_type != 'magic_measurements': print(file_type) print(file_type, "This is not a valid magic_measurements file ") sys.exit() # # # get sorted list of unique specimen names ssort = [] for rec in meas_data: spec = rec["er_specimen_name"] if spec not in ssort: ssort.append(spec) sids = sorted(ssort) # # # work on each specimen # specimen, npos = 0, 6 RmagSpecRecs, RmagResRecs = [], [] while specimen < len(sids): nmeas = 0 s = sids[specimen] RmagSpecRec = {} RmagResRec = {} BX, X = [], [] method_codes = [] Spec0 = "" # # find the data from the meas_data file for this sample # and get dec, inc, int and convert to x,y,z # data = pmag.get_dictitem(meas_data, 'er_specimen_name', s, 'T') # fish out data for this specimen name if len(data) > 5: RmagSpecRec["rmag_anisotropy_name"] = data[0]["er_specimen_name"] RmagSpecRec["er_location_name"] = data[0]["er_location_name"] RmagSpecRec["er_specimen_name"] = data[0]["er_specimen_name"] RmagSpecRec["er_sample_name"] = data[0]["er_sample_name"] RmagSpecRec["er_site_name"] = data[0]["er_site_name"] RmagSpecRec["magic_experiment_names"] = RmagSpecRec[ "rmag_anisotropy_name"] + ":ATRM" RmagSpecRec["er_citation_names"] = "This study" RmagResRec[ "rmag_result_name"] = data[0]["er_specimen_name"] + ":ATRM" RmagResRec["er_location_names"] = data[0]["er_location_name"] RmagResRec["er_specimen_names"] = data[0]["er_specimen_name"] RmagResRec["er_sample_names"] = data[0]["er_sample_name"] RmagResRec["er_site_names"] = data[0]["er_site_name"] RmagResRec["magic_experiment_names"] = RmagSpecRec[ "rmag_anisotropy_name"] + ":ATRM" RmagResRec["er_citation_names"] = "This study" RmagSpecRec["anisotropy_type"] = "ATRM" if "magic_instrument_codes" in list(data[0].keys()): RmagSpecRec["magic_instrument_codes"] = data[0][ "magic_instrument_codes"] else: RmagSpecRec["magic_instrument_codes"] = "" RmagSpecRec[ "anisotropy_description"] = "Hext statistics adapted to ATRM" for rec in data: meths = rec['magic_method_codes'].strip().split(':') Dir = [] Dir.append(float(rec["measurement_dec"])) Dir.append(float(rec["measurement_inc"])) Dir.append(float(rec["measurement_magn_moment"])) if "LT-T-Z" in meths: BX.append(pmag.dir2cart(Dir)) # append baseline steps elif "LT-T-I" in meths: X.append(pmag.dir2cart(Dir)) nmeas += 1 # if len(BX) == 1: for i in range(len(X) - 1): BX.append(BX[0]) # assume first 0 field step as baseline elif len(BX) == 0: # assume baseline is zero for i in range(len(X)): BX.append([0., 0., 0.]) # assume baseline of 0 elif len(BX) != len( X ): # if BX isn't just one measurement or one in between every infield step, just assume it is zero print('something odd about the baselines - just assuming zero') for i in range(len(X)): BX.append([0., 0., 0.]) # assume baseline of 0 if nmeas < 6: # must have at least 6 measurements right now - print('skipping specimen ', s, ' too few measurements') specimen += 1 else: B, H, tmpH = pmag.designATRM( npos) # B matrix made from design matrix for positions # # subtract optional baseline and put in a work array # work = numpy.zeros((nmeas, 3), 'f') for i in range(nmeas): for j in range(3): work[i][j] = X[i][j] - BX[i][ j] # subtract baseline, if available # # calculate tensor elements # first put ARM components in w vector # w = numpy.zeros((npos * 3), 'f') index = 0 for i in range(npos): for j in range(3): w[index] = work[i][j] index += 1 s = numpy.zeros((6), 'f') # initialize the s matrix for i in range(6): for j in range(len(w)): s[i] += B[i][j] * w[j] trace = s[0] + s[1] + s[2] # normalize by the trace for i in range(6): s[i] = old_div(s[i], trace) a = pmag.s2a(s) #------------------------------------------------------------ # Calculating dels is different than in the Kappabridge # routine. Use trace normalized tensor (a) and the applied # unit field directions (tmpH) to generate model X,Y,Z # components. Then compare these with the measured values. #------------------------------------------------------------ S = 0. comp = numpy.zeros((npos * 3), 'f') for i in range(npos): for j in range(3): index = i * 3 + j compare = a[j][0] * tmpH[i][0] + a[j][1] * tmpH[i][1] + a[ j][2] * tmpH[i][2] comp[index] = compare for i in range(npos * 3): d = old_div(w[i], trace) - comp[i] # del values S += d * d nf = float(npos * 3. - 6.) # number of degrees of freedom if S > 0: sigma = numpy.sqrt(old_div(S, nf)) else: sigma = 0 hpars = pmag.dohext(nf, sigma, s) # # prepare for output # RmagSpecRec["anisotropy_s1"] = '%8.6f' % (s[0]) RmagSpecRec["anisotropy_s2"] = '%8.6f' % (s[1]) RmagSpecRec["anisotropy_s3"] = '%8.6f' % (s[2]) RmagSpecRec["anisotropy_s4"] = '%8.6f' % (s[3]) RmagSpecRec["anisotropy_s5"] = '%8.6f' % (s[4]) RmagSpecRec["anisotropy_s6"] = '%8.6f' % (s[5]) RmagSpecRec["anisotropy_mean"] = '%8.3e' % (old_div(trace, 3)) RmagSpecRec["anisotropy_sigma"] = '%8.6f' % (sigma) RmagSpecRec["anisotropy_unit"] = "Am^2" RmagSpecRec["anisotropy_n"] = '%i' % (npos) RmagSpecRec["anisotropy_tilt_correction"] = '-1' RmagSpecRec["anisotropy_F"] = '%7.1f ' % ( hpars["F"] ) # used by thellier_gui - must be taken out for uploading RmagSpecRec["anisotropy_F_crit"] = hpars[ "F_crit"] # used by thellier_gui - must be taken out for uploading RmagResRec["anisotropy_t1"] = '%8.6f ' % (hpars["t1"]) RmagResRec["anisotropy_t2"] = '%8.6f ' % (hpars["t2"]) RmagResRec["anisotropy_t3"] = '%8.6f ' % (hpars["t3"]) RmagResRec["anisotropy_v1_dec"] = '%7.1f ' % (hpars["v1_dec"]) RmagResRec["anisotropy_v2_dec"] = '%7.1f ' % (hpars["v2_dec"]) RmagResRec["anisotropy_v3_dec"] = '%7.1f ' % (hpars["v3_dec"]) RmagResRec["anisotropy_v1_inc"] = '%7.1f ' % (hpars["v1_inc"]) RmagResRec["anisotropy_v2_inc"] = '%7.1f ' % (hpars["v2_inc"]) RmagResRec["anisotropy_v3_inc"] = '%7.1f ' % (hpars["v3_inc"]) RmagResRec["anisotropy_ftest"] = '%7.1f ' % (hpars["F"]) RmagResRec["anisotropy_ftest12"] = '%7.1f ' % (hpars["F12"]) RmagResRec["anisotropy_ftest23"] = '%7.1f ' % (hpars["F23"]) RmagResRec["result_description"] = 'Critical F: ' + hpars[ "F_crit"] + ';Critical F12/F13: ' + hpars["F12_crit"] if hpars["e12"] > hpars["e13"]: RmagResRec["anisotropy_v1_zeta_semi_angle"] = '%7.1f ' % ( hpars['e12']) RmagResRec["anisotropy_v1_zeta_dec"] = '%7.1f ' % ( hpars['v2_dec']) RmagResRec["anisotropy_v1_zeta_inc"] = '%7.1f ' % ( hpars['v2_inc']) RmagResRec["anisotropy_v2_zeta_semi_angle"] = '%7.1f ' % ( hpars['e12']) RmagResRec["anisotropy_v2_zeta_dec"] = '%7.1f ' % ( hpars['v1_dec']) RmagResRec["anisotropy_v2_zeta_inc"] = '%7.1f ' % ( hpars['v1_inc']) RmagResRec["anisotropy_v1_eta_semi_angle"] = '%7.1f ' % ( hpars['e13']) RmagResRec["anisotropy_v1_eta_dec"] = '%7.1f ' % ( hpars['v3_dec']) RmagResRec["anisotropy_v1_eta_inc"] = '%7.1f ' % ( hpars['v3_inc']) RmagResRec["anisotropy_v3_eta_semi_angle"] = '%7.1f ' % ( hpars['e13']) RmagResRec["anisotropy_v3_eta_dec"] = '%7.1f ' % ( hpars['v1_dec']) RmagResRec["anisotropy_v3_eta_inc"] = '%7.1f ' % ( hpars['v1_inc']) else: RmagResRec["anisotropy_v1_zeta_semi_angle"] = '%7.1f ' % ( hpars['e13']) RmagResRec["anisotropy_v1_zeta_dec"] = '%7.1f ' % ( hpars['v3_dec']) RmagResRec["anisotropy_v1_zeta_inc"] = '%7.1f ' % ( hpars['v3_inc']) RmagResRec["anisotropy_v3_zeta_semi_angle"] = '%7.1f ' % ( hpars['e13']) RmagResRec["anisotropy_v3_zeta_dec"] = '%7.1f ' % ( hpars['v1_dec']) RmagResRec["anisotropy_v3_zeta_inc"] = '%7.1f ' % ( hpars['v1_inc']) RmagResRec["anisotropy_v1_eta_semi_angle"] = '%7.1f ' % ( hpars['e12']) RmagResRec["anisotropy_v1_eta_dec"] = '%7.1f ' % ( hpars['v2_dec']) RmagResRec["anisotropy_v1_eta_inc"] = '%7.1f ' % ( hpars['v2_inc']) RmagResRec["anisotropy_v2_eta_semi_angle"] = '%7.1f ' % ( hpars['e12']) RmagResRec["anisotropy_v2_eta_dec"] = '%7.1f ' % ( hpars['v1_dec']) RmagResRec["anisotropy_v2_eta_inc"] = '%7.1f ' % ( hpars['v1_inc']) if hpars["e23"] > hpars['e12']: RmagResRec["anisotropy_v2_zeta_semi_angle"] = '%7.1f ' % ( hpars['e23']) RmagResRec["anisotropy_v2_zeta_dec"] = '%7.1f ' % ( hpars['v3_dec']) RmagResRec["anisotropy_v2_zeta_inc"] = '%7.1f ' % ( hpars['v3_inc']) RmagResRec["anisotropy_v3_zeta_semi_angle"] = '%7.1f ' % ( hpars['e23']) RmagResRec["anisotropy_v3_zeta_dec"] = '%7.1f ' % ( hpars['v2_dec']) RmagResRec["anisotropy_v3_zeta_inc"] = '%7.1f ' % ( hpars['v2_inc']) RmagResRec["anisotropy_v3_eta_semi_angle"] = '%7.1f ' % ( hpars['e13']) RmagResRec["anisotropy_v3_eta_dec"] = '%7.1f ' % ( hpars['v1_dec']) RmagResRec["anisotropy_v3_eta_inc"] = '%7.1f ' % ( hpars['v1_inc']) RmagResRec["anisotropy_v2_eta_semi_angle"] = '%7.1f ' % ( hpars['e12']) RmagResRec["anisotropy_v2_eta_dec"] = '%7.1f ' % ( hpars['v1_dec']) RmagResRec["anisotropy_v2_eta_inc"] = '%7.1f ' % ( hpars['v1_inc']) else: RmagResRec["anisotropy_v2_zeta_semi_angle"] = '%7.1f ' % ( hpars['e12']) RmagResRec["anisotropy_v2_zeta_dec"] = '%7.1f ' % ( hpars['v1_dec']) RmagResRec["anisotropy_v2_zeta_inc"] = '%7.1f ' % ( hpars['v1_inc']) RmagResRec["anisotropy_v3_eta_semi_angle"] = '%7.1f ' % ( hpars['e23']) RmagResRec["anisotropy_v3_eta_dec"] = '%7.1f ' % ( hpars['v2_dec']) RmagResRec["anisotropy_v3_eta_inc"] = '%7.1f ' % ( hpars['v2_inc']) RmagResRec["anisotropy_v3_zeta_semi_angle"] = '%7.1f ' % ( hpars['e13']) RmagResRec["anisotropy_v3_zeta_dec"] = '%7.1f ' % ( hpars['v1_dec']) RmagResRec["anisotropy_v3_zeta_inc"] = '%7.1f ' % ( hpars['v1_inc']) RmagResRec["anisotropy_v2_eta_semi_angle"] = '%7.1f ' % ( hpars['e23']) RmagResRec["anisotropy_v2_eta_dec"] = '%7.1f ' % ( hpars['v3_dec']) RmagResRec["anisotropy_v2_eta_inc"] = '%7.1f ' % ( hpars['v3_inc']) RmagResRec["tilt_correction"] = '-1' RmagResRec["anisotropy_type"] = 'ATRM' RmagResRec["magic_method_codes"] = 'LP-AN-TRM:AE-H' RmagSpecRec["magic_method_codes"] = 'LP-AN-TRM:AE-H' RmagResRec["magic_software_packages"] = pmag.get_version() RmagSpecRec["magic_software_packages"] = pmag.get_version() RmagSpecRecs.append(RmagSpecRec) RmagResRecs.append(RmagResRec) specimen += 1 pmag.magic_write(rmag_anis, RmagSpecRecs, 'rmag_anisotropy') print("specimen tensor elements stored in ", rmag_anis) pmag.magic_write(rmag_res, RmagResRecs, 'rmag_results') print("specimen statistics and eigenparameters stored in ", rmag_res)
def main(): """ NAME aarm_magic.py DESCRIPTION Converts AARM data to best-fit tensor (6 elements plus sigma) Original program ARMcrunch written to accomodate ARM anisotropy data collected from 6 axial directions (+X,+Y,+Z,-X,-Y,-Z) using the off-axis remanence terms to construct the tensor. A better way to do the anisotropy of ARMs is to use 9,12 or 15 measurements in the Hext rotational scheme. SYNTAX aarm_magic.py [-h][command line options] OPTIONS -h prints help message and quits -usr USER: identify user, default is "" -f FILE: specify input file, default is aarm_measurements.txt -crd [s,g,t] specify coordinate system, requires er_samples.txt file -fsa FILE: specify er_samples.txt file, default is er_samples.txt -Fa FILE: specify anisotropy output file, default is arm_anisotropy.txt -Fr FILE: specify results output file, default is aarm_results.txt INPUT Input for the present program is a series of baseline, ARM pairs. The baseline should be the AF demagnetized state (3 axis demag is preferable) for the following ARM acquisition. The order of the measurements is: positions 1,2,3, 6,7,8, 11,12,13 (for 9 positions) positions 1,2,3,4, 6,7,8,9, 11,12,13,14 (for 12 positions) positions 1-15 (for 15 positions) """ # initialize some parameters args=sys.argv user="" meas_file="aarm_measurements.txt" samp_file="er_samples.txt" rmag_anis="arm_anisotropy.txt" rmag_res="aarm_results.txt" dir_path='.' # # get name of file from command line # 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 "-f" in args: ind=args.index("-f") meas_file=sys.argv[ind+1] coord='-1' if "-crd" in sys.argv: ind=sys.argv.index("-crd") coord=sys.argv[ind+1] if coord=='s':coord='-1' if coord=='g':coord='0' if coord=='t':coord='100' if "-fsa" in args: ind=args.index("-fsa") samp_file=sys.argv[ind+1] if "-Fa" in args: ind=args.index("-Fa") rmag_anis=args[ind+1] if "-Fr" in args: ind=args.index("-Fr") rmag_res=args[ind+1] meas_file=dir_path+'/'+meas_file samp_file=dir_path+'/'+samp_file rmag_anis=dir_path+'/'+rmag_anis rmag_res=dir_path+'/'+rmag_res # read in data meas_data,file_type=pmag.magic_read(meas_file) meas_data=pmag.get_dictitem(meas_data,'magic_method_codes','LP-AN-ARM','has') if file_type != 'magic_measurements': print file_type print file_type,"This is not a valid magic_measurements file " sys.exit() if coord!='-1': # need to read in sample data samp_data,file_type=pmag.magic_read(samp_file) if file_type != 'er_samples': print file_type print file_type,"This is not a valid er_samples file " print "Only specimen coordinates will be calculated" coord='-1' # # sort the specimen names # ssort=[] for rec in meas_data: spec=rec["er_specimen_name"] if spec not in ssort: ssort.append(spec) if len(ssort)>1: sids=sorted(ssort) else: sids=ssort # # work on each specimen # specimen=0 RmagSpecRecs,RmagResRecs=[],[] while specimen < len(sids): s=sids[specimen] data=[] RmagSpecRec={} RmagResRec={} method_codes=[] # # find the data from the meas_data file for this sample # data=pmag.get_dictitem(meas_data,'er_specimen_name',s,'T') # # find out the number of measurements (9, 12 or 15) # npos=len(data)/2 if npos==9: # # get dec, inc, int and convert to x,y,z # B,H,tmpH=pmag.designAARM(npos) # B matrix made from design matrix for positions X=[] for rec in data: Dir=[] Dir.append(float(rec["measurement_dec"])) Dir.append(float(rec["measurement_inc"])) Dir.append(float(rec["measurement_magn_moment"])) X.append(pmag.dir2cart(Dir)) # # subtract baseline and put in a work array # work=numpy.zeros((npos,3),'f') for i in range(npos): for j in range(3): work[i][j]=X[2*i+1][j]-X[2*i][j] # # calculate tensor elements # first put ARM components in w vector # w=numpy.zeros((npos*3),'f') index=0 for i in range(npos): for j in range(3): w[index]=work[i][j] index+=1 s=numpy.zeros((6),'f') # initialize the s matrix for i in range(6): for j in range(len(w)): s[i]+=B[i][j]*w[j] trace=s[0]+s[1]+s[2] # normalize by the trace for i in range(6): s[i]=s[i]/trace a=pmag.s2a(s) #------------------------------------------------------------ # Calculating dels is different than in the Kappabridge # routine. Use trace normalized tensor (a) and the applied # unit field directions (tmpH) to generate model X,Y,Z # components. Then compare these with the measured values. #------------------------------------------------------------ S=0. comp=numpy.zeros((npos*3),'f') for i in range(npos): for j in range(3): index=i*3+j compare=a[j][0]*tmpH[i][0]+a[j][1]*tmpH[i][1]+a[j][2]*tmpH[i][2] comp[index]=compare for i in range(npos*3): d=w[i]/trace - comp[i] # del values S+=d*d nf=float(npos*3-6) # number of degrees of freedom if S >0: sigma=numpy.sqrt(S/nf) else: sigma=0 RmagSpecRec["rmag_anisotropy_name"]=data[0]["er_specimen_name"] RmagSpecRec["er_location_name"]=data[0]["er_location_name"] RmagSpecRec["er_specimen_name"]=data[0]["er_specimen_name"] RmagSpecRec["er_sample_name"]=data[0]["er_sample_name"] RmagSpecRec["er_site_name"]=data[0]["er_site_name"] RmagSpecRec["magic_experiment_names"]=RmagSpecRec["rmag_anisotropy_name"]+":AARM" RmagSpecRec["er_citation_names"]="This study" RmagResRec["rmag_result_name"]=data[0]["er_specimen_name"]+":AARM" RmagResRec["er_location_names"]=data[0]["er_location_name"] RmagResRec["er_specimen_names"]=data[0]["er_specimen_name"] RmagResRec["er_sample_names"]=data[0]["er_sample_name"] RmagResRec["er_site_names"]=data[0]["er_site_name"] RmagResRec["magic_experiment_names"]=RmagSpecRec["rmag_anisotropy_name"]+":AARM" RmagResRec["er_citation_names"]="This study" if "magic_instrument_codes" in data[0].keys(): RmagSpecRec["magic_instrument_codes"]=data[0]["magic_instrument_codes"] else: RmagSpecRec["magic_instrument_codes"]="" RmagSpecRec["anisotropy_type"]="AARM" RmagSpecRec["anisotropy_description"]="Hext statistics adapted to AARM" if coord!='-1': # need to rotate s # set orientation priorities SO_methods=[] for rec in samp_data: if "magic_method_codes" not in rec: rec['magic_method_codes']='SO-NO' 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) # continue here redo,p=1,0 if len(SO_methods)<=1: az_type=SO_methods[0] orient=pmag.find_samp_rec(RmagSpecRec["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 az,pl=orient['sample_azimuth'],orient['sample_dip'] s=pmag.dosgeo(s,az,pl) # rotate to geographic coordinates if coord=='100': sampe_bed_dir,sample_bed_dip=orient['sample_bed_dip_direction'],orient['sample_bed_dip'] s=pmag.dostilt(s,bed_dir,bed_dip) # rotate to geographic coordinates hpars=pmag.dohext(nf,sigma,s) # # prepare for output # RmagSpecRec["anisotropy_s1"]='%8.6f'%(s[0]) RmagSpecRec["anisotropy_s2"]='%8.6f'%(s[1]) RmagSpecRec["anisotropy_s3"]='%8.6f'%(s[2]) RmagSpecRec["anisotropy_s4"]='%8.6f'%(s[3]) RmagSpecRec["anisotropy_s5"]='%8.6f'%(s[4]) RmagSpecRec["anisotropy_s6"]='%8.6f'%(s[5]) RmagSpecRec["anisotropy_mean"]='%8.3e'%(trace/3) RmagSpecRec["anisotropy_sigma"]='%8.6f'%(sigma) RmagSpecRec["anisotropy_unit"]="Am^2" RmagSpecRec["anisotropy_n"]='%i'%(npos) RmagSpecRec["anisotropy_tilt_correction"]=coord RmagSpecRec["anisotropy_F"]='%7.1f '%(hpars["F"]) # used by thellier_gui - must be taken out for uploading RmagSpecRec["anisotropy_F_crit"]=hpars["F_crit"] # used by thellier_gui - must be taken out for uploading RmagResRec["anisotropy_t1"]='%8.6f '%(hpars["t1"]) RmagResRec["anisotropy_t2"]='%8.6f '%(hpars["t2"]) RmagResRec["anisotropy_t3"]='%8.6f '%(hpars["t3"]) RmagResRec["anisotropy_v1_dec"]='%7.1f '%(hpars["v1_dec"]) RmagResRec["anisotropy_v2_dec"]='%7.1f '%(hpars["v2_dec"]) RmagResRec["anisotropy_v3_dec"]='%7.1f '%(hpars["v3_dec"]) RmagResRec["anisotropy_v1_inc"]='%7.1f '%(hpars["v1_inc"]) RmagResRec["anisotropy_v2_inc"]='%7.1f '%(hpars["v2_inc"]) RmagResRec["anisotropy_v3_inc"]='%7.1f '%(hpars["v3_inc"]) RmagResRec["anisotropy_ftest"]='%7.1f '%(hpars["F"]) RmagResRec["anisotropy_ftest12"]='%7.1f '%(hpars["F12"]) RmagResRec["anisotropy_ftest23"]='%7.1f '%(hpars["F23"]) RmagResRec["result_description"]='Critical F: '+hpars["F_crit"]+';Critical F12/F13: '+hpars["F12_crit"] if hpars["e12"]>hpars["e13"]: RmagResRec["anisotropy_v1_zeta_semi_angle"]='%7.1f '%(hpars['e12']) RmagResRec["anisotropy_v1_zeta_dec"]='%7.1f '%(hpars['v2_dec']) RmagResRec["anisotropy_v1_zeta_inc"]='%7.1f '%(hpars['v2_inc']) RmagResRec["anisotropy_v2_zeta_semi_angle"]='%7.1f '%(hpars['e12']) RmagResRec["anisotropy_v2_zeta_dec"]='%7.1f '%(hpars['v1_dec']) RmagResRec["anisotropy_v2_zeta_inc"]='%7.1f '%(hpars['v1_inc']) RmagResRec["anisotropy_v1_eta_semi_angle"]='%7.1f '%(hpars['e13']) RmagResRec["anisotropy_v1_eta_dec"]='%7.1f '%(hpars['v3_dec']) RmagResRec["anisotropy_v1_eta_inc"]='%7.1f '%(hpars['v3_inc']) RmagResRec["anisotropy_v3_eta_semi_angle"]='%7.1f '%(hpars['e13']) RmagResRec["anisotropy_v3_eta_dec"]='%7.1f '%(hpars['v1_dec']) RmagResRec["anisotropy_v3_eta_inc"]='%7.1f '%(hpars['v1_inc']) else: RmagResRec["anisotropy_v1_zeta_semi_angle"]='%7.1f '%(hpars['e13']) RmagResRec["anisotropy_v1_zeta_dec"]='%7.1f '%(hpars['v3_dec']) RmagResRec["anisotropy_v1_zeta_inc"]='%7.1f '%(hpars['v3_inc']) RmagResRec["anisotropy_v3_zeta_semi_angle"]='%7.1f '%(hpars['e13']) RmagResRec["anisotropy_v3_zeta_dec"]='%7.1f '%(hpars['v1_dec']) RmagResRec["anisotropy_v3_zeta_inc"]='%7.1f '%(hpars['v1_inc']) RmagResRec["anisotropy_v1_eta_semi_angle"]='%7.1f '%(hpars['e12']) RmagResRec["anisotropy_v1_eta_dec"]='%7.1f '%(hpars['v2_dec']) RmagResRec["anisotropy_v1_eta_inc"]='%7.1f '%(hpars['v2_inc']) RmagResRec["anisotropy_v2_eta_semi_angle"]='%7.1f '%(hpars['e12']) RmagResRec["anisotropy_v2_eta_dec"]='%7.1f '%(hpars['v1_dec']) RmagResRec["anisotropy_v2_eta_inc"]='%7.1f '%(hpars['v1_inc']) if hpars["e23"]>hpars['e12']: RmagResRec["anisotropy_v2_zeta_semi_angle"]='%7.1f '%(hpars['e23']) RmagResRec["anisotropy_v2_zeta_dec"]='%7.1f '%(hpars['v3_dec']) RmagResRec["anisotropy_v2_zeta_inc"]='%7.1f '%(hpars['v3_inc']) RmagResRec["anisotropy_v3_zeta_semi_angle"]='%7.1f '%(hpars['e23']) RmagResRec["anisotropy_v3_zeta_dec"]='%7.1f '%(hpars['v2_dec']) RmagResRec["anisotropy_v3_zeta_inc"]='%7.1f '%(hpars['v2_inc']) RmagResRec["anisotropy_v3_eta_semi_angle"]='%7.1f '%(hpars['e13']) RmagResRec["anisotropy_v3_eta_dec"]='%7.1f '%(hpars['v1_dec']) RmagResRec["anisotropy_v3_eta_inc"]='%7.1f '%(hpars['v1_inc']) RmagResRec["anisotropy_v2_eta_semi_angle"]='%7.1f '%(hpars['e12']) RmagResRec["anisotropy_v2_eta_dec"]='%7.1f '%(hpars['v1_dec']) RmagResRec["anisotropy_v2_eta_inc"]='%7.1f '%(hpars['v1_inc']) else: RmagResRec["anisotropy_v2_zeta_semi_angle"]='%7.1f '%(hpars['e12']) RmagResRec["anisotropy_v2_zeta_dec"]='%7.1f '%(hpars['v1_dec']) RmagResRec["anisotropy_v2_zeta_inc"]='%7.1f '%(hpars['v1_inc']) RmagResRec["anisotropy_v3_eta_semi_angle"]='%7.1f '%(hpars['e23']) RmagResRec["anisotropy_v3_eta_dec"]='%7.1f '%(hpars['v2_dec']) RmagResRec["anisotropy_v3_eta_inc"]='%7.1f '%(hpars['v2_inc']) RmagResRec["anisotropy_v3_zeta_semi_angle"]='%7.1f '%(hpars['e13']) RmagResRec["anisotropy_v3_zeta_dec"]='%7.1f '%(hpars['v1_dec']) RmagResRec["anisotropy_v3_zeta_inc"]='%7.1f '%(hpars['v1_inc']) RmagResRec["anisotropy_v2_eta_semi_angle"]='%7.1f '%(hpars['e23']) RmagResRec["anisotropy_v2_eta_dec"]='%7.1f '%(hpars['v3_dec']) RmagResRec["anisotropy_v2_eta_inc"]='%7.1f '%(hpars['v3_inc']) RmagResRec["tilt_correction"]='-1' RmagResRec["anisotropy_type"]='AARM' RmagResRec["magic_method_codes"]='LP-AN-ARM:AE-H' RmagSpecRec["magic_method_codes"]='LP-AN-ARM:AE-H' RmagResRec["magic_software_packages"]=pmag.get_version() RmagSpecRec["magic_software_packages"]=pmag.get_version() specimen+=1 RmagSpecRecs.append(RmagSpecRec) RmagResRecs.append(RmagResRec) else: print 'skipping specimen ',s,' only 9 positions supported','; this has ',npos specimen+=1 if rmag_anis=="":rmag_anis="rmag_anisotropy.txt" pmag.magic_write(rmag_anis,RmagSpecRecs,'rmag_anisotropy') print "specimen tensor elements stored in ",rmag_anis if rmag_res=="":rmag_res="rmag_results.txt" pmag.magic_write(rmag_res,RmagResRecs,'rmag_results') print "specimen statistics and eigenparameters stored in ",rmag_res